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https://f1000research.com/articles/12-1210/v1	26 Sep 23	{ "type": "Systematic Review", "title": "An exploration of the use of accessory dwelling units for senior housing in Honolulu", "authors": [ "Eric Youn" ], "abstract": "The island of Oahu (Honolulu County, Hawai’i) is facing a shortage of housing for its growing senior population. The construction of accessory dwelling units (ADUs), or small, second homes built on the same lot. for senior housing may be a possible solution. A qualitative document review was utilized to examine the existing Honolulu ADU cost reduction for those wishing to build an ADU on their properties for the purposes of senior housing. There were several publications and articles found through the search. From these articles, four major themes emerged: tax breaks, financing options, green building, and sharing of utilities. These themes led to a secondary level document review and analysis of each of these themes.", "keywords": [ "ADU", "affordable senior housing", "Housing", "Advanced care planning", "Home and community-based services" ], "content": "Introduction\n\nHonolulu County, which consists of the entire island of Oahu, has a high and growing senior population. Residents 65 years and older consist of over 18.2% of the population of Honolulu County compared to 16% nationwide (United States Census Bureau, 2022). This population has grown from 14.5% of the total population for Honolulu County since the last census in 2010 (United States Census Bureau, 2022). Honolulu is the most populated county in the state of Hawai’i by far. Its population of almost one million consists of well over half of Hawai’i’s total population of 1.416 million (United States Census Bureau, 2022).\n\nIn addition to having a high percentage of seniors in the community, Hawai’i residents also experience a longer than average life span than their mainland counterparts. According to a study by Wu et al. (2017), “The life expectancy at birth in Hawai’i in 2010 was 82.4 years, 3.7 years higher than the national average for the total US population (78.7 years)”. These factors all play a role in issues of senior housing in Honolulu County.\n\nHawai’i has a long history of using homes as multigenerational housing. It is not uncommon for two to three generations to live in one house and for the house to be held within the family from generation to generation (Peterkin, 2017). According to Hoff (2020), “Using 2018 data from US Census Bureau’s 1-year American Community Survey estimates, … the share of multigenerational households in each state [was calculated]. Hawai’i had the largest share, where 7.72% of households were multigenerational.” Honolulu County also has the third highest median home cost in the United States only behind New York City and San Francisco (Burrows, 2021).\n\nDespite the strategy of using homes as multigenerational housing, an economic strain still remains on families when an older family member requires extra care. Care homes and assisted-living facilities, although very prevalent, in the Honolulu County area are sometimes a large economic burden on families (Kukaua, 2019). Combined with this, there is also an Asian and Pacific Islander cultural factor in which the desire is for the senior family member to live at home. This desire is often shared by both the senior family member and the rest of the family (Peterkin, 2017). Taking these factors into consideration, it is determined that there is a need for a study that explores various cost reduction options in building ADUs and their application for use in senior housing.\n\n\nThe accessory dwelling unit (ADU) concept\n\nAccording to the American Planning Association (2022), “an accessory dwelling unit (ADU) is a smaller, independent residential dwelling unit located on the same lot as a stand-alone (i.e., detached) single-family home … Internal, attached, and detached ADUs all have the potential to increase housing affordability (both for homeowners and tenants), create a wider range of housing options within the community, enable seniors to stay near family as they age, and facilitate better use of the existing housing fabric in established neighborhoods.”\n\nThis concept has been popular in areas where property values and cost of living are on the higher end of the national average. There have been several awareness campaigns to increase the knowledge of the general public about this option. This includes an ADU being built on the grounds of the state capital in Honolulu (Cerbal, 2017).\n\nUsing an ADU as an option for disadvantaged individuals has also been recognized by well-known non-profits such as Habitat for Humanity (Friend, 2020). The American Association of Retired Persons (AARP) has also recognized the potential of ADUs for seniors (Spevak & Stanton, 2019).\n\nIn 2015, the ability for homeowners to construct an ADU on their property had easier regulations than building an “Ohana Unit”. An Ohana Unit is another type of smaller, independent residential dwelling unit located on the same lot as a stand-alone (i.e., detached) single-family home however, Ohana units were required to “have a ‘wet bar,’ or an eating area with a sink, refrigerator, and stovetop–not a full oven. They also can only be rented to a family member, which is agreed upon through the signing of a restricted covenant agreement” (Arakaki, 2022). The ADU regulations permitted additional allowances such as the benefit of having a full kitchen (Arakaki, 2022). In 2018, Mayor Kirk Caldwell signed into law a tax break for those wishing to build an ADU on their properties (Pang, 2018).\n\n\nAn exploration of options of the use of ADUs for senior housing in Honolulu\n\nThe concept of using ADUs in Honolulu for various disadvantaged populations as well as senior populations has resulted in some interesting ideas and proposals. One that stands out has been the concept of putting ADUs on moveable platforms and then transporting them by truck to various properties in which they can be used either singly or in groups (Olsen, 2017). Although the concept of using ADUs for senior housing in Honolulu is not new, there is a gap in the literature in exploring various cost reduction options.\n\nThe remainder of this article shall explore various cost reduction options in using ADUs and applying them for use in senior housing. As detailed in the methods section, a qualitative document review was utilized to examine the existing Honolulu ADU cost reduction that occurred after the 2018 tax break for those wishing to build an ADU on their properties.\n\nIt would also be inappropriate to assume that any of these options; alone or in combination would be a solution for every senior in Honolulu that is faced with the financial burden of senior housing. Some of these options would only be cost-effective through a return of finances through equity/home value and would not appropriate for everyone. This notion will also be touched on later in this article.\n\n\nMethods\n\nA qualitative document review was utilized to examine the existing literature on Honolulu ADU cost reduction that occurred after the 2018 tax break for those wishing to build an ADU on their properties.\n\nThe inclusion criteria for review consisted of documents written about possible strategies and cost saving measures when building or purchasing a home with an ADU in Honolulu County. Documents published before 2018 or published by a potentially biased party such as a real estate company, contractor, architect, or any party that would benefit directly from the sale of a specific brand of product or service provider within the ADU market were excluded from the study.\n\nThe methods used to collect data/information is as follows. A Google search was used with the keywords “ADU”, “Honolulu”, “saving”, “financing”, “cost savings” and “building” with no filters or limits. Of the 40 results, four articles from the publications: Pacific Business News, Civil Beat – Hawai’i, Hawai’i Life, and Hawai’i Business Magazine were found to meet the content requirements, detailed in the inclusion and exclusion criteria above, and specifically spoke to the use of an ADU as a senior housing option in Honolulu and/or Hawaii. These articles were used as the primary source of information for the review.\n\nIt was determined that after the 40 results from the keyword search were reviewed, four articles were enough as a sample size. This conclusion was drawn due to the specificity of the topic and that this was a preliminary study. These articles were searched for and selected during the time frame of July to October 2022. A protocol for the review was not prepared.\n\nDocument analysis was used as an appropriate method as this is an initial exploration study focused on giving meaning to the assessment topic of ADU cost reduction options when the ADU is used for senior housing. Document analysis is a method of qualitative research where documents are interpreted by the researcher to give meaning on an assessment topic (Bowen, 2009).\n\nThe process and methods used to synthesize the results were those commonly used in qualitative document analysis (Rasch, 2020). This included: 1) forming the research question (examine the existing Honolulu ADU cost reduction for those wishing to build an ADU on their properties for the purposes of senior housing), 2) Collecting the data (using the google keyword search) and 3) Analyzing and comparing patterns (identifying the four themes).\n\nFor purposes of methods duplication, Step 3 involved: a) Analyzing the data from the google keyword search to isolate findings that had a focus on possible strategies and cost saving measures when building or purchasing a home with an ADU in Honolulu County, b) Disqualifying data published by a potentially biased party such as a real estate company, contractor, architect, or any party that would benefit directly from the sale of a specific brand of product or service provider within the ADU market, and c) Disqualifying data published before the 2018 ADU tax break in Honolulu County went into effect.\n\nThe remainder of this paper will 4) Interpret and present the findings.\n\n\nResults\n\nFrom the articles, four major themes emerged: tax breaks, financing options, green building, and sharing of utilities. The theme of tax breaks included the 2018 City and County of Honolulu tax break as well as other associated tax breaks concerning new constructions of ADUs and senior housing construction. The financing options theme centered on various incentives involved in constructing an ADU. The green building and sharing of utilities themes focused on solar electricity and hot water construction and sharing various utilities with the main house.\n\nThese themes led to a secondary level document review in which several organization websites were found to have relevant ADU sections and information. These websites and brief descriptions of their characteristics are as follows: AARP (general resources for seniors), U.S. Department of Agriculture (information of loans), Hawaiian Electric (information on local electric usage and costs), American Planning Association (ADU definitions and resources), and the California Department of Housing and Community Development (2020) (a resource of ADU information from a state with the longest history of use).\n\nSeveral other sources were referenced to support and clarify information that was referenced in the four primary articles and the websites (benefits.gov, 2022; Chai & Wesley, 2022; Fujii-Oride, 2022; Gregory, 2022; G. Udagawa, personal communication, June 8, 2018; HECO, 2021; LaPonsie, 2022; Nagle, 2020; Pang, 2018; Robinson, 2019; Shelton, et al., 2022). The rest of this article expands on these themes and their relevance to strategies and cost saving measures when building or purchasing a home with an ADU in Honolulu County for senior housing purposes.\n\n\nADU cost reduction options\n\nAs previously mentioned, in 2018, Honolulu Mayor Kirk Caldwell offered tax breaks to those wishing to build an ADU on their property. The bill (known as Bill 64) “would make homeowners who receive ADU building permits eligible for an annual exemption of $60,000 per tax year for up to five years. At the current residential homeowner rate of $3.50 per $1000 of property value, the break would amount to $210 annually” (Pang, 2018). O‘ahu and Kaua‘i have tried to incentivize the construction of ADUs by waiving building permits, sewers and other fees, which can save homeowners thousands of dollars. This led to “a separate bill giving those applying for ADU permits as much as USD 11,000 in incentives by waiving all building permits, grading permits, inspection fees, wastewater facility charges and park dedication fees (Fujii-Oride, 2022).\n\nAs far as acceptability and demand, these tax breaks do provide some financial relief for those looking into the ADU option. For implementation, practicality, and adaptation, the key issues here concern knowledge about the particular bills, laws, and regulations and if they are applicable for the particular situation. Knowledge about the future and other tax beak opportunities are also key.\n\nAnother cost-saving opportunity lies with them the financing of the building of the ADU itself. There are several Government backed loans and grant programs that fall into this category. The Single-Family Housing Direct Home Loans Program and the Rural Housing: Repair Loans and Grants program are two examples.\n\nThe Single-Family Housing Direct Home Loans Program, also known as the Section 502 Direct Loan Program (USDA, 2022) lists several criteria for eligibility. In the case of building an ADU for senior housing in Honolulu County, the key criteria that would have to be met is to indicate the current home without the ADU would not be considered “safe and sanitary” as well as having the family “be unable to obtain a loan from other resources on terms and conditions that can reasonably be expected to meet” (USDA, 2022).\n\nThe Rural Housing: Repair Loans and Grants program (benefits.gov, 2022) is much more specific to seniors (as it is for those aged 62 and older living in rural areas). However, it provides a much lower benefit amount than the Single-Family Housing Direct Home Loans Program, capping the total benefit amount at USD 7500 and/or a 1% loan at USD 20,000 (USDA, 2022).\n\nAs far as acceptability and demand, these programs provide some financial relief for those looking into the ADU option. It is particularly key, as modifications to the financing of the ADU have a direct effect on the monthly payment required. For implementation, practicality, and adaptation, the key issues, here again, concern knowledge about the particular bills, laws, and regulations and if they are applicable for the particular situation. These programs are generally for rural area construction, so knowledge about what the definition “rural” entails as well as other qualifying factors are key.\n\nAnother resource for those looking at the ADU option lies in utility costs. The National Foundation for Credit Counseling recommends that utilities today constitute less than 10% of one’s total income (Nagle, 2020). However, advancements in technology may allow this amount to be significantly reduced using green and shared utility processes. For one of the two major utilities of electricity and water, solar power allows for a significant reduction in electric utility costs. For secondary utilities such as cable and internet, technology allows you to now share resources with the main house that also creates a significant reduction in overall cost.\n\nGreen building\n\nThere are several factors involved in generating electricity from solar panels for ADUs. These factors include the number of panels that can be placed on the roof that have exposure to the sun. Another factor is the number of batteries, if any, that are to be used to store excess electricity to be used at night or during times in which there is not enough energy being gathered from the panels to offset the usage of energy in the house. Yet another factor is whether the house will be connected to the electrical grid or if the house will be completely independent from an electric power standpoint.\n\nTo give a rough example of the costs involved and overall savings for a solar powered ADU, one may consider these figures. If the ADU is built to the standard 800 square feet and has 14 solar panels that face the sun as well as two batteries to store excess electricity, the unfinanced start-up cost is approximately USD 34,000 (G. Udagawa, personal communication, June 8, 2018). On average, a property with a system such as this will be electrically independent with the rare need to access excess power from the grid.\n\nOn average in Oahu, an 800 square feet ADU with two residents and having average electricity usage will use 796 kWh a month (Gregory, 2022). At the 2021 Hawaiian Electric Company (HECO) rate of USD 32.47 cents per kWh (HECO, 2021), this would equal USD 258.46 for electricity.\n\nThe approximate $34,000 solar start-up cost mentioned earlier can be broken as follows search: USD 1332.50 for each panel, USD 6165.50 for each battery, and USD 3050.00 for labor and supportive hardware (G. Udagawa, personal communication, June 8, 2018).\n\nOne can use these rough estimates to determine the start-up costs based on their desires, roof size, and available capital. It should also be noted that Tesla provides a possible USD 15,000 Incentives/Rebates and Federal Tax Credit discount (G. Udagawa, personal communication, June 8, 2018).\n\nShared utilities\n\nAlthough this may be obvious to some, others may be unaware of the advantages of wireless technology when it comes to using secondary utilities such as internet and cable television. The internet may be provided throughout the main house and the ADU wirelessly using a wireless router attached to the main house modem. If the ADU is too far away, alternate solutions can be found in using mesh systems or signal boosters to expand and boost the wireless signal (Chai & Wesley, 2022). Similarly, cable and satellite TV boxes have wireless models that get their signal from a signal router in the main house.\n\nThe average internet subscription in Hawai’i costs USD 15–80 (Shelton, et al., 2022) while the average cable/satellite television subscription costs USD 78.58 (LaPonsie, 2022). Although this is not as much as major utilities such as electricity and water, by bundling and sharing these, the savings can add up in the long run.\n\n\nDiscussion\n\nThe various subsidized loans, tax breaks, green construction, and shared utility options may provide cost relief to the family seeking out ADU construction as a possible senior housing option. These cost saving options provide cost relief both during and after construction.\n\nTo reiterate, these options may not be for everyone. Various factors must be considered in choosing which options should be pursued and whether the ADU option for senior housing is the most feasible option overall; not just cost-wise but for the overall goals of the senior family members being housed and the rest of the family.\n\nOther factors that should come into consideration is if the house (along with the ADU) is intended to be sold after the death of the senior family members. Within this consideration is the likelihood of whether caretakers will be needed or if a hospice facility will be used as another residence for the senior family members.\n\nAll of these considerations tie into the overall cost of the ADU. If the entire property is to be sold after the death/hospice of the senior family member, the increase in home value that the ADU adds to the predicted sale price should be considered in the decision to build the ADU. Also, if the family does not want to sell the property after the death/hospice of the senior family member, the ADU may be used as a source of passive rental income. (Note that this is different from the ohana units allowed by Hawai’i law, as ohana units may only be used/rented by family members [Robinson, 2019].)\n\nThe relatively simple and straightforward approach in the review process of finding articles and gathering information and evidence from them on the topic was appropriate for a preliminary study such as this one. However, this simple and preliminary approach should be noted to have limitations to the review process (primarily sample size and lack of interviews and other sources aside from the published sources used in this study) and evidence in comparison to a more in-depth study that used interviews with members of the ADU building and senior care industries.\n\nThese last points of the previous section are a good segue into recommendations for future studies. The cost reduction options of finding subsidize loans, tax breaks, using green building techniques, and sharing utilities with the main house are all things to be considered and explored when building an ADU. However as repeatedly stated in this article, the ADU option is not for everybody and there are many economic considerations that should be reflected upon before proceeding with building an ADU for senior housing purposes.\n\nTherefore, the recommendation for future studies would involve an exploration into the best practices for the various categories of these economic considerations. These categories are:\n\n1) When it is planned that the main house (along with the ADU) is intended to be sold after the death of the senior family members\n\n2) When it is planned that the main house (along with the ADU) is NOT intended to be sold after the death of the senior family members and may be used as a source of passive rental income.\n\n3) In consideration of both of the scenarios above; When it is planned that the senior family members will be moved to a managed care or hospice facility at an appropriate time OR\n\n4) When it is planned that in-home care services will be brought in to the ADU to care for the senior family member at an appropriate time.\n\nIf the analysis and best practices of each of these situations are well laid out it will give the family that is considering the option of building an ADU for the senior family members of their household a strong template to guide their decision making. The laws and regulations that allowed for the ADU option on the island of Oahu were strongly rooted in the purpose of creating more senior housing options (Cerbal, 2017), and a strong template to guide decision making in this process would be a valuable resource.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: PRISMA checklist for “An exploration of the use of accessory dwelling units for senior housing in Honolulu”. https://doi.org/10.5281/zenodo.8187712 (Youn, 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\nAmerican Planning Association: Accessory Dwelling Units.2022, September 14. Reference Source\n\nArakaki A: ADUs in Hawaii.2022, July 29. Reference Source\n\nBenefits.gov: Rural Housing: Housing Repair Loans and Grants.2022, September 14. Reference Source\n\nBowen GA: Document analysis as a qualitative research method. Qual. Res. J. 2009; 9(2): 27–40. Publisher Full Text\n\nBurrows D: 15 U.S. Cities with the Highest Average Home Prices. Kiplinger. 2021, October 20. Reference Source\n\nCalifornia Department of Housing and Community Development: Accessory Dwelling Unit Handbook.2020. Reference Source\n\nCerbal A: ADU built on State Capitol lawn to highlight statewide need for affordable housing. KHON2. 2017. Reference Source\n\nChai W, Wesley D: DEFINITION - wireless mesh network (WMN). TechTarget. 2022. Reference Source\n\nFriend Z: Partnering with Habitat for Humanity on Accessory Dwelling Units. Times Publishing Group; 2020, October 20. Reference Source\n\nFujii-Oride N: ADUs Seemed Like a Simple Solution to Hawai‘i’s Housing Crisis. Hawai’i Business Magazine. 2022. Reference Source\n\nGregory B: How do I determine how many kWh I use?n.d. Retrieved November 7, 2022. Reference SourceReference Source\n\nHawaiian Electric: Average Price of Electricity.2021. Reference Source\n\nHoff M: Social distancing may be harder for families who live with elderly relatives. Here are the 15 states with the largest share of multigenerational households. Bus. Insid. 2020, April 25. Reference Source\n\nKukaua K: Pacific Business News.2019, June 24. Reference Source\n\nLaPonsie M: How much is cable per month? U.S. News and World Report. 2022. Reference Source\n\nNagle C: How Much Should You Plan to Spend on Utilities Each Month? National Foundation for Credit Counseling; 2020. Reference Source\n\nOlsen AO: Promoting Healthy Aging Through Transportable Accessory Dwelling Unit Communities [Doctoral Dissertation, University of Hawai’i at Manoa].2017. Reference Source\n\nPang GYK: Caldwell’s bill offers tax breaks to build accessory dwelling units. Honolulu Star-Advertiser; 2018, August 10. Reference Source\n\nPeterkin O: Why Hawai’i Trends Toward Large And Extended Families. Hawai’i. 2017, November 21. Reference Source\n\nRasch D: A QDA recipe? A ten-step approach for qualitative document analysis using MAXQDA. MAXQDA; 2020, January 20. Reference Source\n\nRobinson B: Guest House or Ohana – Whatʻs the Difference? Hawai’i Life. 2019. Reference Source\n\nShelton S, Kinney J, Brooks O: Best Internet Service Providers of 2022. U.S. News and World Report. 2022. Reference Source\n\nSpevak E, Stanton M: The ABCs of ADUs: A guide to Accessory Dwelling Units and how they expand housing options for people of all ages. AARP; 2019. Reference Source\n\nUnited States Census Bureau: 2020 Census Results.2022, September 14. Reference Source\n\nUnited States Department of Agriculture: Single Family Housing Direct Home Loans.2022, September 14. Reference Source\n\nWu Y, Braun K, Onaka AT, et al.: Life Expectancies in Hawai‘i: A Multi-ethnic Analysis of 2010 Life Tables. Hawai’i Journal of Medicine and Public Health. 2017; 76(1): 9–14. PubMed Abstract\n\nYoun E: An exploration of the use of accessory dwelling units for senior housing in Honolulu. [Data]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "211300", "date": "20 Oct 2023", "name": "Fabio Musso", "expertise": [ "Reviewer Expertise Business 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 manuscript has the objective to examine the existing cost reduction in Honolulu for those wishing to build an accessory dwelling unit on their properties for the purposes of senior housing.\nThe study can be considered just a preliminary review which highlights the factors to be considered when assessing the opportunities related to the accessory dwelling units-related projects.\nA valuable aspect of the study is that it tries to make an economic assessment of the factors to be considered when thinking about solutions related to the creation of accessory dwelling units and how tax breaks can stimulate the creation of such solutions.\nHowever, the study presents some critical issues. The first is related to the limited field of documentary sources examined, without having considered sources regarding other areas of the country or other countries. Similarly, a review of the literature on the topic would be necessary, even analyzing similar experiences at the national and international level.\nAnother limitation is in the perspective adopted for the evaluation: costs and benefits should be assessed also in the light of innovations in digital technologies (e.g. telemedicine, telesurveillance, domotics) that can lower the costs of elderly care. In this regard, the following publications should be taken into consideration:\nAngioni M., Musso F. (2020) “New perspectives from technology adoption in senior cohousing facilities”, The TQM Journal, Vol. 32, n. 4, pp. pp. 761-777. doi 10.1108/TQM-10-2019-0250\nMorris, M.E., Adair, B., Miller, K., Ozanne, E., Hampson, R., Pearce, A.J., Santamaria, N., Viegas, L., Long, M. and Said, C.M. (2013), “Smart-Home Technologies to Assist Older People to Live Well at Home”, Journal of Aging Science, Vol. 1 No. 1, pp. 1-9.\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? Partly", "responses": [] }, { "id": "222214", "date": "20 Nov 2023", "name": "Yifat Holzman-Gazit", "expertise": [ "Reviewer Expertise Regulation of accessory dwelling units (ADUs)", "zoning and property law", "land expropriation", "law and urban forests", "media coverage of supreme courts." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is a preliminary literature review (not a Systematic Review type of research) of factors to consider when assessing the costs of building accessory dwelling units for senior housing in Honolulu. This literature review highlights financing, tax breaks, and cost savings assessments that are relevant to creating ADUs as a housing option for senior family members. The study, however, has some limitations. To begin with, no comparisons are made between the experiences of this state with those in other states in the US or in other countries. Furthermore, it is unclear what are the differences between an \"Ohana Unit\" and an ADU, given the study's focus on providing family members with housing solutions. ADUs and Ohana units enable multigenerational families, aging in place, and economic security. Comparing the economic factors to be considered when building each type of housing is necessary. Lastly, the study ignores the link between ADUs and illegal vacation rentals. Instead of providing senior native Hawaiians (family members and non-members) with affordable housing, ADUs' may be used for vacation rentals. This avenue is likely to affect the costs and benefits of building an ADU along the prospect of using it after the death of a family member.\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? Partly", "responses": [] }, { "id": "222196", "date": "23 Nov 2023", "name": "Hafiszah Ismail", "expertise": [ "Reviewer Expertise Elderly Housing", "Quality of Life", "Generational Differences & Housing Studies" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? - NO - There are no explanations given on of the objectives which should be included in the Introduction of the paper\nAre sufficient details of the methods and analysis provided to allow replication by others? - NO - As for the method of the study, the author only conducted Google Searching with no other protocols of the proper method. Google Searching is not a proper method for Schematic Review type of paper. The Author is advised to follow proper protocols for Schematic Literature Reviews Paper (if the author intends to use the method - Schematic (SLR)).\nIs the statistical analysis and its interpretation appropriate? - NO - The are no statistical/proper analyses conducted in this paper. The author is advised to apply the SLR method for this type of paper.\nAre the conclusions drawn adequately supported by the results presented in the review? - PARTLY - A proper/suitable method of analysis needs to be conducted to derive to more comprehensive conclusion on the matter discussed.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? No\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1210
https://f1000research.com/articles/12-1209/v1	25 Sep 23	{ "type": "Case Report", "title": "Case Report: Metastatic central compartment in tongue carcinoma and it’s management", "authors": [ "Shreya Pawar", "Nitin Bhola", "Anchal Agarwal", "Bhushan Jajoo", "Nitin Bhola", "Anchal Agarwal", "Bhushan Jajoo" ], "abstract": "Tongue malignancies predominantly drain into Level I, II and III cervical lymph nodes. Metastasis of tongue primaries into these lymph nodes of the neck is a common phenomenon which warrants neck dissection. After the surgical intervention, there could be alteration in the lymphatic drainage of the oral cavity causing metastasis to aberrant levels of the neck. We present one such case which was previously operated for tongue cancer where wide local excision of lesion and neck dissection was done. The patient then reported with metastasis over Level VI and VII. Involvement of the central compartment of the neck in oral cavity cancers is a very rare occurrence but is possible. It is imperative to evaluate all the levels of neck for metastasis especially in previously operated cases.", "keywords": [ "Level VI", "Level VII", "central compartment", "metastasis", "oral cancer" ], "content": "Introduction\n\nOral cancer is ranked sixth amongst all the cancers.1 India harbours the most amount of oral cancer patients and it has one-third of all the oral cancer cases around the world.1 Metastasis to the cervical group of lymph nodes is a critical prognostic factor in cases with oral squamous cell carcinoma.2 Presence of cervical metastasis in oral cancer is indicative of aggressive behaviour.3 Node-positive (N+) patients have a 50% reduction in survival compared with node-negative (N−) patient.4 About 30% of oral cancer patients have subclinical metastasis to the neck lymph nodes.5 Kalnins et al., quote survival rates of 75% for a true N0 neck, falling to 49% if one node is involved, 30% if two nodes are involved, and 13% if three or more nodes are involved.6\n\nOral squamous cell carcinoma (OSCC) predominantly captivates the level I, II and III cervical lymph nodes and less commonly it spread to cervical lymph nodes in the level IV and level V groups, which represent 20% and 4% of cases, respectively.7\n\nInvolvement of the central compartment secondary to oral squamous cell carcinoma involving the Level VI and VII neck nodes is extremely unconventional which is also ascertained by Likhterov et al. in 2015 who reported two cases with central compartment involvement in recurrent oral squamous cell carcinoma for the first time in English literature.8 We report a certainly rare case of central compartment involvement in a recurrent case of squamous cell carcinoma of tongue.\n\n\nCase report\n\nA 41-year-old Indian daily wage construction site male worker came to our institute with a non-healing growth over the lateral border of tongue of the right side. There was no relevant family or medical history. On examination, there was a proliferative growth over the right lateral border of tongue of size 1.5×1.5 cm. The biopsy of this growth was reported as ‘well differentiated squamous cell carcinoma’. The MRI report was suggestive of a heterogeneously enhancing altered signal intensity lesion seen over the right lateral border of tongue of size 1×0.5×0.5 cm. The patient underwent wide local excision of the lesion, modified radical neck dissection (type III) of right side and primary closure which was done under general anaesthesia.\n\nThe post-operative margin report was suggestive of ‘well differentiated squamous cell carcinoma’. All margins were clear, pT size 2×1 cm, lymph nodes level I to level V bilaterally were negative for infiltration by malignant cells. The lesion was pT1N0Mx. He was under observation after that, no adjuvant therapy was given. After 8 months, the patient noticed a nodular swelling over the left submandibular region of size 2×1 cm. All other cervical lymph nodes were clinically non-palpable. Fine needle aspiration cytology from left submandibular gland was done which was suggestive of “metastasis of squamous cell carcinoma with foreign body granulomatous reaction” following which he underwent modified radical neck dissection of left side. The histopathological report of the specimens suggested the level IB node to be positive for infiltration by malignant cells. Radiotherapy was given to bilateral face and neck to a dose of 60 Gy in 30 fractions using the intensity modulated radiation therapy [IMRT] technique with weekly Inj. Cisplatin 50 mg/mL. The patient was on follow up after that.\n\nThe patient then reported 1 year later, complaining of swelling over suprasternal region [Figure 1] which gradually increased to the size of 3×2.5 cm and was associated with dull aching pain. On oral examination, there was no evidence of any recurrence of lesion or any second primary tumor in the oral cavity.\n\nFine needle aspiration cytology of the swelling over the suprasternal region was suggestive of “deposits of squamous cell carcinoma”. The PET scan showed no evidence of any distant metastasis [Figure 2].\n\nWide local excision of the lesion over the sternoclavicular joint was carried out with 1 cm of margin [Figure 3]. The tumor was seen encroaching the bone [Figure 4]. Hence, removal of the right sternoclavicular joint was carried out [Figure 5]. Histopathological report of the resected specimen was suggestive of “Moderately differentiated squamous cell carcinoma”. The decalcified bone was positive for infiltration by malignant cells. The patient was on regular follow up. On 6 months clinical follow up, the surgical site was healthy. There was no evidence of recurrent lesion. Nor were there any signs of lymphadenopathy.\n\n\nDiscussion\n\nThe level VI or the tracheoesophageal group of lymph nodes is surrounded superiorly by the hyoid bone, inferiorly by the suprasternal and laterally by the strap muscles.9 The anterior aspect of the neck, pharynx, larynx, oesophagus, thyroid drain lymph into level VI cervical group of lymph nodes. Lymph nodes in the tracheoesophageal groove and the anterior upper mediastinum are considered to be level VII lymph nodes. It reaches the innominate artery from the suprasternal notch.9\n\nFerlito et al. suggested that the skip metastasis of the oral tongue to clinically negative nodes is seen in 20% to 30% of patients.10 The patients who have undergone surgical ablation of the primary tumor and neck dissection followed by adjuvant radiation therapy, the rates of local, regional, and locoregional recurrence are 16.5%, 5.3%, and 4.9%, respectively.11 The predominant lymphatic drainage of the tongue takes place in Level I, II and III cervical lymph nodes.\n\nMetastasis is a familiar sequela of oral carcinoma. If the metastasis skips any regional lymph node and show dysplastic features into the peripheral lymph node then it is known as ‘skip metastasis’ (SM) or ‘nodal skip metastasis’ (NSM). Byers RM., et al. (1997) concluded that the usual supra-omohyoid neck dissection is inadequate for a complete pathologic evaluation of all the nodes at risk for patients with squamous cell carcinoma of the oral tongue due to skip metastasis to level IV in 15.8% of population.12 Pantvaidya et al. (2014) prospectively studied 583 cases of oral cancer through lymph node mapping and found that in 95.7% the metastasis was seen in Level I to Level IV cervical lymph nodes.13\n\nCancer of oral cavity metastasizes to the cervical lymph nodes in a predictable fashion based on the primary sites or subsites. Metastasis of tumor cells to level VI and level VII group of lymph nodes is rare. The incidence of this distinctive phenomenon of level VI lymph node involvement in primary oral squamous cell carcinoma was noted by Zhang et al. in 2021 to be 0.69% of incidence for the first time in the literature.7 Level VII lymph node involvement is uncommon but it does exist. Five of the 779 head and neck cancer patients depicted by Probert et al. acquired mediastinum metastasis, of which four cases were found by autopsy.14\n\nThere are a few theories mentioned about this odd occurrence. Lymphatic drainage is altered after previous surgical interventions. This theory's most likely interpretation is that the obstruction of the afferent lymphatic vessels causes the lymphatic drainage to be diverted along other pathways.\n\nThis is well established in breast cancer studies. Estourgie et al. reported on lymphoscintigraphy studies before and after excisional biopsies of breast masses. Changes in axillary and internal mammary lymph node drainage were noted in 68% of patients.15\n\nAn alternative hypothesis is the seeding of malignant cells in the middle aspect of the neck during previous tracheotomy as is mentioned by Likhterov et al.8 In our case, the patient did not undergo tracheostomy or any intervention in the central compartment during the previous surgery. Hence, seeding of tumor cells would not be applicable in this case.\n\nIn this case, the lesion was seen encroaching the bone but did not involve the thoracic cavity. In PET scan, there was no evidence of distant metastasis. Hence, wide local excision of the lesion was done. The lesion was fixed to the sternoclavicular joint of the right side. Removal of the right sternoclavicular joint was done which was found to be positive for infiltration by malignant cells. With the surgical approach, the lesion was removed with adequate margins. The patient could resume his work 4 weeks after the surgery and could carry out everyday chores smoothly.\n\nThere are no extensive studies in the literature which have assessed the aberrant lymphatic drainage after neck dissection in head and neck cancer surgeries.\n\n\nConclusion\n\nNodal involvement of central compartment in level VI and level VII is a rather very rare finding, but is still possible in cases of oral cavity cancers. This could be expected in cases which have undergone neck dissection previously. Thorough evaluation of the entire neck should be done to rule out metastasis at these aberrant areas of the neck and appropriate management should be carried out.\n\n\nConsent\n\nWritten informed consent for the publication of the case report and associated images was duly taken from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nBorse V, Konwar AN, Buragohain P: Oral cancer diagnosis and perspectives in India. Sens. Int. 2020; 1: 100046. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen CC, Lin JC, Chen KW: Lymph node ratio as a prognostic factor in head and neck cancer patients. Radiat. Oncol. Lond. Engl. 2015 Aug 25; 10: 181. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontoro JR d MC, Hicz HA, de Souza L , et al.: Prognostic factors in squamous cell carcinoma of the oral cavity. Braz. J. Otorhinolaryngol. 2008 Nov 1; 74(6): 861–866. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTankéré F, Camproux A, Barry B, et al.: Prognostic value of lymph node involvement in oral cancers: a study of 137 cases. Laryngoscope. 2000 Dec; 110(12): 2061–2065. PubMed Abstract \| Publisher Full Text\n\nShah JP: Patterns of cervical lymph node metastasis from squamous carcinomas of the upper aerodigestive tract. Am. J. Surg. 1990 Oct; 160(4): 405–409. Publisher Full Text\n\nKalnins IK, Leonard AG, Sako K, et al.: Correlation between prognosis and degree of lymph node involvement in carcinoma of the oral cavity. Am. J. Surg. 1977 Oct; 134(4): 450–454. PubMed Abstract \| Publisher Full Text\n\nZhang S, Zhang R, Wang C, et al.: Central neck lymph node metastasis in oral squamous cell carcinoma at the floor of mouth. BMC Cancer. 2021 Mar 5; 21: 225. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLikhterov I, Rowe ME, Khorsandi AS, et al.: Oral cavity squamous cell carcinoma metastatic to central compartment (level 6) lymph nodes. Laryngoscope. 2016; 126(8): 1803–1805. PubMed Abstract \| Publisher Full Text\n\nKoroulakis A, Jamal Z, Agarwal M: Anatomy, Head and Neck, Lymph Nodes. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023 [cited 2023 Mar 29]. Reference Source\n\nFerlito A, Shaha AR, Rinaldo A, et al.: “Skip Metastases” from Head and Neck Cancers. Acta Otolaryngol (Stockh). 2002 Jan 1; 122(7): 788–791. Publisher Full Text\n\nNisa L, Khanfir K, Giger R: Recurrence due to neoplastic seeding in head and neck cancer: report of two cases and review of the literature. Tumori. 2013; 99(4): e144–e147. PubMed Abstract \| Publisher Full Text\n\nByers RM, Weber RS, Andrews T, et al.: Frequency and therapeutic implications of “skip metastases” in the neck from squamous carcinoma of the oral tongue. Head Neck. 1997 Jan; 19(1): 14–19. PubMed Abstract \| Publisher Full Text\n\nPantvaidya GH, Pal P, Vaidya AD, et al.: Prospective study of 583 neck dissections in oral cancers: implications for clinical practice. Head Neck. 2014 Oct; 36(10): 1503–1507. PubMed Abstract \| Publisher Full Text\n\nProbert JC, Thompson RW, Bagshaw MA: Patterns of spread of distant metastases in head and neck cancer. Cancer. 1974 Jan; 33(1): 127–133. Publisher Full Text\n\nEstourgie SH, Nieweg OE, Olmos RAV, et al.: Lymphatic drainage patterns from the breast. Ann. Surg. 2004 Feb; 239(2): 232–237. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "249378", "date": "07 Mar 2024", "name": "Devaraja K", "expertise": [ "Reviewer Expertise Head and neck surgeon" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting case report on metastatic lymphadenopathy involving the central compartment in recurrent oral cancer. The report is well-written, with an adequate description of the case details and illustrations. It would be useful if authors could provide details on reconstruction after the wide local excision of the node with involved skin and sternoclavicular joint, whether it was primary closure. or a deltopectoral flap/pectoralis major was used? And, if possible, a clinical picture of the final healing of the surgical site. As mentioned by the authors, such reports are reported only a couple of times in the earlier literature, and the working hypothesis of altered lymphatic drainage pathway due to prior surgical (and even possibly radiotherapy-induced) treatment seems fitting. Overall, this report is quite educative and adds to the literature. As such metastatic lesions are rarely reported in the literature, it would be interesting to learn the long-term outcome of this case, that is, if the authors can update on that subsequently in any way possible.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1209
https://f1000research.com/articles/12-1208/v1	25 Sep 23	{ "type": "Research Article", "title": "Effect of clinical risk factors on bacteriological profile in neonatal sepsis: A descriptive cross-sectional study at a tertiary care center, Nepal", "authors": [ "Prem Shankar Chaurasiya", "Umesh Kumar Singh", "Bibek Kumar Yadav", "Ajay Kumar Chaurasiya", "Poonam Rani Shah", "Umesh Kumar Singh", "Bibek Kumar Yadav", "Ajay Kumar Chaurasiya", "Poonam Rani Shah" ], "abstract": "Background: Neonatal sepsis is an important cause of neonatal mortality and morbidity worldwide. The common causative bacteria are Group B Streptococci, Escherichia coli, Listeria monocytogenes, Staphylococcus, Enterococci, Klebsiella, and Enterobacter. The risk factors are premature rupture of membrane, meconium-staining, foul-smelling amniotic fluid, low birth weight, prematurity, low Apgar score, mode of deliveries, and mechanical ventilation. The treatment for neonatal sepsis is a beta-lactam antibiotic combined with an aminoglycoside. The aim of the study was to find the incidence and factors associated with culture-positive neonatal sepsis, and common bacterial isolates. Methods: A hospital-based retrospective cross-sectional study was conducted among 385 neonates admitted with neonatal sepsis at Narayani Central Hospital, Birgunj from July 2021 to July 2022. Ethical approval was taken from the Institutional Review Committee, Nepalese Army Institute of Health Sciences, Nepal (Reference no. 669/ 2022). A convenient sampling was followed. Data regarding different clinical factors were collected in a structured questionnaire. The data was entered and analyzed through SPSS version 22.0 using a binary regression model. Results: The study revealed the mean age, weight, and gestational age of neonates were 2.79kg±0.55kg, 6.19±3.87 days, and 37.64±1.27 weeks respectively. Out of the total cases, 26.5% (102) were culture-positive neonatal sepsis. Staph aureus was the predominant pathogen (40, 39.2%) followed by Klebsiella (25, 24.5%) and Acinetobacter (16, 15.7%). The Premature rupture of membrane (OR=4.32, 95% CI: 2.20–8.47) and Mothers with foul-smelling amniotic fluid (OR=3.03, 95% CI: 1.32–6.92) are statistically associated with culture-positive neonatal sepsis. Conclusion: The factors responsible for the high burden of neonatal sepsis such as premature rupture of membrane, foul-smelling amniotic fluid, prematurity, low birth weight, unhygienic home delivery practices, can be avoided dramatically. The role of pediatricians, nurses, hospital administrations and general awareness among mothers about hygienic practices during parturition are essential to minimize neonatal mortality and morbidity.", "keywords": [ "amniotic fluid", "antibiotics", "demography", "gestation", "hospitalization" ], "content": "Introduction\n\nNeonatal sepsis is an important etiology of neonatal mortality and morbidity. The global incidence of neonatal infection in a study was 7.3 per 1000 live births.1 At national level, 16% of total perinatal death was because of neonatal sepsis in Nepal.2 The common organism of neonatal sepsis are Group B Streptococci, Escherichia coli, Listeria monocytogenes, Staphylococcus sp, Enterococci, Klebsiella, Enterobacter, and Pseudomonas.3 The responsible major factors associated with early-onset neonatal sepsis are foul-smelling amniotic fluid, premature rupture of membrane, meconium-stained amniotic fluid, prematurity (<37 weeks gestation), low birth weight(<2.5kg), low Apgar score (<7)4 and mode of deliveries. The risk factors for late onset neonatal sepsis are invasive mechanical ventilation, intravascular catheterization, delay of early enteral feeding with breast milk, prolonged parenteral nutrition, cardio-pulmonary diseases, and hospital admission.5 The beta-lactam antibiotic combined with an aminoglycoside are mainstay of the treatment of neonatal sepsis. However, cephalosporin (cefotaxime) and a glycopeptide (vancomycin) have been frequently used to treat late-onset sepsis.6 The aim of this study is to find the incidence and risk factors associated with culture-positive neonatal sepsis, and common bacterial agents responsible for it.\n\n\nMethods\n\nThe Institutional Review Committee (IRC), Nepalese Army Institute of Health Sciences, Nepal provided ethical clearance in September 2022 with reference no 669/2022 after submitting the proposal letter beforehand. A proper parental informed written consenting process was followed before the study began via a validated proforma. The consent was also taken regarding their case notes to be used for the study purpose. Those who refused were excluded from the study. The study began with face-to-face interviews that lasted approximately 10 to 15 minutes.\n\nPatients were not involved in the design, conduct, reporting, or dissemination plans of our research.\n\nThe methods used for data collection was a questionnaire,27 which was completed via face to face interviews and case notes available from record section of the hospital. This hospital-based retrospective cross-sectional study was conducted among neonates admitted to neonatal intensive care unit (NICU) from July 2021 to July 2022 at Narayani Central Hospital in Birgunj, Nepal. The data collection was performed in September 2022 after ethical clearance was obtained.\n\nNarayani Central Hospital is one of the tertiary-level central government hospitals running under the Ministry of Health and Population of Nepal, with a total of 200 beds. The hospital lies in Parsa, the southern part of Nepal, bordering India. The hospital is a referral center for the population from province number two as well as the Bihar state of India. It provides many specialist services in addition to general health services. The pediatric department reports a high number of neonatal sepsis cases per month (n = 26 on average).\n\nThe Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines were strictly followed during the study.28\n\nA minimum sample of 380 samples were calculated considering an infinite population proportion of neonatal sepsis (44.96%) based on a previous study.7 However, we included 385 samples meeting the selection criteria for the study.\n\nThe detailed calculation is the following:\n\nn = required sample size\n\nz = 1.96 at alpha 5% level of significance\n\np = prevalence = 0.11; q (compliment of prevalence) = 0.89\n\nE = allowable error, 5%\n\nAfter ethical clearance from IRC of the Nepalese Army Institute of Health Sciences, the study began by reviewing hospital records from the Department of Pediatrics, Narayani Hospital, and the record section of the hospital. A proper parental consent process was followed before commencement of study proper via a validated proforma. We selected 385 neonates with sepsis through convenience sampling methods from all cases admitted to NICU from July 2021 to July 2022. All newborns born and admitted to NICU from July 2021 to July 2022 were included. Cases with incomplete data and ambiguous information were excluded.\n\nThe sample cases were selected via convenient type of sampling methods. All suspected, as well as culture-positive neonatal sepsis cases were included in the study. A clinically suspected neonatal sepsis is defined as a positive septic screen but no growth within 72 hours of culture. The demography section of the questionnaire comprises both qualitative and quantitative data such as the mother’s name, age, sex, and address. These were recorded carefully in the questionnaire during interview processes. Similarly, different maternal risk factors (such as mode of delivery, premature rupture of membrane, foul-smelling amniotic fluid) and neonatal risk factors (such as weight, prematurity) were recorded in the questionnaire from the clinical case notes. The types of different bacterial growth with corresponding drug sensitivity were also recorded.\n\nThe collected data26 were entered and analyzed using Statistical Packages for Social Sciences (SPSS), IBM SPSS® version 22. Descriptive statistics such as frequency, percentage, mean, ranges, and standard deviations were used to express the statistics. An appropriate graph/chart was used to represent the study results. A multivariate regression analysis tool was applied for the risk association of different above-mentioned clinical risk factors with neonatal sepsis. For binary logistic regression analysis, odds ratios (OR) and 95% Confidence Interval (CI) were calculated, and significance was established at 5% level.\n\n\nResults\n\nOur study revealed 2.79 kg±0.55 kg as the mean birthweight of neonates (Table 1). Likewise, the mean age of neonates who participated in the study at the time of neonatal sepsis diagnosis was 6.19 days with a standard deviation of 3.87 days. The neonates had an average gestational age of 37.64±1.27 weeks at the delivery time. Among 385 participants, more than half 225 (58.4%) were male, and the remaining were female.\n\nMoreover, neonates with a weight less than 2500 g (low Birth weight, LBW) were 107 (27.8%) (Table 2). Only 8.3% (32) neonates were born prematurely (<37 weeks). Premature rupture of membrane was reported in 11.4% of mothers. The record showed only 28 mothers had foul-smelling amniotic fluid at the time of delivery. Most women had a normal vaginal delivery (222, 57.7%) followed by cesarean section (153, 39.7%).\n\nMost of the neonatal sepsis diagnoses were clinically diagnosed (283, 73.5%) (Table 3). The remaining cases (102, 26.5%) were culture-positive neonatal sepsis.\n\nAccording to chronology (Table 4), late neonatal sepsis was the predominant diagnosis (85.5%. 329).\n\nOut of 102 culture-positive neonatal sepsis, Staph aureus was found to be the predominant pathogen (40, 39.2%) in culture isolates followed by Klebsiella (25, 24.5%) and Acinetobacter (16, 15.7%) (Table 5).\n\nThere is a statistically significant association between culture-positive neonatal sepsis and prematurity and foul-smelling amniotic fluid. While association with gender, types of neonatal sepsis (early or late), low birth weight, prematurity, and mode of delivery were insignificant. The premature rupture of membrane was four times more likely to have associations with culture-positive neonatal sepsis (OR=4.32, 95% CI: 2.20–8.47). Similarly, mothers with foul-smelling amniotic fluid were three times more likely to have culture-positive neonatal sepsis (OR=3.03, 95% CI: 1.32–6.92) (Table 6).\n\na Low birth weight <2.5 kg.\n\nb Premature rupture of membrane (rupture of amniotic membrane before 37 weeks period of gestation).\n\n\nDiscussion\n\nThe incidence of culture-positive neonatal sepsis was low in our study (26.5%). The results were close to a study done in Ethiopia (29.3%)8 and Tamil Nadu, India (26.2%).9 A study based in Nepali, showed 42.7% of cases were blood culture positive and 57.3% (110 cases) had culture-negative but clinically suspected neonatal sepsis with features of sepsis.10 The late type neonatal sepsis was major category in our study and about four times the early type of neonatal sepsis (73.5%). The findings are similar to a study in Australia where an incidence of early-onset and late onset neonatal sepsis was 0.51% and 1.3% per 1000 live births (2.5 times that of early neonatal sepsis).11 This may partly be due to the high prevalence of risk factors associated with late neonatal sepsis. At a global level, the early onset type is 2.6 times more common with respect to late-onset neonatal sepsis according to a study in a systematic review and meta-analysis.12 The bacterial spectrum demonstrated Staphylococcus aureus as a common pathogen to cause neonatal sepsis followed by Klebsiella. The results are different in other similar studies. Similar studies found Escherichia coli and Streptococcus agalactiae were the most frequent organisms associated with early-onset neonatal sepsis whereas Coagulase-negative Staphylococcus (co-NS) was the main culprit of late-onset neonatal sepsis.13 Similarly, a Nepali hospital based study found Klebsiella pneumoniae (34%) and Enterobacter spp. (25%) as the most common bacterial isolates.14 A study concluded that Escherichia coli was the predominant organism in both early-onset and late-onset type neonatal sepsis, however, Staphylococcus aureus was common in late-onset sepsis.15 A hospital study done in Saudi Arabia reported that the proportion of neonatal sepsis (clinical and culture positive) was almost equivalent in both males (52%) and females (48%).16 However, males had a slightly higher association (59%) with culture-positive sepsis in our study. The current study demonstrated that late-onset neonatal sepsis is nine times more associated with culture-positive sepsis. The above findings are supported by a Myanmar based study that concluded that neonates with late-onset sepsis (LOS) were more probable to have bacteriologically confirmed sepsis (45%) versus early onset sepsis (38%) (aPR: 1.2 (95% CI: 1.1–1.4)).17 But in a similar study, positive blood culture was found in equal proportion in early (47.1%) and late-onset (51.4%) neonatal sepsis respectively.18 As per our study, neonates with low birth weight constitute 23.5% of culture-positive neonatal sepsis. Furthermore, prematurity was present in 7.8% of all culture-positive neonatal sepsis. A similar study based in USA, concluded that the incidence of sepsis is significantly higher in premature infants, as well as those with very low birth weight (<1000 grams).19 The current study also showed normal vaginal and cesarean delivery modes were equally prevalent in culture-positive sepsis. A study completed in Nepal revealed the highest incidence of positive bacterial growth in male newborns (52.3%); 72 hours or more age (71.2%); low birth weight (62.7%); preterm (31.4%); and post cesarean cases (63.3%).10 Our study has demonstrated a statistically significant association between premature rupture of membrane (PROM) and foul-smelling amniotic fluid with culture positive type neonatal sepsis. A significant association was seen between blood culture positivity with foul-smelling amniotic fluid (p = 0.025), PROM (p = 0.016), birth asphyxia, and low birth weight (p = 0.003) in other similar studies.20 A hospital based study showed neonatal sepsis was present in 2.7% of mothers who had early rupture on membranes.21 Similarly, in a study done in B.P. Koirala Institute of Health Sciences (BPKIHS) institute, PROM, meconium-stained and foul-smelling amniotic fluid, low birth weight, prematurity, and low Apgar score were significant risk factors leading to neonatal sepsis.22 Another study established an association of early type Neonatal Sepsis with PROM, foul-smelling amniotic fluid, traditional midwife handling, and maternal urinary tract infection (p < 0.05).23 The major perinatal factors for neonatal sepsis in a similar study were prolonged labor, PROM, maternal pyrexia within 2 weeks (>38°C), foul-smelling amniotic fluid (13%), low apgar score (20%) and unhygienic or >3 sterile per vaginal examinations.24 A meta-analysis and systemic review study based in India, found that male sex, outborn neonates, mechanical ventilation, prematurity, and PROM as significant clinical factors for neonatal sepsis.25\n\nThe sample was taken from the study population visiting the hospital. Therefore, its findings cannot be generalized to other places. As the study design is cross-sectional, the associated risk factors cannot establish casualty.\n\n\nConclusions\n\nNeonatal sepsis is prevalent mostly in an underdeveloped countries like Nepal. The contributing factors for the high burden of neonatal sepsis are premature rupture of membrane, foul-smelling amniotic fluid, prematurity, and low birth weight, unhygienic home delivery practices. Addressing the factors above, the incidence and its impact can be avoided dramatically. The role of pediatricians, nurses, hospital administrations and general awareness among mothers about hygienic practices during parturition is essential to minimize overall neonatal mortality and morbidity.\n\n\nPatient consent\n\nParents’ written informed consent was received after full explanation of research purposes and processes.", "appendix": "Data availability\n\nFigshare: Data neonatal sepsis. https://doi.org/10.6084/m9.figshare.21505314. 26\n\nThis project contains the following underlying data:\n\n- Data neonatal sepsis.sav (Raw data entered into SPSS)\n\nFigshare: Questionnaire neonatal sepsis. https://doi.org/10.6084/m9.figshare.21304599. 27\n\nThe project contains the following extended data:\n\n- questionnaire neonatal sepsis.pdf (Tool used for data collection)\n\nFigshare: STROBE checklist for “Effect of clinical risk factors on bacteriological profile in neonatal sepsis: A descriptive cross-sectional study at a tertiary care center, Nepal”. https://doi.org/10.6084/m9.figshare.22353955. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe would like to express our heartfelt gratitude to the hospital record section and the staff working at the NICU department of Narayani Hospital for supporting us to conduct this research work.\n\n\nReferences\n\nBudhathoki SS, Sunny AK, Paudel PG, et al.: Epidemiology of neonatal infections in hospitals of Nepal: evidence from a large- scale study. Archives of Public Health. 2020 May 7 [cited 2022 Nov 12]; 78(1): 39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNepal Demographic and Health Survey: 2016.\n\nYadav NS, Sharma S, Chaudhary DK, et al.: Bacteriological profile of neonatal sepsis and antibiotic susceptibility pattern of isolates admitted at Kanti Children’s Hospital, Kathmandu, Nepal. BMC. Res. Notes. 2018 May 15 [cited 2022 Nov 12]; 11(1): 301. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDirirsa DE, Degefa BD, Gonfa AD: Determinants of neonatal sepsis among neonates delivered in Southwest Ethiopia 2018: A case-control study. SAGE Open Med. 2021 Jan [cited 2022 Nov 12]; 9: 205031212110270. PubMed Abstract \| Free Full Text\n\nBhutta ZA, Yusuf K: Early-onset neonatal sepsis in Pakistan: a case control study of risk factors in a birth cohort. Am. J. Perinatol. 1997 [cited 2022 Nov 12]; 14(9): 577–581. Publisher Full Text Reference Source\n\nKorang SK, Safi S, Gluud C, et al.: Antibiotic regimens for neonatal sepsis - a protocol for a systematic review with meta-analysis. Syst. Rev. 2019 Dec 5 [cited 2022 Sep 4]; 8(1): 306. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNamrata KC, Shrestha B, Bhattarai A, et al.: Pattern of morbidity and mortality among neonates admitted to neonatal intensive care unit in tertiary care centre, western Nepal. J. Gandaki Med. Coll. Nepal. 2021 Jul 3; 14(1): 24–28. Publisher Full Text\n\nSorsa A: Epidemiology of Neonatal Sepsis and Associated Factors Implicated: Observational Study at Neonatal Intensive Care Unit of Arsi University Teaching and Referral Hospital, South East Ethiopia. Ethiop. J. Health Sci. 2019 May 1 [cited 2022 Sep 4]; 29(3): 333–342. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPavan Kumar D, Mohan J, Rakesh P, et al.: Bacteriological profile of neonatal sepsis in a secondary care hospital in rural Tamil Nadu, Southern India. J. Family Med. Prim. Care. 2017; 6(4): 735–738. PubMed Abstract \| Publisher Full Text\n\nSingh DS, Rpb S, Shrestha S: Unproven Early Onset Sepsis in NICU. Kathmandu Univ. Med. J. 2013; 44.\n\nWright N, Francis L, Bonney D, et al.: Epidemiology of early and late-onset neonatal sepsis in an Australian regional special care nursery with a high proportion of Aboriginal and Torres Strait Islander births. J. Paediatr. Child Health. 2022 Sep 1 [cited 2022 Oct 26]; 58(9): 1594–1600. PubMed Abstract \| Publisher Full Text\n\nFleischmann C, Reichert F, Cassini A, et al.: Global incidence and mortality of neonatal sepsis: a systematic review and meta-analysis. Arch. Dis. Child. 2021 Aug 1 [cited 2022 Oct 26]; 106(8): 745–752. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nGuo J, Luo Y, Wu Y, et al.: Clinical Characteristic and Pathogen Spectrum of Neonatal Sepsis in Guangzhou City from June 2011 to June 2017. Med. Sci. Monit. 2019 [cited 2022 Oct 26]; 25: 2296–2304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nManandhar S, Amatya P, Ansari I, et al.: Risk factors for the development of neonatal sepsis in a neonatal intensive care unit of a tertiary care hospital of Nepal. BMC Infect. Dis. 2021 Dec 1 [cited 2022 Oct 26]; 21(1): 511–546. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShrestha N, Subedi K, Rai G: Bacteriological Profile of Neonatal Sepsis: A Hospital Based Study. J. Nepal Paediatr. Soc. 2011 Jan 1 [cited 2022 Oct 26]; 31(1): 1–5. Publisher Full Text Reference Source\n\nAlmudeer AH, Alibrahim MA, Gosadi IM: Epidemiology and risk factors associated with early onset neonatal sepsis in the south of KSA. J. Taibah Univ. Med. Sci. 2020 Dec 1; 15(6): 509–514. PubMed Abstract \| Publisher Full Text\n\nOo NAT, Edwards JK, Pyakurel P, et al.: Neonatal sepsis, antibiotic susceptibility pattern, and treatment outcomes among neonates treated in two tertiary care hospitals of Yangon, Myanmar from 2017 to 2019. Trop. Med. Infect. Dis. 2021; 6(2). Publisher Full Text\n\nKayange N, Kamugisha E, Mwizamholya DL, et al.: Predictors of positive blood culture and deaths among neonates with suspected neonatal sepsis in a tertiary hospital, Mwanza- Tanzania. BMC Pediatr. 2010 Jun 4 [cited 2022 Nov 3]; 10(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSingh M, Alsaleem M, Gray CP: Neonatal Sepsis. StatPearls.2022 Sep 29 [cited 2022 Nov 3]. Reference Source\n\nPankaj KC, Ganguly S, Upadhyay MR: Forecasting the possibility of neonatal early onset sepsis based on perinatal risk factors. Int. J. Contemp. Pediatrics. 2020 Jun 24 [cited 2022 Nov 4]; 7(7): 1534–1539. Publisher Full Text Reference Source\n\nAlam MM, Saleem AF, Shaikh AS, et al.: Neonatal sepsis following prolonged rupture of membranes in a tertiary care hospital in Karachi, Pakistan. J. Infect. Dev. Ctries. 2014; 8: 067–073. Publisher Full Text\n\nShah GS, Budhathoki S, Das BK, et al.: Risk factors in early neonatal sepsis. Kathmandu Univ. Med. J. (KUMJ). 2006 Apr-Jun; 4(2): 187–191. PubMed Abstract\n\nChacko B, Sohi I: Early onset neonatal sepsis. Indian J. Pediatr. 2005 Jan 1 [cited 2022 Nov 4]; 72(1): 23–26. Publisher Full Text\n\nVolume 16 Issue 3.[cited 2022 Nov 4]. Reference Source\n\nMurthy S, Godinho MA, Guddattu V, et al.: Risk factors of neonatal sepsis in India: A systematic review and meta-analysis. PLoS One. 2019 Apr 1 [cited 2022 Nov 4]; 14(4): e0215683. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaurasiya P: Data Neonatal Sepsis.sav. [Data]. Figshare. 2022. Publisher Full Text\n\nChaurasiya P: questionnare COPD.pdf. [Data]. Figshare. 2022. Publisher Full Text\n\nChaurasiya P: STROBE-checklist-v4-cross-sectional Neonatal sepsis.doc. Figshare. 2023. Publisher Full Text" }	[ { "id": "239011", "date": "11 May 2024", "name": "Adeyemi Temitayo Adeyemo", "expertise": [ "Reviewer Expertise Clinical bacteriology", "anaerobic bacteriology", "antimicrobial resistance and stewardship", "infection prevention and 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\nAbstract: Conclusion should be re-written to reflect the findings from the study. Title:\nThe title in this present form lacks clarity clear and it does not completely reflect what the study was about. I suggest it be recast as “Bacteriology and clinical risk factors of culture-positive neonatal sepsis: A descriptive cross-sectional study at tertiary care center, Nepal” Introduction:\nConcise and good. Methods: 1. Ethical clearance- The last statement in this section, i.e “The study began with face-to-face interviews that lasted approximately 10 to 15 minutes”, does not say anything bordering on ethical clearance. It should be moved to the appropriate section, 2. Study Design and Setting- Citations 27 and 28 are not relevant to this study, they should be removed. 3. The section on sample size calculation should be followed by another section with a heading “Data Collection” 4. It is stated that some data were collected by face-to-face interview. The author should state with who the face-to-face interview was conducted, the study being retrospective. 5. Statistical Analysis: citation 26 is out of chronological order Results: Parameters in Table 2 can not be regarded to as risk factors having not been subjected to multivariate statistical analysis as they are presented. It can be changed to “Clinical parameters of mothers and neonates” Discussions: 1. The author should give reasons for low rate of culture positive neonatal sepsis in their setting if known. Could it be because of the laboratory method deployed or possibility of infection by difficult to isolate bacteria or other non-bacterial agents which the laboratory is not set out to identify. 2. To discuss that culture positive neonatal sepsis is common with prematurity as intended, rather than stating that “prematurity was present in 7.8% of all culture-positive neonatal sepsis”, it is better to express this as “culture-positive neonatal sepsis was recorded in a third of premature neonates” Conclusions:\nThe author gave general remarks that are not findings from the study. The conclusion should be drawn from the study findings. References:\nReference 24 should be written properly to type.\n\nIs the work 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? No", "responses": [] }, { "id": "274378", "date": "11 May 2024", "name": "Vishnu Bhat Ballambattu", "expertise": [ "Reviewer Expertise Neonatology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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.This is a retrospective descriptive study. There is no comparison group and authors looked at culture positive cases 2.A case-control design would have been better 3.Authors mention that they have taken consent from parents. How did they achieve it in a record based study? 4.The data indicates that there were more near term babies with mean time of sepsis onset >6days. This suggests that most of them had (>85%) late onset sepsis. Hence nosocomial factors are more important. 5.Conclusion should be derived from the results. Authors have not looked into hygienic conditions while concluding that they will reduce morbidity and mortality. 6.As indicated by authors, culture positivity was only 26.5%\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1208
https://f1000research.com/articles/12-1205/v1	25 Sep 23	{ "type": "Software Tool Article", "title": "Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.", "authors": [ "Felipe Marques de Almeida", "Tatiana Amabile de Campos", "Georgios Joannis Pappas Jr", "Felipe Marques de Almeida", "Tatiana Amabile de Campos" ], "abstract": "Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago. However, transforming raw reads into a complete genome model is a significant computational challenge due to the varying quality and quantity of data obtained from different sequencing instruments, as well as intrinsic characteristics of the genome and desired analyses. To address this issue, we have developed a set of container-based pipelines using Nextflow, offering both common workflows for inexperienced users and high levels of customization for experienced ones. Their processing strategies are adaptable based on the sequencing data type, and their modularity enables the incorporation of new components to address the community’s evolving needs. Methods: These pipelines consist of three parts: quality control, de novo genome assembly, and bacterial genome annotation. In particular, the genome annotation pipeline provides a comprehensive overview of the genome, including standard gene prediction and functional inference, as well as predictions relevant to clinical applications such as virulence and resistance gene annotation, secondary metabolite detection, prophage and plasmid prediction, and more. Results: The annotation results are presented in reports, genome browsers, and a web-based application that enables users to explore and interact with the genome annotation results. Conclusions: Overall, our user-friendly pipelines offer a seamless integration of computational tools to facilitate routine bacterial genomics research. The effectiveness of these is illustrated by examining the sequencing data of a clinical sample of Klebsiella pneumoniae.", "keywords": [ "bacterial genomics", "pipelines", "nextflow", "antibiotic resistance", "public health", "virulence" ], "content": "Introduction\n\nAs whole genome sequencing has been established as a routine procedure in research projects worldwide, the computational analysis of sequencing data takes center stage, and it is often the main operational barrier to which biologists stumble (Xuan et al., 2013; Berger and Yu, 2022). Over the years, many open-source software tools were created to tackle different processing steps along intricate computational protocols geared toward different data processing scenarios. Notwithstanding, materializing the data analysis workflow is a non-trivial stage that many biologists face, given challenges ranging from the selection and installation among a vast assortment of computational tools to the logic of enactment of processing steps. Consequently, analyses can be performed in many ways by different groups raising issues of reproducibility and provenance (Grüning et al., 2018; Djaffardjy et al., 2023). Also, individual teams face problems implementing the processing workflow, inventorying the requirements, and optimizing performance and scalability (Wratten et al., 2021; Mölder et al., 2021).\n\nBacterial whole-genome sequencing has become mainstream in many microbiological settings, such as taxonomy, ecology, and clinical diagnostics. In concert with these applications, several tailored computational workflows, also known as pipelines, were created for bacterial genomics, each with a different underlying design and implementation approach (Petit and Read, 2020). Despite their similarities, each pipeline is unique and may provide different outcomes, considering that they were developed with different components and parameters. Most of the pipelines are designed to work with limited sequencing data types while focusing on specific annotation tasks, such as functional annotation of open reading frames, antibiotic resistance genes, and variant calling using reference genomes (Olawoye et al., 2020; Quijada et al., 2019; Ruiz-Perez et al., 2021; Sserwadda and Mboowa, 2021). Thus, there is still a need for more generic pipelines that give the user an extensive overview of their data while creating visually rich outputs whilst guaranteeing reproducibility.\n\nHere we describe three pipelines built using the workflow composition system Nextflow (Tommaso et al., 2017). These were specifically designed in a modular way to standardize and facilitate bacterial genomic analysis from the standpoint of non-bioinformaticians relieving the issues of installation, configuration, and execution. Altogether, the pipelines are usable in different analytical scenarios, capable of handling data from different sequencing platforms, ranging from small single-genome projects executed on a personal computer to larger multi-genome projects to be executed in cloud computing platforms. We also leverage the use of operating system virtualization, packing the pipelines to use software containers that provide all required supporting programs without the need to install the required operating system and pipeline components.\n\nTogether, they offer a seamless exposition of computational tools to provide an easy framework for analyzing and interrogating data in routine bacterial genomics. To illustrate the system’s functionality, we provide a full analytical illustration of the processing of a multi-drug-resistant Klebsiella pneumoniae strain.\n\n\nMethods\n\nThe pipelines have been implemented with Nextflow, a workflow composition and orchestration tool that allows the execution of tasks across multiple heterogeneous computing environments in a portable manner (Tommaso et al., 2017). We have used many concepts discussed and established by the nf-core community and adhered to their development framework (Ewels et al., 2020).\n\nIn the pipeline design process, several auxiliary scripts were developed to aid in processing and summarizing intermediate steps and graphical annotation report generation. Several programming languages were used, like Python, R, RMarkdown, and Bash shell scripts. However, the utilization of scripting languages in the pipelines comes with the drawback of increased complexity, as it necessitates the installation of language interpreters and support libraries. To make this as transparent as possible to the end user, all the scripts and core dependencies have been packed into Docker® container images to ensure a consistent distribution and uniform execution regardless of the endpoint hardware and operating system.\n\nWe have adopted a modular development approach, resulting in three independent pipelines specializing in the critical steps of a general bacterial genomics pipeline (Figure 1). The first pipeline focuses on data pre-processing and quality control, the second on genome assembly, and the third on genome annotation. Pipelines 1 and 2 can be used independently for any general-purpose sequencing project, while pipeline 3 is optimized for prokaryotic genomes. The pipelines are autonomous, meaning they can be used separately or in combination with other methods, giving users complete control and flexibility (Figure 1). The pipelines provide a comprehensive end-to-end solution for bacterial genomics analyses when used sequentially. When invoked sequentially, the pipelines provide an end-to-end solution for bacterial genomics analyses. The architecture and implementation of each pipeline are detailed in the following sections.\n\nThe available whole genome assembly module in bacannot is considered limited compared to MpGAP, because it only contains two assembler options. Dashed arrows connected to the crossed circles represent the optional flow of data, highlighting that chaining the pipelines is not required. Gray boxes highlight the pipeline’s outputs.\n\nThe ngs-preprocess pipeline can perform several quality-control steps required for Next-Generation Sequencing (NGS) data assessment. Short or long sequencing reads can be used as input data, and the subsequent steps are determined automatically by the read type or via user configuration settings. These include contamination checking, quality trimming, adapter removal, demultiplexing, file conversion, and graphical report generation (Figure 2). The pipeline accepts data from local storage or deposited in the public repository Sequence Read Archive (SRA). When a list of SRA IDs is given, raw sequencing data (in fastq format) will be automatically downloaded using the entrez-direct and sra-tools tools.\n\nThe following steps in the pipeline will be handled automatically based on the sequencing technology indicated in the configuration file. For sample demultiplexing, Porechop (Wick et al., 2017a) is used for Oxford Nanopore Technologies (ONT) reads and lima for PacBio reads. Long-read qualities and statistics are evaluated, and a quality report is generated using NanoPack (Coster et al., 2018). PycoQC (Leger and Leonardi, 2019) can also be used to perform quality control checks on ONT reads. The program fastp (Chen et al., 2018) is used for preprocessing short sequencing reads, including quality assessment, adapter sequence removal, trimming, and reporting. Tools included in the pipeline are summarized in Table 1.\n\nThe MpGAP pipeline for de novo genome assembly has been designed in an organism and platform-independent manner to perform short or long-read only assemblies, as well as hybrid assemblies using a combination of sequencing technologies (Figure 3). Given the user input, the pipeline automatically selects the assembly mode. When using only short-reads, it performs the genome assembly using any of the programs: SPAdes (Bankevich et al., 2012), Unicycler (Wick et al., 2017b), Shovill and Megahit (Li et al., 2015). On the other hand, when only using long-reads, it uses one or more of the following assemblers: Unicycler, Canu (Koren et al., 2017), Flye (Kolmogorov et al., 2019), Raven (Vaser and Šikić, 2021), Shasta (Shafin et al., 2020), and Wtdbg2 (Ruan and Li, 2019). When both short and long-reads are available, the pipeline is capable of performing two types of hybrid assemblies: (1) A direct hybrid assembly using both short and long-reads sets using HASLR (Haghshenas et al., 2020), SPAdes and Unicycler hybrid assembly modes and (2) A hybrid assembly methodology where long-reads only assembly is produced with one of the assemblers above followed by an error-correction procedure (polishing) using the available short-reads.\n\nMpGAP is capable of polishing long-reads only assemblies using the appropriate tool based on user input: (1) Pilon (Walker et al., 2014) for polishing with short-reads data; (2) Medaka and Nanopolish (Loman et al., 2015) for polishing with nanopore data and (3) GCpp for polishing with PacBio data. Ultimately, assembly statistics are assessed using QUAST (Gurevich et al., 2013) and summarized by MultiQC (Ewels et al., 2016). All the tools that are part of the pipeline are outlined in Table 2.\n\nThe bacannot pipeline is dedicated to annotating prokaryotic genomes. It covers gene prediction, annotation of gene families, mobile genetic elements, and identification of medically relevant features. The pipeline generates dynamic annotation reports and facilitates the navigation of annotated features through a genome browser.\n\nThe bacannot workflow is summarized in Figure 4. The pipeline needs a sample sheet file to initiate the process. This file should contain information about the input files, specifying whether they have preprocessed sequencing reads or assembled genomes. If the sample comprises sequencing reads, the pipeline will utilize either Unicycler (Wick et al., 2017b) for short-reads or hybrid assembly or Flye (Kolmogorov et al., 2019) for long-reads assembly.\n\nThe process starts with a generic genome annotation using Prokka (Seemann, 2014) or Bakta (Schwengers et al., 2021), followed by the prediction of rRNA sequences using barrnap, identification of closest NCBI RefSeq genome with RefSeq Masher and Multilocus Sequence Type (MLST) assignment with mlst package. Subsequently, plasmid replicons are annotated using the Plasmidfinder (Carattoli et al., 2014) and Platon (Schwengers et al., 2020a) software. Antimicrobial resistance genes are predicted with AMRFinderPlus (Feldgarden et al., 2019), CARD-RGI (Jia et al., 2017), ARGMiner database (Arango-Argoty et al., 2020), and Resfinder (Bortolaia et al., 2020). Virulence genes are annotated with the Virulence Factor Database (VFDB) (Liu et al., 2018) and Victors (Sayers et al., 2018) databases. Prophages are predicted by Phigaro (Starikova et al., 2019), PhiSpy (Akhter et al., 2012; Edwards et al., 2019), and PHASTER database (Arndt et al., 2016). Genomic islands are predicted with IslandPath-DIMOB (Bertelli and Brinkman, 2018) and plotted with gff-toolbox. Insertion sequences and integrative and conjugative elements (ICEs) are annotated with the ICEberg database (Liu et al., 2018) and the digIS software (Puterová and Martínek, 2021). Orthologs are assigned using KofamScan (Aramaki et al., 2019) and visualized with KEGGDecoder (Graham et al., 2018). Secondary metabolites are annotated with AntiSMASH (Blin et al., 2021). Optionally, users can provide custom databases (with genes of interest) in FASTA files for additional targeted annotations with BLAST+ (Camacho et al., 2009).\n\nThe main characteristic of this pipeline is that it is built to aid users less familiar with the tools to investigate and interpret its results with graphically rich reports. The pipeline generates HTML reports summarizing all the results using customizable document templates written in RMarkdown (Xie et al., 2020). A genome browser created with JBrowse (Buels et al., 2016) is also available to explore the annotated features. A custom web application has been developed using the R Shiny framework (Chang et al., 2023) to facilitate further results exploration. It offers users additional features such as dynamic annotation filtering, as well as a built-in sequence similarity search (BLAST) functionality with an interface for executing and visualizing the results produced by SequenceServer (Priyam et al., 2019). The software and databases used in the pipeline are listed in Table 3.\n\nThe sample KpBSB53 was collected at the University Hospital of Brasilia, Brazil, in April 2016 from the tracheal aspirate of a 41-year-old man. The VITEK 2 system (BioMérieux) was used for microbial identification. Antibiotic susceptibility was tested by the disk diffusion method as described by de Campos et al. (2021). The following antibiotics were tested: Amikacin, Aztreonam, Cefepime, Ceftazidime, Ciprofloxacin, Gentamicin, Imipenem, Levofloxacin, Meropenem, Norfloxacin, Ofloxacin, Piperacillin/tazobactam, Polymyxin, Tobramycin, Ticarcillin/clavulanate (Sensidisc DME - Diagnósticos Microbiológicos Especializados). After 24 h of incubation at 37°C, the sample was classified as susceptible, resistant multiresistant based on what was described by the manufacturer. DNA extraction was performed as described by Ausubel et al. (1992), and extracted DNA was quantified with Nanodrop™. DNA sequencing was performed with both long and short-read technologies. Long-read sequencing was performed using an Oxford Nanopore Technologies MinION Mk1b device, using the rapid barcode kit (SQK-RBK-004) in a R9.4.1 SpotON flowcell (FLO-MIN106D). Short-read sequencing was performed by BGI (Shenzhen, China) using paired-end reads with 150 bp on a DNBseq® platform.\n\nFor the processing of the bacterial genome above, the raw long and short-reads have been analyzed sequentially with the developed pipelines. Quality assessment, filtering, and trimming were performed using the ngs-preprocess pipeline v2.6. In our use case, aside from the default parameters, we set the pipeline to correct the short paired-end reads with fastp and filter long-reads based on quality (≥10) and length (≥750) using the parameters --lreads_min_length and --lreads_min_quality, respectively.\n\nThe preprocessed sequencing reads were assembled using the MpGAP pipeline v3.1.4. Genome assembly was performed using the hybrid method where long-reads are first assembled with long-reads assemblers and afterward polished using the short-reads data (--hybrid_strategy 2). The hybrid assembly strategy was executed only with the Flye assembler (Kolmogorov et al., 2019) instead of using all the available options to limit the computational burden. The BUSCO (Simão et al., 2015) completion assessment was performed with the bacteria_odb9 dataset, containing 148 expected bacterial genes.\n\nThe final polished genomes were annotated using the bacannot pipeline v3.1.5. The pipeline’s required databases, such as VFDB (Liu et al., 2018), were downloaded in May 2022. The parameter --resfinder_species has been set to “Klebsiella”. We used Prokka (Seemann, 2014) for generic annotation, and the tool’s database was enhanced with the public NCBI Prokaryotic Genome Annotation Pipeline (PGAP) HMM library (Li et al., 2020) by using the --prokka_use_pgap parameter.\n\nThe pipeline requires POSIX-compliant systems (e.g., Linux or OS X) or Windows with Windows Subsystem for Linux (WSL2). Pre-installation requirements on the executing computer are Nextflow, and a software management tool (Conda) or a container platform, either Docker or Singularity. Each pipeline requires a configuration file describing the samples and corresponding data to be used. These files also set the specific software to be used in pipeline steps with numerous alternatives (e.g., assembler program) and execution parameters for the whole pipeline or specific software. The configuration files are text files (in YAML format) that should be modified by the user.\n\nWith all these requirements satisfied, the execution is conducted non-graphically in a terminal. For example, to trigger the sequential execution of the pipelines, the following command lines should be issued sequentially:\n\nnextflow run fmalmeida/ngs-preprocess -profile docker -latest -params-file preprocess-params.yml\n\nnextflow run fmalmeida/mpgap -profile docker -latest -params-file assembly-params.yml\n\nnextflow run fmalmeida/bacannot -profile docker -latest -params-file annotation-params.yml\n\nThe exemplified command lines would trigger the execution of the latest version of the pipeline’s code using docker as the container engine, with all the required parameters configured in the YAML file. Optionally, it is possible to launch specific versions of the pipeline for reproducibility using the “-r” parameter, e.g., “-r v3.2”.\n\nIn order for users to replicate the analyses of this paper, the configuration files and command lines executed have been made available in a Zenodo project. The configuration file and the sample sheet used for the annotation pipeline have been provided as Supplementary Material (1 and 2) for quick visualization of the expected format. All pipelines have a complete description of workflows and input files in the online manuals.\n\n\nResults\n\nThis paper showcases the utilization of the developed pipelines to conduct a thorough genome examination of an unpublished bacterial sample sequenced with both short and long-reads. The sample, namely KpBSB53 (see Methods), microbiologically classified as Klebsiella pneumoniae, was isolated from the tracheal aspirate of a 41-year-old man at the University Hospital of Brasilia. The isolate was susceptible to all the antibiotics tested.\n\nThe pipeline assembles and annotates genes for prokaryotes and performs additional annotation steps when examining a clinical sample. This feature makes the tool especially useful for investigating antimicrobial resistance. Using a clinical sample exposes additional tasks included in the pipeline that apply to antimicrobial resistance studies. Subsequently, the KpBSB53 sample will be used to demonstrate the operation of the pipelines to analyze a clinically relevant bacterial genome, as well as a description of the generated results and how to interpret them.\n\nThe process begins with the ngs-preprocess pipeline, which carries out quality control and cleaning actions essential for subsequent genome assembly and annotation tasks. Additionally, it offers the user an important assessment of the sequencing outcomes of the samples.\n\nThe output of the ngs-preprocess pipeline is a directory containing the preprocessed sequencing reads organized according to the sequencing technology of the input files, as indicated in the user configuration file. The preprocessed reads can have sequencing adapter or low-quality stretches removed (trimming) or be discarded entirely if a minimum number of good-quality bases is not reached. The pipeline also provides plots and reports for quality control (QC) inspection.\n\nIn the particular case of the KpBSB53 sample, the short-reads obtained were of outstanding quality, displaying quality values ≥60 before preprocessing (Figure 5A and B). The nanopore data fluctuated around the expected average quality and length, with median values of ≈10 and ≈4 kb, respectively (Figure 5C and D).\n\nFigures A and B are generated by the fastp tool and display the base quality of one of the short-read pairs and the summary of reads statistics, respectively. Figures C and D are generated by the NanoPlot tool and display the average read quality per read length and the weighted read length histogram, respectively.\n\nAfter running ngs-preprocess pipeline, users can evaluate the quality of the input sequencing reads and ensure that only data with enough quality will be used for genome assembly. Once selected, the user manually supplies the preprocessed sequencing reads (such as short-reads, Nanopore, or PacBio) to the MpGAP pipeline using a sample sheet in a text file (see Methods), allowing users to choose from an assortment of assembly programs and strategies to perform the assembly. The pipeline will automatically select the appropriate assembly program based on the sequencing reads provided.\n\nThe KpBSB53 sample illustrates the pipeline’s versatility and ability to work with both short and long-reads. For this sample, the Flye assembler (Kolmogorov et al., 2019) was chosen for a hybrid assembly approach (Chen et al., 2020), which initially has errors owing to sequencing technology, later corrected by including short-read data (polishing) using Pilon (Walker et al., 2014).\n\nThe pipeline generates a sub-directory for each sample containing the assembly results, including the initial and polished assembly files, and creates a report using MultiQC (Ewels et al., 2016) that includes assembly quality metrics from Quast (Gurevich et al., 2013) and BUSCO (Simão et al., 2015) to facilitate comparison between the assemblies. The user can choose different programs to analyze the same data, and report files are available to aid in selecting the best assembly.\n\nAfter analyzing the KpBSB53 sample with this pipeline, we found that it consists of two circular contigs - one representing a chromosome (5.2 Mb) and the other a plasmid (142 kb), essentially a full replicon resolution. The BUSCO metrics results highlight the reference quality level of this genome, with 98.65% ortholog completeness in the bacterial chromosome.\n\nThe assembly reports offer guidelines to assist users in choosing the most suitable assembly alternative for their sample. After making their selection, users can manually indicate the chosen assembly results to the annotation pipeline through the configuration file. Bacannot provides a structured and consistent output, allowing straightforward summarization and examination of its contents. Though multiple annotation stages produce outputs, the primary focus will be on the pipeline’s essential results, namely:\n\n1. Complete genome annotation.\n\n2. A web-based application for results visualization and exploration (Figure 6).\n\n3. Automatic HTML reports for resistance, virulence, mobile elements, and annotations from specialized databases (Figure 7).\n\n4. A genome browser for visualization of annotated features (Figure 8).\n\nFigure A is the homepage of the application for navigation between available features. Figures B and C display the dynamic text-filtering of annotation results. Figures D and E exemplify the interactive results filtering and investigation based on sequence alignment. Figure F shows the SequenceServer tool included in the application for execution and visualization of BLAST alignments.\n\nFigures A and B are screenshots of the antimicrobial resistance (AMR) automatic report, highlighting its homepage containing the annotation description and summary along with a bar plot displaying all the features annotated by the AMRFinderPlus tool. Figure C shows a partial screenshot of the KEGG annotation heatmap autogenerated using KOfamscan and KEGGDecoder tools.\n\nFor illustration, the annotation tracks showing predicted antibiotic resistance genes and insertion sequences are activated in a region of the KpBSB53 plasmid.\n\nAfter all the specialized programs in bacannot have finished their analysis, the results are consolidated into a single General Feature Format file (GFF) and a GenBank format file (GBK) containing the complete genome annotation. These files can be used in other general investigation programs or submitted to NCBI databases. The annotated features are also saved as nucleotide and protein sequences in FASTA format. Moreover, these files are processed internally and presented in the web application as interactive web pages (Figure 6A). This workbench allows users to filter results by text or sequence using the SequenceServer and BLAST applications. The filtered results can be converted into tables of varying formats (Figure 6B and C). The BLAST function included in this workbench allows users to easily annotate other target sequences even after the pipeline is finished. Users can find intersections of alignment results with the genome annotation (Figure 6E and E) or visualize alignments with SequenceServer (Figure 6F).\n\nMoreover, detailed reports are generated for feature-specific analyses, such as antibiotic gene prediction, consolidating the results, and providing cross-references to the source databases used for annotation (Figure 7). Besides these clinically-relevant features, the pipeline also has other generic annotation modules that are useful for any bacterial strain, such as prophage and secondary metabolites annotation, KEGG KO annotation, and the possibility of using custom annotation databases or a list of NCBI protein IDs. The KO module, for instance, outputs a text file ready for the KEGG mapper tool to generate pathway figures.\n\nThe genome browser allows users to visually explore the annotation results and investigate the genomic context of relevant genes. The browser contains various specialized tracks for the targeted annotations performed by the pipeline, such as for resistance, virulence, prophages, and more. For example, in Figure 8, one can quickly observe a cassette of stress-related resistance genes surrounded by insertion sequences in the plasmid contig.\n\nOne of the first results generated by this pipeline is the strain classification based on the alignment-free sequence distance against a database of bacterial genomes (NCBI RefSeq) as calculated by RefSeq Masher. The strain BIDMC 55 (GCF_000692955.1) isolated in the USA was the closest genome to strain KpBSB53 (Mash distance=0.000715202). Additionally, an in silico multilocus sequence typing (MLST) is executed using the mlst program against the BIGSdb PubMLST database (Jolley and Maiden, 2010), revealing that our strain belongs to the Klebsiella pneumoniae ST 105 group, which has been reported as the driver of a plasmid-mediated outbreak of NDM-1-producing strains in China (Zheng et al., 2016). Using Prokka (Seemann, 2014) for generic annotation, 4937 coding sequences (CDS) have been detected, alongside 25 rRNAs and 87 tRNAs. Another pipeline result is the prediction of plasmid replicons using PlasmidFinder (Carattoli et al., 2014). For the KpBSB53 strain, a single plasmid was predicted and classified as IncFIB(K), a very dynamic replicon that is mostly associated with MDR plasmids in K. pneumoniae (Lahlaoui et al., 2015; Tian et al., 2021) and important for virulence as well (Tian et al., 2021).\n\nThe pipeline includes several analyses for annotating antimicrobial resistance genes as default. Strain KpBSB53 has only a few acquired antibiotic-resistance genes, namely blashv-1, fosA, and oqxAB, all considered intrinsic to the species and located in the chromosome (Bernardini et al., 2019; Holt et al., 2015). This agrees with our experimental results, which show that this strain is susceptible to all antibiotic classes tested.\n\nAdditionally, a set of stress-related genes (Supplementary Material 3) conferring resistance to copper, silver, and other metalloids have been detected in the plasmid sequence (Figure 7). On the other hand, several virulence genes have been detected in the sample’s genome using the Virulence Factor Database (VFDB) (Liu et al., 2018). Despite the classical virulence genes normally found in Klebsiella pneumoniae strains (Paczosa and Mecsas, 2016), strain KpBSB53 encodes three operons for siderophore biosynthesis: enterobactin (entABCDEFS, fesABCDG), salmochelin (iroE) and aerobactin (iutA). Moreover, the type 1 and 3 fimbriae and an ecp (E. coli common pilus) gene have also been detected. These three fimbriae types are directly related to the adhesion to surfaces, interaction with host cells, and biofilm formation (Alcántar-Curiel et al., 2013). Taken together, the presence of several virulence factors suggests that the KpBSB53 sample may be a hypervirulent strain or at least more virulent than the classical K. pneumoniae strains, as discussed by Paczosa and Mecsas (2016).\n\nTable 4 presents the expected computer resources and timings for the execution of all pipelines on a standard Linux laptop. A Linux Ubuntu 22.04 laptop, with 4 CPUs (8 cores) and 18 Gb RAM, was used in this study. The computational requirements of the ngs-preprocess pipeline are low. However, the time it takes to finish is positively related to the amount of data. A single tool called fastp is used for short-read preprocessing, which takes around 7 minutes to complete and requires approximately 3 Gb of RAM. For nanopore reads, porechop is the most resource-intensive module, taking approximately 1 hour to finish and using approximately 5 Gb of RAM. In terms of the MpGAP assembly pipeline, the execution depth highly depends on the amount of sequencing data provided and is the most resource-intensive step in the workflow. In our hybrid assembly use case, it accounts for half of the overall processing time and requires 11 Gb of RAM (Table 4).\n\nFor bacannot, only the most time and memory-consuming tasks are shown.\n\n\nDiscussion\n\nIn the last decade, advances in DNA sequence generation resulted in a steadfast incorporation of genomics into routine microbiological research practice, ranging from clinical to environmental applications (Didelot and Parkhill, 2022). Despite the significant progress made by the establishment of multiple computational protocols to process genomic data, a considerable gap still needs to be bridged for these to be readily integrated into laboratory practices. The primary reason behind the problem is the lack of necessary bioinformatics foundations, including a shortage of skilled personnel or proper infrastructure.\n\nOur belief is that genomics pipelines should possess certain inherent characteristics to promote their widespread use. These attributes include easy installation and execution, modularity and extensibility, and the generation of user-friendly reports that consolidate the results and foster biological interpretation.\n\nConsidering these tenets, we have created a comprehensive set of bacterial genomics pipelines (ngs-preprocess, MpGAP, and bacannot). These specialized pipelines should be invoked in sequence, taking raw data from any sequencing platform and converting them into an annotated genome, emphasizing antimicrobial resistance and virulence genes. The first two modules are not restricted to bacterial data, making it possible to analyze data from other organisms. Conversely, the bacannot pipeline is specific to bacteria but can accept sequencing reads as input, allowing users to assemble and annotate their genome with a single command, which is particularly helpful for those less experienced with bioinformatics.\n\nBy following a few simple steps (available online), users can customize the execution of these pipelines and obtain complete results in under a day using a commodity computer. These pipelines utilize technology for modular workflow composition, installation, and execution through virtual containers that package all necessary software requirements. This modularity enables incremental updates in response to community requirements which are transparently pushed to the users unless a specific version is requested for reproducibility purposes.\n\nCurrently, we are aware of six established bacterial genomics pipelines that are actively maintained and have comparable characteristics to our three pipelines. These include ASA3P (Schwengers et al., 2020b), TORMES (Quijada et al., 2019), Nullarbor, Bactopia (Petit and Read, 2020), MicrobeAnnotator (Ruiz-Perez et al., 2021) and MicroPIPE (Murigneux et al., 2021). Although they have some common elements and comparable assembly and annotation modules, each software has unique features tailored for specific purposes. Their goals and designs vary, providing users with high-quality options for various analytical scenarios. Table 5 outlines the differences in capabilities among the annotation pipelines. We now highlight some of the distinctive features of these pipelines.\n\nOur three pipelines provide a comprehensive bacterial genomics analysis from unprocessed reads to annotation similar to what ASA3P, TORMES, Nullarbor, and Bactopia offer. The analysis provided by MicroPIPE and MicrobeAnnotator is less comprehensive than the other pipelines. MicroPIPE is crafted for genome assembly and covers the process from base-calling to genome polishing. However, our MpGAP genome assembly pipeline is more versatile as it can accommodate data from Illumina, PacBio, and ONT sequencing technologies and has nine assemblers with distinctive assembly strategies. This flexibility enables users to select the most suitable choice for their requirements. MicrobeAnnotator is a pipeline that specializes in functional genome annotation. It offers a KEGG Orthology annotation step through Kofamscan, also available in bacannot. However, MicrobeAnnotator only focuses on the functional annotation of predicted genes using KEGG, UniProt, RefSeq, and Trembl. Unlike other pipelines, it does not include extra modules like virulence and resistance gene annotation.\n\nAnalogous to Bactopia, our pipelines are very flexible and customizable. Compared to bacannot, Bactopia has more functionalities but cannot currently produce visual reports for results inspection. Moreover, those with limited bioinformatics experience may find the additional configuration steps more complex. Additionally, Bactopia provides extensions to its core workflow with post-processing tools intended, for example, for pangenome and phylogenetic analyses. Bacannot does not offer these as default, but the standardization of its outputs enables users to adapt them for such tasks.\n\nBacannot stands out for its added ability to annotate various genomic feature classes as part of its central workflow, including secondary metabolites, prophages, genomic islands, integrative and conjugative elements (ICEs), and DNA methylation, without requiring additional executions. This analytic range permits the annotation of clinically relevant traits and provides valuable attributes for non-clinical samples. As a result, bacannot has been used in various scenarios, including the analysis of clinical samples (de Campos et al., 2021), environmental samples from a lake (Janssen et al., 2021), soil (Belmok et al., 2023), and plant-associated bacteria (Bartoli et al., 2022; Ramírez-Sánchez et al., 2022).\n\nLastly, bacannot is the only tool that includes a comprehensive set of dynamic reports, presented as a built-in web application, along with a genome browser, offering a unified and interactive platform for interrogation and visualization of the annotation results.\n\nUsing the developed pipelines, we analyzed a strain of Klebsiella pneumoniae (KpBSB53) isolated from a patient at the University Hospital of Brasilia. We aimed to characterize its antibiotic resistance profile and virulence at the genome sequence level. We used sequencing data from short and long-read platforms to conduct a comprehensive genomic analysis of the strain on a laptop with 18 Gb of memory in less than a day. Our findings revealed that the strain belongs to the ST 105 group, associated with a neonatal unit outbreak in China (Zheng et al., 2016). The annotation of resistance genes only identified components considered intrinsic to the species (Bernardini et al., 2019; Holt et al., 2015). Additionally, mutations in acrR, ompK36, and ompK37 genes were found, which may play a role in resistance. These findings are consistent with the experimentally observed susceptibility to the tested antibiotics.\n\n\nConclusions\n\nThis work showcases three bioinformatics pipelines that, together, provide a complete workflow for a thorough analysis of bacterial genomics using next-generation sequencing data. These computational protocols encompass the entire process, from the initial raw reads to the final genome assembly and gene annotation. It is recommended to execute them in succession, but they can also function independently by incorporating external data provided by the user.\n\nThe pipelines were designed to simplify the installation process by incorporating the many specialized software tools required for all stages in the form of virtualized containers. This eliminates the complexity of setup tasks, allowing the pipelines to be deployed and executed with a single command line. We also provide thorough documentation to expand the user base and make them accessible to those without bioinformatics expertise.\n\nWe not only focused on processing data but also on creating graphical reports and visualizations to improve result interpretation. To achieve this, we developed a web-based tool that allows users to analyze and refine the results using text or sequence annotation, distinguishing bacannot from other pipelines.\n\nThe existence of several comparable pipelines indicates that there is no one-size-fits-all approach to genomics. Generating DNA sequence data is becoming more widespread, but there is a significant challenge in analyzing this data. Our set of tools has been developed to address this issue and aid in the study of bacterial genomics.\n\n\nEthical considerations\n\nThe studies involving human participants were reviewed and approved by the ethical approval received from the Faculdade de Medicina, Universidade de Brasília, Brasília, DF, Brazil (approval no. CEP/FMUnB 1.131.054; CAEE: 44867915.1.0000.558). The patients provided their written informed consent to participate in this study.", "appendix": "Data availability\n\nSample sequencing data has been made in NCBI, BioProject PRJNA955456, BioSample: SAMN34178607. Additionally, the code required to reproduce the analysis performed in this paper has been made available in a Zenodo repository containing bash scripts with all required configurations.\n\nZenodo. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation (Sup. Material) https://doi.org/10.5281/zenodo.7859428.\n\nThis project contains the following underlying data:\n\n• input/sra_ids.txt (list of SRA ids for the preprocessing pipeline)\n\n• preprocess-params.yml (pre-set parameters file for the preprocessing pipeline)\n\n• run_preprocess.sh (script to run preprocessing pipeline with pre-set configutations)\n\n• assembly-params.yml (pre-set parameters file for the assembly pipeline)\n\n• assembly.config (pre-set resources configuration file for the assembly pipeline)\n\n• assembly_samplesheet.yml (pre-generated samplesheet for the assembly pipeline)\n\n• run_assembly.sh (script to run assembly pipeline with pre-set configuration)\n\n• annotation-params.yml (pre-set parameters file for the annotation pipeline)\n\n• annotation_samplesheet.yml (pre-generated samplesheet for the annotation pipeline)\n\n• run_annotation.sh (script to run annotation pipeline with pre-set configuration)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe thank Rodrigo de Paula Baptista for conducting the nanopore sequencing experiment.\n\n\nReferences\n\nAlcántar-Curiel MD, Blackburn D, Saldaña Z, et al.: Multi-functional analysis of Klebsiella pneumoniae fimbrial types in adherence and biofilm formation. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSserwadda I, Mboowa G: rMAP: The Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial Genomics. June 2021; 7(6). 2057-5858. Publisher Full Text\n\nStarikova EV, Tikhonova PO, Prianichnikov NA, et al.: Phigaro: High throughput prophage sequence annotation. bioRxiv. April 2019; page 598243. Publisher Full Text\n\nTian D, Wang M, Zhou Y, et al.: Genetic diversity and evolution of the virulence plasmids encoding aerobactin and salmochelin in Klebsiella pneumoniae. Virulence. December 2021; 12(1): 1323–1333. 2150-5594, 2150-5608. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVaser R, Šikić M: Time- and memory-efficient genome assembly with Raven. Nat. Comput. Sci. May 2021; 1(5): 332–336. Publisher Full Text\n\nWalker BJ, Abeel T, Shea T, et al.: Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. November 2014; 9(11): e112963. 19326203. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWick RR, Judd LM, Gorrie CL, et al.: Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial. Genomics. October 2017a; 3(10). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWick RR, Judd LM, Gorrie CL, Holt KE: Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. June 2017b; 13(6): e1005595. 15537358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWratten L, Wilm A, Göke J: Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nat. Methods. September 2021; 18(10): 1161–1168. PubMed Abstract \| Publisher Full Text\n\nXie Y, Dervieux C, Riederer E: R Markdown Cookbook. Boca Raton, Florida: Chapman and Hall/CRC; 2020.\n\nXuan J, Ying Y, Qing T, et al.: Next-generation sequencing in the clinic: Promises and challenges. Cancer Lett. November 2013; 340(2): 284–295. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZheng R, Zhang Q, Guo Y, et al.: Outbreak of plasmid-mediated NDM-1-producing Klebsiella pneumoniae ST105 among neonatal patients in Yunnan, China. Ann. Clin. Microbiol. Antimicrob. February 2016; 15(1): 10. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "210163", "date": "18 Oct 2023", "name": "Abdolrahman Khezri", "expertise": [ "Reviewer Expertise Bioinformatics and bacterial genomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper entitled \"Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation\", takes advantage of several well-known tools for NGS data processing, assembly, and downstream analyses. The GitHub page seems to provide enough information too. However, the paper still needs to improve in some aspects.\n\nThe aim of this paper is not clear. The authors developed a pipeline based on existing tools. However, the aim is not easy to find, and the work lacks novelty.\n\nThe other drawback of this paper is the fact that the authors tested the pipeline only using a clinical isolate. How this pipeline handles, for instance, gram-positive bacteria or other bacteria with different genome sizes is not clear.\n\nThe figures are not accurate. They do not provide enough/precise information regarding the steps, tasks, or tools.\n\nIt is necessary to implement the Bandage tool into the pipeline right after assembly to visualize the assembly.\nIs there any specific reason the author chose fastp as a quality check tool? Obviously, fastqc provides much more details compared to fastp.\nI understand that different tools make different assembly, however many publications already benchmarked them, for instance, it is well known that SPAdes, Flye, and Unicycler provides a better assembly for short, long, and hybrid assembly, respectively. Please see Wick et al. (20191) or Khezri et al. (20212). However, in my opinion in a pipeline, an author should stick to the best overall tool and avoid providing many tools as pipelines are designed for less experienced users.\nIn Table 4, some of the tasks such as annotation with Prokka as well as Quast and Busco took a tremendous amount of time which is not how it should be. What is the author's comment on this?\nAlthough the authors presented the differences between their pipeline and other published pipelines, the samples in this study should be tested using other pipelines in order to have a clear demonstration of performance.\n\nPorechop is out of date and no longer supported. This is important when it comes to new chemistry and sequencing kits, where, for instance, 24 barcodes in rapid barcoding kits are not recognized by Porechop. Here it would be better to take advantage of ONT guppy software not only for trimming but also for other tasks.\n\nVery little is written regarding BLAST. How can the user benefit from BLAST in this pipeline? Does it come with ore-indexed reference databases?\nThe Prokka output can be used for many different purposes including core genome and pan genome analyses which are important for people working on epidemiology. It would be nice if the author could extend their pipeline to cover this.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No", "responses": [] }, { "id": "218196", "date": "14 Nov 2023", "name": "Abhinav Sharma", "expertise": [ "Reviewer Expertise Mycobacterium tuberculosis", "Reproducible methods", "Machine learning", "Variant calling", "Reference Alignment", "Resistance profiling and Scientific workflow managers." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The authors present 3 modular piplines aimed at (non-)bioinformaticians and applicable in different stages of bacterial analysis such as data download, assembly and annotation and generates reports to facilitate the interpretation of the results. The pipelines also support the analysis of data from multiple sequencing platforms, aiding the reuse of the pipeline for both short and long read sequences, which adds value to the bioinformatical toolkit given the increasing use of long-read sequences and the current prevalence of short-read sequences.\nFurthermore, these pipelines have been written in Nextflow and generally follow the best practices of modularization outlined by the nf-core community pipeline template.\n\nSuggestion (ref documentation website): As far as the design of the pipeline and description of the design choices goes, it is well explained. The interpretation of the generated results has been neatly described for bacannot in the documentation page (https://bacannot.readthedocs.io/en/latest/outputs/), including the directory structure and the relevant links for the tool-specific reference material. However as the pipelines are modular and the user is expected to run them separately, it is recommended that the documentaiton websites for MpGAP pipeline and ngs-preprocess pipelines should also have an \"Output\" page to facilitate users on the output structure and refer the correct tools-specific links.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "10597", "date": "28 Nov 2023", "name": "Felipe Almeida", "role": "Author Response", "response": "Dear Reviewer, Thank you for the words addressed when reviewing the paper. I would like to reply saying that we will indeed work on the suggestion you made. It is indeed a very important note you have brought to our attention that, even though each pipeline is independent, we forgot to add a proper specification and explanation of all Outputs in the ngs-preprocess and MpGAP pipelines. We have already created issues on the repositories so we do not forget to address this suggestion. Sincerely, Felipe." } ] }, { "id": "219643", "date": "14 Nov 2023", "name": "Austin G Davis-Richardson", "expertise": [ "Reviewer Expertise Metagenomics", "Microbial Genomics", "Microbiome" ], "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 developed a suite of open source workflows implemented in Nextflow for microbial WGS preprocessing, de novo assembly, and annotation. The goal of this work is to provide re-usable workflows that can be tailored to the end-user's needs, therefore several interchangeable tools (e.g., de novo assemblers) are wrapped in a common Nextflow framework. Interoperability between bioinformatics tools is a significant challenge therefore these workflows provide a useful resource for tailoring a set of tools to meet one's needs based on sequencing technology.\nThe workflows are then applied to a real world problem of analyzing genomic sequences from a Klebsiella isolate with recapitulation of antibiotics resistance phenotypes from genomic data as the \"ground truth\" for validating the workflow. While this is a limited dataset, the purpose of the paper is to not validate all of the bioinformatics tools used in the workflow but to demonstrate how it could be used to generate a useful output from genomic sequencing data.\nThe paper would benefit from either demonstrating the first two pipelines (excluding annotation) on a non-bacterial dataset as the authors claim that only the annotation pipeline is prokaryote-specific.\nI was able to download and start the Nextflow pipelines however I do not have access to sufficient computational resources required to complete the pipelines. Therefore, I am unable to evaluate the outputs of the pipelines at this time. It would be useful for the authors to provide example outputs on Zenodo.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "10598", "date": "28 Nov 2023", "name": "Felipe Almeida", "role": "Author Response", "response": "Dear Reviewer, Thanks for the thoughtful words addressed when reviewing our paper. We are on full agreement with your suggestion and indeed the paper and the pipelines ngs-preprocess and MpGAP would enormously benefit from us displaying its usage in a non-bacterial dataset. We would like to reply saying that we are going to work on that, together with the comments of Reviewer 2. First, we are going to generate a new page in the web documentation for this 2 pipelines, showing the analysis of a fungi or plant sequencing dataset. We will make sure that they have the necessary command lines from input to output, so one can reproduce, but also, add an overview of the generated results in the web page. Finally, we are first going to work as making all these changes and enhancements of providing explanation and example of outputs in the web page itself. Once done, we are going to check how easily can we update the paper to provide an additional Zenodo for the non-bacterial analysis, and also to update the bacterial-analysis Zenodo to have the outputs. We have already created issues in the pipelines' repositories so we do not forget to address them. Sincerely, Felipe." } ] } ]	1	https://f1000research.com/articles/12-1205
https://f1000research.com/articles/12-1204/v1	25 Sep 23	{ "type": "Research Article", "title": "Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics", "authors": [ "Mitsutaka Kadota", "Kaori Tatsumi", "Kazuaki Yamaguchi", "Atsuko Yamaguchi", "Takashi Asahida", "Keiichi Sato", "Tatsuya Sakamoto", "Yoshinobu Uno", "Shigehiro Kuraku", "Kaori Tatsumi", "Kazuaki Yamaguchi", "Atsuko Yamaguchi", "Takashi Asahida", "Keiichi Sato", "Tatsuya Sakamoto", "Yoshinobu Uno" ], "abstract": "Estimate of nuclear DNA content serves as an independent tool for validating the completeness of whole genome sequences and investigating the among-species variation of genome sizes, but for some species, the requirement of fresh cells makes this tool highly inaccessible. Here we focused on elasmobranch species (sharks and rays), and using flow cytometry or quantitative PCR (qPCR), estimated the nuclear DNA contents of brownbanded bamboo shark, white spotted bamboo shark, zebra shark, small-spotted catshark, sandbar shark, slendertail lanternshark, basking shark, megamouth shark, red stingray, and ocellate spot skate. Our results revealed their genome sizes spanning from 3.18 pg (for ocellate spot skate) to 13.34 pg (for slendertail lanternshark), reflecting the huge variation of genome sizes already documented for elasmobranchs. Our qPCR-based method ‘sQuantGenome’ enabled accurate genome size estimation without using live cells, which has been a severe limitation with elasmobranchs. These findings and our methodology are expected to contribute to better understanding of the diversity of genome sizes in elasmobranchs even including species with limited availability of fresh tissue materials. It will also help validate the completeness of already obtained or anticipated whole genome sequences.", "keywords": [ "nuclear DNA content", "C-value", "shark", "ray", "genome size" ], "content": "Introduction\n\nGenome size refers to the amount of DNA in a haploid genome, expressed either by weight or number of nucleotides. Development of DNA sequencing technologies and related methods have yielded chromosome-scale sequence information with higher completeness than before, but the total number of nucleotides in resultant genome sequences rarely match the genome size, mainly because of incomplete sequencing that results from highly heterochromatic or repetitive regions in the genome. For example, the axolotl genome sequencing, a pioneering effort on a large vertebrate genome, yielded an assembly consisting of 28 gigabases1 (Gb), but it still lacks a large fraction larger than a whole human genome, to complete its huge genome that is estimated to amount to 32 Gb.2\n\nIn the early days, genome size was determined by measuring the amount of DNA extracted from a defined number of cells or nuclei. The technique revealed variable genome size among species and differential DNA contents between somatic and germ cells.3–5 Other methods based on reassociation kinetics6 also provided estimations on genome size or the degree of genome complexity in various experimental settings, i.e., repetitive and non-repetitive content of the genomic DNA.7–9 Currently, the most commonly used methods for genome size estimation are DNA staining followed by densitometry or cytometry measurement, i.e., Feulgen densitometry or flow cytometry.10,11 These methods, however, require fresh biological samples, which is sometimes challenging, especially when the target species are elusive in the wild.\n\nOne of the taxa with scarce genome size reports is the vertebrate class of cartilaginous fishes (Chondrichthyes) comprised of chimaeras, sharks, and rays. This taxon includes some species with enlarged genome sizes over 10 picogram (pg), making it a class with a remarkable genome size variation among vertebrates,12 next to amphibians in which genome size enlargement is observed particularly in salamanders.13 As posed in ‘C-value enigma’,12 what drives genome size increase/decrease remains inexplicable, and the taxon Chondrichthyes provides an intriguing system to scrutinize it in relation to the variation of habitat environment, body size, propagule size, prey, population size, and lifespan (reviewed in Ref. 14). Among cartilaginous fishes, genome size reports are currently available only up to 134 species (based on the information in the Animal Genome Size Database: http://www.genomesize.com) among approximately 1,300 described species, which is largely due to their inaccessibility—many of them inhabit open ocean or deep-sea and thus are not immediately subjected to laboratory experiments using fresh animal tissues.\n\nAn alternative method for genome size estimation based on quantitative PCR (qPCR) was developed15 and is expected to circumvent the limitation of existing methods with elusive species. The method requires prior information on the genomic or transcriptomic sequences of single-copy genes to design specific oligonucleotide primers, as well as genomic DNA as a template, for PCR. Genome size is then estimated by calculating the DNA copy number contained within a defined amount of DNA. Although the qPCR-based method has been used to assess genome sizes of several plant and animal species,16–19 its utility has been questioned. The qPCR-based method can be more labor-intensive than established methods. Moreover, in some cases, qPCR-based estimates deviated from the values obtained by other established methods such as Feulgen densitometry or flow cytometry.20,21 Thus, establishing a streamlined protocol will allow a wide application of the qPCR-based method to provide accurate genome size estimates even in species with low sample availability.\n\nIn this study, we selected several elasmobranch species and estimated their genome sizes. We primarily adopted flow cytometry, and in parallel, we optimized the previously introduced qPCR-based method to achieve higher accuracy. This yielded genome size estimation of the species including those with low availability of fresh tissue samples, and for the brownbanded bamboo shark, zebra shark, small-spotted catshark, ocellate spot skate, the estimates were cross-validated between the two methods. Our technical optimization has been summarized in a protocol that laboratory personnel can refer at the bench for reliable genome size estimation. Based on the data we obtained, we discuss the genome size variation among elasmobranchs.\n\n\nMethods\n\nThe sources of the animal individuals used for the study (see below) are described in Supplementary Table 1 in the separately supplied file.22 Red blood cells, tissue or embryo of sandbar shark Carcharhinus plumbeus, basking shark Cetorhinus maximus, white-spotted bamboo shark Chiloscyllium plagiosum, brownbanded bamboo shark Chiloscyllium punctatum, slendertail lanternshark Etmopterus molleri, red stingray Hemitrygon akajei, megamouth shark Megachasma pelagios, ocellate spot skate Okamejei kenojei, small-spotted catshark Scyliorhinus canicula, zebra shark (or leopard shark) Stegostoma tigrinum (formerly Stegostoma fasciatum), and mouse Mus musculus were used for the analysis. Animal sampling was conducted in accordance with the institutional guideline Regulations for the Animal Experiments specified by the Institutional Animal Care and Use Committee of RIKEN Kobe Branch and the official guideline for animal experiments at Okinawa Churaumi Aquarium. Phylogenetic relationship of the elasmobranch species covered in the study are described in Figure 1.\n\nDetails of the animals used (e.g., source, developmental stage, and cell type) are included in Supplementary Table 1 in the separately supplied file.22 The branch lengths in the tree are not scaled to relative divergence times.\n\nElasmobranch blood was collected using a syringe containing heparin sodium salt solution (MOCHIDA, cat: 5,000 units/5 mL; use 10 μL for 2-3 ml of blood) or EDTA (0.5 M EDTA, Gibco, cat: 15575-020; use 10 μL for 1-2 ml of blood). Elasmobranch cells from the tissue and embryo were prepared by mincing and dissociation with trypsin (0.5% solution in shark PBS) at 25-28°C for 15-30 min with rotation. Mouse embryonic fibroblast cells prepared from E14.5 embryos of C57BL/6 strain mice, or mouse lung fibroblast cells prepared from an adult male C57BL/6 strain mouse were cultured in DMEM (Nacalai tesque), supplemented with 10% FBS (Gibco) and 1× Antibiotic-Antimycotic solution (Gibco). Human GM12878 lymphoblastoid cell line (Coriell Institute) which has a relatively normal karyotype was cultured in RPMI (Gibco) supplemented with 10% FBS, 1× L-glutamine (Gibco), and 1× Antibiotic-Antimycotic solution. Two million elasmobranch cells or one million reference cells (mouse fibroblast cells or GM12878 cells) were permeabilized in PBS (shark PBS or PBS) containing 0.1 % Triton-X100 and stained with propidium iodide (PI/RNase Staining Buffer, BD Pharmingen).\n\nEstimation of the nuclear DNA content by flow cytometry was performed as follows.23,24 The PI intensity of the elasmobranch cells and reference cells were measured separately in a flow cytometer (Ploidy Analyser; Sysmex). Then, a single analysis setting applicable for both sample types was determined by adjusting the gain and the threshold in the CyView analysis software (Sysmex). Subsequently, the elasmobranch cells and reference cells were mixed at equal ratio and analyzed again. Genome size of the elasmobranch species was estimated relatively from the calibration curve between the 2c (G0/G1 phase) and the 4c (G2/M phase) peaks of the reference cells with known genome size information, i.e., C-value = 3.25 pg25 for mouse or C-value = 3.37 pg for human GM12878 cells determined by flow cytometry using mouse MEF cells as reference. The estimation is also based on the assumption that the elasmobranch species analyzed are diploid organisms. Step-by-step procedures of cell preparation, flow cytometer operation, and genome size calculation are described in the Supplementary Protocol.\n\nFrozen samples (red blood cells or powderized tissue) were used for the genomic DNA (gDNA) extraction with NucleoBond AXG 100 or AXG 500 with NucleoBond Buffer Set IV (Clontech) or DNeasy Blood and Tissue kit (Qiagen). Genomic DNA was analyzed by 4200 TapeStation (Agilent Technologies) with the Genomic DNA ScreenTape analysis kit to confirm high molecular weight (HMW) DNA extraction. 1-4 μg of genomic DNA, adjusted to the total volume to 150 μL with TE buffer, was sheared to 10 kb using g-TUBE (Covaris) in an MX-300 high-speed centrifuge (TOMY) equipped with an AR015-24 rotor (TOMY) at 6,100 rpm for 1 min, at 25°C. After the shearing, size distribution of the DNA was confirmed to be around 10 kb by 4200 TapeStation with the Genomic DNA ScreenTape analysis kit. The sheared gDNA were stored at 4°C until use.\n\nTarget genes for the analysis were selected from the previously defined set of Core Vertebrate Genes26 (CVG), consisting of 233 genes that are shared as one-to-one single-copy orthologs in the genomes of 29 selected vertebrate species. We selected the components of CVG that are also included in Core Eukaryotic Genes27 (CEG) and BUSCO28 (Benchmarking Universal Single-Copy Orthologs) vertebrate gene set identified by Hara et al.26 (see Supplementary Table S3 in the separately supplied file22 for detailed information of the selected genes). Orthologs of those CVGs of the target species were identified by performing BLAST (TBLASTN) search in transcriptome assemblies of the target species in the Squalomix elasmobranch sequence archive (https://github.com/Squalomix/sequences; Ref. 29), using amino acid sequences of human CVG orthologs as the query. Also, the deduced amino acid sequences of the longest open reading frame of the identified transcripts were used for the BLAST (BLASTP) search against the human protein database. Transcripts of the target species that displayed the best hits reciprocally in the BLAST searches were considered orthologous and retained for further analysis (see Supplementary Tables S3 and S4 in the separately supplied file22 for the CVG transcripts used for the study). Primers were designed inside the putative last exon of the transcripts inferred by aligning the target species’ transcript sequences to the last exon of the human counterpart. Primers for the first round of PCR to generate copy-number standards were designed using the Primer3 program30 (https://bioinfo.ut.ee/primer3/), and primers for the nested qPCR were designed using the Primer Express software (ThermoFisher Scientific). The sequences of CVG transcript of the target species and the oligonucleotide sequences of the PCR primers are included in Supplementary Table S3 and S4 in the separately supplied file,22 respectively.\n\nThe first PCR was carried out using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with 5 ng of the sheared gDNA and 0.3 μM concentration of each primer in 20 μL reaction volume at [98°C for 3 min, 34 cycles of (98°C for 20 sec, 58°C-66°C in 2°C increments of temperature gradient for 15 sec, 72°C for 15 sec), 72°C for 1 min]. A portion (5 μL) of the PCR products were analyzed by electrophoresis on a 2% Agarose S gel (Nippon gene) in 1× TBE buffer and stained with GelStar (Lonza). The remaining PCR product of the condition that displayed a single-band or near single-band product on the gel was double size-selected and purified using AMPure XP beads (Beckman coulter) and eluted in 30 μL of TE. The optimal annealing temperature of the PCR reaction and size-selection condition by AMPure XP beads for each gene are included in Supplementary Table S4. Purified PCR products were sequenced directly by Sanger sequencing using the same forward and reverse primers used in the initial PCR reaction to identify possible polymorphic sites. If the polymorphic sites overlapped qPCR primer sequences, the qPCR primers were re-designed. As the first PCR was performed at a high PCR cycle number and may have reached the plateau phase resulting in the PCR product to possess a complex secondary structure, the second PCR was performed with a low cycle number using a small aliquot of the first PCR product as template. The number of PCR cycles in the second PCR was determined with QuantiTect SYBR Green PCR Kit (Qiagen) using 1 μL of the first PCR product after 5-folds of dilution or H2O as the template with 0.3 μM concentration of each primer in 10 μL reaction volume in a duplicate measurement setting, at [95°C for 15 min, 30 cycles of (94°C for 15 sec, 60°C for 15 sec, 72°C for 20 sec)] with QuantStudio 7 Flex system. The baseline signal was set to the 1st cycle only. Ct (cycle threshold) that reached 1/4th of the maximum signal intensity observed at the 30th cycle of PCR was determined as the number of PCR cycles for the second PCR. The second PCR was performed using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems) at the optimal annealing temperature determined earlier. The second PCR product was double-size-selected and purified using AMPure XP beads and eluted in 30 μL of TE buffer. The size distribution analysis was performed again by 2100 Bioanalyzer (Agilent Technologies) to confirm that the purified second PCR product is truly a single-band DNA. The purified second PCR product, which will be used as the DNA copy number standard (DNA standard) in the qPCR reaction, were stored at 4°C until use.\n\nOn the day of qPCR, DNA standards and the sheared gDNA were diluted to 1-10 ng/μL in 1× DB (dilution buffer; 10 mM Tris-HCl pH8.0, 0.05% Tween-20) using 50× DB stock solution (500 mM Tris-HCl pH8.0, 2.5% Tween-20), and 5 μL solution was used for quantitation with QubitFlex fluorometer (ThermoFisher Scientific) in four independent measurements. DNA concentration was determined by taking the average of the four independent measurements. The molecular weight (MW) of the double-strand DNA standards was calculated by the OligoCalc program (http://biotools.nubic.northwestern.edu/OligoCalc.html). The concentration of the DNA standards in copy numbers was calculated with the following formula: DNA copy number in 1 μL DNA = ((DNA concentration (ng/μL)) / (MW (g) × 109)) × (6.02214076 × 1023/mol). DNA standards were diluted hundred-folds in 1× DB, followed by another hundred-folds dilution in 1× DB, and further diluted in 1× DB to generate 100 μL of DNA standard at 50,000 copy DNA/μL (will be STD1). STD1 was diluted five-fold in 1 ×DB by mixing 5 μL of STD1 with 20 μL of 1× DB to generate STD2 at 10,000 copy DNA/μL. Similarly, STD3, 4, and 5 at 2,000 copy DNA/μL, 400 copy DNA/μL, and 80 copy DNA /μL were generated by serial dilution. qPCR for genome size estimation was performed with the QuantiTect SYBR Green PCR Kit (Qiagen) using 1 μL of the sheared gDNA (at 1-10 ng/μL in 1× DB), STD DNAs (STD 1~5) in 1× DB, or H2O as templates with 0.2 μM concentration of each primer in 10 μL reaction volume in 4 technical replicate setting, at [95°C for 15 min, 40 cycles of (94°C for 15 sec, 60°C for 15 sec, 72°C for 20 sec)] with the dissociation curve analysis option in QuantStudio 7 Flex system. Quantification was performed with the QuantStudio Real-Time PCR Software v1.3. The R2 of the standard curve and the dissociation curve were also analyzed to confirm specific amplification and quantification of the target region. C-value was determined with the following formula: C-value = amount of gDNA in the qPCR reaction (ng)/DNA copy number of the gDNA. Genome size was estimated by averaging the C-values from multiple (at least three) target gene regions. Step-by-step procedures for gDNA preparation, DNA standard preparation, qPCR, and genome size calculation are described in the Supplementary Protocol in the separately supplied file.22\n\nIn parallel with the genome size estimate using the flow cytometry and qPCR, those of the zebra shark and thorny skate were estimated in silico based on k-mer frequency distribution with a conventional procedure. For the zebra shark, short-read genomic data produced previously by us (see Yamaguchi et al., 2022)31 were used. For the thorny skate, short-read genomic data produced by the Vertebrate Genomes Project32 was downloaded from VGP GenomeArk (s3://genomeark/species/Amblyraja_radiata/sAmbRad1/genomic_data/illumina/). Sequencing reads were trimmed with trim_galore v0.6.4 to remove low quality bases and the Illumina adaptor sequences. The processed reads (both read 1 and read 2; 351 and 751 M read pairs for the zebra shark and the thorny skate, respectively) were analyzed by jellyfish v2.3.0 program with the k value set at 21. The resultant .histo file was uploaded onto the GenomeScape webserver (http://qb.cshl.edu/genomescope/) to obtain estimates of the genome size.\n\n\nResults\n\nGenome size estimation of ten elasmobranch species that belong to the orders of Orectolobiformes, Lamniformes, Carcharhiniformes, Squaliformes, Rajiformes, and Myliobatiformes, namely eight shark and two skate/ray species (Figure 1), was performed by flow cytometry or qPCR. The flow cytometry method utilizes propidium iodide (PI) that binds to the double-strand DNA to estimate genome sizes relative to the reference mouse or human cells with known genome size information. The reference cells at G0/G1 phase (2c) and G2/M phase (4c) were given a pre-defined nuclear genome content of 6.5 pg and 13 pg for mouse cells and 6.74 pg and 13.48 pg for human GM12878 cells to draw a calibration line. Then, the genome size of the target elasmobranch species was estimated based on the calibration line, assuming that they are diploid organisms (Figure 2). See Supplementary Table 2 in the separately supplied file22 for detailed information on the PI-signal values and the reference cells used in each measurement.\n\na) Flow cytometry analysis of the bamboo shark Chiloscyllium punctatum with Ploidy Analyser (Sysmex). Red blood cells of the bamboo shark and the reference mouse lung fibroblast cells were analyzed together. PI signal of the cells corresponding to mouse 2c (cells at G0/G1 phase), mouse 4c (cells at G2/M phase), and bamboo shark 2c (cells at G0/G1 phase) were obtained. b) Genome size estimation of the bamboo shark based on the standard line of the mouse cells. C-value of the reference mouse cells was set to 3.25 pg.25 The PI-signal values and the estimated genome sizes for the species analyzed by flow cytometry are included in Supplementary Table 2 in the separately supplied file.22\n\nThe qPCR-based method requires the target species’ nucleotide sequence information and materials, i.e., transcriptome sequences for primer design and the genomic DNA for PCR amplification. We followed the method reported by Wilhelm et al.15 while improving the existing protocol to achieve more accurate estimation (Figure 3). The major modifications in the protocol were 1) selection of multiple (at least three) genes from the established single-copy orthologue gene set CVG, 2) use of the sheared gDNA instead of HMW gDNA for DNA quantification and PCR, 3) careful evaluation of the DNA standards; sequence analysis by Sanger sequencing and size distribution analysis by 2100 Bioanalyzer, 4) Use of a dilution buffer that contains a surfactant in the qPCR reaction. We first determined the PCR condition that gives a single-band product in the PCR reaction. The nucleotide sequence of the PCR product was confirmed by Sanger sequencing to avoid overlap of the qPCR primers with possible polymorphic sites inside the target region of the selected CVGs. The second PCR was performed using a limited number of PCR cycles, not to let the PCR amplification hit the plateau. Finally, qPCR was performed using the sheared gDNA of the target species and the DNA standards of 80~50,000 copy/μL diluted in dilution buffer.\n\na) Workflow of the genome size estimation by quantitative PCR. b) Agarose gel electrophoresis of the first PCR product at various annealing temperature conditions. Shown is the result for the brownbanded bamboo shark MPI gene (CpMPI). c) qPCR-based determination of the PCR cycles for the second PCR. Amplification curve for CpMPI (red), negative control (H2O; blue lines), and the threshold (green line) are shown. d) Size distribution analysis of the DNA standard by Agilent Bioanalyzer with the High Sensitivity DNA Kit. Shown is the result for CpMPI. e) Amplification of CpMPI for the sheared gDNA, copy number standards (STD1-5), and negative control (NTC). HMW, high molecular weight; Rn, normalized reporter.\n\nThe reliability of our analysis methods was assessed by comparing our estimates based on flow cytometry and qPCR in four species. C-values of the brownbanded bamboo shark were estimated to be 4.83 pg by flow cytometry (Figure 2) and 5.05 pg by qPCR; C-values of the zebra shark were estimated to be 3.79 pg by flow cytometry and 3.39 pg by qPCR; C-values of the small-spotted catshark were estimated to be 5.46 pg by flow cytometry and 5.49 pg by qPCR; C-values of the ocellate spot skate were estimated to be 3.40 pg by flow cytometry and 3.18 pg by qPCR. Close correlation in the estimated genome size values based on two independent methods suggested high reliability of the data except one case. The values were also compared to the genome size information documented previously (see Table 1). The estimated C-values from this study for sandbar shark (3.43 pg) by flow cytometry, brownbanded bamboo shark (4.83) by flow cytometry, red stingray (3.82 pg) by qPCR, ocellate spot skate (3.40 pg) by flow cytometry, and small-spotted catshark (5.46 pg) by flow cytometry were comparable to previous reports.33–37 The estimated C-value of the house mouse, a control non-elasmobranch species, was 3.18 pg by qPCR and was within 3 % of difference compared to the previous documentation (3.25 pg; Ref. 25). For the rest of the study species selected, genome size was obtained for the first time in this study, namely for the basking shark: C-value = 4.31 pg, white spotted bamboo shark: C-value = 4.96 pg, slendertail lanternshark: C-value = 13.34 pg, megamouth shark: C-value = 5.81 pg, and zebra shark: C-value = 3.79 pg. Our results of genome size estimation are tabulated under the Squalomix consortium gateway page (https://github.com/Squalomix/c-value), which will be kept up-to-date.\n\nWe also estimated genome sizes using DNA sequences with the k-mer-based method38 as supplementary references. For the thorny skate Amblyraja radiata whose nuclear DNA content was previously estimated to be 4.25 Gb,39 the total sequence length of the publicly available genome assembly32 (sAmbRad1.1.pri; GCF_010909765.2) amounts to only 2.56 Gbp. Our k-mer-based estimate of its genome size using raw sequence reads resulted in an even smaller value of approximately 1.7 Gbp. Similarly, for the zebra shark Stegostoma tigrinum whose nuclear DNA content was estimated to be 3.70 Gb (C-value = 3.79 pg), the total sequence length of the genome assembly released previously by us31 (sSteFas1.1; GCA_022316705.1) amounts to only 2.771 Gbp. Our k-mer-based estimate of its genome size using raw sequence reads resulted in approximately 2.805 Gbp.\n\n\nDiscussion\n\nRecent advances in DNA sequencing technologies have enabled genome sequencing in unprecedented scale and accuracy. For setting reasonable goals in the genome sequencing project that can affect overall expenses, it is instrumental to know the karyotype and the total lengths of nucleotide sequences (namely the genome size) of the target species. Upon complete sequencing of the whole genome, the total genome sequence length should be equal to the that measured with nuclear DNA content, but in reality, the severe gap of the lengths appears especially when early technologies such as short-read sequencing is employed (see Introduction). This is the case with all cartilaginous fish species for which whole genome sequencing was conducted (Figure 4a; reviewed in Ref. 14). In the small-spotted catshark genome assembly, more than 1 Gb, in comparison to its genome size, is missing. Also, a huge fraction (1.7 Gb, 40%) is missing in the genome assembly of the thorny skate (Figure 4). The severe gap is also often observed when genome size is estimated using k-mers, as demonstrated for the zebra shark and thorny skate in this study. As shown previously,40 the unreliability of sequence length-based genome size estimate demands independent measurements with more reliable methods. However, the widely used methods for genome size estimation employ flow cytometry and densitometry and require fresh live materials to give an accurate estimation, which was difficult for some elusive species. To circumvent this limitation, we optimized a previously introduced qPCR-based method.\n\na) Total lengths of genome assembly sequences compared with genome sizes. Included in this plot are species with unequivocal genome size estimates33,39,45,50,51 and whole genome assemblies,32,52–55 namely, whale shark (NCBI Assembly ID, GCA_013626285.1), thorny skate (GCA_010909765.2), small-spotted catshark (GCA_902713615.2), white-spotted bamboo shark (GCA_004010195.1), white shark (GCA_003604245.1), elephant fish Callorhinchus milii (GCA_018977255.1). The genome sizes were measured with flow cytometry except for the elephant fish with the measure by Feulgen densitometry. b) Results of our genome size estimation. Species with two estimate values (out of qPCR-based estimate, flow cytometry-based estimate, or at least one estimate from previous study) are included. Estimates from previous reports are included for reference. Multiple estimates for an individual species are shown with multiple data points and lines (see Table 1).\n\nOur cell preparation method for flow cytometry utilized an isotonic solution (shark PBS solution)41,42 allowing mild permeabilization of live elasmobranch cells. Data acquisition with a flow cytometer was performed similarly to genome content analysis (e.g., ploidy level, cell cycle) using fluorescent dyes. The reference cells were cultured mouse or human cells under exponential growth conditions. Using cultured cells enabled the acquisition of PI signals for 2c (G0/G1 phase) and 4c (G2/M phase) cells to draw a regression line between these two data points. In all the measurements based on flow cytometry, we confirmed that the PI signal of the reference 4c cells is about double of the 2c cells (Supplementary Table 2 in the separately supplied file22), assuring that the reference data points are within the quantitative range and applicable for the estimation of relatively large elasmobranch genomes. The qPCR-based method was used for several non-shark species in past studies.16–19 However, it received criticism about the accuracy of the estimate.20,21 We suspected that the possible inaccuracy resulted from the lack of careful evaluation of the DNA copy number standards, careful handling in qPCR, and the use of a single target gene (instead of multiple target genes) for estimation.\n\nIn our preliminary trials, we identified several keys for improving the accuracy in qPCR-based genome size estimation and derived a protocol implementing the following modifications (see Supplementary Protocol for the entire procedure). This protocol is designated sQuantGenome (streamlined protocol for quantitative PCR-based genome size estimation) and is publicly available at the Squalomix consortium gateway (https://github.com/squalomix/c-value/). First, we used low-bind plasticwares (tubes and tips) to minimize the loss of DNA during the laboratory handling. Second, we used Qubit Fluorometer (ThermoFisher Scientific) to measure the concentration of double-stranded DNA (dsDNA) specifically. Third, we sheared HMW gDNA to approximately 10 kb-long fragments for DNA quantification (by Qubit), PCR, and qPCR. Use of un-sheared HMW DNA causes inconsistent measurements in both DNA quantification and qPCR. Fourth, DNA standards were prepared with maximal caution. We designed PCR and qPCR primers within the putative last exon (that tends to be the longest among multiple exons in most eukaryotes43,44) of the target gene by aligning the target species’ transcript sequence to its human ortholog, based on the assumption that the exon-intron structure is conserved between elasmobranchs and mammals. The first PCR was performed at multiple annealing temperatures to identify a condition that gives a single- or near single-band product on agarose gel. We performed Sanger sequencing to confirm the identity of the nucleotide sequence of the first PCR product to the sequence from the transcriptome assembly which was obtained from the Squalomix sequence archive.29 We also confirmed that qPCR primers (to be used for genome size estimation) do not overlap heterozygous polymorphic sites inside the DNA standard sequence. qPCR primers were re-designed if they overlapped heterozygous polymorphic sites. The second PCR was performed at a low PCR cycle number within the exponential amplification phase (confirmed by qPCR for cycle determination) to ensure that the amplified DNA is double-stranded and does not contain incomplete or chimeric PCR products. We size-selected first and second PCR products to remove DNA fragments outside the target size range. We also analyzed the DNA standards with 2100 Bioanalyzer to confirm their uniform DNA size. Fifth, we reduced the sources of variability in the qPCR reaction to improve quantification accuracy. We used a DNA dilution buffer (DB) that contains a surfactant (0.05% Tween-20) to minimize binding of the DNA to the plasticwares (tubes and tips). We prepared template DNAs (sheared gDNA and the DNA standards) in DB and quantified them with Qubit in four independent replications, using a large liquid volume (of 5 uL) containing at least 5 ng of DNA, for improved accuracy. We used an electronic 8-well pipette for consistent dispensation of the qPCR mixture into the 384-well reaction plate. We also performed the experiment with proper liquid handling techniques, e.g., pre-rinsing of the pipette tip, reverse-pipetting, etc. Sixth, our technical consideration also encompassed the in silico steps for selecting adequate amplification targets and primer pairs to amplify them. Choosing multiple single-copy orthologous genes (ideally no fewer than three) as amplification targets per species is a must to take a variation of estimates into consideration and to identity inappropriate choice of genes, e.g., genes with variable copy number caused by structural variation or genes on sex chromosomes.\n\nRecently, transcriptome sequencing with RNA-seq, as well as whole genome sequencing has led to the large-scale production of exonic sequences including protein-coding regions of various genes. This allows efficient identification of single-copy genes from the de novo transcriptome assembly of the target species, even when high-quality whole genome assembly is unavailable. The rigorous selection of such genes has been facilitated by the introduction of already prepared sets of single-copy orthologs, such as CEG,27 CVG,26 and BUSCO,28 that were pre-selected to assess the completeness of whole genome sequence assemblies. Targeting genes from the single-copy ortholog set is a highly recommended approach for gene selection in the qPCR-based method. However, one should be aware of the possibility of lineage- or species-specific gene duplication or a gene-loss event that may cause the qPCR-based estimate to diverge from the actual genome size. In case of gene duplication, the prepared DNA standards may contain DNA of alternative sequence or alternative fragment size which should be identified with Sanger sequencing or size distribution analysis with 2100 Bioanalyzer. In case of gene loss, the candidate transcript of the target species belonging to a non-orthologous gene, may display a low similarity score or may fail to be identified as the transcript with reciprocal best hit in the BLAST analysis. In any of these cases, choosing multiple genes from the single-copy orthologous gene set and performing rigorous evaluation of the DNA standards will help prevent errors caused by the use of inappropriate genes for the analysis.\n\nAmong the ten elasmobranch species analyzed in this study, genome size information was previously documented for five species (Table 1); sandbar shark (reported to be 2.98 pg using red blood cells with Feulgen staining36), brownbanded bamboo shark (reported to be 4.56 pg or 4.83 pg using red blood cells with Feulgen staining or flow cytometry10,45), red stingray (reported to be 4.02 pg, 4.15 pg, or 4.32 pg using red blood cells with Feulgen staining or flow cytometry34,35,37), ocellate spot skate (reported to be 3.09 pg using red blood cells with flow cytometry37), and small-spotted catshark (reported to be 5.65 pg using red blood cells with Feulgen staining33). Whether the estimation was based on flow cytometry or qPCR, our estimates were mostly comparable to the existing reports, suggesting its high accuracy. Among the species with a relatively large gap, the sandbar shark exhibited a difference of as much as 15%, between 3.43 pg (qPCR-based estimate in the present study) and 2.98 pg from a past study.36\n\nWe have demonstrated the utility of the qPCR-based method for genome size estimation of species whose fresh tissue material is difficult to obtain. The qPCR-based method is also recommended when suitable reference cells with known comparable genome size to the study species are not available in Feulgen densitometry or flow cytometry-based analyses, e.g., for genome size estimation of animal and plant species with extremely large genome sizes. In the case of the South American lungfish Lepidosiren paradoxa, the C-value was estimated to be 80.55-123.90 pg46–48 based on flow cytometry and Feulgen densitometry using reference cells with C-values of 3.3-6.7 pg. In the case of the canopy plant Paris japonica (Melanthiaceae) which has the largest genome quantified among eukaryotes to date (C-value = 152.23 pg),49 the genome size was estimated by flow cytometry using multiple reference cells at the C-value of 16.75 pg, 27.11 pg, and 54.08 pg. In both cases, C-value of the reference cells is much smaller than the target species, which in principle should be avoided in reference-based genome size estimation as it harbors risks of calibration error due to extrapolation. On the other hand, the qPCR-based method, which does not require any reference cells, is expected to provide accurate estimation for a wide variety of species with a wide range of genome sizes.\n\n\nAuthor contributions\n\nS.K. and M.K. conceived the study. S.K., A.Y., T.A., K.S., T.S., K.Y., Y.U., and K.T. collected samples. M.K. and K.T. performed experiments, and S.K. and M.K. analyzed data. S.K. and M.K. wrote the manuscript, which was approved by all authors.", "appendix": "Data availability\n\nFigshare: Extended data. https://doi.org/10.6084/m9.figshare.23974383.v1. 56\n\nData are available under the terms of the Creative Commons Attribution (CC BY 4.0).\n\n\nAcknowledgments\n\nWe thank Hatsune Makino-Itou of Molecular Life History Laboratory, National Institute of Genetics, for assistance with qPCR, Hiroshi Kiyonari and Mayumi Watase of Laboratory for Animal Resources and Genetic Engineering, RIKEN BDR, for providing mouse cells, Itsuki Kiyatake and Takaomi Ito of Osaka Aquarium Kaiyukan, Kiyomi Murakumo, Rui Matsumoto, Ryo Nozu, and Taketeru Tomita of Okinawa Churaumi Aquarium, Tomoyuki Satonaka of Shima Marineland Aquarium, Nobuyuki Higashiguchi of Suma Sea Life Park, and Kazuhiro Saito and Waichiro Godo of Ushimado Marine Institute of Okayama University for providing elasmobranch fish samples. 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Publisher Full Text" }	[ { "id": "210076", "date": "23 Oct 2023", "name": "Jochen Wilhelm", "expertise": [ "Reviewer Expertise qrtPCR", "RNA-seq", "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 report presents optimized procedures to determine the genome sizes of shark species based on quantitative real-time PCR and gives results for 10 shark species (plus M. musculus as a mammalian control), 5 of which were determined by established methods in previous studies.\nMost of the relevant details of the protocols and results are given in the online supplement.\nA statistical analysis of the results is missing. It would be good to have some measure of the precision of the estimates, not just the point estimates. I'd prefer seeing 95% confidence intervals from samples of 3-5 independent determinations (ideally from different subjects/animals, if this is possible; the individual values could be listed in the supplement). This would also allow judging if the differences between the methods are systematic or within the margin of error and strengthen the conclusions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "236221", "date": "27 Jan 2024", "name": "Nancy Saavedra-Sotelo", "expertise": [ "Reviewer Expertise Population genomics", "phylogeny", "phylogeography", "and reproductive behavior" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a research focus on estimations of the size of the genomes of sharks and rays using qPCR. I consider that it is research that has value to science because this knowledge will serve as to base for future studies. Abstract Reading the paper, I consider that its results do not show this sentence: “Our qPCR-based method ‘sQuantGenome’ enabled accurate genome size estimation without using live cells”. I invite the authors to write more objective sentences. I make this observation because there is no methodology that allows us to assess the accurate genome size estimation of their results. Introduction I considered that the introduction contained enough information to understand the utility of using qPCR to quantify the genome sizes in wild species with difficult-to-obtain fresh samples. Methods I wonder if it is impossible to have shark cells in 4c? or use gametes to have another reference in addition to the mouse cells (2c and 4c). Maybe this comment is for future experiments. Results. I consider that it is too bold to say: “Close correlation in the estimated genome size values based on two independent methods suggested high reliability of the data except one case”. There is no statistical analysis that verifies the real difference, much less a statistical correlation. I recommend the authors simply mention that the results can be similar without any apparent pattern. This is because in some cases the qPCR presents higher values but in others lower than cytometry. Discussion 1. The authors say: “The pPCR-based method was used for several non-shark species in past studies. However, it received criticism about the accuracy of the estimate…” This is precisely why my comment about not ensuring that there is a correlation between methods is good. Although the authors standardize to a single gene, this method still has certain sensitivity biases when making measurements. 2. The section “Optimization of qPCR-based method our protocol” should be in methods. In this case, if authors need to convince the readers, they should write about the high points of methods, at what point the DNA quantification of the protocol can be biased, and how it is reduced with their methodology. However, they cannot give the detailed methodology under discussion. 3. The authors say: “Whether the estimation was based on flow cytometry of pPCR, our estimates were mostly comparable to the existing reports, suggesting its high accuracy”. I find this sentence to be pretentious, I think the authors should consider that they do not have a statistical method to say the results are comparable and reliable. Although it is an advance in the knowledge of the size of the genomes in no model organisms, the methodologies have biases and are evident in the difference in values when visually comparing the results. 4. The last two sentences of the discussion may be controversial. I believe that any approach can have biases when quantifying the size of the genomes, including qPCR. I invite the authors to write these sentences mentioning the usefulness of making comparisons between methods to have greater certainty of the genome sizes, I mean that it will always be useful to have genome data with cytometry, qPCR, and other methods that allow us to give an idea of the average genome size of no model species.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1204
https://f1000research.com/articles/11-218/v1	23 Feb 22	{ "type": "Research Article", "title": "Eye image effect in the context of pedestrian safety: a French questionnaire study", "authors": [ "Cédric Sueur", "Anthony Piermattéo", "Marie Pelé", "Anthony Piermattéo", "Marie Pelé" ], "abstract": "Human behavior is influenced by the presence of others, which scientists also call ‘the audience effect’. The use of social control to produce more cooperative behaviors may positively influence road use and safety. This study uses an online questionnaire to test how eyes images affect the behavior of pedestrians when crossing a road. Different eyes images of men, women and a child with different facial expressions -neutral, friendly and angry- were presented to participants who were asked what they would feel by looking at these images before crossing a signalized road. Participants completed a questionnaire of 20 questions about pedestrian behaviors (PBQ). The questionnaire was received by 1,447 French participants, 610 of whom answered the entire questionnaire. Seventy-one percent of participants were women, and the mean age was 35 ± 14 years. Eye images give individuals the feeling they are being observed at 33%, feared at 5% and surprised at 26%, and thus seem to indicate mixed results about avoiding crossing at the red light. The expressions shown in the eyes are also an important factor: feelings of being observed increased by about 10-15% whilst feelings of being scared or inhibited increased by about 5% as the expression changed from neutral to friendly to angry. No link was found between the results of our questionnaire and those of the Pedestrian Behavior Questionnaire (PBQ). This study shows that the use of eye images could reduce illegal crossings by pedestrians, and is thus of key interest as a practical road safety tool. However, the effect is limited and how to increase this nudge effect needs further consideration.", "keywords": [ "prosociality", "road crossing", "reputation", "accident prevention", "pedestrian behavior" ], "content": "1. Introduction\n\nWhatever the size and complexity of the society we live in, social life involves respecting rules or norms in order to maintain peace and cohesion (Coleman, 1994; Elster, 1989; Fehr and Fischbacher, 2004). Violating these social norms can unbalance the public good insofar that law-breakers will gain more benefits than their honest counterparts, or other individuals will be put at risk. In order to balance costs and benefits, punishment or police behaviors have evolved in humans societies (Fehr and Gächter, 2000, 2002), and in other primate societies (Boyd and Richerson, 1992; Flack et al., 2006; Mendes et al., 2018; Riedl et al., 2012). Like other primate species, humans have developed emotional bases for prosocial behaviors allowing cooperation. These emotions are concerns, empathy and a sense of morality and of reputation (De Waal, 2006; Jensen et al., 2014; Keltner and Anderson, 2000; Penner et al., 2005; Tomasello and Vaish, 2013) and they are defined as moral emotions by Haidt (2003). Being concerned or empathic enables humans to recognize when they are doing something wrong and correct their behavior in order to maintain a prosocial reputation and continue interacting cooperatively with their conspecifics (Alexander, 1987; Bateson et al., 2006; Burnham and Johnson, 2005).\n\nOur behavior is therefore influenced by the presence of others, which scientists also call ‘the audience effect’ (Filiz-Ozbay and Ozbay, 2014; Kurzban et al., 2007; Zuberbühler, 2008). Feeling observed by real persons or an imagined audience, therefore has an impact on human behavior. Embarrassment, for instance, is defined as the ‘acute state of flustered, awkward, abashed chagrin that follows events that increase the threat of unwanted evaluations from real or imagined audiences’ (Eller et al., 2011; Miller, 1996). Being observed also tends to make individuals more compliant (Dear et al., 2019; Rodriguez Mosquera et al., 2011). With this in mind, Bateson et al. (2006) conducted an experiment to test the effect of eye images on cooperative behavior. In the coffee area of a building at the University of Newcastle, an honesty box was used for people to make contributions to the coffee fund. The experiment consisted of placing pictures of eyes or flowers close to this box and assessing whether they led to differences in the contributions made. The authors found that in the presence of eye images, subjects paid on average 2.76 times more than when flowers images were displayed. Still comparing the effect of these flowers images as control to those of eye images, other studies have found similar prosocial effects during everyday events. For example, eye images had prosocial effects such as cooperation for the clearing of trays in a university cafeteria (Ernest-Jones et al., 2011) and for waste sorting at a bus stop (Francey and Bergmüller, 2012). Similar results were found in experiments in more specific contexts such as blood donations: While eye images on flyers did not result in differences in pledge with a logo as control, more “real” donations were made by students who got the flyers with eyes image (Sénémeaud et al., 2017). Other than the activation of a “sense of being seen” (Pfattheicher and Keller, 2015) or the desire to maintain a pro-social reputation (Bateson et al., 2006), it is important to note that humans possess neurons that respond to faces and eyes and activate such prosocial behaviors (Emery, 2000; Haxby et al., 2000). Bateson et al. (2013) suggest that eye images induce more pro-social behavior regardless of local norms, thus suggesting that the application of eye images could be a means to combat anti-social behavior by triggering a feeling of shame (Nugier et al., 2007).\n\nThe use of social control to produce more cooperative behaviors may positively influence road use and safety. The limitation of conflicts and accidents on road infrastructures is directly dependent upon the respecting of rules by the numerous pedestrians and drivers. However, more than 8000 pedestrians die in road accidents in Europe every year, 25% of whom die when using crosswalks (Guéguen et al., 2015, 2016). These lethal accidents are due to cars not stopping at signalized intersections but also to pedestrians crossing illegally at the red signal (Sueur et al., 2013). Past studies show that individuals do not cross illegally when other pedestrians are present (Pelé et al., 2017, 2019a, 2019b). Visual communication between two individuals can lead to a change in the receiver's behavior and this effect can be found in a road context. For example, eye contact is an important element. Some studies explored the effect of gaze and smile on the propensity of drivers to stop at signalized intersections and allow pedestrians to cross (Guéguen et al., 2015, 2016). A pedestrian waiting at the edge of an unmarked crosswalk has a greater likelihood to cross if s/he seeks to make visual contact with an approaching driver than if s/he is not looking towards the approaching car, with 67.7% of cars stopping versus 55.1%, respectively (Guéguen et al., 2015). If in addition to this visual contact the pedestrian smiles, 62.9% of drivers stopped compared to 50.1% if the pedestrian sought visual contact with a neutral face (Guéguen et al., 2016). These studies show that visual contact can modify the behavior and speed of drivers, and highlight that the facial expression of the pedestrian also has an impact (Ren et al., 2016). However, these studies are rare and more research is needed on how human facial expressions affect the probability that pedestrians will cross the road illegally. This research may have great potential in terms of applications in the field of road safety, especially regarding the regulation of pedestrian behaviors.\n\nThis study aims to test the effect of eye images on the behaviors of pedestrians crossing at the red light. We collected different images of eyes from five different persons (two men, two women and one child) expressing different facial expressions (neutral, friendly and angry) and one image of flowers for use as a control (Figure 1). These images were used in an online questionnaire that asked participants what they would feel if they saw these images before crossing a road. Would they feel observed, scared or surprised? Would the images discourage or encourage them to cross at the red light? These questions were chosen with caution in order to make the questionnaire valid and are based on previous studies (Bateson et al., 2013; Ernest-Jones et al., 2011; Francey and Bergmüller, 2012; Saeed et al., 2020). We compared their answers to these questions with sociodemographic variables (gender, age, geographical zone and city size) and also with a previous well-known questionnaire called ‘Pedestrian Behavior Questionnaire’ (hereafter referred to as PBQ, Appendix A: Deb et al., 2017; Granié et al., 2013), which tested the propensity of pedestrians to violate rules, make errors or lapses, or show positive or aggressive behaviors. The angry eye images are expected to have a stronger emotional impact on participants and thus prevent them from crossing illegally (Bateson et al., 2006). We also expect a gender effect and an age effect, with a stronger impact of eye images on women and younger individuals. Indeed, women might feel more observed or scared than men when looking at the eye images; studies have shown women to be more empathic and thus more receptive in different situations (Flynn, 2000; Furnham et al., 2003; Kellert & Berry, 1987; Miller et al., 2009). In the context of road crossing, fewer illegal and risky behaviors are observed in women than in men (Holland and Hill, 2007; Pelé et al., 2017; Sueur et al., 2013; Tom and Granié, 2011), with more positive behaviors and fewer rule violations or aggressive behaviors (Deb et al., 2017; Tom and Granié, 2011). Studies show that younger people are less respectful of rules (Holland and Hill, 2007; Pelé et al., 2017; Pfeffer and Hunter, 2013). We also expect regional differences in reactions to eye images, as interregional differences were observed in road accidents (Eksler et al., 2008; Lassarre and Thomas, 2005). Correlations are expected between the responses to the eye image questionnaire and the PBQ. Indeed, participants showing higher scores for violations or aggressive behaviors in the PBQ (i.e. the less prosocial individuals) should be less affected by eye images than participants who show more positive behaviors (i.e., the more empathic and cooperative individuals).\n\nThe flower image is a control. The effect of eye images was tested using three different expressions (friendly, neutral and angry respectively from left to right) in the eyes of five different persons. Five questions were asked about feelings for each eye image: Do you feel observed, scared, inhibited, surprised or encouraged? (See methods for details). The score for each feeling and each image is the average score for all participants. Image credits: Cédric Sueur.\n\n\n2. Methods\n\nThe questionnaire was designed in three steps: 1. Eye images, 2. Pedestrian behavior questionnaire and 3. Sociodemographic questions.\n\nEye images: To test the effect of eye images, pictures were taken of five different individuals (one child, two women and two men) with three different facial expressions (friendly, neutral and angry). A picture of flowers was used as a control. Each picture was taken in black and white with the same contrast and brightness calibration (see Figure 1). For each of the 16 pictures (15 eyes and 1 control), participants were asked to answer five questions about their feelings when looking at the picture:\n\n1. Observation: Do you feel observed when looking at this picture? Answer: yes/maybe/no\n\n2. Fear: Are you scared when looking at this picture? Answer: yes/maybe/no\n\n3. Inhibition: Would looking at this picture prevent you from crossing at the red light? Answer: yes/maybe/no\n\n4. Surprise: Would this picture make you feel surprised if you saw it before crossing the road? Answer: yes/maybe/no\n\n5. Incitation: Would seeing this picture encourage you to cross at the red pedestrian signal? Answer: yes/maybe/no\n\nThese five questions were chosen with caution. In order to check the validity of the questionnaire, we chose the four first questions to evaluate the negative effects of the eyes images and the fifth question to evaluate a positive effect. This means that we expected to have the scores of the fourth first questions to be positively correlated between them but negatively correlated with the fifth question. The questionnaire was validated with results (Section 3.1.) following our predictions.\n\nAs five questions for 16 pictures results in a very long questionnaire of 80 questions, 4 images (with for each image the five questions) were randomly selected for the participants to answer. We checked for a homogeneous distribution of questions to participants by making packages of 20 questions (for 4 images).\n\nSociodemographic questions: Participants were asked to indicate their gender (female or male), age (as numeric) and French postal code. The French postal code provides the city population size (DataNova Opensource, 2014 census) and the Defense and Security Zones (French Homeland Ministrysee https://doi.org/10.5281/zenodo.5745446.\n\nPedestrian behavior questionnaire (PBQ): Participants completed a questionnaire of 20 questions about pedestrian behaviors by Deb et al. (2017). We used a pedestrian behavior questionnaire (PBQ) with 20 questions, developed by (Deb et al., 2017) and taken from (Tom and Granié, 2011). The order of questions was randomly attributed. In parenthesis, the average±stdv of the score (from 1 – never - to 6 – always -) attributed by participants to each question (N=611).\n\nViolations (V)\n\nV1 I cross the street even though the pedestrian light is red. (3.73 ± 1.35)\n\nV2 I cross diagonally to save time. (3.45 ± 1.42)\n\nV3 I cross outside the pedestrian crossing even if there is one (crosswalk) less than 50 m away. (3.51 ± 1.49)\n\nV4 I take passageways forbidden to pedestrians to save time. (2.35 ± 1.36)\n\nErrors (E)\n\nE1 I cross between vehicles stopped on the roadway in traffic jams. (3.34 ± 1.43)\n\nE2 I cross even if vehicles are coming because I think they will stop for me. (2.36 ± 1.19)\n\nE3 I walk on cycling paths when I could walk on the sidewalk. (1.91 ± 0.96)\n\nE4 I run across the street without looking because I am in a hurry. (1.27 ± 0.63)\n\nLapses (L)\n\nL1 I realize that I have crossed several streets and intersections without paying attention to traffic. (1.52 ± 0.82)\n\nL2 I forget to look before crossing because I am thinking about something else. (1.65 ± 0.78)\n\nL3 I cross without looking because I am talking with someone. (1.65 ± 0.85)\n\nL4 I forget to look before crossing because I want to join someone on the sidewalk on the other side. (1.45 ± 0.70)\n\nAggressive Behaviors (A)\n\nA1 I get angry with another road user (pedestrian, driver, cyclist, etc.), and I yell at him. (1.94 ± 1.17)\n\nA2 I cross very slowly to annoy a driver. (1.45 ± 0.87)\n\nA3 I get angry with another road user (pedestrian, driver, cyclist, etc.), and I make a hand gesture. (2.08 ± 1.20)\n\nA4 I have gotten angry with a driver and hit their vehicle. (1.25 ± 0.70)\n\nPositive Behaviors (P, Reverse-scaled items)\n\nP1 I thank a driver who stops to let me cross. (5.55 ± 0.82)\n\nP2 When I am accompanied by other pedestrians, I walk in single file on narrow sidewalks so as not to bother the pedestrians I meet. 4.05 ± 1.46)\n\nP3 I walk on the right-hand side of the sidewalk so as not to bother the pedestrians I meet. (4.04 ± 1.48)\n\nP4 I let a car go by, even if I have the right of way, if there is no other vehicle behind it. (3.60 ± 1.49)\n\nQuestions were presented in random order. PBQ was the first complete questionnaire to study a broad range of aspects of pedestrian behavior on the road for all age groups. This questionnaire was originally developed by Tom and Granié (2011) with 47 questions. We chose the short version, which is considered as reliable as the long version according to Deb et al. (2017) and Tom and Granié (2011), in order to avoid demotivating participants. The 20 questions are categorized into five items as followed:\n\n1. Transgression: deliberate deviation from social rules without intention to cause injury or damage, Reason et al., 1990;\n\n2. Error: deficiency in knowledge of traffic rules and/or in the inferential processes involved in making a decision, Rasmussen, 1980; Reason et al., 1990;\n\n3. Lapse: unintentional deviation from practices related to a lack of concentration on the task; forgetfulness, Reason et al., 1990;\n\n4. Aggressive Behavior: tendency to misinterpret other road users’ behavior, resulting in the intention to annoy or endanger, Baxter et al., 1990; Lawton et al., 1997;\n\n5. Positive Behavior: behavior that seeks to avoid violation or error and/or seeks to ensure traffic rule compliance, Özkan and Lajunen, 2005.\n\nThe participants were required to answer the questions using a 6-point Likert scale (1-very infrequently or never, 2-quite infrequently, 3-infrequently, 4-frequently, 5-quite frequently, 6-very often or always).\n\nThe survey was created using LimeSurvey (Engard, 2009; Jayasundara et al., 2010; LimeSurvey Project Team, 2012) and administered online to the French population through mails and social media (Facebook and Twitter).\n\nThe questionnaire was received by 1,447 participants, 610 of whom answered the entire questionnaire (all three steps). The resulting dataset was used in our analyses (N=610). The mean time to answer the entire questionnaire was seven minutes. 71% of participants were women, and the mean age was 35 ± 14 years. The geographic repartition of the population is as follows: Hauts-de-France (N=17), Ile-de-France (N=100), Ouest (N=92), Est (N=219), Sud-Ouest (N=18), Sud-Est (N=75), Sud (N=89). These factors were included in statistical analyses to avoid selection biases selection.\n\nAll data were anonymous, and participants were given sequential numerical identities corresponding to the moment they answered the questionnaire. Participants could obtain information about the study and its results by contacting the authors via an email address provided at the end of the questionnaire. We followed the ethical guidelines of our institution (CNRS-IPHC, Strasbourg, France). This study received ethical approval from the road security direction of the French Homeland Ministry (RefCNRS190529).\n\nFormal written agreement or parental consent was obtained from the five people photographed for the eye images. They were aware of, and agreed to, the intended use of the photographs in the questionnaire and in the publication.\n\nWe first calculated the mean score for each question and each image. This score ranges from 0 to 1, where 0 indicates 100% of participants answering “No” to the question and 1 corresponds to 100% answering “Yes”. The scores concerning all three answers [Yes, maybe, No] and the scores concerning only two answers [Yes, No] are correlated at 95% (linear regression, P<0.0001, R2 = 0.95, N = 80). For this reason and in order to simplify statistical analyses, we only used the [Yes, No] answers.\n\nA Pearson correlation test was used to check the correlation between each feeling. We then performed a principal component analysis (PCA), followed by Hierarchical Clustering on Principal Components (HCPC) in order to assess which images resulted in higher scores. Following these analyses, the incitation question was excluded from the next statistical tests (see results) and a mean score was calculated for each participant, combining all four remaining questions.\n\nWe assessed whether this score is influenced by the age, gender, geographical zone of their city or the city population size (categorized according to quartiles). A general linear model (glm) with a normal law was used with the R package “MultComp” for multiple comparisons (Bretz et al., 2016). A separate GLM tested the interactions between age/sex factors and the expression of eye images (i.e., neutral, angry, friendly). The conditions of application (normality and homoscedasticity of residuals) were graphically verified.\n\nThe 20 PBQ questions with values from 1 to 6 were analyzed using a PCA with a varimax rotation (Package R Psych; Revelle, 2011; Revelle & Revelle, 2015), following the procedure explained in Granié et al. (2011, 2013). In order to fit with the PCA axes of these studies, we set a maximum number of four loadings (as a preliminary analysis of five PCA dimensions shows a division of the positive behaviors in dimensions 4 and 5, we combined both dimensions as described by Granié et al., 2011, 2013). The coordinates of participants in each dimension (five with loadings higher than 1.00) were then compared with the eye images mean score using a Pearson correlation test. GLM analysis was also carried out to test coordinates with gender, age and city data of participants using. The four dimensions were scaled and normalized using the scale function in R. For the “zone” variable, an Anova followed by a Tukey posthoc test was performed on the GLM residuals.\n\nAll tests were carried out with R 3.6 (R Development Core Team, 2009). The significance level was set at 0.05. Results are indicated with mean ± stdv.\n\n\n3. Results\n\nWhatever the eye image, the mean score for the ‘Observation’ question is 0.33 ± 0.14 (meaning that 33% of participants answered ‘Yes’ to this question and therefore feel observed). The mean score for the ‘Fear’ question is 0.05 ± 0.07. The mean score for the ‘Inhibition’ question is 0.10 ± 0.08. The mean score for the ‘Surprise’ question is 0.26 ± 0.12. Finally, the mean score for the ‘Incitation’ question is 0.02 ± 0.01. Scores for each image and each question are provided in Table 1 and are shown in Figure 1.\n\nImages are ranked according to their values in dimension 1 of the PCA, without the incitation variable. Colors indicate the clusters assessed by the HCPC, from the least intense (green) to the most intense (red) feeling.\n\nPearson’s correlation tests between scores (Figure 2) showed a high correlation between all feelings (r > 0.8, p < 0.001) excluding incitation (r < 0.39, p > 0.05). Indeed, a PCA showed that dimension 1 was composed of four feelings (Observation, Fear, Inhibition and Surprise, r > 0.85see https://doi.org/10.5281/zenodo.5745446 for details) and explained 72.73% of variance in the scores, whilst dimension 2, which was solely composed of the Incitation feeling (r = 0.89), explained 19.28% of variance. These results validate our questionnaire with participants answering coherently following our predictions. A HCPC following this PCA produced five clusters, without including picture 2 (Child’s friendly eyes). When the incitation question was removed from analyses, dimension 1 (r > 0.88) explained 87.06% of score variance whilst dimension 2 (r < 0.45) explained only 7.28%. The resulting HCPC produced four clusters, with picture 2 regrouped with another cluster. In view of these results and the aims of our study, we decided to discard the incitation question for the following analyses. The images were then grouped into four clusters. The first cluster includes the flower, and a man and a woman with neutral expressions. It has a lower influence on the scores (see green elements in Table 1; participants do not feel surprised, scared, observed or inhibited). The fourth and last cluster (see red elements in Table 1) is composed of the child and a man with an angry expression. This cluster shows the highest scores (i.e. participants felt observed, scared, surprised and inhibited). Gender is therefore equally distributed in these four clusters, but the picture of a child’s eyes has a strong effect on feelings (ranked 10, 14 and 15 on the 16 images, Table 1). Moreover, whilst the first cluster includes only ‘neutral’ images and the second cluster includes ‘friendly’ and ‘neutral’ images, all the angry images are found in the third and fourth clusters, meaning that these expressions lead to stronger feelings.\n\nValues indicate the Pearson correlation. Stars indicate statistical significance (Absence = p > 0.05; *** = p < 0.001).\n\nThe mean score for each participant was influenced by gender and age (Figure 3) but not by the geographical zone or the city population size (see Table 2 for statistical values). Men have a lower score than women, meaning that they feel less scared or observed by eyes. Age negatively influences the score, meaning that older participants have a lower score and feel less observed or scared than youngers. When we tested the effect on the mean score of the interactions of age and sex with the eye expressions (i.e., neutral, angry or friendly), we did not found any interaction between age and eye expression (\|t-value\| < 1.086, p > 0.277) or between sex and eye expression (\|t-value\|< 1.449, p > 0.147).\n\nHDF for Hauts-de-France, IDF for Ile-de-France.\n\nThe 20 PBQ questions were analyzed in the same way as those in referenced studies (Deb et al., 2017; Granié et al., 2013; Tom and Granié, 2011). Results are in accordance with the precited studies (see https://doi.org/10.5281/zenodo.5745446 for details). The results explain 49.7% of total variance. The Kaiser-Meyer-Olkin measure of sampling adequacy was satisfactory (0.80) and the Bartlett’s test of sphericity was significant (p < 0.0001). The first dimension explains 15.7% of variance and corresponds to “lapses” (following a loading above 0.4). The second dimension explained 14.7% of variance and corresponds to “transgressions”, meaning violations and errors. The third dimension explains 11.2% of variance and corresponds to “aggressive behaviors”. Finally, the fourth dimension explains 8.2% of variance and corresponds to “positive behaviors”.\n\nAll statistical results are indicated in Table 3. Posthoc Tukey multiple comparisons are detailed in https://doi.org/10.5281/zenodo.5745446. The “lapses” dimension is only influenced by the city population size, with a larger city population size leading to higher occurrence of unintentional deviation from rules. The “transgressions” dimension (violations and errors) is influenced by age, with younger people making more transgressions, and also by geographical zones, with a higher transgressions score for the “Sud” (South) Zone than the “Est” (East) area (however, see the Tukey test for further details). The “aggressive behaviors” axis is influenced only by the zone but the posthoc test revealed no differences. Finally, the positive behaviors dimension is influenced by gender, with women showing more positive behavior than men do.\n\nHDF for Hauts-de-France, IDF for Ile-de-France. QuartilePop indicates size of towns populations as quartiles.\n\nWe did not identify any statistical correlation between the eye image questionnaire score and the four PBQ dimensions (Figure 4). Lapses dimension: r= 0.05, t = 1.2843, df = 608, p-value = 0.1995; Transgressions dimension: cor = 0.02, t = 0.47498, df = 608, p-value = 0.635, Aggressive behaviors dimension: r = -0.07, t = -1.8156, df = 608, p-value = 0.06993; Positive behaviors dimension: r = 0.05, t = 1.129, df = 608, p-value = 0.2593.\n\n\n4. Discussion\n\nThis study tested the potential impact of different eye images – friendly, neutral, and angry –and one image of flowers as a control on pedestrians crossing at the red light. In their responses to an online questionnaire about their feelings on seeing these images, participants revealed that they initially felt observed (about 33%), then surprised (26%), then inhibited to cross at the red signal (10%). Finally, few were scared (5%) or felt encouraged to cross at the red signal (2%). Eye images encourage cooperative behavior because unlike pictures of flowers, they make participants feel like they are being watched (Pfattheicher and Keller, 2015). Our results are in line with this explanation, as flowers obtained a null score for being observed or scared. Moreover, the expression conveyed by the eyes also affects participants, as feelings of being observed increased by about 10-15% whilst feelings of being scared or reluctant to cross the road increased by about 5% as the expression changed from neutral to friendly to angry. This study confirms that humans react to faces but rates of negative reactions to the eyes are low, indicated a mixed effect. Indeed, we expected more participants to answer that they feel observed, afraid or surprised by the eyes images. Previous studies have shown that this reaction can play a role in maintaining the cooperative behaviors that are essential to life in societies (Alexander, 1987; Bateson et al., 2006; Burnham and Johnson, 2005) and it is interesting to put in light our results with these studies.\n\nAs predicted by our hypothesis, we found that the gender and age of participants affected their feelings when looking at the eye images. Women were more affected by the images than men were, and younger participants also reacted more than older individuals. Few studies have analyzed the effect of these two variables on the reaction to eye images, maybe because of anonymity in questionnaires or the low number of participants. Two studies report that gender did not influence reactions to eye images (Rodriguez Mosquera et al., 2011; Sparks and Barclay, 2013). However, it is not surprising to find that women felt more observed or scared than men when looking at the eye images, as studies showed women to be more empathic and therefore more receptive in different situations (Flynn, 2000; Furnham et al., 2003; Kellert & Berry, 1987; Miller et al., 2009). In the context of road crossing, women show also fewer illegal andrisky behaviors than men (Holland and Hill, 2007; Pelé et al., 2017; Sueur et al., 2013; Tom and Granié, 2011). Women also show more positive behaviors, as shown in our study, and fewer violations or aggressive behaviors than men do (Deb et al., 2017; Tom and Granié, 2011).\n\nAlthough we expected the effect of eye images on feelings to increase with age, the contrary was observed. To our knowledge, this is the first study on the effect of eye images to date that has reported such a result. However, studies of pedestrian behaviors showed younger people to be less respectful of rules (Holland and Hill, 2007; Pelé et al., 2017; Pfeffer and Hunter, 2013). This is confirmed in our study, which shows more violations by younger participants than by their older counterparts. Elder pedestrians can also display some illegal behaviors but these are generally due to cognitive or physical disorders (Laurin et al., 2001; Yaffe et al., 2001). Contrary to past studies using PBQ (Deb et al., 2017; Granié et al., 2013), we did not find an age effect on each pedestrian behavior axis. Our results show an effect of the city population size on the lapses dimension, meaning that citizens living in big cities show more unintentional violations and/or are more distracted than the inhabitants of small cities, probably because of the density of the population or visual distractions such as shops, signs or public transport. Participants from the South of France seem to display more violations and aggressive behaviors than those from the rest of France.\n\nNo link was found between the results of our questionnaire and those of the Pedestrian Behavior Questionnaire (PBQ). We expected participants showing high scores for violations and aggressive behaviors in the PBQ (or low scores for positive behaviors) to feel less observed or scared by the eye images. However, no correlation was found. This can be explained by a number of reasons. A participant may feel concerned by the eye image but will behave aggressively towards a driver because as a pedestrian, s/he considers that the driver is wrong (and thus seeks to communicate this anger). Alternatively, a participant may not feel concerned by the eyes image because irrespective of who is watching him/her, s/he will always behave well and consider the behavior of the driver - if the latter also behaves well - as reciprocal (Burnham and Johnson, 2005; Fehr and Fischbacher, 2004). This absence of correlation may be due to differences in the empathic profiles of the population, ranging from people who are naturally cooperative and/or react to eye images in order to ensure they are seen in a positive light, to those who are not cooperative at all and are more likely to react to punishment (Boyd and Richerson, 1992; Fehr and Gachter, 2000). Although we expected people who followed the rules to be non-violent, the two traits may not be correlated. In other words, a person may react to eye images and be cooperative or follow the rules but be aggressive towards people who do not do likewise. Conversely, another person may be indifferent to others, and will therefore not react to eye images or behave aggressively towards people who do not respect the rules. A second explanation is that the questionnaire is based on a virtual situation that did not affect participants’ feelings in the same way as the real situation, thus decreasing the potential correlation between our variables (Francey and Bergmüller, 2012). Past studies have indeed shown a great variability of participants responding to eye images according to the experimental setup that is used (see for instance Fehr & Schneider, 2010; Northover et al., 2017 for negative results). Anonymity also has a negative impact on the effect of eye images (Lamba and Mace, 2010), and this could have an impact in our study.\n\n\n5. Conclusion\n\nA better understanding of human cooperative behavior in real life is of key interest for social management, from both theoretical and practical perspectives. The present study shows that the use of eye images could help to reduce illegal crossings by pedestrians. However, this effect is limited as not a majority of participants answered that they felt observed, afraid and so on. Drivers react to the smiles and gaze of pedestrians by permitting them to cross a road (Guéguen et al., 2015, 2016). Pedestrians behaving in this way could also be more cooperative. The mechanisms involved in maintaining a good reputation can also produce investments to serve the common good (Bshary and Bshary, 2010; Francey and Bergmüller, 2012). Our findings are of practical interest for those designing honesty-based systems, or wishing to maximize contributions to public commodities and services. In a meta-analysis of 15 experiments from 13 research papers (Dear et al., 2019), found a 35% reduction in the risk of antisocial behavior when eye images are present. In contrast, systematic reviews have suggested that CCTV cameras reduce crime by only 16%. Settling such eyes images nudges on pedestrian signals could have an effect, even a small one, but this could be enough to decrease significantly accidents, particularly considering the group effect of crossings (Pelé et al., 2017). However, how such effect persist in time as pedestrians could get habituated to the eyes as reprimand is absent. However, our study is based on a questionnaire and this nudge needs to be tested in real situations. We encourage authorities to adopt the use of eye image systems in crossing signals in order to decrease the number of illegal crossings and increase pedestrian safety. Field research as well as more ecologically valid situations must be added to laboratory-based studies to show the real effect of these eye images on human cooperative behaviors.\n\n\nData availability\n\nZenodo. Dataset for Eye image effect in the context of pedestrian safety: a French questionnaire study. DOI: https://doi.org/10.5281/zenodo.5745446", "appendix": "Acknowledgements\n\nWe thank Joanna Munro for paper editing service.\n\n\nReferences\n\nAlexander RD: The biology of moral systems, The biology of moral systems. Hawthorne, NY, US: Aldine de Gruyter; 1987.\n\nBateson M, Callow L, Holmes JR, et al.: Do Images of ‘Watching Eyes’ Induce Behaviour That Is More Pro-Social or More Normative? A Field Experiment on Littering. PLoS One. 2013; 8(12): e82055. PubMed Abstract \| Publisher Full Text\n\nBateson M, Nettle D, Roberts G: Cues of being watched enhance cooperation in a real-world setting. Biol. Lett. 2006; 2(3): 412–414. PubMed Abstract \| Publisher Full Text\n\nBaxter JS, Macrae C, Manstead AS, et al.: Attributional biases and driver behaviour. Soc. Behav. 1990.\n\nBoyd R, Richerson PJ: Punishment allows the evolution of cooperation (or anything else) in sizable groups. Ethol. Sociobiol. 1992; 13(3): 171–195. 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Publisher Full Text" }	[ { "id": "167907", "date": "17 Apr 2023", "name": "Yunchang Zhang", "expertise": [ "Reviewer Expertise Social Behavior", "human interactions." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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-established paper, and I enjoyed reading this paper. Several comments:\nFor the design of experiment, I’m wondering whether eye contact is enough to explain the feeling of friendly, neutral, surprise, anger, etc. I think more rigorous design or evidence is needed here to prove your control and treatment.\n\nI felt that a power analysis is missing in this paper, although fruitful statistical analyses have been conducted. A power analysis will be helpful to demonstrate you have enough samples for the following analyses.\n\nSection 3.3, the authors should list the procedures of Kaiser-Meyer-Olkin measure and Bartlett’s test procedures and explain them in detail in this section. For example, a question will be why does a 0.80 of Kaiser-Meyer-Olkin measure is considered satisfactory?\n\nWhen I read Tables 2 and 3, I got lost by the meanings of variables. What are the values of these variables? Indicators or continuous variables? I recommend using a table for these explanatory variables.\n\nAdditionally, the authors should state the number of comparisons in the Tukey multiple comparisons and the confidence level you choose to make the adjustments since 2 comparisons and 20 comparisons have significant differences.\n\nThe discussion of sociodemographic factors on behavior is vague. Neither did the authors provide statistical numbers, nor persuasive explanations about the differences between South of France and the rest of France.\n\nI understand that there is limited literature regarding the impact of eye contact on pedestrian behavior, but I expected a well-established paragraph regarding the future directions of your research. For example, is a questionnaire adequate for the study? Would a simulator study or site observations be better 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? 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": "9803", "date": "25 Sep 2023", "name": "Cédric Sueur", "role": "Author Response", "response": "This is a well-established paper, and I enjoyed reading this paper. Several comments: For the design of experiment, I’m wondering whether eye contact is enough to explain the feeling of friendly, neutral, surprise, anger, etc. I think more rigorous design or evidence is needed here to prove your control and treatment. Response: We based our experiment on previous studies showing the importance of eyes in social control. Specifically, in sad and angry facial expressions, the eyes received more attention than the mouth (Eisenbarth and Alpers, 2011). It is right that different studies show also the importance of the mouth in facial expression recognition (Calvo and Fernández-Martín, 2013) but eyes tend to attract the highest proportion of fixations (Guo and Shaw, 2015). However, we wanted to build a protocol comparable to eye effect experiments as indicated in our introduction: “With this in mind, Bateson et al. (2006) conducted an experiment to test the effect of eye images on cooperative behavior. In the coffee area of a building at the University of Newcastle, an honesty box was used for people to make contributions to the coffee fund. The experiment consisted of placing pictures of eyes or flowers close to this box and assessing whether they led to differences in the contributions made. The authors found that in the presence of eye images, subjects paid on average 2.76 times more than when flowers images were displayed. Still comparing the effect of these flowers images as control to those of eye images, other studies have found similar prosocial effects during everyday events. For example, eye images had prosocial effects such as cooperation for the clearing of trays in a university cafeteria ( Ernest-Jones et al., 2011) and for waste sorting at a bus stop ( Francey and Bergmüller, 2012). Similar results were found in experiments in more specific contexts such as blood donations: While eye images on flyers did not result in differences in pledge with a logo as control, more “real” donations were made by students who got the flyers with eyes image ( Sénémeaud et al., 2017). Other than the activation of a “sense of being seen” ( Pfattheicher and Keller, 2015) or the desire to maintain a pro-social reputation ( Bateson et al., 2006), it is important to note that humans possess neurons that respond to faces and eyes and activate such prosocial behaviors ( Emery, 2000; Haxby et al., 2000). Bateson et al. (2013) suggest that eye images induce more pro-social behavior regardless of local norms, thus suggesting that the application of eye images could be a means to combat anti-social behavior by triggering a feeling of shame ( Nugier et al., 2007).” So eye effect is well showed in the literature and we obtained in our study the results we expected. However, we added a part in the discussion: “This might be due to the fact that eyes are not enough to convey a facial expression and the presence of the mouth on the face pictures could conduct to stronger effects than the ones we obtained (Calvo and Fernández-Martín, 2013; Eisenbarth and Alpers, 2011; Guo and Shaw, 2015)” I felt that a power analysis is missing in this paper, although fruitful statistical analyses have been conducted. A power analysis will be helpful to demonstrate you have enough samples for the following analyses. Response: We added the power analysis: As per power computation of sample size using GPower version3.1.9.7, reported 262 participants were required for this research at an α value 0.05, power equal to 0.95 and with effect size 0.20. Section 3.3, the authors should list the procedures of Kaiser-Meyer-Olkin measure and Bartlett’s test procedures and explain them in detail in this section. For example, a question will be why does a 0.80 of Kaiser-Meyer-Olkin measure is considered satisfactory? Response: We indicated more details about this part: “The results explain 49.7% of total variance. The Kaiser-Meyer-Olkin measure of sampling adequacy (indicating the proportion of variance in your variables that might be caused by underlying factors with high values, close to 1.0, generally indicate that a factor analysis may be useful with your data, Trujillo-Ortiz et al., 2006) was satisfactory and good (0.80) and the Bartlett’s test of sphericity was significant (p < 0.0001) indicating a homogeneity of variances.” When I read Tables 2 and 3, I got lost by the meanings of variables. What are the values of these variables? Indicators or continuous variables? I recommend using a table for these explanatory variables. Response: We indicated these details in the statistical analyses: “We assessed whether this score is influenced by the following dependent variables: the age (continuous variable), gender (factor: Male or Female), geographical zone of their city (factor with seven zones) or the city population size (as a factor categorized according to quartiles).” We added details about the values of these variables: “The questionnaire was received by 1,447 participants, 610 of whom answered the entire questionnaire (all three steps). The resulting dataset was used in our analyses (N=610). The mean time to answer the entire questionnaire was seven minutes. 71% of participants were women, and the mean age was 35 ± 14 years (min = 16, max = 84). The geographic repartition of the population is as follows: Hauts-de-France (N=17), Ile-de-France (N=100), Ouest (N=92), Est (N=219), Sud-Ouest (N=18), Sud-Est (N=75), Sud (N=89). Population size of cities was 237535±252149 (min = 46; max = 2220445). These factors were included in statistical analyses to avoid selection biases selection.” Additionally, the authors should state the number of comparisons in the Tukey multiple comparisons and the confidence level you choose to make the adjustments since 2 comparisons and 20 comparisons have significant differences. Response: The Tukey multiple comparisons were made on the seven zones. We indicated the details in the statistical analyses: “For the “zone” variable (n = 7), an Anova followed by a Tukey posthoc test (df = 6, 603, confidence level = 0.95) was performed on the GLM residuals.” The discussion of sociodemographic factors on behavior is vague. Neither did the authors provide statistical numbers, nor persuasive explanations about the differences between South of France and the rest of France. Response: We have looked for explanations about high violence rate in France but it is difficult to find some, first because it is forbidden in France to make link between sociodemographic factors, religion and criminality. However, we added sentences: Indeed, studies from the French Homeland Ministry reported that South of France is one of the regions with the highest violence rate. This region is also one with the highest road accident rate, mostly due to the population density (ONISR, 2021). However, reported per inhabitant, South of France, with Ile-De-France are the two regions with the highest contravention rate (ONISR, 2021). I understand that there is limited literature regarding the impact of eye contact on pedestrian behavior, but I expected a well-established paragraph regarding the future directions of your research. For example, is a questionnaire adequate for the study? Would a simulator study or site observations be better etc? Response: We added sentences about this in the conclusion. We realised a real-world situation experiment and submitted a paper. Moreover, we are working on a simulator study. References Calvo, M.G., Fernández-Martín, A., 2013. Can the eyes reveal a person’s emotions? Biasing role of the mouth expression. Motiv Emot 37, 202–211. https://doi.org/10.1007/s11031-012-9298-1 Eisenbarth, H., Alpers, G.W., 2011. Happy mouth and sad eyes: Scanning emotional facial expressions. Emotion 11, 860–865. https://doi.org/10.1037/a0022758 Guo, K., Shaw, H., 2015. Face in profile view reduces perceived facial expression intensity: An eye-tracking study. Acta Psychologica 155, 19–28. https://doi.org/10.1016/j.actpsy.2014.12.001 Trujillo-Ortiz, A., Hernandez-Walls, R., Castro-Perez, A., Barba-Rojo, K., Otero-Limon, A., 2006. kmo: Kaiser-Meyer-Olkin Measure of Sampling Adequacy. A MATLAB file.[WWW document]. URL http://www. mathworks. com/matlabcentral/fileexchange/loadFile. do." } ] }, { "id": "172758", "date": "25 May 2023", "name": "Rahul Raoniar", "expertise": [ "Reviewer Expertise Walkable and Cyclable Cities", "Road Safety", "Injury Prevention", "Transport Psychology", "Transportation Accessibility", "and Quantitative Social Research." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study focuses on exploring the effect of eye image on pedestrian road crossing behavior (signal violation). The overall work is good; still, the authors need to address the following comments to strengthen the manuscript further:\nAbstract None\nIntroduction Human eye contact, facial expressions (smile), and hand gestures could lead to changes in driver behavior (page 3 of the pdf) and also helps pedestrian to cross busy roads.\nThese might not be the only factors that determine the signal violation behavior. There are numerous factors like non-social (traffic volume, composition, infrastructure) and social (presence of others and in a group), and individual (gender, age, speed, and waiting patience).\n\nThe literature should highlight these aspects as well, which will add more value to the current study context.\n\nMethod\nQuestionnaire Participants completed a questionnaire of 20 questions about pedestrian behaviors by Deb et al. (2017).\nAre these questions about general pedestrian behavior (compliance) at signalized crosswalks?\n\nWhether the short version questionnaire set tested locally to optimize the time?\n\nWhat was the average completion time and response rate?\n\nAs this is an online survey, does this represent the French population? If not, isn’t it introduce bias in the study results?\n\nWhether the sample size is enough?\n2.4 Statistical Analysis The statistical analysis part is a little bit difficult to understand. It is recommended to add a flowchart of the entire method and describe the methodology systematically. This will provide a better understanding to the readers and help them reproduce the results.\nPCA and clustering techniques are common to identify internal relationships (similarities). The authors should explain the methods briefly to improve the understanding of the statistical analysis.\n\nResults The first cluster includes the flower, and a man and a woman with neutral expressions. It has a lower influence on the scores (see green elements in Table 1; participants do not feel surprised, scared, observed or inhibited).\nThere are no green elements in Table 1. The color coding for the clusters is missing.\nTable 1: Colors indicate the clusters assessed by the HCPC, from the least intense (green) to the most intense (red) feeling.\nThe colors are not visible in Table 1. Fix the color coding in the table.\nDue to missing color coding (green and red) in Table 1, it is impossible to validate some of the statements. The authors should fix the table.\nDiscussion No link was found between the results of our questionnaire and those of the Pedestrian Behavior Questionnaire (PBQ). We expected participants showing high scores for violations and aggressive behaviors in the PBQ (or low scores for positive behaviors) to feel less observed or scared by the eye images. However, no correlation was found.\nThe online response and real-world scenario of crossing decisions are different. A crossing decision in a dangerous situation is not just born by what eye expression other gives when going against the social norm (like violating a signal). Still, it also depends on many factors (traffic, infrastructure, and situational). The author should explore and add these factors to explain the study outcomes.\nConclusions In a meta-analysis of 15 experiments from 13 research papers (Dear et al., 2019), found a 35% reduction in the risk of antisocial behavior when eye images are present. In contrast, systematic reviews have suggested that CCTV cameras reduce crime by only 16%.\nThe example presented by the author is context specific. The presence of CCTV indeed reduces crime (in particular places). But jaywalking or signal violation is not considered a crime in many countries, especially in developing countries, where rules and regulations are not strict and there are no penalties for signal violation. Thus, just promoting the positive value of social control alone is not enough to enhance compliance; traffic and infrastructure-related safety measures are also needed. Authors should explore and add more transportation study examples that would help better explain the outcomes.\n\nAn online questionnaire survey won’t reflect how pedestrians respond in real-world traffic situations. Past studies showed that other people's presence impacts signal compliance:\na) Rosenbloom, T., 2009. Crossing at a red light: Behaviour of individuals and groups. Transp. Res. Part F: Traffic Psychol. Behav. 12 (5), 389–394. b) Faria, J.J., Krause, S., Krause, J., 2010. Collective behavior in road crossing pedestrians: the role of social information. Behav. Ecol. 21 (6), 1236–1242. c) Raoniar, R. and Maurya, A. K., 2022. Pedestrian Red-Light Violation at Signalized Intersection Crosswalks: Influence of Social and Non-Social Factors, Safety Science, vol. 147. pp. 105583.\n\nSeeing different emotions disseminated through eye expressions could reflect the emotional response from a peer or group member while someone in the group goes against the norm. But a person might not see others' facial reactions (non-peers) while making the final crossing decision.\n\nDo facial expression/eye image alone enough to improve compliance? If not, why?\n\nAuthors need to validate the findings in a controlled experimental setting or through a real-world observational setting. If not possible in the current study context, it should be highlighted in the study limitations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9804", "date": "25 Sep 2023", "name": "Cédric Sueur", "role": "Author Response", "response": "The study focuses on exploring the effect of eye image on pedestrian road crossing behavior (signal violation). The overall work is good; still, the authors need to address the following comments to strengthen the manuscript further: Abstract None Introduction Human eye contact, facial expressions (smile), and hand gestures could lead to changes in driver behavior (page 3 of the pdf) and also helps pedestrian to cross busy roads. These might not be the only factors that determine the signal violation behavior. There are numerous factors like non-social (traffic volume, composition, infrastructure) and social (presence of others and in a group), and individual (gender, age, speed, and waiting patience). The literature should highlight these aspects as well, which will add more value to the current study context. Response: We added a new section in the introduction about all these factors. Method Questionnaire Participants completed a questionnaire of 20 questions about pedestrian behaviors by Deb et al. (2017). Are these questions about general pedestrian behavior (compliance) at signalized crosswalks? Response: We indicated the information: “The Pedestrian Behaviour Scale (PBS) is a self-report questionnaire that distinguishes five dimensions of pedestrian behaviour. Most questions concern pedestrian crossing at signalised crosswalk but some not (Vandroux et al. 2022).” Whether the short version questionnaire set tested locally to optimize the time? Response: Yes, this is indicated in the paper (This questionnaire was originally developed by Tom and Granié (2011) with 47 questions. We chose the short version, which is considered as reliable as the long version according to Deb et al. (2017) and Tom and Granié (2011), in order to avoid demotivating participants.) but we added details : “We used a pedestrian behavior questionnaire (PBQ) with 20 questions, developed by ( Deb et al., 2017) and taken from ( Tom and Granié, 2011) to optimise time as some original questions gave correlated answers (Vandroux et al. 2022).” What was the average completion time and response rate? Response: The response rate was 42.15%. The average completion time was 334±310 sec. We added this information. As this is an online survey, does this represent the French population? If not, isn’t it introduce bias in the study results? Response: Yes, this is indicated in the paper: “The survey was created using LimeSurvey ( Engard, 2009; Jayasundara et al., 2010; LimeSurvey Project Team, 2012) and administered online to the French population through mails and social media (Facebook and Twitter).” Whether the sample size is enough? Response: Yes, we indicated the information: As per power computation of sample size using GPower version 3.1.9.7, reported 262 participants were required for this research at an α value 0.05, power equal to 0.95 and with effect size 0.20. 2.4 Statistical Analysis The statistical analysis part is a little bit difficult to understand. It is recommended to add a flowchart of the entire method and describe the methodology systematically. This will provide a better understanding to the readers and help them reproduce the results. Response: We added an introduction sentence and some bullet points to make the understanding easier. PCA and clustering techniques are common to identify internal relationships (similarities). The authors should explain the methods briefly to improve the understanding of the statistical analysis. Response: We added a paragraph on PCA and HCPC: PCA is a statistical method of reduction of variables in new dimensions usually meaningful. Variables are automatically corrected to be comparable (mean and range). Dimensions (groups of different variables) with eigenvalue superior to 1 are kept. We examined loadings of each variable on each dimension. The loadings are interpreted as the coefficients of the linear combination of the initial variables from which the principal components are constructed. The loadings are equal to the coordinates of the variables divided by the square root of the eigenvalue associated with the component. The goal of HCPC is to identify groups (i.e. clusters) of similar objects within a data set of interest. Results The first cluster includes the flower, and a man and a woman with neutral expressions. It has a lower influence on the scores (see green elements in Table 1; participants do not feel surprised, scared, observed or inhibited). There are no green elements in Table 1. The color coding for the clusters is missing. Response : sorry about that, this is not our fault but an editing error. This is corrected. Table 1: Colors indicate the clusters assessed by the HCPC, from the least intense (green) to the most intense (red) feeling. The colors are not visible in Table 1. Fix the color coding in the table. Response : sorry about that, this is not our fault but an editing error. This is corrected. Due to missing color coding (green and red) in Table 1, it is impossible to validate some of the statements. The authors should fix the table. Response : sorry about that, this is not our fault but an editing error. This is corrected. Discussion No link was found between the results of our questionnaire and those of the Pedestrian Behavior Questionnaire (PBQ). We expected participants showing high scores for violations and aggressive behaviors in the PBQ (or low scores for positive behaviors) to feel less observed or scared by the eye images. However, no correlation was found. The online response and real-world scenario of crossing decisions are different. A crossing decision in a dangerous situation is not just born by what eye expression other gives when going against the social norm (like violating a signal). Still, it also depends on many factors (traffic, infrastructure, and situational). The author should explore and add these factors to explain the study outcomes. Response: We agreed, but here we based this point on only psychological/intrinsic factors as both the PBQ questionnaire and the eye image questionnaire were made online. So we still think that participants showing high scores for violations and aggressive behaviors in the PBQ (or low scores for positive behaviors) should feel less observed or scared by the eye images. However, we added the other factors influencing the pedestrian behaviours in the introduction. Conclusions In a meta-analysis of 15 experiments from 13 research papers (Dear et al., 2019), found a 35% reduction in the risk of antisocial behavior when eye images are present. In contrast, systematic reviews have suggested that CCTV cameras reduce crime by only 16%. The example presented by the author is context specific. The presence of CCTV indeed reduces crime (in particular places). But jaywalking or signal violation is not considered a crime in many countries, especially in developing countries, where rules and regulations are not strict and there are no penalties for signal violation. Thus, just promoting the positive value of social control alone is not enough to enhance compliance; traffic and infrastructure-related safety measures are also needed. Authors should explore and add more transportation study examples that would help better explain the outcomes. Response: You are right, we added your point in the discussion. An online questionnaire survey won’t reflect how pedestrians respond in real-world traffic situations. Past studies showed that other people's presence impacts signal compliance: a) Rosenbloom, T., 2009. Crossing at a red light: Behaviour of individuals and groups. Transp. Res. Part F: Traffic Psychol. Behav. 12 (5), 389–394. b) Faria, J.J., Krause, S., Krause, J., 2010. Collective behavior in road crossing pedestrians: the role of social information. Behav. Ecol. 21 (6), 1236–1242. c) Raoniar, R. and Maurya, A. K., 2022. Pedestrian Red-Light Violation at Signalized Intersection Crosswalks: Influence of Social and Non-Social Factors, Safety Science, vol. 147. pp. 105583. Response: We added this element and references in the introduction. Seeing different emotions disseminated through eye expressions could reflect the emotional response from a peer or group member while someone in the group goes against the norm. But a person might not see others' facial reactions (non-peers) while making the final crossing decision. Response: We added this limitation of our study in the conclusion. Do facial expression/eye image alone enough to improve compliance? If not, why? Response: We based our experiment on previous studies showing the importance of eyes in social control. Specifically, in sad and angry facial expressions, the eyes received more attention than the mouth (Eisenbarth and Alpers, 2011). It is right that different studies show also the importance of the mouth in facial expression recognition (Calvo and Fernández-Martín, 2013) but eyes tend to attract the highest proportion of fixations (Guo and Shaw, 2015). However, we wanted to build a protocol comparable to eye effect experiments as indicated in our introduction: “With this in mind, Bateson et al. (2006) conducted an experiment to test the effect of eye images on cooperative behavior. In the coffee area of a building at the University of Newcastle, an honesty box was used for people to make contributions to the coffee fund. The experiment consisted of placing pictures of eyes or flowers close to this box and assessing whether they led to differences in the contributions made. The authors found that in the presence of eye images, subjects paid on average 2.76 times more than when flowers images were displayed. Still comparing the effect of these flowers images as control to those of eye images, other studies have found similar prosocial effects during everyday events. For example, eye images had prosocial effects such as cooperation for the clearing of trays in a university cafeteria ( Ernest-Jones et al., 2011) and for waste sorting at a bus stop ( Francey and Bergmüller, 2012). Similar results were found in experiments in more specific contexts such as blood donations: While eye images on flyers did not result in differences in pledge with a logo as control, more “real” donations were made by students who got the flyers with eyes image ( Sénémeaud et al., 2017). Other than the activation of a “sense of being seen” ( Pfattheicher and Keller, 2015) or the desire to maintain a pro-social reputation ( Bateson et al., 2006), it is important to note that humans possess neurons that respond to faces and eyes and activate such prosocial behaviors ( Emery, 2000; Haxby et al., 2000). Bateson et al. (2013) suggest that eye images induce more pro-social behavior regardless of local norms, thus suggesting that the application of eye images could be a means to combat anti-social behavior by triggering a feeling of shame ( Nugier et al., 2007).” So eye effect is well showed in the literature and we obtained in our study the results we expected. However, we added a part in the discussion: “This might be due to the fact that eyes are not enough to convey a facial expression and the presence of the mouth on the face pictures could conduct to stronger effects than the ones we obtained (Calvo and Fernández-Martín, 2013; Eisenbarth and Alpers, 2011; Guo and Shaw, 2015)” Authors need to validate the findings in a controlled experimental setting or through a real-world observational setting. If not possible in the current study context, it should be highlighted in the study limitations. Response: We added sentences in the conclusion to discuss this point. Indeed, we performed a controlled experiment in real-world situations and the paper is submitted. However this current study is still interesting as it allows to get sociodemographic information and a wide spectrum of people and cities that we cannot get in an empirical study." } ] } ]	1	https://f1000research.com/articles/11-218
https://f1000research.com/articles/12-1202/v1	25 Sep 23	{ "type": "Study Protocol", "title": "Comparison of rheumatoid arthritis factors, adenosine deaminases and uric acid in arthritis and non-arthritis patients: A protocol", "authors": [ "Priyanka A. Makhe", "Anjali Vagga", "Archana Dhok", "Anjali Vagga", "Archana Dhok" ], "abstract": "Rheumatic disorders are viewed as a public health issue because they affect thousands of individuals around the world and increase health care expenses. Numerous biochemical markers may play a role in the pathophysiology and etiology of rheumatoid arthritis (RA) due to its local as well as systemic inflammatory effects. Rheumatoid factors (RF) can be found in a variety of people, including young, healthy people, the elderly, and people with RA. In this study we will assess and compare the occurrence, clinical presentation, effects and possible risk of biochemical parameters such as uric acid, adenosine deaminase (ADA,), RA factor between arthritis patients and non - arthritis patients. A total of 82 participants — 41 RA patients and 41 healthy controls (non-arthritis patients) —will be included in the study. The levels of serum ADA, uric acid, and rheumatoid factor will be examined, and independent tests will be used for the statistical analysis. Serum ADA rheumatoid factors levels in RA patients is higher in healthy control. When comparing the uric acid levels of RA patients with healthy controls, there is no significant change in the uric acid level. The degree underlying ADA activity between RA patients and healthy individuals should differ noticeably, confirming the test’s value in the diagnosis of the condition.", "keywords": [ "Uric Acid", "Adenosine Deaminases", "Ra Factor", "Rheumatoid Arthritis", "Non-Arthritis Patients", "Biochemical Parameters", "Healthy Control", "Antibodies." ], "content": "Introduction\n\nTargeting the Fc region, which is a part of immunoglobulin G, are antibodies with various isotypes and affinities that are referred to as rheumatoid factors. As mentioned in the literature, since the first discovery of rheumatoid factors 80 years ago, the identification of both anticitrullinated protein antibody and anti-carbamylated protein antibodies has greatly facilitated approaches for early diagnosis of RA.1 Patients started exhibiting signs of rheumatoid arthritis before 70 years ago.1\n\nAn antibody described by Waaler in 1940 boosted the agglutination of sheep red blood cells when subagglutinating doses of rabbit antibodies were used. Meyer first identified serum gamma-globulins as a target of these antibodies in 1922 in Ref. 2 patients with chronic bronchitis and liver cirrhosis. In 1948, Rose became the first to describe these antibodies among rheumatoid arthritis patients.3 They were finally given the name “rheumatoid factors” in 1952 because of their link to rheumatoid arthritis (RA).4 Adenosine deaminase (ADA) breaks down adenosine. ADA has been proposed as a helpful indicator5 to assist in the diagnosis, prognosis, as well as therapy assessment of RA.6 It is recognised as a reliable sign of cell-mediated immunity. ADA activity is increased in rheumatoid arthritis patients.7\n\nAdenosine deaminase is an enzyme that promotes the unchangeable hydrolytic deamination of adenosine to inosine and 2′-deoxyadenosine to 2′-deoxyinosine in red blood cells and the arterial wall. Hypoxanthine, xanthine, and then uric acid (UA) are produced from inosine and 2′-deoxyinosine.8 In humans, both endogenous as well as dietary purine metabolism produce UA.9 The substantial correlation between the level of blood including interleukin-6 (IL-6), C-reactivity protein (CRP), tumour necrosis factor (TNF) and serum UA raises the possibility that UA plays a significant role in systemic inflammation in inflammatory-related diseases, including RA.10\n\nThe oxidant-antioxidant status of RA patients can be assessed by measuring their serum UA and ADA.\n\nPatients with a variety of nonrheumatic arthritic disorders can have RFs. The majority of the time, CD5-positive B cells naturally generate polyreactive, low-affinity IgM antibodies as RFs.11,12 RFs are detectable in 40–50% of hepatitis C virus-infected patients, while their frequency might reach 76%.13\n\nRA constitutes a symmetrical, chronic, inflammatory autoimmune disease which initially affects cartilage and joints as well as the eyes, skin, heart, kidneys, and lungs. Inflammation (painful swelling) takes place in the affected body parts as a result of the body’s immune system mistakenly attacking healthy cells in the body.14\n\nJoint destruction is frequently a gradual result of synovial inflammation and degradation.15 The most prevalent autoimmune systemic illness in the world is RA.16 In the general population, RA affects 1-2% of people.17 Approximately 70% patients have irreparable joint injury, and 80% of active young individuals in the workforce suffer from stiffness and agonising pain.18 Approximately 0.5–1% of people worldwide have RA19 and 1% worldwide.20\n\nRA affects around 10 million people in India alone.21 Women are far more likely than men to develop RA between the ages of 40 and 60.22 RA patients are 1.5–2 times more likely to develop cardiovascular disease (CVD) than persons without the condition who are the same age and sex.23\n\nTo assess the occurrence, prevalence, clinical presentation and possible risk factors of UA, ADA, RA factor in arthritis and non-arthritis patients.\n\n• To measure the prevalence of ADA in people with RA.\n\n• To measure the prevalence of UA in people with RA.\n\n• To calculate the prevalence of RA factors in people with RA.\n\n• To calculate the prevalence of RA factors in patients without RA.\n\n• To calculate the prevalence of ADA in patients without RA.\n\n• To calculate the concentration of UA in patients without RA.\n\n\nProtocol\n\nThe study will be conducted among the common population of the Vidarbha district in AVBRH hospital. Between RA patients and their healthy controls, there should be significant variations in the levels of the ADA RA factor as well as the activity of UA, which may suggest the test’s effectiveness in RA diagnosis.\n\n\nMaterial and methods\n\nThe following study will be started in collaboration on behalf of Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi (Meghe), Wardha, in the Biochemistry division of the Department of Biochemistry, Jawaharlal Nehru Medical College (JNMC), Sawangi (Meghe), conduct the study between October 2022-2024. A total of 41 RA patients will be enrolled as cases and 41 healthy patients will be enrolled as controls. Only patients between the ages of 30 and 60 will be chosen for this study. Before and throughout the trial, all ethical procedures will be followed and written consent form will be obtained at the time of sample collection. Patients with RA factor positivity will be considered for the trial. Patients with primary inflammatory joint illness, either currently or in the past, septic arthritis in a native joint, malignancy, demyelinating disease, soft tissue swelling, rheumatoid nodules, osteopenia in hand/wrist joints, radiographic erosive changes, and gout will be excluded from the study.\n\nFor collection of blood sample, the right arm’s antecubital site will be mostly selected. To puncture the site, a tourniquet, cotton, syringe, and rubbing alcohol will be needed. We will be applying the tourniquet about 3-4’ above the venipuncture site, after which we will clean the area by using a cotton and alcohol, and then the needle will be insert. According to requirements, samples will be collected in a plain vial (up to 5 mL). After collection of the sample, the tourniquet will be removed and cotton will be apply to prevent bleeding. Then the vial will be labelled with the patient’s name and required test name. After labelling, the sample will be sent to the biochemistry processing lab. In the lab, to process the sample, first the serum will be separated by using a REMI R-8C Plus centrifuge at 3000rpm for 5-7 min. Then the level of UA, ADA, RA (required test) will be measured by using a Vitros 5600 Dry Chemistry Analyzer Machine manufactured by Ortho Clinical Diagnostics.\n\nAfter centrifuge, the serum levels of UA, ADA, and RA factors will be measured using a Vitros 5600 Dry Chemistry Analyzer Machine manufactured by Ortho Clinical Diagnostics.\n\n1. For statistical analysis, SPSS software for windows version 27.0 will be used.\n\nStatical significance will be defined at p<0.001.\n\nThis study will be cross-analytical.\n\nThe study will be conducted at Aacharya Vinoba Bhave Rural Hospital Sawangi (Meghe), Wardha.\n\nThis research will include a total of 82 patients between 30-60 years old.\n\nSubjects of both sexes will be included.\n\nThe study will exclude patients experiencing swelling, rheumatoid nodules, osteopenia in hand/wrist joints, radiographic erosive changes, gout.\n\nAll necessary measures to control bias at all levels will be taken by using random sampling.\n\nFormula for sample size estimation:\n\nA total of 82 participants will be needed in the study, in which 41 will be patients and 41 will be healthy controls.\n\nThe data analysis will be done using relevant Chi-squared test for understanding the comparative difference between groups and among groups, whereas the results obtained during the research will be analyzed [using appropriate statistical method by a qualified statistician]. All the response will be calculated using software version 4.3.\n\nAll the results for the outcome variables will be presented in tables and will be described over descriptive statistics. Outcome variables (RA factor [IU/mL], ADA [U/L] and UA [mg/dL]) will first be tested for normality for the quantitative measurement of mean and standard deviation (SD). Positional average (median) statistics will be used to look for skewed distributions and calculating the interquartile range (IQR). All the binary and categorical variables will be described over the frequency and percentages for qualitative assessment. Results will be calculated using R software free version 4.3.2 for all statistical analyses.\n\nThe inferential statistics for testing the significant difference over the outcome variables will be evaluated at 5% level of significance (p ≤ 0.05). If data for the outcome variable shows a non-normal distribution for the quantitative assessment, it will be converted for normal distribution following mathematical algorithm. If data persist with a non-normal distribution we will use alternative non-parametric tests (Chi-square, Mann-Whitney U, Wilcoxon tests). Outcome variables like RA factor (IU/mL), ADA (U/L) and UA (mg/dL) will be subjected to a t-test (independent) to find the significance of the mean.\n\nThe study currently ongoing with sample collection and is expected to be completed before October 2024.\n\nA normal rheumatoid factor value may be less than 15 IU/mL, and one over 100 IU/mL is strongly associated with autoimmune diseases like RA. All RA patients should have their serum ADA levels (IU/L) checked, and these levels should be significantly greater in RA patients. In RA patients as well as healthy controls, UA levels may or may not vary significantly.\n\n\nDiscussion\n\nRheumatoid arthritis (RA) is a complex illness that affects many body tissues and the immune system. Overall, 80% of RA patients experience the initial symptoms and signs of the disease between the ages of 30 and 60, and females are likely to be affected by it two times more frequently than males. T cells may localise and increase the effector activities of monocyte/macrophages in rheumatoid illness, according to the predominance among T cells as well as monocyte/macrophages in rheumatoid synovium.24,25\n\nNeha Singh and co-workers (2021) aimed to evaluate patient education regarding rheumatoid arthritis. They found that the severity of RA, a chronic, inflammatory, and systemically autoimmune disease, on a patient” joints varies. Sex, age, genetics, environmental factors (tobacco use, exposure to air pollution, and occupational hazards) are risk factors. If left untreated, Felty syndrome can develop into a variety of consequences, including rheumatoid vasculitis, persistent joint damage needing arthroplasty, and Felty syndrome necessitating splenectomy. The objectives of treatment for RA are to alleviate discomfort and prevent/slow additional damage because there is no known cure. Here, we give a succinct overview of the numerous previous and present therapy options for RA problems.14\n\nZahra Zakeri et al. (2012) discovered that patients with osteoarthritis and RA differed in their serum as well as synovial fluid levels of ADA. It is crucial to ascertain the degree of inflammation and the response to treatment because of the chronic nature of RA, the disease’s poorly understood pathophysiology, and the disabling character of the condition. Therefore, the ability of the synovial fluid ADA to diagnose RA was assessed in this study as a result of non-specific clinical characteristics and a lack of diagnostic assays.26\n\nAccording to Zamani et al., there is a correlation between the ADA and disease activity, and blood ADA levels may aid in predicting activity of the disease in RA patients.27\n\nAccording to Nalesnik et al., ADA activation is directly linked to inflammation, and it may be an effective biochemical measure of the inflammatory process in people with RA.28\n\nChanchal Garg et al. (2019) observed the CRP, UA and ADA levels in patients with RA. Synovial membrane inflammation is a hallmark of RA, while a state of oxidative stress is frequently linked to tissue damage. UA and inflammation are both significantly influenced by ADA, an endogenous antioxidant with the ability to scavenge free radicals. According to the study’s findings, RA patients had considerably higher serum levels of ADA, CRP, and rheumatoid factor as compared to controls.29 This studyalso assessed how much UA is present. UA acts as a protective antioxidant that is especially good at binding hydroxyl, superoxide, and peroxinitrite radicals, which helps to avoid lipid peroxidation. There was no discernible difference in the levels of UA between RA patients and healthy participants. The study exhibited normal UA levels; however, this may be due to raised utilisation of UA in capturing free radicals and converting them to allantoin. An increase in UA levels due to enhanced ADA levels among RA patients is expected.27,30,31\n\nPeople all throughout the world are afflicted by RA. There are around 10 million RA sufferers in India. Over 70% of those who have rheumatoid arthritis and experience exhaustion on a daily basis and have symptoms of chronic fatigue syndrome.\n\nHigh-affinity RFs are associated with more severe and long-lasting illness in RA patients, and low-affinity RFs have been shown to be important players in immunological responses to numerous pathogens.\n\nThe determination of RA and its consequences, which are brought on by the presence of UA and ADA among rheumatoid arthritis patients, were the main focus of this study. It has been discovered that ADA levels are elevated in RA patients, indicating the value of ADA in illness detection. The extracellular release of ADA during RA inflammation causes cell-mediated immunity to significantly boost its activity. It suggests that while UA may be considered a marker for the diagnosis of RA patients, it is not a meaningful signal in these individuals. In RA patients, UA levels are a significant predictor of renal impairment. Patients with increased UA who have RA may need to be screened for renal failure and given the proper care. According to one study, women who self-reported having RA had noticeably higher serum UA levels. Gout can be brought on by too much of this metabolic waste product in the blood. It results from increasing and crystallising urate. Joints could then become clogged with these crystals, which would hurt and inflame them.32\n\nBy conducting this study, we will be able to carry out early assessment of RA patients with their consent. This study will be helpful for prevention of autoimmune diseases like RA which causes high levels of UA and ADA in patients.\n\nOur study has a smaller sample size.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nThis study was approved by the Datta Meghe Institute of Higher Education Institutional Ethics Committee (DMIHER (DU)/IEC/2023/599).\n\n\nReferences\n\nWu CY, Yang HY, Luo SF, et al.: From rheumatoid factor to anti-citrullinated protein antibodies and anti-carbamylated protein antibodies for diagnosis and prognosis prediction in patients with rheumatoid arthritis. Int. J. Mol. Sci. 2021 Jan 12; 22(2): 686. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaaler E: On the occurrence of a factor in human serum activating the specific agglutination of sheep blood corpuscles. Acta Pathol. Microbiol. Scand. 1940 May; 17(2): 172–188. Publisher Full Text\n\nRose HM, Ragan C, Pearce E, et al.: Differential agglutination of normal and sensitized sheep erythrocytes by sera of patients with rheumatoid arthritis. Proc. Soc. Exp. Biol. Med. 1948 May; 68(1): 1–6. PubMed Abstract \| Publisher Full Text\n\nPike RM, Sulkin SE, Coggeshall HC: Serological Reactions in Rheumatoid Arthritis: I. Factors Affecting the Agglutination of Sensitized Sheep Erythrocytes in Rheumatoid-Arthritis Serum. J. Immunol. 1949 Dec; 63(4): 441–446. Publisher Full Text\n\nSalesi M, Ghazvini RA, Farajzadegan Z, et al.: Serum adenosine deaminase in patients with rheumatoid arthritis treated with methotrexate. J. Res. Pharm. Pract. 2012 Oct; 1(2): 72–76. PubMed Abstract \| Publisher Full Text\n\nSullivan JL, Osborne WR, Wedgwood RJ: Adenosine deaminase activity in lymphocytes. Br. J. Haematol. 1977 Sep; 37(1): 157–158. Publisher Full Text\n\nErkiliç K, Evereklioglu C, Çekmen M, et al.: Adenosine deaminase enzyme activity is increased and negatively correlates with catalase, superoxide dismutase and glutathione peroxidase in patients with Behçet’s disease: original contributions/clinical and laboratory investigations. Mediat. Inflamm. 2003 Apr 1; 12(2): 107–116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoshino T, Yamada K, Masuoka K, et al.: Elevated adenosine deaminase activity in the serum of patients with diabetes mellitus. Diabetes Res. Clin. Pract. 1994 Sep 1; 25(2): 97–102. PubMed Abstract \| Publisher Full Text\n\nFenech G, Rajzbaum G, Mazighi M, et al.: Serum uric acid and cardiovascular risk: state of the art and perspectives. Joint Bone Spine. 2014 Oct 1; 81(5): 392–397. PubMed Abstract \| Publisher Full Text\n\nLyngdoh T, Marques-Vidal P, Paccaud F, et al.: Elevated serum uric acid is associated with high circulating inflammatory cytokines in the population-based Colaus study. PLoS One. 2011 May 20; 6(5): e19901. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDresser DW: Most IgM-producing cells in the mouse secrete auto-antibodies (rheumatoid factor). Nature. 1978 Aug 3; 274(5670): 480–483. PubMed Abstract \| Publisher Full Text\n\nSlaughter LA, Carson DA, Jensen FC, et al.: In vitro effects of Epstein-Barr virus on peripheral blood mononuclear cells from patients with rheumatoid arthritis and normal subjects. J. Exp. Med. 1978 Nov 1; 148(5): 1429–1434. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPalazzi C, Buskila D, D’Angelo S, et al.: Autoantibodies in patients with chronic hepatitis C virus infection: pitfalls for the diagnosis of rheumatic diseases. Autoimmun. Rev. 2012 Jul 1; 11(9): 659–663. Publisher Full Text\n\nLee JE, Kim IJ, Cho MS, et al.: A case of rheumatoid vasculitis involving hepatic artery in early rheumatoid arthritis. J. Korean Med. Sci. 2017 Jul 1; 32(7): 1207–1210. Publisher Full Text\n\nMcInnes IB, Schett G: The pathogenesis of rheumatoid arthritis. N. Engl. J. Med. 2011 Dec 8; 365(23): 2205–2219. Publisher Full Text\n\nHaro I, Gómara MJ, Pérez ML, et al.: Antibodies against β-fibrin synthetic peptides: A study of their association with the immunogenetic background and disease course of rheumatoid arthritis patients. Eur. J. Med. Chem. 2011 Apr 1; 46(4): 1095–1102. Publisher Full Text\n\nKoehn C, Palmer T, Esdaile J: Rheumatoid arthritis: plan to win. Oxford University Press; 2002 Jan 10.\n\nFilipovic I, Walker D, Forster F, et al.: Quantifying the economic burden of productivity loss in rheumatoid arthritis. Rheumatology. 2011 Jun 1; 50(6): 1083–1090. PubMed Abstract \| Publisher Full Text\n\nHambright D, Henderson RA, Cook C, et al.: A comparison of perioperative outcomes in patients with and without rheumatoid arthritis after receiving a total shoulder replacement arthroplasty. J. Shoulder Elb. Surg. 2011 Jan 1; 20(1): 77–85. PubMed Abstract \| Publisher Full Text\n\nChopra A, Abdel-Nasser A: Epidemiology of rheumatic musculoskeletal disorders in the developing world. Best Pract. Res. Clin. Rheumatol. 2008 Aug 1; 22(4): 583–604. Publisher Full Text\n\nRani HS, Madhavi G, Srikanth BM, et al.: Serum ADA and C-reactive protein in rheumatoid arthritis. Int. J. Hum. Genet. 2006 Sep 1; 6(3): 195–198. Publisher Full Text\n\nEbringer A, Rashid T, Wilson C: Rheumatoid arthritis, Proteus, anti-CCP antibodies and Karl Popper. Autoimmun. Rev. 2010 Feb 1; 9(4): 216–223. PubMed Abstract \| Publisher Full Text\n\nLiao KP: Cardiovascular disease in patients with rheumatoid arthritis. Trends Cardiovasc. Med. 2017 Feb 1; 27(2): 136–140. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMonaco C, Andreakos E, Kiriakidis S, et al.: T-cell-mediated signalling in immune, inflammatory and angiogenic processes: the cascade of events leading to inflammatory diseases. Curr. Drug Targets Inflamm. Allergy. 2004 Mar 1; 3(1): 35–42. PubMed Abstract \| Publisher Full Text\n\nStamp LK, James MJ, Cleland LG: Interleukin-17: the missing link between T-cell accumulation and effector cell actions in rheumatoid arthritis? Immunol. Cell Biol. 2004 Feb; 82(1): 1–9. PubMed Abstract \| Publisher Full Text\n\nZakeri Z, Izadi S, Niazi A, et al.: Comparison of adenosine deaminase levels in serum and synovial fluid between patients with rheumatoid arthritis and osteoarthritis. Int. J. Clin. Exp. Med. 2012; 5(2): 195–200. PubMed Abstract\n\nZamani B, Jamali R, Jamali A: Serum adenosine deaminase may predict disease activity in rheumatoid arthritis. Rheumatol. Int. 2012 Jul; 32: 1967–1975. PubMed Abstract \| Publisher Full Text\n\nNalesnik M, Nikolić JM, Jandrić S: Adenosine deaminase and C-reactive protein in diagnosing and monitoring of rheumatoid arthritis. Med. Glas (Zenica). 2011 Feb 1; 8(1): 163–168. PubMed Abstract\n\nGarg C, Mishra MK, More NV: A STUDY FOR THE LEVEL OF ADENOSINE DEAMINASE CRP AND URIC ACID IN RHEUMATOID ARTHRITIS PATIENTS.\n\nMahajan M, Kaur S, Mahajan S, et al.: Uric acid a better scavenger of free radicals than vitamin C in rheumatoid arthritis. Indian J. Clin. Biochem. 2009 Apr; 24(2): 205–207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaring SW, Webb DJ, Maxwell SR: Systemic uric acid administration increases serum antioxidant capacity in healthy volunteers. J. Cardiovasc. Pharmacol. 2001 Sep 1; 38(3): 365–371. PubMed Abstract \| Publisher Full Text\n\nMagnus JH, Doyle MK, Srivastav SK: Serum uric acid and self-reported rheumatoid arthritis in a multiethnic adult female population. Curr. Med. Res. Opin. 2010 Sep; 26(9): 2157–2163. PubMed Abstract \| Publisher Full Text" }	[ { "id": "210010", "date": "27 Oct 2023", "name": "Bogdan Cylwik", "expertise": [ "Reviewer Expertise Rheumatic diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study protocol article of Priyanka Makhe et al. evaluates the diagnostic usefulness of serum rheumatoid factor (RF), uric acid (UA) levels and adenosine deaminase activity in rheumatoid arthritis (RA) patients. In short, this is an interesting project and research idea, however, the authors should better explain its purpose. The authors need to explain why ADA activity determination in RA would be so important. Finally, the authors stated that ADA could be a promising test for the diagnosis of RA patients. I have a few comments and suggestions to the authors.\nThe following points need improvement:\nAbstract:\nIs: “Rheumatoid factors (RF)”. Should be: “Rheumatoid factor(RF)”.\nIs: “The levels of serum ADA….”. Should be: “The serum ADA activity…”.\nIs: “ Serum ADA rheumatoid factors levels in RA patients is higher in healthy control” (?).\nShould be: “Serum ADA activity in RA patients is higher than that in controls”.\nIs: “When comparing the uric acid levels of RA patients with healthy controls, there is no change in the uric acid level”. Maybe: “When comparing the uric acid levels between RA patients and controls, there is no significant difference”.\nIs: “The degree underlying ADA activity between RA patients and healthy individuals should differ noticeably, confirming the test's value in the diagnosis of the condition”. Maybe more precisely: “The ADA activity between RA patients and healthy individuals should differ noticeably, confirming the usefulness of the test in the diagnosis of the condition”.\nKeywords:\nIs: “Ra Factor”. Should be: “Rheumatoid Factor”.\nIntroduction:\nIs: “C-reactivity protein”. Should be: “C-reactive protein”.\nObjective:\nThe goals are not clear and poorly written. Rather should be:\nTo determine the serum ADA activity in RA patients\nTo determine the serum UA level in RA patients\nTo determine the serum RF level in RA patients\nTo determine the serum ADA activity, UA and RF concentrations in patients without RA\nProtocol:\nThe purpose of the research should be clarified. The sentence “Between RA patients and their healthy controls, there should be significant variations in the levels of ADA RA factor…” needs to be corrected.\nMaterial and methods:\nThe study group collected over a 3-year period appears to be small. Diagnostic criteria for RA should be provided. Exclusion criteria are unclear. Control group - it should be specified whether these will be healthy people or hospitalized patients. I don't understand what \"healthy patients\" means.\nSample collection: too detailed description.\nMethods: there are no principles of the methods for determining uric acid, rheumatoid factor and ADA.\nStatistical analysis:\nWhat will the Wilcoxon test be used for?\nWhat p-value will be considered statistically significant (p<0.001 or p<0.05)?\nWhy will research results be processed by 3 different software versions?\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? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "290130", "date": "10 Sep 2024", "name": "Marta Benito-Miguel", "expertise": [ "Reviewer Expertise Rheumatoid Arthritis" ], "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 is a protocol and has no data. It addresses an important topic because rheumatic disorders affect thousands of individuals around the world.\nDespite the protocol is very simple, they are only 2 variables to evaluate, but if there is a correlation, it should make an important contribution to be a simple evaluation method to add to detect rheumatoid arthritis.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1202
https://f1000research.com/articles/11-968/v1	22 Aug 22	{ "type": "Case Report", "title": "Case Report: Optical coherence tomography angiography findings in radiation retinopathy", "authors": [ "Wafa Ammari", "Asma Zaghdoudi", "Olfa Berriche", "Riadh Messaoud", "Olfa Berriche" ], "abstract": "We report the observation of a 31-year-old patient followed for a nasopharyngeal carcinoma since 2009, treated by locoregional radiotherapy, with a cumulative dose of 70 Gray. This case presented all ocular complications of radiotherapy; radiation retinopathy (RR), which is the most severe complication, could be diagnosed earlier and have a better prognosis if optic coherence tomography angiography (OCTA) was performed. She presented with a progressive decline in bilateral visual acuity. Ophthalmologic examination revealed bilateral posterior subcapsular cataract, radiation retinopathy, and optic neuropathy. The OCT B-scan showed more pronounced macular edema in the right eye. The OCTA revealed enlargement of the central avascular zone and loss of the deep and superficial retinal vascular network. The patient received three consecutive monthly intravitreal injections of anti-vascular endothelial growth factor (VEGF), without improvement in visual acuity. The aim of this case report is to present the contribution of OCT-A in the diagnosis of radiation maculopathy, and attribute these changes to ischemia at the level of the retinal vascular network.", "keywords": [ "Superficial retinal capillary plexus", "Deep retinal capillary plexus", "Ischemic cascade", "Radiation retinopathy", "OCT angiography" ], "content": "Introduction\n\nLocoregional radiotherapy is the most effective treatment against nasopharyngeal carcinoma (NPC).1 The proximity with orbit tissues exposes them to severe damages.2 However, late-onset, sight-threatening ocular complications may occur, including cataract, optic neuropathy, radiation retinopathy (RR), and ocular surface disease.2 The early diagnosis of these lesions allowed to better prognosis.1 The optical coherence tomography angiography (OCT-A) allowed to investigate neovascular alteration for patients suffering from RR even before the inset of loss of vision.1\n\nWe report a case of radiation retinopathy in a 31-year-old female with NPC, treated by locoregional radiation therapy (LRT). She presented all post-radiotherapy ocular complications with late diagnosis of RR and poor prognosis.\n\nThe purpose of this case report is to analyze the findings and the usefulness of OCT-A.\n\n\nCase report\n\nA 31-year-old Tunisian, unemployed female with a history of nasopharyngeal carcinoma was diagnosed in 2009 and treated by locoregional radiotherapy. The overall administered dose was about 75 Gy. She presented with adrenal insufficiency, hypothyroidism, and osteonecrosis as side effects of the treatment. She complained of progressive painless loss of vision in both eyes. On examination, her best-corrected visual acuity was 20/40 in both eyes. The ocular motility was full, and no afferent pupillary defect was noted. A symmetrical subcapsular cataract was found. The rest of the anterior segment examination was unremarkable. No vitreous cells were noted. Fundoscopy showed microvascular changes mainly marked by vascular tortuosity and microaneurysms, optic disc pallor, and decreased foveal reflex. Fluorescein angiography was not performed because the patient was allergic to fluorescein. OCT in B-scan showed bilateral macular edema with a central macular thickness of, respectively, 532 μm in the right eye (RE), and 406 μm in the left eye (LE). OCT angiography (OCT-A) disclosed enlargement of the central avascular zone, and hypoperfusion of both superficial and deep retinal capillary networks (Figures 1 and 2). The vessel density was reduced to 38.12 % in the inferior macular area of the RE, and to 39.34 % in the superior macular area of the LE. A systemic workup was performed to rule out other causes of ischemic retinopathy (diabetes mellitus, blood dyscrasias, and carotid insufficiency). Based on medical history, ocular findings, and negative systemic workup the diagnosis of radiation retinopathy was finally established. After informed consent, and a negative pregnancy test, the patient underwent three monthly intravitreal bevacizumab injections (1.25 mg). The improvement of visual acuity was poor.\n\na. Fundoscopy showing vascular tortuosity and dilation of peripheral retinal vessels, the disappearance of foveolar reflection, and mild pallor of the optic disc.\n\nb. Optical coherence tomography (OCT) showed macular edema.\n\nc. Optical coherence tomography angiography (OCT-A) showing enlargement of the centralavascular zone, and hypoperfusion of both superficial and deep retinal capillary network.\n\na. Fundoscopy showing vascular tortuosity and dilation of peripheral retinal vessels, the disappearance of foveolar reflection, and mild pallor of the optic disc.\n\nb. The optical coherence tomography (OCT) shows macular edema.\n\nc. Optical coherence tomography angiography (OCT-A) showing enlargement of the central avascular zone, and hypoperfusion of both superficial and deep retinal capillary network.\n\n\nDiscussion\n\nRadiation retinopathy (RR) was first described in 1933 by Stallard,3 as a predictable complication of radiation exposure. It most commonly occurs between six months and three years after irradiation.4 In this case, the diagnosis was later, twelve years after irradiation. A higher total radiation dose is the highest risk factor, as the incidence of RR increases at doses greater than 45 Gy. This patient received 75 Gy. Histopathological studies have illustrated a vasculopathy with the destruction of the endothelial cells followed by vascular occlusion and capillary dropout.3,4 The microvascular alterations are associated with a reduction of retinal oxygenation, blood flow, and ischemia.2–4 Contrast sensitivity decrease and visual field impairment were notified in patients treated with radiotherapy.1 Our patient had gradually decreased bilateral visual acuity, as well as cataract and optic neuropathy. The clinical appearance mimics many lesions of diabetic retinopathy such as microaneurysms, macular edema, cotton-wool spots, retinal neovascularization, vitreous hemorrhage, and tractional retinal detachment.4 The main tests usually performed on patients are fluorescein fundus angiography (FFA) and optical coherence tomography (OCT). The first exam hallmarks are capillary dilatation and microaneurysms, frequently in combination with ischemia or macular edema.5 On OCT images, we found a disappearance of the macular depression with macular edema, a significant thinning of the inner plexiform, inner nuclear, and outer plexiform layers.5 However, FFA is an invasive diagnostic technique. Intravenous dye injection used may cause severe anaphylaxis, particularly in immunocompromised patients. It was not performed on our patient. Besides, OCT cannot capture vessel network status. Recently, OCT-A, has shown to be a safe and non-invasive examination that combines traditional OCT and FFA. It can provide high-resolution images of each layer of the retina and quantify the retinal microvascular networks without the use of exogenous dyes. OCTA has been introduced for the detection of subtle microvascular changes in radiation retinopathy.6,7 Vascular abnormalities are manifested by an enlargement of the central avascular zone and a reduction of vessel density in the deep vascular plexus of the foveal area. Whereas it’s less reduced in superficial layers. The susceptibility of the deep layer can be explained by the direct connection of the superficial capillary plexus to the retinal arterioles with greater perfusion and oxygen supply.3 This change in structure can be explained by direct compression of the retinal vascular network, deep in the first place, by intra-retinal fluid cysts. Li et al.1 found that OCTA detects early vascular alterations of the retina in patients with normal-ranged visual acuity. It provided a quantitative measurement of retinal capillary changes which may predict future development of radiation-induced retinal toxicity.5 They suggested the implementation of OCTA for the early detection and consistent monitoring of RR. In this sense, a grading system was proposed based on clinical findings in OCTA, increased central macular thickness, evident cysts, and ophthalmoscopy findings.5 The disadvantage is the presence of several artifacts, especially after treatment.\n\nFurthermore, due to the clinical and pathophysiological similarities with diabetic retinopathy, it inspired the treatment of radiation retinopathy.8 Initially, treatments were based on the use of retinal laser.8 Sector photocoagulation improves clinical signs, but the visual outcome is poor.8 Intravitreal injection of anti-VEGF or corticosteroids has been shown to improve visual acuity, reduce cystoid macular edema, and the risk of the development of radiation retinopathy.3,8 The visual acuity of our patient didn’t change, probably because she presented with several complications of local radiotherapy, such as cataract and optic neuropathy, and ischemia affecting deep layers. Continuous treatment is necessary to maintain acuity improvement7; this requires good patient adherence.8 The optimal regimen for anti-VEGF therapy is not yet identified.7 There have been recent preventive efforts to avoid signs that radiation damage has already occurred, particularly since there is still no curative treatment.9\n\n\nConclusions\n\nRadiation retinopathy manifests itself on OCTA by an enlargement of the foveolar avascular zone and a rarefaction of the vascular network at the level of the deep and vascular networks, even in eyes without clinical evidence of radiation retinopathy.\n\n\nData availability\n\nAll data are included as part of the article and no additional data are required.\n\n\nConsent\n\nThe patient has consented to the submission of the case report for submission to the journal.", "appendix": "References\n\nZijing L, Zongyi Z, Jianhui X, et al.: Radiation-Induced Optical Coherence Tomography Angiography Retinal Alterations in Patients with Nasopharyngeal Carcinoma. Front Med (Lausanne). 2020; 7: 630880.\n\nAkagunduz OO, Yilmaz SG, Tavlayan E, et al.: Radiation-Induced Ocular Surface Disorders and Retinopathy: Ocular Structures and Radiation Dose-Volume Effect. Cancer Res Treat. 2021; 54: 417–423. Publisher Full Text\n\nRose K, Krema H, Durairaj P, et al.: Retinal perfusion changes in radiation retinopathy. Acta Ophthalmol. 2018; 96(6): e727–e731. PubMed Abstract \| Publisher Full Text\n\nWang D, Au A, Duker JS, et al.: PAMM and the ischemic cascade associated with radiation retinopathy. Am J Ophthalmol Case Report. 2020; 20: 100918. PubMed Abstract \| Publisher Full Text\n\nSkalet AH, Liu L, Binder C, et al.: Longitudinal Detection of Radiation-Induced Peripapillary and Macular Retinal Capillary Ischemia Using OCT Angiography. Retina. 2020; 4(3): 320–326. PubMed Abstract \| Publisher Full Text\n\nSeibel I, Vollhardt D, Riechardt AI, et al.: Influence of Ranibizumab versus laser photocoagulation on radiation retinopathy (RadiRet) - a prospective randomized controlled trial. Graefes Arch Clin Exp Ophthalmol. 2020; 258(4): 869–878. PubMed Abstract \| Publisher Full Text\n\nFallico M, Chronopoulos A, Schutz JS, et al.: Treatment of radiation maculopathy and radiation-induced macular edema: A systemic review. Surv Ophthalmol. 2021; 66(3): 441–460. PubMed Abstract \| Publisher Full Text\n\nSay T, Ferenczy S, Magrath GN, et al.: Image Quality and Artifacts on Optical Coherence Tomography Angiography: Comparison of Pathologic and Paired Fellow Eyes in 65 Patients with Unilateral Choroidal Melanoma Treated with Plaque Radiotherapy. Retina. 2017; 37(9): 1660–1673. Publisher Full Text\n\nReichstein D: Current treatments and preventive strategies for radiation retinopathy. Curr Opin Ophthalmol. 2015; 26(3): 157–166. PubMed Abstract \| Publisher Full Text" }	[ { "id": "148253", "date": "31 Aug 2022", "name": "Helmi Ben Saad", "expertise": [ "Reviewer Expertise Medical writing skills", "physiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 case-report entitled “Case Report: Optical coherence tomography angiography findings in radiation retinopathy”. The rationale of the study is interesting. However, a revision is needed.\nHere are my remarks:\nGENERAL REMARKS\nI recommend that authors apply the CARE guidelines1.\n\nFor the abstract, I recommend that authors apply the IOC plan in the abstract: Introduction, observation, conclusion.\n\nAll abbreviations should be explained the first time they are used - unless it is a standard unit of measurement - and thereafter the use of abbreviations should be consistent throughout the paper. Avoid excessive use of abbreviations.\n\nThe paper should be checked by a person fluent in English.\n\nSometimes Gy sometime Gray: please use one term\n\nThe patient received 70 Gy (see the abstract) or 75 Gy (see the observation and the discussion)?\nSPECIFIC REMARKS\n1. Abstract:\nSome corrections are needed. For example write ‘A 31 year-old female”, delete (RR) and (VEGF), write “The patient presented with…”. Please use OCTA or OCT-A not both.\n2. Manuscript:\nAvoid abbreviating LE and RE, instead using full text: left-eye, right-eye.\n\nMisuse of abbreviations: for examples, write “*We report a case of RR in a 31-year-old”, “history of NPC was”, “treated by LRT”, OCT-A disclosed enlargement’, “diagnosis of RR was finally”, “RR was first described in 1933”, “angiography (FFA) and OCT”, “microvascular changes in RR”, “the treatment of RR8”, “of RR. 3,8 The visual”, “complications of LRT”, “RR manifests itself”, “clinical evidence of RR”.\n\nMore precision is needed: for example, L3 of the Case report, write ‘The patient complained from “ rather than “She complained from progressive’. In this sentence (L11page 5/6) “retinopathy, it inspired”: it refers to what?\n\nIn the beginning of the case report, please mention the following sentence “This observation was reported according to the CARE guidelines (ref)”.\n\nSome mistakes related to references: for examples you wrote “by Stallard,3”, but reference 3 is the one of Rose K et al. You also wrote “Li et al1 found”, however the reference number 1 is of Zijing et al?\n\nSome sentences are lacking references: for example, add a reference for these sentences: “A higher total radiation dose is the highest risk factor, as the incidence of RR increases at doses greater than 45 Gy”, “However, FFA is an invasive diagnostic technique.”, “Intravenous dye injection used may cause severe anaphylaxis, particularly in immunocompromised patients”.\n3. References:\nPlease verify all your references, especially references number 1 and 3.\n4. Figures:\n\nFigure 1 Title: c. OCT angiography showing…. Figure 2 Title: c. OCT angiography showing….\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "8722", "date": "02 Sep 2022", "name": "WAFA AMMARI", "role": "Author Response", "response": "Thank you for the remarks and the attention paid to this original article. General remarks 1 and 2 we followed the journal recommendations. 3. All abbreviations were explained first time they are used. In ophthalmology, we always used abbreviations. 4. The paper was checked by newspaper experts who appreciated the English used. 5.Gy and Gray are both used, but we rectified this. 6.The patient received 75 Gy. It was a keyboard typo for the abstract. Specific remarks: 1.Abstract: 2.Manuscript: Stallard is the first person to describe this entities and this is mention in the article of Rose K et al. The Author’s name is Zijing Li 3.References: All references were verified 4. Figures: The figures showing multimodal imaging. The OCT-A is the c only. For the other remarks, they have been corrected on the article." } ] }, { "id": "165708", "date": "11 Apr 2023", "name": "David Solá-Del Valle", "expertise": [ "Reviewer Expertise Glaucoma/Ophthalmology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, it's a well written report. One small discrepancy between the dose of Gray received (70 or 75?) in abstract and body of paper. I wish the introduction had a paragraph on OCTA (how does it work? and how is it different from regular OCT) for the general practitioner. I would encourage the writers to proof read the report one more time for typographical errors and syntax (ensure reading flows well, especially the abstract). It would also be important to better summarize data on OCTA in the discussion, especially data from trials or large studies that could be relevant to this patient.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "9688", "date": "19 Jul 2023", "name": "WAFA AMMARI", "role": "Author Response", "response": "Thank you for your interest to this article and for your precious remarks. The total dose was 75 Gray. We had introduced a paragraph about the difference between regular OCT and OCTA in introduction. We had reported the necessary correction for the typographical errors and syntax and we had mad changes for abstract. There are not yet large studies in this topic (The OCT angiography findings in radiation retinopathy)." } ] } ]	1	https://f1000research.com/articles/11-968
https://f1000research.com/articles/12-445/v1	26 Apr 23	{ "type": "Software Tool Article", "title": "Numerical Scheme for Compartmental Models: New Matlab Software Codes for Numerical Simulation", "authors": [ "Samuel Okyere", "Joseph Ackora-Prah", "Ebenezer Bonyah", "Samuel Akwasi Adarkwa", "Joseph Ackora-Prah", "Ebenezer Bonyah", "Samuel Akwasi Adarkwa" ], "abstract": "Background: This paper presents a newly developed Matlab code for the numeri- cal simulation of compartmental/deterministic models. It addresses modeling and simulation issues concerning compartmental models. The code is easy to under- stand and edit for the simulation of compartmental models. An alternative codes for statistical software package R has been proposed for the same model. R software is freely available for use. Methods: We proposed a basic SEIR model for illustration purposes. Matlab and R software codes are developed for the SEIR model which users can follow and easily understand the computations. Results: The two codes work on all Matlab and R versions. For models with more compartments, we suggest using higher version of Matlab and R. Matlab works on windows, Mac and Linux Conclusions: New Matlab software codes purposely for numerical simulations of classical deterministic models which can run on any version of Matlab has been introduced in this paper. This code can be edited/modify to suit any deterministic models and any desired output required. An alternative open source free version has been written in R has been provided as well", "keywords": [ "Compartmental Models", "Numerical Simulation", "Matlab software codes", "R software codes" ], "content": "Introduction\n\nWith the help of a programming language that represents matrix and array mathematics directly, MATLAB combines a desktop environment tailored for iterative analysis and design processes.1 The Live Editor for writing scripts that mix code, output, and formatted text in an executable notebook is part of it.1 The Windows requirements are Windows 10 (version 20H2 or higher), Windows 11, Windows Server 2019, and Windows Server 2022. Many scientists and mathematicians choose to use this program since it can be accessed across all popular platforms, including Linux, Mac, and Windows, and because it can be used to explore, model, and analyze data.1 Matlab software has been used to run numerical simulations of compartmental models in epidemiology.2–11\n\nThere are several fundamental compartmental models described using differential equations. The basic ones include Susceptible - Infected (SI), Susceptible - Infected - Recovered (SIR),12,13 Susceptible - Infected - Susceptible (SIS),14 Susceptible - Infected - Recovered - Vaccinated (SIRV),15 Susceptible - Exposed - Infected - Recovered (SEIR) models.4 The purpose of this study is to make public new Matlab codes that authors have been utilising in their work to aid researchers, especially students, who rely on deterministic or compartmental modeling of epidemiology in the numerical simulation of their research projects. This well-detailed code, in our opinion, might be extremely helpful to them as many of them struggle to do the numerical simulations due to the dearth of research that specifically tackles numerical simulation of deterministic models and also to provide users more freedom for coding in Matlab. Recently, researchers have started sharing their codes and providing detailed explanation on how to use them. To provide users extra coding freedom, Guo et al.16 presented newly developed visualization framework called OpenSeesPyView, which is a Python programming-based graphical user interface (GUI) for OpenSeesPy, a prevalent finite element solver in earthquake engineering. The R package ag5Tools was written by Brown et al.17 and offers a streamlined interface for downloading and retrieving AgERA5 data. With the help of the program, time-series data for groups of geographic points may be easily extracted and converted into a format that can be employed in statistical models used in agricultural research. The Rcall interface, developed by Egert and Kreutz,18 gives users access to a large range of techniques written in MATLAB and R. The program is MATLAB-based and offers direct access to R-based tools and methodologies, such as those found on Bioconductor or CRAN. ShinyGAStool, an open source tool created by Hoffmann et al.,19 allows users to easily execute a candidate gene association analysis from a web browser using huge datasets. The remaining section are group as follows: The method section, where we demonstrate how to use the Matlab software codes. we look at the implementation, operation and discussions and limitations. The last section is the concluding section. The software section has the alternative software codes in R.\n\n\nMethods\n\nWe demonstrate how to use the matlab software codes with the SEIR compartmental model depicted in Figure 1. The population is partitioned into four (4) compartments: Susceptible, exposed, infected and recovered. Individuals are recruited into the susceptible class at a rate Ω and they die at a rate μ. The transmission rate is β and the recovery rate is γ. The rate at which exposed individuals become infectious is α and the disease-induced death rate is σ.\n\nThe model is described by the following ordinary differential equations.\n\nFor the purposes of the simulations, the following parameter values are chosen and is given in Table 1. The initial conditions chosen are S0=1000,E0=0,I0=1,R0=0\n\nOnce you have your model and parameter values clearly defined, you can then open the matlab editor window which is shown in Figure 2. Input or copy the codes and paste at the new script.\n\nThe numerical Matlab software codes used for model (1) functiontSEIR=SEIRMODELΩβμσαγNS0E0I0R0MaxTime\n\nif nargin==0\n\nΩ=20;β=0.3;μ=0.00004252912;α=0.3;σ=0.003286;γ=0.1;\n\nS0=1000;E0=0;I0=1;R0=0.0;\n\nMaxTime=120; % The MaxTime stands for the duration of the simulation\n\nend\n\nS=S0;E=E0;I=I0;R=R0; N=S+E+I+R;\n\n% The main iteration\n\noptions=odeset(’RelTol’,1e-5);\n\ntpop=ode45@Diff260MaxTimeSEIRoptionsΩγβμσαN;\n\nS=pop:1;E=pop:2;I=pop:3;R=pop:4;\n\n% plots the graphs with scaled colours\n\nfigure(1)\n\nY=plot(t,S,’b.’);\n\nlegend(Y,’Susceptible’)\n\nxlabel’Time (days)’\n\nylabel’S(t)’\n\nfigure(2)\n\nT=plot(t,E,’.g’);\n\nlegend(T,’Exposed’)\n\nxlabel’Time (days)’\n\nylabel’E(t)’\n\nfigure(3)\n\nf=plot(t,I,’.m’);\n\nlegend(f,’Infected’)\n\nxlabel’Time (days)’\n\nylabel’I(t)’\n\nfigure(4)\n\nh=plot(t,R,’.g’);\n\nlegend(h,’Recovered’)\n\nxlabel’Time (days)’\n\nylabel’R(t)’\n\n% calculates the differential rates used in the integration.\n\nUpon running the codes, some of the simulation results are shown in Figures 3–6.\n\n\nDiscussion\n\nIn Figures 3–6, are reported, the numerical solutions of system (1) for a period of 120 days. These codes can be modified for any compartmental models. The ‘figure’ command produces the output given in Figures 3–6. The steps or procedures listed in the codes have to be followed carefully in order not to encounter errors. The parameters can be represented with letters for instance Ω can be written in the codes as Omega as Matlab doesn’t recognize the parameters listed in the code. The code written in the editor window can be seen in Figure 7. The SEIR model is extended, and an alternative software, R codes has been provided at the appendix section. Using the same initial conditions and parameter values given in Table 1, the output figures for the R code are given by Figures 8–10. Users who cannot afford Matlab software can freely use the R software codes for the numerical simulation. The two software codes gives the same output results.\n\nMATLAB can disable some advanced graphics rendering features by switching to software OpenGL by ignoring extra legend entries.\n\nR on the other hand, has a limited memory capacity which can be a problem when working with large data sets or running computationally-intensive analyses. It can be relatively slow compared to other programming languages like Matlab, C++ or Python, especially for certain types of calculations. It also has limited graphical capabilities.\n\n\nConclusion\n\nThis work seeks to introduce new matlab software codes purposely for numerical simulations of classical compartmental models which can run on any version of Matlab. The intended targets are researchers and students who uses Matlab for their analysis. This codes can be edited/modify to suit any deterministic models and any desire output required. The SEIR deterministic model was used to give a much insight about the codes. Alternatively, a deterministic SEIR codes written in R software is provided for those who wants to use freely available software. Despite the limitations of the R software, the deterministic model implemented in the R code can still be a useful tool for understanding the basic dynamics of disease transmission.", "appendix": "Data availability statement\n\nOSF: Raw_data_monkeypox. DOI: 10.17605/OSF.IO/2J5R9.\n\nThis project contains the following underlying data:\n\nData_used.pdf (data input into matlab simulations)\n\nOSF: Output_data DOI: 10.17605/OSF.IO/7EJUP.\n\nThis project contains the following extended data:\n\nMATLAB Command Window1.pdf (Matlab output data that accompanied the numerical simulation figures)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nSource code available from: https://github.com/okyere2015/Matlab_codes/releases/tag/v2.0.1.\n\nArchived source code at the time of publication: https://doi.org/10.5281/zenodo.7671815.\n\nLicense: Apache 2.0\n\n\nReferences\n\nMATLAB, Math: Graphics. Programming.Reference Source\n\nOkyere S, Ackora-Prah J: A mathematical model of transmission dynamics of SARS CoV-2 (COVID-19) with an underlying condition of diabetes. Int. J. Math. Math. Sci. 2022; 2022: 1–15. Article ID 7984818. Publisher Full Text\n\nOkyere S, Ackora-Prah J: Modelling and analysis of monkeypox disease using fractional derivatives. Results in engineering. 2023; Vol. 17: 100786. 2590–1230. Publisher Full Text\n\nOkyere S, Oduro FT, Bonyah E, et al.: Epidemiological model of Influenza A (H1N1) transmission in Ashanti Region of Ghana. J. Public Health Epidemiol. April, 2013; 5(4): 160–166. Reference Source\n\nKim S, Seo YB, Jung E: Prediction of COVID-19 transmission dynamics using a mathematical model considering behavior changes in Korea. Epidemiol. Health. 2020; 42: e2020026. Publisher Full Text\n\nHabenom H, Aychluh M, Suthar DL, et al.: Modeling and analysis on the transmission of covid-19 Pandemic in Ethiopia. Alex. Eng. J. 2022; 61(7): 5323–5342.Publisher Full Text\n\nAhmed I, Modu GU, Yusuf A, et al.: A mathematical model of coronavirus disease (COVID-19) containing asymptomatic and symptomatic classes. Elsevier public health emergency collection, Results Phys. 2021; 21: 103776. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgarwal P, Nieto JJ, Ruzhansky M, et al.: Analysis of Infectious disease problems (Covid-19) and their global impact. J. Nanobiotechnol. 2021.\n\nGhosh S, Chatterjee AN, Roy PK, et al.: Mathematical Modeling and Control of the Cell Dynamics in Leprosy. Comput. Math. Model. 2021; 32: 52–74. Publisher Full Text\n\nClark A, Jit M, Warren-Gash C, et al.: Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: A modelling study. Lancet Glob. Health. 2020; 8: e1003–e1017. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNana-Kyere S, Boateng FA, Jonathan P, et al.: Global Analysis and optimal control model of COVID-19. Comput. Math. Methods Med. 2022; 2022: 20. Article ID 9491847.\n\nHarko T, Lobo FS, Mak MK: Exact analytical solutions of the Susceptible-Infected-Recovered (SIR) epidemic model and of the SIR model with equal death and birth rates. Appl. Math. Comput. 2014; 236: 184–194. Publisher Full Text\n\nSchlickeiser R, Kröger M: Analytical solution of the SIR-model for the temporal evolution of epidemics. Part B: Semi-time case. J. Phys. A. 2021; 54(17): 175601. Publisher Full Text\n\nAlah MA, Abdeen S, Tayar E, et al.: The story behind the first few cases of monkeypox infection in non-endemic countries. J. Infect. Public Health. 2022; Volume 15(Issue 9): Pages 970–974. Publisher Full Text\n\nSchlickeiser R, Kröger M: Analytical Modeling of the Temporal Evolution of Epidemics Outbreaks Accounting for Vaccinations. Physics. 2021; 3(2): 386–426. Publisher Full Text\n\nGuo J, Ye A, Wang X, et al.: OpenSeesPyView: Python programming-based visualization and post-processing tool for OpenSeesPy. SoftwareX. 2023; Volume 21: 101278.Publisher Full Text\n\nBrown D, de Sousa K , van Etten J : ag5Tools: An R package for downloading and extracting agrometeorological data from the AgERA5 database. SoftwareX. 2023; 21: 101267.Publisher Full Text\n\nEgert J, Kreutz C: Rcall: An R interface for MATLAB. SoftwareX. 2023; Volume 21: 101276.Publisher Full Text\n\nHoffmann TJ, Miaskowski C, Kober KM: ShinyGAStool: A user-friendly tool for candidate gene association studies. SoftwareX. 2023; volume 21: 101274.Publisher Full Text" }	[ { "id": "200352", "date": "04 Sep 2023", "name": "Belela Samuel Kotola", "expertise": [ "Reviewer Expertise Mathematical modeling" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst and for most I would like to acknowledge the editor for giving me this chance for reviewing the article. Depend up on my back ground knowledge I have reviewed the article as follow.\nThe researcher has been defined MATLAB as a programming language that represents matrix and array mathematics directly, providing a desktop environment for iterative analysis and design processes. Moreover, the area where it is widely used was described by the authors so that to be by scientists and mathematicians for exploring, modeling, and analyzing data across various platforms.\nThe study has been aimed to make public new Matlab codes that authors have been using to aid researchers in numerical simulations of deterministic or compartmental models in epidemiology; which is the fundamental and timely objectives. Researchers have also started sharing their codes and providing detailed explanations on how to use them.\nThis work introduces an editable and modified Matlab software codes for numerical simulations of classical compartmental models, suitable for researchers, students and for those seeking freely available software.\nFinally I recommend the article to be indexed after the following question and recommendation are addressed.\nRECOMMENDATION:\nSome of the graphs can be plotted in a single window, so I recommend the authors plot some of the graphs, such as susceptible class, infected class, and exposed class, in a single window editor. Plotting in such a way can help us compare the relationships and differences among the plotted classes.\n\nAn author has stated the disadvantage of MATLAB as it disables advanced graphics rendering features by using OpenGL, and while R also has limited memory capacity, slowness, and limited graphical capabilities, making it suitable for large data sets and computationally intensive analyses, which one is the best? As an author, which software do you recommend to researchers? For what reason do you recommend it?\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [] }, { "id": "188924", "date": "04 Sep 2023", "name": "Shewafera Wondimagegnhu Teklu", "expertise": [ "Reviewer Expertise Numerical Analysis", "Mathematical Modelling", "Mathematical Biology and 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\nComments to the Authors\nTitle: Numerical Scheme for Compartmental Models: New Matlab Software Codes for Numerical Simulation\nThe authors proposed new Matlab Software Codes for Numerical Simulation and also an alternative codes for statistical software package R has been proposed for the same compartmental model.\n\nIn their discussion section the authors written as the SEIR model is extended, and alternative software, R codes has been provided at the appendix section. In their manuscript I did not find the appendix section and I have seen only the MATLAB code to illustrate the proposed SIER model. Give the R code on the revised manuscript!\n\nThe authors needs to disclose the numerical codes using MATLAB and R software for potential new researchers and possibly students but they should refine the two codes separately and compare and contrast them with the proposed trivial SIER model.\n\nI do not think, with these current details, that the manuscript can be accepted. It needs a modification.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-445
https://f1000research.com/articles/12-735/v1	23 Jun 23	{ "type": "Study Protocol", "title": "Current trends, barriers, and facilitators of use of core outcome sets in Cochrane systematic reviews: Protocol", "authors": [ "Ian Saldanha", "Karen Hughes", "Susanna Dodd", "Toby Lasserson", "Jamie Kirkham", "Samuel Lucas", "Paula Williamson", "Karen Hughes", "Susanna Dodd", "Toby Lasserson", "Jamie Kirkham", "Samuel Lucas", "Paula Williamson" ], "abstract": "Background: Core outcome sets (COS) represent agreed-upon minimum outcomes that should be reported in all studies in a given topic area. Cochrane reviews are considered among the most rigorously conducted systematic reviews (SRs). In 2019, seven of the first 100 published Cochrane SRs (7%) cited a COS in relation to choosing outcomes. A relevant COS existed but was not mentioned (or cited) for 27 of the remaining 93 SRs (29%). Among Cochrane Review Group editors surveyed in 2019, 86% felt that COS should definitely/possibly be used in Cochrane SRs. As of September 2019, the Cochrane Handbook recommends that SR teams consult resources that host relevant COS when choosing outcomes for the SR. Objectives: (1) Examine the extent to which authors are currently considering COS to inform outcome choice in Cochrane protocols and completed SRs. (2) Understand author barriers and facilitators of using COS in Cochrane protocols and completed SRs. Methods: We will examine the extent to which all Cochrane SRs published in the last 3 months of 2022 and all Cochrane protocols published in 2022: (a) cited a COS, (b) searched for COS, and (c) reported outcome inconsistency among included studies and/or noted the need for COS. One investigator will extract information from SRs and protocols; a second extractor will verify all information, discussing discrepancies to achieve consensus. Using Jisc Online Surveys®, we will conduct an online anonymous survey of authors of all the included completed SRs and protocols to assess author awareness of COS and identify barriers and facilitators of using COS to inform outcome choice. Discussion: This study will provide key information regarding uptake of COS by Cochrane SR authors and the barriers and facilitators that they experience. Our findings will inform approaches to increasing awareness and uptake of COS in future SRs, both with and beyond Cochrane.", "keywords": [ "core outcome sets", "systematic reviews", "Cochrane", "outcome choice", "barriers", "facilitators" ], "content": "Background\n\nCore outcome sets (COS) represent agreed-upon minimum outcomes that should be reported in all research studies in a given topic area.1 COS are intended to increase the usefulness of research evidence and facilitate comparisons across studies. Although COS have traditionally been developed for use in clinical trials, increasingly COS are also developed for all research as well as other parts of the evidence ecosystem, such as for routine care.2,3 A systematic review (SR) is a research effort whose goal is to identify and synthesize all relevant studies that fulfill pre-specified eligibility criteria to answer a specific research question(s).4,5 Thus, systematic reviewers not only evaluate primary research that should have considered COS6 but they should themselves also consider COS when choosing outcomes for the SR.\n\nCochrane SRs are considered among the most rigorously conducted SRs in the world. We previously conducted an analysis and reported that only seven of the first 100 published Cochrane SRs in 2019 (7%) cited a COS in relation to choosing outcomes.7 A relevant COS existed but was not mentioned (or cited) for 27 of the remaining 93 SRs (29%). For a further 6 reviews, a relevant COS was published after the protocol of the SR was developed.7 We similarly conducted an analysis of all 67 comparative effectiveness SRs that were published between 2018 and 2020 by Evidence-based Practice Centers (EPCs) with funding from the U.S. Agency for Healthcare Research and Quality (AHRQ) (EPC SRs are also highly rigorous SRs).8 We found relevant COS for 36 of the 67 EPC SRs (54%).8 In the Cochrane analysis paper, we also reported results of a survey of editors of 36 (of the then 52) Cochrane Review Groups; most editors (31/36; 86%) felt that COS should definitely/possibly be used in Cochrane SRs.7\n\nConsiderations regarding COS scope and contextual relevance to the SR notwithstanding, there is no obvious reason why COS should not be used when choosing outcomes to be examined in SRs.8 Use of existing COS represents an opportunity for systematic reviewers to leverage the efforts of COS developers in identifying outcomes for their SRs. Indeed, the 2nd (i.e., most recent) edition of the Cochrane Handbook for Systematic Reviews of Interventions now recommends that SR teams consult resources that host relevant COS when choosing outcomes for the review.9 However, this edition of the Handbook was first published in September 2019, which was after outcome choices were made for all SRs in the sample of Cochrane SRs published in 2019 that we analyzed. Therefore, the extent to which recent Cochrane SRs (and protocols) are considering COS during outcome choice is unclear.\n\nUse of COS to inform choice of outcomes can be considered a behavior.10 In 2022, based on a survey of authors of clinical trials submitted to the top five medical journals (in terms of impact factor), Matvienko-Sikar and colleagues reported that the most common barrier to COS use was trialist preferences and choices regarding outcomes (68% of respondents), and the most common facilitator was trialist awareness and knowledge about COS (90%).11 Also in 2022, Hughes and colleagues conducted qualitative interviews of clinical trialists in the UK and reported that the biggest barriers to COS uptake were trialist perceptions regarding COS characteristics (e.g., increased patient burden, COS being out of date) and the COS development process (e.g., the lack of inclusion of all relevant clinical specialties).12 The biggest facilitators were trialist awareness and understanding of COS and funder and journal editor recommendations to use COS.12\n\nOutcomes chosen for trials and for SRs, even within the same topic area, have been shown sometimes to be inconsistent, perhaps reflecting differing priorities.13,14 Moreover, for Cochrane SRs, these decisions are often shared between the authors and the editorial team (with input from the peer reviewers, including people with lived experience of the condition of interest).7 It may be that these various parties have different priorities, although the SR authors are primarily responsible for choosing which outcomes to assess and this will likely influence the final set of outcomes for a Cochrane SR. The stages of protocol development and subsequent peer review help vet the choice of outcomes.\n\nWe are aware of two surveys assessing barriers to COS use by SR authors, specifically in the topic area of pain.15,16 Boric and colleagues surveyed authors of SRs of interventions for neuropathic pain and reported that the main barrier to use of the Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (IMMPACT) COS was the lack of awareness of the full COS.15 Similarly, Dosenovic and colleagues surveyed authors of SRs of interventions for postoperative pain in children and reported that the main barriers to use of the pediatric version of the IMMPACT COS (PedIMMPACT) were the lack of awareness, difficulties with implementation, and the lack of resources.16\n\nTo our knowledge, the barriers and facilitators of use of COS have not been examined among Cochrane SR authors (in our previous analyses, we did not survey the authors of either the Cochrane SRs or EPC SRs). The insights that could be gained from such an examination would be crucial to inform approaches to increasing awareness and uptake of COS in future SRs, both with and beyond Cochrane.\n\n\nObjectives\n\nThis study has two objectives:\n\n(1) Examine the extent to which authors are currently considering COS to inform outcome choice in Cochrane protocols and completed SRs.\n\n(2) Understand author barriers and facilitators of using COS in Cochrane protocols and completed SRs.\n\n\nMethods\n\nFor Objective 1, we will assess recent Cochrane SRs for the extent to which they (a) cited a COS, (b) mentioned searching for COS, and (c) reported outcome inconsistency among included studies and/or noted the need for COS. For Objective 2, we will conduct an online anonymous survey of authors of these recent Cochrane SRs to identify barriers and facilitators of their using COS to inform outcome choice in SRs.\n\nEligibility Criteria for Cochrane SRs: We will include all completed Cochrane SRs published in the last 3 months of 2022 and all Cochrane SR protocols published throughout 2022. This period restriction will enable us to examine contemporary practices regarding outcome choice in Cochrane SRs. We will not restrict SRs or protocols by topic area or location of the authors or Cochrane Review Group.\n\nIdentifying Cochrane SRs: We will identify relevant completed SRs and protocols by searching the Cochrane Database of Systematic Reviews through the Cochrane Library, restricting by the periods of interest.\n\nData extraction:\n\nFor all relevant SRs, we will extract information about whether the SR authors:\n\n(1) Cited a COS in the context of choosing outcomes for the review, and\n\n(2) Mentioned having searched for a COS to choose outcomes for the review.\n\nFor completed SRs only, we will extract information about whether the SR authors:\n\n(3) Noted any problems with outcome inconsistency across the included studies and/or the need for outcome standardization/COS development.\n\nFor all SRs that cited or mentioned using a COS (i.e., yes to #1 or #2 above), we will also extract:\n\n(4) The extent to which the SR authors used outcomes from the COS. In other words, we will assess the extent of overlap between the COS outcomes and the SR outcomes using a framework that we developed8 and has been used since.17 Briefly, we will focus on the outcome domains (the “what,” e.g., pain) but will not examine whether the “how” of the outcome (e.g., one instrument for measuring pain versus another) matched. The framework we developed considers matches to be general (i.e., nonspecific) or specific. Our approach to determining the type of match for pairs of outcomes is consistent with an approach that has been used previously.3,17,18\n\nFor SRs that did not cite or mention having considered a COS (i.e., no to both #1 and #2 above), we will also extract whether:\n\n(5) A relevant COS exists. We will do this by searching the Core Outcome Measures for Effectiveness Trials (COMET) database. Maintained by the COMET Initiative, this is a free, online, regularly updated, searchable database of COS. One investigator will assess the potential relevance of each identified COS to the topic of each SR following an approach used previously.7,17,19 For identified COS, we will also extract information regarding when the COS was published. This will allow us to assess whether the COS was available during the stage of outcome choice for the SR/protocol.\n\nFor information extraction, we will review all sections of the SR/protocol report. One investigator will extract information from each SR/protocol and a second investigator will independently verify the extracted information.\n\nStatistical analysis: We will calculate descriptive statistics (percentages and medians with interquartile ranges [IQRs]). We will conduct all data analyses using Stata Version 16 (College Station, Texas, USA).\n\nEligibility Criteria for Cochrane SR authors: We will email a survey to the corresponding authors of all completed relevant Cochrane protocols and completed SRs from Objective 1. If a corresponding author does not respond to the survey or our email, we will send the survey to the senior (i.e., last) author. If similar nonresponse occurs, we will send the survey to another author from the author list (e.g., first author). At each request, we will suggest that the person(s) most familiar with the considerations during outcome choice for the SR complete a single response for the SR.\n\nSurvey design and implementation: We will design and distribute the anonymous survey using Jisc Online Surveys® in English. We will send the author(s) of each relevant SR one of four versions of the survey:\n\n• Version A: For SRs that cited/mentioned searching for a COS and the full COS was used.\n\n• Version B: For SRs that cited/mentioned searching for a COS and some but not all COS outcomes were used.\n\n• Version C: For SRs that did not cite/mention searching for a COS, but we identified a potentially relevant COS that could have been used.\n\n• Version D: For SRs that did not cite/mention searching for a COS and we did not identify a potentially relevant COS that could have been used.\n\nItems of interest for the surveys include:\n\n1. Author process for outcome choice for the SR\n\n2. Awareness of COS in general\n\n3. Whether the authors searched for COS (regardless of whether the SR mentions that the authors searched for it)\n\n4. Awareness of a relevant COS (if one exists for the SR)\n\n5. Reasons for non-use of relevant COS (if one exists for the SR)\n\no In instances where a COS exists but was not used, we will also ask authors whether they will consider incorporating the unused outcomes from the COS when completing the SR (for protocols) or when updating the review (for completed SRs).\n\n6. Perceived barriers to COS use\n\n7. Perceived facilitators of COS use.\n\nFor items 5, 6, and 7 above, Box 1 lists examples of prespecified as well as open-ended response options.\n\n\n\n\n\n• Did not know there was a COS.\n\n• COS target population was too narrowly/broadly defined for the SR population of interest.\n\n• COS target intervention was too narrowly/broadly defined for the SR intervention of interest.\n\n• COS was too old.\n\n• Other, specify: _____________\n\n\n\n• Systematic reviewers’ preference to use their own outcomes\n\n• Inadequate knowledge about the existence of COS\n\n• Inadequate knowledge about how to use core outcomes\n\n• Poor quality and design of COS\n\n• Systematic reviewers were not involved in COS development\n\n• Belief that primary study outcomes are different from SR outcomes\n\n• Other, specify: _____________\n\n\n\n• Use of COS can facilitate incorporating more studies into meta-analyses\n\n• Positive perceptions of COS\n\n• Good knowledge about the existence of COS\n\n• Good knowledge about how to use core outcomes\n\n• Availability of well-designed COS\n\n• Belief that primary study outcomes should be fundamentally akin to SR outcomes\n\n• SR funder recommended COS use\n\n• Guideline developer (that the SR was meant to inform) recommended COS use\n\n• Other, specify: _____________\n\nInstitutional Review Board (IRB) approval: Before we distribute the surveys, we will obtain Research Ethics Committee approval from the University of Liverpool, UK.\n\nData analysis: We will analyze the data by calculating descriptive statistics. For open-ended responses to the survey, we will use content analysis. For overlapping questions across versions of the survey, we will analyze and report overall results as well as separate results by survey version. We will report information from the survey only in the aggregate.\n\nWe will disseminate the findings regarding both objectives of this study through publication of peer-reviewed manuscripts and presentation at international conferences, such as the Cochrane Colloquium.\n\nWe have identified the Cochrane SRs and protocols and are currently extracting information for the study.\n\n\nDiscussion\n\nUse of COS in Cochrane SRs is important to improve outcome standardization, reduce research waste, and improve evidence synthesis regarding the effects of interventions in particular health areas. This study will provide useful findings regarding the extent of uptake of COS by Cochrane reviewers and key insights regarding author views and reasons for using, or not using, COS when deciding on outcomes for Cochrane SRs. The findings and insights are essential to better understand barriers and facilitators of COS uptake in Cochrane SRs, so that interventions to promote uptake can be developed and improved.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nWilliamson PR, Altman DG, Blazeby JM, et al.: Developing core outcome sets for clinical trials: issues to consider. Trials. Aug 6 2012; 13: 132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKearney A, Gargon E, Mitchell JW, et al.: A systematic review of studies reporting the development of Core Outcome Sets for use in routine care. J. Clin. Epidemiol. Mar 20 2023; 158: 34–43. PubMed Abstract \| Publisher Full Text\n\nDodd S, Harman N, Taske N, et al.: Core outcome sets through the healthcare ecosystem: the case of type 2 diabetes mellitus. Trials. Jun 25 2020; 21(1): 570. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nInstitute of Medicine. Finding What Works in Health Care: Standards for Systematic Reviews. The National Academies Press; 2011; 340.\n\nLasserson TJ, Thomas J, Higgins JPT: Chapter 1: Starting a review.Higgins JPT, Thomas J, Chandler J, et al., editors. Cochrane Handbook for Systematic Reviews of Interventions version 60. 2nd ed.John Wiley & Sons; 2019.\n\nWilliamson PR, Barrington H, Blazeby JM, et al.: Review finds core outcome set uptake in new studies and systematic reviews needs improvement. J. Clin. Epidemiol. Oct 2022; 150: 154–164. Publisher Full Text\n\nWilliamson PR, de Ávila OR , Clarke M, et al.: Assessing the relevance and uptake of core outcome sets (an agreed minimum collection of outcomes to measure in research studies) in Cochrane systematic reviews: a review. BMJ Open. Sep 6 2020; 10(9): e036562. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaldanha IJ, Dodd S, Gorst SL, et al.: More than half of systematic reviews have relevant core outcome sets. J. Clin. Epidemiol. Aug 2021; 136: 168–179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiggins JPT, Thomas J, Chandler J, et al.: Cochrane Handbook for Systematic Reviews of Interventions version 6.1. 2nd ed. John Wiley & Sons; 2019.\n\nMatvienko-Sikar K, Byrne M, Clarke M, et al.: Using behavioural science to enhance use of core outcome sets in clinical trials: protocol. [version 1; peer review: 1 approved]. HRB Open Res. 2022; 5(23). Publisher Full Text\n\nMatvienko-Sikar K, Avery K, Blazeby JM, et al.: Use of core outcome sets was low in clinical trials published in major medical journals. J. Clin. Epidemiol. Feb 2022; 142: 19–28. PubMed Abstract \| Publisher Full Text\n\nHughes KL, Williamson PR, Young B: In-depth qualitative interviews identified barriers and facilitators that influenced chief investigators' use of core outcome sets in randomised controlled trials. J. Clin. Epidemiol. Apr 2022; 144: 111–120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaldanha IJ, Li T, Yang C, et al.: Clinical trials and systematic reviews addressing similar interventions for the same condition do not consider similar outcomes to be important: a case study in HIV/AIDS. J. Clin. Epidemiol. Apr 2017; 84: 85–94. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaldanha IJ, Lindsley K, Do DV, et al.: Comparison of Clinical Trial and Systematic Review Outcomes for the 4 Most Prevalent Eye Diseases. JAMA Ophthalmol. Sep 1 2017; 135(9): 933–940. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoric K, Boric M, Dosenovic S, et al.: Authors' lack of awareness and use of core outcome set on postoperative pain in children is hindering comparative effectiveness research. J. Comp. Eff. Res. May 2018; 7(5): 463–470. PubMed Abstract \| Publisher Full Text\n\nDosenovic S, Nikolic Z, Ivancev B, et al.: Awareness and acceptability of Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials core outcome set for chronic pain among surveyed neuropathic pain authors. J. Comp. Eff. Res. Jul 2019; 8(9): 671–683. PubMed Abstract \| Publisher Full Text\n\nSaldanha IJ, Dodd S, Fish R, et al.: Representation of core outcomes in regulatory guidance from the FDA and EMA. BMJ Medicine. 2022; 1: e000233. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDodd S, Fish R, Gorst S, et al.: Representation of published core outcome sets for research in regulatory guidance: protocol. HRB Open Res. 2021; 4: 45. Publisher Full Text\n\nHughes KL, Kirkham JJ, Clarke M, et al.: Assessing the impact of a research funder's recommendation to consider core outcome sets. PLoS One. 2019; 14(9): e0222418. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "194904", "date": "29 Aug 2023", "name": "Theresa Sipe", "expertise": [ "Reviewer Expertise Methods for systematic reviews and efficacy reviews that identify individual evidence-based interventions", "HIV 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 protocol entitled ‘Current trends, barriers, and facilitators of use of core outcome sets in Cochrane systematic reviews: Protocol’ is describing a protocol of a study that will examine systematic review (SR) protocols and completed reviews for inclusion of core outcome sets (COS) as well as conduct a survey of SR protocol/review authors for barriers and facilitators of using COS.\nIn general, the protocol is well written and thorough in descriptions. There is some repetition and long sentences that could be reduced. The background does a good job explaining COS and some additional context will help readers not familiar with this concept.\nBackground, p. 3 of 8, 1st paragraph. Term ‘evidence ecosystem’ needs explanation. Seems that time context is needed. The time context will help with understanding the study done in 2019 that is cited in next paragraph.\n\n2nd paragraph – 1st sentence needs citation.\n\n3rd paragraph – 1st sentence is long and has a double negative, making it confusing. It also is a conclusion statement without evidence. Encouragement to do the action may be a better way to word the sentence or re-word to become common practice. 2nd sentence - ‘(i.e., most recent)’ may not be necessary. Last sentence is unclear and Cochrane SRs are personified. It would be the extent in which authors of Cochrane SRs/protocols are considering COS.\n7th paragraph, 1st sentence – the text in parentheses is long and can be shortened ‘(in our previous analyses, we did not survey the authors…)’. Last sentence should ‘both with and beyond Cochrane’ be ‘both within and beyond Cochrane’? If so, this fix is needed for the abstract.\n\nMethods p. 4 of 8. The design of the study is not stated. It seems to have systematic review components (literature search, inclusion/exclusion criteria, data abstraction) but does not meet all of the requirements for a systematic review. However, it could be considered a rapid review. Regardless, please state what the study design is.\nMethods for Objective 1, p. 4 of 8, eligibility criteria - Will there be any exclusions?\n(4) ‘since’ at the end of the sentence may not be grammatically correct.\nStatistical analyses, p. 4 of 8 – the authors stat that medians and IQRs will be used, however this term is often misused. IQRs are a single number (75th percentile minus 25th percentile). So maybe the authors mean ‘interquartile interval’ or more simply 25th and 75th percentiles.\nEligibility Criteria for Cochran SR authors, p. 5 of 8 – the summary of methods on p. 4 says that the surveys are anonymous. How will the nonresponse be known if the surveys are anonymous?\nSurvey design and implementation, p. 5 of 8 - ‘complete a single response for the SR’. It may be more clear to say ‘complete a single survey for the SR’ so as not to confuse with responses to questions on the survey. Will there be a pilot test of the survey?\nItems of interest for the surveys include, p. 5 of 8. #5: Reasons for non-use of relevant COS. The sub-bullet stats that the researchers ‘will ask authors whether they will consider incorporating the unused outcomes from COS when completing the SRs…’. This is not an objective of the paper. It seems to be putting the respondents in an awkward position and could lead to socially desirable responses. There may be many reasons why authors cannot add the COS at this time. Perhaps changing to an intention question that asks how likely they would be to add COS in the future would be better. Also, add this component to the objectives if needed.\n\nBox 1, p. 6 of 8 – Suggest making all bulleted items match grammatically. For example, some bullets have verbs and some do not. For the next to last bullet about Guideline developer: the text in parentheses is confusing. Also it could be made broader than Guideline developer as not all SRs are used for guidelines.\nDiscussion, p. 6 of 8 – Please add something about expected limitations of the evidence.\nNote: The peer review of this protocol is that of the reviewer and does not necessarily represent the official position of the Centers for Disease Control and Prevention.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "10261", "date": "11 Oct 2024", "name": "Ian Saldanha", "role": "Author Response", "response": "This protocol entitled ‘Current trends, barriers, and facilitators of use of core outcome sets in Cochrane systematic reviews: Protocol’ is describing a protocol of a study that will examine systematic review (SR) protocols and completed reviews for inclusion of core outcome sets (COS) as well as conduct a survey of SR protocol/review authors for barriers and facilitators of using COS. In general, the protocol is well written and thorough in descriptions. There is some repetition and long sentences that could be reduced. The background does a good job explaining COS and some additional context will help readers not familiar with this concept. Response: We thank Dr. Sipe for reviewing this manuscript and for providing useful comments. We have edited the manuscript and responded to the comments below. Background, p. 3 of 8, 1st paragraph. Term ‘evidence ecosystem’ needs explanation. Seems that time context is needed. The time context will help with understanding the study done in 2019 that is cited in next paragraph. Response: We have removed reference to the evidence ecosystem. Instead, we specifically note the other targets of core outcome sets (i.e., for routine care and for registries). 2nd paragraph – 1st sentence needs citation. Response: We have added references to support the first sentence. 3rd paragraph – 1st sentence is long and has a double negative, making it confusing. It also is a conclusion statement without evidence. Encouragement to do the action may be a better way to word the sentence or re-word to become common practice. 2nd sentence - ‘(i.e., most recent)’ may not be necessary. Last sentence is unclear and Cochrane SRs are personified. It would be the extent in which authors of Cochrane SRs/protocols are considering COS. Response: We have reworded the first sentence to remove the double-negative phrasing. We have retained the “most recent” in the second sentence because it illustrates the currency of the guidance from Cochrane and because it was released after our prior work, which is discussed in the previous paragraph. We have clarified the last sentence as suggested. 7th paragraph, 1st sentence – the text in parentheses is long and can be shortened ‘(in our previous analyses, we did not survey the authors…)’. Last sentence should ‘both with and beyond Cochrane’ be ‘both within and beyond Cochrane’? If so, this fix is needed for the abstract. Response: In the first sentence, we have removed the parenthetical text to be a full sentence and reworded it for clarity. We have made the suggested fix to the last sentence in paragraph 7 as well as in the Abstract. Methods p. 4 of 8. The design of the study is not stated. It seems to have systematic review components (literature search, inclusion/exclusion criteria, data abstraction) but does not meet all of the requirements for a systematic review. However, it could be considered a rapid review. Regardless, please state what the study design is. Response: We have added a design descriptor for Objective 1 (“cross-sectional analysis”). The text for Objective 2 includes a design descriptor (“online survey”). Methods for Objective 1, p. 4 of 8, eligibility criteria - Will there be any exclusions? Response: We have added the following exclusions: “We will exclude SRs of qualitative studies, SRs of methodological topics, and SRs that only address prognosis, diagnostic accuracy, or etiology.” (4) ‘since’ at the end of the sentence may not be grammatically correct. Response: We have inserted the word “then” after “since”. Statistical analyses, p. 4 of 8 – the authors stat that medians and IQRs will be used, however this term is often misused. IQRs are a single number (75th percentile minus 25th percentile). So maybe the authors mean ‘interquartile interval’ or more simply 25th and 75th percentiles. Response: We have replaced IQRs with “25th and 75th percentiles”. Eligibility Criteria for Cochran SR authors, p. 5 of 8 – the summary of methods on p. 4 says that the surveys are anonymous. How will the nonresponse be known if the surveys are anonymous? Response: We have removed the word “anonymous” throughout the manuscript. Survey design and implementation, p. 5 of 8 - ‘complete a single response for the SR’. It may be more clear to say ‘complete a single survey for the SR’ so as not to confuse with responses to questions on the survey. Will there be a pilot test of the survey? Response: We have made this change. Items of interest for the surveys include, p. 5 of 8. #5: Reasons for non-use of relevant COS. The sub-bullet stats that the researchers ‘will ask authors whether they will consider incorporating the unused outcomes from COS when completing the SRs…’. This is not an objective of the paper. It seems to be putting the respondents in an awkward position and could lead to socially desirable responses. There may be many reasons why authors cannot add the COS at this time. Perhaps changing to an intention question that asks how likely they would be to add COS in the future would be better. Also, add this component to the objectives if needed. Response: We have modified the sentence to indicate that we will ask authors of such SRs about the factors that would influence their decision to incorporate the unused outcomes from the COS in future SRs. Box 1, p. 6 of 8 – Suggest making all bulleted items match grammatically. For example, some bullets have verbs and some do not. For the next to last bullet about Guideline developer: the text in parentheses is confusing. Also it could be made broader than Guideline developer as not all SRs are used for guidelines. Response: We have made the text in the bullet items match grammatically. We have edited the guideline developer text to state “Recommendation of COS use from guideline developer who intended to use the SR findings”. Discussion, p. 6 of 8 – Please add something about expected limitations of the evidence. Response: We have added the following limitation to the Discussion section: “A possible limitation of the current study’s findings (if the survey response rate is poor) is that the findings may not be generalizable to all current Cochrane reviewers.”" } ] }, { "id": "191471", "date": "31 Aug 2023", "name": "Roger Chou", "expertise": [ "Reviewer Expertise Systematic reviews and systematic review 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\nThis is a protocol for a study evaluating the extent to which Cochrane reviews utilize core outcomes sets, and to understand barriers and facilitators to use of core outcome sets through author surveys. The objectives and methods are clear and the study will provide interesting and useful information to inform future systematic reviews and guidance on reviews.\nRe: the methods, for reviews that don't use a core outcome set, the study basically focuses on whether a core outcome set is available. In cases where there is a core outcome set, I think it would be useful and perhaps more meaningful to also compare the degree to which the review evaluated outcomes in the core outcome set i.e. even if they don't cite a core outcome set they could have evaluated most or all of the outcomes.\nI also think it is important to consider that for some Cochrane review groups (e.g., Back and Neck) there is a set of outcomes that authors are asked to include. This is not a formal \"core outcome set\" but may be utilized like one (and these outcomes are often based on core outcome sets). In these cases I am not sure that not citing/using a core outcome set is necessarily problematic.\nIn terms of barriers to use of core outcome sets, one thing that comes up is that Cochrane/GRADE restrict the number of outcomes to be evaluated. This can create issues when a core outcomes specifies many outcomes.\nRegarding reasons for not using core outcome sets (Box 1), some reviews could be focused on a particular outcome e.g. a particular harm.\nIn the Methods would be useful to describe the number of reviews/authors that are expected to be included, to give some sense of how robust the data and surveys will be.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "10262", "date": "11 Oct 2024", "name": "Ian Saldanha", "role": "Author Response", "response": "This is a protocol for a study evaluating the extent to which Cochrane reviews utilize core outcomes sets, and to understand barriers and facilitators to use of core outcome sets through author surveys. The objectives and methods are clear and the study will provide interesting and useful information to inform future systematic reviews and guidance on reviews. Response: We thank Dr. Chou for reviewing this manuscript and providing useful comments. Re: the methods, for reviews that don't use a core outcome set, the study basically focuses on whether a core outcome set is available. In cases where there is a core outcome set, I think it would be useful and perhaps more meaningful to also compare the degree to which the review evaluated outcomes in the core outcome set i.e. even if they don't cite a core outcome set they could have evaluated most or all of the outcomes. Response: We believe in the second sentence of this comment, Dr. Chou is referring to cases where there isn’t a core outcome set cited. We agree with the suggestion and have modified the text in the Data Extraction section of the Methods accordingly. I also think it is important to consider that for some Cochrane review groups (e.g., Back and Neck) there is a set of outcomes that authors are asked to include. This is not a formal \"core outcome set\" but may be utilized like one (and these outcomes are often based on core outcome sets). In these cases I am not sure that not citing/using a core outcome set is necessarily problematic. Response: We agree that this is likely the case for some Cochrane review groups. We anticipate that this sentiment will come through during the surveys when we ask authors what influenced the choice of outcomes for the SRs. Regardless, we believe that whether core outcome sets are used or not used should be clearly reported. Searching for core outcome sets is in keeping with current guidance in the Cochrane Handbook for Systematic Reviews of Interventions. In terms of barriers to use of core outcome sets, one thing that comes up is that Cochrane/GRADE restrict the number of outcomes to be evaluated. This can create issues when a core outcomes specifies many outcomes. Response: We agree that this may be the case for some core outcome sets but not most (the average number of outcomes in core outcome sets is about 6). It will be of interest to see if this is stated as an ‘other’ barrier by survey respondents. Regarding reasons for not using core outcome sets (Box 1), some reviews could be focused on a particular outcome e.g. a particular harm. Response: We don’t agree that being made to include a particular harm precludes a systematic review author from considering core outcome sets. By definition, a core outcome set is a minimum set of outcomes. Systematic reviewers should feel free to include additional outcomes. But, to Dr. Chou’s earlier comment, there may be restrictions to the number of outcomes in the systematic review. In the Methods would be useful to describe the number of reviews/authors that are expected to be included, to give some sense of how robust the data and surveys will be. Response: We have inserted the following sentence at the end of the Eligibility Criteria for Cochrane SRs section of the Methods: “A total of 294 SRs are eligible for Objective 1.”" } ] } ]	1	https://f1000research.com/articles/12-735
https://f1000research.com/articles/12-1198/v1	25 Sep 23	{ "type": "Research Article", "title": "L2 acquisition of Wh-interrogatives at the syntax-discourse interface: interface hypothesis again", "authors": [ "Mohammed Shormani" ], "abstract": "This study sets out to answer one major question: do linguistic phenomena relating to syntax-discourse interface constitute difficulty for Yemeni learners of English? It presents data from an experiment on the acquisition of L2 English wh-interrogatives by L1 Yemeni Arabic speakers, aiming to provide empirical evidence either in support of the Interface Hypothesis (IH) or against it. Two learner groups, intermediate and advanced, were recruited as participants of the study, and a native speaker group of (British) English was also recruited as the control group. The advanced group learners have a near-native proficiency in English. The data utilized consisted of 20 (D-)iscourse linked and non-d-linked wh-interrogatives presented to the three groups in the form of a (decontextualized) bi-modal multiple-choice paced judgement task. Results showed that both learner groups, specifically the advanced learners, performed near-native like in the non-d-linked, but far short of near/native-like performance in the d-linked wh-interrogatives. The study concluded that L2 learners’ English is still vulnerable at the syntax-discourse interface, hence supporting the IH.", "keywords": [ "L2 acquisition", "wh-interrogatives", "Interface Hypothesis", "Syntax-discourse Interface", "D-linking", "(pronoun) resumption" ], "content": "1. Introduction\n\nRecent second language acquisition (SLA) research has witnessed a remarkable shift in scope and orientation, focusing more on the acquisition of interfaces of syntax with other modules of the grammar rather than on the syntax proper. Studies conducted in this line of thought focused on examining second language (L2) acquisition of two or more typologically different languages. The interest in examining two or more typologically different languages in such bilingual SLA studies is to see to what extent these (typological) differences cause difficulty for L2 learners. The differences may include a “partial structural overlap across the two languages where language A uses construction X in context X and construction Y in context Y, while language B uses construction X in both context X and context Y” (Sorace and Serratrice 2009: 196). In other words, such studies aim to identify the influence of this bilingual overlap and whether, and to what extent it causes non-convergence from native or near-native L2 endstate grammar. However, the focus of these studies may be different in the sense that each study may focus on one particular aspect to investigate. For instance, some studies focus on the ability of L2 learners to re-set the parameters according to L2 they are acquiring (see e.g. Belletti et al. 2007). Some others investigate L2 learners’ residual optionality in interpreting uninterpretable features in their endstate L2 grammars (see e.g.Tsimpli and Dimitrakopoulou 2007). And some others aim to find out where these difficulties lie and which module of the grammar they belong to (see.e.g., Sorace 2005, 2006; Sorace and Serratrice 2009): do they belong to syntax proper, or syntax interfaces with other cognitive domains?\n\nThis study examines the availability of the Interface Hypothesis (IH), first proposed by Sorace and colleagues (Sorace and Filiaci 2006) that L2 learners’ endstate grammars are vulnerable at the syntax-discourse interface by first language (L1) Yemeni Arabic (YA) learners, who acquire English as L2, through examining the participants’ rejection of resumptive pronouns in English ungrammatical wh-interrogatives and acceptability of gaps/empty categories in grammatical ones. The study concerns primarily two sets of wh-interrogatives: grammatical and ungrammatical, at two main levels, namely (D-)iscourse linking and non-d-linking conditions, and in terms of subject and object contexts. It involves three groups of participants (n=41): intermediate learner group (IMG, n=17), advanced learner group (AVG, n=14) and control group (NSG, n=10). The intermediate learners are BA English students, at their fourth year, and the advanced learners are MA English students (after completing three semesters of courses, and before commencing writing their MA Theses). Both learner groups are native speakers of YA, and the criterion followed to determine their proficiency in English is the Online University of Michigan grammar (placement) Test (OUMG) parts 1-4. The control group are native speakers of (British) English, MA students at the University of Essex.\n\nThe reason why I study this phenomenon is threefold: first, YA is a null/pro subject language, while English is not.1 Therefore, wh-question formation mechanism is expected to be different in both languages. For example, while YA uses base-generation strategy, English uses wh-movement strategy.2 These two different mechanisms lead to two different resumption options: YA accepts resumptive pronouns in wh-interrogatives, English does not. Second, since YA typologically differs from English, YA (and its speakers) provides a good model for an experimental study. Thus, it is expected that L1 (i.e.YA) interference may have a role to play in the difficulty encountered by YA learners of L2 English. And third, the paucity of studies in Yemeni context that tackle this important aspect of L2 acquisition research. To the best my knowledge, there has been no study in the literature investigating L2 acquisition at the syntax-discourse interface by L1 YA learners of English as L2. Thus, this study serves to fill this gap, by giving empirical support to the IH in SLA and contributing to the ongoing controversy on this unprecedented hypothesis.\n\nThe study not only provides strong support to the IH’s findings, but also for its further refinements that, while it is relatively easy to acquire linguistic phenomena related to the core syntax and those related to syntax and internal interfaces such as syntax-semantics, acquiring linguistic phenomena related to syntax and external interfaces like syntax-discourse is vulnerable even at advanced stages of L2 acquisition. The results show that whereas both groups, specifically advanced learners, performed near-native like at the syntax proper (non-d-linking condition), they were far short of native or near-native competence at the syntax-discourse interface (d-linking condition). Their performance was also better in object condition than in subject condition.\n\nThe article is set up as follows. Section 2 lays out the theoretical foundations of SLA at the interfaces, reviewing some important related studies, specifically those supporting the IH. Section 3 articulates the typological syntactic differences between wh-interrogative formation in YA and English, placing emphasis specifically on the wh-mechanism and resumption strategy used in both languages. Section 4 spells out the design and methods of the study, focusing among other things on the participants of the study, the nature of the data utilized, instrument used and analysis of the data collected from the questionnaires administered to the three groups. Section 5 presents the results, tabulating these results in terms of d-linked and non-d-linked, and subject and object wh-interrogatives, and presenting the One-way ANOVA and Post hoc Scheffe analyses of the findings at the level (p = .05). Section 6 discusses the results reached in terms of three aspects, namely learners’ performance in d-linking versus non-d-linking conditions, their performance in object versus subject conditions, and Access to UG and L1 interference, and Section 7 concludes the article.\n\n\n2. L2 acquisition at the interfaces\n\nWithin earlier generative approaches to syntax, Principles and Parameters (P&P) framework,3 for example, SLA studies focused on the role of Universal Grammar (UG), and whether L2 leaners still have access to it in the acquisition of L2 (or even Ln). There are actually three positions: i) Full Access (see e.g. White 1986, Cook 1988; Flynn 1996; Shormani and AlSohbani 2015), ii) Partial Access (see e.g. Hawkins and Chan 1997; Smith and Tsimpli, 1995), and iii) No Access (see e.g. Bley-Vroman 1989).4 While it was somehow difficult in P&P Framework to account for the difficulties encountered by (adult) L2 learners, and more importantly where (exactly) they lie within L2 grammars (i.e. either within the core syntax or within its interfaces with other high cognitive domains that are not part of the core grammar), recent conceptions and developments in generative approaches to syntax such as the Minimalist Program (Chomsky 2000, 2008), cartography approaches (see e.g. Cinque 2002; Rizzi 2004; Belletti et al. 2007),5 discourse interface studies (see e.g. Reinhart 2006; Erteschik-Shir 2007; Frascarelli 2007; Shormani 2017) explicitly assist SLA scholars to account for the non-ultimate (or ultimate) attainment, the failure of native-like competence.\n\nFrom a minimalist perspective, consider feature (un)interpretability; for instance, it is held that interpretable features at the syntax–discourse interface involve considerable difficulty for L2 learners (Sorace 2005). For others, (see e.g. Tsimpli and Dimitrakopoulou 2007), however, it is uninterpretable features that constitute considerable difficulty for L2 leaners at the syntax-discourse interface, which results in variability in L2 endstate grammar. It was reported that these higher interface domains can also be extended to interpret “delays” experienced in L1 acquisition by children (e.g. Platzack 2001) and L1 attrition (e.g. Chamorro and Sorace 2018). Given this, it was not surprising to find evidence of variability or residual optionality in adult L2 leaners’ endstate grammar (see e.g. Sorace 2000, 2005, 2006, 2011, 2016; Tsimpli and Dimitrakopoulou 2007; Tsimpli and Mastropavlou 2007; Sorace and Serratrice 2009, Sorace et al., 2009).\n\nCartography approaches and discourse studies also help scholars identify where the difficulty encountered by L2 learners lies, in that they make explicit the structural representations beyond the syntax proper, or relating it to other cognitive domains. For example, cartography approaches make available linking the syntax proper with discourse/pragmatics interface (see e.g. Shormani 2017). Discourse has been identified in the left-periphery of constituent structure, specifically with the informational/coda structure, while the syntax proper with the propositional structure, the C-domain and T-domain, respectively (see e.g. Rizzi 1997, 2004, 2006; Cinque 2006; Shormani 2017; Shormani and Qarabesh 2018). To represent the discourse, the CP layer has been proposed to project to three (and sometimes four including FiniteP) projections, namely ForceP, TopicP, and FocusP (Rizzi 1997, 2004, 2006; Cinque 2006), and sometimes even SpeakerP/AddresseeP (see e.g. Espinal 2013). In Rizzi’s (1997: 283) own words, the C-domain is “the interface between a propositional content (expressed by IP) and the superordinate structure (a higher clause or, possibly, the articulation of discourse, if we consider a root clause).” Thus, TopicP, for instance, has been referred to as a projection structurally representing left-dislocation phenomena such as clitic-left dislocation, or topicalization, which is a discourse property. Several studies have tackled this aspect to account for the difficulty encountered by L2 learners at the syntax-discourse interface (see e.g. Tsimpli and Sorace 2006; Dugarova 2014; Chamorro and Sorace 2018; Smeets 2018).\n\nThus, such recent conceptions and developments give SLA scholars enough room to interpret the difficulties encountered by L2 learners, as well as L1 acquirers alike, like the residual optionality, deficit parsing or misanalyzing of L2 structures, variability, permanent fossilization, etc. in adult L2 acquisition (cf. also Long 2003; Shormani 2013). For example, Sorace and colleagues (Sorace and Filiaci 2006) propose the Interface Hypothesis in an attempt “to explain the non-convergence and optionality revealed in very advanced adult second language learners in the comprehension and production of certain structures” (Chamorro and Sorace 2018: 2). The interface Hypothesis states that learners’ endstate knowledge of L2 is vulnerable and this vulnerability is due to interface effects (Sorace and Filiaci 2006; Sorace and Serratrice 2009). That L2 advanced learners encounter considerable difficulty acquiring linguistic phenomena at the syntax-discourse interface, according to Sorace and colleagues, is due to the fact that this interface is a higher level of cognitive domains which requires high processing to be acquired.\n\nThe term Interface has been used to signify a level at which a module of the grammar is linked with other cognitive domains such as syntax-semantics, syntax-morphology, syntax-discourse (see e.g. Sorace 2005, 2006, 2011, 2016; Sorace and Serratrice, 2009). There are two types of interface: internal and external. The former refers to “those between narrow syntax and the other linguistic modules (phonology, morphology, semantics) and external interfaces, those between syntax and other cognitive modules” (Slabakova and Ivanov 2011: 638). Put differently, internal interfaces are said to be between internal modules of the grammar such as syntax-semantics, and syntax-morphology, while external interfaces take place between syntax and external cognitive domains such as syntax-discourse, syntax-pragmatics.\n\nAs for the difference between internal and external interface, Tsimpli and Sorace (2006: 653) postulate that “[t]he distinction between the two interfaces is based on the assumption that the syntax-discourse interface is a ‘higher’ level of language use, integrating properties of language and pragmatic processing, whereas syntax-semantics involve formal properties of the language system alone” (emphasis mine). Furthermore, Sorace and Serratrice (2009) argue that the difference between internal and external interfaces lies in that the former involves operations internal to the ‘core computational system’, while the latter involves operations external to this computational system.6 In their own words, “the syntax-semantic interface involves formal features and operations within syntax and Logical Form, whereas the syntax-discourse interface involves pragmatic conditions that determine appropriateness in context” (p. 197). The overall view held regarding these two types of interfaces, and which causes difficulty for L2 learners is that external interfaces are more difficult to acquire than internal ones. Sorace (2011: 1) writes: “language structures involving an interface between syntax and other cognitive domains are less likely to be acquired completely than structures that do not involve this interface” (see also Chamorro and Sorace 2018).7 The claim is that external interfaces require high processing because they lie out of the core computational system, as has been alluded to above. In what follows, I will discuss some example studies whose results provide support to the IH.\n\nThe IH effects, as well as the difference between internal and external interfaces, were supported by empirical studies cross-linguistically with a wide range of L1s and L2s (see e.g. Sorace 2006, et seq; Tsimpli and Sorace 2006; Sorace and Serratrice 2009; Belletti et al. 2007; Antonova-Ünlü 2015; Chamorro and Sorace 2018; Smeets 2018). For example, Tsimpli and Sorace (2006) investigate the interface hypothesis in a study involving 27 adult Russian learners of Greek. They investigated learners’ ability to distinguish between focus (a syntax-semantics interface property) and clitic-left dislocation, or topicalization (a left-periphery, or more specifically a syntax-discourse interface property). The results indicate that the leaners involved were able to analyze focus data, but not left-dislocated clitics. They conclude that while the syntax-semantics interface is relatively (completely) acquirable, the syntax-discourse interface is vulnerable.\n\nFurthermore, Sorace and Filiaci (2006) conducted a study examining the Anaphora resolution in near-native speakers of Italian. They recruited a control group of monolingual Italian native speakers and a group of native English speakers who had attained near-native proficiency in Italian. Their study supported the IH, pointing out that the residual optionality they found is still persistent at the syntax–discourse interface, which may be attributed to “indeterminacy”, failing to link pronouns to their antecedents. Similar findings were also reported by Belletti et al. (2007) who conducted a study to examine the null subject parameter (which is a discourse related phenomenon) pro versus overt subject pronoun in L2 Italian by 17 learners whose native language is (American) English. They concluded that there is significant divergence between L2 learners and native speakers, attributing this divergence to two sources: i) the visible outcome is the overproduction of overt subject pronouns, and the misinterpretation of overt subject, and ii) the unsystematic use of the low focus position in the VP-periphery of the clause dedicated to the new-information postverbal subjects (Belletti et al. 2007: 682). Further, Antonova-Ünlü (2015) conducted a study whose focus was L2 acquisition of Case markers in Turkish by highly proficient learners of L1 Russian. According to Antonova-Ünlü, Case markers in Turkish involve syntax-semantics/morphology interface and syntax-discourse interface, the latter of which requires pragmatic understanding for accurate interpretation. She concluded that while L2 learners easily acquire syntax-semantics/morphology interface materials, syntax-discourse interface linguistic phenomena, however, were vulnerable.\n\nIn addition, Tsimpli and Dimitrakopoulou (2007) conducted a study on the acquisition of English wh-interrogatives by L1 Greek learners. In this study, the authors examined the residual optionality in L2 acquisition, proposing the Interpretability Hypothesis, which states that uninterpretable features, but not interpretable features, constitute considerable difficulty for L2 learners. The study recruited two groups of learners, 21 intermediate and 27 advanced, and 26 native speakers of English, as a control group. The data utilized consisted of 30 wh-interrogatives (and 21 distractors). They examined resumption, d-linking and animacy effects on the responses of their participants. They found that while non-d-linked wh-questions were relatively easy to learn by both learner groups, d-linked ones were difficult. They concluded that L2 acquisition is vulnerable at the syntax-discourse interface, thus adding strong support to the IH. In addition, Smeets (2018) conducted a study examining near-native grammars at the syntax–discourse interface of two different domains of object movement in Dutch exhibiting two properties lied within syntax-semantics and syntax-discourse interfaces. In this study, the author recruited 56 participants, 15 of which were native speakers of Dutch, 16 native speakers of German and 25 native speakers of English. Her instrument was felicity judgment tasks and a truth value judgment task. The results showed that while syntax-semantics interface properties were easy to acquire, syntax-discourse were not so. However, she opines that for L2 convergence, discourse cues should be sufficiently salient in the input. She added that due to L1-L2 typological differences, “L2 learners may not fully acquire L2 discourse conditions on syntax when their L1 allows the relevant syntactic construction as well but does so in different discourse settings” (p. 21).\n\n\n3. Wh-interrogatives in English and Arabic\n\nRecall that YA is a null subject, or pro-drop language, while English is not. Therefore, it is expected that both languages differ in the way each forms wh-interrogatives. I will discuss the differences between English and YA in terms of d-linked [+DL] and non-d-linked [-DL] wh-interrogatives.8 Section 3.1 addresses the former, and Section 3.2 tackles the latter.\n\nConsider (1a) which exhibits subject d-linked wh-interrogatives, and (1b) which exemplifies object d-linked ones.\n\n(1) a. ʔayyan rajjaal qaal ʕali (ʔinn-uh) jaaʔ ʔams?\n\nwhich man said Ali that-he came yesterday\n\n‘Which man did Ali say (that he) came yesterday?’\n\nb. ʔayyan dars qaal ʕali (ʔinn-uh) katab(-uh)?\n\nwhich lesson said Ali that-he wrote-it\n\n‘Which lesson did Ali say that he wrote (it)?\n\nAs can be observed in (1), it is clear that in YA wh-questions the complementizer and the resumptive (clitic) pronoun attached to it ʔinn-uh is obligatory in both subject and object d-linked wh-questions, as in (1a) and (1b), respectively. As for subject d-linked wh-questions, English behaves exactly in the reverse manner in that the complementizer and the resumptive pronoun ‘that-he/it’ must be absent in English subject d-linked wh-interrogatives, as the English translation shows. This could be noted as the first difference between both languages. And to account for this difference, it is plausible to look at the mechanism each language uses in forming wh-questions. It is well-known that English uses movement strategy by moving the wh-word/phrase to Spec, CP, leaving a gap in the base (cf. e.g. Ross 1986; Chomsky 1977, 1995). However, YA uses base-generation strategy, i.e. the wh-word/phrase is base-generated in Spec, CP (see e.g. Demirdache 1991: 43; Boeckx 2003; Shormani 2015), with a matching resumptive pronoun in the base.\n\nRegarding the object wh-interrogatives, YA uses the complex ‘that-he/it’ and a resumptive object pronoun. However, English does allow ‘that-he/it’, but does not allow object resumptive pronouns. This could be termed as the second difference between English and YA.\n\nIn this section, I address the differences between English and YA in the non-d-linked wh-interrogatives both in subject and object contexts exemplified in (2a) and (2b), respectively:\n\n(2) a. manu qaal ʕali (ʔinn-uh) jaaʔ ?\n\nwho said Ali that-he came\n\n‘Who did Ali say (that he) came?’\n\nb. mu qaal ʕali (ʔinn-uh) ʔaštri(-uh) ?\n\nwhat said Ali that-he bought-it\n\n‘What did Ali say (that) he bought (it)?\n\nIn subject non-d-linked wh-questions, and unlike English, YA accepts the complex ‘that-he/it.9 English, however, does not allow the complex ‘that-he/it’ in subject non-d-linked wh-questions. In object wh-questions, however, English differs from YA in that it does not allow the resumptive pronoun it.\n\nTheoretically, the English properties found above are due to the fact that English does not allow wh-extraction out of a subject position, but it allows such extraction out of an object position, a phenomenon known classically as that-t effects (see e.g. Pesetsky 2017, for a recent discussion). For example, in the English translation in (2a), English does not allow either the complementizer that, the pronoun he or both that-he in subject wh-interrogatives. However, English allows the complementizer that in object position, but not the resumptive pronoun it, as the English translation of (2b) clearly indicates.\n\nTo conclude, the differences observed between English and YA in the way each forms wh-interrogatives could be summarized as follows:\n\nIn wh-interrogative formation,\n\n1. YA uses the base-generation strategy while English uses the movement strategy,\n\n2. YA accepts resumptive pronouns in both subject and object d-linked and non-d-linked wh-interrogatives, while English does not allow resumptive pronouns, English accepts gaps/empty categories, instead, and,\n\n3. English exhibits that-t effects, while YA does not.\n\nBased on these differences between YA and English, the hypotheses of the study are as follows:\n\na) Given (1) above, it is predicted that L1 YA learners of L2 English will not recognize the effects caused by the movement strategy in English, which will result in non-target performance,\n\nb) Given (2), it is predicted that L1 YA learners of L2 English will accept resumptive pronouns in both d-linked and non-d-linked wh-interrogative, and,\n\nc) Given (3), it is predicted that L1 YA learners of L2 English will be unsensitive to that-t effects, and hence inappropriately respond to that-t stances as well-formed structures.\n\n\n4. The present study\n\n4.1.1. Ethical statement\n\nFirst, the ethical approval for this study was obtained from the Department of English Studies, Faculty of Arts, Ibb University, Yemen. Second, written Informed Consent Forms were presented to all the participants in the study, both the experimental groups, viz., intermediate and advanced learners, and the control group. The Informed Consent Forms were presented along with the questionnaire, through which the consent was obtained from all the participants prior to their participation in the study. In the consent forms, it was clearly stated that their participation is voluntary and that all their responses and anonymous data will be used only for scientific research purposes. The participants were also assured that their participation will be acknowledged in the study.\n\n4.1.2. Participants\n\nThe study involves three groups of participants (n=41): control group/native speaker group (NSG), and two learner groups, intermediate group (IMG) and advanced group (AVG). The NSG involves 10 participants (n=10), native speakers of (British) English, Masters of Arts (MA) students, studying at the University of Essex. The IMG consists of 17 participants (n=17), BA students at the final (fourth) year. AVG consists of 14 (n=14), MA students who completed their three semesters of courses (and before commencing writing their MA Theses). Both learner groups were recruited from Ibb University, Yemen. The Mean Age (M) of the three groups is as follows: NSG is 29.3 years, IMG 25.8 years and AVG 34.2 years. The IMG participants have studied English for 10 years. They studied English as a compulsory subject in schools for six years. They have also studied English for four years at the university in BA Degree. Furthermore, the AVG participants have studied English for about 12 years, as a compulsory subject in schools for six years, four years in BA Degree, and one and half years in MA program.\n\n4.1.3. Instrument\n\nThe wh-interrogative data were presented to the participants in three forms: i) an online questionnaire constructed on Google.Forms for native speakers of English). The link of this instrument was sent to an MA student at the University of Essex, requesting her to ask 10 MA students to respond to the items of the questionnaire, ii) a hardcopy of the same questionnaire was administered to the IMG participants, and iii) a hardcopy of the same questionnaire was also administered to the AVG participants (see Shormani 2023).\n\nThe task was a (decontextualized) bi-modal paced judgement task, whereby the participants were asked to judge the acceptability/unacceptability of 20 wh-interrogatives on a 1-4 Linkert scale, ranging from Natural to Very Odd. The responses are Natural, Ok, Odd and Very Odd. Both intermediate and advanced learners were allotted 20 minutes to judge the 20 wh-questions, i.e. one minute for each wh-question. I tested these 20 wh-interrogatives considering d-linking versus non-d-linking, and subject versus object as conditions. Groups is the dependent variable. Concerning the acceptability of the wh-interrogatives, I count the options Natural and Ok as target, and Odd and Very Odd as non-target.\n\n4.1.4. Data utilized\n\nThe data utilized in the study are wh-interrogatives, involving 20 wh-interrogatives. They involve 10 wh-interrogatives for d-linking and 10 for non-d-linking. Both categories involve both subject and object wh-interrogatives. Table 1 presents these categories along with their frequency.\n\nThe data also involved 10 grammatical and 10 ungrammatical wh-interrogatives. Table 2 presents two examples for (+DL) wh-phrase, i.e. Which-NP, and two examples for each (-DL) wh-words, namely Who and What. (For the full set of wh-interrogatives along with number of occurrences, see Shormani 2023).10\n\nAs Table 2 shows, three wh-words/phrases were utilized, namely Who, What and Which-NP; Who and What are non-d-linked wh-words, and Which-NP is a d-linked wh-phrase. Who and What represent subject and object non-d-linked wh-words, respectively, and Which-NP represents subject and object d-linking.\n\nThe data utilized involved complex wh-interrogatives, complex in the sense that each consists of matrix and complement (embedded) clauses, and the participants were told about this fact. In the matrix clauses, verbs that require sentential complements were used. These are say, think, suggest, remember, etc. The responses were collected from the three questionnaires. The data were analyzed by the researcher using SPSS V. 27. One-way ANOVA was used to analyze the statistical differences between groups. As for comparisons within groups, a Post hoc Scheffe was used.\n\n4.1.5. Criterion\n\nThe criterion that was utilized to determine the division of both experimental groups is the Online University of Michigan Grammar (placement) Test (OUMG) parts 1-4. The OUMG Test assesses different and several aspects of English grammar.11 The participants were allotted 20 minutes to answer 40 multiple-choice questions, i.e. each question was given ½ minute. IMG’s minimum score was 67 % and maximum 78% accuracy, and AVG’s minimum score was 83 %, and maximum 91% accuracy (cf. Table 3). Based on these results, IMG participants were considered to have an intermediate level in English, and those in AVG an advanced level. Table 3 presents the results of the OUMG test.\n\nThe variables tested in this study are presented in Table 4.\n\n\n5. Results\n\nThe results collected from the acceptability judgment from the three groups are presented in Tables 5 and 6. The results are presented in two formats according to the conditions, i.e. d-linking and non-d-linking, and subject and object. I first count the participants’ responses for the d-linked wh-interrogatives in both subject and object contexts. Then I count the responses for the non-d-linked wh-interrogatives also in both subject and object contexts. For differences between groups, I used One-way ANOVA analysis for the differences between groups, and Post hoc Scheffe test was used for differences within groups.\n\nAs Table 5 shows, the IMG participants performed less significantly than the AVG participants in both subject and object d-linked wh-interrogatives [IMG: (subject) 42.4%; and (object) 54.1%; AVG: (subject) 58.6%, and (object) 65.7%, accuracy]. It is also clear that both learner groups performed better in object d-linked wh-interrogatives than in subject d-linked ones. However, both groups differ significantly from the control group.\n\nTable 6 shows that both learner groups do not differ significantly; they both fare somehow better than in d-linking condition, particularly in object contexts [IMG: (subject) 68.2%, and (object) 78.9%; AVG: (subject) 82.8%, and (object) 87.2%, accuracy].\n\nThe overall results in both d-linking and non-d-linking conditions, presented in Tables 5 and 6, show that the control group performed as expected. They rejected the resumptive pronouns in ungrammatical sentences and accepted gaps in grammatical ones. Both learner groups fare in non-d-linked better than in d-linked wh-interrogatives. This shows that non-d-linked wh-interrogatives are easier to acquire than d-linked ones, which in turn implies that they have encountered less difficulty in the syntax proper data than that at the syntax-discourse interface.\n\nAs for the d-linking condition, the two experimental groups performed significantly less than the control group (cf. Table 5). A One-way ANOVA performed on the d-linked wh-interrogatives revealed statistically significant differences between the control group and each of the learner groups on both subject and object conditions F(2, 38) = 91.248, p <.001], and F(2, 38) = 19.961, p < .001], respectively.\n\nFor comparisons within groups, Post hoc Scheffe test indicated high statistically significant differences between the control group and each of the learner groups [IMG: (subject) MD = 4.364, p <.001, p <.05; (object) MD = 5.723, p <.001, (p<.05); AVG: (subject) MD = 2.417, p =.01, (p <.05), (object) MD =3.351, p =.01)].12\n\nAs for the learner groups, there were significant differences between the intermediate and advanced learners in both subject and object conditions [IMG: (subject), MD =3.907, p <.001, (p<.05), (object) MD = 3.037, p <.001), (p<.05); AVG: (subject) MD =3.015, p <.001), (p <.05), (object) MD = 1.907, p = .01, (p <.05)].\n\nThe above findings in terms of the d-linking condition clearly indicate that both learner groups performed far short of the control group. Put differently, both learner groups seem to accept resumptive pronouns in d-linking condition in ungrammatical wh-interrogatives, and reject gaps in grammatical ones, which results in bad performance. They also show clearly that the advanced group performed better in the object condition than the intermediate group.\n\nTurning now to the non-d-linking condition, the intermediate learners and the advanced learners fare better in the object condition. However, they both differ significantly from the control group, though they performed better than they did in the d-linked wh-interrogatives (cf. Table 6). A one-way ANOVA conducted on the non-d-linked wh-interrogatives indicated that there were statistically significant differences between the control group and the learner groups each [F(2, 38) = 88.985, p <.001] for subject, and [F(2, 38) = 4.119, p <.024] for object.\n\nAs for comparison within groups, Post hoc Scheffe test revealed statistically significant differences between the control group and the intermediate group [IMG: (subject) MD= 9.623, p <.001, (p<.05); (object) MD = 1.764, p =.01, (p < .05)]. However, there were no significant differences between the control group and advanced group [AVG: (subject) MD= .481, p = 1, (p >.05), (object) MD = .341, p = 1, (p >.05)].\n\nThis is an important finding of this study, because it highlights the better performance of the advanced group at the syntax proper. That is to say, they performed near-native like in judging the non-d-linked wh-interrogatives.\n\nHowever, Scheffe test also revealed that there were no statistically significant differences between the intermediate group and advanced group [IMG: (subject) MD=1.714, p =.058, (p >.05), (object) MD =.514, p =1, (p >.05); AVG: (subject) MD=.462, p =1, (p>.05), (object) MD = .317, p = 1, (p >.05)].\n\nThis is also a significant finding due to the fact that both groups, intermediate and advanced learners, seem to perform near-native like in wh-interrogatives. This implies that the linguistic phenomena related to the syntax proper is easier to acquire.\n\nThe overall findings reached regarding the d-linking condition suggest that: i) both learner groups, though with a varying degree in favor of the advanced group, performed better in the non-d-linked than they did in the d-linked wh-interrogatives, indicating that (a) they have acquired the syntax proper linguistic phenomena, and (b) the fact that the advanced learners performed like native speakers indicates that they face no difficulty in processing the non-d-linked wh-structures, ii) both learner groups, particularly the advanced learners, performed much better in both ungrammatical and grammatical wh-questions, which suggests that they rejected resumptive pronouns and accepted gaps, respectively, relatively close to native speakers’ performance in the non-d-linking condition, and iii) the fact that the advanced group performed like native speakers in the non-d-linked, but far less than them in the d-linked wh-questions shows clearly that they have acquired the proper way of using the [-DL], but not [+DL] features, and iv) the fact that both groups performed far better in the non-d-linked than in the d-linked wh-questions indicates that they encountered considerable difficulty in processing or analyzing linguistic phenomena in the d-linking condition, or more specifically, at the syntax-discourse interface.\n\n\n6. Discussion\n\nThe overall results reached revealed that the intermediate and advanced learners performed significantly differently from the native speakers in the d-linking condition, and significantly far less than they did in the non-d-linking condition, in both subject and object contexts. This indicates that both groups accepted the resumptive pronouns in the ungrammatical, but did not accept gaps in the grammatical wh-interrogatives. This otherwise clearly indicates that they were successful in acquiring the syntax proper wh-questions, but were not so in acquiring the syntax-discourse ones, thus supporting the IH. Thus, I will discuss the results of the study in terms of:\n\ni. learners’ performance in d-linking versus non-d-linking conditions,\n\nii. learners’ performance in subject versus object contexts and,\n\niii. Access to UG and L1 interference\n\nAs for (i), given the statistics in section 5 above, briefly repeated below for convenience, both learners performed in the d-linking condition statistically significantly less than the control group [IMG: (subject) 42.4%; and (object) 54.1%; AVG: (subject) 58.6%, and (object) 65.7%, accuracy] (cf. Table 5). It is also clear that advanced learners performed better than intermediate learners. A One-way ANOVA performed on the d-linked wh-interrogatives revealed statistically significant differences between the control group and each of the learner groups both in subject and object conditions [F(2, 38) = 91.248, p <.001], and F(2, 38) = 19.961, p < .001], respectively.\n\nAs for the non-d-linking condition, both learner groups performed much better than they did in the d-linked wh-questions [IMG: (subject) 68.2%, and (object) 78.9%; AVG: (subject) 82.8%, and (object) 87.2%, accuracy] (cf. Table 6). This means that both learner groups have acquired the syntax proper in which these non-d-linked wh-interrogatives are processed and analyzed, more specifically in object contexts. A one-way ANOVA conducted on the non-d-linked wh-interrogatives indicated that there were statistically significant differences between the control group and the learner groups each [F(2, 38) = 88.985, p <.001] for subject, and [F(2, 38) = 4.119, p <.024] for object.\n\nPost hoc Scheffe test, however, shows that there were no significant differences between the control group and advanced group [AVG: (subject) MD= .481, p = 1, (p >.05), (object) MD = .341, p= 1, (p >.05)]. As noted so far, this is a very significant result which clearly highlights the fact that both learner groups performed near-native like in non-d-linked constructions, which in turn indicates that they have acquired the syntax proper relatively well.\n\nRegarding (ii), the fact that both learner groups’ performance in object condition is far better than in subject condition is not surprising. Given the syntactic facts of YA: i) YA is a null subject language, ii) YA does not use wh-movement strategy, but rather base-generation one, and iii) YA does not exhibit that-t effects, this finding is again not surprising. Given the base-generation strategy utilized by YA, and the assumption that resumptives are the spell out of (uninterpretable) agreement features and Case (cf. Alexiadou and Anagnostopoulou 1998), resumptive pronouns are likely to persist in L1 YA learners’ endsate grammars, or their Interlanguage (cf. Lardiere 2009). Thus, when the wh-word/phrase is base-generated in the topmost Spec, CP, these agreement features and Case are likely to spell out as resumptives, which is not the case in English, which in turn indicates that learners will have a “tendency” to accept these resumptives in their English production.\n\nThe fact that YA does not exhibit the that-t effects results in YA learners being unsensitive to such effects in English. If this is on the right track, the learners will accept resumptives in ungrammatical wh-questions, and will not accept gaps in grammatical ones. Given that that-t effects are related to subject wh-questions, but not to object ones, their bad performance in subject wh-questions could be a direct result of that.\n\nAnother possible interpretation of this subject-object asymmetry is to look at the nature of the object wh-questions in English, i.e. English wh-questions allow the complex ‘that-he/it’, which is not different from YA. Examples in (3a) and (3b) illustrate the point in question.\n\n(3) a. ʔayyan dars qaal ʕali (ʔinn-uh) katab(-uh)? D-linked\n\nwhich lesson said Ali that-he wrote-it\n\n‘Which lesson did Ali say that he wrote (it)?\n\nb. mu qaal ʕali (ʔinn-uh) ?aštri(-uh) ? Non-D-linked\n\nwhat said Ali that-he bought-it\n\n‘What did Ali say (that) he bought (it)?\n\nThus, the only difference between YA and English in object -wh-questions turns to be the obligatory-optional use of the resumptive pronoun it, which suggests that YA learners find object wh-questions easier to process/acquire than subject ones. This may be thought of as a “facilitator” aiding the learners to perform better in object wh-questions than in subject ones. In fact, the subject-object asymmetry found in our study provides support to previous studies (see e.g. Tsimpli and Dimitrakopoulou 2007, and the references there).\n\nAs for (iii), considering the nature of the data utilized, they are complex wh-interrogatives, involving long-distance wh-movements, because they each consist of a matrix and complement clause. These complex wh-interrogatives involve resumptive pronouns “as a saving device to redeem derivations and structures that would otherwise violate a fundamental principle of the grammar” (Rouveret 2011: 2, see also Leal Méndez and Slabakova 2012). These structures are expected to be more difficult to process or analyze by the learners, specifically if the L1 does not use wh-movement strategy and allows resumptive pronouns. Put differently, the wh-movement in these complex structures will undergo several cyclic wh-movements from the base position to the topmost Spec, CP. Thus, learners will face considerable difficulty in processing these A’-chain wh-questions much more than that faced in processing simple wh-questions (i.e. one-clause wh-questions).13\n\nAt the level of the syntax proper, i.e. non-d-linked wh-questions, L2 learners in this study performed approximately well. The fact that they performed well, at least at the syntax proper indicates that the learners, specifically the advanced learners, have acquired how resumptive pronouns are used in English (non-d-linked) wh-interrogatives, by rejecting these pronouns in ungrammatical sentences and accepting gaps/empty categories in grammatical ones. This is evidence that the UG activated by the learners’ L1 (before puberty, cf. Pinker 1995; Shormani 2014c) has worked its path in L2 acquisition, and is still accessible, allowing them to re-set the resumptive parameter according to L2 grammar in the syntax proper. Form a minimalist perspective, L2 learners were able to use Merge and Agree operations properly. As for Merge, one could argue that learners, specifically the advanced ones, were able to apply the internal Merge (wh-movement) accurately, and the wh-movement was applied cyclically, involving several wh-movement stances. Assuming with Chomsky (2000, 2001), for instance, that the head C has an EPP (Extended Projection Principle) (or [uwh]) feature, EPP triggers the wh-word/phrase to remerge in Spec, CP, and the learners seem to have acquired it. Regarding Agree, it is possible to argue that L2 learners have acquired where to or not to apply it in YA and English wh-questions. That is to say, while Agree applies in YA resulting in resumption, learners did not apply it in English (non-d-linked) wh-questions.\n\nHowever, at the syntax-discourse interface, L2 learners involved in this study fail to apply the parameter re-setting, or Merge and Agree operations successfully. In other words, L2 learners were not able to re-set the parameters of L1 according to L2, in such a way as to reject resumptive pronouns in their L2 grammars at the syntax-discourse interface, i.e. when discourse comes to play. The fact that [+DL] features are imposed by discourse such as discourse (co)referentiality (see e.g. Shormani 2017), context, situation, etc. in resumption, for instance, to disambiguate a grammatical structure, or what has been referred to by Tsimpli and Dimitrakopoulou 2007) as “garden-path effects”, manifests itself clearly in their L2 vulnerability. This suggests that L2 learners’ grammar cannot reach endstate or native speakers’ competence, which also suggests that access to UG is partially restricted, the reason of which might be attributed to L1 interference, among other reasons.14 One could assume that though these L2 learners have reached high level of learnability in I-language of L2 (cf. Chomsky 2013), they were just unable to re-set the parameters concerning the use of resumptive pronouns in L2 English. From a minimalist perspective, it seems that L2 learners even at advanced levels are not able to distinguish where to apply the operations Merge and Agree appropriately in their performance. Put simply, they were unable to figure out that a resumptive pronoun cannot be merged with a moved wh-word/phrase in L2 English, and while Agree is spelled out as a resumptive pronoun in YA (cf. Alexiadou and Anagnostopoulou 1998, see also Tsimpli and Dimitrakopoulou 2007, for Greek), it is not the case in English wh-questions at the syntax-discourse interface. Having this deficit characterization of wh-interrogatives at the syntax-discourse interface, L2 learners fail to perform like native speakers, as predicted by the IH.\n\nThis makes it clear, though, that L1 interference may play a role in the learners’ performance. That is, the difficulty encountered by L2 learners could be attributed to L1 interference in acquiring linguistic phenomena relating to the syntax-discourse interface. Or, L2 learners find it difficult to process and analyze a particular structure involving discourse-domain related phenomena, thus, resulting in resorting to their L1, as a “subconscious” strategy to overcome such difficulties (Shormani 2014a &b). The resumption strategy of YA could be said to have been transferred to L2 counterpart structures, hence resulting in ungrammatical performance. Assuming with Alexiadou and Anagnostopoulou (1998) and Tsimpli and Dimitrakopoulou (2007) that features like subject-verb agreement and Case are uninterpretable features and spell out as resumptive pronouns, it could be argued that these features are transferred from L1 YA to L2 English at the syntax-discourse interface. This L1 interference could also be said to make L1-L2 counterpart wh-structures “difficult to identify and analyse in the L2 input due to persistent, maturationally-based, L1 effects on adult L2 grammars” (Tsimpli and Dimitrakopoulou 2007: 217).\n\n\n7. Conclusions and further implications\n\nThis study examined L2 acquisition at the syntax-discourse interface by L1 YA learners acquiring English wh-interrogatives, at both d-linking and non-d-linking conditions, or syntax proper and syntax-discourse interface, respectively. The aim was to answer one major question: do linguistic phenomena relating to syntax-discourse interface constitute difficulty for Yemeni learners of English? According to the results reached, it is clear that the answer is yes; L1 YA learners’ competence of English at the syntax-discourse interface is still vulnerable.\n\nIn our corpus, I found strong support to IH predictions, i.e. L2 acquisition is vulnerable at the syntax-discourse interface. Both groups of learners, intermediate and advanced, involved in this study found considerable difficulty in acquiring the wh-interrogatives at the syntax-discourse interface. However, they performed significantly better in the syntax proper, i.e. the non-d-linked wh-questions. Given this, our study, thus, provides strong support to previous studies on this phenomenon (see e.g. Tsimpli and Sorace 2006; Sorace and Filiaci 2006; Tsimpli and Dimitrakopoulou 2007; Tsimpli and Mastropavlou 2007; Sorace and Serratrice 2009; Sorace 2005, 2006, 2016).\n\nIn addition, our study provides important findings that could be employed by university teachers while prescribing textbooks for their students, or even while their teaching of syntax courses. In the latter aspect, university teachers are advised to involve comprehensive comparisons of YA with English wh-question formation in both languages, concerning specifically the different wh-mechanism and resumption strategies utilized by each language. In this way, teachers could provide students with linguistic input sufficient for acquiring such differences, and students would be made aware of these differences between their L1 and L2 they are acquiring from early stages of their acquisition, and more specifically before these structures get fossilized.\n\nTo conclude, it is true that the results of this study support numerous previous studies, but these studies were conducted in different contexts, different L1s, and L2s, different from those of this study. Thus, it goes without saying that further research be conducted to see whether the results concluded with in this study are supported, not only concerning wh-interrogative acquisition, but also including acquisition of other linguistic phenomena such as articles, focus, topicalization, subject-verb agreement, etc. in English, and I leave these for future research.", "appendix": "Data availability\n\nFigshare: L2 Acquisition of Wh-interrogatives at the Syntax-discourse Interface: Interface Hypothesis again. F1000Reseacrh. https://doi.org/10.6084/m9.figshare.23792385.v5. (Shormani, Mohammed. 2023)\n\nThis project contains the following underlying data:\n\n• Underlying data-total results.pdf. (The tabulated results indicating the group (IMG, AVG & NSG), item number, number of responses and D-linking condition: d-linked and non-d-linked wh-interrogatives).\n\nData is available under the terms of the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: L2 Acquisition of Wh-interrogatives at the Syntax-discourse Interface: Interface Hypothesis again. F1000Reseacrh. http://dx.doi.org/10.6084/m9.figshare.23792385. (Shormani, Mohammed. 2023)\n\nThis project contains the following extended data:\n\n• Sentence.order:\n\n• Example of participants’ responses (Intermediate Learner Group (IMG))\n\n• Example of participants’ responses (Advanced Learner Group (AVG))\n\n• Example of participants’ responses (Native Speaker Group (NSG))\n\nAny further individual responses can be requested from the author.\n\nData utilized in this article are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nI would like to very much thank the learner participants taking part in this study for their valuable contribution. I also extend my sincere thanks and appreciation to the control group who willingly participated in this study. I also thank my friend and colleague Fahd Al Hussain, King Saud University for his help in data analysis.\n\n\nReferences\n\nAlexiadou A, Anagnostopoulou E: Parametrizing AGR: word order, V-movement and EPP-checking. Nat. 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Oxford: Pergamon Press; 1986; 55–72.\n\n\nFootnotes\n\n1 Null/pro subject is a covert subject, i.e. not phonetically realized as in the Arabic sentence in (i):\n\n(i) kataba d-darsa\n\nwrote the-lesson\n\n‘He wrote the lesson.’\n\nIn (i), the subject in Arabic is considered to be null/pro, because Arabic allows the subject pronoun to be dropped.\n\n2 Base-generation strategy is a syntactic process in which the wh-word does not move to its final position, viz., Spec,CP, but rather first merges in this position and remains there throughout the derivation.\n\n3 In early 1980s, Chomsky proposed the Principles and Parameters Framework as a theoretical solution to several problems including what knowledge of language is, and how humans acquire it. He proposed that humans are innately, genetically and tacitly endowed with a Language Faculty, which contains UG (Chomsky 1981). UG, Chomsky argues, contains two types of linguistic/syntactic rules, viz., Principles and Parameters. Principles are rules universal to all human languages e.g. Extended Projection Principle, which states that every clause must have a subject. Parameters, on the other hand, are syntactic rules specific to every language, e.g. Null Subject Parameter, which states that, in some languages, the subject could be null/covert, while in others it is overt (see e.g. Shormani 2014b & c, 2016).\n\n4 As will be discussed in subsequent sections of this article, this study examines this view as well. It argues that this Partial Access to UG is due to L1 interference/persistence in L2 endstate grammar. In other words, L1 influence restricts the access to UG only in relation to linguistic phenomena relating to syntax and external interfaces such as syntax-discourse/pragmatics.\n\n5 With the view that in minimalism language acquisition is acquisition of features, there have been several calls that SLA studies, particularly those done within the generative approach, should be conducted at interfaces (see e.g. Marantz 1995; Chomsky 2005; Lardiere 2009). This is due to the fact that most of the difficulties encountered by L2 learners have been attributed to these interfaces, be they within syntax and its interfaces or within other modules and their interfaces.\n\n6 This line of thought is also supported by Reinhart (2006). She proposes that the interface difficulties encountered by L2 learners are caused by reference set computations, resulting in non-native like performance/proficiency.\n\n7 However, a recent study conducted by Jin et al. (2022) claims exactly the opposite. Their study’s purpose was to examine the adult heritage speakers’ mastery of referential nominal expressions regulated at the syntax-semantics and syntax-discourse interfaces in Mandarin Chinese. The participants of the study are 58 adult heritage speakers of Chinese from overseas and 29 native speakers of Chinese. In their study, they found that their heritage participants performed in linguistic phenomena relating to syntax- discourse interface better than they did in linguistic phenomena relating to syntax- semantics interface.\n\n8 The assumption that wh- phrases are considered d-linking constituents is advocated in several studies (e.g. Pesetsky 1987, 2000; Aoun & Li 2003). The term d-linking was first proposed by Pesetsky (1987) holding that it is a discourse property. Pesetsky (1987, 2000) argues that a wh- phrase is considered a D-linked constituent if the question introduced by it requires an answer which individualizes an entity or a set of entities from that previously referred to in the discourse, understood to both interlocutors of, say, a conversation. Thus, it should be noted that English and YA use similar wh- phrases for d-linking and non-d-linking: YA uses the wh- phrase ʔayyan-NP (English Which-NP ) for subject and object d-linking, and manu and mu (English Who and What, respectively) for non-d-linking, subject and object, respectively.\n\n9 See also Tsimpli and Dimitrakopoulou (2007), for somewhat similar data from Greek, however the differences between Greek and YA. Greek, for example, uses wh-movement strategy, and allows (in)animacy effects while YA use base-generation strategy and does not allow (in)animacy, among other differences.\n\n10 Note that the wh-data were presented to the participants randomly, i.e. without numbering. The numbers in Table 2 indicate the order in which the wh-word/phrase occurs in the questionnaires.\n\n11 This is the link to the OUMG Test: https://www.press.umich.edu/elt/compsite/cleargrammar/CG_part1\n\n12 MD = Mean Difference (I-J)\n\n13 One-clause wh-questions in YA can be exemplified in (i), in which we observe that the complex ‘that-he/it’ is obligatorily absent in YA examples, exactly like English ones. Thus, it is obviously clear that such English one-clause wh-questions could be easier for L2 learners to process and analyze than those consisting of matrix and complement clauses, like the ones utilized in this study.\n\n(i) ?ayyan rajjaal (ʔinn-uh) jaaʔ ?ams ?\n\nwhich man (that-he) came yesterday\n\n‘Which man (*that he) came yesterday?’\n\n14 Somewhere else, I argued that UG is available and accessible to language learners alongside their lifespan, provided that it has been activated by L1 before puberty (see e.g. Pinker 1995). The learners’ inability to re-set the UG parameters, or apply Merge, Agree (or even Move, Internal Merge) operations according to L2 ones cannot be ascribed to accessibility to UG per se. However, this inability could be ascribed to non-linguistic factors such as residual optionality caused by, for instance, insufficient linguistic input, the way this linguistic input was presented to the learners in (or out of ) classroom, and/or the deficit competence of those who present it, among many other reasons irrelevant to UG such as “age, motivation, attitudes towards L2 and its speakers, interest, etc.” (Shormani 2014c: 84)." }	[ { "id": "210085", "date": "19 Oct 2023", "name": "Arif Ahmed Al-Ahdal", "expertise": [ "Reviewer Expertise Professor of Applied Linguistics" ], "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 addresses L2 acquisition, focusing on acquiring English wh-interrogatives by L1 Yemeni learners at the syntax-discourse interface; it examines interface hypothesis proposed by Sorace and colleagues (2006). The study findings indicate that the learners’ endstate knowledge of wh-interrogatives is vulnerable at the syntax-discourse interface, while their knowledge at the syntax proper is not. These findings support a wide range of findings reached and articulated by a great number of studies in this area of language study in general, and L2 acquisition, in particular. Considering the Yemeni context, the study contributes greatly and substantially to the body of research on L2 acquisition process, in general, and acquisition of wh-interrogatives, per se.\nThe paper develops the subject matter in an academic and logical way, which vividly mirrors the author’s sound knowledge in this area of research, and syntax interfaces with other cognitive modules of the grammar. It is well-written, with no grammar or stylistic problems.\nThe originality of topic researched is obvious as the topic is not over-researched, and the findings arrived at would be of great significant to all those interested in the field. A valuable and current bulk of related literature has been consulted and cited, comparing this study to other studies in terms of context, participants, instrument, approach, method of analysis and findings. The introduction section provides a comprehensive account of the nature of the study, scope, purpose, research design, and the gap it tends to fill. The conclusion section skillfully summarizes the whole paper and its findings, and provides tertiary-level instructors with salient pedagogical implications that could be applied in teaching syntax course(s) in order to improve the acquisition process of syntactic phenomena, specifically wh-interrogatives.\nThere are, however, three minor comments to be considered and addressed before the manuscript is indexed. These are:\nThe following example, given in Footnote 13, should be incorporated into the text:\n(i) ?ayyan rajjaal (ʔinn-uh) jaaʔ ?ams ?\n\nwhich\n\nman (that-he)\n\ncame yesterday\n\n‘Which man (*that he) came yesterday?’\n\nInconsistency:\ni) Phonetic symbols: the question mark /?/ is sometimes used instead of the phonetic symbol /ʔ/, which should be used throughout the Arabic data.\nii) Comma “ , ” in in-text referencing: there are few instances where “ , ” between the author’s name and date as in “(…Sorace et al., 2009)” is used. This should be fixed. There are also a few instances of using “&” instead of “and” between two authors’ names as in “…Aoun & Li 2003”, in Footnote 8, which should be checked throughout.\n\nFragment: there is a fragment in the introduction section: “And third, the paucity of studies in Yemeni context that tackle this important aspect of L2 acquisition research”, The verb “is” is missing and “the” should be added before “Yemeni. It should, thus, be rewritten as “And third is the paucity of studies in the Yemeni context that tackle this important aspect of L2 acquisition research.”\nApart from the flaws referred to above, I find that the work is in a good shape and would certainly be a valuable reference for English syntacticians and syntax practitioners across the globe.\n\nIs the work 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": "210086", "date": "30 Oct 2023", "name": "Wagdi Rashad Ali Bin-Hady", "expertise": [ "Reviewer Expertise Applied lingustics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research work is original. The researcher examined the L2 acquisition of Wh-interrogatives in three learner groups. I strongly recommend the work for indexing after mangling a few comments:\nThe first sentences in the introduction need justification, so you are recommended to add some sources.\n\nThe author is required to mention some of the previous studies which have been conducted on YA to set this research in its field.\n\nSome paragraphs should be shifted from the introduction into other sections e.g.,\n\"It involves three groups of participants (n=41): intermediate learner group (IMG, n=17), advanced learner group (AVG, n=14) and control group (NSG, n=10). The intermediate learners are BA English students, at their fourth year, and the advanced learners are MA English students (after completing three semesters of courses, and before commencing writing their MA Theses). Both learner groups are native speakers of YA, and the criterion followed to determine their proficiency in English is the Online University of Michigan grammar (placement) Test (OUMG) parts 1-4. The control group are native speakers of (British) English, MA students at the University of Essex.\"\n\nUnder the method section, add research design.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1198
https://f1000research.com/articles/12-1195/v1	25 Sep 23	{ "type": "Research Article", "title": "Prevalence of Helicobacter pylori infection in dyspeptic patients presenting to a tertiary care center of a developing country: a cross-sectional study", "authors": [ "Ram Chandra Subedi", "Binit Upadhaya Regmi", "Bishnu Deep Pathak", "Bishal Dhakal", "Deekshanta Sitaula", "Ujjawal Paudel", "Prabal KC", "Srijana Maharjan", "Anurag Karki", "Sunil Baniya", "Sushil Joshi", "Chiranjibi Pant", "Kumar Roka", "Ram Chandra Subedi", "Binit Upadhaya Regmi", "Bishal Dhakal", "Deekshanta Sitaula", "Ujjawal Paudel", "Prabal KC", "Srijana Maharjan", "Anurag Karki", "Sunil Baniya", "Sushil Joshi", "Chiranjibi Pant", "Kumar Roka" ], "abstract": "Background: Among the various causes for dyspepsia in patients presenting to the gastroenterology department, Helicobacter pylori is the most common etiological agents. Here, we explore the prevalence of Helicobacter pylori infection, particularly, in dyspeptic patients and different endoscopic findings in such patients. Methods: We conducted a simple observational study in the gastroenterology department of a tertiary care center of Nepal. The Helicobacter pylori was detected using rapid urease test and endoscopic findings were collected from gastroduodenoscopy unit. The obtained data was analyzed using Statistical Package for Social Sciences (IBM-SPSS), version 22. Results: The overall prevalence of Helicobacter pylori infection in dyspeptic patients in our center was found to be 0.329 (0.259 – 0.406) at 95% Confidence Interval (CI). There was significant association of Helicobacter pylori infection with alcohol history (12 [52.17] vs 44 [29.93], p = 0.035) and endoscopic findings of duodenal ulcer (3, 100%) followed by gastritis (29, 50.88%). Conclusions: Amidst various etiology for dyspepsia, Helicobacter pylori was still prevalent at our center. However, considering the variability of its prevalence due to factors like alcohol history, more comprehensive studies are needed to estimate actual proportion in patients presenting with dyspeptic symptoms.", "keywords": [ "Helicobacter", "dyspepsia", "peptic ulcer", "gastritis" ], "content": "Introduction\n\nDyspepsia is defined as having a combination of one or more symptoms among epigastric pain, epigastric burning sensation, postprandial fullness or early satiation. These symptoms are thought to originate from gastrointestinal region in the absence of organic or systemic disorders.1 Although symptoms such as nausea and bloating may co-occur in dyspeptic patients and may point towards the disorder, newer definitions do not include these as cardinal or localizing symptoms of dyspepsia.2 Of all patients with dyspeptic symptoms, 20-25 percent have an underlying organic cause on diagnostic evaluation such as peptic ulcer disease, Helicobacter pylori gastritis, gastroesophageal reflux, biliary pain, malignancy, gastroparesis, pancreatitis, medication, etc.3 while the rest are attributed as functional dyspepsia which is defined as at least three months of symptoms without definite structural or biochemical explanation.4\n\nHelicobacter pylori is a spiral-shaped, microaerophilic, Gram negative, urease positive bacterium that is adapted to survive the harsh, acidic environment of the stomach.5 H. pylori infection is often an underlying cause of dyspepsia and reports verify that eradication of H. pylori improves the symptoms in dyspeptic patients.6,7 The principal mechanism mostly involves altered gastric acid secretion and persistent active inflammation of gastric mucosa, in addition to delayed gastric emptying and antral gastric secretion.8,9 Among different invasive and non-invasive tests available for detection of H. pylori, the rapid urease test is a simple, cheap and quick test to detect urease activity in the gastric mucosa, which requires sampling of the mucosa with an endoscopic approach. The upper GI endoscopy with biopsies has an increasing diagnostic yield with increasing age in patients with dyspepsia, particularly in patients above the age of 60 or those with warning signs. The common endoscopic findings in a background of dyspepsia include erosive esophagitis, gastritis, duodenitis and peptic ulcer disease.10\n\nLimited studies have estimated the prevalence of H. pylori in the Nepalese population with specific targeting of patients suffering from dyspepsia, with varying results depicted in available studies. The purpose of this study was to estimate the prevalence of H. pylori infection among dyspeptic patients presenting at the gastroenterology department of a tertiary care centre in Nepal and to stratify the different endoscopic findings seen among such patients.\n\n\nMethods\n\nThis study was conducted at Shree Birendra Hospital, Kathmandu Nepal. It is a tertiary care hospital dedicated to serving the Nepalese army and their dependent families.\n\nThis study is a cross-sectional, analytical study done on the patients who presented to the Gastroduodenoscopy unit of Shree Birendra Hospital from May 2019 to March 2020. Patients with dyspepsia aged 18 years and above were included in the study. Patients not tolerating endoscopy, previously diagnosed with active peptic ulcer, or stomach cancer, and those who had received H. pylori eradication therapy in the last three months were excluded from the study. Patients with a history of partial or complete gastrectomy, and patients with active UGI bleeding were also excluded.\n\nNon-probability consecutive sampling method was used. Dyspeptic patients presenting for gastroduodenoscopy during the study period were included consecutively. The sample size was calculated by using Cochran’s formula1 where:\n\nStudies done in similar populations in Nepal had shown a prevalence of 70 to 90%.2,3 Thus, p was taken as 70%, q = 100 – p = 30%, Z = 1.96 for 95% confidence, and e = margin of error = 10%. Sample size was calculated to be 164. The final sample size was 170 considering a few non-responses.\n\nA pre-designated proforma was used to record the data. Socio-demographic data and a brief history were collected. The patient’s age, sex, address, occupation, alcohol and smoking history, any history of dyspepsia, or any significant medical history were recorded. They were also asked about dyspeptic symptoms such as epigastric pain, epigastric burning, postprandial fullness, early satiety, bloating, and nausea/vomiting.\n\nEndoscopic findings were categorized as gastritis, duodenitis, gastric ulcer, duodenal ulcer, malignancies; normal, and others. UGI endoscopy was performed using the PENTAX and FUJINON scope by a trained and experienced specialist. A flexible endoscopy tube was introduced after applying a local anesthetic agent and a biopsy sample was taken. Rapid Urease Test (RUT) was done using Helikochek and Pylochek. Biopsy samples, approximately 2–3 mm each were taken from the antrum and placed on the yellow-colored well-containing urea and a pH indicator. The urease enzyme produced by H. pylori breaks down urea into bicarbonate and ammonia, which causes the pH to rise and the color of the dot to change from yellow to red or pink.4 The positive results were read within 24hrs. No color change after 24 hours was considered negative.\n\nThe ethical clearance for this study was obtained from Institutional Review Committee, Nepalese Army Institute of Health Sciences (IRC-NAIHS) with the reference number of 245 (Ref. No. 245). Written informed consent was obtained from each respondent. Data were de-identified and kept on password protected computer.\n\nAll data were entered and analyzed using Statistical Package for Social Sciences (IBM-SPSS), version 22. Both descriptive and inferential statistics were used for analysis. Frequencies, mean/standard deviation and median/interquartile range (IQR) were calculated for descriptive analysis. The Chi-square test was used to check the association between independent and dependent variables of categorical data and a p-value of <0.05 was considered to be statistically significant.\n\n\nResults\n\nA total of 170 patients with dyspeptic symptoms presenting to the Gastroduodenoscopy unit were taken for the study. The median age was 49 (36 – 60) years with majority of patients below sixty years age group (125, 73.53%). The females (87, 51.18%) constituted majority among the total participants. Out of the total, fewer patients had smoking (49, 28.82%) and alcoholic (23, 13.53%) history. The mean years of smoking and alcohol units per day were 6.54 ± 12.349 years and 1.29 ± 5.034 respectively. Similarly, the endoscopic findings revealed gastritis (57, 33.53%) as a major pathology depicted in patients presenting with dyspeptic symptoms. Pantoprazole (131, 77.06%) was the drug taken by most of the patients for their dyspepsia (Table 1).\n\nThe overall prevalence of H. pylori was found to be 0.329 (0.259 – 0.406) at 95% Confidence Interval (CI). The males were found to have H. pylori infection more as compared to females (31 [37.35] vs 25 [28.74], p = 0.232). Individuals equal to or above sixty years of age tend to be infected more with H. pylori (16 [35.56] vs 40 [32.00], p = 0.663). And the smoker group was associated more with the infection (19 [38.78] vs 37 [30.58], p = 0.303). However, none of them were statistically significant.\n\nThe patients with alcoholic history were significantly associated with H. pylori infection (12 [52.17] vs 44 [29.93], p = 0.035). Likewise, based on endoscopic findings, patients with duodenitis (3, 100%) followed by gastritis (29, 50.88%) were associated more with H. pylori infection. But, this was statistically significant (p < 0.001).\n\n\nDiscussion\n\nThe present study reported an overall prevalence rate of 32.9% of H. pylori infection among the studied dyspeptic patients. Previous studies from Nepal have reported wide variation in the prevalence of H. pylori infection among patients with dyspepsia (20.0%-68.1%).11–14 In the studies conducted in North India and Bangladesh, the prevalence of H. pylori infection was 85% and 78% respectively.15,16 As compared to the present study, the prevalence of H. pylori infection was relatively lower in developed countries like the United Kingdom 27.4%, Sweden 26.2% and New Zealand 24%.17,18 In contrast, higher prevalence rates than our study have been reported from other developing countries like Kenya 40.86%, Cameroon 64.39%, Mongolia 80.0%, Nigeria 64.0%.19–22 The variations in H. pylori prevalence rates throughout studies around the world may be caused by a variety of influencing factors, such as socioeconomic status, standard of living, ethnicity, and geographic location, different diagnostic methods and prior antibiotic use.19,23 In our study, RUT was used as a diagnostic method for H. pylori infection. Among the previous studies conducted in Nepal, some used histological examination as the diagnostic method.12,14 Chaudhary et al. used H. pylori stool antigen test for diagnosing H. pylori11 while Shrestha et al. diagnosed H. pylori using rapid urease test in his study.13 Khalifehgholi et al. conducted a study comparing various diagnostic methods of H. pylori in which the sensitivity of histology, RUT and stool antigen test was reported to be 95.6%, 95.6% and 73.9% respectively. In that study, RUT showed the highest specificity (100%), followed by stool antigen test (86.7%) and histology (77.8%).24\n\nIn the present study, the most common endoscopic findings among the H. pylori positive patients were Duodenal ulcer (100.0%), Gastritis (50.88%) and Gastric Ulcer (50.00%). In a study by KC et al., the most common endoscopic findings were Gastric Ulcer (87.3%), Duodenal Ulcer (85%) and Gastritis (63.9%).14 In another study reported from Saudi Arabia, Duodenal ulcer (47.1%), Gastric Ulcer (45.2%) and Gastritis (44.0%) were the most common endoscopic findings.23 These kinds of disparities may be attributed to other factors like ethnicity, socio-economic status and geographical location. In the present study, no significant association was found between the H. pylori infection and smoking habit. 38.78% smokers were found to be H. pylori infected while 30.58% non-smokers were H. pylori positive. This finding is in agreement with Akeel et al. and Khalifa et al. who also reported no significant difference in H. pylori infection between smokers and non-smokers.23,25 There have been conflicting reports from studies regarding the H. pylori infection and smoking. Ogihara et. al. reported significant negative association between smoking and H. pylori infection, whose study showed 1.5-fold greater risk of H. pylori infection among non-smokers than smokers. This study suggested the hypothesis that smoking causes an increase in acid and pepsin production that shields the stomach mucosa from H. pylori infection.26 In contrast, another study reported a strongly positive correlation between H. pylori infection and current smoking.27 There was a significant association between history of alcohol consumption and H. pylori infection in our study. Similar finding was reported by Chaudhary et al.11 However, few studies have reported that moderate alcohol intake is associated with decreased prevalence of H. pylori infection and may facilitate elimination of H. pylori.28,29\n\nThere has been a wide variation in the prevalence of H. pylori infection from different hospital-based studies conducted in different parts of Nepal. There seems to be a need for another more comprehensive study in this region to examine the relationship between various socio-economic factors, presenting complaints, the effectiveness of various diagnostic methods, premorbid conditions and H. pylori infection.\n\nThe present study was a hospital-based study. The findings of the study may not be generalizable to the entire population. As the present study was a cross-sectional study, it could not assess the risk factor for H. pylori infection.\n\n\nConclusions\n\nH. pylori infection was still prevalent among a sizable majority of dyspeptic patients in our setting. It was significantly associated with alcohol consumption. More comprehensive studies are necessary in this region to study the relationship between socio-economic factors, diagnostic methods, premorbid conditions and H. pylori infection.", "appendix": "Data availability\n\nFigshare: Prevalence of Helicobacter pylori infection in dyspeptic patients presenting to a tertiary care center of a developing country (spss), https://doi.org/10.6084/m9.figshare.22815713.v1. 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nTack J, Talley NJ, Camilleri M, et al.: Functional gastroduodenal disorders. Gastroenterology. 2006 Apr; 130(5): 1466–1479. Publisher Full Text\n\nTalley NJ, Stanghellini V, Heading RC, et al.: Functional gastroduodenal disorders. Gut. 1999 Sep; 45 Suppl 2(Suppl 2): II37–II42. PubMed Abstract \| Publisher Full Text\n\nTalley NJ, Silverstein MD, Agréus L, et al.: AGA technical review: evaluation of dyspepsia. American Gastroenterological Association. Gastroenterology. 1998 Mar; 114(3): 582–595. PubMed Abstract \| Publisher Full Text\n\nTalley NJ, Colin-Jones D, Koch KJ, et al.: Functional dyspepsia: a classification with guidelines for diagnoses and management. Gastroenterol. Int. 1991; 4: 145–160.\n\nIeni A, Barresi V, Rigoli L, et al.: Morphological and Cellular Features of Innate Immune Reaction in Helicobacter pylori Gastritis: A Brief Review. Int. J. Mol. Sci. 2016 Jan 15; 17(1): 109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDu LJ, Chen BR, Kim JJ, et al.: Helicobacter pylori eradication therapy for functional dyspepsia: systematic review and meta-analysis. World J. Gastroenterol. 2016; 22(12): 3486–3495. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao B, Zhao J, Cheng WF, et al.: Efficacy of Helicobacter pylori eradication therapy on functional dyspepsia: a meta-analysis of randomized controlled studies with 12-month follow-up. J. Clin. Gastroenterol. 2014; 48(3): 241–247. PubMed Abstract \| Publisher Full Text\n\nPotamitis GS, Axon AT: Helicobacter pylori and nonmalignant diseases. Helicobacter. 2015; 20(Suppl 1): 26–29. Publisher Full Text\n\nSuzuki H, Moayyedi P: Helicobacter pylori infection in functional dyspepsia. Nat. Rev. Gastroenterol. Hepatol. 2013; 10(3): 168–174. Publisher Full Text\n\nFaintuch JJ, Silva FM, Navarro-Rodriguez T, et al.: Endoscopic findings in uninvestigated dyspepsia. BMC Gastroenterol. 2014 Feb 6; 14: 19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaudhary NK, Paudel S: Helicobacter pylori infection among dyspeptic patients in Chitwan, Nepal. J. Chitwan Med. Coll. 2021 Dec 25; 11(4): 69–72. Publisher Full Text\n\nShrestha S, Paudel P, Pradhan GB, et al.: Prevalence study of H. pylori infection in dyspeptic patients coming to Nepal Medical College Teaching Hospital, Jorpati, Kathmandu. Nepal Med. Coll. J. 2012 Sep; 14(3): 229–233. PubMed Abstract\n\nShrestha R, Chhetri G, Deo A, et al.: A descriptive cross-sectional study of helicobacter pylori infection in non-ulcer dyspepsia patients in a tertiary care teaching hospital In the Eastern part of Nepal. J. Nobel. Med. Coll. 2016 Dec 26; 5(2): 10–16. Publisher Full Text\n\nShiva Raj K, Lakhey A, Koirala K, et al.: Prevalence of Helicobacter pylori among patients with dyspepsia and correlation between endoscopic and histological diagnosis. J. Pathol. Nepal. 2016 Mar 17; 6(11): 942–946. Publisher Full Text\n\nAgarwal PK, Badkur M, Agarwal R, et al.: Prevalence of Helicobacter pylori infection in upper gastrointestinal tract disorders (dyspepsia) patients visiting outpatient department of a hospital of North India. J. Fam. Med. Prim. Care. 2018; 7(3): 577–580. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahman MM, Ghoshal UC, Kibria MG, et al.: Functional Dyspepsia, Peptic Ulcer, and Helicobacter pylori Infection in a Rural Community of South Asia: An Endoscopy-Assisted Household Survey. Clin. Transl. Gastroenterol. 2021 Apr 16; 12(4): e00334. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarvey RF, Lane JA, Nair P, et al.: Clinical trial: prolonged beneficial effect of Helicobacter pylori eradication on dyspepsia consultations - the Bristol Helicobacter Project. Aliment. Pharmacol. Ther. 2010 Aug; 32(3): 394–400. PubMed Abstract \| Publisher Full Text\n\nHooi JKY, Lai WY, Ng WK, et al.: Global Prevalence of Helicobacter pylori Infection: Systematic Review and Meta-Analysis. Gastroenterology. 2017 Aug; 153(2): 420–429. Publisher Full Text\n\nPrevalence and Endoscopic Findings of Helicobacter pylori Infection among Dyspeptic Patients in Kenya.[cited 2022 Sep 17]. Reference Source\n\nKouitcheu Mabeku LB, Noundjeu Ngamga ML, Leundji H: Potential risk factors and prevalence of Helicobacter pylori infection among adult patients with dyspepsia symptoms in Cameroon. BMC Infect. Dis. 2018 Jun 15; 18(1): 278. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhasag O, Boldbaatar G, Tegshee T, et al.: The prevalence of Helicobacter pylori infection and other risk factors among Mongolian dyspeptic patients who have a high incidence and mortality rate of gastric cancer. Gut Pathog. 2018 Apr 4; 10: 14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbiodun Christopher J, Jesse Abiodun O, Samuel Olawale O, et al.: Prevalence of helicobacter pylori among Nigerian patients with dyspepsia in Ibadan. Pan Afr. Med. J. 2010 Sep 19; 6: 18. Publisher Full Text\n\nAkeel M, Elmakki E, Shehata A, et al.: Prevalence and factors associated with H. pylori infection in Saudi patients with dyspepsia. Electron. Physician. 2018 Sep 9; 10(9): 7279–7286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhalifehgholi M, Shamsipour F, Ajhdarkosh H, et al.: Comparison of five diagnostic methods for Helicobacter pylori. Iran. J. Microbiol. 2013 Dec; 5(4): 396–401. PubMed Abstract\n\nKhalifa MAAA, Khodiar SE, fadly, Almaksoud AA.: Cigarette smoking status and Helicobacter pylori infection in non-ulcer dyspepsia patients. Egypt J. Chest Dis. Tuberc. 2014 Jul 1; 63(3): 695–699. Publisher Full Text\n\nOgihara A, Kikuchi S, Hasegawa A, et al.: Relationship between Helicobacter pylori infection and smoking and drinking habits. J. Gastroenterol. Hepatol. 2000 Mar; 15(3): 271–276. Publisher Full Text\n\nBateson MC: Cigarette smoking and Helicobacter pylori infection. Postgrad. Med. J. 1993 Jan; 69(807): 41–44. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu SY, Han XC, Sun J, et al.: Alcohol intake and Helicobacter pylori infection: a dose-response meta-analysis of observational studies. Infect. Dis. Lond. Engl. 2016 Apr; 48(4): 303–309. Publisher Full Text\n\nKuepper-Nybelen J, Thefeld W, Rothenbacher D, et al.: Patterns of alcohol consumption and Helicobacter pylori infection: results of a population-based study from Germany among 6545 adults. Aliment. Pharmacol. Ther. 2005 Jan 1; 21(1): 57–64. PubMed Abstract \| Publisher Full Text\n\nPathak BD: Prevalence of Helicobacter pylori infection in dyspeptic patients presenting to a tertiary care center of a developing country. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "209218", "date": "17 Nov 2023", "name": "Sushma Thapa", "expertise": [ "Reviewer Expertise My areas of research includes - Histopathology", "Cytopathology", "Hematology." ], "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 would like to congratulate all the authors for the successful accomplishment of a research work with the coverage of common but important issues of the current situation. Further comments about the manuscript includes: The study design of the work is appropriate and the work is technically sound. The details of methods and analysis are sufficiently provided in the study. The required statistical analysis and its interpretation has also been done but I would like to suggest for a quick review by a qualified statistician. All the source data underlying the results are available in the manuscript for the full reproducibility. The work is clearly and accurately presented however it needs citation with more current literatures. In Table 1 - the heading at the top row -- the normal value and percentage can be denoted by n(%). And also the value of 100 within the bracket in all the presumed normal value should be clarified.\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": "297911", "date": "24 Sep 2024", "name": "Fernando Javier Barreyro", "expertise": [ "Reviewer Expertise H. pylori", "Functional dyspepsia" ], "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 conducted by Subedi et al. investigates the prevalence of Helicobacter pylori (H. pylori) and associated endoscopic findings in dyspeptic patients at a single center in Nepal. The research included 170 patients who underwent upper endoscopy for the evaluation of dyspepsia. The authors reported a 32.9% prevalence of H. pylori infection. However, no significant differences related to the severity of the diseases were observed. The study also found a significant association between a history of alcohol consumption and H. pylori infection. Additionally, the authors noted that H. pylori infection was linked to endoscopic findings indicative of duodenitis and gastritis. This study provides data on H. pylori infection in patients with dyspeptic symptoms, potentially contributing to the local epidemiological data.\n\nEndoscopic Assessment: It is recommended that the authors utilize the Kyoto classification for endoscopic evaluation of gastritis. Dyspepsia Evaluation: The authors should reanalyze the data using the Rome IV classification for dyspepsia syndromes, as it is crucial for a comprehensive assessment of dyspeptic symptoms. Sample Size Justification: The rationale for the chosen sample size is unclear. Please specify the prevalence rate used for the sample size calculation. The study currently appears to be exploratory in nature. Symptom Evaluation: The methodology for evaluating dyspepsia symptoms is not clearly described. It is advised to use a validated dyspepsia symptom scale. proton pump inhibitors (PPIs) Usage: Continuous intake PPIs before upper endoscopy can lead to false-negative H. pylori results. The authors should clarify whether patients were required to discontinue PPIs before undergoing endoscopy. Clinical and Biochemical Data: The manuscript should include a detailed description of clinical variables (e.g., BMI, diabetes, obesity, dyspepsia syndrome) and relevant biochemical variables in Table 1. Gastric Pathology Analysis: From an epidemiological perspective, the study should include an analysis of gastric pathologies such as gastric atrophy and intestinal metaplasia.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1195
https://f1000research.com/articles/12-1194/v1	25 Sep 23	{ "type": "Case Report", "title": "Case Report: Tuberculous abscess of the popliteal fossa: A case report", "authors": [ "Hedi Belhassen", "Mohamed Ali Khlif", "Mohamed Achraf Ferjani", "Yosri Abcha", "Maher Barsaoui", "Mohamed Ali Khlif", "Mohamed Achraf Ferjani", "Yosri Abcha", "Maher Barsaoui" ], "abstract": "Introduction Tuberculosis of the soft tissues is a rare form of extra pulmonary tuberculosis, and isolated localization in the popliteal fossa is particularly exceptional. Atypical clinical presentation can lead to delayed diagnosis and serious complications. Case report We report the case of a 17-year-old patient who was diagnosed with tuberculosis of the popliteal fossa. He presented with a painful inflammatory swelling of the right popliteal fossa associated with a homolateral inguinal lymph node, without knee joint effusion. Standard chest and knee X-rays were normal, while MRI showed an 8 cm well vascularized, partly liquefied mass in the popliteal fossa, developed in contact with the semimembranosus and medial gastrocnemius muscles, associated with a popliteal lymph node without synovial effusion or thickening. Microbiological tests did not isolate any germs. The diagnosis was made on histological examination after biopsy, which revealed a caseous granuloma surrounded by epithelioid cells. The patient was treated with anti-tuberculosis therapy for 9 months. The clinical and radiological regression of the swelling was observed without recurrence at 2 years of follow-up. Conclusion\nAny soft tissue abscess should raise suspicion of tuberculosis, especially in endemic countries. The importance of histopathological examination should be emphasized to establish the diagnosis in the absence of signs in favor of a primary localization.", "keywords": [ "Tuberculosis", "knee", "abscess", "diagnosis", "therapeutic" ], "content": "Introduction\n\nOsteoarticular tuberculosis remains prevalent in countries where tuberculosis is endemic. It represents 1 to 5% of all forms of the disease. It predominantly affects the spine (40%), hip (25%), and knee (8%).1,2\n\nThe symptoms of the extra-spinal form are non-specific, with an insidious clinical picture and inconsistent general signs, which explains the diagnostic difficulties. Early management is necessary to prevent serious complications.3 In the knee, tuberculosis typically presents as joint involvement: synovitis, arthritis, or an infected Baker’s cyst, and rarely as extra-articular involvement.4,5\n\nCurrently, antitubercular antibiotics are the standard treatment. Moreover, surgical treatment is limited to cases resistant to medical treatment.4\n\n\nCase report\n\nThis is a 17-year-old male, Tunisian high school student, from central-western Tunisia (Sbeïtla, Kasserine) with no notable medical history but with a history of exposure to tuberculosis seven years ago (his brother had pulmonary tuberculosis) and a history of regular consumption of unpasteurized milk. The patient presented with a painful, red, hot swelling in the right popliteal fossa that was resistant to first-line medical treatment with analgesics. Furthermore, he reported a weight loss of 5 kilograms over the past 2 months, as well as fever and night sweats over the past 2 weeks.\n\nOn examination, the patient had a limp due to an antalgic stance in the knee flessum. An inflammatory swelling of 10 cm in diameter was found in the right popliteal fossa. It was a painful, soft, and mobile swelling. In addition, there was no joint effusion in the knee and no metaphyseal pain in the femur and tibia. An inguinal lymph node on the same side was found.\n\nLaboratory tests showed a biological inflammatory syndrome with a white blood cell count of 12,040 and a C-reactive protein level of 67.3 mg/L. Chest and knee radiographs were normal (Figures 1 and 2).\n\nDoppler ultrasound of the lower limb showed a collection of the right popliteal fossa with an echogenic content, a clean wall independent of the popliteal pedicle, and thrombophlebitis of the right saphenous vein (Figure 3). The patient was treated with anticoagulant therapy in the form of low-molecular-weight heparin overlap and Sintrom (acenocumarol).\n\nA magnetic resonance image (MRI) showed a well-vascularized mass of 8 cm in diameter that was partly liquefied and developed in contact with the semimembranosus and medial gastrocnemius muscles, popliteal vessels, and posterior tibial nerve, with muscle and adipose edema and popliteal lymphadenopathy but no synovial effusion or thickening. This aspect suggested an infectious etiology (Figure 4).\n\nThe etiological investigation showed negative tuberculin skin test, negative direct examination and culture for Koch’s bacillus in urine and sputum, negative Rose Bengal serology and negative Wright serology.\n\nAn ultrasound-guided biopsy puncture was done. The bacteriological results were negative. Histopathological examination revealed the presence of inflammatory granulation tissue with acellular eosinophil deposits and epithelioid cells, suggesting a tuberculous origin (Figure 5).\n\nThe decision was to start an antituberculosis trial treatment with isoniazid (H), rifampicin (R), pyrazinamide (Z), ethambutol (E) and a pre-treatment assessment. The patient was treated with anti-tubercular drugs for 9 months according to the 2HRZE/7HR regimen with regular monitoring of liver and hematological function. The dosage was 4 HRZE tablets per day associated with 3/4 Sintrom tablets to control the thrombophlebitis of the internal saphenous vein. The patient’s condition improved, and a control MRI was performed in the eighth week of treatment that demonstrated complete disappearance of the previously described mass in the popliteal fossa, with no joint effusion or synovial thickening. Muscular and fatty edema had disappeared, and the bone signal was normal (Figure 6).\n\nWith 2 years of follow-up, the clinical and radiological evolution was favorable (Figure 7): clinical examination showed complete disappearance of the swelling and inguinal lymphadenopathy, with no joint effusion and full active mobility of the knee, and radiography revealed no bone lesions.\n\n\nDiscussion\n\nSoft tissue tuberculosis, defined as involvement of tendons, bursae, muscles, or deep fascia, is a rare form of musculoskeletal tuberculosis. It is usually associated with immunocompromised patients.6 Isolated localization in the popliteal fossa is also exceptional.7\n\nSeveral authors8–10 have reported in the literature that isolated or primary soft tissue tuberculosis without bone involvement in immunocompetent patients represents a rare form of extrapulmonary tuberculosis and its exact incidence is not known. Its clinical manifestations can mimic malignant diseases or other inflammatory diseases, making diagnosis difficult. The main differential diagnoses are pyogenic abscesses, atypical mycobacterial abscesses, hydatid cysts, and certain tumors.11\n\nIt is interesting to note that most cases of soft tissue tuberculosis reported in the literature were located near joints and bursae. The pathophysiology of this isolated involvement remains difficult to understand.12 However, extension from an adjacent joint, bone, or bursa and even direct inoculation have all been reported. In this context, Lupatkin et al.13 reported that tuberculous abscesses resulted from hematogenous, lymphatic, or local contamination from adjacent or other primary infection areas and, in rare cases, direct inoculation.\n\nIn our case, there was no clear explanation for the focal origin of the popliteal fossa involvement. Furthermore, this isolated and primary involvement could be attributed to hematogenous spread or extension from neighboring bursae. This hypothesis is most likely due to the presence of nearly 13 bursae around the knee.\n\nTuberculosis of soft tissues mainly affects the extremities, presenting as localized masses accompanied by local inflammatory signs and pain. General symptoms such as fever and weight loss are inconsistent.14,15 Recent cases of soft tissue tuberculosis published in the last 10 years were identified by conducting a search on PubMed (Table 1). We found 17 reported cases in the literature, including 10 males and seven females. The patients ranged from 7 to 79 years old. 12 cases were reported in Asian countries, four cases in African countries, and one case in America. In 13 patients, the lesions were predominantly in the extremities including the thigh, calf, forearm, and wrist. The other four patients had lesions in the buttocks, back, chest, and iliopsoas. The diagnosis of tuberculosis was made by a combination of bacteriological and pathological examination. The majority of cases improved under medical treatment based on antituberculosis drugs without any associated surgical procedure.\n\nPCR: Polymerase chain reaction, NS: Not specified.\n\nIn the literature,7 to confirm a definitive diagnosis, it is essential to identify the Koch bacillus. However, tuberculous soft tissue disease is paucibacillary. Often, the Ziehl-Nielsen test is negative and it is necessary to wait for the results of Lowenstein culture. Histological examination is more sensitive than microbiological tests and can confirm the diagnosis in 80% of cases.31 A normal chest radiograph, the absence of systemic symptoms, or the absence of detectable tuberculosis focus should not deter from considering this diagnosis.\n\nIn our case, faced with a history of tuberculosis exposure and a painful isolated swelling of the popliteal fossa, we performed an ultrasound-guided biopsy puncture of the swelling. The diagnosis was finally established by histopathology, which showed pathognomonic caseating granulomas of tuberculosis.\n\nIn the literature,10 the treatment protocol is not clearly defined. The main debated questions concern the duration of medical treatment as well as the need and modalities of any surgical treatment. Some authors32,33 advocated for primary medical treatment with a combination of antituberculous antibiotics. The choice of drugs is generally the same as for pulmonary tuberculosis (isoniazid, rifampicin, pyrazinamide, and ethambutol). This treatment is divided into two phases: an initial phase based on quadritherapy that lasts two months and a secondary phase with a bitherapy that lasts 4 to 7 months or longer in extensive cases. Moreover, surgical drainage is reserved for cases resistant to medical treatment.16 Postoperative outcomes are marked by local recurrence in 50% of cases within a year.25 Indeed, our patient responded well to exclusive medical treatment for 9 months. The evolution was spectacular with complete regression of the mass and no recurrence with a follow-up of 2 years. The patient expressed a high level of satisfaction regarding the clinical outcomes following the treatment. He reported a successful recovery and the ability to resume his normal physical activity level.\n\nOur case study had several strengths: we conducted a meticulous clinical examination, along with radiological investigations using ultrasound and MRI of the knee. Given that we are in an endemic country and taking into account the patient’s history of tuberculosis exposure, the diagnosis of tuberculous abscess should always be considered as a first possibility. Therefore, we decided to perform a biopsy to confirm the etiology before proceeding with surgery. After confirming the diagnosis through histology and reviewing the literature, we opted for antibiotic treatment and monitoring of the progression. Consequently, the lesion regressed totally overtime.\n\n\nConclusion\n\nTuberculosis of soft tissues is a rare form of the disease. It is even rarer for it to present as a primary abscess in the popliteal fossa. The lack of specificity of clinical and radiological signs and the insidious and progressive course make the diagnosis difficult.\n\nThis case report emphasizes the importance of considering the diagnosis of tuberculosis in the differential diagnosis of any unexplained soft tissue swelling in endemic areas, despite the absence of systemic and pulmonary symptoms. Thus, a more thorough investigation can prevent delayed diagnosis and its devastating complications.\n\n\nConsent\n\nWritten informed consent for the publication of the patient’s clinical details and clinical images was obtained from the patient and his parents.", "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\nUboldi FM, Limonta S, Ferrua P, et al.: Tuberculosis of the Knee: A Case Report and Literature Review. Joints. 2017; 05: 180–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRindi L: Rapid Molecular Diagnosis of Extra-Pulmonary Tuberculosis by Xpert/RIF Ultra. Front. Microbiol. 2022; 13: 817661. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMbChb EO: Diagnosis and The Surgical Management of Hip and Knee Mycobacterium Tuberculous Arthritis. Surg. Res. 2019; 1. Publisher Full Text\n\nSuresh Babu TV, Kiran KR, Deepti K: Tuberculous Arthritis of Knee Presenting as Bakers Cyst: A Case Report. Int. J. Clin. Med. 2014; 05: 319–324. Publisher Full Text\n\nHamabuchi M, Takeda Z: Isolated tuberculosis of the popliteal cyst. Nihon Geka Hokan Arch. Jpn. Chir. 1990; 59: 337–343.\n\nPuttick MP, Stein HB, Chan RM, et al.: Soft tissue tuberculosis: a series of 11 cases. J. Rheumatol. 1995; 22: 1321–1325. PubMed Abstract\n\nChan YLC, Lui TH: Endoscopic Resection of Recalcitrant Tuberculous Bursitis of the Popliteal Fossa. Arthrosc. Tech. 2021; 10: e1929–e1933. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTrikha V, Gupta V: Isolated tuberculous abscess in biceps brachii muscle of a young male. J. Infect. 2002; 44: 265–266. PubMed Abstract \| Publisher Full Text\n\nTrikha V, Varshney MK, Rastogi S: Isolated tuberculosis of the vastus lateralis muscle: a case report. Scand. J. Infect. Dis. 2006; 38: 304–306. PubMed Abstract \| Publisher Full Text\n\nHayoun S, Ouazzani HE, Habibi B, et al.: Tuméfaction du muscle pectoral révélant une tuberculose musculaire isolée. Pan Afr. Med. J. 2017; 27: 44. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChahbouni M, Eloukili I, Lamrani MO, et al.: Abcès tuberculeux de la face postérieure de la cuisse: à propos d’un cas. Pan Afr. Med. J. 2014; 19: 50. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbdelwahab IF, Kenan S: Tuberculous abscess of the brachialis and biceps brachii muscles without osseous involvement. A case report. J. Bone Joint Surg. 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PubMed Abstract \| Publisher Full Text\n\nElshafie KT, Al-Hinai MM, Al-Habsi HA, et al.: A Massive Tuberculosis Abscess at the Erector Spinae Muscles and Subcutaneous Tissues in a Young Man. Sultan Qaboos Univ. Med. J. 2013; 13: 601–605. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNeogi DS, Bandekar SM, Chawla L: Skeletal muscle tuberculosis simultaneously involving multiple sites. J. Pediatr. Orthop. Part B. 2013; 22: 167–169. PubMed Abstract \| Publisher Full Text\n\nMeena M, Dixit R, Samaria JK, et al.: Tuberculosis of the triceps muscle. BMJ Case Rep. 2015; 2015: bcr2014207032. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDhakal AK, Shah SC, Shrestha D, et al.: Tuberculosis presenting as multiple intramuscular nodules in a child: a case report. J. Med. Case Rep. 2015; 9: 72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSbai MA, Benzarti S, Msek H, et al.: Pseudotumoral form of soft-tissue tuberculosis of the wrist. Int. J. Mycobacteriol. 2016; 5: 99–101. PubMed Abstract \| Publisher Full Text\n\nAl-Khazraji A, Takher J, Alkhawam H, et al.: Primary Tuberculous Pyomyositis of the Calf Muscles. Am. J. Med. Sci. 2017; 353: 187–188. PubMed Abstract \| Publisher Full Text\n\nAlaya Z, Osman W: Isolated muscular tuberculosis: unusual location of the Koch bacillus. Pan Afr. Med. J. 2017; 26: 158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHashimoto K, Nishimura S, Oka N, et al.: Tuberculoma with phlegmon-like symptoms mimicking soft tissue sarcoma in the wrist: A case report. Mol. Clin. Oncol. 2018; 9: 207–210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZeng Y, Liu Y, Xie Y, et al.: Muscular Tuberculosis: A New Case and a Review of the Literature. Front. Neurol. 2019; 10: 1031. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZitouna: Isolated tuberculous abscess in longissimus muscle. n.d. (accessed March 26, 2023). Reference Source\n\nMoyano-Bueno D, Blanco JF, López-Bernus A, et al.: Cold abscess of the chest wall: A diagnostic challenge. Int. J. Infect. Dis. IJID Off. Publ. Int. Soc. Infect. Dis. 2019; 85: 108–110. PubMed Abstract \| Publisher Full Text\n\nFahad S, Baloch N, Din NU: Tuberculosis of the flexor carpi radialis muscle - a case report. JPMA J. Pak. Med. Assoc. 2020; 70: 1645–1647. PubMed Abstract \| Publisher Full Text\n\nMurugesh Anand S, Edwin Fernando M, Srinivasaprasad ND, et al.: Tuberculous myositis and cellulitis in a renal transplant recipient. Indian J. Tuberc. 2020; 67: 353–356. PubMed Abstract \| Publisher Full Text\n\nAl-Saleh S, Al-Arfaj A, Naddaf H, et al.: Tuberculosis arthritis: A review of 27 cases. Ann. Saudi Med. 1998; 18: 368–369. Publisher Full Text\n\nZendeoui A, Oueslati A, Tounsi A, et al.: Knee tuberculosis: A misleading clinical entity (case report). Int. J. Surg. Case Rep. 2022; 96: 107236. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmerican Thoracic Society, CDC, Infectious Diseases Society of America: Treatment of tuberculosis. MMWR Recomm. Rep. Morb. Mortal Wkly. Rep. Recomm. Rep. 2003; 52: 1–77." }	[ { "id": "213649", "date": "08 Feb 2024", "name": "Saoussen Miladi", "expertise": [ "Reviewer Expertise rheumatology", "orthopedics" ], "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 report a case report of a tuberculous abcess of the popliteal fossa occurring on a 17 year old boy.\n\nThis is an interesting case since the localisation of tuberculosis is rare in the popliteal fossa.\n\nThe diagnosis relayed on anatomopathology typical findings.\n\nThe case is well described and follow-up is mentioned.\n\nFigures are with good quality.\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": "271423", "date": "08 May 2024", "name": "Mouadh Nefiss", "expertise": [ "Reviewer Expertise spine surgery", "orthopedic 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\nDear author Thank you for the interesting case you submitted. the paper is well written, however I propose to rephrase certain sentences in particular:\n\"On examination, the patient had a limp due to an antalgic stance in the knee flessum. An inflammatory swelling of 10 cm in diameter was found in the right popliteal fossa. It was a painful, soft, and mobile swelling\" you can say: \"the patient had a limp when walking due to knee flessum as well as a painful, inflammatory swelling of the popliteal fossa that was soft and mobile.\"\nI propose also to change: \"The decision was to start an antituberculosis trial treatment......saphenous vein\" with: \"The treatment was based on anti-tuberculosis chemotherapy after pre-therapeutic assessment and for a total duration of 9 months. Anticoagulant treatment was prescribed for associated thrombophlebitis.\"\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": "209226", "date": "14 May 2024", "name": "Mohamed Ben Jemaa", "expertise": [ "Reviewer Expertise orthopedic surgery", "spine surgery", "bone and joint infectious diseases", "Extra-pulmonary Tuberculosis research Unit (University of sfax", "faculty of medicine)" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt presents a rare form of tuberculosis. This location remains rare also in endemic areas. This case report is well written and described. Clinical and paraclinical features are well analysed not only in the first paragraph of the clinical case but also in the paragraph of discussion. Figures provided by the authors are complete and englobe all clinical and paraclinical aspects. The conclusion is appropriate.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1194
https://f1000research.com/articles/12-1192/v1	25 Sep 23	{ "type": "Research Article", "title": "In vitro comparison of color stability and surface roughness of bulk fill flowable composite and universal packable composite", "authors": [ "Khalid S. Almulhim", "Ashwin C. Shetty", "Hanan Alkathiri", "Dalal Alabdulqader", "Fatimah Al-Yami", "Ashwin C. Shetty", "Hanan Alkathiri", "Dalal Alabdulqader", "Fatimah Al-Yami" ], "abstract": "Background: Bulk fill composites have been introduced as restorative material, where they can be cured up to 4 mm thickness. In this research, we evaluated several flowable bulk fill composite material that can be used as anterior restorations, by testing color stability and surface roughness and compare them to the universal packable composite. Methods: 120 disc-shaped specimens were made from four composite materials shade A1: One universal packable composite (Filtek Z250 XT Universal), and three bulk fill flowable composite (G-aenial Flo X, Filtek Bulk Fill, SDR Plus Bulk Fill). Composite specimens were randomly divided into two groups according to the finishing and polishing system: Sof-lex discs, and Rubber stone system. The baseline color test was performed for each specimen, and the surface roughness was measured at three different points. Specimens were further divided equally and immersed in three different solutions (Distilled Water, Coffee and Cola). Readings were taken at three different time intervals: at the baseline, after 3 days, and after 10 days. Results: Comparing the tested materials in terms of color change, Kruskal Wallis test showed no statistically significant difference (p<0.05) among the composite materials immersed in same solution. On the other hand, Filtek bulk fill composite material presented the least surface roughness compared to the other materials. However, there were no statistically significant difference in surface roughness comparing the two polishing systems, except in SDR bulk fill flowable composite material which had less surface roughness with rubber stone system at the baseline.\n\nConclusions: Within the limitation of our study, it can be concluded that there was no major difference in color change between materials regardless of other factors. The three used bulk fill flowable composites are not recommended as anterior restorations as they yield color change detected by the naked eye (∆E where ≥ 3.3).", "keywords": [ "Color stability", "Surface roughness", "Bulk fill", "Flowable composite", "Anterior restorations." ], "content": "Introduction\n\nComposite resin materials have been one of the most common choices for restoring the anterior region of the oral cavity, as they have high aesthetic characteristics with medium and long term durability and are considered inexpensive for the patients.1,2 With conventional composites, layering technique has been used to overcome polymerization shrinkage in restorations.3\n\nRecently a new advancement of resin materials was introduced which is bulk fill composite materials that claim to be cured at depth of 4 mm.4,5 There are several ways to classify bulk-fill flowable composite but the most common one is by the way of applying which it can be divided into two main categories: non-flowable (paste-like) bulk fill, and flowable bulk fill which is usually characterized by having large amount of resin matrix and lower amount of filler compared to non-flowable bulk fill.6–8 Bulk fill flowable composite materials have been used as: base, liner under class I and II restorations, pits and fissure sealant and as core build up. However, manufacturers have claimed that they can be used for aesthetic restorations as well such as: class III and V.9–11\n\nSeveral advantages have been found in bulk fill flowable composite materials like, less time-consuming procedure compared to conventional composite materials, better adaptation, better access to small cavities, and being highly flexible which makes them bear the stress in high stress bearing areas.5,12 On the other hand, flowable bulk fill composites have some drawbacks such as low mechanical properties in comparison to universal packable composites.13\n\nDiscoloration of restorative material in general is another disadvantage of the esthetic dental resin composite. It can happen due to many reasons; one of them is degradation in the matrix because of the hygroscopic absorption of water which expose the fillers. This is called intrinsic discoloration. The matrix degradation also leads to increased surface roughness which attributes to the discoloration process by providing a place for coloring agents and bacteria.2,14,15 Moreover, extrinsic discoloration may occur as well due to adsorption and absorption of the staining agents that exists in food and drinks.2,16 Studies have also shown that composite resin immersed in coffee, tea and cola have shown great change in color respectively.2,17\n\nA number of studies have investigated composite resin by immersing them in different solutions such as water, tea, coffee, grape juice and cola. In 2011 a study done by Patricia et al. that used four immersing solutions (coffee, tea, cola and artificial saliva), revealed that coffee showed the greatest color change, while cola exhibited the least color change.18 On the contrary in 2007 a study done by Groos et al. that used water, tea, and coffee as immersing solutions, manifested likewise results except when composite resin materials were immersed in tea as they showed a higher color change.19 Additionally, turmeric solution showed the maximum color change in a study done by Kumari et al. in 2015 were they used Turmeric solution, coffee, tea, cola and artificial saliva as immersing solutions.20 In our study distilled water, coffee and cola were used as immersing solutions of four different composite materials in 10 days duration.\n\nIn addition to discoloration of direct restorations, surface roughness is also considered one of the most common associated problems that it could eventually lead to discoloration of the restoration, susceptibility of gingival inflammation due to the plaque retention and possibility of recurrent caries. Therefore, to increase the longevity of a direct restoration and to avoid the previously mentioned issues finishing and polishing is a crucial step.21,22 Finishing and polishing procedure can be defined as “gross contouring of restoration to obtain the desired anatomy. Ideally it consists of multiple steps (3-4) with multiple instruments. Well finished restorations should meet certain important requirements, like: good contour with ideal occlusion, healthy form of embrasures, tightness of the margin that blends with structure of the natural tooth.21 The final finishing step of the restoration depends on several factors and one of the most important factors is within the material itself which are the matrix and the filler. Also, the curing and post curing time are considered an important factor too.22\n\nThere are several finishing and polishing systems which are available in the market, like: silicon disks, abrasive diamond tips, aluminum oxide discs, polishing pastes, hard and soft rubber type cups, wheels and points impregnated with various abrasives grits.23,24 One of the most common finishing polishing systems is So-flex discs, which are color coded with convenient sequence that snaps easily in the mandrel. Another popular and commonly used finishing and polishing system is Astropol rubber stone system, which is especially designed for composite materials.\n\nThis study aimed to evaluate the color stability of the bulk fill flowable composite that were suggested to be used in the anterior teeth, compared to universal packable composite by immersing them in different solutions, and to evaluate the surface roughness of the bulk fill flowable composite compared to universal packable composite by using different polishing systems.\n\n\nMethods\n\nThis study was conducted at the laboratory of Imam Abdurahman bin Faisal University College of Dentistry, after gaining a waiver of ethical approval from the Scientific Research Unit.\n\nThe procedure consisted of the following steps:\n\nA total of 120 disc-shaped specimens were fabricated from four different types of composites materials (30 from each material) with standardized shade (A1): One universal packable composite: Filtek Z250 XT Nano Hybrid Universal Restorative “UNI” (3M ESPE, St. Paul, MN, USA), and three bulk filled flowable composites: G-aenial Flo X GC Flowable Composite “GAN” (GC, Tokyo, Japan), Filtek Bulk Fill Flowable Restorative “FIL” (3M ESPE, St. Paul, MN, USA), and SDR Plus Bulk Fill Flowable “SDR” (Dentsply Sirona, Konstanz, Germany).\n\nSample size was determined according to a previous study17 that used five different resin composites material, where the sample size was 25 specimens for each composite material that was tested for color stability after immersion in different drinks. In the present study, four different resin composite materials were used, accordingly the sample size was increased to 30 from each composite material.\n\nAll specimens are disc-shaped, with 10 mm in diameter and 2 mm thickness. A metal frame with inner plastic circular openings of the desired dimensions was used to fabricate the specimens. The process of fabricating the specimens included a glass slab of 2 mm thickness covered by a Mylar strip (SNA, Universal Strips, Germany). The metal mold was then placed over, and the composite material then added in each circular opening of the mold. Another Mylar strip and glass slab of 2 mm thickness were placed above the mold. Afterwards, composite was polymerized by using LED curing device (Mini LED, Acteon Satelec, Merignac, France) for 40 seconds. After curing, the Mylar strip and glass slab are removed and the samples were taken out from the mold.\n\nA custom-made holder of rubber-base material was fabricated and used to hold the specimens during the finishing and polishing process. Composite specimens were divided into two main groups in this study, each group was finished and polished by a either a Sof-Lex discs system (3M™ ESPE, St. Paul, MN, USA), or a Rubber stone system “RS” (Astropol, Ivoclar Vivadent AG, Schaan, Liechtenstein), starting from the most coarse to the extra fine bur. The SL system included using four discs (Course, Medium, Fine, Ultra-fine) and attached to mandrel on low-speed handpiece (Gentle-Power Lux 20LP; KaVo, Biberach, Germany). The RS system consisted of three burs (Gray, Green, Pink) in flat wheel shape. When using SL disc and mandrel engage in a low-speed handpiece with water spray at 15000 rpm in intermittent brushing movement with gentle pressure. Whereas, when using RS, a low-speed handpiece is used at 25000-30000 rpm in circular movement with gentle pressure. Both speed and pressure were increased gradually while moving toward finer burs in both systems.\n\nSpecimen measurements were performed after 24 hours from storing the specimens in room temperature (25-35°C). The color of the specimens was measured with a spectrophotometer (X-Rite, Grand Rapids, MI, USA) for digital color measurements. The machine is calibrated with black and white ceramic tiles as it compares colors by measuring the amount of light reflected from the specimen.25 The color measurements were recorded by means of the CIELAB (Commission International de L’Eclairage Lab) color notation system.25 ΔE was calculated using the following formula:\n\nWhere:\n\nΔ represents the difference between the object being measured and its reference\n\nL* represents lightness\n\na* and b* are the chromaticity coordinates\n\nAlso, a Profilometer (3D profilometer. Bruker, AZ. USA) machine was used as a 3D optical non-contact surface scan that is accompanied with Vision64 software to test surface roughness.26 Measurements were taken from three random points in each specimen then the average was calculated.\n\nThe baseline measurements of all specimens were made (immediately after the finishing and polishing), and then after immersing in different staining solutions.\n\nThe specimens were divided equally to three groups, each group was immersed in different solutions: Coffee “CF” (Nescafé® Classic Instant Coffee), Cola “CL” (regular Pepsi®), and Distilled Water “W”. Composite specimens were fixed to the container using utility wax covering the bottom surface of the specimens, each sample identified by a code that is written on the container from outside. W and CL were used directly for specimens’ immersion, while coffee required 150 ml of boiled water mixed with 1 full tablespoon (3 grams) of instant coffee to make 1 cup of coffee according to the manufacture instructions, then the solution was left to cool until it reaches room temperature (25-35°C) then used for specimens’ immersion. The acidity of solutions was measured with pH litmus paper strips, the pH for CL was 2, 6 for the CF, and 7 for W. All specimens were kept in an incubator (Thermo Scientific Heraeus Incubator) at (37°C) in the dark, and solutions were changed every day to avoid bacteria or yeast contamination. After 3 days, and 10 days of immersion, the samples were removed from the solutions, rinsed for 60 seconds with a high-pressure water airbrush (Minivapor 93, Effegi Brega, Piacenza, Italy), and air dried. The specimens of all groups were then re-evaluated for surface roughness and color stability after the immersion.\n\nResults were presented as mean and standard deviations. Kruskal-Wallis H test was used to calculate the statistical significance between the groups. In post hoc analyses, Mann-Whitney tests was performed to ascertain which pairs of groups differ significantly from one another. Bonferroni correction was applied to the significances obtained from the Mann-Whitney test results. The significance was considered at p≤0.05. For the pairwise comparisons, adjusted significance levels were given by multiplying the unadjusted significance values by the number of comparisons. Statistical analysis was carried out using SPSS version 23.0 (SPSS Inc., Chicago, II, USA).\n\n\nResults\n\nMeans and standard deviations (SD) of ΔE values are presented in Table 1.37 Kruskal-Wallis H test was used to evaluate the color change among the tested materials, comparing the polishing systems and the immersing solutions, which revealed statistically significant differences (p<0.05). A Mann Whitney post-hoc test with Bonferroni correction manifested that Delta E was significantly less in FIL specimens when polished with SL and immersed in CF (p<0.017). Likewise, the specimens that were polished with RS system and immersed in CL have presented statistically significant difference between (UNI) and (GAN) (p<0.017) where the (UNI) showing less color change (Table 2). In addition, CF exhibits the greatest staining ability on materials, whereas CL exhibits the least staining ability on materials (Table 2).\n\n* Significant at p-value <0.05.\n\nAmong the three materials, (FIL) have manifested the least surface roughness (Table 3). Kruskal-Wallis H test showed statistically significant difference in the roughness between the materials, when polished using Sof-lex disc system immersed in water and coffee, and when polished with Rubber stone system immersed in coffee and Pepsi (p<0.05) with less roughness values in (FIL). Furthermore, statistical significance was found between G-aenial flowable and Filtek bulk fill when polished using Rubber stone system and immersed in coffee (p<0.017) (Table 4).\n\n* Significant at p-value <0.05.\n\n\nDiscussion\n\nDiscoloration of tooth colored resin-based composite has been one of the most common reasons for restorations’ replacements, which consumes time and money.27 There have been several studies that have discussed the effect of different beverages on the color stability on resin composites. However, not enough information was introduced regarding the color stability of bulk fill flowable composites.28 In this study, four types of composites have been used, one universal packable and three bulk fill flowable composites (GAN, SDR, and FIL). Each group have been finished and polished with one of the two systems either SL and RS, then specimens were divided according to solutions (CF, CL and W) into three different groups. The solutions have been chosen as they are most commonly used. The pH of the solutions is constant and changed daily. Readings were taken in three different time intervals at baseline, 3 days and 10 days, using spectrophotometer which is a device used to measure the reflected and transmitted light from materials quantitatively, to measure the color stability.29\n\nSpecimens that were immersed in CF have had the highest ∆E value compared to the other specimens with the same group, which was in line with previous investigations, where CF has stronger chromatogen than CL, this is due to the less polar yellow colorants in CF than the yellow colorants of CL. The absorption and adsorption of CF pigments into the organic phase of resin based composites is probably due to the compatibility of the polymer phase with yellow colorants of CF. In addition to that, CF has large amounts of staining agents like Gallic acid which facilitate the staining.21,28 Also, a slight increase in ∆E was noticed in two of the groups that were immersed in water which have been noticed in previous studies due to degree of water absorption and the hydrophilic/hydrophobic nature of the resin matrix. The absorption of water mainly happens as a direct absorption of resin matrix.27 Kruskal Wallis H test manifested no statistically significant difference in the color between the materials when polished using SL system or RS system immersed in W, CF, or CL at 3 or 10 days (p>0.05). While using the same test in between the polishing systems and the immersing solutions regardless of time displayed, a statistically significant difference between the materials was noticed when polished with SL system and immersed in CF, whereas the specimens that are polished with RS system have exhibited a color change when immersed in CL regardless of time (p<0.05). According to the readings of Table 2, CF exhibits the greatest color change on materials whereas, CL exhibits the least color change on materials.\n\nPrevious studies showed that when ∆E vales are between 1.0-3.7 color change is visually detectable by the naked eyes.30,31 Also, it was agreed by multiple former studies that if ∆E ≥ 3.3, it considered clinically unacceptable and that was applied to this study’s results.31,32 In the current study all four materials ∆E where ≥ 3.3 except U that was polished with SL system at 3 days of immersion, which lead to clinically unacceptable color stability outcomes regarding the tested materials to be used for direct restorations especially in anterior teeth. However, the difference was statistically not significant (p>0.05).\n\nThroughout years companies have been working on improving the surface roughness of composites as studies have shown how it affects the final results aesthetically and biologically. Surface roughness has been related to filler particle size, as the smaller the filler size will result in less porosity, and better polishability, hence less surface roughness.33 Increased surface roughness leads to food accumulation, inflammation of the surrounding gingiva and staining of the composite material itself.33 In our study a profilometer 3D device was used to measure surface roughness with four types of composite materials and two types of the most commonly used polishing systems RS system and SL system. A Kruskal Wallis H test had revealed that (FIL) material had the least surface roughness among the tested materials in spite of other factors. Differing from Karadaş et al. study,34 where (FIL) wasn’t the material with the least surface roughness and that may be due to many factors such as different polishing systems, immersing solutions, and bulk fill materials from other companies that were included. Moreover, surface roughness is believed to be mainly contributed by the material composition, for instance the filler particle size and the filler weight content as many studies have shown.33\n\nIn our study, the 1st null hypothesis “there is no significant difference between bulk fill flowable composites (GAN, SDR and FIL) and (UNI) in color stability” was approved, as there was no significant statistical difference between the materials when other factors are excluded. This is in agreement with Bahbishi N et al.’s35 study where there was no major difference between the Universal composite and bulk fill composite tested. On the other hand, Silva MF et al.’s study36 found that Universal composite had better color stability than bulk fill composites. Our 2nd null hypothesis “there is no significant difference between bulk fill flowable composites (GAN, SDR and FIL) and (UNI) in surface roughness” has been disproved, as there was statistically significant difference between the materials with (FIL) displaying the least surface roughness. In addition to that, our study has approved that there was no significant correlation between polishing systems and color stability.\n\nThere are certain limitations of the present study that are important to mention. One of the main limitation was that it was performed in laboratory conditions, which differs from the oral environment. Furthermore, the composite specimens were prepared in the form of a discs, however, the restoration shapes and surfaces differ in clinical conditions.\n\nThe manufacturer instructions of all four materials used in this study claimed that the materials are indicated to be used as direct dental restorations in posterior teeth, and anterior teeth in cases like Class III and V that commonly demands higher aesthetic features in the dental restorative material. Within the limitations of this study, our results showed no statistically significant difference between the tested materials in terms of color stability and surface roughness, except of FIL. However, it is recommended to have a more well-controlled laboratory environment for further testing the aesthetic and mechanical properties in order to suggest the use of the bulk fill flowable composite materials as final restorative treatment in the anterior teeth.\n\n\nConclusion\n\nIn summary, CF affected the four materials similarly in terms of color stability. However, in terms of surface roughness, FIL showed the least surface roughness compared to the other tested materials. There was no significant difference in surface roughness between the two polishing systems and the four tested materials. The three used bulk fill composite materials (GAN, SDR and FIL) in this study are not recommended to be used as anterior restorations as they all yield a color change that is detected by the naked eye where ∆E where ≥ 3.3. Further investigations about bulk fill materials should be done in vivo studies to have more valid results with better explanation of the materials nature.\n\n\nData availability\n\nZenodo: in vitro comparison of color stability and surface roughness of bulk fill flowable composite and universal packable composite. https://doi.org/10.5281/zenodo.7034847.37\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgments\n\nThe authors would like to thank Mr. Robert Caravana for his assistance in conducting the tests.\n\n\nReferences\n\nLopes I, Monteiro P, Mendes J, et al.: The effect of different finishing and polishing techniques on surface roughness and gloss of two nanocomposites. The Saudi Dental Journal. 2018; 30(3): 197–207. PubMed Abstract \| Publisher Full Text\n\nBarutcigil Ç, Yıldız M: Intrinsic and extrinsic discoloration of dimethacrylate and silorane based composites. J. 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PubMed Abstract \| Publisher Full Text\n\nIkeda I, Otsuki M, Sadr A, et al.: Effect of filler content of flowable composites on resin-cavity interface. Dent. Mater. J. 2009; 28(6): 679–685. PubMed Abstract \| Publisher Full Text\n\nGC Australasia: G-ænial Flo X new, G-ænial universal Flo Strong universal composites with beautiful flow Pure genius [Brochure].2019.Reference Source\n\nDental Sirona: SDR® Plus Bulk Fill Flowable [Brochure].2017.Reference Source\n\n3M: FiltekTM Bulk Fill Flowable Restorative The bulk fill flowable that’s easier to inject [Brochure].2019.Reference Source\n\nHervás A, Martínez A, Cabanes J, et al.: Composite resins. A review of the materials and clinical indications. Med. Oral Patol. Oral Cir. Bucal. 2006; 11(2): E215–E220.\n\nMonterubbianesi R, Orsini G, Tosi G, et al.: Spectroscopic and Mechanical Properties of a New Generation of Bulk Fill Composites. Front. Physiol. 2016; 7. PubMed Abstract \| Publisher Full Text\n\nPoggio C, Ceci M, Beltrami R, et al.: Color stability of esthetic restorative materials: a spectrophotometric analysis. Acta Biomater. Odontol. Scand. 2016; 2(1): 95–101. Publisher Full Text\n\nTavangar M, Bagheri R, Kwon T, et al.: Influence of beverages and surface roughness on the color change of resin composites. J. Investig. Clin. Dent. 2018; 9(3): e12333. PubMed Abstract \| Publisher Full Text\n\nReis A: Effects of various finishing systems on the surface roughness and staining susceptibility of packable composite resins. Dent. Mater. 2003; 19(1): 12–18. PubMed Abstract \| Publisher Full Text\n\nErtas E, Güler AU, Yücel AA, et al.: Color Stability of Resin Composites after Immersion in Different Drinks. Dent. Mater. J. 2006; 25(2): 371–376. PubMed Abstract \| Publisher Full Text\n\nDomingos PADS, Garcia PPNS, Oliveira ALBMD, et al.: Composite resin color stability: influence of light sources and immersion media. J. Appl. Oral Sci. 2011; 19(3): 204–211. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGross MD, Moser JB: A colorimetric study of coffee and tea staining of four composite resins. J. Oral Rehabil. 1977; 4(4): 311–322. PubMed Abstract \| Publisher Full Text\n\nKumari RV, Nagaraj H, Siddaraju K, et al.: Evaluation of the Effect of Surface Polishing, Oral Beverages and Food Colorants on Color Stability and Surface Roughness of Nanocomposite Resins. J. Int. Oral Health. 2015; 7(7): 63–70. PubMed Abstract\n\nChhabra N, Patel B, Jain D: Effect of different polishing systems on the surface roughness of nano-hybrid composites. J. Conserv. Dent. 2016; 19(1): 37–40. PubMed Abstract \| Publisher Full Text\n\nKorkmaz Y, Ozel E, Attar N, et al.: The Influence of One-step Polishing Systems on the Surface Roughness and Microhardness of Nanocomposites. Oper. Dent. 2008; 33(1): 44–50. PubMed Abstract \| Publisher Full Text\n\nRathakrishnan M, Abzal M, Prakash V, et al.: Evaluation of surface roughness of three different composite resins with three different polishing systems. J. Conserv. Dent. 2016; 19(2): 171–174. PubMed Abstract \| Publisher Full Text\n\nAbzal MS, Rathakrishnan M, Prakash V, et al.: Evaluation of surface roughness of three different composite resins with three different polishing systerms. J. Conserv. Dent. 2016; 19(2): 171–174. PubMed Abstract \| Publisher Full Text\n\nJohnston W, Kao E: Assessment of Appearance Match by Visual Observation and Clinical Colorimetry. J. Dent. Res. 1989; 68(5): 819–822. PubMed Abstract \| Publisher Full Text\n\nAlaqeel S: Effect of Grit-blasting on the Color Stability of Zirconia Ceramics Following Exposure to Beverages. Cureus. 2020; 12(3). Publisher Full Text\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(01): 50–56. Publisher Full Text\n\nShamszadeh S, Sheikh-Al-Eslamian SM, Hasani E, et al.: Color Stability of the Bulk-Fill Composite Resins with Different Thickness in Response to Coffee/Water Immersion. Int. J. Dent. 2016; 2016: 1–5. Publisher Full Text\n\nAllen DW, Cooksey C, Tsai BK: Spectrophotometry. NIST;Nov 13, 2009. Retrieved Dec 23, 2018.\n\nJohnston W, Kao E: Assessment of Appearance Match by Visual Observation and Clinical Colorimetry. J. Dent. Res. 1989; 68(5): 819–822. PubMed Abstract \| Publisher Full Text\n\nRagain JC, Johnston WM: Color acceptance of direct dental restorative materials by human observers. Color. Res. Appl. 2000; 25(4): 278–285. Publisher Full Text\n\nYildiz E, Sirin Karaarslan E, Simsek M, et al.: Color stability and surface roughness of polished anterior restorative materials. Dent. Mater. J. 2015; 34(5): 629–639. PubMed Abstract \| Publisher Full Text\n\nGumus H, Kocaagaoglu H, Aslan T, et al.: Efficacy of polishing kits on the surface roughness and color stability of different composite resins. Niger. J. Clin. Pract. 2017; 20(5): 557–565. PubMed Abstract \| Publisher Full Text\n\nKaradaş M, Demirbuğa S: Evaluation of Color Stability and Surface Roughness of Bulk-Fill Resin Composites and Nanocomposites. Meandros Med. Dent. J. 2017; 18(3): 199–205. Publisher Full Text\n\nBahbishi N, Mzain W, Badeeb B, et al.: Color Stability and Micro-Hardness of Bulk-Fill Composite Materials after Exposure to Common Beverages. Materials. 2020; 13(3): 787. PubMed Abstract \| Publisher Full Text\n\nSilva M, Dias M, Lins-Filho P, et al.: Color stability of Bulk-Fill composite restorations. J. Clin. Exp. Dent. 2020; 12: e1086–e1090. PubMed Abstract \| Publisher Full Text\n\nAlmulhim K, Ashwin S, Alyami F, et al.: In vitro comparison of color stability and surface roughness of bulk fill flowable composite and universal packable composite. [Dataset].2022. Publisher Full Text" }	[ { "id": "275108", "date": "22 May 2024", "name": "Mohamed M. Awad", "expertise": [ "Reviewer Expertise Adhesive Dentistry", "Restorative 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\nIntroduction: - The authors are encouraged to identify the gap in literature related to the study. - please mention the hypothesis clearly.\nMaterials and methods:\n- The authors used a light-curing with a 7.5 mm-diameter tip for curing 10-mm diameter samples, in one light-curing interval. This definitely resulted in inadequate light-curing of the samples. Please, justify.\n- How did the authors standardize the pressure (force) during polishing? - What was the handpiece water flow per min ?\n- the surface roughness: the methodology should be more detailed.\n- The statistical variables and reasons to apply the statistical tests should be clearly identified.\n\n-Results: surface roughness: representative images of polished and unpolished composite materials should be added\nDiscussion: The selection of materials (resin-based composites) should be justified. What are the main compositional differences between the composite materials used and how did it affect the study outcome?\nconclusion Filter Z250 XT is a commonly used material used for both anterior and posterior restorations. The conclusion part should be rewritten. There are several clinical studies evaluated the three materials tested.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "257500", "date": "26 Jul 2024", "name": "Ayse Tugba Erturk-Avunduk", "expertise": [ "Reviewer Expertise restorative dentistry", "esthetic dentistry", "dental materials", "caries", "bleaching." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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'd like to thank you for the submission of the present manuscript and to commend for the work performed. However, there are several concerns regarding the methods, results, discussion, and conclusions that impede the acceptance of the paper. In addition, there are many previous published studies on this topic, so the novelty of the study, if exists, should be emphasized.\n- English grammar should be reviewed and edited throughout the entire text.\nAbstract:\nStatistical analysis should be given in the abstract section. Material names should be written standard throughout the text.\n\nIntroduction:\n“esthetic or aesthetic” it should be standardized. “coloring or staining” it should be standardized. “So-flex” There is a spelling error.\nMaterials and Methods:\nAlthough many abbreviations are used, there is a confusion of long names and abbreviations in the text. It should be rearranged. The power analysis should be more detailed. The power of the LED light device must be specified. Where the abbreviation \"SL\" is first mentioned, its long name should be given. How many times were color measurements taken on each specimen? Were the measurements averaged? ΔE∗ threshold should be given. The measurement parameters of the 3D profilometer device should be detailed. How many ml of immersion solutions were prepared for cola and distilled water? What was used to test normality in statistical analysis?\n\nResults:\nWithout a threshold value, a comment was made as to why it was colored more or less. The name of statistical analysis should be removed in this section. Why the abbreviations of materials and immersion solutions was not used in tables? No statistically significant differences are seen in Table 1. Also in Table 3. Many abbreviations are used, but abbreviations are not used everywhere.\n\nDiscussion\nThe discussion part is quite weak, it should be compared and discussed with the current literature.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1192
https://f1000research.com/articles/12-1191/v1	25 Sep 23	{ "type": "Research Article", "title": "Effect of epigallocatechin gallate nanoemulsion on submandibular salivary glands following application of botulinum neurotoxins in albino rats: potential therapeutic effects", "authors": [ "Omneya Wahba", "Nahla Gamaeldin Elhelbawy", "Ola M. El-Borady", "Doaa Ahmed Labah", "Ahmed Abdelaziz Mohamed Essa", "Omneya Wahba", "Nahla Gamaeldin Elhelbawy", "Ola M. El-Borady", "Doaa Ahmed Labah" ], "abstract": "Background: Injecting botulinum neurotoxin (BoNT) into the salivary glands is a common treatment for certain diseases. Green tea's active compound, epigallocatechin-3-gallate (EGCG), has been linked to a variety of health benefits, including the reduction of free radicals and inflammation. This study compared the effects of BoNT and BoNT/EGCG on the submandibular salivary glands (SMG) histology and ultrastructure. Methods: Both BoNT and BoNT/EGCG nanoemulsions were injected into the submandibular salivary glands (SMGs) in adult male albino rats, which were then euthanized, and the right SMGs were thoroughly dissected and prepared for histological, immunohistochemical, and transmission electron microscopic analysis. Results: When compared to the BoNT group, the BoNT/EGCG nanoemulsion group significantly improved SMG acinar and ductal cells using both H&E and immunohistochemical stainings. Ultrastructural findings of the BoNT/EGCG nanoemulsion group revealed marked improvement in the SMG structure, almost normal acini, and striated ducts. Conclusion: Salivary gland histological structures are significantly altered after BoNT administration, but the addition of EGCG causes only minor alterations and can be used to treat hyperfunction.", "keywords": [ "EGCG", "Nanoemulsion", "Botulinum Neurotoxins", "BoNT", "salivary", "hyperfunction" ], "content": "Introduction\n\nOne of the most potent natural toxins ever discovered by humans is botox, also known as botulinum neurotoxins (BoNTs). Various spore-forming anaerobic Clostridium botulinum strains produce seven BoNT serotypes (A–G) (Pirazzini et al., 2017). BoNTs, or metalloproteinases, inhibit neurotransmitter Sherif et al. (2018) release at peripheral cholinergic nerve terminals by cleaving one or more core proteins of the neuroexocytosis apparatus. These substances have demonstrated efficacy in treating a variety of human syndromes brought on by excessively active cholinergic nerve terminals due to their focused mechanism of action. BoNT/A is also a pharmaco-cosmetic, and its clinical uses are expanding. Parkinson’s disease, head and neck cancer, stroke, neurodegenerative disease, focal dystonia, spasticity, and other focal muscle hyperactivity conditions are treated with BoNT/A. Focal hyperhidrosis (axillary perspiration, palmer perspiration, or gustative perspiration), sialorrhea, pathological lacrimation, and rhinorrhea are some of the autonomous hypersecretory alterations that have been significantly affected by this discovery (Thenganatt & Fahn, 2012).\n\nDrooling in children with central nervous system disorders is often treated with BoNT salivary gland injections. Most patients experience a reduction in saliva production and drooling after receiving an intratglandular injection of BoNT because this treatment blocks acetylcholine release at nerve terminals. Even though BoNT can impair oral motor functions such as swallowing, eating, drinking, and articulation and cause sore throats, dry mouths, and teeth grinding, it is increasingly used to treat drooling (Karen et al., 2017). Additionally, BoNT’s safety and effectiveness have their limits. Drooling can be controlled with BoNT, but it has some undesirable side effects that need to be addressed with an adjunctive therapy for optimal effectiveness (Chan et al., 2013).\n\nGreen tea is made from Camellia sinensis leaves. According to recent research, drinking green tea may have important health benefits. According to studies, green tea has chemopreventive, antimicrobial, antiviral, antioxidant, anti-inflammatory, anti-proliferative, and anti-mutagenic properties (Jayakeerthana, 2016). Additionally, it protects neurons, lowers the risk of cardiovascular disease, boosts bone health, and regulates metabolic processes like glucose, cholesterol, blood pressure, and body weight. Green tea’s health benefits come from over 75% of its polyphenol compounds, including catechins. Catechins, one of the most important components of tea leaves, are thought to reduce the formation of free radicals in the body and protect cells from damage because of their intense antioxidant and representative physiological activities. In addition to contributing to the aging process, these free radicals have been linked to numerous diseases (Bae et al., 2020).\n\nGreen tea contains 65% catechins, with EGCG (epigallocatechin gallate) being the most abundant and therapeutically effective. Among the catechins found in green tea, EGCG has the highest antioxidant capacity.(16) EGCG is used to prevent and treat many diseases, including cancer, metabolic syndrome, Parkinson’s disease, Alzheimer’s disease, obesity, and cardiovascular diseases. This makes using this natural substance for these applications a popular choice. The two main drawbacks that regrettably prevent the use of EGCG as a preventative or therapeutic agent are its inability to be absorbed by intestinal cells and its inherent instability (Musial et al., 2020).\n\nAn approach that has been taken to address these deficiencies is the utilization of nanoencapsulated EGCG. The incorporation of EGCG into nanocarriers possesses the potential to increase the permeability of the intestinal barrier, which, in turn, results in the compound’s increased stability and increased therapeutic efficacy. This is because the increased permeability of the intestinal barrier allows more nutrients to pass through (Legeay et al., 2015). Nanoemulsion delivers EGCG well due to its ease of preparation and industrialization. Because it possesses both advantages, this is the reason for this fact. Encapsulating EGCG in a nanoemulsion increases its bioavailability, stability, and biological activity (Eng et al., 2018).\n\nNanoemulsions improve the bioavailability, stability, and biological activity of EGCG. This increases compound solubility. Because of this, a study was conducted to determine how intraglandular injection of BoNT affects the structure of rats’ SMG and how EGCG nanoemulsion reduces this effect.\n\n\nMethods\n\nMaterials\n\nSigma Aldrich Company (St. Louis,USA) provided the EGCG. Tween 80 (ADWIC, Egypt). Absolute ethanol (99.5–99.8%) was purchased from Merck. For the immunohistochemical analysis of cell apoptosis and epithelial cell-to-cell adhesion, Dako (Glostrup, Denmark) supplied mouse monoclonal antibodies against human Bcl-2 (JC70A, IgG1) and E-cadherin (1A4, IgG2a).\n\nEGCG nanoemulsion was prepared by a modified oil-in-water (O/W) emulsification method referring to (Gadkari et al., 2017) using Tween 80 as an emulsifier. To get an O/W nanoemulsion, the prepared ethanolic solution containing EGCG was added drop-wise over a beaker containing 100 ml distilled water and homogenized via probe ultrasonicator (20,000 Hz) for 20 min under an ice bath. Firstly, 100 mg of EGCG was dissolved in 10 ml of ethanol then 0.01 gm of Tween 80 was added over it and mixed very well. The mixture was then stirred to get out the organic solvent (ethanol) with a magnetic stirrer (2,000 rpm) for 4 hours at room temperature. The obtained nanoemulsion was stored in the refrigerator for further use.\n\nUsing a high-resolution transmission electron microscope (TEM) from Japan (JOEL JEM-2010) that operated at an accelerating voltage of 200 kV, the morphology and size of the nanoemulsion were examined. The Fourier transform infrared (FTIR) technique was utilised to carry out the spectral analysis of the nanoemulsion. Spectroscopy was performed using a JASCO spectrometer, Japan, and the scan ranged from 4000–400 cm−1. To measure the surface charge of nanoemulsion and its average size, a zeta analyzer (Zetasizer Nano ZS Malvern) was used to investigate the zeta potential and size distribution.\n\nMorphological analysis\n\nUsing a transmission electron microscope, an examination of the size and shape of the EGCG nanoemulsion that had been manufactured revealed the formation of a spherical nanoemulsion that possessed a high degree of homogeneity in shape. Around 130 nanometers was the average size of the particles that were developed (Figure 1A).\n\nSize distribution and Zeta potential\n\nWhen determining the colloidal stability and surface charges of the particles, the measurement of the zeta potential is considered. The fact that the Zeta potential of the prepared EGCG nanoemulsion was found to be negative 13.5 mV demonstrates the successful formation of a nanoemulsion (Figure 1B). The size distribution as well as the polydispersity index (PDI) for the EGCG nanoemulsion as measured by DLS. The measurements detect the size distribution to be 228 nm with PDI =1 (Figure 1C).\n\nThe Fourier transformed infrared spectroscopy (FTIR)\n\nThe FTIR spectrum of original EGCG displayed a broad peak in the range of 3500-3300 cm−1 attributed to the eight OH groups present in its structure. The presence of a fingerprint peak in the EGCG FTIR spectrum at 3357.46 cm−1 referred to OH groups directly attached to the aromatic ring. Additionally, the EGCG IR spectrum revealed the presence of other bands at 1692 cm−1, 1616 and 1149 cm−1 due to vibrations of C=O, C-C (aromatic ring), and C-O bonds (pyranose heterocyclic chain), respectively. Other bands were detected at 1235 cm-1 for the O-C=O group and 1035 cm-1 for the C-O-C group. On the other hand, the EGCG nanoemulsion showed the peaks corresponding to the OH, C=O, C-C (aromatic ring), and C-O bonds, O-C=O group and C-O-C group at 3367 cm−1, 1692 cm−1, 1621 cm−1, 1140 cm−1, 1243 cm−1, and 1028 cm−1, respectively. The shift observed in the EGCG nanoemulsion peak compared to than the original EGCG confirms its change to the nano form (Figure 1D).\n\nThis study made use of thirty adult male albino rats, each of which weighed between 150 and 180 grammes on average. An earlier method developed by Charan and Biswas was used in the computation of the estimation of the sample size. Five rats in each cage were housed in polycarbonate cages with wire lids at Zagazig University’s Faculty of Medicine. Each cage was numbered, and the rats were kept in a well-ventilated animal house. A normal photoperiod was maintained while the room temperature was kept at 23 degrees Celsius and the humidity was kept at 60 percent. The rats were provided with a dry diet of rat pellets, and they had unrestricted access to water throughout the experiment. After an adjustment period of one week, the rats were randomized into three separate groups of equivalent size: Group I rats were a negative control for other groups. Group II (BoNT) rats were anesthetized by intramuscular injection of xylazine (6 mg/kg) (Sigma-Aldrich, USA) and ketamine (70 mg/kg) (Hospira, USA). The SMG was exposed via surgical incision, and then 5 units of BoNTA (Botox®, Allergan Inc., Irvine, CA, USA) diluted in 0.1 ml saline were injected once at the center of the right SMG (24). Group III (BoNT + EGCG nanoemulsion group) rats were anesthetized then the SMG was exposed, and BoNTA was injected at the center of the right SMG, similar to group II. Then, the rats received EGCG nanoemulsions in a once-daily dose of 0.1 ml by oro-gastric intubation (Koutelidakis et al., 2017). The first oral dose of EGCG nanoemulsions was given on the day of intraglandular BoNTA injection and continued daily for four weeks.\n\nAll animal experiments followed ARRIVE’s guidelines and the National Institutes of Health’s lab animal protocol (NIH Publications, revised 1985). The Zagazig University Institutional Animal Care and Use Committee (ZU-IACUC/3/F/368/2022) approved animal care and experimental protocols.\n\nEach rat was euthanized at the end of the experiment using a sodium thiopental overdose (EIPICO, Egypt), which was then followed by cervical dislocation. Five samples from each group were prepared for histological and immunohistochemical analysis after carefully dissecting the appropriate SMGs. The remaining five samples from each group were processed for transmission electron microscopy analysis.\n\nThe SMG specimens were first fixed in a formalin solution buffered at 4%, followed by a series of increasing concentrations of ethanol used to dehydrate the glands. Finally, the entire gland was then embedded in paraffin. H&E was used to stain sections that represented the entire sample, which were cut into five micrometer sections. At the Zagazig University Faculty of Medicine, a digital color CCD camera examined and photographed the slides (Olympus, DP73, Tokyo, Japan). A light microscope held it (Olympus BX53, Tokyo, Japan).\n\nEach paraffin block was divided into sections with a thickness of 4 micrometers for immunohistochemical staining. These sections were deparaffinized in xylene and dehydrated in increasing alcohol concentrations. To inhibit internal peroxidase activity, they were submerged in 3% hydrogen peroxide in PBS. Antigen retrieval was carried out in a Panasonic 1380-watt microwave oven for 10 minutes at 2 atm and 120°C. Further incubations with prediluted, ready-to-use primary mouse monoclonal antibodies (anti-Bcl-2, clone MIB-5; Sigma-Aldrich, USA, and anti-E-cadherin; clone HECD-1, Biocare Medical, USA) were used as the primary antibody for 30 min and was incubated in a moist chamber at room temperature (24 h) with a working dilution of 1:50 and 1:100, respectively, followed by the application of secondary antibody (for 15 min), DAB (to produce brown staining), and Meyer’s hematoxylin (for background staining). Following each step mentioned, the samples were put into PBS. According to the manufacturer’s instructions, the positive controls for Bcl-2 and E-cadherin were the kidney and skin, respectively. PBS was used in place of the primary antibody to create the negative control. Brown-colored reaction concentrated in the cytoplasm or nucleus was regarded as a positive reaction. In a blinded analysis carried out by two skilled research associates using a traditional light microscope and Image J software (version 4.10.03, Nikon, Tokyo, Japan), the intensity of the immunostaining was categorized as being negative, weak, moderate, or strong in three fields.\n\nFor two hours at room temperature, the 1 mm cubes of SMGs were submerged in a solution of 4 percent paraformaldehyde and 1 percent glutaraldehyde. Before being postfixed in osmium tetroxide at a concentration of 1%, the samples underwent one last rinse in buffer. Following the fixation procedure, the samples were dehydrated in increasing grades of ethanol, immersed in absolute acetone, and then embedded in Epon. At the Mansoura University Electron Microscopy Unit, the RMC-USA ultramicrotome was used to cut the ultrathin slices, then placed on copper grids, stained with uranyl acetate and lead citrate, and viewed with a JEOL JEM-2100 transmission electron microscope (Jeol Ltd, Tokyo, Japan).\n\nImmunohistochemical data were tabulated and statistically analyzed using one-way analysis of variance (ANOVA) to determine group differences Following that, Dunnett’s post-hoc test was utilized to compare the control group to the test group. For the findings to be considered statistically significant, P had to be lower than 0.05. SPSS, version 11.0, was used for the collection and analysis of all statistical data. This software was developed by SPSS Inc. in Chicago, Illinois, in the United States of America.\n\n\nResults\n\nThe architecture of a standard SMG was revealed by the control group. The gland was formed of two main components; the stroma and the parenchyma. Serous acini and various duct types made up the parenchyma. The serous acini were small, rounded, and had narrow lumens. Each acinus is lined with pyramidal cells that have basophilic cytoplasm and large, basal spherical nuclei. Simple cuboidal epithelium with central rounded nuclei and little cytoplasm lining intercalated ducts. Columnar cells with open face nuclei lined the granular convoluted tubules, and the cytoplasm had eosinophilic granules. The striated ducts had high cubical or columnar cells with rounded nuclei and apical brush borders, and basal eosinophilic striations (Figure 2A). Examination of BoNT group revealed many changes in the SMG. Some acinar cells showed There are many cytoplasmic vacuoles, and there are different types of nuclear shape, size, and number. Other acinar cells had darkly stained cytoplasm and appeared lodged with retained secretory granules. Also, separation between acini was evident. The ducts revealed abnormal architecture, and many ductal cells exhibited cytoplasmic destruction and vacuolization (Figure 2B). Cells in the ducts and acini showed striking improvement in the BoNT + EGCG nanoemulsion group, in contrast to the BoNT group (Figure 2C).\n\nBcl-2 immunohistochemical expression\n\nIn the control and BoNT + EGCG nanoemulsion groups, anti-Bcl-2 antibody staining of the cells was found to be weak to moderate. However, the BoNT group’s cells were strongly stained (Figure 3A-C).\n\nThe BoNT group had more Bcl-2-positive immunostained cells than the control and BoNT + EGCG nanoemulsion groups, according to the statistical analysis (Figure 4 & Table 1).\n\nE-cadherin immunohistochemical expression\n\nExamination of E-cadherin immunoreactivity revealed moderate staining of cells in the control group, weak staining of cells in the BoNT group, and strong staining of cells in the BoNT + EGCG nanoemulsion group (Figure 5A-C).\n\nWhen compared to the control and BoNT groups, the E-cadherin positively immunostained cells of the BoNT + EGCG nanoemulsion group showed a significant increase, according to the statistical analysis of the data. The control group had more E-cadherin-positive immunostained cells than the BoNT group (Figure 6 & Table 2).\n\nThe SMG’s normal ultrastructure was visible in the control group. Pyramidal cells with basal nuclei lined the acinar cells. RER parallel arrays were present in well-developed arrays at the base of the cells (Figure 7A). The epithelium lining the striated duct was simple and columnar in shape, characterized by round euchromatic nuclei, infolded basal membranes, and vertically arranged mitochondria (Figure 7B). The BoNT group SMG showed many degenerative changes. Acinar cells had many abnormally shaped secretory granules and RER (Figure 7C). The striated duct showed a loss of normal architecture, and the ductal cells exhibited cytoplasmic rarefaction, dispersed RER, and an abnormal distribution of abnormally configured mitochondria (Figure 7D). The ultrastructural findings in the BoNT + EGCG nanoemulsion group revealed marked improvement in the SMG compared to the BoNT group and showed nearly normal acini and striated ducts (Figure 7E & F).\n\nControl group I reveals normal shape of SMG.\n\n\nDiscussion\n\nBoNT is a novel treatment for many diseases, including salivary gland diseases. Treatment for sialorrhea has included the injection of BoNT into the salivary glands, which is thought to be a secure and minimally invasive procedure. Accidental injections may also occur into the SMG when treating facial wrinkles at the platysma or under the chin for cosmetic reasons. But there hasn’t been enough research done on BoNT injection’s negative effects (Granja et al., 2017). The current study produced some novel results and attempted to address the damaging effect of SMG injection of BoNT in rats and the capability of EGCG nanoemulsion to subside this harming effect.\n\nRats were chosen as the study’s preferred experimental model because of their resemblance to humans in terms of physiology, anatomy, and genetics. In addition to their small size, they have low maintenance requirements, a quick lifespan, ample genetic resources, accessibility, and an affordable price (Tsai & Chen, 2016).\n\nControl SMGs revealed normal histological structures devoid of significant histological and ultrastructural alterations in the serous acini and duct system. In rabbit SMGs injected with normal saline Chen et al. (2020), found regular acinar and ductal cells without morphological changes. In BoNT-injected SMGs, some serous acini lost their spherical shape and had cytoplasmic vacuoles. In addition, the loss of basal striations and faulty borders in striated ducts were observed. These results agreed with those of Al-Allaf et al. (2022). Whereas compared to controls, parotid glands treated with BoNT had smaller acinar cells and a wider striated duct lumen. These effects may be the result of glandular denervation brought on by the inhibition of soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors involved in acetylcholine release at the neuroglandular junction, particularly those involved in acinar cell granule exocytosis. Additionally (Younis et al., 2013), proposed that the molecular mechanism of action of BoNT involves inhibiting the muscarinic receptor (M3) and preventing the expression of aquaporin 5, which is involved in the secretion of water.\n\nIn the current study, quantitative Bcl2 immunohistochemical expression in the BoNT group was significantly higher than in other groups. This discovery may be explained by the degenerative modifications and apoptosis brought on by BoNT in the SMG cells. Moreover, in this work, E-cadherin immunohistochemical expression in the BoNT group was significantly lower than that in other groups, indicating a decline in parenchymal cell adhesions. These findings matched previous research, which evidenced apoptosis and necrosis along with a reduction in the proliferative activity in SMG cells following BoNT intraglandular injection (Regueira et al., 2019; Oliveira et al., 2017).\n\nFinally, while BoNT application clearly damages both histological and ultrastructural levels, the BoNT/EGCG nanoemulsion combination showed the least changes. So, as a minimally invasive treatment method for SMG hyperfunction, BoNT/EGCG nanoemulsion can be used in place of surgical intervention or duct ligation.\n\nAhmed Abdelaziz Mohamed Essa: Conceptualization, Data Curation, Resources, Writing – Original Draft Preparation, Writing – Review & Editing\n\nOmneya Mohamed Wahba: Data Curation, Formal Analysis, Investigation, Methodology\n\nNahla Gamaeldin El-Helbawy: Data Curation, Methodology, Resources, Supervision, Visualization, Writing – Review & Editing\n\nOla M. El-Borady: Data Curation, Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing\n\nDoaa Ahmed Labah: Data Curation, Formal Analysis, Investigation, Methodology, Writing – Review & Editing", "appendix": "Data availability\n\nFigshare. Essa, Ahmed (2023): Effect of Epigallocatechin Gallate Figures and Figure legends. DOI: https://doi.org/10.6084/m9.figshare.23055356 (Essa, 2023).\n\nFigshare. ARRIVE. DOI: https://doi.org/10.6084/m9.figshare.23691360.v1\n\n\nReferences\n\nAl-Allaf L, Mammdoh J, Ahmed A: The histologic effects of high doses of botulinum toxin a on the rabbit’s salivary gland. Iraqi Journal of Veterinary Sciences. 2022; 36(4): 1111–1117. Publisher Full Text\n\nBae J, Kim N, Shin Y, et al.: Activity of catechins and their applications. Biomed Dermatol. 2020; 4: 8. Publisher Full Text\n\nChan KH, Liang C, Wilson P, et al.: Long-term safety and efficacy data on botulinum toxin type A: an injection for sialorrhea. JAMA Otolaryngol. Head Neck Surg. 2013; 139(2): 134–138. Publisher Full Text\n\nChen BH, Hsieh CH, Tsai SY, et al.: Anticancer effects of epigallocatechin-3-gallate nanoemulsion on lung cancer cells through the activation of AMP-activated protein kinase signaling pathway. Sci. Rep. 2020; 10(1): 5163. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEng QY, Thanikachalam PV, Ramamurthy S: Molecular understanding of Epigallocatechin gallate (EGCG) in cardiovascular and metabolic diseases. J. Ethnopharmacol. 2018; 210: 296–310. PubMed Abstract \| Publisher Full Text\n\nEssa A: Effect of Epigallocatechin Gallate Figures and Figure legends figshare. Figure. 2023. Publisher Full Text\n\nGadkari PV, Shashidhar M, Balaraman M: Delivery of green tea catechins through Oil-in-Water (O/W) nanoemulsion and assessment of storage stability. J. Food Eng. 2017; 199: 65–76. Publisher Full Text\n\nGranja A, Frias I, Neves AR, et al.: Therapeutic Potential of Epigallocatechin Gallate Nanodelivery Systems. Biomed. Res. Int. 2017; 2017: 5813793.\n\nJayakeerthana S: Benefits of Green Tea: A Review. J. Pharm. Sci. Res. 2016; 8(10): 1184–1187.\n\nKaren V, Carlyn V, Pieter H, et al.: Negative effects of submandibular botulinum neurotoxin A injections on oral motor function in children with drooling due to central nervous system disorders. Dev. Med. Child Neurol. 2017; 59(5): 531–537.\n\nKoutelidakis AE, Argyri K, Sevastou Z, et al.: Bioactivity of Epigallocatechin Gallate Nanoemulsions Evaluated in Mice Model. J. Med. Food. 2017; 20(9): 923–931. PubMed Abstract \| Publisher Full Text\n\nLegeay S, Rodier M, Fillon L, et al.: Epigallocatechin Gallate: A Review of Its Beneficial Properties to Prevent Metabolic Syndrome. Nutrients. 2015; 7(7): 5443–5468. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMusial C, Kuban-Jankowska A, Gorska-Ponikowska M: Beneficial Properties of Green Tea Catechins. Int. J. Mol. Sci. 2020; 21(5): 1744. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOliveira JB, Evêncio-Neto J, Baratella-Evêncio L: Histological and immunohistochemical findings of the action of botulinum toxin in salivary gland: Systematic Review. Braz. J. Biol. 2017; 77(2): 251–259.\n\nPirazzini M, Rossetto O, Eleopra R, et al.: Botulinum Neurotoxins: Biology, Pharmacology, and Toxicology. Pharmacol. Rev. 2017; 69(2): 200–235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRegueira LS, Baratella-Evêncio L, de Oliveira JB , et al.: Effects of chronic treatment with botulinum toxin type A in salivary glands of rats: Histological and immunohistochemical analyses. J. Oral Pathol. Med. 2019; 48(8): 728–734. PubMed Abstract \| Publisher Full Text\n\nSherif H, Esmail A, Abdelfattah M, et al.: Effects of Botulinum Toxin A (Botox) on cellular organs of Submandibular Salivary Gland in Rats (Ultrastructural study). Al-Azhar Journal of Dental Science. 2018; 21(5): 503–510. Publisher Full Text\n\nThenganatt MA, Fahn S: Botulinum Toxin for the Treatment of Movement Disorders. Curr. Neurol. Neurosci. Rep. 2012; 12: 399–409. Publisher Full Text\n\nTsai YJ, Chen BH: Preparation of catechin extracts and nanoemulsions from green tea leaf waste and their inhibition effect on prostate cancer cell PC-3. Int. J. Nanomedicine. 2016; 11: 1907–1926. PubMed Abstract \| Publisher Full Text\n\nYounis RE, Abou Elkhier MT, Mourad MI, et al.: Ultrastructural changes in the parotid gland of rats after intraglandular injection of Botulinum toxin A. Ann. Oral Maxillofacial Surg. 2013; 1(4): 38. Publisher Full Text" }	[ { "id": "209240", "date": "09 Oct 2023", "name": "Anjalee Vacharaksa", "expertise": [ "Reviewer Expertise Tissue regeneration in rat models" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nExperimental design\nTo observe the damaging effect of injection, another control should be added with normal buffer, without and chemical intervention. There is no detail on the Group I control if the animals in this group got a sham injection or not.\n\nThe authors should explain the rationale of not adding another control group with \"only EGCG injection\".\n\nThe authors should explain the rationale of giving EGCG nanoemulsions in a once-daily dose of 0.1 ml by oro-gastric intubation.\n\nDetails of methods and analysis\nNumber of animals of each experimental group should be clearly written in text, and displayed in the figure.\n\nGroup III (BoNT + EGCG nanoemulsion group) should be written in the figure legend, not just \"EGCG nanoemulsion\".\n\nSome data can be analyzed quantitatively, including Table 1 and 2. However, normal distribution of the data should be demonstrated before selecting parametric analysis. The statistical comparison should be displayed in the figure, rather than adding tables of statistic analysis.\n\nDiscussion and conclusions\nThe original purpose of this study remains unclear in discussion. It is confused whether the injection of BoNT is necessary for a therapeutic purpose. If EGCG can reduce the damage, the effect of EGCG on therapeutic purpose of BoNT should be discussed.\n\nTissue damage by the injection technique should be discussed.\n\nThere is not statement why an \"albino\" rat was chosen as a model. The aim of this study could be concluded with other rat models?\n\nThere is no discussion (only one sentence with no detail) on the benefits of adding EGCG.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1191
https://f1000research.com/articles/11-274/v1	03 Mar 22	{ "type": "Systematic Review", "title": "Efficacy of vitamin D supplementation on the severity of atopic dermatitis in children: A systematic review and meta-analysis", "authors": [ "Afif Nurul Hidayati", "Sawitri Sawitri", "Desiana Widityaning Sari", "Cita Rosita Sigit Prakoeswa", "Diah Mira Indramaya", "Damayanti Damayanti", "Iskandar Zulkarnain", "Irmadita Citrashanty", "Yuri Widia", "Sylvia Anggraeni", "Sawitri Sawitri", "Cita Rosita Sigit Prakoeswa", "Diah Mira Indramaya", "Damayanti Damayanti", "Iskandar Zulkarnain", "Irmadita Citrashanty", "Yuri Widia", "Sylvia Anggraeni" ], "abstract": "Background: Atopic Dermatitis (AD) is a common dermatosis in children, that includes skin architecture defects, immune dysregulation, and changes of skin flora. Several new drugs have been found to reduce the severity of AD. Vitamin D is one of the new therapies that is still controversial. The purpose of this research is to conclude the efficacy of vitamin D on atopic dermatitis severity in children aged 0-18 years old. Methods: A systematic search was conducted on the PubMed, Cochrane, ProQuest, Google Scholar, Clinical Trial website, and university repositories including studies published from January 2010 through October 2020. We compared populations, intervention, study design, and outcomes. Statistical analysis was done with Review Manager 5.4.1. Results: Eight articles met eligibility and inclusion criteria, four articles provided complete data and were analysed. Not all studies demonstrated the efficacy of vitamin D but a meta-analysis of four studies of vitamin D supplementation vs placebo found a mean difference of -0.93 (95%CI -1.76, to -0.11, p<0.001) of patient outcome, but statistically, there was no difference in cure rate (risk ratio 1.46 (95%CI 0.72, to 2.97, p=0.008) in vitamin D supplementation groups compared to placebo groups. Conclusions: Vitamin D supplementation in paediatric atopic dermatitis patients could offer improvement of disease severity but the recommended dose and duration of administration cannot be concluded yet.", "keywords": [ "atopic dermatitis", "children", "efficacy", "vitamin D", "human health" ], "content": "Introduction\n\nAtopic Dermatitis (AD) is now considered a complex multifactorial disease that includes defects in skin barrier structures, immune dysregulation, genetic susceptibility, and changes in skin flora which mostly occur in infancy and childhood. Based on the clinical features, AD can be divided into 3 forms, namely AD in infants (2 months-2 years), children (2–12 years), and adolescents (over 12 years).1 Increasing prevalence of AD has been reported in areas including the Asia-Pacific region, where it is reported that 88% of children with AD have either mild or moderate and 12% have severe AD. However, Indonesia still has a lower prevalence in children between 6-7 years old when compared to Thailand and Malaysia, and a lower prevalence in children aged 13-14 years when compared to Pakistan.2\n\nIn addition to the reduction of skin inflammation, recently, AD treatment has focused more on the regulation of the immune response and enhancing the barrier function of the skin.3 Poor compliance with the use of topical drugs makes some researchers try to find other drugs that are not only safe, cheap, easy to use but also effective. Several recent studies have shown that vitamin D supplementation may be an option, although the results of intervention trials are still conflicting.4\n\nIn AD patients, defects in the skin barrier structure, as well as decreased functional integrity and reduced ability to regenerate have roles in inducing immune responses and specific inflammatory reactions.5 In acute lesions, there will be a decrease in AMP (Antimicrobial Peptide) production, an increase in S. aureus colonization, and an effect on the severity of the disease and reduce the risk of infection. Vitamin D can increase barrier function, induce AMP and enhance monocyte and macrophage cell function.6 Vitamin D has been known to have some effects on the innate and adaptive immune systems. Several mechanisms can modulate the progression of AD lesions, such as increasing epidermal differentiation, increasing production of cathelicidin, decreasing Th2 cytokines, decreasing Ig E production, decreasing B cell proliferation, and upregulating of T cells.7\n\nA previous systematic review and meta-analysis in 2019 on vitamin D and AD had reported a highly statistically significant reduction in SCORAD (Scoring of Atopic Dermatitis) on intervention with vitamin D, in the paediatric and adult population.8 While a systematic review published by Huang on the paediatric AD population in 2018 concluded that 67% of the collected studies reported a significant improvement in AD severity with vitamin D supplementation, but this systematic review did not include a meta-analysis.9 We conducted a meta-analysis with research published in last 10 years because there has been an increase in publications regarding vitamin D supplementation during this time.10\n\nThe main objective of our systematic review and meta-analysis is to provide an updated review of the interventional study of vitamin D in the paediatric AD population to investigate clinical outcomes from measuring scales.\n\n\nMethods\n\nWe conducted a systematic search of the literature on several databases, namely PubMed, Cochrane Library, ProQuest, and a clinical trial website, ClinicalTrials.gov with keywords showed in Table 1 (see also Extended data33). We also did manual hand searching on Google Scholar and searched for grey literature on the repository (including research from January 1st 2010 to October 31st 2020, and the databases were last searched on 2nd November 2020). The search procedure was based on Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). The completed PRISMA checklist is available in Reporting guidelines.33 This search of titles and abstracts was limited to articles that were human-focused and published in English and Bahasa Indonesia. Statistical analysis was carried out with Review Manager (RevMan, Cochrane, London, UK) version 5.4.1 with standardized mean difference and risk ratio as a measure of the effect of therapy.\n\nIn studies that include children and adults as participants, we contacted the author to obtain separate data that contained child subjects only. The ethical clearance of this study has been published from the Ethical Committee of Dr. Soetomo General Academic Hospital Surabaya number 0206/LOE/301.4.2/XI/2020. We did not register the protocol.\n\nIntervention studies including Randomized Control Trials and Prospective Cohort studies with clinical outcomes measured on a scale in both groups, before and after the intervention were assessed. Inclusion criteria were as follows: (1) studies with age group 0-18 years old and diagnosed as mild, moderate, or severe atopic dermatitis in both females and males; (2) No restriction to the duration of intervention, type of vitamin D, doses used, frequency and route of administration, and clinical outcome measuring scale: SCORAD, EASI (Eczema Area and Severity Index), IGA (Investigator Global Assessment). (3) studies that provided complete data for clinical outcomes. Exclusion criteria were articles that did not provide full text.\n\n\n\n1. Evaluating the outcome of the disease (changes in SCORAD or EASI) in the Vitamin D supplementation groups compared to placebo groups.\n\n2. Calculating the clinical importance of both groups so that the CER (Control Event Rate), EER (Experimental Event Rate) and NNT (Number Needed to Treat) values can be obtained.\n\nThis analysis included all articles that qualified for selection criteria. Two author, ANH and SS extracted data from each included study including author, country, publication year, study population, AD severity, supplementation dose, frequency, route of administration, duration and outcome scale. The clinical outcome was measured by scale: SCORAD, EASI or IGA. We defined the clinical outcomes as follows:\n\n(1) SCORAD: A clinical measurement tool used to calculate the severity of Atopic Dermatitis patients. The lesion area was calculated based on the rule of nine with a value of 0-100. Intensity was measured in a representative area by looking at the form of skin abnormalities that were erythema, edema, oozing or crusts, excoriations, lichenification, and dry skin, and each was assigned a value of 0 if there was no lesion, 1 if the lesion was mild, and 2 if the lesion was moderate and 3 if the lesion was severe, then the scores were summed to get B (0-18). Subjective symptoms were measured by Visual Analog Scale (VAS), calculated on average for every 3 night whether there were symptoms of itching and sleep disturbances, with a score of 0 if there was no itching or sleep disturbances, and 10 for the most severe itching or sleep disturbances. These numbers are summed to give C (0-20). The results of the three parameters were submitted into the formula A5+7B/2+C, then grouped into mild AD (<25), moderate AD(25-50) and severe AD(>50) categories.11\n\n(2) EASI: an instrument used by examiners (doctors, dermatologists) to quantify lesion progression and severity of AD patients, by assessing the extent of the disease at four body sites (head/neck, trunk including genitalia, superior and inferior extremities) and measures four clinical signs: (1) erythema, (2) induration/papulation, (3) excoriation, and (4) lichenification each on a scale of 0 to 3. The score can then be divided into 0 (clean), 0.1-1.0 (nearly clean), 1.1-7 (mild), 7.1-21 (moderate), 21.1-50 (severe), 50,1-72.0 (very severe). EASI confers a maximum score of 72.11\n\n(3) IGA: an instrument used to assess overall disease severity at one given time point, and it consists of a 6-point severity scale from clear to very severe disease (0 = clear, 1 = almost clear, 2 = mild disease,3 = moderate disease, 4 = severe disease and 5 = very severe disease). IGA uses clinical characteristics of erythema, infiltration, papulation, oozing and crusting as guidelines for the overall severity assessment.12\n\nThe covidence quality assessment template was customized for this study and the quality of each study was assessed by three authors (ANH, SS and DWS) independently by using the Centre for Evidence-Based Medicine’s RCT (Randomized Control Trial) worksheet, by conducting a critical appraisal to determine validity, importance and applicability. Validity was assessed based on Recruitment, Allocation and Measurement Blinding Outcome. Importance was assessed based on clinical data as well as statistical data. Applicability was assessed by answering several questions related to the author’s setting (Table 2). Critical appraisal for prospective (cohort) study was conducted using critical appraisal skill programme worksheet (Table 3). Another author resolved any disagreement between them (CRSP, DMI, and DD). Quality analysis of the interventional studies had showed three studies scoring randomized double-blind clinical trials with adequate randomization and blinding. These were Refs. 13, 14 and 15. The other study did not mention randomization but confirmed the blinding of both participants and researchers.16\n\nThe risk of bias in RCT studies was assessed with The Cochrane Collaboration's tool for assessing risk of bias17 by ANH, SS and DWS, then we discussed the outcome until we were in agreement. The assessment results were categorized as “yes” for low-risk bias, “unclear”, and “no” for high-risk bias (Figure 1). Cohort studies was assessed with Newcastle-Ottawa Scale (NOS)18 and comprised several items including comparability of the groups (2 points), and ascertainment of exposure (3 points). Each study was interpreted to be low quality (scores <4), moderate quality (scores of 5–6), or high quality (scores ≥7) that was shown in Table 4.\n\nWe performed the data with Review Manager (RevMan, Cochrane, London, UK) version 5.4.1. Three authors, DWS, IC, and SA conducted statistical analysis and presented the result in a forest plot and funnel plot. Statistical analysis was done by calculating the standardized mean differences (SMDs), with 95% CIs, of pre- and post-intervention in both groups, and the standard deviation of each study, and was also calculating risk ratio (RR), with 95% CIs, by counting the number of events in each group with a dichotomy table (Table 5). Significance of RRs was determined using the Z test (p<0.05 was considered statistically significant). We assessed the heterogeneity among the studies using I2 (considered heterogeneity existed if I2 > 25%), then Random Effect Model was adopted. For publication bias, we used funnel plot and it can be seen that the four studies are distributed symmetrically, that is, the distribution of research is balanced on the left and right of the centre line boundary. This means that there is no potential for publication bias regarding the conclusions.\n\n\nResults\n\n570 articles were initially retrieved, and the results of the evaluation of duplicate articles by title showed 157 articles with similar titles and were subsequently excluded from this study. The next evaluation was carried out by reviewing the title of each piece of literature that had been searched based on keywords. There were 11 literatures by excluding 402 literature that was irrelevant with the study design. We did further evaluation of 11 kinds of literature based on eligibility criteria, critical appraisal, and quality assessment, and excluded two articles with subject included aged > 18 years old and one article with non-AD subjects as a comparison group. Qualitative synthesis then resulted two studies that could not be included in the meta-analysis due the fact that no standard deviation was reported19 and.20 A further two studies were also excluded due to the study design which was single-arm cohort21 and22 so that the final results were four articles which were then analysed in this study.\n\nFour articles were included in meta-analysis, as described in Figure 2. The years of publication for all studies were ranging from January 2010 to October 2020. Three studies were conducted with paediatric participants only13,14 and16 and one study was conducted with adult and paediatric participants.15 There were different doses and durations in supplementing vitamin D among studies. One study reported that vitamin D supplementation did not significantly improve the severity of the disease,13 but the other three studies reported otherwise. This study only included AD participants with deficiency or insufficiency status of serum vitamin D. We summarized all studies including population, sample size, intervention, and mean difference outcome of both groups (Vitamin D and placebo groups). All outcomes listed as positive (p<0.05) or negative (p>0.05) are shown in Table 7.\n\nFour randomized controlled trials assessed the efficacy of vitamin D supplementation. The characteristics of the included studies are summarized in Table 6. Three studies measured the SCORAD indexes, whereas only one of the included studies assessed the efficacy of vitamin D supplementation by using EASI. One study used both adults and children as a participant, so we contacted the author to obtain the data associated with the children only. A meta-analysis of four trials showed that the SCORAD index and EASI score decreased significantly after vitamin D supplementation (standardized mean difference = -0.93, 95% CI = -1.76 to -0.11). We observed statistical heterogeneity among the studies (I2 > 25%; Figure 3). We also assessed the potency of the publication bias in those included studies with funnel plot and the result was symmetrical indicated that there was no potency of the publication bias in the four included studies.\n\nWe used the three studies that provided raw data so that the risk ratio of those studies could be measured. The forest plot (see Underlying data33) showed that statistically, there was no difference risk ratio between vitamin D group and placebo group (risk ratio =1.46 , 95% CI = 0.72 to 2.97). We observed statistical heterogeneity among the studies (I2 > 25%; Figure 4) so Random Effect Model was adopted.\n\n\nDiscussion\n\nVitamin D can modulate the innate immune system and also increases the phagocytic ability of immune cells and strengthens the barrier function of epithelial cells.6\n\nAn in vitro study reported that cathelicidin and defensin (which are antimicrobial-like peptides) increased after vitamin D supplementation.23 Another clinical trial also demonstrated that cathelicidin production could be increased and LL-37 expression could be induced by vitamin D supplementation. Thus, vitamin D could increase antimicrobial activity and external tolerability against pathogens.24\n\nVitamin D stimulates the production and regulation of skin antimicrobial peptides, such as cathelicidins which exert direct antimicrobial activity and induce host cellular responses to produce cytokine release, inflammation, and angiogenesis, thus, based on the above theory, vitamin D deficiency may predispose to secondary infection in AD patients.25 This is following what was reported by Haridas, Udompataikul et al. who found a reduction in S. aureus colonization in a paediatric population, as well as Rahmawati et al, who have reported that there was a significant difference in the reduction of S. aureus colonization after vitamin D3 supplementation in children with AD Refs. 26 and 27.\n\nThis theory is following the results of the meta-analysis of our forest plot. Our findings showed a statistically significant difference between the vitamin D supplementation group and the placebo group. In our study, we found high heterogeneity and we assumed that it was caused by variation of the doses and duration. The meta-analysis published by Kim in 201628 reported the same results but for the paediatric and adult population, as well as the meta-analysis reported by Haridas in 2018. To our knowledge, our study is the first one that reported vitamin D supplementation efficacy only in children population with AD as the meta-analysis.\n\nThe outcome of cure rate is one of the risk ratio, wherein this study the risk ratio calculated is the comparison of the probability of recovered participant between vitamin D and placebo. In the forest plot with risk ratio output, three squares were obtained, each represented 3 studies, with a weight of 45.4%; 48.6%, and 6%. All of these studies have heterogeneity above 50% and p-value <0.05 so that the forest plot used the Random Effect Model as seen from the heterogeneity test results and with the eyeball test. Diamond, the result of all studies is on the left side, with a pooled result of 1.46 (CI between 0.72 to 2.97) and touched the vertical line, which means that statistically, there was no difference in cure rate in the vitamin D group and the placebo group. Previously, there were no published meta-analysis with a forest plot with risk ratio outcomes so to our knowledge, our finding is the first meta-analysis with the risk ratio outcome, by point of interest “cure rate” in the experimental group compared to placebo.\n\nIn this study, the clinical significance could only be calculated from 3 studies that provided data on the proportion of subjects who recovered and did not recover or had persistent symptoms from the start of the study to the end. As a determination of the criteria for recovery, we had referred to a journal that mentioned MCID (Minimal Clinically Important Difference) in AD, MCID could be described as a clinical improvement that significantly along with reduction of SCORAD of 9 points and EASI by 6 points and IGA score reduced by 1 point.29 From Table 5, Figure 1 it can be calculated that the CER or incidence in the control group (placebo) was 38/86, which is 44%, means that 44% of cases were cured in the group of subjects who were given placebo and EER or the incidence in the experimental group was 61/91, which is equal to 67%, which means that 67% of cases of cure were found in the vitamin D group. ARR (Absolute risk reduction) in both groups was enabled by reducing CER and EER by 23%, and NNT (number needed to treat) was the amount subjects who must be treated at one time to prevent 1 adverse outcome. In these studies, NNT = 4.34 or required 5 subjects to be treated to prevent 1 unwanted event.\n\nIf toxicity occurs, there will be an increase in 25(OH) D levels which can trigger hypercalcemia by increasing calcium absorption and bone resorption. Hypercalcemia can lead to hypercalciuria, and persistently elevated calcium levels can lead to polyuria and dehydration.30 Vitamin D toxicity is caused by hypercalcemia, which is described by the appearance of symptoms in several organs that can be involved, such as the central nervous system (lethargy, apathy, depression to coma), heart and blood vessels (hypertension, heart rhythm disturbances), gastrointestinal (vomiting), recurrent abdominal pain, anorexia, constipation, and weight loss), and kidney (hypercalciuria is an early symptom, polyuria, polydipsia, nephrocalcinosis, up to life-threatening symptoms such as dehydration and kidney failure requiring haemodialysis).31 The diagnosis of vitamin D toxicity was established based on a detailed examination and history of taking medication, as well as supporting examinations. Laboratory tests show suppression of parathyroid hormone, which results in increased levels of 1,25(OH)2D.32\n\nDose and duration among studies are not similar, and not all studies have observed vitamin D levels before and after supplementation so it has not been seen whether there is an increase in vitamin D levels that exceeds the limit, which could potentially cause signs of vitamin D toxicity in several organs.\n\nThe limitation of our study was that we did not perform sub-group analysis outcome according to the measuring scale and the severity of AD due to the limitations of the studies included, so that the result of our study should be used carefully.\n\nFurther trials with vitamin D3 with the same dose and duration, followed by observation of serum vitamin D levels as an evaluation of the occurrence of side effects.\n\n\nConclusions\n\nOur study has showed that statistically, vitamin D supplementation can improve the outcome of atopic dermatitis in children as assessed by SCORAD, EASI or IGA Score and clinically, vitamin D supplementation can increase the cure rate in AD patients. Observation of side effects and monitoring of 25(OH) D levels in AD patients are required as the toxicity can lead into morbidity. The recommendation of the proper dose of vitamin D supplementation cannot be determined yet because there were no studies with the same dose and duration of administration of the vitamin D supplementation.\n\n\nData availability\n\nFigshare: Data for Efficacy of vitamin D supplementation on the severity of atopic dermatitis in children: A systematic review and meta-analysis. https://doi.org/10.6084/m9.figshare.19091474.v2.33\n\nThis project contains the following underlying data:\n\n- Data untuk forest plot.xlsx (data underlying forest plot).\n\nFigshare: Data for Efficacy of vitamin D supplementation on the severity of atopic dermatitis in children: A systematic review and meta-analysis. https://doi.org/10.6084/m9.figshare.19091474.v2.33\n\nThis project contains the following extended data:\n\n- Cochrane.jpeg (Cochrane search strategy).\n\n- PubMed.jpeg (PubMed search strategy).\n\n- ProQuest.jpeg (ProQuest search strategy).\n\n- PRISMA flowchart.pdf\n\nFigshare: PRISMA checklist for ‘Efficacy of vitamin D supplementation on the severity of atopic dermatitis in children: A systematic review and meta-analysis’. https://doi.org/10.6084/m9.figshare.19091474.v2.33\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgments\n\nAuthors wish to thank Dra. Judith Domínguez Cherit, Irene Lara-Corrales, MD, MSc and Dr. Nanda Earlia, Sp.KK for their support in completing our study.\n\n\nReferences\n\nKennedy K, Heimall J, Spergel JM: Advances in atopic dermatitis in 2017. J. Allergy Clin. Immunol. 2017; 142(6): 1740–1747. PubMed Abstract \| Publisher Full Text\n\nTsai TF, Rajagopalan M, Chu CY, et al.: Burden of atopic dermatitis in Asia. J. Dermatol. 2019 Oct; 46(10): 825–834. PubMed Abstract \| Publisher Full Text\n\nKim J, Kim BE, Leung DYM: Pathophysiology of atopic dermatitis: Clinical implications. Allergy Asthma Proc. 2019; 40(2): 84–92. PubMed Abstract \| Publisher Full Text\n\nBorzutzky A, Camargo CA Jr: Role of vitamin D in the pathogenesis and treatment of atopic dermatitis. Expert. Rev. Clin. Immunol. 2013; 9(8): 751–760. Publisher Full Text\n\nKim BE, Leung DYM: Significance of Skin Barrier Dysfunction in Atopic Dermatitis. Allergy, Asthma Immunol. Res. 2018; 10(3): 207–215. PubMed Abstract \| Publisher Full Text\n\nSassi F, Tamone C, D'Amelio P: Vitamin D: Nutrient, Hormone, and Immunomodulator. Nutrients. 2018; 10(11): 1656. PubMed Abstract \| Publisher Full Text\n\nMartens P-J, Gysemans C, Verstuyf A, et al.: Vitamin D’s Effect on Immune Function. Nutrients. 2020; 12(5): 1248. PubMed Abstract \| Publisher Full Text\n\nHattangdi-Haridas SR, Lanham-New SA, Wong WHS, et al.: Vitamin D Deficiency and Effects of Vitamin D Supplementation on Disease Severity in Patients with Atopic Dermatitis: A Systematic Review and Meta-Analysis in Adults and Children. Nutrients. 2019; 11(8): 1854. PubMed Abstract \| Publisher Full Text\n\nHuang CM, Lara-Corrales I, Pope E: Effects of Vitamin D levels and supplementation on atopic dermatitis: A systematic review. Pediatr. Dermatol. 2018; 35(6): 754–760. Publisher Full Text\n\nScragg R: Emerging Evidence of Thresholds for Beneficial Effects from Vitamin D Supplementation. Nutrients. 2018;3; 10(5): 561. PubMed Abstract \| Publisher Full Text\n\nLara-Corrales I, Bergman JN, Landells I, et al.: Approach to the Assessment and Management of Pediatric Patients With Atopic Dermatitis: A Consensus Document. Section I: Overview of Pediatric Atopic Dermatitis. J. Cutan. Med. Surg. 2019; 23(5_suppl): 3S–11S. PubMed Abstract \| Publisher Full Text\n\nRehal B, Armstrong A: Health Outcome Measures in Atopic Dermatitis: A Systematic Review of Trends in Disease Severity and Quality-of-LifeInstruments 1985–2010. PLoS One. 2011; 6(4): e17520. PubMed Abstract \| Publisher Full Text\n\nLara-Corrales I, Huang CM, Parkin PC, et al.: Vitamin D Level and Supplementation in Pediatric Atopic Dermatitis: A Randomized Controlled Trial. J. Cutan. Med. Surg. 2019; 23(1): 44–49. PubMed Abstract \| Publisher Full Text\n\nCamargo CA Jr, Ganmaa D, Sidbury R, et al.: Randomized trial of vitamin D supplementation for winter-related atopic dermatitis in children. J. Allergy Clin. Immunol. 2014; 134(4): 831–835.e1. Publisher Full Text\n\nSanchez-Armendáriz K, García-Gil A, Romero CA, et al.: Oral vitamin D3 5000 IU/day as an adjuvant in the treatment of atopic dermatitis: a randomized control trial. Int. J. Dermatol. 2018; 57(12): 1516–1520. PubMed Abstract \| Publisher Full Text\n\nEarlia N, Maulida M, Hidayati A, et al.: Pengaruh Pemberian Vitamin D Terhadap Perbaikan Gejala Klinis Pada Penderita Dermatitis Atopik Di Poliklinik Kulit Kelamin RSUD Dr. Zainoel Abidin Banda Aceh Tahun 2018: Uji Klinis Ketersamaran Ganda. J. Med. Sci. 2020; 1(1): 31–37.\n\nAltman DG, Higgins JPT: Assessing risk of bias in included studies. Higgins JPT, Green S, editors. Cochrane handbook for systematic reviews of intervention. London: John Wiley & sons; 2008; p. 196.\n\nStang A: Critical evaluation of the Newcastle-Ottawa scale for the assessment of the quality of nonrandomized studies in meta-analyses. Eur. J. Epidemiol. 2010; 25(9): 603–605. PubMed Abstract \| Publisher Full Text\n\nGalli E, Rocchi L, Carello R, et al.: Serum Vitamin D levels and Vitamin D supplementation do not correlate with the severity of chronic eczema in children. Eur Ann Allergy Clin Immunol. 2015; 47(2): 41–47. PubMed Abstract\n\nMansour NO, Mohamed AA, Hussein M, et al.: The impact of vitamin D supplementation as an adjuvant therapy on clinical outcomes in patients with severe atopic dermatitis: A randomized controlled trial. Pharmacol. Res. Perspect. 2020; 8(6): e00679. PubMed Abstract \| Publisher Full Text\n\nDi Filippo P, Scaparrotta A, Rapino D, et al.: Vitamin D Supplementation Modulates the Immune System and Improves Atopic Dermatitis in Children. Int. Arch. Allergy Immunol. 2015; 166: 91–96. PubMed Abstract \| Publisher Full Text\n\nRaj KAP, Handa S, Narang T, et al.: Correlation of serum vitamin D levels with severity of pediatric atopic dermatitis and the impact of vitamin D supplementation on treatment outcomes [published online ahead of print, 2020 Oct 12]. J. Dermatolog. Treat. 2020: 1–4. PubMed Abstract \| Publisher Full Text\n\nWang TT, Nestel FP, Bourdeau V, et al.: Cutting edge: 1,25-dihydroxyvitamin D3 is a direct inducer of antimicrobial peptide gene expression. J. Immunol. 2004; 173: 2909–2912. PubMed Abstract \| Publisher Full Text\n\nLeung DY, Boguniewicz M, Howell MD, et al.: New insights into atopic dermatitis. J. Clin. Invest. 2004; 113(5): 651–657. PubMed Abstract \| Publisher Full Text\n\nUmar M, Sastry KS, Al Ali F, et al.: Vitamin D and the Pathophysiology of Inflammatory Skin Diseases. Skin Pharmacol. Physiol. 2018; 31(2): 74–86. PubMed Abstract \| Publisher Full Text\n\nUdompataikul M, Huajai S, Chalermchai T, et al.: The Effects of Oral Vitamin D Supplement on Atopic Dermatitis: A Clinical Trial with Staphylococcus aureus Colonization Determination. J. Med. Assoc. Thail. 2015; 98(9): S23–S30.\n\nRahmawati YW, Zulkarnain I, Listiawan MY, et al.: Pengaruh Vitamin D3 pada Dermatitis Atopik Anak di Indonesia. Berkala Ilmu Kesehatan Kulit dan Kelamin. 2019; 31(2): 123–129. Publisher Full Text\n\nKim MJ, Kim SN, Lee YW, et al.: Vitamin D Status and Efficacy of Vitamin D Supplementation in Atopic Dermatitis: A Systematic Review and Meta-Analysis. Nutrients. 2016; 8(12): 789. PubMed Abstract \| Publisher Full Text\n\nSchram ME, Spuls PI, Leeflang MMG, et al.: EASI, (objective) SCORAD and POEM for atopic eczema: responsiveness and minimal clinically important difference. Allergy. 2012; 67(1): 99–106. PubMed Abstract \| Publisher Full Text\n\nVogiatzi MG, Jacobson-Dickman E, DeBoer MD: Drugs, and Therapeutics Committee of The Pediatric Endocrine Society. Vitamin D supplementation and risk of toxicity in pediatrics: a review of current literature. J. Clin. Endocrinol. Metab. 2014; 99(4): 1132–1141. PubMed Abstract \| Publisher Full Text\n\nJain D, Manoj A, Patel G, et al.: Hypervitaminosis D: A Rare Pediatric Case Report. European J. Biomed. Pharm. 2019; 345(7): 66–67. Publisher Full Text\n\nMarcinowska-Suchowierska E, Kupisz-Urbańska M, Łukaszkiewicz J, et al.: Vitamin D Toxicity-A Clinical Perspective. Front. Endocrinol. (Lausanne). 2018; 9: 550. PubMed Abstract \| Publisher Full Text\n\nHidayati AN, Sawitri S, Sari DW, et al.: Data for Efficacy of vitamin D supplementation on the severity of atopic dermatitis in children: A systematic review and meta-analysis. figshare. Dataset. 2022. Publisher Full Text" }	[ { "id": "126213", "date": "21 Mar 2022", "name": "PRASETYADI MAWARDI", "expertise": [ "Reviewer Expertise dermatology and venereology" ], "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 provides optimal knowledge about the administration of vitamin D supplementation in children with atopic dermatitis. In this study, the results of a meta-analysis of 4 data included in the inclusion criteria had differences in the duration of vitamin D supplementation. Two data were given within a 3 month period, two data were provided within a 1 month period.\nHow do authors present their arguments? Although this has become part of the limitations of the study, it is not explained much in the discussion. Can researchers provide appropriate advice on dosing and duration of treatment with vitamin D supplementation? Vitamin D supplementation in children remains to be understood as an adjuvant therapy. The absence of an adequate dose of vitamin D supplementation should be a consideration for clinicians. It is known that in atopic dermatitis there is a filagrin mutation that causes the stratum corneum barrier system to not function properly and there is a second defect in tight junction abnormalities. Even though we know that an excessive increase in vitamin D levels will have a negative impact on the function of filagrin as the main barrier in patients with atopic dermatitis.\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": "8013", "date": "28 Mar 2022", "name": "Afif Nurul Hidayati", "role": "Author Response", "response": "Dear Dr. Mawardi, We would like to firstly express our gratitude for having our manuscript reviewed thoroughly, and we would like to thank you for the helpful advice. Currently, there is no guideline for recommended dose and duration of vitamin D administration that can be given to patients. However, in several studies, it is stated that patients with AD have low serum vitamin D levels, so some doctors use the dosage recommendations from the AAP (American Association of Pediatrics) and several health organizations. In children aged 0-6 months, the maintenance dose for vitamin D administration is 400 IU with an upper limit of 2000 IU/day if including patients at risk of vitamin D deficiency. The largest group of children aged 11-18 years is recommended to give a dose of vitamin D 400 IU by the AAP and 600-1000 IU by the Endocrine society and 4000 IU at the upper limit dose. Therapeutic doses in patients with vitamin D deficiency or insufficiency range from 1000 IU to more than 5000 IU per day, according to age group." } ] }, { "id": "126212", "date": "24 May 2023", "name": "Windy Keumala Budianti", "expertise": [ "Reviewer Expertise Dermatology and Venereology", "Allergy and Immunology", "Dermatosis occupational." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nVitamin D is a therapy that is often used in several inflammatory skin diseases because it has an immunomodulatory effect. One of the diseases is atopic dermatitis (AD), which in children is a problem that is often faced by dermatologists. The cause of AD is based on the disruption of the skin barrier and impaired regulation of the immune response. However, there are still few evidence-based studies on the benefits or efficacy of vitamin D. The authors attempted to conduct a systematic review and meta-analysis with the aim of studying the effectiveness of vitamin D in pediatric atopic dermatitis using several validated measures, such as SCORAD, EASI, and IGA.\nI appreciate the work the authors have done, but there are a few things that might be added to this article.\nAt the introduction, the prevalence of AD in children was presented, it might be better if data were added on the prevalence of vitamin D deficiency or insufficiency in atopic dermatitis in children, which is a risk factor for AD.\n\nThe method used starts from a literature search, determining eligible criteria for inclusion and exclusion, data extraction and quality analysis, and statistical analysis using Revman version 5.4.1. is already good and clearly visible on the PRISMA flow chart.\n\nAs for the results, the data for the duration, dose and improvement of AD on vitamin D administration from the literature varied. The study of Earlia et al. showed that with vitamin D supplementation at a dose of 600 IU / day for 1 month of administration showed significant improvement compared to standard therapy alone. In contrast, the Lara-Corrales et al study using a dose of 2000 IU/day for 3 months did not significantly improve AD severity.\n\nMeta-analysis studies show that statistically vitamin D supplementation when compared with placebo improves the severity but not cure rate of atopic dermatitis.\n\nThe conclusion can be added regarding the results of the meta-analysis related to the risk ratio although the results are not statistically significant.\n\nIn the discussion section, it can be discussed more deeply about the literature included in the study other than the facts that are generally known.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [ { "c_id": "9711", "date": "30 May 2023", "name": "Afif Nurul Hidayati", "role": "Author Response", "response": "Dear Dr. Budianti, Firstly, we would like to thank you for having our manuscript reviewed thoroughly, and for the helpful advice. Based on our study, there were limitations of the data we used. Some of our literatures did not measure the level of Vitamin D in their subjects. Therefore, there was some studies showing improvement and otherwise did not show any significant improvement. For the conclusion sections, to our knowledge, the supplementation of Vitamin D in atopic dermatitis patients is one of therapy that offer improvement in disease severity in despite of the doses and duration. Thank you for the suggestions in your review Best regards, Afif Nurul Hidayati" } ] } ]	1	https://f1000research.com/articles/11-274
https://f1000research.com/articles/11-223/v1	24 Feb 22	{ "type": "Research Article", "title": "Emvolio - A battery operated portable refrigerator preserves biochemical and haematological integrity of biological samples in preclinical studies", "authors": [ "Swastika Maity", "Jaya Aakriti", "Suman Manandhar", "Sharad B Anchan", "Ashlesh Bhat", "Mayur U Shetty", "Yogendra Nayak", "Swastika Maity", "Jaya Aakriti", "Suman Manandhar", "Sharad B Anchan", "Ashlesh Bhat", "Mayur U Shetty" ], "abstract": "Background: Emvolio is a non-medical device, indigenously developed portable refrigeration for maintaining the internal temperature 2–8˚C. The Indian Patent Office has granted patent for applications such as preservation and transport of medicines, vaccines, food, beverages, dairy etc. Further, use of Emvolio can be utilized in transport and store biologicals to preserve their biochemical and cellular integrity. The objective of this study was to evaluate the biochemical and haematological integrity of biological samples such as rat blood, serum and liver. Methods: The steady temperature was maintained inside the Emvolio, and it was compared to that of thermocol and polypropylene boxes aided with frozen gel packs. The blood and liver samples were isolated from Wistar rats and kept in Emvolio, thermocol and polypropylene boxes for 10 hrs, and the temperature was monitored. The blood parameters, namely red blood cells (RBC), white blood cells (WBC), platelets, haematocrit, haemoglobin, mean corpuscular volume (MCV), mean corpuscular haemoglobin concentration (MCHC) and red cell distribution width (RDW), serum parameters like alanine transaminase, alkaline phosphatase, total protein, albumin, creatine kinase, blood urea nitrogen and liver parameters like superoxide dismutase (SOD), glutathione (GSH), catalase were estimated and compared. Results: Emvolio maintained a constant inner temperature range of 2–8˚C, whereas a significant temperature variation was seen in thermocol and polypropylene boxes. There was no significant deviation in the parameters tested when samples were kept in Emvolio for six hours compared to the zero hour readings. In contrast, there was a significant deviation among the parameters for the samples kept in thermocol and polypropylene boxes for six hours compared to zero hour parameters. Conclusions: Emvolio maintained constant temperature and preserved the biological integrity of rat blood, serum and liver. Thus, Emvolio can be efficiently used as a biological sample carrier, especially in preclinical studies.", "keywords": [ "Emvolio", "portable refrigerator", "biologicals", "storage", "transportation" ], "content": "Introduction\n\nCollection, storage and transportation of biologicals has become the chief investment by industry, academia and public research organizations1. Due to the highly sensitive nature of the biologicals to environmental conditions like heat and moisture, samples such as blood, serum, saliva, tissue, and organ samples are utilized in the hospital and medical industry to diagnose and experiment for preclinical or clinical studies2,3. The international agency for research on cancer (IARC) describe the storage conditions for different biologicals4. The guidelines for the transportation and preservation of biological products are as per the National Institute of Health (NIH), International Society for Biological and Environmental Repositories (ISBER)5, Center for Biologics Evaluation and Research (CBER), and Food and Drug Administration (FDA). The biological sample collection, storage, transportation and preservation includes multidisciplinary collaboration among experts in drug discovery, engineering, and other health professionals. The stocks for the use of biologicals in the health care sector is rising every day, especially in pharmaceutical sectors6. This condition has made the health care system rely on technology to ensure the maintenance of temperature. Over the past ten years, dependence on technology has increased for cold chain management7. Especially during the COVID-19 pandemic, the importance of cold-chain management became more prominent8. Generally, 2–8°C temperature is maintained by freezing, whereas for some products freezing should not be done. As per WHO guidelines, biologicals must not be frozen and should be transported and stored at 36–46°F (2–8°C). Particular reference to vaccines, ensuring compliance with temperature in all stages of storage and transport is a must. Researchers are using thermocol based units, polypropylene units, or insulated plastic containers extensively. The thermocol box and polypropylene chillers are the cheapest alternatives that researchers and hospitals can use to transfer biological and blood samples. But due to lack of adequate temperature control, unavailability of information of the sample inside without opening the box itself results in loss of effectiveness in transportation. Hence, technological advancement is required for maintaining the cold chain requirement of biologicals at their optimum level.\n\nEmvolio is a portable active cooling device developed by Blackfrog technologies Pvt Ltd, Manipal, India, for the transportation, delivery and storage of biologicals, especially medicines, vaccines, food, beverages, dairy etc. However, this can also be used to preserve and transport serum, blood and culture samples that are required to be kept strictly between 2–8°C (Figure 1). A 20 MAh rechargeable battery powers this portable device. This battery is roughly equivalent to a commercial cell phone battery. Emvolio device gives 100% accountability to ensure temperature and aims to replace the standard thermocol based carrier or polypropylene-based containers. This device can maintain 2–8°C for 10 hrs, have 1.5 L of capacity and weighs 5 kg. This technology supports rapid cooling and quick stabilization of temperature. It has 96% faster cooling capacity than ice-based technology in all weather conditions, and the device was tested by the company with operational capability at a temperature between –10°C to 43°C. Emvolio device works on a thermoelectric refrigeration principle and has an embedded temperature monitoring device controller, which helps in the dynamic temperature control feedback mechanism (Figure 2). Emvolio has been certified by the Directorate General of Health Services, Ministry of Health and Family Welfare and National Regulatory Authority (NRA), India, following the Central Drugs Standard Control Organisation (CDSCO) guidelines as a non-medical device. The manufacturing company Blackfrog Technologies, Pvt. Ltd., also owns a patent for the same (Indian patent no 201941013056).\n\nThe device has a cooling assembly made up of Peltier chips units. The cross-section of a simple Peltier effect based heat pump is presented in the figure. The blue side is the principal cooling mechanism known as the cold side, and the red as the hot side. Most Peltier chips have multiples of the structure in the figure in parallel to having higher power heat pumps. The device is linked with proportional–integral–derivative (PID) controller process to get accurate setpoint control and fast reaction to disturbance.\n\nThe current objective was to estimate whether Emvolio can maintain steady temperature control of 2–8°C in comparison with thermocol, polypropylene-based boxes supported by ice packs and room temperature conditions. The objective was also to identify deviation in blood, serum and organ biochemical parameters stored in Emvolio, thermocol based boxes, polypropylene-based boxes supported by ice packs and room temperature.\n\n\nMethods\n\nEmvolio was fully charged before the investigation. The gel pads were kept in a deep freezer for 24 hrs before the experiment. A temperature monitoring device, model RC-5 by Elitech, which follows the gold standard for monitoring thermal conductivity, was used. All four groups had their separate RC-5, Elitech devices for monitoring the temperature fluctuation. All three boxes were kept at room temperature. The RC-5, Elitech device was kept in Emvolio once it reached the temperature of 4°C as per the protocols set by the manufacturer. The RC-5, Elitech device was kept in the thermocol and polypropylene boxes 1 hr after keeping the gel pads as per the guidelines of cold chain management. The study was conducted forenoon 8.30–9 AM to 11.20–12 AM daily for seven days. Emvolio was charged after 9 hrs, and the gel pads were changed at 10 hrs. The data was collected each day after the experiment and analyzed.\n\nEmvolio and the other alternatives were validated by the use of Q-tag®. The Q-tag® is a range of WHO Performance Quality Safety (PQS) certified wireless temperature-sensors manufactured by Berlinger, a Swiss temperature monitoring solution company. Q-tag® is the gold standard for the cold chain monitoring system for biologicals and vaccines as per WHO.\n\n\nProcuring the rats and sample collection\n\nAll the applicable international, national and institutional guidelines for the care and use of animals were applied in the experiments. The experimental work was approved by IAEC (#IAEC/KMC/81/2019) of Manipal Academy of Higher Education (MAHE), and the experiments were carried out at the Central Animal Research Facility, Manipal, Karnataka, India (CPCSEA Reg no. 94/Po/ReBi/S/1999/CPCSEA). Rats were procured and acclimatized for seven days in 12 hrs light and dark cycle. Rats were fed with a standard pellet diet and water ad libitum. Each cage made up of polypropylene was used to cage two rats in each. The study was conducted as per the ARRIVE guidelines 2.0 using the ARRIVE Essential 10 checklist for pre-clinical animal studies9 and all efforts were made to ameliorate any suffering of animals during the experiments.\n\nThree months old female Wistar rats weighing 150–180 g were used for the study. The rats were sacrificed after anaesthetising with intraperitoneal ketamine and xylazine solution (9:1) solution. The blood was collected by cardiac puncture in small test tubes coated with anticoagulant 10% EDTA (Cat. No.: 10378-23-1; Sigma-Aldrich). EDTA 10% solution was made using Milli-Q water. Part of the blood was also collected in the Eppendorf tubes, and the serum was isolated after coagulation. The livers were perfused and isolated from the rat body. The samples of blood with anticoagulant, serum and liver were stored in a different container as per the following grouping. Each group contained n=6 female Wistar rats.\n\nGroup I: Emvolio (instrument for consideration)\n\nGroup II: Thermocol box padded with gel pads (common method for biological transfer in hospital and labs)\n\nGroup III: Polypropylene box with gel pads (common method for biological transfer in hospital and labs)\n\nGroup IV: Room temperature (control group)\n\nThe blood, serum and liver from each group of rats were stored in Emvolio, thermocol box, polypropylene box and room temperature. The storage at room temperature was kept as a control group for comparison (Figure 3). The biochemical data from the groups thermocol box, polypropylene box, room temperature and Emvolio groups were compared.\n\nContainers of four groups, namely A: Emvolio; B: Thermocol box and Polypropylene box; C: Room temperature for the study loaded with biologicals.\n\nThe RC-5, Elitech device was kept in Emvolio once it reached the temperature of 4°C as per the protocols set by the manufacturer Blackfrog technologies, Manipal. The RC-5, Elitech device was placed in the thermocol and polypropylene boxes to monitor the temperature fluctuations. Blood was collected in a test tube with 10% EDTA solution to avoid coagulation of blood10 and was kept in the respective group containers. The blood samples were tested at a time interval of 3 hr intervals, 0 hr, 3 hr and 6 hrs, using the Veterinary blood cell counter (PCE-210VET, ERMA Inc., Tokyo, Japan). The blood samples were tested for total red blood cells (RBC), white blood cells (WBC), platelet, haemoglobin (Hb), haematocrit, mean corpuscular volume (MCV), mean corpuscular haemoglobin concentration (MCHC) and red cell distribution width (RDW)11. The temperature of each box was noted after the biological sample analysis was completed.\n\nThe serum and organs were preserved in their respective labelled containers for further investigation. The serum enzymes were analyzed using kits from Agappe, Sigma, and Elabsciences in the Agappe UV auto-analyser. The following kits were procured to conduct the study: blood urea nitrogen kit (Cat. No. 11610002), alanine transaminase (ALT) (Cat. No: 11409005; 11409006), alkaline phosphatase (ALP) (Cat. No: 11401010), lactate dehydrogenase (LDH) (Cat. No: 12011015), serum creatinine (creatinine) (Cat. No: 11420002), albumin (ALB) (Cat. No: 12011002) and total protein (TP). Around 1.5 mL of blood was collected for each sample of individual groups and was centrifuged at 8,000 rpm for 10 min to collect the serum sample. The parameters selected for the serum analysis were reported to be highly temperature-sensitive standardized studies; so, selective parameters were analyzed to find out the temperature variation effect on the serum sample of each group12.\n\nThe liver sample was homogenized in 10% ice-cold KCl (150 mM) solution (Merck, Cat. No: 60142)13. The homogenate was then centrifuged at 8,000 rpm for 10 min, and the supernatant was separated and kept in their respective labelled container (Emvolio, thermocol box, polypropylene box and room temperature). The samples for the group room temperature were kept on a centrifuge tube stand. Organ parameters were performed by homogenization of the liver sample and estivation of its antioxidant property. Superoxide dismutase (SOD), glutathione (GSH) analysis was done using the fluorescent plate reader (FLx800, Biotek), and catalase were estimated using UV spectrophotometer (UV-1650pc TBS instrument). This experiment was carried out throughout 12 hrs. Each sample for both serum and organ analysis was performed over a time interval of 3 hrs to estimate the effect of temperature on the biologicals. Therefore, the samples were analyzed at 0 hr, 3 hr and 6 hrs for their biochemical estimation.\n\nStatistical analysis was done using two-way ANOVA in GraphPad Prism version 8.0 p<0.05 was considered a significant difference for the comparison of all the parameters. The calculations which were done in GraphPad Prism can be done in Microsoft Excel by adding the free extension Analysis ToolPak by Microsoft®.\n\n\nResults\n\nThe temperature recording done for 10 hrs over seven days in different cooling systems is represented in Figure 4. Constant maintenance of temperature within the range of 4–8°C was observed in the Emvolio cooling system kept at normal room temperature (30°C). Both gel-based cooling systems in the thermocol box and polypropylene box could not maintain the temperature in the 4–8°C range, and temperature fluctuations above 8°C was observed during the 10 hrs observation period. After the duration of the 4 hrs, in both polypropylene and thermocol boxes, an increase in the temperature from 8°C to 10°C was noticed. In contrast, the Emvolio cooling system maintained constant temperature (4–8°C) without significant deviations throughout the study duration.\n\nTable 1 represents the changes observed in the blood cell concentrations analyzed in the blood samples stored at different storage systems. For the complete blood count analysis the blood parameters like RBC count, haemoglobin, haematocrit, WBC, MCV, MCHC, RDW were analyzed9. It was observed that at 6 hrs, RBC, haemoglobin and haematocrit values in the samples showed significant differences compared to 0 hrs. But WBC, MCV, MCHC and RDW did not produce any statistical changes compared to 6 hrs. The samples stored in the polypropylene box showed significant differences in the RBC and haemoglobin after 3 hrs and 6 hrs of storage. There was no significant change in WBC, MCV, MCHC and RDW during the observed duration. The samples stored in gel pad aided cooling in thermocol box showed a significant difference in the RBC after 3 hrs and 6 hrs of the sample storage (Table 1). The samples stored at room temperature showed a significant increase in the RBC count, haematocrit after 3 hrs of storage, and a significant increase in RBC, haemoglobin, haematocrit, and MCV level 6 hrs after the storage. This signifies the effect of the storage temperature on the blood cell count.\n\nData are represented as Mean ± SD, n=6. * represents p<0.05, p<0.01, * p<0.001, **** p<0.0001 as compared with 0 hr concentrations.\n\nAmong the estimated serum enzymatic parameters, only three parameters, namely alkaline phosphatase, total protein, and albumin, significantly varied with temperature increase. The serum samples stored at room temperature had increased alkaline phosphatase, total protein, and albumin after 6 hrs of collection compared to the 0 hr reading. However, no significant difference was observed in other estimated serum parameters during the observed duration. Serum alkaline phosphatase and total protein were significantly high in samples stored in thermocol box for 6 hrs. A significant change in the total protein was observed in the serum stored in thermocol box after 3 hrs. In contrast, other parameters had no significant changes during the storage condition. The serum stored in polypropylene box showed a significantly higher alkaline phosphatase and albumin after a 6 hr duration (Table 2). The samples stored in Emvolio with well-maintained temperature showed fewer fluctuations in the serum parameters. However, a significant change in the alkaline phosphatase was observed and the device was able to maintain a stable enzyme concentration in the stored samples for about 6 hrs.\n\nData are represented as Mean ± SD, n=6. * represents p<0.05, p<0.01, * p<0.001, **** p<0.0001 as compared with 0 hr concentrations.\n\nThe liver samples stored in the different storage boxes were homogenized and used to estimate the markers like SOD, GSH and catalase. There were no significant differences in liver catalase and GSH when stored in Emvolio for 6 hrs. In contrast, SOD had a few fluctuations. The samples stored in polypropylene boxes showed a significant difference in SOD after 3 hrs and 6 hrs of storage. A significantly higher SOD was observed in the samples stored in the thermocol box after 3 hrs and 6 hrs, and GSH and catalase after 6 hrs of storage. Samples kept at room temperature showed a significant increase in the SOD level after 3 hrs and 6 hrs; catalase after 6 hrs of storage (Table 3).\n\nData are represented as Mean ± SD, n=6. * represents p< 0.05, p<0.01, * p<0.001, **** p<0.0001 as compared with 0 hr concentrations.\n\n\nDiscussion\n\nEmvolio is a precision refrigeration system with an inbuilt internet-of-things (IoT) element that aids in remote-monitoring of vital statistics such as adherence to 2–8°C. The study conducted aimed to evaluate Emvolio for its efficacy as a biological carrier. The data was compared against the conventionally used non-medical biological carriers, such as thermocol boxes and polypropylene boxes filled with gel-pads. Room temperature was kept as the control group for our data analysis. The temperature recording done for a period of 10 hrs (over seven days) in different cooling systems is represented in Figure 4. Constant temperature within the range of 4–8°C was maintained only in the Emvolio cooling system compared to other systems. Both gel-based cooling system in the thermocol box and polypropylene box did not maintain the steady temperature in the 4–8°C range, and fluctuations above 8°C were observed during the 10 hrs period. A sharp increase in the temperature from 8°C to 10°C was noticed in the polypropylene box and thermocol box after the 4 hrs duration.\n\nThe serum samples stored at room temperature showed a significant increase in alkaline phosphatase (p<0.001), total protein (p<0.01), and albumin (p<0.05) 6 hr after the collection. A significant change in the total protein (p<0.05) level was observed in the serum stored in thermocol box after 3 hrs. In contrast, other parameters had no significant changes during the storage condition. The serum stored in the polypropylene box showed a significant increase in alkaline phosphatase (p<0.01) and albumin (p<0.05) after 6 hrs duration. The samples stored in Emvolio with well-maintained temperature showed fewer serum fluctuations and maintained stable enzyme concentration in the stored samples for 6 hrs. The organs stored in the different storage boxes were homogenized and the antioxidant markers, like SOD, GSH and catalase, were estimated. The samples stored in Emvolio showed a significant increase in SOD concentration (p<0.001) after 6 hrs of storage and no significant changes in the other parameters. The samples stored in polypropylene box showed a significant increase in SOD after 3 hrs (p<0.01) and 6 hrs (p<0.0001) of the storage. A significant increase in the SOD was observed in the samples stored in the thermocol box after 3 hrs (p<0.05) and 6 hrs (p<0.01), GSH (p<0.0001) after 6 hrs and catalase (p<0.05) after the 6 hr duration. Samples kept at room temperature showed a significant increase in the SOD level both after 3 hrs (p<0.0001) and 6 hrs (p<0.0001); and catalase (p<0.05) after 6 hrs of storage. Therefore, it can be inferred that Emvolio maintained a constant temperature of 2–8°C throughout the study with minimum fluctuation. Hence, it comes closest to meeting the requirements laid out by the Drug and Cosmetics Act 1940 for a biological carrier. Therefore, Emvolio is a better alternative to maintain the integrity of biological samples.\n\nGel pads are widely used in the manufacturing and health care industry as coolants. It helps in the maintenance of temperature below the freezing point of the stored sample14. The gel pad weighs approximately 500 g/pack and contains a liquid cocktail of chemicals that dampen heat conduction of the cold pack, allowing the gel pack to retain the heat, in return keeping its surroundings cool for a more extended period. As per cold chain management guidelines, it is recommended for the use of biologicals. The gel pads need to be frozen 24 hrs before use to act as an aid for the biological carrier. These gel pads are used in traditional transporters such as thermocol boxes and polypropylene boxes. The thermocol boxes are made up of Styrofoam. The heat transfer from the outside environment/surroundings makes the thermocol boxes an efficient heat insulator. Generally, a thermocol box is loaded with gel packs for the biological transportation technique. This helps retain the coolness for a more extended period. Styrofoam with an extremely low density of 890–910 kg/m3, when packed in between two plastic walls of polypropylene box, the cooling effect will be better. Further, polypropylene is a low density, chemical resistant, non-corrosive, high temperature resistant biodegradable material. Hence, polypropylene boxes are widely used in the healthcare industry to carry biologicals.\n\nIn a developing nation like India, with a high population and a majority residing in rural areas, biological samples are regularly transported over long distances for diagnosis. Research has assessed temperature during vaccine transfers at various levels under the Universal Immunization Program in 21 districts of India - Bihar, Kerala, and Gujarat. A significant episode of sub-zero exposure was reported, and the study concluded that rigorous monitoring of temperature control is essential to ensure vaccines potency and efficacy15. Thus, the thought of a technical solution for this is dependent on the availability of continuous electricity for the refrigeration unit to maintain the pre-set temperature and provide a conducive environment to biologicals with special reference to vaccines. However, poor connectivity and erratic power supply had rendered this unviable, especially in the context of rural India16.\n\nIn Emvolio, the thermoelectric effect is the conversion of voltage difference to temperature difference and vice-versa. In a thermoelectric cooler, when a voltage difference is applied, a temperature difference is observed. The thermoelectric effect in it comprises three different outcomes: Peltier effect, Seebeck effect and Thomson effect. If a direct current is passed through the junction of two differently doped semiconductors, heat flux is generated, called a Peltier effect. This Peltier effect is used for the thermoelectric cooling and heating application17. Effectively this device is a heat pump moving heat from one side to the other when a current runs through it. The device has a thermoelectric cooler built around the Peltier chip to achieve cooling. In this system, two different heatsinks are attached to the hot side and the cold side to effectively release and absorb heat. To improve the heat exchange, on the heatsink, fans are mounted. Insulation foam is placed between the heatsinks around the Peltier chip to isolate the hot and cold heat sinks thermostatically. The main advantage of using a thermoelectric cooler over a compressor-based refrigerator is that it has no moving parts or circulating liquids. Further, the thermoelectric cooler is lightweight so makes a very compelling case for use in a portable system18, and a digital sensor in the cooling chamber is used for feedback. There are multiple ways to control the temperature of the chamber, Emvolio uses a method called proportional-integral-derivative (PID) controller. PID controller has been an industry standard due to its fast response, accurate setpoint control and fast reaction to disturbance19. In most cases, a traditional compressor-based refrigerator uses an on-off based controller, which creates an oscillation in the temperature20, which is not suitable for most biological samples. The PID controller consists of three different controllers in itself proportional, integral and differential. The proportional controller gives an output directly proportional to the error in the current temperature21. Due to limitations in the PID-controller a steady-state error in temperature may exist, which can be eliminated by an integral controller that sums up all the past errors to give a uniform output. The differential controller predicts the future behaviour of the temperature error and gives the output. Combining all these controllers into a PID controller and a digital sensor helps Emvolio maintain a strict temperature with an error of less than 0.5°C.\n\nBlood, plasma, and serum analysis are key diagnostic activities in preclinical studies and are also followed in most hospitals to identify health problems22. Healthcare has drifted from high facility hospitals, to easy and affordable clinics, to ultimately home services with easy accessibility. Hence, it is now crucial that technology and medicine/healthcare goes hand-in-hand for better efficacy and minimizing the chances of error23. This could help transform an untenable health system into a tenable one. This will further reduce the chances of personal and environmental error and provide a faster and cheaper method for diagnosing biological samples and organ transportation24. To upgrade healthcare with technology, Emvolio can be an aid that can make the patient the point of care. It has the ability to support the diagnostics of one’s health at home and transport the sample to their physician at a far-off laboratory. Emvolio can not only fill the gap of the lack of technology access in the rural area, but also can help the healthcare workers to get accurate sample data with minimum damage. Pharma-logistics, as well as academia, have suffered from a lack of reliable last-mile transport25. So, technical support is required to aid the healthcare sector in coping with the storage and transportation facility of biologicals. Our study showed that Emvolio could maintain a constant temperature, and the samples stored in Emvolio showed significantly less deflection in the parameters estimated compared to thermocol box and polypropylene box aided with pre-frozen gel pads. The thermocol box and polypropylene box showed deviation from the required temperature range after 0 hrs, and thus, it was observed that the biochemical parameters showed fluctuation by the end of 6 hrs. Therefore, there is a critical need to upgrade the transportation and storage facility with appropriate technological support. Emvolio can be adapted for the safe transport of most thermally-sensitive biologicals, and it can be an ideal solution to upgrade the cold chain management system. Thielmann et al., 2019 have carried out a study to verify the quality of vaccine refrigerator management, and they have followed the visual inspections of refrigerators used to store vaccines. As per their study, none of the practises fulfilled the quality criteria of standard practices. Important to them is the non-availability of temperature recording devices and logbooks26. Emvolio has inbuilt documentation and temperature recording system and can be used effectively.\n\nEmvolio can be used for samples and specimen transportation for pandemic diseases like COVID-19 and minimize the risk of false negatives arising due to thermally-degraded samples or contamination. Emvolio head cap (lid) seals the device completely. The cold chamber isolates the inside environment from the outer world by using dual-layered stainless steel chambers that maintain a vacuum. So, Emvolio is a much safer option for the transportation of COVID-19 samples with minimal risk of exposure or cross-contamination. The inner metal walls of Emvolio makes it easy for the user to sanitize the device after use, and no additional technical training is required to handle the device. Emvolio is an ideal solution to maintain the integrity of the COVID-19 samples and shows promising potential for effective last-mile transport. The future smart healthcare networks are expected to combine the 5G and IoT devices and use drones from transportations27,28. We propose that Emvolio has the adaptability for these technologies. Further, we propose cold chain management of biologicals with Emvolio, as depicted in Figure 5.\n\nThe villages or remote labs do not have direct access to analysis facilities; Emvolio can serve as a supporting aid to transport the sample by maintaining the desired temperature. Such technology will reduce the chances of degradation of the sample and have a higher accuracy rate.\n\n\nConclusion\n\nEmvolio maintains the constant internal temperature between 2–8°C, preserving rat blood, serum, and liver for six hours and maintaining biological integrity. Thus, Emvolio can be efficiently used as a biological sample carrier, especially in preclinical studies.\n\n\nData availability\n\nMendeley Data: ‘Effect of temperature on hematological and biochemical parameters when the biological sample from rats kept in room temperature, thermocol, polypropylene box and innovative portable refrigerator’ https://doi.org/10.17632/vgdm3299fp.2.9.\n\nThis project contains the following underlying data:\n\nTemperature effect – Comparison of Biochemical & Hematological parameter_v2.xlsx (Effect of temperature fluctuations on the haematological parameters such as total RBC, WBC, platelets, and haemoglobin, haematocrit, MCV, MCHC, RDW in the blood samples, serum parameters such as ALT, ALP, total protein, albumin, creatinine kinase, blood urea nitrogen, and biochemical parameters in liver such as catalase, SOD and GSH stored in different cooling systems).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nMendeley data: ARRIVE checklist for ‘Emvolio - A battery operated portable refrigerator preserves biochemical and haematological integrity of biological samples in preclinical studies’ https://doi.org/10.17632/vgdm3299fp.9.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgements\n\nAuthors acknowledge the Blackfrog Technologies Pvt. 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World J Gastroenterol. 2018; 24(30): 3361–73. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBunney PE, Zink AN, Holm AA, et al.: Orexin activation counteracts decreases in nonexercise activity thermogenesis (NEAT) caused by high-fat diet. Physiol Behav. 2017; 176(5): 139–48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBreslin M, Lam P, Murrell GA: Acute effects of cold therapy on knee skin surface temperature: gel pack versus ice bag. BMJ Open Sport Exerc Med. 2015; 1(1): e000037. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas MK, Arora NK, Mathew T, et al.: Temperature integrity and exposure of vaccines to suboptimal temperatures in cold chain devices at different levels in three states of India. Trop Dis Travel Med Vaccines. 2020; 6(1): 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMohan P, Kumar R: Strengthening primary care in rural India: Lessons from Indian and global evidence and experience. J Family Med Prim Care. 2019; 8(7): 2169–72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang J, Wang JB, Long ZY, et al.: Design and application of a cooling device based on peltier effect coupled with electrohydrodynamics. Int J Therm Sci. 2021; 162: 106761. Publisher Full Text\n\nGarrido J, Manzanares JA: Heat and work fluxes in thermoelectric coolers. Therm Sci Eng Prog. 2021; 22: 100817. Publisher Full Text\n\nHamid NHA, Kamal MM, Yahaya FH: Application of PID controller in controlling refrigerator temperature. In: 2009 5th International Colloquium on Signal Processing & Its Applications. Kuala Lumpur: IEEE; 2009; 378–84. Publisher Full Text\n\nYalawar MS, Challa MK, Yalawar S: Enhancing the Smart Refrigerator using the IoT. Int J Recent Technol Eng. 2019; 8(2S8): 1734–40. Publisher Full Text\n\nOkochi GS, Yao Y: A review of recent developments and technological advancements of variable-air-volume (VAV) air-conditioning systems. Renew Sustain Energy Rev. 2016; 59: 784–817. Publisher Full Text\n\nGillio-Meina C, Cepinskas G, Cecchini EL, et al.: Translational research in pediatrics II: blood collection, processing, shipping, and storage. Pediatrics. 2013; 131(4): 754–66. PubMed Abstract \| Publisher Full Text\n\nDyb K, Berntsen GR, Kvam L: Adopt, adapt, or abandon technology-supported person-centred care initiatives: healthcare providers' beliefs matter. BMC Health Serv Res. 2021; 21(1): 240. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKara-Junior N: Technology, teaching, and the future of ophthalmology and the ophthalmologist. Arq Bras Oftalmol. 2018; 81(3): V–VI. PubMed Abstract \| Publisher Full Text\n\nArgiyantari B, Simatupang TM, Hasan Basri M: Pharmaceutical supply chain transformation through application of the Lean principle: A literature review. J Ind Eng Manag. 2020; 13(3): 475. Publisher Full Text\n\nThielmann A, Puth MT, Weltermann B: Visual inspection of vaccine storage conditions in general practices: A study of 75 vaccine refrigerators. Pakhare AP, editor. PLoS One. 2019; 14(12): e0225764. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhad A, Tahir M, Yau KLA: 5G-Based Smart Healthcare Network: Architecture, Taxonomy, Challenges and Future Research Directions. IEEE Access. 2019; 7: 100747–62. Publisher Full Text\n\nZailani MAH, Sabudin RZAR, Rahman RA, et al.: Drone for medical products transportation in maternal healthcare: A systematic review and framework for future research. Medicine (Baltimore). 2020; 99(36): e21967. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "150286", "date": "06 Oct 2022", "name": "Ciro Aprea", "expertise": [ "Reviewer Expertise Applied thermodynamics", "Refrigeration" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title of the paper is \"A battery operated portable refrigerator preserves biochemical and haematological integrity of biological samples in preclinical studies\". In this paper the authors present a refrigerated system equipped with a Peltier module finalized to vaccine preservation in the range 2°C-8°C. The aim of their study is to obtain a system capable of maintaining the vaccine storage temperature when the system is picked up from a refrigerated space where it has been located to reach the correct storage temperature. The Peltier module can contribute to maintain the \"cold chain\".\nThe device presented is interesting but some aspects have to be evidenced.\n\nWhich is the autonomy of the battery of the refrigerator when the ambient temperature is of 32°C?\n\nAnd the autonomy of the battery when the refrigerator is opened and closed every hour for thirty seconds (simulation for withdraw the vaccine inside)\n\nIn this last case which is the time necessary for restore the correct temperature?\n\nIn this last case which is the maximum temperature reached with reference to the temperature set-point?\n\nThe temperature of 2°C-8°C are useful only for some vaccines. For Covid-19 the correct conservation temperature of some vaccines are also -20°C (Moderna for example).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "8943", "date": "19 Jan 2023", "name": "Yogendra Nayak", "role": "Author Response", "response": "Dear Ciro Aprea, We thank for your valuable questions and suggestions. Authors are obliged to the reviewer comments. Followings are the answers to your comments. Q1. Which is the autonomy of the battery of the refrigerator when the ambient temperature is of 32°C? Response: The product (Emvolio) has been tested and successfully passed the stringent WHO/PQS/E003/TS01.1 standard for a transportable, powered vaccine appliance. One of the primary requirements for the test is the autonomy of the battery for a minimum of 12 hours at extreme heat of 43°C ambient temperature. Please see the archived test reports at an independent WHO-accredited test facility wherein Emvolio ran for 13+ hours. Q2. And the autonomy of the battery when the refrigerator is opened and closed every hour for thirty seconds (simulation for withdraw the vaccine inside) Response: The autonomy during temperature excursions due to human interference is also captured in the above-mentioned report. Q3. In this last case which is the time necessary for restore the correct temperature? Response: We have conducted internal testing to determine the rate of temperature excursions and cool-down period due to human interference, i.e. opening/closing the lid. The results have also been contrasted against routinely used ice-based refrigeration systems. This report is also archived in a similar manner. Q4. In this last case which is the maximum temperature reached with reference to the temperature set-point? Response: The maximum temperature reached typically is dependent on the ambient temperature. We conducted our interference testing at 34°C, wherein the maximum temperature inside the cold chamber was between 9-11°C. Q5. The temperature of 2°C-8°C are useful only for some vaccines. For Covid-19 the correct conservation temperature of some vaccines are also -20°C (Moderna for example). Response: There is a popular misconception that since the Moderna vaccine requires -20°C and the Pfizer vaccine requires an even colder -80°C, it could be incompatible with typical vaccine carriers. These ultra-cold temperatures are meant for long-term storage and transport of the vaccines in the early parts of the supply chain. Incidentally, the Moderna vaccine is thermostable at 2-8°C up to 30 days, and the Pfizer vaccine is thermostable at 2-8°C up to 7 days as per the regulator’s data (For reference, click here for the report). This implies that regardless of their strict storage requirements, the last-mile transport will always be dependent on a 2-8°C cold chain, which Emvolio fulfils. Any vaccine, regardless of extreme storage temperatures, must be thawed before being administered to a recipient to avoid shock/injury. Once thawed, the vaccines cannot be refrozen again, which underlines the need for precision temperature control that other ice-based coolers fall short in. Further, we thank the reviewer for the input which made the reader a clear idea about the paper. Authors are obliged to the reviewer comments" } ] } ]	1	https://f1000research.com/articles/11-223
https://f1000research.com/articles/12-1190/v1	22 Sep 23	{ "type": "Study Protocol", "title": "Evaluating awareness of oral cancer and attitudes towards its screening practice in Vidarbha: A cross-sectional study", "authors": [ "Sweza Bhaisare", "Gaurav Mude", "Gaurav Mude" ], "abstract": "Background: In various parts of the country, oral cancer is a serious and rapidly growing issue. India has an elevated number of mouth cancer and is growing year after year. mouth cancer is a disease that can be avoided and is mostly affected by lifestyle habits such as chewing tobacco and smoking. Awareness concerning the risk factors, signs, and symptoms of mouth cancer may assist in the early detection and therapy of the condition, which will help in increasing the survival rate of the population. The purpose of this investigation is to estimate mouth cancer awareness in terms of symptoms, signs and causal factors, and information sources. Methods: A cross-sectional population-based questionnaire survey of randomly selected participants will be conducted among 381 participants however we will try to include a larger sample size in order to improve the precision in the Wardha district. The results will be analysed using appropriate statistical methods and a conclusion will be drawn on the basis of observation. This is a research protocol and this study aims to evaluate the awareness about oral cancer and attitude towards dental screening of oral cancer.", "keywords": [ "Oral Cancer", "Awareness", "dental screening", "knowledge", "Attitude", "condition", "detection", "educating" ], "content": "Introduction\n\nCancer is a scientific term for a large group of diseases that can affect any part of the body.1 The other term which can be used for it is malignant tumors and neoplasms. It can influence the different areas of the mouth such as the lips, mouth, and oral cavity. Cancer is the growth of abnormal cells throughout the body which can affect neighboring parts of the body and can develop into various organs which is referred to as metastasis. The prime source of death is widespread metastasis. In 2020, 10 million deaths have been reported, the most common were breast (2.26 million cases), lung (2.21 million cases), colon and rectum (1.93 million cases), prostate (1.41 million cases), and stomach cancer (1.09 million cases).1\n\nOral cancer is described as squamous cell carcinoma of the oropharynx, oral cavity, and lip. It is a major issue and particularly for dental surgeons. Each year 400,000 cases of mouth cancer are reported and most of them developed in Asian nations, such as Indonesia, Bangladesh, Pakistan, Sri Lanka, and India. Oral cavity and lip cancer was common in 2020 and has reported more than 377,700 cases and is the sixteenth most common cancer, the eleventh most common cancer in males, and the eighteenth usual cancer in females. The mouth cancer occurrence rate in 2020 in India was 219,722 and ASR (age-standardized rates) = 16.0 followed by women 45,347 and ASR of 6.7. Mouth and oral cancer mortality in 2020 were 121.096 and ASR = 8.9. followed by women at 26,399 and ASR = 3.9.2\n\nOral cancer is a life-threatening disease all over the world and has a very poor prognosis with a five-year survival rate. Its survival rate can improve by 80% if identified within early tiers (1 and 2 stages).3 50% of patients with oral cancer are diagnosed at the last stage (stages 3 and 4) as most patients do not seek medical attention until they discover signs such as bleeding, pain, or tumors in the oral area.4 Radiotherapy or concurrent chemotherapy is still a conventional treatment in oral cancer but has effects on the daily functionality of the oral cavity.5 When there is a diagnostic delay the chance of having last-stage oral cancer is remarkably higher.6 And the diagnostic delay is linked to low awareness of oral cancer among people and its symptoms and risk factors.7\n\nPoor compliance (25.7%) to oral cancer screening after the invitation has been linked to a possible lack of public awareness of this disease.8 So, the first step in which we can contribute in decreasing the occurrence of mouth cancer is by informing and educating the population on troubles relating to the known risk factors and dental screening. As the awareness about oral cancer study had not been concluded previously in our Wardha District. so here is our aim to appraise the awareness of oral cancer and attitudes toward screening practices for oral cancer among the rural and semi-urban population in district Wardha. With the help of its outcome, the health professional will try to educate and inform people about oral cancer which will help in reducing the incidence of mouth cancer in Wardha district (India).\n\n\nObjectives\n\n\n\n• To assess the awareness of mouth cancer and attitudes towards its screening practice for oral cancer among the ruler and semi-urban population in district Wardha.\n\n• To match their level of knowledge and attitude related to oral cancer based on their age, gender, and level of education.\n\n\nProtocol\n\nThe population used in this study is part of a larger population that can also be found in the upcoming article ‘Awareness regarding breast cancer among the female population in Wardha District’ (Shraddha Banmare, Gaurav Mude).\n\nStudy design: The observational cross-sectional study of awareness and attitude towards screening will be done by using a standardized questionnaire. A conceptual study of oral cancer and its awareness will be done. The study will be completed over a period of 4 months. Prior ethics committee permission has been obtained from the institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research. The standardized questionnaire is derived from previously published articles. After explaining the objectives of the study informed consent will be obtained from the volunteers who are willing to participate. The subject will complete the standardized questionnaire24 which includes a list of questions that will help in assessing the awareness of mouth cancer and attitudes toward its screening practice for oral cancer. The primary outcome will be assessing the awareness of mouth cancer and attitudes toward its screening practice in the Wardha district. The secondary outcome will be to match their level of knowledge and attitude related to oral cancer based on their age, gender, and level of education. The gathered information using a standardized questionnaire will be compiled and examined.\n\nCochran Formula for sample size:\n\nWhere,\n\nZ12 – α/2 = is the level of significance at 5% i.e., 95%\n\nP = Where aware of oral cancer = 55% = 0.55\n\nConfidence interval = 1.96\n\nE = 5% will be Error of Margin = 0.05\n\nn = 381.24\n\nn = 390 participants needed in the sample.\n\nThe study will however try to include a larger sample in order to improve its precision.\n\nRef. 9.\n\nTechniques of sampling: Simple random sampling will be used.\n\nInclusion criteria\n\nAge range\n\n• Subjects aged above 18 to 65.\n\nGender\n\n• Both male and female subjects will be included randomly.\n\n• Participants who are willing to participate after explaining the protocol.\n\nExclusion criteria\n\n• Participants who are not willing to participate after explaining the protocol.\n\nParticipants will be randomly assigned from the rural, semi-urban, and urban residential areas of Wardha district. Subjects will be recruited from various locations like hospitals, local institutions, homes, and from the campaigns in public spaces.\n\n\n\n• Instrument: the researchers prepared a structured questionnaire consisting of MCQs.\n\nSteps of data collection\n\nStep 1: Permission is obtained prior from the ethics committee for the data collection.\n\nStep 2: Introduction between the participants and the researcher.\n\nStep 3: The participants will be assigned by using a random sampling method.\n\nStep 4: ICF25 will be taken from the participants who are willing to participate, after explaining the study purpose.\n\nStep 5: A standardized questionnaire will be filled out by the subjects with the help of face-to-face interaction.\n\nExpected dates of data collection\n\nThe data will be collected from May 2023 to August 2023.\n\nExpected dates of recruitment\n\nThe first subject was recruited on the 1st of May and 390 participants will be recruited by the end of August 2023\n\nData analysis and statistical plan\n\nThe data will be analyzed according to socio-demographic and geographic factors and attitudes toward dental screening. Frequency percentage, mean, and SD will be calculated and, to understand the relationship between various demographic variables and knowledge, the chi-square test will be used. All the statistical analysis will be performed using SPSS Software, version 27.0 p < 0.05.\n\nDissemination\n\nOnce the study is completed it will be published in an indexed journal.\n\nStudy status\n\nThe study has started. The study has not been completed and no data analysis has been performed.\n\n\nDiscussion\n\nOral cancer can build at the lips, salivary glands, tongue, lining of the mouth, buccal area, and other locations. Many different habits such as drinking, smoking, chewing tobacco, Paan, and flavouring agents are used in high amounts in different parts of the country.10 Tobacco use is widespread among the residents and the community.11 Consuming alcohol and use of tobacco are regarded as the primary factor for the occurrence of mouth cancer.12 Snuff is the most widely used smokeless tobacco in Pakistan and sun and heat dried tobacco leaves, slaked lime, tree bark ash, and flavouring and colouring agents are used to make it.13 50% of oral cancers are thought to be caused by precursor lesions.14 Changes in the concentration of intrinsic fluorophores such as collagen, nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD), and porphyrin in human oral tissue mark the progression of oral mucosal lesions.15 Therefore, it’s important to do proper management and early detection of malignant lesions which helps in prevention.16\n\nGenetics also plays a crucial part in the development of cancer and a high chance of developing buccal mucosa and tongue cancer.17 However, it’s hard to link genetics or family with oral cancer as there is the existence of other causal factors such as chewing tobacco, etc. Some researchers believe that some people are vulnerable to developing oral cancer those who are born with the inability to metabolize carcinogens are unable to restore DNA damage.18 Chronic inflammation is also one of the vital parts in the occurrence of cancers such as the mouth and pharyngeal neoplasm. The main viruses involved in the growth of mouth cancer are HPV infection and human immunodeficiency virus (HIV). Human papillomavirus is a tiny virus with a circular double-stranded DNA genome of approximately 8 kb in size. HPV infection is the main causal factor for oropharyngeal squamous cell carcinoma caused by sexual activity. The prevalence peak was found in older people, especially in men showing a longer duration of infection at older ages.19\n\nHaving knowledge about the prior detection and sign and symptoms of oral cancer will assist human beings to diagnose early before getting to the higher stage of oral cancer. However, more than 30% of patients delay for extra three months prior to seeking medical attention for the signs and symptoms of oral cancer.20 The prevalent reason for the delay in seeking medical treatment for signs and symptoms of oral cancer has been reported as a lack of awareness about mouth cancer which leads to the misattribution of symptoms.21 Warnakalasuriya reported a need for awareness about oral cancer in the United Kingdom, as well as a lack of awareness about the prior signs and symptoms of the disease.22 In India Gorakhpur, the highest rate of awareness was observed among high school graduates and was low among the illiterates which pointed to further knowledge among Indian people about oral cancer.23\n\nOpportunistic screening for signs and symptoms among patients who receive dental routine care settings could aid in the early detection of oral cancer. Informing the patient that they are being screened for the early detection of oral cancer, especially the people who are at high risk could be an opportunity for the clinician to provide people with details about the existence, risk factors, sign and symptoms, and prevention of mouth cancer. The British Dental Association (BDA) recommends the patient must be informed that mouth cancer screening is being performed.8\n\nMinimum bias will occur as patients will be randomly selected based on the exclusion and inclusion criteria.\n\nThe studies involving human participants were reviewed and approved by the institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (Deemed to be University) Wardha – 442107, Maharashtra, India.\n\nRef. No. DMIHER (DU)/IEC/2023/593.\n\nThe study protocol will be explained to the participating subjects.\n\nFurther, a written informed consent form will be obtained from the participants.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: questionary for oral cancer awareness, https://zenodo.org/record/8005341. 24\n\nZenodo: English ICF and consent form, https://zenodo.org/record/8229957. 25\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe author would like to acknowledge the support from the Department of Clinical Research, DMIHER, AVBRH, Sawangi, Wardha, India.\n\n\nReferences\n\nCancer: Accessed: August 9, 2023. Reference Source\n\nMouth and oral cancer statistics. Reference Source\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\nSilverman S, Kerr AR, Epstein JB: Oral and Pharyngeal Cancer Control and Early Detection. J. Cancer Educ. 2010; 25: 279–281. PubMed Abstract \| Publisher Full Text \| Free Full Text .\n\nYuwanati M, Gondivkar S, Sarode SC, et al.: Oral Health-Related Quality of Life in Oral Cancer Patients: Systematic Review and Meta-Analysis. Future Oncol. 2021; 17(8): 979–990. Publisher Full Text .\n\nMcCullough M, Prasad G, Farah C: Oral mucosal malignancy and potentially malignant lesions: An update on the epidemiology, risk factors, diagnosis and management. Aust. Dent. J. 2010; 55(Suppl. 1): 61–65. PubMed Abstract \| Publisher Full Text .\n\nAbu-Serriah M, Critchlow H, Whitters CJ, et al.: Removal of partially erupted third molars using an Erbium (Er):YAG laser: a randomised controlled clinical trial. Br. J. Oral Maxillofac. Surg. 2004; 42: 203–208. PubMed Abstract \| Publisher Full Text\n\nJullien JA, Zakrzewska JM, Downer MC, et al.: Attendance and compliance at an oral cancer screening programme in general medical practice. Eur. J. Cancer (Oral Oncol). 1995; 31: 202–206. Publisher Full Text .\n\nBhat PK, Sushma SG, Jayachandra MY, et al.: Awareness about oral cancer among nonhealth professional students - A cross-sectional study in Bengaluru city. J. Oral Maxillofac. Pathol. JOMFP. 2020; 24: 492–498. Publisher Full Text\n\nGómez I, Seoane J, Varela-Centelles P, et al.: Is diagnostic delay related to advanced-stage oral cancer? A meta-analysis. Eur. J. Oral Sci. 2009; 117: 541–546. PubMed Abstract \| Publisher Full Text .\n\nGoyal A, Sharma A, Agarwal S, et al.: Determinants of Tobacco Use among Children of a Rural Village in India: An Exploratory Qualitative Study. Asian Pac. J. Cancer Prev. 2020; 21(1): 81–86. PubMed Abstract \| Publisher Full Text \| Free Full Text .\n\nHamada GS, Bos AJ, Kasuga H, et al.: Comparative epidemiology of oral cancer in Brazil and India. Tokai J. Exp. Clin. Med. 1991; 16: 63–72. PubMed Abstract\n\nZahir R, Khan ZA, Aleem B, et al.: Association of High Immunohistochemical Expression of Minichromosome Maintenance 3 with Human Oral Squamous Cell Carcinoma—A Preliminary Study. Diagnostics. 2023; 13: 13. Publisher Full Text\n\nJensen K, Afroze S, Munshi MK, et al.: Mechanisms for nicotine in the development and progression of gastrointestinal cancers. Transl. Gastroint. Cancer. 2012; 1: 81–87.\n\nSah AN, Kumar P, Pradhan A: In-vivo Testing of Oral Mucosal Lesions with an In-house Developed Portable Imaging Device and Comparison with Spectroscopy Results. J. Fluoresc. 2023; 33: 1375–1383. Publisher Full Text .\n\nSathiasekar AC, Mathew DG, Jaish Lal MS, et al.: Oral field cancerization and its clinical implications in the management in potentially malignant disorders. J. Pharm. Bioallied Sci. 2017; 9(Suppl 1): S23–S25. PubMed Abstract \| Publisher Full Text .\n\nIrani S: miRNAs signature in head and neck squamous cell carcinoma metastasis: A literature review. J. Dent (Shiraz, Iran). 2016; 17: 71–83.\n\nKim KM, Kim YM, Shim YS, et al.: Epidemiologic survey of head and neck cancers in Korea. J. Korean Med. Sci. 2003; 18: 80–87. Publisher Full Text .\n\nShivappa N, Hebert JR, Rosato V, et al.: Inflammatory potential of diet and risk of oral and pharyngeal cancer in a large case-control study from Italy. Int. J. Cancer. 2017; 141: 471–479. PubMed Abstract \| Publisher Full Text \| Free Full Text .\n\nShigeishi H, Sugiyama M: Risk factors for oral human papillomavirus infection in healthy individuals: A systematic review and meta-analysis. J. Clin. Med. Res. 2016; 8: 721–729. PubMed Abstract \| Publisher Full Text \| Free Full Text .\n\nScott SE, Grunfeld EA, Mcgurk M: Patient’s delay in oral cancer: a systematic review. Community Dent. Oral Epidemiol. 2006; 34: 337–343. PubMed Abstract \| Publisher Full Text .\n\nSpeight PM, Palmer S, Moles DR, et al.: The cost-effectiveness of screening for oral cancer in primary care. Health Technol. Assess. 2006; 10: 1–144. Publisher Full Text .\n\nAgrawal M, Pandey S, Jain S, et al.: Oral Cancer Awareness of the General Public in Gorakhpur City, India. Asian Pac. J. Cancer Prev. 2012; 13: 5195–5199. PubMed Abstract \| Publisher Full Text .\n\nBhaisare S, Mude G: Questionary-Sweza bhaisare (Version V1). Zenodo. 2023. Publisher Full Text\n\nBhaisare SS, Mude G: English Informed consent form (Version V1). Zenodo. 2023. Publisher Full Text" }	[ { "id": "246824", "date": "26 Feb 2024", "name": "Mohammad Daud Ali", "expertise": [ "Reviewer Expertise Pharmacy practice and clinical pharmacy." ], "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\nKindly write the rationale of the study in the last paragraph separately Kindly align the introduction with the study's primary and secondary objectives.\n\nKindly add the identification of the study population. How survey tools kindly were designed. Kindly describe the questionnaire/Tools validation description. Kindly add an ethical approval number under the heading Ethical consideration Kindly add the study site Kindly add study participants' inclusion and exclusion criteria How invited the study participants. How to minimize study participants' biasing How is sample size calculated kindly add in the manuscript under methods Kindly add how data is collected as well as how study participants are enrolled in the study for data collection. How was the survey conducted through a hard copy of the questionnaire or online?\nOthers\nKindly add study limitations.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] }, { "id": "252600", "date": "02 May 2024", "name": "Derk Hendrik Jan Jager", "expertise": [ "Reviewer Expertise Knowledge and attitudes of oral health students and professionals related to HPV-related oropharyngeal cancer", "Sjogren's syndrome", "Hyposalivation" ], "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: - Name in which country the research will take place. Readers may not know where Vidarbha is.\nOverall - Try to adhere to the SPIRIT guidelines and checklist. See here: https://www.equator-network.org/reporting-guidelines/spirit-2013-statement-defining-standard-protocol-items-for-clinical-trials/\nAbstract: - Mouth cancer and oral cancer are used both. I would like to recommend using oral cancer. - Name in which country the Wardha district is located. Furthermore, it is confusing that a different name is used in the title (Vidarbha).\nIntroduction - Second paragraph: the definition of Oral cancer is incorrect. Carcinoma of the oropharynx does not fall under oral cancer but under Oropharyngeal squamous cell carcinoma (OPSCC). So it is better to use the following division: Oral Cancer (OC)/Oral Squamous Cell carcinoma (OSCC): oral cavity and lip Oropharyngeal squamous cell carcinoma (OPSCC): oropharynx - It is preferable not to use “mouth cancer” but use OC/OSCC. See above - A prevalence of 400,000 new cases per year is mentioned. In which countries/region? Does this only concern oral cancer (OC) or also OPSCC? Or even Head and Neck cancer? Please clarify. - “The mouth cancer occurrence rate in 2020 in India was 219,722 and ASR (age-standardized rates) = 16.0 followed by women 45,347 and ASR of 6.7. Mouth and oral cancer mortality in 2020 were 121,096 and ASR = 8.9. followed by women at 26,399 and ASR = 3.9”. This sentence is unclear. Explain better to the reader what ASR is. Rewrites this sentence. Do not use a “=” sign in the sentence. Why are both “mouth” and “oral” cancer used here? What's the difference? - “Oral cancer is a life-threatening disease all over the world and has a very poor prognosis with a five-year survival rate.” What is the 5-year survival rate? - Explain “stages 1 to 4”. - “As the awareness about oral cancer study had not been concluded previously in our Wardha District. so here is our aim to appreciate the awareness of oral cancer and attitudes toward screening practices for oral cancer among the rural and semi urban population in Wardha district”. Please rewrite this sentence. Furthermore, the objectives are also mentioned in the next paragraph.\nObjectives: - The 2nd objective is not clear to me. Match to what?\nProtocol: - Sample size and selection of subjects: please transform these to a narrative form. - MCQs: please write this abbreviation in full - Please use a narrative way of presenting the protocol - Exclusion: is a history of cancer an exclusion criterion? What are the in/exclusion criteria?\nDiscussion: - “oral cancer can build” Please rewrite - What is Paan? - Much attention is paid in the Discussion to the possible causes of OC and OPSCC. This has only limited relevance for this study. Nothing is said about possible pitfalls or other complicating matters when conducting the study. Also discuss expected outcomes.\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": [] } ]	1	https://f1000research.com/articles/12-1190
https://f1000research.com/articles/12-128/v1	02 Feb 23	{ "type": "Research Article", "title": "Performance of home-based self-tonometry (iCare HOME (TA022)) for measuring intraocular pressure among healthy and glaucoma patients", "authors": [ "Anush Nayak", "S Ve Ramesh", "Neetha I R Kuzhuppilly", "Vijaya H Pai", "Aditya Chaitanya", "Anush Nayak", "S Ve Ramesh", "Neetha I R Kuzhuppilly", "Vijaya H Pai" ], "abstract": "Introduction: The purpose of this study was to compare iCare HOME (TA022) with Goldmann applanation tonometer and to evaluate the self-tonometry measurements among the Indian population. Methods: Eligible patients underwent iCare HOME training through guided demonstration (verbal, pictorial, video) and practised self-tonometry measures using iCare HOME. Certification for independent iCare HOME measure was provided if first iCare HOME intraocular pressure (IOP) measurement fell within ± 5 mmHg of Goldmann applanation tonometer (GAT) measurement which was measured by the trained clinician (principal investigator). Certified participants underwent simulated home self-tonometry measurements using iCare HOME, and agreement with GAT IOP measurements was assessed. Results: Seven of 83 participants (8.43%) failed to complete the study due to difficulty in performing the task, leading to non-certification. Patients who could use the iCare HOME had a mean age of 53 ± 15.55years (53% males; 46% females). Only one in 12 subjects did not qualify to use iCare HOME. The overall mean difference between iCare HOME and GAT was 0.83 mmHg (95%, 3.92 and -2.25). At various pressure ranges, 7-16 mmHg, 17-23 mmHg and >23 mmHg, the mean difference between iCare HOME and GAT was 1.22 mmHg (95%, 4.32 and -1.86), 0.77 mmHg (95%,3.69 and -2.19), -0.11 mmHg (95%, 2.52 and -2.74) respectively. The intra-class correlation coefficient of the iCare HOME device was 0.997(95% CI,0.995-0.998). Conclusions: Patients were able to perform self- tonometry using iCare HOME with good reliability and safety. iCare HOME can be used to address the issue of difficulty in acquiring frequent and diurnal IOP measurements by patients doing self-tonometry from home.", "keywords": [ "Intraocular pressure", "Glaucoma", "Goldmann applanation tonometry", "iCare HOME" ], "content": "Introduction\n\nTraditionally, intraocular ocular pressure (IOP) management through various medical and surgical procedures is the key factor in controlling the progression of glaucoma. IOP is not constant throughout the day but is subject to change based on the circadian rhythm of the body and other pathological factors. Therefore, managing the IOP of the patient based on a single IOP measurement from one day every four to six months is not effective in controlling the progression of glaucoma. In routine clinical practice, setting a predetermined target for maximum and range of IOP based on diurnal variation test is the key part of management for stabilizing and delaying progression of glaucoma.1–3 Continuous measurement of IOP using Goldmann applanation tonometry (GAT) is deferred because of factors like invasive procedures, need for inpatient registration, time requirements, lack of comfort, and required specialized skills and manpower. iCare TA01i rebound tonometer (RBT) (iCare Oy, Vanda, Finland), which works based on the impact-induction principle, is simple to use, and doesn’t require anesthetic drops and slit lamp use.4 However, it was developed for a trained professional and not for self-use by patients. The iCare HOME tonometer (TA022; iCare Oy) designed for self-use by patients at home and for regular monitoring of IOP measurements as well as automatic recording of those readings.\n\nRecent guidelines on post-coronavirus disease 2019 (COVID-19) glaucoma care recommend the use of a rebound tonometer as the best IOP measuring device considering patient safety and reduced contamination risks. Since glaucoma patients fall in the age group that is high-risk for COVID-19 infection, reducing their visits to the hospital only for IOP measurements is warranted. iCare HOME has a great potential for in-home self-monitoring of IOP, and demonstrating its usability in the Indian population is important.\n\nThis study aimed to investigate the agreement of IOP measurements between self-measurement with an iCare HOME tonometer and Goldmann applanation tonometry, and to assess the precision and feasibility of the iCare HOME tonometer compared to the Goldmann applanation tonometer among the Indian population.\n\n\nMethods\n\nThe study was performed at the Department of Ophthalmology, Kasturba hospital, Manipal Academy Higher Education, Manipal, from August 2018 to April 2019. All patients underwent routine comprehensive ocular examination including visual field testing and ultrasound pachymetry. Patients with central corneal thickness (CCT) between 450 to 620 μm were included and pachymetry was performed at the end of the study. Palpebral fissure height (PFH) and Hertel exophthalmometry were also measured at the beginning of the study. Patients with near visual acuity lower than 20/200 (binocular), one functional eye and having poor or eccentric fixation were excluded. We also excluded patients with hearing impairment to the extent that the individual cannot hear and converse with others without an assistive aid and/or sign language, as well as patients with inability to demonstrate proficiency with the iCare HOME tonometer after training and failure to complete certification procedures described in the protocol. Patients with any kind of corneal pathologies, disabling arthritis or limited motor coordination limiting self-handling of the iCare HOME tonometer and any history of glaucoma filtering surgery, as well as cataract extraction from subjects’ eyes within the previous two months were excluded. Written informed consent was obtained from all the eligible patients after an explanation of the nature and consequences of this study, and told they could withdraw from the study at any time. Ethical approval was obtained from the Kasturba Hospital Institutional ethics committee (IEC:137/2018). The study was conducted following the Declaration of Helsinki and the ICH-GCP (E6 R1) guidelines. The study was registered in clinical trial registry India (CTRI number CTRI/2018/07/014818).\n\nEnrolled patients underwent baseline slit-lamp examination and corneal staining grading (Oxford) using a fluorescein strip to review the corneal health. This was followed by iCare HOME tonometer training and certification. Patients were given verbal, pictorial and video instructions explaining the use of iCare HOME tonometer then the principal investigators (AN or AC) demonstrated the use of the device for self-tonometry on himself. After the detailed demonstration, patients were asked to perform the self-tonometry using the iCare HOME in the chosen study eye. The eye meeting the eligibility criteria was included in the study. If two eyes were eligible, the eye with high IOP on baseline screening was included. A new disposable probe was used for each patient. During the training session, investigator supervised the patients to provide feedback and required instructions to enhance the performance. The training session was followed by the certification procedure, which involved five self-tonometry measurements by the patients and one GAT measurement by an investigator. As part of the certification process, the investigator silently observed the patients’ performance in handling and positioning of the device without any instructions to ensure the competency of the patient to do self IOP measurements. Later, corneal stain grading was performed and IOP measurement was obtained using fluorescein strip and GAT by an investigator. To get the certification, apart from good handling and positioning, the average of the five self-tonometry measurements obtained by the patient using iCare HOME had to be within 5 mmHg of the measurement using GAT; the range of the five iCare HOME values obtained by the patient also had to be less than or equal to 7 mmHg. After the training and certification procedure, a safety assessment was done by clinical observations of corneal epithelial staining and the patient’s discomfort or any other complications during the procedure was noted to rule out further complications.\n\nOnce the patients were certified for the use of iCare HOME, they were given a 20-minute break. Then, patients were instructed to take five self-tonometry measurements using the iCare HOME independently under simulated home-based environment beginning from device setup, loading the probe, and positioning the device without any direct supervision. The number of attempts required to achieve five successful measurements was recorded for each patient in this home-simulated phase. Patients had to decide whether the measurements obtained from the device were correct or not based on the inbuilt device feedback. A maximum of ten attempts was allowed for each patient to get five successful measurements and patients were excluded from the study if they failed to do so. All successful IOP measurements obtained from the device were stored in memory. Unlike other iCare tonometers, iCare HOME does not display the measured IOP, which helps in reducing the bias. Therefore, both patient and investigator knew the patient's measurements at the end of the study once the device was connected to the computer with installed iCare software. After the five successful IOP measurements were obtained from the iCare HOME, each patient underwent GAT apart from corneal stain grading. The calibration of the GAT device was checked every day of the study before the test patients were recruited. Five GAT measurements were obtained from each patient by the investigator and an average of those five measurements was used. Later, corneal thickness was measured for each patient using pachymetry. Both bi-prism used for IOP measurements and pachymetry probe used for corneal thickness measurements were disinfected every time, using alcohol swabs before and after the measurements obtained from the patients to avoid possible infections. At the end of the study, slit lamp examination was repeated and fluorescein grading was done to assess the health of the corneal epithelium. Patients’ complaints of discomfort or any other complications during the procedure were also recorded to assess any possible adverse effect.\n\nThe Oxford grading scale was used to grade corneal staining after the certification procedure and at the end of the study.5 Patient discomfort was graded with the help of a visual analogue scale (VAS).6 Patients were asked to mark the VAS scale based on the discomfort. The scoring was measured with the help of a ruler and was converted into a percentage. Discomfort scoring from 1 to 30 % was graded as 1, 31 to 60 % was graded as 2 and a score higher than 61% was graded as 3. By the end of the study, participants were classified into different eye pressure: 7 to 16 mm Hg, 17 to 22 mm Hg and > 23 mm Hg.\n\nData were recorded in Microsoft Excel 2016 and analyzed using IBM Statistical Package for the Social Sciences (SPSS) software version 20.0. The Shapiro-Wilk test and Kolmogorov-Smirnov test was used to check the normality of the outcome variables. An independent t-test was used to check the significance of age and central corneal thickness; a Chi-square test was used for gender, study eye and handedness to check the significance between participants who were and were not able to perform iCare HOME. A Bland-Altman plot was used to determine the agreement and Spearman’s ρ correlation coefficient was used to calculate the correlation between iCare HOME and GAT. PFH and exophthalmometric values were analyzed using the Mann Whitney U test as the variables were not normally distributed.\n\n\nResults\n\nA total of 83 patients agreed to participate and were recruited for the study. Seven of 83 patients (8.43%) failed to complete the study; four of 83 participants (4.82%) were excluded during simulated home measurements as the number of attempts to achieve five successful measurements were more than 10; two of 83 participants (2.41%) were excluded because self-measured IOP did not agree within 5 mmHg of GAT measurements during certification, and one of 83 participants (1.20%) stopped because of difficulty in using the iCare HOME device during the certification process.\n\nA total of 76 patients completed the study and were included in the final data analysis. The mean age of the participants was 53.12 ± 15.55 years, and the percentage of males and females were 53% and 47% respectively. The majority of the study was done in the right eye 70% and 76% of the participants were right-handed (Table 1).\n\n* Independent –t-test was used for Age, central corneal thickness (CCT), Number of iCare attempts and practicing iCare HOME\n\n* Chi-square test was used for gender, handedness and study eye\n\nFor 75 of 76 participants (98.6%) iCare HOME measurements agreed within 5 mmHg of GAT. one participant (1.32%) had a difference of more than 5 mmHg of GAT. The overall mean difference between iCare HOME and GAT measurement was 0.83 mmHg with 95% limits of agreement (LOA) between 3.92 and -2.25. Figure 1 shows the Bland-Altman plot of the agreement between iCare HOME and GAT measurements of the patients.\n\nAgreement between iCare HOME and GAT was also assessed at various pressure ranges. At lower IOP (7-16 mmHg) the mean difference between iCare HOME and GAT was 1.22 mmHg with 95% LOA between 4.32 and -1.86. iCare HOME underestimated IOP by more than 5 mmHg in one of 39 participants (2.56%). At the middle IOP range (17-23 mmHg) all the measurements agreed within 5 mmHg with a mean difference of 0.77 mmHg with 95% limits of agreement between 3.69 and -2.19. At a higher IOP range (>23 mmHg) there was a slight overestimation of IOP when compared to GAT measurements with a mean difference of -0.11 mmHg with 95% LOA between 2.52 and -2.74. Figure 2 A-C shows the Bland-Altman plots of agreement between the iCare HOME measurements and GAT measurement over the three different IOP ranges.\n\nSpearman’s ρ correlation coefficient for the association between iCare HOME measurements and GAT measurements was 0.944. The association between the measurements of iCare HOME and the GAT is represented in Figure 3.\n\nThe reliability of the iCare HOME device was estimated by the co-efficient of variation (COV). Five iCare HOME measurements and five GAT measurements of each participant were analyzed. The COV was assessed separately for each participant for iCare HOME and GAT measurements. The mean COV for each participant was used to find the overall COV for both instruments. The overall COV for iCare HOME was 6.6 and GAT was 3.4. COV for both instruments at various pressure ranges is shown in Figure 4. The precision of iCare HOME was 0.996 (95% confidence interval: 0.994-0.998) calculated by using an intra-class correlation coefficient.\n\nComfort scale and corneal staining grade were assessed separately before certification, after certification and at the end of the study. The mean discomfort score before certification was 0.20% which increased significantly to 2.50% during certification. The final score after the simulated home condition was 5.14% with a standard deviation of 12%. None of the patients reported discomfort levels at grade 3 (Table 2). In 23% of the participants, corneal staining grade became worse, whereas it remained the same in 76% of the participants. Corneal staining grading, grade 1, grade 2, grade 3 and grade 4 were seen in eight, 8,1 and one participants respectively at the end of the study as shown in Figure 5.\n\nPalpebral fissure height and Hertel exophthalmometer measurement of participants were taken during the baseline examination. The median palpebral fissure height was taken;<10mm was considered a small palpebral fissure and >10mm was considered to be a wide palpebral fissure height. Similarly, the median was taken for Hertel’s exophthalmometry values, Hertel 1 being <17mm and Hertel 2 being >17mm, for analysis. These measurements were compared against the iCare HOME measurements, iCare attempts, time taken for iCare measurement and COV (Table 3). No significant difference was found between lower and higher PFH and exophthalmometry values.\n\n* Results are expressed in Median(Q1-Q3) - Mann-Whitney test\n\n\nDiscussion\n\nIn our study, results showed that iCare HOME self-measuring of IOP can be interchangeably used with GAT. Eligible and certified patients who could perform iCare HOME measurements without supervision, simulating their home environment, showed good agreement (mean difference 0.83 mmHg (95%, 3.92 and -2.25) to the measurements obtained by GAT. This could be used as the best alternative option to conduct a diurnal variation test (DVT) from home in routine clinical practice to monitor glaucoma progression. iCare HOME is also of great benefit to glaucoma care practice in post-COVID care, reducing the number of visits by glaucoma patients to the clinic for IOP examination.\n\nSeveral studies have reported the accuracy of the iCare rebound tonometer (RBT) in comparison with GAT among different age groups and both in healthy and glaucoma subjects.7–24 Another iCare self-tonometer, iCare ONE (RT-ONE), also showed good accuracy and agreement with GAT, even in children.24–29 These studies showed that a higher percentage of patients were able to perform self-tonometry using iCare ONE.24,26,29\n\nSimilar studies done by Mudie LI et al.30 and Dabasia PL et al.31 Mudie LI et al.30 evaluated the use of iCare HOME in 127 patients with glaucoma or suspected glaucoma. There was a good agreement within 5 mmHg between iCare HOME and GAT in 91.3% of patients with a mean difference of -0.33 ± 3.11 mmHg. Overall, 84% of patients were able to obtain IOP measurements with the iCare HOME within 5 mmHg range of GAT measurements with proper training and certification procedures. The intraclass correlation coefficient for iCare HOME was 0.91 (95% CI, 0.89-0.94). Dabasia et al.31 reported an underestimation of IOP by iCare HOME compared to GAT. In this study, 56 (74%) of 76 patients were able to perform self-tonometry with a mean bias of 0.3 mmHg (-4.6 to 5.2) for self-assessment, and 1.2 mmHg (-3.9 to 6.3) for investigator measurement.\n\nAnother study by Julia et al.32 reported the accuracy of IOP with iCare HOME compared with GAT, and showed a mean IOP difference of -0.8 mmHg (-7.2 to 5.6) between the iCare HOME and GAT. At lower IOP ranges iCare HOME underestimated values, whereas for high IOP it overestimated the measurements compared to GAT. A recent study published by Cvenkel et al.33 reported that 88% of patients were able to perform self-tonometry using iCare HOME and 82% of patients fulfilled the requirement for the certification process. The mean (SD) difference in IOP between GAT and iCare HOME was 1.2 (2.4) mmHg (95%, -3.4 to 5.9). This study also reported that 78.5% of patients felt iCare HOME was easy to use and 80.6% of patients expressed their confidence to use the device at the home.\n\nIn this study, we validated the iCare HOME among the Indian population. The facial anthropometric differences across ethnic populations and comprehensibility in different populations might influence the reliability of iCare HOME self-tonometry measurements.34 In this study, 91.57% (76) of patients were able to use iCare HOME and fulfilled the certification process. Only 2.41% (2) patients were excluded because self-measured IOP did not agree within 5 mmHg of GAT measurements during certification. The certification criteria were adopted as per the best guidelines recommended by the manufacturer. In our study, at a higher IOP range (>23 mmHg) there was a slight overestimation of IOP when compared to GAT measurements with a mean difference of -0.11 mmHg with (95%, 2.52 and -2.74). Mudie et al. also reported a slightly higher estimated IOP with iCare HOME for a higher IOP range. Our study also showed good intra-patient reliability of iCare HOME (ICC= 0.996, 95%, 0.994-0.998) similar to reports by Mudie et al. Several previous studies also showed the good reliability of iCare RBT.\n\nIn this study, only 3.9% (3) patients showed grade 2 level discomfort according to the VAS scale at the end of the study. Also, only two patients showed grade 3 and grade 4 corneal stainings at the end of the study as per the Oxford corneal staining scale. Comparatively, iCare HOME is safer and comfortable to use than GAT. It does not require anesthetic drops and corneal staining to measure IOP as opposed to GAT, making it more comfortable. Demirci et al.35 reported that there was no significant difference between GAT and iCare tonometry IOP measurements for all age (7-75) groups; therefore, it is an easy-to-use and reliable alternative to GAT across all age groups. However, iCare HOME cannot be used in a wide range of patients like those with Parkinson’s, arthritis, or dry eyes among others, because of difficulties in handling the tools. In the case of dry eyes, extra precautions may be required as it causes more discomfort. Caregiver can be trained to take IOP measurements for these subsets of patients, however, further research is required to address this issue.\n\nIn our study, results showed that 91.57% of the patients were able to perform self-tonometry using iCare HOME with good reliability and safety. There was also a very slight overestimation of IOP with iCare HOME at higher pressure levels. iCare HOME can be used to address the issue of difficulty in acquiring frequent and diurnal IOP measurements by patients doing self-tonometry from home. Therefore, it provides more clinical information to eye care practitioners to monitor and stabilize glaucoma progression.\n\n\nData availability\n\nHarvard Dataverse: Performance of Home-based self-tonometry (I care HOME (TA022) for measuring intraocular pressure among Normal and Glaucoma patients, https://doi.org/10.7910/DVN/RXRXLS.36\n\n- This project contains the following underlying data: Data entry Master data.xlsx\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\nKonstas AG, Quaranta L, Bozkurt B, et al.: 24-h Efficacy of Glaucoma Treatment Options. Adv. Ther. 2016; 33(4): 481–517. 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PubMed Abstract \| Publisher Full Text\n\nRosentreter A, Jablonski K, Mellein A, et al.: A new rebound tonometer for home monitoring of intraocular pressure. Graefes Arch. Clin. Exp. Ophthalmol. 2011; 249: 1713–1719. PubMed Abstract \| Publisher Full Text\n\nMudie LI, LaBarre S, Varadaraj V, et al.: The ICare HOME (TA022) Study: Performance of an Intraocular Pressure Measuring Device for Self-Tonometry by Glaucoma Patients. Ophthalmology. 2016; 123(8): 1675–1684. PubMed Abstract \| Publisher Full Text\n\nDabasia PL, Lawrenson JG, Murdoch IE: Evaluation of a new rebound tonometer for self-measurement of intraocular pressure. Br. J. Ophthalmol. 2016; 100(8): 1139–1143. PubMed Abstract \| Publisher Full Text\n\nTermühlen J, Mihailovic N, Alnawaiseh M, et al.: Accuracy of Measurements With the ICare HOME Rebound Tonometer. J. Glaucoma. 2016; 25(6): 533–538. PubMed Abstract \| Publisher Full Text\n\nCvenkel B, Velkovska MA, Jordanova VD: Self-measurement with ICare HOME tonometer, patients' feasibility and acceptability. Eur. J. Ophthalmol. 2020; 30(2): 258–263. PubMed Abstract \| Publisher Full Text\n\nZhuang Z, Landsittel D, Benson S, et al.: Facial anthropometric differences among gender, ethnicity, and age groups. Ann. Occup. Hyg. 2010; 54(4): 391–402. PubMed Abstract \| Publisher Full Text\n\nDemirci G, Erdur SK, Tanriverdi C, et al.: Comparison of rebound tonometry and non-contact airpuff tonometry to Goldmann applanation tonometry. Ther Adv Ophthalmol. 2019; 11: 251584141983573. Publisher Full Text\n\nAkkali AC: Performance of Home-based self-tonometry (I care HOME (TA022) for measuring intraocular pressure among Normal and Glaucoma patients.2022. Harvard Dataverse, V1. Publisher Full Text" }	[ { "id": "162324", "date": "14 Mar 2023", "name": "Bhaskaran Mani", "expertise": [ "Reviewer Expertise Glaucoma", "IOP", "IMaging", "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\nGeneral Authors looked at ICARE Home and suggest the readings can be interchageable with GAT and diurnal tests need to be done using the ICARE Home as self tonometry by patients.\nThe Bland Altman test and other results in the study like COV, indicate greater variation and interchangeablility is only moderate. In this context, does the conclusion still hold good?\nSpecific\nAbstract: Conclusion - \"iCare HOME can be used to address the issue of difficulty in acquiring frequent and diurnal IOP measurements by patients doing selftonometry from home\". This is not studied, Preferable to say agreement with GAT or not. Then suggest diurnal study comparisons may be warranted,\n\nAbstract Results: Please provide Bland Altman 95% agreement limit values instead of mean difference and 95% of mean values, it may be misleading.\n\nIntroduction - \"Recent guidelines on post-coronavirus disease 2019 (COVID-19) glaucoma care recommend the use of a rebound tonometer\" - Provide the reference for this.\n\nMethods: Inclusion criteria: Mention healthy and glaucoma patients - Define both clearly. Provide the break up of the glaucoma cases as proper diagnosis in results.\n\nMethods: Patients were provided video instructions - Please provide a link to the same or mention if it is from the manufacturer.\n\nMethods: Mention Icae LINK software or otherwise in full with manufacturer name for the first time.\n\nTable 1 - Age group has a large SD, please provide the median and range as well.\n\nFigures 1 and 2 - Is the X axis should be Mean of Icare Home and GAT, rather than GAT mean only?\n\nFigure 2 - Mention N in each subgroup.\nTable 3: Check title and correct sentence.\n\nDiscussion: Segregate RBT studies and Icare Home studies. Both are different and serve different purposes.\n\nDiscussion should address the strengths and limitations of your study, besides the LOA in Bland Altmann need to be discussed in the context of repeatability. CCT influence is not studied.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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": "10238", "date": "29 Nov 2023", "name": "Aditya Chaitanya", "role": "Author Response", "response": "Dear Sir, We thank you for your thoughtful and constructive review of our paper. Your reviews have helped us make important additions and changes to our manuscript (outlined below). We have added these changes in the latest submitted version of article. Kindly please go through it. With kind regards, Aditya Chaitanya (on behalf of all authors). _____________________________________ Response to Comments: 1. Abstract: Conclusion - \"iCare HOME can be used to address the issue of difficulty in acquiring frequent and diurnal IOP measurements by patients doing self tonometry from home\". This is not studied, Preferable to say agreement with GAT or not. Then suggest diurnal study comparisons may be warranted, Modification: \"Patients were able to perform self- tonometry using iCare HOME with good reliability and safety. iCare HOME shows good agreement with GAT. Further studies with proper home environment will be recommended to study the diurnal comparisons with GAT.\" 2. Abstract Results: Please provide Bland Altman 95% agreement limit values instead of mean difference and 95% of mean values, it may be misleading. We have provided the Bland-Altman 95% agreement limit values in both abstract and results sections in the latest submitted version. 3. Introduction - \"Recent guidelines on post-coronavirus disease 2019 (COVID-19) glaucoma care recommend the use of a rebound tonometer\" - Provide the reference for this. Modification: ‘'Considering the current post-coronavirus disease 2019 (COVID-19) pandemic rebound tonometer will be the best IOP measuring device for patient safety and less contamination risk\". 4. Methods: Inclusion criteria: Mention healthy and glaucoma patients - Define both clearly. Provide the break up of the glaucoma cases as proper diagnosis in results. Modification: Glaucoma patients inclusion criteria: \"Patients with structural glaucomatous optic disc changes that include RNFL defects, loss of neuro retinal rim, disc haemorrhages, disc asymmetry more than 0.2, with or without corresponding functional visual field changes were categorised as glaucoma\". - same mentioned in the methods sections. 5. Methods: Patients were provided video instructions - Please provide a link to the same or mention if it is from the manufacturer. Modification: \"We have made a detailed video showing usage of iCare Home with proper instructions and easy to understand as per the language preferences. This video was approved by the manufacturer to use in iCare Home related studies.\" - same mentioned in the methods sections. 6.Methods: Mention Icae LINK software or otherwise in full with manufacturer name for the first time. Modification: \"http://www.icarefinland.com/products/icare-link/.\" -Mentioned this link in the methodology section. 7.Table 1 - Age group has a large SD, please provide the median and range as well. We have provided Median and range for age group in table - 1. 8.Figures 1 and 2 - Is the X axis should be Mean of Icare Home and GAT, rather than GAT mean only? Both Figure-1 and Figure -2 Modified as per your suggestion 9. Figure 2 - Mention N in each subgroup. Mentioned N in each subgroup in Figure-2. 10. Table 3: Check title and correct sentence. Modification: \"iCare Home findings comparison between two different groups of Palpebral fissure height and Exophthalmometry.\" This table renamed as Table-4. 11.Discussion: Segregate RBT studies and Icare Home studies. Both are different and serve different purposes. Slightly modified as per your suggestion. Second paragraph of the discussion section initially discusses about RBT studies and its reliability. Latter part, discusses about iCare ONE studies. Rest of discussion section particularly discusses about iCare Home studies. 12. Discussion should address the strengths and limitations of your study, besides the LOA in Bland Altmann need to be discussed in the context of repeatability. CCT influence is not studied. Modification: Limitations: \" One of the limitations of the study is that we have performed this study, i.e. validation of iCare Home, in a simulated home environment at hospital set up. Even though each patient underwent proper training and had a simulated home environment, it may not produce the same results as regular home environment. It also does not address the learning effect that comes from use over a period of time. So, the future studies should focus on validation of iCare home through a real time home/work place environment. It helps to understand both regular short term and long term diurnal fluctuations of IOP of the patients.\" - same mentioned in discussion section ." } ] }, { "id": "162323", "date": "02 May 2023", "name": "Rashima Asokan", "expertise": [ "Reviewer Expertise Optometry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 has an impact in testing the usability of the ICare Home tonometer by subjects with glaucoma. The study has a well designed methodology which was explained in detailed in the manuscript. The authors have taken efforts in minimizing the expected bias in the study.\n\nI have only few comments which needs to be addressed by the authors:\nIn the methodology classification, IOP was grouped differently than what was shown in the results. Clarify the range appropriately\nResults first section, it is not clear with the total no of participants. If you are explaining about the 7 participants reasons for not included be specific and do not state as out of 83 again and again as it creates confusion for the reader.\n\nWhile describing the participants age in the results section, the mean age of 76 subjects were given whereas in table for 83 participants were given. What is the justification for this?\nIn table 1, number of icare attempts, mean and SD was used, it would be better represented as Median and IQR\nTable 1 should also include IOP values for paticipants measured using GAT and Icare.\nBland altman was represented well in figure 1 and 2. In Figure 2, A B C description should be in detail in the legend\nScatterplot Figure 3, shows IOP of 50. What were the range of IOP\n\nTable 2, representation can be modified. Difficult to process\nFigure 4, COV, Overall IOP to be removed.\n\nTable 3 - Legends to be incorporated.\n\nDiscussion was well elaborated.\n\nIs the work 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": [ { "c_id": "10247", "date": "29 Nov 2023", "name": "Aditya Chaitanya", "role": "Author Response", "response": "Dear Madam, Greetings! We thank you for your thoughtful and constructive review of our paper. Your reviews have helped us make important additions and changes to our manuscript (outlined below). We have added these changes in the latest submitted version of article. Kindly please go through it. With kind regards, Aditya Chaitanya (on behalf of all authors). _____________________________________ Response to Comments: 1. In the methodology classification, IOP was grouped differently than what was shown in the results. Clarify the range appropriately It is typo error. Group -2 range has been changed from 17-22 mm Hg to 17 -23 mm Hg in methodology. 2. Results first section, it is not clear with the total no of participants. If you are explaining about the 7 participants reasons for not included be specific and do not state as out of 83 again and again as it creates confusion for the reader. Modification: “A total of 83 patients agreed to participate and were recruited for the study. Seven of 83 patients (8.43%) failed to complete the study. Among those seven patients, four (4.82%) were excluded during simulated home measurements as the number of attempts to achieve five successful measurements were more than 10, two participants (2.41%) were excluded because self-measured IOP did not agree within 5 mmHg of GAT measurements during certification, and one participant (1.20%) stopped because of difficulty in using the iCare HOME device during the certification process.” - same mentioned in the results section of the new version. 3. While describing the participants age in the results section, the mean age of 76 subjects were given whereas in table for 83 participants were given. What is the justification for this? In the table-1 we have given mean age for both 76 subjects and 83 participants. 4. In table 1, number of icare attempts, mean and SD was used, it would be better represented as Median and IQR We have provided Median and range for number of iCare attempts in table – 1 as per your suggestion. 5.Table 1 should also include IOP values for participants measured using GAT and Icare. We have provided IOP values of participants measured using both GAT and iCare Home in newly added table – 2 as per your suggestion. 6. Bland altman was represented well in figure 1 and 2. In Figure 2, A B C description should be in detail in the legend We have Modified both Figure -1 and 2 as per your suggestion 7. Scatterplot Figure 3, shows IOP of 50. What were the range of IOP IOP range in normal participants is from 5 to 20.4 using iCare Home and 7 to19.8 using GAT. In glaucoma patients it ranges from 7 to 50 using iCare Home and 10 to 50 using GAT. IOP range has been added as per your suggestion in Table -2. 8. Table 2, representation can be modified. Difficult to process We have Modified table to understand easily as per your suggestion. This table renamed as Table-3. 9. Figure 4, COV, Overall IOP to be removed. We have Modified figure-4 as per suggestion. 10. Table 3 - Legends to be incorporated. Modification: \"iCare Home findings comparison between two different groups of Palpebral fissure height and Exophthalmometry.\" This table renamed as Table-4." } ] } ]	1	https://f1000research.com/articles/12-128
https://f1000research.com/articles/11-1285/v1	10 Nov 22	{ "type": "Research Article", "title": "The role of IL-6, ferritin, and coagulopathy in COVID-19 clinical progression", "authors": [ "Alvin Tagor Harahap", "Cosphiadi Irawan", "Adityo Susilo", "Kuntjoro Harimurti", "Dewi Gathmyr", "Hamzah Shatri", "Anna Mira Lubis", "Leonard Nainggolan", "Murdani Abdullah", "Alvin Tagor Harahap", "Adityo Susilo", "Kuntjoro Harimurti", "Dewi Gathmyr", "Hamzah Shatri", "Anna Mira Lubis", "Leonard Nainggolan", "Murdani Abdullah" ], "abstract": "Background In COVID-19, the release of pro-inflammatory mediators in the cytokine storm, primarily interleukin-6 (IL-6), has been hypothesized to induce pulmonary intravascular coagulation. However, the relationship between IL-6 and coagulopathy remains unclear in COVID-19 progression. We aimed to investigate the correlation of IL-6 with D-dimer, fibrinogen, prothrombin time (PT), and ferritin. Furthermore, we also analyzed the effect of those parameters on the worsening of COVID-19 patients.\nMethods A prospective cohort study was conducted in moderate and severe COVID-19 patients from June 2020 to January 2021. A serial evaluation of IL-6, D-dimer, fibrinogen, ferritin, and PT was performed and correlated with the patient's condition at admission and on the 14th day. The outcomes (improvement, worsening, or discharged patients) were recorded during the study.\nResults Of 374 patients, 73 study subjects (61 severe and 12 moderate COVID-19) were included in this study. A total of 35 out of 61 severe and one out of 12 moderate illness subjects had experienced worsening. Spearman-rank correlation of IL-6 with with ferritin, D-dimer, fibrinogen, and PT was 0.08 (p=0.5), −0.13 (p=0.27), 0.01 (p=0.91), and 0.03 (p=0.77), respectively. In ROC analysis, D-dimer (74,77%) and IL-6 (71,32%) were the highest among other variables (>60%).\nConclusions In COVID-19 patients, there was a correlation between elevated IL-6 and D-dimer levels with disease deterioration. There was no correlation between elevated IL-6 levels with ferritin, D-dimer, fibrinogen, and PT levels. Therefore, changes in IL-6 and D-dimer can predict worsening in moderate and severe COVID-19 patients.", "keywords": [ "D-dimer", "Ferritin", "Fibrinogen", "IL-6", "Prothrombin Time" ], "content": "Introduction\n\nThe SARS-CoV-2 virus is a β-coronavirus with an enveloped, positive-sense, and single-stranded RNA. The COVID-19 pandemic due to SARS-CoV-2 virus poses a serious threat due to systemic inflammation and coagulopathy. Interleukin-6 (IL-6) is a cytokine that has a positive pleiotropic effect on inflammation. This cytokine can amplify the coagulation system to activate the epithelial cells, monocytes, and neutrophils,1 that can inhibit anticoagulant protein S and antithrombin and enhance the activity of clotting factor VII, von Willebrand, and fibrinogen.\n\nPreviously considered, increased ferritin was associated with hemophagocytic lymphohistiocytosis/macrophage activation syndrome in COVID-19. However, the absence of five out of eight characteristics in the previous COVID-19 study explains the differences between the disease.2 Several retrospective studies have been conducted to observe the relationship between IL-6, PT, fibrinogen, and ferritin with COVID-19 progression.3–7 In this current prospective cohort study, we aimed to investigate the effectiveness of these parameters in COVID-19 progression.\n\n\nMethods\n\nIn this prospective cohort study conducted from July 2020 to January 2021, COVID-19 patients aged ≥18 years at the Pertamina Central Hospital Modular Extension Simprug (Simprug Modular Extension Hospital, SMEH, Jakarta, Indonesia) were included. Patients with COVID-19 were detected based on nasopharyngeal and oropharyngeal swab examination by polymerase chain reaction (PCR). Inclusion criteria: aged 18 years or older; moderate and severe COVID-19 (according to COVID-19 WHO guideline confirmed by positive BALF PCR SARS-CoV-2); willingness to provide blood sample. Exclusion criteria: history of chronic bleeding; undergoing hemodialysis; undergoing plasma convalescent clinical trial, or taking immunomodulation therapy (particularly IL-6 and intravenous immunoglobulin therapy).\n\nPatients who fulfilled the criteria were observed on the first day of hospital admission, and blood samples (i.e., first sample collection) were collected to analyze IL-6, D-dimer, ferritin, fibrinogen, and prothrombin time. The collected blood samples were stored in the fridge at -20° celcius at Clinical Pathology laboratory of Pertamina Central Hospital.\n\nAfter collected, IL-6 was analyzed in the Integrated Laboratory of the Faculty of Medicine, Universitas Indonesia. During transferring IL-6 samples were maintained at constant temperature -20° celcius accoding to Guidance on regulations for the Transport of Infectious Substances Guidance on regulations for the Transport of Infectious Substances 2007. IL-6 was analyzed using an ELISA IL6 Vmax microplate reader. Complete blood count, D-dimer, fibrinogen, and prothrombin time (PT) were analyzed using Sysmex CS2100i. Ferritin was analyzed using Cobas 601 Roche in the Clinical Pathology laboratory of Pertamina Central Hospital.\n\nThe severity of the illness was classified according to the WHO interim guidance (version 18th May 2020)8 as moderate, severe, or critical illness. Patients were observed up to day 14th or considered completed when the patients improved, worsened, died, or were discharged earlier. Afterward, samples were collected at the end of the observation (i.e., second sample collection). Worsening was defined as COVID-19 disease severity progression from moderate to severe, critical illness or death. All patients received antibiotics, antivirals, corticosteroids, and anticoagulants according to the standard hospital therapy (Fondaparinux, LMNH, or UFH).\n\nAll collected data were analyzed using Anaconda package program9 and reported in the text, table, or figures. All p-values < 0.05 were considered statistically significant. Correlation test was used to analyze correlation between IL-6 with ferritin and coagulopathy. Method of cutoff points obtained using area under curve method. Cutoff points by receiver operator characteristic obtained by calculating the optimum sensitivity and specificity.\n\nThis study has been approved (approval date: June 29th 2020) by the ethical committee, Universitas Indonesia (approval number: KET-650/UN2.F1/ETIK/PPM.00.02/2020), and Pertamina Central Hospital (approval number: 3315/B00000/2020-S8).\n\n\nResults\n\nDuring the study period from July 2020 to January 2021, 374 severe and moderate COVID-19 patients were treated at the SMEH. Of those, 117 patients were randomized, 42 were excluded due to incomplete data, one received convalescent plasma therapy, and 1 had lysis of blood samples. The remaining 73 patients were further analyzed.\n\nThe characteristics of the study subjects are summarized in Table 1. Of the 73 COVID-19 patients, 61 (84%) were classified as having severe COVID-19 and 12 (16%) were classified as having moderate COVID-19. The majority of the patients were male and the mean age of patients was 61 years (SD±12.74). Most of the patients were overweight, hospitalized at day 6th of the illness with duration of 7 days. As the final observation outcomes, most of the subjects with moderate disease experienced improvement, and subjects with severe disease experienced worsening on day 14 of the illness. The majority of the patients had at least one comorbidity, with hypertension was the most common. All subjects were given the combination of remdesivir, favipiravir, and oseltamivir. They also received corticosteroids (dexamethasone or methylprednisolone) and anticoagulants (unfractionated heparin, enoxaparin, or fondaparinux).\n\nThe variable distributions were analyzed according to disease severity and the worsening or improvement of patients' condition, as shown in Table 2.\n\nCorrelation coefficient analysis using the Spearman method showed p≥0.05 between IL-6 and ferritin, fibrinogen, D-dimer, and PT (Table 3).\n\nFigure 1 and Table 4 displayed the analysis of the receiver operating characteristic (ROC) curve (AUC) for correlation between elevated IL-6, ferritin, fibrinogen, D-dimer, and PT levels with COVID-19 patients' deterioration.\n\nNotes: (1) dDdimer: D-dimer difference, dFibrinogen: Fibrinogen difference, dFerritin: Ferritin difference, dProthrombin Time: Prothrombin Time difference, dIL-6: IL-6 difference. (2) Difference is defined as the value at the end of observation – value at initial observation.\n\nWe found no correlation between IL-6 and other variables. Thus, as one of the disease severity index components, we aimed to investigate the correlation between the oxygen saturation (SpO2)/fraction of inspired oxygen (FiO2) ratio and IL-6, ferritin, fibrinogen, D-dimer, and PT (Figures 2 and 3). As a result, our study demonstrated the correlation between IL-6, ferritin, fibrinogen, D-dimer, and PT and SpO2/FiO2 ratio as the severity determinants.\n\nSpearman correlation test. CRP: C-reactive protein.\n\nNotes: A–D: correlation between SpO2/FiO2 ratio and inflammatory markers CRP, IL-6, ferritin, and fibrinogen with a statistical significance was found between SpO2/FiO2 ratio and inflammatory markers CRP, ferritin, and fibrinogen, but not with IL-6. Figure E and F: correlation between SpO2/FiO2 ratio and coagulation markers D-dimer and prothrombin Time with a statistical significance was found between SpO2/FiO2 ratio and D-dimer, but not with prothrombin time.\n\nSpearman correlation test. CRP: C-reactive protein.\n\nNotes: A–D: correlation between SpO2/FiO2 ratio and inflammatory markers CRP, IL-6, ferritin, and fibrinogen with a statistical significance was found between SpO2/FiO2 ratio and inflammatory markers CRP and ferritin, but not with IL-6 and fibrinogen. Figure E and F: correlation between SpO2/FiO2 ratio and coagulation markers with a statistical significance was found between SpO2/FiO2 ratio and D-dimer and prothrombin time.\n\n\nDiscussion\n\nMales were predominant in this study (64%) with the age range 52–68 years old.10,11 Hypertension (44.4%) and diabetes (31.8%) were the most common comorbidities, and similar results were also reported in other studies from China.12,13 This study found that the comorbidity was not associated with the patient's deterioration. Subjects with hypertension tend to experience worsening, as stated by Li Yongheng et al.13\n\nIn this study, most subjects with moderate disease experienced improvement. Despite the standard therapy, subjects with severe disease experienced worsening on day 14 of the illness. Meanwhile, all the subjects with moderate illness and 55.7% with severe illness survived (Table 2).\n\nThe courses of the COVID-19 disease have been reported comprehensively, with mild symptoms occurring mainly on the 5th day until the 10th day of illness (phase II disease).14,15 In this phase, most patients begin to feel shortness of breath accompanied by hypoxia. Our study subjects visited the emergency department during the mild symptom phase on the sixth day of hospitalization. Furthermore, they showed increased IL-6 and APR of ferritin and fibrinogen. Subjects who visited the emergency department for more than 6 days (mean 7.5 days) had almost three times greater risk of worsening than those who came for less than 6 days (mean 4 days).\n\nSubjects with severe disease had higher levels of D-Dimer (Table 1), which is consistent with previous studies conducted by Chen et al, Zhou et al, and Guan et al.16–18 Additionally, levels of D-dimer were higher in the worsening compared with the improved group. This study reports that levels of D-Dimer tend to increase at the second sample collection (Table 2).\n\nAccording to Chen et al.16 and Zhou et al.,17 non-survivor COVID-19 subjects had higher ferritin levels than the survivors. At admission, this study shows that subjects with moderate and severe conditions had higher ferritin levels (Table 1).\n\nLevels of IL-6 at the first sample collection (Table 1) were similar to the previous study.17 In contrast to the study by Jin Zhang et al.10 and Awasthi et al.,19 study subjects did not show a significant difference in IL-6 levels at the first measurement between moderate to severe illness.\n\nIn acute phare response (APR), IL-6 is a pro-inflammatory cytokine that increases and determines infection-associated ferritin levels.20,21 However, we found no correlation between ferritin levels and IL-6 in the first and second sample collection (Figure 3).\n\nAlthough subjects did not experience an inflammatory process at admission, we found an increase in ferritin and fibrinogen levels, indicating that inflammation occurred in most study subjects. Furthermore, other factors contributing to increased ferritin levels, such as epithelial damage, were also considered. Since a decrease in the SpO2/FiO2 ratio was due to an acute respiratory distress syndrome (ARDS) manifestation,13,22 the correlation between SpO2/FiO2 ratio with ferritin and fibrinogen was investigated to determine whether the epithelial damage affected IL-6 and other the inflammatory variables. Our result showed a statistically significant correlation between SpO2/FiO2 ratio with ferritin and fibrinogen (Figure 2). This correlation showed that inflammation affected the SpO2/FiO2 ratio from the onset of the illness. However, since the increase of IL-6 was not correlated with SpO2/FiO2 ratio, we assumed that inflammation and ferritin release was not affected by IL-6.7,23 According to a study by Zhi et al., several possibilities cause the increase of ferritin: 1) pro-inflammatory cytokines stimuli (i.e., IL-1β, tumour necrosis factor α (TNF-α), and IL-6) caused an inflammatory reaction that damaged the cells, 2) intracellular ferritin leakage due to cell damage and inflammation, and 3) the ferritin leakage from the injured cells further triggers the damage of other cells via Fenton and Haber–Weiss's reaction.24\n\nInflammation will trigger the coagulation system characterized by changes in the value of D-dimer, fibrinogen, and PT at the time of viral entry.25 Thus, we investigated the correlation between levels of IL-6 and markers of coagulopathy and inflammation.\n\nSince there was no correlation found between IL-6, ferritin, and the incidence of coagulopathy, we concluded that coagulopathy in COVID-19 patients could occur without the role of IL-6 and ferritin. Such explanations for this finding are: 1) ARDS pathophysiology in the infected subjects with moderate and severe illness is related to a massive loss of the angiotensin-converting enzyme (ACE)-2 enzyme, causing damage to the alveolar epithelium and vascular endothelium,26 2) compartmentalization of the inflammatory cascade, as described by Chow and Tisoncik et al.,27,28 and 3) an acute phase response (APR) increase may be due to other pro-inflammatory cytokines, such as TNF-α or IL-1,23,25,29–31 and the aforementioned vicious cycle of cellular destruction.\n\nAn analysis was carried out on the second blood collection after patients had a worsening during treatment to determine whether the incidence of coagulopathy correlates with IL-6 levels, in which the effect of IL-6 and cytokine storm was the utmost. The data from the second blood collection showed a significant correlation between the SpO2/FiO2 ratio and the D-dimer, ferritin, PT, and IL-6 (Figure 3). Furthermore, the D-dimer, fibrinogen, and PT were correlated with ferritin, while there was no correlation with IL-6. Our result demonstrated that inflammation correlates with coagulopathy, but conceivably not via a direct IL-6 pathway. To explain this finding, according to a study described by Sinha et al. that the interaction of mediators and pathways involved is not always constantly linear or uniform.32\n\nWorsening subjects showed significant changes in D-dimer, fibrinogen, and PT. Since there was no correlation between IL-6, ferritin and PT, fibrinogen, and D-Dimer, we determined the changes in the variables' mean values between the first and second blood collections. Furthermore, Wilcoxon's non-parametric test was performed since the data was not normally distributed (Figure 4).\n\nNotes: Ddimer1, Fibrinogen1, Prothrombin Time1, Ferritin1, IL-61: D-dimer, fibrinogen, prothrombin time, ferritin, and IL-6 at the first sample collection; Ddimer2, Fibrinogen2, Prothrombin Time2, Ferritin2, IL-62: D-Dimer, fibrinogen, prothrombin time, ferritin, and IL-6 at the second sample collection.\n\nIn worsening subjects, the second IL-6 blood collection had a higher value than the first one, albeit not statistically significant. Possible reasons include: 1) cytokines other than IL-6 affect the increase in D-dimer, fibrinogen, and ferritin levels, or 2) external factors, such as administration of anti-inflammatory corticosteroids and heparin, also have anti-inflammatory effects,33 resulting in an insignificant increase of IL-6 and ferritin. During the study period, corticosteroids and heparin were administrated following the standard therapy for moderate and severe COVID-19 patients, or 3) large amounts of soluble IL-6 receptors production binds free IL-6 to reduce the concentration, as described by Garbers et al.,34 or 4) the presence of other cytokines (IL-6 cytokine family), including IL-11,35 that also has a pro-inflammatory effect.36\n\nThe disease may be influenced by the period between the onset and the patient's admission to the hospital. However, we found no differences between severe and moderate illness subjects. This result demonstrated that the disease onset was not correlated with the disease severity.\n\nThe disease severity was determined using WHO criteria for oxygen saturation, respiratory rate, and radiological findings. Most subjects were admitted to the emergency department with severe illness (83%), with a median SpO2/FiO2 ratio was 97. In moderate illness, there were no differences in IL-6 at the baseline.\n\nOur study found a negative correlation between D-dimer, fibrinogen, and PT levels with the SpO2/FiO2 ratio, reflecting the disease severity. This finding demonstrated that coagulopathy had a role in the patient's deterioration even though SpO2/FiO2 ratio showed no correlation with IL-6. The worsening lung function was due to pre-existing inflammation before the increase in IL-6 may explain the correlation with the coagulation system.\n\nSinha,32 and Leisman31 proposed that the pathophysiology of moderate and severe COVID-19 ARDS differs from typical ARDS, where the inflammatory system activation marked by increased IL-6 occurred only in a few COVID-19 ARDS patients. Our study showed that only 15.1% of subjects had IL-6 elevation at the initial examination, with an increase of 10-times the lower standard limit. Furthermore, if COVID-19 ARDS is considered a hyperinflammatory type, the IL-6 will be much lower than the value found in studies of the hyperinflammatory type that showed an increase of more than 100-times the lower standard limit.\n\nThe second blood collection sample showed that IL-6, ferritin, D-dimer, and PT had a statistically significant negative correlation with the SpO2/FiO2 ratio, suggesting that deteriorating lung function is also correlated with inflammation and coagulopathy. However, we found no statistically significant correlation between IL-6 with D-dimer, fibrinogen, PT, and ferritin. As mentioned previously, this phenomenon may be caused by administering anti-inflammatory drugs that can reduce APR levels.\n\nFibrinogen is a soluble glycoprotein synthesized by the liver, and the activation can produce insoluble fibrin in the plasma. This process occurs via intrinsic and extrinsic pathways, and the activity is assessed by measuring PT.\n\nFibrinogen level is elevated in inflammatory conditions.23 In patients who experienced worsening, we found that the fibrinogen levels at admission were higher than normal, with no changes in PT values. Thachil argued that the initial increase of fibrinogen would regulate inflammation. However, when the D-dimer levels continue to elevate with decreased fibrinogen levels, the protective role of fibrinogen ceases, and thrombus formation begins.37 In our finding, the initial fibrinogen levels in moderate and severe COVID-19 were increased but decreased at the second blood collection sample analysis, which showed a tendency towards normal compared to the worsening group. This result demonstrated that hypercoagulable conditions might have a role in the pathology of the worsening group, a condition that differs from the hypothesis as reported by Thachil.37 The hypercoagulable state can result from neutrophils’ subsequent pulmonary capillary endothelial activation, namely the formation of neutrophil extracellular traps (NETs).38–42\n\nAs part of APRs, ferritin was negatively correlated with the SpO2/FiO2 ratio (Figure 2). We assumed that the inflammation process had occurred prior to the patients' hospitalization, which explains the presence of a correlation between ferritin and the disease severity (moderate and severe). In the early phase, ferritin levels did not correlate with D-dimer, PT, and fibrinogen levels, which unlikely indicate that inflammation triggers coagulopathy.\n\nOn the initial observation, there was an elevation in ferritin levels in the subjects with moderate and severe illness (Table 1). In the second blood collection sample, ferritin levels increased in the worsening but decreased in the improved group. Finally, we found the most significant changes in the improved group of moderate illness subjects (Table 2), as also reported by Zhi et al.24 To explain this finding, we hypothesized that 1) pro-inflammatory cytokines such as IL-1β, TNF-α, and IL-6 can increase ferritin synthesis, 2) damage to the cellular level due to inflammation will release intracellular ferritin,30 and 3) in acidosis, increased production of reactive oxygen species induce the release of iron from the ferritin. In addition, Fenton and Haber–Weiss reaction increases the concentration of hydroxyl radicals and eventually damages the cells. Overall, this process will initiate a vicious cycle of cell damage by increasing ferritin concentration.\n\nRosario,43 explained that ferritin has immunosuppressant and pro-inflammatory effects. The immunosuppressant properties were found in the ferritin H fraction, supressing B lymphocyte antibodies' production. Additionally, ferritin also reduces granulocytes' phagocytosis, regulates the production of granulocytes-monocytes, and induces the production of IL-10 in lymphocytes. Moreover, it also inhibits the function of CXCR4 (chemokine receptor 4), an activator of the mitogen-activated protein kinase system that plays a role in the proliferation, differentiation, and migration of the cells. The role of ferritin in the inflammatory process has been described in hepatic stellate cells. For example, increased nuclear factor κB can promote the expression of inflammatory mediators, including IL-1β, and induce the production of nitric oxide synthase. This immunomodulatory process belongs to ferritin H and L properties. However, the role of ferritin as an inducer of inflammation or anti-inflammatory in COVID-19 infection has not been proven since the elevated ferritin type is still unknown.20,30,43\n\nThe correlation between ferritin with fibrinogen, D-dimer, and PT in COVID-19 patients is recognized as a damage-associated molecular pattern that can modulate IL-6 concentrations.30\n\nThere was no correlation between decreased SpO2/FiO2 ratio and IL-6 in the first blood collection sample, but SpO2/FiO2 ratio was correlated with acute-phase protein ferritin and fibrinogen. Albeit D-dimer, fibrinogen, and PT were correlated with the SpO2/FiO2 ratio, we found no correlation between ferritin and those. Based on this finding, we demonstrated that the increase in APR does not correlate with the incidence of coagulopathy in COVID-19 since the condition has different mechanisms, including epithelial damage due to the entry of the SARS-CoV-2 virus and the increased production of NETs by neutrophils, as previously described.\n\nTheoretically, inflammatory (IL-6 and ferritin) and coagulopathy (D-dimer, fibrinogen, and PT) markers are correlated with patients' deterioration. Interleukin-6 regulates the inflammatory process, and the elevation is associated with the worsening of COVID-19 patients. This study found that increased levels of IL-6 can predict the deterioration of subjects, but it is insufficient to justify it as a routine examination. Additionally, uncorrelated IL-6 with coagulopathy markers, perhaps due to the ability of IL-6 to activate the inflammatory cascade in multiple body systems,32 inducing amplification of the cascade.\n\nInflammation due to COVID-19 can activate epithelium, endothelium, macrophages, and neutrophils. Massive recruitment of neutrophils to the lungs and release of NETs regulates coagulation and IL-6 activation.40,44 We found that alteration in D-dimer levels can predict the patients' deterioration. Therefore, the availability of D-dimer in hospitals can justify its function as a routine examination.\n\nAlthough the alteration of ferritin and fibrinogen can not predict the patient's deterioration, these APR markers can be elevated in inflammatory conditions.20,23 Thus, administration of corticosteroid therapy or anti-inflammatory agents, such as heparin, can reduce the inflammation process,33,45 as marked in our study by the unaltered ferritin and decreased fibrinogen levels (Table 2).\n\nProthrombin time is the period required for plasma to clot after adding tissue factor. The reaction velocity is the result of coagulation factors activation that consist of coagulation factors XII to X. Furthermore, Yu Zhang et al. found that PT had a sensitivity of 83.54% and specificity of 65.22% for sepsis patients at the cut-off 20.46 Our study showed a 75% quartile of 12 in severe COVID-19 subjects, describing that levels of PT were insensitive to measure patient's deterioration. A similar finding was also reported in a retrospective study by Long et al.,47 where the initial measurement of PT was not correlated with the disease severity. This phenomenon may demonstrate the effect of hypercoagulation as the dominant pathophysiology in the early phase of the disease, in contrast to DIC in sepsis.48,49\n\nOur study limitation is that the IL-6's diurnal variation cannot be eliminated since the use of a consecutive sampling method and the disease phase factor.\n\n\nConclusion\n\nIn moderate and severe COVID-19 patients, there was a correlation between elevated IL-6 and D-dimer levels with disease deterioration. There was no correlation between elevated IL-6 levels with ferritin, D-dimer, fibrinogen, and PT levels.\n\n\nInformed consent statement\n\nWritten informed consent from the patient/patient’s family for the use and publication of the patient’s data was obtained from all subjects involved in the study. Informed consent was conceptualized according to local ethics committee, and hospital review committee.", "appendix": "Data availability statement\n\nUnderlying data cannot be shared due to privacy concerns. Data will be made available to readers and reviewers on request from Alvin Tagor Harahap (alvinharahap@gmail.com).\n\n\nReferences\n\nYoshikawa T, Hill T, Li K, et al.: Severe acute respiratory syndrome (SARS) coronavirus-induced lung epithelial cytokines exacerbate SARS pathogenesis by modulating intrinsic functions of monocyte-derived macrophages and dendritic cells. J. Virol. 2009; 83(7): 3039–3048. PubMed Abstract \| Publisher Full Text\n\nMcGonagle D, O'Donnell JS, Sharif K, et al.: Immune mechanisms of pulmonary intravascular coagulopathy in COVID-19 pneumonia. Lancet Rheumatol. 2020; 2(7): e437–e445. PubMed Abstract \| Publisher Full Text\n\nZhu Z, Cai T, Fan L, et al.: Clinical value of immune-inflammatory parameters to assess the severity of coronavirus disease 2019. Int. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "164119", "date": "13 Mar 2023", "name": "Azlan Bin Husin", "expertise": [ "Reviewer Expertise Clinical hematology", "malignant hematology", "benign hematology", "autologous hematopoietic stem cell transplant" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall writing of this manuscript requires extensive language and grammatical improvement. Subject matter of interest were properly introduced but some of methodology parts were not defined. Hence, there is a missing connection between the subject of interest, methodology, results and discussion.\nIntroduction The introduction needs to be revised to better contextualize on the work performed.\nProvide rationale of evaluating only prothrombin time and D-dimer instead of adding partial thromboplastin time too whereas it was mentioned in introduction that von Willebrand activity also enhanced.\n\nThe term \"effectiveness of parameters\" in Introduction, para 2 is inappropriate.\n\nProvide rationale of evaluating SpO2/FiO2 ratio as the chosen severity index to compared with selected inflammatory markers.\nMethods This section requires substantial revision and improvement\n\nDefine the term \"BALF\" in Study design.\n\nClarify what happen if enrolled patients received IL-6 inhibitor or Ig later part of hospital stay? Example before day 14. Were they withdrawn or included in the analysis?\n\nCRP was not mentioned in the sample collection and tables but is showed in the graphs.\n\nProvide rationale and appropriate reference of using cut off point 14 days for assessment in the Assessment of patient's severity. What if patient stay longer than that and changed in clinical status?\n\nRevise the term \"or considered complete\" used in Assessment of patient's severity. Perhaps use 'censored'?\n\nProvide reference and appropriate citations used for definition of COVID-19 disease severity progression or worsening.\n\nProvide more information on the standardized approach of administering antibiotics, antivirals, corticosteroids and anticoagulant in the study center. This is to understand the different types of these agents used and possible interaction with the variables assessed.\n\nThe term \"coagulopathy\" used in Statistical analysis, para 1 should be defined earlier.\n\nThe term \"randomized\" in Results, para 1 is incorrect because the study population was not randomized. Perhaps 'randomly selected' is more suitable?\nResults\nFor Table 1; should add normal reference range as foot note.\n\nStatement \"subjects with severe disease experienced worsening on day 14...\" should be \"subjects with severe disease experienced worsening within 14 days of...\"\n\nPercentage of hypertension should be reflected in the table 1; can be as footnote.\n\nThe statement \"All subjects were given the combination of remdesivir, favipiravir, and oseltamivir\" is not consistent with the actual number of patients received it.\n\nAuthor should describe the approach or basis of how different types of antibiotics given to these patients. This important to understand factors may influence the inflammatory markers evaluated in different category of patients.\n\nStatement \"Correlation coefficient analysis using the Spearman method showed p≥0.05 between IL-6 and ferritin, fibrinogen, D-dimer, and PT\" should be, \"Correlation coefficient analysis using the Spearman method showed p≥0.05 between IL-6 and ferritin, fibrinogen, D-dimer, and PT levels\".\n\nDisease severity index was not mentioned in introduction and methodology.\nDiscussion; Characteristics of the study subjects\nPara 3, line 2: statement \"In this phase, most patients begin to feel shortness of breath accompanied by hypoxia\" is this refers to all mild cases? If so, then it is incorrect statement.\nDiscussion: Correlation between increased levels of IL-6 and ferritin\nPara 2, line 1: statement should be \"...patient did not show raised inflammatory markers...\".\n\nThe argument using Zhi et al., findings was rather contradicting to author's finding of no correlation with IL-6.\nDiscussion: Correlation between levels of IL-6 with D-dimer, fibrinogen, and PT\nIt is difficult to analyze and to explain what really happened among worsening patients as no clear definition of this event and what type of treatment they received?\nConclusion\nPerhaps should include differences in inflammatory and hemostatic response between initial presentation and as patient became worse.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10235", "date": "22 Sep 2023", "name": "Cosphiadi Irawan", "role": "Author Response", "response": "Dear Azlan Bin Husin We thank you for your constructive feedback. We made revisions in our article and hope you would not mind to review once again our article if it is eligible for indexing. Introduction The introduction needs to be revised to better contextualize on the work performed. 1. Provide rationale of evaluating only prothrombin time and D-dimer instead of adding partial thromboplastin time too whereas it was mentioned in introduction that von Willebrand activity also enhanced. we added explanations in the introduction 2. The term \"effectiveness of parameters\" in Introduction, para 2 is inappropriate. we fixed the grammar 3. Provide rationale of evaluating SpO2/FiO2 ratio as the chosen severity index to compared with selected inflammatory markers. we added explanations in the introduction Methods This section requires substantial revision and improvement 1. Define the term \"BALF\" in Study design. we added some explanations 2. Clarify what happen if enrolled patients received IL-6 inhibitor or Ig later part of hospital stay? Example before day 14. Were they withdrawn or included in the analysis? the subjects were exempted. We revised the statement regarding the exclusion criteria 3. CRP was not mentioned in the sample collection and tables but is showed in the graphs. We added some explanations in sample collection but we 4. Provide rationale and appropriate reference of using cut off point 14 days for assessment in the Assessment of patient's severity. What if patient stay longer than that and changed in clinical status? We used 14 days as cutoff based on studies reported the mean duration of disease progression typically occur at 7-14 days after onset of symptoms Revise the term \"or considered complete\" used in Assessment of patient's severity. Perhaps use 'censored'? We agreed with your feedback. we fixed the sentence Provide reference and appropriate citations used for definition of COVID-19 disease severity progression or worsening. We added references and explanations regarding Covid-19 disease severity Provide more information on the standardized approach of administering antibiotics, antivirals, corticosteroids and anticoagulant in the study center. This is to understand the different types of these agents used and possible interaction with the variables assessed. We added explanations of management protocol used in our center, but mostly were based on clinical judgement The term \"coagulopathy\" used in Statistical analysis, para 1 should be defined earlier. We added definition of coagulopathy in introduction The term \"randomized\" in Results, para 1 is incorrect because the study population was not randomized. Perhaps 'randomly selected' is more suitable? We revised the sentence like you suggested Results For Table 1; should add normal reference range as foot note. We added normal reference in table footnote Statement \"subjects with severe disease experienced worsening on day 14...\" should be \"subjects with severe disease experienced worsening within 14 days of...\" We revised the statement Percentage of hypertension should be reflected in the table 1; can be as footnote. We decided to not mention any comorbidities percentage The statement \"All subjects were given the combination of remdesivir, favipiravir, and oseltamivir\" is not consistent with the actual number of patients received it. We revised the statements Author should describe the approach or basis of how different types of antibiotics given to these patients. This important to understand factors may influence the inflammatory markers evaluated in different category of patients. We added explanations in results section regarding the selection of type of antibiotics given to the patients Statement \"Correlation coefficient analysis using the Spearman method showed p≥0.05 between IL-6 and ferritin, fibrinogen, D-dimer, and PT\" should be, \"Correlation coefficient analysis using the Spearman method showed p≥0.05 between IL-6 and ferritin, fibrinogen, D-dimer, and PT levels\". We revised the sentence like you suggested Disease severity index was not mentioned in introduction and methodology. We added explanations regarding disease severity index in introduction Discussion; Characteristics of the study subjects Para 3, line 2: statement \"In this phase, most patients begin to feel shortness of breath accompanied by hypoxia\" is this refers to all mild cases? If so, then it is incorrect statement. We revised the statement. What we meant was most patients begin to feel chest discomfort and in moderate or severe cases, begin to feel shortness of breath. Discussion: Correlation between increased levels of IL-6 and ferritin Para 2, line 1: statement should be \"...patient did not show raised inflammatory markers...\". The argument using Zhi et al., findings was rather contradicting to author's finding of no correlation with IL-6. We reconstructed the statements. Discussion: Correlation between levels of IL-6 with D-dimer, fibrinogen, and PT It is difficult to analyze and to explain what really happened among worsening patients as no clear definition of this event and what type of treatment they received? We tried to explain the management protocol used in the result section and explain what happened in worsening group based on the markers analysed Conclusion Perhaps should include differences in inflammatory and hemostatic response between initial presentation and as patient became worse We added more explanations regarding the difference in inflammatory and coagulation marker between initial and later sample." } ] }, { "id": "168232", "date": "22 May 2023", "name": "Gopal Krishna", "expertise": [ "Reviewer Expertise Neuroendocrine disorders", "Coagulation disorders in Neurosurgery", "Neurospinal disorders", "vascular Neurology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 good study. However, the parts of article are not properly organized. There is extensive overlap of results and discussion. The write up needs extensive revision. Some important aspects to be addressed:\nIntroduction:\nThe introduction is very brief. Basic concepts regarding pathophysiological aspects of inflammation in COVID-19 may be described here. The role of parameters included in metadata and their behaviour in COVID-19 may be elucidated.\n\nThe treatment protocol pertaining to corticosteroids, low molecular weight heparin or UFH, and antiviral medications e.g. remdesivir etc. should be mentioned. And the modifications of these drugs according to the severity of disease.\nMethods\n\nThe exclusion criteria should explain whether patients on oral anticoagulants, liver dysfunction were included or not. As a large size of study population had diabetes and hypertension, underlying coronary artery disease is likely to be present. Such population may have been on oral anticoagulant therapy prior to COVID-19.\n\nC-reactive protein have been also studied and detailed in result section. It is a new parameter which is described by authors in results bearing no mention in methods.\n\nThe criteria of worsening of patients need to be described well according to citation used or modification, if any.\nResults:\n\"The patients were randomized\" is not correct as selection of patients and their classification was the decision of authors.\n\nThe part of discussion, \"Fig 4.Variable alterations between the first and second sample collection in the worsening group\" should be explained in the result section.\n\nWith using terms like \"most\" and \"majority\", the percentages must be mentioned next to them.\n\nRepetition of many result parameters in discussion e.g., \"males were most commonly affected in this study\" is not appropriate.\n\nAttempt may be made to include data on patients who worsened.\n\nThe normal reference laboratory values should be given for all parameters used in the study.\nDiscussion:\nThis section needs to be rewritten as there are many grammatical errors. The authors must seek professional help.\n\nMany lines and paragraphs are not correct. e.g., ”This study found that increased levels of IL-6 can predict the deterioration of subjects, but it is insufficient to justify it as a routine examination. Additionally, uncorrelated IL-6 with coagulopathy markers, perhaps due to the ability of IL-6 to activate the inflammatory cascade in multiple body systems,32 inducing amplification of the cascade\".\n\nThe part, “Although subjects did not experience an inflammatory process at admission\" is not acceptable. Subjects do not experience inflammatory process they suffer with symptoms.\n\nIn subheading \"Correlation between levels of IL-6 with D-dimer, fibrinogen, and PT\", \"Since there was no correlation found between IL-6, ferritin, and the incidence of coagulopathy, we concluded. The word \"concluded\" may be changed to \"assumed\". Authors should mention e.g., \"in the first sample analysis...\" and then start elaboration. The entire part does not fit well with subsequent portions of discussion. Authors are advised to write in flow oriented manner.\n\nThe authors are also advised to discuss the results and its implications with a statistician.\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? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10232", "date": "22 Sep 2023", "name": "Cosphiadi Irawan", "role": "Author Response", "response": "Thank you for your constructive review. We have made some corrections in respond to your feedback. Introduction 1. The introduction is very brief. Basic concepts regarding pathophysiological aspects of inflammation in COVID-19 may be described here. The role of parameters included in metadata and their behaviour in COVID-19 may be elucidated. We have reconstructed the introduction part to be more comprehensive and narrative. We included the concept of pathophysiological aspect of inflammation in Covid 19 and the reason we did the study 2. The treatment protocol pertaining to corticosteroids, low molecular weight heparin or UFH, and antiviral medications e.g. remdesivir etc. should be mentioned. And the modifications of these drugs according to the severity of disease. We have added the protocol of covid 19 management used in this study Methods 1. The exclusion criteria should explain whether patients on oral anticoagulants, liver dysfunction were included or not. As a large size of study population had diabetes and hypertension, underlying coronary artery disease is likely to be present. Such population may have been on oral anticoagulant therapy prior to COVID-19 We have added more detailed criteria of exclusion in the methods section and corrected ambiguous statement in the methods. The population with prior anticoagulant therapy was excluded 2. C-reactive protein have been also studied and detailed in result section. It is a new parameter which is described by authors in results bearing no mention in methods We have added explanation of CRP analysis in this study in method section. CRP was not the main focus of this study thus we did not describe CRP comprehensively in the method section. 3. \"The patients were randomized\" is not correct as selection of patients and their classification was the decision of authors. we agreed and have revised the grammar 4. The part of discussion, \"Fig 4.Variable alterations between the first and second sample collection in the worsening group\" should be explained in the result section. We added more explanations about fig 4 5. With using terms like \"most\" and \"majority\", the percentages must be mentioned next to them. We agreed and added percentages next to them 6. Repetition of many result parameters in discussion e.g., \"males were most commonly affected in this study\" is not appropriate. we reconstructed the statements and reduced repetitions 7. Attempt may be made to include data on patients who worsened. we added some narratives about worsened patients in discussion 8. The normal reference laboratory values should be given for all parameters used in the study. We added normal reference laboratory values as footnotes below the table Discussion: 1. This section needs to be rewritten as there are many grammatical errors. The authors must seek professional help. We already consulted with professional translator and we made corrections in discussion. We hope the corrected version will convey the study result more clearly 2. Many lines and paragraphs are not correct. e.g., ”This study found that increased levels of IL-6 can predict the deterioration of subjects, but it is insufficient to justify it as a routine examination. Additionally, uncorrelated IL-6 with coagulopathy markerss due to the ability of IL-6 to activate the inflammatory cascade in multiple body systems,32 inducing amplification of the cascade\"., we reconstructed the statements 3. The part, “Although subjects did not experience an inflammatory process at admission\" is not acceptable. Subjects do not experience inflammatory process they suffer with symptoms. we reconstructed the statement 4. In subheading \"Correlation between levels of IL-6 with D-dimer, fibrinogen, and PT\", \"Since there was no correlation found between IL-6, ferritin, and the incidence of coagulopathy, we concluded. The word \"concluded\" may be changed to \"assumed\". Authors should mention e.g., \"in the first sample analysis...\" and then start elaboration. The entire part does not fit well with subsequent portions of discussion. Authors are advised to write in flow oriented manner. we tried to reconstruct the structure and add more conjunctive narrations. 5. The authors are also advised to discuss the results and its implications with a statistician." } ] } ]	1	https://f1000research.com/articles/11-1285
https://f1000research.com/articles/12-1189/v1	22 Sep 23	{ "type": "Research Article", "title": "Correlation of serum interleukin-6 levels and neutrophil-lymphocyte ratio in the severity of COVID-19", "authors": [ "Tenri Esa", "Budu Budu", "Budi Mulyono", "Gita Vita Soraya", "Andi Nilawati Usman", "Umi Solekhah Intansari", "Budu Budu", "Budi Mulyono", "Gita Vita Soraya", "Umi Solekhah Intansari" ], "abstract": "Background: Interleukin-6 (IL-6) is a pro-inflammatory cytokine that is produced at varying levels in patients with coronavirus disease 2019 (COVID-19). The neutrophil–lymphocyte ratio (NLR) is one of the new inflammatory markers of COVID-19. This study aimed to evaluate the differences in IL-6 level and the NLR in mild and severe COVID-19 and assess their correlation with COVID-19 severity and the correlation of IL-6 and NLR in COVID-19. Methods: A total of 91 patients with COVID-19 were divided into mild (n = 57) and severe (n = 34) COVID-19 groups. IL-6 levels were measured using the electrochemiluminescence immunoassay method on Roche Cobas e411. The NLR was the ratio of the total neutrophil and lymphocyte counts from complete haematology on the Sysmex XS-800i. Data were analysed using the Kolmogorov–Smirnov, Mann–Whitney, receiver operating characteristic curve, chi-square and Spearman correlation tests. The statistical test was significant at p <0.05. Results: Serum IL-6 levels and NLR significantly differed in mild and severe COVID-19. The median (min–max) IL-6 levels for mild and severe COVID-19 were 3.59 (1.50–638.30) pg/mL and 28.82 (5.52–926.30) pg/mL, respectively (p <0.001). The median (min–max) NLR in mild and moderate COVID-19 was 2.18 (0.69–15.58) and 8.13 (2.24–30.90), respectively (p <0.001). The obtained cut-off values for IL-6 and NLR were >6.99 pg/mL and >4.18, with odds ratios of 29.29 and 26.19, respectively. A positive correlation was found between IL-6 and NLR and COVID-19 severity (r = 0.612; p <0.001). Conclusions: The results indicated that serum IL-6 levels and NLR are higher in severe COVID-19 than in mild COVID-19. Patients with IL-6 levels >6.99 pg/mL and NLR >4.18 are 29 and 26 times more likely to suffer from severe COVID-19, respectively. Serum IL-6 levels and NLR are strongly correlated with COVID-19 severity. Serum IL-6 levels correlate with NLR in COVID-19.", "keywords": [ "Coronavirus disease-19", "COVID-19", "Interleukin-6", "IL-6", "neutrophil–lymphocyte ratio", "serum level", "disease severity", "inflammation" ], "content": "Introduction\n\nCoronavirus disease 2019 (COVID-19) is atypical pneumonia caused by the novel coronavirus of the coronaviridae class, i.e. severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).1 The World Health Organisation (WHO) declared this disease a pandemic.1,2 SARS-CoV-2 can fatally lead to acute respiratory distress syndrome (ARDS) or multiple organ distress syndrome (MODS).1,3\n\nBased on WHO and the Indonesian Ministry of Health data for COVID-19 as of 19 August 2021, the number of confirmed cases globally reached 209,201,939, with a total of 4,390,467 deaths (case fatality rate [CFR] 2.1%).4,5 In Indonesia, as of 19 August 2021, 3,930,300 confirmed cases, 3,472,915 recovered cases and 122,633 deaths from COVID-19 were reported (CFR 3.1%). South Sulawesi recorded 99,791 confirmed COVID-19 cases, 86,349 recovered cases and 1,807 deaths from COVID-19.4\n\nThe main characteristic of people with COVID-19 is an increase in the production of pro-inflammatory cytokines.6 Excessive increase in cytokines and inflammatory mediators such as interleukin (IL)-1β, IL-2, IL-6, IL-7, IL-8 and IL-10 and chemokines (CXCL 10 and CCL2) can exacerbate COVID-19 symptoms, which is characterised by a picture known as a ‘cytokine storm’.6,7 In patients with COVID-19, high IL-6 levels were found as an immunological response to SARS-CoV-2.8 Similarly, Coperchini et al. (2020) and Liu et al. (2020) demonstrated high serum IL-6 levels in patients with COVID-19 and circulating levels were positively related to disease severity.6,8 Several studies have found high IL-6 levels in severe conditions or ARDS compared with mild cases; thus, IL-6 could be a biomarker of COVID-19 severity.9,10\n\nLuo et al. (2020) and Liu et al. (2020) stated that the combination of IL-6 levels >20 pg/mL and CD8+ T lymphocytes <165 cells/μL is a prognostic indicator and can predict COVID-19 death.11,12 An increase in IL-6 levels of more than 10 times correlated with severe COVID-19, and decreased levels were related to successful therapy.11,12\n\nStudies have also found that the neutrophil–lymphocyte ratio (NLR) increased in COVID-19. This ratio is a new marker for assessing inflammation, including COVID-19. The NLR is obtained from a comparison of neutrophil and lymphocyte counts from a complete blood count.13 A high NLR is caused by an imbalance in the expressions of inflammatory cytokines and the upregulation of genes involved in the apoptotic pathway of lymphocyte cells during SARS-CoV-2 infection.14,15 A high NLR in patients with severe COVID-19 is characterised by lymphopenia and increased absolute neutrophil count; thus, the NLR may reflect an imbalance in inflammatory and immune responses in patients with COVID-19.16\n\nOngoing research on IL-6 and NLR in COVID-19 reveals a correlation between IL-6 and NLR with COVID-19 severity. Several studies have also reported different cut-offs. However, currently, no study in Indonesia has reported cut-offs for IL-6 and NLR. The results of this study are expected to provide information regarding the body’s immune response and inflammation in COVID-19, which is characterised by differences in serum levels of the pro-inflammatory cytokine IL-6 and an imbalance of inflammatory cells with the NLR. The results can be included in COVID-19 management.\n\nThe hypothesis is:\n\n1. IL-6 levels and NLR are higher in severe COVID-19 sufferers than mild ones.\n\n2. IL-6 and NLR are positively correlated with the severity of COVID-19.\n\n3. The higher the IL-6 and NLR cutoff, the more severe the symptoms of COVID-19.\n\n4. IL-6 serum levels are associated with NLR in COVID-19 sufferers.\n\n\nMethods\n\nThe study population included individuals suspected of COVID-19 who underwent examinations and received treatment at the UNHAS Public Hospital and Makassar City Hospital, Makassar, South Sulawesi, Indonesia. The research participants were COVID-19 sufferers who met the inclusion and exclusion criteria. Patients with COVID-19 are those with COVID-19 confirmed by reverse-transcription polymerase chain reaction (RT-PCR) and diagnosed by a clinician at the Department of Internal Medicine/Pulmonary Medicine, Hasanuddin University, through anamnesis and physical, laboratory and radiological examinations. While the exclusion criteria were lipemic, icteric or hemolytic specimens, insufficient sample volume and incomplete data.\n\nSufferers were categorised based on symptoms that have been determined by the Indonesian Ministry of Health 2020. Mild COVID-19 included confirmed COVID-19 cases showing mild and moderate symptoms. Mild symptoms include symptomatic cases without evidence of viral pneumonia or hypoxia. Symptoms include fever, cough, fatigue, anorexia, shortness of breath and myalgia. They may be accompanied by sore throat, nasal congestion, headache, diarrhoea, nausea, vomiting, loss of smell (anosmia), or loss of taste (ageusia). Moderate symptoms include cases with clinical signs of pneumonia (fever, cough, shortness of breath and rapid breathing) without signs of severe pneumonia, including SpO2 >93% on room air. Severe COVID-19 included confirmed COVID-19 cases with severe and critical symptoms. Severe symptoms include clinical signs of pneumonia (fever, cough, shortness of breath and rapid breathing) plus either respiratory rate >30 times/minute, severe respiratory distress, or SpO2 <93% on room air. Critical COVID-19 included cases with ARDS, sepsis, or septic shock.\n\nSerum IL-6 levels (pg/mL) were measured by the electrochemiluminescence immunoassay (ECLIA) method using the reagent of Elecsys IL-6 in an automatic Cobas e411 analyzer from Roche diagnostics. The NLR is a comparison in percentage value of total neutrophil and total lymphocyte counts obtained from a complete blood count on Sysmex XS-800i.\n\nOur complete method has been published on protocol.io (DOI: dx.doi.org/10.17504/protocols.io.rm7vzbworvx1/v1).17\n\nThe inclusion criteria were as follows: patients with COVID-19 confirmed by RT-PCR; the diagnosis was made by a clinician in the Department of Internal Medicine/Pulmonology based on anamnesis and physical, laboratory and radiological examinations; and willingness to participate in the study by providing written informed consent. The exclusion criteria were as follows: lipemic, icteric, or hemolysed specimens, insufficient sample volume and incomplete data.\n\nThis study was conducted in several research locations in Makassar, Indonesia: the Outpatient and Inpatient Department/ICU, RSPTN Hasanuddin University (UH RSPTN) Makassar and Makassar City Hospital for sampling, Laboratory of Siloam Hospital Makassar for the IL-6 measurement and Clinical Pathology Laboratory at RSPTN UH for complete haematology examination. The research was conducted in August 2020.\n\nIn this study, 3 mL of whole blood placed in ethylenediaminetetraacetic acid (EDTA) tubes was used for NLR examination from complete haematology, and 3 mL of the serum placed in plain tubes was used for IL-6 examination.\n\nThe research design was an analytic observational study with a cross-sectional approach. Each task in this study was carried out with the permission and knowledge of the patients who provided written informed consent. The study met the ethical requirements of the Health Research Ethics Commission, Faculty of Medicine, Hasanuddin University - Hasanuddin University RSPTN - RSUP Dr. Wahidin Sudirohusodo Makassar (KEPK FKUH-RSPTN UH-RSWS) No. 422/UN4.6.4.5.31/PP36/2020 dated 12th August 2020 at Hasanuddin University.\n\nSubjects consisted of 91 patients diagnosed with COVID-19 were recruited using exhaustive sampling. Namely, the researchers approached all patients suffering from COVID-19 at the Hasanuddin University Hospital and Makassar City Hospital, South Sulawesi, Indonesia. Research subjects who met the inclusion criteria were divided into two groups, namely mild and severe COVID-19. The identity of patients who met the inclusion criteria was recorded and they were provided with a complete explanation of what would be done to them and if they agreed they filled out and signed a written informed consent.\n\nStudy subjects who met the inclusion criteria had 3 mL of venous blood taken in an EDTA tube and a normal tube. The blood in the EDTA tube was checked for complete hematology. Serum was obtained after the EDTA tube containing blood formed a clot after 30 minutes at room temperature and was centrifuged for 20 minutes at 3000 rpm. Serum samples were collected until sufficient was obtained and it was stored at -20°C. A minimum of 3 ml of K2-EDTA plasma to prepare for minimum 30 μL of serum is required for the measurement of IL-6. Samples were thawed at 25°C prior to analysis. The following tools and materials were used during the study:\n\n• Cobas e 411 instruments (Cobas e411 analyzer; RRID:SCR_018369)\n\n• IL-6 reagent (Elecsys IL-6; RRID: AB_2938994)\n\n• IL-6 calibrator and control\n\n• Diluents\n\nThe test principle used was sandwich with the electrochemiluminescence immunoassay (ECLIA) method. Test work was carried out in advance with a series of preparations including daily calibration and quality control. Sample work was carried out according to the manufacturers’ instructions (https://diagnostics.roche.com/). The detailed protocol is as follows:\n\nIntended use: Elecsys IL-6 immunoassay is an in vitro diagnostic test for the quantitative determination of IL-6 (interleukin-6) in human serum and plasma\n\nTest principle: Sandwich principle.\n\n• First incubation: The sample are at (20-25)0 C before measurement. Then 30 μL of each sample was incubated with 0.9 μg/mL biotinylated monoclonal anti-IL-6-specific mouse antibody (Roche diagnostics, catalogue no. 05109442190).\n\n• Second incubation: After adding a monoclonal IL-6-specific antibody labelled with a ruthenium complex and streptavidin-coated microparticles, the antibodies form a sandwich complex with the antigen of the sample.\n\n• The reaction mixture is aspirated into the measuring cell, where the microparticles are magnetically captured onto the surface of the electrode. Unbound substances are then removed with ProCell/ProCell M/ProCell II M. Application of a voltage of 220V to the electrode induces chemiluminescent emission, measured by a photomultiplier, which is included in Cobas E411instrument.\n\n• Results are determined via a calibration curve which is an instrument- generated explicitly by 2-point calibration, and a master curve provided via the reagent barcode or e-barcode.\n\nMeasuring range: 1.5–5000 pg/mL (or 50000 pg/mL if diluted up to 10 times) Reference value: up to 7 pg/mL.\n\nElecsys IL-6 reagent pack\n\nThe Elecsys IL-6 immunoassay is an electrochemiluminescence immunoassay “ECLIA” intended for use on cobas e immunoassay analyzers. In this study, we used the Cobas e411 analyzer, which is related to use with the reagent rack pack labeled as IL-6. It consists of:\n\nM Streptavidin-coated microparticles (transparent cap), 1 bottle, 6.5 mL: Streptavidin-coated microparticles 0.72 mg/mL; preservative.\n\nR1 Anti-IL-6-Ab~biotin (gray cap), 1 bottle, 9 mL: Biotinylated monoclonal anti-IL-6 antibody (mouse) 0.9 μg/mL; phosphate buffer 95 mmol/L, pH 7.3; preservative.\n\nR2 Anti-IL-6-Ab~Ru (bpy) (black cap), 1 bottle, 9 mL: Monoclonal anti-IL-6 antibody (mouse) labeled with ruthenium complex 1.5 μg/mL; phosphate buffer 95 mmol/L, pH 7.3; preservative.\n\nCalibration\n\nTraceability: This method has been standardized against the NIBSC (National Institute for Biological Standards and Control) 1st IS 89/548 Standard.\n\nCobas e 411 analyzers: Every Elecsys reagent set has a barcoded label containing specific information for calibration of the particular reagent lot. The predefined master curve is adapted to the analyzer using the relevant CalSet.\n\nThe calibration interval may be extended based on acceptable verification of calibration by the laboratory.\n\nData were grouped according to the purpose and type, and appropriate statistical methods were selected. Basic data characteristics were described descriptively, and the normality of data was determined by the Kolmogorov–Smirnov test using IBM SPSS statistics version 26 (RRID:SCR_019096). Differences in IL-6 levels and NLR values between the mild and severe COVID-19 groups were analysed using the Mann–Whitney test, and the IL-6 and NLR cut-off values were determined from the receiver operating characteristic (ROC) curve. The correlation between IL-6 and NLR levels and COVID-19 severity was analysed using the chi-square test and the correlation between IL-6 and NLR and COVID-19 was analysed with the Spearman correlation test. The statistical test was significant at p <0.05.\n\n\nResults\n\nDuring the study period, 96 patients with COVID-19 met the inclusion criteria. Five patients were excluded because they did not meet the sample criteria, namely, one patient was lipemic, two involved lysate and two had small serum volumes; thus, they could not be examined. In total, the sample included 91 patients, consisting of 57 (62.6%) with mild COVID-19 and 34 (37.4%) with severe COVID-19. As shown in Table 1, 46 (50.5%) patients were male and 45 (49.5%) were female, and the age range 21–40 years had the highest number of patients. Patients were divided into mild and severe COVID-19, and no significant difference in sex was found among these patients (Table 2).\n\n* Chi Square test.\n\n** Kolmogorof Smirnov test.\n\n* Mann Whitney test.\n\nTable 1 shows that in the mild COVID-19 group, the highest number of patients were in the age range of 21–40 years, whereas in the severe COVID-19 group, most of the sufferers were in the age range of ≥41 years. A significant difference was found between the two groups, and this indicates that older age can be a comorbid factor in the development of COVID-19, which becomes more severe.\n\nBased on the NLR cut-off category of 3.13, most of the patients (n = 57 [78.9%]) in the mild COVID-19 group had NLR below the cut-off; in the severe COVID-19 group (n = 34 [94.1%]), the NLR values were above the cut-off (P <0.005). In a 2020 study in China, Yang found that old age and NLR were significantly related to COVID-19 severity.18\n\nIn this study, the IL-6 level and NLR were not normally distributed (Kolmogorov–Smirnov); thus, the differences in IL-6 levels and NLR in the two COVID-19 groups were analysed using the Mann–Whitney test. The median serum IL-6 in the mild COVID-19 group was significantly lower (3.59 pg/mL [min–max of 1.50–638.30]) than that of the severe COVID-19 (28.82 pg/mL [min–max of 5.52–926.30], P <0.005). The median NLR in the mild COVID-19 group was significantly lower (2.18 [min–max of 0.69–15.58]) than that of the severe COVID-19 group (8.13 [min–max of 2.24–30.90, P <0.005]).\n\nIn Figure 1 in the mild COVID-19 group, two patients had IL-6 levels higher than the average IL-6: a female patient (aged 68 years) who had an IL-6 level of 638.3 pg/mL and NLR of 2.81, who was diagnosed with mild COVID-19 accompanied by diabetes mellitus and hypertension; a male patient (aged 29 years) who had an IL-6 level of 485.4 pg/mL and NLR of 1.26, who was diagnosed with mild COVID-19 accompanied by fever, cough and nausea.\n\nIn the severe COVID-19 group, three patients had IL-6 levels higher than the average IL-6: a male patient (aged 73 years) who had an IL-6 level of 926.3 pg/mL and NLR of 30.9 and C-reactive protein (CRP) of 340.2 mg/dL, who was diagnosed with severe COVID-19 accompanied by bilateral pneumonia, cardiomegaly and aortic dilatation; a female patient (aged 60 years) who had an IL-6 level of 515.8 pg/mL and NLR of 2.82, who was diagnosed with severe COVID-19 accompanied by diabetes mellitus and hypertension; and a female patient (aged 54 years) who had an IL-6 level of 105.7 pg/mL, NLR of 17.68 and CRP level of 399.88 mg/dL, who was diagnosed with severe COVID-19 accompanied by hematochezia with suspected malignancy. In the severe COVID-19 group, two patients had an NLR higher than the existing average: a male patient (aged 73 years), with NLR of 30.9, who also had very high IL-6 levels, and was diagnosed with severe COVID-19 accompanied by bilateral pneumonia, cardiomegaly and aortic dilatation and a male patient (aged 58 years) who had an NLR of 23.68 and was diagnosed with severe COVID-19 accompanied by pneumonia and aortic atherosclerosis.\n\nFigure 2 shows the IL-6 and NLR cut-off; the ROC curve was used. In the IL-6 ROC curve, the area under the ROC curve (AUC) was 0.89 (95% CI 0.818–0.957; p <0.0001, and the IL-6 cut-off was >6.99 pg/mL). In the NLR ROC curve, the AUC was 0.93 (95% CI 0.881–0.984; p <0.0001), and the cut-off NLR was >4.18.\n\nThe relationship between IL-6 and NLR and COVID-19 severity was assessed using the chi-square test. The results are shown in Tables 3 and 4. As shown in Table 3, more patients with mild COVID-19 (n = 43, 75.44%) had IL-6 levels below the cut-off compared with those (n = 14, 24.56%) who had levels above the cut-off. In the severe COVID-19 group, more patients (n = 33, 97.06%) had IL-6 levels above the cut-off. In the chi-square test, a significant relationship was found between IL-6 levels and COVID-19 severity (P = 0.004; P <0.05). Patients with high IL-6 levels have 29 times the risk of suffering from severe COVID-19.\n\n* Chi-square-test.\n\n* Chi-Square test.\n\nThe results of the correlation analysis between NLR and COVID-19 are shown in Table 4. In the mild COVID-19 group, more patients (n = 50, 87.72%) had NLR values below the cut-off than those (n = 7, 12.28%) who had levels above the cut-off. In the severe COVID-19 group, 31 (91.18%) patients had NLR values above the cut-off. In the chi-square test, a significant relationship was found between the NLR and the degree of COVID-19 severity (P = 0.000; P <0.05). Patients with a high NLR had 26 times the risk of suffering from severe COVID-19.\n\nThe correlation between the serum IL-6 level and the NLR in COVID-19 was analysed using the Spearman correlation test, and the results are shown in Table 5 and Figure 3. After the Spearman correlation test, a P value of <0.001 was obtained, which indicated a significant correlation between the IL-6 level and the NLR in patients with COVID-19. A correlation coefficient of 0.612 (95% CI 0.459–0.729) was obtained indicating a moderate positive correlation. This suggested that an increase in the NLR is associated with an increase in IL-6 levels. However, this relationship may still be influenced by other internal factors. Our raw data has been published on figshare (https://www.doi.org/10.6084/m9.figshare.22736474).19\n\n* Spearman test.\n\n\nDiscussion\n\nThe COVID-19 guidelines in Australia and New Zealand, released in March 2020, identified lymphopenia and neutrophilia as prognostic markers of severe COVID-19, and the Centers for Disease Control and Prevention in the United States released guidelines emphasising that leukopenia (9%–25%), leukocytosis (24%–30%) and lymphopenia (63%) are the results of routine blood tests in patients who are hospitalised for COVID-19 (https://www.who.int/).20\n\nHaematological parameters in patients with COVID-19 demonstrated significant changes including decreased lymphocyte, haemoglobin and platelet counts, whereas combined parameters such as NLR, monocyte–lymphocyte ratio (MLR) and platelet–lymphocyte ratio (PLR) in patients with COVID-19 significantly increased, indicating that changes in routine blood parameters have clinical significance.21,22 In patients with severe COVID-19 and poor outcomes, the lymphocyte, eosinophil and platelet counts increased, whereas neutrophil, NLR, IL-6, procalcitonin, D-dimer, ferritin, amyloid A protein and CRP levels increased.23,24\n\nThe NLR was identified as a marker of systemic inflammation and a prognostic factor for mortality in patients with COVID-19. An imbalance in neutrophil and lymphocyte counts can indicate severe inflammation leading to complications such as sepsis, MODS and ARDS.14,25\n\nA high NLR can be caused by the dysregulation of inflammatory cytokine expression and the upregulation of genes involved in the lymphocyte apoptosis pathway caused by SARS-CoV-2 infection.26,27 A high NLR in patients with severe COVID-19 is characterised by an increase in neutrophil count and a decrease in lymphocyte count. The NLR may reflect an imbalance in the inflammatory and immune response in patients with COVID-19.23,27 Zhu et al. (2020) reported that the AUC for IL-6 was 0.84 (95% CI 0.708–0.962) and NLR was 0.69 (95% CI 0.537–0.842), which were slightly lower than our values, but similarly showed better sensitivity in predicting severe COVID-19.\n\nHaematological parameters in patients with COVID-19 change significantly, including a decrease in lymphocyte, haemoglobin and platelet counts. Meanwhile, combined parameters such as the NLR, MLR and PLR in patients with COVID-19 increased significantly.6,15 This suggests the clinical significance of changes in routine blood parameters. This is reflected in the results of this study, revealing higher NLR in patients with severe COVID-19.\n\nTo determine IL-6 and NLR cut-offs, ROC curves are used (Figure 2). Very few studies have investigated IL-6 and NLR cut-offs as predictors of COVID-19 severity. Several existing studies have found different IL-6 cut-offs. For example, Harold et al. (2020) found that at an IL-6 cut-off of >80 pg/mL, the patient may experience respiratory failure and require a ventilator. Liu et al. (2020) reported that an IL-6 cut-off of >34.1 pg/mL indicated severe complications.7,9 Meanwhile, Liu et al. (2020) obtained an NLR cut-off of >4.87 (95% CI 0.659–0.850) with a sensitivity of 56.52% and a specificity of 86.89%, which indicated an 8.5 times probability of experiencing critical/severe COVID-19 compared with a lower NLR.28 The combination of NLR and CRP was recommended as a potential predictor of severe COVID-19. AP et al. (2020) obtained an NLR cut-off of >3.3, with a sensitivity of 88% and a specificity of 64%, and Liu et al (2020) reported that an NLR of >3.13 and age >50 years indicated severe COVID-19 that required intensive care unit (ICU) admission.13,29\n\nAs shown in Table 3, the chi-square test revealed a significant relationship between IL-6 levels and COVID-19 severity (P = 0.004; P <0.05). Patients with high IL-6 levels have 29 times the risk of suffering from severe COVID-19.30 Zhu et al. (2020) analysed several inflammatory markers in mild and severe COVID-19 and assessed the association of these markers with COVID-19 severity. They found that high IL-6 levels, CRP and hypertension were independent risk factors of COVID-19 severity. IL-6 levels are significantly higher in severe than in mild COVID-19 at the first onset and 5–10 days afterward.10 Liu et al. (2020) found that IL-6 was greatly increased in severe COVID-19 and was significantly associated with fever, increased CRP, LDH and ferritin. IL-6 was positively related to COVID-19 severity. Thus, IL-6 could be a marker for severe COVID-19.12\n\nFu et al. (2020) compared haematological and inflammatory markers in mild and severe COVID-19 and found that leukocytes (white blood cells), NLR, D-dimer and fibrinogen values were significantly higher in severe COVID-19 than in mild COVID-19. The highest NLR AUC value was obtained among the four parameters, with 0.88, and the value was slightly lower than our results; however, their value similarly showed a strong association between NLR and COVID-19 severity.31\n\nUpon the entry of SARS-CoV-2 into the body, the immune system is activated, which causes an increase in several immune cells and the release of pro-inflammatory cytokines, resulting in an inflammatory response in the area of infection. Subsequently, the inflammation spreads throughout the body. Pro-inflammatory cytokines such as IL-6 are produced, and their levels are indirectly affected by the imbalance of neutrophils and lymphocytes. In severe COVID-19, IL-6 production and NLR values are also higher. Zhu et al. (2020) found a positive relationship between IL-6 and NLR (r = 0.428, P <0.001).30\n\nIn patients with severe COVID-19 and poor outcomes, the lymphocyte, eosinophil and platelet counts decreased, whereas neutrophil, NLR, IL-6, procalcitonin, D-dimer, ferritin, amyloid A protein and CRP levels increased. The NLR was identified as a marker of systemic inflammation and a prognostic factor for mortality in patients with COVID-19. AP et al. (2020) and Liu et al. (2020) analysed patients with mild and severe COVID-19 in China and found that high NLR and age were closely related to disease severity and were markers of poor prognosis. Thus, the NLR can be an independent prognostic biomarker in the management of COVID-19. Moreover, Liu et al. (2020) set an NLR cut-off of 3.13 and an age of 50 years as risk factors of severe COVID-19 requiring ICU admission.\n\n\nConclusions\n\nSerum IL-6 levels and NLR are higher in severe COVID-19 than in mild COVID-19 cases. Serum IL-6 levels and NLR are positively correlated with COVID-19 severity. If an IL-6 level is more than 6.99 pg/mL, then the patient has a 29 times risk of suffering from COVID-19 and if the NLR level is more than 4.18 pg/mL, then the patient has a 26 times risk. Serum IL-6 levels correlate with NLR in COVID-19.\n\nThis study was conducted using a cross-sectional design by collecting data when COVID-19 sufferers were hospitalised, no further observations were made on the course of the patient’s illness and the results of IL-6 and NLR examinations were not monitored. Thus, further research is needed to measure serum IL-6 levels and NLR in patients with COVID-19 using an IL-6 cut-off of >6.99 pg/mL and NLR of >4.18, which can be included in the laboratory parameters for the management of patients with COVID-19.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details was obtained from the patients.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Correlation of serum interleukin-6 levels and neutrophil-lymphocyte ratio in the severity of COVID-19’, https://www.doi.org/10.6084/m9.figshare.22736474. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nAll authors would like to thank Unhas General Hospital and Makassar City General Hospital, Indonesia for their infrastructure support.\n\n\nReferences\n\nKemenkes RI: Current Situation of Novel Coronavirus Development (Covid-19) 11 Agustus 2020.2020. Reference Source\n\nDirektorat Jenderal Pencegahan dan Pengendalian Penyakit (P2P), K. K. R: Guidelines for Prevention and Control of Coronavirus Disease (Covid-19). 5th revision.Juli 2020.\n\nWang L-S, Wang Y-R, Ye D-W, et al.: A review of the 2019 Novel Coronavirus (COVID-19) Based on Current Evidence. Int. J. Antimicrob. Agents. 2020; 55: 105948. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKemenkes G: Current Situation Development of COVID-19, update data 19 Agustus 2021.2021.\n\nWHO, W. H. O: COVID-19 Weekly Epidemiological Update: Edition 51, published 3 August 2021.2021.\n\nChen R, Sang L, Jiang M, et al.: Longitudinal hematologic and immunologic variations associated with the progression of COVID-19 patients in China. J. Allergy Clin. Immunol. 2020; 146: 89–100. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu F, Li L, Xu, et al.: Prognostic val ue 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\nCoperchini F, Chiovato L, Croce L, et al.: The cytokine storm in COVID-19: an overview of the involvement of the chemokine/chemokine-receptor system. Cytokine Growth Factor Rev. 2020; 53: 25–32. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHerold T, Jurinovic V, Arnreich C, et al.: Elevated levels of IL-6 and CRP predict the need for mechanical ventilation in COVID-19. American Academy of Allergy, Asthma & Immunology. 2020; 146: 128–136.e4. Publisher Full Text\n\nZhu Z, Cai T, Fan L, et al.: Clinical value of immune-inflammatory parameters to assess the severity of coronavirus disease 2019. Int. J. Infect. Dis. 2020; 95: 332–339. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLuo M, Liu J, Jiang W, et al.: IL-6 and CD8+ T cell counts combined are an early predictor of in-hospital mortality of patients with COVID-19. JCI insight. 2020; 5(13). Publisher Full Text\n\nLiu T, Zhang J, Yang Y, et al.: The potential role of IL-6 in monitoring severe case of coronavirus disease 2019. medRxiv. 2020.\n\nLiu J, Liu Y, Xiang P, et al.: Neutrophil-to-lymphocyte ratio predicts severe illness patients with 2019 novel coronavirus in the early stage. medRxiv. 2020.\n\nPonti G, Maccaferri M, Ruini C, et al.: Biomarkers associated wiith COVID-19 disease progression. Crit. Rev. Clin. Lab. Sci. 2020; 1–11.\n\nSun X, Wang T, Cai D, et al.: Cytokine storm intervention in the early stages of COVID-19 pneumonia. Cytokine Growth Factor Rev. 2020; 53: 38–42. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKong M, Zhang H, Cao X, et al.: Higher levels of neutrophilto-lymphocyte is associated with severe COVID-19. Epidemiol. Infect. 2020; 148: e139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEsa T, Budu, Mulyono B, et al.: Correlation of serum interleukin-6 levels and neutrophil-lymphocyte ratio in the severity of COVID-19. Research protocol. Protocol.io.2023.\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. Publisher Full Text\n\nEsa T, Budu, Mulyono B, et al.: Correlation of serum interleukin-6 levels and neutrophil-lymphocyte ratio in the severity of COVID-19. [Dataset]. Figshare. 2023. Publisher Full Text\n\nKhartabil T, Russcher H, van der Ven A , et al.: A summary of the diagnostic and prognostic value of hemocytometry markers in COVID19 patients. Crit. Rev. Clin. Lab. Sci. 2020; 1–17.\n\nSun S, Cai X, Wang H, et al.: Abnormalities of peripheral blood system in patients with COVID-19 in Wenzhou, China. Clin. Chim. Acta. 2020; 507: 174–180. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen X, Zhao B, Qu Y, et al.: Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely correlated with drastically elevated interleukin 6 (IL6) level in critically ill COVID-19 patients. Clin.Infect. Dis. 2020.\n\nChen R, Sang L, Jiang M, et al.: Longitudinal hematologic and immunologic variations associated with the progression of COVID-19 patients in China. J. Allergy Clin. Immunol. 2020; 146: 89–100. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen G, Zhao J, Ning Q, et al.: Clinical and immunological features of severe and moderate coronavirus disease 2019. J. Clin. Investig. 2020; 130: 2620–2629. Publisher Full Text\n\nLiu J, Liu Y, Xiang P, et al.: Neutrophil-to-lymphocyte ratio predicts severe illness patients with 2019 novel coronavirus in the early stage. medRxiv. 2020.\n\nKong M, Zhang H, Cao X, et al.: Higher level of neutrophilto-lymphocyte is associated with severe COVID-19. Epidemiol. Infect. 2020; 148: e139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBedel C, Korkut M: Neutrophil-to-Lymphocyte Ratio and Covid-19. Shock. 2021 Nov 1; 56(5): 874. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu YP, Li GM, He J, et al.: Combined use of the neutrophil-to-lymphocyte ratio and CRP to predict 7-day disease severity in 84 hospitalized patients with COVID-19 pneumonia: a retrospective cohort study. Ann. Transl. Med. 2020; 8(10): 635. 1-11. Publisher Full Text\n\nYang AP, Liu JP, Tao WQ, et al.: The diagnostic and predictive role of NLR, d-NLR and PLR in COVID-19 patients. Int. Immunopharmacol. 2020; 84, 106504. 1-8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu Z, Cai T, Fan L, et al.: Clinical value of immune-inflammatory parameters to assess the severity of coronavirus disease 2019. Int. J. Infect. Dis. 2020; 95: 332–339. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang A-P, et al.: The diagnostic and predictive role of NLR, d-NLR and PLR in COVID-19 patients.2020; 1–8." }	[ { "id": "209210", "date": "28 Sep 2023", "name": "Zhongheng Zhang", "expertise": [ "Reviewer Expertise ICU", "mortality", "sepsis" ], "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 study comparing the IL-6 and NLR in severe versus mild COVID-19 patients; however, due to the pandemic of COVID-19; the sample size is too small and the simple biomarker to associate severity of COVID-19 lacks novelty. More specifically, I have several comments:\nIL-6 is a well known biomarker in COVID-19, and this has already been used in clinical practice to guideline immunomodulatory therapy. I wonder what the rationale was to perform the current study.\n\n\"no study in Indonesia has reported cut-offs for IL-6 and NLR\" - this motivation does not make sense because COVID-19 is a global threat; there is no special traits for Indonesia patients.\n\nIL-6 is a simple marker of the inflammatory system; there are many other biomarkers, and one marker cannot fully reflect the immnue profile.\n\nTable 1 should give full characteristics of the cohorts, many important aspects are missing such as comorbidities, PF ratio, and severity of illness by SOFA.\n\nTable 2 is redundant, and can be combined with Table 1.\n\nThe lack of external validation prohibits use of the current results to other institutions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "222926", "date": "29 Nov 2023", "name": "Mukta Pujani", "expertise": [ "Reviewer Expertise Immunology", "hematology", "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 article is a little late as a lot of literature has been published on various parameters in Covid 19. But this article can be improved with several suggestions:\n1. A comparative table maybe drawn on the literature on NLR and IL-6 in Covid-19 from across the world especially South-East Asia. A few articles published early on and latest may be added in the table as mentioned below:\nPujani et al. (20211). Sayah et al. (20212). Pujani et al. (20213). Făgărășan et al. (20234).\n\n2. Since CBC forms the basis of the calculated index like NLR, other indices like PLR, MLR may also be compared if deemed fit.\n3. Were NLR and IL-6 co-related with any co-morbidities in Covid-19 patients?\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": [] }, { "id": "222933", "date": "04 Dec 2023", "name": "Luis Del Carpio-Orantes", "expertise": [ "Reviewer Expertise Internal Medicine", "Infectology", "Virology", "COVID-19", "Long COVID", "Arbovirus" ], "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\nAfter reviewing the document, I appreciated an interesting research effort where it was possible to establish IL-6 levels with INL levels, which is relevant since in many scenarios the measurement of IL-6 or other interleukins was not available, which was extremely serious and made it difficult to follow up on patients, mainly those affected by severe COVID-19 who warranted starting treatments such as tocilizumab or other anti-IL6 drugs. Likewise, in those latitudes with great deficiencies, various indices were used, of which the most significant was the INL, predominating its use over other hematological indices, so this work unites the ideal world where IL-6 levels could be measured and the unreal world where great deficiencies meant that other resources that were easily measurable with cytometry were used. Hematology, so I consider its relevance lies in this point, demonstrating that correlation between both measurements. Given the above, I consider it to be a study worthy of indexing.\nI leave a reference in which various hematological indices have been used (Carpio-Orantes et al., 20201).\n\nIs the work 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": "222937", "date": "13 Dec 2023", "name": "Satyendra K. Tiwary", "expertise": [ "Reviewer Expertise Surgery", "Sepsis", "Wound", "Oncology", "Surgical Gastroenterlogy", "Phlebology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n\"Correlation of serum interleukin-6 levels and neutrophil-lymphocyte ratio in the severity of COVID-19\" is the research article which was conducted more than 3 years back in August 2020 and after 3 years a lot of spectrum and problem with COVID-19 has changed globally leading to less relevance of the article in current situation globally. Although a good correlation of the IL-6 and NLR with severity of the COVID-19 is obvious from this research, there are a lot of inclusions to enrich this article in content and relevance. 1.Sample size of 91 is quite small considering the volume and epidemic of the disease which may be more value if sample size increased as almost every indoor COVID-19 patient were investigated for IL-6 and NLR almost everywhere.\n\n2. Only two markers are useful in COVID-19, but inclusion of more biomarkers may be of more scientific message considering more strength in the study.\n\n3. External Validation of the study is lacking which should be included for the authencity and strength in the study.\n\n4. Flow chart of the methodology should be included for the better perspectives in the understanding.\n\n5. Immunoassay images added may enrich the manuscript.\n\n6. Table 1 and Table 2 should be merged for compact data analysis.\n\n7. Limitation of the study must be added in the conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1189
https://f1000research.com/articles/12-1188/v1	22 Sep 23	{ "type": "Study Protocol", "title": "Comparative evaluation of accuracy of cranial prosthesis designed by four different workflow protocols analysed by software", "authors": [ "Ritul Jain", "Sweta Kale Pisulkar", "Sweta Kale Pisulkar" ], "abstract": "Cranioplasty aims to reconstruct skull defects from tumours, congenital anomalies, decompressive craniectomies, and fractures in a cosmetically acceptable manner. Since the 1970s, polymethyl methacrylate (PMMA) prostheses have been manually prefabricated using a variety of techniques. However, more recent computer-aided design and computer-aided manufacturing (CAD/CAM) techniques appear to have eclipsed these older methods. These techniques essentially involve using imaging from the patient's cranial defect and prefabricating the PMMA prosthesis using a 3D printer. The traditional methods for producing prostheses require a number of intricate stages, can be extremely stressful for the patient, and their success depends on the expertise of the maxillofacial team. Although there have been advances in digital fabrication for prosthetics, there are still some constraints that prevent a full transition to digital fabrication for the final stages of prosthesis construction. Advance training and modification of current treatment procedures are required due to the introduction of new technologies and methods in the field of maxillofacial prosthodontics. The aim of this study is to compare and evaluate the accuracy of cranial prosthesis designed by conventional, digital and two hybrid workflows We will report on 10 consecutive patients who have undergone cranioplasty surgery or had trauma for an extensive skull defect. The final prosthesis will be analyzed using the software CloudCompare for its accuracy by using reverse engineering principle. The purpose of this research is to develop a hybrid protocol for fabricating a prosthesis that is both cost-effective and more dimensionally accurate than its conventional counterpart, thereby providing ease for both the patient and the maxillofacial team.", "keywords": [ "Craniomaxillofacial defects", "Cranial Prosthesis", "Digital Workflow", "Conventional Workflow", "Hybrid Workflow", "Cranioplasty" ], "content": "Introduction\n\nCranioplasty aims to reconstruct skull defects from tumours, congenital anomalies, decompressive craniectomies, and fractures in a cosmetically acceptable manner. In addition to attempting to safeguard underlying brain tissue from cranium defects, cranioplasty also seeks to re-establish normal calvarial shape in a way that is aesthetically appropriate. It can be carried out using either alloplastic devices for repair or osteoplastic reconstruction. Among the materials used for cranial alloplastic implants are metal, acrylic resin, polyethylene, and silicone.1\n\nSeveral centers now consider methyl methacrylate cranioplasty to be preferable to titanium mesh due to its radiolucency, cheaper cost, ease of shaping, light weight, and lower rates of infection when compared to titanium implants.1 Previous studies have demonstrated the potential to transform a conventional workflow from one that is highly skill-dependent, time-consuming, labour-intensive, costly, and unpleasant for the patients due to discomfort of the procedure, to one that is straightforward and predictable digitally.1\n\nOne of the earliest publications on digital maxillofacial prosthesis Penkener et al. in 1999 described a method for creating a patient’s unique, life-sized, three-dimensional ear model using a computer and a CT scan Endoplan (Medical Diagnostic Computing, Zeiss, Germany) with a semiautomatic contouring program for CBCT segmentation of the soft tissue, based on Hounsfield units (HU) thresholding.2\n\nRecently, maxillofacial prosthodontics has adopted digital technology more and more. The studies on the production of maxillofacial prostheses with CAD and CAM (computer-aided design and computer-aided manufacturing) technology that have been published in the last 20 years2 have shown that it is feasible to switch from a traditional workflow that is extremely skill-dependent, laborious, costly, and unpleasant for the patients to a digitized version.\n\nAlthough there have been advances in digital fabrication for prosthetics, there are still some constraints that prevent a full transition to digital fabrication for the final stages of prosthesis construction. Advanced training and modification of current treatment procedures are required due to the introduction of new technologies and methods in the field of maxillofacial prosthodontics.3\n\nAs of right now, only highly skilled dental professionals or CAD engineers may utilise the interface and software used for processing and developing maxillofacial prosthesis as CAD software is expensive and requires a skilled personnel to carry out the fabrication process.4\n\nDigital dentistry currently faces something of a split; industry-driven technological solutions (primarily in the CAD-CAM and imaging sectors) are already realities, whereas AI-technologies concentrating on diagnosis and treatment planning are currently theoretical rather than reliable applications. One important job in the future is to bridge this gap. There is great need for collaborative and interdisciplinary research that combines technology and dental care.\n\nThe purpose of this research is to develop a hybrid protocol for fabricating a prosthesis that could be more accurate than the conventional technique in terms of accuracy, precision and fit of the prosthesis, and provide ease for both the patient and the maxillofacial team. This research will help prosthesis providers understand the application of a digital workflow with the addition of a conventional workflow and how they could use this in providing the finest prosthesis.\n\nThe aim of this study is to evaluate the accuracy of cranial prosthesis designed with conventional, digital and hybrid workflow, using software analysis.\n\nThe objective of this study is to evaluate the accuracy of prostheses fabricated from the conventional, two hybrid, and 3D workflow and then compare their accuracy with the help of software analysis, i.e. reverse engineering principle.\n\n\nProtocol\n\nEthical approval for this protocol was granted by Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha, with IEC reference number DMIHER (DU)/IEC/2023/853 on 31st March 2023.\n\nWritten informed consent will be taken from the participants. In the case of unconscious patients, the relatives including the parents or spouse can provide written informed consent instead. In the case of minors the parents can provide written informed consent.\n\nThis will be a hospital-based study with an observational and analytical design.\n\nThis research comprises a hospital based observational and analytical study, carried out in the Department of Prosthodontics, Sharad Pawar Dental College, Sawangi (Meghe), Wardha, Datta Meghe Institute of Higher Education and Research (Deemed to be University).\n\nData will be collected after the IEC approval and this study will be completed in 2 years.\n\nEligible patients will be those above 10 years of age, who have been referred from the Department of Neurology to the Department of Prosthodontics with a cranial defect, which may be due to a congenital or acquired anomaly. Only patients who have given full consent to participate in the study will be included.\n\nThe exclusion criteria for the study will be the patients who are not willing to participate and give consent.\n\n\nMethods\n\nThis will be a hospital-based study on patients who report to Department of Prosthodontics, referred from the Department of Neurology for the fabrication of their outer cranial stent for defects due to congenital and acquired anomalies. In prosthodontics, we deal with maxillofacial prostheses which includes fabrication of stents and cranial rehabilitation for patients from the neurosurgery department. The cranial stent will be fabricated from polymethyl methacrylate with four different workflow protocols for the research, for the purpose of checking their accuracy. Each patient will have four stents fabricated. The cranial stent fabricated using CT scan 3D workflow will be taken as gold standard. This stent will be then compared for accuracy using reverse engineering principle using a software analysis.\n\nInitially, the impression of the patient will be taken and the CT scan will be taken of the defect.\n\nFirst, the impression of the defect will be created using the traditional method by the primary investigator for the conventional prosthesis, and the prosthesis will be designed with conventional workflow i.e., an impression will be made and then the cast will be fabricated in type 3 dental stone, and over the master cast the wax pattern is fabricated. This wax pattern is flasked and packed with polymethyl methacrylate, and after this finishing and polishing is done (Figure 1).\n\nFor the 3D prosthesis, a CT scan will be taken of patient in the neurology department, and the prosthesis will be designed in the prosthodontics department with CAD software and, with the help of mirroring the image, the 3D print will be created (Figure 2).\n\nFor the first hybrid prosthesis, an impression will be taken of the defect by the primary investigator using conventional alginate, and the cast will be fabricated with the type 3 dental stone. The cast will then be scanned and the mould will be fabricated with rapid prototyping, i.e., we will 3D print it and the prosthesis will be fabricated conventionally from PMMA (Figure 3).\n\nThe second hybrid prosthesis will be made from the CT scan of the patient and the stl file that it generates. The prothesis will be fabricated by rapid prototyping, i.e., 3D printing and designed conventionally from PMMA (Figure 4).\n\nAll four prosthesis will be designed using conventional, 3D, and the two hybrid workflows, and will be scanned using an extraoral EinScan Pro 2x 2020 scanner, and will be converted into point cloud data that is the points taken from the four prostheses on a 3D shape in software depicting its coordinates in the X,Y, and Z axis. This data will be compared by overlapping the prosthesis on the control group, i.e. 3D group, and compared for its change in the surface deviation in 3D space. Charts will be prepared for the surface deviation thus depicting the dimensional accuracy of prosthesis (Figure 5).\n\nThe study will measure the accuracy of all the prostheses made from the 4 different workflows, which will check the size, shape, and fit of the prostheses. As this study is an in vitro study, the fit cannot be checked on a patient. Since the prosthesis is fabricated with different protocols, the cost will differ for each prosthesis; the best fitting and most accurate prosthesis may be more expensive, so this is a variable that can act as a confounding factor and will be considered in the analysis.\n\nThe expected outcome of the study is that the hybrid prosthesis would be a better fit and more accurate than its conventional counterpart. For dental professionals the paradigm shift towards digital technology has many obstructions, such as in infrastructure and costly equipment, so for an accurate prosthesis opting for a hybrid solution is needed so that we can benefit from both technology and the conventional process.\n\nBias will be minimized by random selection of patients based on inclusion and exclusion criteria.\n\nThe calculation of sample size is described in this section. The primary variable is the cranial prosthesis defect measurement.\n\nConventional method\n\nMax (positive) deviation in conventional prosthesis = 3.5, max (negative) deviation in conventional mould = 1.0\n\nAverage deviation for prosthesis mould = (3.5+1)/2 = 2.25\n\nDigital CAD method\n\nMax (positive) deviation in CAD fabricated prosthesis mould = 2.5, max (negative) deviation in CAD mould = 1.0\n\nAverage deviation for prosthesis mould = 1.755\n\nMean difference of deviation between two treatments = 0.5\n\nEstimated standard deviation = (0.4) mean difference [mean difference between the two average deviations of prosthesis mould from conventional and digital method].\n\nAssumption\n\nZα=1.64\n\nα=Type I error at 5%\n\nZβ=0.84atequivalence1−β=Power at 80%\n\nσ=std.dev\n\nMinimum sample size required N = 2 *[(1.64+ 0.84)2(0.4)2] / (0.5)2 = 10 per group\n\nAll results obtained from the comparison of the prostheses fabricated from the four different workflows will be analyzed using R software version 4.3.2. Data collection from the prostheses fabricated for patients with congenital and acquired cranial defects who are undergoing cranioplasty, made with four different workflows, will be converted into point cloud i.e. the points of all four prostheses on 3 dimensional axis, X,Y, and Z. This data will be fetched from (point cloud) software and will be comparatively analysed for surface deviation in the 3 dimensional axes, defect significance (mean) in size, shape, fit and accuracy, using the one way ANOVA test. A p-value <0.05 will be considered as significant value for providing greater accuracy.\n\nThe findings related to this study will be published in indexed journals and presented in scientific tracks/conferences. This study will help us in standardizing a protocol for hybridization of digital technology with conventional methodology to establish a more accurate and precise treatment deliverance of maxillofacial prosthesis.\n\nThe craniomaxillofacial prostheses made with different workflows can be checked for their accuracy and cost efficacy, and the best suited one can be further used in patients.\n\nThe limitations for this study are that only cranial defects will be considered, but the branch of maxillofacial prosthodontics as a whole deals with all the maxillofacial prosthesis. This is an in vitro study; as the prosthesis is not fitted in a patient its final fit cannot be assessed.\n\nThe study is not yet started. It will begin in September 2023.\n\n\nDiscussion\n\nDe La Pena et al. conducted a case study of a 3D-designed PMMA cranial prosthesis in 2018 and found that the prosthesis conformed precisely to the osseous defect. No problems, such as rejection, toxicity, local or systemic infection, were seen at the 6-month follow-up, and the cosmetic improvement was extremely noticeable and pleasing. A customised 3D PMMA prosthesis has benefits in terms of price, cosmetic quality, operation time, and biocompatibility.6\n\nSchon et al. in 2020 in 16 patients demonstrate that systematic in-hospital manufacture of patient-specific implants made of conventional PMMA with 3D printer assistance is viable for severe calvaria deformities and may be simply applied in routine practise. When a patient needs a cranioplasty but does not have access to a bone flap, this manufacturing method may lower treatment expenses.7\n\nRotaru et al. did a study to assess quantitatively whether a symmetric reconstruction of the calvaria could be achieved using 3-dimensional (3D) custom-made implants and to examine any complications caused by the cranioplasty. He found out that the implants could be highly helpful for treating significant and irregularly shaped cranial abnormalities.8\n\nBeri et al did in year 2022 published a trial to evaluate the impression making process in the craniomaxillofacial defects by traditional method 3D scanning and photogrammetry. In these trial all the impression was assessed by the point cloud data and checked for its accuracy.9\n\n\nConclusion\n\nThe purpose of this research is to develop a hybrid protocol for fabricating a prosthesis that could be more accurate than the conventional technique in terms of accuracy, precision and fit of the prosthesis, and provide ease for both the patient and the maxillofacial team. This research will help prosthesis providers understand the application of a digital workflow with the addition of a conventional workflow and how they could use this in providing the finest prosthesis.", "appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nZenodo: STROBE checklist for ‘Comparative evaluation of accuracy of cranial prosthesis designed by four different workflow protocols analysed by software’, https://doi.org/10.5281/zenodo.8172894.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSorour M, Caton WL, Couldwell WT: Technique for methyl methacrylate cranioplasty to optimize cosmetic outcome. Acta Neurochir. 2014 Jan; 156: 207–209. PubMed Abstract \| Publisher Full Text\n\nCristache CM, Tudor I, Moraru L, et al.: Digital Workflow in Maxillofacial Prosthodontics—An Update on Defect Data Acquisition, Editing and Design Using Open-Source and Commercial Available Software. Appl. Sci. 2021 Jan; 11(3): 97. Publisher Full Text\n\nMishra SK, Chowdhary R: Does Complete Digitization in Maxillofacial Rehabilitation Become a Reality in Near Future? Int. J. Prosthodont. Restor. Dent. 2019; 9(3): 67–68. Publisher Full Text\n\nBansod AV, Pisulkar SG, Dahihandekar C, et al.: Rapid Prototyping in Maxillofacial Rehabilitation: A Review of Literature. Cureus. September 09, 2022; 14(9): e28969. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeel S, Eggbeer D, Burton H, et al.: Additively manufactured versus conventionally pressed cranioplasty implants: an accuracy comparison. Proc. Inst. Mech. Eng. H J. Eng. Med. 2018 Sep; 232(9): 949–961. PubMed Abstract \| Publisher Full Text\n\nDe La Peña A, De La Peña-Brambila J, Pérez-De La Torre J, et al.: Low-cost customized cranioplasty using a 3D digital printing model: a case report. 3D Print Med. 2018 Apr 12; 4: 4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchön SN, Skalicky N, Sharma N, et al.: 3D-Printer-Assisted Patient-Specific Polymethyl Methacrylate Cranioplasty: A Case Series of 16 Consecutive Patients. World Neurosurg. 2021; 148: e356–e362. PubMed Abstract \| Publisher Full Text\n\nRotaru H, Stan H, Florian IS, et al.: Cranioplasty with custom-made implants: analyzing the cases of 10 patients. J. Oral Maxillofac. Surg. 2012 Feb 1; 70(2): e169–e176. PubMed Abstract \| Publisher Full Text\n\nBeri A, Pisulkar SK, Bagde AD, et al.: Evaluation of accuracy of photogrammetry with 3D scanning and conventional impression method for craniomaxillofacial defects using a software analysis. Trials. 2022; 23: 1048. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "260417", "date": "04 Apr 2024", "name": "Gopi Chander", "expertise": [ "Reviewer Expertise Prosthodontics", "Dental materials", "Implantology", "Maxillofacial prosthodontics" ], "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\nSince the study has not yet been conducted (as mentioned in the study status), there are no results or findings presented in the manuscript. Including preliminary results or anticipated outcomes could provide readers with a clearer understanding of the expected impact of the research. sample size calculation section includes several assumptions, such as the estimated standard deviation and mean difference of deviation between two treatments. These assumptions may influence the accuracy of the calculated sample size. Providing justification or sensitivity analysis for these assumptions would enhance the robustness of the sample size estimation. Include a discussion section would allow the authors to interpret the findings, compare them with existing literature, discuss limitations, and propose future directions for research. Some sections of the manuscript could be further clarified and organized for readability. For example, the methods section could be structured more coherently, with clear subheadings for each workflow (conventional, digital, hybrid). While the manuscript outlines the statistical analysis plan, providing more details on specific statistical tests and assumptions (e.g., one-way ANOVA) would enhance the transparency and reproducibility of the study.\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? No", "responses": [] }, { "id": "260421", "date": "09 May 2024", "name": "Ping Di", "expertise": [ "Reviewer Expertise oral implantology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Inclusion criteria \"Eligible patients will be those above 10 years of age, who have been referred from the Department of Neurology to the Department of Prosthodontics with a cranial defect, which may be due to a congenital or acquired anomaly. \" The question is, besides age and cranial defect, are there any other requirements for inclusion criteria? 2.This is an in vitro study; as the prosthesis is not fitted in a patient its final fit cannot be assessed. Each of the four methods has its own systematic errors, and since the true value can not be obtained, how can one determine which method yields more accurate?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] }, { "id": "246771", "date": "25 May 2024", "name": "Andrew J. Kobets", "expertise": [ "Reviewer Expertise Craniofacial neurosurgery" ], "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 series of 10 patients in which a hybrid methodology for creating PMMA cranial implants in order to improve upon classical methods. First, why was there no input from the neurosurgery team, who are the experts in cranioplasty surgery? The standard of care for this procedure if far beyond the days of PMMA and the literature review on this topic as included in the discussion is far from complete, limiting this report's academic validity. Why is there no mention of PEEK or new sonolucent materials? PMMA is no longer the standard of care, and it is unclear as to why the hybrid workflow is even measured against a \"classic\" workflow, as no one fabricates these cranioplasties today, or over the last decade without using a CT to create a matched cranioplasty. There are many protocols that we can demonstrate as being much more efficient than standard of care over 30 years ago. The Discussion as mentioned is just so sparse and neglects so much of the current literature. It just feels disconnect from current care and its relevance to current patient management if difficult to ascertain. The authors should review the current standard of care and compare their methodology to it in order to support the academic validity of this report.\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": [] } ]	1	https://f1000research.com/articles/12-1188
https://f1000research.com/articles/12-1187/v1	22 Sep 23	{ "type": "Research Article", "title": "Corporate social responsibility & students’ perceptions: evidence from Indian higher education institutions", "authors": [ "Premendra Kumar Singh", "Raju Ganesh Sunder", "Pravin Narayan Mahamuni", "Elangbam Nixon Singh", "Bidhu Kanti Das", "Anand G. Jumle", "Rajeshkumar Kashayp", "Premendra Kumar Singh", "Pravin Narayan Mahamuni", "Elangbam Nixon Singh", "Bidhu Kanti Das", "Anand G. Jumle", "Rajeshkumar Kashayp" ], "abstract": "Background: For many, the understanding of Corporate Social Responsibility (CSR) may sound a rather new topic, but it has been pondered upon by great thinkers of the world for many decades. The initial form of CSR was more of philanthropic which has become more of mandatory norm in Indian context. We believe the future of a nation are the youth of the nation and their perceptions on the matter of CSR are of great importance. Therefore, the purpose of the current study is to investigate the many viewpoints that students have about CSR and to determine whether or not socioeconomic characteristics (gender, age, professional experience, and academic degree) influence these views.\nMethods: The research methodology comprises of utilization of an accepted scale (PRESOR) for collecting data of perception on CSR. Data was collected using an online questionnaire, distributed to students at Higher Educational Institutes of Northeast India. Responses from 272 students were received out of which we rejected unengaged responses of 25 students, and we continued with responses from 247 students. We have utilized Factor Analysis, Multivariate analysis of variance (MANOVA), & t-test for the scrutinizing the collected data.\nResults: The perceptions of students show a variety of dimensions, which may be categorised as: (a) value CSR, (b) against CSR, and (c) neutral to CSR. It is also found that the sociodemographic variables have a statistically significant influence on students' notion of CSR.\nConclusions: This study is one of the first investigative works that has utilized modified PRESOR model for examining the perception of CSR in Indian context. The model was found to be fit to be used in Indian context. The study concluded that sociodemographic variables such as Age, Education, Professional Experience influences perception of CSR.", "keywords": [ "Corporate Social Responsibility", "Perceptions", "Higher Educational Institutes." ], "content": "Introduction\n\nCorporate social responsibility (CSR) has received symbolic recognition in the eyes of corporations, customers, and academic professionals due to the considerable societal consequences that corporations have (Džupina, 2016; Ortiz-Avram et al., 2018; Schmidt and Cracau, 2018). Companies evolving progressively are mindful of the role of corporate social responsibility (CSR) in terms of global competitiveness (Petrović-Ranđelović et al., 2015). This understanding allows them to concentrate not just on delivering profits, but also to make informed choices that are morally & socially acceptable to all concerned stakeholders, such as the community, the climate, and investors (Bir et al., 2009; Teixeira et al., 2018).\n\nRegardless of the fact that there has been extensive research on CSR for more than five decades, (e.g., Bowen, 1953; Davis, 1973), many academicians maintain to be interested in this area (e.g., Burton & Goldsby, 2009; Ortiz-Avram et al., 2018). Despite this, many respected academics have moved their attention from CSR to the achievement of corporations in the sphere of social responsibility (Wartick and Cochran, 1985) and how it affects the company's overall success (Ciampi, 2018; Waddock and Graves, 1997) and if CSR plays role in customer loyalty (Park and Kim, 2019). According to Maignan (2001), concerns pertaining to CSR, on the other hand, continue to be a subject of research that receives little attention. This is especially true with research on the perception that students have about CSR, particularly in the Indian context.\n\nIn simple terms, social responsibility may be viewed as a collection of a course of action adopted by corporations to boost economic, societal, and environmental situations, efforts that go above and beyond the requirements of law (Godfrey et al., 2009). As a result, given the fact that responsibilities towards the society are gaining more and more significance in the corporate world, it is essential to explore the opinions of workers, executives, and entrepreneurs, or, more specifically, the perceptions of Higher Education Institutions (HEIs) students, on this aspect (Teixeira et al., 2018).\n\nA person’s positive, negative or neutral perceptions of CSR are influenced by culture and the nation they are brought up in (Usunier and Lee, 2013). Available literature also shows that students from various cultural backgrounds have varied perspectives on CSR (Akbaş et al., 2012; Pätäri et al., 2017; Wong et al., 2010). The intention of this paper is to contemplate if students of India have different perceptions on understanding of CSR and also to substantiate if sociodemographic factors instigate students’ perception on the area of CSR.\n\nThis paper initiates itself with a literature review indicating the applicability of the topic in Higher Education Institution (HE). This also comprises of the various important definition of CSR, the importance and actions leading to socially responsible actions apart from set of hypotheses and purpose of studying the students’ perception on CSR. These are addressed by utilizing questions used earlier in a study which assessed students’ notion of corporate social responsibility (Fitzpatrick, 2013; Teixeira et al., 2018).\n\nThis study is conducted to investigate the perception by taking a representative sample of students from Indian Higher Education Institutions by employing the model proposed by Fitzpatrick (2013) and Teixeira et al. (2018) and utilized various univariate and multivariate statistical techniques that were most appropriate for the study's objectives.\n\nCSR becomes a crucial business choice as a result of globalization's influence on the business, climatic and economic development (McGuire et al., 1988) so that companies can meet the expectations of a wider range of customers and stakeholders (Dahlsrud, 2008). Corporations that practise corporate social responsibility (CSR) recognise that their actions have consequences for a wide range of people and places, including consumers, suppliers, workers, shareholders, communities, and the climate (Wymer and Rundle-Thiele, 2017). Although CSR is a hot issue, there are no mutual agreement on how the concept should be defined. This is because various scholars propose different definitions based on different aspects, with just a few sharing anything in common (Dahlsrud, 2008).\n\nCSR seems like it ought to be part of the \"triple bottom line,\" which holds that an organization’s success is determined by three factors: its financial health, its commitment to the environment, and its impact on society (Zadek et al., 2003). Thus, CSR has the potential to initiate corporate social progress, which can come in a variety of forms. Some of these forms include internal changes regarding manufacturing methods, minimised environmental impacts, increases in satisfaction among employees, and new interactions along the chain. Investments in the building infrastructure of local communities and growth of community-based activities are also possible outcomes of CSR (Aguilera et al., 2007).\n\nTherefore, companies need to integrate social consciousness into their overarching strategies by doing things like differentiating their goods depending on the social traits they possess. This will increase brand loyalty and establish the business as a trustworthy and ethical option for consumers (Siegel and Vitaliano, 2007).\n\nThe number of socially responsible investment funds has grown, and so has the amount of money invested in them, as noted by Fitzpatrick (2013, p. 86). CSR is a widely debated issue in the commercial and academic spheres because of its pervasiveness in today's global economy (Doh and Guay, 2006). Carroll (2016) argues that creativity, market distinctiveness, enthusiastic staff participation are the reasons for companies to adopt CSR whereas Kurucz et al., 2009, suggest that cost and risk reductions, enhancement of competitive advantage, bolstering of firm legitimacy and reputation, and the creation of win-win scenarios for both the company and society are the reason why companies must accept and work towards the advancement of CSR. Companies should focus on producing value rather than merely following current procedures since there is a risk that huge corporations would engage in unethical behaviour in their pursuit of profit maximisation (Santos, 2012).\n\nAlthough CSR has not yet permeated every sector of industry (Sánchez-Hernández and Mainardes, 2016), this topic is focus of fresh research from a wide range of institutions, most notably, Higher Education Institutes (HEI) (Vallaeys et al., 2009; Vázquez et al., 2014, 2016). Vallaeys et al., (2009), defined CSR as competent leadership in all areas of educational institutions at a higher level (teaching, research, extension, and administration) is central to this approach. As a result, several universities' business programmes now emphasise ethical behaviour and accountability to society topics in their curriculum to better meet the needs of businesses and the community (Assudani et al., 2011).\n\nIn regard to Higher Education Institutions, CSR must include all phases of an institution's teaching, research, and knowledge transfer activities, including planning, design, implementation, and evaluation (Esfijani et al., 2013). The terminology \"University Social Responsibility\" (USR) refers to collective responsibilities of Higher Education Institutions in areas such as Increasing access to higher education, creating market-relevant curriculum, producing high-quality graduates, reducing waste, bolstering research capacity, and meeting other societal demands are all goals of changing the academic system (Esfijani et al., 2013). Institutions committed to morality, good administration, and ecological consciousness, social participation, and the promotion of values; HEIs shape society through educating its members and expanding their horizons via the dissemination of information (Vallaeys et al., 2009).\n\nTherefore, higher education institutions (HEI) are crucial in producing ethical and socially conscious business leaders (Alsop, 2006), and because of this reason an increase courses devoted to CSR is observed (Wymer and Rundle-Thiele, 2017). Sánchez-Hernández & Mainardes (2016) note that a combination of factors—including increased competitiveness and shifting demographics—has resulted in higher education institutions (HEIs) being increasingly student-centric.\n\nGiven that corporate social responsibility (CSR) has grown in importance and relevance in the corporate world, studying the views of today's students—the employees, employers, and company owners of tomorrow - on the topic is intriguing (Assudani et al., 2011, p. 103). As a result, HEIs should aid in the preparation of socially responsible persons by emphasising the significance of upholding ethical standards in the workplace (Wymer and Rundle-Thiele, 2017). It is because, according to these authors, “education on ethical topics increases moral cognition and deliberation” (Lau, 2010).\n\nThere has been some empirical work done to quantify students' a conscience of duty to others (Elias, 2004), several categories and dimensions can be identified as a result (González-Rodríguez et al., 2013). Despite widespread agreement that CSR helps businesses thrive and raises their profile in the public eye, and despite CSR's maturation into a useful strategic tool, opinions on it among students are split (Mcguire et al., 1988; Schmidt & Cracau, 2018; Ugwuozor, 2020)).\n\nThe distinct aspects of the social responsibility identified included charity (Akbaş et al., 2012; Wong et al., 2010); statutory mandates or duty to obey the law (Akbaş et al., 2012; Arli et al., 2014a; Wong et al., 2010); edge over competitors through innovation and continuous learning; economic & ethical commitment (Akbaş et al., 2012; Arli et al., 2014a). Also, studies employing the PRESOR instrument reveal that profit, longevity, and rapid growth are all characteristics of ethical behaviour (Elias, 2004; Fitzpatrick, 2013; Singhapakdi et al., 1996).\n\nHowever, when more instances of corporate hypocrisy are brought to light, customers acquire a natural mistrust towards the CSR promises made by businesses (Connors et al., 2017). This is even though consumers' perspectives could vary since CSR has developed at various rates in Western countries and in Eastern countries, and even within regions (González-Rodríguez et al., 2013). As a result, certain aspects of CSR views that are identified in the literature that are not in a good light. One such aspect is the prevalent assumption that businesses may enhance their image if they are sensitive to concerns raised by the public (Wals, 2007). Therefore, CSR may be perceived as a manufactured performance; in addition, students who embrace the principles of altruism are more likely to have good opinions of CSR than students who adopt self-centred values (Pätäri et al., 2017).\n\nTherefore, the plethora of previously listed notions proves that there is no mutual acceptance on how CSR ought to be defined as the preceding examples of overlapping ideas, investigation of the likelihood that there is a plurality of elements in this material might benefit by identifying the many characteristics that influence students' views of CSR. Within this context, we propose the following hypothesis in light of the research demonstrating that students' attitudes of corporate social responsibility are influenced by their nationality (Pätäri et al., 2017; Wong et al., 2010) as well as the fact that the study conducted by Fitzpatrick (2013) at an American higher education institution did not investigate the many facets that influence students' views of CSR.\n\nStudents’ perceptions of CSR can be considered in different dimensions, including having supporting perception about CSR, negative perception or maybe neutral positioning.\n\nIn conjunction with the uniqueness of each nation's culture and set of natural advantages, sociodemographics are taken into account as a factor that might affect how people view CSR and ultimately shape their moral judgements (Arli et al., 2014b; Fitzpatrick, 2013; González-Rodríguez et al., 2013; Wong et al., 2010). When examining students' perspectives on CSR, we may generalise about the effects of sociodemographic factors play a role in shaping how students feel about the organization's commitment to social and environmental responsibility (Fitzpatrick, 2013; Ugwuozor, 2020). These studies allow us to formulate the suggested hypothesis:\n\nSociodemographic students’ characteristics can influence their perception of CSR\n\n\nMethods\n\nAs the research was conducted on the students in order to measure their perceptions, necessary approval was taken from the ethical committee. The Human Ethics Committee of Mizoram University, India in their letter, bearing the reference number MZU/HEC/2023/011, dated 04.07.2023 reviewed the questionnaire and proposal and approved the collected data for further processing.\n\nThe questionnaire, which was provided to the students, clearly mentioned that the “The information given by student will be used for academic purpose only” and the students agreeing to this statement have filled up the questionnaire.\n\nIn order to determine whether or not the hypotheses proposed are valid, a quantitative approach was utilised. The motive is to have an insight and determine whether students’ perceptions in the present study may be linked to other variables and to assess the influence of sociodemographic attributes in their perceptions of issues pertaining to CSR and other social concerns.\n\nFor measuring the students’ perceptions, a slightly modified version of PRESOR, which was initially designed to assess the views of marketers’ perception with relation to the significance in terms of morality and civic duty (Singhapakdi et al., 1996) and was then used by (Fitzpatrick, 2013; Teixeira et al., 2018) to measure the perception of students about CSR was adopted.\n\nPerceived Role of Ethics and Social Responsibility (PRESOR), a measurement having three major dimensions namely Social Responsibility and Profitability, Long Term and Short-Term Gains was developed with potentials of supplementing in making concrete decision in situations which involves ethical and social issues (Singhapakdi et al., 1996). The scale was modified and was adapted to investigate how gender, job experience, and spirituality impact students' opinions of corporate social responsibility (CSR) (Fitzpatrick, 2013). On the basis of the same adapted scale (Teixeira et al., 2018), investigated the many views that students hold on CSR, therefore giving a platform with an accepted scale for measurement of CSR perceptions which are shown in Table 2, underlying data and on basis of prior research, the relations that are mentioned in Table 1, underlying data was expected to be found. All Tables can be found as Underlying data (Sunder, 2023).\n\nThe data was collected from students of Master of Business Administration (MBA) & Bachelor of Business Administration (BBA) from the various reputed Central Universities, State Universities and Private Universities in the North-eastern States of India between April to September 2022. Online Survey method was deployed as it can have a larger reach and higher number of responses could be collected. Responses from 272 students were received out of which 25 responses were filtered out because of unengaged responses and we continued with a total of 247 responses which were collected by convenience sampling through a well-structured 16 questions Likert scale-based survey plus five demographic questions.\n\nThe data that was obtained was evaluated employing IBM SPSS statistics version 21, included both univariate analyses, such as descriptive analysis, t-tests, and Pearson tests, and multivariate analyses, which included confirmatory factor analysis and Multivariate analysis of variance (MANOVA), were performed. The selection of the aforementioned statistical methods was guided by the proposed study framework as depicted in Table 1, underlying data (Sunder, 2023).\n\nTable 3, underlying data (Sunder, 2023) represent while most students (89.1%) were in the age range 17 and 26, responses came from students as young as 17 and as old as 50. It was estimated that about 93% of the students were unmarried, while the residual 7% were married. Most respondents (54.3%) had some bachelor's degree, while 4.9% having earned a master's degree and 40.9% obtained professional courses. Regarding employment, 75.3% of respondents were enrolled as full-time students while 12.1% were working full-time (student worker).\n\n\nResults\n\nComplementary to study of Fitzpatrick, (2013) and Teixeira et al., (2018), Table 2, underlying data takes into account and compiles students' judgment of CSR in this study (Sunder, 2023).\n\nThe same table presents the means and is viable to deduce that statements with the higher means are the statements which support CSR, for instance, perceptions 15, 6, 4, 1 and 11. On the contrary, perceptions 5, 8 and 13, with lower average suggests that CSR is not a significant choice that companies should address.\n\nTaking into consideration the above findings, Factor Analysis was conducted on the perception of the students about CSR to deduce the dimensions to meet our first objective of the study.\n\nThe value of Kaiser-Meyer-Olkin (KMO) computed was 0.914, which indicates that the sample size is suitable for carrying out factor analysis. On top of that, significance level of the Bartlett Test is 0 (0.000), which means that the sample is suitable for this method at a significance level of 1%. Table 4, underlying data shows the results, and in particular when individual MSA values are considered, it becomes clear that the samples were sufficiently representative, as there is no parameter with an MSA score below 0.5 (Sunder, 2023). As a consequence, all of these factors are deemed crucial to the investigation, and they have enough properties with the order variables for viability metrics to be produced from them. The values of the rotated components demonstrate that the variables are associated to one another, with the three extracted constructs having a variation explained by the factors that accounts for about 56% of the variance of the overall variance involving the variables. Using the factor analysis shown in Table 4, underlying data (Sunder, 2023) and drawing on earlier explanation of PRESOR (Fitzpatrick, 2013; Singhapakdi et al., 1996), we may deduce that there are three distinct dimensions at play here: component 1 contains positive views of CSR (averaging 5.16), component 2 comprised negative perceptions of CSR (averaging 4.16), and factor 3 comprises neutral perceptions of CSR (averaging 4.68).\n\nSince the values in Table 4 are more than 0.60 (Sunder, 2023), suggesting that the measures are trustworthy, a reliability study utilising the Cronbach's Alpha coefficient may be employed to validate the results of the confirmatory factorial analysis (Nunnally and Bernstein, 1994; Pallant, 2001). As the questions were adopted, we did not do exploratory factor analysis, but to see if the model fits a different geographical location, Confirmatory Factor Analysis was conducted by making use of IBM SPSS Amos version 21 software to evaluate the model fit by utilizing the plugin \"Model Fit Measure\" (Gaskin and Lim, 2016). A satisfactory match with the model was observed by various indicatives namely CFI = 0.936; CMIN/DF = 2.512; RMSEA = 0.078; SRMR = 0.066 which is in line with the cutoff criteria of good fit values suggested by Hu & Bentler, (1999).\n\nBecause of this, it is feasible to draw the conclusion, on the basis of the findings of the factor analysis, that the results of these views demonstrate that there are several ways in which students understand CSR, and that CSR is not universally seen as a major regard for businesses. Therefore, the first goal was successfully completed, and hypothesis 1 was verified.\n\nTo understand if the sociodemographic variables taken in the research have any impact on the notion of students about CSR, Pearson Corelation investigation into whether or not any corelation reside between the variables under study. Students' views on CSR were broken down into their constituent dimensions through factor analysis, and a correlation test was run between these elements and sociodemographic factors. The corelation test at 5% significance level reflects relationship between the dimensions of student perception about CSR and the sociodemographic characteristics which is contrary to the findings of (Teixeira et al., 2018). Positive corelation is observed between the three dimensions of CSR: positive attitudes towards CSR, attitudes that cast doubt on the significance of CSR, and the prioritisation of business activities that push CSR to the back burner and the sociodemographic characteristics in the context of Indian students. It is not statistically significant that if there is any corelation between variable age and civil Status and the three dimensions of CSR perception.\n\nIn order to address to the other hypotheses which were related to the sociodemographic variables, we used MANOVA for those hypotheses testing where the independent variables were Age, Academic Degree and Experience and t-test was conducted on the variables which had only two options namely Gender and Civil Status. The use of MANOVA was preferred over using multiple ANOVAs to test statistical significance difference between several groups (Maroco, 2003). For the purpose of MANOVA, the reduced dimensions were used as the dependent variables and the sociodemographic variables were considered as independent variables. But before the hypotheses were tested, assumptions of multivariate analysis of variance (MANVOA) namely multivariate normality, homoscedasticity and existence of corelation between the independent variables were fulfilled as depicted in Table 5 (Sunder, 2023).\n\nAddressing hypothesis 2.1, \"The influence of age on students' perceptions of CSR,\" the Wilks' Lambda = 0.907, F (15, 660) = 1.578, p = 0.074, illustrates that the dependent variable has a statistically significant impact on the independent factors at a significance level of 10%. However, the Test of Between Subjects Effects reflects that the first reduced dimension is significant at 10% level, instead of one-way ANOVA we did a Levene’s test of equality of error variances and it was found to be insignificant. We did a Scheffe Post-hoc test to confirm the findings and it was confirmed that there was no significant difference between age interval and the reduced dimensions. As all the values are greater than 0.10, the results show no significant differences across age groups. Therefore, we conclude that age positively influences students’ perception of CSR.\n\nFor Hypothesis 2.2, we used MANOVA again and the values of Wilks' Lambda = 0.951, F (6, 484) = 2.032, p = 0.060, indicates that the dependent variable has a statistically significant impact on the independent factors at a significance level of 10%. Levene’s test was conducted and it was found to be insignificant, which meets the presumption of homogeneity of variance. The output of the Test of Between Subjects Effects reflects significant difference between second and third reduced dimension. Based on the contrast results upon comparison of undergraduate and professional technical courses there was significant difference in all the three reduced dimensions. Therefore hypothesis 2.2 i.e., “academic degree positively influences the students’ perceptions of CSR” is accepted.\n\nFor the hypothesis 2.3, we continued with MANOVA and it was observed that, the Wilks' Lambda = 0.919, F (12, 635) = 1.515, p = 0.060 was observed which implies that the dependent variables have statistically significant effect on the independent variables at 10% significance level. Besides that, the Levene’s test (used in place of ANOVA) reflets insignificant values and the p-values of Test of Between Subjects Effects were all insignificant implying that the hypothesis is accepted: “professional experience positively influence the students’ perception of CSR”.\n\nTo test hypothesis 2.4 and 2.5, We conducted t-tests to look at whether or not there is a correlation amongst students' views on CSR and their gender, civil status, comparison is made between the means of the two groups taking into consideration three reduced dimensions. The Levene’s test in all the dimensions are insignificant implying that the equality of variances is verified and the insignificant p-value presented in the t-test concludes that no statistical difference prevails among gender, civil status and students’ perception of CSR thereby rejecting the hypothesis 2.4 & hypothesis 2.5.\n\n\nDiscussion & conclusions\n\nA primary goal of this study was to see if students' perspectives of CSR were different from one another, and a preliminary examination of the means of the students' replies concerning perceptions suggested that there were really two unique groups of students' perceptions. Individuals may be roughly divided into two groups: those who did better overall and who tend to have more positive views of CSR, and those who did worse overall and who reject these views.\n\nAccordingly, the analysis is expected to support the first hypothesis, \"Students' perceptions about CSR can be considered in different dimensions,\" which affirm the outcomes of the literature review, particularly regarding, that students are mindful of morally as well as socially accountable practises/strategies but are not necessarily making responsible decisions and assert behaviour that contribute to the betterment of community (Assudani et al., 2011). Factor analysis findings, which delineated three main aspects in students' opinions of CSR, confirm the findings that Students’ perceptions about CSR can be considered in different dimensions.\n\nAccording to the available data, most students have favourable opinions on sustainability and CSR initiatives (Bahaee et al., 2014). High social perceptions are associated with CSR because the new age of human values is linked with things like harmony, standard of living, environmental considerations, care for and concern for others' well-being (González-Rodríguez et al., 2013). Our first derived dimension, pro-CSR attitudes, has a mean score of 5.16, corroborating findings from the studies that CSR is seen as a crucial vital decision, providing growing and positive prequisite to businesses (Mcguire et al., 1988) which is effective for organizations eminence (Gallardo-Vázquez and Sanchez-Hernández 2014).\n\nThere are certain less favourable impressions of CSR that may drive people into adopting a poor consciousness while processing CSR information. This is since consumer cynicism has a significant repercussion on the attitudes and perceptions of customers (Connors et al., 2017). The second component addresses attitudes that call into question the significance of CSR and address beliefs that are resistive to CSR. According to the findings of Wymer and Rundle-Thiele, 2017, about only one third of the universities are offering courses that are related to the sustainability. This might be related to the notion that HEI's implementation of a responsible education framework is still in its early stages. Students may not be aware of this problem due to the fact that there is a significant lack of expertise amid educators regarding the value of CSR, their unpreparedness for educating ethics and doubt their ability to influence how students make moral decisions (Wymer and Rundle-Thiele, 2017).\n\nIn the third and final component, company prioritisation is discussed. While it's true that offering products or services with a solid reputation may provide a business an edge in the marketplace, (Brei and Böhm, 2011), the responses to this component place corporate social responsibility in a secondary plan, in the background, with an average score of 4.68. Many of these students believe that corporate social responsibility (CSR) should take a back seat; a socially conscious business, in their eyes, is one that puts its money where its mouth is in terms of helping people and the planet; as a result, the principal management policy of maximisation of wealth is called into question by the expenses associated with socially conscious conduct (Wymer and Rundle-Thiele, 2017). Decisions are skewed in favour of CSR because managers are motivated by a pursuit of power, control, and riches rather than by considerations of ethics and social responsibility. Therefore, CSR is given top priority only if it is expected to generate a financial return and advance the company's objectives (Giacalone and Thompson, 2006).\n\nWith regard to the study's secondary goal, which is to determine how students' demographic information affects their views on CSR, differentiation based on age, level of education, and professional experience was supported by the data in this study, which strongly indicates that students' CSR perceptions is influenced by the sociodemographic variables which is in line with the findings of (Almutawa and Hewaidy, 2020) and is in contradiction to the findings of (Anand and Singh, 2021; Burcea and Marinescu, 2011; Pätäri et al., 2017; Teixeira et al., 2018; Ugwuozor, 2020). Whereas the t-tests on gender and civil status depicted that there is no statistical relationship between these two variables and the reduced dimensions of students’ impression of CSR which is in line with finding of (Almutawa and Hewaidy, 2020; Chan et al., 2021).\n\nIn a nutshell, we may remark the presence of three main aspects of students' perspectives: i) value CSR, ii) against CSR, and iii) neutral to CSR, and we can claim that positive attitudes to CSR offer the greatest average, suggesting that, generally speaking, students appreciate CSR. Thus, the majority of people agree that CSR is crucial, yet different people have different conceptions about what it entails. What's more, the findings demonstrate that there are no statistically significant variations in students' perspectives on CSR across demographic characteristics including age, gender, educational attainment, and professional experience.\n\nThe management implications of this study for higher education institutions are substantial. In their roles as future workers, business owners, and customers, students play an essential role in assessing the effectiveness of CSR actions. Distributing sustainable production and consuming practises will influence transitions toward a more sustainable activity (Pülzl et al., 2014), and the youths have the potential to be extremely major Influencers on society (Pätäri et al., 2017). It is of the utmost importance to comprehend and foresee how the students' moral and environmentally conscious actions will develop in their future roles as staff members, managers, and business owners, as well as in the context of their customer roles.\n\nThe quantity of participants in the study is one of the constraints of the study as HEIs considered for the data collections were limited to a specific region of the country and the sample size may be considered too little to draw any firm conclusions. Therefore, to have a better perspective of whether the hypotheses that were provided in this work would lead to different results, potential future research may entail a sample that is both more complete and more varied. This would require extending to include new HEIs as well as students of varying ages and regions.", "appendix": "Data availability\n\nZenodo: Corporate Social Responsibility & Students’ Perceptions: Evidence from Indian Higher Education Institutions. https://doi.org/10.5281/zenodo.8328583 (Sunder, 2023).\n\nThis project contains the following underlying data:\n\n- Blank Instrument.doc\n\n- Coding File.csv\n\n- Data File.csv\n\n- Raw Data.csv\n\n- Table 1 - Methodology\n\n- Table 2 - Affirmations on CSR under study\n\n- Table 3 - Characterization of the Sample\n\n- Table 4 - Factor Analysis Results\n\n- Table 5 - Validation of the assumptions of MANOVA\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAguilera Rv, Rupp DE, Williams CA, et al.: Putting the S back in corporate social responsibility: A multilevel theory of social change in organizations. Acad. Manag. Rev. 2007; 32(3): 836–863. 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United Kingdom: Copenhagen Centre; 2003." }	[ { "id": "209451", "date": "03 Mar 2024", "name": "VJ Byra Reddy", "expertise": [ "Reviewer Expertise Inequalities", "Development", "Third Sector and Rights and Responsibilities." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is very well conceptualized and studying the perception of young business students on 'corporate social responsibility' who would don the roles in corporate corridors for the next 30-40 years is very salient. The hypotheses formed and tested appear to be consistent with the objectives of this study. What is very appreciable throughout the study is the 'robust' review cited in all areas of the study and not just the review of literature. Moreover, the literature is current and appropriate. The methods and methodology followed does complete justice to the objectives of the study.\n\nHowever:\n\nThe study may need to change its title from the current - Corporate social responsibility & students’ perceptions: evidence from Indian higher education institutions – to - Corporate social responsibility & students’ perceptions: evidence from Indian higher education institutions from Northeast India. It is very important to change the title to the effect of the suggestion as the sample collected is from Northeast Indian higher educational institutions. The current title is misleading in the sense that the prospective readers and particularly the research fraternity including research scholars searching this article going by its current title would think that, this study is from the Indian higher educational institutions instead of from where this study actually is from – Northeast India.\n\nA question which maybe asked to the researchers is, how using an instrument developed for studying the perception in non-Indian context, answers questions regarding student perception in the Indian context?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "225196", "date": "26 Mar 2024", "name": "Partakson Romun Chiru", "expertise": [ "Reviewer Expertise Corporate Social Responsibility", "Finance and Accounting and Marketing" ], "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: Corporate Social Responsibility & Students’ Perceptions: Evidence from Indian Higher Education Institutions\nRelevance and Significance: The research article addresses a pertinent topic concerning the perceptions of students on Corporate Social Responsibility (CSR) within Indian Higher Education Institutions (HEIs). Given the growing importance of CSR in the corporate landscape and the role of HEIs in shaping future business leaders, understanding students' perceptions holds significant relevance. By investigating how sociodemographic factors influence these perceptions, the study offers valuable insights that can inform CSR education and practice in India.\nComprehensive Literature Review: The article provides a thorough literature review on CSR, HEIs, and students' perceptions, demonstrating a clear understanding of the research context. It covers key theoretical frameworks, empirical studies, and conceptual discussions, thereby providing a comprehensive background for the study. The review effectively sets the stage for the research by highlighting the gaps and emphasizing the need for further investigation.\nClear Research Question and Objectives: The research question and objectives are clearly articulated, focusing on exploring students' perceptions of CSR and examining the influence of sociodemographic factors. This clarity helps guide the study's direction and ensures alignment between research aims and methodologies. The objectives are specific, measurable, and relevant, contributing to the overall rigor of the research design.\nIntegration of Concepts: The article effectively integrates concepts from CSR literature, educational theory, and sociodemographic research to construct a robust analytical framework. By drawing on established models such as the PRESOR scale and adapting them to the Indian context, the study demonstrates a thoughtful approach to theoretical integration. This integration enhances the validity and applicability of the research findings.\nIdentification of Research Gaps: The literature review skillfully identifies gaps in existing research, particularly regarding students' perceptions of CSR in Indian HEIs. By highlighting the need for empirical investigation and the lack of studies addressing sociodemographic influences, the article contributes to knowledge development in the field. The research aims to fill these gaps by providing empirical evidence and addressing the identified research questions.\nBroader Implications: The study's findings have broader implications for CSR education, organizational practice, and policy development in India. By understanding students' perceptions and the factors influencing them, HEIs can tailor their curriculum and initiatives to promote ethical leadership and social responsibility. Moreover, organizations can leverage these insights to enhance their CSR strategies and engage with future stakeholders effectively.\nRecommendations for Future Research: The article offers insightful recommendations for future research, including expanding the sample size, incorporating diverse geographical regions, and examining longitudinal trends. By suggesting avenues for further investigation, the study encourages scholars to build on its findings and advance knowledge in the field of CSR and education. Additionally, exploring the long-term impact of CSR education on students' attitudes and behaviors could provide valuable insights for both academia and practice.\nOverall, the research article demonstrates a strong theoretical foundation, methodological rigor, and relevance to current debates in CSR and education. With its clear research objectives, comprehensive literature review, and insightful findings, the study makes a significant contribution to the scholarly discourse on CSR perceptions in Indian HEIs.\n\nIs the work 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/12-1187
https://f1000research.com/articles/12-667/v1	14 Jun 23	{ "type": "Study Protocol", "title": "Effectiveness of multi-component modular intervention among adults with prehypertension in a village of Dakshina Kannada district - a community-based interventional study – protocol", "authors": [ "Neneh Feren", "Rekha Thapar", "B Unnikrishnan", "Prasanna Mithra", "Nithin Kumar", "Ramesh Holla", "Darshan BB", "Himani Kotian", "Neneh Feren", "B Unnikrishnan", "Prasanna Mithra", "Nithin Kumar", "Ramesh Holla", "Darshan BB", "Himani Kotian" ], "abstract": "Introduction: The Joint National Committee (JNC 7) report on Prevention, Detection, Evaluation, and Treatment of Hypertension, defined \"prehypertension,\" as individuals with a Systolic Blood Pressure (SBP) in the range of 120–139 mmHg and a (diastolic blood pressure) DBP of 80–89 mmHg. Prehypertension is directly linked with hypertension which is a precursor of CVDs. Owing to its high conversion rate to hypertension, it is important to identify individuals with blood pressures in this category and bring about lifestyle modifications in them that can prevent them from being hypertensive and from developing cardiovascular diseases later in life. Methods: This randomized controlled trial will be done among the selected pre-hypertensive adults of all genders residing in Kateel Gram panchayat, Dakshina Kannada district, Karnataka. A baseline survey will be done initially to assess the level of prehypertension among the study population. To study the effectiveness of the intervention, 142 individuals will be randomly allocated using block randomization technique to intervention and control groups. A multi-component module (educational intervention) will be developed, validated, and administered to participants in the intervention group, while the control group receives standard care. Each participant will then be followed up once in four months till the end of the study period of one year to assess for changes in SBP, DBP, WHR, BMI, stress levels, and usage of tobacco and alcohol. Ethics and dissemination: Institutional Ethics Committee approval was obtained from Kasturba Medical College in Mangalore, India. The plans for dissemination of findings include presenting at scientific conferences and publishing in scholarly journals.", "keywords": [ "Hypertension", "Prehypertension", "Randomized controlled trials", "Block randomization", "Non Communicable diseases", "WHO-STEPS." ], "content": "Introduction\n\nHypertension is a modifiable risk factor for cardiovascular diseases (CVD) and a major cause of premature death. Early Identification and prevention lower the risk for the same.1\n\nIn 2003, the Joint National Committee in their 7th report on the Prevention, Detection, Evaluation, and Treatment of Hypertension introduced a new term ‘Prehypertension’ which included SBP (Systolic blood pressure) ranging from 120 – 139 mmHg and DBP (Diastolic blood pressure) from 80 – 89 mmHg. This was a redefined new criterion to increase the emphasis on the excess risk factors associated with BP in this range and to bring public attention to the importance of the prevention of hypertension among all genders.2–4\n\nGlobally, the prevalence of prehypertension is 31% with a high conversion rate to hypertension of 30%.2 It is responsible for almost 62% of cardiovascular and 49% of ischemic heart diseases.5 The prevalence of pre-hypertension in the Indian subcontinent from a study conducted in 2016 was approximately 47% among young urban residents.6 A prevalence of 31.5% was observed in South India, 30% in West India, 24.6% in North India, and 20.9% in East India7\n\nPrehypertension is directly linked with hypertension which is a precursor of CVDs. Owing to its high conversion rate to hypertension, it is important to identify individuals with blood pressures in this category and bring about lifestyle modifications in them that can prevent them from being hypertensive and from developing cardiovascular diseases later in life.\n\nStudies demonstrate that multiple lifestyle modifications lower blood pressure by modifying the risk factors which control hypertension.8 The nutritional requirements of a pre-hypertensive individual can be addressed by adopting a DASH (Dietary Approaches to Stop Hypertension) diet. This diet promotes the reduced intake of salt, incorporating fruits, vegetables, micro-nutrients, and lean meat instead of full-fat meat, low-fat dairy, nuts, and legumes.9\n\nPhysical Inactivity and a sedentary lifestyle are major risk factors for hypertension.10 According to multiple studies, exercise training lowers blood pressure in about 75% of the individuals diagnosed with hypertension, with systolic blood pressure and diastolic blood pressure reductions of 11 and eight mmHg, respectively.10 Another risk factor for hypertension is salt consumption. Salt being the main source of sodium in our diet, is usually consumed in large quantities and often ends up being two times higher than the recommended quantity. Reducing salt intake has been identified as one of the most cost-effective measure to reduce the risk of cardiovascular diseases, stroke, and coronary artery disease.11\n\nTobacco use is one of the biggest public health threat world has ever faced and is one of the major causes of cardiovascular diseases.12 There is a causal relationship between the harmful use of alcohol and increased levels of blood pressure which poses it as a risk factor.13 Several studies have also observed the causal association between high levels of stress and high blood pressure measurements.14\n\nThe early identification of individuals with prehypertension along with risk behaviors is important to reduce the burden of non-communicable diseases. Effective non-pharmacological interventions, health education, and lifestyle modifications have been used extensively for lowering the blood pressure among the pre-hypertensive individuals\n\nEven though a high prevalence of pre-hypertension is observed in India, there is a paucity of literature on its prevalence in rural areas of South India. Also, adequate emphasis is not given to the importance of halting progression of pre-hypertension blood pressure levels to hypertension levels in preventive programs. The present study is undertaken to fill the gap in existing information on the effectiveness of multi-component intervention in preventing the progression of pre-hypertension to hypertension among adults in a rural area of South India.\n\nThe term “pre-hypertension” was used by the Joint National Committee's Seventh Report to describe a group of people who have elevated blood pressure and a greater burden of other risk factors, like obesity, diabetes, dyslipidemia, and coronary artery disease.2–4\n\nIn the Cross-sectional study conducted by McNiece KL et al, the prevalence of prehypertension and hypertension was 15.7% and 3.2% respectively. The factors like risk for overweight or overweight along with the racial trait and gender were associated with pre-hypertension independently.14\n\nIn a cross-sectional study done by Parek A et al. in Vadodara, the prevalence of prehypertension was found to be 24.2%. The mean systolic and diastolic blood pressures were directly proportional to age. The study concludes that periodic screening of people, especially high-risk people regularly, can help in the early detection of hypertension and thus prevent cardiovascular diseases.15\n\nIn the study conducted by Parthaje PM on the prevalence of prehypertension in adults in urban South India, blood pressure levels in the prehypertensive range were found in 343 (55%) of the total 643 adults and 185 (29.6%) had previously undiagnosed hypertension. Among the study subjects, a higher proportion were females (69.1) and people in the age group 20 to 39 years (40.5%). A high prevalence of prehypertension was found among the study population3\n\nA study, done by Pimenta E. et al which evaluated the effects of pre-hypertension concluded that all prehypertensive patients should get non-pharmacological treatment with lifestyle changes such as weight loss, dietary changes, and an increase in daily physical activity because these measures significantly lower the risk of cardiovascular events.16\n\nIn an interventional trial conducted by Darviri C. et al. to examine the effectiveness of an 8-week health promotion program consisting of multiple lifestyle modifications intended to lower blood pressure (BP) in pre-hypertensive and patients with hypertension, a significant decline in the blood pressures and anthropometry measurements in the intervention arm was observed when compared to the control arm.17\n\nIn a randomized controlled trial studying the importance of multiple lifestyle modifications for patients with prehypertension and hypertension, the intervention tool included health education modules regarding various food pattern changes and increased physical activity. The lifestyle modification and follow-up lasted for two months. The study concluded that combination of various lifestyle interventions, physical activity, and dietary interventions diminished blood pressure and reduced CVD events.18\n\nA study conductedby Rubinstein A in Latin American countries, showed that after 12 months of mHealth (mobile Health) interventions consisting of diet and physical activity among prehypertensives, there was an increase in daily intake of fruits and vegetables and a decrease in daily dietary fat, refined sugar, and high sodium post intervention. A reduction in body weight was also observed at the end of the study period.19\n\nTo study the effectiveness of the multi-component modular intervention on pre-hypertension among adults in a rural area of Dakshina Kannada District in Karnataka.\n\nThe objectives are:\n\n- To develop a comprehensive multi-component module for people with pre-hypertension.\n\n- To assess the effectiveness of modular interventions among prehypertensive individuals.\n\n\nMethods\n\nThe study will be conducted in the three selected villages of Kateel, a temple town in the Moodubidri taluk20 of Dakshina Kannada District of Karnataka. The population of all the selected villages within Kateel Gram panchayat, according to the census India 2011 is 4470 with 2378 in Kondemula (literacy rate of 87.87%), 1454 in Nadugodu (literacy rate: 85.82%) and 658 in Kilinjur (89.84%).21\n\nThe initial baseline survey estimated 32% prevalence of prehypertension. One forty-two hypertensive individuals, as per the sample size calculation will be included in the trial.\n\nThis will be an open-label study RCT with the parallel group. The trial will be reported along with the Consolidated Standards of Reporting Trials (CONSORT).22\n\nThe protocol for this study is reported along with Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) Guidelines. The Reporting guideline criteria include a completed SPIRIT checklist.23\n\nThe study population will be selected from the prehypertensive individuals identified during the baseline by simple random sampling.\n\nThe study will be conducted for one year from June 2021 to Dec 2022.\n\nA sample size of 142 prehypertensive individuals (71 in each group with 1:1 allocation) was calculated using the formula mentioned below and considering a difference in change score of 0.37 (standard deviation- 0.88)19 in SBP between the intervention and control groups, assuming a clinically acceptable difference of 0.5 irrespective of gender, 95 % confidence interval, 90% power, and along with 10 % non-response error\n\nWhere Z 1-α =1.96 for a 95% confidence interval, Z1-β = 1.281 for 90% power. δ - δ0 = 0.5 (clinically acceptable difference). S is the combined standard deviation.\n\nAdults of all genders above the age of 18 who are diagnosed with prehypertension will be eligible to participate. Pregnant women, individuals diagnosed with hypertension, genetic disorders/disabilities, and those who are bedridden will be excluded. Those who do not give consent will also be excluded from the study.\n\nSimple random sampling will be used to select the study participants from the prehypertensive individuals identified at the baseline assessment. In this randomized controlled Trial (RCT), 142 individuals irrespective of gender, who are pre-hypertensives will undergo random allocation to the intervention and control group. i.e. intervention (A) and control group (B). Applying the block randomization technique, for allocating the 142 participants into two groups 36 blocks are needed, with 4 participants in each block (36 blocks x 4 participants =144 participants).\n\nFor getting a block of four participants with an equal no of participants from the intervention & control group the six possible permutations are AABB, BBAA, ABAB, BABA, ABBA & BAAB, which will be numbered as one, two, three, four, five and six respectively. To begin with, a random permutation numbered from one-six will be selected using the lottery technique and the first four participants will be allocated according to the selected permutation. The participants will be allocated into either group in a batch of four.\n\nA health education module will be developed based on the inputs from the subject experts, an extensive literature review, and in-depth interviews with the local stakeholders. This will be a multi-component audio-visual module with relevant textual information.\n\nThe creation and curation of the educational module will be done in the vernacular language and local context. Before the modules are used in the study environment, their content validity will be assessed. It will contain four parts.\n\nPart I will include general knowledge about hypertension, its causes, and risk factors. It will emphasize the importance of treating it on a prehypertensive level and preventing the conversion to hypertension.\n\nPart II will include pictorial demonstrations of various dietary modifications, the food that they should avoid to prevent the progression of prehypertension to hypertension, and the food that they should eat more to improve their health.\n\nPart III will be about the importance of physical activities, their benefits, different types of exercises, and the guidelines to follow them.\n\nPart IV will consist of different kinds of stress and anxiety relieving techniques and the guidelines to follow them.\n\nThree sessions of modular intervention with a duration of 20 minutes each will be administered to the pre-hypertensive individuals in the intervention group at an interval of three months. Sessions will be conducted in groups at the Rural Health Training Centre of Kasturba Medical College at Kateel. The participants missing one intervention session will be contacted and will be rescheduled with a different group. Participants in the study who miss two or more sessions will be deemed to have dropped out.\n\nA Pretested, content validated and semi-structured questionnaire will be used. The instrument will include the following sections: A) General participant information B) Knowledge about high blood pressure, C) WHO STEPS Questionnaire24, D) Perceived Stress Scale25, E) Socio-economic scale26\n\nThe study area will be visited on a pre-informed date. All the selected individuals (n=142) with prehypertension from the three villages of Kateel will be included. Participants will be then approached in their houses. They will be explained in their vernacular language regarding the objectives of the study and a participant information sheet will be provided to each one of them which consists of details regarding any queries on dropping out. Written informed consent will be obtained from the participants who are willing to take part. Each eligible participant will be interviewed, and their anthropometric measurements and blood pressure will be measured using standard methods.24 Stress levels will be assessed. It will be in the form of a 5-point Likert scale will be used. The responses ranging from strongly agree (5) to strongly disagree (1) will be recorded. The control group will receive standard patient care.\n\nThe intervention and control groups will be followed up every four months. On each visit, the blood pressure and anthropometry of the intervention group will be recorded at Rural Health Training Centre (RHTC), Kateel. The study participants allocated to the control group will be followed up in their houses.\n\nA weekly track record of diet, physical activity, and stress reduction activities will be maintained by the participants. This will be verified by the investigator during each intervention session. At the end of the fourth follow-up session, an assessment will be done concerning their perception of hypertension, perceived stress, usage of tobacco and alcohol, and anthropometric measurements.\n\nCONSORT diagram22\n\n\n\nMeasurement of weight24\n\nA portable digital weighing scale will be used to measure weight. The person will be requested to take off their shoes, slippers, sandals, and socks before being instructed to step one foot onto either side of the scale. The instructions will be given to the participant to stand still with their arms at their sides and to face forward. On the instrument, the weight will be measured in kilos to the nearest 0.1 cm. After each use, the scale will be reset to zero.\n\nMeasurement of height24\n\nA portable length measuring board will be used to measure height. The participant will be required to take off their shoes, slippers, sandals, and/or headgear which includes a hat, cap, hair bows, comb, etc It will be measured over a thin fabric. The participant will be instructed to face the investigator while standing on the board. The contestant must stand with their feet together, their heels pressed up against the backboard, and their knees straight. The subject is instructed to maintain a straight-ahead gaze with eyes level with ears. By lowering the measuring arm to the patient's head, the reading will be measured to the nearest 0.1 cm.24\n\nBody mass index24\n\nThe formula to calculate BMI will be\n\nAsian BMI Classification:\n\n< 18.5 kg/m2 = underweight\n\n>18.5-22.9 kg/m2 = ideal\n\n>23-24.9 kg/m2 = overweight\n\n> 25 kg/m2 = obese\n\nMeasurement of waist-circumference24\n\nA tape with consistent tension will be used to measure waist circumference. It will be measured at the midpoint between the bottom of the last rib and the top of the iliac crest at the end of regular respiration while the arms are relaxed at the sides. The participant will be instructed to wrap the tape over themselves, and the investigator will assist them in positioning it properly. The subject will be instructed to stand with their feet together, their weight spread evenly over both feet, and\n\ntheir arms relaxed by their sides. Only one reading of the measurement will be made at the level of the tape, to the closest 0.1 cm.\n\nMeasurement of hip-circumference24\n\nHip circumference will be measured using a constant tension tape. The measurement will be taken with the subject minimally clothed. The individual is instructed to stand with their feet together, their weight evenly spread over both feet, and their arms at their sides. The tape would be positioned horizontally over the maximum circumference of the buttocks. Measurement will be read at the level of the tape to the nearest 0.1 cm. It will be measured only once.24\n\nWaist - hip ratio (WHR)24\n\nWHR will be calculated using the formula\n\nAs recommended by the WHO,\n\nBlood pressure measurement24\n\nUsing a digital automatic blood pressure monitor, blood pressure will be measured. Participants will be requested to sit on a chair with their feet flat on the floor, their legs uncrossed, and their backs supported. At the level of the heart, the cuff will be placed on the patient's uncovered upper arm. It will be placed over the brachial artery. A maximum of two fingers should fit between the distal portion of the cuff and the skin when it is properly positioned. A few centimeters (one-two) above the antecubital fossa will be where the distal portion of the cuff is placed. After detecting a pulse, the monitor will begin taking measurements.\n\n\n\n• Mean change in blood pressure measurements (SBP, DBP)\n\n• Change in mean BMI, waist circumference and hip circumference, WHR\n\n• Difference in the usage of tobacco and alcohol\n\n• Change in mean stress levels.\n\nThe collected data will be entered into an excel sheet. After the entry, the data will be cleaned and the missing information will be obtained by reaching out to the study participant. Validation of the proforma will be checked with 10% of the data obtained. A committee for data management will not be formed. The data will be kept confidential with password protection. It will be coded and analyzed using the software ‘IBM Corp. Released 2017. IBM SPSSStatistics for Windows, Version 25.0. Armonk, NY: IBM Corp.27\n\nResults will be expressed as proportions and summary measures (Mean±SD). Appropriate tables and figures will be used. Intention to treat analysis (ITT) will be followed.\n\nThe variables will be compared across the prehypertensive and the normotensive groups using the chi-square test. The factors associated with prehypertension will be studied using Binary logistic regression and multivariate logistic regression. The ‘Hosmer and Lemeshow goodness-of-fit test will be used to assess the fit of the logistic model. A P value < 0.05 will be considered a significant association between predictive and outcome variables (Prehypertension). The confidence intervals (95%) for both the unadjusted and adjusted odds ratios will be reported.\n\nThe baseline and post-intervention values across the intervention and control groups will compare using the Mann- Whitney U test for the data that are non-normally distributed and an independent t-test will be used for the normally distributed data (SBP, DBP, BMI, WHR, and stress levels) and chi-square test (Usage of Alcohol and Tobacco). The change score within the group will be compared using repeated measures of ANOVA (WHR) and Friedman’s test (SBP, DBP, BMI, and Stress). A 'p-value less than < 0.05 will signify statistical significance.\n\n\n\n‐ The findings of this study may help in prioritizing the resources towards the reduction of NCD risk factors.\n\n‐ The multi-component module developed can be used for conducting health education sessions among pre-hypertensive adults in rural areas of South India.\n\nCurrently, the participants have been recruited and two sessions of multi-modular comprehensive intervention have been conducted for the participants in the intervention group.\n\nIEC (Institutional Ethics Committee) of Kasturba Medical College, Mangalore has approved the study (IECKMCMLR-12/2020/399)\n\nAny changes in the protocol during the course of the study will be submitted to the IEC and approval will be obtained.\n\nThis trial is registered prospectively in CTRI India (CTRI/2021/11/037852). Necessary permissions will be obtained from the district health authorities.\n\nA participant information sheet will be administered to all participants. Participants who agree to take part in the study will be asked for a written statement of informed consent. The participant information data will be kept in confidence.\n\nData Monitoring\n\nInterim analysis will be conducted at 6 months after the initiation of the study. Trial conduct audit will be carried out by the investigators at regular interval of 3 months. No known adverse effect is associated with this study. A separate Data Monitoring Committee (DMC) will not be constituted. The modular intervention will be administered among the participants in the control group at the end of the study.\n\n\nAuthor Contributions\n\nNeneh Feren\n\nRoles: Conceptualization, Validation, Writing – Original Draft Preparation, Writing – Review & Editing\n\nRekha Thapar\n\nRoles: Conceptualization, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nPrasanna Mithra\n\nRoles: Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nNithin Kumar\n\nRoles: Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nRamesh Holla\n\nRoles: Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nDarshan BB\n\nRoles: Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nHimani Kotian\n\nConceptualization, Data Curation, Software, Review and Editing", "appendix": "Data Availability\n\nNo underlying data is associated with this article\n\nOpen Source Framework: Effectiveness of multi-component modular intervention among adults with prehypertension in a village of Dakshina Kannada district - a community-based interventional study – protocol\n\nhttps://osf.io/ywsj4/?view_only=2fb4312ecb09483d872ce2e0ebbd14dc\n\nThe supplementary materials available are:\n\n- Informed consent form and participant information sheet\n\n- Questionnaire\n\n- SPIRIT checklist\n\n- Consort diagram\n\nSPIRIT checklist. Open Science Framework. EFFECTIVENESS OF MULTI-COMPONENT MODULAR INTERVENTION AMONG ADULTS WITH PREHYPERTENSION IN A VILLAGE OF DAKSHINA KANNADA DISTRICT - A COMMUNITY-BASED INTERVENTIONAL STUDY – PROTOCOL. DOI: https://doi.org/10.17605/OSF.IO/YWSJ4\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank the Manipal Academy of Higher Education in Manipal, India, the Durga Sanjeevani Manipal Hospital in Kateel, Dakshina Kannada, and Kasturba Medical College in Mangalore for their assistance in making this study possible.\n\n\nReferences\n\nWorld Health Organisation: Non-communicable diseases. Hypertension. Geneva:World Health Organisation;2011 [updated 2020; cited 2020 Nov 1].Reference Source\n\nZhang W, Li N: Prevalence, risk factors, and management of prehypertension. Int. J. Hypertens. 2011; 2012: 1–6.\n\nParthaje PM, Unnikrishnan B, Thankappan KR, et al.: Prevalence and Correlates of Prehypertension among Adults in Urban South India. Asia-Pac Public Health. 2016; 28: 93S–101S. Publisher Full Text\n\nRuilope LM: Can the effectiveness of hypertension management be improved? Expert. Rev. Cardiovasc. Ther. 2013; 11(6): 689–695. Publisher Full Text\n\nWorld Health Organisation: Health topics. Sustainable Development Goals. Geneva:World Health Organisation;2015 [updated 2020; cited 2020 Nov 1].Reference Source\n\nMoinuddin A, Gupta R, Saxena Y: Assessment of anthropometric indices, salt intake and physical activity in the etiology of prehypertension. J. Clin. Diagn. Res. 2016; 10(2): 11–14.\n\nSingh RB, Fedacko J, Pella D, et al.: Prevalence and risk factors for prehypertension and hypertension in five Indian cities. Acta Cardiol. 2011; 66(1): 29–37. PubMed Abstract \| Publisher Full Text\n\nAppel LJ: Effects of Comprehensive Lifestyle Modification on Blood Pressure Control: Main Results of the PREMIER Clinical Trial. JAMA. 2003; 289(16): 2083–2093. PubMed Abstract\n\nMahmood S, Shah KU, Khan TM, et al.: Non- pharmacological management of hypertension: in the light of current research. Ir. J. Med. Sci. 2019; 188(2): 437–452. PubMed Abstract \| Publisher Full Text\n\nHagberg JM, Park JJ, Brown MD: The role of exercise training in the treatment of hypertension: An update. Sports Med. 2000; 30(3): 193–206. Publisher Full Text\n\nWorld Health Organisation: Newsroom. Healthy diets: Fact sheet. Geneva:World Health Organisation. 2018 [updated 2020; cited 2020 Nov 1].Reference Source\n\nWorld Health Organisation: Newsroom. Tobacco Factsheet. Geneva:World Health Organisation;2015 [updated 2020; cited 2020 Oct 20].Reference Source\n\nWorld Health Organisation: Health Topics. Harmful use of Alcohol. Geneva:World Health Organisation;2014 [updated 2020; cited 2020 Sept 30].Reference Source\n\nMcNiece KL, Poffenbarger TS, Turner JL, et al.: Prehypertension: epidemiology, consequences, and treatment. J. Pediatr. 2007; 150(6): 640–644.e1. Publisher Full Text\n\nParekh A, Parekh M, Vadasmiya D, et al.: Study of Prehypertension & Hypertension in a rural area of Vadodara district. Int. J. Med. Sci. Public Health. 2013; 2(1): 117–120. Publisher Full Text\n\nPimenta E, Oparil S: Prehypertension: epidemiology, consequences, and treatment. Nat. Rev. Nephrol. 2010; 6: 21–30. PubMed Abstract \| Publisher Full Text\n\nDarviri C, Artemiadis AK, Protogerou A, et al.: A HEALth promotion and STRESS Management Program (HEAL-STRESS study) for prehypertensive and hypertensive patients: a quasi-experimental study in Greece. J. Hum. Hypertens. 2016; 30(6): 397–403. PubMed Abstract \| Publisher Full Text\n\nLi J, Zheng H, Du HB, et al.: The multiple lifestyle modifications for patients with prehypertension and hypertension patients: a systematic review protocol. BMJ Open. 2014; 4(8): e004920. Publisher Full Text\n\nRubinstein A, Miranda JJ, Beratarrechea A, et al.: Effectiveness of a mHealth intervention to improve the cardio-metabolic profile of people with prehypertension in low-resource urban settings in Latin America: a randomized controlled trial. The Lancet Diabetes Endocrinol. 2016; 4(1): 52–63. PubMed Abstract \| Publisher Full Text\n\nTNN: Moodabidri, Kadaba becomes new taluks. Times of India;2019 May 9 [cited 2020 Oct 14].Reference Source\n\nMinistry of Home Affairs, Office of the Registrar General and Census Commissioner: Census 2011, Primary Census Abstracts. New Delhi:Government of India, Office of the Registrar General and Census Commissioner;2011 [cited 2020 Oct 30].Reference Source\n\nConsort: The CONSORT Flow Diagram:[cited 2020 Nov 13]. Reference Source\n\nThe SPIRIT Statement: Standard Protocol Items: Recommendations for Interventions Trials. [cited 2022 Oct 22] Reference Source\n\nWorld Health Organisation: WHO STEPS Instrument. Geneva:World Health Organisation;[updated 2017; cited 2020 Nov 1].Reference Source\n\nCohen S, Kamarck T, Mermelstein R: A global measure of perceived stress. J. Health Soc. Behav. 1983; 24: 385–396. Publisher Full Text\n\nPandey VK, Aggarwal P, Kakkar R: Modified BG Prasad Socio-economic Classification, Update-2019. Indian J. Community Health. 2019 Jan; 31(1): 150–152. Publisher Full Text\n\nIBM Corp: IBM SPSS statistics for Windows, version 25.0. ArmonkNY:IBM Corp;2017.Reference Source" }	[ { "id": "178663", "date": "04 Jul 2023", "name": "Karani Magutah", "expertise": [ "Reviewer Expertise Medical physiology and epidemiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have 2 major and 1 minor comments as here below:\nThis is a trial and will have interventions in the one group and not the other (control). Participants are drawn from the same villages/community and this is likely to have contamination where individuals in the control group may see and be influenced by those in the intervention group. There is need for careful quality control considerations to fend off likely cross-over mainly from control to intervention arm when the investigators do not want this. One way to do this is having separate but homogenous villages for intervention and the control group.\n\nTo avoid a likely recall bias that may be introduced by weekly tracking of diet that participants were on throughout a week that has already passed, this could either be done more regularly (like twice a week) or have participants fill daily record-logs after every meal or at the end of every day. These records can thereafter be collected at the end of the week. This will help reduce recall bias that may compromise quality of the results.\n\nPhysical activity (PA) should be defined such that the intensity to be considered, the length and the frequency is clear for the reader. Usually, we have mild, moderate and vigorous intensity PA. Because participation in either may yield differing outcomes, the investigators may need to in their intervention have only form form that the participants could adopt. Similarly, the number of minutes in a week that is determined by the frequency and the length for each session could be clarified.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "10184", "date": "22 Sep 2023", "name": "Rekha Thapar", "role": "Author Response", "response": "1.This is a trial and will have interventions in the one group and not the other (control). Participants are drawn from the same villages/community and this is likely to have contamination where individuals in the control group may see and be influenced by those in the intervention group. There is need for careful quality control considerations to fend off likely cross-over mainly from control to intervention arm when the investigators do not want this. One way to do this is having separate but homogenous villages for intervention and the control group. Response Thank you sir for your suggestion. At the designing stage, we thought of assigning one of the selected villages for intervention and another selected village as control. However, this approach might result in an unequal number of prehypertensives in the intervention and control arm. Only one prehypertensive from every household will be recruited for the study to prevent cross-contamination. 2. To avoid a likely recall bias that may be introduced by weekly tracking of diet that participants were on throughout a week that has already passed, this could either be done more regularly (like twice a week) or have participants fill daily record-logs after every meal or at the end of every day. These records can thereafter be collected at the end of the week. This will help reduce recall bias that may compromise the quality of the results. Response Thank you sir. We have incorporated your suggestion to record-log every meal of the participant on a daily basis. The manuscript has been modified accordingly 3. Physical activity (PA) should be defined such that the intensity to be considered, the length and the frequency is clear for the reader. Usually, we have mild, moderate and vigorous intensity PA. Because participation in either may yield differing outcomes, the investigators may need to in their intervention have only form that the participants could adopt. Similarly, the number of minutes in a week that is determined by the frequency and the length for each session could be clarified. Response The definition and recommendations for physical activity have been incorporated from the WHO-STEPS questionnaire. The STEPS questionnaire includes questions to assess an individual's level of physical activity. It typically covers aspects such as the frequency, duration, and intensity of physical activity, as well as the types of activities individuals engage in (e.g., walking, cycling, sports)." } ] }, { "id": "178670", "date": "06 Jul 2023", "name": "Hon Lon Tam", "expertise": [ "Reviewer Expertise Cardiometabolic diseases", "controlled trial", "systematic review", "meta-analysis", "gerontological nursing" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: The use of abbreviation in abstract is not a common practice. CVD was not introduced before the first use. Please add a section to describe the significance and contribution of the study to current research and practice.\n\nIntroduction\nThe use JCN7 was good, but the it was very old. Also, none of the cited Reference #2-4 was the direct JNC7 document. There are many updated hypertension guidelines you can refer to (1-3).\n\nYou mentioned lifestyle modifications were important to pre-hypertension people. Please summarize the points as it was too long now.\n\nPlease summarize the prevalence of pre-hypertension from various studies.\n\nYou may mention that many people with hypertension did not adhere to healthy lifestyles (4). You can use this point to link with the development of interventions for pre-hypertensive people.\n\nYou described that several studies had shown the effectiveness of using multi-components to improve blood pressure and lifestyles among pre-hypertensive people, What was the value/significance of current study?\n\nMethods:\nWhere are the villages, South, North, East or West India? Any specific reasons to select these villages?\n\nThe study had been done in Dec 2022. Why to publish a study protocol, but not the study findings?\n\n\"For getting a block of four participants with an equal .... The participants will be allocated into either group in a batch of four.\" Might not be necessary.\n\nPlease describe the development of the intervention. Any guideline to follow the development of the content?\n\nWhat will be the expected group size? Who delivered the education? What was the interval between each session, daily, weekly?\n\nIt was unclear that there were 4 modules, but only 3 sessions. Please describe with modules will be delivered in session 1, 2, and 3.\n\nHow to control subject contamination between intervention and control groups?\n\nPlease update blood pressure measurement. It has been suggested to measure at least twice in one measurement (1-3).\n\nWho collect the data from the participants? Who assign the participants to groups?\n\nThe use of ITT is good, but how to treat missing data?\n\nThe change score within the group will be compared using repeated measures of ANOVA and Friedman’s test. Any test to examine the change between groups (intervention vs control)?\nImplications:\nPlease use paragraph format. Urban-rural disparities in hypertension management has been shown globally for years (4, 5, 6). The authors need to make further discussion.\nFigure: There was only 71 participants assigned to intervention group, but 72 will receive the modules?\nSuggested references:\nUnger T, Borghi C, Charchar F, et al. 2020 International Society of Hypertension Global Hypertension Practice Guidelines. Hypertension. 2020;75(6):1334-1357.\n\nWhelton PK, Carey RM, Aronow WS, et al. 2017 ACC/AHA/AAPA/ABC/ACPM/AGS/APhA/ASH/ASPC/NMA/PCNA Guideline for the Prevention, Detection, Evaluation, and Management of High Blood Pressure in Adults: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. Journal of the American College of Cardiology. 2018;71(19):e127-e248.\n\nWilliams B, Mancia G, Spiering W, et al. 2018 ESC/ESH Guidelines for the management of arterial hypertension. European Heart Journal. 2018;39(33):3021-3104.\n\nTam HL, Chair SY, Leung ISH, Leung LYL, Chan ASW. US Adults Practicing Healthy Lifestyles Before and During COVID-19: Comparative Analysis of National Surveys. JMIR Public Health and Surveilance. Mar 31 2023;9:e45697.\n\nBa HO, Camara Y, Menta I, et al. Hypertension and Associated Factors in Rural and Urban Areas Mali: Data from the STEP 2013 Survey. International Journal of Hypertension. 2018:6959165.\n\nRatovoson R, Rasetarinera OR, Andrianantenaina I, Rogier C, Piola P, Pacaud P. Hypertension, a Neglected Disease in Rural and Urban Areas in Moramanga, Madagascar. PLoS One. 2015;10(9):e0137408.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "10185", "date": "22 Sep 2023", "name": "Rekha Thapar", "role": "Author Response", "response": "1.The use of abbreviation in abstract is not a common practice. CVD was not introduced before the first use. Please add a section to describe the significance and contribution of the study to current research and practice. Response Thank you sir for the suggestion. We have included a section on the importance of the study in the abstract. The use of abbreviations before the first use has been rectified in the manuscript. 2.The use JCN7 was good, but the it was very old. Also, none of the cited Reference #2-4 was the direct JNC7 document. There are many updated hypertension guidelines you can refer to (1-3). Response Thank you sir for your observation. The term prehypertension was a classification introduced in JNC VII. The main objective of the trial is to study the effect of modular intervention in halting the progress of prehypertensives to overt hypertension. Prehypertension was initially redefined in JNC 7. Our focus is on individuals with prehypertension as they can progress to hypertension. Since the main focus of our study is on pre-hypertensives we have used the JNC-VII report. 3.You mentioned lifestyle modifications were important to pre-hypertension people. Please summarize the points as it was too long now. Response Thank you, sir. We have summarized the points as per your suggestion. 4.Please summarize the prevalence of pre-hypertension from various studies. Response Thank you. We have incorporated the suggestion in the manuscript. 5.You may mention that many people with hypertension did not adhere to healthy lifestyles (4). You can use this point to link with the development of interventions for pre-hypertensive people. Response Thank you sir We have incorporated your suggestion in the manuscript. 6.You described that several studies had shown the effectiveness of using multi-components to improve blood pressure and lifestyles among pre-hypertensive people, What was the value/significance of current study? Response Thank you, sir. Studies using multi-component modular interventions have not been conducted previously in our study setting. The intervention in our study will be administered using a module that is easy to comprehend and practice with the participants. Modular interventions break down the process of improving health into manageable steps or modules, making it easier for individuals to implement changes gradually. The active food tracking component will self-motivate the participants to adopt healthy behaviour. 7.Where are the villages, South, North, East or West India? Any specific reasons to select these villages? Response The villages selected for the study are located in the southern part of India. These villages are the rural field practice area of the Department of Community Medicine, KMC Mangalore, to which the authors of the study are affiliated to. 8.The study had been done in Dec 2022. Why to publish a study protocol, but not the study findings? Response Analysis of the data is still underway. 9.\"For getting a block of four participants with an equal .... The participants will be allocated into either group in a batch of four.\" Might not be necessary. Response Thank you, sir. We have removed the same from the manuscript. 10.Please describe the development of the intervention. Any guideline to follow the development of the content? Resposne The intervention module is prepared based on the recommendations from WHO STEPS and National programme for prevention & control of cancer, diabetes, cardiovascular diseases & stroke (NPCDCS. 11. What will be the expected group size? Who delivered the education? What was the interval between each session, daily, weekly? Response The expected group size is 10 and the sessions are delivered by the principal investigator once in three months. 12. It was unclear that there were 4 modules, but only 3 sessions. Please describe with modules will be delivered in session 1, 2, and 3. Response The intervention tool (module) consists of four components. All the components are delivered during all three sessions. 13. How to control subject contamination between intervention and control groups? Response At the designing stage, we thought of assigning one of the selected villages for intervention and another selected village as control. However, this approach might result in an unequal number of prehypertensives in the intervention and control arm. Only one prehypertensive from every household will be recruited for the study to prevent cross-contamination. 14. Please update blood pressure measurement. It has been suggested to measure at least twice in one measurement (1-3). Response Thank you sir. We have updated the measurements. 15. Who collect the data from the participants? Who assigns the participants to groups? Response The data is collected by the principal investigator (NF). Randomization and record keeping was done by co-investigators 16. The use of ITT is good, but how to treat missing data? Response The imputation technique will be used to treat the missing data. Also, the sample size was calculated considering a 10% loss to follow-up. The same has been incorporated in the manuscript. 18. The change score within the group will be compared using repeated measures of ANOVA and Friedman’s test. Any test to examine the change between groups (intervention vs control) Response Thank you, sir. Mann Whitney U tests will be used to examine the change between groups. The same has been included in the manuscript. 19. Please use paragraph format. Urban-rural disparities in hypertension management have been shown globally for years (4, 5, 6). The authors need to make further discussion. Response Thank you, sir. We have incorporated the changes as per your suggestion. 20. There was only 71 participants assigned to intervention group, but 72 will receive the modules? Response Thank you sir for pointing out the mismatch in the number. The same has been corrected in the manuscript." } ] } ]	1	https://f1000research.com/articles/12-667
https://f1000research.com/articles/12-748/v1	26 Jun 23	{ "type": "Systematic Review", "title": "Prognostic role of C-reactive protein-to-albumin ratio in acute pancreatitis: a systematic review and meta-analysis", "authors": [ "I Ketut Mariadi", "Gde Somayana", "Christina Permata Shalim", "Dwijo Anargha Sindhughosa", "Dian Daniella", "Made Lady Adelaida Purwanta", "Gde Somayana", "Christina Permata Shalim", "Dwijo Anargha Sindhughosa", "Dian Daniella", "Made Lady Adelaida Purwanta" ], "abstract": "Background: Acute pancreatitis (AP) is a common disorder and although most of the cases are mild, the mortality risk is high when it comes to severe AP. It is therefore important to determine the severity of AP as early as possible. This review aimed to determine the prognostic value of C-reactive protein-to-albumin ratio (CRP/alb ratio) in patients with AP. Methods: We performed a systematic search on the electronic databases PubMed, Cochrane Library, and Google Scholar up to January 2023. Studies reporting CRP/alb ratio on admission and its association with severity or mortality in AP patients were included. We calculated pooled mean difference (MD) and their 95% confidence intervals (CI) using a random-effects model. Quality assessment of the included studies was appraised using a Newcastle–Ottawa scale. Results: A total of six studies comprising 2244 patients were included in this meta-analysis. Severe AP had higher CRP/alb ratio on admission than mild-moderate AP (pooled MD: 3.59; 95% CI: 2.51-4.68; p<0.00001). CRP/alb ratio was also significantly higher on non-survivor AP patients compared to survivor AP patients (pooled MD: 2.12; 95% CI: 0.43-3.8; p < 0.01). Conclusion: High CRP/alb ratio can be used as an early predictor of poor prognosis in patients with AP.", "keywords": [ "c-reactive protein", "albumin", "acute pancreatitis", "prognostic", "meta-analysis" ], "content": "Introduction\n\nAcute pancreatitis (AP) is an inflammation of the pancreas characterized by sudden and severe onset of abdominal pain and elevated pancreatic enzyme.1,2 This condition is mostly caused by bile stones or heavy use of alcohol. Even though most of the cases are mild, the mortality risk is high when it comes to severe AP. The overall mortality rate of AP is 3% to 10%, but in severe AP the mortality rate rises to 36% to 50%.3 Thus, early determination of the disease severity to choose appropriate therapeutic strategy are of great importance.\n\nSeveral scoring systems are commonly used to determine the severity and prognosis of AP, such as Ranson scores, bedside index for severity in acute pancreatitis (BISAP), acute physiological assessment and chronic health evaluation II (APACHE II), and Atlanta classification.4 These scoring systems use multiple blood test results and clinical parameters, and almost all of them need repeated blood tests 48 hours after admission to increase its accuracy on predicting AP severity. There is a need for tools to predict the prognosis of AP within the first hour of admission.\n\nC-reactive protein (CRP) is an inflammatory marker that is widely used in clinical practice to determine the severity of various inflammatory and infective conditions. Inflammation and infection boost this liver-produced acute phase reactant.5 Albumin, on the other hand, is a liver-produced negative acute phase reactant that diminishes during inflammation. Albumin is also associated with disease severity and mortality.6\n\nCRP-to-albumin (CRP/alb) ratio was recently discovered as a new prognostic score associated with inflammation severity and mortality even though there is still no consensus on normal values of CRP/alb ratio. Some studies already tried to establish the relationship between CRP/alb ratio to AP severity and mortality and most of them yielded positive results. However, there is no meta-analysis that is currently available that summarizes all of these studies findings.\n\nIn this study, a systematic review and meta-analysis were conducted to investigate the prognostic value of CRP/alb ratio in AP.\n\n\nMethods\n\nThis systematic review and meta-analysis conforms to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standards. We registered this review in PROSPERO (registration number: CRD42023427438).\n\nWe performed a systematic literature search using PubMed, Science Direct, and Cochrane Library to find eligible journals from their commencement to January 31st, 2023. We employed keywords “pancreatitis” AND (“CRP albumin ratio” OR “C-reactive protein/albumin” OR “C-reactive protein albumin” OR “CRP/albumin” OR “CRP alb ratio” OR “CRP/alb”). Additionally, we examine the references of pertinent articles. Duplicate results were removed after the initial search.\n\nThree authors (IKM, CPS, DAS) independently performed study selection. A screening of study titles and abstracts was undertaken to exclude irrelevant literature. The inclusion and exclusion criteria for this review were applied to studies that passed the initial screening. The studies were included if they met all of the mentioned criteria: (1) observational studies reporting patients with acute pancreatitis, (2) reporting CRP/alb ratio on admission, (3) adult patients, (4) reporting the AP severity and/or patient’s mortality, (5) articles in English or Indonesian. Moreover, the studies were excluded if they meet one of the following criteria: (1) no full text available, (2) case reports, (3) conference papers, (4) review articles, (5) non research letters and (6) commentaries, (7) did not provide the necessary data for conducting meta-analysis.\n\nData of the included studies that were extracted are the first author’s name, year of publication, country, type of study, number of patients, age, CRP/alb ratio means or median value, and outcomes (severity or mortality).\n\nThe primary outcome studied in the present systematic review and meta-analysis is severity of AP. The secondary outcome was the mortality of AP patients. All authors utilized an electronic data collection form to acquire the necessary information from each article.\n\nThe Newcastle–Ottawa scale (NOS) was adopted to assess the risk of bias in each study included. Three authors (IKM, CPS, DAS) independently conducted this process. The investigations were divided into three categories: low risk (6), moderate risk (4–5), and high risk (3).\n\nReview Manager 5.4 and Stata 17 were used as the softwares for statistical analysis. We estimated the pooled mean difference (MD) with 95% confidence intervals (CI) using the mean difference (MD) and standard deviation (SD) from each study. We utilized a calculator by Luo et al. and Wan et al. to determine the mean if data were provided as median with Q1 and Q3 or range.7,8 Heterogeneity was assessed using the I2 statistic, which reveals which percentage of the variation in observed impacts across studies is related to the variation in true effects, with values greater than 60% indicating significant heterogeneity. All P values were two-tailed, and <0.05 was regarded statistically significant. Forest plot was generated to give a visual suggestion of the amount of study heterogeneity and the estimated effect. The leave-one-out method (repeating the analysis after eliminating one study at a time) was used to conduct a sensitivity analysis.\n\n\nResults\n\nThe keywords search yielded a total of 21 publications. After eliminating the duplicates, we retrieved 18 publications. By screening the titles and abstracts, we excluded 7 studies, leaving us with 11 potential studies. Then, the full texts of the potential studies were obtained and reviewed to see if they were eligible for inclusion in the meta-analysis. Publications that did not offer all the necessary data for this meta-analysis and that did not fulfill all the inclusion criteria were excluded. Thereby, in the present study, a total of 6 studies were included.9–14 PRISMA study flow diagram is described in Figure 1.\n\nAll 6 included studies were retrospective cohorts, with a total of 2244 patients. All studies were published in 2017–2022. Based on the study location, 4 studies were conducted in Turkey and 2 in China. There were 5 studies that evaluated CRP/alb relationship with AP severity. Meanwhile, the relationship between CRP/alb ratio with AP mortality were evaluated in 2 studies. Table 1 showed the characteristics of the included studies.\n\nUsing the NOS to evaluate the risk of bias, five studies were found to be at low risk, while one study was at high risk. Table 2 showed the risk of bias assessment.\n\nFive studies with a total of 1960 patients analyzed the relationship between CRP/alb ratio and AP severity. Severe AP patients had higher CRP/alb ratio than non-severe AP patients (pooled MD: 3.59; 95% CI: 2.51-4.68; p < 0.00001) (Figure 2). In addition, a sensitivity analysis was performed with leave-one-out method due to severe heterogeneity (I2 = 89%). Leave-one-out analysis showed no significant change in results after excluding one study at a time (Figure 3).\n\nWe found only two studies evaluating AP mortality and CRP/alb ratio that fulfilled the inclusion criteria. Based on these studies, non-survivor patients had higher CRP/alb ratio than survivor patients (pooled MD: 2.12; 95% CI: 0.43-3.8; p < 0.01) (Figure 4).\n\n\nDiscussion\n\nIn patients with AP there is a local inflammation that can cause systemic effects. This systemic inflammation is prone to develop systemic organ dysfunction and later organ failure.15 Severity of AP is classified based on the presence of these systemic complications and organ failure, with severe AP is defined as persistent organ failure. Meanwhile in mild AP there are no systemic complications or organ failure.16\n\nBecause the severity of AP is determined by how much inflammation there is, markers of inflammation are thought to determine the prognosis of AP. CRP, as one of the most commonly used biomarkers, has been shown to correlate well with AP severity. The problem was CRP levels alone at admission showed poor predictive value, and the correlation only significant when assessed later at 48 hours from admission. The accepted number by international consensus for prediction of severe AP was CRP >150 mg/L within the first 48 hours.17 Several studies discovered that both CRP and albumin can be beneficial in prognosis determination of various diseases. Combination of these two markers is expected to produce a more superior predictive value than using only one of them.\n\nIn this meta-analysis, we noted that the CRP/alb ratio is a promising prognostic score that can be used for the prediction of severity and mortality in AP patients. We analyzed 6 studies that fulfilled our inclusion criteria. Four studies from Turkey and 2 studies from China. Several included studies have different measurement units of CRP and albumin and some did not mention specifically what measurement units that were used. We tried to contact each corresponding author of the study in question to clarify this problem but none gave a response, thus we estimate the measurement units based on other relevant data from each study and make it all in the same measurement units.\n\nWe found that severe and non-survivor AP patients had higher CRP/alb ratio at admission than those with non severe and survivor AP patients. These findings were in line with results from other studies in recent years that showed the benefit of CRP/alb ratio as a prognostic marker in a variety of diseases. Because inflammation and carcinogenesis are linked, several systematic studies revealed the predictive practicality of CRP/alb ratio in different types of cancers.18,19 Several studies tried to determine this association focusing on critically ill patients. Park et al. in their single center retrospective study found out that higher CRP/alb ratio was associated with increased mortality in ICU patients.20 Wang et al. discovered that critically ill acute kidney injury patients with greater CRP/alb ratios had higher in-hospital mortality and 2-year all-cause mortality.21\n\nA retrospective cohort by Oh et al. showed that a high CRP/alb ratio in intensive care unit-admitted patients is an independent risk factor for a 30-day mortality rate.22 The results from this current meta-analysis reveal that CRP/Alb ratio may also serve as a reliable prognostic marker in patients with AP. AP is a disease that in severe form often leads to admission in the intensive care unit. This might explain the similar findings of this current study and previous study that focuses on critically ill patients.\n\nBased on our knowledge, this is the first meta-analysis that evaluates CRP/alb ratio as a prognostic marker in AP patients. There is one systematic review by Tarar et al. that also assessed the prognostic value of CRP/alb ratio in AP patients, but that study just did the qualitative analysis based on 3 retrospective cohort studies and did not conduct meta-analysis. That study discovered an overall beneficial connection between the CRP/alb ratio at admission and the occurrence of severe AP as well as a longer hospital stay.23 These outcomes are consistent with the results of our study.\n\nNevertheless, our research has its own limitations. First, 6 studies that included in this meta-analysis only came from 2 countries, which are Turkey and China. We cannot explain this lack of variety in study location, but we can say that this lack of diversity has been a limitation in this current study. Second, the differences in the units of measurement that were used in each study lead to the possibility of inaccurate comparisons made in this study.\n\n\nConclusion\n\nOur meta-analysis showed that high CRP/Alb ratio is associated with severe AP and mortality in patients with AP. Thus, CRP/alb ratio can be used as an early predictor of poor prognosis in patients with AP. However, due to the study’s limitations, large-scale trials involving patients of various ethnicities will be needed to verify the results we obtained.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Prognostic role of C-reactive protein-to-albumin ratio in acute pancreatitis: a systematic review and meta-analysis (extended data), https://doi.org/10.5281/zenodo.8003368. 24\n\nThis project contains the following extended data:\n\n- Search strategy.docx\n\nZenodo: PRISMA checklist for ‘Prognostic role of C-reactive protein-to-albumin ratio in acute pancreatitis: a systematic review and meta-analysis (extended data)’, https://doi.org/10.5281/zenodo.8003368. 24\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nLeppäniemi A, Tolonen M, Tarasconi A, et al.: 2019 WSES guidelines for the management of severe acute pancreatitis. World J. Emerg. Surg. 2019 Jun 13; 14(1): 27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJaber S, Garnier M, Asehnoune K, et al.: Guidelines for the management of patients with severe acute pancreatitis, 2021. Anaesth. Crit. Care Pain Med. 2022 Jun 1; 41(3): 101060. PubMed Abstract \| Publisher Full Text\n\nSilva-Vaz P, Abrantes AM, Castelo-Branco M, et al.: Multifactorial Scores and Biomarkers of Prognosis of Acute Pancreatitis: Applications to Research and Practice. Int. J. Mol. Sci. 2020 Jan; 21(1): 338. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Zhang J, Zou J: Evaluation of four scoring systems in prognostication of acute pancreatitis for elderly patients. BMC Gastroenterol. 2020 Jun 1; 20(1): 165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSproston NR, Ashworth JJ: Role of C-Reactive Protein at Sites of Inflammation and Infection. Front. Immunol. 2018 Apr 13; 9: 754. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEckart A, Struja T, Kutz A, et al.: Relationship of Nutritional Status, Inflammation, and Serum Albumin Levels During Acute Illness: A Prospective Study. Am. J. Med. 2020 Jun 1; 133(6): 713–722.e7. PubMed Abstract \| Publisher Full Text\n\nLuo D, Wan X, Liu J, et al.: Optimally estimating the sample mean from the sample size, median, mid-range, and/or mid-quartile range. Stat. Methods Med. Res. 2018 Jun; 27(6): 1785–1805. PubMed Abstract \| Publisher Full Text\n\nWan X, Wang W, Liu J, et al.: Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med. Res. Methodol. 2014 Dec 19; 14: 135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKarabuga B, Gemcioglu E, Konca Karabuga E, et al.: Comparison of the predictive values of CRP, CRP/albumin, RDW, neutrophil/lymphocyte, and platelet/lymphocyte levels in determining the severity of acute pancreatitis in patients with acute pancreatitis according to the BISAP score. Bratisl. Lek. Listy. 2022; 123(2): 129–135. PubMed Abstract \| Publisher Full Text\n\nKiyak M, Tanoglu A: Comparison of the Efficacy of Balthazar Score and C-Reactive Protein-Albumin Ratio for Determination of Acute Pancreatitis Severity. Curr. Health Sci. J. 2022; 48(1): 81–87.\n\nUgurlu ET, Yurekli UF: The effect of procalcitonin and immature granulocyte ratio in predicting the development of acute necrotizing pancreatitis: evidence from 582 cases. Eur. Rev. Med. Pharmacol. Sci. 2022 Oct; 26(20): 7514–7521. PubMed Abstract \| Publisher Full Text\n\nYılmaz EM, Kandemir A: Significance of red blood cell distribution width and C-reactive protein/albumin levels in predicting prognosis of acute pancreatitis. Ulus Travma Ve Acil Cerrahi Derg. Turk. J. Trauma Emerg. Surg. TJTES. 2018 Nov; 24(6): 528–531. Publisher Full Text\n\nZhao Z, Yu Y, Xie R, et al.: Prognostic value of the creatinine-albumin ratio in acute pancreatitis debridement. BMC Surg. 2020 Dec 9; 20(1): 322. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao Y, Xia W, Lu Y, et al.: Predictive value of the C-reactive protein/albumin ratio in severity and prognosis of acute pancreatitis. Front. Surg. 2022; 9: 1026604. Publisher Full Text\n\nGarg PK, Singh VP: Organ Failure due to Systemic Injury in Acute Pancreatitis. Gastroenterology. 2019 May; 156(7): 2008–2023. PubMed Abstract \| Publisher Full Text \| Free 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; 62(1): 102–111. PubMed Abstract \| Publisher Full Text\n\nStirling AD, Moran NR, Kelly ME, et al.: The predictive value of C-reactive protein (CRP) in acute pancreatitis – is interval change in CRP an additional indicator of severity? HPB. 2017 Oct 1; 19(10): 874–880. PubMed Abstract \| Publisher Full Text\n\nFang Y, Zheng T, Zhang C: Prognostic Role of the C-Reactive Protein/Albumin Ratio in Patients With Gynecological Cancers: A Meta-Analysis. Front. Oncol. 2021 Oct 28; 11: 737155. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiao CK, Yu YL, Lin YC, et al.: Prognostic value of the C-reactive protein to albumin ratio in colorectal cancer: an updated systematic review and meta-analysis. World J. Surg. Oncol. 2021 May 1; 19(1): 139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPark JE, Chung KS, Song JH, et al.: The C-Reactive Protein/Albumin Ratio as a Predictor of Mortality in Critically Ill Patients. J. Clin. Med. 2018 Oct; 7(10): 333. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang J, Zhao K, Mao X, et al.: Relationship between CRP Albumin Ratio and the Mortality in Critically Ill Patients with AKI: A Retrospective Observational Study. Biomed. Res. Int. 2021 Sep 30; 2021: 1–9. Publisher Full Text\n\nOh TK, Song IA, Lee JH: Clinical usefulness of C-reactive protein to albumin ratio in predicting 30-day mortality in critically ill patients: A retrospective analysis. Sci. Rep. 2018 Oct 8; 8(1): 14977. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTarar MY, Khalid A, Choo XY, et al.: Use of the C-Reactive Protein (CRP)/Albumin Ratio as a Severity Tool in Acute Pancreatitis: Systematic Review. Cureus. 2022; 14(9): e29243. Publisher Full Text\n\nMariadi IK, de Somayana G , Shalim CP, et al.: Prognostic role of C-reactive protein-to-albumin ratio in acute pancreatitis: a systematic review and meta-analysis (extended data).2023. Publisher Full Text" }	[ { "id": "182368", "date": "24 Jul 2023", "name": "Hasan Maulahela", "expertise": [ "Reviewer Expertise Gastroenterology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an important topic in the search for a simple prognostic marker for acute pancreatitis. The method chosen by the authors is strong (meta-analysis). Some additional information should be stated in the manuscript:\nIn the methods, who performed the literature search and what are their qualifications?\n\nAny other attempts to acquire unpublished data?\n\nFrom the studies we see that the severity criteria used are different for each study, how do the authors analyze this? Please explain more about it.\n\nExplain more the possibility of more robust studies being excluded from the analysis because the authors cannot obtain the data (in the discussion).\n\nIs there any risk of bias concerning the patient characteristics from the studies that were included in the analysis?\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "10233", "date": "22 Sep 2023", "name": "I Ketut Mariadi", "role": "Author Response", "response": "Dear Dr. Hasan Maulahela, We sincerely appreciate the time and consideration you have provided in reviewing our manuscript. Here we provide responses to your comments: 1. In the methods, who performed the literature search and what are their qualifications? Our response: The literature search and study selection performed by three authors (IKM, CPS, DAS) independently. IKM and DAS are internists in the Division of Gastroenterology and Hepatology, Faculty of Medicine, Udayana University/Prof Dr. I.G.N.G. Ngoerah Hospital, Denpasar, Bali, Indonesia. While CPS is a medical doctor at one of hospital in Jakarta 2. Any other attempts to acquire unpublished data? Our response: We are not seeking any unpublished data since we could not determine the quality of the study. However, we try to obtain any incomplete data by tracking the supplementary information of the respective articles in our study. 3. From the studies we see that the severity criteria used are different for each study, how do the authors analyze this? Please explain more about it. Our response: Thank you for your suggestion. We have added the discussion about different severity criteria that were used in each study in the “Discussion” section. Different severity criteria from each study were expected because each study was conducted in different countries and different centers. Each center usually has severity criteria of acute pancreatitis that is more often used than the other. But, we thought this difference did not significantly affect the results, because all the criteria were standardized criteria that are often used and in few studies already compared and showed no significant differences in their prognostic value. 4. Explain more the possibility of more robust studies being excluded from the analysis because the authors cannot obtain the data (in the discussion). Our response: Thank you for your suggestion. We added the discussion about this in the discussion as you suggested. Some studies passed the screening process and fulfilled the inclusion criteria but eventually excluded because the statistical data provided by those studies were not clear. We tried to contact the corresponding author for those studies but none gave us response, thus the studies were excluded. 5. Is there any risk of bias concerning the patient characteristics from the studies that were included in the analysis? Our response: Based on the risk of bias that we conducted using Newcastle-Ottawa Scale, most of the studies included were considered low risk of bias, with the exposed and non exposed individuals considered truly or somewhat representative of the target population. Thank you for your attention. Sincerely, I Ketut Mariadi Division of Gastroenterology and Hepatology, Faculty of Medicine, Udayana University/Prof Dr. I.G.N.G. Ngoerah Hospital, Denpasar, Bali, Indonesia" } ] }, { "id": "182364", "date": "26 Jul 2023", "name": "Bogi Pratomo Wibowo", "expertise": [ "Reviewer Expertise Gastroenterologist" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nREVIEW ARTICLE\nThis article addresses the prognostic value of CRP/albumin ratio in severity and mortality of acute pancreatitis. It addresses an important topic, especially the high CRP/albumin ratio as an early predictor of severity to conduct the doctors in charge immediately choose an appropriate therapeutic strategy. Despite the rather small study included in this meta-analysis, it should make an important contribution.\nThere are a number of issues with the inconsistency in the words chosen and the statistic analysis that need to be clarified. Below are more specific comments by section:\nAbstract\nThe title stated prognostic role, in my opinion it should be prognostic value in conjunction with the statement of prognostic value of C-reactive protein-to-albumin ratio on the background of the abstract. The conclusion also stated the poor prognostic seems to be uncorrelated with the data reported in the article. It would be better using the term of severity or mortality in state of poor prognostic.\nIntroduction\nMore information about the epidemiology of acute pancreatitis would provide welcome context here. A bit more detail of incidence rate of acute pancreatitis in population would be helpful since you explicitly state acute pancreatitis is a common disorder on the background of the abstract.\nResults\nOn the page 6 of 9, the double subtitles of CRP/alb ratio and AP severity should not be used. In my opinion, the subtitle should be CRP/alb ratio and AP severity and CRP/alb ratio and AP mortality. It is based on the primary and secondary outcome studied in this meta-analysis.\nTable 2 – you indicate one study is moderate risk of bias with score 5, but in the text report of quality assessment is written high risk. This should be minimalized by cross-checking between the table shows and the text reported.\nFigure 2 and 3 – the titles of forest plot are severe vs non severe patients, since you already make a case definition of non-severe as mild-moderate patients. It would be consistent if you use the title of severe vs mild-moderate patients.\nFigure 4 – the heterogeneity of the forest plot is I2=0% which means low heterogeneity, with p value 0.42 which means the heterogeneity test is not significant, so it would be better if you used the Fixed model rather than Random model analysis.\nDiscussion\nDiscussion of the CRP/alb ratio in cancer and critically ill patients is interesting, but it could be made much more succinct in keeping with the focus of acute pancreatitis patients on this article. More detail of the cut-off level of CRP/alb ratio here would be welcome.\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": "10234", "date": "22 Sep 2023", "name": "I Ketut Mariadi", "role": "Author Response", "response": "Dear Dr. Bogi Pratomo Wibowo, We sincerely appreciate the time and consideration you have provided in reviewing our manuscript. Here we provide responses to your comments: Abstract The title stated prognostic role, in my opinion it should be prognostic value in conjunction with the statement of prognostic value of C-reactive protein-to-albumin ratio on the background of the abstract. The conclusion also stated the poor prognostic seems to be uncorrelated with the data reported in the article. It would be better using the term of severity or mortality in state of poor prognostic. Our response: Thank you for your suggestion. After the discussion by the authors, we agreed that “prognostic value” was more suitable for this study title, thus we changed the title with “Prognostic value of C-reactive protein-to-albumin ratio in acute pancreatitis: a systematic review and meta-analysis”. For the conclusion in the abstract we tried to summarize our findings. Our findings showed that high CRP/alb ratio is associated with severe AP and mortality in patients with AP, thus we conclude that findings as poor prognostic. In the conclusion section in the full text we describe it in more detail than in the abstract. Introduction More information about the epidemiology of acute pancreatitis would provide welcome context here. A bit more detail of incidence rate of acute pancreatitis in population would be helpful since you explicitly state acute pancreatitis is a common disorder on the background of the abstract. Our response: Thank you for your suggestion. We already added data of acute pancreatitis incidence rate in the introduction section as you suggested. Results On the page 6 of 9, the double subtitles of CRP/alb ratio and AP severity should not be used. In my opinion, the subtitle should be CRP/alb ratio and AP severity and CRP/alb ratio and AP mortality. It is based on the primary and secondary outcome studied in this meta-analysis. Our response: Thank you for the correction. We already corrected the subtitles to the correct one: “CRP/alb ratio and AP severity” and “CRP/alb ratio and AP mortality”. Table 2 – you indicate one study is moderate risk of bias with score 5, but in the text report of quality assessment is written high risk. This should be minimalized by cross-checking between the table shows and the text reported. Our response: Thank you for the correction. We already corrected the mistakes. The score range of Newcastle-Ottawa Scale should be: low risk (7-9), moderate risk (4–6), and high risk (0-3). The one study that you mentioned has a score of 5, thus considered moderate risk of bias. Figure 2 and 3 – the titles of forest plot are severe vs non severe patients, since you already make a case definition of non-severe as mild-moderate patients. It would be consistent if you use the title of severe vs mild-moderate patients. Our response: Thank you for your suggestion. We already changed the title of figure 2 and 3 with severe vs mild-moderate patients as you suggested. Figure 4 – the heterogeneity of the forest plot is I2=0% which means low heterogeneity, with p value 0.42 which means the heterogeneity test is not significant, so it would be better if you used the Fixed model rather than Random model analysis. Our response: Thank you for your suggestion. We already changed the statistical models that we used for the analysis between CRP/alb ratio with mortality as shown in figure 4 with the fixed-effect model as you suggested. Discussion Discussion of the CRP/alb ratio in cancer and critically ill patients is interesting, but it could be made much more succinct in keeping with the focus of acute pancreatitis patients on this article. More detail of the cut-off level of CRP/alb ratio here would be welcome. Our response: Thank you for your suggestion. We already reduced the discussion about CRP/alb ratio in critically ill patients to keep the discussion focus on CRP/alb ratio in acute pancreatitis patients. Thank you for your attention. Sincerely, I Ketut Mariadi Division of Gastroenterology and Hepatology, Faculty of Medicine, Udayana University/Prof Dr. I.G.N.G. Ngoerah Hospital, Denpasar, Bali, Indonesia" } ] } ]	1	https://f1000research.com/articles/12-748
https://f1000research.com/articles/12-1185/v1	21 Sep 23	{ "type": "Case Report", "title": "Case Report: Langerhans cell histiocytosis involving the cervical spine in an adult patient", "authors": [ "Dipak Chaulagain", "Volodymyr Smolanka", "Andriy Smolanka", "Taras Havryliv", "Volodymyr Smolanka", "Andriy Smolanka", "Taras Havryliv" ], "abstract": "Langerhans Cell Histiocytosis (LCH) is a typically benign disorder that affects infants predominately, with adult occurrence being uncommon. We discuss the case of a 22-year-old guy who visited our clinic complaining of three months of acute nape pain and upper limb radiculopathy. Notably, the patient had no history of trauma, fall injuries, or tuberculosis. Radiological tests identified a single osteolytic lesion within the C3 vertebral body. The lesion was removed, an anterior C3 corpectomy and discectomy were performed, and the patient's spine was reconstructed with a titanium cage and plating. The patient's nape discomfort and radiculopathy vanished almost instantly after surgery. A definitive diagnosis of LCH was confirmed through histological examination. This case report illustrates the unusual and uncommon occurrence of LCH at the C3 vertebral body, for which fusion surgery was the only viable therapeutic option. The patient's recovery from radiating pain following the surgical procedure demonstrates the effectiveness of the intervention. LCH in the cervical spine is rather rare, but it is nevertheless important to be aware of the possibility of developing it.", "keywords": [ "Langerhans cell histiocytosis", "Histiocytosis", "Cervical spine" ], "content": "Introduction\n\nLangerhans cell histiocytosis (LCH) is a rare disease that causes Langerhans cells to multiply in a way that isn’t normal. This causes sores on the skin, the bones, the liver, the spleen, and the lymph nodes.1,2 The localized form of LCH is the most common presentation, typically manifesting as a solitary bone lesion predominantly seen in children.3,4 In about 7–15% of cases, the spine is affected. The thoracic spine is most often affected (54%), followed by the lumbar spine (35%), and then the cervical spine (11%).5\n\nThe clinical presentation of LCH can vary widely, ranging from self-healing bone lesions to life-threatening multi-system involvement. Consequently, determining the most appropriate treatment approach poses a significant challenge, as therapeutic options span from watchful waiting to aggressive interventions.6,7\n\nLesions of the adult spine in the context of Langerhans cell histiocytosis do not appear to have any particular therapeutic recommendations or treatment regimens in the existing research. In addition, there is a paucity of research devoted to surgical treatments for LCH of the spine, therefore there is little in the way of specifics or established protocols for how to treat this condition in adults.\n\nIn this report, we describe a case of adult Langerhans cell histiocytosis (LCH) involving the C3 vertebrae, a location seldom affected by this disease. The patient initially presented to our hospital with pain in the nape region, which prompted the decision to pursue surgical intervention. During the surgery, an anterior lesion was removed, an anterior corpectomy with discectomy was done, and then the area was put back together with a titanium cage and plating.\n\n\nCase report\n\nThe Regional Clinical Centre of Neurosurgery and Neurology in Uzhhorod, Ukraine, had a visit from a 22-year-old male patient of Ukrainian nationality. The patient, who is now pursuing studies, reported experiencing neck discomfort for a duration of three months. There was no familial history indicating the presence of similar symptoms. The patient’s neurological problems did not improve in spite of getting non-steroidal anti-inflammatory medicines and physical therapy. The cranial nerves were confirmed to be intact, and no localized weakening was observed during the motor assessment. The patient exhibited normal physiological reflexes. However, he experienced increasing discomfort in the posterior neck region.\n\nA magnetic resonance imaging (MRI) of the cervical spine revealed that there were anomalies in the C3 vertebral body. An enlarged mass-like lesion may be seen on contrast-enhanced T1-weighted imaging; this lesion has migrated to the anterior epidural region, which reveals central spinal stenosis (Figure 1).\n\nThe patient had a titanium cage and plating restoration after a discectomy and anterior corpectomy at C3 (Figure 2).\n\nThese specimens revealed fragments of connective tissue and bone with a histiocytic lesion upon microscopic examination. The histomorphological aspect and the immunohistochemical staining profile argue for a Langerhans cell histiocytosis. LCH was the histological diagnosis. Positive immunohistochemical stains were observed for CD1a, S-100, CD68, and KiM1p.\n\nFollowing the surgical procedure, there was a full recovery from the pain in the neck. One month following the operation, MRI scans revealed that the C3 vertebral body had not shown any signs of new tumor development (Figure 3). We found no evidence of a previous history of problems or a worsening of the symptoms.\n\n\nDiscussion\n\nInterleukin-17A, among other inflammatory cytokines, is recognized to have a role in the development of Langerhans cell histiocytosis (LCH).8,9 Estimates place the incidence of LCH in adults between 1 and 2 cases per million population, while in children, the incidence ranges from 2 to 10 cases per million. However, it is likely that these numbers underestimate the true incidence of the disease.10 In the case presented here, the patient’s age of 22 years suggests the possibility of a delayed diagnosis, which may have contributed to the later presentation of the disease.\n\nLangerhans cell histiocytosis (LCH) exhibits a predilection for various skeletal sites, with the skull being the most commonly affected (26%), followed by the ribs (12%), mandible and upper extremities (9%), and other bones of the extremities (11%).11 In terms of spinal involvement, LCH is relatively infrequent, accounting for only a small percentage of cases. Only 6.5% (14 cases) of the 214 cases reported by Bunch et al. were localized in the spine. Spinal lesions mostly affect the vertebral bodies, with the thoracic spine (54% prevalence) being greater than the lumbar (35% prevalence) and cervical (11% prevalence).11 LCH is so uncommon that determining its prevalence as a single cervical lesion is challenging. Just 0.02% of 342 cases evaluated by Howarth et al. 9 had spinal involvement, and of those, exclusively in the cervical vertebrae. The fact that LCH rarely presents as a single lesion in the cervical spine is highlighted by this.\n\nThis patient is a rare example of an adult with Langerhans cell histiocytosis (LCH) of the cervical spine. Radiological alterations shown on imaging investigations, along with certain pathological and immunohistochemical results, are often used to make a diagnosis of LCH. Confirming the presence of LCH and differentiating it from other illnesses with comparable clinical presentations rely heavily on these methods of diagnosis.\n\nHistopathological examination of Langerhans cell histiocytosis (LCH) under the microscope reveals eosinophils, large cells, neutrophils, foamy cells, and fibrosis, among other possible findings. As compared to other cell types, Langerhans cells may be identified thanks to their positive immunostaining both CD1a with S-100 protein.12 In addition to aiding in a diagnosis of LCH, these microscopic features and immunohistochemistry markers can be used to set LCH apart from other histiocytic illnesses and inflammatory syndromes.\n\nDetermining an optimal treatment strategy for Langerhans cell histiocytosis (LCH) remains a highly controversial issue. Previous literature suggests that the prognosis for vertebral involvement is generally considered benign, with favorable outcomes. Specifically, there have been no reported cases of significant neurological deficits resulting from vertebral spine involvement in LCH.13 These findings imply that the vertebral types of LCH typically exhibit a less aggressive disease course and are associated with a relatively good prognosis.\n\nIn a study by Monalti et al., two patients with a solitary eosinophilic granuloma (EG) of the spine experienced rapid pain alleviation after receiving corticosteroid infiltrations. However, post-interventional imaging did not match the clinical manifestations observed in these patients. In particular, computed tomography (CT) imaging revealed a reduction in lesion size in one patient while the morphology of the vertebral lesion remained unchanged in the second patient.14 There are a number of methods for dealing with Langerhans cell histiocytosis (LCH), including close surveillance, NSAIDs, chemotherapy, radiation, intralesional steroid injection, surgical removal of the lesion, and spinal repair.15\n\nLangerhans cell histiocytosis (LCH) indications for radical surgery remain inadequately documented. Nevertheless, given the patient’s presentation with radiculopathy, we decided to pursue radical surgical intervention. This decision was made based on the clinical condition of the patient and the urgency need to relieve compression and preserve neurological integrity. Prior studies have reported successful resolution of Langerhans cell histiocytosis (LCH) via observation, surgery, chemotherapy, and radiation therapy, among others. Individual patient characteristics, the severity of the disease, and the presence of associated symptoms or complications determine which of these treatment options are employed. Thus, a titanium cage and plating reconstruction with anterior cervical C3 corpectomy and discectomy was performed. Further research is needed with a larger sample size to provide firm guidelines and criteria for LCH surgical treatment in the adult cervical spine. The sample tissue was examined under a microscope to confirm the diagnosis of LCH.\n\nFollowing the surgical intervention, the patient experienced complete resolution of posterior neck pain. Subsequent postoperative MRI studies conducted one month after the surgery indicated no evidence of tumor re-growth and the absence of any lesions or signs of tumor regrowth within the fusion construct. These results suggest that surgical decompression may be a viable alternative for relieving pain and preventing neurologic impairment when other treatments have failed.\n\n\nConclusion\n\nWe suggest an anterior cervical corpectomy with discectomy and titanium cage and plating for the treatment of adult Langerhans cell histiocytosis (LCH). This technique, which is performed through a direct, anterior access to the cervical vertebrae, has the potential to alleviate pain, achieve stability, and restore function, particularly in cases involving significant cortical bone destruction and concomitant neurological deficits in the cervical spine. It is essential to note, however, that these results are founded on a singular case study; therefore, additional research employing more extensive research methodologies is necessary. Further research is required to ascertain whether LCH in the adult cervical spine should be surgically treated and how the procedure should be carried out.\n\n\nConsent\n\nWe are pleased to confirm that we have received written consent from the patient, for the publication of their clinical details and images in the manuscript. This consent statement is a vital aspect of our submission, and we are committed to upholding the highest ethical standards in medical research. The consent statement, duly signed by the patient’s parent, has been provided. This statement outlines the patient and parent of patient’s clear understanding and agreement regarding the publication of their clinical information and images for educational and research purposes. We would like to reiterate our commitment to maintaining patient confidentiality and ensuring that all ethical guidelines are adhered to throughout the publication process.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReference\n\nImashuku S, Shioda Y, Kobayashi R, et al.: Neurodegenerative central nervous system disease as late sequelae of Langerhans cell histiocytosis. Report from the Japan LCH study group. Haematologica. 2008; 93: 615–618. Publisher Full Text\n\nDerenzini E, Fina MP, Stefoni V, et al.: MACOP-B regimen in the treatment of adult Langerhans cell histiocytosis: Experience on seven patients. Ann. Oncol. 2010; 21: 1173–1178. Epub 2009 Oct 27. PubMed Abstract \| Publisher Full Text\n\nAzouz EM, Saigal G, Rodriguez MM, et al.: Langerhans’ cell histiocytosis: pathology, imaging and treatment of skeletal involvement. Pediatr. Radiol. 2005; 35: 103–115. PubMed Abstract \| Publisher Full Text\n\nRamzi C, Vinay K, Abul A, et al.: Robbins and Cotran Pathologic Basis of Disease. St. Louis, Mo: Elsevier Saunders; 2005; 701.\n\nSayhan S, Altinel D, Erguden C, et al.: Langerhans cell histiocytosis of the cervical spine in an adult: A case report. Turk. Neurosurg. 2010; 2: 409–412. Publisher Full Text\n\nPorto L, Schoning S, Hattingen E, et al.: Central nervous system imaging in childhood Langerhans cell histiocytosis - a reference center analysis. Radiol. Oncol. 2015; 49(3): 242–249. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGong L, Zhang WD, Li YH, et al.: Clonal status and clinicopathological features of Langerhans cell histiocytosis. J. Int. Med. Res. 2010; 38(3): 1099–1105. PubMed Abstract \| Publisher Full Text\n\nBadalian-Very G, Vergilio JA, Degar BA, et al.: Recurrent BRAF mutations in Langerhans cell histiocytosis. Blood. 2010; 116(11): 1919–1923. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJang KS, Jung YY, Kim SW: Langerhans cell histiocytosis causing cervical myelopathy in a child. J. Korean Neurosurg. Soc. 2010; 47(6): 458–460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNg-Cheng-Hin B, O’Hanlon-Brown C, Alifrangis C, et al.: Langerhans cell histiocytosis: old disease new treatment. QJM. 2011; 104(2): 89–96. Publisher Full Text\n\nSayhan S, Altinel D, Erguden C, et al.: Langerhans cell histiocytosis of the cervical spine in an adult: a case report. Turk. Neurosurg. 2010; 20(3): 409–412. PubMed Abstract \| Publisher Full Text\n\nGong L, Zhang WD, Li YH, et al.: Clonal status and clinicopathological features of Langerhans cell histiocytosis. J. Int. Med. Res. 2010; 38(3): 1099–1105. Publisher Full Text\n\nJouve JL: Expert’s comment concerning grand rounds case entitled “Langerhans cell histiocytosis of the atlas in an adult” (by Wo Quan Zhong, Liang Jiang, Qing Jun Ma, Zhong Jun Liu, Xiao Guang Liu, Feng Wei, Hui Shu Yuan, Geng Ting Dang). Eur. Spine J. 2010; 19(1): 23–24. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontalti M, Amendola L: Solitary eosinophilic granuloma of the adult lumbar spine. Eur. Spine J. 2012; 21(4): 441–S444. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGirschikofsky M, Arico M, Castillo D, et al.: Management of adult patients with Langerhans cell histiocytosis: Recommendations from an expert panel on behalf of Euro-Histio-Net. Orphanet J. Rare Dis. 2013; 8: 72. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "240234", "date": "05 Feb 2024", "name": "Abhilash Thatikala", "expertise": [ "Reviewer Expertise Neurology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the author for writing this manuscript. The article presents a case report of a 22-year-old patient with Langerhans cell histiocytosis (LCH) affecting the cervical spine. The patient initially presented with nape pain and radiculopathy, and the diagnosis was confirmed through imaging and biopsy. The patient underwent a successful surgical procedure to remove the tumor in the C3 vertebral body, resulting in complete pain relief and no evidence of new tumor development one month later. The report emphasizes the rarity of LCH in the cervical spine and underscores the significance of prompt diagnosis and treatment for optimal outcomes. Below are my comments for the author: Abstract : Well written and concise. Please mention the which side the patient had radicular symptoms. Intro: Well written. Case report: Please describe the radicular symptoms as mentioned in the abstract. Please provide histopathology slides if available. Discussion: Well written. Conclusion: Agree with the comments that this cannot be generalized to broader population.\n\nSome potential strengths of the article include:\nThe article presents a unique case report of Langerhans cell histiocytosis involving the cervical spine in an adult patient, which could contribute to the understanding of the disease and its management. The article provides a detailed description of the surgical procedure performed to treat the patient's condition, which could be useful for clinicians and researchers interested in this area.\n\nSome limitations of the article may include: The article is based on a single case report, which limits the generalizability of the findings to a broader population. The article may not provide information on the long-term outcomes of the patient, such as recurrence of the disease or complications, which could impact the assessment of the treatment efficacy.\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": "246281", "date": "08 Jun 2024", "name": "Mohammad Alfawareh", "expertise": [ "Reviewer Expertise Spine Deformiy and Tumors" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nwell described well formatted manuscript the introduction gave details about the disease and how common histiocytosis\n\ncase report well described the case scenario, covering all the needed details images gave great explanation to the case post operative CT scan well informative discussion well constructed and exploring possible deferential and management details were included\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1185
https://f1000research.com/articles/12-1184/v1	21 Sep 23	{ "type": "Study Protocol", "title": "Assessing the efficacy of hemoglobin electrophoresis as a diagnostic tool in moderate to severe anemia: a study protocol", "authors": [ "Rakhi Bhongade", "Sahitya Vodithala", "Sunita Vagha", "Sahitya Vodithala", "Sunita Vagha" ], "abstract": "Patients with hemoglobinopathy may experience short-term benefits from nutritional support and blood transfusions, but long-term results may be better if a precise diagnosis is obtained and a precise course of treatment or safety measures is adopted. The goal of the study is to determine the prevalence of haemoglobin abnormalities in people who presented with moderate to severe anaemia using haemoglobin electrophoresis They will undergo haemoglobin electrophoresis to test for the presence of any haemoglobin abnormalities. For anaemia classification, the WHO reference range is used. The outcome and quality of life of patients with haemoglobin disorders can be improved when they are properly managed, and since a significant portion of the patients in our study have hemoglobinopathies of varying severity, it would be prudent to conduct investigations to determine the precise cause of anaemia, particularly in rural areas where supportive management remains the mainstay of treatment in most scenarios.", "keywords": [ "hemoglobinopathy", "haemoglobin electrophoresis", "severe anemia", "WHO" ], "content": "Introduction\n\nThe branch of medicine known as haematology deals with a variety of physiological, pathological, clinical, and disorders that impact the platelets, white blood cells, and red blood cells that make up blood. The most prevalent haematological disorder, anaemia is defined as a reduction in haemoglobin or red blood cell (RBC) as a result of several causes. Anaemia in varied degrees can have a variety of clinical repercussions.1\n\nThe essential oxygen-transporting metaloprotein found in erythrocytes is called haemoglobin (Hb). An iron-containing porphyrin ring, often known as a heme group and a tetramer of the globin polypeptide chain make up the two primary parts of the haemoglobin molecule. The globin chains protect and make the heme soluble while the heme serves as an oxygen-carrying group. Porphyrias are uncommon inherited abnormalities of the porphyrin ring1,2\n\nIn developing countries, anaemia is the most prevalent issue among the rising age group. Iron deficiency anaemia (IDA), which has detrimental effects on health, especially in children and adolescents, results from a decrease in haemoglobin (Hb) concentration in the blood when iron deficiency is sufficiently severe. The different forms of haemoglobins present are measured using a procedure called haemoglobin electrophoresis.2\n\nTwo dimers of globin chains that are similar to one another make up the globin tetramer. The - and -chains, which are encoded on chromosome 16, are the globins that resemble globins. The -, and -chains, which are encoded on chromosome 11, are the globins that resemble globins. The embryonic Hbs, which are present in healthy embryos and foetuses less than three months gestation, are made up of the - and -chains. Hb F (22) predominates during foetal life. The correct maternal-fetal oxygen exchange in pregnancy depends on foetal red blood cells (RBCs) with Hb F having a higher oxygen affinity than adult RBCs. Before 20 weeks of pregnancy, adult Hb, Hb A (22), is only minimally created; production starts as soon as -chain synthesis is initiated.2,3\n\nHb A makes about 15–40% of the total Hb at birth. At six months of age, Hb F makes up about 8% of the total Hb due to the ongoing increase in the ratio of Hb A to Hb F. Adults typically have 97% Hb A, 1% Hb F, and 1.5-3.5% Hb A levels. Haemoglobin (Hb) is a crucial metaloprotein that transports oxygen and is present in erythrocytes. The two main components of the haemoglobin molecule are a tetramer of the globin polypeptide chain and an iron-containing porphyrin ring, commonly referred to as a heme group. Heme functions as an oxygen-carrying group and is shielded and made soluble by the globin chains. Rare inherited anomalies of the porphyrin ring are known as porphyrias.3\n\nThe most common condition affecting children in underdeveloped nations is anaemia. Over the past few decades, the diagnosis of haemoglobin disorders has changed, moving from being predominately driven by symptomatic patients, aberrant lab results, or peripheral blood smears, to the present emphasis on universal screening in the majority of developed healthcare systems. This evolution has kept pace with our growing understanding of these illnesses and the improvement of diagnostic techniques.3,4\n\nDr. Linus Pauling made the first molecular analysis of disease in 1949 by connecting sickle cell disease to a molecular abnormality. Since his groundbreaking study, more than 400 thalassemias and 1,000 Hb variations have been discovered. Haemoglobin (Hb), hematocrit (HCT), or RBC count reductions are all indicators of anaemia. It can be classified as macrocytic, microcytic, or normocytic and is a manifestation of an underlying ailment. Patients with anaemia often exhibit nebulous symptoms such lethargicness, weakness, and fatigue. Syncope, shortness of breath, and a decreased ability to tolerate physical activity are symptoms of severe anaemia. This exercise describes anaemia assessment and management, as well as the function of the interprofessional team in treating individuals with this condition. Over 2 billion individuals worldwide suffer from anaemia, which is the most prevalent haematological condition and a significant health burden. It is a symptom of a problem that is underlying and is indicated by a decrease in the percentage of red blood cells (RBCs). Anaemia can be caused by a wide range of conditions, including nutritional deficiencies, chronic illnesses, inflammatory conditions, medicines, cancer, renal dysfunction, genetic diseases, and bone marrow problems. Although cation-exchange HPLC is rapidly becoming the method of choice for the identification and quantification of Hb variants, Hb electrophoresis has been used since the 1960s and continues to be a viable tool for diagnosing Hb abnormalities. The Bio-Rad Variant (Bio-Rad Laboratories) is the most widely used commercial cation-exchange HPLC system. By using cellulose acetate and zone electrophoresis at an alkaline pH, the naturally occurring Hb A and Hb A2 are separated from the often found variations, Hb S, Hb F, and Hb C. Using citrate agar electrophoresis, the co-migrating Hbs (Hb S from Hb D and Hb G. Densitometric scanning is used to quantify Hb in electrophoresis, however it can be unreliable when variations are present in low concentrations. Isoelectric focusing (IEF), a relatively recent technique for high-resolution electrophoresis, divides haemoglobin variations according to their electric charge in a pH gradient produced by carrier ampholytes present in the medium. Capillary electrophoresis, a technique that uses haemoglobin electrophoresis in a negatively charged capillary system, has also gained favour recently.4\n\nAnother significant factor contributing to anaemia globally is infection-related anaemia, which is thought to account for around 12% of all cases in 2019-12 and is closely correlated with the geographic distribution of infection. Infections can affect how nutrients are metabolised and absorbed, or they might result in nutritional loss. The immune-driven anaemia known as anaemia of inflammation can also be brought on by prolonged illness and inflammation. Pro-inflammatory cytokines boost the production of the hormone hepcidin, which regulates iron absorption. Hepcidin then causes iron to be sequestered as ferritin, preventing iron from being transferred to erythrocyte precursor cells in the bone marrow and reducing erythropoiesis as well as erythrocyte survival.4,5\n\nA blood test called a haemoglobin electrophoresis is performed to assess and distinguish between the various forms of haemoglobin in the bloodstream. Disease diagnosis is no exception to the automation that already permeates nearly every part of life, including medicine. It is now easier, quicker, and less expensive to diagnose diseases because to computer-aided disease diagnosis technologies. By saving time and effort, they make decision-making easier. A further advantage of automated diagnosis is that it is less susceptible to variations in physician preferences. Computers may also be useful in the detection and forecasting of anemia. It is estimated that nearly every second child under the age of five has anaemia, which is a serious ailment that primarily affects women and children. Although there are several procedures, the Hb electrophoresis test technique is straightforward. In a nutshell, haemoglobin is released from red blood cells and dissolved into a solution. This lysate is then used to perform electrophoresis on a suitable electrophoresis medium, such as a cellulose acetate strip. The different Hb variants move across different distances because of differences in ionic charge. Blood samples from many patients (up to eight patients) are included in the Hb electrophoresis test photographs on a single cellulose sheet.6\n\nThe purpose of the study is to offer a precise method of analysing chemicals, such your blood and DNA (deoxyribonucleic acid), which are challenging to separate using conventional techniques. Haemoglobin electrophoresis analyses samples of blood to detect abnormal haemoglobin types. Most frequently, it is used to aid in the diagnosis of anaemia, sickle cell disease, and other haemoglobin abnormalities. The laboratory professionals includes lab technicians, pathologists, healthcare providers, supporting staffs, and students of medical lab technology can help to minimise the risk and provide safe and effective care to their patients at DMIHER, Sawangi.\n\nTo assess the efficacy of haemoglobin electrophoresis in moderate to severe anemia.\n\n\n\n1. To detect hemoglobin disorders in patients with anemia in a tertiary care hospital.\n\n2. To analyse the results of hemoglobin electrophoresis.\n\n3. To assess the efficacy of hemoglobin electrophoresis routinely for screening patients with anemia.\n\nThe study is conducted among the common population of the Vidarbha district in AVBRH hospital. The study is about the assessing the efficacy of hemoglobin electrophoresis as a diagnostic tool in moderate to severe anemia The study is helpful in the awareness of anemia among people. The conceptual research on anemia will be done. The recruitment of the people is independently done and the awareness will be observed.\n\n\nMethods\n\nThe following study is a diagnostic investigative study that will be conducted in the hematology division of the Dept. of Pathology, Jawaharlal Nehru Medical College (JNMC), Sawangi (Meghe), Wardha, in collaboration with the Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi (Meghe), Wardha, from 2022 to 2024.\n\nParticipant recruitment\n\nAll the samples which are routinely received in the section of hematology will be used for the study. The patients who have the features of moderate to severe anemia based on Complete Blood Count (CBC) and peripheral smear will be selected for the study.\n\nSample collection\n\nA typical blood draw will be used for the haemoglobin electrophoresis test. The patient’s arm will be tourniqueted, and a technician will feel for a suitable vein. An alcohol wipe will be used to clean the patient’s skin before a needle is used to draw blood from a vein. A tiny bandage or gauze patch will be put following the blood sample. After that, the patient will be free to leave.\n\nSample for hemoglobin electrophoresis\n\n1. Hemolysate will be prepared from blood in EDTA, citrate, or heparin.\n\n2. Fresh or refrigerated samples will be used.\n\nSteps to prepare the hemolysates\n\n1. The EDTA blood will be centrifuged and the upper liquid portion (supernatant plasma and buffy coat) will be removed.\n\n2. These cells with saline will be washed three times, and the saline will be discard from the last centrifuge.\n\n3. An equal volume of distilled water and 1/2 volume of carbon tetrachloride will be added.\n\n4. Then, will be shaked it vigorously.\n\n5. For 5 minutes at 1500 G will be centrifuged.\n\n6. Three layers will be formed:\n\n1. Upper hemolysate.\n\n2. Middle RBC leftover (stroma).\n\n3. Carbon tetrachloride (CCl4).\n\n7. The upper layer of the hemolysate (supernatant) will be pipetting carefully. This will look ruby color and will be clear.\n\n8. The hemoglobin concentration with distilled water 70 to 100 g/L will be adjust.\n\n9. The hemoglobin electrophoresis will be ready to run.\n\nIt is a prospective observational study.\n\nSample size: - Minimum sample size required\n\nZ1 − α/2 = 1.96, at 5% level of significance\n\nPrevalence of anemia in Wardha district P = 61.19%. (As per reference article)\n\nMinimum sample size required for the study was 92.\n\nIt will be published in an Index Journal.\n\nApproved by the Institutional Ethics Committee Ref. No. DMIHER (DU)/IEC/2023.Datta Meghe Institute of Higher Education and Research Sawangi (M) Wardha- 442001 Maharashtra, India.\n\nThe study is yet to be started; expected to complete before October 2024.\n\n\nDiscussion\n\nR Hafeez et al.(2022) did a study to concluded that the most frequent causes of severe anaemia in local kids were found to be 89 cases of malaria, 37 cases of septicemia, 7 cases of sickle cell anaemia, and 232 cases of iron deficiency (63.6%%). It must be remembered that these factors may eventually lead to severe anaemia because anaemia is a global health issue and can negatively affect children’s cognitive and physical development. To reduce the risk of severe anaemia in these kids, preventative and therapeutic measures must be taken.7 S Krishnamurthy et al.(2022) did a study to concluded that identifying anaemia in the elderly is important, as is classifying the kind and severity of the anaemia, looking for the underlying reason, and then treating the aetiology that has been found. In senior people with iron deficiency anaemia, it’s crucial to convince them of this and test their GIT with bilateral scopes. Despite having received the best workup possible, some individuals may appear with anaemia that is undiagnosed or without a known cause. It is satisfying to notice that we can greatly contribute to the general improvement in the quality of life of the elderly and their ability to carry out their daily activities wherever a reversible cause of anaemia is found and treated. Although natural and inevitable, remaining healthy as you age is a fundamental human right.8 LM Rogers et al. (2023) did a study to concluded that Nutritional, physiological, social, and environmental factors should all be taken into account when determining anemia’s occurrence. In order to address and combat anaemia and the related cause(s), a diagnosis of anaemia and the determination of its causes are necessary. The optimum method for determining haemoglobin (Hb) is to use venous blood that has undergone automated haematology analysis and undergone high-quality control procedures. Actions toward anemia diagnosis and control at public health levels will require global, regional, and country actions, It should include both general and context-specific qualities. New instruments to diagnose anaemia and its determinants in a single, more cost, practical, and quick test could be developed as a result of research into the biology, epidemiology, diagnosis, and treatment of anaemia. The introduction of sandwich ELISAs and other technologies that can assess numerous markers simultaneously has made it easier to identify anaemia risk factors, while commutability studies are still needed. For other indicators to assess causes of anemia, relatively large volumes of blood are needed, the costs are higher, and specialized laboratories are required. The WHO Comprehensive framework for integrated action on the prevention, diagnosis, and management of anaemia seeks to provide strategic, effective, and implementable actions to reduce anaemia, accelerate progress towards the global target on anaemia, and optimise health and well-being. Establishing a correct diagnosis of anaemia and its causes would also support this framework. Stakeholders must comprehend and agree that a multispectral, coordinated response is necessary for anaemia prevention and management.9 AK Shrestha et al.(2022) did a study to concluded that Haemoglobin Hb J is a rare variety, and research on it is still going strong and quickly; 71 new variants have been discovered so far. Although the Hb J is typically clinically asymptomatic, hemolysis and severe anaemia may occasionally be present. Where Hb J manifests as a P3 peak, CE-HPLC is the gold standard for differentiating these haemoglobin types. When Hb J is present, anaemia as such should cause a search for a coexisting hemoglobinopathy or the presence of an unstable form. When analysing differentials for any case of anaemia, this case prompts us to consider Hb J as a probable cause.10 T Milovanovic et al.(2021) did a study to concluded that GPs are a patient’s initial point of contact with the healthcare system. In addition to the inadequate research data from primary care units, the scarcity of anaemia recommendations may be motivated by worries about overburdened endoscopy services due to patient referrals or local priorities, as well as opinions about the costs and advantages of diagnostic testing.11 V Geetha et al. (2022) did a study to concluded that The hazards to the mother and foetus are reportedly increased when anaemia is prevalent in pregnant women. It is advised that primary healthcare be reinforced and that treating anaemia in pregnancy should be prioritised in order to prevent it from occurring in the first place. There are five key factors that affect the elimination of iron deficient anaemia. The main contributing factor is low iron supplementation compliance because to its negative effects. Some of the other factors are as follows: due to the difficulties of obtaining and getting to healthcare facilities, people with parasite and worm-related infections, symptoms that go undiagnosed, a shortage of micronutrients, and insufficient monitoring or evaluation of the supplementing plan. Additionally, it is necessary to enhance the healthcare programme, including the dietary intake and the health environment.12 M Salman Khan et al. (2022) did a study to conclude that for the automated assessment of thalassaemia, a novel deep-learning-based screening method has been investigated. The main goal was to identify whether strips of electrophoresis pictures of human beings were normal or abnormal in relation to thalassaemia by automatically extracting the lanes from the strips and classifying the subjects. When employing the InceptionV3 network, the proposed technique has a thalassaemia classification accuracy of 95.8% when tested on data from 524 cases. This was the first attempt to categorise electrophoresis test photos using a deep learning classifier model, and the technique produced passable accuracy. In the pipeline for thalassaemia screening, the suggested technique replaces manual assessment with automated assessment and detection. The findings also demonstrated that electrophoresis pictures combined with CNNs can provide superior results for thalassaemia screening when compared to more costly tests and methods. We plan to eventually add more electrophoresis picture data to the created database. In addition, we want to create gear that would enable automated thalassaemia screening.13 Kamran DS et al. (2023) did a study to concluded that peripheral smear can be used in high-risk locations and, although though it is not a very sensitive tool for screening for the Sickle trait, it can be supported by more advanced methods in ambiguous circumstances.14 Kharche K et al.(2023) did a study to concluded that in order to treat microcytic hypochromic anaemia with a hemolytic component that is resistant to treatment, a systematic review of 14 research from four regions and across India was conducted. The rare haemoglobin variations that the electrophoresis was unable to identify are likely best discovered by the HPLC. This review also comes to the conclusion that anaemia in children can result from both extremely unusual hemoglobinopathies like Hb J and common hemoglobinopathies like TM. The evaluation of haemoglobin abnormalities in the form of characteristics and diseases is advised for all paediatric patients with refractory anaemia.15 F Afshin et al. (2021) did a study to concluded that the examination of Hb Bart’s and Hb H are direct approaches for the diagnosis of thalassemia, however only a few cases of thalassemia were found in this study, and the most of them were missed. Because of this, -thalassemia must be confirmed in Hb Bart’s newborns, and molecular investigation is required to count the number of defective genes. In fact, lower MCV and MCH along with normal or low HbA2 levels appear to be a good opportunity to identify -thalassemia carriers. The CE result, whether generated from established genotypes or novel mutant genotypes, may be used as proof of Hb Hb and Hart Bart’s illness. Capillary electrophoresis is an effective method for identifying Hb H and Hb Bart’s disease due to the specificity of anaemia in blood analysis.16 VS Hariharan et al. (2023) did a study to concluded that the current research offers significant background data on PHT epidemiology among children and adolescents with SCA globally. PHT is one of the significant problems among SCA patients, regardless of their age, according to the findings of this systematic research. This study also emphasises how little research have looked into the degree of PHT among SCA patients in low- and middle-income areas. Clinicians in high-risk environments should create and implement diagnostic and intervention packages that are specifically aimed at these patients. It is important to conduct more research on the causes of the high prevalence of PHT in SCA patients since doing so will enable clinicians to better grasp the process, act decisively, and develop patient-specific therapies.17 N Kim et al. (2023) did a study to concluded that a specific Ampliseq-based panel was created for the genetic screening of HHA people, and it found 10 pathogenic mutations and 1 VUS. Although just a small number of people were chosen for our cohort, the data give a general idea of the molecular traits found in HHA. While we cannot rule out the possibility that genetic factors are not the primary causes of disease in these people, mutation-negative individuals from our cohort will need additional testing to identify the probable molecular flaws underlying their HHA.18 SR Menakuru et al. (2022) did a study to concluded that due to the description of the rare phenomena of HHS and the procedures necessary to identify the disease, this case is crucial to the body of current literature. As additional blood transfusions could result in a life-threatening anaemia, doctors need to have a high level of clinical suspicion when treating HHS patients. Usually, IVIG and steroids are used in the treatment to reduce macrophage activation; but, in a few, very uncommon cases, such as this one, HHS may be resistant to these methods. Given that macrophages are the cause of the syndrome and that SCD is a pro-inflammatory state, using tocilizumab, an IL-6 inhibitor, in SCD-induced acute HHS may be justified. More investigation into the relationship between cytokine levels and HHS is advised by the authors since it may be possible to administer tailored therapy once testing is more widely accessible.19 H Luo et al.(2022) did a study to concluded that presented the most thorough mutation spectrum of thalassemia and aberrant Hb variants in the HBB gene among Jiangxi Province people of reproductive age to date. Additionally, we offered comprehensive genetic counselling and prenatal testing to couples who had reasons to delay the conception of foetuses with ß-thal intermediate or significant. Our work may serve as a foundation for genetic counselling, public awareness campaigns, and as a guide to enhance ß-thal prevention.20 ME Fields et al.(2022) did a study to concluded that children with non-SCAs had higher OEF than unaffected children, indicating that anaemia is the main cause of this compensatory mechanism. However, even adjusting for the effect of anaemia, children with SCA have considerably higher OEF than kids without SCAs, indicating that there are other pathophysiologic mechanisms in SCA than anaemia that affect cerebral metabolic demand. Future treatment options for neuroprotection in this vulnerable population may be revealed by a better knowledge of the variables causing this rise in cerebral metabolic stress in SCA.21\n\n\nConclusion\n\nConclusion will be drawn on the basis of observation, result and interpretation of result pertaining to the study.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nLamsal KS: Clinical profile of patients with anemia.2009.\n\nHemminger JA, Sheikh NA, Kahwash SB: Identification and Reporting of Common Hemoglobin Disorders: A Review. Ibnosina J. Med. BS. 2012; 04(3): 63–77. Publisher Full Text http://www.ijmbs.org\n\nNaser Alamiry AA, Ali TH, Majeed MN: Detection Of Hemoglobinopathies In Hypochromic, Microcytic And Sickeled Cell Blood Films By Hemoglobin electrophoresis. Thi-Qar Med. J. 2011; 5(1): 139–148.\n\nKhanam B, Maurya S, Gupta P, et al.: A study on hemoglobin electrophoresis profile in patients with moderate to severe anemia. Int. J. Contemp. Med. Res. 2018; 5(3): C21–C24. Publisher Full Text\n\nSinha AK, Sanjay Yadav M: Nazrul Islam, Birendra Yadav and Bijay Arya Assessment of Anemia Based on Hb Levels in Children of 2 to 12 Years Age Group in Biratnagar, Nepal. Int. J. Pharm. Biol. Arch. 2012; 3(3): 552–554.www.ijpba.info\n\nHess SY, Owais A, Jefferds MED, et al.: Accelerating action to reduce anemia: Review of causes and risk factors and related data needs. Ann. NY Acad. Sci. 2023; 1523: 11–23. PubMed Abstract \| Publisher Full Text https://nyaspubs.onlinelibrary.wiley.com/journal/17496632\n\nHafeez R, Amir S: Frequency of Common Causes of Severe Anemia in Children under 5 Years of Age Admitted in Children Hospital, Lahore. P J M H S. MAR 2022; 16(03): 717–719. Publisher Full Text\n\nKrishnamurthy S, Kumar B, Thangavelu S: Clinical and hematological evaluation of geriatric anemia. J. Family Med. Prim. Care. 2022; 11: 3028–3033. Publisher Full Text\n\nGarcia-Casal MN, Dary O, Jefferds ME, et al.: Diagnosing anemia: Challenges selecting methods, addressing underlying causes, and implementing actions at the public health level. Ann. NY Acad. Sci. 2023; 1524: 37–50. PubMed Abstract \| Publisher Full Text\n\nShrestha AK, Rijal A, Belbase K, et al.: Hemoglobin J in a patient with severe anemia, a case report from Nepal. Ann. Med. Surg (Lond). 2022 Sep 15; 82: 104703. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMilovanovic T: Anemia as a Problem: GP Approach. Dig. Dis. 2022; 40: 370–375. PubMed Abstract \| Publisher Full Text\n\nDr. Geetha V , Dr. Gomathy CK , Keerthi K, et al.: Diagnostic Approach To Anemia In Adults Using Machine Learning.Publisher Full Text\n\nSalman Khan M, Ullah A, Khan KN, et al.: Deep Learning Assisted Automated Assessment of Thalassaemia from Haemoglobin Electrophoresis Images. Diagnostics. 2022; 12: 2405. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKamran DS, Siraj S, Ishaq I, et al.: Validity of peripheral blood smear as a screening tool for Sickle Cell Anemia: Comparison with Electrophoresis. RMJ. 2023 [cited March 04, 2023]; 48(1): 47–49.\n\nKharche K, Bhake A: Hemoglobin Variants in Patients With Microcytic Hypochromic Anemia: A Review of Indian Studies. Cureus. April 30, 2023; 15(4): e38357. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFathi A, Valizadeh M, Damandan M, et al.: Detection of Hb Bart’s and Hb H Diseases Caused by -α3.7 Prevalent Deletion Using Capillary Electrophoresis in Ardabil Province. Jorjani Biomed. J. 2021; 9(3): 61–68.\n\nShankar V, Pulmonary H: Hypertension among Children and Adolescents with Sickle Cell Anemia:A Systematic Review and Meta-analysis. INNOSC Theranostics and Pharmacological Sciences. 2023; 6(1): 35–45. Publisher Full Text https://accscience.com/journal/ITPS\n\nKim N, Kim TY, Han JY, et al.: Five Years’ Experience with Gene Panel Sequencing in Hereditary Hemolytic Anemia Screened by Routine Peripheral Blood Smear Examination. Diagnostics. 2023; 13: 770. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMenakuru SR, Priscu A, Dhillon V, et al.: Acute Hyperhemolysis Syndrome in a Patient with Known Sickle Cell Anemia Refractory to Steroids and IVIG Treated with Tocilizumab and Erythropoietin: A Case Report and Review of Literature. Hematol. Rep. 2022; 14: 235–239. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLuo H, Huang T, Lu Q, et al.: Molecular prevalence of HBBassociated hemoglobinopathy among reproductive-age adults and the prenatal diagnosis in Jiangxi Province, southern central China. Front. Genet. 2022; 13: 992073. Publisher Full Text\n\nFields ME, Mirro AE, Binkley MM, et al.: Cerebral oxygen metabolic stress is increased in children with sickle cell anemia compared to anemic controls. Am. J. Hematol. 2022; 97(6): 682–690. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "220742", "date": "23 Nov 2023", "name": "Youqiong Li", "expertise": [ "Reviewer Expertise hemoglobinopathy", "thalassemia", "capillary electrophoresis" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript attempts to de-evaluate the efficacy of hemoglobin electrophoresis as a diagnostic tool for moderate to severe anemia. From the description of the text, the authors may be trying to show that hemoglobin electrophoresis can detect abnormal hemoglobin and thus be used to assess anemia. As we all know, the vast majority of abnormal hemoglobins are not anemic, therefore, the manuscript is designed to use hemoglobin electrophoresis to assess anemia, which is difficult to achieve the purpose.\nThe manuscript does not provide relevant testing data and testing may not have been initiated.\nIn the third sentence of the fifth paragraph of the introduction, the 1.5-3.5% content should be Hb A2.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] }, { "id": "220744", "date": "12 Dec 2023", "name": "Kritsada Singha", "expertise": [ "Reviewer Expertise Thalassemia and hemoglobinopathies" ], "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 will use Hb electrophoresis to diagnose Hb disorders in patients with moderate and severe anemia. I have comments as follows;\nThe introduction is very long and irrelevant. The authors should focus on hemoglobinopathies. Other causes of anemia can be written shortly. It is well known that β-thalassemia carriers, β-thalassemia diseases, α-thalassemia diseases, and Hb variants can be detected by Hb analysis. I’m not sure that will they find the crucial new knowledge? If you have a sample size of about 100 samples, I think that thalassemia diseases and sickle cell anemia should be found less than 10%. Most patients will be other causes of anemia such as IDA, ACD, infections, etc. I recommended that this study should investigate not only Hb disorders but also all causes of anemia. What kind of Hb electrophoresis will you use in this study? CAE, CE, or IEF? Many abbreviations have no full name, for example, GIT, CNNs, PHT, SCA, HHA, VUS, HHS, IVIG, OEF, etc. There is some mistake in this sentence “The CE result, whether generated from established genotypes or novel mutant genotypes, may be used as proof of Hb Hb and Hart Bart’s illness.” The discussion looks like a literature review. Some references are from local publishers and cannot be downloaded to read further.\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": [] } ]	1	https://f1000research.com/articles/12-1184
https://f1000research.com/articles/12-1182/v1	21 Sep 23	{ "type": "Research Article", "title": "Implementation of distributed arithmetic-based symmetrical 2-D block finite impulse response filter architectures", "authors": [ "Pratyusha Chowdari Ch", "J.B. Seventline", "J.B. Seventline" ], "abstract": "Background: This paper presents an efficient two-dimensional (2-D) finite impulse response (FIR) filter using block processing for two different symmetries. Architectures for a general filter (without symmetry) and two symmetrical filters (diagonal and quadrantal symmetry) are implemented. The proposed architectures need fewer multipliers because of the symmetry of the filter coefficients.\nMethods: A distributed arithmetic (DA)- based multiplication method is used in the proposed architecture. A dual-port memory-based lookup table (DP-MLUT) is used in the multiplication instead of lookup-table (LUT) to reduce the area and power of the FIR filter. The filter's throughput is increased by using block processing. Memory reuse and memory sharing methods are introduced, which reduces the need for many registers and hence the circuit complexity. The architectures are written in Verilog Hardware Description Language and synthesized using Genus Synthesis tool-19.1 in 45nm technology with a generic library of Cadence vendor constraints. The synthesis tool generates the area, delay, and power reports. Power consumption of architectures is calculated with an image size of 64 X 64 and at 20 MHz frequency.\nResults: Compared to existing architectures, the synthesis results show improvements in power, area, area delay product (ADP), and power delay product (PDP). The proposed MLUT-based 2-D block Quadrantal Symmetry Filter (QSF) for length 8 with block size 4 consumes 58.94% less power, occupies 59.5% less area, 48.44% less ADP and 47.78% less PDP compared to best existing methods.\nConclusions: A novel DA-based 2-D block FIR filter architecture with various symmetries is realized. Symmetry is incorporated into the filter coefficients to minimize the number of multipliers. The LUT size is optimized by odd multiples or even multiples storage techniques. Also, the overall area of the architecture is decreased by DP-LUT-based multipliers. The proposed filter architecture is area-power-efficient. It is best suited for applications that have fixed coefficients.", "keywords": [ "Systolic architecture", "block processing", "distributed arithmetic", "2-D finite impulse response", "symmetries in FIR filter" ], "content": "Introduction\n\nMany image and video processing applications, including image enhancement, template matching, image restoration, and video communication, use 2-D digital filters.1,2 Finite impulse response (FIR) filters are preferred over infinite impulse response (IIR) filter when the numerical stability, ease of design and linear phase are the primary concerns.1 Because 2-D FIR filters need numerous computations, the efficient structure design is challenging for researchers. In,1 Parhi proposed a systolic structure for a 2-D FIR filter and suggested many techniques to optimize the implementation of 1-D and 2-D FIR and IIR filter architectures with more computational blocks. The block-based 2-D FIR filter banks consisting of separable and non-separable architectures with a significant reduction in memory are described.3,4 In,3 conventional multipliers, which consume power, are used for the convolution of input samples and filter coefficients, and there is no consideration of the internal architectures of symmetry filters.\n\nThe power-efficient and memory-efficient 2-D FIR filter architectures (FIRAs) are constructed with high-speed multipliers and parallel prefix modified carry look ahead adder (MCLAA).5 The low area-memory-based non-symmetry type 2-D FIRA is proposed with a new multiplication technique.6 In the above works, no symmetry concept is considered. The arithmetic computations are decreased by coefficient symmetry in the systolic filter architecture.7,8 The low-power multimode architectures for 2-D IIR filters are designed and implemented with four symmetries. The critical path analysis is addressed for symmetry filters, but the architectures are implemented only for single input processing. Another single input processing-based quadrantal symmetry is implemented using the 2-D L1- technique to minimize the filter coefficients and hardware blocks.9 Recently, Chowdari et al.24–26 have proposed efficient implementation of DA based adaptive filter.\n\nMohanty et al.10 proposed a 1-D block filter for narrowband applications using a Distributed Arithmetic (DA)-based reconfigurable filter for the software define radio SDR channelizer. Introduced the memory sharing concept to implement a 1-D finite impulse response (FIR) filter with a low area-power-delay. Several authors have implemented only DA-based 1-D filters. In recent years, DA techniques have attained great importance in FIR filter implementation to reduce the complexity of the architecture with high throughput and regularity. Kumar et al.11,12 recently proposed block-based 2-D FIR and IIR filter architectures using DA with a memory-sharing approach but did not discuss the symmetry of coefficients. DA-based FIRAs are described in,13,14 and the review of DA methods for cost-effective and efficient FIRAs is summarized. Park et al.15 have suggested reconfigurable FIR architecture using DA.\n\nIn all the DA-based filter implementation schemes, the authors focused only on the decreasing adders' quantity and multiplier complexity. Memory complexity is one of the key factors while designing the filter, affecting power consumption and area. Many researchers have addressed the 1-D and 2-D filters using symmetry or block processing in filters.16,17 Few researchers have realized the filter structures with Lookup Table (LUT)-based or DA multipliers without block processing or symmetry.\n\nA new approach to memory-based DA multiplication is proposed by Meher et al.18,19 This memory-based LUT (MLUT) multiplication approach is used to realize the 1-D FIR filters. The comparison analysis is presented with conventional multiplier-based filter architectures. Vinitha et al.6,20 also developed the LUT-based multiplication and incorporated it into the filer architectures with fewer hardware blocks. Chiper et al.21 suggested the dual-port concept in the MLUT-based DA multiplication rather than Single-Port LUT (SPLUT) multipliers. The modified memory-based multipliers are realized to implement an efficient filter architecture by Sharma et al.22 Alawad et al.23 presented a stochastic-based 2-D FIRA with low hardware complexity and high throughput. The probabilistic convolution theorem is used for the proposed non-separable systolic 2-D FIRA. The proposed work solves this problem within a predetermined accuracy range. The probability density function represents the 2-D input signal kernels by exploiting the convolution theorem. This well-known probabilistic convolution theorem replaces the expensive multipliers with simple adders. The memory storage complexity is also reduced by memory sharing and memory reuse. This work is more suitable for applications like perception-based image processing, which can inherently tolerate some computing inaccuracy.\n\nThe addressed points motivate developing and implementing the block-based 2-D FIRAs using various symmetries and multiplier-less DA-based approaches. In this research, two types of symmetries, diagonal symmetry and quadrantal symmetry, are considered to reduce the multipliers. The hardware in adders is increased by block processing in symmetry filters, although multipliers are more complex than adders. A novel MLUT multiplication approach is introduced in the 2-D block FIRAs. Two types of symmetries for 2-D FIRA and one non-symmetry filter are explored to decrease the number of multipliers. Conventional multipliers are replaced with MLUT multipliers to decrease each symmetry filter's power consumption, delay, and area.\n\nThe paper is organized as follows: The novel approach to designing the two types of symmetries and an optimized memory-based multiplication approach for 2-D FIRAs are discussed in background section. The next section describes the proposed 2-D FIRAs, and the individual symmetry filter architectures are explored according to the block processing using enhanced Dual-Port Memory-based LUT (DP-MLUT)-based multipliers.\n\n\nBackground: Block-based design and symmetry of 2-D FIR filters\n\nThis section explains the various coefficient symmetry concepts and the MLUT multiplication approach to replacing normal multipliers.\n\nIn the digital filters, the block processing concept increases the throughput of the architecture. If the input block size is ‘N’, the filter produces ‘N’ outputs per one iteration, which means N-times throughput increases. The input matrix Xn1n2 is needed at different systolic stages to generate a 2-D filter output Yn1n2is of the length of the filter (L).3\n\nLet us consider xn1n2−m is the m+1th input of the 2-D FIR filter, wpq represents filter coefficients. The m+1thoutput of the filter is expressed as3:\n\nwpq is expressed as equation (3).3\n\nThus, the 2-D FIR filter block output at each systolic stage is expressed as11:\n\nThe filter coefficient vector required at each stage is expressed as11:\n\nEach iteration of the 2-D block FIRA needs the parallel calculation of a block of input samples and produces a block of output. At each systolic stage, a set of L−1 delayed inputs is required to generate a block of input. The input pixels at p+1th the stage is represented by Gn1n2, which is given in matrix form as11:\n\nTo facilitate parallelism, we further decompose the input pixel matrix Gn1n2 and coefficient vector by a factor of s. The input pixel matrix Gn1n2 is decomposed into LSsub matrices represented as Xpq of dimension GNXS, and also the coefficient vector wpqof dimension 1XS; 0≤q≤LS−1. Equation (4) is modified as11\n\nWhere11\n\nwpq=wpsqwpsq+1…wpsq+q−1, u=n1−p and v=(n2−sq). Equation (7) is re-writtenas\n\nWhere\n\nThe symmetry concept is considered for the reduction of complex multipliers. In this paper, two types of symmetry, Diagonal Symmetry Filter (DSF) and Quadrantal Symmetry Filter (QSF)7,8 for 2-D FIRAs, are studied and explored. The following transfer functions are used to design the two types of symmetries in the 2-D FIRA.7,8\n\nA) DSF 2-D FIR Filter: The transfer functions of DSF in magnitude response as Hz1z2=Hz2z1, where z1=ejθ1and z2=ejθ2, ∀θ1,θ2. The filter coefficients are related ashij=hji for all i,j. Equation (11) expresses the transfer function of diagonal symmetry.17\n\nB) QSF 2-D FIR Filter: The QSF’s magnitude response isHz1z2=Hz1−1z2, where z1=ejθ1and z2=ejθ2, ∀θ1,θ2. The filter coefficient symmetry is given by hij=hL−ij for all i,j. Equation (12) expresses the transfer function of the filter.17\n\nThe general filter coefficients and two types of symmetry coefficient matrices are shown in Figure 1.\n\nThe proposed work implements two efficient symmetrical 2-D FIRAs and one generic filter architecture. Because of the symmetry of the filter coefficient, fewer multipliers are needed to design the filter.\n\nA LUT is treated as memory in memory-based multiplication, and the precomputed outputs of filter coefficients are saved in the LUT. DA multiplication is the process of shifting and accumulating LUT output values. The input sample and coefficient are multiplied in the process of memory-based multiplication. The LUT memory can save 2w possible values for the binary input of word length of w bits and a coefficient of bit length of c bits. In the process of standard LUT-based multiplication, it requires 2w words to save the precomputed partial products in LUT.\n\nEven multiples can be obtained from memory using left shift operations on odd multiples. This work uses (2w/2) words to save the odd multiples of coefficient C. This approach is shown for w = 4-bits of input sample in Table 1. In this table, the 8-address locations are stored by odd multiples of coefficient C, such as C, 3C, 5C, 7C, 9C, 11C, 13C, and 15C. Even multiples are evaluated using left shift operations of C, such as 2C, 4C, and 8C by 1-, 2-, and 3-times left shift operation to C, respectively. Next, 6C and 12C products are produced by a left shift of 3C; the remaining 10C is derived from 5C, and 14C is derived from 7C, respectively. The product output for the input sample consists of all zeros x=0000 produced by resetting the LUT.\n\nThe single-port MLUT-DA multiplier is realized with reference to Table 1, as shown in Figure 2A. The structure has one 4-to-3 encoder block, one 3-to-8 decoder block, one control logic to produce Reset (RST), and control lines {S0, S1} to accommodate the shifts required for the computation of even multiples of coefficients such as 2C, 4C, 8C, 10C, 12C, and 14C. A maximum of three shifts are required, so two bits of control signals are contemplated in the structure.\n\nWhere MUX is multiplexer and RST is reset.\n\nUsing a control logic block, the RST is formed from the applied input sample. It results in eight odd multiples of coefficients with c+4 bits. An extra 4 bits are essential to computing the highest odd multiple value 15C is precomputed and stored in the LUT. The decoder output corresponding location is read and fed to the NOR cell, which is made up of c+4 NOR gates with one common input of RST. The NOR cell outputs are shifted by a barrel shifter based upon the control signals {S0, S1} coming from the control logic. The barrel shifter has 2×(c + 4) AOI (AND_OR_INVERT) gates or 2×1 multiplexers (MUXs). Finally, the barrel shifter output is the multiplication result of the input sample and coefficient.\n\nThe combinational logic expression of the 4-to-3 encoder, employed in the LUT multiplier, is indicated in equations (13), (14), and (15).\n\nIn very large scale integration (VLSI) design, the conventional multipliers consume more power and occupy more area, whereas the LUT-based multipliers save area and power consumption. Hence, a further reduction in the hardware is achieved by LUT-DA multipliers.\n\nIn the LUT, only the even multiples of the coefficients are saved. Hence, only 2w/2 words are required instead of all 2w words. Even multiples can be translated into odd multiples by adding one filter coefficient magnitude. The barrel shifter and encoder blocks are not required for this modified multiplier, and one 2 × 1 MUX is required to choose the odd or even-multiple coefficients. Table 2 depicts the even multiples storing technique for w = 4. The even values of constant-coefficient 02C4C…12C14C are precomputed corresponding to x3x2x1 using the 3-to-8 decoder and saved in the 8-LUT locations. The other input for the 2 × 1 MUX is the LUT even output, and the other input is the odd output from the adder. The selection lines of the MUX are the least significant bit LSB-bits of the input sample x0. Whether the coefficients are even or odd multiples depends on the input sample’s LSB bit. Figure 2B represents the modified LUT-based multiplier.\n\nLikewise, odd multiples of the coefficient can be saved in an improved LUT-DA multiplier by using a subtractor to generate the required even multiples. In the proposed work, the SPLUT multiplier is converted into a DPLUT multiplier using the DA approach. When the input sample bits are more, the dual-port memory helps decrease the LUT size. The common filter coefficient is multiplied simultaneously with two separate input samples using a DPMLUT-based multiplier. The following section explains how the proposed filters use an improved MLUT-DA multiplier with even multiples storage.\n\n\nMethods\n\nThe block-based 2-D FIRA is shown in Figure 3 for L = 4, with N = 2 without any symmetry, and is considered a general filter. The input samples {xk0, xk1} are from the same row of the image input matrix given to the shift register unit (SRU) array, and input samples are given in serial order, block by block and row by row. The SRU array contains L−1 SRUs, each with L shift registers with M words. Here, SRU1 is termed as {SR1, SR2}. Likewise, SRU2 and SRU3 are placed in an array form considered the SRU array for order L = 4. Each L - Delay Unit Block (DUB) produces NL samples by applying each set of past N and present samples to the total L sets.\n\nWhere PU is Processing Unit, Xkm is input and Ykm is output.\n\nThe input block of L input samples from the image matrix M×M are applied as present inputs. The (L−1) SRU array receives these parallel inputs. Figure 4A represents the structure of SRU using the L number of registers. The present input sample and the past input sample blocks are applied to the N-DUBs of the DUB array. Each DUB consists of (L−1) flipflops. It produces the present and past samples required for block processing. As shown in Figure 4B, each DUB generates LN samples. The L-DUBs give the L×LN of input samples to the filter’s arithmetic module.\n\nStructures of block-based symmetric 2-D FIR filter arithmetic modules\n\nThis section explores two symmetry-type 2-D FIR filters and one general filter of L = 4 with N = 2.\n\nGeneral filter structure with MLUT multipliers\n\nThe arithmetic module of the general filter architecture is realized by the L number of Processing Units (PU) and an Adder Tree (AT) block, which receives LN samples from DUB.\n\nEach PU block is constructed by N number of Product Cells (PC), which are used to multiply the input sample by the corresponding filter coefficients. Generally, the product is done by conventional multipliers. MLUT multipliers are used in place of these power-hungry conventional multipliers. At last, the AT adds the outputs of the PU block and generates the Nfilter outputs corresponding to the N block of inputs.\n\nThis general filter architecture is modified by DPMLUT multipliers, as presented in Figure 5. In this architecture, the inputs multiplied with the common filter coefficients are given to a DPLUT-multiplier. Hence, a total of L×L DPLUT multipliers are needed to process the complete multiplication of input samples of L= 4 and filter coefficients. 2L×L multipliers are needed if SPLUT-based multipliers are used. The DPLUT-based multipliers save 50% of the area compared to SPLUT multipliers. Each DPLUT-based multiplier produces the L number of filter outputs. Total L memory multipliers generate L×LN number of outputs, and these are parallelly added by N -AT blocks and give N outputs with a size of (c+4)-bits.\n\nSRU, shaft register unit; DUB, Delay Unit Block; LUT, look up table.\n\nIn this work, the multiplier quantity is decreased by symmetry in the filter coefficients. Two different symmetries are described in this section, and these symmetry filters can be used to design circular symmetry, fan-type and diamond filters.\n\nStructure of 2-D FIR Diagonal Symmetry Filter (DSF)\n\nIn the DSF coefficient matrix, the sixteen coefficients are reduced to ten, such as {h00,h01,h02,h03,h11,h12,h13,h22,h23,h33} for L = 4 as shown in Figure 1B. Figure 6 represents the arithmetic module of the DSF-based 2-D FIRA, and it is designed by diagonal symmetry. Before the multiplication process, the input samples to be multiplied with common filter coefficients are added.\n\nSRU, shaft register unit; DUB, Delay Unit Block; LUT, look up table.\n\nFor the one input of N = 2, seven adders are required to accumulate symmetry input samples. The seven highlighted colored adders indicate the adders for the other input sample. The adder is a simple block than the multiplier. The diagonal symmetry filter requires 2L+2Nmultipliers instead of L×LN,but extra L−1Nadders are required. Next, these2L+2Nmultipliers are only designed for 2L+2N/2 DPLUT-based multipliers. Hence, half of the area is optimized. Finally, all the multiplier output samples are accumulated by N- AT blocks to produce N outputs.\n\nBecause multipliers are responsible for most of the power consumption, DPLUT-based multipliers are used to optimize them. Hence, ten DPMLUT multipliers are needed to produce the N = 2 outputs from the diagonal symmetry filter. The DSF architecture for L = 4 with N = 2 needed 20 individual SPLUT multipliers.\n\nDPLUT decreases the LUT size for input samples with greater bit lengths by adding an additional shifter. Because of parallel block processing, two inputs are multiplied with the common filter coefficient in a 2-D FIR filter. This concept can be used to replace two SPLUT multipliers with a single DPLUT multiplier. The internal structure of the conventional DPLUT-based multiplier and the modified DPLUT-based multiplier are shown in Figure 7A and B.\n\nRST, reset.\n\nThe common filter odd coefficient multiples are precomputed and placed in the LUT memory. According to the input bits, the address of the location in the LUT is determined by the address encoder and address decoder. DPLUT fetches the corresponding locations based on the given addresses of two ports and provides two parallel outputs. Furthermore, each output is shifted by barrel shifters after passing through the corresponding NOR gate. The control lines for shifting are generated from the input sample bits handled by some control circuit logic, as explained earlier.\n\nThis conventional DPLUT-DA multiplier has been revised, shown in Figure 7B for w = 4 bits of input sample using even multiples storage in LUT. It can be observed that the modified even multiples storage LUT-DA multipliers need less memory and area. Control logic for RST, barrel shifter, NOR cell, 4-to-3 encoder, and control signals of barrel shifter sos1 are not needed to enhance the DPLUT multiplier, and this feature reduces area further.\n\nThe conversion of SPLUT into DPLUT is a critical task. The common filter coefficients stored in the LUT must be shared by two inputs simultaneously. For this, the control logic is introduced related to the clock signal to choose the address locations with a slight delay. Figure 8 represents the control logic using multiplexers for a DPLUT-DA multiplier.\n\nMUX. Multiplexer; LUT, look up table.\n\nStructure of a 2-D FIR Quadrantal Symmetry Filter (QSF)\n\nThe QSF consists of eight unique filter coefficients are given as {.h00,h01,h02,h03,h10,h11,h12,h13.}. Figure 9 represents the architecture of QSF for L = 4 with N = 2. A total of 16 SPLUT multipliers are needed for this structure, and it is modified with eight DPLUT multipliers to produce N -block outputs.\n\nDUB, Delay Unit Block; SRU, shaft register unit; LUT, look up table.\n\nThe summary of the number of single-port and dual-port multipliers needed for each symmetry is presented in Table 3.\n\nExperiment/validation\n\nThis section analyzes the implementation and results for the proposed 2-D FIRAs. Multipliers, registers, and adders construct the architecture of the proposed filters. The hardware block's complexity depends on the filter input sample bits, length L, input block size N, and filter coefficients. Hence, DSF and QSF symmetry-based 2-D FIR filters are designed and explored to reduce the quantity of the multipliers. Next, the multiplier architectures are optimized by dual-port even multiples storage LUT- based multipliers. The architectures are synthesized using the Genus Synthesis tool-19.1 in 45nm technology with a generic library of Cadence vendor constraints. There is a free synthesis tools available like Xilinx Integrated Synthesis Environment, which can be used instead of Genus Synthesis tool in Cadence to replicate our methods. Power consumption of architectures is calculated with an image size of 64 X 64 and at 20 MHz frequency. The synthesized results (reports in Underlying data27) have been analyzed and compared with the existing architecture’s results. All Verilog code associated with the work is available in Software availability.28\n\n\nResults and discussion\n\nThe data associated with the results is available in Underlying data.27 Table 4 presents synthesis results of two individual types of symmetry 2-D FIR filters and general filters for L = 4 with N = 2.\n\nSPLUT, Single-port look-up table; DPLUT, Dual-port look-up table; DSF, Diagonal Symmetry Filter; QSF, Quadrantal Symmetry Filter.\n\nThe power consumption, delay, and area results are represented in graphs, as shown in Figures 10, 11, and 12, respectively. The proposed DPLUT-based 2-D FIR DSF-filter architecture needs 20.54% and 5.84% less area than normal and SPLUT multiplier-based filter architectures. 34.2% and 3.2% of power savings are obtained by the proposed filter architecture compared to the normal and single-port multiplier-based filter architectures, respectively. The proposed DSF architecture is 27.9%, and 10.4% has less delay than normal multiplier and SPLUT-based architectures. Similarly, the proposed QSF 2-D FIRA power is decreased by 44%, 20%, than normal and SPLUT multipliers, the area is decreased by 33%, 18.6%, and delay is decreased by 24.7%, 5.3% than normal and SPLUT multipliers, respectively.\n\nWhere DSF is diagonal symmetry filter, QSF is quadrantal symmetry filter and LUT is look up table.\n\nWhere DSF is diagonal symmetry filter, QSF is quadrantal symmetry filter and LUT is look up table.\n\nWhere DSF is diagonal symmetry filter, QSF is quadrantal symmetry filter and LUT is look up table.\n\nThe filter architectures of 2-D FIR with two symmetries and one general filter are implemented by block processing and dual-port memory-based multipliers. Here, the memory reuse concept is used to get the filter outputs, and memory saving is obtained. The VLSI performance metrics, such as area, delay, and power values of the proposed filters, are compared for input bits w = 4 and 8 in Table 5.\n\nThe area of the proposed DSF and QSF symmetry filter architectures is reduced by 24.1% and 39.3% to the general 2-D FIRA for w = 4. The power-saving obtained by DSF and QSF is 9.9% and 27.8% less than the general filter architecture. The delay values of DSF, QSF and general filter are almost the same. Figure 13 represents the comparison of area, delay, and power consumption of the proposed DPLUT-based 2-D FIRAs for w = 4 and 8. It can observe that the VLSI performance metrics increase correspondingly when the filter's input sample bits increase.\n\nDSF, diagonal symmetry filter; QSF, quadrantal symmetry filter; LUT, look up table.\n\nfor w = 4 and 8. Where DSF is diagonal symmetry filter, QSF is quadrantal symmetry filter and LUT is look up table. The proposed symmetry 2-D FIR filters with DPLUT-based multipliers are compared to previous works. The performance metrics obtained from the synthesis tool are tabulated in Table 6.\n\nDSF, Diagonal Symmetry Filter; QSF, Quadrantal Symmetry Filter; ADP, area delay product; PDP, power delay product.\n\nThe proposed filter architecture implementation is extended for L =8 with N = 4. The 2-D FIRA for L =8 with N = 4 is also compared with the state-of-the-art works in Table 6. It can be observed that the proposed architecture is improved in terms of power, area, delay, ADP, and PDP than existing architectures.\n\nA graphical comparison of results of rea, power consumption, delay, ADP, and PDP of the proposed structure with existing filter architecture for L = 8 with N = 4 is shown in Figure 14.\n\nThe proposed MLUT-based 2-D block DSF filter for L= 8 with N= 4 requires 62.50%, 76.81%, and 54.79% less area compared to [23], [3], and [11], respectively. It has 20.49%, and 30.72% less delay compared to [23], and [3], respectively. It consumes 76.39%, 63.10%, and 54.49% less power than [23], [3], and [11], respectively. It has 70.3%, 83.99%, and 41.72% less ADP than [23], [3], and [11], respectively. It has 81.22%, 74.43%, and 41.24% less PDP compared to [23], [3], and [11] respectively.\n\nThe proposed MLUT-based 2-D block QSF filter for L= 8 with N= 4 requires 66.47%, 79.26%, and 59.57% less area compared to [23],[3], and [11], respectively. It has 21.67%, and 31.74% less delay compared to [23], and [3], respectively. It consumes 78.69%, 66.71% and 58.94% less power than [23], [3], and [11], respectively. It has 73.72%, 85.83%, and 48.44% less ADP than [23], [3], and [11] respectively. It has 83.31%, 77.27%, and 47.78% less PDP compared to [23], [3], and [11] respectively.\n\n\nConclusions\n\nThis paper implements two novel symmetry 2-D block FIRAs using QSF and DSF and one general filter (without symmetry) with DPMLUT-based multipliers. The conventional multipliers are replaced with the MLUT multipliers; DPMLUT-based multipliers save power and area compared to SPMLUT-based multipliers. Individual symmetry filters are implemented using fewer multipliers. Block processing is used to achieve memory reuse.\n\nThe proposed MLUT-based 2-D block DSF filter for L= 8 with N= 4 requires 54.79% less area, consumes 54.49% less power, has 41.72% less ADP, and 41.24% less PDP, but has 29% more delay compared to existing HLUT-based 2-D block FIR filter.11\n\nOn the other hand, the proposed MLUT-based 2-D block QSF filter for L= 8 with N= 4 requires 59.5% less area, consumes 58.94% less power, 48.44% less ADP and 47.78% less PDP, but has 27% more delay compared to existing HLUT-based 2-D block FIR filter.11 The 2-D block FIRA using QSF has fewer unique coefficients than the 2-D block FIRA using DSF. Hence, QSF performs well in terms of performance metrics.", "appendix": "Data availability\n\nFigshare: Untitled ItemFIR FILTER. https://doi.org/10.6084/m9.figshare.22058801.v1. 27\n\nThis project contains the following underlying data:\n\n- Data set.xlsx (testbench which defines the operational relation between input and output, results for different values of block length and also the results table in which existing and proposed models be compared).\n\n- larea_DSF.rep (area report of DSF_2D FIR filter, a tool generated area report downloaded while executing).\n\n- larea_QSF.rep (area report of QSF_2D FIR filter, a tool generated area report downloaded while executing).\n\n- lpower_DSF.rep (power report of DSF_2D FIR filter, a tool generated area report downloaded while executing).\n\n- lpower_QSF.rep (power report of QSF_2D FIR filter, a tool generated area report downloaded while executing).\n\n- ltiming_DSF.rep (timing report of DSF_2D FIR filter, a tool generated area report downloaded while executing).\n\n- ltiming_QSF.rep (timing report of QSF_2D FIR filter, a tool generated area report downloaded while executing).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nParhi KK: VLSI Digital Signal Processing Systems: Design and Implementation, ch. 7. 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I: Regular Papers. 2005; 52(6): 1125–1137. Publisher Full Text\n\nSharma D, Johnson J, Sharma A: Memory-based FIR digital filter using modified OMS-LUT design. Applications of Computing, Automation and Wireless Systems in Electrical Engineering. Singapore: Springer; 2019; pp. 1007–1017. Publisher Full Text\n\nAlawad M, Lin M: Memory-Efficient Probabilistic 2-D Finite Impulse Response (FIR) Filter. IEEE Transactions on Multi-Scale Computing Systems. 2017; 4(1): 69–82.\n\nChowdari CP, Seventline JB: An efficient FIR Filter Architecture Implementation using Distributed Arithmetic (DA) for DSP Applications. International journal of Innovative Technology and Exploring Engineering. 2019.\n\nChowdari CP, Seventline JB: Systolic architecture for adaptive block FIR filter for throughput using distributed arithmetic. Int. J. Speech Technol. 2020; 23(3): 549–557. Publisher Full Text\n\nChowdari CP, Seventline JB: VLSI implementation of distributed arithmetic-based block adaptive finite impulse response filter. Materials Today: Proceedings. 2020; 33: 3757–3762.\n\nch, pratyushachowdari: Untitled ItemFIR FILTER. [Dataset]. figshare. 2023. Publisher Full Text\n\npratyusha chowdari ch: FIR filter [Software]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "208433", "date": "01 Nov 2023", "name": "Sirish Kumar Pagoti", "expertise": [ "Reviewer Expertise Communication", "signal processing", "wireless networks", "embedded system" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. This paper presents a well-structured and highly efficient approach to 2-D finite impulse response (FIR) filter design, focusing on symmetry-based optimizations. The incorporation of various symmetries to minimize multipliers is a commendable strategy.\n2. The utilization of distributed arithmetic (DA) and the dual-port memory-based lookup table (DP-MLUT) in multiplication is a noteworthy innovation. It not only reduces area and power consumption but also enhances the overall efficiency of the FIR filter.\n3. The introduction of memory reuse and memory sharing methods is a clever technique to reduce the need for registers and, consequently, circuit complexity. This approach contributes significantly to the practicality of the proposed architectures.\n4. The comparative results provided in the paper clearly demonstrate the advantages of the proposed architectures in terms of power, area, area delay product (ADP), and power delay product (PDP). These improvements are substantial and hold promise for a wide range of applications.\n5. The synthesis results in a 45nm technology environment showcase the real-world applicability of the proposed architectures. The power and area savings, especially in the Quadrantal Symmetry Filter (QSF), are quite impressive.\n6. The paper's conclusion emphasizes the suitability of the proposed filter architecture for applications with fixed coefficients. This insight into potential applications adds practical value to the research.\n7. Overall, this paper offers a valuable contribution to the field of FIR filter design. The innovative approaches, clear presentation, and substantial improvements in efficiency make it a significant advancement in the area of signal processing.\n\nIs the work 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": "242160", "date": "29 Feb 2024", "name": "M Balaji", "expertise": [ "Reviewer Expertise FIR FIlter Design", "Distributed Arithmetic", "Residue Number System", "VLSI Signal Processing" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study focuses on symmetry-based optimizations and offers a well-organized and very effective method for designing 2-D finite impulse response (FIR) filters. It is a good method to decrease multipliers by incorporating different symmetries. One notable innovation is the multiplication process that uses distributed arithmetic (DA) and the dual-port memory-based lookup table (DP-MLUT). It increases the FIR filter's overall efficiency while also consuming less space and power.\nOne ingenious way to lower the requirement for registers and, hence, circuit complexity is to implement memory reuse and memory sharing solutions. The suggested architectures' practicality is greatly enhanced by this method. The benefits of the suggested designs in terms of power, area, area delay product (ADP), and power delay product (PDP) are well demonstrated by the comparison data presented in the study. These are significant advancements that have potential for many different uses.\n\nThe synthesis produces a 45 nm technological environment that demonstrates how the suggested designs may be used in practical settings. Particularly with the Quadrantal Symmetry Filter (QSF), the power and area savings are very noteworthy. The appropriateness of the suggested filter design for applications with fixed coefficients is emphasized in the paper's conclusion. This understanding of possible uses gives the research more usefulness.\nRequest the Corresponding author to provide justifications for these queries.\n\n1) Please explain how the area (micrometers square) was calculated. 2) The proposed filter was designed with L=8 and N=4, it can be further extended to 32-bit with 64 taps. 3) If the comparisons of your proposed results with existing results within a table format is appreciable.\"\n\nIs the work 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/12-1182
https://f1000research.com/articles/12-339/v1	27 Mar 23	{ "type": "Research Article", "title": "Comparing the effectiveness of pterostilbene and sitagliptin on modulating inflammatory levels and inducing autophagy to improve atherosclerosis outcome: A preclinical study in rabbits", "authors": [ "Hussam H Sahib", "Bassim I Mohammad", "Najah R Hadi", "Azhar Al-Shaibany", "Anil K Philip", "Wisam J Mohammed", "Dina A Jamil", "Hayder A Al-Aubaidy", "Hussam H Sahib", "Bassim I Mohammad", "Najah R Hadi", "Azhar Al-Shaibany", "Anil K Philip", "Wisam J Mohammed", "Dina A Jamil" ], "abstract": "Background: Inflammation is the key contributor to the development of atherosclerotic plague. This study aims to evaluate the protective and autophagy induction properties of pterostilbene and sitagliptin on modulating the degree of atherosclerosis in rabbit models treated with an atherogenic diet. Methods: 80 rabbits were randomly placed into one of four study groups (20 in each group): normal control diet (NC) fed normal diet for eight weeks, atherogenic control (AC) fed atherogenic diet for eight weeks, pterostilbene treated group (PT) fed atherogenic diet with pterostilbene (at 10 mg/kg/day) orally daily for eight weeks, and sitagliptin treated group (ST) fed atherogenic diet with sitagliptin (at 12 mg/kg/day) orally daily for eight weeks. Results: While serum lipids and F2-isoprostane were elevated significantly in the AC study cohort compared to NC study cohort, (P < 0.001), both pterostilbene and sitagliptin supplementations provided significant improvements in serum lipid parameters and F2-isoprostane in the PT study cohort and ST study cohort, respectively, when compared to the AC study cohort, (P<0.001). Total cholesterol, triglycerides and LDL levels were significantly reduced among the PT and ST study cohorts as compared to the AC study cohort. This was coupled with a significant rise in LC3B levels (marker of tissue autophagy) among the PT study cohort and the ST study cohort, as compared to the AC study cohort, (P < 0.001). The RNA expression of mTORC1 was reduced significantly at both PT study cohort and ST study cohort, (P<0.001). Pterostilbene supplementation induced a significant reduction in tissue expression of PI3K and AKT, (P<0.01), while sitagliptin induced significant reduction in 5’ adenosine monophosphate-activated protein kinase (AMPK) levels, (P<0.001). Conclusions: The results indicate that pterostilbene and/or sitagliptin supplementation can significantly improve the outcome of atherosclerosis due to their effects on the inflammatory pathways which hinder the progression of atherosclerotic plaque formation.", "keywords": [ "Pterostilbene", "Sitagliptin", "Atherosclerosis", "PI3K", "AMPK", "AKT", "Rabbits." ], "content": "Introduction\n\nAtherosclerosis is a chronic inflammatory condition which affects various tissues and organs and can lead to serious complications including the development of cardiovascular disease, stroke, and diabetes mellites.1 As part of disease progression, the atherosclerotic plaque could be detached from the vascular wall and can lead to a major cardiovascular complication.1 There is still a knowledge gap about the exact mechanisms for plaque rupture, however, previous studies have illustrated the action of inflammation and oxidative damage in atherogenic plaques progression.2 Hence, there is a close correlation among the degree of oxidation and inflammation and atherosclerosis, and so it is important to monitor the inflammatory markers as they may help to provide information about atherosclerosis progression which is of clinical usefulness.\n\nAutophagy is a normal physiological mechanism through which the body can recycle cytoplasmic components (such as damaged/aged organelles and other cellular proteins), which are phagocytosed, and flagged for destruction by lysosomes.3 Autophagy plays a key role in cellular homeostasis and can help get rid of damaged cells in disease conditions such as cancer and chronic illnesses.4 Therefore, induction of autophagy in blood vessels can protect endothelial cells and smooth muscle cells damage, which may occur due to atherosclerosis and reduce the vulnerability of the plaques.4 Macrophage autophagy can be useful in inhibiting atherosclerotic plaque rupture, which could reduce the severity of the condition.4 mTOR is Ser/Thr protein kinase, considered to be a key control in cellular nutrition and energy expenditure, thus playing a central role in regulation of autophagy.5 It can integrate multiple signals from upstream pathways and block the formation of autophagosomes.5 Accordingly, there are several signaling paths which monitor autophagy induction. These include PI3K-Akt-mTOR and AMPK-mTOR pathways.6 Previously, it was indicated that the (PI3K-Akt-mTOR) represent the primary pathway which is responsible for regulating a variety of cellular behaviors such as growth, apoptosis, and autophagy.6 The activation of (PI3K/Akt/mTOR) signaling pathway in atherosclerosis may provide insight on the therapeutic role of inhibiting this pathway to control the development of atherosclerosis. LC3B is defined as an RNA-binding protein, which can be used to initiate mRNA degradation during autophagy, and hence will be measured in the current study to indicate the degree of autophagy.4\n\nPterostilbene is a di-methylated analog of resveratrol. It has been known for its potent anti-inflammatory properties7; hence it can be used to reduce the degree of inflammation and improve the outcome of atherosclerosis. It was previously shown that pterostilbene downregulates NF-κB and Toll like receptor 5 expression.8 In addition, pterostilbene can inhibit smooth muscle activation via its effects on adenosine-monophosphate-activated-protein-kinase (AMPK) pathway.7 This signaling pathway (AMPK - STAT3) provides an index about the degree of inflammation of the endothelial cells in the vascular wall.7 Sitagliptin is a known oral antidiabetic medication of gliptins family, which is used as a second line treatment to treat hyperglycemia in patients with diabetes mellitus.9 Gliptins work through their effects of stimulating insulin production and secretion via inhibiting dipeptidyl peptidase-4 enzyme and thus increasing the half-life of incretin hormones in response to diet.10 Thus, the use of sitagliptin can help in improving insulin sensitivity and reduce the development of diabetic complications including atherosclerosis.\n\nThe current study aims to highlight the benefits of pterostilbene and sitagliptin supplementations in improving the outcome of atherosclerosis in rabbits treated with an atherogenic diet.\n\n\nMethods\n\nAll the procedures were performed according to the guidelines approved by the National Institutes of Health. The research study received ethics approval from the Animal Research Ethics, College of Medicine, University of Kufa, Iraq (approval no. 15792, on 14th December 2020) where the research took place. All experimental procedures involving animals were carried out in keeping with guidelines from the National Institutes of Health Guide for the Care and Use of Laboratory Animals to ameliorate any suffering of animals.\n\nThis study included 80 rabbits (New Zealand White; 26 males and 54 females). Rabbits were aged between 1-3 years old and weighed between 1300 grams – 3000 grams. All the rabbits were housed individually in polycarbonate cages (0.90 × 0.60 × 0.60 m) for two weeks on a 12-h light/dark cycle at a steady temperature of 25°C and humidity of 50% for acclimatization to the environment. Animals were fed a standard pellet diet with tap water ad libitum and were routinely inspected for food consumption and fecal characteristics. These animals have not been included in previous research. Animals were excluded if they appeared unwell prior to being included in the study.\n\nFollowing the first two weeks, animals were randomly divided into one of the four study groups (20 animals in each study group). A sample size of 20 animals in each group would present more than 85% power to detect significant differences with 0.45 effect size and at a significance level of α=0.05. Sample groups were chosen utilizing simple random sampling. Each animal was assigned a tag number, the blind-folded researcher (B.M.) then picked numbered tags from the hat.\n\n• Normal control study cohort (NC): In this group, rabbits received traditional chow diet and water ad libitum for eight weeks.\n\n• Atherogenic control study cohort (AC): In this group, animals were given an atherogenic diet, consisting of 2% cholesterol enhanced diet and water for 8 weeks.\n\n• Pterostilbene treated study cohort (PT): In this group, rabbits received an atherogenic diet, water and pterostilbene (purity 98%, Hangzhou Hyper Chemicals Limited, China; CAS No. 537-42-8) supplements at 10 mg/kg orally daily for 8 weeks.\n\n• Sitagliptin treated group (ST): In this group, rabbits received atherogenic diet, water and sitagliptin (Purity 98%, Hangzhou Hyper Chemicals Limited, China; Batch No. 20112301) supplements at 12 mg/kg orally daily for 8 weeks.\n\nTo induce hyperlipidemia and subsequent development of atherosclerotic changes, animals were provided with 2% high cholesterol (BDH Chemicals Ltd, England), in their food to develop atherosclerotic changes in the aorta following 8 weeks supplementation.11 During the study, animals were monitored on a daily basis to check their vital signs. In addition, blood pressure, body weight and blood samples were collected fortnightly to measure blood glucose levels.\n\nAt the conclusion of the study, rabbits were kept fasted overnight, then they were euthanized using ketamine (HIKMA Pharmaceuticals, 3310), using (66 mg/kg), and xylazine (Alfasan, 1004111-07), sing (6 mg/kg), via intramuscular injection.12,13 Following euthanasia, thoracotomy was performed to expose the heart and collect blood. Aortic arch was dissected, and samples collected as well as the following:\n\n• Serum lipid profile (total cholesterol – TC, triglyceride – TG, low density lipoprotein cholesterol – LDL, high density lipoprotein cholesterol – HDL, and very low-density lipoprotein cholesterol – VLDL. Serum lipids were measured using enzymatic methods (Abbott, Alcyon 300 Chemistry Analyzer, USA).\n\n• Serum F2-isoprostane to assess lipid peroxidation. This has been assessed colormetrically via ELISA (Sunlong, China, SL0284Rb).\n\n• Tissue LC3B as a marker of tissue autophagy marker using the LC3 Antibody Kit for Autophagy (Thermo Fisher, USA, catalogue number: L10382).\n\n• Assessments of mTOR (PI3K, AKT, AMPK, and mTORC1) using RT-PCR (see details below).\n\n• Histopathological examination of the aorta looking for atherosclerotic changes.\n\nTotal RNA was extracted from heart tissue samples by using a TRIzol® reagent kit (Thermo Fisher, Catalogue number 12183555): 100 mg heart tissue sample was homogenized by adding 750 μl of TRIzol® reagent. Add 200 μl chloroform, and stir for 15 seconds, then place on ice for 5 minutes before centrifugation. Transfer 500 ul into a new tube and add 500 ul isopropanol and incubate in a fridge for 10 minutes, before centrifugation. Discard the supernatant, add 1 ml of ethanol and repeat the mixing and centrifugation as above. Discard the supernatant and leave the RNA pellet until dried out, then add 100 ul of free nuclease H2O to dissolve before RNA extraction.\n\nAs for the reverse transcriptase polymerase chain reaction (RT-PCR), using a mixture containing 3 μg total RNA, 2.5 μM oligo (dT), 1.5 mM magnesium chloride (MgCl2), 0.01 M dithiothreitol, and 200 units of SuperScript III reverse transcriptase in a total volume of 20 μl. The RT steps consisted of an RT step (42°C for 60 minutes) and a denaturation step (70°C for 5 minutes). The PCR steps consisted of a denaturation step (95°C for 30 seconds), a primer annealing step (60°C for 30 seconds), and an elongation step (72°C for 30 seconds) for 30 cycles. In the final step, the duration of the elongation step was seven minutes. Finally, the samples were loaded onto a 1% agarose gel. The gels were then observed and photographed under ultraviolet light.\n\nMeans and standard error of means (SEM) were analyzed utilizing Statistical Package for Social Sciences (version 26, IBM, USA). One-way ANOVA for multiple comparisons followed by LSD-post-hoc test. Significant P value of <0.05 was considered. The Mann-Whitney test used to assess histopathological grading. A significant P value was set at ≤0.001.\n\n\nResults\n\nThe mean serum levels of total cholesterol, TG, and LDL increased significantly in the AC study cohort versus the NC study cohort, (P<0.001). Pterostilbene supplementation significantly reduced serum levels of TC, and LDL, while sitagliptin supplementation significantly reduced TC, TG, and LDL (P<0.001) (Figure 1, Table 1).\n\n* Significance (P<0.001) among the pterostilbene & the atherogenic study cohorts.\n\n# Significance (P<0.01) among the sitagliptin & the atherogenic study cohorts.\n\nSerum HDL levels were increased in the ST study cohort in comparison to the AC study cohort, (P<0.01), something which was not achieved with the PT study cohort (Figure 1, Table 1). In addition, mean serum HDL level was reduced significantly in the AC study cohort in comparison to the NC study cohort and then improved significantly following sitagliptin supplementation (P<0.001) (Table 1, Figure 1).\n\nAs a lipid peroxide marker, plasma F2-Isoprostane was significantly increased following the ingestion of atherogenic diet for 8 weeks (AC study cohort) when compared to the NC study cohort (P<0.001). Moreover, the mean plasma level of F2-isoprostane was reduced significantly in response to 8 weeks supplementation of pterostilbene 523.4±72.4 pg/ml, and sitagliptin 598.3±59.3 pg/ml, when compared to the atherogenic study cohort 798.3±66.3 pg/ml (P<0.05) (Figure 2, Table 1).\n\nUsing the Mann-Whitney test to look for the significance across the four study groups, we identified significant reduction in the degree of atherosclerotic changes when using pterostilbene and or sitagliptin supplementation with atherogenic diet for 8 weeks (P<0.001) (Figure 3). Atherosclerotic changes were assessed following the American Heart Association classification of atherosclerosis: Type-1 (initial lesions), Type-2 (fatty streak lesions), Type-3 (moderate lesions), Type-4 (atheroma lesion), Type-5 (advance lesion), and Type-6 (complicated lesion).\n\nA: Normal arterial appearance in the control group; B: Initial atherosclerotic changes – lipid-laden foam cells in the sitagliptin study cohort; C: fatty streak and D: Intermediate atherosclerotic changes – extracellular lipid pool in the Pterostilbene study cohort; E: Advance atherosclerotic changes – a core of extracellular lipid and F: Complicated atherosclerotic changes – hemorrhagic thrombus as seen in the atherogenic study cohort (no supplementations).\n\nWe have used the scoring methodology to interpret the lesions (Table 2).\n\nIn addition, the tissue levels of LC3B were significantly reduced in the atherogenic control study cohort (35.4±7.8) compared to the NC study cohort (70.2±10.7, P<0.001). Both pterostilbene and sitagliptin supplementations appeared to induce significant improvements in the level of LC3B index, 80.6±14.3 and 97.5±21.2, respectively, in relation to the atherogenic study group (Figure 4) (P<0.001).\n\nThe atherogenic diet caused a significant increase in the degree of inflammation as manifested by the significant rise in the expression of mTORC1, PI3K and AKT (P<0.001). Following the 8 weeks of supplementations, the expression of mTORC1 was significantly reduced in response to pterostilbene and sitagliptin supplementations as compared to the atherogenic study cohort (P<0.001) (Figure 5).\n\nPterostilbene supplementation exerted beneficial effect on improving the expression of aortic tissue levels of AKT and PI3K, something which could not be achieved with sitagliptin supplementation (P<0.001) (Figure 5).\n\nMoreover, the mean AMPK index significantly dropped in the AC study cohort in comparison to the NC study cohort (P<0.05). It then significantly increased following sitagliptin therapy (P<0.001) (Figure 5).\n\n\nDiscussion\n\nThe current study compared the beneficial use of pterostilbene and sitagliptin supplementation on reducing the degree of inflammation and improving the outcome of atherosclerosis. We have demonstrated that the use of an atherogenic diet can significantly impair all components of lipids when compared to the normal control diet.14 Following 8 weeks of supplementation in rabbits fed with atherogenic diet, both pterostilbene and sitagliptin significantly improved serum lipids in terms of significantly reducing TC and LDL and significantly increasing HDL levels. Previous studies revealed that pterostilbene induces similar effects to peroxisome proliferator-activated receptor α-isoform (PPAR-α) in reducing serum lipid profile.15 In addition to its lipid lowering effects, PPAR-α can also reduce gene transcription for lipogenesis, a key step for lipid peroxidation which can precipitate the development of multiorgan disease, such as liver disease and heart failure.15\n\nWe have also revealed a statistically significant reduction in plasma F2-Isoprostane in response to pterostilbene supplementation. Although we could not find any previous data related to this correlation, we hypothesize that this effect could be achieved due to the inhibitory effect of pterostilbene on the 8-iso-prostaglandin – alpha production.16 F2-isoprostane level is a known marker for lipid peroxidation, and hence, it would make sense to measure this marker to get an estimation about the oxidized LDL and the degree of oxidative stress.17\n\nWe have also identified increased mRNA expression of PI3K, AKT and mTORC1 in cholesterol-fed rabbits compared with normal control.18 This can be explained due to the fact that oxidized LDL, a key risk factor for atherosclerosis development, can induce PI3K signaling in macrophages and foam cells, which can stimulate inflammatory cells’ synthesis and release which leads to monocyte chemotaxis, macrophage migration, and amplified intracellular lipid accumulation. The increased mTORC1 activity contributes to atherosclerosis progression in animal studies.19 It is worth mentioning that earlier studies found that (PI3K-Akt-mTOR) pathway was associated with autophagy in vascular dysfunction.19,20 As an example, the development of advanced glycation end products, due to persistent hyperglycemia, can inhibit the (PI3K-Akt-mTOR) pathway resulting in the development of serious vascular dysfunction. Hence, Pterostilbene can be used as an effective compound to inhibit the PI3K/Akt/mTOR pathway, regulates autophagy of macrophages and therefore may affect the progression of atherosclerotic plaque.19,20 We have also revealed that LC3B level was significantly elevated following pterostilbene treatment, suggesting that the reduction in autophagosome formation in the atherogenic group was significantly prevented by pterostilbene treatment.21\n\nFinally, autophagy induction of macrophages may inhibit foam cell formation. This could be done via reducing oxidized LDL particles engulfing by macrophages and increasing cholesterol outflow into macrophages. These findings suggest that pterostilbene improves serum lipids, inhibits inflammation, and promotes autophagy which eventually improves the outcome of atherosclerotic plaque.\n\nMoreover, this study illustrated that sitagliptin supplementation could increase expression of AMPK in aortic tissue when compared to the atherogenic group, something which could not be achieved with pterostilbene supplementation. Upregulation of AMPK following sitagliptin therapy could induce beneficial effects on atherosclerosis outcome by increasing plaque’s stability.22 Sitagliptin supplementation was also beneficial in stimulating cellular autophagy via increasing tissue expression of LC3B23 and suggests that the reduction in autophagosome formation in the atherogenic group was significantly prevented by sitagliptin treatment. Sitagliptin protects atherogenic rabbits against inflammation through reduction of macrophage accumulation, and prevention of the inflammatory pathway concurrent with improved autophagic processes via activation of the AMPK/mTORC1 pathway.23\n\nDue to the timeframe of this study, we could not measure the autophagy induction at other areas of the large blood vessels. In addition, scoring of atherosclerotic changes was calculated from the hematoxylin and eosin stain which may possess medium sensitivity. It would be best to use alternative, more sensitive measures for a higher accuracy using electron microscopy.\n\n\nConclusion\n\nWe conclude that supplementation with pterostilbene or sitagliptin can significantly reduce the degree of oxidative stress, lipid peroxidation and inflammation which may ultimately help reduce the severity of atherosclerotic lesions in animal models with an atherogenic diet. This could be explained through the effects of these supplements on inhibiting inflammation through their effects on PI3K/Akt/mTOR, and AMPK/mTOR pathways.\n\n\nAuthor contributions\n\nThe authors responsibilities were as follows: Conceptualization, H.S., W.M., B.M., and N.H.; methodology, H.S., D.J., and N.H.; formal analysis, H.S., A.A., A.P., and H.A.; investigation, H.S., B.M., N.H., and H.A.; writing—original draft preparation, H.S., B.M., and N.H.; writing—review and editing, B.M., A.A., W.M., D.J., A.P., and H.A.; supervision, B.M., and N.H. All authors have read and agreed to the published version of the manuscript.", "appendix": "Data availability\n\nfigshare: Pterostilbene versus sitagliptin study, https://doi.org/10.6084/m9.figshare.22028744.v4. 24\n\nThis project contains the following data:\n\n- Pterostilbene vs sitagliptin study.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nARRIVE checklist for ‘Comparing the effectiveness of pterostilbene and sitagliptin on modulating inflammatory levels and inducing autophagy to improve atherosclerosis outcome: A preclinical study in rabbits’, https://doi.org/10.6084/m9.figshare.22028744.v4. 24\n\n\nAcknowledgments\n\nThe authors thank members of the Pharmacology and Therapeutic Department of Al-Qadisiyah Medical College.\n\n\nReferences\n\nHassanpour M, Rahbarghazi R, Nouri M, et al.: Role of autophagy in atherosclerosis: foe or friend? J. Inflamm. 2019; 16(1): 8. 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PubMed Abstract \| Publisher Full Text\n\nSasani M, Yazgan B, Celebi I, et al.: Hypercholesterolemia increases vasospasm resulting from basilar artery subarachnoid hemorrhage in rabbits which is attenuated by Vitamin E. Surg. Neurol. Int. 2011; 2: 29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHayashi T, Fukuto JM, Ignarro LJ, et al.: Basal release of nitric oxide from aortic rings is greater in female rabbits than in male rabbits: implications for atherosclerosis. Proc. Natl. Acad. Sci. U. S. A. 1992; 89(23): 11259–11263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHadi NR, Mohammad BI, Ajeena IM, et al.: Antiatherosclerotic Potential of Clopidogrel: Antioxidant and Anti-Inflammatory Approaches. Biomed. Res. Int. 2013; 2013: 790263.\n\nAl-Aubaidy H: Pterostilbene vs sitagliptin. figshare. Dataset. 2023. Publisher Full Text" }	[ { "id": "199143", "date": "14 Sep 2023", "name": "Jelica Grujic Milanovic", "expertise": [ "Reviewer Expertise oxidative stress", "polyphenols", "hypertension", "cardiovascular diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Sahib et al. has been clearly defined. The methodology applied is overall correct. The authors support their paper with recent references.\nHowever, the following changes to the main text are suggested:\nIn the results, use the abbreviation TC instead of total cholesterol. In Figure 1 and Table 1 the authors presented the same results. The authors must improve this part of the results. In Figure 1, use the same colors for marking as a group as in Figure 1/4/5. Does the letter F in Figure 3 stand for the ST group?\n\nIs the work 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": "10231", "date": "06 Oct 2023", "name": "Hayder Al-Aubaidy", "role": "Author Response", "response": "Dear Professor Grujic, Many thanks for reviewing the manuscript and providing us with your comments. We confirm addressing all your comments in Version 2 of the manuscript. A summary of the changes has been listed below: The article by Sahib et al. has been clearly defined. The methodology applied is overall correct. The authors support their paper with recent references. However, the following changes to the main text are suggested: In the results, use the abbreviation TC instead of total cholesterol. Response: Thank you for your comment. This has been fixed across the results section. In Figure 1 and Table 1 the authors presented the same results. The authors must improve this part of the results. Response: We have removed Figure 1 (serum lipid parameters) and kept Table 1 to avoid duplication of data. We have renamed the remaining figures accordingly. In Figure 1, use the same colors for marking as a group as in Figure 1/4/5. Response: Figure 1 – Serum lipid parameters has been removed from the manuscript as per the comment above. Does the letter F in Figure 3 stand for the ST group? Response: In this figure, letter F shows complicated atherosclerotic changes - hemorrhagic thrombus as seen in the atherogenic study cohort (no supplementations). The changes in the sitagliptin group are shown in letter B. Please refer to the figure legend for more details about the changes in the other study groups. Best Regards Prof. Hayder Al-Aubaidy On behalf of all authors for this manuscript" } ] } ]	1	https://f1000research.com/articles/12-339
https://f1000research.com/articles/11-1138/v1	05 Oct 22	{ "type": "Research Article", "title": "Development and validation of sonological classification and scoring system for uterine adenomyosis: A pilot study", "authors": [ "Sudwita Sinha", "Mukta Agarwal", "Punam Prasad Bhadani", "Ria Roy", "Upasna Sinha", "Punam Prasad Bhadani", "Ria Roy", "Upasna Sinha" ], "abstract": "Background: Adenomyosis is a common disorder in women of reproductive age. The gold standard for diagnosis is histopathological examination of hysterectomy specimen. However, only a small percentage of women undergo surgery as treatment is primarily hormonal. Non-invasive methods of diagnosis include transvaginal sonography and magnetic resonance imaging. Patient management in adenomyosis is often based on ultrasonographic diagnosis alone, highlighting the importance of a uniform, reproducible, clinically relevant and validated sonological classification and scoring system. Although a few investigators have proposed classification and scoring system for diagnosis of adenomyosis, none of those have been validated yet. This study aimed to propose and validate a new sonological classification and scoring system for adenomyosis. Methods: This was a prospective observational pilot study. A new sonological classification and scoring system of adenomyosis was proposed based on topography, type, size and extent, which was validated by comparing the sonological reporting with histopathological reporting. The main outcome measures that were measured were rate of agreement (Cohen’s kappa) between the findings of sonologist and pathologist; and diagnostic accuracy of the sonological classification of adenomyosis. Results: This pilot study included 30 women who underwent hysterectomy over a time period of one year with ultrasonographic diagnosis of adenomyosis. The rate of agreement (Cohen’s kappa) between the findings of sonologist and pathologist showed substantial agreement (0.703) for topography and almost perfect agreement for type (0.896), extent (0.892) and size (0.898). Conclusions: Our newly proposed sonological classification and scoring system for adenomyosis is valid and can be used for clinical application in interpersonal communication between clinicians, to prognosticate patients about the disease severity, to assess the candidates for surgical management and in further studies to correlate with symptoms severity and effectiveness of medical therapies.", "keywords": [ "sonological classification of adenomyosis", "validation of sonological scoring system", "adenomyosis", "sonological and pathological agreement", "diagnostic accuracy of sonological system of adenomyosis", "hysterectomy", "heavy menstrual bleeding", "dysmenorrhoea" ], "content": "Introduction\n\nAdenomyosis or ‘cystosarcoma adenoides uterinum’, as initially described by Rokitansky (1860), was defined by Von Recklinghausen (1896) as migration of endometrium glands and stroma into the myometrium.1 Angiogenesis of spiral vessels and smooth muscle hyperplasia and hypertrophy is incited by these migrated endometrium glands leading to junctional zone thickening and diffuse enlargement of the uterus.2 The gold standard for diagnosis is histopathological examination of hysterectomy specimen.3 However, not all women suffering from adenomyosis undergo surgery as the treatment of choice is primarily hormonal – oral progestins, levonorgestrel intrauterine system (LNG-IUS), etc.3 Therefore, tools for non-histologic confirmation of adenomyosis are indubitably required. The non-invasive methods of diagnosis of adenomyosis include transvaginal sonography (TVS) and magnetic resonance imaging (MRI).3 Ultrasonography (USG) is readily available, relatively inexpensive, has no contraindications, and requires no preparation, making it the imaging modality of choice.3 Currently there are no guidelines on USG based classification and scoring system of adenomyosis.\n\nPatient management in adenomyosis is often based on USG diagnosis alone, highlighting the importance of a uniform, reproducible, clinically relevant and validated scoring system for USG findings. Many new sonological classifications of adenomyosis have been proposed in the recent years.4–6 However, it is necessary to validate such tools so that it can be used in clinical practice. After extensive literature research, we found that to date none of the proposed classification and scoring systems for adenomyosis have been validated yet.\n\nA uniform classification and scoring system for USG findings of adenomyosis can be applied in clinical practice only after validation. Classification of type and degree of adenomyosis will be useful in interpersonal communication between clinicians, to prognosticate patients about the severity of the disease, to assess the candidates for management options and in further research studies to correlate with symptoms severity and effectiveness of medical therapies. This study aimed to propose and validate a new classification and scoring system for adenomyosis. The primary objective was to calculate the rate agreement between the findings of sonologist and pathologist. A secondary objective was to determine the diagnostic accuracy of the sonological classification of adenomyosis described using sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio and area under receiver operator curve.\n\n\nMethods\n\nThis was a single-centered, hospital-based, prospective, observational pilot study conducted in the Departments of Obstetrics and Gynecology, Radiology and Pathology, AIIMS, Patna after ethical approval over a time period of one year from August 2021 to July 2022. Since this was a pilot study, a sample size of 30 was chosen for the study. A new sonological classification and scoring system for adenomyosis was proposed based on topography, type, size and extent. This classification system was validated by comparing the sonological reporting with the histopathological reporting which is the gold standard investigation to confirm the diagnosis of adenomyosis. Patients attending the Gynecology outpatient department of AIIMS, Patna, with symptoms suggestive of adenomyosis – heavy menstrual bleeding, dysmenorrhea, dyspareunia, pelvic pain and infertility – were asked to get a transvaginal sonography done, which was performed by a sonologist with six years of experience in the Department of Radiology. Patients were asked to evacuate the bladder and then were laid down in lithotomy position. After taking proper consent, conventional two-dimensional transvaginal sonography (by ACCUVIX-XG machine) was done using a 5-9 Megahertz (MHz) transducer. Firstly, the pelvis was assessed to rule out any obvious pathology. Then the uterus was visualized and focused in the transverse and longitudinal planes. Myometrium was examined to look for the presence of any abnormalities. Color doppler analysis was done. Identical ultrasound settings, both grayscale and doppler were set for all patients. Diagnosis of adenomyosis was made when any of the recognized ultrasound feature of adenomyosis was observed (2015 MUSA group consensus – the international morphological uterus sonographic assessment).3 MUSA features of adenomyosis includes enlarged globular uterus, asymmetrical thickening of myometrium, myometrial cysts, echogenic sub-endometrial lines and buds, hyperechogenic islands, fan shaped shadowing, irregular or interrupted junctional zones and trans-lesional vascularity on color doppler study.3 Those with confirmed diagnosis of adenomyosis based on USG were classified into different types according to the proposed classification system and a score was given based on the type, size and extent. Their data (including their contact information) was recorded in a register. Patients were counselled regarding different management options. Among these patients, those opting for hysterectomy were included in the study.\n\nInclusion criteria included premenopausal women (defined by having had menstruation in the last six months), in the age group of 18–52 years, on no hormonal treatment for the past three months, who gave written informed consent, had hysterectomy planned with a USG based provisional diagnosis of adenomyosis and in whom hysterectomy did not require morcellation (uterus was allowed to be divided into two to three pieces, given that the orientation of the specimen was still possible for the pathologist). Exclusion criteria were postmenopausal women or women with no menstrual bleeding for the last six months, ongoing pregnancy, reproductive tract cancer, fibroid uterus, use of gonadotropin-releasing hormone (GnRH) agonist or antagonist or oral progestins or LNG-IUS within last three months prior to USG evaluation and need for morcellation of the uterus.\n\nThe patients undergoing hysterectomy were admitted in the Gynecology ward two days prior to surgery. A detailed history including chief complaints, history of presenting illness, past medical or surgical history, menstrual history, obstetric history, family history, drug and allergy history and associated co-morbidities were taken from all patients. General examination, systemic examination and pelvic examination was done and findings were noted. Hysterectomy was performed after proper pre-anesthetic check-up, pre-operative investigations, negative Pap smear and normal endometrial biopsy. Hysterectomy specimens were sent for histopathological examination in the Department of Pathology to confirm the diagnosis, type, topography, size, extent and scoring of adenomyosis (observed on USG) by a pathologist, who was blinded to the findings and score of the sonologist. Data regarding patient’s history, examination findings, associated co-morbidities, investigation results, sonological classification and soring, and peri-operative management were collected from the patients’ file records while they were admitted in the Gynecology ward. Histopathological reporting, classification and scoring data were collected from the Department of Pathology using patients’ clinical reference number.\n\nAdenomyosis on USG was reported as follows:\n\n1. Topography: anterior, posterior, left lateral, right lateral or fundal.\n\n2. Type: on a sagittal section through the uterus where the adenomyotic lesion appeared to be at its largest – localized if >25% of the circumference of the lesion was surrounded by normal myometrium, diffuse if <25% of the circumference of the lesion was surrounded by normal myometrium, adenomyoma when focal adenomyosis was demarcated distinctly and surrounded by hypertrophic myometrium, and mixed if features of both localized and diffuse adenomyosis were seen.\n\n3. Extent: assessed subjectively based on proportion of affected uterine corpus – superficial if <25% was affected, deep if >25% was affected but serosa was not involved and full thickness if entire myometrial thickness was affected.\n\n4. Size of lesion: the largest diameter of the largest lesion was measured and in case of diffuse lesion, uterine size was measured.\n\nTable 1 shows the proposed LAD (localized, adenomyoma, diffuse) classification and scoring system for adenomyosis. Minimum possible score is 3 and maximum possible score is 10.\n\nMinimum score-3, maximum score-10.\n\n\n\nI. Localised-1\n\n\n\na. Superficial-1\n\n\n\nII. Adenomyoma-2\n\n\n\nb. Deep-2\n\n\n\nIII. Diffuse-3\n\n\n\nc. Full thickness-3\n\n\n\nIV. Mixed-4\n\nThe outcome measures that were estimated included rate agreement between the findings of sonologist and pathologist and diagnostic accuracy of the sonological classification of adenomyosis described using sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio and area under receiver operator curve.\n\nData was collected offline, entered into Microsoft Excel version 16 and analyzed on SPSS v25 (Statistical package for the social sciences version 25). Cohen’s kappa was calculated by entering the number of agreements in each score. The diagnostic accuracy parameters were estimated by calculating the area under the receiver operator characteristic curve, along with finding the optimum sensitivity and specificity through Youden’s index (sensitivity + specificity -1). The predictive values and likelihood ratios were subsequently calculated taking prevalence of adenomyosis as 23.5%, according to a study done in India by Bupathy Arunachalam and Jayasree Manivasakan.7\n\nThe study was conducted after approval of the ethics committee of the institute (IEC-AIIMS-P ALL INDIA INSTITUTE OF MEDICAL SCIENCES, PATNA PHULWARISHARIF PATNA BIHAR-2021/761), dated 27th July 2021. Written and informed consent were taken from all participants.\n\n\nResults\n\nA total of 30 women were included in the study who underwent hysterectomy with a diagnosis of adenomyosis based on USG.8 The age distribution was as follows: three women were less than 40 years, 13 women were between 40–45 years, 10 women were between 46–50 years and four women were above 50 years of age. All patients were multiparous except for one nulliparous patient. All the patients had a history of heavy menstrual bleeding (HMB) with varying duration of symptom; four patients had HMB for less than a year, 17 patients had HMB for 1–5 years, six patients had HMB for 5–10 years and three patients had HMB for more than 10 years. It was observed that 11 out of 30 patients had symptoms of dysmenorrhea of which three patients had symptoms for more than 10 years, two patients had symptoms for 5–10 years, five patients had symptoms for 1–5 years and one patient had symptoms for less than a year. Only one patient had the symptom of dyspareunia. Only one patient had infertility. Chronic pelvic pain was seen in 14 patients of which two patients had symptoms for more than 10 years, two patients had symptoms for 5–10 years, six patients had symptoms for 1–5 years and four patients had symptom for less than a year. Pelvic organ prolapse was an accompanying symptom seen in four out of 30 patients. The medical co-morbidities associated with adenomyosis included hypothyroidism (10 out of 30 patients), hypertension (eight out of 30 patients) and diabetes mellitus (three out of 30 patients). A history of prior treatment with hormonal therapy was given by 11 out of 30 patients. Anemia was present in 16 patients with pre-operative hemoglobin less than 10 g/dl (grams per deciliter) of which eight required peri-operative blood transfusion. The surgeries that were done in these patients included total abdominal hysterectomy in six patients, total laparoscopic hysterectomy in 20 patients, vaginal hysterectomy with pelvic floor repair in two patients and total laparoscopic hysterectomy with pelvic floor repair in two patients. On histopathology, diagnosis of adenomyosis was confirmed for all patients except for one (29 out of 30 patients). The topographic distribution showed 13 patients with adenomyosis in the anterior wall of the uterus, 10 patients with adenomyosis in the posterior wall of the uterus, five patients with adenomyosis in the fundus of the uterus, three in the right lateral wall and two in the left lateral wall of the uterus. On classifying the type of adenomyosis, localized adenomyosis was seen in 15 patients, diffuse adenomyosis in nine patients and adenomyoma in five patients. Coming to the extent distribution in patients – 16 patients had superficial adenomyosis, seven patients had deep adenomyosis and six patients had full thickness adenomyosis. The size of the largest lesion of adenomyosis was less than 2 cm in 14 patients, 2–5 cm in eight patients and more than 5 cm in seven patients. The total score showed a score less than or equal to 3 in 12 patients, a score between 4–6 in eight patients and a score more than or equal to 7 in nine patients.\n\nThe sonographic scoring system had an overall visible agreement with the histopathological scoring system and findings of the pathologist. In Table 2, the agreement was determined by Cohen’s kappa. The kappa value for topography of adenomyosis is 0.703, indicating substantial agreement (0.61–0.80). The sonographic findings of the type, extent and size of adenomyosis had almost perfect agreement to the histopathological findings, as shown by the kappa value of 0.896, 0.892 and 0.898 respectively.\n\nTable 3 shows the diagnostic accuracy characteristics of the proposed sonographic scoring system which diagnosed adenomyosis as being present in the participants. All the parameters had 100% sensitivity, and the extent of adenomyosis had the highest specificity of 69.6% and highest positive predictive value of 50%. There was only one participant who did not have any adenomyosis according to histopathology, but came highly positive on sonography, resulting in the test being non-specific for topography. Except for topography, every other parameter can be successfully determined by sonography, as shown by the area under receiver operator characteristic curve being 0.600 and above.\n\n\nDiscussion\n\nThe above study shows that most of the patients with adenomyosis who landed up in surgery (hysterectomy) belonged to the age group of 40–50 years. This may be due to the fact that medical and hormonal treatments are tried first in younger age groups and surgery is done only when hormonal therapy fails. All the patients undergoing surgery were multiparous except for one nulliparous patient who was so much affected by the symptoms that desire of fertility was not her first priority, and she was ready to go for adoption. The reason behind maximum patients undergoing surgery being multiparous can also be explained by the conservative attitude towards treatment in nulliparous women so as to conserve the uterus. The most common symptoms seen in adenomyosis patients undergoing hysterectomy were heavy menstrual bleeding (100%), chronic pelvic pain (46.67%) and dysmenorrhea (36.67%). Heavy menstrual bleeding resulted in anemia in many patients as is shown by the fact that 53.33% of patients had hemoglobin less than 10 g/dl before surgery that necessitated blood transfusion in half of these patients (26.67%). Only one patient had infertility as we generally don’t do hysterectomy in an infertile patient. This patient was however so much burdened with the disease symptoms that she wanted complete surgery to relieve her symptoms despite counselling against surgery and offering conservative management options. It is also seen that dyspareunia was complained by only one out of 30 patients. This might be underreporting of this symptom due to several factors in this part of the country with the majority of women belonging to lower socio-economic status. Some of the factors may include considering it a taboo, stigma or shameful topic, shyness, embarrassment, reluctance to raise the topic of sexual problems with clinicians, patriarchal dominance where females don’t have any say against sexual discomfort, etc. Pelvic organ prolapse was seen in four patients which may be unrelated to the etio-pathogenesis of adenomyosis. The most common associated medical co-morbidities were hypothyroidism (33.33%), hypertension (26.67%) and diabetes mellitus (10%). These factors may have also contributed to heavy menstrual bleeding independently. In 11 out of 30 patients, prior treatment with hormonal therapy had failed which resulted in patients opting for surgery for relief of symptoms. On histopathology, diagnosis of adenomyosis was confirmed in 29 out of 30 patients (96.67%). The topographic distribution showed 43.33% anterior wall adenomyosis, 33.33% posterior wall adenomyosis, 16.67% fundal adenomyosis, 10% right lateral wall and 6.67% left lateral wall adenomyosis. Thus, it can be concluded that adenomyosis is more common in fundo-anterior and posterior regions of the uterus. On classifying the type of adenomyosis, the most common type seen was localized adenomyosis (50%), followed by diffuse adenomyosis (30%) and adenomyoma (16.67%). Adenomyoma was the least common type of adenomyosis seen. More than half (53.33%) of patients had superficial adenomyosis, 23.33% of patients had deep adenomyosis and 20% of patients had full thickness adenomyosis. Majority of the patients had small size adenomyosis (46.67%), whereas adenomyosis of more than 5 cm was seen in 23.33% of patients. The total score showed a score less than or equal to 3 (mild) in 40%, a score between 4–6 (moderate) in 26.67% and a score more than or equal to 7 (severe) in 30% of patients.\n\nThe sonographic scoring system had an overall visible agreement with the histopathological scoring system and findings of the pathologist with topography of adenomyosis having substantial agreement whereas type, extent and size of adenomyosis having almost perfect agreement to the histopathological findings. This suggests that our proposed classification and scoring system for adenomyosis is valid and can be used in clinical practice.\n\nAmong the diagnostic accuracy characteristics of the proposed sonographic scoring system which diagnosed adenomyosis as being present in the participant, sensitivity was 100% for all parameters and specificity was highest for extent of adenomyosis (69.6%). The highest positive predictive value of 50% was also seen for extent of adenomyosis. However, there was only one participant who did not have any adenomyosis according to histopathology, but came highly positive on sonography, resulting in the test being non-specific for topography. Except for topography, every other parameter can be successfully determined by sonography, as shown by the area under receiver operator characteristic curve being 0.600 and above.\n\nThe limitations of this study include its small sample size and unavailability of three-dimensional (3-D) ultrasound machines for transvaginal sonography which could have given more accurate imaging diagnosis.\n\n\nConclusion\n\nTo conclude, the present study successfully proposed and validated a sonological classification and scoring system for adenomyosis which can be applied in clinical practice for interpersonal communication between clinicians, further research studies correlating disease severity with severity of clinical symptoms, to prognosticate patients about the severity of their disease, deciding the different management options for patients and following up patients for effectiveness of medical and hormonal therapies. Further studies with larger sample size are still required to correlate disease severity according to score with the severity of clinical symptoms.\n\n\nData availability\n\nFigshare: adenomyosis data file 1. https://doi.org/10.6084/m9.figshare.20708965.8\n\nThis project contains the following underlying data:\n\n• adenomyosis data file 1.csv (data mentioning the age, parity, symptoms, co-morbidities, sonological and histopathological classification and scoring and the surgeries performed)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nSakhel K, Abuhamad A: Sonography of adenomyosis. J. Ultrasound Med. 2012 May; 31(5): 805–808. PubMed Abstract \| Publisher Full Text\n\nCunningham RK, Horrow MM, Smith RJ, et al.: Adenomyosis: A Sonographic Diagnosis. Radiographics. 2018 Sep-Oct; 38(5): 1576–1589. PubMed Abstract \| Publisher Full Text\n\nVan den Bosch T, Dueholm M, Leone FP, et al.: Terms, definitions and measurements to describe sonographic features of myometrium and uterine masses: a consensus opinion from the Morphological Uterus Sonographic Assessment (MUSA) group. Ultrasound Obstet. Gynecol. 2015 Sep; 46(3): 284–298. PubMed Abstract \| Publisher Full Text\n\nLazzeri L, Morosetti G, Centini G, et al.: A sonographic classification of adenomyosis: interobserver reproducibility in the evaluation of type and degree of the myometrial involvement. Fertil. Steril. 2018 Nov; 110(6): 1154–1161.e3. PubMed Abstract \| Publisher Full Text\n\nGordts S, Grimbizis G, Campo R: Symptoms and classification of uterine adenomyosis, including the place of hysteroscopy in diagnosis. Fertil. Steril. 2018; 109: 380–388.e1. PubMed Abstract \| Publisher Full Text\n\nExacoustos C, Morosetti G, Conway F, et al.: New Sonographic Classification of Adenomyosis: Do Type and Degree of Adenomyosis Correlate to Severity of Symptoms? J. Minim. Invasive Gynecol. 2020; 27: 1308–1315. Publisher Full Text\n\nArunachalam B, Manivasakan J: A clinico- pathological study of adenomyosis. J. Clin. Diagn. Res. 2012; 6(3): 428–430.\n\nSinha S, Agarwal M: adenomyosis data file 1. figshare. [Dataset].2022. Publisher Full Text" }	[ { "id": "153725", "date": "07 Nov 2022", "name": "Rooma Sinha", "expertise": [ "Reviewer Expertise Minimally invasive Gynecology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is well designed and written and can be used in clinical setting to confirm the diagnosis of adenomyosis.\nIt's clinical relevance can be more in infertility patients where hysterectomy is not being considered and an accurate diagnosis of adenomyosis can help fertility specialists to plan treatment appropriately or counsel and prognosticate such patients. This point can be included in the discussion.\n\nAlthough this study attempts to validate this scoring system, the number of participants is small. Perhaps the authors can continue this study in future and revalidate it. This at present can be considered as a pilot study.\n\nDid the authors take all the characters described in MUSA into consideration for sonological diagnosis of adenomyosis or a minimum number. Could the authors clarify this as all features described are not seen in all patients. This would be important for diagnosis in clinical setting.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10240", "date": "16 Nov 2023", "name": "Mukta Agarwal", "role": "Author Response", "response": "Thank you for taking the time to review this article. As suggested, we will include your point in discussion section regarding clinical relevance of the study in infertility patients. We would also be continuing this study in the future and re-validate it, considering the present study as a pilot study. A minimum number of MUSA features were considered for sonological diagnosis, this point will also be clarified in our next version." } ] }, { "id": "168055", "date": "12 Apr 2023", "name": "Maria Grazia Porpora", "expertise": [ "Reviewer Expertise Endometriosis", "minimally invasive gynecology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for inviting me to review the manuscript entitled “Development and validation of sonological classification and scoring system for uterine adenomyosis: A pilot study” by Sudwita Sinha et al.\nThe aim of this pilot study is to assess a valuable sonological classification and scoring system able to better address the diagnosis of uterine adenomyosis.\nThe Abstract is clear and accurately summarizes the contents of the paper. Methods are well explained. The Results are consistent with the objectives of the study. References are updated. English language is clear and easily understood.\nThe greatest limitation of the study, as reported by Authors, is the low sample size. Authors should emphasize on the need of a larger group of patients to validate this study model.\nMoreover, as the well-known MUSA criteria are the most suitable accepted classification system for adenomyosis, Authors should clarify why and how their sonological classification and scoring system is ought to be more useful and adoptable by experts in this field.\nTherefore, the article will be suitable for indexing in F1000 Research 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": "10241", "date": "16 Nov 2023", "name": "Mukta Agarwal", "role": "Author Response", "response": "Thank you for reviewing this article. All the suggestions regarding revision will reflect in our revised version. Thank you." } ] } ]	1	https://f1000research.com/articles/11-1138
https://f1000research.com/articles/12-359/v1	03 Apr 23	{ "type": "Research Article", "title": "Toward esthetically and biomechanically reliable anterior resin composite restorations: Current clinical experiences among dental practitioners in Saudi Arabia", "authors": [ "Khalid S. Almulhim", "Rasha AlSheikh", "Moamen Abdalla", "Rasha Haridy", "Amr Bugshan", "Stephen Smith", "Mohammed Zeeshan", "Moataz Elgezawi", "Khalid S. Almulhim", "Rasha AlSheikh", "Moamen Abdalla", "Rasha Haridy", "Amr Bugshan", "Stephen Smith", "Mohammed Zeeshan" ], "abstract": "Background: Esthetic anterior composite restorations are very challenging. They constitute a main part of the clinical practice of restoring teeth with resin composites. Distinctive variations in composite material selection and technique of application in anterior teeth exist when compared to the practice of restoring posterior teeth with resin composites. In a continuation of a previous assessment of class II resin composite practice, a cross-sectional survey study was performed to determine the awareness of general dental practitioners in Saudi Arabia about resin composite restorations in anterior teeth and to provide evidence-based recommendations to improve their practice. Methods: A total of 500 dental practitioners from different provinces in Saudi Arabia were invited to participate in an online questionnaire which comprised four domains and included a total of sixteen questions addressing aspects regarding the selection of resin composites, cavity configuration, etching protocol, light-curing technique, liner application, application of poly-chromatic composite, as well as finishing and polishing procedures. Chi square testing and descriptive statistics were used to analyze the attained data. Results: From 250 respondents, the greatest participation was from the Eastern and Middle provinces of Saudi Arabia. Female dentists participated less than males. There was no general agreement between participants regarding the resin composite material or the employed technique of application in restoring anterior tooth defects. Respondents indicated that discoloration and hypersensitivity were the most common reasons for patient’s dissatisfaction with resin composites in anterior teeth. Conclusions: Dental practitioners are highly encouraged to improve their clinical practice of restoring anterior teeth using resin composites with the focus upon continuous education programs, online webinars, and workshops.", "keywords": [ "Keywords: cross-sectional survey", "resin composite", "anterior teeth", "general dentists", "Saudi Arabia." ], "content": "Introduction\n\nThe main objective of the modern practice of restorative dentistry is the reestablishment of optimum esthetics and effective biofunction of hard structural tooth defects in an evidence-based and patient-centered manner with long term clinical durability.1 The central focus for dental clinicians, researchers as well as patients constitutes the optimization of procedural outcomes when restoring defective anterior teeth into esthetically pleasing, biologically healthy and mechanically sound integral units of the dental arch.2–4\n\nPresently, direct resin composites are the principle and most widely used option for restoring anterior teeth as they can produce restorations with optimum esthetics and effective biomechanical rehabilitation with long-term clinical reliability and patient satisfaction.5 Furthermore, they can conserve and reinforce sound tooth structure.6–10 Modern resin composites have particularly upgraded optical properties, surface finish color stability, wear resistance, flexure strength and fracture toughness.11 In comparison to the indirect options of dental ceramics, direct resin composites are timesaving, less costly and allow for repairable options.12–14\n\nRestoration of defects in the esthetic zone is challenging. According to World Dental Federation (FDI) commission 2-95, the quality of the restoration is directly related to the utilized materials, to the clinician's individual skills and preferences as well as to patient’s particular oral environment and post-operative care.2,3 Operator related factors have been considered as being instrumental in determining the quality and clinical performance of dental restorations. This includes procedural excellence variations, clinical judgement, and differences between operators regarding cavity design, material selection and manipulation.15\n\nVarious resin composite materials are currently available in the market with variations in composition, clinical performance and application technique as recommended by manufacturers.16–18 Micro-filled, micro-hybrid, nano-hybrid, flowable, incremental, and bulk-fill composites are amongst the available resin composites widely used in restoring tooth defects.16–18\n\nRestoring anterior tooth shape and optical characteristics involve a variety of procedural techniques which are determined by the material used, extent of the defect and operator preference.19,20 Anterior tooth defects may be small or extensive, resulting from caries or non-carious developmental defects, as well as traumatic lesions. Freehand, palatal putty index and different matricing techniques have been suggested for restoring anterior tooth defects, especially involving the incisal angle or extensive coronal tooth structure defects.19,20\n\nNatural teeth consist of translucent enamel and relatively opaque dentin which is influenced by the pulp and investing gingiva.21 This necessitates a polychromatic manner of restoring anterior tooth defects requiring consideration of tooth optical characteristics and chameleon effects.22,23 Individual shading patterns and translucency variability of teeth are demanding. A single shade mono-laminal versus different shade multilaminate techniques have been alternatively implemented to optimize results that will match tooth optical characteristics when restoring anterior tooth defects.24,25 Dentists differ in their judgment regarding the necessity of using an intermediate liner beneath resin composites in anterior teeth.26 Moreover, they differ in selecting a particular brand of resin composite material and a specific restoration technique for a particular clinical situation when restoring anterior tooth defects.\n\nThis cross-sectional survey was therefore designed to investigate the current clinical practices of general dental practitioners in Saudi Arabia regarding the restoration of anterior tooth defects using resin composites. In our previous publication, class II resin composite practices of general dental practitioners in Saudi Arabia were assessed.27 The objective of the current study was to assess the knowledge and attitude of general dental practitioners in Saudi Arabia toward anterior resin composites.\n\n\nMethods\n\nGeneral non-university governmental hospitals in each of the following Saudi provinces; North, Middle, East, West, and South were considered in the study. The hospitals were enumerated in sequence according to the number of available dental units. The first five hospitals with the largest number of dental units in each of the study provinces with the largest number of appointed dentists were selected for the study and included 500 dental practitioners. The study was conducted over a period of four months starting mid-September 2021. E-mail addresses of general dentists were collected through administrative contacts in hospitals included in the study after explaining the study objective. Personal data including names, gender or years of employment were not available to the study investigators prior to sending the invitations, and all e-mail invitations were anonymous. Potential sources of bias were minimized by avoiding leading answers, extreme answers, questions framing, question order bias and sampling bias.\n\nThis cross-sectional study was conducted utilizing an online uploaded survey questionnaire using Google’s free online survey platform. E-mail invitations stated clearly that participation was anonymous and voluntary and that participants were free to leave the survey or to skip any questions. The targeted population of 500 resulted in a calculated sample size of 218 dentists. Calculations were performed at the 95% confidence level using a free online sample size calculator.\n\nThe validity and reliability of the questions were tested for content validation. Ten experts were invited to validate each question of the survey before the beginning of the study using the following scale: the question is not relevant, the question is somewhat relevant, the question is quite relevant, or the question is highly relevant. The experts ranked all questions as either relevant or highly relevant. Therefore, no modifications were made in the designed questions.\n\nThe questionnaire comprised four domains; the first domain focused on the demographic data of the participants. Demographic data included age, gender, and city of appointment. The second domain targeted the professional record (profession duration and frequency of utilizing anterior composite resin restorations). The third domain addressed the individual personal preferences in the selection and utilization of resin composites for restoring anterior tooth structure defects. The fourth domain investigated patients' feedback regarding previously placed resin composite restorations. Moreover, it considered suggestions for anterior resin composites practice improvement. The questionnaire included a total of 18 questions of which 3 questions allowed two optional answers while the rest of the questions included more than two optional answers. Chi square testing using SPSS 27 software at a level of significance of p ≤ 0.05 and descriptive statistics were employed in analyzing the received responses. Minitab statistical software is an example of free online software that can be used to perform similar statistical analysis.\n\nThis research received an ethical approval (IRB-2022-02-102) from IRB Committee, Imam Abdulrahman Bin Faisal University.\n\nDuring the research, participants were invited to join the survey through emails that clarified the objectives of the study and included necessary information and that joining the survey is anonymous and voluntary. The invite explained that by completing the survey, they were consenting to participate in the study. Participants were informed that they could leave the study at any step if they did not wish to continue, and that the data collected would be used for research purposes. The IRB approval of Imam Abdulrahman bin Faisal University deemed this method of implied consent as sufficient.\n\n\nResults\n\nOut of the 500 email invitations, 250 responses were obtained. The questionnaire domains, questions, answers, and relative responses in percentages and the P values are depicted in Tables 2-4 and Figures 1-2: Responses with different upper-case letters in each question have statistically significant difference (p ≤ 0.05). Domain 1 comprised the demographics of participants (n=250), see Table 2.\n\n\n\n1. Age\n\n\n\n2. Gender\n\n\n\n3. Status\n\n\n\n4. Where you have been practicing in Saudi Arabia\n\nDomain 2 comprised the dentists’ professional records (profession duration and frequency of utilizing anterior composite resin restorations).\n\n\n\n5. How long have you been practicing dentistry? (n=250)\n\n6. How many resin composite restorations in anterior teeth do you place per week? (n=250)\n\nDomain 3 comprised the individual personal preferences in the selection and utilization of resin composites for restoring anterior tooth structure defects (n=250), Table 3.\n\n\n\n7. What is the isolation technique that you usually use?\n\n\n\n8. What is the most frequent type of composite resin restoration you practice?\n\n\n\n9. What is the type of resin composite material you use to restore each class?\n\n\n\n10. Type of etching/adhesive system you use:\n\n\n\n11. Type of light-curing unit you use:\n\n\n\n12. Duration of curing per layer:\n\n\n\n13. In class IV restorations, what is the technique that you use?\n\n\n\n14. Do you usually use a liner under a composite restoration?\n\n\n\n15. In class IV restorations, do you use a polychromatic approach in the form of enamel and dentin shades?\n\n\n\n16. The technique used for finishing and polishing of the composite resin restoration\n\nDomain 4 comprised anterior composites failure & suggestion for practice improvement (n=250) Table 4.\n\n\n\n17. What are the principal forms of failure and patient dissatisfaction with old resin composite restorations in anterior teeth?\n\n\n\n18. How can the practice of anterior composites be improved?\n\n\nDiscussion\n\nThis study analyzed the current practice of restoring anterior tooth defects with direct resin composites by dentists in Saudi Arabia. This cross-sectional survey was utilized to collect and analyze dental practitioners’ responses at one single time. The study was designed and conducted over a period of four months which was initiated in mid-September 2021. The number of anticipated participants at the time of the study design as well as the number of respondents to the survey could have affected the results of the survey. A broader study outcome could have been provided if greater population sizes and larger numbers of respondents were utilized.28,29 The inclusion of general governmental hospitals granting dental treatments completely free of charge to patients is another possible limitation of the current study. The flow of patients seeking free dental treatments versus the availability of time and facilities may also have had an influence. Study outcomes in this study could have been expanded by the addition of private dental centers and clinics as well as university clinics and hospitals. This would thus have included general dentists exposed to socioeconomically different patients and distinctive facilities. The current survey was conducted as an online questionnaire. This method facilitated the ease of collecting data instead of utilizing a physical paper method. Invitations to participants was sent via e-mail. E-mail addresses of the general dentists in the included hospitals were anonymously collected through administrative contacts after explaining the study objective. Participants were anonymously and voluntarily invited to participate in the survey without any bias and with assurance of confidentiality so as to follow ethical guidelines. To assure reliability and validity of questions, ten experts in restorative dentistry were requested to validate the questionnaire before starting the survey. All invited experts validated questions as either highly relevant or relevant.28 Participants were from all Saudi Arabia provinces, with the highest participation from the Eastern and Middle provinces. Though it was not anticipated for gender to have any impact on the collected data, it was included in the general demographic information. Most of the dental schools in the Kingdom are segregated with more male schools available compared to female’s, that said, more female dentists have graduated from King Saud University since 198230 and later from other universities with the number continuing to increase. The results from our study showed that male dentist’s participation was more than females which is in line with a previous study.27\n\nData from the Saudi Commission for Health Specialties in 2016 shows that 70.27 % of licensed dentists are registered as general dentists in Saudi Arabia, therefore the current study design targeted general dentists who constitute the greatest fraction of licensed dentists in Saudi Arabia.27 The used population size and distribution in the current study was previously used in a cross-sectional survey that studied class II resin composites practice of general dentists in Saudi Arabia.31\n\nIn a former survey-based study performed in southern Brazil, a sample size of 276 dentists and descriptive statistics were used to draw the study conclusions about the clinical practice of general dentists in anterior composite restorations.3 The study revealed that most dentists in southern Brazil use hybrid composite, simplified adhesives, LED light curing and immediate polishing while only few dentists use of rubber dam isolation.3\n\nA recent systematic review that studied the clinical reliability of anterior composites has summarized the factors influencing the quality and evaluation process of restorations. The first group of factors are restoration related (material type, composition, insertion technique, curing mode, finishing and polishing, shading concept, and accuracy). The second group is preparation related (form and configuration, volume, margin design, and proximal extension). The third group is operator related (experience, skills, and handling). The environment in terms of public academic centers, private centers, public social centers, multiple or single operator practice was listed as the fourth group.7,32,33\n\nIn designing the questionnaire of the current study and the targeted population, the previous factors were considered.\n\nModern resin composite formulations include developments and modifications in materials technology regarding the structural components of resin matrix, fillers, coupling agents, photo initiator as well as shading and color pigments.34–38 This has greatly influenced the physico-mechanical and biological properties of different brands of resin composites which eventually impact clinical application techniques and final clinical behavior during function in the oral cavity. Bulk-fill, self-adhesive, single shade, self-healing, and antibacterial composites are examples of such recent developments. Similarly, modern finishing and polishing tools of resin composites have also become available in the market. The increasing demand from patients for excellent esthetic quality has been met with distinctive clinical application techniques utilizing direct resin composites for restoring defects of particularly anterior teeth, this by means of combining art with knowledge and color selection.5 Based on the natural layering concept, a polychromatic layering technique has been suggested.39 An example of this practice is the utilization of palatal indices to optimize the designed form and contours.40\n\nIsolation of the operative field and control of moisture during various operative restorative procedures are essential for developing optimum physical and mechanical properties of the restoration. This is particularly true for resin composite restorations in anterior teeth where developing optimum adhesion and superior esthetics is mandatory for clinical reliability and patient satisfaction. In agreement with previous studies, rubber dam followed by cotton rolls isolation were the two methods of operative field isolation used by participants of the current survey.41\n\nAssessing the ability to reliably restore esthetics is a principal aspect of the current cross-sectional study. The chameleon effect has been reported by manufacturers of resin composites as a property of the material to adapt to the color of the surrounding tooth tissues. The color adjustment potentials of resin composites have been reported to be influenced by the material type, the cavity design, and configurations as well as the substrate surrounding the restoration. Understanding the optical characteristics of teeth and properties of incident light is essential for optimum shade selection and faithful restoration of esthetic derangements.42 Making use of the optical illusion phenomenon is essential for optimum esthetic outcomes and excellence in restoring anterior tooth form, contour, and emergence profile. Accordingly, the best esthetic outcomes are achievable when scientific knowledge is coupled with artistic potential.43 Consequently, dentists should be continuously updated in materials and color selection technologies so as to be able to select and implement the best application technique for each clinical indication. Selection of the most appropriate brand of resin composite material, adhesive approach and insertion technique for a specific clinical case is crucial for a clinically satisfactory result, particularly when restoring deranged esthetics in anterior tooth defects. This should be based on thorough knowledge of color dimensions, optical properties, principles, and technologies of shade selection,44 familiarity of the respective material properties, indications and contraindications, comprehensive esthetic analysis including tooth forms, alignment, symmetry, the correlation with adjacent and opposing teeth,45 and in addition, the clinical factors related to the specific lesion or tooth defect.46 Moreover, full recognition of complex oral environmental factors influencing decision making in the designing of treatment plans has a major influence on the quality and clinical reliability of the final anterior resin composite restoration and is mandatory for assuring patient satisfaction.17,18,47,48 The third domain of our questionnaire therefore aimed to study the awareness of general dentists concerning the different composite classes of material and the respective clinical indications. Participants were asked about class V resin composite restorations for restoring cervical tooth defects including abfraction lesions. These restorations are used to restore cervical tooth defects where the greatest flexure of teeth occurs during functioning, and includes higher risks of developing tooth cracking, abfraction defects and loss of retention with the usage of rigid and higher inorganic filler containing restorations. Accordingly, the need for more flexible and less filler containing restorations that yield upon repeated flexure at cervical locations, including having superior surface finish ability and polish ability, is clearly advocated in these cases. Our results showed that for class V lesions, 28% of participants use microfilled resin composites while 28% apply nanohybrid composites, 26% use flowable composites and 16% insert micro-hybrid composite, raising strong concerns.\n\nBecause of their initial low viscosity and high post gel flexibility, many previous studies have recommended the use of flowable composites for restoring non-carious cervical tooth defects.49 Nevertheless, our collected data indicated that in class III restorations, 37 % work with nano-hybrid, and 28% of participants use micro-filled, and 32% use micro-hybrid composites. In a randomized clinical control trial over 12 months,50 micro-hybrid resin composite was found to provide the best color match over microfilled and nanohybrid composite while microfilled and nanofilled composite showed better 12-month surface quality than microhybrid composite.\n\nOur results for class IV restorations where high strength resin composite materials are highly recommended, showed that 33% of the respondents employ nano-hybrid while another 33% use micro-hybrid resin composites, and 26% used microfilled composite, 16% use other resin composite classes, and 2% of non-respondents, deserves attention. In a comprehensive metanalysis,51 the main reason for replacement of class IV resin composites was bulk fracture which occurred more frequently with microfilled composite than with hybrid and macrofilled composites.\n\nThe literature shows that there is no one single class of resin composite for all purposes and that it is the responsibility of the restorative dentist to select the most appropriate type of composite for a particular indication. In response to the current questionnaire, many dentists indicated that selection of composite material conforms to sound and relevant evidence-based criteria for selection in respective clinical situations. On the other hand, other responses indicated unjustified selections with poor clinical relevance and judgement.\n\nThe survey indicated a clear variation between respondents regarding the specific adhesive regularly used. The easier and less time-consuming usage of self-etching adhesives have apparently played a role in individual operator preference at the expense of the proven long-term clinical reliability and more consistent performance of total-etch adhesives. This might explain that only 45% of participants use total-etch adhesives, while 31% and 23% used self-etching and selective etching technology, respectively. This is in line with a similar study3 finding.\n\nPresently, most resin-based composites are visible light-activated materials. This allows for more controlled and command curing and adequate working time before curing, while at the same time requiring incremental placement of material into the prepared cavity to ensure an optimum degree of curing.52–54 Adequate light curing is crucial to achieve the desired biomechanical and biocompatibility properties of the resin composite material. Adequate curing requires appropriate criteria of light intensity, curing time, direction of the curing light and proximity of the light curing source to the surface of the curing resin composite.55–57 Dental light-curing units are handheld devices that are used for the polymerization of visible light-activated dental materials. Different light-curing units of variable technologies are currently available in the market. Each has specific set-up and light intensity output. Respondents showed variation in their practice of light curing and specific curing devices.58 It is evident that light curing awareness and practices need urgent reconsideration and correction in many cases. LED followed by QTH are the most widely used light curing devices while Laser and Plasma Arch are the least used light curing devices. This is in line with many pervious reports indicating the popularity of LED and QTHs.59 A previous study found LED units to have higher curing light intensity than that of QTH. Moreover, it reported that QTHs have greater frequency than LEDs.60 Due to the higher radiant emmitance of plasma arch light and argon ion laser, less light curing time is needed. However, greater polymerization shrinkage stresses and marginal discrepancies were reported with this mode of light curing.58\n\nPrevious reports have advocated that in anterior teeth with extensive loss of coronal tooth structure involving the incisal edge, the controlled application of resin composite restorations using a palatal putty consistency rubber base index is more recommended than the freehand application. Cumulating evidence indicates that the palatal index technique allows multiple chromatic layering, leading to improved tooth optical characteristics in addition to optimizing the restoration of tooth form and contours with a minimal need for occlusal adjustment.61–64 The results of the current survey indicated that 46% of participants used both techniques while only 10% exclusively used the palatal index technique. This contradicts evidence-based research and therefore reflects the need for practice correction. Moreover, the survey indicated that many dental practitioners in Saudi Arabia should consider changing their practice from using single shades of resin composite to the polychromatic approach of applying several shades of resin composite when restoring anterior tooth defects, so as to achieve the best esthetic quality. A previous report described the multiple layering approach using different enamel and dentin composite shades, a palatal hybrid composite layer, and a buccal microfilled composite with selective addition of transparent and white spot characters as a biomimetic direct composite stratification technique duplicating the physical and optical properties of natural teeth in class IV restorations.65\n\nFinishing and polishing of resin composites are essential for long-term clinical reliability and esthetically pleasing restorations. Smooth surfaces will not accumulate plaque and stains with subsequent discoloration and secondary decay.66 Respondents commonly selected various tools in finishing and polishing resin composite rather than using one single tool for finishing and polishing, thereby reflecting the general keenness of respondents to perform optimum finishing and polishing procedures. Finishing and polishing strips were the preferred tools for 69% of respondents that might be related to their ease of usage, especially with class III restorations. Participants also reported other tools like white stones, Soflex, and impregnated rubber tips and polishing paste as other validated options which are in line with previous studies.67–69 The current survey responses from dentists in Saudi Arabia showed that discoloration is most common form of failure and patient dissatisfaction of resin composites in anterior teeth, which is generally in line with previous outcomes of systematic reviews listing reasons for failure of resin composite restorations.70 Accordingly, upon restoring anterior tooth defects with resin composites, clinical practices of dentists in Saudi Arabia should confirm superior long-term pleasing esthetics and minimization of future caries recurrence. Furthermore, it is recommended that dental practitioners in Saudi Arabia implement clinical protocols that will prevent or minimize post-restoration hypersensitivity, ensure best tooth form, and provide durable structural integrity without chipping or fracture of the restored anterior tooth. The current survey outcomes have also identified the need for dental practitioners in Saudi Arabia to upgrade their awareness and to modify their practices of resin composite restorations in anterior tooth defects. Participation in continuous dental educational and training programs is strongly suggested. Improving the clinical skills and broadening the experiences of undergraduates and recent graduates in complex esthetic resin composite restorative techniques under close supervision of senior clinical experts is vital.71\n\n\nConclusions\n\nIn consideration and within the limitations of this study, the following conclusions can be made:\n\n1- Dental practitioners in Saudi Arabia are not consistent in their clinical practice of restoring anterior tooth defects using resin composites, regardless of the location of their practice or length of their clinical experience.\n\n2- Improvement in clinical practice and awareness of resin composite restorations in anterior teeth appears to be of high necessity for some dental practitioners in Saudi Arabia. Dental practitioners should actively and dynamically be familiar with updates in resin composites technologies and clinical techniques of restoring anterior teeth through continuous education programs, workshops, and online webinars.", "appendix": "Data availability\n\nZenodo: Toward esthetically and biomechanically reliable anterior resin composite restorations: current clinical experiences among dental practitioners in Saudi Arabia. https://doi.org/10.5281/zenodo.7738566.\n\nThis project contains the following underlying data:\n\n- Responses collected-Anterior Composite.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nThe authors would like to thank the experts who validated the questions of this survey: Dr Dalia Kaisarly, Dr Stephen Smith, Dr Hala Bahgat, Zahraa Aldawakhly, Dr Murad Benhameurlaine, Dr Dana Alsenan, Dr Amal Elsawi, Dr Abeer Elembabi, Dr Khalid Almas and Dr Mohamed Gad.\n\n\nReferences\n\nBlatz MB, Chiche G, Bahat O, et al.: Evolution of Aesthetic Dentistry. 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Publisher Full Text\n\nDietschi D, Fahl N: Shading concepts and layering techniques to master direct anterior composite restorations: an update. Br. Dent. J. 2016; 221(12): 765–771. PubMed Abstract \| Publisher Full Text\n\nGao Y, Li J, Dong B, et al.: Direct composite resin restoration of a class IV fracture by using 3D printing technology: A clinical report. J. Prosthet. Dent. 2021; 125(4): 555–559. Publisher Full Text\n\nWang Y, Li C, Yuan H, et al.: Rubber dam isolation for restorative treatment in dental patients. Cochrane Database Syst. Rev. 2016; 9(9): CD009858. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmeling M: Color Selection and Reproduction in Dentistry Part 2: Light Dynamics in Natural Teeth. Odovtos-Int. J. Dent. Sc. 2016; 18(2): 23–40. Publisher Full Text\n\nIsmail EH, Paravina RD: Color adjustment potential of resin composites: Optical illusion or physical reality, a comprehensive overview. J. Esthet. Restor. Dent. 2022; 34(1): 42–54. PubMed Abstract \| Publisher Full Text\n\nChu SJ, Trushkowsky RD, Paravina RD: Dental color matching instruments and systems. Review of clinical and research aspects. J. Dent. 2010; 38(Suppl 2): e2–e16. PubMed Abstract \| Publisher Full Text\n\nFradeani M: Evaluation of dentolabial parameters as part of a comprehensive esthetic analysis. Eur. J. Esthet. Dent. 2006; 1(1): 62–69. PubMed Abstract\n\nMcLaren EA, Rifkin R: Macroesthetics: facial and dentofacial analysis. J. Calif. Dent. Assoc. 2002; 30(11): 839–847. PubMed Abstract \| Publisher Full Text\n\nLutz F, Phillips RW: A classification and evaluation of composite resin systems. J. Prosthet. Dent. 1983; 50(4): 480–488. Publisher Full Text\n\nPrakash V, Banu S, Sukumaran V, et al.: Comparision of True Nano with Microhybrid and Nanocluster Composite Before and After Tooth Brushing. Biosci. Biotechnol. Res. Asia. 2016; 13(4): 2365–2370. Publisher Full Text\n\nKubo S, Yokota H, Hayashi Y: Three-year clinical evaluation of a flowable and a hybrid resin composite in non-carious cervical lesions. J. Dent. 2010; 38(3): 191–200. Publisher Full Text\n\nLoguercio AD, Lorini E, Weiss RV, et al.: A 12-month clinical evaluation of composite resins in class III restorations. J. Adhes. Dent. 2007; 9(1): 57–64. PubMed Abstract\n\nHeintze SD, Rousson V, Hickel R: Clinical effectiveness of direct anterior restorations--a meta-analysis. Dent. Mater. 2015; 31(5): 481–495. PubMed Abstract \| Publisher Full Text\n\nChandrasekhar V, Rudrapati L, Badami V, et al.: Incremental techniques in direct composite restoration. J. Conserv. Dent. 2017; 20(6): 386–391. PubMed Abstract \| Publisher Full Text\n\nMahn E: Clinical criteria for the successful curing of composite materials. Revista Clínica de Periodoncia, Implantología y Rehabilitación Oral. 2013; 6(3): 148–153. Publisher Full Text\n\nStein PS, Sullivan J, Haubenreich JE, et al.: Composite resin in medicine and dentistry. J. Long-Term Eff. Med. Implants. 2005; 15(6): 641–654. PubMed Abstract \| Publisher Full Text\n\nStrazzi-Sahyon HB, Passos Rocha E, Gonçalves Assunção W, et al.: Influence of Light-Curing Intensity on Color Stability and Microhardness of Composite Resins. Int. J. Periodontics Restorative Dent. 2020; 40(1): 129–134. PubMed Abstract \| Publisher Full Text\n\nPar M, Marovic D, Attin T, et al.: The effect of rapid high-intensity light-curing on micromechanical properties of bulk-fill and conventional resin composites. Sci. Rep. 2020; 10(1): 1–10.\n\nPirmoradian M, Hooshmand T, Jafari-Semnani S, et al.: Degree of conversion and microhardness of bulk-fill dental composites polymerized by LED and QTH light curing units. J. Oral Biosci. 2020; 62(1): 107–113. PubMed Abstract \| Publisher Full Text\n\nScotti N, Baldi A, Vergano EA, et al.: Light-Curing Units. Modern Operative Dentistry. Springer; 2020; pp. 435–464. Publisher Full Text\n\nLima AF, de Andrade KM , da Cruz Alves LE , et al.: Influence of light source and extended time of curing on microhardness and degree of conversion of different regions of a nanofilled composite resin. Eur. J. Dent. 2012; 06(2): 153–157. Publisher Full Text\n\nOmidi BR, Gosili A, Jaber-Ansari M, et al.: Intensity output and effectiveness of light curing units in dental offices. J. Clin. Exp. Dent. 2018; 10(6): e555–e560. Publisher Full Text\n\nPaolone G: Direct composite restorations in anterior teeth. Managing symmetry in central incisors. Int. J. Esthet. Dent. 2014; 9(1): 12–25.\n\nKorkut B: Smile makeover with direct composite veneers: A two-year follow-up report. J. Dent. Res. Dent. Clin. Dent. Prospects. 2018; 12(2): 146–151. Publisher Full Text\n\nAmmannato R, Ferraris F, Allegri M: The “index cutback technique”: A three-dimensional guided layering approach in direct class IV composite restorations. Int. J. Esthet. Dent. 2017; 12: 450–466.\n\nEspíndola-Castro LF, de Melo Monteiro GQ , Ortigoza LS, et al.: Multidisciplinary Approach to Smile Restoration: Gingivoplasty, Tooth Bleaching, and Dental Re-anatomization. Compend. Contin. Educ. Dent (Jamesburg, NJ: 1995). 2019; 40(9): 590–599.\n\nArdu S, Krejci I: Biomimetic direct composite stratification technique for the restoration of anterior teeth. Quintessence Int. 2006; 37(3): 167–174. PubMed Abstract\n\nCarneiro P, Ramos T, de Azevedo C , et al.: Influence of finishing and polishing techniques and abrasion on transmittance and roughness of composite resins. Oper. Dent. 2016; 41(6): 634–641. PubMed Abstract \| Publisher Full Text\n\nJang J, Kim H, Shin S, et al.: Clinical effectiveness of different polishing systems and self-etch adhesives in class V composite resin restorations: two-year randomized controlled clinical trial. Oper. Dent. 2017; 42(1): 19–29. Publisher Full Text\n\nDaud A, Gray G, Lynch CD, et al.: A randomised controlled study on the use of finishing and polishing systems on different resin composites using 3D contact optical profilometry and scanning electron microscopy. J. Dent. 2018; 71: 25–30. Publisher Full Text\n\nBabina K, Polyakova M, Sokhova I, et al.: The Effect of Finishing and Polishing Sequences on The Surface Roughness of Three Different Nanocomposites and Composite/Enamel and Composite/Cementum Interfaces. Nanomaterials (Basel). 2020; 10(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDemarco FF, Collares K, Coelho-de-Souza FH, et al.: Anterior composite restorations: A systematic review on long-term survival and reasons for failure. Dent. Mater. 2015; 31(10): 1214–1224. Publisher Full Text\n\nElgezawi M, Hassan K, Alagl A, et al.: Complexity of comprehensive care treatments in undergraduate dental programs: The benefits of observing and assisting experienced faculty members. Saudi Dent. J. 2017; 29(4): 161–166. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "186404", "date": "28 Jul 2023", "name": "Hatem M. El-Damanhoury", "expertise": [ "Reviewer Expertise Restorative Dentistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-written manuscript, that investigated the awareness of general dental practitioners in Saudi Arabia about resin composite restorations in anterior teeth using a cross-sectional survey study design. The sample size and methodology is appropriate, the statistical analysis is suitable for the data type and the presentation of the results is adequate to draw conclusions. A few points have to be addressed by the authors before accepting this manuscript for indexing:\nMore details of the sample size calculation method are required.\n\nFor the validity and reliability of the questions, it is recommended to run an inter-examiner agreement test.\n\nPlease explain why the Chi-square test was used and whether the assumption of the test was met or not.\n\nPlease delete the sentence \"Minitab statistical software is an example of free online software that can be used to perform similar statistical analysis\", as it is not needed, and adds nothing to the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10206", "date": "06 Oct 2023", "name": "Moataz Elgezawi", "role": "Author Response", "response": "The Authors would like to thank both reviewers, Dr. Nesrine A. Elsahn and Dr. Hatem M. El.Damanhoury for the time they gave to provide their constructive feedback and comments to improve the quality of the article. The authors have tackled each comment and respectively responded to. All changes in the manuscript were red highlighted. Moreover, below is a detailed response consistently progressing with both reviewers. Kindly refer to our response below: Reviewer 2, Dr Nesrine Alsahn Comment #1: The highlighted parts in the following paragraphs contain information that was stated twice. The authors have to revise and rephrase these parts to avoid repetition. \"This cross-sectional study was conducted utilizing an online uploaded survey questionnaire using Google’s free online survey platform. E-mail invitations stated clearly that participation was anonymous and voluntary and that participants were free to leave the survey or to skip any questions. The targeted population of 500 resulted in a calculated sample size of 218 dentists. Calculations were performed at the 95% confidence level using a free online sample size calculator.\" Response: \"During the research, participants were invited to join the survey through emails that clarified the objectives of the study and included necessary information and that joining the survey is anonymous and voluntary. The invite explained that by completing the survey, they were consenting to participate in the study. Participants were informed that they could leave the study at any step if they did not wish to continue, and that the data collected would be used for research purposes.\" The paragraphs were revised and rewritten. (See the word doc attached) The first highlighted sentence was deleted, and the second sentence was modified. Comment #2: Why was the Nanofilled composite not listed as an option to restore different classes of anterior tooth defects? Response: Because of the close similarity of clinical performance of nanofilled and nanohybrid composites with no superiority over nanohybrid composites regarding surface polishability , wear and gloss stability indicated in a recent systematic review and meta analysis and following a similar pervious survey conducted in Brazil, nanofilled composites were not listed in our study as a separate option in our questionnaire. Moreover, we have used the categories of composite materials usually provided by suppliers to our selected governmental hospitals included in the study (added to the Discussion section) References: Nanofilled/nanohybrid and hybrid resin-based composite in patients with direct restorations in posterior teeth: A systematic review and meta-analysis Anterior composite restorations in clinical practice: Findings from a survey with general dental practitioners Comment #3: In Domain 2: There is no table number or legend/ header for the information related to questions 5 and 6. If the authors decided to present this part in a table, a table number must be given and all the changes required in the following tables’ numbering and in the text must be done. The sample size (n=250) has to be written before the table for questions 5 and 6, as it was done for the other tables, not at the end of the questions. The authors didn’t include answer options, participants’ responses, or relative responses in percentages for question #6. Although this information was presented in Figure 2, the authors have either to present domain 2 in figures only or to use figures and a table, provided that the table is written following the same format used for the other tables. Response: -Domains 5 & 6 were combined and presented using table 3 -Rest of tables numbers were adjusted accordingly. - Done - Done table 3. Comment #4: In question 8, what does option build-up mean or represent? Was it clarified for the participants? Response: In our questionnaire, the option ‘build up’ was employed to describe a large resin composite restoration used for restoring grossly mutilated anterior teeth including incisor teeth with incisal edge fracture involving more than 1/3 of the coronal tooth structure or with bilateral incisal angle involvements extending at least to the middle third of the crown or anterior teeth with bilateral complex class III cavities involving greater than 1/3 of coronal tooth structure. This was clearly stated in the online link at the beginning of the questionnaire. (added to discussion section) Comment #5: In question 10, the authors mentioned in the discussion that only 45% of participants use total-etch adhesives, while 31% and 23% used self-etching and selective etching technology, respectively. The authors used the correct terminology for the adhesive strategies in the discussion. Meanwhile, in Table 3,question 10, the authors used a different terminology for the adhesive types (self-adhesive, selective self-etching, total-etching). The answer options for question 10 need to be replaced by the correct terminology for adhesive strategies. Otherwise, the authors need to clarify in the text the adhesive strategies' terms they used. Response: Adjusted Comment# 6: Why the statistical analysis was done only for domains 3 and 4? Response: In the current study, all questionnaire domains were subjects of descriptive statistics using percentages and histograms. Furthermore, domains 3 and 4 were subjects of chi square testing since they are testing the actual clinical practice and individual practice preference. In our previous questionnaire study testing that tested the practice of resin composite light curing using similar population, demographic factors of age, gender, location, and duration of practice did not have a significant influence when analyzed using chi square testing. Comment #7: The authors used reference 65 to describe the multiple-layering approach. Please add a recent reference that introduces the latest techniques and composite materials used in the multiple-layering approach. Response: Done (added: Ajay Singh Rao, Shreya Bhor, Nimisha Shah, Naveen Chhabra: Comparative evaluation of aesthetic outcome of direct polychromatic composite layering and the \"index cut-back technique\" for restoring class IV defects using a newly patented simulated 3D printed mould: An in vitro study. J Oral Biol Craniofac Res. 2022;12(5):552-556. doi: 10.1016/j.jobcr.2022.07.007.) Reviewer 1 Dr. Hatem El-Damanhouri: Comment #1- More details of the sample size calculation method are required. Response: In the current study, the targeted population, selected hospitals, and sample size calculation followed the same methodology detailed in our previously published studies. Toward optimum light curing of Resin Composite Restorations: A survey on Current Awareness and Practice among General Dentists in Saudi Arabia Toward a Clinically Reliable Class II Resin Composite Restoration: A Cross-Sectional Study into the Current Clinical Practice among Dentists in Saudi Arabia Comment #2- For the validity and reliability of the questions, it is recommended to run an inter-examiner agreement test. Response: The literature has listed experts opinion as a satisfactory tool to pretest the reliability and validity of a survey questionnaire. “ An Examination of Questionnaire Evaluation by Expert Reviewers Kristen Olson” Olson reported that despite the efforts spent to select reviewers of same background skills, disagreements among raters were found which did not adversely affect the outcome. In our study and following our previously published surveys, we did not perform inter raters agreement testing since all our invited experts evaluated all questions as highly relevant or relevant. References: An Examination of Questionnaire Evaluation by Expert Reviewers, Kristen Olson A cross-sectional multicenter survey on the future of dental education in the era of COVID-19: Alternatives and implications Toward optimum light curing of Resin Composite Restorations: A survey on Current Awareness and Practice among General Dentists in Saudi Arabia Comment #3-Please explain why the Chi-square test was used and whether the assumption of the test was met or not. Response: Following many previous similar survey studies , the current study used Descriptive statistics in the form of percentages and histograms to summarise the survey qualitative data. Moreover, Chi square test using received frequencies was employed to analyze the study qualitative data at a level of significance (P <0.05) In the present study, all Chi square test assumptions listed by Mary L. McHugh biomedica, 2013 were met. References: Puja C. Yavagal, Hitashi Singla,Prevalence of dental caries based on personality types of 35–44 years old residents in Davangere city, Journal of Oral Biology and Craniofacial Research,Volume 7, Issue 1,2017, Pages 32-35. Aksha Sharen, Hima Sandeep: survey on indirect tooth coloured restorations among dental students and specialist. Journal of Pharmaceutical Negative Results. 2022, 13 (3). Singh RP, Gopalakrishnapillai AC, Bhat N, Pawar A. Perception of Dental and Medical Teaching Faculty Regarding Mobile Dental Application. J Pharm Bioallied Sci. 2019 Nov;11(Suppl 3):S530-S539. doi: 10.4103/jpbs.JPBS_261_18. PMID: 31920270; PMCID: PMC6896578. Comment #4-Please delete the sentence \"Minitab statistical software is an example of free online software that can be used to perform similar statistical analysis\", as it is not needed, and adds nothing to the manuscript. Response: Deleted" } ] }, { "id": "186405", "date": "10 Aug 2023", "name": "Nesrine A. Elsahn", "expertise": [ "Reviewer Expertise Adhesive Dentistry", "Restorative Dentistry", "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\nThe article presents a comprehensive and well-executed study that investigates the awareness of dental practitioners in Saudi Arabia about resin composite restorations in anterior teeth. The authors have clearly outlined the research problem, framed it within the relevant literature and the methodology employed is appropriate for addressing the research questions posed. Moreover, the study provided evidence-based recommendations to improve anterior restorations in Saudi Arabia. However, the authors need to address the following points and answer the following questions.\n\nComment #1: The highlighted parts in the following paragraphs contain information that was stated twice. The authors have to revise and rephrase these parts to avoid repetition.\n\"This cross-sectional study was conducted utilizing an online uploaded survey questionnaire using Google’s free online survey platform. E-mail invitations stated clearly that participation was anonymous and voluntary and that participants were free to leave the survey or to skip any questions. The targeted population of 500 resulted in a calculated sample size of 218 dentists. Calculations were performed at the 95% confidence level using a free online sample size calculator.\"\n\"During the research, participants were invited to join the survey through emails that clarified the objectives of the study and included necessary information and that joining the survey is anonymous and voluntary. The invite explained that by completing the survey, they were consenting to participate in the study. Participants were informed that they could leave the study at any step if they did not wish to continue, and that the data collected would be used for research purposes.\"\nComment #2: Why was the Nanofilled composite not listed as an option to restore different classes of anterior tooth defects?\nComment #3: In Domain 2:\nThere is no table number or legend/ header for the information related to questions 5 and 6. If the authors decided to present this part in a table, a table number must be given and all the changes required in the following tables’ numbering and in the text must be done.\n\nThe sample size (n=250) has to be written before the table for questions 5 and 6, as it was done for the other tables, not at the end of the questions.\n\nThe authors didn’t include answer options, participants’ responses, or relative responses in percentages for question #6. Although this information was presented in Figure 2, the authors have either to present domain 2 in figures only or to use figures and a table, provided that the table is written following the same format used for the other tables.\nComment #4: In question 8, what does option build-up mean or represent? Was it clarified for the participants?\nComment #5: In question 10, the authors mentioned in the discussion that only 45% of participants use total-etch adhesives, while 31% and 23% used self-etching and selective etching technology, respectively.\nThe authors used the correct terminology for the adhesive strategies in the discussion. Meanwhile, in Table 3 question 10, the authors used a different terminology for the adhesive types (self-adhesive, selective self-etching, total-etching). The answer options for question 10 need to be replaced by the correct terminology for adhesive strategies. Otherwise, the authors need to clarify in the text the adhesive strategies' terms they used.\nComment# 6: Why the statistical analysis was done only for domains 3 and 4?\nComment #7: The authors used reference 65 to describe the multiple-layering approach. Please add a recent reference that introduces the latest techniques and composite materials used in the multiple-layering approach.\n\nIs the work 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": "10206", "date": "06 Oct 2023", "name": "Moataz Elgezawi", "role": "Author Response", "response": "The Authors would like to thank both reviewers, Dr. Nesrine A. Elsahn and Dr. Hatem M. El.Damanhoury for the time they gave to provide their constructive feedback and comments to improve the quality of the article. The authors have tackled each comment and respectively responded to. All changes in the manuscript were red highlighted. Moreover, below is a detailed response consistently progressing with both reviewers. Kindly refer to our response below: Reviewer 2, Dr Nesrine Alsahn Comment #1: The highlighted parts in the following paragraphs contain information that was stated twice. The authors have to revise and rephrase these parts to avoid repetition. \"This cross-sectional study was conducted utilizing an online uploaded survey questionnaire using Google’s free online survey platform. E-mail invitations stated clearly that participation was anonymous and voluntary and that participants were free to leave the survey or to skip any questions. The targeted population of 500 resulted in a calculated sample size of 218 dentists. Calculations were performed at the 95% confidence level using a free online sample size calculator.\" Response: \"During the research, participants were invited to join the survey through emails that clarified the objectives of the study and included necessary information and that joining the survey is anonymous and voluntary. The invite explained that by completing the survey, they were consenting to participate in the study. Participants were informed that they could leave the study at any step if they did not wish to continue, and that the data collected would be used for research purposes.\" The paragraphs were revised and rewritten. (See the word doc attached) The first highlighted sentence was deleted, and the second sentence was modified. Comment #2: Why was the Nanofilled composite not listed as an option to restore different classes of anterior tooth defects? Response: Because of the close similarity of clinical performance of nanofilled and nanohybrid composites with no superiority over nanohybrid composites regarding surface polishability , wear and gloss stability indicated in a recent systematic review and meta analysis and following a similar pervious survey conducted in Brazil, nanofilled composites were not listed in our study as a separate option in our questionnaire. Moreover, we have used the categories of composite materials usually provided by suppliers to our selected governmental hospitals included in the study (added to the Discussion section) References: Nanofilled/nanohybrid and hybrid resin-based composite in patients with direct restorations in posterior teeth: A systematic review and meta-analysis Anterior composite restorations in clinical practice: Findings from a survey with general dental practitioners Comment #3: In Domain 2: There is no table number or legend/ header for the information related to questions 5 and 6. If the authors decided to present this part in a table, a table number must be given and all the changes required in the following tables’ numbering and in the text must be done. The sample size (n=250) has to be written before the table for questions 5 and 6, as it was done for the other tables, not at the end of the questions. The authors didn’t include answer options, participants’ responses, or relative responses in percentages for question #6. Although this information was presented in Figure 2, the authors have either to present domain 2 in figures only or to use figures and a table, provided that the table is written following the same format used for the other tables. Response: -Domains 5 & 6 were combined and presented using table 3 -Rest of tables numbers were adjusted accordingly. - Done - Done table 3. Comment #4: In question 8, what does option build-up mean or represent? Was it clarified for the participants? Response: In our questionnaire, the option ‘build up’ was employed to describe a large resin composite restoration used for restoring grossly mutilated anterior teeth including incisor teeth with incisal edge fracture involving more than 1/3 of the coronal tooth structure or with bilateral incisal angle involvements extending at least to the middle third of the crown or anterior teeth with bilateral complex class III cavities involving greater than 1/3 of coronal tooth structure. This was clearly stated in the online link at the beginning of the questionnaire. (added to discussion section) Comment #5: In question 10, the authors mentioned in the discussion that only 45% of participants use total-etch adhesives, while 31% and 23% used self-etching and selective etching technology, respectively. The authors used the correct terminology for the adhesive strategies in the discussion. Meanwhile, in Table 3,question 10, the authors used a different terminology for the adhesive types (self-adhesive, selective self-etching, total-etching). The answer options for question 10 need to be replaced by the correct terminology for adhesive strategies. Otherwise, the authors need to clarify in the text the adhesive strategies' terms they used. Response: Adjusted Comment# 6: Why the statistical analysis was done only for domains 3 and 4? Response: In the current study, all questionnaire domains were subjects of descriptive statistics using percentages and histograms. Furthermore, domains 3 and 4 were subjects of chi square testing since they are testing the actual clinical practice and individual practice preference. In our previous questionnaire study testing that tested the practice of resin composite light curing using similar population, demographic factors of age, gender, location, and duration of practice did not have a significant influence when analyzed using chi square testing. Comment #7: The authors used reference 65 to describe the multiple-layering approach. Please add a recent reference that introduces the latest techniques and composite materials used in the multiple-layering approach. Response: Done (added: Ajay Singh Rao, Shreya Bhor, Nimisha Shah, Naveen Chhabra: Comparative evaluation of aesthetic outcome of direct polychromatic composite layering and the \"index cut-back technique\" for restoring class IV defects using a newly patented simulated 3D printed mould: An in vitro study. J Oral Biol Craniofac Res. 2022;12(5):552-556. doi: 10.1016/j.jobcr.2022.07.007.) Reviewer 1 Dr. Hatem El-Damanhouri: Comment #1- More details of the sample size calculation method are required. Response: In the current study, the targeted population, selected hospitals, and sample size calculation followed the same methodology detailed in our previously published studies. Toward optimum light curing of Resin Composite Restorations: A survey on Current Awareness and Practice among General Dentists in Saudi Arabia Toward a Clinically Reliable Class II Resin Composite Restoration: A Cross-Sectional Study into the Current Clinical Practice among Dentists in Saudi Arabia Comment #2- For the validity and reliability of the questions, it is recommended to run an inter-examiner agreement test. Response: The literature has listed experts opinion as a satisfactory tool to pretest the reliability and validity of a survey questionnaire. “ An Examination of Questionnaire Evaluation by Expert Reviewers Kristen Olson” Olson reported that despite the efforts spent to select reviewers of same background skills, disagreements among raters were found which did not adversely affect the outcome. In our study and following our previously published surveys, we did not perform inter raters agreement testing since all our invited experts evaluated all questions as highly relevant or relevant. References: An Examination of Questionnaire Evaluation by Expert Reviewers, Kristen Olson A cross-sectional multicenter survey on the future of dental education in the era of COVID-19: Alternatives and implications Toward optimum light curing of Resin Composite Restorations: A survey on Current Awareness and Practice among General Dentists in Saudi Arabia Comment #3-Please explain why the Chi-square test was used and whether the assumption of the test was met or not. Response: Following many previous similar survey studies , the current study used Descriptive statistics in the form of percentages and histograms to summarise the survey qualitative data. Moreover, Chi square test using received frequencies was employed to analyze the study qualitative data at a level of significance (P <0.05) In the present study, all Chi square test assumptions listed by Mary L. McHugh biomedica, 2013 were met. References: Puja C. Yavagal, Hitashi Singla,Prevalence of dental caries based on personality types of 35–44 years old residents in Davangere city, Journal of Oral Biology and Craniofacial Research,Volume 7, Issue 1,2017, Pages 32-35. Aksha Sharen, Hima Sandeep: survey on indirect tooth coloured restorations among dental students and specialist. Journal of Pharmaceutical Negative Results. 2022, 13 (3). Singh RP, Gopalakrishnapillai AC, Bhat N, Pawar A. Perception of Dental and Medical Teaching Faculty Regarding Mobile Dental Application. J Pharm Bioallied Sci. 2019 Nov;11(Suppl 3):S530-S539. doi: 10.4103/jpbs.JPBS_261_18. PMID: 31920270; PMCID: PMC6896578. Comment #4-Please delete the sentence \"Minitab statistical software is an example of free online software that can be used to perform similar statistical analysis\", as it is not needed, and adds nothing to the manuscript. Response: Deleted" } ] } ]	1	https://f1000research.com/articles/12-359
https://f1000research.com/articles/11-1277/v2	20 Sep 23	{ "type": "Research Article", "title": "Development and thermophysical analysis of binary eutectics phase change materials for solar drying application", "authors": [ "Saurabh Pandey", "Abhishek Anand", "Dharam Buddhi", "Atul Sharma", "Abhishek Anand", "Dharam Buddhi", "Atul Sharma" ], "abstract": "Background: In the past 30–40 years, conflicts over limited conventional energy sources and the negative climate change caused by them have attracted researchers and analysts to new, clean, and green energy technologies. Thereby reducing the consumption of conventional fuel and the negative impact on the climate. The production of alternative energy in the form of thermal energy storage using phase change materials (PCMs) is one of the techniques that not only reduces the gap between the supply and demand of energy but also increases the stability of the energy supply. The tendency of PCMs to melt and solidify over a wide temperature range makes them more attractive for use in many applications. The effective and efficient storage of solar energy by PCM has the potential to significantly advance the use of renewable energy. Methods: Organic non-paraffin compound beeswax (BW) mixed with other non-paraffin compounds stearic acid (SA), Palmitic acid (PA), Myristic acid (MA), and Lauric acid (LA) in different compositions with the help of magnetic stirrer at 50–60°C for 3–4 hours to prepare BWSA, BWPA, BWMA, and BWLA eutectic PCM. Results: Prepared eutectics melt and solidify in the temperature range 36–56°C and with latent heat in the range of 155–211 kJ/Kg. Conclusions: Due to suitable temperature and good latent heat storage range, it is a good choice as thermal energy storage, for solar drying applications.", "keywords": [ "Eutectic", "Phase change materials", "Non-paraffins", "Thermal energy storage", "Solar dryer" ], "content": "Introduction\n\nModern civilization has grown and developed mostly as a result of energy, which has always been important from the perspective of the development of the global economy. However, along with increased efficiency in the energy sector, significant barriers must also be overcome, including the creation of conventional energy sources, reducing the use of fossil-based fuels, as well as reducing greenhouse gas emissions i.e., CO2 (carbon dioxide), SOX (oxides of sulfur), CH4 (methane), NOX (nitrogen oxides).1 Researchers around the world have been looking for new technologies in the last 30–40 years that will reduce the use of fossil fuels and, lessen the detrimental effects that energy production has on the climate and environment. A practical way of using alternative energy is through energy storage, in addition to conserving energy, energy storage also improves the stability and quality of the energy supply and reduces the variation between supply and demand. One of the popular techniques of energy storage is thermal energy storage (TES), which can be classified as2: i) Latent heat storage and ii) sensible heat storage.\n\nLatent heat storage is reliant on heat absorption or release phenomenon, during the phase transition of material from solid to liquid or liquid to gas or vice versa. These materials involved in phase transition are known as phase change materials (PCMs). Whereas in sensible heat storage, energy is stored by increasing the temperature of liquid or solid. In the charging and discharging process, a sensible heat storage system makes use of the material's heat capacity and temperature variation. Stored heat in materials depends on the amount of storage material, the specific heat of the medium, and the temperature change.3\n\n\nPhase change materials (PCMs)\n\nDue to applied thermal energy, some materials change their state by storing some amount of latent heat during the state/phase transition, such materials are known as PCMs. During the transition from solid to liquid or from liquid to solid, thermal energy is transferred. These solid-liquid PCMs function initially like traditional storage materials, as they absorb heat, their temperature increases, but release heat at a practically constant temperature, in contrast to conventional (sensible) storage materials.4 PCMs use chemical bonds for energy storage and release. Although in a sense every material is a PCM, the materials are only categorized as PCM if they have some characteristics of energy storage. High thermal conductivity and significant latent heat should be present in phase transition materials used for energy storage. Additionally, the materials melting points should be within a practical application range; materials should melt consistently with the least amount of supercooling and should be chemically stable. The materials should not be toxic, or chemically corrosive, and should be economical for practical applications.5 PCMs are often divided into three groups i.e., organic, inorganic, and eutectics, which is the combination of two or more materials.\n\nThis group of PCMs is divided into salt hydrates and metallics. Due to their low cost, better thermal conductivity, cost-effectiveness, and minor volumetric changes for storage, salt hydrates are very appealing materials for phase change energy storage. Salt hydrates are a typical crystalline solid that are a mixture of water (H2O) and inorganic salts and is written as AB.nH2O. Salt hydrates can change from a solid to a liquid state by dehydrating or hydrating the salt, even though this process thermodynamically mimics melting or freezing. Generally, a salt hydrate melts into water, and salt hydrate6 i.e.,\n\nAnd in anhydrous form\n\nMost salt hydrates have the problem of incongruent melting. The hydrate crystals disintegrate into anhydrous salt and water, or a lower hydrate and water, at the melting point. The fact that the water released during crystallization is insufficient to completely dissolve all of the solid phases present causes incongruent melting, which is one issue with the majority of salt hydrates. The lower hydrate (or anhydrous salt), due to the density difference, descends to the bottom of the container. Many salt hydrates also have weak nucleating capabilities, which causes the liquid to supercool before crystallization starts. The addition of a nucleating agent, which supplies the nuclei on which crystal formation is started, is one approach to solving this issue. Another option is to keep some crystals in a small, cold area so they can act as nuclei. Some of the salt hydrates with their latent heat of fusion and melting point are listed in Table 1.\n\nMost of the metal eutectics and low melting metals come under the inorganic metallic PCM category, but due to their heavy weight, metallics have not been given substantial consideration for PCMs. They are reasonable candidates when the volume is taken into account due to the high latent heat of fusion output per unit volume. The employment of metallics brings forth a variety of peculiar technical issues. The strong heat conductivity of the metallics distinguishes them significantly from other PCMs.8\n\nOrganic PCMs are divided into the paraffin and non-paraffin subgroups. Without any loss in their latent heat of fusion and phase segregation, these materials have the property of congruent melting i.e., repeatedly melting and freezing. It also exhibits the property of non-corrosiveness and self-nucleation.\n\nParaffin is mostly made up of an alkanes chain (CH3–CH2–CH3…), and the crystallization of these chains generates a significant amount of latent heat. In general, paraffin is stable below 500°C, and there are no significant changes in the volume on their melting; also they have low vapor pressure while melting.9 The melt-freeze cycle of paraffin is often relatively long. With more carbon atoms present, alkane has a higher melting point. The fact that paraffin is accessible in a wide range of temperatures is the primary factor in its qualification as an energy storage material. Along with other beneficial traits like consistent melting and good nucleating qualities, paraffin has several other advantages.10 They have a few unfavorable characteristics, including low thermal conductivity, incompatibility with plastic containers, and considerable flammability. By slightly modifying the wax and the storage unit, all these negative effects can be somewhat removed. Some of the most desirable and moderate desirable paraffin are shown in Table 2.\n\nOf all phase transition materials, non-paraffin organics are the most prevalent and have the widest range of features.11 Unlike paraffin, which has extremely comparable properties, each of these materials will have unique characteristics. This is the broadest group of potential PCMs. After conducting a thorough analysis of organic materials, Buddhi and Sawhney found several esters, fatty acids, alcohols, and glycols that might be useful as energy storage materials.12 Fatty acids and other non-paraffin organic compounds are other subgroups of these organic molecules. Due to their flammability, fatty acids and non-paraffin organic materials cannot be subjected to extreme heat, flames, or oxidizing agents. Compared to paraffin, fatty acids have high heat of fusion and have repeatable behavior in their melting and freezing. Fatty acids also freeze without supercooling. All fatty acids are described by the chemical formula CH3(CH2)2n.COOH. Their main disadvantage is that they are 2–2.5 times more expensive than technical-grade paraffin. They are also barely corrosive. Some of the non-paraffin compounds are listed in Table 3 with their melting point and latent heat of fusion.\n\nA minimal-melting composition of at least two or more materials is known as a eutectic, and during crystallization, each of these materials melts and freezes concurrently to form a mixture of the material crystals.13 Because they freeze to a close-knit combination of crystals, eutectic materials rarely melt or freeze without the components segregating. Both components simultaneously liquefy when heated, making separation unlikely. Since they are minimum melting, some segregated PCM compositions have been wrongly referred to as eutectics. But it would be more accurate to refer to them as peritectic as they undergo a peritectic reaction during phase change. Some of the compositions of the eutectics are shown in Table 4.11\n\nNow, if there is a discussion on the merits and demerits of the three types of PCMs mentioned above (inorganic, organic, and eutectic), there are many discrepancies, some of which are listed in Table 5.\n\nPCMs, Phase change materials.\n\n\n\n• Ease of availability\n\n• Economically feasible\n\n• Non-flammable\n\n• High thermal conductivity\n\n• High latent heat of fusion\n\n\n\n• Supercooling\n\n• Corrosive in nature\n\n\n\n• Wide temperature range\n\n• Chemically stable\n\n• Non-reactive\n\n• No supercooling\n\n• Non-hazardous\n\n\n\n• Flammable\n\n• Large volume change\n\n• Costly except technical grade paraffin\n\n• Low thermal conductivity\n\n\n\n• Sharp melting point\n\n• Large volumetric storage density\n\nOther than the listed eutectic PCMs, many more eutectic mixtures were prepared with the good latent heat of fusion and melt-freeze cycle. In this series, beeswax-Stearic (BWSA), beeswax-Palmitic (BWPA), beeswax-Myristic (BWMA), and beeswax-Lauric (BWLA) are prepared and tested. These four prepared eutectic mixtures are a composition of organic non-paraffin PCMs.\n\n\nMethods\n\nOrganic non-paraffin compound beeswax (BW) in different compositions mixed with another organic non-paraffin compound, Palmitic (PA), Myristic (MA), and Lauric (LA) acid at a temperature range of 50–60°C with the help of a magnetic stirrer at 200 rpm for 3–4 hrs followed by sonication for 15 minutes using Sonics Vibracell probe sonicator and get eutectic PCMs. Organic non-paraffin compounds are mixed in different compositions to get desired eutectics. A total of 20 wt % of BW mixed was with 80 wt % of SA to prepare BWSA28. Similarly, 40, 10, and 10 wt % of BW were mixed with 60, 90, and 90 wt % of PA, MA, and LA, respectively, to form BWPA46, BWMA19, and BWLA19 eutectic PCMs. Each sample is prepared in a quantity of 10 gm and acids SA, PA, MA, and LA used here were sourced from MOLYCHEM with product codes 19060, 16705, 16392, and 12520, respectively. Whereas BW was sourced from the center of Excellence on Honey Bees (Nalanda College of Horticulture, Nalanda, Bihar).\n\nThe PerkinElmer DSC 4000 equipment was used for the differential scanning calorimetry (DSC) study. In order to measure this little amount (mg) of the samples, an analytical digital weighing machine with a precision of 0.00001 g was used. The weighted sample between 10 to 15 mg was filled into an aluminum pan, and the DSC procedure was carried out in a nitrogen environment at a flux of 20 ml/min at a heating rate of 2°C/min. The accuracy of the DSC device was ±2% for enthalpy measurement and ± 0.1°C for temperature measurement. The reference pan and the sample pan are heated at the same rate during the DSC analysis. The latent heat of fusion, peak melting temperature, and other thermophysical parameters was measured. The top point of the curve offers the peak melting temperature, while the area that comes under the curve explicated latent heat of fusion and crystallization, and the tangent of the highest slope explicated the onset melting point.\n\n\nResults\n\nEutectic PCM molecules start to oscillate when heated, this oscillation causes the atoms to move farther apart, occupying more space and resulting in an increase in volume. Further raising the temperature caused molecules to move more quickly due to an increase in kinetic energy, quick movement of molecules disrupting the supramolecular link between the individual atoms. The ordered crystal structure transforms into a randomly oriented liquid state as the temperature rises to a specific critical point, DSC is used to measure this critical point of temperature known as phase transition temperature. Therefore, using DSC analysis, the thermal energy storage properties of BWSA28, BWPA46, BWMA19, and BWLA19 were determined. The DSC curves for BWSA28, BWPA46, BWMA19, and BWLA19 are shown in Figure 1. The DSC curves for BWSA28, BWPA46, BWMA19, and BWLA19 displayed comparable patterns and nearly equal forms. For BWSA28, BWPA46, BWMA19, and BWLA19, the onset melting points were 49.59°C, 48.85°C, 50.91°C, and 41.02°C, respectively, which are listed in Table 6. Similarly, the peak melting temperatures for these materials were 55.17°C, 56.85°C, 55.22°C, and 44.96°C, respectively. Onset and freezing temperatures obtained from BWSA28, BWPA46, BWMA19, and BWLA19 were 50.79°C, 50.22°C, 45.44°C, 36.77°C, and 48.93°C, 49.59°C, 45.34°C, 36.08°C, respectively. In the DSC plot, the area under the curve provides latent heat of fusion and latent heat of crystallization as shown in Figure 1 and marked with the arrow. So, the obtained latent heat of fusion and latent heat of crystallization for BWSA28, BWPA46, BWMA19, and BWLA19 were 174.52 kJ/kg, 166.03 kJ/kg, 192.85 kJ/kg, 195.73 kJ/kg, and 177.94 kJ/kg, 155.55 kJ/kg, 211.52 kJ/kg, and 201.04 kJ/kg, respectively.\n\nDSC, differential scanning calorimetry; BWSA, Beeswax-Stearic; BWPA, Beeswax-Palmitic; BWMA, Beeswax-Myristic; BWLA, Beeswax-Lauric.\n\nPCMs, Phase change materials; BWSA, Beeswax-Stearic; BWPA, Beeswax-Palmitic; BWMA, Beeswax-Myristic; BWLA, Beeswax-Lauric.\n\n\nDiscussion\n\nFoods and agricultural products can be stored using drying techniques, which is a better technique for reducing the moisture content of products that will also not reduce their quality. Fruits and vegetables are dried at an operating temperature of 40–60°C.15 Where humidity level and operating temperature can be used to regulate the moisture content and product quality (such as nutritional characteristics).16 The food and agricultural industries have focused their attention on the solar drying technique as it is an inexpensive way to preserve food and agricultural products. Additionally, it has significant ecological advantages.17 The prepared eutectic PCMs had melting and freezing temperatures in the range of 36°C to 56°C, which is very much suitable for the solar drying application.\n\n\nConclusions\n\nDue to its capability to enhance system performance, energy storage is particularly alluring to a wide range of parties. Technology development is more efficient and practical when excess energy is stored for later use rather than being replaced by new power plants. The latent heat of the phase change is associated with prepared eutectic PCMs and has a crucial influence on their ability to store greater amounts of energy. A target-oriented settling temperature is also supported by PCMs due to the fixed phase change temperature. This paper deals with the development of eutectics PCM. The foremost advantages of these prepared eutectic PCMs were their low cost and eco-friendly nature. DSC analysis of this prepared eutectics BWSA28, BWPA46, BWMA19, and BWLA19 showed good thermal energy storage capacity, and it lies between 155–211 kJ/Kg. These eutectics have a temperature range between 36–56°C.", "appendix": "Data availability\n\nFigshare: Dataset, https://doi.org/10.6084/m9.figshare.23496929.v1. 18\n\nThis project contains the following underlying data:\n\n• BWSA 28.xlsx\n\n• BWPA(46).xlsx\n\n• BWLA(19).xlsx\n\n• BWMA(19).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\nAnand A, Shukla A, Sharma A: Recapitulation on latent heat hybrid buildings. Int. J. Energy Res. 2020; 44(3): 1370–1407. Publisher Full Text\n\nNazir H, Batool M, Bolivar Osorio FJ, et al.: Recent developments in phase change materials for energy storage applications: A review. Int. J. Heat Mass Transf. 2019; 129: 491–523. Publisher Full Text\n\nFarid MM, Khudhair AM, Razack SAK, et al.: A review on phase change energy storage: Materials and applications. Energy Convers. Manag. 2004; 45(9–10): 1597–1615. Publisher Full Text\n\nNkwetta DN, Haghighat F: Thermal energy storage with phase change material - A state-of-the art review. Sustain. Cities Soc. 2014; 10: 87–100. Publisher Full Text\n\nPielichowska K, Pielichowski K: Phase change materials for thermal energy storage. Prog. Mater. Sci. 2014; 65: 67–123. Publisher Full Text\n\nXie N, Huang Z, Luo Z, et al.: Inorganic salt hydrate for thermal energy storage. Appl. Sci. 2017; 7(12). Publisher Full Text\n\nPurohit BK, Sistla VS: Inorganic salt hydrate for thermal energy storage application: A review. Energy Storage. 2021; 3(2): 1–26.\n\nGonzalez-Nino D, Boteler LM, Ibitayo D, et al.: Experimental evaluation of metallic phase change materials for thermal transient mitigation. Int. J. Heat Mass Transf. 2018; 116: 512–519. Publisher Full Text\n\nChang Z, Wang K, Wu X, et al.: Review on the preparation and performance of paraffin-based phase change microcapsules for heat storage. J. Energy Storage. 2022; 46: 103840. Publisher Full Text\n\nDash L, Mahanwar PA: A Review on Organic Phase Change Materials and Their Applications. Int. J. Eng. Appl. Sci. Technol. 2021; 5(9): 268–284. Publisher Full Text\n\nSharma A, Tyagi VV, Chen CR, et al.: Review on thermal energy storage with phase change materials and applications. Renew. Sust. Energ. Rev. 2009; 13: 318–345. Publisher Full Text\n\nBuddhi D, Sawhney RL: Proc: Thermal energy storage and energy conversion. Sch. Energy Environ. Stud. Devi Ahilya Univ. Indore, India. 1994.\n\nSingh P, Sharma RK, Ansu AK, et al.: A comprehensive review on development of eutectic organic phase change materials and their composites for low and medium range thermal energy storage applications. Sol. Energy Mater. Sol. Cells. 2021; 223: 110955. Publisher Full Text\n\nQiu J, Huo D, Xia Y: Phase-change materials for controlled release and related applications. Adv. Mater. 2020; 32(25): 2000660. PubMed Abstract \| Publisher Full Text\n\nKant K, Shukla A, Sharma A, et al.: Thermal energy storage based solar drying systems: A review. Innov. Food Sci. Emerg. Technol. 2016; 34: 86–99. Publisher Full Text\n\nShalaby SM, Bek MA, El-Sebaii AA: Solar dryers with PCM as energy storage medium: A review. Renew. Sust. Energ. Rev. 2014; 33: 110–116. Publisher Full Text\n\nGetahun E, Delele MA, Gabbiye N, et al.: Importance of integrated CFD and product quality modeling of solar dryers for fruits and vegetables: A review. Sol. Energy. 2021; 220(March): 88–110. Publisher Full Text\n\nPandey S: DataSet. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "346917", "date": "24 Dec 2024", "name": "Deepika P. Joshi", "expertise": [ "Reviewer Expertise composite", "core-shell nanomaterials", "thermal energy storage" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReviewer Report\n\nThe manuscript presents a study on “Development and thermophysical analysis of binary eutectics phase change materials for solar drying application ” Summary of the work: In the Manuscript,\nNon-paraffin organic PCM beeswax (BW) was mixed in another non organic PCMs Palmitic (PA), Myristic (MA), and Lauric (LA) acid. 20 wt % of BW mixed was with 80 wt % of SA to prepare BWSA28. 40, 10, and 10 wt % of BW were mixed with 60, 90, and 90 wt % of PA, MA, and LA, respectively, to form BWPA46, BWMA19, and BWLA19 eutectic PCMs. DSC analysis was carried out to obtain phase transition properties. The PCMs are good candidate for solar drying applications.\nComments:\nBeewax PCM was mixed in other PCMs in random composition. The author didn’t provide a reason for selecting a particular composition for a particular eutectic. In the DSC analysis only results are provided, Discussion part is missing completely. The entire manuscript contains only a single characterization (DSC). Other characterization should be performed to get an idea about morphological, structural and thermal changes by mixing that may occurring in eutectic PCM. TGA should be performed to get the effect on thermal stability of individual PCM.\nReviewer Report: The article provides details only of single characterization technique (DSC). Therefore, it lacks primary information about the prepared composite. Manuscript does not provide substantial discussion and practical applications of the findings.\n\nTherefore, at its current stage, the manuscript does not provide sufficient information to draw meaningful conclusions. Significant revisions are required to draw impactful conclusions from the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "337593", "date": "30 Dec 2024", "name": "Abuelnuor Abdeen Ali Abuelnuor", "expertise": [ "Reviewer Expertise Phase Change Materials", "Solar Drying" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWas the choice of specific compositions for BW, PA, MA, and LA (e.g., 20:80 for BWSA28) based on prior experimental optimization or theoretical predictions? Could alternative ratios yield better eutectic properties, and were these tested? The onset and peak melting temperatures for the eutectic PCMs are close but show variations. Were these differences attributed to specific interactions between the molecular components, and how do these differences influence the practical applications of these PCMs? The latent heat of fusion and crystallization values for the PCMs vary significantly (e.g., BWSA28 vs. BWMA19). What factors contribute to these differences, and how do they affect the efficiency of thermal energy storage in real-world scenarios? How do the specific melting and freezing temperature ranges of the prepared eutectic PCMs (36°C to 56°C) ensure optimal performance in maintaining product quality during solar drying, particularly for sensitive nutritional characteristics of fruits and vegetables? The discussion of the results needs to be expanded, as well as a comparison of your results with those of other studies.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	2	https://f1000research.com/articles/11-1277
https://f1000research.com/articles/12-333/v2	16 Jun 23	{ "type": "Research Article", "title": "Integrated Management of Corn Marigold (Glebionis segetum) in Tef Field at Western and Southwestern Shewa Zones in Ethiopia", "authors": [ "Niguse Hundessa", "Nagassa Dechassa", "Shashitu Bedada", "Getachew Bekele", "Mosisa Duguma", "Niguse Hundessa", "Shashitu Bedada", "Getachew Bekele", "Mosisa Duguma" ], "abstract": "Background: Corn marigold (Glebionis segetum (L.) Frourr.) is a serious weed species of agricultural crops in many parts of Ethiopia. However, there is a lack of information on its management in tef fields in the country. Therefore, the current work was designed with the objectives of evaluating integrated management of the weed and determining the most economical integrated weed management options in tef fields. Methods: The field experiments were conducted in naturally corn marigold infested fields of Cheliya and Woliso districts of West and Southwest Shewa Zones in Ethiopia, respectively, during 2020 to 2021 cropping seasons. Results: Different corn marigold management practices exhibited different responses to different parameters of the target weed and the test crop differently. Application of Pyroxsulam 45g L-1 at a rate of 0.40 l ha -1 supplemented with once-hand weeding and Halauxifen-methyl 100g kg-1 + Florasulam 100g kg-1 sprayed at a rate of 50 g ha -1 supplemented with once-hand weeding increased grain yield by about 70 and 50%, respectively, over the weedy check. The marginal revenue and benefit-cost ratio obtained from the marketing of goods for the application of Pyroxsulam 45g L-1 with one supplementary hand weeding of corn marigold increased by110 89%, respectively, as compared to the weedy check. Conclusions: The present study revealed the role of integrated management of corn marigold in improving tef production and productivity by combating the weed. Future research should be directed towards scaling up and popularizing these technologies among the growers.", "keywords": [ "Benefit-cost ratio", "Effective management", "Glebionis segetum", "Pallas", "Quelex" ], "content": "Introduction\n\nTef (Eragrostis tef) is the most important staple grain for over 60-72% of Ethiopia’s population (Gizaw et al., 2018). Its cultivation predates historical records by Ethiopian farmers, and it has a comparative advantage over other cereals in terms of farming and utilization (Minten et al., 2018). It is one of the most widely cultivated and economically important cereal crops in Ethiopia, but one of the lowest in production. Because of its weak root system and short stem with narrow leaves, it is vulnerable to weed competition (Tessema, 2002). Tef-weed competition is a big threat to the crop production and productivity, causing great yield loss.\n\nParticularly, corn marigold (Glebionis segetum (L.) Fourr.) is considered as one of the most difficult weed species in many countries of the world in general (Karamaouna et al., 2019) and in Ethiopia particularly (Asres & Das, 2011; Shashitu, 2019). They are specifically harmful in the high land part of Ethiopia and can significantly reduce crops yield (Asres & Das, 2011; Shashitu, 2019). Corn marigold has been reported to cause 56% yield losses in wheat in Ethiopia if appropriate management measures are not implemented (Shashitu et al., 2018).\n\nSimilar to other weeds, corn marigold competes with agricultural crops for water, nutrients, minerals, space and light. Its competitive advantage is enhanced by its extreme fast growth rate, fast spreading ability, rapid multiplication via seeds, and strong competitiveness with crop (Shashitu, 2019). It is a noxious weed which highly adapted to a wide range of nutrient and environmental conditions. Its complicated root system, large number of branches that are difficult to uproot, and cutting worsen its infestation (Shashitu, 2019) Figure 1.\n\nCorn marigold is observed spreading fast and invading grazing and crop lands at an alarming rate at Dabat (Assefa, 2019), Debark districts (Asres & Das, 2011) in Amhara regional state and Cheliya and Woliso districts (Shashitu, 2019) in Oromia regional state in Ethiopia. It is becoming a noxious weed to crop production and causes yield and seed quality reduction in crops at highland parts of the country. As evidenced from Figure 2A-F, it infests grazing land, faba bean, tef, wheat, and linseed fields at Cheliya and Woliso areas in Oromia regional state in Ethiopia.\n\nHand weeding is the most often utilized weed management approach in tef fields to reduce the detrimental impact of corn marigold. Due to overlapping operations with other crops, farmers' family labor is insufficient during the main cropping season for timely and adequate control of corn marigold in tef fields (Nagassa et al., 2022). Hand-weeding tef fields takes time and is typically done late in the season, after the weed have reduced crop growth and development. It's especially tough because of the constant rain during the primary cropping season, which inhibits people from getting out into the field and conducting field activities.\n\nThough the threat of corn marigold in tef production is increasing spatially and temporally in Ethiopia, few studies have been conducted on its management and feasibility of the management option in the country. Therefore, this study was conducted with the objectives of developing effective integrated management of corn marigold, determining the grain yield benefit and yield losses derived from the use of integrated management of the weed, and determining the most economical integrated weed management options tested in tef production in the selected sites of the western and southwestern zones of Ethiopia.\n\n\nMethods\n\nThis experiment was conducted within an appropriate ethical framework of Ethiopian Institute of Agricultural Research as confirmed by institutional letter with Ref. No.: 9.7/4712/2023 written on 3rd March 2023.\n\nThe study was conducted at Cheliya and Woliso districts in Oromia regional state in farmers’ fields during the main cropping season of 2020 to 2021 (Figure 3). A naturally corn marigold infested field per district was selected (Table 1 and Figure 3).\n\nThe experiment consisted of six treatments arranged in randomized complete block design with three replications on the plot size of 4 m × 5 m. Spacing 1.5 m between blocks and 1m between plots were used. Tef seed rate of 10 kg ha-1 of “Kuncho” variety was drilled in rows 20 cm apart. NPS and urea fertilizers were applied at rates of 150 and 200 kg ha-1, respectively. NPS was applied at sowing time, whereas urea was applied in two split half amounts at sowing time and the remaining amount at the tillering stage of the crop. The herbicide amount required for the treatment was calculated and measured using a sensitive digital balance and measuring cylinder and applied 30 days after sowing (DAS) Table 2. For all herbicide treatments, a uniform spray volume of 200 l ha-1 was used. Moreover, all experimental plots management activities were executed to the standard level.\n\nBoth corn marigold weed and tef crop data were recorded. The weed parameters such as the number of corn marigold before and after treatment, biomass and visual scoring scale were recorded using appropriate materials and procedures. The weed control efficacy percentage was calculated using the appropriate formula. Tef parameters plant height, biomass, and grain yield were recorded, and a harvest index was calculated.\n\nNumber of corn marigold: was counted at 30th and 60th days after sowing using 1 m * 1 m quadrat.\n\nVisual scoring: was undertaken using 1-5 scale scoring system at 15th and 30th, days after herbicide application (Taye et al., 2007).\n\nBiomass of corn marigold (kg/plot): the weed shoot biomass at crop physiological maturity from the net plot area was recorded and weed control efficacy was calculated using the following formula:\n\nWhere, WDC and WDT are weed dry weight in control and any particular treatment, respectively.\n\nPlant height: was measured from the ground level to the tip of ten randomly selected plants from harvestable rows at physiological maturity.\n\nGrain yield (kg ha-1) was measured by harvesting the crop from the net plot area.\n\nShoot biomass yield: At physiological maturity, the shoot biomass of ten plants selected randomly from the destructive rows was measured after oven drying the harvested produce till a constant weight.\n\nHarvest index: The plants harvested for shoot biomass yield at physiological maturity was used to calculate the harvest index by dividing grain yield by the total shoot dry biomass yield.\n\nRelative tef yield loss due to weed was calculated as follows:\n\nWhere, MY = maximum yield from a treatment, YT = yield from particular treatment\n\nWhere, CFy = crop yield in corn marigold free plots, FPy = crop yield in farmers’ practice, and CCy = crop yield in corn marigold un-weeded check plot.\n\nData on inputs and their costs were collected for each evaluated weed control option/treatment, including the costs of procuring herbicides and planting materials, labor expenses for land preparation, tillage and herbicide application, hand weeding, and tef harvesting.\n\nThe costs of Pyroxsulam 45g L-1 (2974-birr L-1), Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 (10913-birr kg-1), and Flurasulam 75 g L-1 + Flumetsulam 100 g L-1 175 SC (8400-birr kg-1) were obtained from the prevailing local market (53.37 Ethiopian Birr = $1 United State during merchandising). The shopping unit value of the knapsack sprayer was 1200 birr as information gathered from Addis Ababa (central market), Ethiopia. Around West and Southwest Shewa zones, the labor cost man-1 day-1 was ranges from 50-150 birr. In addition, data on the market price of tef per kilogram were collected at each site. The current market price (as of January 2023) was taken from farmers who sell tef in local markets and district extension workers to compute benefit cost ratio.\n\nThe collected data were subjected to analysis of variance using SAS computer software version 9.4. However, Means were separated using LSD procedure at the 95% confidence level, when they found statistically significantly different.\n\nThe cost-benefit analysis for the proposed management practices, which included herbicidal and cultural (manual weeding) strategies, was determined using the (Program et al., 1988) process. During the cost-benefit analysis, the total input cost of production, gross revenue, marginal revenue and benefit-cost ratio were all taken into account. The total input cost (additional expenses for weed and trial management) was calculated by adding all costs (variable + fixed input costs) incurred during the study. Tillage and fertilizer costs, as well as planting and harvesting wages, were considered fixed production costs. While the knapsack sprayer, herbicides, and manpower for pesticide spraying and manual weeding were considered variable production costs.\n\nThe gross revenue was concluded by multiplying of commercialized price and grain yield (Daramola et al., 2019). The marginal revenue was computed as subtracting the total variable costs from the gross revenue (Daramola et al., 2019) In addition, the benefit cost ratio was computed as the proportion of marginal revenue (numerator) and total variable cost (denominator) (Daramola et al., 2019).\n\n\nResults and discussions\n\nThe variance analysis revealed statistically significant differences in the evaluated weed management strategies on both the corn marigold and tef characteristics (Tables 3 and 4). Different corn marigold management approaches produced different results in weed parameters including weed biomass and weed control efficiency, as well as crop factors like plant height, biomass yield, grain yield, and harvest index.\n\nThere was statistically significant difference in corn marigold dry weight among management strategies (Table 3). In the weed-free plots, there was no weed dry weight recorded. Following the weed free plots, the application of Pyroxsulam 45 g L-1 supplemented with once-hand weeding significantly decreased the weed dry weight by about 33-fold, followed by the application of Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 supplemented with once-hand weeding, which decreased the weed dry weight by 30-fold as compared to the weedy check. However, farmers' family labor is insufficient for timely and adequate management of corn marigold in tef field, as it needs continuous removal of the weed as it emerges. Hand-weeding tef fields is time-consuming and usually done late in the season, after the weeds have reduced crop plant growth. It is especially difficult because of the heavy rain during the main cropping season.\n\nThe effects of weed management strategies on weed control efficiency were significantly different (Table 3). Continuous hand weeding of corn marigold as it appeared in the field resulted in complete eradication, whereas Pyroxsulam 45 g L-1 supplemented with once hand weeding followed by Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 supplemented with once hand weeding resulted in effective corn marigold destruction. However, frequent hand-weeding of the weed in tef field is one of the most difficult tasks faced by farmers, especially during the main cropping season. It requires 3–4 rounds of continued weed removal per season to make the field weed-free. Uprooting the weed is difficult due to its complex root system, and cutting it worsens its infestation. Additionally, tef seedlings are also uprooted and the crop population reduced during frequent hand weeding.\n\nThe effect of weed management practices on plant height, biomass yield, grain yield, and harvest index were significantly different whereas there was a statistically insignificant difference among all management practices on the crop harvest index (Table 4). However, in tef crop yield, there was a statistically insignificant difference among weed free plots, Pyroxsulam 45 g L-1 spray supplemented with once hand weeding, and Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 spray supplemented with once hand weeding (Table 4). The application of Pyroxsulam 45 g L-1 supplemented with once hand weeding increased the tef yield by about 70%, followed by Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 sprayed with once supplementary hand weeding with the crop yield increment of 50%. Overall, the results showed a good agreement in the trends of all yield related parameters.\n\nThe highest yield was obtained from weed free plots, followed by the application of Pyroxsulam 45 g L-1 at 0.40 l ha-1 with supplementary hand weeding. The minimal relative yield loss (0.44%) due to corn marigold was obtained from application of Pyroxsulam 45 g L-1 at 0.40 l ha-1 with supplementary hand weeding, followed by application of Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 at 50 g ha-1 with one supplementary hand weeding with intermediate relative yield loss (12.10%) (Table 5).\n\nBased on corn marigold density per area, the potential tef yield loss by the weed ranged from 23.75 to 62.93%, whereas the actual tef yield loss was 13.67 to 47.09% (Table 6). Both actual and potential yield losses due to the weed were highest at West Shewa Zone (Cheliya District), whereas yield losses due to the weed were lowest at Southwest Shewa Zone (Woliso District). This might be due to the fact that the weed density in Cheliya District was higher than that in Woliso District.\n\nFor the integrated use of herbicide application and supplementary hand weeding for corn marigold management, the marginal revenue (MR) and benefit-cost ratio (BCR) were computed for treatment combinations. The cost-benefit analysis showed that significant variation in MR and BCR was observed among the evaluated experimental treatments (Table 7). Comparing the management practices, the most prominent MR 72459- and 71210-birr ha-1) and BCR (2.86 and 2.63) were calculated from application of Pyroxsulam 45 g L-1 supplemented with hand weeding and weed free plots, respectively. Conversely, the lowest MR (34633- and 46571-birr ha-1) and BCR (1.51 and 1.97) were computed from weedy check and application of Flurasulam 75 g L-1 + Flumetsulam 100 g L-1 supplemented with hand weeding, respectively, whereas the intermediate MR and BCR were obtained from the application of Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 with supplementary hand weeding. The MR and BCR obtained from the marketing of goods for application of Pyroxsulam 45 g L-1 supplemented with hand weeding of corn marigold increased by 110 and 89% as compared to corn marigold weedy check (control plot) (Table 7). Cost-benefit analysis indicated that integration of Pyroxsulam 45 g L-1 with supplementary hand weeding exhibited the topmost MR 72459 Birr ha-1) and BCR (2.86), followed by the weed free plots correspondingly with the MR of 71210-birr ha-1 and BCR of 2.63. Overall, integrated use of broad leaf killer herbicides with supplementary hand weeding provides a better MR and BCR than single weed management practices (Table 7).\n\n\nSummary and conclusion\n\nCorn marigold is one of the aliens weed species that has seriously infested cereal and pulse crops in many parts of Ethiopia since its introduction. It is a noxious weed that is difficult to manage due to its: prolific seed production, fastest growth and spread, adaptation to a wide range of environmental conditions, and strong competitiveness with crops. Integrated effects of herbicide application and hand weeding significantly lowered the weed infestation in the study locations. The current study revealed that application of Pyroxsulam 45 g L-1 at a rate of 0.40 l ha-1 supplemented with once-hand weeding and Halauxifen-methyl 100 g kg-1 + Florasulam 100 g kg-1 at a rate of 50 g ha-1 supplemented with once-hand weeding effectively manage the weed and increased tef grain yield. The marginal revenue and benefit cost ratio obtained from the marketing of goods for application of Pyroxsulam 45 g L-1 at a rate of 0.40 l ha-1 supplemented with hand weeding of corn marigold increased by about 110 and 89% as compared to a weedy check. In conclusion integrated management of corn marigold by integrating broad spectrum and/or broad-leaf killer herbicides with hand weeding practices played a crucial role in improving tef production and productivity by contesting the weed. Forthcoming studies should focus on scaling up and popularizing these technologies in corn marigold weed-infested tef fields in Ethiopia.", "appendix": "Data availability\n\nAll data supporting the results are included in the article, and no extra source data are necessary.\n\n\nAcknowledgement\n\nWe would like to express our gratitude to Ethiopian Institute of Agricultural Research (EIAR) for financially sponsoring the research. A special appreciation also goes to Ambo Agricultural Research Centre (AmARC) for providing logistical help during the research periods. We also thank our colleagues at AmARC, particularly Mr. Tadele Gudeta, for his valuable technical assistance during the project.\n\n\nReferences\n\nAsres B, Das T: Diversity and integrated management of weeds in highland wheat of Northern Ethiopia. Plant Prot. Q. 2011; 26(1): 8–16.\n\nAssefa S: Weed flora survey in field crops of Northwestern Ethiopia. Afr. J. Agric. Res. 2019; 14(16): 749–758. Publisher Full Text\n\nDaramola OS, Adeyemi OR, Adigun JA, et al.: Economics of row spacing and integrated weed management in soybean (Glycine max L.). J. Agric. Sci (Belgrade). 2019; 64(3): 265–278. Publisher Full Text\n\nGizaw B, ZerihunTsegay GT, Aynalem E, et al.: Traditional knowledge on teff (Eragrostis tef) farming practice and role of crop rotation to enrich plant growth promoting microbes for soil fertility in East Showa: Ethiopia. Agric. Res. Technol. 2018; 16: 39–55.\n\nKaramaouna F, Kati V, Volakakis N, et al.: Ground cover management with mixtures of flowering plants to enhance insect pollinators and natural enemies of pests in olive groves. Agric. Ecosyst. Environ. 2019; 274: 76–89. Publisher Full Text\n\nMinten B, Taffesse AS, Brown P: The economics of teff: Exploring Ethiopia’s biggest cash crop. Intl. Food Policy Res. Inst. 2018.\n\nNagassa D, Niguse H, Takele N: A Manual for Integrated Weed Management in Wheat (9994466305).2022.\n\nProgram CE, Maize I, Center WI: From agronomic data to farmer recommendations: an economics training manual. CIMMYT. 1988.\n\nShashitu B: Study of Phenology of Chrysanthemum segetum L. and Its Impact on Crop Productivity in Cheliya District, Ethiopia. J. Biol. Agric. Healthc. 2019; 9(2): 25–30.\n\nShashitu B, Nigusie H, Gectachew B, et al.: Herbicidal Control of Chrysanthemum segetum in Wheat Field at Cheliya District. Results of Plant Protection Research. 2018.\n\nTaye T, Rezene F, Yirefu F: Invasive alien weed species in Ethiopia: Biology, distribution and importance, and available control measures. J. Rev. Weed Sci. 2007; 10(1): 33–39.\n\nTessema T: Investigation of Pathogens for Biological Control of Parthenium (Parthenium hysterophorus L.) in Ethiopia University of Berlin].2002." }	[ { "id": "196230", "date": "14 Aug 2023", "name": "Abdellatif Boutagayout", "expertise": [ "Reviewer Expertise Agroecology and Agroecological weed 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\nReview Report, August 13, 2023\nComments to the author(s): Below are both general and specific comments that I hope the authors will find helpful in revising the manuscript.\nGeneral Comments: This article delves into a significant issue within Ethiopian agriculture, shedding light on an integrated approach involving hand weeding and herbicide application for the management of corn marigold. Nonetheless, there are aspects that require further elucidation and enhancement. These encompass the reference list, trial duration, lack of citations in the Methods section, and the method of presenting results for distinct districts. While the findings gleaned from this study hold great value, it is imperative to incorporate a comprehensive discussion section that can holistically interpret the results, establish context, and address potential ramifications.\nSpecific Comments and Recommendations\nTitle: The current title does not align with the article's content, as it lacks consistency with the concept of \"Integrated Management.\" It is suggested to revise the title to \"Integrated Hand Weeding and Herbicide Application for Corn Marigold (Glebionis segetum) Management in Tef Fields across Western and Southwestern Shewa Zones in Ethiopia.\"\nAbstract and Keywords: The abstract provides a succinct overview of the study's design, results, and implications, accentuating the integrated approach adopted for corn marigold management across the Western and Southwestern Shewa Zones in Ethiopia.\nIntroduction: The introduction effectively outlines the issue of corn marigold infestation and underscores the importance of effective weed management in tef fields. To fortify the introduction, briefly touch upon potential environmental and sustainability concerns arising from herbicide usage and elaborate on how the integrated approach could serve to address these concerns.\nMethods: Ethical Considerations: If the study involved human subjects, it provided pertinent details regarding ethical considerations. This would facilitate readers’ comprehension of the ethical framework underpinning this research.\nMaterial and methods:\nElucidate whether the trial was conducted over two discrete years (2020 and 2021) or confined within a single growing season (2020-21).\n\nInformation concerning weather conditions during the growing season encompasses parameters such as precipitation and temperature. This provides insights into the potential climatic influences on the outcomes. Additionally, please state clearly whether the collected data were subjected to normality checks.\n\nOffer a rationale for the selected statistical methods to enhance readers' grasp of the appropriateness of the approach. Furthermore, the Methods section should feature citations, particularly for calculations related to biomass, weed control efficiency, and corn marigold density. Recent studies, such as those by Boutagayout et al. (2023a)1 and Boutagayout et al. (2023b)2, can be referenced to comprehensively detail the methodologies employed.\nResults:\nEnsure that the data presentation is lucid and succinct, and that suitable tables or figures are incorporated to illustrate noteworthy trends and findings.\n\nThe study encompassed two districts: Cheliya and Woliso. However, the Results section provides only a single value for each assessed parameter. To accurately encapsulate the scope and findings of the study, we segregated the results for each district. This would facilitate an understanding of potential divergences in outcomes due to geographical nuances.\nDiscussion:\nGiven the absence of a discussion section, it is imperative to incorporate this section in the revised article. The discussion should be pivotal, encompassing the interpretation of results, comparisons with prior research, and contextualization of the study's implications.\n\nAddressing plausible environmental concerns stemming from herbicide application and expounding on how the integrated approach of hand weeding and herbicide usage could potentially ameliorate these effects.\n\nThe findings are analyzed within the context of agricultural sustainability. The integrated approach aligns with sustainable weed management practices and explores trade-offs between weed control efficacy and potential ecological repercussions.\n\nSynthesize the findings with the extant literature. Draw parallels between your results and studies investigating analogous weed-management approaches. Illuminate the contribution of your findings to the existing knowledge base.\n\nDelving into the limitations of the study, knowledge of any constraints or obstacles encountered during the research process may impinge on the generalizability of the findings.\n\nProvide insights into the pragmatic implications of the results for farmers, policymakers, and researchers. How can an integrated approach be scaled and adopted? Are there any policy recommendations based on your findings?\nConclusion:\nConcisely encapsulate the primary findings of this study and their implications for corn marigold management in tef fields.\n\nPotential avenues for future research in the domain of integrated weed management include factoring in efficacy and sustainability.\nFormatting and References\nThe reference list should encompass no more than 12 sources and should be enriched with references that are more recent. Eliminate older references (1988, 2002, 2007, etc.)\n\nHarmonize reference formatting with a specific citation style mandated by the target journal.\nOverall Impression: This study has the potential to contribute significantly to the realm of integrated hand weeding and herbicide application for weed management in tef fields. By addressing the suggestions of the review, including clarifying trial duration, bolstering method citations, segmenting results for each district, and delving into environmental considerations, the article aims to gain robustness, impact, and informativeness.\nFinally, while cost-benefit analysis remains crucial for farmers, burgeoning environmental costs demand attention. It is our role as scientists to explore ecologically sound alternatives to herbicides, ensuring the sustenance of African agro-ecosystems and food security for future generations.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "196661", "date": "29 Aug 2023", "name": "Ioannis Gazoulis", "expertise": [ "Reviewer Expertise WEED MANAGEMENT/WEED 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\nKeywords should include herbicide active ingredients onstad of trade names.\nUse species full scientific names when species are mentioned for the first time in the text.\nIntroduction is precise and without generalities. Good work here. Materials and methods\nFertilizer trade names and company name should be cited. Crop rotation history should be added. Something more abou your tef genotype should be added.\n\nHerbicide application pressure and sprayer trade name should be added. Number and type of nozzles should be also mentioned.\n\nFor statistical analysis, did you include year's effects in the ANOVA as fixed? Did you pool data over growing seasons and why was that possible?\nI do not see any reference cited in the Discussion section. Please include references when trying to explain why phenomena occurred.\nDo not forget to mention that except for herbicides, non-chemical cultural practices should be considered to build Integrated Weed Management (IWM) systems in this \"novel\" crop as also in other crops where herbicide options are still limited1.\n\nThe Conclusion section should summarize your key findings highlight research gaps and state your future research objectives on the topic.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	2	https://f1000research.com/articles/12-333
https://f1000research.com/articles/12-1179/v1	20 Sep 23	{ "type": "Review", "title": "Contemporary Role and Applications of Artificial Intelligence in Dentistry", "authors": [ "Talal Bonny", "Wafaa Al Nassan", "Khaled Obaideen", "Maryam Nooman Al Mallahi", "Yara Mohammad", "Hatem M. El-damanhoury", "Talal Bonny", "Wafaa Al Nassan", "Khaled Obaideen", "Maryam Nooman Al Mallahi", "Yara Mohammad" ], "abstract": "Artificial Intelligence (AI) technologies play a significant role and significantly impact various sectors, including healthcare, engineering, sciences, and smart cities. AI has the potential to improve the quality of patient care and treatment outcomes while minimizing the risk of human error. Artificial Intelligence (AI) is transforming the dental industry, just like it is revolutionizing other sectors. It is used in dentistry to diagnose dental diseases and provide treatment recommendations. Dental professionals are increasingly relying on AI technology to assist in diagnosis, clinical decision-making, treatment planning, and prognosis prediction across ten dental specialties. One of the most significant advantages of AI in dentistry is its ability to analyze vast amounts of data quickly and accurately, providing dental professionals with valuable insights to enhance their decision-making processes. The purpose of this paper is to identify the advancement of artificial intelligence algorithms that have been frequently used in dentistry and assess how well they perform in terms of diagnosis, clinical decision-making, treatment, and prognosis prediction in ten dental specialties; dental public health, endodontics, oral and maxillofacial surgery, oral medicine and pathology, oral & maxillofacial radiology, orthodontics and dentofacial orthopedics, pediatric dentistry, periodontics, prosthodontics, and digital dentistry in general. We will also show the pros and cons of using AI in all dental specialties in different ways. Finally, we will present the limitations of using AI in dentistry, which made it incapable of replacing dental personnel, and dentists, who should consider AI a complimentary benefit and not a threat.", "keywords": [ "Artificial Intelligence", "Digital Dentistry", "Dentistry", "Deep Learning", "Artificial Neural Networks", "‎Dental Specialty" ], "content": "Introduction\n\nArtificial intelligence (AI) is the process of training a computer in such a way that it starts thinking like human beings.1 With the advancement in technology in AI, the idea behind the machine that performs tasks for human beings is becoming old-fashioned. Devices and systems that can perform basic calculations and fundamental tasks or detect the text with various recognition applications are now considered standard computer applications and does not lie under AI. This globally recognized technique constantly improves many sectors, including medical, engineering,2–6 energy,7,8 mechanical,9 computer science,10,11 psychology,12 and other disciplines.13–19 This constant improvement in AI makes it an important constituent of almost every field. Along the same line, AI is one of the enablers of achieving the United Nations Sustainable Development Goals (SDGs).20 More specifically, AI could accelerate the achievement of SDG 3: Good Health and Well-being.21,22\n\nIn dentistry, AI is becoming an important constituent owing to its use in improving the diagnostic facility to provide excellent patient care and the ability to get excellent results.23–26 Dentists are capable enough with their training to analyze and suggest the best possible treatment and provide the best clinical decision based on their experiences.27,28 However, sometimes, dentists do not have sufficient information and knowledge to predict the best clinical practice.29 This may result in poor clinical decision-making and bad effects on human well-being.30 However, the dentist can perform better using AI systems by making accurate decisions.31 They can rely on computer and AI software to make clinical decisions.32,33 Several papers intend to explore and review the role of AI in dentistry.34,35 However, most of these papers were very technical or focused on the technical perspective of AI's application in dentistry, making them quite difficult for dental practitioners.\n\nThis paper attempts to review the solutions used in digital dentistry that engineers have developed from various fields of knowledge. As a result, this knowledge is critical for dentists, surgeons, clinicians, and laboratory technicians. Moreover, most of the previous papers did not explore the role of AI in different dental specialties; diagnosis, clinical decision-making, treatment, and prognosis prediction in ten dental specialties; dental public health, endodontics, oral and maxillofacial surgery, oral medicine and pathology, oral & maxillofacial radiology, orthodontics and dentofacial orthopedics, pediatric dentistry, periodontics, prosthodontics, and digital dentistry in general, so this paper intends to fill this gap by reviewing the application of AI in dentistry using simplified terms and showing the role of AI in different dentistry specializations. As a result, this paper focuses on answering the following research questions:\n\n• What are the trends, applications, and innovations of AI in dentistry and digital dentistry that are expected to influence the direction of dental research in the coming years?\n\n• What are the strengths and weaknesses of AI in dentistry?\n\n• What are the challenges of using AI in dentistry?\n\nThe paper is structured as follows. The next section reviews artificial intelligence and its application in healthcare. The application of AI in dentistry and digital dentistry is then described. The strengths and weaknesses of AI in dentistry are presented in the section after. Then we present the main challenges of using AI in dentistry. Finally, the conclusion is given in the final section.\n\n\nArtificial Intelligence (AI) for Healthcare\n\nThe science of AI contains different branches, such as machine learning (ML) and deep learning (DL). ML is a system that can be trained by different problem-solving training and models to gain the ability to automate the process of solving tasks.36 DL is a part of ML in which the learning module is based on artificial neural networks.37 DL provides an excellent ability to beat state-of-the-art techniques in its application to perform various tasks and analyze and evaluate data from various sources, including audio,38,39 sensors,40 and visual data.41 On the other hand, there are several types of artificial intelligence. Under two main categories based on their functionalities and capabilities, as shown in Figure 1.\n\nSince its inception, AI has significantly improved our daily lives and activities in various ways. Emerging fields, including surgery,42 automatic disease diagnosis,43 and the recently established personalized medicine, can benefit from AI support.44 Figure 2 demonstrates the key aspects of artificial intelligence, ranging from ML, Neural Networks (NN), and DL.\n\nMoreover, AI models were implemented to central processing unit (CPU) and graphics processing unit (GPU) architectures, so detection\\recognition-based algorithms can achieve practical needs. However, recent AI algorithms, especially deep learning models, demonstrated efficiency in solving many problems. Those algorithms demand an intensive CPU and memory, which prevents standard CPUs from achieving the desired performance levels.45 As a result, hardware processors, specifically field-programmable gate arrays (FPGAs) platforms, have been used to effectively maximize those models' performance.46–48 FPGA is an integrated circuit customized for a specific application where the configuring process is applied after manufacturing.49 Consequently, FPGA is the perfect candidate for implementation from various perspectives, including but not limited to performance for parallel tasks, cost-effectiveness, prototyping, and real-time applications.50,51\n\n\nApplication of AI in Dentistry\n\nArtificial intelligence has a large number of advantages in various businesses as well as various domains. In healthcare, AI has been getting attention in the medical and pharmaceutical fields by providing self-driven operating applications. AI applications in the healthcare domain include Robotic systems, Diagnostic Aids, and Drug Discovery.52,53\n\nAI emerged in the healthcare field to \"train\" computer programs to reach highly intelligent capabilities. AI, a superior diagnostic aid that minimizes daily practice mistakes, might enhance patient care.54 The interpretation of medical images has progressed from expert systems through atlas-based models toward the potential of deep learning. The huge data from digital radiographs may be utilized since it has much potential for improving radiology diagnosis with AI. Through automated data mining, AI with DL might help medical radiology.55 New information will be found with only a little human understanding.56–59\n\nThe identification and management of systemic conditions during dental treatment has always been a challenge to the dentists. AI can examine electronic medical records and scientific datasets practically and efficiently. With the advent of huge scientific data, the diagnosis of human congenital abnormalities has improved. In medical research, the support vector machine (SVM), a machine-learning model, has become a typical way of analysis. SVM may be used to classify complex situations like traumatic brain damage.60,61 DL may play a crucial role in advancing cardiovascular medicine due to the requirement for precision in diagnosis and therapy.62 With the adoption of deep learning, it will be feasible to identify numerous cardiovascular disorders with high-precision diagnosis.63 Wearable technology combined with intelligence applications can anticipate a patient's life-threatening crisis such as a stroke, allowing physicians to deliver effective, early therapies.54 Using AI to examine viruses has boosted transitional studies in viral immune monitoring.64\n\nAI can help fill knowledge gaps while also lowering costs and increasing benefits. AI is commonly utilized in disease management to examine treatment outcomes and provide precision medicine. These cutting-edge machine-learning algorithms are powerful analytic tools that assist clinicians in understanding and analyzing moods.\n\nTraditional components of dentistry have been modernized by using AI. In dentistry, AI-based diagnostic systems and patient data are widely used. They are mostly decision systems based on clinical knowledge, which leads to helping and advising specialists in making better judgments. This highly efficient technology has been employed to analyze treatment planning, diagnosis, and prognosis prediction. Because of their usefulness in offering explanations and logic, these systems are in high demand. AI has transformed dentistry, resulting in reducing the work of a dentist.65 AI-based technology in dentistry is mainly aimed at providing expert assistance to healthcare providers.66–68 Any computer software created to assist health professionals in making clinical choices and dealing with medical knowledge essential for understanding such data is referred to as a clinical decision support system.32 Figure 3 displays the structure and major dental applications of AI.\n\nAfter reviewing various scientific journals, key information such as applications, AI techniques, and field of research was investigated and categorized, as shown in Figure 4.\n\nThis section describes the state of the art of AI technology in the dentistry field. AI provides essential help to automate different activities, such as the assessment of a radiographic image to detect a dental disease faster and more accurately than other activities. It has been shown how appropriately trained algorithms can be extremely successful for the diagnostician and how AI can determine the direction of public health and clinical services.\n\nArtificial neural networks (ANN’s) are systems based on algorithms, learning on a neural network with biological functionality. Such systems address various challenges, including supervised, unsupervised, and reinforcement learning. An ANN's fundamental structure is a series of data layers interconnected by operational neurons. The most promising area of study in this discipline is undoubtedly DL applications in dentistry. Because these approaches allow discovering particular arrangements from massive data sets of pictures, they can help build a high-performance system with excellent decision-making capabilities.69\n\nAlthough it may not appear that advances in AI have had a significant impact on dentistry, various areas, including automated detection of oral diseases, enhancement and analysis of dental x-rays and images, are some of the benefits of AI in dentistry. On the robotics front, various advancements are allowing robotic assistance in dentistry.70\n\nSeveral variables have played a role in the latest AI revolution in biomedicine. For starters, data collection has grown exponentially over the past few decades. However, data alone is insufficient. New sophisticated AI algorithms have permitted a complete and helpful extraction of information from acquired data because of improvements in high-performance computing (HPC). This information extraction technique is called ML, the data-driven component of AI that seeks to enable machines (algorithms implemented in computer systems) to learn about a specific topic from a specific dataset.71 This sort of information extraction is often carried out utilizing supervised learning approaches, which have proven to be quite effective in solving many issues. Supervised learning aims to train a function that converts an input sample to the desired output using a dataset of input-output pairings. After learning this function using the training dataset, new predictions can be formed over incoming samples.72\n\nThese technologies have also seen substantial medical adoption, namely in computer vision. A variety of factors has been recognized as driving this adoption. Diagnostic imaging is critical in many healthcare disciplines,73 and AI is particularly well suited to overcoming the diversity in individual subjective inspection and increasing the effectiveness of therapy while cutting costs by removing mundane activities. Digital health data are being collected everywhere, and while these data are currently somewhat heterogeneous, businesses are progressively aiming to deliver cleansed, curated, and organized data.74\n\nThe convolutional neural network (CNN) is the ANN's most often utilized subclasses in medicine and dentistry.75 A CNN employs a unique neuron connection architecture and the mathematical function convolution to handle digital data such as sound, pictures, and videos. CNNs evaluate a larger picture or signal by scanning a small neighborhood of inputs simultaneously, from left to right and top to bottom, using a sliding window. They are the most often used image recognition method because they are particularly well matched to picture categorization.76\n\nDental care is a one-of-a-kind career in the medical field, and it is incredibly required as it is a necessity hence the incorporation of a vast quantity of data and the development of clinical skills.77 A technology that superimposes a computer-generated picture over a user's perspective of the actual world, producing a composite vision, according to the definition of augmented reality.78 The development of augmented reality has generated appealing prosthetics resulting in better and improved overall patient experiences. The patient can try on the augmented reality that can be altered until they are satisfied using AI algorithms and augmented reality. The final prosthesis is produced precisely to these specifications.79,80\n\nIrrespective of augmented reality, virtual reality is a simulation based on a 3D picture generated by the computer, which can interact with the real and physical world and electrical and electronic equipment. In combination with virtual reality, AI systems have been utilized to alleviate dental concerns and as a strong tool for treating a patient with pain that cannot be cured by medicine.81\n\nThe field of intelligent teaching organizations has advanced greatly since its inception in the 1980s. To create scenarios that simulate clinical work on patients while removing the risks associated with teaching a live patient, augmented reality and virtual reality are both extensively used in dentistry education.82 The preclinical virtual patient has greatly improved the quality of feedback provided since AI was recently included in intelligent teaching systems, namely the Unified Medical Language System (UMLS). In the interactive interphase, students can evaluate their work and compare it to the ideal, resulting in high-quality training settings. Studies has highlighted the importance of these systems and reported that students achieve competency-based skill levels faster than those using standard simulator modules.83,84\n\nWhile ML makes predictions based on an analytical approach to available data, data mining is concerned with discovering causal links and similarities in current data. Data mining of digitized dental data allows for the analysis of variance across dentists when detecting and predicting dental caries, dental age estimation.33,85–87\n\nDental public health, endodontics, oral and maxillofacial surgery, oral medicine and pathology, oral and maxillofacial radiology, orthodontics and dentofacial orthopedics, pediatric dentistry, periodontics, and prosthodontics are dental specialties recognized by the Canadian Dental Association as shown in Figure 5.88\n\nVirtual dental assistants working on AI are now working for various domains in the market. Like virtual assistants, these designed systems can perform specific tasks in dental clinics more precisely and accurately, using less power, resulting in less error than human beings.80\n\nSome of the virtual assistant work in the field of dentistry includes,\n\n▪ Offering the patient a convenient appointment time reduces the potential for commotion and activity arising due to the large number of patients coming in a day.89\n\n▪ Informing the dentist and the patients regarding the upcoming checks when hereditary or lifestyle factors suggest a higher vulnerability to oral problems. (e.g., diabetic patient's periodontal screening and users of smoked and smokeless tobacco regularly will be tested for oral cancer screening).90\n\n▪ Taking care of paperwork and insurance.\n\n▪ Helping in better diagnosis and planning after the patient's disease diagnosis is carried out.\n\n▪ Provide the dentist with information about the allergies and diseases the patient already has before the patient visit.\n\n▪ Providing the dentist with the associate medical background. This will help the doctor finalize the plan regarding the patient's diagnosis. This also helps in planning surgery for the patient.33\n\n▪ Offering telephone-based services on time in the cases when the dentist cannot reach the hospital and urgent medical care is required.91\n\nFigure 6 demonstrates a comprehensive dental care system for the future with AI. Aside from this, AI-based software allows us to develop a comprehensive data history for each patient, which may be incredibly thorough and accessible.27,92 The AI software can recognize the voice, which will help the dentist improve their performance. AI software can perform documentation and display all the data relevant to the dentist at a rather efficient and faster speed than a human equivalent. (For example, gathering all relevant patient records on their dental visits, supplementary oral pictures, x-rays, and diagnostic graphs related to their disease). Owing to these exceptional learning abilities, it can be trained to execute various tasks. Such devices can be used alongside dental x-rays and CT-scans to detect changes in human teeth from their normal teeth that the dentist's eyes may not have noticed.27,93\n\nIt can be divided into pre-appointment, inter-appointment, and post-appointment AI systems. These three types of AI gather data that will be used to enhance patient care.\n\nThis technique may also be used to reach orthodontic diagnosis by analyzing the cephalometric radiographs and detecting dental and skeletal abnormalities.94 Simply by successfully obtaining the patient's data and synchronizing it with the decision system already in place for the patient in the dental labs, this is accomplished.95 In pathology, scanning numerous sections to find minute details that aid in diagnosis and clinical decision-making is possible. The program can do different analyses of images and radiographs in orthodontics to aid in diagnosis and treatment planning.96 Taking a dental impression might soon be obsolete due to advancements in intra-oral scanners and cameras. These digital impressions minimize all laboratory operations, which sharply lowers the frequency of errors and is quicker and more accurate.\n\nUsing AI, the computer can notify the dentist throughout the process of creating a digital imprint and assist in making an excellent impression.97 Taking a dental impression may soon be a thing of the past thanks to advancements in intra-oral scanners and cameras. In addition to being quicker and more accurate, these digital images also do away with all laboratory procedures, which greatly reduces the possibility of mistakes. Using AI, the computer can guide the dentist as they create a digital impression, optimize the final scan by eliminating the unwanted frames during scanning, automatically detect the margins of the preparations and develop a restoration design that imitate the anatomy of the lost tooth structure.98 Computer Aided Design (CAD) Computer Aided Manufacturing (CAM) techniques, like subtractive milling, and additive manufacturing techniques, like 3D printing, are currently used to create prostheses. It has replaced the labor-intensive and challenging traditional casting process while dramatically lowering human error in the finished prosthesis. These technologies can also be employed to create precise orthodontic appliances.98\n\nAI software has aided in pre-surgical planning procedures to the smallest detail in oral surgery and implantology. The introduction of robotic surgery has made one of the most significant uses of AI in oral and maxillofacial surgery. Simulating human body motion and intellect is critical in robotics science.99 However, the discipline of surgery has been revolutionized by artificial intelligence. The number of robotic surgeons doing semi-automated surgical procedures under the supervision of a skilled surgeon has increased significantly in recent years. Last but not least, one of the most cutting-edge uses of AI is found in the field of \"bioprinting,\" which allows living tissue and even organs to be built into successively thin layers of cells. This technology could one day reconstruct oral hard and soft tissues lost due to pathological or unintentional causes.100\n\nArtificial intelligence (AI) can be used in Dental Public Health, which involves diagnosing, preventing, and controlling dental diseases through research, education, and group dental care programs.\n\nAs an example, an AI-assisted diagnosis method is developed by employing Faster-Recurrent Convolutional Neural Network (RCNN) to predict the number and locations of caries lesions based on periapical films, which in the end, will help doctors diagnose the diseases with higher efficiency and precision.101\n\nAlthough root canal configuration in a group of mandibular molars may seem similar, numerous unusual deviations may exist.73 Cone-beam computed tomography (CBCT) has established the gold standard for reducing treatment failures due to these morphological variations and hence, optimizing endodontic therapy clinical results.102 However, due to its increased radiation dosage compared to traditional radiography, CBCT is not widely employed.103 To address such issues, AI has been applied to categorize the supplied data using a CNN to determine the anatomical variation in root canals.104,105\n\nAI can be used in the diagnosis, surgical, and adjunctive treatment of disorders, diseases, injuries, and defects involving the functional and aesthetic aspects of the hard and soft tissues of the oral and maxillofacial regions and related structures.\n\nAI technology has been widely applied for predicting facial attractiveness after orthognathic surgery. The above artificial intelligence models are built on either ANNs or CNNs.106\n\nDeep-learning-based algorithms can predict the virtual soft tissue profile after mandibular advancement surgery and compare its accuracy with the mass tensor model (MTM).107\n\nANNs have enormous potential to help in clinical decision-making. To get predictable outcomes for patients, orthodontic treatments must be meticulously planned. Teeth extractions, on the other hand, are not uncommon in orthodontic treatment plans. As a result, ensuring that the best clinical choice is taken before embarking on irreversible operations is critical.108–110 Using DL for automated tooth segmentation on a 3D model of the jaw, the segmented teeth can be reconstructed with their roots from the CBCT using iterative closest point (ICP) algorithm to form a complete digital dental model, and to obtain the necessary information for orthodontic treatment simulation.111,112\n\nThere are two clinical categories of periodontitis, according to the American Academy of Periodontology's classification of periodontal disease in 1999: aggressive (AgP) and chronic (CP). Due to the disease's complex pathophysiology, no clinical, microbiological, histological, or genetic test can distinguish AgP patients from CP patients.113 Many non-surgical and surgical techniques have been developed to manage periodontally compromised teeth and supporting structures. Despite advancements in treatment methods, there has been no major improvement in diagnosing and forecasting the prognosis of periodontally compromised teeth (PCT).114 Clinical diagnosis and prognosis are highly reliant on empirical data. Deep CNN algorithms have shown a high potential for usefulness and accuracy in diagnosing and predicting the need for extraction of PCT.115\n\nIn detecting and identifying anatomical structures, CNNs have demonstrated promise. For instance, some people have been taught to identify and name teeth using periapical radiographs. When it comes to identifying and classifying teeth, CNN's accuracy rating of 95.8-99.45 percent closely resembles that of clinical specialists, whose accuracy score is 99.98 percent. Dental cavities can be found and diagnosed with CNNs as well. In 3000 periapical radiographs of posterior teeth, a deep CNN algorithm identified carious lesions with an accuracy of 75.5-93.3 percent and a sensitivity of 74.5-97.1 percent.116 With sensitivity ranging from 19 percent to 94 percent; this represents a considerable advancement over the use of radiographs alone for diagnosis by medical personnel. When combined with their speed, deep CNNs have a high potential for improving the sensitivity of dental caries diagnosis, making them one of the most effective technologies in this field.117,118 Another application of the AI in dental radiology is the use of artefact reduction algorithms that help the enhancement of the radiographic images and eliminate the distortion effect radio-opaque objects on the fine details of the acquired image, while reducing the need for high radiation dose and large voxel size.119,120\n\nEarly identification and diagnosis of oral lesions are critical in dental offices since early detection improves prognosis greatly. Because certain oral lesions might be precancerous or cancerous, obtaining an accurate diagnosis and treating the patient appropriately.121 CNN has been demonstrated to be a potential tool in diagnosing head and neck cancer lesions. CNN offers excellent promise for recognizing tumoral tissues in tissue samples or on radiographs, with specificity and accuracy of 78–81.8 percent and 80–83.3 percent, respectively (compared to specialists' 83.2 percent and 82.9 percent, respectively).117\n\nAI in Pediatric Dentistry can be used in the same way it is used in adults by providing primary and complete preventative and therapeutic oral health diagnosis, care, and consultation knowledge for infants and kids through adulthood.\n\nAI has the potential to solve discrepancies that may arise throughout the analysis of growth data, and AR augmented reality methodologies have been developed to educate patients and families about growth disorders and their treatments.122\n\nAI models serve as a dependable diagnostic tool for tooth shade selection, automated restoration design, mapping the preparation finishing line, optimizing manufacturing casting, predicting facial changes in patients with removable prostheses, and designing removable partial dentures.105,114 (See Table 1) which summarizes a set of applications for dental activities that integrates AI technology.\n\nDigital dentistry has changed the dental industry by introducing fresh methods, tools, and interactions. Research directions and opportunities for material scientists have been prompted by innovation. Many digital processes for production processing, particularly computer-aided designing and manufacturing (CAD/CAM), have already been integrated into dental treatment procedures.123–126\n\nNowadays, the advances in Artificial Intelligence (AI) and 3D imaging systems make dentists rely more and more on digital technologies for detection and treatment.127,128 Adopting AI-based digital technology for clinical solutions and dental laboratories allows the dentist to digitally repeat the whole procedure and treatments. Furthermore, assure sharing of information across the entire process of the digital dental system, shown in Figure 7. Using a digitalized dental system brings real advantages in accuracy and quality, is time-consuming, and decreases costs.129\n\nDigital dentistry now incorporates diagnostics, decision-making, treatment conduct, and re-evaluation of lifelong management of patient's oral health, as well as computer-aided designing and manufacturing (CAD/CAM) and rapid prototyping fields.\n\nRapid prototyping (RP) is a subset of rapid manufacturing and a type of (CAM). It is a method of creating three-dimensional (3D) models of a finished product or a component of a larger whole using 3D printers quickly and automatically. The recent revolutionary application of 3D scanning and printing is AI-based orthodontic treatment.130–132 AI is applied in orthodontics at all stages, from diagnosis to treatment planning and follow-up supervision. Where the Aligners and treatments can be designed with the help of these 3D scans. After the aligners are printed, a data algorithm is developed that intelligently specifies how the teeth should be managed to move, the amount of pressure that should be applied, and sometimes even recognizes the pressure points for that particular tooth.133\n\nLarge dental labs in Europe and USA have increasingly implemented CAD/CAM technology. Recent advancements in 3D printing have broadened its applications that involve dental models, orthodontic appliances, mouth guards, and appliances for guided implant surgery.\n\nAll CAD/CAM systems are made up of three parts:\n\n• 3D Scanners convert geometric features into digital data that a computer can process.\n\n• CAD is a data processing software that produces a dataset for the component to be manufactured, depending on the application.\n\n• CAM is a manufacturing technology that transforms a dataset into the desired component.\n\nCAD/CAM technology has revolutionized the concept of dentistry. Standardized production processes have significantly improved the quality of dental prostheses. This provides extremely effective quality management. It enhanced productivity significantly and changed dental laboratories from manufacturers into sophisticated computerized production centers. Increased productivity. In addition, it leads to a competitive capability to make dental prostheses independent of the manufacturing site, which could be a crucial reason for high-wage countries to maintain business volume in the country.134 Lastly, CAD/CAM technology has enabled the high-precision machining of novel materials such as high-performance ceramics and titanium.\n\nRecently, researchers have been looking into ways to improve the accuracy of 3D scanning, CAD\\CAM, and 3D printing, such as using AI models. This can save money and time and reduce the number of visits required for precise fitting. Table 1 includes a summary of the applications of AI in 3D digital dentistry during recent years.\n\nEven so, some drawbacks of this manufacturing technology should be handled. The rising cost of machines may exceed the limits of smaller laboratories. Additionally, some applications are limited due to software and manufacturing procedures. CAD/CAM technology has already changed dentistry and will gradually replace traditional methods of fabricating dental restorations.\n\n\nStrengths and Weaknesses of AI in Dentistry\n\nAI enables the integration of many heterogeneous data domains, such as patient data, clinical knowledge of the patient, imaging results, and so on, creating the greatest use of these data obtained and understanding their contact. Artificial intelligence-based supports discoveries by supplementing other research levels and current modeling methodologies within silico experimentation choices in traditional research hierarchies.\n\nAs previously noted, AI may simplify mundane tasks and enhance the contact time between patient and doctor. This might include not just diagnostic aid technology but also data from patients' voices and speech to help the dentist keep track of the record and help in saving time.135\n\nUsing these continually obtained data will reduce the effect of \"on-off-medicine,\" in which patients only meet the doctor for a few seconds. However, the health issues develop over the year leading to an increase and decrease in the symptoms of the disease over time. Continuous and constant health and behavior analysis will allow for a far deeper, personalized knowledge of the underlying drivers and processes of health and illness.136\n\nDiagnostic and treatment expenses are expected to reduce due to betterment in the healthcare field by embedding AI in the system resulting in more early diagnoses of chronic diseases. However, the disadvantage of the use of AI in dentistry includes.137\n\nAI may also help alleviate labor scarcities, which have been noted and are projected to remain in many regions of the world, therefore assisting in achieving the sustainable development goals defined by WHO.\n\nAI-based apps will expedite treatment, freeing the dental staff of time-consuming, mundane duties, improving health at a cheaper cost for a larger population, and eventually enabling customized, predictive, preventative, and participative dentistry. However, AI solutions have not yet been widely adopted in routine dental practice, owing to fewer data and development standards and ethical concerns.34\n\nThe misuse of data and security concerns of AI is other important parameter in dentistry. relying entirely on the machine to decide the health care services is critical, and entrusting a machine will not be okay regarding human health. It would be suitable only if AI provides low cost with excellent patient benefits and, as a result, improve society.138 Figure 8 provides of summary of the strengths and weaknesses of AI within the dentistry area.\n\n\nThe Main Challenges of using AI in Dentistry\n\nClinical data storage and interchange present significant challenges when using AI algorithms in the healthcare industry. The initial training of the AI system and further training, validation, and improvement require patient-specific data. Additionally, the development of AI will promote data flow within different businesses and, in some circumstances, across international boundaries. When integrating AI into healthcare operations, systems must be changed to protect patient privacy and confidentiality. Personal data must therefore be anonymized before further distribution is considered. Despite being able to implement these precautions, the healthcare industry is still dubious about secure data sharing.139\n\nAI systems raise safety issues as well. It is necessary to create controls for the effectiveness of AI algorithms. The US Food and Medicine Administration created a new drug classification called \"Software as Medical Device\" to address this problem,140 which is in charge of ensuring patient safety and safe innovation. Ambiguous responsibility in applying AI technologies is a further cause for concern. The replacement of people with autonomous agents raises a number of legal and ethical concerns because the legal system is based on the core tenet that blame and crime are ultimately attributed to people. For the foreseeable future, these challenges will continue to pose a significant challenge to the judicial system.141\n\nThe openness of AI algorithms and data is a major concern. The precision of the annotations and labeling of the training dataset significantly influences the quality of predictions generated by AI systems. Poor outcomes may stem from wrongly tagged data. Clinic-labeled datasets could be of different quality, making the developed AI systems less effective. Additionally, healthcare professionals should be able to argue the results and projections of an AI system and have a complete understanding of them. The interpretability of AI technology is a well-known problem, and much advancement is required before some algorithms, like neural networks, can provide clinical diagnoses or treatment recommendations with total transparency.142\n\n\nConclusion\n\nIn the recent decade, the field of AI has evolved enormously. While breakthroughs in AI, such as neural networking, natural language processing, image identification, and speech recognition, have revolutionized medicine and dentistry in many ways, they are not without downsides and obstacles. One example is the high upfront capital equipment expenses. When applied to clinical medicine, the methods sought for adoption in the medical profession have certain severe limitations. At some point, simple flowcharts and statistical pattern matching become unmanageable. Algorithms frequently make incorrect assumptions, leading to doubt regarding their responsibility in healthcare. Although AI systems are a big help in the field of dentistry and dental education, biological processes are far more complicated, and AI systems will never be able to replace human knowledge, competence, and decision-making capacity.\n\nDespite numerous studies showing potential applications of AI in dentistry, these systems are far from being able to completely replace dental professionals. AI should be viewed as an additional benefit for dentists and other professionals. To ensure that humans can continue to oversee the care and make informed judgments in dentistry, AI must be implemented in a safe and controlled manner. Most institutions are currently unprepared for the duty of providing dental and continuing education training, which is necessary for effective AI integration in dentistry. Additionally, augmented reality (AR) and virtual reality (VR) both benefit from AI. Mixed reality is a novel concept that incorporates parts of generative AI, VR, and AR into computer-superimposed information overlays to improve learning and surgical planning. As many AI systems for various dentistry disciplines are being researched and have yielded promising early results, a future for AI in the healthcare system cannot be ruled out. AI systems offer significant promise as a valuable tool for oral health practitioners.\n\nThe results of this review indicate that embracing AI-based technologies for clinical solutions and dental laboratories enables dentists to digitally repeat procedures and treatments and ensure data sharing throughout the entire digital dental system process. 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Oral Investig. 2022/01/01 2022; 26(1): 651–658. PubMed Abstract \| Publisher Full Text\n\nPoedjiastoeti W, Suebnukarn S: Application of Convolutional Neural Network in the Diagnosis of Jaw Tumors. hir. 07 2018; 24(3): 236–241. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhanagar SB, Alfouzan K, Awawdeh M, et al.: Performance of Artificial Intelligence Models Designed for Diagnosis, Treatment Planning and Predicting Prognosis of Orthognathic Surgery (OGS)—A Scoping Review. Appl. Sci. 2022; 12(11): 5581. Publisher Full Text\n\nCorbella S, Srinivas S, Cabitza F: Applications of deep learning in dentistry. Oral. Surg. Oral. Med. Oral. Pathol. Oral. Radiol. 2021; 132(2): 225–238. Publisher Full Text\n\nRomanini J, Kanomata LM, De Figueiredo RM: ARTIFICIAL INTELLIGENCE: AID IN EARLY ORAL CANCER DIAGNOSIS AT THE DENTAL CLINIC. Oral. Surg. Oral. Med. Oral. Pathol. Oral. Radiol. 2020; 130(3): e282–e283. Publisher Full Text\n\nSingh NK, Raza K: Progress in deep learning-based dental and maxillofacial image analysis: A systematic review. Expert Syst. Appl. 2022; 199: 116968. Publisher Full Text\n\nLee J-H, Kim D-H, Jeong S-N, et al.: Detection and diagnosis of dental caries using a deep learning-based convolutional neural network algorithm. J. Dent. 2018; 77: 106–111. PubMed Abstract \| Publisher Full Text\n\nLeonardi R, Giudice AL, Farronato M, et al.: Fully automatic segmentation of sinonasal cavity and pharyngeal airway based on convolutional neural networks. Am. J. Orthod. Dentofac. Orthop. 2021; 159(6): 824–835.e1. PubMed Abstract \| Publisher Full Text\n\nGil S-M, Kim I, Cho J-H, et al.: Accuracy of auto-identification of the posteroanterior cephalometric landmarks using cascade convolution neural network algorithm and cephalometric images of different quality from nationwide multiple centers. Am. J. Orthod. Dentofac. Orthop. 2022; 161(4): e361–e371. PubMed Abstract \| Publisher Full Text\n\nAmantini SNSR, Montilha AAP, Antonelli BC, et al.: Using augmented reality to motivate oral hygiene practice in children: protocol for the development of a serious game. JMIR research protocols. 2020; 9(1): e10987. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZafar S, Zachar JJ: Evaluation of HoloHuman augmented reality application as a novel educational tool in dentistry. Eur. J. Dent. Educ. 2020; 24(2): 259–265. PubMed Abstract \| Publisher Full Text\n\nLee J-H, Jeong S-N: Efficacy of deep convolutional neural network algorithm for the identification and classification of dental implant systems, using panoramic and periapical radiographs: A pilot study. Medicine (Baltimore). 2020; 99(26): e20787–e20787. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRen R, Luo H, Su C, et al.: Machine learning in dental, oral and craniofacial imaging: a review of recent progress. PeerJ. 2021; 9: e11451. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYamaguchi S, Lee C, Karaer O, et al.: Predicting the debonding of CAD/CAM composite resin crowns with AI. J. Dent. Res. 2019; 98(11): 1234–1238. PubMed Abstract \| Publisher Full Text\n\nLerner H, Mouhyi J, Admakin O, et al.: Artificial intelligence in fixed implant prosthodontics: a retrospective study of 106 implant-supported monolithic zirconia crowns inserted in the posterior jaws of 90 patients. BMC Oral Health. 2020; 20(1): 1–16. Publisher Full Text\n\nLi H, Sakai T, Tanaka A, et al.: Interpretable AI Explores Effective Components of CAD/CAM Resin Composites. J. Dent. Res. 2022; 101: 1363–1371. Publisher Full Text\n\nKurt Bayrakdar S, Orhan K, Bayrakdar IS, et al.: A deep learning approach for dental implant planning in cone-beam computed tomography images. BMC Med. Imaging. 2021; 21(1): 1–9.\n\nRojek I, Mikołajewski D, Dostatni E, et al.: AI-optimized technological aspects of the material used in 3D printing processes for selected medical applications. Materials. 2020; 13(23): 5437. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNg WL, Chan A, Ong YS, et al.: Deep learning for fabrication and maturation of 3D bioprinted tissues and organs. Virtual and Physical Prototyping. 2020; 15(3): 340–358. Publisher Full Text\n\nLiu Y, Shang X, Shen Z, et al.: 3D Deep Learning for 3D Printing of Tooth Model. IEEE. 2019; 274–279.\n\nAriji Y, Fukuda M, Kise Y, et al.: Contrast-enhanced computed tomography image assessment of cervical lymph node metastasis in patients with oral cancer by using a deep learning system of artificial intelligence. Oral. Surg. Oral. Med. Oral. Pathol. Oral. Radiol. 2019; 127(5): 458–463. PubMed Abstract \| Publisher Full Text\n\nKnoops PG, Papaioannou A, Borghi A, et al.: A machine learning framework for automated diagnosis and computer-assisted planning in plastic and reconstructive surgery. Sci. Rep. 2019; 9(1): 1–12.\n\nZanjani FG, Moin DA, Verheij B, et al.: Deep learning approach to semantic segmentation in 3D point cloud intra-oral scans of teeth. PMLR. 2019; 557–571. Publisher Full Text\n\nKim T, Cho Y, Kim D, et al.: Tooth segmentation of 3D scan data using generative adversarial networks. Appl. Sci. 2020; 10(2): 490. Publisher Full Text\n\nLian C, Wang L, Wu T-H, et al.: Deep multi-scale mesh feature learning for automated labeling of raw dental surfaces from 3D intraoral scanners. IEEE Trans. Med. Imaging. 2020; 39(7): 2440–2450. PubMed Abstract \| Publisher Full Text" }	[ { "id": "209464", "date": "17 Oct 2023", "name": "Reham Osman", "expertise": [ "Reviewer Expertise Prosthodontics", "Oral implanvology", "Digital Dentistry", "3D- printing", "Biomechanics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 at hand had described the concept of AI and its different types, its application in health care sector in details and some of its applications in dental field. As well, the article has highlighted the strength and weakness point of technology and came up with some future recommendations.\n\nThe reviewer thinks that a huge effort has been made in writing this review and that it is recommended for publication after addressing all of the below mentioned points.\n\nThe title “Application of AI in Dentistry”\nDifferent paragraphs beneath this title are more towards describing and explaining the application of AI in general health sector generally rather than in dentistry as the title entails;\n\nexample “With the advent of huge scientific data, the diagnosis of human congenital abnormalities has improved. In medical research, the support vector machine (SVM), a machine-learning model, has become a typical way of analysis. SVM may be used to classify complex situations like traumatic brain damage.60,61DL may play a crucial role in advancing cardiovascular medicine due to the requirement for precision in diagnosis and therapy.62 With the adoption of deep learning, it will be feasible to identify numerous cardiovascular disorders with high-precision diagnosis.63 Wearable technology combined with intelligence applications can anticipate a patient's life-threatening crisis such as a stroke, allowing physicians to deliver effective, early therapies.54 Using AI to examine viruses has boosted transitional studies in viral immune monitoring.” This paragraph should be shifted to the title above it “Artificial intelligence for health care”.\nThe title: State-of-the-art AI technology in Dentistry\nSame comment as in previous point. The whole paragraph under this title seems to be describing more the components and different types of artificial intelligence rather than describing Art of AI in dentistry.\n\nReviewer would suggest that the authors rename this paragraph differently so it is not misleading to reader.\n“Taking a dental impression might soon be obsolete due to advancements in intra-oral scanners and cameras. These digital impressions minimize all laboratory operations, which sharply lowers the frequency of errors and is quicker and more accurate.”\nThis is a very sharp statement not supported by current state of art in literature. Digital impressions are effective and comparable to conventional impressions in cases of unilateral partially dentate patients with up to 4 missing units. However, in fully edentulous cases and extensive cases crossing midlines, accuracy of digital impressions is inferior to their conventional counterparts. Digital impression acquisition is challenging in fully edentulous cases because of lack of anatomic landmarks that allow images stitching during the scan process besides mobility of soft tissue especially floor of mouth of arch during scan process of mandibular arches. All of these factors cast a shadow about the possibility of digital impression obliterating the need for conventional impression.\n“Taking a dental impression may soon be a thing of the past thanks to advancements in intra-oral scanners and cameras. In addition to being quicker and more accurate,”\nSame comment as mentioned in point above\nThe reviewer suggests that the authors either modify and rephrase this statement as per current state of literature and add necessary references and citations or totally delete it.\nIn image six, there is a typo error in post-appointment bullets: should be “AI Clinician evaluation”.\n\nResolution of image 3 & image 5 is low, and images are not clear and cannot be easily read, please re-provide with a better resolution one that could be easier read.\n\nUnder the title: “Weakness of AI in Dentistry”.\n\nThe first statement in the paragraph “Diagnostic and treatment expenses are expected to reduce due to betterment in the healthcare field by embedding AI in the system resulting in more early diagnoses of chronic diseases.” is considered an advantage rather than a disadvantage or a weakness.\n\nThe last statement in the first paragraph “However, the disadvantage of the use of AI in dentistry includes” The sentence is incomplete and it is not mentioned what is the disadvantage of using AI in Dentistry.\n\nUnder the title: “oral medicine and pathology”\nThe statement “Because certain oral lesions might be precancerous or cancerous, obtaining an accurate diagnosis and treating the patient appropriately.” The statement is not complete and need to be adjusted.\nCan the authors please add a reference for this statement: “AI may also help alleviate labor scarcities, which have been noted and are projected to remain in many regions of the world, therefore assisting in achieving the sustainable development goals defined by WHO.”\n\nThis Statement “AI may also help alleviate labor scarcities, which have been noted and are projected to remain in many regions of the world” under the weakness of artificial intelligence title is the opposite of increasing the unemployment which is mentioned in Figure 8 and which is properly described as one of AI weakness in health care sector.\n\nUnder the title: “AI application in 3D digital dentistry”\n“Using a digitalized dental system brings real advantages in accuracy and quality, is time-consuming, and decreases costs.” Can the authors please check this sentence that one of the advantages of digital dentistry is time consumption?\n“This provides extremely effective quality management. It enhanced productivity significantly and changed dental laboratories from manufacturers into sophisticated computerized production centers. Increased productivity.” Please delete increased productivity as it does not form a comprehensible sentence.\n\n“Lastly, CAD/CAM technology has enabled the high-precision machining of novel materials such as high-performance ceramics and titanium.” Can the authors please add a reference for this statement.\nFINAL GENERAL RECOMMENDATION: that the authors alter the title of paper into “Contemporary Role and Applications of Artificial Intelligence in Health care sector with specific interest in dental applications”. It is in the reviewer’s opinion will better fit the content of the paper more than the current title. Further, the applications of AI in different fields of dentistry are very briefly described considering\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": [] }, { "id": "212091", "date": "26 Oct 2023", "name": "Hemant Sawhney", "expertise": [ "Reviewer Expertise Artificial Intelligence in Dentistry and Radiology", "Oral Medicine", "Maxillofacial Radiology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary:\nThe manuscript titled \"Contemporary Role and Applications of Artificial Intelligence in Dentistry\" provides a comprehensive overview of the current state of artificial intelligence (AI) in the field of dentistry. The author discusses various applications of AI, from diagnosis and treatment planning to predictive analytics, virtual consultations, and the use of robotics in dental surgery. Overall, the paper is well-structured and informative, making a valuable contribution to the field of AI in dentistry.\nGeneral Comments:\nClarity and Organization: The manuscript is well-organized, with a clear introduction and structured sections that make it easy for readers to follow the discussion.\n\nCitations and References: The paper adequately cites relevant sources to support the discussed points.\n\nDepth of Coverage: The paper covers a wide range of topics related to AI in dentistry, providing a comprehensive overview. However, it might be beneficial to delve deeper into specific case studies or examples of successful AI applications in dentistry to offer a more practical understanding for readers.\n\nTechnical Accuracy: The manuscript appears to be technically accurate, and the concepts related to AI are well-explained. It would be helpful if the author could provide a glossary or definitions for any technical terms that might be unfamiliar to the general reader.\nSpecific Comments:\nCase Studies and Examples: The manuscript could benefit from the inclusion of specific case studies or real-world examples of AI applications in dentistry. This would illustrate the practical benefits of AI to the readers.\n\nEthical and Legal Considerations: It would be valuable to address the ethical and legal considerations surrounding AI in dentistry, such as patient data privacy, liability, and informed consent. This would provide a more well-rounded perspective on the topic.\n\nFuture Trends: Discussing future trends and potential advancements in AI within the field of dentistry could be an excellent addition. This would give the paper a forward-looking perspective and help readers understand the evolving landscape.\nConclusion:\nThe manuscript, \"Contemporary Role and Applications of Artificial Intelligence in Dentistry,\" provides a valuable and informative overview of AI applications in dentistry. To enhance the paper, I recommend including case studies, addressing ethical considerations and discussing future trends. With these improvements, the manuscript will offer a more comprehensive understanding of the topic.\nOverall, this paper contributes to the growing body of knowledge on AI in dentistry and should be considered for publication with the suggested revisions.\nRecommendation: I recommend accepting this manuscript with minor revisions.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "212090", "date": "07 Nov 2023", "name": "Dipmala Salunke", "expertise": [ "Reviewer Expertise Dental image processing", "Deep learning", "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\nSummary of the article:\nThe article provides a detailed exploration of the role of Artificial Intelligence (AI) in dentistry, its potential applications, and its limitations. It covers a range of topics, including AI algorithms, the pros and cons of using AI in dental specialties, and the need for AI to complement rather than replace dental professionals. The article also discusses the integration of AI with augmented and virtual reality technologies in dentistry.\n\nStrengths of the Article:\n\nComprehensive Coverage: The article comprehensively explores the potential applications of AI in various dental specialties and discusses both the advantages and limitations of AI in the field.\nClarity of Purpose: The article clearly states its purpose, which is to assess the advancement of AI algorithms in dentistry and their performance in diagnosis, clinical decision-making, treatment, and prognosis prediction.\nIntegration with Emerging Technologies: The discussion of AI's integration with augmented reality and virtual reality is valuable, as it highlights innovative approaches to dental education and surgical planning.\nReal-World Applications: The mention of AI's potential benefits in clinical solutions and dental laboratories demonstrates the practical advantages of AI in the dental field, such as data sharing, accuracy, and cost savings.\n\nAreas for Improvement:\n\nEthical Considerations: While the article touches on the limitations of AI, it could expand on ethical considerations in more detail, such as patient data privacy, potential biases in AI algorithms, and the need for human oversight in clinical decision-making.\n\nIllustrations: Authors are suggested to include images of good resolution specially, figure number 1.\nConclusion:\nThe article “Contemporary Role and Applications of Artificial Intelligence in Dentistry”, offers a promising exploration of AI's impact on dentistry.However, it could be enhanced by addressing topics such as patient data privacy, potential biases in AI algorithms, and the essential role of human oversight in clinical decision-making.The content of the article is not only informative but also relevant, especially for readers who are starting research in the field of dentistry, therefore, I wholeheartedly recommend accepting this manuscript for publication with reservations outlined above.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1179
https://f1000research.com/articles/12-1178/v1	20 Sep 23	{ "type": "Study Protocol", "title": "Mapping the theories, content, and outcomes of family-based interventions for children and young people with gaming disorder: A scoping review protocol", "authors": [ "Harshini V S", "Mariam Abraham", "Samyuktha Prabhu", "Jing Shi", "Deena Dimple Dsouza", "Harshini V S", "Mariam Abraham", "Samyuktha Prabhu", "Jing Shi" ], "abstract": "Background: Despite the growth of gaming disorders globally, evidence of the formal involvement of family in treating gaming disorders is limited. When children are affected by gaming disorder, the family may encounter challenges in managing the behavior and in the lack of information regarding the gaming disorder, resulting in inconsistent parenting, which may further exacerbate the problem. Thus, it is essential to involve the family in formal interventions. The current scoping review plans to identify the theories, content, and outcomes of family-based interventions for children and young people with gaming disorders. Methods: This scoping review will follow the Joanna Briggs Institute (JBI) methodology. The population, Concept, and Context (PCC) were used to develop the review question. The studies published in the indexed databases will be searched systematically, and the reference list of included full texts will be searched for relevant studies. Intervention studies published in English from January 2010 to December 2022 will be included. Two independent reviewers will screen the studies against eligibility criteria. The data will be extracted and presented in a tabular and narrative style. Discussion: This scoping review will help better understand content, outcomes, and theories underpinning family-based interventions for children and young people with gaming disorders. Findings will inform the stakeholders about the current topic and guide the potential research areas. Registration details: The protocol has been registered in Open Science Framework with the DOI: https://doi.org/10.17605/OSF.IO/TXWBH", "keywords": [ "Gaming Disorder", "Family-Based Interventions", "family", "scoping review", "video gaming", "treatment" ], "content": "Introduction\n\nOnline gaming is a popular leisure activity in the present digital age. The highly evolving process includes no gaming to occasional gaming, high-frequency gaming, and uncontrolled gaming. Online gaming has attracted an increasing number of children and adolescents1 i. Furthermore, its availability 24/7 makes online gaming possible to engage children and adolescents any time of the day and for a prolonged period. Undoubtedly, the Coronavirus disease 2019 (COVID-19) pandemic has caused increased numbers in gaming disorders2.\n\nGaming may become problematic if it causes disruptions in school and work life3,4, sleep5–7 and social life5. Dysfunctional gaming patterns have become a significant concern for children and adolescents in recent years, with increasing research publications since the World Health Organization’s inclusion of gaming disorders in the International Classification of Diseases 11th edition8. Problematic gaming behavior may not be connected only to intra-personal characteristics of an individual but also involve social variables, including parental and family factors9.\n\nThe family is the primary unit for social skills development for children, and the parent-child relationship remains vital. Families assist in organizing a child’s daily needs, and a supportive family offers the most reliable network throughout childhood, early adulthood, and beyond. The family develops a special emotional bond with their child through nurturing10. From a clinical perspective, including families in intervention is critical as parents may help regulate the gaming behavior of children and young people, as positive parenting and family dynamics were associated with decreased rates of problematic gaming while positive attachment with parents was associated with lower rates of problematic gaming9. However, an authoritative or demanding parenting style correlated with higher rates of problematic gaming9. In addition, the dysfunctional family relationship also contributed to an increase in gaming behavior11.\n\nA dearth of literature exists on interventions to prevent or treat gaming disorders. The current interventions available for gaming disorders include cognitive behavioural therapy, family therapy, motivational interviewing, individual counselling, solution-focused therapy, and combinations of these12. Despite the growing gaming behavior among children and young people, there is limited research on family-based interventions. Including parents in the intervention promotes children’s initial engagement and ongoing participation. It also helps the parents learn to set limits on playing video games and (re)establish communication with children13. To the best of our data search, no previous reviews have been carried out to methodically map and categorize family-based interventions for children and young people with gaming disorders. Therefore, this review is aimed to map the theories, content, and outcome of family-based interventions.\n\nThis scoping review aims to map the theories, content, and outcome of family-based interventions for children and young people with gaming disorders.\n\n1. What are the theories, content, and outcomes presented across interventions for families with children and young people with gaming disorders?\n\n2. Which interdisciplinary health care professionals (e.g., educational background, qualifications) are involved in family-based interventions for children and young people with gaming disorders?\n\n3. What functional outcomes are reported regarding family-based interventions with children and young people with gaming disorders?\n\n\nProtocol\n\nThis scoping review is developed following Joanna Briggs Institute (JBI) Manual for scoping review14. The results will be reported according to the Preferred Reporting Items for Systematic Reviews and the Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The Population, Concept, and Context (PCC) were used to develop the review question. JBI manual for scoping review guides the inclusion of studies that will be included in this review. A pilot search of PubMed and the Cochrane Database of Systematic Reviews was conducted, and no reviews were identified. If there are any changes to the protocol, the final review will amend with justification. The primary outcome of this review is to identify the theories, content and outcome of family-based interventions for children and young people. The secondary outcome health professionals involved and the functional outcome. The scoping review protocol is registered on 23rd April 2023 in Open Science Framework (Registration DOI: https://doi.org/10.17605/OSF.IO/TXWBH)15.\n\nParticipants. This scoping review will consider the studies investigating family-based interventions to prevent or treat gaming disorders between parents of children and young people, primary caregivers, and professionals (psychiatrists, nursing, occupational therapist, and schoolteachers). The age range selected for children is from (0–10 years) and young people from (10–24 years), a term used by World Health Organization to combine adolescence and youth16. Studies with participants receiving unimodal or multi-model family-based interventions will also be included. Studies with children and young people with co-occurring conditions will also be considered.\n\nConcept. The concept of interest is any research addressing family-based interventions to prevent or treat gaming disorders for children and young people. The review will consider family defined as parents, primary caregivers such as grandparents who live with the child, and legal guardians. The studies included in this review must explicitly discuss family-based interventions for gaming disorders. In addition, the program development and validation of family-based interventions will be considered.\n\nContext. This scoping review will consider studies involving family-based interventions for children and young people with gaming disorders conducted in physical contexts such as schools, hospitals, private clinics, outpatients, community, or digital platforms. The studies eligible for review will not be limited to any geographical location.\n\nTypes of evidence sources. This scoping review will consider all interventional studies, such as randomized controlled trials, pre-test-post-test study designs, non-randomized controlled trials, quasi-experiments, pilot studies, case series, case reports, and prospective and retrospective clinical studies. In addition, reviews and mixed-method studies will be included. Qualitative studies focusing on developing and evaluating the effects of interventions will also be eligible. The following studies will be excluded: studies that are not written in English, conference presentations, abstracts, theses, studies with participants older than 24 years old and studies published before 2010.\n\nStudies published in indexed databases PubMed, Scopus, EMBASE, and CINAHL will be searched. An initial search was developed and trailed in PubMed, Scopus, and CINAHL. Subsequently, the most suitable keywords and indexed terms were identified, and a complete search strategy was developed and trailed in PubMed, Scopus, and CINAHL. The strategy was adapted for each search since the index terms varied in some databases (Table 1). A librarian was consulted with search terms, words, and databases. Reference lists of included studies will be hand searched to identify other relevant studies. The studies published in the years 2010–2022 will be included in the review. An extensive study range was considered, as no previous reviews were published on family-based interventions for children and young people with gaming disorders.\n\n*MeSH headings will be used in PubMed when appropriate\n\nThe studies will be collated and exported to Microsoft Excel for Microsoft 365 with citation details and abstract keywords from all the electronically searched databases. Subsequently, duplicates will be removed. The two independent reviewers will screen selected sources' titles and abstracts to identify the eligibility criteria for full-text extraction. The reason for exclusion will be recorded in the scoping review presented in a PRISMA-ScR. A third reviewer will be consulted for any conflicts. The final results of the search will be reported in the scoping review and represented in the PRISMA-ScR flow diagram17.\n\nTwo independent reviewers will extract the data, and the third reviewer will be consulted on any discrepancies and perform a final check. The data to be extracted is outlined in Table 2 with the basic summary of the studies. The main interest of the review is presented in Table 3.\n\nA summary table will be provided with detailed information on every included source as per the predefined data extraction sheet. We will summarize the first objective by grouping the theories used in family-based interventions along with content of the development program and what was the outcome of the intervention. The second objective will list health care professionals involved in the intervention. The third objective will report the functional outcome of the intervention. Descriptive analysis will include frequencies of theories used and outcomes. Furthermore, the findings will be described in a narrative style, organized according to the theories underpinning the family-based interventions.\n\n\nEthics and dissemination\n\nWe will conduct the scoping review of existing studies and will not recruit any participants directly; thus, ethical approval will not be required. We intend to submit the paper for publication in a peer-reviewed journal.\n\n\nStudy status\n\nWe have developed the keywords for the search strategy and will run the search in predefined databases by the end of August 2023.\n\n\nDiscussion\n\nFamily-based interventions' underpinning theories and content with children and young people with gaming disorders are relatively new. A scoping review will be the best method as it will ensure the literature covered is as broad as possible from all the multidisciplinary studies. It is anticipated that the results of this review will provide clear and in-depth evidence of the theories applied in family-based interventions. Publishing a planned scoping review protocol is in keeping the good transparent research practice. The synthesized knowledge will describe family-based interventions and the theories, content, and outcomes they entail. This review will help inform various stakeholders, including researchers, clinicians, and therapists from various disciplines, on the importance and applications of family-based interventions. The outcome of the scoping review will also inform future research planning. For example, researchers can collaborate with the existing family-based interventions that various healthcare professionals, organizations and schools implement, and evaluate them in different locations and cultures. The limitations expected in the scoping review will be only studies published in English will be included, studies with important data is missed if published in other languages.", "appendix": "Data availability\n\nNo data associated with this article.\n\nOSF: Mapping the theories, content, and outcomes of family-based interventions for children and young people with gaming disorder: A Scoping Review Protocol. https://doi.org/10.17605/OSF.IO/TXWBH15\n\nOSF: PRISMA-P and PRISMA-ScR checklist for “Mapping the theories, content, and outcomes of family-based interventions for children and young people with gaming disorder: A Scoping Review Protocol” https://doi.org/10.17605/OSF.IO/TXWBH15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nStevens MW, Dorstyn D, Delfabbro PH, et al.: Global prevalence of gaming disorder: A systematic review and meta-analysis. Aust N Z J Psychiatry. 2021; 55(6): 553–568. PubMed Abstract \| Publisher Full Text\n\nHan TS, Cho H, Sung D, et al.: A systematic review of the impact of COVID-19 on the game addiction of children and adolescents. Front Psychiatry. 2022; 13: 976601. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrunborg GS, Mentzoni RA, Frøyland LR: Is video gaming, or video game addiction, associated with depression, academic achievement, heavy episodic drinking, or conduct problems? J Behav Addict. 2014; 3(1): 27–32. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuss DJ, Griffiths MD: Online gaming addiction in children and adolescents: A review of empirical research. J Behav Addict. 2012; 1(1): 3–22. PubMed Abstract \| Publisher Full Text\n\nTurel O, Romashkin A, Morrison KM: A model linking video gaming, sleep quality, sweet drinks consumption and obesity among children and youth. Clin Obes. 2017; 7(4): 191–198. PubMed Abstract \| Publisher Full Text\n\nHawi NS, Samaha M, Griffiths MD: Internet gaming disorder in Lebanon: Relationships with age, sleep habits, and academic achievement. J Behav Addict. 2018; 7(1): 70–78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKristensen JH, Pallesen S, King DL, et al.: Problematic gaming and sleep: a systematic review and meta-analysis. Front Psychiatry. 2021; 12: 675237. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShi J, van der Maas M, Yu L, et al.: Current prevention strategies and future directions for problem Internet use. Curr Opin Behav Sci. 2022; 48: 101231. Publisher Full Text\n\nNielsen P, Favez N, Liddle H, et al.: Linking parental mediation practices to adolescents' problematic online screen use: A systematic literature review. J Behav Addict. 2019; 8(4): 649–663. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorris AS, Silk JS, Steinberg L, et al.: The role of the family context in the development of emotion regulation. Soc Dev. 2007; 16(2): 361–88. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTorres-Rodríguez A, Griffiths MD, Carbonell X, et al.: Internet gaming disorder in adolescence: Psychological characteristics of a clinical sample. J Behav Addict. 2018; 7(3): 707–718. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZajac K, Ginley MK, Chang R: Treatments of internet gaming disorder: a systematic review of the evidence. Expert Rev Neurother. 2020; 20(1): 85–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonnaire C, Liddle HA, Har A, et al.: Why and how to include parents in the treatment of adolescents presenting Internet gaming disorder? J Behav Addict. 2019; 8(2): 201–212. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeters MDJ, Godfrey C, McInerney P, et al.: Best practice guidance and reporting items for the development of scoping review protocols. JBI Evid Synth. 2022; 20(4): 953–968. PubMed Abstract \| Publisher Full Text\n\nDsouza DD, Shi J, Harishini VS, et al.: Mapping the theories, content, and outcomes of family-based interventions for children and young people with gaming disorder: A Scoping Review Protocol.OSF. [Data], 2023. http://www.doi.org/10.17605/OSF.IO/TXWBH\n\nWorld Health Organization: Adolescent health. World Health Organization. (n.d.-a). Retrieved January 30, 2023. Reference Source\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann Intern Med. 2018; 169(7): 467–473. PubMed Abstract \| Publisher Full Text" }	[ { "id": "233826", "date": "07 Feb 2024", "name": "Ben J Riley", "expertise": [ "Reviewer Expertise Problem gambling", "cognitive behavior therapy", "literature reviews" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article reports a priori protocol for a scoping review. The scoping review intends to review the theories, content, and outcomes of family-based interventions for children and young people with gaming disorder.\nAbstract The abstract is clear and provides all the necessary information.\nIntroduction The term online gaming is introduced. Gaming can of course occur both on and offline. The opening paragraph suggests this scoping review will focus on online gaming. If this is correct, I suggest an explanation as to why online gaming is the focus along with a distinction between on and offline gaming (gaming disorder naturally can include both on and offline gaming). If the focus is not intended to be online gaming only, I suggest removing the first word “Online” and simply opening with “gaming”.\n\nThe negative effects of excessive gaming are often sensationalised by the media. Gaming indeed increased during COVID-19, however, this was also associated with many benefits for people (as several articles report). Gaming, as we know, has many benefits for young and older people. I like to see a sentence or two noting such benefits in the introductions of articles that address the harms associated with gaming. E.g., “While there are several positive effects of engaging in gaming such as [creativity, cognition, social, physical…] excessive gaming can be harmful….”\nThe justification for the scoping review is sound. The three review questions are clear and measurable.\nProtocol A word is missing from the sentence “The secondary outcome health professionals…” suggestion: “The secondary outcomes comprise health professionals involved, and the functional outcome reported.” Are there two or three outcomes – later in the protocol it refers to three objectives. Please check this sentence. It may be clearer to write “The second and third objectives comprise health professionals involved and the functional outcome.”\nEligibility criteria Check if “between” is the correct word for the sentence This scoping review will consider the studies investigating family-based interventions to prevent or treat gaming disorders between parents of children and young people, primary caregivers, and professionals (psychiatrists, nursing, occupational therapists, and schoolteachers). “among” may be a better word.\nContext Were online/internet-delivered interventions considered? If not, I suggest make it clear if they were excluded.\nTypes of evidence sources. If grey literature will be excluded, I suggest making this clear. E.g., “This scoping review will consider all peer-reviewed interventional studies, such as…” Then add “grey literature” to the sentence that lists the exclusion criteria.\nI suggest please justify why the search will involve articles published from 2010. Yes, 12 years is an extensive range, however, internet gaming took off in the '90s; why limit it to 2010-22? This is not a problem, but the decision should be justified.\nDiscussion A further limitation will be articles published before 2010 will not be included.\nI hope these comments are helpful, and best of luck with this interesting and relevant review.\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": "252048", "date": "09 Mar 2024", "name": "Marcos Bella-Fernández", "expertise": [ "Reviewer Expertise Literature reviews", "video games", "gaming disorder." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article describes a protocol for a scoping review which the authors are intended to perform on family-based interventions in gaming disorders in young patients (children, adolescents, and young adults). Family-based interventions have been designed to treat gaming disorders on the basis that family and social variables may impact its appearance and treatment.\nAbstract The abstract clearly summarizes the goal and the rationale of this scoping review. It also emphasizes that the protocol is registered in OSF. No improvement is needed.\nIntroduction The background states that gaming disorder is a prevalent disorder among young people. Research on gaming disorder is growing to the point that it was included in the ICD-11 as a disorder. I would add that it was also recently mentioned in the DSM-5-TR under the name of Internet Gaming Disorder.\nThe introduction focuses on therapies and specifically on family-based interventions. They also argue that family and social variables have an impact on gaming disorder appearance; here lies the rationale for this type of interventions.\nReview question The authors pose three review questions, regarding the theories, content, and outcomes of these interventions, which professionals administer them, and the reported functional outcomes. The questions are scientifically sound and easily operationalized. I have no comments on them.\nProtocol The authors will follow the Joanna Briggs Institute Manuslfor scoping review. I am not familiar with this, so perhaps the authors could briefly say what characterizes this manual, if that is possible. They will elaborate a report following the PRISMA-ScR guidelines. There is one sentence in the protocol paragraph which appears to have something missing: \"The secondary outcome health professionals involved and the functional outcome\". Maybe it should be something like: \"The secondary outcome is health professionals involved and the functional outcome\"?\nThe authors used the Population, Concept, and Context approach to develop the research questions. As mentioned earlier, the questions are perfectly developed in my opinion.\nRegarding the sources, the authors are in general including peer-reviewed articles and excluding these and other grey literature sources. Also, the syntaxes described in Table 1 appear to we exhaustive enough to capture many valuable entries, so perhaps grey literature is not necessary in this review. However, if the authors see that they have not retrieved a sufficient number of entries, perhaps they will have to contemplate including these and other grey literature. I would also suggest the authors to include searches in PsycInfo, apart from the many other databases they are already going to use.\nThe plan to present and disseminate the results seems perfectly valid for me. The only issue is the date for the research; perhaps it should be updated if the authors have not performed the searches in August 2023.\nIn summary, this scoping review promises to be a valuable addition to the existing literature. Best of luck with it.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1178
https://f1000research.com/articles/12-1177/v1	20 Sep 23	{ "type": "Study Protocol", "title": "Comparative evaluation of the efficacy of BlueM active oxygen gel and Coe-pak dressing on post-operative healing of gingival depigmentation: a study protocol", "authors": [ "Shweta Bhagat", "Priyanka Jaiswal", "Deepika Masurkar", "Priyanka Jaiswal", "Deepika Masurkar" ], "abstract": "Introduction Dark colored gingiva is an esthetic concern that cannot be ignored, especially when accompanied by a high lip line or gummy smile. Gingival depigmentation is a periodontal plastic surgical procedure wherein the hyperpigmentation is removed or reduced by various techniques. Protecting the wound from mechanical trauma and stability of the surgical site during the healing process are among the most important advantages of periodontal dressing application after surgery. Aim This study is aimed to comparatively evaluate the effectiveness of reactive oxygen gel species (BlueM gel) and the traditional Coe-Pack dressing on gingival healing and pain after surgical depigmentation. Protocol This split-mouth randomized clinical trial will be conducted on 20 patients aged 18–45 years with maxillary physiologic gingival pigmentation classes (II) (III) and (IV) according to the Dummett–Gupta Oral Pigmentation Index (40 treated sites). The maxilla will be randomly divided into two symmetrical parts—from the right second premolar to the midline and from the midline to the left second premolar—to receive either BlueM gel or Coe- Pack as a dressing after surgical depigmentation with a scalpel. Various indices will be assessed, such as plaque index, papillary bleeding index, pain index, healing index and reepithelization index with toluidine blue, and the follow-up period will be one month. Expected results- A total of 20 patients will be included in this study. Statistically significant differences are expected to show in the pain index and healing index after one, two, three, four, and five days. The BlueM gel group is expected to show a higher significant difference after one, two, three and four weeks in the reepithelization index.", "keywords": [ "Keywords- Gingival pigmentation", "Scalpel technique", "BlueM gel", "Active oxygen species", "Coe-pack", "wound healing", "Gingival hyperpigmentation", "Esthetics." ], "content": "Introduction\n\nThe smile is a significant element of social relationships and has an immense effect on making a positive first impression because it conveys emotions and confidence. Dark-coloured gingiva looks aesthetically unpleasant and is a matter of concern that should be taken into account, especially with a gummy smile or high lip line. Dark pigmentation is frequently caused by an excessive accumulation of melanin in the gingival epithelium; a brown pigment that can range in colour from pale pink to dark brown. In every ethnic group, gingiva have some degree of melanin pigmentation, which is a physiological process, and its presence is not indicative of risk.1\n\nPeriodontal plastic surgery called gingival depigmentation uses a range of techniques to eliminate or to reduce hyperpigmentation. The primary rationale for depigmentation in patients is a desire for better aesthetics.2 One of the earliest and most widely used methods used is the scalpel technique which requires removal of undesirable pigmentation of epithelium of gingiva and underneath connective tissue layer with surgical scalpel. Thus, the connective tissue denudation healing occurs by secondary intention. It is a conventional, simple, non-invasive, and economical technique.3 But also, it results in an open wound where bleeding tissues are visible, and it heals by secondary intention. Thus, to reduce undesirable bleeding, pain, and the possibility of postoperative infection, a periodontal dressing must be required.4\n\nDr. A.W. Ward pioneered the use of periodontal dressings in 1923 and recommended using them after periodontal surgery. One of the key advantages of using periodontal dressings is preventing mechanical damage to the wound and maintaining stability at the surgical site throughout the healing process after surgery. Other advantages includes decrease in tooth hypersensitivity in the early postoperative hours, providing additional comfort as the surgical site heals, providing support in free gingival grafts, preventing post-operative haemorrhage or infection, protecting the clot from pressures generated by speech or mastication, preventing detachment of gingiva from the surface of the root, preventing coronal flap displacement in apically repositioned flaps, and preserving and protecting denuded bone during the process of healing.5\n\nOver the years, composition of the periodontal dressing has been modified. There are three distinct categories of materials: those that contain both eugenol and zinc oxide (Ward’s Wonderpak), those that contain zinc oxide only (Coe-Pak, PeriPac, Vocopac, SeptoPack, Periocarea), and those that don’t have zinc oxide and eugenol (Resopac, Mucotect, Barricaid).5\n\nThe cytotoxic effects of Coe-Pak may become more pronounced with continued use and cause oral allergenic reactions and allow plaque to build up underneath them thus, slowing the healing process.5\n\nBlueM gel has components that release oxygen in addition to antibacterial elements which provides therapeutic effects such as neovascularization, eliminating toxins, aids in the stimulation and synthesis of new blood cells, increases stem cell proliferation which promotes faster healing, and has antihistamine and antimycotic effects.1\n\nTherefore, the current study will be implemented to overcome the limitations of the periodontal dressings as there is the scarcity of the literature regarding newer material. BlueM gel will therefore present novel perspectives on the proper management of a periodontal dressing.\n\nTo compare the effectiveness of BlueM active oxygen gel with Coe-pack dressing on post-surgery healing of gingival depigmentation in a split-mouth trial.\n\n\n\n1. To evaluate the effectiveness of BlueM oxygen gel on pain, healing of the gingival tissue and reepithelization acceleration on post-operative gingival depigmentation healing.\n\n2. To evaluate the effectiveness of Coe-pack dressing on pain, healing of the gingival tissue and reepithelization acceleration on post-operative gingival depigmentation healing.\n\n3. To compare the effectiveness of BlueM active oxygen gel and Coe-pack dressing on pain, healing of the gingival tissue and reepithelization acceleration on post-operative gingival depigmentation healing.\n\nComparative split-mouth randomised parallel group trial will be performed at the Sharad Pawar Dental College, Datta Meghe Institute of Higher Education and Research, Sawangi, Meghe, from the outpatient department of periodontics. 20 systemically healthy patients with maxillary gingival hyperpigmentation will be selected using following criteria.\n\nInclusion criteria\n\n• Patients with maxillary gingival hyperpigmentation\n\n• Age between 18 and 45 years.\n\n• Patient with scoring criteria for Dummet Oral Pigmentation (DOP) index >1\n\nExclusion criteria\n\n• Recent periodontal surgery within the last three months\n\n• Gingival hyperpigmentation linked to many disorders and lesions\n\n• Plaque and gingivitis indices scores more than 1 and\n\n• DOP index scores lower than 1 were excluded.\n\n• Smokers\n\n• Pregnant and lactating women\n\n• Patients with medically compromised health\n\nCoe-Pack dressing\n\nThe well-known non-eugenol periodontal dressing, Coe-Pack, is composed of two pastes: a base paste and a catalyst paste to physically protect the surgical sites. The Coe-Pack dressing will be applied to the denuded sites in the control group during surgery, and it will be removed out at the initial recall appointment after one week.1\n\nBlueM oxygen gel\n\nIngredients like sodium perborate and honey enzymes are used in an active oxygen formula (Blue M gel). In the affected tissues, it is capable of releasing oxygen at a therapeutic concentration. BlueM gel contains additional antibacterial components along with its oxygen-releasing elements.1\n\nInitial therapy\n\nThe objectives will be discussed and explained to the patients. Before enrolling them, informed consent will be acquired orally and in writing by the primary investigator. After proper oral examination and diagnosis, initial treatment will be carried out including scaling until a plaque score of 1 or less is achieved plaque control instructions will be reinforced. Oral hygiene instructions will be given. Ethical committee of Datta Meghe Institute of Higher Education and Research will first provide its approval to the study protocol before it may proceed further.\n\nAt baseline, clinical parameters will be assessed and again at the first, second, third, and fourth weeks, respectively, prior to the surgical procedures. These are:\n\n1. Patient with scoring criteria for Dummet Oral Pigmentation (DOP) index >1\n\nScore 0: Pink tissue (No clinical pigmentation)\n\nScore 1: Mild light brown color (Mild clinical pigmentation)\n\nScore 2: Medium brown or blue -black tissue (Heavy clinical pigmentation)\n\nScore 3: Deep brown or blue -black tissue (Heavy clinical pigmentation)6\n\n2. Plaque index at first week, sixth weeks and three months post-surgery.\n\n3. Papillary bleeding index will be assessed at six weeks and three months after surgery.\n\n4. Pain index i.e severity of pain experienced after 2 hours (as soon as the effect of anesthesia gets resolved), and after 24 hours, 48 hours, after 72 hours will be marked post-operatively and assessed by Visual analogue scale (VAS).\n\nAll the patients will be asked to mark the level of pain (0–10) experienced on each side based on the numeric pain rating scale (Visual Analog Scale, VAS) where scores will suggest the level of pain from “no pain” to “severe pain” [0 = no pain; 1–3 = mild pain; 4–6 = moderate pain; 7–10 = severe pain].7\n\n5. Healing index- Early healing index [Wachtel et al.] or postoperative healing will be assessed after 1- and 2-weeks post-surgery by EHI differentiating into five different closure types.8\n\na. Complete flap closure – no fibrin line in the interproximal area\n\nb. Complete flap closure – fine fibrin line in the interproximal area\n\nc. Complete flap closure – fibrin clot in the interproximal area\n\nd. Incomplete flap closure – partial necrosis of the interproximal tissue\n\ne. Incomplete flap closure – complete necrosis of the interproximal tissue\n\n6. Reepithelization index- All surgically depigmented sites on test and control group will be stained with toluidine blue at one-week, two-week, three-week and four-week follow-up postoperatively.\n\n20 systemically healthy patients will be selected which will be considered suitable for the study after initial therapy. Prior to surgery, randomly 20 defects from the test and control groups will be assigned to each group by a coin flip in keeping with a randomised parallel design and sequentially numbered.\n\nFollowing all the aseptic precautions, two symmetrical halves of the maxillary gingival pigmentation between the two second premolars will be divided. Each half will undergo the required steps: Using a no. 15 surgical blade, the entire gingival epithelium’s pigmented layer and layer of connective tissue underlying will be removed after topical anaesthesia with 2% lidocaine has been given. The depigmentation procedure will be carried out, and procedure will be continued till the removal of pigmented layer. Direct pressure will be applied with a sterile gauze to control haemorrhage during surgery.\n\nEach half will undergo surgical depigmentation using a conventional scalpel, with a one-week interval to assess pain indices and reepithelization indices accordingly. As a postoperative dressing, Coe-Pack or Blue gel will next be distributed at random to the split sections. After the procedure, periodontal dressing will be applied over the open wound. In the test group. The depigmented area will be covered with BlueM oxygen gel, whereas the control group will be provided with Coe-Pack periodontal dressing and will ask patient to apply BlueM gel three times per day for one week at home. Patients will be recalled for follow up visit after 24 hours and 1 week post-operatively for the removal of Coe-pack dressing.\n\nThere will be no special criteria for discontinuing or modifying allocated interventions.\n\nThere will be follow ups involved in the study and outcomes will be checked at the specific time points for each outcome.\n\nThere is no concomitant care permitted or prohibited during the trial as this is a surgical procedure carried out for the purpose of improving aesthetics.\n\n\n\n1. Assessment of pain based on the numerical scale for grading pain will be done by Visual analogue scale (VAS) i.e severity of pain experienced post-operatively. Patients will be addressed to rate their degree of pain (0–10) each side after two hours (immediately after the anaesthetic effect subsided), after twenty-four hours, after two days, and after three days, respectively.7\n\n2. Reepithelization index study\n\nToluidine blue staining will be performed on all surgically depigmented sites in the respective test groups and control groups at the postoperative follow-up intervals of one, two, three, and four weeks. 1% Toluidine Blue solution is used in accordance with the application protocol to measure re-epithelialization. The patient is instructed to rinse for 20 seconds with water to get rid of food particles, then to rinse for 20 seconds with 1% acetic acid to eliminate salivary components. Then, using a piece of cotton, 1% toluidine blue is applied for 20 seconds. In addition, participants rinse for again 20 seconds with 1% acetic acid. After that, sterile water is used to rinse for 20 seconds with a syringe. The amount of stain that a given area absorbs reflects the inflammatory concentration beneath it. The presence of inflammatory cells in the operated area is well demonstrated by the toluidine blue score. Connective tissues bind to toluidine blue dye, which gives them a blue colour. Therefore, if dye is not retained it suggests that clinically, the wound is healed which indicates the formation of keratinized epithelium. The interpretation depends upon the colour. When no colour is visible, it is considered as a negative stain otherwise a heavy blue stain is viewed as positive, a light blue stain as questionable.9\n\nThe results will be recorded on the 7th, 14th, 21st, 28th day post-surgery by putting the cellophane sheet over the surgical site. The cellophane sheet’s dark blue color’s surface area is calculated. The overall wound area is subtracted from the dark blue area to determine the re-epithelialization surface area. At one week, two-week, three-week, and four-week follow-ups, complete reepithelization of gingiva in the BlueM group and Coe-Pack group will be assessed, respectively.10\n\nClinical measurements to record will be plaque index, papillary bleeding index, pain index, healing index and reepithelization index. For three days following surgery, analgesics like Ibuprofen 400 mg or Paracetamol 500 mg twice a day will be prescribed. Patients will be asked to rinse with 0.2% chlorhexidine gluconate twice daily for a period of six weeks. One week after surgery, the periodontal dressing will be taken off. For six weeks after treatment, chewing or mechanical oral hygiene procedures are prohibited, and given cleaning instructions for an extra two to three weeks after treatment using cotton pellets soaked in 0.12% chlorhexidine gluconate and later using a soft toothbrush. Following this period, patients will be instructed to resume mechanical oral hygiene practices, such as gentle brushing with a soft toothbrush, using an interdental brush to clean between teeth, and discontinue chlorhexidine usage.\n\nPatient recalls will take place at 1st, 2nd, 3rd day and 4th day for assessment of pain and after 1st, 2nd, 3rd, and 4th week post operatively for assessment of healing and re-epithelization.\n\nAt follow-up appointments, a thorough post-operative evaluation will be carried out. The clinical parameters will all be assessed.\n\n20 patients in all will be a part of this study. After one, two, three, four, and five days of using BlueM gel, statistically significant differences are anticipated to appear in the pain index and healing index. After one, two, three, and four weeks, the reepithelization index is anticipated to show a higher significant difference in favour of the BlueM gel group.\n\n\nDiscussion\n\nHuman Post-operative pain is reduced with use of periodontal dressing.11\n\nIn comparison to the control group, the percentage of sites with PPD 5 mm or more was considerably lower in the periodontal dressing group. There may be fewer periodontal dressing group sites that require surgery.12\n\nBy preventing the coagulum from detaching, periodontal dressings can promote healthy healing and improve periodontal indices. The test group experienced a higher PD reduction, measuring 2.4 0.6 mm on average. The improvement in parameters following scaling and root planning procedure is evident from the difference in PAL, which was 2.5 0.4 mm.13\n\nPain score was significantly lower in periodontal flap surgical sites with periodontal dressing.14\n\nBlueM oral gel is a newer formula developed for dental professionals as a local drug delivery system. Wound healing improves significantly due to intensified levels of oxygen which can be delivered to periodontal pockets and oral wounds.15\n\nAccording to Juliana et al. 2022, 50% of patients in the BlueM group had no pain or just mild to moderate discomfort after surgery, but in the Coe-Pack group, after two hours, 30% had no pain, and 70% had just slight pain. After 24 hours, BlueM group experienced 50% no pain and 50% mild pain, compared to 20% no pain, 50% mild pain, and 30% moderate pain in the Coe-Pack group. After two days, 90% of the patients in the BlueM group reported no pain, while 10% reported mild pain, whereas 30% in the Coe-Pack group reported no pain, 40% reported mild pain, and 30% reported moderate pain. After three days, BlueM group had no pain, compared to 20% of the patients in the Coe-Pack group who had no pain, 80% had mild pain, and 20% had moderate pain.1\n\nThe participant timeline is as follows: 01 September 2023 to 01 March 2024.\n\nFigure 1 shows the Flow diagram for patient recruitment.\n\nSample size will be calculated using the reference from the previous study1 using OpenEpi (version 1), open-source calculator – SS Mean (calculation shown at the end).\n\nRatio of sample size (Group 1/Group 2) = 1:1\n\nSample size in Group 1 is 20\n\nSample size in Group 2 is 20\n\nTotal sample size 20\n\nSample size depends on the true mean difference, d, standard deviations for the two groups, and a level of significance α (type\|error), and the power. The total sample size n=n1+n0 is minimized when r = σ1/σ0.\n\nWith the calculation above, a sample size of 20 was determined. To accommodate for dropouts, an estimated sample size of 20 samples per group was used. 20 is the total sample size required to achieve a 90% confidence level.\n\nPrincipal investigator of the department will enrol participants and will assign participants to interventions by flipping the coin and thus sequentially numbered. Trial participants will be blinded.\n\nPatients will be evaluated for primary and secondary outcomes at baseline, one month and three months. The data collected from participants will be entered on case history proforma which also includes the personal information of the participants.\n\nElectronic data management will be done by entering the data from patients into the database by principal investigator.\n\nFor the pain index and re-epithelization index, the mean and standard deviation (Mean SD) values will be determined. Data from the baseline up to four weeks for each treatment group will be correlated using a paired t-test of the students. Comparisons between treatment groups will be made at baseline, 24 hours, 48 hours, 36 hours, and 48 hours as well as at the first, second, third, and fourth weeks using the student’s unpaired t test. The observed difference will be considered significant if the probability value (p) is less than 0.05 and non-significant if it is greater than 0.05.\n\nThe study will be monitored till completion by DMC which includes PG Guide, head of the department, research convener and chief advisor of university research cell.\n\nPrincipal investigator (PI) will have access to these interim results and make the final decision to terminate the trial.\n\nData will be collected, assessed, and spontaneously reported during adverse events and other unintended effects of trial interventions or trial conduct.\n\nThe project management group meet will review the trial conducted every month. The trial steering group and the independent data monitoring and ethics committee meet will review and conduct the trial period till the trial is complete.\n\nThe results will be published in an indexed journal.\n\nProcedures will be performed in keeping with the ethical standards of the institutional and/or national research committee. This protocol is permitted by the Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research, Sawangi, Meghe, Wardha [Ref.No. DMIHER (DU)/IEC/2023/1085].\n\nIn order to protect confidentiality personal information about potential and enrolled participants will be managed by keeping the records in the computer and protected by password.\n\nOnly principal investigator, co-principal investigator and institutional ethics committee will have access to the final trial dataset.\n\nModel consent form and other related documentations will be given to the participants and authorised surrogates.\n\nPersonal information about potential and enrolled participants will be collected and maintained in order to protect confidentiality before, during, and after the trial.\n\nNot yet started.", "appendix": "Data availability\n\nNo data is associated with this article.\n\nZenodo: Spirit checklist for protocol titled Comparative evaluation of the efficacy of BlueM active oxygen gel and Coe-pak dressing on post-operative healing of gingival depigmentation: A study protocol. DOI: 10.5281/zenodo.8213548\n\n\nAcknowledgements\n\nI acknowledge the help from my university, college, professors, department, statistician and resources which provided the necessary data and their inputs for this given clinical study.\n\n\nReferences\n\nJuliana H, Tarek S: Comparative study of the effect of BlueM active oxygen gel and coe-pack dressing on postoperative surgical depigmentation healing. Saudi Dent. J. 2022 May 1; 34(4): 328–334. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussein S, Kotb R: Management of Gingival Hyperpigmentation by scalpel surgery and Bur abrasion. (case Report). Authorea Preprints. 2022 Jun 27.\n\nPatil KP, Joshi V, Waghmode V, et al.: Gingival depigmentation: A split mouth comparative study between scalpel and cryosurgery. Contemp. Clin. Dent. 2015 Mar; 6(Suppl 1): S97–S101. PubMed Abstract \| Publisher Full Text\n\nPera C, Ueda P, Casarin RC, et al.: Double-masked randomized clinical trial evaluating the effect of a triclosan/copolymer dentifrice on periodontal healing after one-stage full-mouth debridement. J. Periodontol. 2012 Jul; 83(7): 909–916. PubMed Abstract \| Publisher Full Text\n\nBaghani Z, Kadkhodazadeh M: Periodontal dressing: a review article. J. Dent. Res. Dent. Clin. Dent. Prospects. 2013; 7(4): 183–191. PubMed Abstract \| Publisher Full Text\n\nDummett CO, Gupta OP: Estimating the epidemiology of oral pigmentation. J. Natl. Med. Assoc. 1964; 56(5): 419–420.\n\nSteigmann S: The relationship between physiologic pigmentation of the skin and oral mucosa in Yemenite Jews. Oral Surg. Oral Med. Oral Pathol. 1965 Jan 1; 19(1): 32–38. PubMed Abstract \| Publisher Full Text\n\nWachtel S, Schenk G, Böhm S, et al.: Microsurgical access flap and enamel matrix derivative for the treatment of periodontal intrabony defects: a controlled clinical study. J. Clin. Periodontol. 2003; 30: 496–504. PubMed Abstract \| Publisher Full Text\n\nSharma V, Kumar A, Puri K, et al.: Application of platelet-rich fibrin membrane and collagen dressing as palatal bandage for wound healing: A randomized clinical control trial. IJDR. 2019 Nov 1; 30(6): 881–888. PubMed Abstract \| Publisher Full Text\n\nSridharan G, Shankar AA: Toluidine blue: A review of its chemistry and clinical utility. J. Oral Maxillofac. Pathol. 2012 May; 16(2): 251–255. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSkoglund LA, Jorkjend L: Postoperative pain experience after gingivectomies using different combinations of local anaesthetic agents and periodontal dressings. J. Clin. Periodontol. 1991 Mar; 18(3): 204–209. PubMed Abstract \| Publisher Full Text\n\nLang NP, Tonetti MS: Periodontal risk assessment (PRA) for patients in supportive periodontal therapy (SPT). Oral Health Prev. Dent. 2003 Jan 1; 1(1): 7–16. PubMed Abstract\n\nGenovesi AM, Ricci M, Marchisio O, et al.: Periodontal dressing may influence the clinical outcome of non-surgical periodontal treatment: a split-mouth study. Int. J. Dent. Hyg. 2012 Nov; 10(4): 284–289. PubMed Abstract \| Publisher Full Text\n\nSoheilifar S, Bidgoli M, Faradmal J, et al.: Effect of Periodontal Dressing on Wound Healing and Patient Satisfaction Following Periodontal Flap Surgery. J. Dent (Tehran). 2015; 12(2): 151–156. PubMed Abstract\n\nSubramanya AP, Vardhan KB, Prabhuji ML: Current Trends and Controversies in Periodontal Dressing–A Narrative Review. RGUHS Journal of Dental Sciences. 2022; 14(2): 32–40. Publisher Full Text" }	[ { "id": "325314", "date": "30 Sep 2024", "name": "Naina Pattnaik", "expertise": [ "Reviewer Expertise Dentistry", "Periodontics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 study presents a novel comparison between BlueM active oxygen gel and Coe-Pack dressing for post-operative healing in gingival depigmentation surgery. The introduction provides a clear rationale for the research, highlighting the aesthetic concerns of gingival hyperpigmentation and the advantages of periodontal dressings. However, some areas could benefit from improvement.\nStrengths: - The aim and objectives are well-defined, and the study design is appropriate for a split-mouth trial. - The inclusion of various clinical indices like the Dummet Oral Pigmentation Index, Visual Analog Scale (VAS), healing index, and reepithelization index adds depth to the study. - The study uses innovative material (BlueM oxygen gel), which has shown promise in wound healing.\nAreas of Concern: 1. Literature Review: Although the introduction provides background on gingival pigmentation and the role of dressings, it could benefit from more recent references, especially on the use of BlueM gel in clinical settings. Some references appear outdated, and more current studies could strengthen the rationale for using BlueM.\n\n2. Sample Size Calculation: The justification for the sample size appears minimal. While the calculation has been done using previous studies, it would be more robust if additional power calculations were explained, especially considering potential dropouts.\n3. Bias and Blinding: The coin-flip randomization method may be subject to bias. A computerized randomization method would reduce the chance of allocation bias. Moreover, the blinding method for both patients and clinicians should be clarified. It is unclear if the clinicians administering the dressings are blinded.\n4. Subjectivity in Measurement: While the VAS for pain is a widely used tool, it is inherently subjective. Future studies could incorporate objective pain measurement methods, like biomarkers, to complement the subjective scales.\n5. Potential Adverse Events: The manuscript briefly mentions adverse events but does not delve into the potential side effects of BlueM gel, particularly any allergic or inflammatory reactions. This should be addressed in the discussion, as it could affect patient outcomes.\n6. Discussion Section: The discussion section could be strengthened by integrating more critical analysis. For example, limitations of the study (small sample size, potential biases) should be explicitly mentioned. Furthermore, how the findings might impact clinical practice or influence future research could be elaborated upon.\nOverall Impression: This study presents an interesting comparison with potential clinical relevance. However, improvements in literature support, bias reduction strategies, and discussion depth are recommended.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1177
https://f1000research.com/articles/12-1176/v1	20 Sep 23	{ "type": "Research Article", "title": "Examining the relationships between contraception and fertility rate in Ghana: Evidence from the 1988 to 2014 Ghana Demographic and Health Surveys", "authors": [ "Fred Y. Gbagbo", "Edward K. Ameyaw", "Edward K. Ameyaw" ], "abstract": "Background: There have been some discrepancies between Contraceptive Prevalence Rate (CPR) and Total Fertility Rate (TFR) in Ghana over the years which we examined in this study. Methods: We adopted a repeated cross-sectional study design to examine the relationship between Ghana's CPR and TFR using data from 1988 to 2014 Ghana Demographic and Health Surveys (GDHS). Results: Our findings show that TFR declined from 6.4 to 4.2 births per woman between 1988 and 2014. Bivariate models fitted revealed that between 1988 and 2014, women using contraceptives had higher prospects of bearing more children than women not using contraceptives. This manifested in 1988 (IRR=1.16, 95% CI=1.11, 1.22) and 2014 (IRR=1.20, 95% CI=1.12, 1.29). The multivariable Poisson regression models also showed the same patterns in all the surveys including the 1988 GDHS (IRR=1.12, 95% CI=1.09,1.19) and 2014 (1RR=1.13,95% CI=1.09,1.17). Contrary to earlier studies reports, and common perceptions held by stakeholders in family planning that there is an inverse relationship between CPR and TFR in Ghana, we did not find any such inverse relationship between CPR and TFR in Ghana during the period under review. Conclusions: Based on our findings we believe, contraception alone does not guarantee low fertility in Ghana, hence we recommend a qualitative study to further investigate the plausible factors behind our results/observations from this current study to inform policy and program decisions.", "keywords": [ "Contraception", "Fertility", "Ghana Demographic and Health Surveys", "Reproductive health", "Ghana" ], "content": "Introduction\n\nFertility regulation has been one of the key responsibilities of the global population, health and development organizations, and governments alike. This originates from the fact that the growth of any given population has enormous implications for present and future populations’ well-being coupled with the direct interrelationship between fertility and socio-economic development, holistic wellbeing, and the natural environment.1 Fertility refers to one’s ability to conceive a child or being able to produce offspring.2 An effective method of fertility regulation with global acclamation is contraceptive use (contraception).\n\nThis is encapsulated in the seventh target of the third Sustainable Development Goal (SDG3), thus “By 2030, ensure universal access to sexual and reproductive health-care services, including for family planning, information and education, and the integration of reproductive health into national strategies and programs.”3 Contraception has also been promulgated by several international organizations for its efficacy.3,4 Easy access to and utilization of an effective birth control method accord women and their families the opportunity to maximize their reproductive health rights to freely decide the spacing and number of children to bear at any point in time and contributes positively towards women’s empowerment.5–7 In addition to the fundamental relevance of offering protection against pregnancy, Kavanaugh and Anderson8 assert that contraception reduces the likelihood of some reproductive cancers, is efficacious for reducing pregnancy-related morbidity and mortality, as well as being useful for the treatment of menstrual-related disorders and symptoms.\n\nIn recent times, scholars have investigated the drivers of Ghana’s fertility rate. For instance, using negative binomial regression modelling, Nyarko9 estimated Ghana’s cumulative fertility from 2003 to 2014. The composition of ever-born children did not vary substantially over the period. Notable factors that affected fertility included employment, place (i.e., urban/rural) and region of residence, educational attainment, and household wealth status.9 Some economic indicators (e.g., wage, non-labour income, and monetary cost of childbearing) are also reported to affect fertility negatively.10 Another 2022 study has investigated the trend of fertility rate over two decades (spanning from 1993 to 2014) and revealed that the fertility rate declined from 5.50 to 4.15 over the period.11 Inequalities in fertility rates were also noted in four main dimensions: wealth index, education, place of residence, and region. Yet, there seems to be limited studies on the relationship between contraceptive use and fertility rate based on national estimates since 1988.\n\nA retrospective investigation into how contraception has shaped Ghana’s fertility rate since the onset of the Ghana Demographic and Health Survey (GDHS) to date, is, therefore, worthwhile to inform national population regulation policies and interventions to brighten the nation’s chances of attaining the SDG targets 3.1 and 3.2. This study, therefore, examines the relationship between contraceptive use and the fertility rate in Ghana using all the six rounds of Ghana’s DHS.\n\n\nMethods\n\nThis study is a repeated cross-sectional study of six distinct national surveys from Ghana. These surveys were conducted between 1988 and 2014 among women of reproductive age (15–49 years old). This study design helped us to investigate the pattern of association between contraceptive use and fertility within a 26-year period in Ghana.\n\nWe used secondary data from all the six Ghana Demographic and Health Surveys of 1988, 1993, 1998, 2003, 2008, and 2014.12–17 All the surveys used standardised DHS model questionnaire which was developed by the Measure DHS programme. The Ghana Demographic and Health Survey is a nationwide survey executed every five years, except in 2014 which was delayed by one year. The survey is implemented by the Ghana Statistical Service and the Ghana Health Service in collaboration with the ICF International, which offers technical support through MEASURE DHS Programme. The focus of the survey is on maternal and child health, and it gathers relevant data for monitoring the population and health situation of Ghana. It collates data on an array of demographic and health issues such as contraceptive use, fertility, child health, nutrition, malaria, HIV/AIDS, health insurance, antenatal care, delivery care, and post-natal care. In this present study, sample included sexually active women from the six surveys.\n\nWomen’s cumulative fertility (i.e., number of children ever born) was the outcome variable for this study. This was a count variable. The main independent variable was contraceptive use. All women who reported that they were using contraceptives, either traditional or modern were categorized as “yes”, whilst those who reported that they were not using contraceptives at all were categorized as “no”. Besides, eight covariates were included, namely age (15–19, 20–24, 25–29, 30–34, 35–39, 40–44, 45–49), education (no education, primary, secondary, higher), union (never in a union, currently in union/living with a man, formerly in union/living with a man), wealth (poorest, poorer, middle, richer, richest), residence (urban, rural), region (Western, Central, Greater Accra, Volta, Eastern, Ashanti, Brong Ahafo, Northern, Upper East, Upper West), knowledge of fertile period within the ovulatory cycle (during her period, after period ended, middle of the cycle, before the period begins, at any time, don’t know) and religion (Catholic, Other Christian, Islam, Traditionalist, no religion). No data were collected on wealth status and knowledge of the fertile period within the ovulatory cycle in 1988 and 1998, respectively. These variables were selected as covariates as a result of their significant association with fertility as reported by previous studies.18–20\n\nThe data were managed and analysed with Stata (version 14). Descriptive analyses were conducted to compute the socio-demographic characteristics of the research participants (see Table 1) and the trend of fertility from 1988 to 2014 (see Figure 1). Considering that the outcome of interest was a count variable without evidence of overdispersion, we conducted Poisson regression to investigate the factors that have underpinned Ghana’s fertility between 1988 and 2014 at a 95% confidence interval. Model 1 is for the first survey (i.e., 1988) and follows chronologically the model for the 2014 survey (Model 6). We exponentiated the Poisson regression coefficients and reported findings as Incidence Rate Ratio (IRR). The data were weighted with the complex survey design to adjust for the multi-stage sampling nature and to ensure that we generate nationally representative and accurate results. Variance inflation factor was used to investigate multicollinearity among the independent variables.\n\nIn all the surveys,12–17 ethical approval for the data collection was provided by the Ethical Review Committee of Ghana Health Service, Accra, Ghana, and the Institutional Review Board of ICF International, USA.12–17 We noticed from these ethics’ approval documents that, each participant engaged in the various GDHS provided verbal or written informed consent prior to data collection. In the case of participants below 18 years (the statutory age for adulthood), parental or legal guardian’s consent was secured in addition to the respondent’s assent.12–17\n\nWhile the original work that provided the data for this work had ethical review and approval,12–17 this report in its own right also obtained ethical approval from the Institutional Review Board and Ethical Review Committee of the Ghana Health Service, Accra, Ghana (GHS-ERC 009/12/21) because we reported on health related information which was predominantly generated through the Ghana Health Service, hence a requirement to seek approval in this particular study as well. However, because we used a secondary data, informed consent was not obtained from individual participants; rather the consent for data use was obtained from the Ghana Statistical Service in line with the use of GDHS data.\n\n\nResults\n\nTable 1 presents the socio-demographic characteristics of the research participants. The analysis of age revealed that women aged 25–29 years old dominated in all the surveys as evidenced in 1988 (21.4%) and 2014 (19.0%). However, those aged 40–44 and 15–19 were the least in the 1988 (9.0%) and 2014 (8.5%) surveys, respectively. More than half of the participants for the 1988 survey had primary education (50.1%), meanwhile, those with secondary education dominated in 2014 (54.7%). Those with higher education were consistently few, as noted in the 1988 (0.9%) and 2014 (6.3%) surveys. Women in union or living with a woman persistently dominated. For instance, almost eight out of 10 of the participants were in union/living with a man (76.5%), whilst 64.8% were in union/living with a man in 2014. Only the 1988 survey lacked wealth data and for the surveys with wealth data, and the analysis revealed dominance of “richest” women in 1993 (24.5%) and 2014 (22.9%) correspondingly.\n\nMost of the research participants were in rural locations in 1988 (67.3%). However, more than half of the women were in urban locations in 2014 (53.2%). During the 1988 survey, two of the current administrative regions of Ghana were part of the Northern region (Upper East and Upper West Regions), and that is why no results were recorded for those regions under the 1988 survey (see Table 1). As displayed in the table, a significant proportion of the research participants resided in the Ashanti region (17.6%). However, in 2014, a greater proportion of the research participants were residents of the Greater Accra region (20.0%). Regarding women’s knowledge of their fertile period during the ovulatory cycle, most of them reported that they did not know the fertile period during the cycle in 1988 (42.4%), whilst 38.4% admitted that it was the middle of the cycle (38.4%). Lastly, on religion, a greater proportion of the participants were other Christians both in 1988 (52.1%) and 2014 (70.5%), as shown in Table 1.\n\nAs shown in Figure 1, Total Fertility Rate (TFR) in Ghana declined from 6.4 births per woman to 4.2 births per woman between 1988 and 2014. Yet, it is worth noting that there was a decline from 1988 to 2008 (4.0 births per woman), before it slightly increased to 4.2 births per woman in 2014.\n\nSource: GDHS 1988, 1993, 1998, 2003, 2008, 2014.\n\nTFR = Total Fertility Rate.\n\nTables 2 and 3 present the inferential results of the study. Table 2 presents the bivariate results, whilst Table 3 presents the multivariate results. From the bivariate models, we noted that between 1988 and 2014, women who reported that they were using contraception had higher prospects of bearing more children relative to women who were not using contraception. This manifested in 1988 (IRR = 1.16, 95% CI = 1.11, 1.22) and 2014 (IRR = 1.20, 95% CI = 1.12, 1.29) as shown in Table 2.\n\nIRR = Incidence Rate Ratio (exponentiated Poisson regression coefficients).\n\nIRR = Incidence Rate Ratio (exponentiated Poisson regression coefficients).\n\nThe multivariable Poisson regression models revealed the same pattern as women who were using contraception showed chances of higher fertility in all the survey rounds, including that of 1988 (IRR = 1.12, 95% CI = 1.09, 1.19) and 2014 (IRR = 1.13, 95% CI = 1.09, 1.17). Throughout the period, women in all age categories had a higher incidence of fertility relative to 15–19-year-old women, especially among 45–49-year-old women in 2003 (IRR = 13.36, 95% CI = 11.16, 15.99).\n\nThe analysis revealed that highly educated women had a lower incidence of fertility compared to those without formal education, with the least incidence in 1998 (IRR = 0.52, 95% CI = 0.46, 0.61). Notably, women who reported that they were currently in a union or living with a man had a higher fertility incidence relative to those who had never been in a union (IRR = 11.58, 95% CI = 8.90, 15.06) in 1993. In 2014, wealthy women had a lower fertility incidence than poor women (IRR = 0.58, 95% CI = 0.55, 0.62). From 1988 to 2014, rural women were noted to have a higher fertility incidence compared to urban women, particularly in 1998 (IRR = 1.19, 95% CI = 1.13, 1.25).\n\nAnalysis of fertility across the erstwhile 10 administrative regions showed that, relative to the Western region, the incidence of fertility was lower in the Upper West region both in 1998 (IRR = 0.85, 95% CI = 0.77, 0.92) and 2003 (IRR = 0.85, 95% CI = 0.77, 0.93). Women of other religions had a higher fertility incidence in 2003 relative to Catholics (IRR = 1.43, 95% CI = 1.28, 1.60) and this trend permeated all the survey rounds, as shown in Table 3.\n\n\nDiscussion\n\nThis study aimed to investigate the association between contraception use and fertility in Ghana, spanning from 1988 to 2014. We noted that between 1988 and 2014, women who reported that they were using contraception had higher prospects of bearing more children relative to women who were not using contraception. The multivariable Poisson regression models revealed the same pattern, as women who were using contraception showed chances of higher fertility in all the survey rounds. Though this seems counter-intuitive to some earlier reports and research findings,21–24 our findings could be attributed to a number of factors. As espoused by some scholars,25,26 fertility is a resultant outcome of an interplay of several factors.\n\nFor instance, women can only derive the full benefits of contraceptives if they are easily accessible and used correctly. If a woman desires to use contraception but has truncated access coupled with limited knowledge, she stands a greater chance of getting pregnant just like someone who does not use contraception. The finding is indicative that contraceptives alone cannot guarantee low fertility, rather there might be other essential factors that need to be unravelled. There is therefore the need for a qualitative study to further investigate the plausible factors behind this observation.\n\nThroughout the period, women in all age categories had a higher incidence of fertility relative to 15–19-year-old women, especially among 45–49-year-old women. This finding is anticipated considering that teenagers (aged 15–19) are typically in school or learning a trade and are usually not married. Besides, childbearing in Ghana is appreciated and dignified particularly when it occurs within marriages. The ability of families and parents to uphold this culture may go a long way to dissuade teenagers from any desire to initiate childbearing at the expense of their educational and career planning and development.\n\nThe analysis revealed that highly educated women had a lower incidence of fertility compared to those without formal education, with the least incidence in 1998. Generally, highly educated women tend to spend many years in school and usually give birth late, partly due to late marriage.20,27 Conversely, women without formal education enter marriage at a relatively early age and hence have a greater part of their reproductive life in socially sanctioned childbearing institutions. It has earlier been reported that Ghanaian women with higher education have an average TFR of between 2 and 3, whilst those without formal education have an average TFR of 6.28 Similarly, Abdul-Salam and Baba27 noted that one more year of education among Ghanaian women will reduce the expected number of children by 0.25.27 Similar findings have been reported from other sub-Saharan African countries.20,29\n\nIn 2014, the “richest” women had lower fertility rates than the “poorest” women. Similarly, rural women had an incidence of fertility compared with urban residents. More often than not, rural settings are typically characterized by poverty compared with urban settings. Due to this, the joint effect of poverty and rurality might have informed the fertility incidence of these women. As espoused by the wealth flow theory Caldwell,30 the rich consider children a liability due to the desire to ensure that their children attend the best schools irrespective of the cost and obtain the best healthcare and other essential services. On the contrary, the poor tend to consider children as assets, and means of financial support and security in old age.30 Due to these, the poor generally have more children as compared with the rich, as affirmed by our study. Fertility regulation interventions may have to prioritize the poor for them to appreciate the need for them to choose quality over quantity with respect to family size.\n\nAnalysis of fertility across the erstwhile 10 administrative regions showed that, relative to the Western region, the incidence of fertility was lower in the Upper West region both in 1998 and 2003. This may suggest the fertility preferences across the respective regions of Ghana. It, therefore, indicates that fertility interventions may have to be sensitive to the contextual variations of the administrative regions of the country.\n\nThe study has a number of limitations and outstanding strengths. This study employed rigorous analytical procedures to investigate the association between contraception and fertility ratio over a 26-year period. It offers insights into the critical factors to be prioritized regarding fertility regulation in Ghana. Also, the representativeness of the sample strengthens the generalisability of our findings to all Ghanaian women within the reproductive age bracket. In spite of these strengths, caution is required in the interpretation of our findings as a causal inference cannot be made between contraception, women’s socio-demographic characteristics, and fertility.\n\nThis study investigated the relationship between Contraceptive Prevalence Rate (CPR) and Total Fertility Rate (TFR) between 1988 and 2014. This study did not show an inverse relationship between CPR and TFR, as reported by earlier studies. Findings from the study suggest that contraception use alone does not necessarily translate into reduced fertility in Ghana, but that other several factors might account for Ghana’s fertility trend between CPR and TFR.\n\n\nConclusion\n\nThe findings suggest that future fertility interventions would have to be informed by women’s socio-demographic characteristics with significant associations with fertility, as revealed by this study. These include age, education, marital status, wealth, and residential characteristics. A qualitative investigation into what women in Ghana do to reduce fertility, other than the use of contraceptives, will be useful in charting a course of action.\n\n\nAuthor contributions\n\nWe declare that we are the sole authors of this manuscript, and our contributions are as follows. Fred Yao Gbagbo: Conceptualization, Data Curation, Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing.\n\nEdward Kwabena Ameyaw: Data Curation, Formal Analysis, Methodology, Validation, Writing – Original Draft Preparation, Writing – Review & Editing.\n\nBoth authors developed the manuscript together and approved the submission for publication.", "appendix": "Data availability\n\nData used in this study are from the Ghana Demographic and Health Survey dataset of 1988, 1993, 1998, 2003, 2008, and 2014. This survey is a population-based survey created to track development in the use and management of health services and provide information to decision-makers. The surveys gather information at the regional and national levels on health seeking behaviours, illness prevalence, nutritional status, mortality, and morbidity. The data sets are available from the Demographic and Health Survey (DHS) website. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.\n\n\nAcknowledgements\n\nWe are grateful to all those who provided information and direction for this paper.\n\n\nReferences\n\nAbel GJ, et al.: Meeting the Sustainable Development Goals leads to lower world population growth. Proc. Natl. Acad. Sci. 2016; 113(50): 14294–14299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFor Women’s, National Collaborating Centre, and U. K. Children’s Health. “Fertility: assessment and treatment for people with fertility problems.”.2013.\n\nUnited Nations: Sustainable development goals. SDGs Transform Our World.2015; 2030.\n\nWorld Health OrganizationReproductive Health et al.: Selected practice recommendations for contraceptive use. 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Publisher Full Text\n\nBongaarts J: The effect of contraception on fertility: Is sub-Saharan Africa different? Demogr. Res. 2017; 37: 129–146. Publisher Full Text\n\nBongaarts J: United Nations Department of Economic and Social Affairs, Population Division World Family Planning 2020: Highlights, United Nations Publications, 2020. 46 p.2020; 857–858.\n\nYland JJ, et al.: Pregravid contraceptive use and fecundability: prospective cohort study. BMJ. 2020; 371. Publisher Full Text\n\nEckart K: How birth control, girls’ education can slow population growth 2020.Reference Source\n\nShallo SA: Roles of proximate determinants of fertility in recent fertility decline in Ethiopia: application of the revised bongaarts model. Open Access J. Contracept. 2020; 11: 33–41. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOzbay DZ: Determinants of fertility rates in Turkey. Int. J. Public Adm. 2020; 43(5): 466–476. Publisher Full Text\n\nAbdul-Salam S, Baba SS, Jabir H: The impact of mother’s education on fertility in Ghana. Int. J. Probab. Stat. 2018; 7(2): 31–43.\n\nPradhan E: Female Education and Childbearing: A Closer Look at the Data 2015.[cited 2022 June 2]. Reference Source\n\nKebede E, Striessnig E, Goujon A: The relative importance of women’s education on fertility desires in sub-Saharan Africa: A multilevel analysis. Popul. Stud. 2022; 76(1): 137–156. PubMed Abstract \| Publisher Full Text\n\nCaldwell JC: On net intergenerational wealth flows: an update. Popul. Dev. Rev. 2005; 31(4): 721–740. Publisher Full Text" }	[ { "id": "284457", "date": "10 Jun 2024", "name": "Frank Götmark", "expertise": [ "Reviewer Expertise Human fertility and factors influencing TFR", "population", "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\nThis is interesting paper with some puzzling results, but it requires much more work. The authors need to provide more explanation of the seemingly contradictory result that contraception does not affect birth rates, or even lead to somewhat increased rates.\nHowever, the data and results presented overlap markedly with another recently published paper in SN Social Sciences, Vol 3, article 112, 2023: Klu D, et. al., 2023 (Ref 1) The authors must explain what is different in their paper, and what motivates its publication.\nIntroduction, first paragraph:\nThere is a new study showing how contraceptive use is linked to declining TFR in developing countries 1970-2014, it should be cited. On-line here: Götmark F, et. al., 2023 (Ref 2)\nMethods:\nIt is stated: \"In this present study, sample included sexually active women from the six surveys.\" Does this mean that some (fertile) women were excluded from the sample?\nIt is stated: \"All women who reported that they were using contraceptives, either traditional or modern were categorized as “yes”,\" I suggest only use of modern contraception is included in the analysis, or that the two forms are treated separately, and presented separately. Use of traditional contraception is risky in preventing child birth, generally considered unsafe - and may have affected the results. This is an important point.\nIt is stated: \"The data were weighted with the complex survey design to adjust for the multi-stage sampling nature and to ensure that we generate nationally representative and accurate results.\" Please explain better, add 3-4 sentences.\nResults\nFigures are important in showing the main results! Figure 1 is fine, but please add a similar Figure showing, by curves, over time the difference TFR between women using (modern) contraception, and those not using contraception (two lines). Judging from the regression data, the difference may not be large, but need to be clearly presented.\nDiscussion\nThe stall in fertility (Fig 1) should be discussed - see the earlier, similar paper, and other papers published by Bruno Schoumaker. For instance, why does not increased education affect birth rates during the last three surveys?\nMore discussion (and analysis) of the main result that contraception seem to have no effect. For instance, could it be that contraception is used only for \"spacing\", not \"limiting\" birth, often discussed in papers from Africa?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "354293", "date": "27 Jan 2025", "name": "Mario Philip R. Festin", "expertise": [ "Reviewer Expertise Maternal Health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting report on the relationship of CPR and TFR, which are usually inversely related. However, this report based on the analyses of serial DHS shows that it is not always the case. It is puzzling what could have contributed to some results. This is a difficult analyses of the finding given the traditional belief about this relationship. I am thinking the authors should look at any of the following as possible causes: 1. The number of pregnancies/ deliveries before contraceptives were used because a high number in these may have influenced the high number of pregnancies in the outcome analyses. 2. The types of contraceptives used, as the use of the traditional or non modern methods, although actual contraceptives, would have lower efficacy rates in reducing pregnancy. May I suggest considering only the defined modern methods, as these are more promoted in country programs. 3. The number of years the contraception was in use at the time the survey was taken as those women who may have had some children but used contraception only for a short time could have influenced the findings. These are among the possible reasons for the findings, which should have been explored before the paper was written, as these would have been gathered as part of DH Surveys. While this paper reports on an unusual finding, we should always be prepared to answer such possibilities, as in this case.\n\nIs the work 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": [] } ]	1	https://f1000research.com/articles/12-1176
https://f1000research.com/articles/12-1175/v1	20 Sep 23	{ "type": "Study Protocol", "title": "Effect of Active Release Technique and Cyriax approach on pain, grip strength and functional performance in individuals with lateral epicondylitis: a randomized clinical trial protocol", "authors": [ "Aditi N. Nagore", "Subrat Samal", "Subrat Samal" ], "abstract": "Background: Tennis elbow, also known as lateral epicondylitis, is a painful condition characterized by irritation of the tendons that link the forearm muscles on the outside of the elbow, which can result from using the elbow too much. Active Release Technique (ART) is defined as a hands-on approach that manages cases to enable the identification and treatment of soft tissue injuries. Through the removal of fibrosis and adhesions that can develop in tissues as a result of overload from frequent use, the aim of ART, a soft tissue treatment, is to lessen tissue stress. Deep transverse friction (DTF) and Mill's manipulation, which are used shortly after DTF, have been used by Cyriax and Cyriax to successfully treat tennis elbow. ART and Cyriax techniques have shown promise for lateral epicondylitis sufferers. There hasn't yet been any research comparing these two approaches for participants with lateral epicondylitis. The aim is to examine the efficiency of ART with the Cyriax technique on lateral epicondylitis pain, strength, and function. Methods: A total number of 60 participants will be included as per the inclusion criteria and then they will be further divided into 30 in each group. The physiotherapy intervention will be given to Groups A (ART) and Group B (Cyriax technique) along with conventional 12 sessions spread across four weeks, three times per week. Each patient will be evaluated during and after treatment on the baseline and after four weeks using the Visual Analogue Scale (VAS), hand grip strength dynamometer, and Patient-rated Tennis Elbow Evaluation (PRTEE) scale. Conclusions: This physiotherapy intervention could be used in the treatment of lateral epicondylitis if our study's hypothesis is found to be accurate. Registration: CTRI (CTRI/2023/06/053660; 08/06/2023).", "keywords": [ "Tennis Elbow", "Active Release Technique", "Cyriax Technique", "Lateral Epicondylitis", "Conventional therapy", "Visual Analogue Scale", "Hand grip strength dynamometer", "and Patient rated tennis elbow scale" ], "content": "Introduction\n\nThe most prevalent elbow overuse ailment is called lateral epicondylitis, also referred to as tennis elbow, and more recently as lateral elbow (or epicondyle) tendinopathy (LET). Using a computer, moving heavy objects, pronating and supinating the forearms, and vibrating frequently are all common repetitive upper limb activities that cause it.1 Fibroblasts, vascular hyperalgesia, and disorganized collagen are histological indicators of tendon deterioration. Normally, the discomfort is localised to the epicondyle, but in more extreme situations, it may extend to the wrist and shoulder. Pressure on the epicondyle, resistance to wrist extension, and strain of the epicondyle muscles are the usual causes of it. The most prevalent age range is 35 to 54 years old, with an estimated incidence of 40% and a frequency of 1% to 3% in the general population.2 The tennis elbow is brought on by pain-inducing tendon injury to the wrist’s short radial extensor on the lateral side. Relevant risk factors include overuse, repeated motions, improper training, misalignment, flexibility problems, aging, poor circulation, muscle weakness or imbalance, and mental variables.3\n\nSimple tests that would elicit discomfort, tenderness over the lateral epicondyle facet on touch, resistant wrist extension, resisted middle finger extension, and passive wrist motion could be used to diagnose tennis elbow flexion. First, Mill’s test is a special test performed to identify lateral epicondylitis. The examiner passively pronates the patient’s forearm, fully extends the elbow, and fully flexes the wrist while palpating the lateral epicondyle. Pain above the lateral epicondyle of the humerus and a second Cozen’s test are signs of a positive test. The examiner’s thumb, which is resting on the patient’s lateral epicondyle, is stabilizing the patient’s elbow. The patient is then instructed to pronate their forearm, extend their wrist radially, and create a fist as the examiner resists them. Sudden, severe pain in the lateral epicondyle of the humerus is indicative of positive information. To determine the source of discomfort, the epicondyle can be felt, and third, resisted. The middle finger extension test stresses the extensor digitorum muscle and tendon by resisting the extension of the third finger of the hand distal to the proximal interphalangeal joint. Pain across the lateral epicondyle of the humerus signifies a positive test.4\n\nThe Active Release Technique (ART) is a manual therapy used to eliminate scar tissue, which can cause pain, stiffness, weakness in the muscles, and other aberrant feelings like mechanical dysfunction in the muscles and the restoration of soft tissue function.5 According to its description, ART is a hands-on approach that handles the cases to make it possible to recognise and cure soft tissue injuries. The foundation of ART is the concept of recognizing and treating cumulative damage disease (CID). The patient actively changes the targeted area’s posture from a shorter to a longer one as the physical therapist repeatedly administers deep manual pressure strokes to the unpleasant and painful location.6 Deep transverse friction (DTF) and Mill’s manipulation, which are used immediately after DTF, have both been used to successfully treat tennis elbow by Cyriax and Cyriax. It is necessary for the two components of Cyriax intervention to be present and combined in the right order. The most well-known kind of physical therapy is referred to as Mill’s manipulation, and it entails pushing with a small-amplitude, high-velocity force while keeping the wrist and hand in a flexed position near the end of the elbow extension.7 This study’s objective is to examine the effectiveness of the Cyriax technique and ART on participants experiencing subacute lateral epicondylitis who are experiencing discomfort, weakness, and functional impairment.\n\n\n\n1. To study the effect of ART along with conventional therapy for pain visual analogue scale (VAS), for grip strength (hand grip strength dynamometer) and for functional performance (Patient-rated Tennis Elbow Evaluation (PRTEE) scale) in individuals with lateral epicondylitis.\n\n2. To study the effect of Cyriax technique along with conventional therapy for pain VAS, for grip strength (hand grip strength dynamometer) and for functional performance (PRTEE) in individuals with lateral epicondylitis.\n\n3. To compare the effect of ART and Cyriax technique along with conventional therapy for pain VAS, for grip strength (hand grip strength dynamometer) and for functional performance (PRTEE) in individuals with lateral epicondylitis.\n\nSingle centre, two arm parallel, open label, randomized clinical trial.\n\n\nProtocol\n\nThe model consent form, data collection form and schedule of enrolment, interventions and assessments can be found as Extended data.21 This study protocol adheres to the SPIRIT checklist.22 After getting approval from the Datta Meghe Institute of Higher Education & Research’s institutional ethics committee participants in this study will be enrolled from the Physiotherapy Outpatient Department (OPD) of Acharya Vinoba Bhave Rural Hospital Sawangi, Ravi Nair Physiotherapy College, Datta Meghe Institute of Higher Education and Research (Deemed to be University) Meghe, Wardha, Maharashtra, and written informed consent will be obtained.\n\nThe study’s inclusion and exclusion criteria will be applied to the population of the region. They will be divided into two groups, Groups A and B. There will be 30 subjects in each group. Group A will receive ART along with conventional treatment that will last for 30 minutes. The participants in group B will receive Cyriax technique for a duration of 30 minutes along with conventional treatment. As part of the inclusion procedure for the study, subjects will be recruited according to inclusion criteria and evaluated according to the assessment and outcome measures. For subject allocation, a computer-generated random number system will be used for the randomization process utilizing the simple envelope method. In this trial, there will be no blinding. The allocation will be generated by the lead investigator, who will also enrol individuals and allocate them to interventions. The project will be overseen by a departmental committee comprised of the Post Graduate (PG), Guide, Head of Department (HOD), Principal of the Ravi Nair Physiotherapy College (RNPC), and a member of the Research Guidance Cell. We will ensure that the patients strictly follow the recommended treatment plan through routine treatment sessions. Individuals will receive counselling or phone reminders about their therapy appointments as necessary. Each patient will be assessed pre and post-treatment on the baseline and after four weeks using the VAS, hand grip strength dynamometer, and PRTEE. The study design is visualized in Figure 1.\n\nInclusion criteria\n\n1. Both male and female patients between the age group of 18 to 45 years old.\n\n2. Patients with pain that has lasted more than 3 months.\n\n3. Patients that have been diagnosed with lateral epicondylitis.\n\n4. Those who intend to take part in the study.\n\nExclusion criteria\n\n1. Patients with the history of cervical and upper limb injuries.\n\n2. Patients who have undergone any procedure involving the cervical area and an upper limb.\n\n3. Patients with any regional infections.\n\n4. Patients with any localized cancer.\n\n5. Patients with lateral epicondylitis that is acute in nature.\n\n6. Patients with cervical radiculopathy.\n\n7. Patients with a recent history of steroidal infusion.\n\nConventional treatment\n\nDescription\n\nAfter identifying the area of pain, the ultrasound will be applied in continuous mode, 3 MHz with the intensity of 1 W/m^2 in slow circular movements or in a longitudinal pattern will be performed three times a week, every other day, for a total of 12 sessions over four weeks. Following which, the treatment area will be exposed and ice pack fomentation will be applied for 10 to 20 mins. Stretching exercises will be given (30 seconds, 10 stretches every session, once per day), isometric for wrist flexion, wrist extension, wrist radial deviation, wrist ulnar deviation (3 to 5 second hold and 10 repetition/ session once daily), and praying position stretches for 10 to 30 seconds hold and 10 repetition/session once daily.8,9\n\nActive Release Technique\n\nPatient position\n\nThe patient will sit with the forearm in mid-prone, elbow extends, wrist in neutral position and resting on the treatment table. Then the therapist will apply pressure to the muscles and the patient will extend the elbow, pronate the forearm, and flex the wrist from a shortened to a lengthened position as the therapist holds the muscles. Following which, the therapist will adjust the pressure proximally in an effort to break up adhesions within and between muscle planes.\n\nDosage\n\nA total of 12 sessions of 10 minutes each will be performed, three times a week, over four weeks.10\n\nCyriax technique\n\nPatient position\n\nThe patient will sit on a chair while holding a pillow.\n\nDeep transverse friction (DTF)\n\nDTF and manipulation, which will be done right after DTF, are both parts of the Cyriax physiotherapy regimen. DTF will be performed by pressing on the teno-osseous junction with the tip of the thumb’s side facing backward. This pressure will be maintained while the therapist applies DTF in the direction of their fingers, which will be placed on the opposite side of the elbow to apply counter pressure. After obtaining the numbing effect, the tendon will be prepared for Mill’s manipulation.7\n\nMill’s manipulation\n\nThe subjects arm will be held under the elbow’s crook while the shoulder joint will be medially rotated and pronated at the forearm. The hand that holds the elbow in the crook will transfer to the back of the elbow joint, and the patient’s elbow will be stretched until all the slack in the tendon had been picked up while preserving full wrist flexion and pronation. Then, while side-flexing away from the arm, the therapist will deliver a small-amplitude, high-velocity thrust while neatly pushing downward with the hand over the patient’s elbow.\n\nDosage\n\nA total of 12 sessions will be performed, three times a week, for four weeks.9,11\n\nCriteria for discontinuing allocated interventions for a given trial participant\n\nIf any patients in any of the allocated groups develop complications (i.e., worsening of disease or rupture of tendon), their participation in the study will be discontinued. The patients will then receive appropriate care and offered outpatient rehabilitation as needed. Study participants will be retained in the trial (unless they withdraw their consent) to enable follow-up data collection and to prevent missing data.\n\nAdherence and concomitant care\n\nFor the purpose of ensuring adherence to the study, the patients will be informed and reminded of the sessions in advance through messages sent to their mobile phones. Additionally, if a patient misses a session for any reason, the standby days from the week will be used so that the patient still receives 12 sessions of intervention throughout the course of the four-week period.\n\nAll enrolled patients will be encouraged to contact the principal investigator directly if experiencing problems related to their allocated group intervention. The principal investigator will then fill out a standardized form at these calls. To avoid study-contamination, patients will be asked to adhere to the allocated rehabilitation intervention and not to seek alternative health-care services during the course of the study. Patients will be advised to contact their general practitioner or the principal investigator as needed.\n\nTime frame: At baseline and 4 weeks later.\n\nPrimary outcome\n\nChange in visual analogue scale (VAS)\n\nFirst employed by Hayes and Patterson in 1921, the VAS is a scale for assessing the intensity of pain1–10 on a subjective basis. The two ratings are based on self-reported indicators of symptoms that are recorded with a single handwritten mark placed at one point along a 10-cm line that represents a continuum between the scale’s two ends—“no pain” on the scale’s left end (0 cm) and “worst pain” on the right end (10 cm)—to determine the scores. The distance in centimetres between the scale’s starting point (left end) and the patient marks how much pain they are experiencing. Additionally, VAS scores exhibit ratio-level scoring characteristics and are correlated with pain behaviours. The information can be used to track an individual’s discomfort rise or to compare patients with similar illnesses’ pain levels.12\n\nSecondary outcome\n\nChange in hand grip strength dynamometer\n\nThe maximal force or tension produced by one’s forearm muscles is measured as grip strength, which is a component of muscular strength. It is an evaluation tool for determining upper limb strength and overall strength. The patient is positioned in a seated position with the shoulder abducted, elbow extended to 90 degrees, forearm neutral, and wrist neutral. The therapist places the dynamometer in the patient’s hand, holding the dynamometer’s base gently while giving the client instructions to squeeze as tightly as they can. Smooth application of grip force is preferred than a quick jerking motion. During the grip, allow the wrist to expand. As we become older, our grip strength weakens, which eventually begins to affect our day-to-day.\n\nChange in Patient-rated tennis elbow evaluation (PRTEE)\n\nThe patient’s pain and function will be estimated by the PRTEE over the previous week. The questionnaire has 15 questions, the first five of which are about pain in the elbow and the following 10 of which are about how the elbow or elbows function. The discomfort and functioning scales include 11 degrees, with 0 denoting no pain or difficulty accomplishing a task and 10 denoting the worst pain possible or complete inability to perform a task. The cumulative score for every question, including the pain and function questions, is the final score. It consists of 15 questions, 10 of which are about functional limitations in everyday life, at work, and in sports, and five of them are about pain. The overall score goes from 0 (no pain or disability) to 100 (worst possible pain and impairment), and both subscales equally contribute to it. Before these cutoffs were validated, scores greater than 54 were considered to indicate serious discomfort and impairment, while values lower than 33 were considered to indicate mild pain and disability.13\n\nUsing a power analysis with 80% power and 5% Type 1 error for the primary variables, we calculated the sample size. The VAS score contrasts with the traditional group’s mean score variance between baseline and end visits. We used the previously calculated effect size difference in percentage from the RCT for the study.7 Formula using mean difference:\n\nPrimary Variable (VAS)\n\nMean ± SD. (Pre) result on VAS for conventional lateral epicondylitis (Control group) = 8.60 ± 0.50.\n\nMean ± SD. (Post) result on VAS for conventional lateral epicondylitis (Control group) = 4.40 ± 0.50.\n\nDifference = 4.2 ± 0.50. (As per the reference article7)\n\nClinically relevant superiority = 10 % = (4.2*10)/100 = 0.42.\n\nAs the reference article.7\n\nTotal samples required = 30 per group.\n\nTotal sample size required = 60\n\nNotations:\n\nData collection methods\n\nThe participants will be evaluated in accordance with the inclusion and exclusion criteria prior to group assignment. The indicated outcome measures’ baseline evaluation will come next. All participants will be randomly assigned to either Group A or Group B after the randomization process. For four weeks, the intervention will be given three days a week for 30 minutes each. After the final day of the intervention session, the post intervention data for the outcomes will be recorded. The information will be gathered and examined in order to study the outcomes. Throughout the course of the study, the guide will supervise the principle investigator as they administer the study interventions. The data collection staff will monitor every recording of the participants during the trial, which will last four weeks. Based on sections and variables, all entries will be saved in a database. This will assure data quality and confidentiality. For the thorough analysis of the dataset, all entities for values will be completely checked that there is no missing data.\n\nData management\n\nThe evaluation data will be gathered from a pre-set spreadsheet with varied baseline characteristics. The research data will be stored in a safe database. Hard copies of evaluation forms, signed informed consent forms, and other non-electronic documents will be safely preserved in the study setting. Every month until the trial is over, a complete backup of the data entries will be performed. The accuracy of the research papers must be properly reviewed. At the end of the study, a Microsoft Excel spreadsheet will be published and delivered to the statistician for the necessary analysis. Checklists can be used to prevent data loss caused by ineffective staff practices. Due to the thorough follow-up assessment of this trial, participant retention and completion of follow-up assessments are anticipated to be quite high. Patients included in this trial are invited to follow-up assessments at four weeks.\n\nThe overall result will be calculated using R studio software 4.3. Descriptive statistics will be calculated on the quantitative assessment for the variable like age with the parameters mean standard deviation maximum, minimum, median. For the qualitative assessment frequency and percentage will be calculated for the variables (hand dominance and occupation, gender). All the results for the inferential statistic will be tabulated and tested for the significance at 5% level of significance P=>0.05. The outcome variables (primary, VAS for the measurement of pain; secondary, hand grip strength dynamometer for the measurement of grip strength and patient- rated tennis elbow evaluation for the measurement of functional performance) will be evaluated for testing the pre post result using paired t-test. Kolmogorov-Smirnov will be used to check the outcome measure’s normalcy at first. If the data cannot be transformed into a normal distribution, the mathematical algorithm for the log, inverse function, exponential, or boxcox transformation will be used. Alternative non-parametric tests will be employed to validate the results of the parametric test if the data’s non-normal distribution continues. Wilcoxon sign test is an alternative for the paired t-test. Unpaired t-test will be used to find the significant difference over the mean of both primary and secondary variables between ART and Cyriax technique. Alternate non parametric Mann Whitney test will be used for the unpaired t-test. Association analysis for finding significance of cofounding parameters will be evaluated by using Chi-squared test or Fisher’s exact test or by using multi-variant analysis.\n\nData monitoring\n\nWe will have a data monitoring committee for maintaining and integrating the data.\n\nHarms\n\nThe whole procedure will be carried out under the direction of a departmental committee and clinical staff. Any injuries or adverse events will be immediately reported to the committee during the trail. The completed dataset will be uploaded on the institutional repository website and made available to the appropriate authorities.\n\nEthical consideration\n\nDatta Meghe Institute of Higher Education and Research, Sawangi Wardha granted ethical approval (date, 21/03/2023; reference number, DMIHER (DU)/IEC/2023/802). This protocol has been registered on Clinical Trials Registry – India (CTRI; trial registration number, CTRI/2023/06/053660; registered on 08/06/2023).\n\nProtocol amendments\n\nThe study received approval from the Scrutiny Committee at the college level on 01/03/2023 and the IEC at the university level on 21/03/2023. CTRI registration has also been completed since these approvals. The study has already been modified and authorized based on the suggestions made through these committees. So further changes cannot be carried out.\n\nConsent\n\nMembers of the trial committee will provide the consent form to the participants in the trial and will inform and explain all the potential benefits and risks to the participants.\n\nConfidentiality\n\nThe participant and a member of their family will be given a detailed explanation of the study plan, and the primary investigator will collect personal data as part of the protocol. The confidentiality statement and the lead investigator, the patient, and two witnesses will all sign the consent form. Every time information for the study needs to be disclosed, the patients consent will be acquired with full assurance of confidentiality.\n\nAncillary and post-trial care\n\nThe whole procedure is going to held under the supervision of clinicians and the departmental committee i.e., Guide, Head of department, Principal and member of Research Guidance Cell. After the trial session, the participations are going to be under supervision for about four weeks so that if there will be any harm, the Principal Investigator will take care of the participants.\n\nAccess to data\n\nThe final trail datasheet will be accessible to the principal investigator who will be conducting the study.\n\nDissemination policy\n\nPreparing to present the work in International Conference Proceedings and publish in an indexed journal.\n\nThe study is yet to be started.\n\n\nDiscussion\n\nTennis elbow is one of the most common lesions of the arm. Pain in the lateral epicondyle gets worse when the extensor carpi radialis brevis muscle contracts against resistance.14 The extensor muscles that arise from the lateral epicondylar portion of the humerus are affected by this overuse injury, with the extensor carpi radialis brevis musculotendinous junction seeing the highest incidence.15 People who work in occupations that frequently require forearm rotation, such as tennis players and carpenters, frequently experience it. It is typically brought on by grasping the wrist and faster, more frequent, cyclic eccentric contractions.16 The incidence of 1-3% in the general population indicates that the dominant arm is the one that is most commonly affected. Tennis elbow occurs 4–7 times per 1,000 patients per year in general practice, peaking in individuals between the ages of 35 and 54 years. Equally affected are both men and women.14\n\nThe main focus of conventional tennis elbow treatment has been pain management with anti-inflammatory drugs, ultrasound, phonophoresis, or iontophoresis. P. Michael Leahy created ART, a deep tissue treatment for removing adhesions and scar tissue and regaining flexibility and function. Deep digital tension is applied over discomfort during ART, and in order to break any formed adhesions, an individual is actively asked to move the tissue from a shortened to a lengthened posture.17 The specific soft tissue massage technique known as “deep friction massage” or “cross friction massage” was created by Cyriax. Deep Friction Massage (DFM) keeps the soft tissue structures of ligaments, tendons, and muscles mobile while preventing the development of adhesion-prone scar tissue.18 Increased friction can also help to break down previously formed adhesions.9\n\nThe present research objective is to evaluate the impact of ART and the Cyriax technique on participants with subacute lateral epicondylitis in terms of pain, strength, and function. In one study conducted by Ramteke and Samal,19 they studied the effect of rotator cuff exercises on tennis elbow. In total, 30 patients were randomly selected and split into two equal groups: Group 1 (the control group) and Group 2 (the interventional group). Group A (15 patients) underwent traditional treatment, good scapular control, and rotator cuff strengthening. Group B (15 patients) received traditional care, mostly using electrotherapeutic modalities and taping for elbow exercises. Before taking part in the study, the players were informed of the specific treatments they would be subjected to over the course of six weeks and need to sign a consent form. Six days a week, the regimen was followed for 10 sittings. The outcome measures were assessed pre and post with the help of patient rated tennis elbow evaluation scale and VAS. After that, both the study group and the experimental group received a home workout regimen. As a result, there was no apparent age difference between the two groups. The mean pain score on the VAS was 4.66 1.77 for group A and 7.13 1.30 for group B. The conclusion of this study infers that a rotator cuff strengthening program is significantly effective in reducing pain and enhancing functional activity.19 In a randomised controlled study conducted by Uttamchandani and Phansopkar,20 the individuals (n=50) with lateral epicondylitis were separated into either an intervention group or a control group, with 25 subjects in each group. Group A used the “PowerBall device” for a strength training programme that was conducted across five sessions per week for three weeks, lasting anywhere between 20 and 64 minutes per session. Depending on the subject’s capacity, the “PowerBall device” frequency was then be determined by the total rounds fired each minute, which ranged from 2,000 to 10,000. Patients with lateral epicondylitis in group B underwent Mulligan Mobilisation with Movement (MMWM). The therapist used the approach 30 times in one session. There was a one-minute break after 10 repetitions. Each session lasted 30 to 60 minutes. Three sets of movement mobilisations were performed during each session, with five sessions scheduled each week over the following three weeks. The patient-rated tennis elbow evaluation scale, Hand Dynamometer, VAS, and range of motion were utilised to measure the outcomes both before and after treatment. The conclusion of this study was that Mulligan Mobilisation was widely regarded as having the biggest impact on pain in patients with lateral epicondylitis, which makes sense given all the factors involved and the treatment’s successful outcomes.20 The ART and the Cyriax technique will be evaluated for their effects on participants with subacute lateral epicondylitis in terms of pain, strength, and function using the primary (i.e., VAS) and secondary (i.e., hand dynamometer and patient-rated tennis elbow evaluation scale) outcome measures. The advantages of the survey allow for a personalised approach to the rehabilitation protocol and the flexibility to adjust to the patients’ increasing abilities throughout the course of therapy. The study’s findings will help future lateral epicondylitis patients by presenting a more effective and advanced rehabilitation strategy.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Aditi- Extended data Sheet-.docx. https://doi.org/10.5281/zenodo.8299769. 21\n\nThis project contains the following extended data:\n\n- Data collection form\n\n- Model consent form\n\n- Flowchart of procedure\n\n- Schedule of enrolment, interventions and assessments\n\nZenodo: SPIRIT checklist for ‘Effect of Active Release Technique and Cyriax approach on pain, grip strength and functional performance in individuals with lateral epicondylitis: a randomized clinical trial protocol’. https://doi.org/10.5281/zenodo.8013637. 22\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nI would like to express my gratitude to Mr. Lakshmikant Umate for data analysis planning and sample size.\n\n\nReferences\n\nTarpada SP, Morris MT, Lian J, et al.: Current advances in the treatment of medial and lateral epicondylitis. J. Orthop. 2018 Mar 1; 15(1): 107–110. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFernández-Carnero J, Fernández-de-las-Peñas C, de la Llave-Rincón AI , et al.: Prevalence of and Referred Pain From Myofascial Trigger Points in the Forearm Muscles in Patients With Lateral Epicondylalgia. Clin. J. Pain. 2007 May; 23(4): 353–360. PubMed Abstract \| Publisher Full Text\n\nLandesa-Piñeiro L, Leirós-Rodríguez R: Physiotherapy treatment of lateral epicondylitis: A systematic review. J. Back Musculoskelet. Rehabil. 2022 Jan 1; 35(3): 463–477. PubMed Abstract \| Publisher Full Text\n\nThe Role of Active Release Manual Therapy for Upper Extremity Overuse Syndromes—A Preliminary Report\|SpringerLink: [cited 2023 Jan 25]. Publisher Full Text\n\nKalaskar G, Gurjalwar I, Phansopkar P, et al.: Effect of Cyriax physiotherapy and conventional ultrasound on lateral epicondylitis.11(2320). Publisher Full Text\n\nBalasuburamaniam A, Kandaswamy M: Effect of Myofascial Release Therapy and Active Stretching on Pain and Grip Strength in Lateral Epicondylitis. J. Riphah. Coll. Rehabil. Sci. 2016 Sep 8; 4: 3–6.\n\nKalaskar G, Phansopkar P: A Comparative Study to Evaluate the Efficacy of Supervised Exercise Program and Cyriax Physiotherapy on Pain and Function in Lateral Epicondylitis.2021 Nov 18 [cited 2023 Feb 21]; 87–97. Publisher Full Text\n\nZaghloul HMS, Ali HA, Ghally SAO, et al.: Comparison of The Effectiveness of Instrument-Assisted Soft Tissue Mobilization Technique, Ultrasound therapy, or Deep Friction Massage on Fast Recovery and Accelerating Tissue Healing in Groin Strain.2020.\n\nDabkara P, Daniel J, Sharma M, et al.: A Study to Compare the Effectiveness of Active Release Technique Versus Deep Friction Massage on Pain, Grip Strength and Functional Performance in Patients with Chronic Lateral Epicondylitis. Indian J. Public Health Res. Dev. 2022 Jun 24; 13(3): 222–227. Publisher Full Text\n\nBasu DS, Bhatia DD, Palekar T, et al.: EFFECTIVENESS OF ACTIVE RELEASE TECHNIQUE IN THE TREATMENT OF CHRONIC LATERAL ELBOW PAIN.\n\nAshfaquzzaman M: Effectiveness of a mill’s manipulation for tennis elbow patient [Thesis]. Bangladesh Health Professions Institute, Faculty of Medicine, the University of Dhaka, Bangladesh.2020 [cited 2023 Feb 22]. Reference Source\n\nDelgado DA, Lambert BS, Boutris N, et al.: Validation of Digital Visual Analog Scale Pain Scoring With a Traditional Paper-based Visual Analog Scale in Adults. J. Am. Acad. Orthop. Surg. Glob. Res. Rev. 2018 Mar 23; 2(3): e088. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRompe JD, Overend TJ, MacDermid JC: Validation of the Patient-rated Tennis Elbow Evaluation Questionnaire. J. Hand Ther. 2007 Jan 1; 20(1): 3–11. PubMed Abstract \| Publisher Full Text\n\nCutts S, Gangoo S, Modi N, et al.: Tennis elbow: A clinical review article. J. Orthop. 2019 Aug 10; 17: 203–207. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEVALUATION OF THE EFFECT OF MOBILIZATION WITH MOVEMENT ON PAIN, KINESIOPHOBIA AND ACTIVITIES OF DAILY LIVING IN LATERAL EPICONDYLITIS - AN EXPERIMENTAL STUDY - ProQuest.[cited 2023 Sep 4]. Publisher Full Text\n\nFlanders M: The clinical effectiveness of therapeutic exercises alone and in combination with orthotic bracing in the treatment of lateral epicondylalgia.\n\nKim JH, Lee HS, Park SW: Effects of the active release technique on pain and range of motion of patients with chronic neck pain. J. Phys. Ther. Sci. 2015 Aug; 27(8): 2461–2464. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaves P, Simões D, Paço M, et al.: Cyriax’s deep friction massage application parameters: Evidence from a cross-sectional study with physiotherapists. Musculoskelet. Sci. Pract. 2017 Sep 1; 32: 92–97. PubMed Abstract \| Publisher Full Text\n\nRamteke S, Samal S: To Study the Effect of Rotator Cuff Exercises on Tennis Elbow. Indian J. Public Health Res. Dev. 2020; 11(3): 610–614.\n\nUttamchandani S, Phansopkar P: A Research Protocol to Evaluate the Efficacy of Powerball versus Mulligan Mobilization with Movement on Pain and Function in Patients with Lateral Epicondylitis. J. Pharm. Res. Int. 2021 Oct 9; 33(45B): 491–500. Publisher Full Text\n\nNagore AN: Aditi. Extended data Sheet-.docx. [Dataset]. Zenodo. 2023 Aug 30 [cited 2023 Aug 30]. Reference Source\n\nNagore A: SPIRIT_checklist - Aditi.docx. [Dataset]. Zenodo. 2023 Jun 7 [cited 2023 Aug 30]. Reference Source" }	[ { "id": "247984", "date": "14 May 2024", "name": "Neha Shukla", "expertise": [ "Reviewer Expertise Orthopaedic-related topics", "Physiotherapy 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\nOverall, the protocol exhibits a robust framework for conducting a randomized clinical trial to investigate the effectiveness of the Active Release Technique (ART) and the Cyriax technique in treating lateral epicondylitis. The inclusion of power analysis for sample size determination ensures adequate statistical power, while the clear data collection, management, and analysis plan enhance the study's internal validity and reliability. However, I have further suggestions to improve the quality of the manuscript. 1. While the introduction provides a comprehensive overview of lateral epicondylitis and the interventions under investigation, it could benefit from a more integrated discussion of current evidence supporting the efficacy of ART and the Cyriax technique. 2. The protocol mentions the use of the Visual Analogue Scale (VAS), hand grip strength dynamometer, and PRTEE scale as outcome measures, the authors could provide more information on the reliability, validity, and interpretation of these measures. 3. The decision not to implement blinding is noted in the protocol, but a rationale for this choice is not provided. Lack of blinding can introduce bias, particularly in subjective outcome measures like pain assessment. 4. In eligibility criteria, some exclusion criteria, such as \"recent history of steroidal infusion,\" could benefit from further clarification. Defining what constitutes a \"recent\" history (e.g., within the past six months) would provide clearer guidance for identifying eligible participants. 5. While the inclusion criterion specifies patients diagnosed with lateral epicondylitis, the protocol does not outline how the diagnosis will be validated. Details on the diagnostic criteria or methods used to confirm the diagnosis could be added. 6. Statistical analysis, the plan does not explicitly address how missing data will be handled in the analysis. Including strategies for handling missing data, such as imputation methods or sensitivity analyses, would ensure robustness in the statistical analysis.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1175
https://f1000research.com/articles/12-1174/v1	20 Sep 23	{ "type": "Research Article", "title": "Storage stability of a fluidized-bed agglomerated spray-dried strawberry powder mixture", "authors": [ "Hader Ivan Castaño Peláez", "Misael Cortés-Rodríguez", "Rodrigo Ortega-Toro", "Hader Ivan Castaño Peláez", "Misael Cortés-Rodríguez" ], "abstract": "Background: Strawberry is a fruit with a high antioxidant capacity due to its richness in phenolic compounds that suffer a rapid post-harvest deterioration. Spray drying is an alternative to reduce losses; however, these powders present problems of instantanisation, making it necessary to implement agglomeration processes. During storage, powdered food products can undergo a series of changes in their amorphous state from a product initially in a vitreous state to a gummy state, where all properties are substantially modified due to the increased mobility of water in the matrix. Methods: The research objective was to evaluate the storage stability (6 months) of a fluidized bed agglomerated strawberry powder mixture at three temperatures (15, 25 and 25°C), a controlled environment at 65% relative moisture, and PET foil laminated film bags as packaging. Moisture, water activity, bulk and compacted density, Carr and Hausner indices, solubility, hygroscopicity, wettability, angle of repose, antioxidant capacities, total phenols, anthocyanins, vitamin C, color (CIE-Lab) and particle size were monitored. Results: ANOVA showed statistically significant differences (p<0.05) for all dependent variables concerning storage time; storage temperature had no significant effect on S, ABTS, DPPH and Hu. The time-temperature interaction during storage had no significant effect (p>0.05) on S, ABTS, DPPH, Hu and L. The agglomerate showed moisture and aw values that confer excellent stability against deterioration reactions; it retained good fluidity, low cohesiveness, and retentions above 50% for antioxidant capacity, 76% for total phenols, 39% for anthocyanins, and 40% for vitamin C; particle size was retained during the evaluation. The color was only affected in the 35°C treatment from the fifth month onwards. Conclusions: The study will serve as a tool for the determination of the shelf life of the chipboard once the critical values of the attributes selected as predictors of shelf life are defined.", "keywords": [ "Fragaria ananassa Dutch", "storage stability", "clumping" ], "content": "Introduction\n\nThe strawberry (Fragaria ananassa Dutch.) is a plant belonging to the Rosaceae family, considered a pleasure fruit par excellence. The fruit is noted for its vitamin C (Vit.C), tannins, flavonoids, anthocyanins, catechin, quercetin and kaempferol, organic acids (citric, malic, oxalic, salicylic and ellagic) and minerals (K, P, Ca, Na and Fe, among others). These compounds in strawberries have potent antioxidant power, helping to reduce the risk of cardiovascular events, improve vascular endothelial function and decrease thrombosis (Forbes-Hernandez et al., 2016).\n\nSpray drying (SD) is one of the most widely used technologies in producing food powders, allowing them to increase their shelf life; however, most of these products present fluidity and instantaneousness deficiencies (Samborska et al., 2022). These powders are mainly characterized by being very fine and with particle sizes below 100 μm, where high interparticle cohesion forces are present, especially due to Van der Waals forces, which predominate over gravitational forces by several orders of magnitude (Rosa et al., 2020). The agglomeration process allows the bonding of solid particles improving related physical properties, such as wettability (Hu), cohesion, dispersibility, and solubility (S); in addition, it produces better rheological properties, decreasing the compaction, cohesiveness, and adhesiveness of fruit powders (Jeong & Yoo, 2023). Fluidized bed agglomeration has the potential to achieve superior product quality in terms of oxidation stability because of the encapsulation of spoilage-sensitive compounds; retaining bioactive compounds during storage is paramount for these products' shelf life and final quality (Haas et al., 2020).\n\nStudies on changes in the quality of a product as a function of time are important to ensure compliance with food standards. Several factors affect the shelf life of food, such as the environmental conditions to which the food is exposed (temperature, relative humidity (RH), and presence of light); in addition, the properties of the packaging used (permeability to oxygen, water vapor and light) (Wong & Lim, 2016). Another important result is the kinetic modeling of the change in food quality during storage, which describes the reaction rate as a function of time, and therefore allows prediction of the changes after the product starts its logistic distribution process (Wong & Lim, 2016; Chang et al., 2018).\n\nDuring storage, powdered products may experience changes in the nature of the amorphous state of matter from a vitreous to a gummy state; where the physical, chemical, sensory, microbiological, and nutritional properties are substantially modified due to the increased molecular mobility of water in the matrix (Hernández-Sandoval et al., 2014). These changes, like the material, are caused by the adsorption of moisture from the medium and storage temperatures above the glass transition temperature (Tg) (Rahman, 2017), resulting in progressive compaction and an irreversible state of caking (Chang et al., 2018).\n\nAlthough the integration of the SD and agglomeration processes allows high preservation of the functional properties of strawberries and improvement of the flowability and instantaneousness properties of the strawberry powder mixture, the physicochemical properties of the fruit powders during storage change due to the hygroscopicity (H) and stickiness characteristics of the particles, in response to the food-environment interaction (Robaina et al., 2019; Samborska et al., 2022), there is evidence of many studies evaluating the storage stability of fruit powder blends: bael (Aegle marmelos) (Sornsomboonsuk et al., 2019), papaya (Gomes et al., 2018), coconut (Carlos et al., 2018), soursop (Chang et al., 2018) and blackberry. However, no reported studies evaluate the stability of fruit powder blends, especially strawberries. In this context, this study aimed to evaluate the storage stability of a strawberry powder mixture agglomerated by a fluidized bed.\n\n\nMethods\n\nFresh strawberries (Fragaria ananassa Duch, var. Monterrey) were purchased at the wholesale market in Medellín and refrigerated at 4 °C until use was used. The degree of ripeness of the strawberries corresponded to a scale of 5-6 according to the Colombian Technical Standard NTC 4103. Additionally, gum Arabic (GA) (Tic Pretested gum Arabic FT Powder, Tic Gums, USA) and maltodextrin (MD) with dextrose equivalent 19-20 (Ingredion) were used as drying additives.\n\nStrawberries without stalks and sepals were washed and disinfected with Citrosan® (0.25% v/v). They were then processed in an IKA colloid mill, model MK 2000/5, coupled to a water-cooling system (≅ 5 °C) (3660 rpm, minimal clearance of the grinding disc, flow rate: 240 mL/minute), until a homogenized strawberry pulp (HSP) with total solids (TS) of 8.9% was obtained; this pulp was stored frozen (-18 °C) until use. An industrial batch of 100 kg of feed suspension SD (SSD) with a total TS content equivalent to 19.6% was prepared under the following procedure: 1) thawing of HSP, 2) weighing of ingredients: HSP with a contribution of 8.9% of the ST of the SSD, GA (0.22% w/w) and MD (11.5% w/w), and 3) slow addition of the GA and MD under homogenization in an Ultra Turrax, IKA - UTL 50 (10000 rpm and time = 5 minutes). The development of the strawberry base colloidal suspension formulation without including MD and its processing has been reported by Castaño-Peláez et al., 2022a.\n\nThe SD process was carried out in an industrial tower (Lemar, China, with a water evaporation capacity of 200 kg/h), model LPG320, co-current flow, and operating under sub-atmospheric conditions. The process conditions were air inlet temperature (154 °C), air outlet temperature (89 °C), and atomizer disc speed (15000 rpm). The formulation of the colloidal suspension of feed to the SD (MD included) and the drying process conditions was established from the investigation at the pilot level, reported by Castaño-Peláez et al., 2022b; where the air inlet and outlet temperatures were kept at the pilot level; while the speed of the industrial spray disc (rpm) was recalculated, keeping the same tangential speed used in the pilot equipment (Vibrasec spray dryer, model PASALAB 1.5).\n\nA Lemar (China) fluidized bed agglomerator, model FL5, with a 3000 g charge and operating at a fluidizing air temperature of 70 °C, binder solution atomization pressure of 1 bar, binder solution flow rate of 10-15 mL/min at 25 °C and with a vitamin C (Vit.C) concentration of 3.33 g/L and a blower frequency of 30-34 Hz was used. SiO2 (Pirosil®) at 0.5 w/w was used to improve the fluidization of the filler in the agglomeration process. The basis for the operating conditions in the FL5 agglomerator equipment was established from the research work reported by Castaño-Peláez et al., 2022c.\n\nThe storage study of the strawberry agglomerated powdered mix (StPM) was carried out using a completely randomized factorial design, considering two independent variables: temperatures (T) (15, 25 and 35 °C) and time (t): 0, 30, 60, 90, 120, 150 and 180 days, and the dependent variables: moisture (Xw), water activity (aw), solubility (S), wettability (Hu), hygroscopicity (Hy), bulk density (ρb), compacted density (ρc), Carr's index (CI), Hausner's index (HI), angle of repose (AR), particle size in terms of equivalent surface diameter (D[3;2]), antioxidant activity (ABTS and DPPH methods), total phenols (TF), Vit. C, total anthocyanins (TA) and color in CIE-Lab* space. Samples were packed in laminated PET film bags, aluminum foil with O2 permeability <1 mL/(m224hatm), water vapor permeability < 1 g/(m224hatm), ALICO® brand, and stored in climate chambers conditioned with a controlled relative humidity (RH) of 65%. The dependent variables were evaluated from three replicates per storage condition.\n\nXw was determined according to the official AOAC method (2003); aw was determined using a dew point hygrometer at 25 °C (Aqualab 3TE series, Decagon). The ρb was determined according to the methodology described by Pereira et al., (2020), modified by weighing 5 g of sample and recording the volume occupied in a test tube. The ρc was determined according to the methodology described by Haas et al. (2020) modified, by weighing 5 g of powder in a falcon tube, then centrifuging for 5 min at 8000 rpm, and finally, the compacted volume was recorded. The CI and HI parameters were determined according to equations 1 and 2, respectively, whose flowability and cohesiveness classification (Table 1) was described by (Jinapong et al., 2008).\n\nAR was determined according to the methodology described by (Barbosa-Cánovas & Juliano, 2005). S was determined according to the method described by Marulanda et al. (2018), 1g of product was weighed and dispersed in 50 mL of water. The mixture was centrifuged at 3000rpm/5min at 25°C, and 25mL of the supernatant was taken and dried in an oven at 105°C for 5 hours. The S (%) was calculated as the difference between the initial and final weight of the dried. Hu was determined as the time required for 1 g of powder to disappear from the surface of a 100 mL volume of water at 20 °C (Marulanda et al., 2018). Hy was determined according to the gravimetric method for sorption isotherms by controlling the ambient RH inside an airtight bottle at 68% (supersaturated KI solution). Particle size was determined on the Mastersizer 3000 particle analyzer (Malver Instrument), Aero S module, and reported as equivalent surface area diameter (D[3;2]). TF content was determined by the colorimetric method using phosphomolybdic-phosphotungstic acid reagents (Singleton & Rossi, 1965). The extract obtained from the powdered agglomerate was mixed with a methanolic solution of the 2,2-Diphenyl-1-picrylhydrazyl (DPPH°) radical and reacted for 30 minutes to evaluate the antioxidant activity. The reduction in DPPH° absorbance was measured at 515 nm, and the percentage inhibition of the radical was calculated. Trolox was the positive control (Brand-Williams et al., 1995). Likewise, the antioxidant activity was determined by the ABTS method, where performed radical cation of 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS•+) was generated through the oxidation of ABTS with potassium persulfate. The ABTS•+ was subsequently reduced in the presence of the extract obtained from the powdered agglomerate. The extent of radical discoloration was quantified as a reduction in absorbance of the radical cation at 734 nm, and this reduction was calculated as the percentage inhibition of ABTS•+. Trolox was employed as the reference standard (Re et al., 1999).\n\nVit.C was determined by HPLC (Shimatzu Prominence 20A), column: Luna® 5 um C18(2) 100A - 2504.6 mm, mobile phase: KH2PO4 0.02M - pH: 3.06, flow: 1 mL/min, pressure: 1172 psi, retention times: 4.317-4.456 min, injection volume: 5 μL and wavelength: 244 nm. An analytical standard L-Ascorbic acid (Sigma Aldrich 47863, Lot LRAC1812) was used. The extraction process was performed by weighing 0.25 g of StPM in a graduated test tube and adding a 0.02M KH2PO4 buffer solution adjusted to pH 3.0 with 85% orthophosphoric acid to make up 20 mL. The mixture was vortexed for 2 min, centrifuged at 5000 rpm, 4 °C and 15 min, and the supernatant was passed through a 0.45 μm acetate-cellulose membrane filter and made up to 25 mL. The results were expressed in mg/100g bs.\n\nThe quantification of TA in the form of Cyanidin-3-glucoside (C3G) was performed by HPLC (Shimadzu), DAD-Uv-vis detector (200-700 nm), C18 column and mobile phase acetonitrile/water/formic acid (80:18:2), in a gradient mode at a constant flow rate (0.5 mL/min). The extract for TA quantification was obtained by weighing 0.25 g of sample in 50 mL falcon tubes, adding 25 mL of the solvent (1% HCl in methanol), placing in an ultrasonic bath for 15 min, centrifuged at 8000 rpm (Universal 320) for 15 min at 25 °C, filtered on 0. 45 mm in a 50 mL volumetric balloon, washed three times with 10 mL of the solvent, repeating the operations of the ultrasonic bath, centrifugation, filtration, and finishing with gauging with the HCl/methanol mixture. The sample was filtered by syringe and 0.25 uL filter in an amber vial. The results were processed with Chromeleon 7.2. software (Dionex, Thermo Scientific, United States), using chromatograms at 517 nm, expressed as mg C3G/100g bs.\n\nData were analyzed from ANOVA, using the LSD (Least Significant Difference) method for multiple comparisons, with a confidence level of 95%, and using STATGRAPHICS XVI software (Statpoint Inc, USA).\n\n\nResults and Discussion\n\nFigure 1 and Table 2 present the behaviors during storage of the StPM quality attributes, and the values of the p-value statistic derived from the ANOVA, respectively. The ANOVA showed significant differences (p<0.05) of the variables Xw, aw, Hy, ρb, ρc, CI, HI, AR, D[3;2], TF, DPPH, Vit. C, TA, L, a, and b concerning T; while all the dependent variables presented significant differences (p<0.05) concerning t. On the other hand, the variables Xw, aw, Hy, S, Hu. ρb, ρc, CI, HI, AR, D[3;2], Vit. C, L, a, and b* presented significant differences (p<0.05) concerning the T-t interaction.\n\n* Not significant. Continued.\n\nThe mean values of Xw and aw during storage at 180 days reached maximum values of 4.79±0.06, 4.48±0.20, 6.23±0.11%, and 0.350±0.009, 0.287±0.018, 0.361±0.006 at the temperatures of 15, 25 and 35 °C, respectively (Figure 1a-b); values that confer excellent stability against physicochemical and microbiological deterioration reactions (Varastegani et al., 2019). Xw presented an increasing behavior over time, being, in general, higher with increasing T. The behavior of aw was corresponding to that of Xw; however, these behaviors were not consistent concerning T, which could be attributed to the microstructural heterogeneity of the agglomerates, where the binder solution does not homogeneously impregnate the active points of the StPM surfaces, some agglomerates concerning others, which affects the levels of water adsorption during storage. In general, Xw and aw are critical variables involved by T, t, and T-t, whose behavior is considered as the result of two phenomena mainly: 1) The environment-packaging-StPM interaction at the conditions of the study generated a driving force in favor of Xw adsorption on the StPM, due to the chemical potential difference between the interior of the chamber (aw: 0.650) and the surface of the StPM (aw < 0.361) (Marulanda et al., 2018; Chang et al., 2018), and 2) Higher storage temperature generates higher partial pressure of water at the StPM surface, which contributes to lower Xw content.\n\nStorage of StPMs at 25 °C was the most favorable temperature for the sixth month of control (< Xw and aw), with values of 4.45% and 0.297, respectively. This Xw value is like the monolayer moisture in dry products and is very suitable for food preservation (Varastegani et al., 2019). It is highlighted that the results in the present study were lower than those reported for soursop powders obtained by SD (Chang et al., 2018) and similar to those reported by Varastegani et al., (2019) on black cumin powder obtained by SD and by Wong & Lim, (2016) on papaya powder obtained by SD.\n\nThe values of ρb and ρc varied between 0.3753±0.003-0.420±0.000 and 0.463±0.001-0.509±0.015 g/mL, respectively. Although these variables presented significant differences concerning T, t and T-t interaction, in general, their variations were small (≅ 5%) (Figure 1c-d), behavior that has also been reported during storage for black cumin powders obtained by SD (Varastegani et al., 2019). On the other hand, it is highlighted that the values of the present study were similar to those reported by Oliveira et al., (2013) during storage of strawberry powder obtained by SD. Lower variations of the densities were observed at low T (15 and 25 °C), which is explained due to the small changes of Xw during storage, whereas, at 35 °C, this variation becomes larger and consistent with the increase of Xw content (higher molecular mobility of water in the agglomerate structure), which could generate changes of the non-thermodynamic state (rubbery amorphous) and higher plasticity of the material (Liu et al., 2017).\n\nAccording to the variations of the CI values (%) found (16.606±0.005-20.001±0.888), the flowability of the material during storage was little affected, retaining good flow characteristics. The cohesiveness of the agglomerate during storage through monitoring at HI allowed identifying that the material retains a low - intermediate cohesiveness (1.198±0.136-1.250±0.018), an important aspect that positively impacts the instantaneity of the material. The CI and HI variables showed an increasing trend but fluctuated concerning t. When applying Fischer's test, storage at 35 °C showed a higher significance concerning storage at 15 and 25 °C, showing at 35 °C a better fluidity and cohesiveness of the agglomerate and, at the same time, an increase in the densities (Figure 1e-f).\n\nThe monitoring of the AR behavior during storage identified the preservation of the agglomerate fluidity by decreasing with increasing t; however, this variation was low (5.7° → 4.1°), corresponding to a change rate of 28.1%. These low RA values are favored by the presence of SiO2 in the StPM, which has fluidizing and anti-compacting properties, reducing the likelihood of particles sticking together by reducing the cohesive forces, thus reducing potential caking (Chang et al., 2018). Additionally, it was observed from month 4 and in all T that AR values tend to be asymptotic (Figure 1g); however, this behavior is in contrast with what was reported by Wong & Lim, (2016) in papaya powder obtained SD. A similar situation was observed in D[3;2], whose maximum variation was between 56.3 and 52.3 μm; however, this dependent variable did not show a well-defined trend concerning the independent variables considered (Figure 1h).\n\nIt is highlighted that from month 5 the StPM stored at 35 °C presented a caking of the material in the form of the lump (D[3;2] >>>) or the possible start of crystallization of the fructose and glucose present in the StPM (Wong & Lim, 2016), with the respective loss of agglomerate structure, which could favor the increase in particle size due to: 1) change of the non-thermodynamic state from vitreous amorphous to rubbery amorphous (Saavedra-Leos et al., 2018); aspect related to the high Xw contents (> 5.5%) discussed above at this T and t, and 2) the interaction Xw- pectic content of the food matrix that favors inter-particle forces (Einhorn-stoll, 2018), which is why it was only plotted up to day 120.\n\nThe instantaneity of food powders is a property highly valued by consumers and industry when used as a raw material in producing other food products. Instantaneity is made explicit by assessing S, Hy, and Hu properties (Dhanalakshmi et al., 2011). The S of agglomerates is directly related to properties affecting the microstructure of the material, where the higher the degree of preservation of the vitreous state, the better the conditions for wetting, sinking, and dispersion; a collapsed structure in a rubbery state restricts the diffusional processes of water in the aggregate (Bhandari et al., 2013).\n\nIn general, the S of StPM presented an excellent water solubility during storage (86.0-92.8%), being very stable during 6 months at 15 and 25 °C (Figure 1i) (correlated with the stable behavior observed in properties such as ρ, AR and Hy) (Hogekamp & Schubert, 2003). Similar S values have been reported by Varastegani et al., (2019) on black cumin powder (92.6 and 91.9%), stored at 4 °C for 12 months and, using Gum Arabic and Maltodextrin as drying agents.\n\nOn the other hand, the S of the StPM stored at 35 °C after month four shows an accelerated decrease associated with the increase in Xw and the aforementioned caking. According to the results found for the densities at this T and t, their values were higher, an indicator of the compaction experienced by the material, a negative aspect for a good interaction of the material with water in the solubilization process (Chang et al., 2018). These authors have identified reductions of 35% of S in the storage of SD soursop powders using aluminum foil PET laminated film packaging at 35 °C. On the other hand, in the storage stability study of papaya powder obtained by SD at 38±2 °C and 90% relative humidity, using aluminum PET foil laminated film packaging, S decreased in week 7 from 97.1 → 85.1% (Wong & Lim, 2016), which represents a more significant reduction compared to the findings of the present study.\n\nThe packaging material plays an important role as a barrier to water vapor, O2, and CO2, which is why the choice of material is a fundamental decision to guarantee the stability of the product during storage. In general terms, a decrease in the Hy of the StPM during storage was observed, with the statistical analysis describing two homogeneous groups: 1) 15 and 25 °C and 2) 35 °C, where the rate of change was (14.4 → 12.1%), (14.4 → 12.3%) and (14.4 → 10.3%), respectively (Figure 1j). The decrease in StPM Hy is a favorable aspect for the stability of the material and its shelf life; this phenomenon can be explained by the formation of a surface layer on the agglomerate structure in response to the interaction of the adsorbed water with the pectin, gum Arabic and maltodextrin of the StPM, which generates a barrier for the adsorption and subsequent diffusion of water into the matrix. The behavior of these results was contrary to those reported by Wong & Lim (2016) on papaya powder obtained by SD. It was stored for seven weeks, 38.2 °C and RH 90%, in aluminum foil PET (8% increase) and PET (13% increase) laminated film packaging.\n\nHu showed an increasing trend with t, independent of T; however, at 35 °C from five months onwards, it could not be determined due to caking problems of the StPM, discussed above (Figure 1k). The behavior of Hu during storage was not favorable due to its increase (3.12±0.01 → 4.01±0.05 min), which contributed to a decrease in the reconstitution capacity of the material in water by 28.5%. This situation is consistent with the observed increases in ρb and ρc caused by moisture adsorption in the packaging, which reduces the material's porosity, affecting its capillarity and increasing the wetting time (Cuq et al., 2013). No evaluations of Hu stability studies of SD powders or agglomerated powders during storage are reported in the literature to contrast the findings.\n\nGenerally, these values are favorable when at least minimal agitation is performed in the reconstitution system. On the other hand, these Hu values of the StPM compared to those of the strawberry powder mixture dried by SD and used in the binder loading (Hu: 11-19 min) show a significant reduction and preservation during storage, which translates into an improvement in the instantaneousness of the product.\n\nIn general, the behavior of ABTS, DPPH, and, TF decreased with t, the latter being the most critical variable during storage (Figure 1l, m-n); furthermore, ANOVA showed that T exerts a greater affectation mainly on DPPH and TF.\n\nFor ABTS, it is observed that during the first 4 months, there is a low rate of change due to the good level of protection of the MD and GA on these components; subsequently, a higher rate of degradation was observed, mainly at T of 35 °C, which corresponds to the caking discussed above due to the possible change in the state of matter (vitreous → gummy), which increases the molecular mobility of water and degradation phenomena. Oliveira et al., (2013) reported preserving the antioxidant capacity of strawberry powder obtained by SD during the first 90 days of storage at 25 °C, using laminated PET film bags and aluminum foil.\n\nRegarding DPPH, similar behavior is observed for 15, 25 and 35 °C, showing a linear trend with slopes of 3.155, 3.013 and 3.039 (mg TE/day) (average degradation rate = 3.069 mg TE/day); however, it is considered that the level reached at 180 days represents an important nutritional contribution. The literature does not report comparative values on DPPH for agglomerated products; no effect of T on DPPH stability during storage of Bael powder obtained by SD has been reported (Sornsomboonsuk et al., 2019).\n\nThe results at the end of storage showed a similar level of preservation for ABTS and DPPH concerning the study T (15, 25, and 35 °C), being of the order of (53.9, 55.1 and 48.2%) and (53.6, 55.3 and 54.4%), and with correlation coefficients of 0.70, 0.62, and 0.63, respectively. The Xw further favors this preservation and aw conditions reached by the products, which slow down the deterioration reactions (Hedegaard & Skibsted, 2013). On the other hand, the presence of SiO2 contributes to an increase in the Tg of the StPM (45 °C), which guarantees adequate matrix stability, mainly at 15 and 25 °C, where (Tg - Tstorage) ≥ 20 °C (Chang et al., 2018). The ABTS and DPPH preservation levels in the present study are higher than those Varastegani et al., (2019) reported in black cumin powders obtained by SD, stored for 12 months at 4 °C and RH of 40 and 60% (33 and 29%, respectively).\n\nThe stability of TF during storage is an important aspect of quality assurance of food products, which modern consumers highly appreciate. Strawberries are a rich source of phenolic compounds, specifically flavonoids, the most representative being catechin, quercetin, and anthocyanins, which are responsible for metal chelation and antioxidant capacity. Generally, high retention percentages were presented at 15, 25, and 35 °C during the 180 days of storage: 76.8, 79.9, and 83.2%, respectively. The degradation was a consequence of the statistical effect of T and t, which favors oxidation processes (Varastegani et al., 2019); furthermore, the higher retention of TF with increasing T could be attributed to a possible higher extraction of these compounds or the hydrolysis of condensed phenolic compounds when subjecting the StPM to these conditions (Tonon et al., 2010).\n\nThe results obtained for vitamin C during storage at 15, 25, and 35 °C showed a good regression fit for zero-order kinetics (R2: 0.941, 0.910, and 0. 940 respectively), showing 2 homogeneous groups, one at 15 and 25 °C, and the other at 35 °C, with lower vitamin C levels at all control times at higher T and t; i.e. with degradation kinetics for 15-25 °C of 1.28 mg Vit. C/100 g bs x day and for 35 °C of 1.44 mg Vit. C/100 g bs x day (Figure 1o). This situation revalidates an increased sensitivity to temperature and oxidation reactions of vitamin C at high t and T, as reported by Lucas-Aguirre et al., (2020).\n\nThe retention levels of vitamin C in the StPM at t = 0 corresponded to an average of 110.8 mg Vit. C/25g serving, corresponding to 123.1% of the recommended dose according to the World Health Organization (WHO), whereas, at month 6 for the homogeneous groups 15-25 and 35 °C, the levels reached 51.9 and 39.6 mg Vit. C/25 g serving (58 and 44% of the recommended dose), respectively. It is noted that 25 g of StPM dissolved in water to complete 250 g corresponds to a beverage with a soluble % solids content of ≅ 10%.\n\nDegradation of the vitamin is due to the highly reactive structure of enediol; the main degradation route is oxidation to dehydroascorbic acid and subsequent oxidation of the latter compound to 2,3-dicetogulonic acid, which has no biological activity. Depending on the system conditions, 2,3-dicetogulonic acid is cycled through Strecker degradation. It produces carbon dioxide and furfural; the latter polymerizes to form melanoidins, compounds responsible for non-enzymatic browning. This mechanism is considerably complicated in the presence of reducing sugars and amino acids that favor various degradation pathways.\n\nIn the storage of acerola and Camucamu powders obtained by SD at 30 °C, 75% RH, and 30 days, vitamin C reductions of 78 and 39.5%, respectively, were observed (dos Santos et al., 2020). Another study reported increased sensitivity of vitamin C in microcapsules in Taro starch at 50 °C with increasing RH (13, 22, 46, 57, and 72%) (Hoyos-Leyva et al., 2018).\n\nAnthocyanins are the substances of the group of phenolic compounds responsible for the characteristic coloring of strawberries; cy-3-glucoside (cy-3-glu), pg-3-glucoside, and Pg-3-rutinoside stand out. Color changes in food products during storage depend on independent variables such as T, t, RH, packaging atmosphere, and packaging, among others, which contribute to a greater or lesser extent in the deterioration reactions of the matrix (Ramachandra & Rao, 2013).\n\nThe behavior of TA at 15, 25 and 35 °C was similar to that of vitamin C, showing a decrease with increasing storage t and T, presenting a good regression fit for zero-order kinetics (R2: 0.9922, 0.949, and 0.9953 for 15, 25 and 35 °C, respectively); additionally, they presented 2 homogeneous groups: 15-25 °C and 35 °C, and degradation rates of 0.116 and 0.204 mg TA/100g bs x day respectively. Similar behavior of TA in bayberry powder obtained by SD has been reported by Mahdavi et al., (2016); however, some research has reported first-order kinetics for TA, for example, Mahdavi et al., (2016) on blackberry powder obtained by SD and stored for 5 months in environments at 25 and 35 °C and an RH of 32.8%.\n\nThe retention levels of TA in the StPM at t = 0 corresponded to a mean of 63.3±2.0 mg cy-3-Glu/100g bs (15.3 mg cy-3-Glu/25 g serving), whereas, at month 6 for the homogeneous groups 15-25 °C and 35 °C, the levels reached 38.0 and 25.5 mg cy-3-Glu/100g bs (9.1 and 6.0 mg cy-3-Glu/25 g serving). Thermal degradation of anthocyanins is associated with the formation of Maillard reaction products (furfural and hydroxymethyl furfural), which condense with the anthocyanins, forming brown-colored compounds (Delia et al., 2019). This situation is considered to have occurred in the StPM at 35 °C mainly and more intensely from day 150, where the color change from a soft pink (t=0) to camel (t > 150 days) became noticeable. This situation parallels other changes observed under these conditions: higher Xw content and development of a caked structure. This same behavior was reported in corozo (Acrocomia aculeata) microcapsules obtained by SD and stored at T > 50 °C (shade red → brown) for 40 days (Osorio et al., 2010); however, other investigations did not find significant changes in TA in SD strawberry powders during storage at 25 °C, 90 days, using aluminum foil PET film laminated packaging and placed in a desiccator with silica gel (Oliveira et al., 2013).\n\nThe stability of food color during storage depends on several factors: temperature, time, relative humidity, light, humidity and composition of the product, and atmosphere (O2, N2, modified atmosphere), among others. Color is the first quality parameter the consumer observes; therefore, its assessment is essential.\n\nThe changes of the color parameters observed for 15 °C and 25 °C during storage (0 →180 days) were low: ∆L* (0.81 and 4.76), ∆a* (-0.06 and 1.81), and ∆b* (0.14 and 1.32), respectively. This situation at these conditions defines these parameters as non-critical for StPM, given that the rate of change is less than 5, not even perceptible by the human eye, as has been reported by several authors: in grape (De Souza et al., 2015) and avocado extracts (Marulanda et al., 2018).\n\nConcerning storage at 35 °C, ∆L* (7.8), ∆a* (-10.0) and ∆b* (2.7) were reached, reflecting the following phenomenologist: 1) a higher clarity of the samples with the storage t, with a higher rate of change after 150 days; this situation is explained by the decrease of the reddish pigments due to their degradation, which causes the contents of the other components of the StPM: MD, SiO2 and GA (white powders) bring out their greater clarity (Zanoni et al., 2020) 2) degradation of the pigments responsible for the reddish chromaticity of the StPM (anthocyanins, flavonols, among others) (Weber et al., 2017), and possible condensation reactions of these with the products of the Maillard reactions, which finally produces a camel shade (Figure 2). 3) a slight increase in yellow chromaticity; however, this change is insignificant (∆b* < 5).\n\nIncreasing storage temperature is a critical factor in stability; notable color changes have been reported in fruit powders obtained by SD and stored at 35 °C: corozo (Osorio et al., 2010), blackberry (Weber et al., 2017) and purple cabbage (Zanoni et al., 2020).\n\n\nConclusion\n\nThe StPM presented good physicochemical stability against deterioration reactions due to the low values of Xw and aw reached, which also confers microbiological stability (aw < 0.361 and Xw < 6.2%). The stability achieved in the properties: ρb, ρc, S, Hy, Hu, AR, CI, HI and D[3;2] confers to the food product homogeneous particle size, with good flowability and instantaneity, and low cohesiveness, mainly at 15 and 25°C. At 35°C, caking was observed from month five onwards, mainly caused by the Xw levels and the possible change from amorphous vitreous to a rubbery state. In general, the color corresponded to the above properties, with similar behavior at 15-25°C during the 180 days of storage, whereas, at 35°C, a change in the shade of the StPM was observed at 150 days: pink → camel. Good retention of bioactive compounds was achieved during storage: antioxidant capacities > 50%, TF > 76%, TA > 39%, and Vit. C > 40% (58 and 44% DR according to OMS for 15-25°C and 35°C, for 180 days). Finally, the research defined a storage t of the StPM of 180 days at 15 and 25°C, and 120 days at 35°C, using an aluminum foil PET laminated film bag as packaging. The study will serve as a tool for the determination of the shelf life of the chipboard once the critical values of the attributes selected as predictors of shelf life are defined.", "appendix": "Data availability\n\nFigshare: Evolution over time (days) of StPM quality attributes during storage. DOI: https://doi.org/10.6084/m9.figshare.23915901.v1\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 the Universidad Nacional de Colombia, the Gobernacion de Antioquia and the General Royalty System for providing the resources for the development of this research.\n\n\nReferences\n\nAOAC: Official Methods of Analysis. VoI.17th ed. Washington, DC, USA: Association of Analytical; 2003.\n\nBarbosa-Cánovas GV, Juliano P: Compression and Compaction Characteristics of Selected Food Powders. Prog. Opt. 2005. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "207975", "date": "27 Oct 2023", "name": "Marianela Hazel Álvarez Hernández", "expertise": [ "Reviewer Expertise Agri-food science and technologies", "postharvest conservation techniques." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 correct approach and is quite interesting. Indeed, strawberries are a highly perishable product. In fresh form, its shelf life is about one week under refrigeration.\n\nThe authors mention that spray drying is one of the most common methods for producing food powders. However, the resulting products have certain deficiencies. Therefore, they propose the fluidized bed agglomeration process for developing a strawberry powder mixture.\nThe authors concluded that the fluidized-bed agglomerated strawberry powder mixture retained a good physicochemical quality for up to six months at both 15 and 25 °C due to its low humidity and water activity. Nevertheless, at 35 °C the mixture developed a cake state.\n\nThe methodology is well-detailed. The statistical analysis is appropriate, but standard deviation is missing from graphs and decimal points must be replaced where applicable. It is not explicitly stated what the control was. Do you have any data available for strawberry powder that has been obtained exclusively through spray drying? The chart title \"Vitamina C\" should also be translated. In the ANOVA table, it is preferable to indicate the significance for P ≤ not signiﬁcant, 0.01, and 0.001.\n\nIn general, the letter \"w\" in the designation aw for water activity should be maintained throughout the text as a subscript. It is also important to preserve the homogeneity regarding numbers and units. In this case, I recommend placing a space between the numerical value and its corresponding unit symbol.\nI consider it relevant to mention the following publications: https://doi.org/10.1016/j.powtec.2019.03.010, 10.1016/j.heliyon.2023.e19577 and 10.3233/JBR-220036.\nPlease, condense and clarify sentences for better readability. I dare to suggest the following wording in the abstract: \"The research aimed to analyze the storage stability of a mixture of fluidized bed agglomerated strawberry powder for six months at three different temperatures (15, 25, and 35 °C). The environment was controlled at 65% relative humidity, and PET foil laminated film bags were used for packaging. Moisture, water activity, bulk density, ..., and particle size were monitored to assess the storage stability of the powder mixture.\".\nIn the abstract section, the conclusion should be improved. The final conclusion of the manuscript should avoid abbreviations to facilitate understanding.\n\nIs the work 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": "267506", "date": "16 May 2024", "name": "Martha Rascón Díaz", "expertise": [ "Reviewer Expertise Stability and bioaccessibility of systems carrying bioactive compounds (microencapsulation and nanoencapsulation)." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 evaluates the storage stability of a mixture of strawberry powder agglomerated in a fluidized bed at three temperatures with a controlled environment at 65% relative humidity and laminated film bags with PET foil as packaging. The study is interesting but has some problems:\n\n1. The authors must correct the errors of the finger. For example, in the methods section of the abstract, the temperature of 25°C is repeated.\n2. The authors must correct the errors of citing. For example, the authors assure that most spray-dried (SD) products present deficiencies in fluidity and instantaneity, citing the study carried out by Samborska et al., 2022. Still, this information does not exist in said study. Furthermore, the authors state that the powders obtained by spray drying are mainly characterized by being very fine and with particle sizes less than 100 μm, where high interparticle cohesion forces are present, mainly due to Van der Waals forces and cite a study carried out by Rosa et al., 2020; but again, this information is not found in that study. 3. It is necessary to improve the writing of the conclusions. What the authors mean by \"(58 and 44% DR according to OMS for 15-25°C and 35°C, for 180 days)\"\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": "232901", "date": "25 Jun 2024", "name": "Ramachandra C T", "expertise": [ "Reviewer Expertise Food Process Engineering", "shelf life studies", "post harvest 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\nThe manuscript is well written with a focus on spray fluid-bed dried strawberry powder mixture. 1. What is shelf life of the chipboard mentioned in the conclusion part of the abstract? 2. Arrange key words in alphabetical order 3. What is the predicted shelf life over observed shelf life of the product?\n\nIs the work 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/12-1174
https://f1000research.com/articles/12-743/v1	26 Jun 23	{ "type": "Research Article", "title": "The effect of academic supervision, managerial competence, and teacher empowerment on teacher performance: the mediating role of teacher commitment", "authors": [ "Imron Muttaqin", "Nani Tursina", "Ajat Sudrajat", "Uyung Yuliza", "Novianto Novianto", "Fajar Fahri Ramadhan", "Muhammad Edi Kurnanto", "Nani Tursina", "Ajat Sudrajat", "Uyung Yuliza", "Novianto Novianto", "Fajar Fahri Ramadhan", "Muhammad Edi Kurnanto" ], "abstract": "Background: Teacher commitment and performance are important factors contributing to student achievement and the quality of education. Therefore, it is critical to draw attention to this issue by identifying factors that influence these two variables. Methods: A survey, consisted of 34 closed-ended questions, was used. The total sample comprised 2,203 teachers, including 832 men and 1,371 women. Data analysis was performed using partial least squares (PLS) structural equation modeling (SEM). Model measurement employed indicator loading, convergent and discriminant validity, Cronbach's testing, composite reliability and average variance extracted (AVE) for internal consistency. Structural model measurement employed coefficient determination (R2), effect size (F2), variant inflation factor (VIF), predictive relevance (Q2) and path analysis measures. Results: The results of the study reveal that academic supervision has a significant positive effect on commitment (β; 0.085, t-statistics; 3.792 and p-value 0.000), academic supervision also affects teacher performance (β; 0.096, t-statistics; 4.416 and p-value 0.000), managerial competence affects teacher commitment (β; 0.195, t-statistics; 8.046 and p-value 0.000), managerial competence also affects teacher performance (β; 0.149, t-statistics; 6.561 and p-value 0.000), organizational commitment affects teacher performance (β; 0.163, t-statistics; 7.263 and p-value 0.000), teacher empowerment affects teacher commitment (β; 0.489, t-statistics; 22.601 and p-value 0.000), and teacher empowerment affects teacher performance (β; 0.489, t-statistics; 22.601 and p-value 0.000). Academic supervision affects teacher commitment mediating by teacher performance (β; 0.014, t-statistics; 3.178 and p-value of 0.001). Managerial competence affects teacher commitment with teacher performance mediation (β; 0.032, t-statistics; 5.588 and p-value 0.000), and teacher empowerment affects teacher commitment with teacher performance mediation (β; 0.080, t-statistics; 7.050 and p-value 0.000). Conclusion: Academic supervision, managerial competence, and teacher empowerment significantly positively affect teacher performance directly and through teacher performance as mediating variable. Teacher empowerment is the most significant factor influencing teacher performance and commitment.", "keywords": [ "Academic supervision", "principal managerial competence", "teacher empowerment", "teacher commitment", "teacher performance" ], "content": "Introduction\n\nTeacher commitment and performance are the keys to successful learning because they directly impact students’ commitment (Abu Nasra & Arar, 2020; Sun, 2015) and mediate the quality of work and performance. Teacher commitment is also influenced by teacher performance (Singh, 2022), but there is still little research that discusses the effect of performance on teacher commitment. Meanwhile, teacher empowerment is influenced by several factors: teacher commitment is indispensable to a school (Shirrell, 2016), and a school can also contribute to the improvement of commitment with reasonable management efforts (Karakuş & Aslan, 2009). Teacher empowerment is also influenced by the principal’s managerial competence and supervision.\n\nManagerial competence is part of principal leadership (Rinehart et al., 1998). Previous research discusses the effects of teacher managerial competence and teacher commitment (Ben Sedrine et al., 2021), but few studies discuss such effects in reference to the West Kalimantan and East Java Provinces. However, it has been proven that academic supervision significantly affects teacher performance (Prasetyono et al., 2018) and teacher empowerment (Davis & Wilson, 2000).\n\nTeacher empowerment affects teacher professionalism and the school itself (Moore & Esselman, 1992; Patrick et al., 2003). In addition, teacher empowerment is very important for the government (Reitzug, 1994) because it can improve the quality of national education and positively influence teachers’ professional and organizational commitment (Bogler & Somech, 2004), which in turn can affect the quality of education. Teacher empowerment is carried out by providing teachers with the power to conduct their duties and responsibilities and continuously improve their competencies to influence their organizational behavior (Tindowen, 2019), job satisfaction (Nursyfa & Asmawi, 2018) and mindset development (Seaton, 2018). Research in this area is important because a) few studies link managerial competence, supervision, and empowerment to teacher commitment and b) improving professionalism and teacher performance in Indonesia is pivotal, necessitating an assessment of the relationship between variables that affect professionalism and teacher performance and commitment. Indonesia also needs teachers’ commitment and performance to improve the quality of education. Given the rationality of the importance of factors affecting teacher performance and commitment, it was interesting for our research team to test these factors. The present study focused on teachers based in the West Kalimantan and East Java Provinces. Teachers in West Kalimantan Province were chosen because of the province’s Pontianak State Institute for Islamic Studies system, which requires teachers to synergize and participate in facilitating teachers’ development. The province of East Java was chosen because it has the highest concentration of teachers in Indonesia.\n\n\nTheoretical framework\n\nThe managerial competence of the principal is a form of competency that includes the ability to plan; carry out organizational development; lead and utilize school resources and manage changes, development, and learning in schools such that they are more effective and efficient in achieving the school’s vision and mission. Previous studies have consistently shown that principal leadership affects teachers’ and students’ quality of learning and motivation (Muijs & Harris, 2003). In addition, a principal needs to strive for teacher participation based on his knowledge (Richardson, 2003). Previous studies have revealed that the leadership model affecting teacher empowerment is participatory because it positively impacts teachers’ impact, autonomy, self-efficacy, and job satisfaction (Martino, 2003) and is a mediating variable for teachers’ commitment to schools (Bogler & Somech, 2004). A principal’s leadership also affects teacher performance (Satriadi, 2016).\n\nCompetence is an individual characteristic of effective or superior reference criteria applying to specific work situations (Spencer and Spencer, 2008). Characteristics that appear on the surface include skills and knowledge, while those that are not visible include motivations, traits, self-image, and social roles. These invisible characteristics largely determine a principal’s success in leading and influencing his actions and thoughts. A principal must exhibit managerial communication skills, teamwork, proactiveness, vision, self-management, outcome orientation, strategies, perseverance, decision-making skills, risk-taking, and creativity (Bhardwaj & Punia, 2013). Such abilities strongly support the tasks and functions of leadership in an organization.\n\nOther studies report that managerial competence comprises the ability to analyze, make decisions, apply knowledge, adapt, perform, lead, and communicate (Khoshouei et al., 2013). A principal as an excellent manager has competence in the following areas: 1) impact and influence, 2) achievement orientation, 3) teamwork and cooperation, 4) analytical thinking, 5) initiative, 6) developing others, 7) self-confidence, 8) directive/assertiveness, 9) information searching, 10) team leadership, and 11) conceptual thinking (Spencer and Spencer, 2013). Previous studies have shown that managerial competence is related to performance (Victor, 2017), and the managerial competence of principals and compensation affect teacher performance (Suhardi, 2019). Research by Lourena Fitri May et al. (2020) also proves the effect of managerial competence on teacher performance. Other factors affecting teacher performance include the organizational climate (Jannah et al., 2019) and leadership styles (Verawati Wote & Patalatu, 2019). However, these two variables are not considered in this study.\n\nTeacher empowerment\n\nTeacher empowerment is an effective means to achieve the vision and mission of education and academic and nonacademic achievement in schools. Teacher empowerment is essentially an effort to support teachers in upholding their duties and responsibilities independently. The significant power of teachers affects many aspects of education, such as motivation, performance, student achievement, job satisfaction, and school achievement. Teacher empowerment can be divided into psychological and structural empowerment. Psychological empowerment affords one a feeling of being able to carry out one’s work well, which has dimensions of meaning, competence, self-determination, and impact (Spreitzer, 1995). Teacher empowerment, according to Short and Rinehart (1992) includes six dimensions: involvement in decision-making, impact, status, autonomy, professional development opportunities, and self-efficacy.\n\nTeacher empowerment is the provision of power to teachers to have power, autonomy, choice, responsibility, and status regarding their duties as teachers. To determine the empowerment of teachers in schools, researchers have uncovered the dimensions of teacher empowerment. Melenyzer (1990) states that there are four dimensions of empowerment: organizational culture, social practice with the strengthening of social norms, and the use of transformational leadership. Wunder (1997) added the professional community as a dimension of teacher empowerment.\n\nThese dimensions include instruments specifically used to measure teacher empowerment, including the School Participant Empowerment Scale (SPES) proposed by Short and Rinehart (1992). In 1998, confirmatory factor analysis was conducted to retest the SPES indicators on 4,091 teachers. The study results showed the need for revisions to the six subscales used by Short and Rinehart (Klecker & Loadman, 1998), and Klecker and Loadman (1998) then made his instrument to measure teacher empowerment.\n\nPrevious research findings reveal a relationship between teacher empowerment and joint decision-making (Bernd, 1992). Delegating decision-making power to teachers has also been shown to increase teachers’ organizational commitment (Mohd Ali & Yangaiya, 2015). Additionally, the involvement of teachers as a decision-making team (Dee et al., 2006) makes them part of the leadership team (Srivastava & Dhar, 2016) because the involvement of teachers as members of this team affects their job satisfaction where teachers’ job satisfaction ultimately affects their empowerment. Teacher empowerment can also be achieved by forming a teacher work team (Park, 2004).\n\nTeacher empowerment can be achieved through many activities, such as cognitive training (Cochran & DeChesere, 1995), decision-making involvement, and self-efficacy improvement (Crum, 1996). The continuous professional development of teachers needs to shift from a mechanistic technical approach to a model of social change that is integrated with the community, schools, and teachers (Patrick et al., 2003), and also more specifically, with the culture of local communities. Many research results reveal that in Indonesia, teacher empowerment activities include writing scientific papers (Chairunnisa, 2016), utilization of information and communication technology (Chodzirin, 2016), teacher certification (Permana, 2017), and sustainable professional development (Pratama, 2018; Rohmah, 2018).\n\nSelf-efficacy refers to a teacher’s confidence in his ability to manage and decide what needs to be done when facing problems related to his tasks. Teachers who do not have confidence in their abilities will see an effect on their performance and job (Skaalvik & Skaalvik, 2014). Teachers’ self-efficacy in some countries can differ according to their cultural orientation (Vieluf & Göbel, 2019), self-efficacy measurements must be modified to a specific country’s culture. Previous research has shown that teacher self-efficacy affects teacher job satisfaction (Klassen et al., 2018), and teacher job satisfaction affects teacher performance (Damrus, 2018; Julianingsih & Paramartha, 2018). Another study showed that job satisfaction affects the performance of junior high school teachers in Sekayu (Widayati et al., 2020).\n\nAcademic supervision\n\nSupervision is a service to teachers that aims to improve the learning, methods, and curriculum used to achieve goals. In general, educational supervision involves coaching toward improving educational services through guidance and enhancing and improving the quality of teaching. Such education provides guidance to improve educational services in general and the quality of teaching and learning (Ametembun, 1991). A supervisor must have personality, managerial, academic, educational evaluation, research, and social competencies as stated in the Regulation of the Minister of Education and Culture Number 12 of 2007 concerning School/Madrasah Supervisory Standards (Nasional, 2007). Supervision has several functions: research, assessment, and improvement.\n\nPrincipal supervision affects teacher performance (Magdalena et al., 2020). They also state that supervision from the principal is very important in improving teachers’ performance and commitment because teachers with such supervision feel guided by their superiors. Other studies have also shown similar results; principal clinical supervision, work motivation, work climate, and teacher professional benefits affect teacher job satisfaction (Febrina Subagia et al., 2019). Teacher performance is influenced by supervision (Veloo & Zolkepli, 2011).\n\nTeacher performance\n\nPerformance refers to a person’s achievement in carrying out their duties and obligations based on authority and responsibility. Kane (1986) defines performance as performing one’s position in a certain period, while Otley (1999) argues that performance is only intended for the business and public sectors because it relates to effectiveness, efficiency, and economy in work. Teacher performance can be articulated as a result of a teacher’s work in carrying out his teaching duties, from planning and implementation to evaluation/assessment.\n\nTeacher performance is influenced by several factors, including the leadership of the principal (Abu Nasra & Arar, 2020), which should be supported by several competencies to be done well. One of these competencies is managerial competence, which is needed for a school to be able to organize and achieve its vision and mission. Teacher job satisfaction (Wolomasi et al., 2019), commitment, and performance are also influenced by teacher job satisfaction (Fei & Han, 2019). Teacher performance is related to the tasks assigned to teachers (Sultana, 2020); tasks that demand high performance are also often responded to with high performance. The duties and responsibilities of a teacher require supervision and meeting targets that have been set. Therefore, academic supervision is needed to help teachers carry out their duties properly. Past studies prove the influence of supervision on teacher performance (Prasetyono et al., 2018), and organizational culture also affects teacher performance (Emengini et al., 2020).\n\nTeacher commitment\n\nCommitment is an important trait for any teacher; teaching with full commitment can be judged by the passion and enthusiasm of the teacher when teaching. Commitment is here defined as exhibiting dedication to the goals and values of an organization relating to the role of the teacher in achieving learning objectives. Teachers with high commitment are determined and responsible in their teaching. This attitude is needed to improve student achievement. The term commitment comes from social exchange theory, which underlies the emergence of social relationship theory due to the development of needs in organizations (Cropanzano & Mitchell, 2005). The theory states that social exchange involves continuous interaction that creates obligations (Emerson, 1976).\n\nFurthermore, social exchange theory emphasizes an individual’s contribution to an organization and participation (Angle & Perry, 1981). The theory is ultimately the foundation of organizational commitment theory. In this case, a teacher’s commitment and interaction with the school and its students are at the core. Steers and Spencer (1977) explain that commitment refers to an individual’s positive orientation toward his organization; a teacher behaves positively toward the tasks assigned to him at school. Steers and Spencer stated that there are three indicators of commitment: the desire to remain in the organization, to strive according to the organization’s wishes, and to accept the organization’s values and goals.\n\nSome studies show that teacher commitment is influenced by the leadership of the principal (Yu et al., 2002), leadership behavior (Huang, 2011), authoritarian leadership (Parlar et al., 2022), transformational leadership (Yahaya & Ebrahim, 2016), and distributed leadership (Liu, 2020). Some of the studies above highlight the principal’s leadership role, which requires good managerial abilities to ensure the quality of education. Therefore, it is interesting to examine whether managerial competence affects teacher commitment. In addition, teacher involvement also increases commitment (Jyoti et al., 2021). As an important dimension of empowerment, we explore whether teacher empowerment can affect teacher performance through teacher commitment. Therefore, we propose hypothetic research model as Figure 1.\n\nHypotheses\n\n1: Academic supervision has a significant positive effect on teacher commitment.\n\n2: Academic supervision has a significant positive effect on teacher performance.\n\n3: Managerial competence has a significant positive effect on teacher commitment.\n\n4: Managerial competence has a significant positive effect on teacher performance.\n\n5: Organizational commitment has a significant positive effect on teacher performance.\n\n6: Teacher empowerment has a significant positive effect on teacher commitment.\n\n7: Teacher commitment has a significant positive effect on teacher performance.\n\n8: Academic supervision has a significant positive effect on teacher performance mediated by teacher commitment.\n\n9: Managerial competence has a significant positive effect on teacher performance mediated by teacher commitment.\n\n10: Teacher empowerment has a significant positive effect on teacher performance mediated by teacher commitment.\n\n\nMethods\n\nThe present research uses quantitative methods with surveys. The research variables include five variables: the managerial competence of the principal, teacher empowerment, academic supervision, teacher performance, and commitment.\n\nThe respondent population of this study includes teachers under the auspices of the Ministry of Religious Affairs who were active and registered on the Sistem Informasi Pendidik dan Tenaga Kependidikan (SIMPATIKA) website in semester 1 of the 2020/2021 academic year in West Kalimantan and East Java. A cluster random sampling technique was used based on the large number of respondents involved in this study, respondents came from teacher on East Java (38 districts and West Kalimantan province (14 districts). The research period lasted for seven months running from February 2022 to August 2022.\n\nResearch instruments were adopted and modified from regulations and relevant research results. Data were collected using an online questionnaire including five Likert scale options: (1) strongly disagree, (2) agree, (3) cannot decide, (4) agree, and (5) strongly agree. Validity and reliability of the measurement depend on the score obtained in one group sample, changes in the other group will change the quantitative value of validity and reliability. Validity and reliability was performed directly on one group of participants, with a large sample size - invalid and unreliable items were excluded from the analysis and, re-analysis was conducted only on valid and reliable items (Hadi, 2004), so the present research using indicator validity, not instrument validity, invalid and unreliable indicators are detailed reported and deleted and then re-analyzed only for valid indicators. This research instrument was adapted from another instrument for several reason; 1) indicators are known or pre-tested (Regulation or research findings, 2) large sample with different district and culture, 3) PLS SEM is different from covariance-based SEM which uses theory to be confirmed, PLS SEM (smartPLS) can be used to confirm existing theories or answer hypotheses.\n\nThe questionnaire can be found in the Extended data. There are five constructs of this research: managerial competence, academic supervision, teacher empowerment, teacher performance and teacher commitment. The managerial competence and academic supervision indicators were adapted from the Decree of the Ministry of Educational and Culture of Republic Indonesia number 13 Year 2007 concern about Standards for School/Madrasah Principals (Republik, 2007). There were 16 indicators (pp.5) for managerial competence, while for supervise competence, there were 3 indicators (pp.7). The present study uses 6 indicators of managerial competence (MC1 to MC6) and 6 indicators for academic supervision (AS1 to AS6). The teacher empowerment indicators were modified and adapted from Short’s teacher empowerment scale (Short, 1992), consisting of involvement in decision-making, impact, status, autonomy, professional development opportunities, and self-efficiency. There were 11 indicators (TE1 to TE11) used for measures. The teacher performance indicators were adapted from APKG (Alat Penilai Kinerja Guru/Teacher performance assessment tool) sering digunakan seperti (Aryana et al., 2022; Dahlia & Afriadi, 2020), and this indicator assesses teachers starting from preparation/planning, implementation, and evaluation. Teacher performance indicators of the present study uses 6 indicators (TP1 to TP6). Several indicators in APKG are merged for effectiveness and efficiency, and teachers are light when completing questionnaires. The teacher commitment (TC) instrument was modified from Lei Mee Thien, Nordin Abd Razak, and T. Ramayah instruments (Thien et al., 2014). They made 13 indicators of teacher commitment used for teachers in Malaysia. The dimensions measured were commitment to students, teaching, school, and profession. The present study used 7 indicators for teachers (TC1-TC7).\n\nModel measurements are performed by calculating the validity and reliability of the instrument. The indicator was assessed with three measurements: 1) indicator loading and internal consistency reliability, 2) convergent validity, and 3) discriminant validity (Hair et al., 2019). Internal consistency reliability was assessed with Cronbach Alpha, Composite Reliability (CR), and Average of Extracted Variants (AVE). While structural model measurement of the present study was performed by assessing the collinearity, coefficient of determination (R2), effect size (F2), predictive relevance (Q2) using the blindfolding procedure, and path coefficient.\n\nFirst, A collinearity was used to test whether this model was worth using. If an instrument’s Varian Inflation Factor (VIF) value is less than 3 for the inner model and less than 10 for the outer model, it can move on to the next step (Sarstedt & Cheah, 2019). Second, The coefficient of determination (R2). The R2 value can be used to determine the goodness of fit (GoF) test. A variation in the proportions of endogenous factors that external variables can predict is the coefficient of determination from 0 to 1. Values range from significant (0.75) to moderate (0.50) to weak (0.25) (Chin, 1998). Third, changes in coefficient of determination (R2) values are used to determine effect size (F2). In order to determine if exogenous latent variables have a significant impact on endogenous variables, this change in value is used (Ghozali, 2014). Cohen (1998) also divided into a minimal impact (0.02); a moderate impact (0.15); and a considerable impact (0.35); on the structural level (Chin, 1998). Fourth is predictive relevance. The Stone-Geisser (Q2) test is a statistical test to measure how well the model and the resulting parameters produce the observation value (predictive relevance). If the Q2 value is greater than 0, then the model has predictive relevance. Fifth is the path coefficient. The calculation of the path coefficient between endogenous and exogenous constructs was performed with 5000 bootstrapping.\n\nThe institute for research and community services of Pontianak State Institute for Islamic Studies as ethical committee has approved the study (ethics committee approval number: B-415.1/In.15/LP2M/HM.01/11/2022). Researchers visited on a pre-informed date and obtained permission from Head Office of Ministry of Religious Affairs (MORA) district after explaining the purpose of this study. Teachers who participated in this study were provided with a consent form when opening the questionnaire page. The research instrument was approved by Institutional Review Board (approval number B-43.1/In.15/LP2M/HM.01/2/2022). Teachers who filled out the questionnaire thus agreed to participation in the study, and those who did not participate did not agree (the consent form is provided as extended data).\n\nThe measurement model employed in this study uses three measurements: 1) an item validity measurement using indicator loading and internal consistency measurement using Cronbach’s alpha, composite reliability and the average variance extracted (AVE); 2) a convergent validity measurement; and 3) a discriminant validity measurement. First, the validity of an indicator is determined from the value of the loading factor based on SmartPLS output; this value shows the correlation between an indicator and its construct. An indicator with a low value indicates that it does not work in the measurement model, while a high value is said to be valid.\n\nSecond, internal consistency measurement or construct reliability is used to measure the internal reliability of variable constructs, and the measurement uses composite reliability (CR) and Cronbach’s alpha. Composite reliability values of between 0.6 and 0.7 are considered to indicate good reliability (Sarstedt et al., 2021), while Ghozali recommends composite reliability values of above 0.6 (Ghozali, 2011). In addition, the value of the average variance extracted (AVE) can be used as a guideline for the reliability of a construct. The average variance extracted (AVE) is declared eligible if the value is above 0.50. An AVE value of > 0.50 or higher indicates that a construct can account for more than its indicator variance; conversely, an AVE is less than 0.50 indicates that on average, more variance remains in the item error than the construct describes (Henseler et al., 2009). More details about the validity and reliability tests can be seen in Table 1. For more validity can be seen also on Fornel-Larcker criterion one Table 2.\n\nThird, discriminant validity testing involves comparing the AVE to the root of the AVE or Fornell-Larcker criterion. From the previous table, the AVE value of academic supervision is 0.674, that of managerial competence is 0.693, that of teacher commitment is 0.540, that of teacher empowerment is 0.519, and that of teacher performance is 0.617. When compared to the AVE root in the following Fornell-Larcker table, the AVE root is greater than its correlation with the construct, which means it has discriminant validity.\n\nDiscriminant validity can also be determined from the cross-loading value of each construct. If the loading value of an item/indicator is greater than the cross-loading value, it is said to have discriminant validity. In addition to these criteria, Ghozali added that the cross-loading value should be greater than 0.7.\n\nFor example, the loading value of AS1 is 0.757, which is greater than the value of AS1 for managerial competence (0.420), teacher commitment (0.339), teacher empowerment (0.372) and teacher performance (0.356). In the table above, all loading values are greater than the cross-loading values, which means that they have good discriminant validity. To strengthen discriminant validity further, we also use the Heterotrait-Monotrait (HTMT) criterion. HTMT values should be less than 0.9 to ensure reflective construct validity (Henseler et al., 2009). All values of the HTMT construct for this study are below 0.9, meaning that discriminant validity requirements are met. The detail HTMT table as shown on Table 4.\n\nA structural model serves to predict the relationships between constructs used in a study. We apply the model using bootstrapping and blindfolding procedures using SmartPLS. The procedure is used to determine the coefficient of the determinant (R2)/R-square of the exogenous construct, effect size, and predictive relevance/Q2 of the model. One of the conditions for testing using PLS is a lack of multicollinearity; therefore, before other tests are carried out, whether an intercorrelation between latent/exogenous variables is analyzed. Final model after validity, reliability and collinearity test show on Figure 2 as follows.\n\nCollinearity refers the existence of a close relationship between independent/exogenous variables, as a strong relationship can interfere with the precision of predictions of the proposed model. Therefore, a good model must be free of collinearity. The presence or absence of collinearity can be determined from the tolerance value and variant inflation factor (VIF). The VIF value must be below 5; if it is above 5, multicollinearity exists (Sarstedt et al., 2021). Collinearity checking is performed to calculate the inflation factor (VIF) variant provided by SmartPLS.\n\nThe VIF table shows no multicollinearity between the variables of this study. From Table 5, there is no multicollinearity between the variables of this study.\n\nWe next determine the potential direct or indirect influence of exogenous variables on endogenous variables. SmartPLS provides tables for both direct and indirect path analysis. From the output of the path coefficient table, it can be concluded that academic supervision has a significant positive direct effect on teacher commitment and teacher performance, managerial competence has a significant positive direct effect on teacher commitment and performance, and teacher empowerment has a significant positive direct effect on teacher commitment and performance. Table 6 shows these results in detail.\n\nRegarding the indirect influence of the three variables with the mediation of teacher commitment, Table 7 shows the beta coefficient, t-statistics and p-values. The SmartPLS output shows that all variables have a significant positive effect on teacher performance with the mediation of teacher commitment.\n\nTo predict the effect of exogenous variables on endogenous variables in the structural model of this study, we use the coefficient of determination, which is a means to calculate how much an endogenous construct can be explained by an exogenous construct. The R-squared value ranges from 0 to 1. R-square adjusted, the R-square adapted to the standard error, is more precise because it involves error calculation. Table 8 shows the output of the calculation results of the coefficient of determination. An R-square value of 0.67 is considered high, a value of 0.33 is moderate and a value of 0.19 is low (Chin, 1998). Table 8 shows the R-square results of this study.\n\nTo increase confidence in the R-square value, the influence of exogenous variables on individual variables, including substantive variables, should be considered (Ghozali, 2014). This study also used F-square to calculate the effect size. The value of f2 is used to determine the effect of exogenous variables on endogenous variables, including strong, moderate and weak effects. If the F-square value is less than 0.15 (0.02 ≤ f2 < 0.15), the effect is weak; a value between 0.16 and 0.35 (0.15 ≤ f2 < 0.35) denotes a moderate effect; and a value greater than 0.35 (0.35 ≤ f2) denotes a strong effect. Table 9 shows the F-square output in detail.\n\nTo test predictive relevance, this study uses the Stone-Geisser test (Q2); this calculation is used to see how well a model can predict certain parameters. Results below 0 denote a model with no predictive relevance. In PLS-SEM, predictive relevance is tested using blindfolding, which is an analysis of data used to determine the relevance of predictions produced by a construct; the process uses the Q-square value as a reference. Ghozali created three blindfolding levels: less (0.02), moderately (0.15) and highly predictive (0.35) (Ghozali, 2014). The complete blindfolding calculation results are given in Table 10.\n\n\nDiscussion\n\nThis study aims to determine the influence of academic supervision, managerial competence, and teacher empowerment on teacher commitment directly and with the mediation of teacher performance. Calculations made via bootstrapping with 5,000 repetitions reveal an influence of academic supervision on teacher commitment directly and with the mediation of teacher performance. Principal managerial competence also directly affects teachers’ commitment and the mediation of teacher performance. A teacher’s performance also affects a teacher’s commitment.\n\nWe test how much influence exogenous constructs have on endogenous constructs by calculating the coefficient of determination (R-square). Overall, the influence of the exogenous construct shows an R-square of 0.445 with an adjusted R-square of 0.444. The figure shows that 44.4% of teacher commitment can be explained by academic supervision, managerial competence, and teacher empowerment. The three constructs also affect teacher performance, with an R-square of 0.567 and an R-square of 0.566. To increase the degree of trust, we also used an F test (F-square). Academic supervision’s effect on teacher commitment is 0.008 and the effect on teacher performance is 0.018. The effect of management competence on teacher commitment is 0.040, and the effect on teacher performance is 0.045.\n\nMeanwhile, the effect of teacher empowerment on teacher commitments is valued at 0.291, and the effect on teacher performance is valued at 0.510. To determine how well the model predicts the research constructs, a blindfolding stone-Gaisser (Q2) calculation is used. SmartPLS output shows a figure of 0.235 for teacher commitment, while for teacher performance, we obtain a figure of 0.356. This output shows that predictive relevance is in the moderate category (<0.15).\n\nHypothesis 1 posits a significant positive effect of academic supervision on teacher commitment. This hypothesis is accepted we found a β value of 0.085, t-statistic of 3,792, and p-value of 0.000. A t-statistical value greater than 1.96 indicates a positive influence of academic supervision on teachers’ organizational commitment that is significant with a p-value below 0.05. This finding is consistent with Irawan et al. (2018) who report that academic supervision affects teachers’ organizational commitment. Academic supervision indicators of teacher commitment include assistance from principals and supervisors in syllabus/teaching preparation (AS1), creating teaching materials, media and tests (AS2), material delivery (AS3), learning strategies and media (AS4), the evaluation of learning processes and outcomes (AS5), and question item analysis (AS6).\n\nRegarding Hypothesis 2, academic supervision is found to have a direct influence on teacher performance, as the SmartPLS output shows a β value of 0.096, t-statistic of 4.416 and p-value of 0.000. A t-statistic above 1.96 indicates that a construct has an influence, and p-value below 0.05 indicate a significant effect. The findings of this study are consistent with the results of a study conducted in Malaysia finding a relationship between supervision and teacher performance (Hoque et al., 2020). The findings also corroborate Hidayatullah and colleagues’ (2020) finding that supervision influences teacher performance. Aprida et al. (2020) also reported that school administration and supervision affect teacher performance. Seven indicators of academic supervision affect the performance of teachers in syllabus/teaching preparation (TP1), material development and media and learning evaluation (TP2), the use of appropriate methods (TP3), the use of learning media (TP4), the evaluation of processes and results (TP5), the analysis of question items and learning evaluation (TP6).\n\nHypothesis 3, which states that a principal’s managerial competence affects a teacher’s organizational commitment, is accepted, as the SmartPLS output shows a β value of 0.195, T-statistic of 8,046, and p-value of 0.000. The findings of this study are consistent with those of Rachmawati and Suyatno, who revealed that a principal’s interpersonal and technical competence significantly affects teachers’ commitment (Rachmawati & Suyatno, 2021).\n\nHypothesis 4 states that a principal’s managerial competence has a direct significant effect on teacher performance, which is accepted due to the following statistical results: a β value of 0.149, T-statistic of 6.561, and p-value of 0.000. A t-statistical score greater than 1.96 indicates a direct influence of a principal’s managerial competence on teacher performance. A p-value below 0.05 indicates that the effect is significant. This finding is consistent with Rahman Tanjung et al. (2021), who found an influence of a principal’s managerial competence on teacher performance, and with Susanti (2021), who also reports an effect of a principal’s managerial competence and work climate on teacher performance.\n\nHypothesis 5 states a significant positive influence of direct teacher commitment on teacher performance, which is accepted from the following statistical results: a β value of 0.163, t-statistic of 7.263, and p-value of 0.000. A t-statistical score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. A p-value below 0.05 indicates a significant effect. This finding is consistent with Agung’s study, which identifies the influence of organizational commitment on performance (Agung, 2017), and it corroborates The study of Butar et al. (2020), which finds an effect of organizational commitment on teacher performance both directly and indirectly. The six indicators influenced by teacher commitment in this study include teachers speaking well of their school/madrasah to others (TC1), alignment between a school’s values and a teacher’s personal values (TC2), commitment to students’ success (TC3), enjoyment of teaching (TC5), a desire to teach (TC6), and feeling that becoming a teacher was the right decision (TC7).\n\nHypothesis 6 posits a significant positive influence of direct teacher empowerment on teachers’ organizational commitment, which is accepted due to the following statistical results: a β value of 0.489, t-statistic of 22.601 and p-value of 0.000. A t-statistical score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. A p-value below 0.05 indicates a significant influence. These findings corroborate the work of Lee and Nie (2014) and Toremen et al. (2011), who found an effect of teacher empowerment on teacher commitment. The professional dimension of growth, which refers to the ability of teachers to operate in a professional school environment (TE1) and cooperate and collaborate with other teachers both in and outside of school (TE3), contributes to teacher commitment, as does the status dimension of teacher empowerment, which includes obtaining in-depth knowledge and understanding of the field of science (TE6). One indicator of the autonomy dimension is teachers’ freedom to select strategies, teaching materials and their own materials (TE8). Impact dimensions including the ability to influence other teachers and students (TE9), teachers’ confidence in their impact on their school/madrasah (TE10), and the ability to complete schoolwork well (TE11) also increase teacher commitment.\n\nHypothesis 7 posits a significant positive influence of direct teacher empowerment on teacher performance, which is accepted due to the following statistical results: a β value of 0.494, t-statistic of 22.301 and p-value of 0.000. A t-statistical score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. A p-value below 0.05 indicates a significant influence. The seven teacher dimensions (TE1, TE3, TE6, TE8, TE9, TE10 and TE11) have a significant positive effect on teachers’ performance in compiling a teaching syllabus/preparing for lessons (TP1), material development and media and evaluation (TP2), the use of appropriate methods for learning materials (TP3), the use of learning media that are appropriate to the material and connect with the real world (TP4), evaluation of learning processes and outcomes (TP5) and the implementation of question analysis items and evaluation. These findings are consistent with studies conducted by Lutsilili and East Constituency, which reveal effects of teachers’ empowerment on their performance (Constituency et al., 2014; Lutsilili et al., 2012).\n\nHypothesis 8 posits a significant positive influence of academic supervision on teacher performance through the mediation of teacher commitment, which is accepted due to the following statistical results: a β value of 0.014, t-statistic of 3.178 and p-value of 0.001. A t-statistic score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. An accepted p-value below 0.05 indicates a significant influence. This finding is consistent with the results of Susana, who finds effects of supervision and teacher commitment on teacher performance (Susana, 2018). The commitment variable used in this study is mediation, while Susana studied exogenous variables, which means that teacher commitment affects teachers either as a mediation variable or directly.\n\nHypothesis 9 posits a significant positive influence of principal managerial competence on teacher performance through the mediation of teacher commitment, which is accepted due to the following statistical results: a β value of 0.032, t-statistic of 5.588 and p-value of 0.000. A t-statistic score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. A p-value below 0.05 indicates a significant influence. These findings are consistent with previous studies showing that the managerial competence of school principals consistently affects achievement and other aspects (Grissom & Loeb, 2011). These findings also corroborate the results of Paturusi, who found an effect (Paturusi, 2017), reinforcing the relationship between managerial competence and teacher performance.\n\nHypothesis 10 states that teacher empowerment significantly influences teacher performance through the mediation of teacher commitment, which is accepted due to the following statistical results: a β value of 0.080, t-statistic of 7,050, and p-value of 0.000. A t-statistical score greater than 1.96 indicates a direct influence of teacher commitment on teacher performance. A p-value below 0.05 indicates a significant influence. The seven teacher empowerment indicators used in this study positively and significantly affected teacher performance by intervening teacher commitment. Being in a professional community of fellow teachers to learn influences teacher commitment (Lee et al., 2011) equally. This indicator is also a teacher empowerment dimension. Empowered teachers tend to speak well of their school/madrasah to others (TC1). They also feel alignment between the values adopted by their school and their personal values (TC2), have a mission to make their students successful (TC3), enjoy teaching (TC5), always wanted to be a teacher (TC6) and feel that becoming a teacher was the right decision (TC7).\n\n\nConclusion\n\nTeacher commitment can be increased through academic supervision from the principal and supervisor, managerial competence from the principal, and teacher empowerment. These three factors directly and indirectly affect teachers’ commitment. Independent teacher performance can predict teacher commitment. In addition, teacher performance moderates the impacts of academic supervision, managerial competence, and teacher empowerment on teacher commitment. Among the variables used in this study, teacher empowerment affects teacher commitment and performance most, while supervision has the weakest effect. Therefore, principals, superintendents, and governments are advised to improve programs that empower teachers because they affect teacher commitment and performance.\n\nThe present study is limited by its sample, which, although quite large, cannot be generalized to the rest of Indonesia. However, theoretically, this study proves the effects of academic supervision, managerial competence and teacher empowerment on teacher performance both directly and through the mediation of teacher commitment.\n\nFurther work can determine other factors hypothesized to affect teacher performance and commitment, since the variables used in this study represented 44.4% of the identified effects, while 45.6% of the effects were attributed to other variables.", "appendix": "Data availability\n\nHarvard Dataverse: “Effect of Supervision, Managerial Competence, Empowerment on Performance; Commitment as intervening effect”, https://doi.org/10.7910/DVN/CMLWOU (Muttaqin, 2022).\n\nThis project contains the following underlying data:\n\n- Data CSV for SmartPLS.csv\n\n- Valid instrument\n\nThis project contains the following extended data:\n\n- Questionnaire in English and Indonesia.pdf\n\n- Research Contract.pdf\n\n- Ethical Commission Approval.pdf\n\n- Letter from the Ministry of Religious Affairs Blitar disctric.pdf\n\n- Letter from Head of The Office of Religious Affairs of Bengkayang.pdf\n\n- Letter from Section Chief of Madrasah’s Education of The Office of Religious Affairs of Surabaya City number B-5022/Kk.13.29.2/PP.00/07/2022\n\n- Penma Blitar request permission\n\n- Letter from the Ministry of Religious Affairs Blitar disctric.pdf\n\n- Validity and reliability test.xlsx\n\n- Bootstrap 5000.xlsx\n\n- Blindfolding.xlsx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThe researchers sincerely appreciate and express gratitude for financial support from LP2M under Research Grant Scheme with grant number B.222.34/In.15/Lp2m/PP.00.9/5/2022 Pontianak State Institute for Islamic Studies (IAIN) Pontianak.\n\nThe researchers also express gratitude and special thanks to:\n\nDr. H. Syarif, MA, Rector of State Institute for Islamic Studies (IAIN) Pontianak,\n\nSukardi, M. Hum. Chief of The Institute for Research and Community Services (2018-2022);\n\nDr. Yusriadi, MA, Chief of The Institute for Research and Community Services (2022); Drs. KH. Taufiq Abdul Djalil, MM, Head of The Office of Religious Affairs of Blitar Disctric, East Java Indonesia; Dr. H. Taufiqurrahman, M. Ag, Head of The Office of Religious Affairs of Jombang Disctric, East Java Indonesia; Dr. Ahmad Munir, M. Hum, Head of The Office of Religious Affairs of Tuban Disctric, East Java Indonesia;\n\nDr. Muhajir, S. Pd, M.Ag, Head of The Office of Religious Affairs of Tulungagung Disctric, East Java Indonesia; Dr. H. Taufiqurrahman, M. Ag, Head of The Office of Religious Affairs of Jombang Disctric, East Java Indonesia;\n\nFatkhul Mubin, S. Pd, M.Pd.I, Section Chief of Madrasah’s Education of The Office of Religious Affairs of Surabaya City, East Java Indonesia;\n\nH. Damsir, S. Ag, Head of The Office of Religious Affairs of Bengkayang Disctric, West Kalimantan, Indonesia; The authors would also like to extend thanks to teachers, who participated in this study.\n\nNanik Shobikah, S. Pd., M.Pd. who accompany this research.\n\nAisha Qurrotul Ain, baby researcher who accompany data collection in east java and west borneo.\n\n\nReferences\n\nAbu Nasra M, Arar K: Leadership style and teacher performance: mediating role of occupational perception. Int. J. Educ. Manag. 2020; 34(1): 186–202. Publisher Full Text\n\nAgung BR: Teachers’ job satisfaction, organizational commitment, and performance in Indonesia: A Study from Merauke District. Int. J. Dev. Sustain. 2017; 6(8): 700–711. www.isdsnet.com/ijds.\n\nAmetembun: Supervisi Pendidikan. PT. Remaja Rosdakarya.1991.\n\nAngle HL, Perry JL: An empirical assessment of organizational commitment and organizational effectiveness. Adm. Sci. Q. 1981; 26: 1–14. 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Publisher Full Text\n\nSingh A: The mediating role of employee commitment between quality of work-life and job performance of the faculty. Ind. Commer. Train. 2022; 54(2): 250–266. Publisher Full Text\n\nSkaalvik EM, Skaalvik S: Teacher self-efficacy and perceived autonomy: Relations with teacher engagement, job satisfaction, and emotional exhaustion. Psychol. Rep. 2014; 114(1): 68–77. PubMed Abstract \| Publisher Full Text\n\nSpencer LM, Spencer PSM: Competence at Work models for superior performance. John Wiley & Sons; 2008.\n\nSpencer LS, Spencer PSM: Competence at Work models for superior performance. John Wiley & Son, Inc.; 2013.\n\nSpreitzer GM: Psychological empowerment in the workplace. Acad. Manag. J. 1995.\n\nSrivastava AP, Dhar RL: Authentic leadership for teacher’s academic optimism. Eur. J. Train. Dev. 2016; 40(5): 321–344. Publisher Full Text\n\nSteers RM, Spencer DG: The role of achievement motivation in job design. J. Appl. Psychol. 1977; 62(4): 472–479. 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JIIP-Jurnal Ilmiah Ilmu Pendidikan. 2021; 4(4): 291–296. Publisher Full Text\n\nThien LM, Razak NA, Ramayah T: Validating teacher commitment scale using a Malaysian sample. SAGE Open. 2014; 4(2): 215824401453674. Publisher Full Text\n\nTindowen DJ: Influence of empowerment on teachers’ organizational behaviors. Eurasian J. Educ. Res. 2019; 8(2): 617–631. Publisher Full Text\n\nToremen F, Karakus M, Savas AC:The effect of empowerment on teachers’ organizational commitment. Energy Education Science and Technology Part B: Social and Educational Studies. 2011; 3(4): 545–554.\n\nVeloo A, Zolkepli WH: Atribut Sistem Penilaian Prestasi dengan Kepuasan Kerja dalam Kalangan Guru. Int. J. Manag. Stud. 2011. Publisher Full Text\n\nVerawati Wote AY, Patalatu JS: Pengaruh Gaya Kepemimpinan Transformasional dan Kepuasan Kerja terhadap Kinerja Guru Sekolah Dasar. Jurnal Ilmiah Sekolah Dasar. 2019; 3(4): 465–465. 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The Pennsylvania State University;1997.\n\nYahaya R, Ebrahim F: Leadership styles and organizational commitment: literature review. J. Manag. Dev. 2016; 35(2): 190–216. Publisher Full Text\n\nYu H, Leithwood K, Jantzi D: The effects of transformational leadership on teachers’ commitment to change in Hong Kong. J. Educ. Adm. 2002; 40: 368–389. Publisher Full Text" }	[ { "id": "181580", "date": "14 Jul 2023", "name": "MD. Rahat Khan", "expertise": [ "Reviewer Expertise Quantitative and Qualitative Research", "Business and Management", "Strategic issues in business." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Author\nThank you so much for giving me the chance to read your paper. I found the paper interesting, but there need some adjustments that may enrich the quality and readability of this manuscript.\nThe problem statement is incorrectly designed in the 'Introduction.' You need to develop research questions based on your identified problem. The problem statement is not in-depth; you need to explain the statement based on global context and then focus on various developing country perspectives. Go and search the different databases to strengthen your problem statement.\n\nThe section “literature review” is missing. Develop the section first to deep dive into your problem statement (add the latest citations to the research context) in detail and then develop the \"Theoretical framework and hypotheses\". Please read and cite the following papers to learn how to differentiate the “literature review” and “Theoretical framework and hypotheses” and learn the recent trend of writing hypothesis development.\nKhan, M. R., Rana, S., & Hosen, M. I. (2022). Impact of trustworthiness on the usage of m-banking apps: A study on Bangladeshi consumers. Business Perspectives and Research, 10(2), 234-250.\nKhan, M. R., & Roy, S. K. (2023). Do primary HR functions model work in emerging economies? Sustainable compact perspective for Bangladeshi RMG industry. Review of International Business and Strategy, 33(2), 328-341.\n\nMore information is required in the 'Methodology\" section. There are some mismatches in the 'Methodology\" and \"Result Analysis\" sections. Please see the suggested paper to develop the section. The mediation effect analysis is confusing and the tabulation of the entire hypothesis outcomes can be presented in the same table. See the following papers for mediation analysis writing.\nMitra, A., & Sur, S. (2023). Subjective Knowledge, Perceived Ability, Motivation, and Age: A Mediated Moderation Model of Antecedents of Stock Market Investors’ Information Search. Global Business Review, 09721509221146062.\nAl Ahad, A., & Khan, M. R. (2020). Exploring the mediating effect of demographic attributes on the relationship between employee engagement and organizational citizenship behavior. International Journal of Management and Sustainability, 9(1), 11-23.\n“Ethical considerations” is not an essential highlighting heading in a research paper but rather a dissertation writing. Hence this part can be synthesized under the methodology section.\n\nThe 'Discussion' section is missing and needs to focus more on the novelty of this research. You need to compare the earlier related research to vivid why your research is unique in the international banking business literature.\n\nYour conclusion section needs to add more subheadings on the 'Implications' and 'Future Direction of the research' Implication sections should be separated from this section and be fragmented as managerial and theoretical implications of this research.\n\nI recommend seeing the suggested articles to develop the overall structure of your paper.\n\nBest wishes\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "9969", "date": "16 Nov 2023", "name": "Imron Muttaqin", "role": "Author Response", "response": "Dear Reviewer, Thank you for your insightful feedback and suggestions. In what follows, we provide responses to your six points of suggestion for this article; Dear reviewer, I greatly appreciate your insightful suggestions. In response, I have expanded upon the problem identification and provided a more in-depth examination of the problem statements, supplementing them with explanations based on a global context. Additionally, I have fortified the research statement with more literature. In this revision, I have incorporated 37 new articles into the literature review. I have thoroughly revised the introduction section in accordance with the reviewer's guidance Dear reviewer, thank you for your feedback. I have made the necessary additions to the literature review, theoretical framework, and hypotheses as you suggested. However, I would like to apologize as the articles you recommended for citation do not align with the scientific field of this study. Despite this, I am appreciative of the additional references, which I can use to further enhance this article Dear Reviewer, thank you for your suggestion. I believe there is a fundamental distinction between \"methodology\" and \"method\". In this paper, I've opted for the term \"method\" because referencing \"methodology\" would imply a discussion about the science behind the research method. As my focus lies primarily on the \"method\", this section outlines the actions taken during the research process, without delving into the associated theories. These theories have been previously discussed during the research proposal seminar and the results seminar. The method section specifies that this research is categorized as quantitative, employing a survey design. Data was collected via questionnaires and analyzed using SEM-PLS using SmartPLS software. I am grateful for the valuable analytical materials and examples you provided. I have thoroughly read the article titled \"Exploring The Mediating Effect of Demographic Attributes on The Relationship between Employee engagement and organizational citizenship behavior\". However, there is a key difference between your article and our. In your paper, data analysis was conducted using Parametric Statistics with SPSS/AMOS version 20, while the present study uses non-parametric statistics with SmartPLS. Consequently, the output tables generated by each software are vastly different. Regarding the mediation effect, PLS-SEM uses SmartPLS indeed employs the term \"Indirect\" in the output table, implying a mediation or moderation variable, depending on the researcher's intent. In line with the provided diagram, this study uses mediation, or indirect effect of the SmartPLS software. In terms of ethical considerations, I concur with the reviewer's perspective. However, this crucial section is required to be uploaded as extended data in the F1000 journal for easy reference. Thus, I created a separate subheading for this section. Dear Reviewer, Thank you for your insightful suggestions. In response, I have incorporated a section on the novelty of this research into the discussion section. This includes a comparison with other studies in the field. These additions have been carefully integrated into each segment of the discussion. However, I did not add literature pertaining to the international banking business, as it falls outside the scope of our research group's focus, which is education. We believe that maintaining a strict focus on our area of expertise ensures the research's relevance and applicability. In this revision, I have adhered to the direction you suggested, including aspects of flow, literature review, and theoretical framework. Thank you once again for your guidance and support. Dear Reviewer, I/we appreciate your valuable suggestions. In response, I/we have made revisions to the concluding section of the paper, emphasizing the contribution of this research by specifically incorporating 'Implications' and 'Future Directions of Research' subheadings. Each subheading is accompanied by a detailed explanation to elaborate on these aspects. I/we trust that these additions will provide greater clarity and depth to the paper. Thank you once again for your insightful feedback. Thank you for the articles you recommended have proven to be extremely useful Thank you once again for your insightful feedback. Sincerely, Dr. Imron Muttaqin, S.Pd.I, M.Pd.I" } ] }, { "id": "181578", "date": "20 Jul 2023", "name": "Idi Warsah", "expertise": [ "Reviewer Expertise Education", "Educational Psychology", "Multiculturalism" ], "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, as a whole, has been well-written and the theoretical and data-based details have been appropriate. However, when addressing that the instruments used had been told to be valid, the researchers need to prove it by giving the scores of validities and reliability of each instrument within the paper (though the detailed validity computation has been enclosed).\nAlso, the researchers need to discuss the results by providing argumentations comparing the present results and the previous ones in terms of differences. Most of comparison made in the discussion showcases that the present results are consistent or support the previous ones. If so, what is something new to be highlighted from this study. The researchers should make sure that there are parts of the present research different from the preceding ones to cast light some novel parts of this study.\nLastly, in the section of recommendation, the authors emphasized that there were some external factors affecting the results, so the authors recommend others to conduct future's studies working with such factors. Please give some possible examples of such factors so that further researchers could find their ways to go.\n\nIs the work 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/12-743
https://f1000research.com/articles/12-1171/v1	19 Sep 23	{ "type": "Study Protocol", "title": "Protocol on comparative evaluation of the effect of application of 38% silver diamine fluoride on sealing ability of Biodentine and MTA Angelus as a perforation repair material: a confocal laser microscopic study", "authors": [ "Saee Wazurkar", "Dr. Aditya Singh patel", "Dr. Aditya Singh patel" ], "abstract": "Background: Perforation can occur while performing root canal treatment. Biodentine has been made utilizing MTA (mineral trioxide aggregate) as a base, and claims to improve its properties in aspects such as physical property, durability, and handling, as well as its many other applications in restorative dentistry. The chemical components of SDF (silver diamine fluoride) have been suggested to have the following benefits: fluoride aids in remineralization and prevention, silver salts induce dentin sclerosis/calcification, and exhibit germicidal actions. It works by occluding dentinal tubules thus helping in preventing microleakage. This study aims to focus on the use of SDF on Biodentine and MTA as perforation repair material using a confocal microscope. Methods: Mandibular molars will be selected for the study. The study will be divided into 4 groups: Group 1: Biodentine without application of 38% SDF; Group 2: Biodentine with the application of 38% SDF; Group 3: MTA Angelus without application of 38% SDF; and Group 4: MTA Angelus along with the application of 38% SDF. An artificial perforation 2 mm in diameter will be made directly in the middle of the pulpal floor. 38% silver diamine fluoride (FAMAGAIN) will be applied on the walls of the perforation according to the manufacturer’s instructions for the experimental groups (Groups 2 and 4). In the four groups, Biodentine will be applied in groups 1 and 2 and MTA will be applied in 3 and 4 (perforation repair material). To evaluate the sealing capacity of perforation material in this study, we will use the average values of coronal dye leakage at the perforation site and Escobar’s criteria, which are used to assess the infiltration proportions. Conclusions: It is expected that application of 38% of silver diamine fluoride on MTA Angelus and Biodentine may show better sealing ability than MTA Angelus and Biodentine alone.", "keywords": [ "* MTA", "Biodentine", "perforation", "silver diamine fluoride", "sealing ability", "Confocal laser microscope." ], "content": "Introduction\n\nRoot canal therapy is a dental procedure that helps to alleviate pain caused by a tooth that is diseased or abscessed. The inflamed pulp is removed during the root canal procedure. Procedural errors are often seen during the treatment, which will have an overall impact on the outcome of the tooth. Furcal perforation is one of the most unpleasant and frequent accidents that can occur during endodontic treatment.1 The term “perforations” refers to “mechanical or pathological communication between the root canal system and the tooth surface”.2 Iatrogenic factors, such as root canal treatment, or pathologic factors, such as carious lesions or resorption, can both cause root perforations.3 These root perforations hamper treatment responses and might develop into a bacterial invasion and lead to further endodontic periodontal diseases if not addressed properly.4\n\nMTA (mineral trioxide aggregate) was introduced by Mahmoud Torabinejad in 1993, and was developed to treat perforations. The use of MTA can result in a complete seal between the root canal and the outer surface of the tooth.5 Biodentine is a new calcium silicate-based bioactive cement created to solve several limitations of white MTA, which is difficult to work with and requires a long curing period.6\n\nRoot perforation is thought to be an infinite pit in which repair material frequently escapes along the periodontal area. Some of the most important criteria for furcal perforation repair materials are their capacity to seal the surrounding tissues, their nontoxicity, and their ability to regulate the flow of material.7\n\nSince 1840, silver compounds have been administered in dentistry. Silver inhibits the growth of bacteria, and fluoride aids in remineralization and prevention.8 Numerous in vitro studies have confirmed silver diamine fluoride’s (SDF) clinical efficacy in reducing tooth tissue solubility concerning chemical acid challenges and further aiding in enamel remineralization. SDF can also increase the microhardness of dentin.9\n\nSometimes, perforation can occur due to large carious lesions, and attempts to remove caries can lead to bigger and wider perforation will lead to a poor prognosis of the teeth.2 MTA and Biodentine tend to show limited antimicrobial properties and are not efficient when directly placed on dentine. One of the studies, conducted by Jasim et al., evaluated the microleakage of composite resin and self-cure glass ionomer (GI) restorations in primary molars when the restorations were applied on the same day of SDF treatment. After 14 days, they concluded that there was a substantial decrease in microleakage after the use of SDF before restoration.9 Henceforth, there is a need for an antimicrobial and caries-inhibiting agent that will provide an alternative to enhance the efficacy of MTA and Biodentine as a root repair material.\n\nBiodentine and MTA have been used as root repair materials because of their ability to seal, being nontoxic and compatible with the surrounding tissue, and their ability to promote the regeneration of surrounding tissue. SDF can be used in addition to Biodentine and MTA as it is a widely used antibacterial compound. It has shown effectiveness in both hardening tooth structure and killing bacteria. Studies have been done to evaluate the microleakage of composites and GIC (glass inomer cement) in the application of SDF, and they have reported decreased microleakage after the application of SDF.9 As such, there is a need for research to evaluate the application of SDF in addition to Biodentine and MTA as a perforation repair technique.\n\nTo assess the outcome and sealing ability of the application of Biodentine as a perforation repair material with the application of 38% SDF using dye penetration by a confocal laser microscope.\n\nTo assess the outcome and sealing ability of the application of Biodentine perforation repair material without the application of 38% SDF using dye penetration by a confocal laser microscope.\n\nTo assess the outcome and sealing ability of the application of MTA Angelus as a perforation repair material with the application of 38% SDF using dye penetration by a confocal laser microscope.\n\nTo assess the outcome and sealing ability of the application of MTA Angelus as a perforation repair material without the application of 38% SDF using dye penetration by a confocal laser microscope.\n\nTo compare the above parameters with each other.\n\n\nProtocol\n\nWritten informed consent was taken from patients who underwent extraction regarding the use of extracted teeth in this study.\n\nEthical approval was received from Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha (reference DMIHER (DU)/IEC/2023/581) on 06/02/2023.\n\nThis will be an in-vitro study with samples divided into four groups:\n\nGroup 1: Biodentine without application of 38% SDF.\n\nGroup 2: Biodentine with the application of 38% SDF.\n\nGroup 3: MTA Angelus without application of 38% SDF.\n\nGroup 4: MTA Angelus along with the application of 38% SDF.\n\nThe materials used in this study will be Biodentine™ (Septodont, Saint-Maur-des Fosses, France); MTA Angelus® White (Angelus Lodrina, Parana Brazil); 38% silver diamine fluoride (Fagamin); Rhodamine B fluorescent dye; and a confocal laser microscope.\n\nFreshly extracted permanent mandibular molars with intact tooth structure.\n\nTeeth with caries and teeth with a fractured root will be excluded.\n\nMandibular permanent molars will be selected in this study. Calculus and soft tissue tags will be removed by ultrasonic scaling, and the teeth will be kept in 0.5% chloramine T for 7 days then in normal saline until the next step. After access cavity preparation of each molar, the crown will be sectioned up to the roof of the pulp chamber, and the apical one-third of the roots will be sectioned using straight fissure carbide bur.The root canal orifices in each selected tooth and the terminus of sectioned roots will be sealed using sticky wax. An artificial perforation of 2 mm in diameter will be made directly in the middle of the pulpal floor using a 2 mm width round bur in a high-speed handpiece with water coolant. The area will be then flushed with water and dried with compressed air. 38% silver diamine fluoride (FAMAGAIN) will be applied on the walls of the perforation according to the manufacturer’s instructions for the experimental group. Over which the perforation repair material, that is MTA and Biodentine, will be applied both in control and experimental groups.\n\nThe teeth will be randomly divided into four groups:\n\nGroup 1: Biodentine without application of 38% SDF.\n\nGroup 2: Biodentine with the application of 38% SDF.\n\nGroup 3: MTA Angelus without application of 38% SDF.\n\nGroup 4: MTA Angelus along with the application of 38% SDF.\n\nAfter 24 hours, the teeth will be covered with two layers of clear, air-dry nail varnish leaving 1–2 mm around the perforation site exposed. Then, all teeth will be immersed in 100% humidity at 37°C for 24 hours, followed by immersion in 0.6% aqueous rhodamine B dye for 48 hours. Then each tooth will be sectioned longitudinally in a buccolingual direction and crossing the perforation site with a diamond disc (0.3mm thickness) and a water-cooled handpiece, and the maximum apical extent of dye leakage at the interfacial surface between tooth structure and repair material will be measured using a confocal microscope at 10× magnification. To evaluate the sealing capacity of perforation material in this study, we will use the average values of coronal dye leakage at the perforation site and Escobar’s criteria4 which are “used to assess the infiltration proportions”:\n\n0 – infiltration loss (dye penetration 0–<1.5 mm).\n\n1 – simple infiltration (dye penetration 1.5–3 mm).\n\n2 – medium infiltration (dye penetration > 3 mm).\n\nThe target sample size will be calculated using mean difference.\n\n• Primary variable: microleakage in millimetres\n\n• Microleakage of MTA in mm = 1.24 ± 0.13 (as per reference article)\n\n• Microleakage of MTA in mm = 0.88 ± 0.02 (as per reference article)\n\n• Clinically relevant difference = 0.36\n\n• Pooled std.dev = 0.25 (estimated)\n\n• As per reference articles.\n\n• N1 = 2 *[(1.96+ 1.28)2(0.25)2] / (0.36)2 = 10\n\n• Total samples required = 40\n\n• Study reference: Ref. 7.\n\nAll the data will be analysed using SPSS version 27 software. Data for outcome variables will be tested for normality using the Kalmogorov-Smirnov test. The comparative analysis of the micro tensile bond strength will be evaluated on the measurement of Newton. ANOVA will be used to find the significant difference between the mean of the four groups. Tukey’s test will be used for comparative evaluation of measurement in between two groups pairwise. P-value ≤ 0.05 will be considered as significant at 5% level of significance and 95% confidence of interval.\n\n\nDiscussion\n\nPerforation is an unfortunate mishap that happens while performing root canal treatment. The size of the perforation, level, and position of the perforation, time of healing, and presence of periodontal or pulpal disorders are all factors that influence the result of perforated teeth.10 MTA is one of the most commonly used materials for furcal repair because of its ability to seal and its biocompatibility, bioactivity, and low solubility. Biodentine uses MTA as a base, and it claims to improve its properties in several aspects such as physical properties, durability, and handling, as well as its many other applications in restorative dentistry, such as endodontic treatment and pulp capping.11 In vitro testing is an important tool for the initial screening of dental material as it gives data for further clinical evaluation. Fluoride aids in remineralization and inhibition of caries while silver salts induce dentin sclerosis/calcification and have germicidal properties. It works by occluding dentinal tubules thus helping in preventing microleakage.12 This study aims to focus on the use of SDF on Biodentine and MTA as perforation repair material using a confocal microscope.\n\n\nConclusion\n\nIt is expected that application of 38% of silver diamine fluoride on MTA Angelus and Biodentine may show better sealing ability than MTA Angelus and Biodentine alone.\n\nThe study may provide information about the new protocol which provides a better sealing ability to get the best outcome for the perforation repair by the clinician.\n\nAfter obtaining the results of the data, we will publish them in a scientific journal.\n\nThe study began on 1st August 2023, and is currently at the sample preparation stage.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nI would like to thank my institute, my Guide, HOD and my colleagues.\n\n\nReferences\n\nElDeeb ME, ElDeeb M, Tabibi A, et al.: An evaluation of the use of amalgam, Cavit, and calcium hydroxide in the repair of furcation perforations. J. Endod. 1982 Oct; 8(10): 459–466. PubMed Abstract \| Publisher Full Text\n\nMohammed S, Ashley M, Darcey J: Root perforations: Aetiology, management strategies and outcomes. The hole truth. BDJ. 2016 Feb 26; 220: 171–180. Publisher Full Text\n\nKakani A, Chandrasekhar V: Sealing ability of three different root repair materials for furcation perforation repair: An in vitro study.2020 Oct 22.\n\nEscobar C, Michanowicz AE, Czonstkowsky M, et al.: A comparative study between injectable low-temperature (70 degrees C) gutta-percha and silver amalgam as a retroseal. Oral Surg. Oral Med. Oral Pathol. 1986 May 1; 61(5): 504–507. PubMed Abstract \| Publisher Full Text\n\nAdiga S, Ataide I, Fernandes M, et al.: Nonsurgical approach for strip perforation repair using mineral trioxide aggregate. J. Conserv. Dent. 2010 Apr; 13(2): 97–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDammaschke T: A new bioactive cement for direct pulp capping.2(2).\n\nMohan D, Singh AK, Kuriakose F, et al.: Evaluation of Sealing Potential of Different Repair Materials in Furcation Perforations Using Dye Penetration: An In Vitro Study. J. Contemp. Dent. Pract. 2021 Jan 1; 22(1): 80–83. PubMed Abstract\n\nDelbem ACB, Bergamaschi M, Sassaki KT, et al.: EFFECT OF FLUORIDATED VARNISH AND SILVER DIAMINE FLUORIDE SOLUTION ON ENAMEL DEMINERALIZATION: pH-CYCLING STUDY. J. Appl. Oral Sci. 2006 Apr; 14(2): 88–92. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJasim MZ, Khalaf MS: Comparison of Microleakage of Composite and Glass Ionomer Restorations in Primary Molars Pretreated with Silver Diamine Fluoride at Two Time Intervals: An in vitro study. Dent. Hypotheses. 2022 Oct 1; 13(4): 145. Publisher Full Text\n\nComparative Evaluation of Sealing Ability of Three Materials Used in Furcal Perforation Repair (In Vitro).[cited 2023 Jan 24]. Reference Source\n\nFarea M, Husein A, Pameijer CH: Furcation perforation: current approaches and future perspectives.\n\nMei ML, Lo ECM, Chu CH: Clinical Use of Silver Diamine Fluoride in Dental Treatment. Compend. Contin. Educ. Dent. Jamesburg NJ 1995. 2016 Feb; 37(2): 93–98. quiz100." }	[ { "id": "267845", "date": "25 Apr 2024", "name": "Srinidhi Surya Raghavendra", "expertise": [ "Reviewer Expertise Endodontic microbiology", "sealing ability of perforation repair materials", "outcomes of endodontic treatment" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: has been written in a structured manner giving the background and the method. Key words have been mentioned. Introduction: Etiology of perforations, MTA have been explained well. One point which can be added is an enumeration of the various materials used to seal perforations, apart from MTA and Biodentine. You have to write the formulation available for SDF. Rationale: Have been mentioned Objectives: clearly written Protocol: Groups have been defined. You have to mention the country of origin of Famagain. Statistical tests have been mentioned and the sample size determination has been explained. Estimation of the seal of the materials to the tooth structure will be measured with the CLSM.\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/12-1171
https://f1000research.com/articles/12-1170/v1	19 Sep 23	{ "type": "Systematic Review", "title": "University social responsibility (USR) in the context of Peruvian society: A systematic review", "authors": [ "Oscar Arbieto Mamani", "Miguel Gerardo Mendoza Vargas", "Rosmery Sabina Pozo Enciso", "Elio Huamán Flores", "Teresa Villafuerte Palomino", "Willie Alvarez Chavez", "Oscar Arbieto Mamani", "Miguel Gerardo Mendoza Vargas", "Elio Huamán Flores", "Teresa Villafuerte Palomino", "Willie Alvarez Chavez" ], "abstract": "Background: The university social responsibility (USR) goes beyond the traditional extension and solidary social projection of the universities, but the professional must improve and develop proposals in improvement of the country. The objective is to carry out a systematic review of the scientific production related to USR in Peru and to analyse the most important findings of this production. Method: A systematic review of articles in English and Spanish in Scopus, Redalyc, and SciELO was carried out, searching for research related to USR in the Peruvian context. Articles on USR in Latin America or the world were excluded. The search and filtering of articles was carried out until February 2023. Several filters were applied, starting with the search for titles according to the search equation. Then, articles that did not deal with USR were eliminated. Subsequently, abstracts were read and those that did not meet the inclusion criteria were discarded. Finally, the remaining research was analysed to obtain the necessary information for the research. Results: A total of 20 articles were analysed. The main results showed that university social responsibility in the Peruvian context seeks to benefit society and to form ethical and responsible students. However, more policies and actions are needed to encourage the participation of all universities in USR. It was found that 65% of the literature had a quantitative approach, 30% was qualitative and only 5% was mixed. Conclusion: University Social Responsibility (USR) seeks to benefit society, being students the key actors to improve their country with the professional development acquired in higher institutions. The implication for future research is to carry out more studies on USR but within the national university centres in the highlands and jungle areas of Peru, where it is possible to show the state of this topic in other areas of Peru.", "keywords": [ "University law", "university social responsibility", "Peru", "systematic review", "journal", "Prisma", "Scopus", "Redalyc", "Scielo" ], "content": "Introduction\n\nIn recent years, the production of goods and services has grown rapidly, and although it has allowed for the development of emerging economies, the increase in globalization and the advancement of the media has also led to neglect of labor rights, disregard for the environment, and rising levels of poverty in different countries around the world (Comisión Económica para América Latina y el Caribe, 2018).\n\nDue to the lack of attention to different stakeholder groups, the concept of corporate social responsibility has gained importance in the last century (Palacio, 2020). The initial approach to corporate social responsibility was introduced by Bowen (1953), who stated that social responsibility is “the obligation of businessmen to pursue policies, to make decisions or to follow lines of action that are desirable in terms of the objectives and values of society” (p.44). All decisions made by entrepreneurs in various organizations have an impact on the rest of society (Tiep, Huan, and Hong, 2021).\n\nAs important as understanding the components of social responsibility is measuring and implementing them. However, due to the diversity of organizations and their multiple characteristics, there are various methods used in the implementation of corporate social responsibility programs, and consequently, the results vary (Barragán et al., 2019, 2022).\n\nWhile it is important to understand the implementation and results of this vision in different sectors and types of organizations, there are activities and institutions on which social pressures increase, and it is important to emphasize them given their nature and mission (Garbanzo, 2015). This is the case with Higher Education Institutions and Universities, which have a high responsibility towards society as they are responsible for preparing the professionals of the future (Santana, 2022).\n\nIt should be remembered that the mission of the university and higher education institutions is based on social awareness, as the university, above all, shapes individuals with all that entails culture, ethics, social commitment, and politics (Ruiz and López, 2019). This is because it seeks to build knowledge and fulfil its missions of “education, research, and social dimension” (Beltrán et al., 2014, p.5).\n\nAs evident, the link between the university and society as a principle of responsibility has always existed. This is why university social responsibility (USR) is defined as a set of integral management policies that contribute to the challenges of the 21st century (Ibarra and Fonseca, 2020), aiming to develop a series of actions that improve the university’s relationships with society and fulfil its responsibility towards all stakeholders (administrative staff, professors, students, and administrative personnel, among others) (Medina et al., 2017).\n\nUSR goes beyond traditional solidary social extension and outreach; it is not only about voluntary initiatives of assistance and service to vulnerable groups. It is important to coordinate university actors to transmit responsible knowledge, as it ensures the contribution of competencies and capabilities, which in turn leads to sustainable development and the education of future comprehensive professionals, as stated by Prieto et al. (2015), Cabrejos (2017), and Vallaeys and Álvarez (2019).\n\nThe objective of this study was to conduct a systematic review of scientific production related to university social responsibility (USR) in Peru and analyze the most important findings from that production. To carry out the research, a systematic literature review (SLR) was conducted using three databases: Scopus, Redalyc, and SciELO, which were selected based on the degree of result updates they provide and the bibliometric analysis tools they include.\n\n\nMethods\n\nFor the development of the research, a search for scientific production associated with the topic of USR was conducted through a systematic review of articles. This method aims to identify, interpret, and evaluate different works carried out by scholars on a specific topic or field, based on the text (Pardal and Ochoa, 2017) with the intention to “provide researchers and readers with clarifying information on a particular subject” (Pardal and Pardal, 2020, p.1).\n\nThe systematic review of scientific literature was carried out based on the adaptation of the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) methodology, a method published in 2009. It was designed to assist authors in conducting transparent systematic reviews, documenting the rationale for conducting a review, what the authors investigated and developed, and what their main findings were, based on the text by Page et al. (2021). Based on this, the research question for the review was formulated: How is university social responsibility developed in Peru?\n\nThe search was conducted within the databases of Scopus, SciELO, and Redalyc, as they are among the most important repositories of journals and scientific production in Latin America and the Caribbean, based on the text by Miguel (2011).\n\nThe obtained results were refined after an analysis of titles and keywords, and those documents with titles containing the term ‘responsabilidad social universitaria (USR)’ and ‘Peru’ were used, both in Spanish and English in all three databases. The search for articles was conducted from December 9, 2022, until the last screening on February 5, 2023.\n\nThe equation used for the first search within the three databases only used: ‘Responsabilidad social universitaria’ and ‘university social responsibility’ (Table 1).\n\nThen, in order to identify the articles located in the Peruvian reality, a second filter equation was applied.: AND ‘Perú’ (Table 2).\n\nAs a final filter, all of the included search results were classified and the inclusion and exclusion criteria were applied to them (Figure 1).\n\nFiltered articles from Scopus, Redalyc, and Scielo repositories.\n\nInclusion criteria:\n\n• Articles that have university social responsibility as a premise.\n\n• Articles that have been developed in the Peruvian context.\n\n• Empirical studies, both quantitative and qualitative, investigating aspects related to university social responsibility should be included.\n\n• The studies can include key participants such as students, professors, administrative staff, university authorities, and other stakeholders related to university social responsibility, as well as literature review in the Peruvian context.\n\nExclusion criteria:\n\n• Articles that are within the context of Latin America or the world.\n\nThe process for deciding whether the article met the criteria was first to review the titles of each research paper; where it was assessed whether the article met the university social responsibility theme. After the first filter, we proceeded to read all the abstracts and evaluate whether they were written within the Peruvian context. Finally, the total content of the manuscript was reviewed for the completion of the article. The filtering was performed by two of the authors and the examination of each record and each report retrieved was performed by each author, it should be noted that the distribution was done equally according to the number of articles between the number of authors. The review and analysis of each manuscript was carried out independently, but at the end a final compilation was made, which was done jointly by all authors.\n\nEach author explored the contents of each manuscript in depth, meticulously evaluating the variable ‘university social responsibility’ in the context of the research. Crucial aspects such as the methodology employed, data collected and initial interpretations were considered. The individual analysis allowed a detailed exploration of each manuscript, always leaving diverse contributions from the perspective and experience in the interpretation of the data.\n\nHowever, to ensure consistency and integration of the different analyses, a joint review phase was carried out, where the different approaches and results obtained were collated and contrasted. Constructive discussions and debates were encouraged to resolve discrepancies and ensure that the final interpretation was sound and substantiated. The process culminated in the creation of a final compilation reflecting the results and conclusions reached by consensus from the combination of the individual analyses.\n\n\nResults\n\n20 articles were included in the final results of this study (Table 3).\n\nTable 4 revealed that 65% of the analyzed literature was quantitative in nature, 30% was qualitative, and only 5% was mixed methods.\n\nSocial responsibility is being widely addressed as it has become a fundamental part of university policy (Martí, et al., 2019). From its inception, it was included in the University Law 23733 which stated that “universities extend their educational activities in favor of those who are not their regular students; in this sense, they organize activities to promote and disseminate general culture and professional studies, which can be free or not, and which can lead to certification.” In this way, the law aimed to establish a university-society interrelationship. However, since this was often confused with carrying out social assistance activities or mere cultural activities, the new University Law 30220 was enacted, which incorporated university social responsibility and was regulated through the quality model of the National System for Evaluation, Accreditation, and Certification of Educational Quality (2019) [2016, 2017]. This quality model includes responsibility as part of institutional management, with Factor 6 focusing on responsibility. It states that “the university has a defined policy of social responsibility, and its actions are framed within it, achieving integration with research, technological development, and innovation activities (R&D&I)” (Villegas and Cairampoma, 2021, p.3). This factor undoubtedly urges universities to involve faculty and students in social and environmental development projects and to engage the entire university community with stakeholders from the public and private sectors, thus contributing to society.\n\nFurthermore, Article 125 of the law requires universities to allocate a minimum of 2% of their budget to social responsibility actions and provides instruments to incentivize the development of projects such as social responsibility initiatives or the establishment of competitive funds (Villegas and Cairampoma, 2021).\n\nIn other words, university social responsibility concerns not only students but also other areas, including administrative functions such as purchasing, planning, service provision, enrollment, marketing, and personnel selection, among others. It also extends to the academic dimensions of education and research (Vallaeys and Álvarez, 2019), as we must remember that the university becomes the center for knowledge production and professional training, with a significant impact on students’ lives (Zolezzi, 2010). The university allows all its members to develop social, environmental, and economic awareness (Severino, Sarmiento, Villar, and Ramírez, 2022).\n\nMartí et al. (2018) conducted an analysis of university social responsibility in three countries, including Peru, where they found that it is implemented within the framework of the University Law 30220 (Ley 30220, 2014). They highlighted that the objective of university social responsibility is to generate mutual benefits between the university and the community, aiming to create development improvements that contribute to the well-being of citizens and the nation. In addition to being a requirement in the curriculum, university social responsibility serves as a support base for accreditation. It obliges higher education institutions (HEIs) to implement, develop, and put into practice social responsibility activities within their undergraduate programs. The goal is to prepare graduates who can contribute to and implementing “public policies of social interest and fostering altruistic and supportive behavior that contributes to improving the quality of life of vulnerable groups in our society” (Ley 30220, 2014, p.57), based on the knowledge and skills they have developed during their professional training.\n\nVargas (2021) presents a concept of university social responsibility from the perspective of innovation, indicating that every university should channel “the provision of a public service of knowledge generation where the general interests of citizens, the defense of the common good, and functioning as an agent of change and social improvement must be considered” (p. 442). In line with this, Ruiz (2018) discusses a proposal made by a university in collaboration with the Ministry of Education and three other universities, which involves granting a scholarship to students who have completed their undergraduate studies and wish to pursue a master’s degree within the same institution. This is known as the “Teaching Scholarship,” and its purpose is to provide social and economic support to professionals from any region of Peru, allowing them the opportunity to further their education and become master’s degree holders in their chosen field, with full academic preparation. The aim is to promote a culture of meritocracy within the teaching staff.\n\nIn 2017, the Universidad Los Ángeles de Chimbote implemented 3,716 social development projects, involving over 44,399 students and receiving guidance from 537 teachers. The target population benefited from these projects consisted of vulnerable communities in the region where the university is located. Similarly, the Pontifical Catholic University of Peru has made more concrete progress by engaging in activities across various dimensions such as the academic sphere, society, campus, strategic communication, and administrative strategies. Additionally, each organ, department, faculty, academic department, center, and institute within the university aims to strengthen the integration of this important topic in a comprehensive manner (Villegas and Cairampoma, 2021).\n\nOrtiz (2010) conducted a study on a specific course called “Proyección Social” (PROSODE) offered at the Pontifical Catholic University of Peru (PUCP) in the Law program. PROSODE is based on university social responsibility (USR), and the author emphasizes that the real purpose of USR is to act in the community and have this action benefit the university community as a source of learning. The course is designed for the development and execution of activities and projects for the benefit of citizens. Its objectives include exercising law in favor of those in need, generating experiences related to USR and being a lawyer, understanding the reality of Peru, and preparing students to fulfil their professional roles when the time comes. This perspective is supported by La Cruz, Zelada, Aguirre, and Garro (2022), whose study revealed a direct relationship between USR and four components: ‘Formation’, ‘Research’, ‘Management’, and ‘Extension’. The study concluded that USR is relevant for university institutions to achieve better positioning, as it encompasses aspects such as education, research, management, and extension. It allows for a stronger identity, communication, and image among the target audience. Therefore, policies and procedures should be in place to encourage greater participation of all university members in USR activities (La Cruz et al., 2022, p.341).\n\nHinojosa et al. (2022) also emphasize the importance of university social responsibility in the context of teaching and learning. According to these authors, it is necessary to promote a participatory dynamic in university classrooms, utilizing different methods and virtual tools, all from a perspective of social responsibility. They consider social responsibility as a crucial pillar in the theoretical and practical consolidation of teaching processes and aim to ensure that these practices reflect their own characteristics, adapting to any eventualities that may arise (Hinojosa et al., 2022, p.1094).\n\nIn summary, Kovács’s analysis (2016) highlights the importance of generating knowledge and findings based on the national reality, particularly in remote communities, while respecting their human dignity and cultures. It also emphasizes the need to eliminate the limited view of social responsibility as mere donations or sponsorships and instead promote the creation and management of knowledge for the benefit of society.\n\nDíaz, Castillo, and Criollo (2022) point out that in 2020, with the arrival of COVID-19 in Peru, many higher education institutions (HEIs) had to close their doors and pause all scheduled activities for the start of the academic year due to the pandemic. This led to the suspension of in-person activities in universities and the need to implement contingency measures that would allow teaching to continue for students. The quickest solution was to transition to virtual teaching. This change posed a significant institutional challenge as it required guidance not only for students but also for faculty members. The new method of teaching had to maintain the same level of commitment and moral obligation as the classroom setting, ensuring the production of new knowledge relevant to solving citizens’ problems and the direct application of scientific and technological knowledge, as well as a more humanitarian professional preparation (Díaz et al., 2022, p.335). This means that the essence of university social responsibility should not be neglected. Therefore, “it is necessary for different universities to guarantee the same quality of education in the virtual context as in the in-person setting, which is part of this university social responsibility” (Díaz et al., 2022, p.336). This should be done while upholding the principles of university social responsibility as a social proposal, as expressed by Albertini (2015), who states that “universities can improve and enrich collaborative work experiences between the state and the population through co-production projects. They can provide guidance for the development of realistic participatory budgets and support their monitoring and proper implementation. They should raise the level of political and public debates by scrutinizing the suitability of proposals and demanding efficient and effective solutions for the problems faced by our communities and regions.”\n\nNow all of this must also be seen from the student’s perspective, whether they perceived and felt that their academic preparation was humanistic and geared towards the country’s development. For this reason, a study was conducted by Pumacayo et al. (2020) to investigate the perceptions of USR among students. The study focused on a group of students from various faculties of a public university in Peru, aiming to understand their perception of USR and whether they believed that the university implemented it in their professional preparation. The results showed that 35.4% of students considered USR to be negative at the university, followed by 33.2% who rated it as average, and only 8.2% rated it as very good.\n\nIn universities such as the Hermilio Valdizán National University, activities related to university social responsibility have been carried out through projects and/or plans of University Extension and Social Projection (Saquicoray and Cuadros, 2015). However, since the concept of social responsibility is broader, some studies indicate that these efforts are not sufficient. According to a study conducted by Condori and Reyna (2019), 58% of students from the Faculty of Sociology at the National University of Central Peru still consider social responsibility to be deficient. This perception includes dimensions such as environmental management and governance, where they also believe that social participation is passive. Therefore, there is still a need to work diligently to strengthen the implementation of university social responsibility in public universities in the interior of the country. While effective social participation is already carried out through volunteer actions, university extension, and social projection, it is necessary to include aspects such as knowledge dissemination and transfer through research and sustainable organizational management (Condori et al., 2022).\n\nFlores et al. (2022) questioned the constructs that would allow measuring USR from the perception of university students in Peru. To do this, they designed a rating scale to measure university social responsibility from the perspective of Peruvian students and obtained the following dimensions: “Broad and transformative academic education, socio-environmental engagement, socially focused research, and transformative institutional management and administration” (Flores et al., 2022, p.94). It is worth noting that this scale was validated and reviewed by experts in the field who approved the instrument.\n\nAs observed in Peru, the law regulates processes and encourages universities to promote challenges in the education of their professionals, making them socially responsible, useful, and capable of promoting actions that contribute to equality, societal well-being, and sustainable development. According to Severino et al. (2022), university social responsibility incorporates the dimension of sustainable consumption as part of its improvement processes. It can be understood that a socially responsible university student exercises their consumption in a sustainable manner. This implies that the responsibility exercised by the university has a transformative capacity and is a fundamental axis for the implementation of educational policies in different higher education institutions. Therefore, it is essential to seek qualities in teachers, such as mental and emotional management of guiding environments. They should be able to share motivations, achieve the objectives of proposed plans, and improve educational productivity, thus reinforcing the practical dimension of individuals not only through the curriculum but also in other areas such as management, research, and university outreach to society (Monzón et al., 2022).\n\n\nDiscussion\n\nWithin the literature found, two points are quite clear when discussing university social responsibility. Firstly, the main beneficiary should always be society, as it is where university students coexist, and universities have the fundamental task of implementing and constantly developing USR within their institutions, ensuring its practical application among all members. This is expressed by Ruiz and López (2019) when they state that “the university cannot remain detached from the reality in which it exists; it must be a driver of development and social cohesion.” This should be achieved through various fields, not only through research but also through humanistic, social, and technological practices. Implementing this will provide students with education in principles and ethics, which will positively impact their professional activities and their contribution to society. Bracamonte and Reynafarje (2017) support this by concluding that USR within universities should be oriented towards the commitment that students, teachers, and authorities must have in contributing to the development and formation of a better society.\n\nIt is important to mention that this analysis could have limitations, such as the lack of diversity in the bibliographic sources consulted or the lack of empirical support for the assertions made. In addition, the literature review may be subject to selection biases and limitations in the completeness of the search for sources. It should also be kept in mind that the interpretation of the results may be influenced by the author’s biases or theoretical approaches. The results have implications relevant to practice, policy, and future research. They support the need for universities to assume university social responsibility as a central aspect, developing programs and practices that foster the engagement of students, faculty and authorities in contributing to social development. This implies practical considerations for the design of curricula, extension programs and university policies. It also suggests areas for future research to better understand the impacts and best practices of university social responsibility in the academic context.\n\n\nConclusion\n\nWithin the Peruvian context, it is evident that there is still much work to be done, as the student body does not view the promotion of USR within their educational institutions favourably, indicating that they do not feel their academic preparation is being carried out with a responsible focus that benefits society. Pérez (2020) supports this by finding that the perception level of students in a university in Peru regarding university social responsibility was low. This is often because teachers and/or authorities do not encourage it within their educational institutions. Híjar (2018) found that “university authorities interviewed indicated that there are several aspects that can be improved regarding university social responsibility within the educational institution. However, they do not specify what the university is doing to improve it,” and the teaching staff had a moderate perception of USR.\n\nTherefore, there is a need to create additional policies and procedures that encourage greater participation from all members of the university in USR activities, rather than isolated cases in some universities, as evidenced in certain studies. It is worth noting that with the arrival of COVID-19 and the new forms of virtual teaching, it should not be a reason to give up and neglect USR. On the contrary, the necessary conditions must be created for universities to engage in more innovative work, which, in turn, meets the expectations of the community and the country regarding their university graduates.", "appendix": "Data availability\n\nZenodo. University Social Responsibility (USR) in the context of Peruvian society A systematic review. Version 3. https://zenodo.org/record/8190897 (Arbieto et al., 2023).\n\nThis project contains the following underlying data:\n\n• Manuscripts analyzed.xlsx. (Final manuscripts included in the systematic review).\n\n\n\n• Zenodo: PRISMA checklist for ‘University Social Responsibility (USR) in the context of Peruvian society A systematic review’. https://doi.org/10.5281/zenodo.8190897 (Arbieto et al., 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\nAlbertini J: La vigencia de la responsabilidad social universitaria en el Perú: una propuesta desde el capital social. Ius et Praxis. Revista de la Facultad de Derecho. 2015; 46: 151–178. Publisher Full Text\n\nArbieto O, Mendoza M, Pozo R, et al.: University Social Responsibility (USR) in the context of Peruvian society A systematic review. Zenodo. 2023. 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Publisher Full Text\n\nFlores L, Severino P, Sarmiento G, et al.: Responsabilidad social universitaria: diseño y validación de escala desde la perspectiva de los estudiantes de Perú. Formación universitaria. 2022; 15(3): 87–96. Publisher Full Text\n\nGarbanzo G: Desarrollo organizacional y los procesos de cambio en las instituciones educativas, un reto de la gestión de la educación. Rev. Educ. 2015; 40(1): 67–87. Publisher Full Text\n\nHíjar A: Percepción interna de la responsabilidad social en una universidad nacional. [Tesis de Doctorado, Universidad Cesar Vallejo].2018. Reference Source\n\nHinojosa C, Hernández M, Polo B, et al.: Responsabilidad social universitaria y el proceso formativo de estudiantes en Perú. Revista Venezolana de Gerencia. 2022; 27(8): 1082–1097. Publisher Full Text\n\nIbarra L, Fonseca C: La responsabilidad social universitaria. Misión e impactos sociales. Sinéctica. 2020; 54: 1–18. Publisher Full Text\n\nKovács I: Las relaciones públicas y la responsabilidad social de las universidades peruanas según la nueva ley universitaria. Revista de Investigación Apuntes Universitarios. 2016; 6(2): 147–159. Reference Source\n\nLa Cruz O, Zelada E, Aguirre J, et al.: Responsabilidad social universitaria y posicionamiento de universidades en Lima-Perú. Revista de Ciencias Sociales. 2022; 28(3): 334–344. Publisher Full Text\n\nMartí J, Ignacio A, Fernández A: La responsabilidad social universitaria en Iberoamérica: análisis de las legislaciones de Brasil, España y Perú. Revista Iberoamericana de Educación Superior. 2018; 9(24): 107–124. Publisher Full Text\n\nMartí J, Pérez G, Cano E: Legislación de la responsabilidad social universitaria: Estudio de casos en universidades de Perú y Ecuador. Revista Venezolana de Gerencia. 2019; 23(84): 899–912. Publisher Full Text\n\nMedina R, Franco M, Torres L, et al.: La responsabilidad social universitaria en la actual sociedad del conocimiento. Un acercamiento necesario. Medisur. 2017; 15(6): 786–791. Reference Source\n\nMiguel S: Revistas y producción científica de América Latina y el Caribe: su visibilidad en SciELO, RedALyC y SCOPUS. Revista Interamericana de Bibliotecología. 2011; 34(2): 187–199. Reference Source\n\nMonzón A, Illa-Sihuincha G, Ruiz Villavicencio R, et al.: Neuromanagement y responsabilidad social: Factores clave en la gestión educativa universitaria. Revista de Ciencias Sociales. 2022; 28(5): 135–144. Publisher Full Text\n\nOrtiz I: Proyección Social de Derecho: PROSODE, un aporte de proyección y responsabilidad social. Derecho PUCP. 2010; 65: 373–383. Publisher Full Text\n\nPage M, McKenzie J, Bossuyt P, et al.: Declaración PRISMA 2020: una guía actualizada para la publicación de revisiones sistemáticas. Rev. Esp. Cardiol. 2021; 74(9): 790–799. PubMed Abstract \| Publisher Full Text\n\nPalacio A: Responsabilidad social empresarial: evolución e importancia dentro de las organizaciones. Revista Colombiana de Contabilidad. 2020; 8(15): 75–85. Publisher Full Text\n\nPardal J, Pardal B: Anotaciones para estructurar una revisión sistemática. Revista ORL. 2020; 11(2): 155–160. Publisher Full Text\n\nPardal J, Ochoa C: Revisiones sistemáticas. Revista ORL. 2017; 8(4): 197–203. Publisher Full Text\n\nPérez E: Responsabilidad social universitaria desde la percepción de los estudiantes en la Escuela de Postgrado de la UNPRG de Lambayeque. [Tesis de Licenciatura, Universidad Católica Santo Toribio de Mogrovejo].2020. Reference Source\n\nPrieto R, González D, Paz A: Responsabilidad social universitaria: estrategia para el desarrollo sostenible en América Latina.noviembre de 2015. Reference Source\n\nPumacayo I, Calla K, Yangali J: Responsabilidad social universitaria y la calidad de servicio administrativo. Revista de Investigación Apuntes Universitarios. 2020; 10(1): 46–63. Publisher Full Text Reference Source\n\nRuiz I: Beca docente en el Perú: una experiencia de colaboración público-privada, más allá de la responsabilidad social universitaria. Educación. 2018; 27(52): 219–230. Publisher Full Text\n\nRuiz M, López E: La misión de la universidad en el siglo XXI: comprender su origen para proyectar su futuro. Revista de la educación superior. 2019; 48(189): 1–19. Publisher Full Text\n\nSantana A: Evaluación de la Responsabilidad Social Universitaria: una revisión sistemática de literatura. Emerging Trends in Education. 2022; 4(8): 16–31. Publisher Full Text\n\nSaquicoray P, Cuadros V: Impacto de la responsabilidad social universitaria de la UNHEVAL en el desarrollo multisectorial de la provincia de Huánuco 2010-2013. Investigación Valdizana. 2015; 9(2): 60–65. Reference Source\n\nSeverino P, Sarmiento G, Villar J, et al.: Consumo sustentable socialmente responsable: El caso de estudiantes universitarios de una ciudad de Perú. Formación universitaria. 2022; 15(1): 219–230. Publisher Full Text\n\nSistema Nacional de Evaluación, Acreditación y Certificación de la Calidad Educativa: Información institucional.21 de agosto de 2019. Reference Source\n\nTiep L, Huan N, Hong T: Effects of corporate social responsibility on SMEs’ performance in emerging market. Cogent Business & Management. 2021; 8(1): 1–18. Publisher Full Text\n\nVallaeys F, Álvarez J: Hacia una definición Latinoamericana de responsabilidad social universitaria. aproximación a las preferencias conceptuales de los universitarios. Educación XX1. 2019; 22(1): 93–116. Publisher Full Text\n\nVargas J: Innovación social: ¿Nueva cara de la responsabilidad social? conceptualización crítica desde la perspectiva universitaria. Revista de Ciencias Sociales. 2021; 27(2): 435–446. Publisher Full Text\n\nVillegas P, Cairampoma A: La responsabilidad social universitaria desde el derecho administrativo. Derecho PUCP. 2021; 87: 523–550. Publisher Full Text\n\nZolezzi L: La responsabilidad social en la formación de los abogados. Derecho PUCP. 2010; 65: 251–262. Publisher Full Text" }	[ { "id": "218915", "date": "30 Nov 2023", "name": "Edgard Méndez", "expertise": [ "Reviewer Expertise Business Administrator" ], "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\nInteresting article developed, I highlight the results that could be found from the reviews of the works.\nThe systematic review on USR in Peru found that there is still much work to be done in promoting USR within educational institutions, as the student body does not view it favorably. This is often because teachers and/or authorities do not encourage it within their educational institutions. The review also highlights the need to create additional policies and procedures that encourage greater participation from all members of the university in USR activities, rather than isolated cases in some universities.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "239392", "date": "14 Feb 2024", "name": "David Perez Jorge", "expertise": [ "Reviewer Expertise Educational research", "Special Education Needs", "health 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\nI have had the opportunity to review your article entitled \"University social responsibility (USR) in the context of Peruvian society: A systematic review\". I am pleased to note that your work represents a significant effort in synthesizing research on a topic of increasing importance. However, I would like to suggest some areas for improvement that could further enrich your study.\nCritical Evaluation of Studies: A deeper evaluation of the methodological quality and limitations of the included studies could offer a richer and more contextualized perspective of the findings. Practical and Theoretical Implications: A more detailed discussion on how your findings can influence educational policies and practices would enrich your contribution to the field. Data Analysis Methodology: Providing more details on the techniques used for data analysis would strengthen the transparency and replicability of your study. Continuous Update and Review: Including recent studies and periodically updating the article would ensure that your review continually reflects trends and changes in the field. Diverse Perspectives: Including studies with diverse or contradictory perspectives could provide a more comprehensive view of the topic.\nI hope you find these comments useful for strengthening your work. I appreciate the opportunity to review your valuable research.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1170
https://f1000research.com/articles/12-1169/v1	19 Sep 23	{ "type": "Case Report", "title": "Case Report: Implication of antiangiogenic therapy (bevacizumab) along with dichloroacetate therapy on endometriosis patient seeking infertility treatment", "authors": [ "Saurabh Mehakar", "Akash More", "Shilpa Dutta", "Ritesh Jadhav", "Namrata Chaudhari", "Rukaiya Shaikh", "Saurabh Mehakar", "Shilpa Dutta", "Ritesh Jadhav", "Namrata Chaudhari", "Rukaiya Shaikh" ], "abstract": "Endometriosis is a pervasive gynecological ailment which usually results in unease and infertility and is signified by an accumulation of endometrial-like tissue outside the uterus. Current endometriosis medications, which often entail surgical intervention and hormone therapy, are geared around easing discomfort as well as improving fertility. However, alternative approaches targeting angiogenesis have shown promise in managing endometriosis-associated infertility. This case report highlights the implications of combining antiangiogenic therapy (bevacizumab) with dichloroacetate (DCA) therapy in a patient with endometriosis seeking infertility treatment. A 34-year-old woman presented with a five-year history of severe pelvic pain and primary infertility due to stage IV endometriosis. The patient sought other possibilities after repeated unsuccessful attempts using assisted reproductive technology. A revolutionary therapy strategy combining bevacizumab, a vascular endothelial growth factor (VEGF) inhibitor, and DCA, a metabolic modulator, has been proposed considering the potential significance of angiogenesis in endometriosis-related infertility. The patient underwent a six-month treatment regimen consisting of intravenous bevacizumab infusions combined with oral DCA administration. The theory behind this combination was to target the metabolic reprogramming typically associated with the disease in addition to altering the abnormal angiogenic signaling pathways that contribute to the pathogenesis of endometriosis. Given the scores on the visual analogue scale, the patient's pelvic pain substantially decreased during the time frame of treatment. Additionally, a notable improvement in ovarian reserve markers was observed, including an increase in anti-Müllerian hormone levels and the number of antral follicles. This case report suggests that the combination of bevacizumab and DCA may have a synergistic effect in managing endometriosis-associated infertility. This form of therapy may provide patients who have failed typical infertility treatment options with an innovative therapeutic approach since it targets both angiogenesis and metabolic changes.", "keywords": [ "fallopian tube", "endometriosis", "inflammation" ], "content": "Introduction\n\nEndometriosis is characterized by the presence of inflammation and abnormal tissue growth outside the uterus in the female reproductive system.1 This case study focuses on the management of infertility in a patient with endometriosis as the underlying cause. Endometriosis may culminate in pain and infertility in women who are fertile. Laparoscopy is the gold standard for diagnosing endometriosis, and biopsy in any suspicious lesions is recommended preceded by histological confirmation. The true prevalence of endometriosis in reproductive-aged patients remains unknown due to the difficulties and costs associated with surgical intervention.2\n\nWhen endometrial tissue, which typically originates inside the uterus, becomes apparent on the ovaries, fallopian tubes, or the pelvic lining, endometriosis is a consequence.2 Although numerous hypotheses suggest that a genetic predisposition, hormonal imbalances, immune system problems, and retrograde menstruation—a phenomenon that occurs when menstrual blood flows to the pelvic rather of exiting the body—could be contributing factors, it is not yet understood what exactly causes endometriosis. None of these hypotheses, however, fully explain the development of endometriosis.3\n\nPelvic pain, that may fluctuate from mild to severe and occur prior to or throughout menstruation, sexual activity, bowel and urine movements, is the most characteristic symptom of endometriosis.4 Other common symptoms include infertility or difficulty conceiving, heavy or irregular periods, fatigue, and gastrointestinal issues such as bloating, constipation, or diarrhea.5\n\nNotwithstanding knowing that there is currently no known treatment for endometriosis, there are an assortment of alternatives to cope with the signs and symptoms of the disease while improving the quality of life of the individuals who have been impacted. These may include pain medications, hormone therapy (such as contraceptives or hormonal intrauterine devices), and, in severe cases, surgical removal of endometrial tissue or repair of any organ damage.6 Stage 4 endometriosis is a severe form of endometriosis characterized by extensive infiltration and adhesions involving pelvic organs. The condition has significant adverse effects on the quality of life for those who are impacted by it given that it has been associated to debilitating pain, inflammation, and infertility. Despite the fact that stage 4 endometriosis frequently responds to therapy predominantly through surgical intervention, additional methods of treatment are essential, notably for people seeking in vitro fertilisation. Antiangiogenic therapy, such as Bevacizumab, has shown promise in inhibiting the formation of new blood vessels, known as angiogenesis, which is crucial for the growth and progression of endometriotic lesions. In the field of malignancy, bevacizumab, a monoclonal antibody that inhibits vascular endothelial growth factor (VEGF), went through noteworthy research and has proven to be successful in inhibiting tumour angiogenesis. Dichloroacetate (DCA) therapy has gained attention for its potential in targeting metabolic dysregulation in various diseases, including cancer. DCA acts by modulating the activity of pyruvate dehydrogenase kinase, promoting mitochondrial metabolism and potentially reversing the metabolic alterations observed in endometriosis. In particular for patients seeking treatment for infertility, the simultaneous administration of antiangiogenic therapy with Bevacizumab and dichloroacetate therapy has emerged as an innovative approach in the management of stage 4 endometriosis. By targeting both the angiogenic and metabolic components that make up endometriosis, this combination therapy could significantly increase the probability of regaining fertility. This case report explores the implications and outcomes of using the combination therapy of antiangiogenic therapy (Bevacizumab) along with dichloroacetate therapy in the treatment of stage 4 endometriosis patients seeking infertility treatment. Recognising the prospective benefits of this a combination therapy could assist with establish more productive and comprehensive therapeutic strategies for individuals with stage 4 endometriosis-related infertility.\n\n\nCase presentation\n\nThis case report is based on south Asian patient who is a 34-year-old woman who was nurse by profession who visited our WTTBC (Wardha Test Tube Baby), Wardha, with a medical history of stage IV endometriosis, a severe form of endometriosis characterized by the presence of extensive endometrial tissue outside the uterus. She has also been diagnosed with hypothyroidism, indicating an underactive thyroid gland. Despite these conditions, the male partner’s semen parameters were found to be normal, indicating no significant abnormalities in sperm quality or quantity. There were no notable medical reports in the patient’s family history. It is important to note that the male partner is a non-alcoholic as well as non-smoker, which may have potential implications for their fertility journey. The patient also had history of failed IUI attempt before visiting our center.\n\nBased on the preliminary investigation, we decided to perform Ovum pick up cycle on our patient. In assisted reproductive techniques (ART), such as in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI), the ovum pick-up (OPU) cycle is an essential procedure. It involves the retrieval of oocytes from the woman’s ovaries for subsequent fertilization. Once the follicles had reached an optimal size, a trigger injection was administered to induce final maturation of the oocytes within the follicles. Approximately 36 hours after the trigger injection, oocyte retrieval was performed under ultrasound guidance. The retrieved oocytes were then evaluated and prepared for fertilization through ICSI in our case study. During the first ovum pick-up (OPU) procedure, no oocytes were retrieved due to the patient’s chronic condition of stage IV endometriosis. Subsequently, the first OPU cycle was conducted, followed by Gonadotropins releasing hormone. Low dosage can be given for 24 month and high dosage given for 6 month. So we gave high dosage of 6 month to the patient. The route of administration was injectable. High dosage of 10 mg/day.7 However, the conventional therapy yielded no improvements or discernible outcomes. Notably, in the first OPU cycle, no oocytes were retrieved.\n\nTherefore, in the second ovum pick-up (OPU) procedure, a combination therapy involving bevacizumab treatment (antiangiogenic therapy) 10mcg every 2 week in combination with cyclophosphamide and dichloroacetate (DCA) therapy 12.5 and 10.6 mcg twice-daily was administered orally for 3 months. Following the application of this therapeutic regimen during the second OPU cycle, the patient’s oocytes were successfully retrieved. Specifically, two oocytes in the metaphase II (MII) phase were retrieved after the implementation of bevacizumab treatment (antiangiogenic therapy) and dichloroacetate therapy during the second OPU cycle.\n\nThe process of intracytoplasmic sperm injection (ICSI) was employed to facilitate fertilization of the retrieved oocytes using the male partner’s sperm, thereby enhancing the likelihood of successful conception. To meet the patient’s hormonal needs and prepare the endometrium for embryo transfer, progesterone 200mcg orally and estrogen 1.25 to 2.5mg three times a day orally for 10 days were administered. Subsequently, a high- quality blastocyst was transferred into the patient’s uterus via a transcervical tube. There was no complications faced during the procedure.\n\nFollowing the embryo transfer procedure, the patient was counselled to take prescribed medications, including progesterone supplementation 200mcg orally for next 14 days, to support the development of the uterine lining and enhance implantation. The patient was closely monitored through periodical follow-up visits to assess her progress. The patient was also advised on lifestyle modifications, including recommendations for a healthy diet, physical activity, and avoidance of potential risks. Ongoing support and guidance were provided to address any concerns or queries during the follow-up period. The patient’s well-being and the progression of the pregnancy were closely monitored to optimize the chances of a successful outcome. Following routine follow-up examinations two weeks later, a positive beta-human chorionic gonadotropin (β-hCG) test confirmed the patient’s pregnancy. The value of β-hCG was reported to be 1245 mIU/mL.\n\n\nDiscussion\n\nAgustin Gracia et al observed that the endometriosis is cured by this Bevacizumab therapy was very effective therapy. The limitation of this therapy was Agustin Gracia and et al was observed this therapy only in one patient so this therapy required RCT randomized control trial to validate the result. The goals of endometriosis medication include symptom relief, slowing the disease’s course, and enhancing fertility outcomes. The use of prescription or over-the-counter painkillers, hormonal treatments like Gonadotropins releasing hormone. Low dosage was be given for 24 month and high dosage given for 6 month. So we gave high dosage of 6 month to the patient. The route of administration was injectable. High dosage of 10 mg/day.8\n\nEndometriosis is a chronic and complex condition that significantly affects the lives of women. Its exact cause remains unknown, and the wide range of symptoms and the lack of a definitive diagnostic test contribute to delays in diagnosis. The impact of endometriosis on a woman’s quality of life, fertility, and mental well-being cannot be underestimated.9\n\nA monoclonal anti-angiogenic antibody that targets the VEGF is bevacizumab. Thus, it may have an effect on neo-angiogenesis, one of the key aspects of endometriosis. With this history in mind, we suggested this treatment as off-label to a patient who had a severe case of endometriosis that had failed to respond to traditional treatments.10\n\nA monoclonal antibody known as bevacizumab blocks the creation of new blood vessels by specifically targeting the vascular endothelial growth factor (VEGF) protein. It has been largely approved for the therapy of specific tumors, including ovarian, lung, and colorectal cancer. Angiogenesis (creation of new blood vessels) contributes to the onset and development of endometriosis, an abnormal development of endometrial tissue beyond the uterus. Bevacizumab has been studied for its potential to reduce pain and lesion size associated with endometriosis, but more studies are required to determine the drug’s efficacy and safety in this setting.11\n\nThis research states that a high tolerability profile and a favourable impact on managing pain were attained. Importantly, we noticed that the hormone receptor was expressed more strongly in endometriosis cells. Knowing the crucial role performed by hormones in the prevention of cell/proliferation, inflammation, and neovascularization, these results may be of significant therapeutic value. Reverting to standard hormonal therapy in cases of refractoriness could contribute to a cautious approach to the condition.12\n\nWe also noted a favourable tolerance profile with no adverse effects. Bevacizumab should be used cautiously due to its anti-angiogenic activity, however, since it has been associated with intestinal, renal, and cardiovascular adverse reactions. When organizing a second opinion surgery, it’s important to keep in mind that poor wound healing caused by anti-angiogenesis therapy should also be taken into consideration.13 Finally, our experience suggests that bevacizumab treatment (antiangiogenic therapy) may be impacted by an elevated tissue fibrosis. Less bleeding, but a harder time dissecting implants because to inflammation, should be taken into account.\n\nAfter using bevacizumab treatment (antiangiogenic therapy), endometriosis was significantly cured and improved the chances of fertilization and implantation chances in the patient. Hormonal treatment involving the use of a combined oral contraceptive pill, routine follow-up visits, and conversations about fertility preservation strategies. This case emphasizes the necessity of raising awareness, developing diagnostic methods, and doing additional research to improve the care and quality of life for endometriosis sufferers.13\n\n\nConclusion\n\nThis case report is the testament of an endoemetrisos patient undergoing infertility treatment at WTTBC wardha who underwent bevacizumab treatment (antiangiogenic therapy) and dichloro acetate therapy for treating her ailment and resulted in significant improvement of the same, which resulted in positive clinical pregnancy.\n\n\nConsent\n\nWritten informed consent was obtained from the patient and her partner for the publication of their clinical details.\n\n\nEthical approval\n\nProspective Ethical approval: DMIHER (DU)/IEC/2023/603.", "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\nGardos G, Cole JO: Maintenance antipsychotic therapy: is the cure worse than the disease? Am. J. Psychiatry. 1976 Jan; 133(1): 32–36. PubMed Abstract \| Publisher Full Text\n\nLibíková H, Pogády J, Wiedermann V, et al.: Search for herpetic antibodies in the cerebrospinal fluid in senile dementia and mental retardation. Acta Virol. 1975 Nov; 19(6): 493–495. PubMed Abstract\n\nPoole-Wilson PA, Langer GA: Effect of pH on ionic exchange and function in rat and rabbit myocardium. Am. J. Phys. 1975 Sep; 229(3): 570–581. Publisher Full Text\n\nGardos G, Cole JO: Maintenance antipsychotic therapy: is the cure worse than the disease? Am. J. Psychiatry. 1976 Jan; 133(1): 32–36. PubMed Abstract \| Publisher Full Text\n\nFiddian-Green RG, Silen W: Mechanisms of disposal of acid and alkali in rabbit duodenum. Am. J. Phys. 1975 Dec; 229(6): 1641–1648. Publisher Full Text\n\nKidder GW, Montgomery CW: Oxygenation of frog gastric mucosa in vitro. Am. J. Phys. 1975 Dec; 229(6): 1510–1513. Publisher Full Text\n\nBehre HM, Kliesch S, Pühse G, et al.: High Loading and Low Maintenance Doses of a Gonadotropin-Releasing Hormone Antagonist Effectively Suppress Serum Luteinizing Hormone, Follicle-Stimulating Hormone, and Testosterone in Normal Men. J. Clin. Endocrinol. Metab. 1997 May; 82(5): 1403–1408. PubMed Abstract \| Publisher Full Text\n\nEhrhart IC, Parker PE, Weidner WJ, et al.: Coronary vascular and myocardial responses to carotid body stimulation in the dog. Am. J. Phys. 1975 Sep; 229(3): 754–760. Publisher Full Text\n\nShare JB: Review of drug treatment for Down’s syndrome persons. Am. J. Ment. Defic. 1976 Jan; 80(4): 388–393. PubMed Abstract\n\nBouquet De Joliniere J, Fruscalzo A, Khomsi F, et al.: Antiangiogenic Therapy as a New Strategy in the Treatment of Endometriosis? The First Case Report. Front. Surg. 2021 Dec 8; 8: 791686. Publisher Full Text\n\nTaira K, Okazaki S, Akiyoshi K, et al.: Short bevacizumab infusion as an effective and safe treatment for colorectal cancer. Mol. Clin. Oncol. 2022 Jul 27; 17(3): 139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKahn T, Bosch J, Levitt MF, et al.: Effect of sodium nitrate loading on electrolyte transport by the renal tubule. Am. J. Phys. 1975 Sep; 229(3): 746–753. Publisher Full Text\n\nKidder GW, Montgomery CW: Oxygenation of frog gastric mucosa in vitro. Am. J. Phys. 1975 Dec; 229(6): 1510–1513. Publisher Full Text" }	[ { "id": "208441", "date": "23 Oct 2023", "name": "Mathew Leonardi", "expertise": [ "Reviewer Expertise Gynecology", "Endometriosis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 Impression: The authors of the case report titled “Implication of antiangiogenic therapy (bevacizumab) along with dichloroacetate therapy on endometriosis patient seeking infertility treatment” provided novel evidence of the effectiveness of conjoined treatment using an angiogenic inhibitor and metabolic modulator in the treatment of endometriosis-associated infertility. The current case report suggests improvement in fertility outcomes and disease upon administration of both interventions. Please see the comments below:\nIntroduction\nThe manuscript has several grammatical errors, particularly in the introduction and discussion sections, which need to be revised. I suggest using a grammar software.\n\nPlease stay consistent when referring to stages of disease; in some cases, “Stage 4” was used, and in others, “Stage IV.”\n\nI would suggest breaking the introduction into four sections: 1) introducing the disease, 2) the pathobiology of endometriosis in the context of angiogenesis and metabolic dysregulation, 3) defining the intervention and their past use in malignancies, and 4) case report hypothesis and objective.\nCase presentation\nThe authors describe that the patient was diagnosed with Stage IV disease, assuming rASRM was used. How was the patient diagnosed (i.e. imagining, surgically, clinically)?\n\nHow did the patient present to the clinic? What were the symptoms, and what past treatments were provided?\n\nHas the patient had any past surgeries related to endometriosis?\nClinical Findings\nThe authors state, \"the first OPU cycle was conducted, followed by Gonadotropins releasing hormone. Low dosage can be given for 24 month and high dosage given for 6 month. So we gave high dosage of 6 month to the patient. The route of administration was injectable. High dosage of 10 mg/day. However, the conventional therapy yielded no improvements or discernible outcomes. Notably, in the first OPU cycle, no oocytes were retrieved.\" - Were the number of follicles counted sonographically in the first OPU cycle? If so, what was the count of visible follicles? Were AMH levels assessed at this time?\n\nThe authors suggest this treatment be used among those with Stage IV disease, particularly those who are unresponsive to the current conventional treatments. However, patients with stage IV disease typically present with significant adhesions throughout the pelvis, making imaging and oocyte retrieval difficult. For example, the ovaries may be adherent to pivotal structures such as the uterosacral or pelvic side wall, or the rectouterine pouch is commonly obliterated, making it challenging to retrieve eggs altogether. Similarly, what was the follicle and AMH count?\n\nWere the patients using any self-management strategies during the cycle period?\n\nDid the patient have any adverse reactions to the medication, and if so, what were they?\n\nA large contraindication of bevacizumab is pregnancy or the potential of childbearing, as it can readily pass the placental barrier, transmitting it from the mother to the developing fetus. Do you expect bevacizumab to affect the development period, given the half-life negatively? If so, is bevacizumab a feasible treatment in the context of fertility?\nDiscussion\nThe limitations were reported adequately, though they may be elaborated on, particularly the author's comment on fibrosis.\n\nThe authors state “After using bevacizumab treatment (antiangiogenic therapy), endometriosis was significantly cured and improved the chances of fertilization and implantation chances in the patient.” What do you mean by the endometriosis being cured, followed by treatment? Did the endometriosis disappear?\nReferences\nPlease review the references, as some are irrelevant to the field or topic, such as Share JB: Review of drug treatment for Down’s syndrome persons. Am. J. Ment. Defic. 1976 Jan; 80(4): 388–393\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1169
https://f1000research.com/articles/12-1168/v1	18 Sep 23	{ "type": "Research Article", "title": "Cultural differences in the measurement of self-curiosity within Mexico: a person-centered and variable-centered study", "authors": [ "Filippo Aschieri", "Angélica Quiroga Garza", "Giulia Pascarella", "Michela Zambelli", "Semira Tagliabue", "Angélica Quiroga Garza", "Giulia Pascarella", "Michela Zambelli", "Semira Tagliabue" ], "abstract": "Background: This study assessed the role of culture in the measurement of the Self-Curiosity Attitude-Interest scale (SCAI-M), a measure of attitude and interest in increasing one’s knowledge of self, adopting both a person-centered and variable-centered approach. Methods: The study was conducted on a Mexican sample composed of 484 adult participants who completed both the SCAI-M and a series of instruments that measure cultural dimensions through Qualtrix. Data were collected between November 9, to December 18, 2020, and respondents were contacted using advertisements on social media platforms (Facebook and WhatsApp). Analyses included multigroup confirmatory factor analysis and latent profile analysis. Results: A latent profile analysis allowed for the generation of three groups featuring distinct cultural orientations that were similar to previously found cultural profiles (Consensus-oriented Egalitarians, Flexible Individualists, and Rules-based Competitors). Multigroup Confirmative Factor Analysis showed partial metric and scalar invariance for the SCAI-M between groups; moreover, we found proofs of convergent validity with other cultural dimensions besides the ones linked with the Hofstede model. Our results indicate that cultural profiles and cultural variables are associated with both the level and meaning of self-curiosity among Mexican citizens. Conclusions: Finally, the discussion includes considerations on self-curiosity divergence among minority cultures and relevant clinical applications; a field for which we propose future research.", "keywords": [ "Self-Curiosity Attitude-Interest Scale", "Latent Profile Analysis", "Measurement invariance", "Cultural profiles" ], "content": "Introduction\n\nIn clinical settings, curiosity about oneself is a central construct for psychological assessment, psychopathology and intervention. In the field of psychological assessment, Finn (1996) proposed to engage clients in defining their assessment questions from the onset of the consultation, stressing that promoting clients’ curiosity about themselves and about the origins of their problems increases clients’ participation and utility of the assessment. Kashdan and Fincham (2004) linked curiosity with self-regulation, Borawski (2022) highlighted that loneliness and search for meaning in life are mediated by the capacity to reflect (i.e., develop curiosity about oneself). Finally, the capacity to reflect upon inner conscious thoughts and mental processes has been found as a fundamental component for the patients’ engagement in psychotherapy (Conte et al., 1990) and for their effectiveness (Nyklíček et al., 2020).\n\nTo formally assess how people observe and explore their inner world, the authors proposed the Self-Curiosity Attitude-Interest scale (SCAI). Its structure consists of two positively correlated factors, Attitude toward Self-Curiosity (ASC, disposition to explore their inner world, four items) and Interest in Increasing Knowledge of Self (IKS, interest in understanding better themselves, three items) (r ranging from .35 to .50). The scale had acceptable reliability coefficients considering its short length (Cronbach alpha across studies ranging from .58 to .69 for ASC and from .63 to .72 for IKS) and showed convergent validity coefficients with reflection (r=.60), openness, awareness, and motivation toward knowledge (r=.40), and general curiosity, interest, and desire for stimulating experiences (r=.30). Test-retest reliability for IKS was lower (r=.67) than for ASC (r=.81), indicating that the former is more sensitive to changes, whereas the latter behaves more like a stable trait-like feature. Discriminant validity analyses showed self-curiosity to be unrelated both to fluid intelligence (Aschieri et al., 2016) and current emotional states (Aschieri and Durosini, 2015).\n\nSelf-curiosity could be linked with people’s cultural characteristics. The construct of curiosity itself can be considered a cultural trait (Lindholm, 2018), and its development varied across different cultures: western cultures welcome its early presence, while non-western cultures value more obedience and respect. Among adults, an international survey found curiosity to be one of the most important character strengths; however, its ranking varied among cultures. Indeed, in some cultures curiosity was the most important character strength (e.g., Switzerland, Japan, Denmark), in other cultures it was in the low half of the top ten most important strengths (Brazil, Saudi Arabia, Sri Lanka), and in some other cultures curiosity had an intermediate value (Paraguay, Pakistan, and Turkey; McGrath, 2015).\n\nDue to the expected role of culture on self-curiosity, the SCAI has been studied in different countries. The SCAI’s two-factor structure was replicated in Czech Republic, Colombia, Mexico, and Japan. However, the scale incorporated modifications due to the respondents’ culture. For example, in the SCAI-J (Ushiyama et al., 2022) all negative items related to the IKS were substituted with new items, all positively keyed. The application of the SCAI to non-Italian respondents largely confirmed the same pattern of concurrent validity found in Italy. The SCAI Scale correlated with reflection (rJapan=.43); self-awareness (rColombia=.38, rMexico=.20), interest and deprivation factors of general curiosity (rColombia equal to, respectively, .30 and .23; rMexico equal to, respectively, .26 and .12), personality traits (Openness, rColombia=.34; rMexico=.24; rJapan=.16), and learning motivation (intrinsic motivation Towards Knowledge, rColombia=.35; Intrinsic Motivation Towards Stimulating Experiences, rColombia=.30; Intrinsic Motivation Towards Achievement, rColombia=.24). The administration of the SCAI in different countries showed also differences in the strength of its relations with other variables, such as Extraversion (rColombia=.20, rMexico=-.04; rJapan=-.02) and Agreeableness (rColombia=.15, rMexico=.14; rJapan=.04).\n\nPrevious studies found full metric invariance, but a lack of scalar invariance (Durosini et al., 2018; Aschieri et al., 2021). The lack of scalar invariance affects the final score, so it seemed that people belonging to different countries could obtain different levels of self-curiosity due to differences in the measurement of the construct.\n\nThese findings indicated that self-curiosity possessed some differences in the measurement process linked with cultural aspects. Importantly, all the aforementioned studies were conducted with a unit of analysis based on the country, assuming that the country was representative of a specific culture. However, it has been recently underlined that the country is not always a good proxy for cultural differences in values, and that many of those differences are within-country and more linked with other demographical or environmental factors (Taras et al., 2016). Often, studies that highlight the importance to investigate within-country differences, adopt a person-centered approach by which different cultural profiles within one country can be found.\n\nRecently, the latent profile analysis (LPA) technique has been applied to identify groups of individuals with similar cultural patterns of scores on dimensions of interest. This approach uses multiple attributes from each respondent to identify the boundaries that separate one group of individuals with similar cultural attributes from another, without defining the boundaries ex-ante. For instance, Cooper et al. (2020) investigated cultural profiles through LPA in 1071 participants from five different states (China, Germany, India, Russia, and the USA) using the Cultural Values Scale (CVSCALE, Yoo et al., 2011) that measure the five dimensions of the Hofstede (2001)’s model of cultural differences: power distance, uncertainty avoidance, individualism/collectivism, masculinity/femininity, and long/short term orientation. Three different profiles were found. The first profile (‘flexible individualists’, 14% of the pooled sample) was characterized by moderate levels of masculinity and relatively low power distance, uncertainty avoidance and collectivism. They were very flexible and individualistic. The second profile (‘consensus-oriented egalitarians’, 46% of the pooled sample) was characterized by a significantly higher uncertainty avoidance and collectivism, and low power distance and masculinity. Members of this second group placed great importance on group consensus and typical values of egalitarian perspectives. The third profile (‘rules-based competitors’, 40% of the pooled sample) was characterized by high levels of power distance, masculinity, uncertainty avoidance, and collectivism. They placed an important emphasis on competition for power and status and preferred clear rules relating to hierarchies and social obligations. Another study, conducted on Latino immigrants in the United States (Rojas et al., 2021) also found three cultural profiles: low socio-cultural protection (30%), high socio-cultural protection (4%), and high socio-, low-cultural protection (66%). People in the first profile were characterized by the highest levels of machismo (a socially constructed set of behaviors guiding male gender role, De La Cancela, 1986, in Estrada et al., 2011) along with the lowest levels of familismo (a cultural value that encompasses using family members as role models, turning to family members as sources of support, and prioritizing the family’s well-being over the individual’s (Stein et al., 2014 in Montoro and Ceballo, 2021), social-support, and multi-group identity, whereas people with the lowest levels of machismo and caballerismo (a code of masculine chivalry for a male adopting proper, respectful manners, Arciniega et al., 2008) were the ones with the high socio-cultural protection. The high socio-, low-cultural protection profile showed the highest levels of familismo. Overall, these findings indicate that the cultural dimensions described in Hofstede’s model (2001) can effectively be used to construct groups of respondents with similar cultural profiles.\n\nThe possibility to identify groups based on respondents’ cultural orientation within the same country allows involving participants from a single nation to explore the relationship between psychological constructs such as self-curiosity and culture. Mexican society is an elective context to study the effects of cultural orientation on self-curiosity given the heterogeneity of its society. Although Hofstede (2001) reported Mexico as a highly collectivistic society, with a high-power distance structure, and with a relatively low tolerance for uncertainty, those characteristics do not fully apply to the entire Mexican population. Mexico embraces five regions in which marked economic and social differences exist. Not only there are significant differences in accessing economic opportunities between the North and the South, but the means of production varies significantly across Mexico between agrarian, maritime, pastoral, industrial, and digital cultures. In 10 metropolitan areas, 37.0% of the total population of the country resided in cities; the rest of the population resided in urban and rural spaces. Around 10% of the population described themselves as speaking the indigenous language or identifying themselves as having African origins. Thus, a considerable minority of the population did not primarily affiliate themselves with the westernized Mexican culture as such, with even more being multilingual (National System of Statistical and Geographical Information, 2021).\n\nGiven the variety of Mexican society, ‘traditional’ Mexican cultural pillars such as familism/collectivism, distinctive gender roles, deference to power and authority figures and spirituality have been constantly challenged and shaped by acculturation processes with Western cultural models and by contextual demands, making “impossible to impose stereotypic characterizations to describe the behavior, attitudes, values, or beliefs of members from a particular cultural group” (Rodriguez and Olswang, 2002, p. 157). As an example, in a sample of woman with Mexican origins, a LPA analysis highlighted “that many Mexican heritage young women disavow many of the traditional gender values that are often assumed by others to be the key components of their culture and that they do so while maintaining strong ethnic identities” (Gutierrez and Leaper, 2022, p. 268).\n\nSimilarly, the aim of the present study was to investigate self-curiosity differences by comparing different cultural profiles found within the Mexican population, adopting both a person-centered and a variable-centered approach. More specifically, we aimed to: 1) identify cultural profiles within the Mexican sample; 2) compare, through a multigroup analysis, the structure of the SCAI-M across the cultural profiles identified; 3) investigate level differences of self-curiosity’s dimensions of Attitude and Interest in the different cultural profiles; and 4) correlate SCAI-M’s dimensions and several cultural constructs within a variable-centered approach.\n\nRegarding the identification of cultural profiles, we expected to find similar profiles to those found in the literature. More specifically, we expected to find at least two profiles: one profile characterized by the “traditional” cultural values, similar to the “rules-based competitors” of Cooper et al. (2020) defined by people more collectivist, high in masculinity and avoiding uncertainty; another profile similar to the “flexible individualists” (Cooper et al., 2020), characterized by more individualistic values, and in particular by low power distance, uncertainty avoidance and collectivism and low or moderate levels of masculinity.\n\nRegarding the cultural differences in self-curiosity, we hypothesized that individualistic people would engage in a higher self-curiosity to confirm their uniqueness and separateness from others, would describe themselves as having distinctive characteristics that are not shared by others, and would own a context-independent processing style. Conversely, profiles characterized by high masculinity could show lower scores on both self-curiosity dimensions. People not inclined to bring up their feelings when talking to others could be less likely to be open to self-exploration and interested in their inner world.\n\n\nMethods\n\nThe study was approved by the CONBIOÉTICA, the Ethical Committee of the Universidad de Monterrey (approval number 19-CEI-002-20191210). All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional research committee at the Universidad de Monterrey and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. Written informed consent was obtained from all individual adult participants included in the study.\n\n528 adults participated in this study. We considered only the data of those who compiled at least the SCAI-M. Based on this criterion, we eliminated 44 subjects for a total of 484 participants (see Table 1 for sample’s characteristics). No exclusion criteria were adopted.\n\nAll participants voluntarily agreed to take part in the study without incentives and were recruited through mailing lists and social networks (Facebook and WhatsApp) and completed the questionnaires using the Qualtrics platform (https://www.qualtrics.com/uk/platform/). All participants voluntarily accessed the survey and completed it online between November 9, to December 18, 2020. All data were collected in an anonymized format. No incentives were offered for participation in the study.\n\nNone of the scales were pilot tested prior to the start of the survey. All scales used in this study (except for SCAI-M) were structurally evaluated via confirmatory factor analysis (CFA) and explorative factor analysis (EFA). To find the best initial solutions, we performed CFA, with parallel analyses as an extraction method. The reliability of all dimensions was evaluated using McDonald’s omega (ω; Dunn et al., 2014). We used Jamovi 1.6.21 version to run CFA and reliability analyses. Detailed information about psychometric analyses on the instruments are available in Appendix (see extended data, Aschieri et al., 2023).\n\nSelf-Curiosity Attitude-Interest scale, Mexican version (SCAI-M, Aschieri et al., 2021)\n\nParticipants filled in the Mexican version of the SCAI (SCAI-M, Aschieri et al., 2021). The SCAI is a seven-item scale, originally formulated by Aschieri and Durosini (2015) in Italy, composed of two factors: ASC (four items; e.g., ‘I like to listen to music because it teaches me what I am like as a person’); IKS (three items; e.g., ‘I am not interested in understanding how my past experiences impact my current life’). All items are answered on a seven-point scale, ranging from 1= completely disagree and 7 = completely agree. The psychometric properties of the SCAI-M on the present sample will be presented in the result section.\n\nCultural Values Scale (CVSCALE, Yoo, Donthu & Lenartowicz, 2011)\n\nThe instrument, composed by 26 items answered on a five-point Likert scale, measures five cultural dimensions from Hofstede model: power distance (five items; e.g., ‘People in higher positions should make most decisions without consulting people in lower positions’), uncertainty avoidance (five items; e.g., ‘It is important to have instructions spelled out in detail so that I always know what I’m expected to do’), collectivism (six items; e.g., ‘Individuals should sacrifice self-interest for the group’), long-term orientation (six items; e.g., ‘Giving up today’s fun for success in the future’), and masculinity (four items; e.g., ‘It is more important for men to have a professional career than it is for women’).\n\nCollective-interdependent Self-Construal Scale (SCS, Gabriel & Gardner, 1999)\n\nThis is a 10-item scale designed to assess collective-interdependent self-construal (e.g., ‘When I am in a group, it often feels to me like that group is an important part of who I am’), which is defined as a general orientation toward representing oneself in terms of large group relationships. All items are answered on a seven-point Likert scale.\n\nConformity to Masculine Norms-29 (CMN-29, Hsu & Iwamoto, 2014)\n\nThis is a 29-item scale measuring eight factors of normative masculinity: winning (four items; e.g., ‘Winning is not my first priority’), playboy (three items; e.g., ‘If I could, I would frequently change sexual partners’), self-reliance (three items; e.g., ‘I hate asking for help’), Violence (four items; e.g., ‘I believe that violence is never justified”), heterosexual self-presentation (six items; e.g., ‘I would be furious if someone thought I was gay’), risk taking (three items; e.g., ‘I enjoy taking risks’), emotional control (three items; e.g., ‘I bring up my feelings when talking to others’), and power over women (three items; e.g., ‘Women should be subservient to men’). Items scored on a four-point Likert scale from 0 (strongly disagree) to 3 (strongly agree).\n\nCulture Orientation Scale (COS, Triandis and Gelfand, 1998)\n\nFrom this 16-items scale designed to measured four dimensions of collectivism and individualism we selected only the dimension of horizontal collectivism (four items; e.g. ‘The well-being of my coworkers is important to me’) because of poor fit of the whole factorial structure of the scale. All items were answered on a nine-point Likert scale.\n\nRelational-Interdependent Self-Construal Scale (Rel-IntSC, Cross, Bacon, and Morris, 2000)\n\nThis is an 11-item scale designed to assess relational-interdependent self-construal, defined as a general orientation toward representing oneself in terms of close relationships (e.g., ‘My close relationships are an important reflection of who I am’). In the present study, only nine items were retained to obtain acceptable fit of the scale structure. Items 8 and 9 (‘Overall, my close relationships have very little to do with how I feel about myself’, and ‘My close relationships are unimportant to my sense of what kind of person I am’) were excluded to allow good fit of the scale to the data (see Appendix). All items were answered on a seven-point Likert scale.\n\nSixfold Self-Construal Scale (SSC, Harb and Smith, 2008)\n\nThis is a 30-item scale measuring six subcategories of self-construal: the personal self (five items; e.g., ‘I am a unique person separate from others’); relational vertical (five items; e.g., ‘I think of myself as connected to my family’); relational horizontal (five items; e.g., ‘I control my behavior to accommodate the wishes of my friends’); collective vertical (five items; e.g., ‘I am affected by events that concern to my social organization’); collective horizontal (five items; e.g., ‘I am aware of the needs, desires, and goals of my peers), and humanity (five items; e.g., ‘I feel I have a strong relationship with humankind’). The subdimension of personal self was dropped due to psychometric problems. All items were answered on seven-point Likert-type scales.\n\nThe missingness mechanism was evaluated by Little’s MCAR test on the entire set of measures administered, indicating that data were not distributed randomly [χ2 (1541)=1699.40; p=.003]. Missing data were handled in Mplus 8.4 software (https://www.statmodel.com/) via the full information maximum likelihood (FIML) method.\n\nTo identify different profiles of cultural orientation among participants based on Hofstede’s five-dimension model, we conducted a latent profile analysis (LPA; Collins and Lanza, 2013) using Mplus 8.4. The core assumption of LPA is that individuals are homogeneous within the same profile and dissimilar between the different profiles, with respect to the mean level of the considered indicators. LPA was performed on the five dimensions of the cultural values scale (CVS), for a total of 15 observed indicators, comparing increasing number of profiles (k). The decision about the best profile solution was based on fit indices, parsimony, classification precision and interpretability of the profiles (Marsh et al., 2009).\n\nThen, we tested a CFA of the SCAI-M on the total sample using MLR as the extraction method. To test the measurement invariance of the SCAI-M in relation to the profiles of cultural orientation, a series of multigroup CFA were tested in a step-by-step process. First, we tested the configural invariance of the two-factor structure of SCAI-M. Second, we tested metric invariance by constraining the factor loadings to be equal across the different profiles of cultural orientation. The metric invariance model was then compared with the configural one. Full metric invariance is found when a chi-square difference is non-significant (changes were calculated using the Satorra-Bentler Scaled; www.statmodel.com/chidiff.shtml), the CFI’s decrease is lower than .01, and the RMSEA’s increase is equal to or lower than .015 (Chen, 2007). Following the same procedure, we tested a scalar invariance model in which equality constraints were added on intercepts across the different profiles; this model was compared with the metric invariance model using the same cut-off scores. When full measurement invariance was not found, modification indexes were consulted to remove parameter constraints until reaching satisfactory cut-offs, to obtain a model of partial invariance. We used Mplus 8.4 version to run multi-group confirmatory factor analyses.\n\nFinally, adopting a variable-centered approach, we also evaluated whether the two dimensions of the SCAI-M were associated to several cultural variables. The ‘diffcor’ R package was used for correlations and between-groups comparisons.\n\nAll analyses can be run with non-proprietary software. Here follows a freely accessible alternative software capable of the same analyses. LPA models can be fit in R (version 4.0.3; R-core team, 2020), running in Rstudio (version 1.3.1093), and the package ‘tidyLPA’. CFA and multigroup CFA can be run using R (version 4.0.3; R-core team, 2020), running in Rstudio (version 1.3.1093), and the lavaan package.\n\n\nResults\n\nAnalyses were carried on a total of 484 respondents (female, n = 269), with age ranging from 16 to 23 years old (36.6%), 24 to 43 years old (36.4%) and 44 to 77 (27%). Most of participants were students (40.3%) and employees (29.2%) (Aschieri et al., 2023). Overall our sample was educated, with 62.9% participants having a university degree of higher title of study, and only 1% having finished compulsory education.\n\nWe compared three measurement models, and we stopped in correspondence with the four-profile solution as this model was not identified (Table S1 in Supplementary materials; Aschieri et al., 2023). The three-profile model turned out to be the preferred one according to all the criteria (AIC, BIC, CAIC, AWE; BLRT; Entropy; Profiles’ distribution), and to the inspection of the classification-diagnostics criteria (Table S2 in Supplementary materials; Aschieri et al., 2023). Figure 1 presents the profiles’ solution with standardized values on the y-axis, indicating each profile’s mean deviation from the total sample mean. Specifically, the largest group was made of individuals who scored on average on all the items administered (i.e., their scores were included in the range of 0.5 standard deviations from the sample mean), thus they were named ‘consensus-oriented egalitarians’, as they were like the people found by Cooper et al. (2020) as characterized by high collectivism and uncertainty avoidance and low power distance and masculinity. The second group was made of individuals with very low uncertainty avoidance and low long-term orientation, thus they were named ‘flexible individualists’, as they were similar to people belonging to the profile found by Cooper et al. (2020) which was characterized by low power distance, uncertainty avoidance and collectivism and moderate masculinity. Conversely, the last group represented individuals with extreme scores for power distance and masculinity, and high scores for collectivism. This last group was named ‘rules-based competitors’, as it was like the one found by Cooper et al. (2020) characterized by high power distance, masculinity, uncertainty avoidance and collectivism.\n\nNote. CVS=Cultural Values Scale (P=power distance, U=uncertainty avoidance, C=collectivism, L=long term orientation, M=masculinity.\n\nOn the total sample, the SCAI-M showed acceptable fit with the expected two-factors structure (χ2/df=3.5; CFI=.917; RMSEA=.071 [C.I. .051 - .093] and acceptable reliability coefficients for ASC (four items, ω=.69) and IKS (three items, ω=.69). When multigroup analyses were conducted, the configural invariance model showed acceptable fit indexes (χ2/df=2.25; CFI=.890; RMSEA=.093), so the two-factors structure could be considered suitable for the three cultural profiles. However, when metric invariance was tested, the model resulted in a significant decrease of the fit (Δχ2 (13)=54.82, p<.001; ΔCFI=-.103; ΔRMSEA=.020). An inspection of modification indexes revealed that factor loadings of items four and seven were not similar in the three groups. A partial metric invariance model was then tested by removing the equality constraints on the item four factor loading. Moreover, the factor loading of item seven in the consensus-oriented egalitarian group was set free to account for its different weight in contributing to the IKS (Δχ2 (11)=14.19, p=.223; ΔCFI.000; ΔRMSEA=-.010). Items’ factor loading estimates revealed that the consensus-oriented egalitarian group presented a lower factor loading of item four (‘I select my best friends among those with whom I can grow as a person’; factor loading=0.407) than rules-based competitors (.809), and flexible individualists (1.411). Thus, the meaning of the attitude dimension was more related to social relationships for the rules-based competitors and, especially, for flexible individualists, whereas, for consensus-oriented egalitarians, attitude was more related to individual preferences and less to relational choices. Regarding item seven (‘I am not interested in understanding what motivates my behaviors.’), the consensus-oriented egalitarians group presented a lower factor loading (.916) than the other two groups (1.829), showing that, also in this case, the (absence of) interest dimension was more defined by item seven for the flexible individualists and rules-based competitors groups than for the consensus-oriented egalitarians1.\n\nFinally, a scalar invariance model was tested showing a significant decrease of the fit (Δχ2 (9)=25.24, p=.003; ΔCFI=-.033; ΔRMSEA=.004). An inspection of modification indexes revealed that the intercepts of item four were not similar between the consensus-oriented egalitarians group and the other two groups, so a partial scalar invariance model was tested releasing the intercept of item four only for the consensus-oriented egalitarians group (Δχ2 (8)=11.42, p=.179; ΔCFI=-.010; ΔRMSEA=-.003). Estimates revealed that consensus-oriented egalitarians presented a higher intercept of item four (6.165) than the other two groups (5.643), indicating that scores on that item depended on the different way respondents used the 1-7 scale for item four. That means that those people were more interested in selecting their friends among people who allow them to grow than people belonging to flexible individualists or rules-based competitors profiles.\n\nTable 2 shows the correlations between SCAI-M total scale, SCAI-M Attitude and SCAI-M Interest factors and the cultural dimensions measured by the other scales considered in this study. SCAI-M total scale strongest positive correlations were with relational-interdependent self-construal and horizontal collectivism. Smaller correlations were found with collective-interdependent self-construal, humanity, relational horizontal, relational vertical, and, in a negative direction, with emotional control. SCAI-M Attitude strongest positive correlation was with relational-interdependent self-construal, whereas smaller correlations were with horizontal collectivism, collective-interdependent self-construal, relational horizontal, collective vertical, collective horizontal, and humanity. SCAI-M Interest strongest positive correlation was with Relational interdependent self-construal, whereas smaller positive correlation with Horizontal collectivism, and negative correlations with heterosexual self-presentation, emotional control, and power over woman were found.\n\n* p<.05.\n\n p<.01.\n\n* p=.001.\n\na Fisher's z-tests were computed with the ‘diffcor’ R package (https://CRAN.R-project.org/package=diffcor) to test differences between correlations of scale’s factors with SCAI attitude and SCAI interest.\n\n\nDiscussion\n\nThe principal focus of this study was to investigate cultural differences in self-curiosity measurement by adopting both a person-centered and variable-centered approach. Regarding the person-centered approach, three cultural profiles within the Mexican sample were identified through LPA: consensus-oriented egalitarians were people with average scores on all cultural dimensions, flexible individualists were people that appreciated uncertainty and short-term orientation, and rules-based competitors people showed very high scores in power distance, masculinity, and collectivism. As expected, the profiles were similar to the ones identified by Cooper et al. (2020), although the prevalence of the profiles within the Mexican sample was different especially for the consensus-oriented egalitarians’ profile, that was more represented in our sample than in Cooper et al. (2020), and the rules-based competitors, that was less represented in our sample. Those findings support the variety of cultural profiles present in Mexico and confirm the importance to evaluate within-country cultural differences (Taras et al., 2016). Moreover, Cooper et al. (2020) did not use the dimension of Long/Short Term Orientation to identify latent cultural profiles, so the present study is the first that considers that dimension to enrich the description of the cultural profiles within one country.\n\nAdopting the person-centered approach highlighted some cultural differences in the measurement of self-curiosity that were not previously found. Indeed, beside partial scalar invariance found also in previous cross-country comparisons (Durosini et al., 2018; Aschieri et al., 2021), also partial metric invariance was found. This suggests that the meaning of ASC is more related to the choice of friends for the flexible individualists and rules-based competitors than for the consensus-oriented egalitarians. Moreover, flexible individualists and rules-based competitors perceive IKS more in terms of motivational features than do the consensus-oriented egalitarians. Some differences were also present regarding the mean level of item four related to social relationships, with consensus-oriented egalitarians that scored higher than the other two groups.\n\nSCAI-M is more likely to provide stable assessment results of self-curiosity traits when respondents do not position on the tails of the distribution of cultural dimensions. When this happens, the results should be interpreted with caution, since the relevance that respondents give to their friends in exploring their inner world assumes a unique and higher relevance in the measurement of their self-curiosity. Thus, professionals aiming to promote self-curiosity in traditionalist clients should invest efforts to build relationships with them and join their traditionalist point of view as the first step of their work. This seems coherent with Eriksen et al., (2002), who described the difficulties with conservative Christian clients, and suggested building a solid relationship first, by empathically placing themselves in the client’s shoes, and being open to learn about their worldview. Thus, adopting a person-centered approach in evaluating the cultural profiles helped to understand that cross-cultural differences in the measurement of the construct of self-curiosity need to be considered even when comparisons are made within one country.\n\nAdopting the variable-centered approach showed that the SCAI-M was negatively correlated with power-related definitions of masculinity, and, in particular, to its emotional control component. Contrary to the expectations, the SCAI-M positively correlated with collectivism, with higher correlation coefficients with relational interdependence in the definition of the respondents’ identity. The SCAI-M was associated with the respondents’ ability to conceptualize their identity as strictly connected to a relational network. It might be speculated that self-curiosity can help respondents to make sense of the continuity of their identity in the context of the different people they relate with, and to be more aware of the interconnectedness between their current self-identity and their relational network. However, those findings could also be affected by some issues related to the measurement of cultural variables, indeed, as seen in the Appendix (Aschieri et al., 2023), some of the scales had less than acceptable model fit in the CFA.\n\nThis study tested the structure of the SCAI-M in three groups of Mexican respondents. While the consensus-oriented egalitarians group was large and findings on the SCAI-M metrics with these respondents were reliable, the other two groups were smaller. Thus, to confirm the findings on flexible individualists and rules-based competitors, future research focusing on these marginal cultural orientations are needed.\n\nRegarding the correlation between the SCAI-M’s dimensions and other cultural variables, we should be cautious in the interpretation because of the unsatisfactory fit of many of the instruments used, moreover, we cannot rule out the possible correlations with other cultural dimensions not considered in this study. Furthermore, future additional studies are necessary to increase the generalizability of LPA results obtained with groups collected through convenience sampling, and resulting featured by high levels of education.\n\nTesting the measurement properties of the SCAI with a clinical population is also compelling. Methodologically, LPA could be used to describe the profiles of specific groups of patients including both measures of clinical symptoms and self-curiosity. Results of this typology of studies would allow tailoring interventions to specific typologies of patients by increasing the understanding of their interest and attitude to understand themselves better.\n\nOverall, the present study contributes to both the self-curiosity and cross-cultural literature in several ways. It confirmed that within a country it is possible to find cultural variability, but also proposes an approach to deal with such variability: the use of both person-centered and variable-centered approach in investigating cultural differences. Self-curiosity measurement was also confirmed to be linked with the cultural features, adding that when culture is investigated more in deep than only comparing countries, new findings could rise. Thus, future studies aiming at examining cross-cultural differences in the use of measurement tools could benefit of that approach.", "appendix": "Data availability\n\nRepository name: Cultural differences in the measurement of self-curiosity within Mexico: a person-centered and variable-centered study. https://doi.org/10.17632/zvcc9gvys9.1 (Aschieri et al., 2023).\n\nThe project contains the following underlying data:\n\n• Dataset.sav (List of all variables analyzed).\n\n• Codebook (Items/constructs corresponding to each variable in the dataset).\n\nRepository name: Cultural differences in the measurement of self-curiosity within Mexico: a person-centered and variable-centered study. https://doi.org/10.17632/zvcc9gvys9.1 (Aschieri et al., 2023).\n\nThis project contains the following extended data:\n\n• Supplementary (Appendix: Psychometric properties of all instruments used in the study; Syntax of the analyses; Supplementary Tables 1 and 2)\n\n• Questionnaire/Cuadernillo (list of the items corresponding to columns the dataset)\n\nRepository: SRQR checklist for ‘Cultural differences in the measurement of self-curiosity within Mexico: a person-centered and variable-centered study’. https://doi.org/10.17632/zvcc9gvys9.1 (Aschieri et al., 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\nArciniega GM, Anderson TC, Tovar-Blank ZG, et al.: Toward a fuller conception of Machismo: Development of a traditional Machismo and Caballerismo Scale. J. Couns. Psychol. 2008; 55(1): 19–33. Publisher Full Text\n\nAschieri F, Durosini I: Development of the Self-Curiosity Attitude-Interest scale. TPM-Testing, Psychometrics, Methodology in Applied Psychology. 2015; 22(3): 327–347.\n\nAschieri F, Durosini I, Locatelli M, et al.: Factor structure invariance and discriminant validity of the Self-Curiosity Attitude-Interest scale. TPM-Testing, Psychometrics, Methodology in Applied Psychology. 2016; 23(2): 139–148.\n\nAschieri F, Quiroga-Garza A, Tagliabue S, et al.: Psychometric properties of the Self-Curiosity Attitude-Interest Scale in two paired samples from Italy and Mexico. TPM - Testing, Psychometrics, Methodology in Applied Psychology. 2021; 28(4): 415–426. Publisher Full Text\n\nAschieri F, Tagliabue S, Quiroga-Garza A, et al.: Cultural differences in the measurement of self-curiosity within Mexico: a person-centered and variable-centered study. Dataset. Mendeley Data. 2023; V1. Publisher Full Text\n\nBorawski D: When you are lonely, look inside yourself: The moderating role of reflection in the relationship between loneliness and meaning in life. Personal. Individ. Differ. 2022; 194: 111662. Publisher Full Text\n\nChen FF: Sensitivity of goodness of fit indexes to lack of measurement invariance. Struct. Equ. Model. 2007; 14(3): 464–504. Publisher Full Text\n\nCollins LM, Lanza ST: Latent class and latent transition analysis: With applications in the social, behavioral, and health sciences. Hoboken, NJ: John Wiley & Sons; 2013.\n\nConte HR, Plutchik R, Jung BB, et al.: Psychological mindedness as a predictor of psychotherapy outcome: a preliminary report. Compr. Psychiatry. 1990; 31(5): 426–431. PubMed Abstract \| Publisher Full Text\n\nCooper JT, Stanley LJ, Stevens CE, et al.: Switching analytical mindsets: A person-centered approach to the analysis of cultural values. Int. J. Cross-cult. Manag. 2020; 20(2): 223–247. Publisher Full Text\n\nCross SE, Bacon PL, Morris ML: The relational– interdependent self-construal and relationships. J. Pers. Soc. Psychol. 2000; 78: 791–808. PubMed Abstract \| Publisher Full Text\n\nDe La Cancela V: A critical analysis of Puerto Rican machismo: Implications for clinical practice. Psychotherapy: Theory, Research, Practice, Training. 1986; 23: 291–296. Publisher Full Text\n\nDunn TJ, Baguley T, Brunsden V: From alpha to omega: A practical solution to the pervasive problem of internal consistency estimation. Br. J. Psychol. 2014; 105(3): 399–412. PubMed Abstract \| Publisher Full Text\n\nDurosini I, Fantini F, Escobar-Ramírez CD, et al.: Validation of the Self-Curiosity Attitude-Interest Scale in Colombia. Suma Psicológica. 2018; 25(1): 1–10. Publisher Full Text\n\nEriksen K, Marston G, Korte T: Issues and insights: Working with God managing conservative Christian beliefs that may interfere with counseling. Couns. Values. 2002; 47(1): 48–68. Publisher Full Text\n\nEstrada F, Rigali-Oiler M, Arciniega GM, et al.: Machismo and mexican american men: An empirical understanding using a gay sample. J. Couns. Psychol. 2011; 58(3): 358–367. PubMed Abstract \| Publisher Full Text\n\nFinn SE: Manual for using the MMPI-2 as a therapeutic intervention. Minneapolis, MN: University of Minnesota Press; 1996.\n\nGabriel S, Gardner WL: Are there “his” and “hers” types of interdependence? The implications of gender differences in collective versus relational interdependence for affect, behavior, and cognition. J. Pers. Soc. Psychol. 1999; 77: 642–655. Publisher Full Text\n\nGutierrez BC, Leaper C: Reconstructing culture: A latent profile analysis of Mexican-heritage young women’s cultural practices, gender values, and ethnic identity. Cult. Divers. Ethn. Minor. Psychol. 2022; 28(2): 259–270. PubMed Abstract \| Publisher Full Text\n\nHarb C, Smith PB: Self-Construals across cultures: Beyond independence–interdependence. J. Cross-Cult. Psychol. 2008; 39: 178–197. Publisher Full Text\n\nHofstede G: Culture’s consequences: comparing values, behaviors, institutions and organizations across nations. Sage (co-published in the PRC as Vol. 10 in the Shanghai Foreign Language Education Press SFLEP Intercultural Communication Reference Series, 2008).2001.\n\nHsu K, Iwamoto DK: Testing for measurement invariance in the Conformity to Masculine Norms-46 across white and Asian American college men: Development and validity of the CMNI-29. Psychol. Men Masculinity. 2014; 15: 397–406. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKashdan TB, Fincham FD: Facilitating curiosity: A social and self-regulatory perspective for scientifically based interventions.Linley PA, Joseph S, editors. Positive psychology in practice. New Jersey: Wiley; 2004; pp. 482–503. Publisher Full Text\n\nLindholm M: Promoting curiosity? Sci. & Educ. 2018; 27(9): 987–1002. Publisher Full Text\n\nMarsh HW, Lüdtke O, Trautwein U, et al.: Classical latent profile analysis of academic self-concept dimensions: Synergy of person-and variable-centered approaches to theoretical models of self-concept. Struct. Equ. Model. Multidiscip. J. 2009; 16(2): 191–225. Publisher Full Text\n\nMcGrath RE: Character strengths in 75 nations: An update. J. Posit. Psychol. 2015; 10(1): 41–52. Publisher Full Text\n\nMontoro JP, Ceballo R: Latinx adolescents facing multiple stressors and the protective role of familismo. Cult. Divers. Ethn. Minor. Psychol. 2021; 27(4): 705–716. PubMed Abstract \| Publisher Full Text\n\nNational System of Statistical and Geographical Information: 2020 Census of Population and Housing.2021. Reference Source\n\nNyklíček I, Zonneveld R, Denollet J: Introspective Interest and Insight in the Context of Mindfulness-Based Stress Reduction: a Randomized Trial. Mindfulness. 2020; 11: 2176–2188. Publisher Full Text\n\nR Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020. Reference Source\n\nRodriguez BL, Olswang LB: Cultural diversity is more than group differences: An example from the Mexican American community. Contemporary Issues in Communication Science and Disorders. 2002; 29(Fall): 154–164. Publisher Full Text\n\nRojas LM, Sanchez M, Westrick A, et al.: Socio-cultural subgroups of Latina/o immigrants: A latent profile analysis. Int. J. Intercult. Relat. 2021; 82: 185–196. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStein GL, Cupito AM, Mendez JL, et al.: Familism through a developmental lens. Journal of Latina/o Psychology. 2014; 2(4): 224–250. Publisher Full Text\n\nTaras V, Steel P, Kirkman BL: Does country equate with culture? Beyond geography in the search for cultural boundaries. Manag. Int. Rev. 2016; 56(4): 455–487. Publisher Full Text\n\nTriandis HC, Gelfand M: Converging measurement of horizontal and vertical individualism and collectivism. J. Pers. Soc. Psychol. 1998; 74: 118–128. Publisher Full Text\n\nUshiyama M, Kumamoto M, Aschieri F: Conceptual structure of self-curiosity in Japan. Cogent Psychol. 2022; 9(1). Publisher Full Text\n\nYoo B, Donthu N, Lenartowicz T: Measuring Hofstede’s Five Dimensions of Cultural Values at the Individual Level: Development and Validation of CVSCALE. J. Int. Consum. Mark. 2011; 23: 193–210. Publisher Full Text\n\n\nFootnotes\n\n1 The residual of item seven had to be constrained to 0 for the rules-based competitors group, because otherwise, it generated a negative value." }	[ { "id": "207990", "date": "09 Oct 2023", "name": "Juan Manuel Fernández-Cárdenas", "expertise": [ "Reviewer Expertise Sociocultural research in psychology and education", "linguistics and ethnography", "dialogue and clinical practice" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article aims to investigate the relationship of self curiosity with possible cultural traits in Mexican population. The study found correlation of self-curiosity with three previously found cultural profiles. These profiles are found in different degrees within the Mexican sample studied, confirming that a national culture cannot be assumed as relatively homogenous. The study is relevant for clinical implications, as self-curiosity is a very valuable trait for psychotherapy, given that this allows patients to think and feel about his or her mental states in an exploratory mode, allowing the possibility of alternative explanations about the behavior of others towards him or her, and the resulting feelings he or she can develop as a consequence of those behaviors. See the work of Peter Fonagy and colleagues in terms of mentalization (e.g. 2003), where curiosity about how the mind of others and your own mind works, is a key element for the development of a reflective function, and a key ingredient for mental health. If curiosity can be conceptualized also as a cultural trait, then a psychotherapist could be more aware about the need for constructing more carefully relationships with patients who might need more trust to be developed (Fonagy and Campbell, 2023) in order to feel more secure about disclosing possible hypotheses of mental states that could be felt as more traditional or rigid, and therefore with possible links to shame or guilt, for instance. This is a very interesting article, very useful to identify tests that can reliably measure these traits, and thus promote more effective ways for clinical practice.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "10527", "date": "06 Nov 2023", "name": "Semira Tagliabue", "role": "Author Response", "response": "Thank you for the warm and supportive feedback on our work. We are encouraged to move ahead in this field by your kind words of appreciation. Semira Tagliabue, Filippo Aschieri and co-authors" } ] }, { "id": "217960", "date": "10 Nov 2023", "name": "Stefania Cristofanelli", "expertise": [ "Reviewer Expertise a) Research concerns diagnostic assessment", "with a particular interest in the clinical-diagnostic aspects of psychopathology in adolescence", "b) the evaluation of outcomes and processes in the care pathways of adolescent patients placed in therapeutic and socio-rehabilitative communities." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe aim of the research is to evaluate whether, and possibly how, the culture influences the attitude of curiosity and interest in increasing self-knowledge. To achieve this goal, the authors adopted both a person-centered and a variable-centered approach. The personal disposition to be curious was investigated using the Self-Curiosity Attitude-Interest scale Mexican version (SCAI-M); moreover, five other questionnaires were administered to evaluate further cultural dimensions. The sample was composed of 484 Mexican adults; the data collected were analyzed using a multigroup confirmatory factor analysis and a latent profile analysis. The choice to select a Mexican sample has the advantage of analyzing a social context within which different cultures coexist. The latent profile analysis revealed the presence of three different cultural profiles: flexible individualists, rule-based competitors and consensus-oriented egalitarians. At a clinical level, this result suggests that it is important, even within the same country, to consider the culture of the individual when exploring the construct of self-curiosity. By adopting the person-centered approach, it emerged that in flexible individualists and rule-based competitors profiles, the attitude of self-curiosity was associated with the choice of friends. From a clinical point of view, this data is interesting, because it suggests that when a therapist should promote an attitude of curiosity in a traditionalist client the professional should begin by building a relationship based on adopting the patient's point of view. Furthermore, in flexible individualists and rule-based competitors, the interest in self-knowledge is more understood in terms of motivational characteristics. Adopting the variable-centered approach, the SCAI-M scale negatively correlates with the definitions of masculinity most related to power and, in particular, to its emotional control component. Contrary to expectations, SCAI-M correlates positively with collectivism.\nThe paper is interesting because it places emphasis on how culture influences the attitude of curiosity towards oneself, an internal disposition which, in the clinical field, is crucial both for understanding the functioning of the individual and for change (Kamphuis, & Finn, 2018). Furthermore, the study warns against the mistake of not considering the impact of different cultures even among individuals living within the same country (Taras et al., 2016).\nSuggestions:\nIn the introduction section can be add a brief description of the person-centered approach and the variable-centered approach.\n\nAs stated in the footnote (page 8), in one case the residual had to be constrained to zero because otherwise it generates a negative value. From the literature you consulted, are there any other studies in a similar condition?\n\nCould the SRMR (Standardized Root Mean Square Residual) also be reported in the CFA results as a measure of fit?\n\nIs the work 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/12-1168
https://f1000research.com/articles/12-12/v1	05 Jan 23	{ "type": "Research Article", "title": "Antioxidant and phytometabolite profiles of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland: A study for potential photoaging agent", "authors": [ "Wahyu Lestari", "Kartini Hasballah", "M. Yulianto Listiawan", "Sofia Sofia", "Wahyu Lestari", "M. Yulianto Listiawan", "Sofia Sofia" ], "abstract": "Background: As the most abundant coffee by-product, cascara pulp has been considered a good source of antioxidants which could be used to prevent photoaging. The aim of this study was to determine the phytometabolite profiles, antioxidant and photoaging properties of the ethanolic extract of Coffea arabica cascara pulp. Methods: Ethanolic maceration was performed on the fine powder of C. arabica cascara pulp collected from Gayo Highland, Aceh Province, Indonesia. The filtrate obtained was evaluated for its 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, total phenolic content (TPC), and total flavonoid content (TFC). The phytometabolite profiling was conducted qualitatively using reagents and quantitatively using gas chromatography—mass spectroscopy (GC-MS). The potential of the cascara pulp phytometabolites in inhibiting activator protein-1 (AP-1) was evaluated through molecular docking. Results: The extract had TPC and TFC of 2.04 mg gallic acid equivalent/g extract and 91.81 mg quercetin equivalent/g extract, respectively. The half-maximal inhibitory concentration (IC50) for the DPPH inhibition reached as low as 9.59 mg/L. Qualitative phytocompound screening revealed the presence of alkaloids, saponins, tannins, flavonoids, steroids, quinones, polyphenols, and triterpenoids. GC-MS revealed the extract containing 5-hydroxy-methylfurfural (22.31%); 2,5 dimethyl 4 hidroxy 3(2H) furanone (0.74%); and caffeine (21.07%), which could form interaction with AP-1 with binding energies of -172.8, -150.8, and -63.188 kJ/mol, respectively. Conclusion: Ethanolic extract from C. arabica cascara pulp potentially have anti-photoaging properties which is worthy for further investigations in the future.", "keywords": [ "AP-1", "DPPH", "flavonoid", "in-silico", "natural product", "polyphenol" ], "content": "Introduction\n\nAging, a process that manifests in excessive wrinkle, cutis laxa, degraded collagen and hyperpigmentation, occurs naturally. Other than endogenous factors, the process could be accelerated by exogenous factors.1 Exogenous aging is caused by the surrounding environment that could enhance the oxidative stress in skin tissue including but not limited to cigarette smoke, air pollution, and UV exposure.1,2 The chronic exposure of solar radiation could also contribute to the development of skin cancer.3 As an addition, maintaining youthful appearance has been the goal of many individual recently which create multibillion-dollar industry of anti-aging products.4 Therefore, searching for anti-photoaging has been a crucial research topic in the field of dermatology.\n\nNatural products have been studied for their ability in providing photoprotection, hence preventing photoaging.4,5 These natural products usually have high antioxidant activities which could suppress the excessive UV radiation-induced reactive oxygen species (ROS) generation.6 Coffea arabica and its by-products have been reported multiple times containing abundant antioxidants.7,8 Cascara pulp is one of the widely studied coffee by-products which have been utilized in food and beverage products.9–11 Previously, cascara pulp has been extracted using water, methanol, or even supercritical CO2.12,13 However, the use of ethanol solvent that could attract polar compounds and several non-polar compounds is scarcely reported.14 The present study tried to close the gap by determining the phytometabolite profile of the ethanolic extract of C. arabica cascara pulp along with its antioxidant properties. Furthermore, the potential of the cascara pulp extract as photoaging agent has been evaluated in-silico.\n\n\nMethods\n\nMaterials used in this study included methanol, ethanol 96%, ascorbic acid, gallic acid, quercetin, potassium acetate, and sodium carbonate. Reagents for phytochemical screening included AlCl3 powder, Mg powder, Liebermann-Burchard reagent, Folin–Ciocalteu reagent, Mayer reagent, Dragendorf reagent, and Wagner reagent. All materials and reagents were analytical grade and procured from Merck, Selangor, Malaysia. Other reagents were procured from specific companies as described in each section.\n\nThe cascara of C. arabica was collected from Gayo Highland, Aceh Province, Indonesia. Cascara pulp was crushed into small pieces to produce simplicia powder and air-dried. The maceration was performed on the dried simplicia powder using ethanol 96% (Merck, Selangor, Malaysia) with ratio of 1:10 for 7 days. Thereafter, the filtrate was collected and dried in a rotary evaporator (45°C) (N-1300VW, EYELA, Tokyo, Japan).\n\nAntioxidant activity of the cascara pulp extract was evaluated based on 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. DPPH was procured from Merck, Selangor, Malaysia. Briefly, 1 mg extract was dissolved up to 10 mL using ethanol 96% to produce 100 mg/L extract solution, which was further dissolved into 2–10 mg/L. DPPH solution was prepared by adding its powder (7.9 mg) into 50 mL methanol (Merck, Selangor, Malaysia). One mL of DPPH 0.4 mM was added into priorly-dissolved extract, homogenized, and incubated at 37°C for 30 minutes. The absorbance was measured at 517 nm on UV-Vis spectrophotometer (Uvmini-1250, Shimadzu, Kyoto, Japan). Ascorbic acid (Merck, Selangor, Malaysia) was used as the control.\n\nThe cascara pulp extract (0.2 mL) was added into 15.8 mL distilled water which had been pre-added with 1 mL Folin–Ciocalteu reagent (Merck, Selangor, Malaysia). The mixture was shaken rigorously and rested for 8 minutes before added with 15 mL sodium carbonate 10% (Merck, Selangor, Malaysia) and subsequently incubated at room temperature for 2 h. The absorbance was measured at 765 nm using an UV-Vis spectrophotometer (Uvmini-1250, Shimadzu, Kyoto, Japan). The value in concentration was obtained from the calibration curve constructed using gallic acid (gallic acid equivalent (GAE)/g extract) and assigned as total phenolic content (TPC). Gallic acid was purchased from Merck, Selangor, Malaysia.\n\nAs for the total flavonoid content (TFC), its value was derived from absorbance at 450 nm of a mixture consisting of potassium acetate (0.2 mL) (Merck, Selangor, Malaysia), AlCl3 (0.2 mL), and distilled water (5.6 mL) which was incubated for 30 minutes at room temperature (all from Merck, Selangor, Malaysia). TFC was calculated through a calibration curve based on quercetin concentrations (quercetin equivalent (QE)/g extract). Both TPC and TFC measurements followed the procedure reported previously.15\n\nPhytochemical screenings followed the procedure reported previously.16,17 Flavonoids were detected from a reaction between the cascara pulp extract (0.5 in 10 mL methanol) and Mg powder (0.5 mg) in the presence of HCl 0.5 M. As for saponin contents, the extract (0.5) was shaken to form a stable foam after dissolved in 10 mL boiling water. Three reagents, namely Mayer, Dragendorf, and Wagner (all from Merck, Selangor, Malaysia), were used to identify alkaloid contents. Tannins were identified by reacting the extract (0.5 g in 10 mL distilled water) with FeCl3 10%. Quinones was observed through the appearance of red color following the drop-wising of sulfuric acid (1–2 drops) into the extract (0.5 g in 10 mL methanol). As for the steroids and triterpenoids, their presence was indicated by color change following the a few drops addition of reagent Liebermann-Burchard (Merck, Selangor, Malaysia) to the cascara pulp extract (1 g in 10 mL n-hexane).\n\nThe cascara pulp extract was analyzed for its phytometabolites based on gas chromatography–mass spectrometry (GC-MS) (Shimadzu QP2010, Kyoto, Japan). The analysis was carried out with column temperature of 40°C (10°C/minute), flown with He gas. The retention was made 3 minutes (30°C/minute) until the temperature reached 299°C with total running time of 29.63 minutes through splitless injector (280°C; 4.34 psi) with total current of 8.4 mL/m in a 30 m-long Rti-1MS column. Data from mass spectrometer was compared with the database from National Institute of Standards and Technology (NIST).\n\nTo perform the molecular docking, 3D molecular structure was downloaded from PubChem for the following compounds: caffeine (ID: 2519); 5-hydroxymethylfurfural (ID: 237332); and 2,5 dimethyl 4 hidroxy 3(2H) furanone (ID: 538757). As for the protein, activator protein-1 (AP-1; ID: 5vpf), its structure was downloaded from RSCB Protein Data Bank. Preparation on the protein and active sites prediction was carried out on Molegro Virtual Docker 5. The grid box position was X: -16.5A; Y: 55.64A; Z: -32.78A. The ligand-protein interaction and its visualization were performed on PyMol and Discovery Studio v.21.1.1, respectively.\n\n\nResults\n\nAntioxidant properties of C. arabica cascara pulp were investigated based on the TPC, TFC, and DPPH assay. The TPC and TFC values of the cascara pulp extract were presented in Table 1. The calibration curves obtained from the measurement of gallic acid and quercetin had R2 values of 0.9284 and 0.9868, respectively. When the extract was reacted with Folin–Ciocalteu reagent, the UV-Vis absorbance at 765 nm was found to be 0.055 a.u. Meanwhile, the absorbance of 1.545 a.u. was obtained following the reaction between the reaction with AlCl3 and CH3CO2K. The foregoing absorbance gave the TPC and TFC of the cascara pulp extract as much as 2.04 mg GAE/g extract and 91.81 mg QE/g extract, respectively.\n\nDPPH inhibition percentages yielded by the extract with concentrations ranged from 2 to 10 mg/L have been presented (Figure 1). When the extract concentrations were at 2, 4, 6, 8, and 10 mg/L, the DPPH inhibition percentages reached 25, 29.41, 33.82, 42.65, and 54.41%, respectively. Based on these values, the linear equation with a slope and intercept of 3.603 and 15.44, respectively (R2 = 0.933). As for the ascorbic acid (control), at the same concentration range, the DPPH inhibitions were 41.18–60.29%. The IC50 value of the cascara pulp extract in scavenging free radicals DPPH was 9.59 mg/L, which could be considered highly active as an antioxidant. However, the value still fell short by almost 2-fold when compared with the ascorbic acid (5 mg/L).\n\nResults of the qualitative phytometabolites screening of C. arabica cascara pulp have been presented in Table 2. Positive results were indicated by the Dragendorf and Wagner tests, though the phytometabolites were not sensitive to Mayer test. Members of saponin, steroid, quinone, and tannin families were also found positive in the extract. Flavonoids and polyphenols, widely known antioxidant compounds, were shown to be contained in the extract. The presence of triterpenoids was not observable by the qualitative screening.\n\nAfter the initial screening, GC–MS analysis was carried out to identify the phytoconstituents in the extract. The chromatogram depicting peaks from each phytometabolite detected has been presented in Figure 2. Details of the recorded compounds along with the quantitative information (peak area which could be associated to the metabolite contents) have been presented in Table 3. As many as 30 phytocompounds were identified in this present study. Compounds 5-hydroximethylfurfural; caffeine; n-hexadecanoic acid; cis-vaccenic acid; and 2(1H) naphthalenone, 3,5,6,7,8,8a-hexahydro-4, 8a-dimethyl-6-(1-methylethenyl) topped the phytometabolite abundance rank in the extract with peak areas of 22.31, 21.07, 12.85, 11.94, and 5.26%, respectively. However, only 5-hydroxy-methylfurfural; 2,5 dimethyl 4 hidroxy 3(2H) furanone; and caffeine (peak area = 22.31, 0.74, and 21.07%, respectively) were considered most bioactive based on previous research.18–20 The aforementioned phytocompounds were then selected for molecular docking study against AP-1.\n\nThe summaries of molecular docking results were presented in Table 4. Highest binding energy was exhibited by 5-hydroxy-methylfurfural (-172.8 kJ/mol) attributed to six hydrogen bonds and five Van der Waals interactions. The second most potential AP-1 inhibitor was and 2,5 dimethyl 4 hidroxy 3(2H) furanone with a binding energy of -150.8 kJ/mol involving four H bonds and three non-polar interactions. Caffeine appeared to have the lowest affinity with AP-1, where the binding energy only reached -63.188 kJ/mol despite the seven H bond, six alkyl, and four pi-alkyl interactions. All the three compounds formed interactions with AP-1 through ARG176, ARG177, and LYS289. While both 5-hydroxy-methylfurfural and 2,5 dimethyl 4 hidroxy 3(2H) furanone interacted with ARG173, only caffeine that did not. The 3D representations of the foregoing interactions have been presented in Figure 3.\n\n\nDiscussion\n\nIn this present study, the antioxidant activity of C. arabica cascara pulp could be considered high since the IC50 value of DPPH inhibition reached below 100 mg/L.15 The antioxidant properties of the cascara pulp extract are further supported by the TPC and TFC of 2.04 mg GAE/g extract and 91.81 mg QE/g extract, respectively. C. arabica has previously been reported to possess high antioxidant activities. A study in India revealed that 200 mg/L C. arabica seed extract could yield >90% DPPH inhibition.8 The authors attributed the finding with the donation of hydrogen from hydroxyl groups of the bioactive metabolites which could stop the oxidation process by DPPH via stable end products formation.8 Other studies also observed the strong antioxidant activity of C. arabica along with its high TPC.21,22 In our previous systematic review, we found there are at least 13 studies confirming the antioxidant activities of C. arabica by-products.7 IC50 value obtained from the DPPH assays of arabica coffee husk using supercritical fluid extraction was >0.25 mg/L.13 Arabica coffee pulp extracted with distilled water was reported to contained TPC as high as 0.28 mg GAE/g extract.23 Hence, our ethanolic extract from C. arabica cascara pulp had higher DPPH scavenging activity and TPC value than that of previously studied by-products.\n\nUV radiation could induce aging process (photoaging) by promoting reactive oxygen species (ROS) production which could result in excessive oxidative stress and inflammation in skin. Indeed, ROS is naturally produced in mitochondria resulted from the aerobic metabolism, particularly in electron transport chain, which contributes to slow endogenous aging.24 However, there are studies who suggest that ROS production could be enhanced by UV light exposure. Activities of keratinocytes and fibroblasts in producing ROS are positively correlated with the UV radiation intensity.25,26 The increase of ROS release following the solar light exposure could also attributed to the downregulation of ROS neutralizing enzymes viz glutathione reductase and peroxidase.1 In addition, ROS could mediate several signaling pathways to induce skin damage.6,25,27 A terpenoid isolated from an ethyl acetate fraction of coffee silverskin was reported to be capable of inhibiting ROS production and potential as photoaging agent.12 Taken altogether, the cascara pulp obtained herein is potential in preventing photoaging attributed to its high antioxidant activity that could suppress the oxidative stress in skin tissue following solar radiation.\n\nROS induced from the UV exposure could initiate the cascading reaction of mitogen-activated protein kinases (MAPKs), consisting of extracellular C-Jun N-terminal kinase (JNKs), signal-regulated kinase (ERK), and p38MAPK.28 The activation of JNK and p38MAPK pathways promotes activator protein-1 (AP-1) and cyclooxygenase-2 (COX-2).28 This reaction cascade contributes to the enhanced levels of interleukin (IL)-8, IL-10, prostaglandin G2, and vascular endothelial factor which are responsible for inflammatory reaction, differentiation, immunosuppression, proliferation, as well as angiogenesis.1 Moreover, AP-1 is responsible to aging process by both inhibiting collagen synthesis via direct binding with procollagen promoter and degrading collagen via interaction with matrix metalloproteinase 1 (MMP1).29,30 Based on the foregoing explanations, researchers have used AP-1 as the target for anti-photoaging agents.31–33 Hence, we had performed molecular docking studies to observe the potential of the phytometabolites from the cascara pulp extract to interact with AP-1.\n\nIn this present study, two predominant compounds (5-hydroxy-methylfurfural and caffeine) and one minor compound (2,5 dimethyl 4 hidroxy 3(2H) furanone) were shown to have strong affinity with AP-1 through molecular docking studies. From the highest to the lowest, the phytometabolites could be ranked as follows: 5-hydroxy-methylfurfural > 2,5 dimethyl 4 hidroxy 3(2H) furanone > caffeine. Both 5-hydroxy-methylfurfural and 2,5 dimethyl 4 hidroxy 3(2H) furanone are common food additives, while caffeine is a common compound in coffee products. Similarly, a study found that caffeine was among the isolates obtained from antioxidant assay-guided procedure on Robusta coffee seeds, yet its bioactivity is relatively minimum.34 In our previous in-silico screening using gallic acid, malonic acid, gallic acid, and decanoic acid from water:ethanol combination extract of C. arabia cascara pulp, ARG173, ARG176, ARG177, and LYS289 were also found as common binding sites.35 The highest binding energy found in that previous study was -242.24 kJ/mol.35 Though the highest binding energy in this present study is -172.8 kJ/mol, obtained from 5-hydroxy-methylfurfural, the value is relatively high and could be considered as an effective binding.36,37 Moreover, the antioxidant properties of the cascara pulp herein could contribute to other preventive mechanisms of photoaging. Nonetheless, it is worth noting that in-silico study alone is not sufficient to conclude the AP-1 inhibition by the cascara pulp extract, where in vitro study is a must.14\n\n\nConclusions\n\nThe ethanolic extract from the cascara pulp of C. arabica is highly active as an antioxidant agent. Phytocompound profiling evidences the antioxidant metabolite richness of the cascara pulp extract which could act as anti-photoaging agent. In-silico studies reveal the potential of strong interaction between the bioactive phytometabolites with AP-1. Further research with in vitro or in vivo design is warranted to confirm the anti-photoaging activities of the phytometabolites contained in the C. arabica cascara.", "appendix": "Data availability\n\nPubChem: Molecular structure for caffeine. 2519, https://identifiers.org/pubchem.compound:2519. 38\n\nPubChem: Molecular structure for 5-hydroxymethylfurfural. 237332, https://identifiers.org/pubchem.compound:237332. 39\n\nPubChem: Molecular structure for 2,5 dimethyl 4 hidroxy 3(2H) furanone. 538757, https://identifiers.org/pubchem.compound:538757. 40\n\nPubChem: Molecular structure for activator protein-1. https://doi.org/10.2210/pdb5VPF/pdb. 41\n\nFigshare: ‘Antioxidant and phytometabolite profiles of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland: A study for potential photoaging agent’, https://doi.org/10.6084/m9.figshare.21219323. 42\n\nThis project contains the following underlying data:\n\n• DPPH Inhibition Assay.docx\n\n• Determination of Total Phenolic Content.docx\n\n• Determination of Total Flavonoid Content.docx\n\n• Calibration Curve_Total flavonoid.png\n\n• Calibration Curve_Total Phenolic.png\n\n• DPPH inhibition by cascaara pulp extract and cascorbid acid (control).jpg\n\n• Figure 2. Chromatogram of cascara pulp extract.jpg\n\n• 3D (left and middle) and 2D (right) conformations of the interactions between the phytometabolites and AP-1.jpg\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 Badan Pengembangan Sumber Daya Manusia (BPSDM) Aceh, Indonesia.\n\n\nReferences\n\nChen X, Yang C, Jiang G: Research progress on skin photoaging and oxidative stress. Postepy Dermatol. Alergol. 2021; 38(6): 931–936. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKrutmann J, Bouloc A, Sore G, et al.: The skin aging exposome. J. Dermatol. Sci. 2017; 85(3): 152–161. Publisher Full Text\n\nKrutmann J, Schalka S, Watson REB, et al.: Daily photoprotection to prevent photoaging. Photodermatol. Photoimmunol. Photomed. 2021; 37(6): 482–489. 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Venereol. 2020; 3(1).\n\nRyu JY, Na EJ: MMP expression alteration and MMP-1 production control by syringic acid via AP-1 mechanism. Biomedical. Dermatology. 2018 2018/05/15; 2(1): 15.\n\nKwon K-R, Alam MB, Park J-H, et al.: Attenuation of UVB-Induced Photo-Aging by Polyphenolic-Rich Spatholobus Suberectus Stem Extract Via Modulation of MAPK/AP-1/MMPs Signaling in Human Keratinocytes. Nutrients. 2019; 11(6): 1341. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTomé M, Sepúlveda JC, Delgado M, et al.: miR-335 Correlates with Senescence/Aging in Human Mesenchymal Stem Cells and Inhibits Their Therapeutic Actions Through Inhibition of AP-1 Activity. Stem Cells. 2014; 32(8): 2229–2244. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang L, Lee W, Cui YR, et al.: Protective effect of green tea catechin against urban fine dust particle-induced skin aging by regulation of NF-κB, AP-1, and MAPKs signaling pathways. Environ. Pollut. 2019; 252: 1318–1324. PubMed Abstract \| Publisher Full Text\n\nHerawati D, Giriwono PE, Dewi FNA, et al.: Three major compounds showing significant antioxidative, α-glucosidase inhibition, and antiglycation activities in Robusta coffee brew. Int. J. Food Prop. 2019; 22(1): 994–1010. Publisher Full Text\n\nLestari W, Hasballah K, Listiawan MY, et al.: GC-MS Profiling and Anti-aging Activities of Cascara from Gayo Arabica Coffee. Med. Arch. 2022; 76(3): 206–210.\n\nPurnama A, Mardina V, Puspita K, et al.: Molecular docking of two cytotoxic compounds from Calotropis gigantea leaves against therapeutic molecular target of pancreatic cancer. Narra. J. 2021; 1(2): e37. Publisher Full Text\n\nPurnama A, Rizki D, Qanita I, et al.: Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer. J. Adv. Pharm. Technol. Res. 2022; 13(1): 44–49. PubMed Abstract \| Publisher Full Text\n\nNational Center for Biotechnology Information:PubChem Compound Summary for CID 2519, Caffeine. [Data].2022. Reference Source\n\nNational Center for Biotechnology Information:PubChem Compound Summary for CID 237332, 5-Hydroxymethylfurfural. [Data].2022. Reference Source\n\nNational Center for Biotechnology Information:PubChem Compound Summary for CID 538757, 2,4-Dihydroxy-2,5-dimethyl-3(2H)-furanone. [Data].2022. Reference Source\n\nYin Z, Rudenko G, Machius M:Transcription factor FosB/JunD bZIP domain in complex with cognate DNA, type-II crystal, Protein Data Bank. [Data].2019. Publisher Full Text\n\nHasballah K:Antioxidant and phytometabolite profiles of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland: A study for potential photoaging agent. figshare. [Dataset]. Journal Contribution. 2022. Publisher Full Text" }	[ { "id": "165756", "date": "23 Mar 2023", "name": "Emil Salim", "expertise": [ "Reviewer Expertise Pharmacology and Immunology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors studied the antioxidant properties of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland. Using the DPPH method, they found that the extract has strong antioxidant activity. Moreover, they studied the phytochemical constituent of the extract using phytochemical screening methods using reagents and found that the extract contained saponin, steroid, quinone, tannin, flavonoids and polyphenols. Using GCMC, they found some bioactive compounds exist in the extract, such as 5-hydroxy-methylfurfural, 2,5 dimethyl 4 hydroxy 3(2H) furanone and Caffeine. By performing in silico study, they showed that these compounds have interaction with AP-1, a target for anti-photoaging agents.\nThe study's background, methods, results, discussion, and conclusion have been presented clearly. However, in the title, I would like to suggest that it should be \"anti-photoaging agent\" rather than \"photoaging agent\".\nI spotted a tiny error in the sentence: The second most potential AP-1 inhibitor was and 2,5 dimethyl 4 hidroxy 3(2H) furanone with a binding energy of -150.8 kJ/mol involving four H bonds and three non-polar interactions. I think the word \"and\" should be deleted. Also in some sentences, \"hidroxy\" should be written as \"hydroxy\".\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9761", "date": "13 Jun 2023", "name": "Kartini Hasballah", "role": "Author Response", "response": "We thank and appreciate the reviewer comment regarding our manuscript and we are humbled that our efforts have been well conveyed. We thank and appreciate the reviewer comment about our intention regarding the sources of our manuscript. We’d like to agree about the introduction part and would like to add more sources as soon as possible. Again, we’d like to thank the reviewer regarding her veracity as well as her precision. We apologize about our lack of source, we’d like to correct it soon enough. We’d like to thank the reviewer about the comment regarding our result and we’re content that our purpose have been well received. We’d also appreciate the advice regarding the phenolic and flavonoid matter. About the formula, yes, we’re completely agree that we should write it according to the IUPAC requirement. We’d like to correct it later. We thank and appreciate the reviewer comment regarding the discussion and conclusion section. We really do appreciate the reviewer for taking the time and for giving us her insights in order to make our manuscript better." }, { "c_id": "9865", "date": "18 Sep 2023", "name": "Kartini Hasballah", "role": "Author Response", "response": "Dear Reviewer, We would like thank you for your suggestions and corrections. We have revised our title from \"photoaging agent\" to \"anti-photoaging agent\". We also have replaced all \"hidroxy\" to \"hydroxy\" in the entire article. Authors" } ] }, { "id": "171576", "date": "09 May 2023", "name": "Maria Atanassova", "expertise": [ "Reviewer Expertise My research area is Total Phenols and Total Flavonoids", "Bioactive Compounds and Antioxidant Activity of Extracts from Different Natural Plants" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 \"Antioxidant and phytometabolite profiles of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland: A study for potential photoaging agent\" with authors Wahyu Lest, Kartini Hasballah, M. Yulianto Listiawan, Sofia Sofia is interesting and original. I think it would be of interest not only to readers of F1000Research but also to other researchers. I think that the task that the authors have set themselves is very serious.\nIn the Introduction part, the authors have cited 10 sources from the last 3-5 years, out of a total of 14. This shows that the authors have worked very seriously on their goal to prove the seriousness of the research they have done. I would like to say that I think the Introduction is too short and I ask the authors to add more sources.\nAs for the Methods and Materials section, the methods are generally known, well described, and could be replicated by any researcher. It struck me that two of the methods have no sources noted. I ask the authors to cite where they got the methods because according to the journal's requirements, this omission amounts to plagiarism. These are the methods: DPPH inhibition assay; Determination of total phenolic (TPC). The authors may have modified them in their use but they should also note this.\nResults are presented accurately and clearly. They are supported by relevant tables and figures. Accordingly, the results obtained by the authors enable any reader of this manuscript to get a clear idea. In my opinion, the authors should note Total Phenolics and Total Flavonoids in the table. The phenols and flavonoids for which the authors present the results are not one specific compound and for that they use the corresponding equivalent. For example, if the authors had used another equivalent such as catechin or rutin to prove the flavonoids, I think they would have obtained different results. Another thing that I would like the authors to pay attention to is the formula of potassium acetate CH3CO2K, in my opinion, it should be written according to IUPAC CH3COOK. I also ask the authors to write the formulas of the compounds in the text according to the IUPAC requirements, for example: 2,5-Dimethyl-4-hydroxy-3(2H)-furanone.\nIn the Discussion section, I think the authors presented their results accurately and clearly and supported them with relevant citations. In my opinion, the conclusion supports the results obtained by the authors.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9760", "date": "13 Jun 2023", "name": "Kartini Hasballah", "role": "Author Response", "response": "We thank and appreciate the reviewer comment regarding our manuscript and we are humbled that our efforts have been well conveyed. We thank and appreciate the reviewer comment about our intention regarding the sources of our manuscript. We’d like to agree about the introduction part and would like to add more sources as soon as possible. Again, we’d like to thank the reviewer regarding her veracity as well as her precision. We apologize about our lack of source, we’d like to correct it soon enough. We’d like to thank the reviewer about the comment regarding our result and we’re content that our purpose have been well received. We’d also appreciate the advice regarding the phenolic and flavonoid matter. About the formula, yes, we’re completely agree that we should write it according to the IUPAC requirement. We’d like to correct it later. We thank and appreciate the reviewer comment regarding the discussion and conclusion section. We really do appreciate the reviewer for taking the time and for giving us her insights in order to make our manuscript better." }, { "c_id": "9869", "date": "18 Sep 2023", "name": "Kartini Hasballah", "role": "Author Response", "response": "Dear Reviewer, Thank you for reviewing our article and proving the comments and suggestions. Based on your comments and suggestions we have revised our article: We have added more information about photoaging in Introduction section with nine additional references. We have added the references for both methods of DPPH inhibition assay and total phenolic (TPC). The total of the total phenolics and total flavonoids have been provided in the Table 1. We have revised all the names of the compounds according to IUPAC. We would like to thank you for pick some of them. Best regards, Authors" } ] } ]	1	https://f1000research.com/articles/12-12
https://f1000research.com/articles/12-1167/v1	18 Sep 23	{ "type": "Research Article", "title": "Immunoinformatics design of B-cell multi-epitope peptide for the diagnosis of Methicillin Resistant Staphylococcus aureus (MRSA) infection", "authors": [ "Simeon Kayowa Olatunde", "Joshua Babatunde Owolabi", "Bolaji Oluwabusayo Ayinde", "Shauna Angella Ebanks", "Edla Sophia Vidale", "Elijah Kolawole Oladipo", "Yakubu Adekunle Alli", "Enoch Oluwalonimi Adewara", "Joshua Babatunde Owolabi", "Bolaji Oluwabusayo Ayinde", "Shauna Angella Ebanks", "Edla Sophia Vidale", "Elijah Kolawole Oladipo", "Yakubu Adekunle Alli", "Enoch Oluwalonimi Adewara" ], "abstract": "Background: Methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA) remains a significant clinical and epidemiological pathogen in hospital settings and in the community world-wide. The resistance to methicillin in Staphylococcus aureus is mediated by the mecA gene, which encodes penicillin-binding protein 2a (PBP2A). Rapid patient screening for MRSA is essential for infection control procedures in order to possibly enhance the outcomes of infected patients. In this study, we utilized PBP2A to predict and create a novel synthetic protein with multiple immunodominant B cell epitopes for rapid diagnosis of MRSA using an in-silico approach. Methods: Seven putative PBP2A peptides were used to analyze the protein’s primary, secondary, and tertiary structures (BepiPred). The B cell construct was then evaluated using I-TASSER server, and physicochemical properties, and homology modeling of the 3 D structure of the protein were obtained. Results: In silico analyses revealed regions with high immunogenicity. Altogether, 19 consented epitopes were selected for the in-silico succession; three consented epitopes from ALJ10988.1, three from ORN56903.1, three from AFJ06714.1, one from AEO00772.1, three from WP_000721309.1, three from WP_057521704.1, and three from WP_063851348.1. The constructs have an average length of 503 amino acids, molecular weight of 55,151.78, instability index of 41.44, theoretical PI of 9.28 and a C score −1.50. In addition, the parameters that were examined indicated the newly multi-epitope construct could potentially serve as a theoretical framework for the development of a MRSA diagnostic kit. Conclusions: Overall, we have developed an antigen-based multi-epitope peptide for the rapid and accurate diagnosis of MRSA infection through an in-silico approach, acceptable in terms of antigenicity, physicochemical properties, structural stability and strong immunogenicity.", "keywords": [ "Methicillin Resistant Staphylococcus aureus (MRSA)", "Penicillin binding protein 2A (PBP2A)", "Diagnostic kit", "Antigen", "Multi-epitope" ], "content": "Introduction\n\nMethicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection (BSI) remains a major cause of concern in health systems all over the world, because of the high incidence rates, which correlate positively with significant upward trends in patient age and comorbidities, longer length of stay, access to health care, both non-intravascular and vascular catheter sources, and the associated high morbidity and mortality rates in infected patients (Gasch et al., 2011, 2013). MRSA BSI also occurs in the community, more commonly in patients with a previous MRSA colonization, injection drug use, or who are admitted from a skilled nursing facility, who have had surgery in the previous year, or are on dialysis during hospitalization, or have bone/joint as a common source of CA-BSI (McLaughlin and Smith, 2019; Gouin, 2019).\n\nFurthermore, the hematogenous spread of MRSA in 10-20% of BSI patients is of major concern, causing secondary complications such as abscesses, vertebral osteomyelitis, endocarditis and implant associated infections of prosthetic joints, electronic cardiac devices, and so on, which can occur weeks or months after the primary infection (Tande et al., 2016).\n\nMethicillin resistance in Staphylococcus aureus is mediated by PBP-2a, a penicillin-binding protein produced by the mecA gene that enables the organism to proliferate and replicate when beta-lactam drugs like methicillin are present. The mecA gene is located on a mobile genetic element called staphylococcal chromosome cassette (SCCmec) (Archer et al., 1994). Though there are antibiotics of choice for treating bloodstream infections due to MRSA; vancomycin and daptomycin (Liu et al., 2011), treatment failure has been associated with lower (<15 mg/l) trough levels of vancomycin (Forstner et al., 2013), reduced vancomycin susceptibility (Howden et al., 2004) and growing incidence of “hetero-resistant” vancomycin intermediate susceptible S. aureus (hVISA) strains (Hiramatsu et al., 1997). Thus, the occurrence of MRSA isolates with decreased susceptibility to vancomycin has grown over the past few years, most likely also as a result of patients with MRSA infections using vancomycin more frequently (Hiramatsu, 2001).\n\nExcept for patients with pneumonia, daptomycin is still a viable therapy choice for these MRSA BSI isolates (Moise et al., 2009). As a result, insufficient source control, an uncertain primary focus of infection, or insufficient antibiotic therapy are additional risk factors for BSI consequences (Seifert et al., 2008).\n\nThe impact of MRSA infection prevention on patient outcomes and length of hospital stays has been significantly reduced by adopting tactics including monitoring for MRSA carriers upon arrival, followed by isolation and/or decolonization, and hand hygiene (Kavanagh, 2019).\n\nHowever, up to the present moment, MRSA vaccination attempts have proved unsatisfactory. Phase IIb/III trials have been advanced for three candidates. Bivalent conjugate vaccine StaphVAX, which targets capsular polysaccharide types 5 and 8, failed to produce long-lasting protection (Shinefield et al., 2002). The experiment was prematurely terminated because V710, a monovalent vaccination that targets the iron salvage protein IsdB, was actually linked to higher mortality (Giersing et al., 2016). Most recently, Pfizer reported that the phase IIb trial of their multi-antigen vaccine (PF-06290510) has been suspended due to futility in December 2018 (Pfizer, 2019).\n\nPatients with MRSA infection may require a longer and more expensive course of therapy and recuperation, if their infection is not adequately identified in the early stages of illness progression (Cosgrove, 2006). Any infection control monitoring approach that aims to reduce the exposure of healthcare personnel, other members of the community, or other patients to this disease must include an accurate and prompt diagnosis of the MRSA status. The conventional microbiological culture techniques including the detection of resistance to methicillin among staphylococcal isolates, based on phenotypic assays such as a disk diffusion test, minimum inhibitory concentration determination or broth microdilution testing are assumed to be 100% reliable but require quite some time (up to 5 days for set up, data collection and analysis (Palavecino, 2020). Similarly, there are commercially available chromogenic agars that can be used for MRSA identification with read out in between 24 and 48 hours (Lee et al., 2013). The real-time PCR assay is regarded as the global gold standard for diagnosing MRSA, increasingly the tool of choice to help clinicians understand MRSA and S. aureus infections and to guide patient care; generally faster than the traditional culture methods (by saving 48-72 hours). However, while most real-time PCR methods offer similar sensitivity, they present with different specificity leading to reports of unacceptably high number of MRSA false negative results—ranging from 6% to 30%—and false positive rates as high as 20% (Jeyaratnam et al., 2008; Rossney et al., 2008).\n\nIt is basically understood that MRSA and S. aureus misdiagnoses can result in poor patient management and care delivery as well as serious primary and secondary consequences, including fatalities (Nathwani et al., 2008; Diekema and Saubolle, 2011; Olatunde et al., 2022; Owolabi and Olatunde, 2022; Olatunde and Owolabi, 2022). Therefore, the severity of the damage these strains can bring to infected patients and the potential for community dissemination, infections caused by multidrug-resistant bacteria like MRSA necessitate rapid and accurate diagnosis and elimination at an early stage (Rahman et al., 2018). Immunopeptidomics is a field of study that examines the collections of all peptides connected to human leukocyte antigen (HLA) molecules, and it is frequently fueled by mass spectrometry (MS) technologies. In recent years, several in-silico approaches have been used to predict and design multi-epitope peptides capable of bounding to major histocompatibility complexes (MHC) (Paul et al., 2021; Moradi et al., 2022; Oladipo et al., 2022; Khan et al., 2022; Ghulam et al., 2022; Islam et al., 2022). This study sought to develop a B-cell multi-epitope peptide for the diagnosis of MRSA infection from the blood of individuals with MRSA blood stream infection using an immunoinformatics approach, which may aid in immune response and improve serodiagnosis accuracy while speeding up diagnosis, particularly for those residing in developing and endemic areas. The data and findings from this study could be used as starting points for the designing of improved infection diagnostic methods.\n\n\nMethods\n\nFigure 1 shows the process flow for the steps performed throughout this investigation.\n\nThis figure is an original figure produced by the authors for this article.\n\nWe identified some highly conserved and experimentally verified potential antigenic penicillin-binding protein 2A (PBP2A) from the genomes of Methicillin Resistant Staphylococcus aureus (MRSA), consisting of ALJ10988.1, ORN56903.1, AFJ06714.1, AEO00772.1, WP_000721309.1, WP_057521704.1, and WP_063851348.1. The National Center for Biotechnology Information (NCBI, Retrieved February 23, 2023) was utilized to retrieve the protein sequences. After running a query with their accession numbers, the protein sequences were obtained as a FASTA format.\n\nUsing the Vaxijen V2.0 server program (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html) (Doytchinova and Flower, 2007b), the antigenicity of the retrieved protein sequences was evaluated at a threshold value of 0.5. The Vaxijen investigates the antigenic protein’s capacity to bind to or interact with B-cell receptors.\n\nTMHMM Server 5.0 (https://services.healthtech.dtu.dk/services/TMHMM-2.0/) was used to predict the transmembrane structure of proteins. In order to evaluate if the proteins are constituted within the membrane or not, the protein sequences were uploaded into the server window and three regions (S), comprising the inner and outside transmembrane were examined (Möller et al., 2001; Khazaei and Moghadamizad, 2022; Shams et al., 2021). Additionally, SignalP Server (https://services.healthtech.dtu.dk/services/SignalP-5.0/) investigated the signal peptide prediction of the membrane proteins to ascertain whether the proteins found within the membrane were plasma membrane or subcellular (Almagro et al., 2019).\n\nSetting all our parameters to default, we utilized the BCpred epitope prediction server (http://ailab-projects1.ist.psu.edu:8080/bcpred/) by characterizing the physio-chemical features to examine the linear and continuous B-cell epitopes in the antigenic sequences (EL-Manzalawy et al., 2008). This was further validated with another B-cell epitope prediction tool called BepiPred (http://www.cbs.dtu.dk/services/Bepipred/) which was utilized to examine the epitope most likely to stimulate antigen-antibody interactions (Jespersen et al., 2017). However, from the results of the BepiPred tool, the epitope of interest was determined to be the peptides with the greatest percentile rank of 75% specificity, and those with high intensity gradients were selected.\n\nThe construction of a multi-epitope antigenic structure and the improvement of its sensitivity were both examined utilizing various online biological computing tools. Additionally, predicted were the primary, secondary, and tertiary protein structures. Prior to the construction of 3-dimension multiepitope design, an epitope with the higher B-cell prediction score was linked by an appropriate connector (GGSSGG) as shown in Figure 3A, and submitted to the I-TASSER server (https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S566518/) (Roy et al., 2010). These strategies involving connection of epitopes with flexible linker sequences (Gly-Gly-Ser-Ser-Gly-Gly) can be used to create a more effective diagnostic kit (Zhang, 2008).\n\nThe backtranseq EMBOSS 6.0.1 program was used to translate the constructed B-cell epitopes into a sequence of nucleotides, from which the GC content ratio was determined. (https://www.ebi.ac.uk/Tools/st/embossbacktranseq/). Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons (Oladipo et al., 2022).\n\nCodon optimization tools are online bioinformatics resources that determine the gene expression level of the multiple-epitopes in the vectors and consequently, they enhance the optimal expression of a foreign gene (multiepitope) (Olatunde et al., 2022; Ebrahimi et al., 2020). Because of the shape of the hairpin structure, higher quantities of GC sequences in messenger RNA (mRNA) can inhibit protein translation, boosting the stability of mRNA and considerably raising immunological responses to the designed diagnostic kit (Grote et al., 2005). A codon-adaptation tool-server (http://www.jcat.de/start.jsp) (Geourjon and Deleage, 1995) has been used to optimize constructs with GC content values between 30% and 70%. The back translation was likewise effective due to the insertion of the initiation codon AUG and the termination codon UAA (Oladipo et al., 2022).\n\nThe primary sequence was subjected to I-TASSER to build the tertiary structure of the multi-epitope peptide (Roy et al., 2010). In order to evaluate the secondary structure of the multi-epitope, a self-optimized prediction method using the SOPMA server (https://npsa-prabi.ibcp.fr/cgi-bin/secpred sopma.pl) was employed (Geourjon and Deleage, 1995). This approach analyzes the number of turns, loops, sheets, and helix in the protein’s secondary structure. The tertiary structure of the construct was predicted by the I-TASSER server online prediction tool (http://zhanglab.ccmb.med.umich.edu/I-TASSER) (Roy et al., 2010). I-TASSER is one of the most used tools for predicting protein structure (Iterative Threading Assembly Refinement). This server is an integrated platform that uses cutting-edge algorithms to deliver the most precise structure and function forecasts imaginable (Ebrahimi et al., 2020). The I-TASSER server also functions as an integrated platform for automated protein structure and function prediction, based on the sequence-to-structure-to-function paradigm (Roy et al., 2010).\n\nThe ProSA-web server (https://prosa.services.came.sbg.ac.at/prosa.php) was used to confirm and improve the predicted structures by calculating the Z-score thus, helping to identify any errors (Wiederstein and Sippl, 2007) in the predicted structure. Assessing a protein’s 3-dimensional structure is necessary for understanding its functions and property modification (Wiederstein and Sippl, 2007). Finally, the B-cell construct was studied using the Ramachandran plot server (https://zlab.umassmed.edu/bu/rama/). The main-chain conformational propensity of an amino acid is depicted graphically by a Ramachandran plot (Anderson et al., 2005).\n\n\nResults\n\nAll of the protein sequences from the NCBI’s Protein Database were retrieved for penicillin-binding protein 2a (PBP2A). Each protein sequence was identified and recovered in FASTA format with its corresponding accession number (shown in Table 1).\n\nAntigenic result of the retrieved penicillin-binding protein 2a\n\nAll the protein sequences exhibited a potent antigenic score at ≥0.5. These properties confirmed the suitability of the protein sequences in designing the intended diagnostic kit (Doytchinova and Flower, 2007a). The antigenicity scores are presented in Table 1.\n\nThe TMHMM server was used to screen all the protein sequences retrieved from NCBI at a scale of >0.4 and then subjected to signal peptide prediction using the SignalP server (Table 2) (Möller et al., 2001; Khazaei and Moghadamizad, 2022; Shams et al., 2021). Observation shows that all the sequences possessed three different dimensions, which implies all the proteins selected have inside, outside, and transmembrane helix positions (Table 2). Table 3 displays the outcome of the signal peptide prediction for the protein.\n\nUtilizing different appropriate parameters and bioinformatics software, the predicted linear B-cells of the seven proteins are presented in Figure 2 (EL-Manzalawy et al., 2008). Altogether, 19 consented epitopes were selected for the in-silico succession; three consented epitopes from ALJ10988.1, three from ORN56903.1, three from AFJ06714.1, one from AEO00772.1, three from WP_000721309.1, three from WP_057521704.1, and three from WP_063851348.1.\n\nDesign and modelling of the multi-epitope construct\n\nTable 4 displays a combination of consented results for the prediction of antigenic epitopes using various parameters and bioinformatics software. Each epitope was connected via a flexible linker sequence (Gly-Gly-Ser-Ser-Gly-Gly) (Ghulam et al., 2022).\n\nReverse translation and codon optimization\n\nThe multi-epitope protein sequences were translated into nucleotide sequences using the backtranseq algorithm. There was an optimization in the numbers of the C-G sequence. Considering the pre-optimization values of codon adaptation index (CAI) (0.92) and C-G percentage (66), there was an optimization in the numbers of the CAI and the C-G sequence following the post optimization values of 0.96 and 68% respectively. We explored the process of codon optimization in other to boost the expression of the MRSA diagnostic candidate. The results of this research are consistent with the claims that enhanced expression requires a C-G concentration of 30% to 70% and that CAI values of more than 0.8 are considered to be excellent for target organism expression (Sanami et al., 2021). The immunological response to a diagnostic kit is therefore a necessary factor that can considerably improve and increase the stability of mRNA (Ebrahimi et al., 2020).\n\nThe results from the B cell primary construct with ExPASy server, containing an average buildup length of 503 amino acids, are summarized in the Table 5. To evaluate the solubility in an electric field, the theoretical PIs for the B cell construct were calculated to be 9.28. This structure is stable at a wide range of temperatures because of its 62.72 aliphatic index. The index of instability (41.44) additionally provides an estimate of protein stability in vitro, and the results demonstrate that the structures are averagely stable. Finally, the structure’s GRAVY (Grand Average of Hydropathicity) value was negative (-0.938).\n\nThe SOPMA server results are shown in Figure 3A and B. According to the findings, secondary structures that make up Alpha helixes, Beta turns, Random coil, and Extended strands are, respectively, 24.06%, 13.52%, 42.15%, and 20.28%. The prevalence of random coils and extension strands in the structure of B cells demonstrate how proteins might create antigenic epitopes.\n\nThe B-cell epitopes tertiary structure construct was predicted with the I-TASSER servers and are shown in Figure 4. For each of the targets, I-TASSER simulations provide a vast ensemble of structural conformations, known as decoys. I-TASSER uses the SPICKER program to cluster all the decoys based on pair-wise structural similarity, and then reports up to five models that correspond to the five biggest structure clusters in order to choose the final models (Kimmig et al., 2021). The relevance of threading template alignments and the convergence parameters of the structure assembly simulations are used to calculate the C-score, which provides a quantitative assessment of each model’s confidence. The values of the C-scores for models 1 through 5 are -1.50, -1.70, -1.66, -1.55, and -3.05 respectively. Model 1 with a C-score value of -1.50 was chosen because the C-score of a model typically ranges from -5 to 2, and a higher C-score number indicates that the model has a high level of confidence (Sanami et al., 2021).\n\nA (Model 1): C-score = -1.50, B (Model 2): C-score = -1.70, C (Model 3): C-score = -1.66, D (Model 4): C-score = -1.55, E (Model 5): = -3.05.\n\nThe RAMACHANDRAN PLOT server assessed the modeled structure and produced a Ramachandran plot (Figure 5). According to the results, 83.215% of the residues was discovered in the highly preferred observation, 11.584% in the preferred observation, and 5.201% in the questionable observation. Additionally, the ProSA-web server predicted both the overall model quality (Figure 6A) and local model quality (Figure 6B) with a Z-Score of -0.43 for the 3D structure of B-cell construct. These results demonstrate the 3D model of the structure’s outstanding dependability.\n\n\nDiscussion\n\nMethicillin-resistant Staphylococcus aureus (MRSA) is a significant global source of bacteremia in BSI. These infections are associated with morbidity and excessive mortality. The development of recommendations for the clinical diagnosis of MRSA carriage and infection is fraught with controversies (Kimmig et al., 2021; Hajissa et al., 2015). Among these are the best test methodologies, whether screening should be general or targeted, and the financial repercussions of choosing one strategy over another. It is obvious that there are significant differences in MRSA incidence and health-economic cost not only between different nations, but also between various institutions within a same country and between various patient populations. These variations will have an impact on the selection of the best screening techniques to use at both the national and local levels. What is best for patient safety, however, might not necessarily be practical financially (CDC, 2019).\n\nRecent advancements in molecular and nonmolecular testing technologies have significantly reduced the amount of time necessary to detect MRSA. The traditional MRSA culturing and susceptibility testing takes 48 to 72 hours, including 16 to 24 hours incubation period and another 16 to 24 hours to perform the susceptibility assays. The use of chromogenic agar, which causes a color reaction in bacterial cultures, is an adaptation to the traditional culturing technique, antibiotics are also present in these medium, allowing only resistant bacteria to proliferate (CDC, 2019).\n\nThe mecA gene, which is unique to MRSA, remains a major target of amplification during PCR methods (Milheiriço et al., 2007). These tests can be directly performed on blood, nasal, or wound swab samples and typically yield results within 1 to 3 hours (CDC, 2019; Milheiriço et al., 2007). However, due to the necessity of sample transport, testing, and result communication in clinical settings, the entire time from sample collection to receiving results is frequently longer. Another method for MRSA detection is immunochromatographic assays, which utilize antibodies that react with specific bacterial proteins. If the targeted protein is present in the sample, a visible reaction occurs in the test medium. This method was described by Shin et al. (2010).\n\nAntigen-based immunoassays are increasingly necessary at the point of care for infection detection. In-silico analysis approaches are required to evaluate the structure and functional properties of proteins. These methods could help identify antigenic regions for the development of a multi-epitope diagnostic test kit. Similarly, because of advances in bioinformatics research, epitope prediction has increased considerably in recent years (Sanches et al., 2021; Combet et al., 2000).\n\nA diagnostic kit can be used to detect MRSA specific antibodies in serum samples (Oladipo et al., 2022; Metzger and Mordmüller, 2014). Multi-epitope peptides may be used to improve diagnostic kit accuracy, and antigen-based immunoassays are required for rapid point-of-care detection of MRSA. However, limited biomarker-based diagnostic techniques for MRSA have made it to the point-of-care (Akue et al., 2018; Metzger and Mordmüller, 2014). Consequently, this study sought to develop a diagnostic multi-epitope construct that is as accurate, specific, and efficient as possible. Using a range of immunoinformatics tools, we identified seven unique proteins with potential value as biomarkers of MRSA infection. The antigenicity of the retrieved proteins was evaluated at a threshold of 0.5, suggesting that proteins with this threshold (antigenicity score) or higher are more likely to respond to the presence of their specific antibody, as previously described by Doytchinova and Flower (2007a).\n\nThe newly designated proteins were then examined using the Transmembrane Helices Hidden Markov Model (TMHMM) server (Möller et al., 2001) to determine whether they were membrane proteins or intracellular proteins, this unique trait remains an important factor to consider when designing an antibody-based diagnostic kits. The prediction of transmembrane (TM) helices plays a crucial role when studying membrane proteins, because of the relatively small number (∼0.5% of the PDB) of high-resolution structures for such proteins (Sanches et al., 2021). Furthermore, these proteins were subjected to SIGNALP server to predict the presence and location peptide cleavage sites in the amino acid sequence. Therefore, knowing a protein’s particular signal peptide can help determine where it is most likely to be found. These analyses confirmed that the protein sequences chosen are present within plasma membrane, therefore, BcPred tools were used to identify specific epitopes within each protein sequence at a threshold of 0.5 with a specificity of 75%. According to Kringelum et al. (2012), these two tools were utilized to boost the likelihood of selecting the appropriate epitopes that can induce an immune response.\n\nB-cell epitopes are classified into two categories; linear and conformational. Linear epitopes are continuous amino acid segments in the protein sequence while conformational epitopes are made up of amino acid residues that are physically aligned while being separated in the protein main sequence (Sanchez-Trincado et al., 2017; El-Manzalawy et al., 2017). According to our results in Figure 2, the BepiPred server predicted several linear B-cell epitopes. B-cells are responsible for the conservation of antibody while stimulating a swift response to subsequent antigen exposure (Olatunde et al., 2022; Schneider, 2017). B-cells recognize solvent-exposed antigens through B-cell receptors (BCR) called membrane-bound immunoglobulins (Olatunde et al., 2022; Schneider, 2017). Therefore, to improve the specificity and sensitivity of diagnosing MRSA infected patients, the indicated epitopes were all linked together by a flexible appropriate linker (GGSSGG) at the end of each epitope (Oladipo et al., 2022).\n\nFurther investigation of the multi-epitope construct’s primary and secondary structures revealed both the physicochemical and structural features. It was noted that the molecular weight of the designed kit is significantly greater than 32kD which is an average molecular weight for a multi-subunit diagnostic kit, thus, favoring the antigenicity of the constructs (Onile et al., 2020). The theoretical pI of 9.28 indicates that the construct is slightly basic; the pH level at which a molecule carries no electrical charge is known as the isoelectric point (pI). The idea is crucial for zwitterionic compounds like proteins, peptides, and amino acids. According to Schneider (2017), the physiological pH of human body ranges between 7.35 to 7.45, therapeutic antibodies administered with pI values between 8 and 9 are properly absorbed. Nevertheless, antibodies occasionally have pI values that fall above this range or have been altered to produce higher or lower pI values (cationization or anionization, respectively). The observed elevated aliphatic index score of 62.72 indicates that the construct is thermostable when compared to some previously developed vaccines as suggested by Onile et al. (2020). Additionally, the construct’s overall hydropathicity has a greater negative score of 0.938, indicating that it is hydrophilic. Sanches et al. (2021) established that hydrophilic properties can decrease the likelihood of functional antigen synthesis and their capacity to enhance antigen processing and presentation.\n\nThe highly precise homology modelling (I-TASSER) was utilized to obtain the 3-dimensional structure with sufficient details regarding the arrangement of protein amino acid residues and the percentage disorder. A benchmarked scoring system that enables quantitative evaluations of the I-TASSER models was developed to facilitate the creation of the I-TASSER server, which generated automatic full-length 3D protein structure predictions in Figure 4 (Roy et al., 2010; Zhang, 2008). The C-score values of the models 1-5 were -1.50, -1.70, -1.66, -1.55, -3.05, respectively. Model 1 with a value of -1.50 was chosen because the C-score of a model is typically between -5 and -2, and a higher C-score number denotes a high level of confidence Yang and Zhang (2015). Using the EMBOSS transeq server, the amino acid of the multi-epitope sequence was reverse-translated into a nucleotide sequence to ascertain the epitope’s expression level and it’s compatibility with a cloning vector. Further analysis of the designed kit’s epitopes showed that the construct’s codon adaptation index was 0.96, which was near to a score of 1.0, indicating that the construct was well expressed in a cloning vector (Grote et al., 2005).\n\nAn effective and straightforward method to assess the tertiary structure quality is to use a Ramachandran plot. Our model had 83.215% of residues in the most preferred region, while 16.785% of the remaining residues were deposited in the additional authorized regions, demonstrating the excellent quality of our model (Pande et al., 2021, 2022). Additionally, our model has a Z-score of -0.43, which indicates the overall model quality; models with lower Z-scores were thought to be of greater quality, a positive Z-score often denotes the discovery of an incorrect or inconsistent region in the created 3D protein model (Pande et al., 2021, 2022). The Z-score obtained (Figure 6) validated the high quality of our overall model (Hajissa et al., 2015; Pande et al., 2022; Olatunde et al., 2022). The major aim of developing this multi-epitope construct is to investigate their potential in the diagnosis of MRSA infection. The synthetic recombinant multi-epitope peptide employed in current diagnostic kits has proven to be sufficient and useful for designing a more sensitive and specific diagnostic test than a single epitope peptide. As a result, multi-epitope peptides are promising diagnostic markers with the potential to improve diagnostic kit accuracy.\n\n\nConclusion\n\nMethicillin-resistant Staphylococcus aureus (MRSA) is a significant global source of bacteremia in BSI. Recent advancements in molecular testing technologies have significantly reduced the amount of time necessary to detect MRSA. Several in-silico approaches have been used to predict and design multi-epitope peptides capable of bounding to major histocompatibility complexes (MHC). Antigen-based immunoassays are increasingly necessary at the point of care for infection detection. In the present study, we have developed a novel multi-epitope construct for diagnosis of MRSA infection through an in-silico approach. Furthermore, the study provides an in-silico B-cell epitope mapping analysis for seven peptides, namely: ALJ10988.1, ORN56903.1, AFJ06714.1, AEO00772.1, WP_000721309.1, WP_057521704.1, and WP_063851348.1. The peptide constructs were analyzed for antigenicity, secondary and primary protein structures and physicochemical properties; investigations revealed that the peptide contains potential epitopes, hence, it can serve as a theoretical foundation for further research into its antigenicity as well as a prototype for developing a rapid diagnostic test kit for MRSA infection.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgments\n\nWe wish to acknowledge the management of All Saints University School of Medicine, Commonwealth of Dominica for providing the technical support needed for the project.\n\n\nReferences\n\nAkue JP, Eyang-Assengone ER, Dieki R: Loa loa infection detection using biomarkers: current perspectives. Res. Rep. Trop. Med. 2018; 9: 43–48. 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Publisher Full Text\n\nGouin K: Timing of Methicillin-resistant Staphylococcus aureus (MRSA) Bloodstream Infections among Hospitalized Patients and Its Association with Patient and Prior Healthcare Exposures.2019. Reference Source\n\nGrote A, Hiller K, Scheer M, et al.: JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005; 33(Web Server issue): W526–W531. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHajissa K, Zakaria R, Suppian R, et al.: Design and evaluation of a recombinant multi-epitope antigen for serodiagnosis of Toxoplasma gondii infection in humans. Parasit. Vectors. 2015; 8: 315. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiramatsu K: Vancomycin-resistant Staphylococcus aureus: a new model of antibiotic resistance. Lancet Infect. Dis. 2001; 1(3): 147–155. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJeyaratnam D, Whitty CJ, Phillips K, et al.: Impact of rapid screening tests on acquisition of meticillin resistant Staphylococcus aureus: cluster randomised crossover trial. BMJ. 2008; 336(7650): 927–930. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKavanagh KT: Control of MSSA and MRSA in the United States: protocols, policies, risk adjustment and excuses. Antimicrob. Resist. Infect. Control. 2019; 8(1): 103–108. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan MAS, Miah MI, Rahman SR: Subtractive proteomic analysis for identification of potential drug targets and vaccine candidates against Burkholderia pseudomallei K96243. Inform. Med. Unlocked. 2022; 35: 101127. Publisher Full Text\n\nKhazaei S, Moghadamizad Z: Echinococcus granulosus cyclophilin: Immunoinformatics analysis to provide insights into the biochemical properties and immunogenic epitopes. Inform. Med. Unlocked. 2022; 30: 100925. Publisher Full Text\n\nKimmig A, Hagel S, Weis S, et al.: Management of Staphylococcus aureus Bloodstream Infections. Front. Med. 2021; 7: 616524. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKringelum JV, Lundegaard C, Lund O, et al.: Reliable B cell epitope predictions: Impacts of method development and improved bench narking. PLoS Comput. Biol. 2012; 8(12): e1002829. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee S, Park YJ, Park KG, et al.: Comparative evaluation of three chromogenic media combined with broth enrichment and the real-time PCR-based Xpert MRSA assay for screening of methicillin-resistant Staphylococcus aureus in nasal swabs. Ann. Lab. Med. 2013; 33(4): 255–260. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu C, Bayer A, Cosgrove SE, et al.: Clinical practice guidelines by the Infectious Diseases Society of America for the treatment of methicillin-resistant Staphylococcus aureus infections in adults and children. Clin. Infect. Dis. 2011; 52(3): e18–e55. PubMed Abstract \| Publisher Full Text\n\nMcLaughlin L, Smith S: 559. Two Different Beasts: Comparing Epidemiology of Healthcare-Associated vs. Community-Acquired Methicillin-Resistant Staphylococcus aureus Bacteremia. Open Forum Infect. Dis. 2019, October; 6. Publisher Full Text \| Free Full Text\n\nMetzger WG, Mordmüller B: Loa loa—does it deserve to be neglected? Lancet Infect. Dis. 2014; 14(4): 353–357. PubMed Abstract \| Publisher Full Text\n\nMilheiriço C, Oliveira DC, de Lencastre H : Multiplex PCR strategy for subtyping the staphylococcal cassette chromosome mec type IV in methicillin-resistant Staphylococcus aureus:‘SCC mec IV multiplex’. J. Antimicrob. Chemother. 2007; 60(1): 42–48. PubMed Abstract \| Publisher Full Text\n\nMoise PA, North D, Steenbergen JN, et al.: Susceptibility relationship between vancomycin and daptomycin in Staphylococcus aureus: facts and assumptions. Lancet Infect. Dis. 2009; 9(10): 617–624. PubMed Abstract \| Publisher Full Text\n\nMöller S, Croning MD, Apweiler R: Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics. 2001; 17(7): 646–653. PubMed Abstract \| Publisher Full Text\n\nMoradi M, Golmohammadi R, Najafi A, et al.: A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis. Inform. Med. Unlocked. 2022; 28: 100862. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNathwani D, Morgan M, Masterton RG, et al.: Guidelines for UK practice for the diagnosis and management of methicillin-resistant Staphylococcus aureus (MRSA) infections presenting in the community. J. Antimicrob. Chemother. 2008; 61(5): 976–994. PubMed Abstract \| Publisher Full Text\n\nOladipo EK, Jimah EM, Irewolede BA, et al.: Immunoinformatics design of multi-epitope peptide for the diagnosis of Schistosoma haematobium infection. J. Biomol. Struct. Dyn. 2022; 1–8. PubMed Abstract \| Publisher Full Text\n\nOlatunde SK, Owolabi JB: Knowledge, Attitudes and Practices of Antibiotic Use and Antimicrobial Resistance among Medical Students in a Private University in Dominica, West Indies. Adv. Microbiol. 2022; 12(9): 511–524. Publisher Full Text\n\nOlatunde SK, Oladipo EK, Owolabi JB: Designing a novel in-silico multi-epitope vaccine against penicillin-binding protein 2A in Staphylococcus aureus. Informatics in Medicine Unlocked. 2022; 33: 101080. Publisher Full Text\n\nOnile OS, Fadahunsi AI, Adekunle AA, et al.: An immunoinformatics approach for the design of a multi-epitope subunit vaccine for urogenital schistosomiasis. PeerJ. 2020; 8: e8795. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOwolabi JB, Olatunde SK: A Review of Prevalence, Antimicrobial Susceptibility Patterns and Molecular Characteristics of Methicillin-Resistant Staphylococcus aureus (MRSA) in the Caribbean. Adv. Microbiol. 2022; 12(8): 459–480. Publisher Full Text\n\nPalavecino EL: Rapid methods for detection of MRSA in clinical specimens. Methicillin-Resistant Staphylococcus Aureus (MRSA) Protocols: Cutting-Edge Technologies and Advancements. 2020; 2069: 29–45. PubMed Abstract \| Publisher Full Text\n\nPande M, Kundu D, Srivastava R: Drugs repurposing against SARS-CoV2 and the new variant B. 1.1. 7 (alpha strain) targeting the spike protein: molecular docking and simulation studies. Heliyon. 2021; 7(8): e07803. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPande M, Kundu D, Srivastava R: Vitamin C and Vitamin D3 show strong binding with the amyloidogenic region of G555F mutant of Fibrinogen A alpha-chain associated with renal amyloidosis: proposed possible therapeutic intervention. Mol. Divers. 2022; 26: 939–949. PubMed Abstract \| Publisher Full Text\n\nPaul D, Sharif IH, Sayem A, et al.: In silico prediction of a highly immunogenic and conserved epitope against Zika Virus. Inform. Med. Unlocked. 2021; 24: 100613. Publisher Full Text\n\nPfizer: februray 6, 2019. Retrieved February 23, 2023. Reference Source\n\nRahman MM, Amin KB, Rahman SMM, et al.: Investigation of methicillin-resistant Staphylococcus aureus among clinical isolates from humans and animals by culture methods and multiplex PCR. BMC Vet. Res. 2018; 14(1): 300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRossney AS, Herra CM, Brennan GI, et al.: Evaluation of the Xpert methicillin-resistant Staphylococcus aureus (MRSA) assay using the GeneXpert real-time PCR platform for rapid detection of MRSA from screening specimens. J. Clin. Microbiol. 2008; 46(10): 3285–3290. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoy A, Kucukural A, Zhang Y: I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010; 5(4): 725–738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanami S, Azadegan-Dehkordi F, Rafieian-Kopaei M, et al.: Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches. Sci. Rep. 2021; 11(1): 1–15. Publisher Full Text\n\nSanches R, Tiwari S, Ferreira L, et al.: Immunoinformatics design of multi-epitope peptide-based vaccine against Schistosoma mansoni using transmembrane proteins as a target. Front. Immunol. 2021; 12: 621706. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanchez-Trincado JL, Gomez-Perosanz M, Reche PA: Fundamentals and methods for T-and B-cell epitope prediction. J Immunol Res. 2017; 2017: 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchneider Z: Importance of isoelectric point (pi) of antibodies. The Antibody Society; 2017, June 28. Retrieved January 12, 2023. Reference Source\n\nSeifert H, Wisplinghoff H, Kaasch A, et al.: Epidemiology, course and prognosis of Staphylococcus aureus bacteremia--Preliminary results from the INSTINCT (INvasive STaphylococcus aureus INfection CohorT) cohort. Deutsche Medizinische Wochenschrift (1946). 2008; 133(8): 340–345. Publisher Full Text\n\nShams M, Nourmohammadi H, Basati G, et al.: Leishmanolysin gp63: Bioinformatics evidences of immunogenic epitopes in Leishmania major for enhanced vaccine design against zoonotic cutaneous leishmaniasis. Inform. Med. Unlocked. 2021; 24: 100626. Publisher Full Text\n\nShin KS, Song HG, Kim H, et al.: Direct detection of methicillin-resistant Staphylococcus aureus from blood cultures using an immunochromatographic immunoassay-based MRSA rapid kit for the detection of penicillin-binding protein 2a. Diagn. Microbiol. Infect. Dis. 2010; 67(3): 301–303. Publisher Full Text\n\nShinefield H, Black S, Fattom A, et al.: Use of a Staphylococcus aureus conjugate vaccine in patients receiving hemodialysis. N. Engl. J. Med. 2002; 346(7): 491–496. Publisher Full Text\n\nTande AJ, Palraj BR, Osmon DR, et al.: Clinical presentation, risk factors, and outcomes of hematogenous prosthetic joint infection in patients with Staphylococcus aureus bacteremia. Am. J. Med. 2016; 129(2): 221.e11–221.e20. PubMed Abstract \| Publisher Full Text\n\nWiederstein M, Sippl MJ: ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007; 35(suppl_2): W407–W410. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang J, Zhang Y: I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res. 2015; 43(W1): W174–W181. Publisher Full Text\n\nZhang Y: I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008; 9: 40. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "226412", "date": "11 May 2024", "name": "Potukuchi Venkata Gurunadha Krishna Sarma", "expertise": [ "Reviewer Expertise Development antiS. aureus drugs against MRSA" ], "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 work is primarily carried out using in silico predictions and is quite interesting. Although such work if it is validated through laboratory studies would be great value and will have large impact. Further, it is known that several vaccines and diagnosis kts of MRSA infection both at hospital level and at community level are available, this study will just be another one. Yet, these results minimize the search for the development of diagnosis.\n\nIs the work 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/12-1167
https://f1000research.com/articles/10-151/v1	26 Feb 21	{ "type": "Study Protocol", "title": "Effect of atorvastatin on subclinical atherosclerosis in virally-suppressed HIV-infected patients with CMV seropositivity: a randomized double-blind placebo-controlled trial", "authors": [ "Evy Yunihastuti", "Lusiani Rusdi", "Muhammad Syahrir Azizi", "Riwanti Estiasari", "Chyntia Olivia Maurine Jasirwan", "Endah Ayu T. Wulandari", "Dyah Purnamasari", "Mutiara Shinta Noviar", "Sally Aman Nasution", "Lusiani Rusdi", "Muhammad Syahrir Azizi", "Riwanti Estiasari", "Chyntia Olivia Maurine Jasirwan", "Endah Ayu T. Wulandari", "Dyah Purnamasari", "Mutiara Shinta Noviar", "Sally Aman Nasution" ], "abstract": "Background: Persistent immune activation and inflammation in HIV-infection are linked to excess cardiovascular risk and other non-communicable diseases. Periodic asymptomatic CMV-reactivity in HIV infected patients over a lifetime may contribute to non-AIDS defining morbidity. Despite undetectable levels of HIV and CMV, these patients continue to have increased levels of biomarkers and immune activations. Statin administration is thought to reduce subclinical atherosclerosis by decreasing LDL-C levels. It may also add beneficial effects against CMV infection. Methods: We are conducting a double-blind placebo-controlled trial in which patients are randomized to receive either atorvastatin or placebo with a ratio of 1:1. This trial aims to study the effect of atorvastatin in statin-naive virally-suppressed HIV-infected patients with stable ART and CMV seropositivity on carotid intima media thickness (CIMT), tool that evaluates subclinical atherosclerosis. The study recruits 80 patients at HIV integrated care unit of Cipto Mangunkusumo hospital. All eligible subjects have CIMT evaluation as primary outcome, along with flow mediated vasodilatation (FMD), liver fibrosis and steatosis evaluation, fasting lipid, neurocognitive test, community periodontal index (CPI), and residual immune activation as secondary outcomes in 48 weeks. Ethics and dissemination: This study has received an ethical approval from Health Research Ethics Commitee–Universitas Indonesia and Cipto Mangunkusumo Hospital. Before joining the study, all participants fill in an informed consent form. At the end of study analysis, the trial results will be published and disseminated in peer-reviewed journals. Discussion: The main purpose of our study is to evaluate the effect of atorvastatin administration on CIMT changes in statin naïve virally suppressed HIV-infected patients with stable ART and CMV seropositivity Registration: ClinicalTrials.gov ID NCT04101136; registered on 24 September 2019.", "keywords": [ "HIV", "atherosclerosis", "atorvastatin", "cytomegalovirus", "non alcoholic fatty liver", "cognitive dysfunction", "periodontitis" ], "content": "Introduction\n\nHighly active antiretroviral therapy (HAART) has contributed to significant reduction in AIDS related morbidity and mortality in HIV-infected patients1. Increased longevity in HIV patients results on increased incidence of chronic non-communicable diseases (NCDs), particularly cardiovascular disease that has come out as an important cause of morbidity and mortality. Cardiovascular disease and other NCDs are associated with persistent inflammation and chronic activation that are still ongoing even in the state of viral suppression2.\n\nThere is accumulated evidence that some infectious agents, such as cytomegalovirus (CMV) and varicella zoster virus (VZV), may accelerate the course of atherosclerotic disease in HIV-infected patients3. Cytomegalovirus seropositivity is commonly found in the Indonesian population. Prevalence of CMV seropositivity in pre-marital women is 78.9% while in blood donors is 98.23%4,5. Periodic asymptomatic CMV-reactivity in HIV-infected patients over a lifetime may play a part in non-AIDS defining morbidity, including cardiovascular disease, neurocognitive impairment, renal disease, and cancer6.\n\nSubclinical atherosclerosis has been described in several studies on HIV-infected patients but no special treatment has been confirmed yet. There are some traditional and non-traditional factors that may contribute to the acceleration of atherosclerotic process in HIV patient, such as dyslipidemia, ART-related dyslipidemia, and HIV-associated immune activation and inflammation.\n\nCarotid intima media thickness (CIMT) is known to be the surrogate marker for subclinical atherosclerosis6,7. The direct correlation between CIMT and atherosclerosis among HIV-positive patients has been established in several studies8. A prospective study conducted by Hsu R et al. described that greater CIMT was found in HIV-positive patients compared to that in HIV-negative patients, despite of viral suppression, lipid, and hypertension control9. That study is parallel with our previous study which confirmed the slight rise of CIMT in ART-naïve patients 12 months after commencing ART. The CMV burden measured by using CMV IE level after ART admission was also correlated with right CIMT10. We also found that CMV antibody level was inversely correlated with the Z score of cognitive result before ART admission11.\n\nBesides CIMT, FMD has also gained more attention in recent years despite its tight procedure. Flow-mediated dilatation describes any vasodilatation of an artery following an increase in luminal blood flow and internal-wall shear stress12. The imbalance between vasoconstrictor and vasodilator factors lead to endothelial dysfunction. In addition, the release of inflammatory mediators and altered local shear forces may increase the synthesis of endothelial derived reactive oxygen species (ROS)13. However, the correlation of FMD value in HIV patients remains a controversy14. A small study conducted by Lebech AM et al. revealed no significant difference between FMD value among HIV-infected patients with a low cerebrovascular disease (CVD) risk compared to controls15. Another study on population at risk of cardiovascular diseases stated that failure in FMD improvement after six months of antihypertensive therapy is an independent predictor of coronary events for the next five years16. In a longitudinal study on ART-naïve patients, a considerable decrease in vasomotor function was found on FMD examination five weeks after ART initiation, which could be induced by immune reconstitution. This endothelial function decrease is supported by a handful of studies17–19.\n\nSeveral studies have linked cardiovascular disease with oral inflammation, including periodontitis in the general population. However, its underlying mechanisms and cause-effect relationship remain unclear20,21. A report in 1989 demonstrated a link between periodontitis and myocardial infarction. Periodontitis has now been linked with greater CIMT and impaired FMD21. Moreover, cardiovascular disease and periodontitis share predisposing factors, such as age, low socioeconomic and educational background, poor oral hygiene, smoking habits, and inflammatory genotypes22,23. HIV infection is thought to aggravate the existing periodontitis. This is supported by a recent study in the Netherlands on ART stable patients that linked the co-existence of HIV and periodontitis with higher risk of age-related diseases (cardiovascular diseases, autoimmune diseases, and diabetes mellitus)24. In the general population, higher titers of the anti-CMV antibodies are proportionally correlated with the severity of the periodontal lesions and a subset of cases have detectable CMV DNA in affected tissues25. Biofilm bacteria may initially induce gingivitis, which later results on consequent inflammation that may reactivate latent CMV (possibly from acinar cells) whilst the macrophage drawn into the periodontium may include cells infected with the virus, thus it is able to transfer it to somatic cells26.\n\nNon-alcoholic Fatty Liver Disease (NAFLD), another NCD that is common in HIV-infected patients, is also closely related to cardiovascular disease through different immune and metabolic processes. Patients with fatty liver disease are present with increased visceral adipose tissue (AT) secondary to inadequate intake of food. This causes a dysfunction in the AT generating insulin resistance, thereby increasing lipolysis and resulting in a greater release of free fatty acids (FFAs) into the bloodstream27. Others suggest its relation to high concentration of apoprotein B (APOB) containing atherogenic lipoproteins. These are formed mainly by the process of increased hepatic production of non-high-density lipoprotein (non-HDL) cholesterol in order to decrease cholesterol toxicity from the diet28. Inflammatory factors, pro-coagulation factors, greater formation of stress molecules, such as ROS and ceramides, also favor the progression of NAFLD and increase cardiovascular risk29. The rising evidence of the association between NAFLD and subclinical CVD may suggest that NAFLD is not only a marker but may also be actively involved in pathogenesis of cardiovascular disease30.\n\nStatins, which were first extracted from Pythim sp., Penicillium sp., and Aspergillus sp., are inhibitors of hydroxyl-3-methylglutaryl coenzyme A. Initially, the target of statin therapy was to reduce cholesterol levels. Recent studies showed that the use of statin was also associated with other atherogenic lipid particles reduction, such as oxidized LDL and phospholipase associated with lipoprotein31. Statins remain the primary and secondary key of CVD prevention by improving endothelial function, slowing the progression of atherosclerosis and stabilizing atherosclerotic plaque. In the HIV population, decreased oxidized LDL is independently associated with a decrease in important markers of subclinical atherosclerosis, such as coronary plaque and CIMT. The dual mechanism of statin use reduces LDL cholesterol, and modifies inflammatory responses, antioxidant effects, antithrombic effects (clotting processes), and removal of blood vessel plaques, thereby preventing cholesterol build-up and muscle proliferation32. Treating dyslipidemia with statins has been challenging in HIV-infected patients due to potential drug interaction between statins and antiretroviral drugs as both drugs are metabolized by cytochrome P450. A study comparing pitavastatin and pravastatin in patients using protease inhibitor shows higher virological failure in pravastatin group33. However, pitavastatin is expensive as it is not available in generic formulation. Atorvastatin, another moderate-intensity statin, is available in generic formulation and is widely used in Indonesia. This drug is known to have no interaction with current antiretroviral drugs used in Indonesia. Seropositivity to CMV may jointly predict increased mortality rate in patients with coronary heart disease. Statin therapy is known to decrease lipid level and also has an anti-inflammatory effect. A study shows that statin reduces mortality rate among CMV-infected patients with coronary artery disease34. An in vitro study demonstrates the broad anti-CMV activity of statins. All statin doses are found to dependently reduce CMV titers in human aortic endothelial cells. These findings provide new insight into beneficial effects of statins35. The use of atorvastatin, a cheap and widely accessible drug in Indonesia, has not been specifically studied in term of improving cardiovascular outcome in HIV-infected patients under ART.\n\nWe conduct a randomized double-blind placebo-controlled trial that primarily aims to evaluate the effect of atorvastatin on carotid intima media thickness (CIMT) in virally-suppressed HIV-infected patients with CMV seropositivity. Secondly, this trial also evaluates the other marker values, such as FMD, liver fibrosis and steatosis, fasting lipid, neurocognitive test, CPI, and residual immune activation as secondary outcome for 48 weeks.\n\n\nProtocol\n\nThis study uses randomized control trial in which subjects are assigned to a double blind randomized with placebo-controlled clinical trial study with atorvastatin 20 mg in virally-suppressed HIV-infected patients.\n\nThe study is taking place in a single center, the HIV integrated clinic Cipto Mangunkusumo Hospital, Jakarta. All patients receive government free antiretroviral program according to Indonesian guidelines. The first-line regimen consists of two nucleoside reverse transciptase inhibitors (NRTIs) and one non-nucleoside reverse transcriptase inhibitor (NNRTI), and the second-line regimen of two NRTIs and one protease inhibitor (PI). The majority of patients belong to urban and mainly low- to middle-income families living in Jakarta. Assuming that the effect size is 0.1, standard deviation is 0.12, and the use of 2 sample t-test, the sample size needed for 90% power and 5% significant level is 32 per arm. With an additional 20% drop out rate, each arm (placebo and control group) will need 40 participants.\n\nPatients, men and women aged between 20 to 45 years old, using stable ART for at least a year with positive CMV IgG and viral load of HIV RNA <50 copies/mL are recruited to the study. Patients with the following conditions are excluded from the study:\n\npatients undergoing hepatitis C DAA therapy\n\ndecompensated cirrhosis or acute liver failure\n\nhistory of coronary artery disease\n\nhistory of diabetes mellitus\n\nhistory of brain infection, epilepsy, or stroke\n\nhistory of rhabdomyolysis or myopathy\n\npregnant or breastfeeding during study\n\nsevere depression\n\npatients using statin therapy in the 6 weeks prior to the study\n\nhistory of statin hypersensitivity\n\npatients with a Framingham Risk Score above 10% within LDL ≥130\n\nAll potential participants receive an explanation about the purpose and method of the study and are informed of their rights to stop or refuse to take part in the study. A special mobile number is available for potential participants to obtain additional information should they wish. Viral load, anti-CMV antibody, and lipid panel tests are done before defining the eligibility criteria. Participants are also required to not use any statin therapy 6 weeks before enrollment. All potential participants are contacted again to schedule an appointment if they agree to continue with all of the procedures. After screening is completed, they will be interviewed and examined at the clinic area, which includes CIMT, FMD, and neurocognitive evaluation. The oral examination is conducted at the dentistry clinic and the transient elastography examination will be conducted at the hepatology clinic. Figure 1 presents a CONSORT diagram of the anticipated number of participants needed to be screened in order to reach a target of 80 participants randomized to atorvastatin or placebo.\n\nCONSORT diagram of the anticipated number of participants that need to be screened in order to reach a target of 80 participants randomized to atorvastatin or placebo.\n\nParticipants receive either 48 weeks of 20 mg atorvastatin or placebo once daily. We use oral atorvastatin 20 mg capsule in generic form and a placebo capsule prepared by the hospital pharmacist, composed of starch which is similar to atorvastatin capsule in size, shape, and color. Packagings are identical in appearance for both atorvastatin and the placebo.\n\nThe primary aim of this study is to compare the effect of 48 weeks of 20 mg daily atorvastatin versus placebo on CIMT in virally suppressed HIV patients with CMV seropositivity. Other aims are to evaluate the interaction between baseline CMV copy number and the effect of atorvastatin on CIMT changes, the effect of 48 weeks of 20 mg daily atorvastatin versus placebo on fasting lipid changes, the effect on liver fibrosis and steatosis changes, neurocognitive changes, several immune activation biomarker (sCD14, VCAM, ICAM, hsCRP, and β2M) changes, CPI changes in virally suppressed HIV patients with CMV seropositivity, and to evaluate the interaction between baseline CMV copy number and effect of atorvastatin on FMD, neurocognitive function, liver fibrosis and steatosis, lipid profile, and immune activation biomarkers changes in 48 weeks.\n\nParticipants who meet the inclusion criteria are randomized into atorvastatin groups and placebo groups with a ratio of 1:1 (40 subjects per group). Randomization using STATA version 14.2 based on randomization of permutation blocks with block 4 sizes is carried out by statistical analysts. The administration of study drug is home-based participant self-administration. Participants are asked to swallow the whole capsule without chewing or breaking it. The participants get the medication supply every month along with the prescription of antiretroviral drugs.\n\nThe code of each participant is given to pharmacists who are involved in the study. The pharmacists keep the code in the sealed envelope. Researchers, doctors, and participants do not know the results of randomization. The drug and placebo capsules are administered to patients by a staff member who is privy to the treatment. Each participant should return the unused capsules every month. At the end of the study, the pharmacist and related staff members will count the Medication Possession Ratio (MPR). The study will be discontinued if:\n\nthe participant withdraws informed consent\n\nthe participant develops significant toxicity, intolerance or allergy associated with study drug that causes a risk to participant’s life\n\nthe participant is admitted to hospital for other morbidity that is incompatible with further atorvastatin treatment\n\nblinding is revealed. Unblinding will also be available if a clinician believes that clinical management depends importantly on knowledge of whether the patient is currently receiving statin or placebo.\n\nSubjects who meet eligibility criteria are enrolled and have a baseline visit within 6 weeks following the screening visit. Venous blood sample are collected for fasting blood glucose, ALT, CMV DNA, hsCRP, sCD14, VCAM, ICAM, and β2M examinations.\n\nEach patient has a CIMT and FMD evaluation performed by a trained cardiologist using B mode ultrasonography. CIMT is defined as a double-line pattern visualized by echo 2D on both walls of the common carotid artery (CCA) in a longitudinal view. Two parallel lines (leading edges of two anatomical boundaries) form it: the lumen-intima and media-adventitia interfaces. High-resolution B-mode ultrasound images of the right and left common carotid artery will be used to measure carotid intima-media thickness. The patient is scanned in the supine position using 7–12 MHz linear array transducer (Philips Affiniti 70C, Phillips, UK). CIMT is calculated using both manual and semi-automated (Automated; QLAB, Phillips, UK) methods. Manual CIMT measurements are recorded from the far wall at 1 cm, 1.5 cm, and 2 cm intervals proximal to the carotid bulb. Automated measurements are also recorded from the far wall, using the same image, from the identical 1 cm section proximal to the carotid bulb. The carotid bulb is defined as the point where the far wall deviated from the parallel plane of the distal CCA. Mean manual and automated cIMT measurements for the right and left CCA are calculated from three consecutive cardiac cycles.\n\nFMD is assessed in the brachial artery by ultrasonography. The participant has to abstain from exercise (≥12 hr), caffeine (≥12 hr), smoking or smoke exposure (≥12 hr), vitamin supplementation (>72 hr), and any medication (≥4 hr half-lives of the drug, non-steroidal anti-inflammatory agents for 1 day and aspirins for 3 days). We ensure that the participant is under fasting conditions or has only consumed low-fat meals. The measurements are performed on the right arm when the patient is in the supine position, after 10 to 20 minutes of rest in the supine position36,37 The brachial artery is scanned longitudinally just above the antecubital crease with a linear multifrequency 5- to 12-MHz transducer B-mode. The diameter of the brachial artery is measured on the interface between media and adventitia of the anterior and posterior wall as a baseline. Gain settings are optimized to identify the lumen and the vessel wall interfaces and could not be modified during the examination. Hyperemia is induced by inflation of a pneumatic cuff of 200-250 mm Hg for 5 minutes on the most proximal portion of the forearm. Arterial diameter measurement is repeated just before (30-60 seconds) deflation of the cuff, then just after (30 to 60 seconds) sudden deflation of the cuff. Tracings is recorded on image and file and are read by two investigators (MS, LR) who are unaware of the participant’s clinical data. The measurements of basal and posthyperemia diameter will be used for the analysis. Flow-mediated vasodilation is expressed as the relative increase in brachial artery diameter during hyperemia and defined as 100× [(posthyperemia diameter−basal diameter)/basal diameter].\n\nTransient elastography with CAP will be done by trained hepatologist using Fibroscan (Echosens®) device. The criteria for successful examination are 10 shots and an interquartile range (IQR) for liver stiffness of less than 20% of the median value. The cut-off value for NAFLD diagnosis is CAP measurement of above 238 dB/m and/or fibrosis score higher than 7.1 kPa38.\n\nA trained neurologist performs the neurocognitive evaluation. The cognitive tests are performed in week 0, week 24, and week 48. This study uses tests that are sensitive to domain most affected in HIV but can be delivered in relatively short time. This study uses Trail Making Test (TMT) A and B to measure executive function, Symbol Digit Modalities Test (SDMT) for speed of information processing, and Brief Visuospatial Memory Test Revised for learning and memory. These tests have already been validated in Indonesia and can be administered by non-neuropsychologists who have been trained39. To determine cognitive impairment, we use local normative data that match age and education level.\n\nA trained dentist will assess periodontitis using CPI, which was modified by the World Health Organization (WHO). This assessment uses a 0.5 mm ball tip periodontal probe with black band markers at 3.5, 5.5, 8.5, and 11.5 mm, and involve 10 teeth (17, 16, 11, 26, 27, 37, 36, 31, 46, and 47). The score ranges from 0 for healthy periodontal to score 4 for periodontal pocket ≥6 mm40,41. All examinations will be done within a week before taking study drugs (week 0) and at the end of this study (week 48), except for neurocognitive and blood collection, which are done in baseline, in month 6, and at the end of this study in month 12, as seen in Table 1.\n\nW = week; *extra visit will be done when adverse event occurs during the study.\n\nAt the end study, a total drug consumption adherence will be assessed using MPR. Meanwhile, each patient has monthly clinical follow-ups as standard of care in the clinic. Study follow-up visits include clinical and laboratory procedures as presented in Table 1. MPR is the sum of the days’ supply for all fills of a given drug in a particular time period, divided by the number of days in the time period42.\n\nData management are managed in the HIV Integrated Care Unit, Cipto Mangunkusumo Hospital. All research staff have overall responsibility for maintaining the study CRFs. Corrections to the paper CRF documents must be made by striking through the incorrect entry with a single line (taking care not to obliterate or render the original entry illegible) and entering the correct information adjacent to the incorrect entry. Corrections to paper CRFs must be initialed and dated by the person making the correction. The researchers are responsible for maintaining accurate, complete, and up-to-date records. These forms are to be completed on an on-going basis during the course of the study.\n\nStatistical analyses will be performed with SPSS (version 21). Subjects will be analyzed in the group to which they are randomized, regardless of the treatment received. A T test will be used to compare the mean CIMT changes of virally supressed HIV patients with CMV seropositivity in the atorvastatin group versus the placebo group between the baseline and week 48 to analyze primary endpoints. Meanwhile, secondary endpoints will be analyzed using linear regression with interaction to assess the magnitude of change in the effect of atorvastatin on CIMT associated with the baseline CMV copy number, and a proportional odds logistic regression model will be used to estimate the odds ratios of CPI in treating an increased level of CIMT. Other continuous endpoints will be analyzed using a 2 sample T-test. Missing data will be resolved by comparing subject characteristics in the drop out group with the remaining participants. If there is no difference in characteristics it would assumed that the missing data is at random.\n\nThe study is to be monitored by Cipto Mangunkusumo Hospital Research Unit. Research records for all study subjects including CRFs, laboratory, and other investigation data/results are to be maintained by the investigator in secure storage for five years. These records are to be maintained in compliance with all designated IRBs requirements. It is the investigator’s responsibility to retain copies of these study records until notified in that they can be destroyed. Any severe adverse event or unintended effects of trial intervention will be reported and assessed by the ethics committee.\n\nParticipants begin involvement in the trial when the eligibility criteria are fulfilled and screening examinations are surpassed. Clear information about the trial, including participant’s role, is explained by study team and is written on informed consent form. Each participant has his/her right to decline or withdraw from the trial. The participant also has the right to receive any information regarding test result done during the trial. One of the participants and experienced team member are given the role of patient recruitment.\n\nThis trial has been approved by Health Research Ethics Commitee–Universitas Indonesia and Cipto Mangunkusumo Hospital (HREC-FMUI/CMH) and registered in ClinicalTrials.gov (identification number 19-03-0272). Any amendments or modification regarding the protocol during the trial will be consulted and notified to HREC-FMUI/CMH. All participants are required to give their consent before joining the study. The consent form is written in Indonesian and is composed of the following details: participant’s name, date of birth, investigator contact, and explanation of the study purpose that is easily understood by non-medical personnel, course and duration of the study (as well as the freedom to withdraw at any time and guarantee of confidentiality), details of invasive procedures involved (blood collection), an explanation of blood remnant storage, the type of intervention (atorvastatin vs placebo), and possible side effects. The details of the informed consent form are explained by on-site research staff. Blood collections are collected by professional health workers and processed by lab analysts. The study team receives training on Good Clinical Practices (GCP) to ensure that sensitive research activities will be handled appropriately. The study maintains records of adverse events, as well as copies of the consent forms. All records are placed in a locked filing cabinet at the clinic that is only accessible by the research team. All team members are responsible for data security and record keeping. The datasets that will be used for analysis do not contain any identifying information, specifically, no names of participants are included in the datasets. Identifiers for the participants will be disposed of no more than three years after study completion. To protect confidentiality, identifiers are only accessible by the PI or project coordinator and are kept separated from other records with participants’ responses.\n\nParticipants presenting complaints or adverse event related to the trial will have an extra visit to medical personnel.\n\nAt the end of study analysis, the trial results will submitted and published in peer-reviewed journals. Links of publication will be provided in the applicable trial register. Authorship for all publications will be based on the criteria defined by the International Committee of Medical Journal Editors.\n\n\nDiscussion\n\nThis study is a double-blind and placebo-controlled trial. The main purpose of this study is to evaluate the effect of atorvastatin administration on CIMT changes in statin naïve virally suppressed HIV-infected patients without any comorbidities with stable ART and CMV seropositivity. To our knowledge this is the first study which is conducted in a population of this kind.\n\nA study of statin-intervention with a 48 week follow-up comes with challenges and considerable limitations. First, the possibility of missed visits by study patients. Second, managing the follow-up of treatment and evaluation because this study involves multi-disciplinary specialists. Our solutions to avoid these problems is assigning a research assistant to regularly and preemptively remind patients and specialist teams to attend or carry out scheduled procedures by phone or message. If the patients cannot be contacted, the research assistant will check the schedule of antiretroviral collection at the administration desk. Another challenge arises from the Covid-19 pandemic. We have faced the difficulty of conducting direct monitoring due to the implementation of social restrictions. Many HIV-infected patients using delivery services to get their antiretroviral drugs in order to maintain their medications. We also conduct online monitoring and maintain study drug medications using delivery services. When it comes to procedural examination, physical barriers are provided along with personal protective equipment.\n\nIn sum, if the results as agree with our hypothesis, statin administration may be useful to prevent negative cardiovascular outcomes, especially the carotid intima medial thickness among virally suppressed HIV-infected patients and CMV seropositivity.\n\n\nData availability\n\nNo data are associated with this article\n\nFigshare: SPIRIT checklist for “Effect of atorvastatin on subclinical atherosclerosis in virally-suppressed HIV-infected patients with CMV seropositivity: A randomized double-blind placebo-controlled trial”. https://doi.org/10.6084/m9.figshare.13604831.v143.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nWorld Health Organization (WHO): Global Health Observatory Data: Antiretroviral therapy (ART) Coverage Among All Age Groups. Genève WHO Press. 2015. 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In: Gill EA, Ballantyne CM,Wyle KL, editors. Lipidology, An Issue of endocrinology and Metabolism Clinics of North America, 1st edition. The Clinics: Internal Medicine. 2016; 45-1.\n\nKarim B, Wijaya IP, Rahmaniyah R, et al.: Factors affecting affect cardiovascular health in Indonesian HIV patients beginning ART. AIDS Res Ther. 2017; 14(1): 52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEstiasari R, Aryanto I, Lee S, et al.: Determinants of cognitive health in Indonesian HIV patients beginning antiretroviral therapy. J Neurovirol. 2020; 26(1): 32–40. PubMed Abstract \| Publisher Full Text\n\nThijssen DHJ, Black MA, Pyke KE, et al.: Assessment of flow-mediated dilation in humans: A methodological and physiological guideline. Am J Physiol Heart Circ Physiol. 2011; 300(1): H2–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodriguez-Miguelez P, Seigler N, Harris RA: Ultrasound assessment of endothelial function: A technical guideline of the flow-mediated dilation test. J Vis Exp. 2016; (110): 54011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGokce N, Keaney JF, Hunter LM, et al.: Predictive value of noninvasively determined endothelial dysfunction for long-term cardiovascular events in patients with peripheral vascular disease. J Am Coll Cardiol. 2003; 41(10): 1769–75. PubMed Abstract \| Publisher Full Text\n\nLebech AM, Kristoffersen US, Wiinberg N, et al.: Coronary and peripheral endothelial function in HIV patients studied with positron emission tomography and flow-mediated dilation: Relation to hypercholesterolemia. Eur J Nucl Med Mol Imaging. 2008; 35(11): 2049–58. PubMed Abstract \| Publisher Full Text\n\nModena MG, Bonetti L, Coppi F, et al.: Prognostic role of reversible endothelial dysfunction in hypertensive postmenopausal women. J Am Coll Cardiol. 2002; 40(3): 505–10. PubMed Abstract \| Publisher Full Text\n\nHsue PY, Hunt PW, Wu Y, et al.: Association of abacavir and impaired endothelial function in treated and suppressed HIV-infected patients. AIDS. 2009; 23(15): 2021–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurphy RL, Berzins B, Zala C, et al.: Change to atazanavir/ritonavir treatment improves lipids but not endothelial function in patients on stable antiretroviral therapy. AIDS. 2010; 24(6): 885–90. PubMed Abstract \| Publisher Full Text\n\nTorriani FJ, Komarow L, Parker RA, et al.: Endothelial Function in Human Immunodeficiency Virus-Infected Antiretroviral-Naive Subjects Before and After Starting Potent Antiretroviral Therapy. The ACTG (AIDS Clinical Trials Group) Study 5152s. J Am Coll Cardiol. 2008; 52(7): 569–76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHansson GK: Inflammation, Atherosclerosis, and Coronary Artery Disease. N Engl J Med. 2005; 352(16): 1685–95. PubMed Abstract \| Publisher Full Text\n\nOrlandi M, Suvan J, Petrie A, et al.: Association between periodontal disease and its treatment, flow-mediated dilatation and carotid intima-media thickness: A systematic review and meta-analysis. Atherosclerosis. 2014; 236(1): 39–46. PubMed Abstract \| Publisher Full Text\n\nPereira LC, Nascimento JCR, Rêgo JMC, et al.: Apolipoprotein E , periodontal disease and the risk for atherosclerosis : a review. Arch Oral Biol. 2019; 98: 204–12. PubMed Abstract \| Publisher Full Text\n\nNazir MA: Prevalence of periodontal disease , its association with systemic diseases and prevention. Int J Health Sci (Qassim). 2017; 11(2): 72–80. PubMed Abstract \| Free Full Text\n\nGroenewegen H, Bierman WFW, Delli K, et al.: Severe periodontitis is more common in HIV- infected patients. J Infect. 2019; 78(3): 171–177. PubMed Abstract \| Publisher Full Text\n\nKazi MMAG, Bharadwaj R: Role of herpesviruses in chronic periodontitis and their association with clinical parameters and in increasing severity of the disease. Eur J Dent. 2017; 11(3): 299–304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodrigues PM de S, Teixeira AL, Kustner EC, et al.: Are herpes virus associated to aggressive periodontitis ? A review of literature. J Oral Maxillofac Pathol. 2015; 19(3): 348–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMendez-Sanchez N, Cruz-Ramon VC, Ramirez-Perez OL, et al.: New Aspects of Lipotoxicity in Nonalcoholic Steatohepatitis. Int J Mol Sci. 2018; 19(7): 2034. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZelberSagi S, Salomone F, Yeshua H, et al.: Non-high-density lipoprotein cholesterol independently predicts new onset of non-alcoholic fatty liver disease. Liver Int. 2014; 34(6): e128–35. PubMed Abstract \| Publisher Full Text\n\nValencia-Rodríguez A, Vera-Barajas A, Barranco-Fragoso B, et al.: New insights into the association between non-alcoholic fatty liver disease and atherosclerosis. Ann Transl Med. 2019; 7(Suppl 8): S300. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbdallah LR, de Matos RC, Souza YPD, et al.: Non-alcoholic Fatty Liver Disease and Its Links with Inflammation and Atherosclerosis. Curr Atheroscler Rep. 2020; 22(1): 7. PubMed Abstract \| Publisher Full Text\n\nHemkens LG, Bucher HC: HIV infection and cardiovascular disease. Eur Heart J. 2014; 35(21): 1373–81. Publisher Full Text\n\nEckard AR, McComsey GA: The Role of Statins in the Setting of HIV Infection. Curr HIV/AIDS Rep. 2015; 12(3): 305–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAberg JA, Sponseller CA, Ward DJ, et al.: Pitavastatin versus pravastatin in adults with HIV-1 infection and dyslipidaemia (INTREPID): 12 week and 52 week results of a phase 4, multicentre, randomised, double-blind, superiority trial. Lancet HIV. 2017; 4(7): e284–e294. PubMed Abstract \| Publisher Full Text\n\nHorne BD, Muhlestein JB, Carlquist JF, et al.: Statin therapy interacts with cytomegalovirus seropositivity and high C-reactive protein in reducing mortality among patients with angiographically significant coronary disease. Circulation. 2003; 107(2): 258–63. PubMed Abstract \| Publisher Full Text\n\nPonroy N, Taveira A, Mueller NJ, et al.: Statins demonstrate a broad anti-Cytomegalovirus activity in vitro in ganciclovir-susceptible and resistant strains. J Med Virol. 2015; 87(1): 141–53. PubMed Abstract \| Publisher Full Text\n\nThijssen DHJ, Black MA, Pyke KE, et al.: Assessment of flow-mediated dilation in humans: a methodological and physiological guideline. Am J Physiol Heart Circ Physiol. 2011; 300(1): H2–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCorretti MC, Anderson TJ, Benjamin EJ, et al.: Guidelines for the ultrasound assessment of endothelial-dependent flow-mediated vasodilation of the brachial artery: a report of the International Brachial Artery Reactivity Task Force. J Am Coll Cardiol. 2002; 39(2): 257–65. PubMed Abstract \| Publisher Full Text\n\nLi Q, Dhyani M, Grajo J, et al.: Current status of imaging in non-alcoholic fatty liver disease. World J Hepatol. 2018; 10(8): 530–42. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEstiasari R, Fajrina Y, Lastri D, et al.: Validity and reliability of brief international cognitive assesment for multiple sclerosis (BICAMS) in Indonesia and the correlation with quality of life. Neurol Res Int. 2019; 2019: 4290352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDhingra K, Vandana KL: Indices for measuring periodontis: a literature review. Int Dent J. 2011; 61(2): 76–84. PubMed Abstract \| Publisher Full Text\n\nNomura Y, Okada A, Katuta E, et al.: A new screening method for periodontis: an alternative to the community periodontal index. BMC Oral Health. 2016; 16(1): 64. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKozma CM, Dickson M, Philips AL, et al.: Medication possesion ratio: implications of using fixed and variable observation periods in assesing adherence with disease-modifying drugs in patients with multiple sclerosis. Patient Prefer Adherence. 2013; 7: 509–16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYunihastuti E, Rusdi L, Azizi MS, et al.: Effect of atorvastatin on subclinical atherosclerosis in virally-suppressed HIV-infected patients with CMV seropositivity: A randomized double-blind placebo-controlled trial. Figshare. Fileset. 2021. http://www.doi.org/10.6084/m9.figshare.13604831" }	[ { "id": "97333", "date": "01 Dec 2021", "name": "Vicente Estrada", "expertise": [ "Reviewer Expertise HIV" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 research project that aims to analyze the effect of atorvastatin vs. placebo on carotid IMT variation over 48 weeks of treatment. The hypothesis is interesting, and the methods (double-blind, placebo-controlled) are correct.\nThere are previous publications on this field that addresses the research hypothesis (PMID: 272037151, PMID: 323530622, in the general population PMID: 173844343). Furthermore, the number of patients included seems low; estimates consider that atorvastatin will reduce IMT by 10% at 48 weeks, which seems a bit of an exaggerated estimate. Finally, the 48-week follow-up is scarce because the IMT variations need more time. The age >45 y exclusion criteria are not clearly explained.\nOn the other hand, the hypothesis that atorvastatin will reduce the degree of steatosis after one year does not have a solid background. It has not shown definitive efficacy in the general population without being associated with vitamin E (PMID: 208421094). On the other hand, I believe that it disperses the study's primary objective, and indeed it will not have statistical power to confirm the hypothesis.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "7755", "date": "28 Jan 2022", "name": "Evy Yunihastuti", "role": "Author Response", "response": "Thank you for your comments, In our sample size calculation, we assume that the effect size is 0.1 with a standard deviation of 0.12. With the plan to use of 2 sample t-test, the sample size needed for 90% power and 5% significant level is 32 per arm. Assuming an additional 20% drop in each arm (placebo and control group), we need a minimum of 40 participants. We exclude subjects >45 years because the highest PLHIV prevalence in Indonesia is 20-45 years and we want to see the effect of atorvastatin on subclinical atherosclerosis in virally-suppressed HIV-infected patients with CMV seropositivity. A previous study reported that CVD morbidity and mortality in PLHIV is higher above 45 years old than in negative controls.1 Reference: Chastain DB, Stover KR, Riche DM. Evidence-based review of statin use in patients with HIV on antiretroviral therapy. J Clin Transl Endocrinol. 2017 Feb 22;8:6-14. Thank you and best regards, Evy" } ] }, { "id": "129619", "date": "06 Jun 2023", "name": "Rudi Wisaksana", "expertise": [ "Reviewer Expertise HIV" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 by Yunihastuti et. al. is an interesting attempt to answer intriguing questions regarding CVD prevention in people co-infected with HIV and CMV with low-risk CVD, in a major hospital in Indonesia.\nThe study protocol was extensive with numerous markers evaluations. But the relatively short duration of observations and the limited number of study subjects might have an effect on the results.\n\nMajor:\nMy major concern is that judgment on sample size and duration of the follow-up needed to show the effect of Atorvastatin on subclinical atherosclerosis was based on assumption only. The investigators should have considered this more carefully, given the large number of variables involved.\n\nOther questions is regarding the study population. HIV-infected people still have ongoing low-level HIV viremia and low-level inflammation that exist even in virally-supressed persons. Why the investigators choose this population should be stated in the article.\nMinor:\nIn the Protocol sections:\nParticipants, interventions, and outcomes.\nComment: It was suggested that the subheading be changed to be Participants and interventions as there was another sub consisting of the study outcomes on the later page (page 6 of 11)\n\nStudy setting and sample-size.\nComment: Is there any reference used regarding the SD value utilized in the sample size measurement? Or is it purely based on the investigator clinical assumption?\n\nEligibility and enrollment.\nComments: - Can you provide the clear definition of ‘stable ART’ is?\n- Please add the limit period of the VL result date in the screening process will it be qualified as sourced documents to enroll the subject.\n- Do you hold any extra screening exam regarding the exclusion conditions in the case of subject having no related sourced documents prior to the screening process?\n- Please provide further details about how you define the existence of each exclusion conditions within the potential subjects and what kind of sourced documents will be relied on (maybe you can add bracket form at each exclusion conditions bullets e.g., history of diabetes {fasting glucose >125mg/dL}).\n\nInterventions and participant timeline.\nComment: I believe the sentence “Viral load, anti-CMV antibody, …… the eligibility criteria.” (Line 5-6) and the sentence “Participants are also ….. weeks before enrollment.” (Line 7-8) belongs to the prior sub and should be moved to be written in the Eligibility and enrollment sub.\n\nStudy outcomes. Comments: - Why did you choose those parameters used for the residual immune activation measurement among other parameters?\n- Please rephrase and eliminate the redundant words in the paragraph so it feels more clear and not repetitious.\n\nData collection and management. Comments: - Please use the same terminology in defining the study timeline. Which of the following is considered a baseline? The W-1 or W0?\n- Please use the same terminology in defining the study visit. Consistent with the unit whether it is using months or weeks.\n\nFigure 1:\nIn the box titled \"Excluded”, there were consisted of 2 bullets only (“not meeting inclusion criteria and decline to participate”). On the other hand, in the prior sub it was mentioned that there were certain exclusion conditions and I believe it should be reflected in the diagram. May you add another bullet in the box considering this.\n\nPlease add any footnotes regarding any defined shortened terms used in the diagram.\n\nTable 1:\nPlease add details about what laboratory examinations are done during the blood sample collection in each related study visit.\n\nI think it was more suitable to change the “Allocation” term into “Randomization”, thus the “Post-allocation” into “Post-randomization” and the “Enrollment” term into “Screening and Enrollment”.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "10224", "date": "26 Sep 2023", "name": "Evy Yunihastuti", "role": "Author Response", "response": "Thank you for your comments, Major: The sample size for randomized controlled trial was calculated according to the primary aim: to evaluate the effect of atorvastatin on carotid intima-media thickness in virally-suppressed HIV-infected patients with CMV seropositivity. The assumptions done were meant for the effect size (0.1) with a standard deviation of 0.12. We decided to use 90% for power and 5% for significant level for the sample size, resulting in 32 participants per arm. Considering an additional 20% drop in each arm, a total of 40 participants in each arm was needed. We considered HIV-infected participants the target population due to their sustained inflammation. We included additional information regarding this population in the second paragraph of the introduction. Minor: Protocol sections: Participants, interventions, and outcomes Thank you for the suggestion. We have changed it into “Participants and Interventions”. Study setting and sample size Yes, we used a formula in order to determine the SD value in the sample size measurement. The formula is as follow: n1=n2=[(Z∝+Zβ)S/(x1-x2)]2 with n1 and n2 being sample size for group 1 and 2, Zα = 1.96, Zβ = 1.64, S for standard deviation, and x1-x2 for the minimum difference between the means that is considered meaningful. Eligibility and enrollment Stable ART is defined by “those who were receiving ART for at least 1 year with no adverse drug reactions requiring regular monitoring, no current illnesses or pregnancy, a good understanding of lifelong adherence, and evidence of treatment success”.1 The limit period for VL result date is 1 year for the screening process. The cholesterol level was checked for every participant before statin therapy was given. Other examinations were done not as part of the study protocol, but were taken from medical record or history taking. Each exclusion condition was evaluated from the medical record. Diabetes mellitus, severe depression, and other conditions were defined by the medical record or history taking. Interventions and participant timeline Thank you for the comment. We have moved it to the “Eligibility and enrollment” sub. Study outcomes We chose sCD14, VCAM, ICAM, hsCRP, and β2M as the residual immune activation parameters for these reasons below: sCD14 is expressed on macrophages as receptor for lipopolysaccharides on bacterial surfaces and has been reported to be higher in patients with residual HIV viral load than undetectable. Statin administration has the potency to reduce sCD14.2,3 VCAM is an endothelial activation found higher in viral-suppressed patients than in control. Increased expression of VCAM is associated with inflammation-related vascular complications.4 ICAM is expressed on endothelial cells and leukocytes at low levels but is stimulable to greater density by pro-inflammatory cytokines.5 We hypothesize that statin may reduce ICAM by interfering with the ligand binding.6 hsCRP is a pentametric protein produced by the liver in response to IL-6 secretion and is a biomarker for early inflammation. Statin is thought to reduce CRP by regulating CRP formation directly in hepatocytes.7 β2M is a lymphocyte activation marker that increases in patients with tumors, renal dysfunction, immunoreactive conditions, or infections, including HIV.8 Patients with more progressive disease have higher β2M levels, with highest in AIDS.9 We have modified the sentences so they are not redundant. Thank you for the input. Data collection and management The baseline of the study is W0. Thank you for the input. We have changed the unit with weeks. Figure 1 Thank you for the suggestion. We have added more bullets to the box. We have added footnotes to the diagram. Table 1 We have added the details. We have changed the terms accordingly, as suggested. Reference: Waldrop G, Doherty M, Vitoria M, Ford N. Stable patients and patients with advanced disease: consensus definitions to support sustained scale up of antiretroviral therapy. Trop Med Int Health. 2016 Sep;21(9):1124-30. doi: 10.1111/tmi.12746. Epub 2016 Jul 22. PMID: 27371814. Falasca F, Di Carlo D, De Vito C, Bon I, d’Ettorre G, Fantauzzi A, et al. Evaluation of HIV-DNA and inflammatory markers in HIV-infected individuals with different viral load patterns. BMC Infect Dis. 2017;17: 581. Chastain DB, Kayla RS, Daniel MR. Evidence-based review of statin use in patients with HIV on antiretroviral therapy. J Clin Transl Endocrinol. 2017; 8: 6-14. Eckard AR, Yin J, Sara MD, et al. Effect of 24 weeks of statin therapy on systemic and vascular inflammation in HIV-infected subjects receiving antiretroviral therapy. J Infect Dis. 2014; 209(8): 1156-1164. El-Gohary AM, Fawaz NA, Hassoba HM, Serwah A, Ali M. Soluble ICAM-1 in patients with chronic hepatitis C infection: a prognostic marker of disease activity. Egypt J Immunol. 2004;11: 109–119. Videm V, M Albrigsten. Soluble ICAM-1 and VCAM-1 as markers og endothelial activation. Scandinavian Journal of Immunology. 2008; 67(5). Montecucco F, Burger F, Pelli G, et al. Statins inhibit c-reactive protein-induced chemokine secretion, ICAM-1 upregulation and chemotaxis in adherent human monocytes. Rheumatology (Oxford). 2009; 48(3): 233-42. Grady BPX, Nanlohy NM, van Baarle D. HCV monoinfection and HIV/HCV coinfection enhance T-cell immune senescence in injecting drug users early during infection. Immunity & Ageing. 2016 Dec 31;13(1):10. Rao M, Sayal SK, Uppal SS, Gupta RM, Ohri VC, Banerjee S. BETA-2-MICROGLOBULIN LEVELS IN HUMAN-IMMUNODEFICIENCY VIRUS INFECTED SUBJECTS. Med J Armed Forces India. 1997 Oct;53(4):251-254. doi: 10.1016/S0377-1237(17)30746-3. Epub 2017 Jun 26. PMID: 28769505; PMCID: PMC5531080. Thank you and best regards, Evy" } ] } ]	1	https://f1000research.com/articles/10-151
https://f1000research.com/articles/12-1158/v1	15 Sep 23	{ "type": "Case Report", "title": "Case Report: Rehabilitation of missing lower anterior teeth with Maryland bridge", "authors": [ "Ankita Pathak", "Mithilesh Dhamande", "Seema Sathe", "Smruti Gujjelwar", "Mithilesh Dhamande", "Seema Sathe", "Smruti Gujjelwar" ], "abstract": "Congenital partial hypodontia is a common disorder, and many treatments have been developed for adolescents, but each has had one or more significant drawbacks. Maryland Bridge, a widely available treatment option, appears to offer great strength and aesthetics. The option is discussed in this article along with a successful application of it. A young male patient reported to us with the chief complaint of missing lower anterior teeth. After examination, clinical findings revealed that the patient was receiving orthodontic treatment and two lateral incisors missing in the lower arch. The patient was diagnosed with congenital partial hypodontia. A treatment plan was decided to rehabilitate the missing teeth with a Maryland Bridge. A treatment conundrum for restorative dentists is the presence of congenitally absent lateral incisors. There are numerous therapy alternatives, none of which are perfect. The outcome of this rehabilitation was aesthetically pleasing appearance, hence serving the required purpose. This article offers Maryland Bridge as a feasible substitute for the patient.", "keywords": [ "Maryland bridge", "congenitally missing teeth", "Esthetics" ], "content": "Introduction\n\nA resin bonded bridge’s fundamental design comprises a metal framework that supports a pontic. The lingual surface of one or more abutment teeth is connected to this with composite resin and the acid-etch technique for tooth enamel. The composite resin can be attached to the structure in a variety of ways.1 In cases of good survival rates, resin bonded bridges can be considered as a good treatment option in aesthetic region of missing teeth.2 In spite of disadvantage such as debonding of restoration resin bonded bridges shows high success rates, and minimally invasive procedure in general dental setup.2 Rehabilitation with resin bonded bridge retentive vertical grooves and wing shaped preparation should be done on adjacent teeth3 The prevailing consensus is that implants shouldn’t be placed until definitive evidence of growth completion has been gathered, such as consecutive-year cephalometric radiographs that show growth is incomplete.1 Studies conducted over an extended period of time have demonstrated that implant-supported crowns are the most durable, aesthetically attractive, and stable restoration currently available.2\n\nResin bonded bridges are not a no-prep method, but rather need extensive treatment planning and technical abilities.4 Successful resin-bonded fixed partial denture (FPD) abutment preparations are particular and unique, relying on appropriate enamel changes to establish a distinct incisal-gingival path of insertion and resistance form.4 This clinical report describes a conservative technique for replacing missing lower lateral incisors is described. This technique involves a Maryland bridge, a resin-bonded fixed partial prosthesis.\n\n\nCase report\n\nA 15-year-old Asian male patient who was a student at school came with the main complaint of missing lower anterior teeth and the unfavorable appearance brought on by the missing teeth to the Department of Prosthodontics in Sharad Pawar Dental College and Hospital, Sawangi, Wardha. The patient had congenitally absent right and left lateral incisors and showed excellent general oral health condition (Figure 1, 2). He had been receiving orthodontic treatment for crowding in the lower arch for the past two years and had been wearing a prosthesis in lower lateral incisor regions that was stabilized along with orthodontic braces. After his orthodontic treatment was finished, he was eager to replace the missing tooth with a durable aesthetic option. He had not yet reached full physical development, according to a series of cephalometric radiographs, hence he was not yet a candidate for implant placement. He decided to get a Procera Maryland Bridge as a temporary fix after considering his options. His psychological profile was sound, and his expectations were realistic.\n\nOnly the lingual surfaces of the abutments required minimal tooth preparation using the standard guidelines as follows:\n\n1. Wing shaped preparation of depth 1-2 mm carried out on cingulum area of the canines bilaterally with tapered fissure bur.\n\n2. After which two vertical grooves prepared on central incisors of dimensions 1-1.5 mm occluso-gingivally.\n\n3. All the margins of preparation were finished and the preparations were carefully monitored to make sure they didn’t go past the linguo-proximal line angles of the abutments.\n\n4. With the aid of addition silicone impression material (Express XT,3M ESPE, Germany 36892), impression was made and submitted to the lab. Using non-precious alloy, a metal structure with ‘wings’ extending onto the preparations was created. With the Vita 3-D Master shade guide, shade selection was done. In order to avoid the tooth discoloration caused by the blockage of light transmission, the laboratory technician was advised to keep the metal wings of the prosthesis off the incisal third. Universal self-etch resin cement was used to secure the restoration (Rely X U100, 3M ESPE, Germany). At both centric and eccentric mandibular positions, the occlusion was examined to rule out any interferences (Figure 3, 4). Instructions for post-cementation care were given, such as the patient should avoid eating or drinking anything for 60-90 minutes, biting with anterior teeth for any hard or sticky food should be avoided, use of dental floss in proximal regions to avoid food lodgement and secondary caries, if debonding of the prosthesis occur, the patient should visit the dentist. Followed by periodic visits given to the patient. On the follow up visits there was no debonding of bridge and the patient was happy. The outcome of the procedure was aesthetically satisfactory and pleasing appearance.\n\n\nDiscussion\n\nRehabilitation of congenital partial hypodontia includes various treatment options, however minimally invasive approach with resin bonded Maryland bridge was the treatment of choice. In the literature there are a number of citations providing satisfactory outcomes of the Maryland Bridges.1,2 Success of Maryland Bridge depends on electrolytic etching, micromechanical bonding, accurate construction and fitting of the prosthesis.1 In order to replace lost teeth with a typical fixed partial denture, all of the abutment teeth’s surfaces must be prepared, which, given how big the pulp chambers are in young patients, increases the risk of pulpal damage.3 In this situation, resin bonded fixed dental prostheses are a good option. The “Maryland Bridge” is a resin-bonded permanent dental prosthesis that was created at the University of Maryland. The retention of the resin-bonded prosthesis has improved thanks to the creation of new resin cements that chemically connect to both the tooth surface and the etched metal alloy.4 Micromechanical retention is used to keep the Maryland Bridge in place. Since precious alloys cannot be etched to provide the micromechanical retention, only non-precious alloys can be used with Maryland Bridges.5\n\nFactors contributing to success of Maryland Bridges include proper case selection, ultimate abutment selection, bridge designs such as retainer wing coverage, vertical depth grooves and technical considerations. With confluence and balance with all these factors, the success rates of Maryland Bridges can be raised.6\n\nMaryland Bridges have a number of benefits, including minimal tooth preparation, which preserves the enamel, minimal pulpal trauma, a lower risk of gingival irritation, a single insertion path that prevents displacement, improved aesthetics, patient satisfaction, and the avoidance of local anaesthesia.6 However, it also has several drawbacks, such as its technique-sensitive placement and the metal retainer’s tendency to show through the anterior teeth. For the prevention of caries, certain precautions are required, such as appropriate sealing of the prosthesis and tooth surface margin.7 To maintain healthy gingiva, the pontic’s gingival surface should be heavily glazed and in passive contact with the tissue.8\n\nPartial or complete debonding of the Maryland Bridge can occur. In addition to this with partial debonding and food lodgement secondary caries can take place. In spite of these, Maryland Bridges are the ultimate treatment option for enhancing aesthetics and optimizing results.\n\n\nConclusion\n\nWhen it comes to replacing missing teeth, restoring dental function and aesthetics, and increasing patient satisfaction, resin bonded bridges can be quite effective. The resin bonded bridge should be taken into consideration more frequently as the restoration of choice for small spans, given extensive patient assessment and the application of meticulous clinical methods.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient and the patient’s father.", "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\nSaunders WP: Resin bonded bridgework: a review. J. Dent. 1989 Dec; 17(6): 255–265. PubMed Abstract \| Publisher Full Text\n\nBalasubramaniam GR: Predictability of resin bonded bridges – a systematic review. Br. Dent. J. 2017 Jun; 222(11): 849–858. PubMed Abstract \| Publisher Full Text\n\nEdelhoff D, Sorensen JA: Tooth structure removal associated with various preparation designs for anterior teeth. J. Prosthet. Dent. 2002 May; 87(5): 503–509. Publisher Full Text\n\nBurgess JO, McCartney JG: Anterior retainer design for resin-bonded acid-etched fixed partial dentures. J. Prosthet. Dent. 1989 Apr; 61(4): 433–436. PubMed Abstract \| Publisher Full Text\n\nChan AWK, Barnes IE: A prospective study of cantilever resin-bonded bridges: An intial report. Aust. Dent. J. 2000 Mar; 45(1): 31–36. PubMed Abstract \| Publisher Full Text\n\nDurey KA, Nixon PJ, Robinson S, et al.: Resin bonded bridges: techniques for success. Br. Dent. J. 2011 Aug; 211(3): 113–118. Publisher Full Text\n\nThoma DS, Sailer I, Ioannidis A, et al.: A systematic review of the survival and complication rates of resin-bonded fixed dental prostheses after a mean observation period of at least 5 years. Clin. Oral Implants Res. 2017 Nov; 28(11): 1421–1432. PubMed Abstract \| Publisher Full Text\n\nVerzijden CWGJM, Feilzeri AJ, Creugers NHJ, et al.: The Influence of Polymerization Shrinkage of Resin Cements on Bonding to Metal. J. Dent. Res. 1992 Feb; 71(2): 410–413. PubMed Abstract \| Publisher Full Text" }	[ { "id": "208601", "date": "27 Sep 2023", "name": "R. Scott Conley", "expertise": [ "Reviewer Expertise orthodontics", "orthognathic surgery", "interdisciplinary care" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for your invitation to review the paper.\nThe paper is very nice for what it covers, however there are many missing details that are critical for the reader to understand regarding the potential for long term success of this style of restoration.\n1) There were no x-rays to demonstrate root length, root width, bone height, etc for the reader to understand the ability of the selected teeth to withstand the restorative load.\n2) It would be beneficial to include full pre-orthodontic treatment records, full progress records (i.e. just before the restoration was to be placed) and full post treatment records at the conclusion of treatment by all services.\n3) Given this is a case report on a young individual, a long term assessment (i.e. post-braces removal of at least 1 year) would be very beneficial.\n4) Full facial analysis including face height, masticatory load etc. would be beneficial. With the significant improvement in adhesive technology, this particular reviewer likes the return to minimally invasive restorative approach such as this. At the same time, an understand of the load is essential since short face patients with deep overbite and strong orofacial musculature can fracture the restoration from the teeth or when the adjesive is strong enough, can fracture the teeth themselves. This paper does not provide enough detail in this regard to fully assess the potential for long term success.\n5) Again, given the young age of the patient and the need for a 60+ year replacement, were other treatment options discussed including orthodontic movement of the centrals to create bone, other facial esthetic goals etc.?\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] }, { "id": "212624", "date": "06 Nov 2023", "name": "Matthias Kern", "expertise": [ "Reviewer Expertise Prosthodontics and Dental Materials" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this report, the treatment of a patient with two resin-bonded bridges following the outdated classical Maryland bridge design with two metal retainer-wings is described.\nThe cited references are outdated ignoring original studies and literature published within the last ten years which revealed superior results with single retainer resin-bonded bridges, i.e.\nBotelho MG, Ma X, Cheung GJ, Law RK, Tai MT, Lam WY. Long-term clinical evaluation of 211 two-unit cantilevered resin-bonded fixed partial dentures. J Dent 2014;42:778-784.\nBotelho MG, Chan AW, Leung NC, Lam WY. Long-term evaluation of cantilevered versus fixed-fixed resin-bonded fixed partial dentures for missing maxillary incisors. J Dent 2016;45:59-66.\nAlso the even better outcomes with alumina and zirconia ceramic single retainer resin-bonded bridges are completely ignored, i.e.\nKern M. Fifteen-year survival of anterior all-ceramic cantilever resin-bonded fixed dental prostheses. J Dent 2017;56:133-135.\nKern M, Passia N, Sasse M, Yazigi C. Ten-year outcome of zirconia ceramic cantilever resin-bonded fixed dental prostheses and the influence of the reasons for missing incisors. J Dent 2017;65:51-55.\n\nTherefore, this article describes an outdated treatment method, with inferior longevity and inferior function than the actual concepts with resin-bonded bridges.\n\nIt might potentially mislead readers as the described treatment method dose not yield good results on the long run.\nIn addition, the history of resin bonded bridges is not correctly described as Rochette and Howe and Denehy described the principles years before the researchers from Maryland stated with it, e.g.\nRochette AL. Attachment of a splint to enamel of lower anterior teeth. J Prosthet Dent 1973;30:418-423.;\nHowe DF, Denehy GE. Anterior fixed partial dentures utilizing the acid-etch technique and a cast metal framework. J Prosthet Dent 1977;37:28-31.\nThe discussion does not reflect the limitations and shortcomings of the article.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1158
https://f1000research.com/articles/12-90/v1	24 Jan 23	{ "type": "Research Article", "title": "Comparative analysis of health authorities’ spokespersons and health influencers during the COVID-19 pandemic", "authors": [ "N. Nurlaela Arief", "Andika Putra Pratama", "Vinka Amalia Hasta Barata", "Nyayu Lathifah Tirdasari", "Dicky Budiman", "Andika Putra Pratama", "Vinka Amalia Hasta Barata", "Nyayu Lathifah Tirdasari", "Dicky Budiman" ], "abstract": "Background: Concerns over an infodemic following a surge in health misinformation circulating on social media set out the government's priority for Indonesia. Given the urgent work on the coronavirus disease 2019 (COVID-19) response, the government collaborated with health-related spokespersons and influencers with a medical background by starting a COVID-19 public education campaign on social media. A collaborative initiative involved health spokespersons from government and non-government to clarify misinformation about COVID-19. Methods: The primary purpose of this research is to compare government and non-government spokespersons by examining their roles in educating about COVID-19 vaccines and health services. This study employed comparative factor analysis and non-participatory observation toward the media activity of spokespersons in Indonesia. Using a questionnaire, this study examined the dimensions of public campaigns, risk communication, health and emergency, leadership and communication from Indonesian spokespersons. The data collection was conducted in two stages: a pilot study involving 102 respondents and the actual study involving 276 respondents. Results: Findings show that utilizing spokespersons is important due to its capabilities of reaching diverse audiences and improving public engagement, trustworthiness, and credibility. Conclusions: Combining health authorities’ spokespersons and health influencers in Indonesia, this study provides valuable insights for communication management in developing and supporting the role of health authorities from the government, non-government as well as medical sectors.", "keywords": [ "Omicron", "Spokesperson", "Health Authorities", "Risk Communication", "Health Influencer." ], "content": "Introduction\n\nThe government and health authorities have taken various approaches with diverse strategies during the coronavirus disease 2019 (COVID-19) pandemic. Approaches start by informing and forcing the public to participate in disease prevention and persuading reasonable goals for health.1 In fact, a comprehensive study conducted in seven countries in Europe discussed risk communication during COVID-19: familiarity, compliance, and trust in WHO precautions.2 Further, a former study was conducted in ten European countries, the USA,3,4 Japan, and Australia5 concerning the importance of maintaining distance, self-isolation, and quarantine, the application of which varies from simple methods, social campaigns, and heavy sanctions if violated.\n\nIn global health policy, the World Health Organization (WHO) has provided guidance and coordinated various efforts to deal with COVID-19. However, each country is also fighting the infodemic: the abundance of information, both accurate and inaccurate, makes it difficult for the public to choose which source is prominent, trusted and reliable to support the right decisions for healthy life during the pandemic.\n\nThe infodemic phenomenon is arguably getting stronger because of the high use of social media. With information overload, even false and mythical information. If communities are not targeted appropriately, public health instruction and guidance may not address cultural or linguistic barriers adequately. Therefore, health communication is an essential resource for public health campaigns, seeking behavior change and reducing health gaps in the community.6\n\nSpecifically, the best practice in Indonesia, by compensating for the infodemic, reliable sources of information are needed, and communicators can convey messages effectively. That makes having a high level of critical health literacy particularly important.7 Based on the Google year in search 2021, overall trends that were most searched by people in Indonesia, included those related to covid-19, covid-19 vaccines, Adverse Events Following Immunization (AEPI or KIPI), types of covid-19 vaccines, how to check vaccine certificates, how to list of vaccines, and the nearest vaccination facilities.8\n\nDiscussion about science related to COVID-19 is not easy to design as a public communication campaign. With the increase in the search for science related to COVID-19, the emergence of new models for the formation of hype in science communication and public understanding about science. In this new model, the blame for hypnotizing scientific results and/or the significance of research findings lies not with the traditional structures of public relations and science communication journalists, but with politicians and social media celebrities, with serious consequences for public policy, as perceived in the case of hydroxychloroquine (HCQ) in Brazil.9 As another reference previous research in Japan conclude the effectiveness of refutational two-sided messages for risk communication for new vaccines introduced during the COVID-19 pandemic.10\n\nThe outbreak of the COVID-19 pandemic has resulted in preventive and protective action from the government, healthcare professionals, companies, and medical influencers. Since the first vaccine was approved in Indonesia in January 2021, the government of Indonesia has encouraged the public to support the vaccination program.11 Although, in Indonesia, an increasingly widespread anti-vaccine movement in a group of people or community efforts to persuade people to refuse vaccination.12 In addition, the majority of false information and invalid conclusion were purposively disseminated on social media.\n\nThis condition may create a crisis and emerging risks in the health sector due to the lack of timely and accurate health information. Therefore, WHO supported risk communication intervention contributions from every organization. The organizations define risk communication as various communication required through the preparedness, response, and recovery stage of a serious health situation to encourage informed stakeholders, positive behavior change, and trust maintenance.13 Social media is responsible for the main channels for spreading COVID-19 misinformation content compared to mass media channels.14 The freedom of information through social media may allow people to access valid and invalid information. It would also create potential problems as people would share their pros and cons of vaccination without checking the validity of the information. Information sharing is not only considered as a key source of information, but also a factor in cooperation and modeling problem awareness.15\n\nThe Indonesian government, public health practitioners and even health-related influencers collaborate and counterbalance the spread of negative campaigns about vaccine education and related COVID-19. A group of health spokespersons or influencers from a medical background or voluntarily give objections, provide education and socialization, and clarify misinformation about the COVID-19 topic. Previous research pointed out that risk communication determines and influences an understanding of risk perceptions and shapes public perceptions, leading to behavioral intentions in public health risk situations.16 Accordingly, the purpose of this research is to explore the role of health authorities’ spokespersons and compare government vs non-government spokespersons with the principles of risk communication theory on spokespersons in educating about COVID-19 vaccine and health services in Indonesia. This study has a novelty value because to the best of our knowledge, the exploration of health authorities’ spokespersons during COVID-19 crisis has not been previously discussed in Indonesia. Most of the studies focus on technical aspects, such as treatment & vaccines.\n\n\nLiterature review\n\nThe vaccine refusal in Indonesia and the pro-vaccine against anti-vaccine phenomenon are related to the public communication campaign. It relates to a program as an endeavor aimed at informing or influencing the behavior of a broad audience over a certain period using a set of organized communication strategies and displaying a series of messages mediated in various channels to create collective benefits for individuals and society.17 The term campaign describes a phase designed to achieve specific goals. Furthermore, its application is so broad that it includes communication strategies to produce various social, political, commercial, and health effects. Hence, the incorporation and implementation of communication campaigns with vaccinations should be well-planned routine and integral vaccination programs.\n\nFormer literature18 concludes several key points in designing and implementing a communication plan, including the two-way communication process and knowledge. However, the essence is to change behavior, and the selected communication tools need to be used creatively to promote the positive vaccine campaign. In addition, strengthening social norms, building public trust, and continuing government competency in handling the pandemic are vital to increasing vaccination intentions.19\n\nThe pandemic situations have challenged the importance of communicating risk beyond the everyday challenges of environmental, safety, and health risks to audiences. In terms of risk communication, individuals tend to form attitudes about complex risk-related information by emphasizing existing value systems.20 This form of attitude is due to its hard-to-define nature, as the solutions to address it are often uncertain. Health communication commenced by fostering well-being and basic psychological needs has the potential to promote sustainable behavior prevent the infodemic.6 Delivering the risk communication efforts to curb the spread of communicable disease.21 Although there is broad consensus among health experts, medical professionals, and policymakers regarding the vaccination, there is a required plan on how the information communicates effectively with the public to address their concerns, beliefs, and trust about vaccines.\n\nIt is necessary to design collective values that provide proper guidance since the uncertainty associated with vaccination is a significant issue for public health practitioners.22 Previous literature concludes that public relations play an essential role in managing risks and crises as social media can contribute to real-time dialogue, build trust, and motivate the public to take action for risk and crisis communication around health threats.23 Furthermore, a key mechanism in reducing the spread of misinformation is the timely provision of risk communication regarding the emergency faced.24 The rapid development of the latest technologies during pandemics enables the Indonesian government to implement risk communication messages to reach the public through various channels, including spokespersons. To determine the success of risk communication depends on how the public makes health-related decisions in the face of contradictory information.25 The stream of messages warning and safety are essential to achieve the effectiveness of the communication.21\n\nThe context of health authority’s spokesperson in this research is health communicators involved in campaigning vaccines agenda, health promotion and preventive action. The chosen government spokespersons, non-government spokespersons, medical practitioners, health influencers, pediatricians, and health service providers in Indonesia. Further, the spokesperson includes those mentioned professions. Previous research defines a spokesperson as a credible person who communicates voluntarily to inform their network regarding specific issues. In several developing countries, effective communication should be ‘pro-poor and ‘pro- vulnerable’.26\n\nHence, proper communication methods need to be analyzed and implemented. The problem in communicating healthcare information during COVID-19 is informing the message with proper terminology for the public.27 Similarly, former research found that different populations may acquire different perceptions regarding the crisis, and different spokespersons required for different population segments, especially for younger and older generations.28 The presence of a health spokesperson can become an individual bridging the gap of understanding between fact and fake.\n\nIn the COVID-19 situation, the health communication is an emergency to control the situation, such as to mitigate the spread and also the public reaction. At this moment, the spokespersons have to deliver the potential consequences of the infodemic. Since then, there must be careful strategic communication to be applied for the emergency.\n\n\nMethods\n\nThis study employed comparative factor analysis and non-participatory observation toward the media activity of spokespersons. The health spokespersons were preferred to represent government, medical experts, and non-government or volunteers. The factors of risk and health communication variables were generated from the literature review according to health spokesperson characteristics. The data were collected by an online questionnaire with a seven-point Likert scale. This online assessment tool is preferable when physical restriction contact occurs in this pandemic. The questionnaire was distributed through the researchers’ network by optimizing email, social media, and personally approached by the researchers. Refer to research ethics, this research asked for respondents’ willingness to fill in the questionnaire at the beginning. It also mentioned that all the data are confidential and appropriately used for the research’s purpose. Bias can lead to distorted results and false conclusions. To reduce bias, this study used several points of view within the research team, including health practitioners, communication practitioners, and academics. In addition, probability-based sampling methods was also utilized to avoid sampling bias. The higher sample sizes provide more reliable results.\n\nOverview\n\nThe data collection was conducted in two phases. The first phase was a pilot study collecting data from 102 respondents, the second phase was the actual study collecting data from 276 respondents. Respondents mainly were enrolled through an online survey form between March 7–14, 2022 and 9–12 May 2022. Participation in the survey was voluntary and unpaid.\n\nIn addition, secondary data by optimizing big data retrieval was carried out in January 2021–July 2021 (Phase 1) and December 2021–February 2022 to determine what topics are circulating in the public regarding COVID-19 education (Phase 2) February and March 2022, to determine Indonesia health spokespersons. The period of monitoring was three months when Omicron occurred, which was December 2021 to February 2022. This secondary data helped the studies to identify the name of the spokespersons (Table 3) which will be assessed with the questionnaire.\n\nSample\n\nInitially this study wanted to achieve 500 respondents from Indonesia and Australia. Samples were selected using the Slovin formula with a 10% margin of error and 150 million of population, resulting in the minimum samples of 100 respondents. The equation used n = N/(1+Ne2) = 150,000,000/(1+150,000,000(10%2)) = 100. After distributing 500 online questionnaires through the email, social media, and personally approached, this study received 276 final respondents. The English survey form was translated to its native language (Bahasa Indonesia). The questionnaire can be found as Extended data.35 This study aimed to collect data from respondents aged 16–50 years old. The samples were designed randomly with optimized distribution over the network of ITB (Indonesia), and the public.\n\nAs shown in Table 1 demographic summary, the respondents come from diverse backgrounds. However, to ensure this research effectiveness, the respondents were asked about their ideal spokesperson preferences in health promotion & preventive action. To test the questionnaire requires a small sample to align the public campaign theory and risk and health communication dimensions, the researchers conducted a pilot study with 102 samples. It is essential to test the validity of the early research framework. Therefore, it needs a minimum of fifty questionnaires. It considers adequate even if the larger sample will represent a better result.29\n\nIn total, the questionnaire consists of 54 questions. The component of questionnaire designed and verified by discussion among the expert from medical doctors & the research team.\n\nThe authors state that the work is written with due consideration of ethical standards. The study was conducted following the ethical principles approved by the Ethics Committee of the University on 01 March 2022 (approval number 1132A/IT1.C09.1/TA.00/2022). The research complied with all ethical standards and anonymity; there were no requirements to provide confidential information (name, date of birth or place of residence, etc.). The respondents gave their written consent for the conduct of the research and data processing. The written consent was provided before the survey. Respondents could not proceed to the survey if they were unwilling to provide the consent or quit otherwise.\n\nData processing was deployed using Ms Excel 2019 for the data cleaning process, then using SPSS 27 to find the distribution of data, whether it is the frequency in each respondent’s answer choices, descriptive statistics (mean, mode, median). The process continued with a data visualization process using Ms Excel and Tableau. Table 2 shows reliability statistics. Each questionnaire item using a Likert scale is tested for reliability using Cronbach’s Alpha, and this study is considered valid and reliable if the value exceeds 0.70. In the second phase, this study acquired 276 respondents.\n\nValidity and reliability test were conducted before analyzing the data. A validity test aims to examine the truth of the measurement. The significant score of each item is below 0.05, which indicates that each item is valid. The reliability test was done to check the consistency of the measurement using coefficient α. The questionnaire is considered reliable if the Cronbach alpha > 0.7. Cronbach alpha’s values for all sets of factors (subscales) are more than 0.7. Hence, this study is considered valid and reliable.\n\nSummary statistics, including percentages, were used to analyze the data. We use descriptive statistics, including proportions and graphical representations, such as 100% stacked bar charts to analyze and display the data. The statistical significance of the difference in proportions was tested using a t-test. Additionally, we used graphical representations and simple ranking for summarizing results. Statistical analyses were performed on SPSS. To simplify the analysis of the results, we used code to replace the name of the spokespersons. Table 3 below explains the code for spokesperson.\n\n\nResults\n\nTable 1 displays respondents’ demographic information, including age, gender, employment, and the respondents’ city. The number of respondents was 276 (female = 57,25%; Male = 42,75%), with an average age of 16–45.35 Their employment status was student, private employee, civil servant/government employee, entrepreneur, academician, and other. The respondents were from 11 cities in Indonesia (Bekasi, Surabaya, Malang, Banten, Bogor, Depok, Yogyakarta and Other cities). All respondents included in this study were examined for eligibility and confirmed eligible.\n\nThis question asks the extent to which the message delivered by the spokespersons are beneficial (i.e. Perceived Benefit). Based on the result (Figure 1), it is found that the means of Perceived Benefit for non-governmental medical doctor(s) as spokespersons, specifically for the second one (NGS2, means = 5.53), are relatively higher than for governmental one(s). Particularly for the second non-governmental medical doctor (NGS2), there are more people who strongly agree (26.45%) that the person has a significant influence in communicating messages to people and the communication about COVID-19 in Indonesia, compared to other doctors (below 15%). Particularly interesting is that the governmental, non-medical, official (GS3) has the lowest mean of Perceived Benefit (means = 4.78). The means of Perceived Benefit for the first and second governmental medical doctors are identical to one another (means = 5.23).\n\nThis question asks whether the message delivered by the spokespersons provides an incentive to the respondents to change their behavior (i.e. Behavioral Change). Somewhat mirroring from the trend that can be seen from result of Perceived Benefit, the result of Behavioral Change (Figure 2) shows that the perceived impact of the second non-governmental medical doctor in communicating COVID-19-related matters towards self-behavior. With the means of 5.21, respondents tend to agree more with the respective spokesperson (compared to other spokespersons) being able to influence changes in their behavior. Similar to the previous result, the person with the lowest means regarding perceived behavioral change in people after the message is the governmental, non-medical, person (means = 4.68).\n\nThe question asks whether the message delivered by the spokespersons makes the respondents willing to be vaccinated (i.e. Vaccination Promotion). While there are some differences among the means, the differences do not seem to be significant. However, the second spokesperson (non-governmental, medical, doctor) as shown in Figure 3 is shown to induce more people who strongly agree that the person makes them willing to be vaccinated (40.58%). Again, the governmental, non-medical, spokesperson (GS3) is shown to have the lowest means, indicating that the person is less able (compared to the others) to make the respondents willing to be vaccinated.\n\nAs Figure 4 shows, when asked the extent to which the spokespersons are experts at health-related matters, the first non-governmental, medical, doctor (NGS1) has the highest means (5.88), followed by the second non-governmental, medical, doctor (NGS2, means = 5.78). Governmental, medical, doctors (GS1, GS2) come third and fourth respectively. The governmental, non-medical, spokesperson (GS3) comes last. This figure generally supports the previous results that show people’s agreement with the impact of the non-governmental, medical, doctors as spokespersons regarding COVID-19-related matters.\n\nRegarding the channels perceived (Figure 5) as the most effective and beneficial when it comes to information pertaining to OMICRON, Online media (means = 6.18) and Instagram (means = 6.12) are shown to be the highest. YouTube (means = 5.87), Twitter (means = 5.80), TikTok (means = 5.62), TV (means = 5.61), and WhatsApp (means = 5.08) are within the range of 5-6 of agreement by respondents. The channels perceived to be the least effective and beneficial are Spotify (4.86), Facebook (4.80), Radio (4.70), and Traditional Channel (means = 4.61).\n\nFigure 6 regarding risk and health communication shows that most respondents (61.59%) tend to strongly agree on RHC03 regarding consequence, which is also the highest percentage, while for the lowest percentage is for RHC06 regarding probabilities (39.49%). The rest, an explanation of the findings on this RHC, can be seen in the Table 4.\n\nTable 4 shows that the value of RHC03 regarding the consequences of contracting the disease is the highest, and the value of RHC06 probabilities by getting a COVID-19 vaccine, there is a less risk of omicron is the lowest. This shows that respondents tend to strongly agree that there will be consequences if they do not comply with the health protocols, leading them to be exposed to the COVID-19, while a low RHC04 value indicates that respondents tend to be disobedient and prefer to go on vacation and go home so that they do not reduce the risk of developing Omicron cases.\n\nRegarding the extent to which the respondents trust spokespersons from the government (Figure 7), the means (5.30) lie in between “somewhat trust” and “trust.” Most people generally trust the spokespersons from the government (35.14%), followed by those that somewhat trust the government (28.26%).\n\nRegarding how consistent the spokespersons of their choice providing information regarding OMICRON (Figure 8) in particular, most respondents tend to answer either “consistent” (37.68%) or “somewhat consistent” (33.33%). No one answered “strongly inconsistent.” Overall, the messaging appears to be relatively consistent.\n\nRegarding how interactive the spokespersons of their choice are towards the public (Figure 9), most respondents tend to answer “interactive” (40.58%), followed by “somewhat interactive” (28.99%). Overall, the means for perceived interaction between the spokespersons and the public is 5.41.\n\nRegarding the perception of the extent to which public trust (Figure 10) is important towards the leaders in dealing with the pandemic crisis, the respondents overall lean towards agreeing that it is “important” (35.51%) to “highly important” (32.25%). This indicates the importance of public trust.\n\n\nDiscussion\n\nThe research evaluates how audiences perceive a sample of five spokespersons from both government and non-government sources with medical and non-medical backgrounds. Based on perceived benefits, spokespersons from the non-government sector gain higher trust than the government. On parameters related to risk and health communication, awareness, health promotion, consequences, perceived control, well informed choices, probabilities, and voluntariness show variations. Risk communication designed and delivered by experts, policymakers, and regulators showed less effective results, especially related to risk & health communication. Risk communication should be carefully designed; it requires a scientize and democratize approach30 especially with issues related to covid, vaccines and uncertain scientific and ethical characteristics.31 Risk and health communication has a wide and diverse audience, so it is necessary to design risk communication targeted a specific audience: in the form of a personalized communication strategy on targets who have a high risk of contracting disease., this research shows that trust in the government spokesperson is quite high, and the majority of the respondents agree. Understanding key information is needed, creating messaging that is appropriate and relevant, and disseminating information in whatever means works best are important steps in battling the infodemic.4 To sum up, these results show that to communicate health risks in the COVID-19 pandemic in Indonesia, the government spokespersons gain the same high level of trust as non-government spokespersons. related to consistent and leadership communication. No respondents answered “strongly inconsistent.” Overall, the message appears to be relatively consistent. The consistency and routine of the leaders who become spokespersons are most expected by the audience in anticipation of reducing worries and stress due to the continued emergence of the Omicron variant in Indonesia.\n\n\nConclusions\n\nThe Indonesian government started to perform a collaborative agenda to support the vaccination campaign, which was carried out amid the current COVID-19 pandemic. The vaccine is one of the expected efforts to end the pandemic. The vaccination campaign implementation in Indonesia is facing a massive scope and complexity. There is always an uncertainty factor in vaccines. A carefully crafted communication strategy should be an integral component of the vaccination program, addressing the specific factors influencing the target/population to assess progress toward achieving herd immunity. Hence, the success of public communication theory relies on the public’s acceptability of vaccination. The research provides valuable insights for communication management and government in developing and supporting the role of health authorities from the government, non-government and medical sectors. Based on the results, several factors emerge as important. The proficiency of medical practitioners cannot determine the spokesperson’s effectiveness. A spokesperson who possesses referent power, expert power, and reward power should be more effective than other spokespersons.32 Furthermore, the more significant the social capabilities that are possessed, the greater the ability to influence the behavior of its network. Another study concluded that a spokesperson’s physical attractiveness to be more persuasive for implementing organizational messages.33 How the spokesperson deals with the media request and offers an answer as soon as possible to give other media information from other sources can also reflect as a good spokesperson practice.34 In addition, spokespersons in this pandemic play an important role in filling the information gap between the government and the public. The effectiveness of the spokesperson’s implementation is critical in the rapid advancement and change of digital information. Unfortunately, many methods and application techniques were evolving in vain without proper crisis communication-based implementation. The authority of health spokesperson is crucial to respond to public health risk situations. The organization needs to emphasize the vital role of a spokesperson in these circumstances, as one which helps and assists in developing messages sent or delivered to the public. Another important reason for utilizing spokespersons is their capabilities of reaching diverse audiences, public engagement and empowerment, trustworthiness, and credibility. These practices provide valuable indicators for other countries and make a theoretical contribution. This study implies strengthening the preparedness response during a health crisis, especially in risk & crisis communication. The literature has not explored the study of health authorities spokespersons previously. This, combined with the Indonesian perspectives, brings new insights to the field. Social media use is incredibly high in Indonesia, so it acts as a good exemplar for the field. It also builds on the growing literature about the importance of individual and health practitioners as health authorities, especially in the social media space during the COVID-19 crisis.\n\nThis scoping review has several limitations. First, when the data was collected, Indonesia was experiencing a new type of COVID-19 virus, causing that data collection was not optimal. Second, the literature review on spokespersons was mainly from articles and international reports (e.g., WHO, Satgas COVID), with limited references to the practice of spokespersons in Indonesia and Asia. Thirdly, when grouping spokesperson data presented with big data, many spokesperson figures appeared and were curated to be selected based on the evaluation of the research team. Fourth, some data on spokesperson statements and non-participatory observation are dynamic from time to time and change simultaneously. Therefore, some of the spokespersons as an object of research might have been excluded from this review process.", "appendix": "Data availability\n\nDryad: Comparative analysis of health authorities spokesperson and health influencer during the COVID-19 pandemic: A case in Indonesia. https://doi.org/10.5061/dryad.12jm63z23. 35\n\nThis project contains the following underlying data:\n\n- Response_Spokesperson_2 (Responses to survey)\n\nDryad: Comparative analysis of health authorities spokesperson and health influencer during the COVID-19 pandemic: A case in Indonesia. https://doi.org/10.5061/dryad.12jm63z23h. 35\n\nThis project contains the following extended data:\n\n- Quesionnaire_Spokesperson_1_Rev_(1) (questionnaire - English translation)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nOxman AD, et al.: Health communication in and out of public health emergencies: to persuade or to inform? Heal. Res. Policy Syst. 2022; 20(1): 28–29. PubMed Abstract \| Publisher Full Text\n\nVarghese NE, et al.: Risk communication during COVID-19: A descriptive study on familiarity with, adherence to and trust in the WHO preventive measures. PLoS One. April 2021; 16(4): e0250872–e0250815. PubMed Abstract \| Publisher Full Text\n\nSchneider CR, Freeman ALJ, Spiegelhalter D, et al.: The effects of quality of evidence communication on perception of public health information about COVID-19: Two randomised controlled trials. PLoS One. 2021; 16(11 November): e0259048–e0259020. PubMed Abstract \| Publisher Full Text\n\nKorin MR, Araya F, Idris MY, et al.: Community-Based Organizations as Effective Partners in the Battle Against Misinformation. Front. Public Health. 2022; 10(March): 1–4. PubMed Abstract \| Publisher Full Text\n\nBudiman D, Chu C: A SWOT Analysis of Indonesia’s COVID-19 Pandemic Response Strategy. Int. J. Adv. Heal. Sci. Technol. 2021; 1(2): 50–52. 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PubMed Abstract \| Publisher Full Text\n\nAbu-Akel R, Spitz A, West R: The effect of spokesperson attribution on public health message sharing during the COVID-19 pandemic. PLoS One. 2021; 16(2 February): e0245100–e0245115. PubMed Abstract \| Publisher Full Text\n\nde Winter JCF , Dodou D, Wieringa PA: Exploratory factor analysis with small sample sizes. Multivar. Behav. Res. 2009; 44(2): 147–181. Publisher Full Text\n\nLidskog R: Scientised citizens and democratised science. Re-assessing the expert-lay divide. J. Risk Res. 2008; 11(1–2): 69–86. Publisher Full Text\n\nFuntowicz S, Ravets J:Values and Uncertainties. Handbook of Research Methods and Applications in Empirical Macroeconomics. Springer Science;2008; pp. 361–369.\n\nTom G, Clark R, Elmer L, et al.: The use of created versus celebrity spokespersons in advertisements. J. Consum. Mark. 1992; 9(4): 45–51. Publisher Full Text\n\nWang SW, Scheinbaum AC: Enhancing brand credibility via celebrity endorsement trustworthiness trumps attractiveness and expertise. J. Advert. Res. 2017; 58(1): 16–32. Publisher Full Text\n\nConstantin A, Petruca I: The Role of The Spokesperson in The Process of Public Relations. Int. J. Commun. Res. 2019; 9(3 July): 261–265.\n\nArief NN, et al.:Comparative analysis of health authorities spokesperson and health influencer during the COVID-19 pandemic: A case in Indonesia, Dryad. [Dataset]. 2022. Publisher Full Text" }	[ { "id": "175543", "date": "14 Jun 2023", "name": "Hanny Hafiar", "expertise": [ "Reviewer Expertise Health communication", "Health promotion" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 commend the authors for their efforts. I provide my comments for this article as follows:\nThe abstract section has briefly justified the purpose of this research well, how the research method is applied. I think the keywords are also good and represent the description of the content of this research. However, the author(s) failed to highlight the research results, which are in accordance with the research objective, namely \"to compare.\" What is the outline of the comparison?\n\nThe Introduction section is well-written in the present research context. However, this introductory section does not explain in detail why there is a need for this comparative research. What is the urgency why these health communicators should be compared? Researchers tend to emphasize the importance of risk communication only in the context of a pandemic.\n\nThe method is still problematic. How does the author(s) determine a representative sample size before carrying out one of the sampling techniques? It seems this research applies non-probability sampling, so does the Slovin formula work enough to determine the sample size for a study with non-probability sampling? Where did the author get the population (150 million)? And why is the margin of error 10%? Is the sample strong enough to produce confident findings? Is this research capable of producing confident results? It seems unclear. The author(s) need to clarify it.\n\nThe results section looks fine. However, in the discussion section, the authors seem to have lacked elaboration on the research findings with the literature studies conducted. It makes the manuscript unbalanced between the literature review that underlies this study and the discussion of its findings. The author(s) need to comprehensively discuss the results and what are the implications of these findings.\n\nThis article is quite promising, but the author needs to clarify things that are questionable by reviewers or even readers later.\n\nIs the work 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": "9798", "date": "14 Sep 2023", "name": "Neneng Nurlaela Arief", "role": "Author Response", "response": "1. The abstract section has briefly justified the purpose of this research well, how the research method is applied. I think the keywords are also good and represent the description of the content of this research. However, the author(s) failed to highlight the research results, which are in accordance with the research objective, namely \"to compare.\" What is the outline of the comparison? Authors response: We have improve the research results: Results: This study found that the highest perceived benefits and behavioral change come from the non-government spokesperson, of which 26.45% and 18.48% of respondents strongly agree, while the lowest is from a government spokesperson with no medical background. This study also found from five-health spokespersons, the best two are occupied by non-government with medical backgrounds, with 31.52% and 29.35% of respondents strongly agree. However, most respondents had high trust in the governments, with 14.49% strongly agreeing. Compared to those from the governmental sector, spokespersons from the non-governmental sector are perceived to induce higher perceived benefits in delivering the message. However, this does not mean there is no utility in using governmental sector spokespersons, as they are also shown to induce high levels of trust. Overall, governmental and non-governmental spokespersons show utility in different communication aspects, highlighting the need for targeted communication strategies. To conclude, these findings demonstrate that government spokespersons for the COVID-19 pandemic in Indonesia receive the same high level of trust as non-government spokespersons regarding communicating health hazards. The public looks forward to the regularity and routine of the leaders who serve as spokespersons in hopes of easing concerns and tension brought on by the ongoing appearance of the Omicron variation in Indonesia. 2. How does the author(s) determine a representative sample size before carrying out one of the sampling techniques? Authors response: Regarding the determination of a representative sample size, we apologize for not providing sufficient clarification in our paper. In our research, we employed a probability sampling technique due to practical constraints and the nature of our study population. The author first determines the target population to be studied. Because there is already valid data regarding population figures, the sampling technique and the number of samples needed for the study can be determined. 3. This research applies non-probability sampling, so does the Slovin formula work enough to determine the sample size for a study with non-probability sampling? Authors response: Probability sampling is used because the population size is known to calculate the required sample size. In determining the respondents are also not limited by specific subjective criteria. The slovin formula is also appropriate because the slovin formula can be used for the probability sampling method. The slovin technique is a derivative of the Cochran formula and the confidence level is 95% (significance level α=5%). With a population of 150 million, the required sample size is still 100. 4. Where did the author get the population (150 million)? Authors response: The target respondents are social media users as infodemic recipients from spokespersons in educating about the COVID-19 vaccine and health services in Indonesia. We study it by first mapping the average age of social media users in Indonesia, then collecting data on how many active social media users are in Indonesia. According to several reliable research sources, the number of active social media users in Indonesia in 2019 -2020 is 150 million (Statista, we are social, 2020). Therefore, the population of the study was 150 million people. We employed expert judgment and considered the available resources to determine a feasible sample size that would allow for meaningful analysis and interpretation of the data 5. Why is the margin of error 10%? Is the sample strong enough to produce confident findings? Authors response: A 10% margin of error is commonly used for large populations (Regression Analysis, Quantitative Research Methods, Firdaus, 2021). The Slovin formula can be used with the following conditions: e = 0.1 (10%) for a large population, e = 0.02 (20%) for a small population. So the range of samples that can be taken from the Slovin technique is between 10-20% of the study population. Therefore, this study's sample size is appropriate and valid to represent the population. Note: The significance level differs from the margin of error, so the significance level remains low according to the standard (5%). 6. Is this research capable of producing confident results? Authors response: - Questionnaire Validity Before data collection, a pilot study was conducted to test the validity and reliability of the questionnaire. Each questionnaire item was tested using Cronbach's Alpha, the results of which can be seen in Table 2. - Result Validity The sampling technique and the number of samples have been determined systematically so that they can represent the population. Response to reviewer comments No 1 & 4 the abstract section, result & discussion. Thank you for bringing this important aspect to our attention. Your feedback has been invaluable, and we are committed to incorporating your suggestions to rewrite the abstract, strengthen the introduction and provide a more comprehensive justification for result and discussion section. We will highlight that the findings from such studies can provide valuable insights and evidence-based recommendations for improving communication strategies across diverse health contexts, including but not limited to pandemics." } ] } ]	1	https://f1000research.com/articles/12-90
https://f1000research.com/articles/12-1152/v1	14 Sep 23	{ "type": "Systematic Review", "title": "Associations between physical activity and health outcomes in clinical and non-clinical populations: A systematic meta-umbrella review", "authors": [ "Nektaria Zagorianakou", "Stefanos Mantzoukas", "Fotios Tatsis", "Evangelia Tsiloni", "Spiros Georgakis", "Agni Nakou", "Mary Gouva", "Elena Dragioti", "Nektaria Zagorianakou", "Stefanos Mantzoukas", "Fotios Tatsis", "Evangelia Tsiloni", "Spiros Georgakis", "Agni Nakou", "Mary Gouva" ], "abstract": "Background: The beneficial effect of physical activity in various health conditions is recognised, but the consistency and magnitude of its outcomes remain debated. Therefore, we aimed to chart the evidence of the association between physical activity and health outcomes in clinical and non-clinical populations. Methods: We conducted a meta-umbrella review using a semiquantitative and descriptive analysis. We searched PubMed/MEDLINE, PsycINFO, and CINHAL databases from inception to February 28, 2023, for umbrella reviews that evaluated the relationship between physical activity and health outcomes using validated methods to assess evidence levels. Two reviewers independently screened, extracted data, and assessed quality of the umbrella reviews. The overlap analysis of component meta-analyses within the umbrella reviews was performed using the Corrected Covered Area (CCA) method. To ensure consistency, pooled effect estimates were converted to equivalent odds ratios (eORs). Results: Sixteen umbrella reviews with a total of 130 statistically significant associations were included. The sole risk-demonstrating association, supported by convincing evidence, was between intensive sports and atrial fibrillation (eOR=1.64, 95%CI=1.10-2.43). The strongest protective associations, supported by convincing and highly suggestive evidence, were between any physical activity and the incidence of Parkinson's disease (eOR=0.66, 95%CI=0.57-0.78), Alzheimer's disease (eOR=0.62, 95%CI=0.52-0.72), cognitive decline (eOR=0.67; 95%CI=0.57-0.78), breast cancer incidence (eOR=0.87, 95%CI=0.84-0.90), endometrial cancer incidence (eOR=0.79, 95%CI=0.74-0.85), and between recreational physical activity and the incidence/mortality of cancer (eOR=0.70, 95%CI=0.60-0.83). The remaining ones demonstrated lower levels of evidence, while 60 (46.2%) of those exhibited multiple levels of evidence, displaying a lack of consistency. Conclusion: Despite the inconsistent evidence across associations, the contribution of regular physical activity to maintaining both physical and mental health cannot be underestimated, particularly when it comes to cognitive and cancer outcomes. The association between intensive sports and potential risk of atrial fibrillation requires further consideration though.", "keywords": [ "exercise", "fitness", "physical exercise", "mental health", "physical health", "umbrella review" ], "content": "Introduction\n\nThe gravity of physical activity and its impact on our well-being is widely recognized1–7 and emphasised on a daily routine level by the World Health Organization (WHO).3,4 At the same time, nearly 70% of the global population is afflicted by the pandemic of physical inactivity,3 which raises public health concerns8 and is responsible for a substantial economic burden.9\n\nExisting evidence highlight the beneficial effect of physical activity in various health conditions such as non-communicable diseases,4,10–12 including cardiovascular diseases,5,13,14 like coronary artery disease, stroke, hypertension,12,14 diabetes,12,14–16 and certain types of cancer.12,14,17 It is also found to be of great aid in musculoskeletal conditions18–21 and degenerative diseases like osteoporosis and osteoarthritis,5,14 plays a vital role in in promoting metabolic health22,23 and bear therapeutic effects on mental health disorders, such as depression and anxiety.24–28\n\nWhile physical activity is very beneficial, it should not be considered as panacea or an all-rounder for every situation. Potential harms may exist depending on the level of intensity, the population group, and the health condition.6 For example, individuals with pre-existing cardiovascular conditions may need to exercise with caution and consult with healthcare professionals to ensure that the exercise intensity is appropriate.29,30 Similarly, pregnant women should be mindful of their physical activity levels and choose exercises that are safe for them.31 In some cases, excessive physical activity can also lead to injuries, overuse syndromes, or exacerbation of existing health conditions.6\n\nHence, the concept of a universal physical activity recommendation seems oversimplified, as factors such as exercise type, intensity, duration, and health condition should be considered.6,32 Such recommendations should be tailored and based on individual needs and capabilities.2 Towards this, additional information on the associations between physical activity and different population groups with various health conditions would be of great value.2\n\nDespite numerous umbrella reviews demonstrating the overall positive association between physical activity and health outcomes,33–36 the topic is still partially understood due to variations in objectives and methods across these reviews. A comprehensive analysis examining the consistency and magnitude of physical activity effects is still lacking. To address these issues, we conducted a systematic meta-umbrella review (or in other words, an overview of reviews synthesis) on the associations between physical activity and health outcomes in clinical and non-clinical populations, an approach that allows for an overarching charting and comprehensive assessment of the relevant subject based on published umbrella reviews.37,38\n\nOur aim was to provide an evidence synthesis map on the consistency and magnitude of the health effects of physical activity and its potential protective role across a wide range of physical and mental health outcomes, which, in turn, can contribute to formulating relevant recommendations for further clinical research and practice.\n\n\nMethods\n\nThis meta-umbrella review was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines39 and the Preferred Reporting Items for Overviews of Reviews (PRIOR) checklist (see Reporting Guidelines, https://osf.io/bv27t/).40 The research question, inclusion criteria, and all methods were determined ad hoc prior to the start of the literature searching. The research question was formulated as follows: How strong is the evidence regarding the effects of physical activity and/or exercise, either as exposure or as interventions on physical or mental health in any populations (clinical and non-clinical) of all ages?\n\nA broad search was performed on three electronic databases (PubMed/MEDLINE, PsycINFO and CINAHL) for umbrella reviews published from inception through February 28, 2023, with no language, age, or setting restrictions. The last update was carried out on April 7th, 2023. The search algorithm included the following search terms: “umbrella review” and (“physical activity” OR “exercise” OR “fitness” OR “physical exercise”). The identified umbrella reviews were first screened based on the title and reading of the abstract. After excluding those records that were not relevant to the subject under investigation, the full texts of the remaining records were further examined for inclusion. References to umbrella reviews included in the final dataset were also checked to identify other eligible articles that may have been missed during electronic searches. Two independent reviewers (MG, NZ) screened titles and full texts in duplicate, with discrepancies to be resolved by a third independent reviewer (ED).\n\nIn this study, the unit of analysis was umbrella reviews i.e., a newer form of evidence synthesis from multiple systematic reviews and meta-analyses on a certain question, as previously defined41–43 to achieve overall consistency by summarising these reviews together.43,44\n\nHence our inclusion criteria were: 1) umbrella reviews reporting quantitative data (i.e., with a formal meta-analysis [MA]) from observational individual studies (i.e., case-control, cohort, cross-sectional or ecological studies) and/or randomised controlled trials (RCTs); 2) umbrella reviews reporting data on the association between physical activity and any health outcome in any population of all ages that consider physical activity to be either an etiological factor or an intervention approach; and 3) umbrella reviews using well-known approaches to grading the evidence (e.g., GRADE or similar).41,43,45,46\n\nUmbrella reviews were eligible regardless of the physical activity that were examined in terms of type, delivery mode (e.g., supervised or not supervised, in groups etc.), dose (frequency, intensity, and duration), or comparator (e.g., no exercise, other type of physical activity etc.). In the case of two umbrella reviews examining the same association between physical activity type and health outcome (i.e., overlapping umbrella reviews), we retained only the umbrella review with the largest number of included meta-analyses. Any disagreements were resolved through discussion and consensus within the entire review panel.\n\nOur exclusion criteria were: 1) umbrella reviews of network meta-analysis, methodological umbrella reviews or guidelines, policy studies and protocols; 2) umbrella reviews presenting only narrative description of the data; whenever an umbrella review included systematic reviews with and without a formal MA, we retained only the systematic review presenting a formal MA, 3) umbrella reviews not addressing the physical activity as an exposure or an intervention (i.e., physical activity treated as an outcome e.g., adherence to physical activity) or umbrella reviews not addressing physical or mental health outcomes (e.g., academic achievements); and 4) umbrella reviews did not use established approaches to grade the evidence.\n\nSearch results were imported into EndNote V.X9 (Clarivate, Philadelphia) where duplicates were removed and then exported into an Excel sheet for evaluation against inclusion criteria and data extraction. Six reviewers (NZ, ED, FT, ET, AN, and SG), in groups of two, performed the data extraction from each eligible umbrella review. We recorded the first author, year of publication, type of physical activity and whether a definition was given, health conditions or population analysed, number of systematic reviews reviewed and number of meta-analysis included, number of primary studies included per systematic review and their study design, total sample size, health outcomes tested, years of evidence reviewed, databases searched, grading method used for the credibility of the evidence, and if funding sources were reported.\n\nWe also recorded the dose of physical activity or the comparison group, where reported, the number of studies and cases analysed for each association between physical activity and association-specific estimates (i.e., OR, RR, etc.), as well as the corresponding confidence interval (CI) for each umbrella review. The class of evidence was then recorded as originally reported in the umbrella reviews included, according to our inclusion criteria; all studies must have used an established classification of the robustness of the reported associations. Whenever workable, we recorded the class of evidence from prospective studies as part of a sensitivity analysis.\n\nOutcomes of interest were any reported health outcome (both physical and mental) assessed using risk ratios (RR), hazards ratio (HR), odds ratio (OR), or standardized mean difference (SMD) metrics of association. Risk difference measures of effect or mean difference or weight mean difference measures of effect were not considered unless they can be converted to either RR or SMD.41 To provide a robust and clear evidence map, only outcomes with statistically significant associations were assessed in the current study (i.e., outcomes with non-significant associations (p>0.05) were not examined in the current study, regardless of the certainty level reported in the original umbrella reviews).\n\nThe methodological quality of the included umbrella reviews was assessed independently by two reviewers (NZ and ED) employing the AMSTAR 2 checklist (A Measurement Tool to Assess systematic Reviews),47 as there are no standard criteria for assessing the quality of umbrella reviews. The AMSTAR 2 method was applied by completing an online checklist (https://amstar.ca/Amstar_Checklist.php) including 16 specific items that automatically calculated the quality as high, moderate, low, and critically low, respectively. The AMSTAR 2 does not generate an overall score.47 In cases of discrepancy during the assessment, a third reviewer decided (MG).\n\nFirst, we calculated the overlap in component meta-analyses that were included across the eligible umbrella reviews using the Corrected Covered Area (CCA) method48 with the following cut-offs: 0%–5%=‘slight overlap’; 6%–10%=‘moderate’; 11%–15%=‘high’ and >15%=‘very high’ overlap. In alignment with prior meta-umbrella review publications,37,49,50 we summarised data that had already undergone meta-analysis and grading (and considered statistically significant at p < .05), instead of re-synthesizing and re-grading them. Hence, the results of the included umbrella reviews are summarised descriptively.37 However, since the primary goal of a meta-umbrella review is to allow comparison of the across different types of pooled effect estimates reported in different umbrella reviews,41 we converted pooled effect estimates to equivalent odds ratios (eORs), using the formula previously reported.41,51,52 The results with high and moderate evidence were presented using forest plots using STATA 17.0 (STATA Corp., College Station, TX, USA).\n\n\nResults\n\nThe electronic search identified 240 potentially relevant umbrella reviews. After removing 28 duplicates, 212 umbrella reviews were screened and 131 were further excluded based on title and abstract. No further umbrella review was identified using the hand search method. Eighty umbrella reviews were retrieved in full text and screened against our inclusion criteria (one full text could not be retrieved). Finally, 16 umbrella reviews were deemed eligible and included in the present meta-umbrella study.53–68 Figure 1 depicts the PRISMA flowchart for the study selection process and the Table 1 in Supplementary Material contains the list of full-text articles that were read and excluded along with the specific reasons for exclusion.\n\nThe characteristics of the 16 eligible umbrella reviews are described in Table 2 in Supplementary Material. The 16 umbrella reviews corresponded to a total of 462 systematic reviews, with or without meta-analysis but only 103 were meta-analyses and were included here, examining the effects of physical activity, including all types of physical activity and exercise (or mixed types, including combinations aerobic training, strength training, yoga, tai chi, qigong, mind body interventions, etc.), as well as physical leisure activities, occupational physical activity, and sports practice with marked associations mainly in mixed populations not specified (any population). In specific populations, there were associations with five clinical conditions (mild cognitive impairment, dementia and Alzheimer's disease, cancer [any cancer, breast and lung cancer], chronic kidney disease, and type II diabetes mellitus) and four healthy populations (healthy youth, general healthy population, pregnant women and peri or postmenopausal women).\n\nThe included umbrella reviews were published between 2015 and 2023 and assessed individual systematic reviews published from 1996 to 2021. The minimum and maximum number of primary studies (i.e., observational studies and randomised controlled trials) included in the meta-analyses were 2 and 514, respectively, while the corresponding figures for the included sample sizes were 53 (minimum) and 3,861,201 (maximum), respectively. As for the grading method employed in eligible umbrella reviews, eight were used the GRADE approach,46 seven the Ioannidis Criteria,43 and one the Oxford Centre for Evidence-Based Medicine criteria.69\n\nMore than 700 associations were identified in total, but only 130 of them were found to be statistically significant and have been evaluated herein. These 130 distinct associations concerned a total of 41 outcomes (e.g., cancer incidence and mortality neurocognitive outcomes, hypertension and cardiovascular outcomes, psychological symptoms, metabolic outcomes, fatigue, quality of life, etc.). Ninety of these 130 associations related to physical health outcomes and 40 to mental health ones. The overlap in component meta-analyses CCA method48 indicated a slight overlap (CCA=1.92%; Table 3 in Supplementary Material).\n\nBased on AMSTAR 2 evaluation of methodological quality, two umbrella reviews (12.5%) were rated as high quality, six (37.5%) as moderate quality, seven (43.8%) as low quality, and one (6.2%) as critically low quality (Table 1). The items that most often contributed to lower ratings were items 2 and 3 (50 % of umbrella reviews did not include an explicit statement in the article that the review methods were established prior to the conduct of the review and 81.25% did not explain their selection of the study designs for inclusion in the review) and items 7,8 and 10 (75.1% of umbrella reviews did not provide a list of excluded studies and justify the exclusion in the review, 87.5% described partially the included studies in adequate detail, and 93.8 % did report on the sources of funding for the studies included in the review).\n\n* AMSTAR 2 Items are described in Supplementary material.\n\nA total of 130 statistically significant, non-overlapping associations between physical activity and health outcomes were identified for both clinical and non-clinical population categories (Tables 2 and 3). Notably, 129 out of 130 associations were identified as protective against various health outcomes, while only one posed a risk. As shown in Tables 2 and 3, 70 associations (53.8%) had a unique level of evidence while sixty (46. 2%) of them shared multiple levels of evidence, indicating that many statistically significant associations lack consistency. Moreover, only two (1.5%) were supported by convincing/high evidence and 23 (17.7%) by highly suggestive or moderate evidence (Figure 2). The remaining 105 associations were supported by either a suggestive/low (46.2%) or a weak/very low level of evidence (34.6%) (see Table 4-8 in Supplementary Material). Below, we analytically describe the associations with the highest evidence (high and moderate) by population and physical and mental health outcomes.\n\nAssociations between physical activity and physical health outcomes in clinical populations\n\nIn total, 14 statistically significant associations were identified in clinical populations including people with chronic kidney disease (n=8), dementia (n=2), any cancer (n=3), and type II diabetes mellitus (n=1) (see Table 4 in Supplementary Material). None of them was found to be at increased risk of physical outcomes due to physical activity. In this population category, the most highly protective associations were identified between all types of cancer mortality and any physical activity (eOR = 0.79, 95%CI=0.75-0.85) and other physical activity (non-occupational; eOR = 0.75, 95%CI= 0.68-0.83), in cancer patients, supported by the highest quality of evidence according to the Ioannides approach (highly suggestive). Two also highly protective associations were found between risk of falls and mixed physical activity (eOR = 0.69, 95%CI=0.55-0.85) in dementia situations and between systolic blood pressure and mixed physical activity (eOR = 0.48, 95%CI= 0.28-0.21) in chronic kidney disease (peridialysis), supported by the highest quality of evidence according to the GRADE approach (moderate; Figure 2).\n\nAssociations between physical activity and mental health outcomes in clinical populations\n\nIn total, 30 statistically significant associations were identified in clinical populations including people with Alzheimer’s disease (n=1), breast cancer (n=13), chronic kidney disease (n=4), dementia (n=2), lung cancer (n=1), and mild cognitive impairment (n=9) (see Table 5 in Supplementary Material). None of them was found to be at increased risk of mental outcomes from physical activity. In this population category, the most protective associations were found between delayed memory and aerobic exercise (eOR =1.60, 95%CI=1.11-2.30), global cognition and mixed physical activity (eOR =1.72, 95%CI= 1.22-2.43) in mild cognitive impairment, depressive symptoms and mixed physical activity (eOR =0.72, 95%CI= 0.55-0.96) in dementia, psychological distress and yoga (eOR =0.34, 95%CI= 0.24-0.47) and between fatigue and various combinations of physical activity (i.e., aerobic; resistance; yoga; qigong; pilates; strength & flexibility; eOR =0.58, 95%CI= 0.51-0.67;eOR =0.56, 95%CI= 0.43-0.73; eOR =0.46, 95%CI= 0.34-0.62; eOR =0.53, 95%CI= 0.40-0.71; eOR =0.22, 95%CI= 0.09-0.56, respectively) in breast cancer with the highest quality of evidence according to the GRADE approach (moderate; Figure 2).\n\nAssociations between physical activity and physical health outcomes in healthy populations\n\nIn total, 28 statistically significant associations were identified in healthy populations including pregnant women (n=20), healthy youth (≤ 18 years; n=7), and peri or postmenopausal women (n=1) (see Table 6 in Supplementary Material). None of them was found to be at increased risk of physical outcomes from physical activity. However, as shown in Tables 2 and 3 and Table 6 in Supplementary Material, none of these were supported by the highest level of evidence i.e., high, and moderate according to the GRADE approach. The associations between any physical activity and health outcomes such as gestational diabetes mellitus, gestational hypertension and/or preeclampsia in pregnancy were supported by low evidence according to the GRADE approach. There was also low or very low evidence associating resistance training with health outcomes such as muscular strength and/or strength in healthy adolescents as well as yoga with flash severity peri or postmenopausal women.\n\nAssociations between physical activity and mental health outcomes in healthy populations\n\nOnly one statistically significant association was identified in healthy populations including peri or postmenopausal women (n=1) (see Table 6 in Supplementary Material). A protective association was found between psychological symptoms and Yoga (eOR =0.56, 95%CI= 0.43-0.74) with the highest quality of evidence according to the GRADE approach (moderate; Figure 2).\n\nIn total, 48 statistically significant associations were identified in any population mostly including cancer incidence and/or mortality outcomes (n=45) (see Table 7 in Supplementary Material). The highest risk association was found between atrial fibrillation and intensive sports (eOR =1.64, 95%CI= 1.10-2.43), while the most protective associations were found between breast cancer incidence and any physical activity (eOR =0.87,95%CI=0.84-0.90), colon cancer incidence or mortality and recreational physical activity (eOR =0.70,95%CI=0.60-0.83) and between endometrial cancer incidence and any physical activity (eOR =0.79,95%CI=0.74-0.85), supported by the highest quality of evidence according to the Ioannides approach (convincing and highly suggestive; Figure 2). Additionally, four highly protective associations were also identified between colon cancer incidence (eOR =0.74,95%CI=0.67-0.82), endometrial cancer incidence (eOR =0.81,95%CI=0.75-0.87), prostate cancer incidence (eOR =0.86,95%CI=0.78-0.94), and rectal cancer incidence and occupational physical activity (eOR =0.88, 95%CI=0.79-0.98), supported by the highest quality of evidence according to the GRADE approach (moderate; Figure 2).\n\nIn total, nine statistically significant associations were identified in any population including only neurocognitive health outcomes (see Table 8 in Supplementary Material). None of them was found to be at increased risk of physical outcomes from physical activity. The strongest protective associations were found between Parkinson disease incidence (eOR = 0.66, 95%CI=0.57-0.78), Alzheimer’s disease incidence (eOR = 0.62, 95%CI= 0.52-0.72), cognitive decline incidence (eOR = 0.67; 95%CI= 0.57-0.78) and any physical activity with the highest quality of evidence according to the Ioannides approach (convincing and highly suggestive; Figure 2).\n\nOnly 31 associations were analysed in the umbrella reviews, limited to prospective studies (see Table 9 in Supplementary Material). Most of them remained at the same level as the main analysis. The association between colon cancer incidence or mortality and recreational physical activity was upgraded from highly suggestive to convincing evidence. The association between diabetic retinopathy and total physical activity in people with type II diabetes mellitus was downgraded from suggestive to non-significant evidence. The association between endometrial cancer incidence and any physical activity was downgraded from highly suggestive to suggestive evidence, while the association between oesophageal cancer incidence or mortality and recreational physical activity was downgraded from suggestive to weak evidence.\n\n\nDiscussion\n\nIn this comprehensive meta-umbrella review, we examined sixteen umbrella reviews, collectively comprising 130 associations between physical activity and health outcomes that displayed statistical significance. Overall, all but one of these associations exhibited a protective effect. Among the notable findings, the association between atrial fibrillation and intensive sports posed the highest risk. Several other associations showed strong and moderate protective effects, particularly relevant to cognitive outcomes and cancer risk in both clinical and non-clinical populations. However, almost half of the associations displayed varying levels of evidence, indicating a lack of consistency among the statistically significant findings. Our meta-umbrella review represents the pioneering endeavour in its field, being the first of its kind.\n\nAt an analytical level, we found strong evidence that intensive sports practice, particularly in athletes, is associated with a potential risk of developing atrial fibrillation. In recent years, participation in very demanding physical activities such as marathon running has become very popular.70 Our findings suggest that while physical activity does not have a significant impact on cardiovascular risk, prolonged participation in endurance events does pose a potential risk of atrial fibrillation, which is also consistent with the literature.71–73 The mechanisms behind this association are not fully understood, but several factors have been proposed. Factors such as fluid shifts and electrolyte abnormalities, illicit drugs, atrial anatomical adaptations due to chronic volume or pressure overload, alterations in autonomic nervous system, chronic systemic inflammation and atrial fibrosis and enlargement might contribute to the development of atrial fibrillation in high-demanding sport activity.72,73 Further research is still required to better understand the specific mechanisms and risk factors involved.\n\nContrarily, the most protective identified associations involved Parkinson's disease, Alzheimer's disease incidence, and cognitive decline; supported by high or highly suggestive evidence. Parkinson's disease is a common neurodegenerative condition74 characterised by reduced dopamine and motor symptoms like tremors, bradykinesia, rigidity, and postural instability.75 To date, in absence of cure for Parkinson’s disease, existing medications aim solely at controlling the clinical symptoms.76 Regular physical activity has a positive impact in health outcomes of the Parkinson’s disease as it can reduce tumour necrosis factor alpha in the skeletal muscle (TNF-alpha),77 alleviate neuron loss and enhance nerve regeneration and reduce the accumulation of α-Syn protein which is the main pathogenetic protein of Parkinson's disease.78 Alzheimer's disease, furthermore, is a progressive neurodegenerative disorder with no known cure, that most often occurs in people over the age of 65, causing cognitive decline. Clinical symptoms drastically affect the quality of life and include cognitive dysfunction and behavioural disturbances. In line with our findings, a number of studies79–81 also highlight the protective effects of physical activity and exercise on cognitive and brain health. Although strong evidence does exist, the exact mechanism is not yet specifically identified.82 According to Gallaway et al.82 some of these mechanisms might be the increased brain blood flow, the improved sleep quality, and the improved metabolic and cardiovascular health in physically active people, who at the same time are at lower risk of developing depression, that is highly associated with dementia.\n\nConsistent with previous reports,12,83–88 we also found highly suggestive and moderate-quality evidence between any physical activity or occupational physical activity and a lower risk for the incidence of several types of cancer including breast, endometrial, colon, prostate incidence, and rectal cancer. Towards the same direction,89,90 recreational physical activity was found to have a protective effect against colon cancer incidence/mortality. Physical activity and/or exercise can reduce the risk of cancer occurrence by decreasing markers of systemic inflammation and sex hormone levels, promoting a healthy gut microbiota and improving insulin, leptin, adiponectin levels and function of immune cells.91 General recommendations by health organisations include at least 150 minutes of moderate-intensity aerobic exercise or 75 minutes of vigorous-intensity exercise each week while strength training is recommended for at least twice a week.92,93 However, due to lack of data that precludes more specific recommendations,90 a need for further research into physical activity specifics for the prevention of some types of cancer arises.91\n\nSeveral other associations were supported by moderate levels of evidence, including reduced risk of falls in those with dementia, blood pressure in those with chronic kidney disease (peridialysis), psychological distress and symptoms, and fatigue in women with breast cancer and in postmenopausal women. These findings suggest that participating in various types of physical activities can contribute to reducing falls in individuals with dementia, have a beneficial impact on lowering systolic blood pressure, especially in those receiving peridialysis treatment, and enhance psychological well-being in breast cancer patients and postmenopausal women. According to the literature cardiovascular health is bolstered by regular physical activity,13,14 which strengthens the heart, enhances blood circulation, and lowers blood pressure.94 Additionally, exercise has therapeutic effects on psychological symptoms,24–28 by promoting the release of endorphins,14 which contribute to feelings of happiness and well-being.6,27,32\n\nLimitations of our study should be considered in the interpretation of the findings. Our meta-umbrella approach relied solely on previously published umbrella reviews, making our results susceptible to any limitations or biases present in those reviews. The decision to include only statistically significant associations may be criticised for potentially limiting the generalizability of our findings. However, we believe that this approach has led to a clearer and more concise understanding of the bigger picture in this area. Moreover, the analysis of the extensive body of evidence encountered various challenges. Methodological differences among the included umbrella reviews posed difficulties, and we excluded several reviews with inadequate reporting methods. The lack of a clear definition for physical activity posed challenges in presenting detailed data, including specific populations, as well as conveying the type, frequency, and intensity of physical activity. This could also be the reason for the inconsistencies in the evidence for half of the associations observed herein. Lastly, it is important to acknowledge that our study may not have captured all relevant studies, as it was confined to the available literature up until the time of the review.\n\n\nConclusions\n\nDespite the aforementioned limitations, our findings underscore the significance of physical activity for overall health and well-being. While our review unveiled a potential risk of atrial fibrillation associated with intensive sport activities and most associations were inconclusive, maintaining a regular exercise regimen remains crucial to reducing the risk of various diseases and to alleviate both physical and psychological symptoms. Hence, for optimal health outcomes, it is highly advisable to incorporate physical activity into your daily routine. It's also important to customise recommendations to ensure that they align with personal abilities and goals. However, the lack of data on specific populations and the diverse nature of physical activity make it challenging to provide targeted recommendations based on this study alone. Moreover, physical activity should be balanced with nutrition, rest, and stress management for a healthy lifestyle. Future studies, regardless of their design, should thoroughly investigate the type, intensity, and duration of physical activity as well as personal factors to obtain a comprehensive understanding in terms of both possible benefits and harms. Additionally, there is a great need for a standardised approach in conducting umbrella reviews within this domain.", "appendix": "Data availability\n\nOpen Science Framework: Supplementary material meta-UR. “Associations between physical activity and health outcomes in clinical and non-clinical populations: A systematic meta-umbrella review”, DOI: https://doi.org/10.17605/OSF.IO/BV27T.\n\nOpen Science Framework: PRISMA and PRIOR checklists for Associations between physical activity and health outcomes in clinical and non-clinical populations: A systematic meta-umbrella review”, DOI: https://doi.org/10.17605/OSF.IO/BV27T.\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\nBull FC, Al-Ansari SS, Biddle S, et al.: World Health Organization 2020 guidelines on physical activity and sedentary behaviour. Br. J. Sports Med. Dec 2020; 54(24): 1451–1462. 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Publisher Full Text\n\nGwinnutt JM, Wieczorek M, Cavalli G, et al.: Effects of physical exercise and body weight on disease-specific outcomes of people with rheumatic and musculoskeletal diseases (RMDs): systematic reviews and meta-analyses informing the 2021 EULAR recommendations for lifestyle improvements in people with RMDs. RMD Open. Mar 2022; 8(1): e002168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFaíl LB, Marinho DA, Marques EA, et al.: Benefits of aquatic exercise in adults with and without chronic disease-A systematic review with meta-analysis. Scand. J. Med. Sci. Sports. Mar 2022; 32(3): 465–486. PubMed Abstract \| Publisher Full Text\n\nRibas TM, Teodori RM, Mescolotto FF, et al.: Impact of physical activity levels on musculoskeletal symptoms and absenteeism of workers of a metallurgical company. Rev. Bras. Med. Trab. Mar 3 2021; 18(4): 425–433. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMytinger M, Nelson RK, Zuhl M: Exercise Prescription Guidelines for Cardiovascular Disease Patients in the Absence of a Baseline Stress Test. J. Cardiovasc. Dev. Dis. Apr 27 2020; 7(2). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEvenson KR, Barakat R, Brown WJ, et al.: Guidelines for Physical Activity during Pregnancy: Comparisons From Around the World. Am. J. Lifestyle Med. Mar 2014; 8(2): 102–121. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMahindru A, Patil P, Agrawal V: Role of Physical Activity on Mental Health and Well-Being: A Review. Cureus. Jan 2023; 15(1): e33475. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDipietro L, Evenson KR, Bloodgood B, et al.: Benefits of Physical Activity during Pregnancy and Postpartum: An Umbrella Review. Med. Sci. Sports Exerc. Jun 2019; 51(6): 1292–1302. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDipietro L, Campbell WW, Buchner DM, et al.: Physical Activity, Injurious Falls, and Physical Function in Aging: An Umbrella Review. Med. Sci. Sports Exerc. Jun 2019; 51(6): 1303–1313. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPescatello LS, Buchner DM, Jakicic JM, et al.: Physical Activity to Prevent and Treat Hypertension: A Systematic Review. Med. Sci. Sports Exerc. Jun 2019; 51(6): 1314–1323. Publisher Full Text\n\nZanghì M, Petrigna L, Maugeri G, et al.: The Practice of Physical Activity on Psychological, Mental, Physical, and Social Wellbeing for Breast-Cancer Survivors: An Umbrella Review. Int. J. Environ. Res. Public Health. Aug 20 2022; 19(16). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArango C, Dragioti E, Solmi M, et al.: Risk and protective factors for mental disorders beyond genetics: an evidence-based atlas. World Psychiatry. Oct 2021; 20(3): 417–436. 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PubMed Abstract \| Publisher Full Text\n\nBellou V, Belbasis L, Tzoulaki I, et al.: Environmental risk factors and Parkinson's disease: An umbrella review of meta-analyses. Parkinsonism Relat. Disord. Feb 2016; 23: 1–9. Publisher Full Text\n\nMarkozannes G, Tzoulaki I, Karli D, et al.: Diet, body size, physical activity and risk of prostate cancer: An umbrella review of the evidence. Eur. J. Cancer. Dec 2016; 69: 61–69. PubMed Abstract \| Publisher Full Text\n\nHou W, Zhai L, Yang Y, et al.: Is physical activity effective against cancer-related fatigue in lung cancer patients? An umbrella review of systematic reviews and meta-analyses. Support Care Cancer. Feb 13 2023; 31(3): 161. PubMed Abstract \| Publisher Full Text\n\nCillekens B, Lang M, van Mechelen W , et al.: How does occupational physical activity influence health? An umbrella review of 23 health outcomes across 158 observational studies. Br. J. Sports Med. Dec 2020; 54(24): 1474–1481. PubMed Abstract \| Publisher Full Text\n\nValenzuela PL, Santos-Lozano A, Morales JS, et al.: Physical activity, sports and risk of atrial fibrillation: umbrella review of meta-analyses. Eur. J. Prev. Cardiol. Jul 10 2021; 28(7): e11–e16. PubMed Abstract \| Publisher Full Text\n\nLesinski M, Herz M, Schmelcher A, et al.: Effects of Resistance Training on Physical Fitness in Healthy Children and Adolescents: An Umbrella Review. Sports Med. Nov 2020; 50(11): 1901–1928. Publisher Full Text\n\nZhang F, Bai Y, Zhao X, et al.: Therapeutic effects of exercise interventions for patients with chronic kidney disease: an umbrella review of systematic reviews and meta-analyses. BMJ Open. Sep 19 2022; 12(9): e054887. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSingh B, Olds T, Curtis R, et al.: Effectiveness of physical activity interventions for improving depression, anxiety and distress: an overview of systematic reviews. Br. J. Sports Med. Feb 16 2023; bjsports-2022-106195. PubMed Abstract \| Publisher Full Text\n\nShepherd-Banigan M, Goldstein KM, Coeytaux RR, et al.: Improving vasomotor symptoms; psychological symptoms; and health-related quality of life in peri- or post-menopausal women through yoga: An umbrella systematic review and meta-analysis. Complement. Ther. Med. 2017; 34: 156–164. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartínez-Vizcaíno V, Sanabria-Martínez G, Fernández-Rodríguez R, et al.: Exercise during pregnancy for preventing gestational diabetes mellitus and hypertensive disorders: An umbrella review of randomised controlled trials and an updated meta-analysis. BJOG. 2023; 130(3): 264–275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJiang M, Ma Y, Yun B, et al.: Exercise for fatigue in breast cancer patients: An umbrella review of systematic reviews. Int. J. Nurs. Sci. Apr 10 2020; 7(2): 248–254. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBellou V, Belbasis L, Tzoulaki I, et al.: Systematic evaluation of the associations between environmental risk factors and dementia: An umbrella review of systematic reviews and meta-analyses. Alzheimers Dement. Apr 2017; 13(4): 406–418. PubMed Abstract \| Publisher Full Text\n\nTrott M, Driscoll R, Pardhan S: Associations between diabetic retinopathy and modifiable risk factors: An umbrella review of meta-analyses. Diabet. Med. Jun 2022; 39(6): e14796. PubMed Abstract \| Publisher Full Text\n\nZhang YR, Xu W, Zhang W, et al.: Modifiable risk factors for incident dementia and cognitive impairment: An umbrella review of evidence. J. Affect. Disord. Oct 1 2022; 314: 160–167. Publisher Full Text\n\nOxford Centre for Evidence-based Medicine Levels of Evidence (January 2001).2014.\n\nMalchrowicz-Mośko E, Poczta J: Running as a Form of Therapy Socio-Psychological Functions of Mass Running Events for Men and Women. Int. J. Environ. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKerr J, Anderson C, Lippman SM: Physical activity, sedentary behaviour, diet, and cancer: an update and emerging new evidence. Lancet Oncol. Aug 2017; 18(8): e457–e471. PubMed Abstract \| Publisher Full Text\n\nSchmid D, Behrens G, Keimling M, et al.: A systematic review and meta-analysis of physical activity and endometrial cancer risk. Eur. J. Epidemiol. May 2015; 30(5): 397–412. PubMed Abstract \| Publisher Full Text\n\nWu Y, Zhang D, Kang S: Physical activity and risk of breast cancer: a meta-analysis of prospective studies. Breast Cancer Res. Treat. Feb 2013; 137(3): 869–882. Publisher Full Text\n\nSchmid D, Ricci C, Behrens G, et al.: Does smoking influence the physical activity and lung cancer relation? A systematic review and meta-analysis. Eur. J. Epidemiol. Dec 2016; 31(12): 1173–1190. PubMed Abstract \| Publisher Full Text\n\nShephard RJ: Physical Activity and Prostate Cancer: An Updated Review. Sports Med. 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Publisher Full Text" }	[ { "id": "239227", "date": "26 Feb 2024", "name": "Courtney Bouchet", "expertise": [ "Reviewer Expertise Exercise neuroscience" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the article “Associations between physical activity and health outcomes in clinical and non-clinical populations: A systematic meta-umbrella review” the authors conduct a meta-umbrella review on research investigating the effects of physical activity on physical and mental health. The data presented indicate that exercise has multiple beneficial health outcomes and one very important health risk factor, increasing the incidence of atrial fibrillation in any population (i.e. the population was not specified). This meta-umbrella review does a nice job summarizing the exercise field while accepting limitations of this type of review. Overall, this is a timely and thorough meta-umbrella review, the only major concern is regarding the lack of discussion regarding sex investigated in each umbrella review. Understanding how different exercise regimens affect males versus females is very important and could have major clinical implications. Additional minor concerns are as follows:\nMajor concern:\nThere is no mention of sex examined in each umbrella review and sex differences in outcomes. This is useful information and should be included.\n\nMinor concerns:\nSupplemental tables 4-8 should go into the main text as they contain pertinent information to fully synthesize the data conveyed in this meta-umbrella review. In the abstract, it would be helpful if the authors describe the ‘validated methods to assess evidence levels’. Please specify these validated methods within the abstract. According to PRISMA 2020 guidelines, inclusion and exclusion criteria need to be specified in the abstract methods, please include these criteria in the abstract. In Figure 1, one of the options is “Records marked as ineligible by automation tools” but I do not see any other mention of automation tools. Please specify any automation tools that were used to remove records or make it clear that no automation tools were used. In the methods Data extraction section, please list all association-specific estimates that were used, as opposed to listing “OR, RR, etc.”. In the discussion, it is not clear how illicit drugs are associated with prolonged participation in endurance events, please clarify this. In the Data Synthesis paragraph of the methods, there is a missing word/typo. “However, since the primary goal of a meta-umbrella review is to allow comparison of the across different types of pooled…” Please include page numbers in the supplement.\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": [] } ]	1	https://f1000research.com/articles/12-1152
https://f1000research.com/articles/10-990/v1	30 Sep 21	{ "type": "Research Article", "title": "Green Tea and Decaffeinated Light Roasted Green Coffee Extract Combination Improved Cardiac Insulin Resistance through Free Fatty Acids and Adiponectin/FAS Pathway Amelioration in Metabolic Syndrome Rat Model", "authors": [ "Mifetika Lukitasari", "Mohammad Saifur Rohman", "Dwi Adi Nugroho", "Mukhamad Nur Kholis", "Nila Aisyah Wahyuni", "Nashi Widodo", "Mifetika Lukitasari", "Dwi Adi Nugroho", "Mukhamad Nur Kholis", "Nila Aisyah Wahyuni", "Nashi Widodo" ], "abstract": "Background: Insulin resistance has been independently associated with cardiac diseases. A free fatty acid is recently known to induce cardiac insulin resistance due to low-grade inflammation. Therefore, the improvement of free fatty acid levels can also improve cardiac insulin resistance. This study investigated the combination of green tea and decaffeinated-light roasted green coffee extract in improvement of free fatty acid-induced cardiac insulin resistance by improving the adiponectin/FAS pathway. Methods: This study used 25 males Sprague-Dawley rats induced by a high-fat high sucrose diet and injection of low dose streptozotocin to make a metabolic syndrome (MS) rat model and standard chow as healthy control rats. The MS rats were treated with green tea (200 mg/ b. w.), decaffeinated-light roasted green coffee (300 mg/ b. w.), and the combination of both extracts in 9 weeks. Experimental groups in this study were divided into 5 groups: 1) MS (HFHS diet + STZ) group, 2) NC (normal chow) group, 3) GT (green tea extract) group, 4) GC (decaffeinated-light roasted green coffee extract), 5) CM (combination of both extracts) group. Adiponectin and HOMA-IR level was analysed using ELISA, and the gene expression of Adipo-R1, FAS, PI3K, PDK1, Akt, GLUT4 was measured by RT-PCR. Results: The combination of green tea and decaffeinated-light roasted green coffee showed synergistic effects in improving FFA levels. The adiponectin/FAS pathway was attenuated in the CM group. Moreover, the combination also showed improvement in cardiac insulin resistance markers such as IRS1/2, PI3K, PDK1, Akt, and GLUT4. Conclusions: The combination of green tea and decaffeinated-light roasted green coffee extract improved cardiac insulin resistance better than green tea and green coffee extract administration alone by reducing free fatty acids levels through adiponectin/FAS pathway modulation.", "keywords": [ "metabolic syndrome", "green tea", "green coffee", "cardiac insulin resistance" ], "content": "Editorial note\n\nEditorial Note (4th August 2023): The F1000 Editorial Team has not yet received a new version of this article, as detailed in the Editorial Note published on 16th June 2023. The F1000 Editorial Team is actively contacting the authors to request the new version of the article. Peer review activity remains suspended until the authors publish a new version of this article.\n\nEditorial Note (16th June 2023): Since publication, it has been brought to the attention of the Editorial Team that the article was missing key information regarding animal treatment and ethical approval. The Editorial Team requested further detail and an explanation from the authors in March 2023. The authors provided an adequate response and were requested by the Editorial Team to create a new version of the article to include the additional details. Peer review activity has been suspended until the authors publish a new version of this article.\n\n\nIntroduction\n\nThe incidence of metabolic syndrome (MS) features, such as obesity, hyperglycemia, and insulin resistance has increased and is associated with excessive food consumption.1 MS prevalence has increased about 50–75% in the last decade.2 A previous study showed that insulin resistance had been known to be a significant predictor of heart failure (HF)3 and the major feature in HF patients.4 Many studies have shown that insulin resistance might develop cardiac remodellings such as hypertrophy, fibrosis, and cardiac dysfunction without coronary artery disease or hypertension.5–9 Lipotoxicity by free fatty acids (FFAs) has been the primary cause of insulin resistance10 through low-grade inflammation in cardiac tissue.11 Kim et al. (2009)12 reported that FFAs might cause inflammation and suppress glucose uptake through inhibition IRS-1 in cardiac tissue. Meanwhile, reducing FFAs plasma levels could improve cardiac function in the high-fat diet-induced obese rat model.13 Therefore, improving the lipid profile could prevent the development of cardiac insulin resistance.\n\nRecently, natural compound derivatives revealed beneficial effects in metabolic syndrome improvement. One of the natural compounds that are widely consumed is epigallocatechin-3-gallate (EGCG) which is mainly derived from green tea leaves.14 Many studies have investigated the beneficial effect of green tea administration and its constituents in alleviating metabolic syndrome. Most of those studies revealed that green tea administration modulated insulin sensitivity, reduced blood glucose level, and improved lipid profile in metabolic syndrome animal models.15–17 Additionally, FFAs-induced insulin resistance and hyperglycemia-induced cardiac fibrosis could be attenuated by EGCG administration in vivo.18 Moreover, chlorogenic acid (CGA), a phenolic compound in green coffee beans, has been another natural compound derivative that could alleviate metabolic syndrome.19,20 CGA potentiates insulin activity similar to the therapeutic mechanism of metformin21 but does not induce obesity, unlike thiazolidinedione (TZD) or insulin therapy.22 A previous study also showed that CGA improved FFAs metabolism in rats hepatic tissue.23 Nevertheless, green coffee extract administration has detrimental effects due to the caffeine content,24–26 and the CGA antioxidant activity depends on the roasted level of green coffee beans.27,28 Therefore, this study used decaffeinated light-roasted green coffee beans to avoid the detrimental effects of caffeine content and reach the highest antioxidant activity of CGA. Many studies showed that green tea or green coffee extract administration could treat metabolic syndrome. Still, analysis investigating the beneficial effect of these extract combinations in alleviating metabolic syndrome remains limited, whereas natural compounds have a more significant therapeutic effect when combined.29 This study investigated the combination of green tea and decaffeinated, light roasted green coffee extract to improve free fatty acid-induced cardiac insulin resistance by improving the adiponectin/FAS pathway.\n\n\nMethods\n\nAll experimental procedures were approved by the ethical committee of Faculty of Medicine, Brawijaya University with registration number 405/EC/KEP/10/2016. All efforts were made to ameliorate harm to the animals by using the standard protocol from the Indonesian Ministry of Health ethical research guidelines for animal experimental research.\n\nThis study is part of a larger study30 which used 25 males Sprague–Dawley rats (age 9 weeks) obtained from the National Agency of Drug and Food Control, Indonesia. The ethical committee approved the experimental protocols of the Faculty of Medicine, Brawijaya University. Rats were maintained and acclimatized in the environmentally controlled standard cage as described in our previous study.30 Animals were grouped as the previous study as follows: i) normal control group (NC) that were assigned to standard chow without STZ injection; metabolic syndrome rats were obtained after HFHS diet and low dose STZ (bioWORLD cat.41910012-4) injection intraperitoneally at the second week of the protocol. NCEP ATP III criteria confirmed metabolic syndrome features. The metabolic syndrome rats were assigned to four groups ii) metabolic syndrome group (MS); iii) green tea group (GT) that were given the HFHS diet, STZ injection, and green tea extract (300 mg/kg b.w.) administration per oral; iv) green coffee group (GC) that were assigned to HFHS diet, STZ injection, and green coffee extract (200 mg/kg b.w.) administration; v) combination group (CM) that were assigned to HFHS diet, STZ injection, and combination of green tea (300 mg/kg b. w.) and green coffee (200 mg/kg b. w.) extract administration, respectively.31 Green tea and coffee extract were administered in millilitres via oral gavage daily based on weekly measured body weight.31 After 9 weeks of exact treatment, animals were euthanized by cervical decapitation previously anaesthetized using diethyl ether after a 12-hour fast. As soon as the rats died, the blood samples were obtained from the heart and transferred into a microcentrifuge tube to get serum samples by centrifugation (4,000 ×g for 15 minutes at 4°C).31\n\nThe green tea leaves were obtained from Sukawana, Bandung, Indonesia (1550 MAMSL). Protocol of green tea extraction followed the procedure of Saifur Rohman et al. (2021).31\n\nThe coffee beans used in this experiment were Coffea canephora/robusta. The coffee beans were obtained from Dampit, Malang, Indonesia (800 MAMSL). The protocol of green coffee extraction followed the prodcedure of Saifur Rohman et al. (2021).31\n\nBioactive compound level in green tea extract (EGCG) and green coffee bean extract (caffeine and CGA) were analyzed by high-performance liquid chromatography (HPLC) system using a Shimadzu Brand chromatograph (model SCL10AVP, Japan) that set up with a C-18 reverse-phase column (Shim-pack VP ODS 5μm 150 × 4.6 mm). Details of the method were explained in the previous study.31\n\nOur previous study determined the exact doses based on the optimal doses for each extract.31\n\nDaily food intake and fluid intake were measured each day, and body weight every week. Foods and fluids intake were measured by subtracting the amount provided by the remaining. More information was written in the previous study.31\n\nThe fasting blood glucose (BIOLABO, cat no. 80009), triglycerides (TG) (cat no. 80019), and HDL-Cholesterol (BIOLABO, cat no. 86516) were analyzed with commercial kits (Biolabs, France) enzymatically as in the previous study.31\n\nRat serum was collected at the end of the study and stored at −80oC. ELISA analysis was conducted for measuring non-esterified fatty acid (NEFA) (Ref E-BC-K014, Elabscience, United States), (Ref E-EL-R2466, Elabscience, United States), and adiponectin level (Ref E-EL-R3012, Elabscience, United States). The measurements were conducted using the manual protocol by the manufacturer and read using ELx808 Absorbance Microplate Reader (BioTek, China) to get the result as ng/mL.\n\nThis study measured HOMA-IR using the Commercial ELISA Kit (Ref E-EL-R2466, Elabscience, United States). The measurement was conducted using the manual protocol by the manufacturer and read using EL×808 Absorbance Microplate Reader (BioTek, China) to get the result as ng/mL. HOMA-IR was used to calculate an index from the product of the fasting concentrations of blood glucose (mg/dL) and insulin (microU/L) levels divided by 14.1. Lower levels of HOMA-IR indicate greater insulin sensitivity, and higher levels indicate insulin resistance (Van Dijk et al., 2013).\n\nBlood pressure was measured three times by a tail-cuff sphygmomanometer technique (Ugo Basile 58500) at the baseline and the end of the study. The average of those three measurements was calculated and shown as the final reading for SBP.\n\nTotal RNA was obtained from liver and heart tissues and isolated using the easy-BLUE (Intron Biotechnology, cat no. 17061). Reverse transcription reaction was converted by a ReverTra Ace-α kit (Toyobo, FSK-101). The mRNA expression levels were measured using the touchdown PCR protocol with polymerase chain reaction (PCR) LightCycler 96 system (Takara, cat no. TP600). The PCR process was performed using a GoTaq Green Master PCR Kit (Promega, cat no, M7822) according to the manufacturer's protocols with one of the target gene primers. The primer sequences were as follows: β-actin forward 5′-CGA GTA CAA CCT TCT TGC AG-3′, reverse 5′-CAT TGT AGA AAG TGT GGT GC-3′; FAS forward 5′-TGG AGA AGC CCA GGA ACA ACT CAT-3′, reverse 5′-ACC GAG TAA TGC CGT TCA GTT CCT-3′; Adipo-R1: forward 5′-GAC AGG CCT AGG TGT CCA TCA-3′, reverse 5′-TCG TAT GGG ATG ACC CTC CA-3′; PI3K forward 5′-CCT CTC CTT ATA AAG CTC CTG GAA-3′, reverse 5′-GAT CAC AAT CAA GAA GCT GTC GTA A-3′; IRS1 forward 5′-AAG CAC CTG GTG GCT CTC TA-3′, reverse 5′-TCA GGA TAA CCT GCC AGA CC-3′; IRS2 forward 5′-ATA CCG CCT ATG CCT GTC TG-3′, reverse 5′-AGA AGA AGC TGT CCG AGT GG-3′; PDK1 forward 5′-CGT CCC GCA CGT AGA G-3′, reverse 5′-TCC TCA GCA CTC TTG TCC TTA-3′; AKT forward 5′-TCA CCT CTG AGA CCG ACA CC-3′, reverse 5′-ACT GGC TAG TAG GAG AAC TGG-3′; GLUT4 forward 5′-CTT CCT TCT ATT TGC CGT CCT C-3′, reverse 5′-GCT GCT TTG TCC TTC ATC CTG-3′. Gene expression was defined as the relative expression level after being compared with the housekeeping gene (β-actin).\n\nData were presented as mean ± SD and statistically analyzed using an independent t-test with a confidence level of 95% as significant at p ≤ 0.05.\n\n\nResults\n\nHPLC analysis showed that EGCG concentration in green tea extract was 74.126 μg/g. Meanwhile, CGA, caffeine, and polyphenol concentrations in the green coffee extract was 27.134 μg/g and 43,473 μg/g, respectively.31\n\nOur previous study reported that rats with the HFHS diet and low-dose STZ injection had metabolic syndrome. It was proved by the measurement of systolic blood pressure (SBP), fasting blood glucose (FBG) level, triglyceride (TG), and HDL cholesterol (HDL) plasma level in rats induced HFHS diet with STZ injection (MS) group met the metabolic syndrome characteristic in accordance to NCEP-ATP III criteria in 8 weeks of duration. Significant differences in SBP, FBG, TG, and HDL levels were observed between the normal control group (NC) and the metabolic syndrome group (MS) (p < 0.05).32 The pre- and post-test in all extract-intervention groups showed improvement in SBP, FBG, TG, and HDL levels. Meanwhile, the GC group had no statistically significant difference between pre-and post-test, except the HDL level (data were available in https://doi.org/10.6084/m9.figshare.13249163.v3).\n\nA significant increase was observed in plasma NEFA levels in the MS group compared tothe NC group (p < 0.05). After extract intervention, the plasma NEFA levels in all extract treated rats were significantly lower (p < 0.05) compared to that of the MS group. Interestingly, the CM group had the least plasma NEFA levels and a significant difference than GT (p < 0.05) and GC (p < 0.01) was observed in plasma NEFA levels (Figure 1A). It suggested that combining the green tea extract and decaffeinated light roasted green coffee was more effective in reducing FFAs than green tea or green coffee extract single administration (Figure 1A).\n\nA. Serum level of non-esterified free fatty acids; B. HOMA-IR score index was used as representation of insulin resistance status. Data are expressed as mean ± SEM (N = 4-5). p < 0.05, p < 0.01, p < 0.001, *p < 0.0001 compared with MS. #p < 0.05, ##p < 0.01, ###p < 0.001, ####p < 0.0001 compared with GT. $p < 0.05, $$p < 0.01, $$$p < 0.001 compared with GC.\n\nAdiponectin levels were significantly lower in the MS group than in the NC group (p < 0.05). The GT group showed lower levels of adiponectin than the GT group. Still, the combination extract group showed a better effect in improving adiponectin levels significantly compared to that of the GT and GC groups (p < 0.05) (Figure 2A). Moreover, the relative mRNA expression levels of adiponectin-receptor 1 (Adipo-R1) in this study also significantly lower in the MS group compared to that of the NC group (p < 0.001) (Figure 2B). All extract treated groups, either GT, GC, or CM, revealed a significantly higher of relative mRNA expression in Adipo-R1 gene expression compared to that of the MS group (p < 0.001) (Figure 2B). Moreover, the CM group showed the highest Adipo-R1 mRNA expression levels among other extract treated groups (p < 0.01) (Figure 2B).\n\nA. Adiponectin serum levels; B. Gene expression of Adipo-R1; C. Gene expression of FAS. Data are expressed as mean ± SEM (N = 4-5). p < 0.05, p < 0.01, p < 0.001, **p < 0.0001 compared with MS. #p < 0.05, ##p < 0.01, ###p < 0.001, ####p < 0.0001 compared with GT. $p < 0.05, $$p < 0.01, $$$p < 0.001 compared with GC.\n\nThis study revealed the effect of green tea and green coffee extract administration on the free fatty acid synthesis pathway by analyzing the NEFA levels and adiponectin/Adipo-R1/AMPK/FAS pathway involvement.\n\nThere was an increase in fatty acid synthase (FAS) gene expression in the liver. The expression of relative mRNA level of FAS was significantly higher in the MS group compared to that of the NC group (p < 0.001) (Figure 2C). All extract-treated groups showed a lower of relative mRNA level of FAS gene in the GT, GC, or CM groups and significantly different with the MS group (p < 0.05) (Figure 2C). However, there was no significant difference in FAS gene expression between the GT and GC groups (p > 0.05). Still, the FAS gene expression in the CM group showed a significant difference compared to the GT and GC group (p < 0.01) (Figure 2C). These results were linear with our previous study; we reported that HFHS diet and low dose STZ injection induced metabolic syndrome rats had lower AMPK-α2 gene expression (p < 0.05). Meanwhile, the combination of green tea and green coffee extract showed substantially higher AMPK-α2 expression compared to that of single extract either green tea or green coffee extract administration (p < 0.05).32 Therefore, this study revealed that green tea or green coffee extract administration could ameliorate the FFAs levels by improving the adiponectin/adipo-R1/AMPK/FAS pathway in liver tissue rats. However, the combined extract was more effective.\n\nHFHS diet with STZ injection rats showed a higher homeostatic model assessment for insulin resistance (HOMA-IR) index compared to that of the NC group (p < 0.001) (Figure 1B). All of the extract treated groups revealed a lower HOMA-IR index compared to the MS group (p < 0.05) (Figure 1B). Moreover, the CM group showed the lowest level in the HOMA-IR index among other extract treated groups (p < 0.001). This indicated that the combination revealed a better effect in improving insulin resistance.\n\nThe higher HOMA-IR in HFHS diet with low dose STZ injection induced rats was accompanied by a decrease of cardiac insulin signalling protein gene expression compared to that of the NC group (p < 0.05) (Figure 1B). It was illustrated by the lower expression of IRS1/2, PI3K, PDK1, Akt, and GLUT4. A higher cardiac insulin signalling protein gene expression was observed in all extract treated groups. Nevertheless, the GT group showed higher IRS2, AKT, and GLUT4 gene expressions compared to that of the GC group (Figure 3B, E, F). However, those markers’ relative mRNA expression levels were higher in the CM group than in the GT or GC group (p < 0.001) (Figure 3).\n\nA. Relative mRNA expression level of IRS1; B. Relative mRNA expression level of IRS2; C. Relative mRNA expression level of PI3K; D. Relative mRNA expression level of PDK1; E. Relative mRNA expression level of Akt; F. Relative mRNA expression level of GLUT4. Data are expressed as mean ± SEM (N = 4-5). p < 0.05, p < 0.01, p < 0.001, ***p < 0.0001 compared with MS. #p < 0.05, ##p < 0.01, ###p < 0.001, ####p < 0.0001 compared with GT. $p < 0.05, $$p < 0.01, $$$p < 0.001 compared with GC.\n\n\nDiscussion\n\nMetabolic syndrome is a metabolic disturbance characterized by insulin resistance and a decrease of adiponectin as a biomarker. Adiponectin has essential roles in metabolic profile, such as improved glucose and lipid metabolism and insulin resistance.33 Adiponectin, an inducer of AMP-activated protein kinase (AMPK) has a regulatory effect on glucose and lipid metabolism that had an essential role in free fatty acid production through inhibition of fatty acid synthetase (FAS).34 The present study showed lower adiponectin and higher FFA levels in MS rats than the normal rats and intervention rat groups. The administration of green coffee and green tea in MS rats improved adiponectin and FFA serum levels. The improvement of adiponectin and FFA levels were related to the modulation of adipo-R1 and AMPK gene expression in hepatic tissue.35–37 This study showed improvement in adipoR1 in the extract treated groups. Additionally, FAS gene expression in hepatic tissue was lower in either the green tea or green coffee group. Furthermore, our previous study showed that hepatic AMPK expression was improved in all intervention groups, and the highest level showed in the combination extract group.32\n\nLower adiponectin levels and higher FFA levels are related to insulin resistance in hepatic, skeletal, and cardiac tissue.33,38 This study showed that higher HOMA-IR levels reflected insulin resistance conditions. The highest HOMA-IR was shown in MS group rats compared to that of intervention group rats. Moreover, green tea and green coffee extract administration had significantly lower HOMA-IR levels compared to that of MS group rats. Lower HOMA-IR in the extract treated group was accompanied by improvement of insulin signalling in cardiac tissue. Our study showed cardiac tissue gene expression improvement related to insulin signalling, such as through IRS, Akt, PI3K, PDK1, and GLUT4 in MS rat with green tea and green coffee administration. The results showed that insulin signaling gene expressions were significantly higher in the intervention group compared to MS group rats. Moreover, the combination of green tea and green coffee had the highest expressions.\n\nThe present study aimed to investigate the effect of combining green tea and green coffee on cardiac insulin resistance caused by the elevation of FFA serum and lower adiponectin levels. This study showed that the administration of green tea and green coffee improved cardiac insulin resistance by reducing serum free fatty acids levels and elevating serum adiponectin levels by modulation of adipo-R1, AMPK, and FAS gene expressions. These results were similar to previous studies that improving serum FFA and adiponectin signalling pathway could attenuate insulin resistance.39–42 Although animal and human studies have shown that lowering serum FFAs directly improved insulin resistance in some tissues such as muscles, adipose, hepatic, and endothelial tissues, few studies showed the effect on cardiac tissues. Moreover, green coffee administration could improve blood lipids and increase metabolic rates, fatty acid oxidation, and hepatic triglyceride in obese animal rat or mice models using diet or genetic modification.12,43–45 In addition, a chlorogenic acid compound in the green coffee extract was associated with the improvement of adiponectin levels and had an important role in insulin sensitivity and inflammation.46 Besides, green tea administration was known to have similar effects.47 Li et al. (2018) study showed that the EGCG compound in green tea extract inhibited gene expression involved in synthesizing de novo fatty acids, such as FAS, ACC, and SC.48 Other studies showed that EGCG had a beneficial effect on insulin resistance by improving the AMPK pathway.18\n\nAdministration of a combination of green coffee and green tea extract in this study showed a higher adiponectin level compared to that of green coffee or green tea single extract administration. Additionally, the Adipo-R1 gene expression was higher in the CM group. Previous studies showed that green tea extract had a beneficial effect on the adiponectin signalling pathway through improving adiponectin levels and modulating adipo-R1 expressions.35,36 On the other hand, few studies have revealed the effect of green coffee on the improvement of FFA levels.49,50 Our study also showed that green tea and green coffee administration were adequate to reduce serum FFA levels. This study was in accordance with previous studies that revealed the improvement of adiponectin and adipo-R1 is involved in lower serum FFA levels.18,39,43–45 Interestingly, the combination of both extracts exhibited lower serum FFA levels than green tea or decaffeinated-light roasted green coffee alone.\n\nElevation of serum FFA levels is caused by excess nutrition intake, adipose lipolysis, and de novo fatty acid synthesis (glucose utilization), mainly in the hepatic tissues.37 The present study showed that hepatic de novo fatty acid synthesis was increased in metabolic syndrome rats. It was illustrated by increasing FAS mRNA expressions in the MS group (P < 0.01 vs. NC group). This finding was linear with our previous study that AMPK mRNA expressions were reduced in MS rats.32 AMPK has an inhibitory effect on FAS51; thus, the reduction of AMPK showed a decrease in inhibitory regulation effect. Nevertheless, green tea or green coffee intervention in the present study showed a decrease in FAS expressions, and these were similar to other previous studies43,44,49,52,53; however, our findings showed no significant difference between green tea and green coffee extract rat groups. Meanwhile, the combination of light roasted decaffeinated green coffee and green tea extract significantly reduced FAS mRNA expression compared to that of single extract groups. These findings showed that green tea and green coffee had more practical effects on improving hepatic de novo fatty acid synthesis, thus reducing serum FFAs levels.\n\nIt was known that FFA induced insulin resistance.42,54 This study revealed HOMA-IR accompanied the increase of serum FFA levels in MS rats. Compared with previous studies,55–57 we had similar findings that administration of green tea decaffeinated-light roasted green coffee had beneficial effects on improving insulin resistance. It was illustrated by a lowering of HOMA-IR in all intervention groups. Meanwhile, the administration of the combination of both extracts showed a lower level of HOMA-IR than green tea or green coffee administration alone. A previous study showed that the administration of EGCG52,58 attenuated insulin sensitivity in skeletal and adipose tissue.. Moreover, CGA and other polyphenols in green coffee improved insulin sensitivity in HFD Mice.49 HOMA-IR reflects insulin resistance conditions from multi organs such as adipose, heart, and muscle, including skeletal and cardiac muscle.59,60\n\nMany reviews have revealed that FFA could induce alteration of cardiac structure and function without coronary disease or hypertension,7 which is called diabetic cardiomyopathy, and insulin resistance is the early step in the development of the disease.61 Many studies suggest that an increase of serum FFA levels can induce insulin resistance by inhibiting IRS1/PI3K/Akt in cardiac muscle,62–64 and associated with cardiac remodelling and dysfunction.65,66 It was recently known that FFAs could interact with toll-like receptors (TLR) and induce insulin resistance through the disturbance of insulin signalling pathways in cardiac tissues.11,67 Our findings observed that improvement of serum FFA levels was accompanied by improved cardiac insulin signalling pathway. All treatment groups showed a high of IRS1/2, PI3K, PDK1, Akt, and GLUT4 mRNA expression, but the GT group showed higher IRS2, Akt, and GLUT4 than the GC group. Rebollo-Hernanz et al. (2019) recently showed that phenolic compounds in green coffee, especially CGA, modulate adipogenesis and insulin resistance via PI3K/Akt signalling pathway in adipocytes.68 Another study showed that chlorogenic acid stimulates glucose transport in skeletal muscle via AMPK activation in db/db mice.56 Besides, the green tea administration showed the ameliorating mechanism of hyperglycemia by promoting GLUT4 translocation in skeletal muscle of diabetic rodents.58 Moreover, another study revealed that EGCG administration induced GLUT4 translocation in skeletal muscle through PI3K- and AMPK-dependent pathways.16 Nevertheless, the combination of green tea and decaffeinated-light roasted green coffee extract had the highest expressions. It showed that green tea and green coffee extract had synergistic interaction that consequently improved insulin sensitivity.\n\nThis study had several limitations. Firstly, we did not investigate the biomarker in adipose tissues, which might give a comprehensive understanding of green tea and green coffee administration’s effect on lipid metabolism. Secondly, we could not exhibit the molecular mechanisms for the effects of green tea and green coffee combination administration.\n\n\nConclusion\n\nOur study revealed clear evidence that a combination of green tea and decaffeinated light roasted green coffee extracts improved cardiac insulin resistance better than single extract administration by ameliorating free fatty acids through adiponectin/FAS pathway modulation.\n\n\nData availability\n\nFigshare: Underlying data for ‘Green Tea and decaffeinated light roasted green coffee extract combination improved cardiac insulin resistance through free fatty acids and adiponectin/FAS pathway amelioration in metabolic syndrome rat model’ https://doi.org/10.6084/m9.figshare.13249163.v3.\n\nThis project contains the following underlying data:\n\n- Data of Metabolic Syndrome Rat Model.xlsx (This file contains the analyzed data)\n\n- RAW data metabolic syndrome.xlsx (This file contains the actual observed values of the variables)\n\n- Chlorogenic acid Coffee HPLC.pdf (This file contains the value of coffee chlorogenic acid levels as measured by HPLC)\n\n- Caffeine coffee HPLC.pdf (This file contains the value of coffee caffeine levels as measured by HPLC)\n\n- Green Tea Catechin HPLC.pdf (This file contains the value of the catechin levels in the tea)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthor contributions\n\nM.L: Conceptualization, Data Curation, Methodology, Writing – Review & Editing\n\nM.S.R: Conceptualization, Funding acquisition, Supervision, Writing – Review & Editing\n\nD.A.N: Conceptualization, Data Curation, Methodology, Resources\n\nM.N.R: Data Curation, Formal Analysis, Investigation, Writing – Original Draft Preparation\n\nN.A.W: Data Curation, Investigation, Writing – Original Draft Preparation\n\nN.W: Project Administration, Supervision, Writing – Review & Editing", "appendix": "Acknowledgements\n\nThanks to the Medical Faculty of Brawijaya University, the Molecular Biology Laboratory of the Department of Biology Mathematics and Natural Sciences of Brawijaya University, and the Ministry of Education, Culture, Research, and Technology.\n\n\nReferences\n\nHotamisligil GS, Erbay E: Nutrient sensing and inflammation in metabolic diseases. 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PubMed Abstract \| Publisher Full Text\n\nHamdaoui MH, Snoussi C, Dhaouadi K, et al.: Tea decoctions prevent body weight gain in rats fed high-fat diet; black tea being more efficient than green tea. J Nutr Intermediary Metabolism. 2016 Dec; 6: 33–40. Publisher Full Text\n\nStorz P, Doppler H, Wernig A, et al.: Cross-talk mechanisms in the development of insulin resistance of skeletal muscle cells. Palmitate rather than tumour necrosis factor inhibits insulin-dependent protein kinase B (PKB)/Akt stimulation and glucose uptake. Eur J Biochem. 1999 Nov 15; 266(1): 17–25. PubMed Abstract \| Publisher Full Text\n\nDresner A, Laurent D, Marcucci M, et al.: Effects of free fatty acids on glucose transport and IRS-1–associated phosphatidylinositol 3-kinase activity. J Clin Invest. 1999 Jan 15; 103(2): 253–259. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoden G: Obesity, insulin resistance and free fatty acids: Current Opinion in Endocrinology. Diabetes Obes. 2011 Apr; 18(2): 139–143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurase T, Misawa K, Minegishi Y, et al.: Coffee polyphenols suppress diet-induced body fat accumulation by downregulating SREBP-1c and related molecules in C57BL/6J mice. Am J Physiol Endocrinol Metab. 2011 Jan; 300(1): E122–E133. PubMed Abstract \| Publisher Full Text\n\nCho A-S, Jeon S-M, Kim M-J, et al.: Chlorogenic acid exhibits anti-obesity property and improves lipid metabolism in high-fat diet-induced-obese mice. Food Chem Toxicol. 2010 Mar; 48(3): 937–943. PubMed Abstract \| Publisher Full Text\n\nIlmiawati C, Fitri F, Rofinda ZD, et al.: Green coffee extract modifies body weight, serum lipids and TNF-α in high-fat diet-induced obese rats. BMC Res Notes. 2020 Dec; 13(1): 208. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang Z, Wang S, Zhou S, et al.: Sulforaphane prevents the development of cardiomyopathy in type 2 diabetic mice probably by reversing oxidative stress-induced inhibition of LKB1/AMPK pathway. J Mol Cell Cardiol. 2014 Dec; 77: 42–52. PubMed Abstract \| Publisher Full Text\n\nYuan H, Li Y, Ling F, et al.: The phytochemical epigallocatechin gallate prolongs the lifespan by improving lipid metabolism, reducing inflammation and oxidative stress in high-fat diet-fed obese rats. Aging Cell. 2020 Sep [cited 2021 Jul 17]; 19(9). Reference Source\n\nLi F, Gao C, Yan P, et al.: EGCG Reduces Obesity and White Adipose Tissue Gain Partly Through AMPK Activation in Mice. Front Pharmacol. 2018 Nov 22; 9: 1366. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong SJ, Choi S, Park T: Decaffeinated Green Coffee Bean Extract Attenuates Diet-Induced Obesity and Insulin Resistance in Mice. Evid Based Complement Alternat Med. 2014; 2014: 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Shen D, Tang X, et al.: Chlorogenic acid prevents isoproterenol-induced hypertrophy in neonatal rat myocytes. Toxicol Lett. 2014 May; 226(3): 257–263. PubMed Abstract \| Publisher Full Text\n\nDay EA, Ford RJ, Steinberg GR: AMPK as a Therapeutic Target for Treating Metabolic Diseases. Trends Endocrinol Metab. 2017 Aug; 28(8): 545–560. PubMed Abstract \| Publisher Full Text\n\nLi F, Gao C, Yan P, et al.: EGCG Reduces Obesity and White Adipose Tissue Gain Partly Through AMPK Activation in Mice. Front Pharmacol. 2018 Nov 22; 9: 1366. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang R, Xiao W, Wang X, et al.: Novel inhibitors of fatty-acid synthase from green tea (Camellia sinensis Xihu Longjing) with high activity and a new reacting site. Biotechnol Appl Biochem. 2006 Jan 1; 43(1): 1. PubMed Abstract \| Publisher Full Text\n\nCapurso C, Capurso A: From excess adiposity to insulin resistance: The role of free fatty acids. Vascul Pharmacol. 2012 Sep; 57(2–4): 91–97. PubMed Abstract \| Publisher Full Text\n\nLukitasari M, Nugroho DA, Rohman MS, et al.: Light-Roasted Green Coffee Extract Improved Adiponectin, Insulin Resistance, And Metabolic Profile Of Metabolic Syndrome Rat Model. Asian J Pharm Clin Res. 2017 Sep 1; 10(9): 279. Publisher Full Text\n\nOng KW, Hsu A, Tan BKH: Chlorogenic Acid Stimulates Glucose Transport in Skeletal Muscle via AMPK Activation: A Contributor to the Beneficial Effects of Coffee on Diabetes.Calbet JAL, editor. PLoS ONE. 2012 Mar 7; 7(3): e32718. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu J, Song P, Perry R, et al.: The Effectiveness of Green Tea or Green Tea Extract on Insulin Resistance and Glycemic Control in Type 2 Diabetes Mellitus: A Meta-Analysis. Diabetes Metab J. 2017; 41(4): 251. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUeda-Wakagi M, Nagayasu H, Yamashita Y, et al.: Green Tea Ameliorates Hyperglycemia by Promoting the Translocation of Glucose Transporter 4 in the Skeletal Muscle of Diabetic Rodents. IJMS. 2019 May 16; 20(10): 2436. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZabielski P, Błachnio-Zabielska AU, Wójcik B, et al.: Effect of plasma free fatty acid supply on the rate of ceramide synthesis in different muscle types in the rat.Chan C, editor. PLoS ONE. 2017 Nov 2; 12(11): e0187136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXin Y, Wang Y, Chi J, et al.: Elevated free fatty acid level is associated with insulin-resistant state in nondiabetic Chinese people. DMSO. 2019 Jan; 12: 139–147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPalomer X, Pizarro-Delgado J, Vázquez-Carrera M: Emerging Actors in Diabetic Cardiomyopathy: Heartbreaker Biomarkers or Therapeutic Targets? Trends Pharmacol Sci. 2018 May; 39(5): 452–467. PubMed Abstract \| Publisher Full Text\n\nWitteles RM, Fowler MB: Insulin-Resistant Cardiomyopathy. J Am College Cardiol. 2008 Jan; 51(2): 93–102.\n\nCook SA, Varela-Carver A, Mongillo M, et al.: Abnormal myocardial insulin signalling in type 2 diabetes and left-ventricular dysfunction. Eur Heart J. 2010 Jan; 31(1): 100–111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuniyappa R, Montagnani M, Koh KK, et al.: Cardiovascular Actions of Insulin. Endocr Rev. 2007 Aug 1; 28(5): 463–491. PubMed Abstract \| Publisher Full Text\n\nOuwens DM, Diamant M, Fodor M, et al.: Cardiac contractile dysfunction in insulin-resistant rats fed a high-fat diet is associated with elevated CD36-mediated fatty acid uptake and esterification. Diabetologia. 2007 Sep; 50(9): 1938–1948. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaddingham MT: Contractile apparatus dysfunction early in the pathophysiology of diabetic cardiomyopathy. WJD. 2015; 6(7): 943. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Luca C, Olefsky JM: Inflammation and Insulin Resistance. 2009; 17.\n\nRebollo-Hernanz M, Zhang Q, Aguilera Y, et al.: Phenolic compounds from coffee by-products modulate adipogenesis-related inflammation, mitochondrial dysfunction, and insulin resistance in adipocytes, via insulin/PI3K/AKT signaling pathways. Food Chem Toxicol. 2019 Oct; 132: 110672. PubMed Abstract \| Publisher Full Text" }	[ { "id": "98201", "date": "10 Nov 2021", "name": "Vijaya Anand Arumugam", "expertise": [ "Reviewer Expertise Phytothreapeutics", "Clinical Biochemistry", "Medical Genetics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors intended to evaluate the effects of Green Tea and Decaffeinated Light Roasted Green Coffee Extract metabolic syndrome. It is an interesting and useful study. Firstly, this manuscript is well-organised and well-structured. Secondly, this study observed the differentially expressed genes and provided potential target candidates for the treatment of the metabolic syndrome.\n1. There are some grammatical and syntax errors in the manuscript. For example, the words “A free fatty acid is” may be as “Free fatty acids are”; “improvement” as “the improvement” (in the 7th line of the abstract); “IRS-1” as “of IRS-1”; “Combination green” as “A combination of green”; “study also” as “study were also”; “higher of” as “higher”; “lower of” as “lower”; “different with” as “different from”. The grammar mistakes which are not mentioned here also to be checked and corrected properly.\n2. There are some typing mistakes as well, and authors are advised to carefully proof-read the text. For example, the word “prodcedure” may be as “procedure”; “compound level” as “compound levels”; “tothe” as “to the”; “extract treated” as “extract-treated”; “theMSgroup” as “the MS group”; “theNCgroup” as “the NC group”; “GTgroup” as “GT group”; “theGTandGCgroups” as “the GT and GC groups”; “theCMgroup” as “the CM group”; “injection induced” as “injection-induced”; “pathway” as “pathways”; “tissue..” as “tissue.”; “decaffeinatedlight” as “decaffeinated light”. The typos not mentioned here also to be checked and corrected properly.\n3. The keywords should not be from the title and also the remaining part of the manuscript. The keywords should assist computer searches to find your specific article.\n4. Check the abbreviations throughout the manuscript and introduce the abbreviation when the full word appears the first time in the text and then use only the abbreviation (For example, high-fat high sucrose (HFHS), streptozotocin (STZ), metabolic syndrome (MS), chlorogenic acid (CGA), high-fat diet (HFD), etc.). And it should be in both abstract as well as in the remaining part of the manuscript. Make a term abbreviated in the article when it is repeated at least three times in the text, not all of them need to be.\n6. The weight of the animals should be included in the materials and methods under the heading “Animals and experimental design”. The composition of the standard diet may be included in the materials and methods and also where it has been obtained.\n7. In the statistical analysis the authors should include the software and version of the software used in the present findings under the heading “Data and statistical analysis”.\n8. The referencing in this paper is inconsistent. The authors have not given the references as per the journal format. In many places, the authors used numbers and authors with year and in few places used only numbers and in some places the authors' used names and years only. For example, “Van Dijk et al., 2013” and it should be corrected properly.\n9. The figures should be improved and a proper footnote should be given. All legends should have enough description for a reader to understand the figures without having to refer back of the main text of the manuscript. The authors have used the abbreviations in the axis and expansions that are not given with the graph. The quality of the image is not to be changed since it seems good. The only suggestion here is the authors may include the expansion of the terms used like 1) MS (metabolic syndrome), 2) NC (normal chow) 3) GT (green tea extract) 4) GC (decaffeinated-light roasted green coffee extract), 5) CM (combination of both extracts) as legends.\n10. The author should justify how the dose fixation is done (is it based on toxicity test or previous reference, if previous should be included in the reference section) in materials and methods or discussion section of the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10212", "date": "16 Nov 2023", "name": "Dwi Adi Nugroho", "role": "Author Response", "response": "Dear A. Vijaya Anand, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, Tamil Nadu, India I would like to express my sincere gratitude for taking the time to review our manuscript titled \"Green Tea and Decaffeinated Light Roasted Green Coffee Extract Combination Improved Cardiac Insulin Resistance through Free Fatty Acids and Adiponectin/FAS Pathway Amelioration in Metabolic Syndrome Rat Model.\" Your thoughtful feedback and constructive comments have been invaluable in improving the quality of our work. I have made the necessary revisions to the manuscript as per your recommendations. You will find these changes clearly marked in the revised manuscript. Additionally, I have included a detailed response to each comment in the attached document. Once again, thank you for your time and expertise in reviewing our work. We believe that your feedback has significantly enhanced the quality and rigor of our research. We look forward to your further insights and guidance during the next round of review. Sincerely, M.N. Kholis" } ] }, { "id": "138844", "date": "18 Jul 2022", "name": "Sylvia Riedel", "expertise": [ "Reviewer Expertise Metabolic diseases", "inflammation", "gastrointestinal physiology", "food chemistry" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral impression: The authors determined whether green tea, decaffeinated green coffee, and a combination thereof can reduce features of metabolic syndrome in rats, with a specific focus on insulin resistance. The manuscript in its current form lacks important information as well as clarity. Grammar and sentence construction need to be reviewed critically throughout the manuscript. The work has merit, but there are too many errors and omissions in this version, the authors should rethink and revise the manuscript thoroughly. The referencing requires attention. Specific comments are highlighted below:\nAbstract\nSecond sentence - grammar. What does “improvement of free fatty acid” mean?\n\nAbbreviations need to be explained when first used (e.g. FAS).\n\nIt is unclear how many rats were used per group, is it 25 for all groups or per group?\n\nFrom the abstract, it is not clear whether groups 3, 4, and 5 were given the high-fat high-sucrose (HFHS) diet and streptozotocin (STZ).\n\nWhat is the rationale for the combination group of green tea and green coffee?\n\nWas circulating adiponectin measured and in which tissues were the mentioned genes assessed?\n\nThe results should be stated clearly and vague statements such as “showed synergistic effects” should be avoided.\n\nThe p values should be included. A clear description of which parameters increased and which decreased in which groups should be included.\n\nIntroduction\nThere is a specific set of diagnostic criteria for metabolic syndrome which should be detailed and referenced in the introduction. Reference 10 describes non-alcoholic fatty liver disease (NAFLD) and not insulin resistance (IR) as such, it seems inappropriate to cite here. There are a few sentences that do not make sense. The authors should draw a distinction between cardiac dysfunction and cardiac insulin resistance and define what cardiac insulin resistance entails.\n\nMethods\nThe study outline is not clear enough from the description, an illustration would be helpful. Critical details regarding the animal work are missing, such as the number of animals per group and dosage of STZ applied. What are the “NCEP ATP III” criteria? These need to be explained and referenced and how the rats used for this study meet these criteria needs to be presented with data (can be supplementary data).\n\nWhat is the composition of the HFHS diet?\n\nIt seems that this study and the study by Rohman et al. 2021 (reference 31) are using the same animals. If this is the case, then this should be stated clearly. Both manuscripts could benefit from combining the results to provide a more substantial and comprehensive overview of the study in one single paper.\n\nIt would be preferable if critical references such as 31 were already published/accepted articles, rather than cited while awaiting peer review.\n\nIf the present study and reference 31 are different experiments, then critical data on the animal’s metabolic status (fasting blood glucose, body weights, and data showing that metabolic syndrome was induced, etc.) needs to be provided in the manuscript (the data is shared, but clear visuals would be preferable) and all paragraphs in the methods including extract preparation and the animal study need to clearly reflect this.\n\nThere is also mention that the study is part of a study published previously (reference 30) – it needs to be clarified in which way. It seems that some of the confusion derives from an unclear formulation of sentences.\n\nThe preparation of the extracts can be referenced if the same method was followed as in reference 31, however, it is not clear what was used to gavage the animals and how the solutions were prepared. Were the animals in the normal control group and the metabolic syndrome control also gavaged and if so, with what? For future studies, alternative methods such as administering the extracts in the diet should be considered to replace gavaging. Extracts can be freeze-dried and mixed into the diet.\n\nIt is not clear how the Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) was analyzed using a kit. How was fasting blood glucose determined? This section requires clarification.\n\nStatistical analysis using a t-test is inappropriate. To assess group differences at least a one-way analysis of variance (ANOVA) or better yet a two-way ANOVA should be used for the MS-induced treatment groups. The MS treatment groups fit a 2x2 factorial design, and a two-way ANOVA will give more appropriate insight into the data, especially the combination of treatments. The negative control and positive control can be compared using a t-test. It is unclear whether the authors report standard deviations (SD) as stated in the statistics paragraph or standard error of the mean (SEM) as stated in the graph legends. The distinction is important and requires clarification.\nResults\nLegends to the graphs require more details, such as an explanation of abbreviations and a clear description in which tissues gene expression was analyzed. In general, graph legends should provide enough information to understand the data presented without reading the text.\n\nIt was stated that decaffeinated green coffee was used. An explanation is required as to why the extract seems to contain caffeine. There is a chromatogram for caffeine in the data section. The second sentence in the HPLC results section is not clear, it mentions CGA, caffeine, and polyphenols but only two values are given. These values should also be presented with standard deviations of replicate measurements. This needs clarification.\n\nGraph numbers do not align with the references in the text. For example, on page 6 the first paragraph refers to Fig 2, but the data is displayed in Fig 3. In the last paragraph on page 10, the authors also refer to Fig 2 which should be Fig 3.\n\nThere was no protein expression included or reported. This is an important aspect to add as gene expression does not necessarily correlate with protein levels and function.\nDiscussion\nOnce the manuscript structure has been clarified and revised, the discussion should be refocused and written concisely to clearly work out what new knowledge this study brings to the body of literature. Grammar should be checked.\n\nThe last sentence in the limitations section “…we could not exhibit the molecular mechanisms for the effects of green tea and green coffee combination administration…”, is unclear but seems to contradict the authors' conclusion.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/10-990
https://f1000research.com/articles/12-674/v1	14 Jun 23	{ "type": "Case Report", "title": "Case Report: Atypical presentation of non-functional gonadotropinoma", "authors": [ "Suresh Oommen", "Sam Rice", "Sam Rice" ], "abstract": "Gonadotropinoma is the most common non-functional pituitary adenoma comprising 10%–30% of all pituitary adenomas. They are benign slow-growing tumours originating from adenohypophysis and rarely become malignant. Its presentation can be atypical, such as visual disturbance, and most patients presenting to an ophthalmologist for visual correction are eventually found to have a field defect. Here, we report a case of a 59-year-old patient who presented with a left-sided visual disturbance, which progressed over the years due to a left temporal hemianopia. The patient was referred to us by an ophthalmologist and was diagnosed with a giant non-functional gonadotropinoma. The patient was surgically treated. Postoperative follow-up magnetic resonance imaging after 3 months showed near complete resection of the tumour.", "keywords": [ "Non-functional pituitary adenoma", "gonadotropinoma", "hemianopia" ], "content": "Introduction\n\nNon-functional gonadotropinomas have become increasingly common as part of non-functional pituitary adenoma with estimated prevalence of 78–94 cases per 1,000,000 population and may present with fewer symptoms such as loss of libido, lethargy or visual disturbance because of their slow-growing nature.1 We present, with informed consent, a case report of a patient who had blurring of vision in the left eye and initially presented to an ophthalmologist who made a diagnosis of left temporal hemianopia. The patient was referred to us for urgent magnetic resonance imaging (MRI), which showed a large pituitary mass compressing the optic chiasm with an anterior pituitary hormone profile showing suppressed levels of thyroxine (T4), follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone and mildly elevated levels of prolactin. Immunohistochemistry was positive for steroidogenic (transcription) factor 1 (SF1), indicating silent gonadotropinoma. This article is reported in line with CARE guidelines.11\n\n\nCase report\n\nA 59-year-old Welsh male, self-employed, was referred to us by an ophthalmologist with a left visual disturbance, which worsened since 2019. He complained of blurring in his left peripheral vision and was diagnosed with left temporal hemianopia, confirmed by Humphrey’s perimetry. The patient did not complain of associated headaches, nausea, vomiting upper limb weakness, cold intolerance, or weight gain. He complained of low energy and decreased libido for approximately 10 years, but showed normal development of secondary sexual characteristics and had a normal frequency of shaving. He had no cushingoid, acromegaly, or other features suggestive of multiple endocrine neoplasia syndrome. He had no significant past medical, family or psychosocial history. He was not on any medications at the time of presentation.\n\nOn examination, the patient was overweight, with a height of 175 cm and weight of 85 kg with BMI of 27. His blood pressure was 140/70 mm Hg, with a pulse of 80 bpm. His body temperature was 36.5 °C. His Glasgow coma scale score was 15/15, and eye examination showed right and left eye visual acuity of 6/6 and 6/24, respectively, as well as reduced colour vision and temporal field defect in the left eye with normal fundus examination. Respiratory, cardiac, abdominal and neurological examination findings were normal.\n\nHis initial blood investigations (Table 1) showed biochemical evidence of hypopituitarism with T4 of 9.5 pmol/L, FSH of 1.9 IU/L, LH of 2.0 IU/L, testosterone of 4.4 nmol/L, 9 am cortisol of 228 nmol/L and prolactin of 370 mU/L with a temporal field defect in the left eye, confirmed by Humphrey’s perimetry (Figure 1). Pituitary MRI showed evidence of pituitary macroadenoma with suprasellar extension and optic chiasmal compression (Figure 2).\n\nThe case was discussed among the multidisciplinary team for surgery. He was admitted after 3 months for transsphenoidal hypophysectomy. A complete excision was not possible because of the extent of the lesion. Immunohistological analysis showed gonadotropinoma with SF1 expression and negative FSH and LH beta subunits.\n\nMild postoperative hyponatremia was due to the syndrome of inappropriate antidiuretic hormone secretion (SIADH), which improved with fluid restriction. Perioperative intravenous hydrocortisone 50 mg 6th hourly coverage was administered to prevent adrenal insufficiency. A low T4 level necessitated the administration of L-thyroxine (50 mcg once daily), but cortisol response was adequate and he was discharged with follow-up after 6 weeks. At follow-up, repeat anterior pituitary hormone profile test showed low TSH, T4, LH and testosterone levels, with a good response to the short synacthen test. Postoperative follow-up MRI after 3 months showed a near complete resection of the tumour (Figure 3).\n\n\nDiscussion\n\nNon-functional pituitary adenomas (NFPAs) are increasingly common with a prevalence rate of 78–94 per 1000,000 population.1 They are benign slow-growing tumours that arise from adenohypophyseal cells of the pituitary gland, with no clinical evidence of hormonal secretion. The most common NFPA is gonadrotropinoma, comprising approximately 80% of all NFPAs, expressing mainly LH, FSH, and alpha subunits along with other transcriptional factors such as SF1 and GATA2.2 NFPAs are generally considered clinically silent tumours, but they can secrete small amounts of gonadotropins, rarely causing ovarian hyperstimulation in females and precocious puberty in males.3 Our patient had SF1-positive immunohistochemistry, with patchy nuclear expression, negative FSH and LH subunits, with a Ki67 index of 2%, indicating a non-functional gonadotropinoma.\n\nThe patient was initially diagnosed with a visual field defect by an ophthalmologist and then was referred to an endocrinologist; detailed history taking showed a picture of gonadotropin deficiency. Patients with NFPA can present with acute deterioration in vision with or without headaches due to haemorrhage into the tumour (known as apoplexy), leading to rapid expansion of the tumour within the limited space of the sella turicia.4 The patient had a left-sided visual field defect, with MRI showing a necrotic area within the tumour with no signs of bleeding or haemorrhage. Although bitemporal hemianopia is the most common type of visual field defect seen in 40% of patients, our patient had left superior and inferior temporal deficits without cranial nerve palsy.5\n\nManagement includes screening of anterior pituitary hormones to rule out any functional secreting tumours such as prolactinoma.6 Once deficiencies of two or more hormones are confirmed, the patient should be referred for visual field testing using either Humphrey’s or Goldmann perimetry.7 Pituitary MRI with gadolinium contrast is recommended to identify the pituitary mass.8 Transsphenoidal surgery is the treatment of choice for NFPA, and recovery depends on the tumour size.9 Patients should have adequate perioperative hydrocortisone coverage to prevent adrenal insufficiency along with preoperative thyroid evaluation.9 Transient complications such as diabetes insipidus or SIADH may occur postoperatively, from which patients may recover.10 Our patient developed transient SIADH postoperatively on day 1 and recovered on day 4. Patients should be reassessed after 6 weeks with follow-up testing of the hypothalamo–pituitary–adrenocortical axis and MRI after 3 months; depending on the size of the lesion; 6 months to yearly surveillance may be required thereafter.9\n\nSome distinctive features to point out in our patient were firstly, it’s a Giant pituitary tumour with central necrotic area, resembling radiological features of pituitary apoplexy, which is a life-threatening condition, presented without headaches or vomiting. Secondly, the tumour was large enough to compress the optic chiasm but had affected the left temporal field sparing the right. Limitations to the study are that, since it is a single case study, the clinical features may vary and validation of our findings to a wider population is needed.\n\nIn conclusion, NFPA can remain asymptomatic for years and may present as visual disturbance, as seen in our patient. Most NFPAs are referred by ophthalmologists due to visual field defects on routine eye examinations. Large NFPAs with optic chiasmal compression need urgent referral for surgery.\n\n\nConsent\n\nWritten informed consent for 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\nZenodo: CARE checklist for ‘Case Report: Atypical presentation of non-functional gonadotropinoma’, https://doi.org/10.5281/zenodo.7927437. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nFernandez A, Karavitaki N, Wass JA: Prevalence of pituitary adenomas: a community-based, cross-sectional study in Banbury (Oxfordshire, UK). Clin. Endocrinol. 2010; 72: 377–382. PubMed Abstract \| Publisher Full Text\n\nChaidarun SS, Klibanski A: Gonadotropinomas. Semin. Reprod. Med. 2002; 20: 339–348. Publisher Full Text\n\nBroughton C, Mears J, Williams A, et al.: A clinically functioning gonadotroph adenoma presenting with abdominal pain, ovarian hyperstimulation and fibromatosis. Endocrinol. Diabetes Metab. Case Rep. 2018; 2018. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVargas G, Gonzalez B, Ramirez C, et al.: Clinical characteristics and treatment outcome of 485 patients with nonfunctioning pituitary macroadenomas. Int. J. Endocrinol. 2015; 2015: 756069. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOgra S, Nichols AD, Stylli S, et al.: Visual acuity and pattern of visual field loss at presentation in pituitary adenoma. J. Clin. Neurosci. 2014; 21: 735–740. PubMed Abstract \| Publisher Full Text\n\nFreda PU, Beckers AM, Katznelson L, et al.: Pituitary incidentaloma: an endocrine society clinical practice guideline. J. Clin. Endocrinol. Metab. 2011; 96(4): 894–904. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonneville F: Silent Corticotroph Adenoma.Bonneville JF, Bonneville F, Cattin F, et al., editors. MRI of the pituitary gland. Berlin: Springer; 2016; pp. 113–116. Publisher Full Text\n\nLucas JW, Bodach ME, Tumialan LM, et al.: Congress of neurological surgeons systematic review and evidence-based guideline on primary management of patients with nonfunctioning pituitary adenomas. Neurosurgery. 2016; 79: E533–E535. PubMed Abstract \| Publisher Full Text\n\nMccutcheon IE: Management of Pituitary Tumors: The Clinician’s Practical Guide, 2nd edition. Neuro-Oncology. 2004; 6: 75–76. Publisher Full Text\n\nSata A, Hizuka N, Kawamata T, et al.: Hyponatremia after Transsphenoidal Surgery for Hypothalamo-Pituitary Tumors. Neuroendocrinology. 2006; 83: 117–122. PubMed Abstract \| Publisher Full Text\n\nOommen S, Rice S: Atypical presentation of non-functional gonadotropinoma. Zenodo. 2023. Publisher Full Text" }	[ { "id": "181637", "date": "14 Jul 2023", "name": "Robinson George", "expertise": [ "Reviewer Expertise My area of expertise is gastrointestinal & oncological laparoscopic surgery including endocrine breast." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case of a non-functional pituitary adenoma has been well written with crisp history taking, precise examination findings & relevant investigations performed.\n\nThe case has been described well enough for the benefit of other general practitioners.\n\nThe case report has discussed the relevant investigations required & the precise management for the same.\n\nAs a case report, it fulfills the concise format of information provided to the readers.\n\nPlease check your spellings (sella turcica).\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": "195186", "date": "06 Sep 2023", "name": "Atul Kalhan", "expertise": [ "Reviewer Expertise Endocrinology" ], "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\nA well written case report related to a man who presented with left sided visual disturbance secondary to optic chiasm compression by a non-functioning macroadenoma (immunohistochemistry confirming it to be a gonadotropinoma). Patient had secondary hypogonadism and secondary hypothyroidism on presentation. It would be nice if a table with 6 weeks post-operative endocrine investigations are added as a comparison.\n\nThe last paragraph of the case report mentions about L-thyroxine (50 mcg once a day) being given on follow up. Was the patient put on long term thyroxine therapy (post-operatively)? It will be worth mentioning in the case report that thyroxine therapy should only be initiated if ACTH-cortisol axis integrity has been tested (prior to initiation of thyroxine therapy). A significant proportion of non-functioning pituitary adenomas show positive immunostaining for gonadotropins although the amount of gonadotropin secreted by such tumours is extremely small (to lead to a clinical impact) or it is a biologically inert gonadotropin.\n\nIn the discussion section, paragraph 3 has a statement which is factually incorrect and needs to be changed: Formal visual field assessment needs to be carried out for pituitary macroadenoma especially if these are in proximity of optic chiasm (or compressing the chiasm) irrespective of presence or absence of anterior pituitary hormonal deficiency. I will suggest the authors to change the 2nd line in this paragraph to reflect the above mentioned statement. In addition, the protocol for peri-operative coverage with hydrocortisone varies based on the institute (which is carrying out neurosurgery). I will suggest that the authors go through the following article by Prete et al. published in 2017 for reference (Prete et al., 20171).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "10191", "date": "06 Oct 2023", "name": "Suresh Oommen", "role": "Author Response", "response": "Dear Sir, Thank you for your review. The patient was on put on L-thyroxine after a good cortisol response post surgery. He continued to have central hypothyroidism in follow up visit (after 6 weeks) with adequate cortisol response. Sincerely, Dr Suresh Oommen." } ] } ]	1	https://f1000research.com/articles/12-674
https://f1000research.com/articles/11-550/v1	19 May 22	{ "type": "Case Report", "title": "Case Report: Bilateral peritonsillar abscess with complications of upper airway obstruction", "authors": [ "Rizka Fathoni Perdana", "Elsa Rosalina", "Elsa Rosalina" ], "abstract": "Background: Peritonsillar abscess is a collection of pus between the tonsillar fibrous capsule and the pharyngeal constrictor muscle. Unilateral peritonsillar abscess is a common complication of acute tonsillitis, whereas bilateral peritonsillar abscess is rare. The incidence of bilateral peritonsillar abscess remains unknown but is estimated to be 4.9% of all peritonsillar abscess cases. Case report: A 20-year-old man came to the emergency room with bilateral peritonsillar abscess and complaining of shortness of breath for two weeks. Physical examination showed muffled voice, 82% oxygen saturation, and inspiratory stridor. The isthmus faucium was narrow, with approximately 30% remaining. Peritonsillar puncture revealed pus mixed with blood. The treatment for this patient included bilateral peritonsillar incision and drainage and intravenous antibiotics of levofloxacin and metronidazole. The patient came to the Ear, Nose, Throat, Head, and Neck (ENTHN) Outpatient Unit eight days after the procedure for a control checkup and was in good condition. Conclusion: We have reported a bilateral peritonsillar abscess with complications of upper airway obstruction, in which we performed incision and drainage. Prompt and appropriate management is needed to avoid unwanted morbidity and mortality.", "keywords": [ "bilateral peritonsillar abscess", "upper airway obstruction", "peritonsillar abscess puncture", "incision and drainage", "infectious diseases", "health risk" ], "content": "Introduction\n\nUnilateral peritonsillar abscess is a common complication of acute tonsillitis, whereas bilateral peritonsillar abscess is rare. The incidents of bilateral peritonsillar abscess are unknown, the rough estimate is 4.9% of all peritonsillar abscess cases.1,2 The prevalence of peritonsillar abscess is approximately 1.9% to 24% of tonsillectomy cases since abscess is also exists on the contralateral side.2,3 The comprehensive report of bilateral peritonsillar abscess incidents reaches 4.9%.1,2,4 Peritonsillar abscess patient age ranges from 10 to 40 years old, with an average of 27 to 28 years old. It is mainly found in young adult males on a ratio of 2:1 compared to females.2,4,5 Diagnosis is performed through puncture of the abscess in the most bomban area with CT scan examination to determine the extent of the disease spread. The treatment includes incision and drainage of bilateral peritonsillar abscess and also appropriate medications.2,3,5\n\nThis paper reports the clinical experiences and management of a bilateral peritonsillar abscess patient.\n\n\nCase report\n\nA 20-year-old Javanese Indonesian non-diabetic male came to the emergency room at Dr. Soetomo General Academic Hospital on October 22, 2017, with a chief complaint of shortness of breath going for two weeks that had worsened in the last two days. The shortness of breath came and went and even worsened when the patient laid down. Additional complaints included pain and swallowing difficulty, throat felt lumpy, fever, and cough with a thick sputum consistency. The patient had a history of sore throats approximately two to three times per year that got better after oral amoxicillin 500 mg every 8 hours and normal saline gurgle, drank alcohol frequently, and smoked. Physical examination showed muffled voice, an axillary temperature of 37.2 °C, a pain scale of 7, 82% oxygen saturation (normal > 95%), and inspiratory stridor. Throat examination showed smooth-surfaced T4-T4 tonsils, palate, right and left peritonsillar areas of the bombans, and hyperemia. The isthmus faucium was narrow, with about 30% remaining (Figure 1A).\n\nResults of laboratory blood tests showed an increase in leukocytes at 34,03 × 103/uL (normal 3,80-10,60 × 103/uL), C-reactive protein (CRP) at 86.54 mg/L (normal 0,00-10,00 mg/L) glutamic oxaloacetic transaminase serum (SGOT) and glutamic pyruvic transaminase serum (SGPT) at 51 and 123 U/L (normal SGOT <41 U/L, SGPT 0-35 U/L), and hepatitis B surface antigen (HBsAg) came out reactive. Therefore, based on the history, physical and laboratory examination, a bilateral peritonsillar abscess was suspected with obstruction of the upper airway. Hence, we performed peritonsillar punctures with disposable sterile syringe at the most bomban locations to make the diagnosis, with 1 ml of pus mixed with blood in the right peritonsillar and 3 ml of pus in the left peritonsillar (Figure 1B and C).\n\nWe performed a Computed Tomography Scan (CT scan) on this patient to determine the expansion of the abscess, considering that the patient has immunodeficiency. Results showed hypodense lesions (26–29 HU) with clear boundaries, irregular edges, ±4 cm in diameter on the right and left peritonsillar, which in contrast showed rim enhancement (73 HU). The lesion caused narrowing of the oropharyngeal lumen at 2–3 cervical vertebrae levels. The narrowest lumen diameter was ±0.1 cm—no expansion of abscess to the surrounding area (Figure 2).\n\nWe performed an incision on the right and left peritonsillar using a scalpel number 11 in the most bomban area without topical anesthesia. It resulted in 6 ml of pus mixed with blood in the right peritonsillar and 13 ml of pus mixed with blood in the left. In addition, we carried out swab culture on the peritonsillar incision area. As a result, the isthmus faucium looked more spacious (Figure 3).\n\nChest X-ray suggested left paracardial infiltrates, and the Pulmonology Department diagnosed the patient with community-acquired pneumonia (CAP), which was then treated with levofloxacin injection at 500 mg every 24 hours. In addition, the Internal Diseases department treated the patient with 500 mg of paracetamol tablets every 8 hours and 200 mg of n-acetyl cysteine tablets every 8 hours related to chronic hepatitis B. Furthermore, we diagnosed him with bilateral peritonsillar abscess with CAP and chronic hepatitis B. The patient was also treated with 500 mg of levofloxacin injection every 24 hours, 500 mg of metronidazole injection every 8 hours, 500 mg of paracetamol tablets every 8 hours, 200 mg of n-acetyl cysteine tablets every 8 hours, and gargle with 0.9% sodium chloride solution every 8 hours.\n\nEvaluation on the first day showed reduced bombans, hyperemia, and edema in the right and left peritonsillar. We evaluated the incision area and obtained 0.2 ml of blood from the right peritonsillar and 0.5 ml of blood mixed with pus in the left peritonsillar (Figure 4A). On the second day of evaluation, the peritonsillar area returned to normal. There was a decrease in leukocytes on the third day, namely at 9.5 u/L and CRP 0.5 mg/L. We declared the patient cured and advised him to be outpatient based on the history, physical examination, and laboratory results. The patient was given medications in the form of 500 mg of levofloxacin antibiotics tablets every 24 hours, 500 mg of metronidazole tablets every 8 hours, 500 mg of anti-pain paracetamol tablets every 8 hours and 200 mg of n-acetyl cysteine tablets every 8 hours, and gargle with 0.9% sodium chloride every 8 hours.\n\nPatients came for a control checkup to the ENTHN Outpatient Unit of Dr. Soetomo General Academic Hospital on the eighth day after the incision. There were no complaints, the peritonsillar area was in good condition, and T3/T4 tonsils (Figure 4B). Swab culture results showed Streptococcus equi. We advised the patient to undergo a tonsillectomy, but he preferred first to cure his chronic hepatitis B and pneumonia.\n\n\nDiscussion\n\nPeritonsillar abscess is a disease often found in ENTHN services. In this case, we found it on a 20-year-old man. The main complaints included shortness of breath for two weeks, accompanied by complaints of swallowing pain, difficulty swallowing, and a feeling of a lump in the throat. There was a fever within two weeks and a cough for one month accompanied by thick phlegm. This disease is found at the age of 10–40 years, and the majority are diagnosed at the age of 22–28 years old with a male to female ratio of 2:1.2,4 Complaints with peritonsillar abscess include difficulty swallowing, fever, pain, and a lump in the throat.6,7 Complaint of bilateral peritonsillar abscess is longer than in unilateral peritonsillar abscess. Shortness of breath can be caused by narrowing the upper airway due to bilateral peritonsillar abscesses.5\n\nThe patient has a history of recurrent sore throat with a frequency of two to three times a year. The patient came in an acute state characterized by complaints of a sore throat for two weeks. A 2017 Brazilian study reported acute tonsillitis was the most common predisposing factor for peritonsillar abscess.3 Peritonsillar abscess can evolve from acute tonsillitis to peritonsillitis, then progress to peritonsillar cellulitis, and finally peritonsillar abscess or a consequence of Weber’s gland (salivary gland) abscess located at the supratonsil space.3–5\n\nThe patient has a history of frequent drinking and smoking. The reactive results on HBsAg examination and the CAP indicate the possibility of being immunocompromised, which makes it easier for peritonsillar abscesses to occur. Smoking and drinking alcohol are predisposing factors for peritonsillar abscess due to the adverse effects of smoking on the normal flora in the oropharynx.8 Immunocompromised conditions such as diabetes mellitus and HIV carry a more atypical and challenging risk of head and neck infections.3,9\n\nClinical examination revealed muffled voice, odynophagia, difficulty swallowing, trismus, and fever. T4-T4-sized tonsils, palate, and right and left peritonsillar areas to appear turgid and hyperemic. The uvula is in the middle, pressed by the bomban peritonsillar and the edema on the right and left tonsil area. The faucium isthmus becomes narrow, with about 30% remaining. Unilateral or bilateral peritonsillar abscess signs include muffled voice, odynophagia, difficulty swallowing, otalgia, trismus, hypersalivation, and fever. Unilateral peritonsillar abscess shows the asymmetric peritonsillar area, bulging, and uvula deviation, whereas there are no classic signs in bilateral cases.1–3,10 A midline uvula with bilateral mole bomban palate is a characteristic feature of a bilateral peritonsillar abscess. Trismus due to disruption of the lateral pterygoid muscles can result from either peritonsillar or parapharyngeal abscess.10\n\nThe location of the peritonsillar abscess, in this case, was at the superior right and left peritonsillar spaces. The most common location of peritonsillar abscess was in the superior peritonsillar space (61%), in the middle (33%), and below the peritonsillar space (6%). This unique abscess location is due to the failure of suppurative inflammatory drainage by blockade of crypts on acute tonsillitis, which causes infection to the peritonsillar space.1\n\nRight and left peritonsillar abscesses, in this case, occurred at different levels. The left peritonsillar abscess is more mature, whereas the right peritonsillar is a transition from infiltrates to abscesses, seen in the right-side discharge that is less than the left. Research in Greece in 2011 reported that tonsillitis is an infection of the tonsils that can cause complications in the form of bilateral peritonsillar abscesses with different levels of development on each side.2 Bilateral peritonsillar abscess cases can occur when tonsillitis and abscess develop bilaterally.1–4\n\nBlood laboratory examination showed an increase in leukocytes of 34.020 u/L, 83.8% of neutrophils, and a CRP of 86.54 mg/L, indicating that bacteria caused the infection. Aerobic and anaerobic organisms mainly caused peritonsillar abscesses. Increased leukocytes and CRP are found in unilateral peritonsillar abscesses and even higher in bilateral peritonsillar abscesses.3,7\n\nCT scan showed hypodense lesions (26–29 HU) with clear boundaries, irregular edges at the right and left peritonsillar, and showed rim enhancement on contrast. This outcome indicates the presence of fluid in the form of pus in the peritonsillar. Narrowing of the lumen in the oropharynx at the level of 2–3 cervical vertebrae with a diameter of ±0.1 cm gives a clinical picture of upper airway obstruction, a complication of bilateral peritonsillar abscesses.5 A CT scan determined the density of the mass and the remaining isthmus, and the abscess spread to the surrounding area. Head and neck CT scans also can detect deep neck abscesses that are not clinically visible.2,3,10,11 Upper airway obstruction is a possible diagnosis due to inspiratory stridor and the peritonsillar area being bombans on both sides, pushing the tonsils medially and leaving a small gap between them. A contrast-enhanced CT scan is preferred when the symptoms and signs of a peritonsillar abscess are atypical.5\n\nSwab culture results showed Streptococcus equi. The majority of organisms in peritonsillar abscess are aerobic and anaerobic organisms. Aerobic organisms that often coexist are Streptococcus pyogenes, Streptococcus milleri, Haemophilus influenza, and Streptococcus viridans. Meanwhile, anaerobic organisms that often coexist are Fusobacterium sp. and Bacteroides sp.2,3,6,10\n\nWe performed peritonsillar punctures at the most bomban point to make the diagnosis. We suggest a drainage aspiration or incision if pus occurs at the puncture.12 Immediate tonsillectomy is a definitive procedure when the incision and drainage of the abscess cannot properly evacuate the pus. However, it might cause an increased risk of postoperative bleeding. We recommend interval tonsillectomy 4–6 weeks after the incision and drainage of the peritonsillar abscess, indicated in patients who experience recurrent tonsillitis in the same year after peritonsillar abscess.2,3\n\nWe treated the patient having a peritonsillar abscess with 500 mg of levofloxacin injection every 24 hours and 500 mg of metronidazole injection every 8 hours as antibiotics. The treatment choice is due to Streptococcus sp., the organism that causes the most common peritonsillar abscesses. Penicillin is the first-line antibiotic for peritonsillar abscesses and is not different from other broad-spectrum antibiotics.2,4,10 Meanwhile, broad-spectrum quinolones are third-line therapy for peritonsillar abscess treatment and first line therapy for CAP.13,14 Therefore, antibiotic therapy for this case is a combination of quinolone and metronidazole. Furthermore, the administration of metronidazole depends on the frequency of anaerobic organisms in the peritonsillar abscesses.\n\n\nConclusion\n\nWe report a bilateral peritonsillar abscess with a complication of upper airway obstruction. Bilateral peritonsillar abscesses are rare cases. Puncture in the peritonsillar area resulted in pus. We performed a CT Scan to determine the extent of the abscess to the surrounding area. Then, we carried out incision and drainage to treat the patient. Antibiotic therapy of levofloxacin, metronidazole, anti-pain paracetamol, N-acetyl-cysteine injections, and 0.9% sodium chloride gargle is given to the patient with bilateral peritonsillar abscess after incision and abscess drainage.\n\n\nConsent\n\nWritten informed consent for publication of clinical details and clinical images was obtained from the patient.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nRepository: CARE checklist for ‘Case report: Bilateral peritonsillar abscess with complications of upper airway obstruction’. https://doi.org/10.5281/zenodo.6519444.15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nFarooq M: Local infiltration anesthesia in drainage of quinsy. Int J Pathol. 2015; 13(4): 142–147.\n\nPapacharalampous GX, Vlastarakos PV, Kotsis G, et al.: Bilateral peritonsillar abscesses: a case presentation and review of the current literature with regard to the controversies in diagnosis and treatment. Case Rep Med. 2011; 2011: 1–4. PubMed Abstract \| Publisher Full Text\n\nSeerig MM, Chueiri L, Jacques J, et al.: Bilateral peritonsillar abscess in an infant: an unusual presentation of sore throat. Case Rep Otolaryngol. 2017; 2017: 1–3. PubMed Abstract \| Publisher Full Text\n\nAlAwadh I, Aldrees T, AlQaryan S, et al.: Bilateral peritonsillar abscess: a case report and pertinent literature review. Int J Surg Case Rep. 2017; 36: 34–37. PubMed Abstract \| Publisher Full Text\n\nPham V, Gungor A: Bilateral peritonsillar abscess: case report and literature review. Am J Otolaryngol - Head Neck Med Surg. 2012; 33(1): 163–167. Publisher Full Text\n\nSunnergren O, Swanberg J, Mölstad S: Incidence, microbiology and clinical history of peritonsillar abscesses. Scand J Infect Dis. 2008; 40(9): 752–755. PubMed Abstract \| Publisher Full Text\n\nWatanabe T, Suzuki M: Bilateral peritonsillar abscesses: our experience and clinical features. Ann Otol Rhinol Laryngol. 2010; 119(10): 662–666. PubMed Abstract \| Publisher Full Text\n\nMarom T, Cinamon U, Itskoviz D, et al.: Changing trends of peritonsillar abscess. Am J Otolaryngol - Head Neck Med Surg. 2010; 31(3): 162–167. Publisher Full Text\n\nCheong JP, Chong AW, Mun KS: Bilateral intratonsillar abscesses: a first case report in an adult patient. J Emerg Med Trauma Acute Care. 2015; 2015: 2–7. Publisher Full Text\n\nLin YY, Lee JC: Bilateral peritonsillar abscesses complicating acute tonsillitis. Cmaj. 2011; 183(11): 1276–1279. PubMed Abstract \| Publisher Full Text\n\nMaharani D, Ferriastuti W: Chronic suppurative otitis media complicated by subdural and bezold abscesses: a case report. Radiol Case Reports. 2022; 17(4): 1175–1179. PubMed Abstract \| Publisher Full Text\n\nSowerby LJ, Hussain Z, Husein M: The epidemiology, antibiotic resistance and post-discharge course of peritonsillar abscesses in London, Ontario. J Otolaryngol - Head Neck Surg. 2013; 42(JAN): 1–7. Publisher Full Text\n\nKamila RS, Rochmanti M, Bakhtiar A: Appropriate antibiotic use for community-acquired pneumonia in inpatient settings and its impact on 30-days readmission and mortality rate. Indian J Forensic Med Toxicol. 2021; 15(1): 2765–2772.\n\nAynehchi BB, Har-El G: Deep Neck Infections. Johnson JT, Rosen CA, editors. Bailey’s head and neck surgery otolaringology. 5th ed.Philadelphia: Lippincot-Raven; 2014; Vol 1: pp. 794–812.\n\nPerdana RF: CARE checklist for ‘Case report: Bilateral peritonsillar abscess with complications of upper airway obstruction’. Zenodo. 2022. Publisher Full Text" }	[ { "id": "138440", "date": "30 May 2022", "name": "Susyana Tamin", "expertise": [ "Reviewer Expertise Otolaryngology", "Bronchoesophagology", "Endoscopy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article describes a rare case of bilateral peritonsillar abscess, complicated to upper airway obstructions, with CAP concomitant.\n\nThe case report is very well written. Although there are some minor grammatical errors, for example, \"complaining\" in the abstract and \"first line therapy\" in the discussion.\n\nThe case report conveys appropriate details of the case, including patient's demography, assessment, findings, and investigations.\n\nPlease enhance the discussion with what could be the reasons and the risk factors for peritonsillar abscess in this case occurring bilaterally, not unilaterally. Please consider adding patient's data that could be the risk factors for bilateral peritonsillar abscess in the patient, such as nutritional status, immunocompromised (HIV-AIDS), hepatitis B, etc. In addition, as the literature showed the webers glands as one of the etiology of peritonsillar abscess, please explain whether in this case the peritonsillar abscess is caused by the webers glands' obstruction. Please explain why anaerobic organisms, which often exist in peritonsillar abscesses, were not detected in this swab culture.\nPlease explain the etiology of the pneumonia. Is there any correlation between swallowing difficulty in the patient with the pneumonia (aspiration pneumonia)?\nThis case report mentions the treatment, including the dose and route of drugs. It describes the antibiotic's rationale chosen for peritonsillar abscess treatment with CAP concomitant. It would be better to mention the durations for antibiotics and other drugs. Please explain the reason why antibiotics were given intravenously. Please add some discussion on whether corticosteroids could be considered in this case? Corticosteroids have analgesic and anti-inflammatory mechanisms.\n\nSince the patient complained of swallowing difficulty, it would be better to explain the nonpharmacological treatment, such as dietary for the patient.\nOther than this case is a rare case, please emphasize what the reader could get from this case report because the diagnosis and management of the bilateral and unilateral peritonsillar abscess are quite the same.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/11-550
https://f1000research.com/articles/12-1150/v1	14 Sep 23	{ "type": "Research Article", "title": "Translation, reliability, and validation of the Dutch Safe Use of Mobility Aid Checklist (SUMAC-NL) for walker use in people living with dementia", "authors": [ "Jesper Kroesen", "Hans Hobbelen", "Susan Hunter", "Helen Bruinsma", "Hans Drenth", "Hans Hobbelen", "Susan Hunter", "Helen Bruinsma", "Hans Drenth" ], "abstract": "Background: People with dementia have a yearly risk of falling of 60 to 80 percent. Therefore, a walker is often recommended. However, the use of a walker in people with dementia is associated with a threefold increased odds of falls compared to their healthy peers. Better advice and training could reduce fall risk. Therefore, a tool to assess functional walking skills with a walker is needed. The SUMAC was developed to fill this gap. So far, there is no Dutch instrument available that can assess functional walking skills with a walker in people with dementia.\n\nMethods: Reliability was evaluated by scoring videos of people with dementia (n = 9) using a walker performing the SUMAC-NL. ICC was used to assess inter-rater and test-retest reliability. An expert panel (n = 8) evaluated the content validity using the content validity index (CVI) and the content validity ratio (CVR). Results: Inter-rater reliability of the SUMAC-NL was statistically significant for the PF domain (ICC = 0.94, 95%CI (0.84, 0.98, p < 0.001) and for the EQ domain (ICC = 0.79, 95%CI (0.49 – 0.95), p < 0.001). Test-retest reliability was statistically significant for both the PF domain (ICC = 0.95, 95%CI (0.89, 0.99), p < 0.001) and EQ domain (ICC = 0.92, 95%CI (0.82, 0.98), p < 0.001). The SUMAC-NL shows content validity with a CVI >0.79 for both domains and a CVR of 0.53 on the PF domain and 0.78 on the EQ domain. Conclusions: The SUMAC-NL shows good to excellent reliability and content validity for both the PF and the EQ domain. The SUMAC-NL seems to be a promising tool to assess walking with a walker in people with dementia in the Netherlands.", "keywords": [ "dementia", "walker", "geriatric evaluation", "fall risk", "walking", "translation", "validity", "reliability" ], "content": "Introduction\n\nDementia is a neurocognitive disorder in which mental abilities as associative memory, reasoning and perceptual speed are severely reduced.1 It is estimated that there are approximately 290,000 people with dementia in the Netherlands and it is the fastest-growing cause of death in the Netherlands.1–3 Dementia is characterized by a cognitive decline related to memory and in at least one of the other domains: perceptual-motor function, language, executive function, attention, and social cognition.4,5\n\nPeople with dementia have a high risk of falling and the cause is multifactorial. Intrinsic and extrinsic factors such as vision or balance problems and the use of medication can play a role in falling.6 Also, impairments in attention and executive functions are prominent risk factors for falls among people living with dementia.7 Importantly, balance and gait problems are common and progressive in dementia as well. People with dementia have a yearly risk to fall of sixty to eighty percent. This is twice as high as in their cognitively healthy peers.7,8 Moreover, people with dementia have a high risk of admission to a long-care setting.7,8\n\nTo compensate for deficits in balance, gait and strength that accompany dementia, the use of a walker is often recommended. A walker is known for improving stability during walking in cognitively healthy adults.9,10 However, the use of a walker in people with dementia is associated with a threefold increased odds of falls compared to their healthy peers who walk with a walker.6,11 Lindemann et al. identified obstacles and opening a door towards a person as the main problems for older adults using a walker.12\n\nMany standardized scales for balance and gait developed for cognitively healthy older adults have been evaluated for reliability and validity in people living with dementia.13 The existing measures provide only partial information regarding mobility and few target elements that become relevant as dementia progresses.13 In addition, none of these instruments can assess the functional skills for safe walking when using a walker in people with dementia.\n\nThe high frequency of falls among people with dementia and the absence of a measurement instrument to assess walking skills in walker use led Hunter et al. to develop the Safe Use of Mobility Aid Checklist (SUMAC) in 2020.14 The SUMAC was generated by a focus group (N = 12) consisting of one geriatrician, two registered nurses, five physiotherapists, and four occupational therapists.14 The generated tasks were scored for relevance by an independent panel of five healthcare professionals. This resulted in a final selection of nine tasks in two domains (physical functioning (PF) and interaction with equipment (EQ) that form the SUMAC. The SUMAC can evaluate the skills of walking with a walker in people with dementia who walk with a walker independently or assess the success of training when the walker has been identified as an appropriate level of gait aid to compensate for deficits.14 The SUMAC has a good test-retest and inter-rater reliability (ICC = 0.89 for PF and ICC = 0.88 for EQ) and shows good construct validity (rs = 0.92 for the PF score and rs = 0.82 for the EQ score).14 This makes it a promising tool to give specific advice and training in walker use and to reduce the risk of falling in people with dementia.\n\nCurrently, there is no Dutch assessment instrument that can assess walking skills in people with dementia who need a walker. Therefore, a Dutch measuring instrument must be developed that can assess the safety of walking with a walker in people with dementia. This will lead to better advice and training regarding the use of a walker and thereby reduce the risk of falls in people with dementia in the Netherlands.\n\nTherefore, the primary objective of this study is to 1) translate the SUMAC from English to Dutch and 2) determine the inter-rater reliability, the test-retest reliability, and the content validity of the SUMAC-NL to assess walking skills in older people with dementia living in the Netherlands who walk with a walker.\n\n\nMethods\n\nThis study has an observational clinimetric design and involved two phases. The first part of this study consisted of the translation of the English version of the SUMAC into Dutch (SUMAC-NL). In the second part of this study, the reliability and validity evaluation of the SUMAC-NL was performed. The second part of the study was a replication study of the work by Hunter et al. (2020).14\n\nThe SUMAC was translated into Dutch between July and August 2021. The tasks and domains in the SUMAC remained the same. The translation was done according to the Beaton guideline15 and consisted of five phases. The first phase was the forward translation from English to Dutch by two Dutch native speakers with a medical background. The first translator knew the purpose of the instrument. The second translator did not know the instrument to keep the translation as objective as possible. The second phase was the synthesis of the two translations by the Dutch native translators. The third phase was the backward translation from Dutch to English by two English native speakers. The first translator had a medical background and the second translator did not. Both translators were unaware of the purposes of the SUMAC. The fourth phase consisted of a review of the translations by the researcher, two experts, and the developer of the SUMAC. The fifth phase consisted of getting an understanding of the items. For the feasibility of this study, the last step has been replaced by the evaluation of the content validity (Figure 1). This last step of the Beaton guideline consists of testing the prefinal version of the translated test. This involves administering the translated test to 30 to 40 people and then conducting interviews to ask participants what they thought was meant by the questions and the chosen response.15\n\n▽ = translated version; △ = step in translation.\n\nParticipants\n\nOlder people with dementia who walk with a walker, living in an intramural setting were recruited by their physiotherapist between 1 December 2021 and 28 February 2022 by convenience sampling. The recruiter selected potential participants from the institution’s patient database. Potential participants and their families were informed about the study through the information letter and through verbal explanations. They were then asked for their participation.\n\nThe inclusion criteria were: 1) diagnosed with dementia 2) walking with a walker, 3) Dutch-speaking, 4) able to follow simple instructions, 5) able to walk 60 meters without the supervision of another person, 6) able to perform the SUMAC-NL and 7) having someone available who can make decisions (e.g. on participation) if necessary.16 Exclusion criteria for this study were: 1) comorbidities that limit mobility, such as Multiple Sclerosis (MS), a past Cerebro Vascular Accident (CVA), or (poly) neuropathy, and 2) people who have recently undergone surgery that limits mobility. All participants provided written informed consent. The legal representative of the participant was asked to give informed consent if the participant was deemed unable to do so.\n\nData collection\n\nThe demographic data requested from the participants were age, sex, amount of medication use, number of comorbidities, level of activities of daily living, and fear of falling. The 6-item Katz ADL scale was used to assess the participants’ ability to perform ADL activities and the short-FES-I is administered to determine the fear of falling of the participants. The Katz ADL (ICC = 0.82, p < 0.05) and short-FES-I (α = 0.84) are both reliable instruments to measure these parameters.17–19\n\nThe assessment of the performed tasks by the participants was done by a group of raters consisting of a convenience sample of five physiotherapists who were recruited by one of the researchers (JK). All physiotherapists provided written informed consent for using their demographic data at the start of data collection. The physiotherapists were all legally registered therapists working in the physical therapy primary practice.\n\nThe participants were asked to perform the tasks of the SUMAC-NL while being filmed. Filming took place on 25 February and 4 March 2022 in a corridor with sufficient space in the institution where the participants live. Participants were asked if they wanted to be recognised in the video. If they did not agree, their faces were blurred in the videos so that the participants are unrecognisable in the video. The videos were stored in a 2FA-protected digital location, according to the data management plan and were deleted after the raters finished rating the videos. These videos were only used for the reliability assessment.\n\nEthical considerations\n\nThis study was conducted following the Declaration of Helsinki and the FAIR principle and was approved by the Hanze University of Applied Sciences Groningen’s Ethical Review Board (HEAC), with approval number heac.2021.026. Participants gave informed consent for understanding the information letters and that participating in the study was voluntary. In addition, they gave permission to contact their GP in case of unexpected findings, the collection and use of data and longer storage of the data as well as whether or not they wanted to be contacted again for follow-up studies.\n\nReliability\n\nEach of the raters was asked to watch the provided instruction video and to read the instruction manual of the SUMAC-NL before starting the evaluation of the participants. The instruction video consisted of a detailed instruction of the components and items within the SUMAC-NL and an example of the evaluation with the SUMAC-NL. The videos of the participants performing the SUMAC-NL were sent to the raters on 11 March 2022. The evaluations of the participants was done twice at an interval of one week. The ratings were collected by the researcher on 8 April 2022.\n\nThe order of the tasks in the videos was the same as in the SUMAC-NL. The videos were offered in a random order. This order differed between the first and second evaluation session. Each rater evaluated all participants. The raters could evaluate the videos digitally at a location of their choice.\n\nValidity\n\nThe expert panel consisted of six master of science trained geriatric physiotherapists, one master of science geriatric physiotherapist student, and one master of science trained physiotherapist. The experts in the panel have a mean age of 31.5 ± 2.7 years. Each of them has experience in working with older people with dementia (3.5 ± 3.2 years).\n\nBefore determining content validity, the expert panel received an instructional video explaining how to score the content of the SUMAC-NL. In addition, the expert panel received a digital score sheet in Microsoft Office Word in which the assessment of the SUMAC-NL was recorded. The scores of the experts were compared with each other and the content validity ratio (CVR) and content validity index (CVI) were calculated. Scoring of the SUMAC-NL by the expert panel to determine content validity took place between 18 February 2022 and 25 March 2025.\n\nIBM SPSS statistical package version 28 (IBM Corp, Armonk, NY) was used for descriptive analysis and reliability analysis. Microsoft Office Excel 2019 was used in the content validity calculation.\n\nReliability\n\nAn a priori sample size calculation for the reliability study was done using the formula of Shoukri et al. (2004).20 This formula showed that a sample consisting of nine participants and five raters making two evaluations is required to determine the desired ICC of >0.9 (CI ± 0.1). An ICC of >0.90 is considered excellent reliability.21 The demographic characteristics of the participants are presented using descriptive statistics.\n\nContinuous data (SUMAC-NL subscores) were used and presented quantitatively. Missing data were considered ‘missing completely at random’ (MCAR) and imputed by the Expectation-Maximization (E-M) algorithm.22 Normality checks were done by the Shapiro-Wilk test and using histograms and Q-Q plots.\n\nThe absolute reliability was calculated using the standard error of the measurement (SEM) and minimal detectable change with a 95% confidence interval (MDC95) for the PF and EQ domains of the SUMAC-NL. A smaller SEM means higher absolute reliability.23 The SEM was estimated using the pooled standard deviation and the ICC for each group. The following formula was used: SEmeasurement = s √(1-rxx).24,25 The MDC95 was calculated using the SEM by the following formula: MDC95 = (1.96)(√2)(SEM).25,26\n\nThe relative values of inter-rater and test-retest reliability were calculated using ICC. An average measurement, absolute agreement, 2-way random-effects model (ICC 2,k) was used for determining the ICC.21 An ICC value less than 0.5 is indicative of poor reliability, values between 0.5 and 0.75 indicate moderate reliability, values between 0.75 and 0.9 indicate good reliability and values greater than 0.9 indicate excellent reliability.21\n\nContent validity\n\nContent validity was determined using CVR and the CVI and was calculated separately for both domains of the SUMAC-NL. The CVR was used to show the acceptance of tasks in the instrument and the CVI was used to determine the content validity of both the entire domains.27\n\nFor CVR, the expert panel separately scored each item of the SUMAC-NL on a three-point Likert scale where a score of one is essential, a score of two is useful but not essential and a score of three is not essential. After obtaining the scores of the assessments of the experts, the CVR was calculated based on the following formula in Microsoft Office Excel 2019, where ne represents the number of panel members who have chosen the item of ‘essential’, and N is the number of panel members:\n\nThe CVR varies between -1 and 1. A higher score indicates further agreement of members of the panel on the necessity of an item in the instrument. The CVR of each domain is compared with the values in Lawshe’s table, and if the CVR is equal to or higher than the value (0.75) in Lawshe’s table, the item is preserved.27\n\nTo determine the CVI, all items of the instrument have been scored on three parameters by the experts: relevance, simplicity, and clarity. Each parameter was scored on a 4-point Likert scale from disagree to totally agree. The average of the total scores was taken from the table and the CVI of each item was calculated with the following formula:\n\nThe CVI of both domains of the SUMAC-NL was determined by dividing the sum of the CVI scores per item by the number of items.28,29 A CVI of >0.79 was considered appropriate.29\n\n\nResults\n\nNine participants with dementia participated in this study. The sample consisted of five women (55.6%) and four men with a mean age of 85.56 (± 7.49). See Table 1 for the demographic characteristics of the participants.\n\nThe absolute reliability values were: SEM for the PF domain was 1.20 and for the EQ domain was 2.22; the MDC95 was 3.33 for the PF domain and was 6.15 for the EQ domain (Table 2).\n\nA good to excellent inter-rater reliability in both evaluation moments in the PF domain (ICC = 0.85 (0.63, 0.96), p < 0.001 for assessment 1 and ICC = 0.90 (0.74, 0.97), p < 0.001 for assessment 2) and EQ domain (ICC = 0.86 (0.64, 0.96), p < 0.001 for assessment 1 and ICC = 0.75 (0.41 – 0.94), p < 0.001 in assessment 2) was found (Table 2). In addition, we found excellent test-retest reliability in the PF (ICC = 0.94, 95%CI (0.86, 0.99), p < 0.001) and EQ (ICC = 0.91 95%IC (0.79, 0.98), p < 0.001) domains (Table 2). The full raw data can be found under Underlying data.30\n\nThe evaluation of the content validity was done by an expert panel (N =8) with experience in working with older people with dementia.\n\nIn the evaluation of the content validity, we calculated a CVI of 0.86 on the PF domain and 0.96 on the EQ domain. In addition, we calculated the CVR of 0.53 on the PF domain and 0.78 on the EQ domain (Table 3).\n\nThe CVI of all individual tasks was >0.79. The CVR of tasks 4 and 5 in the PF domain were both 0, of task 7 it was 0.5, and of tasks 8 and 9, it was 0.25. The other tasks showed a CVR >0.75. In the EQ domain, task 4 had a CVR of 0 and task 5 had a CVR of 0.5. The other tasks had a CVR >0.75.\n\n\nDiscussion\n\nThis replication study of the study from Hunter et al.14 includes the translation of the English SUMAC into Dutch and the determination of the test-retest reliability, inter-rater reliability, and validity of the Dutch SUMAC (SUMAC-NL) for people with dementia who walk with a walker. This study found a good to excellent inter-rater reliability and test-retest reliability, and strong support for content validity.\n\nSmall differences were found between our results and the results of the study by Hunter et al.14 The inter-rater reliability of the SUMAC-NL seems to be higher than the English version. The test-retest reliability of the SUMAC-NL seems higher for both the PF domain and the EQ domain (0.94 vs. 0.89 and 0.91 vs. 0.88, respectively). The SEM is smaller for the PF domain (1.20 vs. 1.31) and higher for the EQ domain (2.22 vs. 1.93) in the SUMAC-NL. The MDC95 for the PF domain of the SUMAC-NL is smaller than that of the English-language SUMAC (3.33 vs. 3.64) and greater for the EQ domain (6.15 vs. 5.35). These differences could be explained by the differences in the way the raters were instructed. In the study by Hunter et al.,14 the raters received a one-hour one-on-one training session while, in this study, an online education via an instructional video was chosen due to the COVID-19 pandemic.14 As a result, the interpretation of the scoring method may differ slightly between the two raters’ groups.\n\nThe content validity index (CVI) shows that both the PF domain and the EQ domain are considered valid by the expert panel. However, the content validity ratio (CVR) shows that tasks 4, 5, 7, 8, and 9 are not valid (CVR <0.75) tasks for determining physical function (PF domain) for walking with a walker in people with dementia. This finding is not in line with the results from the study by Hunter et al.14 The content validity was determined by two sets of experts to include these tasks important for observing physical functioning.14 In addition, it appears that walking through a doorway causes serious problems for older people who use a walker, which is observed in tasks 7, 8, and 9.12 Because of the results from previous research and a good CVR (>0.75) for tasks 7, 8, and 9 in the EQ domain, it seems appropriate to keep these tasks in the FF domain of the SUMAC-NL.12\n\nThe expert panel in this study determined tasks 4 and 5 as not valid for both the PF and EQ domain. These tasks involve walking with a double task (horizontal head turns) and a cognitive task. The expert panel scored lower for these tasks on the simplicity parameter within the CVI. One of the reasons given is that the wording of the tasks can be interpreted in different ways. However, different studies show that gait performance decreases and fall risk increases with increasing task complexity with the addition of a second cognitive task in community-dwelling adults or cognitively impaired older adults.31–34 Therefore, it seems appropriate to observe these performances and keep tasks 4 and 5 in the SUMAC-NL but the formulation may have to be modified in the future.\n\nOther measuring instruments can score balance and physical performance to interpret a risk of falls. A commonly used measuring instrument for evaluating physical performance and walking in older adults is the Berg Balance Scale (BBS).35,36 The BBS measures the balance of participants through transfers and static postures, without a walker. The BBS is a reliable instrument for determining the risk of falling and has good reliability in older people with dementia to assess physical functioning.35,37,38 This measuring instrument can have value in determining walking safety but is not specified for determining walking safety in older people with dementia who walk with a walker. The SUMAC-NL seems to be an appropriate tool to fill this gap because of its good reliability in people with dementia and the functional items that are included for walking with a walker. The SUMAC-NL provides professionals a standardised assessment tool to assess safe walking with a walker in people with dementia.\n\nPrevious research shows that people with dementia are well able to learn tasks both implicitly and explicitly, making possible therapy effective.39,40 The SUMAC-NL could be performed in people living with dementia who already walk with a walker or in people who have received training in walking with a walker so that the walking skills and/or the success of the training can be evaluated.\n\nThe translation of the English-language SUMAC into Dutch was carried out systematically using the Beaton guideline.15 This increases the comparability between different cultures.41 For the feasibility of this study, the last step in the guideline has not been reviewed. We have overcome this by determining the content validity and reliability, which also includes the comprehensibility of the instrument.\n\nAnother strength of this study is that the experts involved in the validation assessment of the SUMAC-NL were all master trained physiotherapists who are experts in the field of physical activity who have experience in geriatrics and work with people living with dementia.42\n\nThis study also has some limitations. For the power and feasibility of this study, the reliability phase of this study consisted of several assessors (N = 5) and nine participants. Although the sample size is appropriate to achieve power in the analysis, research with a larger sample size (n >50) is recommended.43 After data collection, there was missing data (<10%). This data was assumed to be missing completely at random (MCAR). After imputation, we did calculations on the imputed data and the raw data. The results of both calculations were similar to each other.\n\nThis study was done in older people with dementia who were able to perform the SUMAC-NL. Therefore, the results cannot be generalised to people with dementia who may not be able to complete the SUMAC-NL. The people in our sample show no severe fear of falling on the FES-I and are largely independent in ADL following the Katz ADL scores. The results are therefore not generalizable to people with severe fear of falling and are more dependent in ADL. Further research is needed on the psychometric properties of the SUMAC-NL in people who are less likely to be able to perform the SUMAC-NL, have a greater fear of falling and are more dependent in ADL.\n\nThe inter-rater reliability, test-retest reliability, and validity support the use of the SUMAC-NL in practice. The SUMAC-NL should be considered to assess the walking skills in people living with dementia who use a walker independently and/or to evaluate the training success of walking with a walker. With the help of the SUMAC-NL, more specific training, education, and advice can be given for walker use.\n\nFuture research must determine whether the use of the SUMAC-NL can improve the walking safety of older people with dementia who walk with a walker and thus can reduce the risk of falling in this population. Because of the lack of generalizability of this study to older people with dementia with more severe fear of falling and are more dependent in ADL, further research into the psychometric properties of the SUMAC-NL in people with dementia is advised.\n\n\nConclusion\n\nIn this study, the English-language SUMAC was translated into the Dutch SUMAC-NL. The SUMAC-NL seems to have good to excellent inter-rater reliability, test-retest reliability, and content validity. The SUMAC-NL seems to be a promising instrument for the assessment of walking with a walker in older people with dementia.", "appendix": "Data availability\n\nDataverseNL: Safe Use of Mobility Aid Checklist (SUMAC) for walker use in people living with dementia. https://doi.org/10.34894/RUKZQP 30\n\nThis project contains the following underlying data:\n\nDataset of the reliability study\n\n- DatastetreliabilitySUMACNL_15-5-2022_raw (.cvs and.sav)\n\n- Syntax1reliabilitySUMAC (.sps)\n\nDataset of the validity study\n\n- Validityworksheet_CVI_CVR-SUMAC-NL (.xlsx)\n\nThis project contains the following extended data:\n\n- README_ENG_ SUMAC_NL_translation_relibility_validation 27-1-2023.pdf\n\n- informatiebrief SUMAC-NL studie 2-12-2021.docx (participant information sheet)\n\n- Handleiding SUMAC-NL_final.docx (manual for using the SUMAC-NL)\n\n- SUMAC-NL_final.docx (The official SUMAC-NL tool for clinical use)\n\n- Dataset definitions.pdf\n\n- The English version of the SUMAC can be found via: http://www.mobility-in-aging-lab.ca/#publications\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nThis research is part of the graduation phase of the Physiotherapy Sciences programme at Utrecht University. 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Publisher Full Text Reference Source\n\nDavis LL: Instrument Review: Getting the Most From a Panel of Experts.1992.\n\nKroesen J, Hobbelen H, Hunter S, et al.: Safe Use of Mobility Aid Checklist (SUMAC) for walker use in people living with dementia. DataverseNL. 2022; V2. Publisher Full Text\n\nHunter SW, Omana H, Madou E, et al.: Effect of dual-tasking on walking and cognitive demands in adults with Alzheimer’s dementia experienced in using a 4-wheeled walker. Gait Posture. 2020 Jan; 77(77): 164–170. Publisher Full Text\n\nMuir-Hunter SW, Wittwer JE: Systematic review Dual-task testing to predict falls in community-dwelling older adults: a systematic review. Physiotherapy. 2016 [cited 2022 May 2]; 102: 29–40. PubMed Abstract \| Publisher Full Text\n\nWoollacott M, Shumway-Cook A: Attention and the control of posture and gait: a review of an emerging area of research. Gait Posture. 2002 [cited 2022 May 2]; 16: 1–14. PubMed Abstract \| Publisher Full Text Reference Source\n\nMontero-Odasso M, Verghese J, Beauchet O, et al.: Gait and Cognition: A Complementary Approach to Understanding Brain Function and the Risk of Falling $watermark-text $watermark-text $watermark-text. J. Am. Geriatr. Soc. 2012; 60(11): 2127–2136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDowns S, Marquez J, Chiarelli P: The Berg Balance Scale has high intra- and inter-rater reliability but absolute reliability varies across the scale: a systematic review. J. Physiother. 2013; 59: 93–99. PubMed Abstract \| Publisher Full Text\n\nBeck Jepsen D, Robinson K, Ogliari G, et al.: Predicting falls in older adults: an umbrella review of instruments assessing gait, balance, and functional mobility. BMC Geriatr. 2022; 22(1): 1–27.\n\nConradsson M, Lundin-Olsson L, Lindelöf N, et al.: Berg Balance Scale: Intrarater Test-Retest Reliability Among Older People Dependent in Activities of Daily Living and Living in Residential Care Facilities Background and Purpose.2007 [cited 2022 May 6]. Reference Source\n\nTelenius EW, Engedal K, Bergland A: Inter-rater reliability of the Berg Balance Scale, 30 s chair stand test and 6 m walking test, and construct validity of the Berg Balance Scale in nursing home residents with mild-to-moderate dementia. BMJ Open. 2015 [cited 2022 Jun 20]; 5: e008321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuzis G, Sabe L, Tiberti C, et al.: Explicit and Implicit Learning in Patients With Alzheimer Disease and Parkinson Disease With Dementia. Neuropsychiatruy, Neuropsychol. Behav. Neurol. 1999; 12(4): 265–269.\n\nvan Tilborg IADA , Kessels RPC, Hulstijn W: Learning by observation and guidance in patients with Alzheimer’s dementia. NeuroRehabilitation. 2011; 29: 295–304. Publisher Full Text\n\nGuillemin F, Bombardier C, Beaton D: Cross-cultural adaptation of Health-Related Quality Of Life Measures: Literature review and proposed guidelines. J. Clio. Itpidemiol. 1993; 46(12): 1417–1432. Publisher Full Text\n\nMutsaers B, Ruitenbeek T, Schmitt M, et al.: KNGF Physical Therapist Professional Profile.2021 Mar.\n\nMokkink LB, Terwee CB, Patrick DL, et al.: The COSMIN checklist for assessing the methodological quality of studies on measurement properties of health status measurement instruments: an international Delphi study. Qual. Life Res. 2010; 19: 539–549. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "270411", "date": "10 May 2024", "name": "Jodie Marquez", "expertise": [ "Reviewer Expertise rehabilitation", "ageing", "exercise", "physiotherapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract:\nThe abstract needs to be revised to clearly outline the reason for the study and the primary aims. Concepts need to be introduced more clearly. For example: “the use of a walker in people with dementia is associated with a threefold increased odds of falls compared to their healthy peers”. This point is misleading – it suggests that walker use is associated with falls, yet it may be that if they didn’t use a walker the falls rate may be much higher. Please revise for clarity.\n\nPlease reconsider ‘Better advice and training could reduce falls risk – is this true in this population where short term memory is problematic? It would seem that the assessment tool would be used to warrant the prescription of the walker rather than to inform education. Please re consider the purpose of this tool. If this point is to be presented, please provide evidence in the introduction of evidence of the use of training /education to improve mobility in this population. The SUMAC was developed but why was the Dutch version required? Don’t use abbreviations not introduced eg PF domain, EQ Was intra-rater/ test-retest reliability assessed?\n\nIntroduction: The background needs to describe what assessments are currently used to determine the need for a mobility aid, such as a walker, in the general population – and why these tools are not suitable for those with dementia Why is a dementia specific tool required? What makes the Dutch population any different to the global population – why is a Dutch specific tool required? Methods: Not clear why a cognitive assessment score was not included in the demographic information –it would seem this information would be very important in determining what level of cognitive functioning is appropriate for clinical application of the tool In the ‘data collection’ section it states ‘ a convenience sample of five physiotherapist who were recruited’ else where it states “8 experts” please clarify. The expert panel are very homogenous with regard to age and experience - this is a potential limitation to widespread adoption of the tool whereby reliability may differ for those outside of this age/experience range Discussion:\nThe authors conclude that the difference in reliability with the previous study may be due to the difference in the format in which the training was provided ( in person vs online) please clarify this. Was the content different? How would this affect the scoring? There were differences in findings but no recommendation to modify the tool for the Dutch population therefore the impact of the study is reduced\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11687", "date": "13 Jun 2024", "name": "Jesper Kroesen", "role": "Author Response", "response": "Dear Jodie, Thank you for taking the time to review our study. We find your suggestions very valuable and will incorporate them into the article. On the advice of F1000research, we will do so after a second review by another researcher. Kind regards, Jesper Kroesen" } ] }, { "id": "351635", "date": "29 Jan 2025", "name": "Brittney Muir", "expertise": [ "Reviewer Expertise aging", "mobility", "device evaluation and translation." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 replication study of the work by Hunter et al. (2020).14 However, the authors have translated the instrument into Dutch, and evaluated its use. The study found that SUMAC-NL shows good to excellent reliability and content validity, and seems to be a promising tool to assess walking with a walker in people with dementia in the Netherlands.\nMajor comments:\nI find the science to be sound, as it is by design a replication of previous work. I have major concerns about the value this study adds to science. While validating the tool in another language is an important step, there is little support on why this is novel publishable scientific work. Towards this, I am requesting the authors revise the introduction and discussion to explain why it is important to evaluate and publish this work on the translated device. Points that could be considered in this revision include: 1) Were you expecting the Dutch version to not be as valid/ reliable? 2) What value does this study bring other than having the tool in Dutch? Does it speak to the robustness of the original tool? Minor comments:\nI have no minor comments, I thought the paper was well-written, scientifically sound, and rigorous work was conducted and documented.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1150
https://f1000research.com/articles/12-1149/v1	14 Sep 23	{ "type": "Review", "title": "Extracorporeal cardiopulmonary resuscitation as a standard of care in the future: a literature review", "authors": [ "Vashistha Patel", "Shreya Patel", "Rayan Saab", "Kalyan Prudhvi", "Miles Cobia", "Allison Rogers", "Alanna Cole", "Shreya Patel", "Rayan Saab", "Kalyan Prudhvi", "Miles Cobia", "Allison Rogers", "Alanna Cole" ], "abstract": "Background: The use of extracorporeal cardiopulmonary resuscitation (ECPR) is limited generally to situations where traditional CPR failed to restore a patient's heart rhythm. Although ECPR is not regarded as the standard of care for cardiac arrest patients, it might be a more effective treatment for some forms of cardiac arrest. This literature review explores the efficacy of ECPR as a potential standard of care for cardiac arrest in the future. Methods: English language publications fulfilling eligibility criteria from 2010 to 2023 were found through a literature search using four electronic databases (PubMed, Google Scholar, Cochrane, and IEEE Explore). Articles were included in this literature review for fulfilling following criteria: empirical primary studies evaluating ECPR in human subjects with either IHCA or OHCA; articles published in English between 2010 and 2023; articles exploring ECPR in cardiac arrest across all ages of patients. Results: 12 studies out of 1,092 search results met the inclusion criteria for data extraction and synthesis. Data extracted included the efficacy of ECPR in both IHCA and OHCA patients based on the PICO framework. The quality of study done by NOS (Newcastle-Ottawa Quality Assessment Scale for Cohort Studies) resulted in three studies with moderate quality while nine were of high quality. Conclusions: ECPR was associated with neurologically intact survival with favorable neurological outcomes compared to a standard CRP for cardiac arrest patients. This study also demonstrates that, at the moment, ECPR is the most successful in centers with a well-trained multidisciplinary ECMO team of experts. On the other hand, cardiac arrest patients in semi-rural areas and underdeveloped locations are likely to benefit less from ECPR interventions due to the lack of necessary ECPR expertise and infrastructure. Those individuals eligible for ECPR benefit from better neurological outcomes and associated higher survival rates.", "keywords": [ "extracorporeal cardiopulmonary resuscitation", "ECPR", "extracorporeal life support", "ECMO", "out-of-hospital cardiac arrest", "in-hospital cardiac arrest" ], "content": "Introduction\n\nCardiac arrest (CA) is one of the leading causes of death worldwide.1,2 CA prevalence accounts for nearly 350,000 cases in the US,3 and whether out-of-hospital (OHCA)4–6 or in-hospital CA (IHCA),7,8 cardiac arrest is responsible for the morality of more than half a million individuals every year worldwide.9,10 Although adult CA survival rates have increased over the past 20 years, only just 22% of IHCA patients and less than 10% of OHCA patients survive.11,12 Notably, less than 10% of survivors have satisfactory neurological outcomes when discharged from hospitals despite standardizing basic cardiac resuscitation, post-arrest care, and application with personalized therapies.3,13 Extracorporeal cardiopulmonary resuscitation (ECPR) is a potentially life-saving therapy for patients in cardiac arrest who otherwise are unresponsive to traditional cardiopulmonary resuscitation (CPR).14,15 ECPR involves cardiopulmonary bypass maintaining circulation and perfusion to vital organs while16 the patient’s body recovers from the underlying condition that caused the cardiac arrest.17–19\n\nCurrently, ECPR is not considered a standard of care for cardiac arrest patients,20 and it is typically reserved for cases where conventional CPR has failed to restore a patient’s heart rhythm.21,22 There is growing evidence to suggest that ECPR may be a more effective treatment for certain types of cardiac arrest,23 particularly those caused by conditions such as pulmonary embolism, hypothermia, or drug overdose.24 As a result, some healthcare systems consider ECPR as an essential standard of care for cardiac arrest patients.25 For instance, in some parts of the world, emergency medical services have implemented ECPR programs that allow trained responders to perform the procedure on eligible patients in the field.26–28 While use of ECPR as a standard of care for cardiac arrest is still the subject of ongoing research, it is clear that this therapy has potential to save many lives. In this regard, our literature review aims to explore the efficacy of ECPR as a potential standard of care for cardiac arrest patients in the future.\n\n\nMethods\n\nWe adhered to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) standards to prepare this literature review.29 Bibliographic searches were conducted using four electronic databases: PubMed, Google Scholar, Cochrane, and IEEE Explore.\n\nUsing a set of keywords, computerized bibliographic searches were carried out in PubMed, Google Scholar, Cochrane, and IEEE Explore. The search was limited to English language articles dating from 2010 to 2023. We utilized the following search terms: (“extracorporeal cardiopulmonary resuscitation” OR “ECPR” OR “extracorporeal oxygenation” OR “extracorporeal life support” OR “percutaneous cardiopulmonary support” OR “ECMO” OR “extracorporeal circulation”) AND (“cardiopulmonary resuscitation” OR “CPR” OR “conventional CPR” OR “CCPR”) AND (“out-of-hospital cardiac arrest” OR “in-hospital cardiac arrest” OR “cardiac arrest” OR “heart arrest” OR “OHCA” OR “IHCA”).\n\nArticles were included in this literature review for fulfilling following criteria:\n\n• Empirical primary studies evaluating ECPR in human subjects with either IHCA or OHCA.\n\n• Articles published in English between 2010 and 2023.\n\n• Articles exploring ECPR in cardiac arrest across all ages of patients.\n\nStudies were eliminated based on the following exclusion criteria:\n\n• Secondary sources including other reviews, newspaper articles, magazines, conference proceedings, and unpublished data sets.\n\n• Non-English language studies.\n\n• Studies older than 2010.\n\nEach eligible publication’s study characteristics and data were extracted by us in adherence to the PICO framework.30 These characteristics and data included the first author’s name, the publication year, the country of origin, the study’s design, the location of the arrest (OHCA or IHCA), the number of patients, the sex ratio, and the mean age.\n\nAuthors pooled the findings from the included articles, and the results of all the research under consideration were then available for synthesis and analysis. A modified version of the Newcastle-Ottawa Quality Assessment Scale for Cohort Studies was used to rate effectiveness of each study (NOS)31 (Table 1).\n\n\nResults and discussion\n\nA total of 1,092 pertinent articles were found in the literature search across four electronic databases. The authors eliminated 373 duplicate articles. The remaining articles’ titles and abstracts were scrutinized for the research subject and 338 were excluded as these studies did not meet the research criteria. The remaining 381 articles were reduced to 140 after the inability to retrieve 241, and the remaining 140 were evaluated based on the predetermined eligibility standards. Eventually, only 12 articles met the requirements after being evaluated using the qualifying criteria (Tabulated in study characteristics in Table 2 and Table 3). The other 140 papers were disregarded on the grounds that 26 were published before 2010, 38 were non-English articles, 39 were abstracts and 25 were systematic reviews, letters to the editor, case reports, and magazines. The study selection process is shown in Figure 1.\n\nThe NOS Scale was used to assess the quality of the collected studies and considered ten factors: selection, comparability, and outcome and rating each study on a range of 0 to 10. High-quality observational cohort studies constituted those with 7 or more stars; a score of less than four denotes low quality, a score of five to six suggests moderate quality, a score of seven to eight indicates good quality, and a score of nine to 10 denotes extremely good quality.44 Four studies were deemed moderate quality, while eight were judged to be of high quality. No studies were deemed to be of low quality. The quality assessment score is shown in Table 1.\n\nThe main objective of the current literature review is to examine the efficacy of ECPR compared to conventional CPR in patients with cardiac arrest across various settings. In doing so, we aim to establish the effectiveness of ECPR as a future intervention for either IHCA or OHCA patients. We also identified the existing gaps that would require further research. Based on the synthesis of included studies, our review showed that employing ECPR in both IHCA and OHCA is associated with improved survival rate and corresponding positive neurological outcomes compared to conventional CPR. Our review entails a total of twelve studies comprising observational and retrospective studies, analyzing a cumulative of 2,897 IHCA and OHCA patients. Six studies examined ECPR in OHCA, while the remaining six explored IHA and OHCA. The outcome measures evaluated across the studies mainly comprised ROSC (return of spontaneous circulation), survival, neurological outcomes, eligibility for ECPR, and time to extra corporeal membrane oxygenation (ECMO). Furthermore, among the 12 studies analyzed, five studies reported an increased long-term neurologically intact survival with the use of ECPR, four of which were OHCA,32,34,37,39 while one evaluated ECPR in IHCA35 (Table 3 in Supplemental Material shows the studies’ design, objectives, interventions, outcomes, and results with neurological outcomes.)\n\nGenerally, studies enrolling adult IHCA and OHCA patients reported improved and favorable neurological outcomes associated with ECPR.38,40 A study by Bartos et al. demonstrated that for CPR durations of less than 60 minutes, ECPR was associated with favorable neurological outcomes and survival despite significantly higher metabolic derangement as compared with CCPR.32 Our observations are consistent with findings of another meta-analysis which compared ECPR and CCPR for patients with CA and found that ECPR was related to statistically significant improvement, 30-day survival, and neurologic outcomes for patients with IHCA (RR = 1.60, 95% CI = 1.25-2.06 and RR = 2.69, 95% CI = 1.63-4.46).45 The findings revealed no effect on neurological outcomes and survival with ECPR on OHCA patients.45 However, another study comparing ECPR and CCPR revealed that neurological outcome and survival were the same in both groups for OHCA.46 This finding particularly contradicts the outcomes of the majority of the included studies, which suggest favorable neurological outcomes associated with ECPR relative to CCPR.36,43\n\nThe disparities in these results can be attributed to selection bias in meta-analyses which are due to inclusion of studies with recruitment periods spanning a decade, a period in which technological advancements could have changed a lot in this field. For instance, these advancements have seen CPR guidelines being changed twice and the emergence of advanced mechanical CPR equipment becoming widely adopted.47 While our literature review evaluated the criteria under which ECPR should be performed, four studies reported the need to evaluate CA patients for eligibility to see if they fit for ECPR therapy.35,39,41,42 These studies report higher survival associated with carefully selected patients after meeting inclusion criteria.39 These results are significant as they demonstrate the need to make early patient selection conceivable and necessary prior to ECPR therapy. In that regard, Te Avest et al. suggest that one of the factors to consider is the effectiveness of in-hospital ECPR, which appears to be of little importance in rural setups, as potentially ECPR-eligible patients would deteriorate prior to their arrival to the hospital.42 This is imperative since as ECPR awareness grows and pre-hospital mechanical CPR is introduced, it is plausible that not only more ECPR eligible cases will present to the emergency department (ED), but may also predict a rise in ECPR ineligible patients.48\n\nTime to return of spontaneous circulation, ROSC, CPR duration, and extracorporeal membrane oxygenation were evaluated as an effect of ECPR in this literature review and were reported in most of included articles. Kim et al. showed that longer durations of CPR were associated with decreased neurological outcomes in CCPR compared to with ECPR.36 In contrast, a significant number of patients who were scheduled for ECPR recovered ROSC before or after hospital admission after receiving prolonged CPR.37 In addition, Patricio et al. showed that the ROSC rates associated with ECPR were significantly higher relative to CCPR (77/80 (96%) vs. 30/80 (38%), (p <0.001)).38 Additionally, ECPR effectively reduced the time from OHCA to ECMO under an ECPR-specific program implementation.40 (Table 3 provided as in Supplemental Material shows the study design, objectives, interventions, outcomes, and results with neurological outcomes.)\n\nThe majority of the included studies were observational studies and retrospective in design. This literature review demonstrates existence of a research gap with the absence of randomized control trials, which would raise the level and quality of evidence and close knowledge gaps, since the majority of the current knowledge is derived from single-center observations, and the preponderance of the evidence is derived from case series and cohort studies, making it susceptible to publication bias.49 As a result of observational studies’ well-known flaws, it is impossible to draw valid conclusions from primary data due to its high bias risk and potential for producing accurate but false results when combined. This indicates the importance and need for high-quality research that would explore the viability and patient-centered results of employing ECPR in innovative settings, such as via EMS-based or ED-based large, randomized trials, further exploring the usefulness of ECPR for cardiac arrest. Ideally, the design of future research would identify a successful and unified approach to ECPR and develop an algorithm that could be used for both IHCA and OHCA.\n\n\nConclusion\n\nOur literature review demonstrates that ECPR has better survival rates and neurological outcomes than standard CPR therapies for CA. ECPR is a development in CPR that allows a bridge to treatment in carefully chosen individuals after meeting the criteria following refractory CA. Furthermore, we establish that individuals who meet the criteria of selection for ECPR are associated with increased neurological outcomes and high survival rates compared to those who are not eligible. This study also demonstrates that, at the moment, ECPR is the most successful in centers with a well-trained multidisciplinary ECMO team of experts. On the other hand, cardiac arrest patients in semi-rural areas and underdeveloped locations are likely to benefit less from ECPR interventions due to the lack of necessary ECPR expertise and infrastructure. Those individuals eligible for ECPR benefit from better neurological outcomes and associated higher survival rates. Therefore, ECPR has the potential to be an effective standard of care for cardiac arrests in the future. There is a need for high quality research in this area to evaluate the feasibility, safety, and efficacy associated with ECPR and the reliability of the findings in our literature review.", "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\nMehra R: Global public health problem of sudden cardiac death. J. Electrocardiol. 2007; 40(6 Suppl): S118–S122. 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Publisher Full Text\n\nPoppe M, Schriefl C, Steinacher A, et al.: Extracorporeal cardiopulmonary resuscitation at the emergency department: A retrospective patient selection evaluation. Eur. J. Anaesthesiol. 2020; 37(4): 280–285. Publisher Full Text\n\nRead AC, Morgan S, Reynolds C, et al.: The effect of a structured ECPR protocol aided by specific simulation training in a quaternary ECMO centre: A retrospective pre-post study. Resusc. Plus. 2022; 10: 100234. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchober A, Sterz F, Herkner H, et al.: Emergency extracorporeal life support and ongoing resuscitation: a retrospective comparison for refractory out-of-hospital cardiac arrest. Emerg. Med. J. 2017; 34(5): 277–281. PubMed Abstract \| Publisher Full Text\n\nter Avest E , Tunnicliff M, Griggs J, et al.: In-hospital extracorporeal cardiopulmonary resuscitation for patients with an out-of-hospital cardiac arrest in a semi-rural setting: An observational study on the implementation of a helicopter emergency medical services pathway. Resusc. Plus. 2022; 12: 100339. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu HY, Wang CH, Chi NH, et al.: Effect of interplay between age and low-flow duration on neurologic outcomes of extracorporeal cardiopulmonary resuscitation. Intensive Care Med. 2019; 45(1): 44–54. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLo CKL, Mertz D, Loeb M: Newcastle-Ottawa Scale: comparing reviewers’ to authors’ assessments. BMC Med. Res. Methodol. 2014; 14(1): 45. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen Z, Liu C, Huang J, et al.: Clinical Efficacy of Extracorporeal Cardiopulmonary Resuscitation for Adults with Cardiac Arrest: Meta-Analysis with Trial Sequential Analysis. Biomed. Res. Int. 2019; 2019: 6414614–6414673. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhn C, Kim W, Cho Y, et al.: Efficacy of extracorporeal cardiopulmonary resuscitation compared to conventional cardiopulmonary resuscitation for adult cardiac arrest patients: a systematic review and meta-analysis. Sci. Rep. 2016; 6: 34208. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang PL, Brooks SC: Mechanical versus manual chest compressions for cardiac arrest. Cochrane Database Syst. Rev. 2018; 8(8): CD007260. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoudoulas KD, Whitson BA, Keseg DP, et al.: Extracorporeal Cardiopulmonary Resuscitation (ECPR) for Out-of-Hospital Cardiac Arrest due to Pulseless Ventricular Tachycardia/Fibrillation. J. Interv. Cardiol. 2020; 2020: 6939315–6939319. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLink MS, Berkow LC, Kudenchuk PJ, et al.: Part 7: Adult Advanced Cardiovascular Life Support: 2015 American Heart Association Guidelines Update for Cardiopulmonary Resuscitation and Emergency Cardiovascular Care. Circulation. 2015; 132(18 Suppl 2): S444–S464. Publisher Full Text" }	[ { "id": "273389", "date": "25 Jun 2024", "name": "Benoît Vivien", "expertise": [ "Reviewer Expertise Prehospital medical emergency 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\nIn this manuscript, the authors presented a literature review on the use of ECPR for cardiac arrest, either IHCA or OHCA. From an extended search collecting 1092 papers between 2010 and 2023, they retained 12 studies which met their inclusion criteria. They concluded that ECPR has better survival rates and neurological outcomes than standard CPR for CA. One very pertinent point is the consideration of rural OHCA and the minimum recruitment in ECPR centers to get sufficient training and expertise.\n\nGeneral Comments: This literature review is interesting and seems to have been accurately performed. The results and conclusions of the authors are relevant. Moreover, the text of the manuscript the figure and the tables are clear and well presented. The Reviewer has no major concern or criticism on this study. Minor Comments\nIntroduction, 3rd line : please correct motality to mortality\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1149
https://f1000research.com/articles/12-1148/v1	13 Sep 23	{ "type": "Research Article", "title": "Validation of the suicidal ideation scale for Hijra (third gender) people in Bangladesh", "authors": [ "Md. Omar Faruk", "Md. Ashiquir Rahaman", "Asibul Islam Anik", "Mohammad Zayeed Bin Alam", "Md. Ashiquir Rahaman", "Asibul Islam Anik", "Mohammad Zayeed Bin Alam" ], "abstract": "Background: Hijra people, recognized as a third gender in Bangladesh, experience a variety of mental health problems, including suicidal ideation. However, there is no psychometric instrument to measure the suicidal ideation of hijra people. The aim of the study was to validate the suicidal ideation scale (SIS) for hijra people in Bangladesh. Methods: Standard validation processes were followed to develop the initial Bangla version of the scale. After the pretest, the final version of the scale was prepared. A cross-sectional survey with a combination of purposive and snowball sampling was conducted. A total of 314 participants were recruited from Dhaka. Exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) were conducted besides the analysis of reliability and validity. Results: The SIS was found to have a two-factor structure, collectively explaining 46.69% of the total variance during EFA. The measurement model was supported by a number of fit indices while conducting CFA. The higher Cronbach’s alpha (0.80) suggested internal consistency reliability. The scale demonstrated acceptable test-retest reliability (0.89). Convergent and divergent validity was tested with the World Health Organisation WHO-5 Well-being Index, and Perceived Stress Scale, respectively. Conclusions: The results suggested that the SIS is a psychometrically valid instrument to measure the suicidal ideation of hijra people in Bangladesh.", "keywords": [ "Suicidal ideation scale", "Factor analysis", "CFA", "EFA", "Hijra people", "Bangladesh" ], "content": "Introduction\n\nThe term hijra represents a minority group of transgender females in the Indian subcontinent (Jayadeva, 2017). Although the term hijra refers to biological males who have a female gender and gender expression, their identities are created by a variety of variables other than sex and gender, such as religion, culture, and community (Jayadeva, 2017). Hijra people experience various mental health problems worldwide, including suicidal ideation. Evidence suggests that they experience perceived and internalized stigma, isolation, discrimination, and victimization leading them to develop mental health problems such as anxiety, depression, and substance use (Jayadeva, 2017). When compared to their heterosexual counterparts, they have a higher prevalence of mental health difficulties (Meyer, 2003; Russell & Fish, 2016). Various psychiatric disorders such as alcohol and substance use and reduced well-being are prevalent among hijra people (Kalra & Shah, 2013; Lin et al., 2021). Evidence suggests the rates of lifetime mental illness among hijra people was 38% (Sartaj et al., 2021). They experience somatoform disorder, eating disorder (e.g., bulimia nervosa) (Sartaj et al., 2021), and lower life satisfaction (Anderssen et al., 2020). Evidence also showed that hijra people have poor mental health than physiological problems (Bhattacharya & Ghosh, 2020) that include a higher susceptibility of HIV and sexually transmitted infections (STIs) (Jayadeva, 2017; Sha et al., 2021).\n\nHigher rates of suicidal ideation, suicidal attempt, and self-harm behaviors were also found to be prevalent among hijra people (Anderssen et al., 2020; Lin et al., 2021). Estimates showed that suicide rate and suicidal attempts among the transgender community, including hijra people, have been reported to be higher compared to the general population (Cochran & Mays, 2000; Proctor & Groze, 1994; Russell & Joyner, 2001; Thoma et al., 2019). For example, it was estimated that the rate of suicide among transgender individuals in India is about 31%, and 50% of them have attempted suicide at least once before their 20th birthday (Virupaksha et al., 2016). Similarly, in Canada’s Ontario the prevalence rate for suicide is 35.1% and, of them, 11.2% attempted suicide in the past year (Bauer et al., 2015). Risk factors for this disproportionately high rate include discrimination, rejection by family, friends, and community, bullying, internalized transphobia, gender-based victimization, policy and public, intimate partner violence, and being denied appropriate bathroom, proper treatment at health-care system, and lack of access to housing, unemployment, mental disorders such as depression, physical assault, desire for gender affirming surgery (Narang et al., 2018; Virupaksha et al., 2016; Zwickl et al., 2021). In addition, the persistent experience of minoritization can cause emotional distress and mental health repercussions among gender diverse people. Therefore, deprivation and minority stress have the potential to develop suicidal ideation among gender diverse people.\n\nTransgender people are generally referred to as hijra in Bangladesh and possess a culture that is distinct and easily identifiable due to their unique way of living, such as feminine clothing with masculine characteristics. They usually live and move in groups (Mozumder, 2017). Their sources of income include claiming and collecting money from shops, which is known as cholla in the hijra community, singing and dancing, and claiming money when babies are born (Jebin, 2018; Mozumder, 2017). Some of them are involved in the sex-trade (Dietert & Dentice, 2009). Hijra people are subject to myriad societal issues ranging from changing official documents (e.g., birth certificates and social benefit cards, etc.) (Dietert & Dentice, 2009) to being treated viciously due to their atypical gender identity that does not conform to societal ideas of gender. Despite the Bangladesh governments’ recognition of hijra as ‘third gender’, this plight continues (Jebin, 2018). They are widely vulnerable and continue to be among the poorest of the poor and often are denied basic education, health care, and employment (Khan et al., 2009). They are also prone to ill-health including sexually transmitted diseases and HIV (Jebin, 2018). Parts of their reluctance to see doctors at hospitals were attributed to a feeling of discomfort due to socio-cultural perceptions toward them and little understanding of diverse sexual identities among health service providers (Chan & Khan, 2007; Joseph, 2013). Employment opportunities are restricted due to their lower education and feminine behavioral attributes (Jebin, 2018). Furthermore, hijra people experience disproportionate verbal harassment and there is little opportunity to seek legal support in response to this (Khan et al., 2008). This plight is even worse for older hijra people living alone with poverty and suffering from illness, who are without family members and restricted social connections as social outcasts (Khan et al., 2008).\n\nThe number of hijra people in Bangladesh is not accurately determined, with some estimates suggesting being between 4,504 and 8,882 (Mozumder, 2017) while other estimates suggest that more than 10,000 hijras live in Bangladesh (Sifat, 2020). It is of note that hijra people in Bangladesh have been granted a social safety net (e.g., allowance for older hijra people) (Jebin, 2018). While the social benefits and legal recognition seem very progressive, the reality is grim with various unexpected accounts of discrimination based on their sexual orientation and gender identity (Chaney et al., 2020). These experiences may synergistically contribute to greater mental health problems including suicidal ideation. Evidence suggests that sexual minority groups including transgender individuals are more susceptible to stressful life events such as physical, sexual, and psychological abuse, financial and legal difficulties (Mozumder, 2017). But little research exists in Bangladesh which documents their mental health experiences. Limited scholarly work suggests that exclusion from greater society has diminished their self-esteem and sense of social responsibility (Khan et al., 2009). They also experienced physical, verbal, and sexual abuse (Khan et al., 2009). These accounts of abuses and social exclusions can contribute to the development of suicidal ideation. Currently there are no known standardized instruments to measure the suicidal ideation for this sexually and gender diverse community (i.e., hijra community) thus our purpose was to assess the psychometric properties of a widely used suicidal ideation scale (SIS) (Luxton et al., 2011) in the context of Bangladesh.\n\n\nMethods\n\nThe study employed a cross-sectional survey with 314 hijra people recruited with snowball and purposive sampling in Dhaka’s Mirpur and Manda (Faruk et al., 2023). A total of 330 responses were collected. However, 314 responses were analyzed after removing the incomplete data. Another 50 participants were recruited to assess test-retest reliability. The socio-demographic characteristics are presented in Table 1.\n\nBangla version of the World Health Organisation WHO-5 Well-being Index\n\nThe self-reported Bangla version of the WHO-5 Well-being Index scale measures the level of well-being for the general population in Bangladesh (Faruk et al., 2021). The scores of the six-point Likert-type scale range from 0 (At no time) to 5 (All of the time). Higher scores represent higher well-being. The scale demonstrated acceptable internal consistency (α = 0.754) and test-retest reliability 0.713, divergent validity -0.443, and convergent validity 0.542 (Faruk et al., 2021). The WHO-5 Well-Being Index has been utilized as a depression screening tool as well as an outcome measure in a variety of research domains (Topp et al., 2015).\n\nPerceived Stress Scale (PSS 10)\n\nThe Perceived Stress Scale (PSS) was originally developed by Cohen and colleagues (Cohen et al., 1983). Among other versions of PSS (PSS 14 and PSS 4), the 10-item PSS was found to be superior (Mozumder, 2017). The Bangla translated version of PSS-10 was used for the present study which is available at Shelden Cohen’s Laboratory for the study of stress. Published data on the validity and reliability were found to be unavailable (Mozumder, 2017). The 5-item Likert-type scale determines the degree to which an individual reports life as stressful. The scale combined with both positive (items no. 4, 5, 7, and 8) and negative (items no. 1, 2, 3, 6, 9, and 10) items ranging from 0 representing ‘never’ to 4 ‘very often’. The 10-item PSS has been tested with varying types of psychometric tools with a view to determining its construct validity. Results suggested a moderate to strong correlation bearing testimony to a robust tool for measuring perceived stress (Mozumder, 2017).\n\nPrior permission was sought from the original author to validate the Suicidal Ideation Scale (Luxton et al., 2011). Standard translation and back-translation processes were followed throughout the preparation of the final scale (Gjersing et al., 2010). The original scale was translated into Bangla by a group of six people. Of them, three were clinical psychologists, one psychiatrist and counseling psychologist while the remaining individual was an English language expert. The accuracy and suitability of the translation were assessed by an expert panel comprising of two mental health professionals (one clinical psychologist and one psychiatrist) and a language expert. The expert panel emphasized the understandability and precision of items for hijra people in Bangladesh. Two words were changed based on an agreed decision. The synthesized version of the scale was given to six people for back-translation, maintaining a similar composition to the forward translation (three clinical psychologist, one psychiatrist, one counseling psychologist, and a language expert). The people involved in the back-translation did not have prior experience of the scale. Three professionals formed another expert panel to review the backward translations of the scale. The items were assessed in terms of their semantic clarity, idiomatic, and conceptual equivalence. The review suggested no change of words. The draft version of the scale was prepared based on the consensus. The draft version underwent a pilot study with a recruitment of 20 hijra people. Understanding the items, words, and meanings were taken into consideration while pilot testing of the scale. No words seemed to have any difficulty in conveying the meaning of each item. The scale was finalized after the piloting. The final scale was administered on a group of 314 hijra people in Dhaka. The first author along with two research assistants collected the data. The research assistants were trained prior to the data collection. Understanding suicidal ideation, administration of scales, and cognitive interviewing were discussed in the training. Starting with a snowball sampling, the study also employed purposive sampling. Data were collected between August and September 2021. Verbal and written consent were taken. A thumb mark was used to indicate consent for those with no formal education or literacy. The nature of the study, benefits, potential risks, rights to withdraw, and a referral directory consisting information of available mental health services were provided prior to the data collection. Participation in the study was completely voluntary, therefore, no monetary compensation was provided.\n\nThe Kaiser-Myer-Oklin (KMO) Test (>.70) (Kaiser & Rice, 1974) and Bartlett’s Test of Sphericity were considered in the exploratory factor analysis. χ2, ratio of χ2 to df (χ2/df), root mean square error of approximation (RMSEA), and comparative fit index (CFI), and Normed fit index (NFI) were used to assess the adequacy of the model fit in confirmatory factor analysis (CFA). The criteria for model fit were χ2 with p ⩾ 0.01, χ2/df ⩽ 2, RMSEA ⩽ 0.06, CFI ⩾ 0.95, SRMR ⩽ 0.08 (18). CFA was performed on AMOS 18.\n\nThe study was approved by an ethical review committee (Project ID: IR201201; approved on February 27, 2021). In addition, Helsinki Declaration guidelines were also followed throughout the study.\n\n\nResults\n\nThe mean age of participants was 29.97 (SD = 11.090) years old. All participants recruited in the study live with guru maa (the leader of the community that offers a living place and food). In addition, all participants were engaged in collecting money. The remaining demographic information is provided in Table 1.\n\n* SSC = Secondary School Certificate.\n\n** HSC = Higher Secondary School Certificate.\n\nThe mean score of the SIS items ranged from 1.79 (SD = 0.79) to 2.29 (SD = 0.79) (Table 2) with overall mean 2.08 (SD = 0.81).\n\nInter-item and item-total correlations were examined (Table 3). All inter-item correlations were statistically significant with a substantial number of them above 0.30 (42.22%). The item-total correlations were also highly significant with a range from 0.568 to 0.658. No negative or extremely low item-total correlation was found. Based on the item analysis, no item was excluded.\n\n* p < 0.05 level.\n\n** p < 0.01 level.\n\nExploratory factor analysis (EFA)\n\nThe structure of the Bangla SIS was evaluated by EFA using principal component analysis (PCA) with direct oblimin rotation. Prior to performing PCA, the suitability of data for factor analysis was assessed. Inspection of inter-item correlation matrix revealed the presence of substantial number (42.22%) of coefficients 0.30 and above. The Kaiser-Myer-Oklin value was 0.863, exceeding the recommended value of 0.6, and Bartlett’s Test of Sphericity reached statistical significance (χ2 = 622.607, p < 0.0001), supporting the factorability of the data. PCA revealed two components with eigen value >1 explaining 46.69% of the total variance. An inspection of the scree plot also revealed a clear break after the second component. However, the result of parallel analysis revealed only one component with eigenvalues exceeding the corresponding criterion values for a randomly generated data matrix of the same size (10 variables × 314 respondents). Nonetheless, we went for two factor solutions because parallel analysis is not the only criteria to determine the number of factors (Lim & Jahng, 2019).\n\nThe two factors solution of the present study addresses two constructs including suicidal desire (ongoing thoughts or desires) and resolved plans and preparation (intense thoughts, plans, courage, and capability to commit suicide). Table 4 presents the rotated factor loadings.\n\nConfirmatory factor analysis (CFA)\n\nFor the solution of two factors of SIS, CFA was conducted with maximum likelihood estimation. The following fit indices were used to estimate the appropriateness of the model fit: (1) chi-square to df ratio (χ2/df), wherein a value of no more than 3 indicates a good fit (Carmines, 1981); (2) the comparative fit index (CFI); (3) the normed fit index (NFI); generally, values of the CFI and NFI exceeding 0.90 indicate a good fit (Hau et al., 2004); and (4) the root-mean-square error of approximation (RMSEA), in which the criterion for a good model fit is <0.06 (Marsh et al., 2004). In the present study, the result of the two factor CFA showed a good fit to the data (χ2/df = 52.31/34 = 1.54, CFI = 0.97, NFI = 0.92, RMSEA = 0.041). The first factor explained 36.06% of the variable and the second factor explained 10.64% of the variable. The correlation between the two factors was 0.79. The CFA factor loadings and squared multiple correlations are displayed in Table 5. Overall, the results of the CFAs support the two factors model of the SIS. Figure 1 represents the two-factor structure of the Bangla SIS scale.\n\nInternal consistency of reliability\n\nInternal consistency reliability was computed using the coefficient alpha method. For the present Bangla SIS, Cronbach Alpha was found to be 0.80, which is usually termed as a respectable level of internal consistency (DeVellis, 2003). The corrected item-total correlation ranged from 0.43 to 0.54 (Table 6). Cronbach’s alpha for subscale Suicidal desire and Resolved plan were found to be 0.729 and 0.669, respectively.\n\nTest-retest reliability\n\nTo estimate the test-retest reliability, the Bangla SIS was administered twice on 50 participants over a period of three weeks. The Pearson correlation between test and retest scores of vthe Bangla SIS was found to be 0.89 (p < 0.01). The paired sample t-test between the two testing periods revealed no significant difference, t(49) = 1.09, p = 0.281, suggesting the temporal stability of the Bangla SIS.\n\nConstruct validity\n\nConstruct validity of the present scale was determined using convergent and divergent validation process (Domino & Domino, 2006). A significant positive correlation of SIS total score with PSS total score (r = 0.12, p < 0.05) and a negative significant correlation of SIS total score with WHO-5 total score (r = -0.21, p < 0.01) ensure the construct validity of the scale.\n\n\nDiscussion\n\nThe present study was conducted amid the absence of an instrument measuring suicidal ideation specific for hijra people in Bangladesh. The cross-sectional study recruited 314 hijra people by means of purposive and snowball sampling. The scale underwent stages of translation, judge evaluation, and pilot testing prior to the field testing. Both exploratory and confirmatory factors analysis were employed. Construct validity was assessed using convergent and divergent methods.\n\nOriginally developed by Rudd (1989), the SIS assesses the severity of suicidal ideation among college students. The original scale demonstrated a high internal consistency (Cronbach’s alpha = 0.86) and adequate item-total correlations (r = 0.45 to 0.74). The concurrent validity assessed with the Centre for Epidemiologic Studies - Depression scale was found to be moderate (r = 0.55). Moderate validity was also found with the Beck Hopelessness Scale (r = 0.49) (Rudd, 1989). The scale has been translated into other languages such as Malay (Ibrahim et al., 2021) and Indonesian (Fitriana et al., 2022). The scale has been used to assess suicidal ideation among a variety of target population and settings [see (Bhargav & Swords, 2022; Che Din et al., n.d.; Ibrahim et al., 2019; Luxton et al., 2011; Morris et al., 2021; Nkwuda et al., 2020)]. The scale has not been validated in Bangladesh among gender and sexually diverse people, especially those who identified themselves as hijra.\n\nThe Bangla version of the scale underwent a series of statistical analyses to assess psychometric properties.\n\nThe scale demonstrated excellent test-retest reliability (r = 0.89) based on the recommended criteria (Cicchetti, 1994). This implies that the scale remained consistent when administered twice with a gap of two weeks. The paired sample t-test showed no significant differences between the two time points which further indicates the stability of the scale.\n\nConstruct validity was determined with regards to convergent and divergent validity. The scale demonstrated a weak correlation with PSS and WHO-5 Well-being Index (Akoglu, 2018) for divergent and convergent validity, respectively. The weak correlations may be interpreted as the measure not adequately reflecting the construct under study. However, this is not always the case, as validity coefficients are sensitive to sample size (Nunnally & Bernstein, 1994) where collecting data from a more diverse group of participants can improve the validity of the measure. In addition, the absence of multiple measures may also result in poor validity coefficients. Evidence suggests that using multiple measures to assess a construct increases the validity of a measure (Havron, 2022; Nassaji, 2020) as multiple measures provide different perspectives on the construct under investigation, eventually leading to an increase of validity. The present study employed PSS and WHO-5 Well-being Index as these measures are short and easy to understand and take relatively a short period of time to administer. Considering the transient nature of hijra peoples’ residences and demand for increased income on a daily basis, using short measures was thought to be a feasible idea. Besides, it is often argued that long measures can lead to response fatigue and vice versa (Tourangeau et al., 2000). Therefore, it is generally suggested that while conducting research, especially survey research, it is important to consider the length of the measures to reduce the likelihood of response fatigue (Tourangeau et al., 2000). The present study recognizes these weak validity coefficients as limitations and recommends using multiple measures to improve the validity in future studies.\n\nThe SIS is a unidimensional scale and yielded a two-factor structure namely suicidal intention and resolved plan. However, not all validation studies yielded the same factor-structure. For example, the Malay version of the scale demonstrated a single factor structure where all of the items loaded into the single factor (Ibrahim et al., 2021). The present study demonstrated the two-factor structure with item no. 5 (I feel life just isn’t worth living) loaded in the resolved plans/preparations as opposed to the original scale where the item was retained in the factor named suicidal desire. This variation can be attributed to the cross-cultural validation of a study where the central construct (in this case resolved plans for suicide) may be subject to indigenous ideas about suicide, sociocultural aspects, and individual factors. The idea of life not worth living may be different across cultures and gender and sexually diverse groups. Giving up life when it is not perceived worthy may lead to a final resolution implying a resolved plan. The other reasons for this discrepancy may include a relatively small sample size (314 in the present study) as opposed to the original study. Factor structures may be susceptible to the small sample size that can lead to the difficulties in identifying the underlying factors of an instrument (Nunnally & Bernstein, 1994). Others have argued that sample size can be problematic in interpreting and replicating the results of a study (Hair, 2009). Future studies are required to investigate whether the discrepancy is related to the small sample size or the inherent cultural differences in construing resolved plans for suicide.\n\nThe same data set was used to carry out CFA as evidence suggests that cross-validation study using different data sets may lead to a lack of correspondence between CFA and EFA (van Prooijen & van der Kloot, 2001). In addition, using the same different data sets can lead to overfitting that occurs when the model fits the data but fails to generalize the new data leading to unreliable factor structures. CFA results demonstrated acceptable fit indices suggesting a good model fit of the two-factor structures of the Bangla SIS scale.\n\nThe validation of a scale for sexually diverse people (e.g., hijra people) can have important implications for research and clinical practice. It may provide a more accurate and comprehensive understanding of the experiences and needs of this hijra population that can inform the development of tailored psychosocial interventions and pertinent policies. The scale can provide an insight into the understanding and severity of suicidal thoughts of the hijra population in Bangladesh. Finally, the scale can help advance the field of sexual orientation research in Bangladesh.\n\nThe study recognizes some limitations. The cross-sectional nature of the study with purposive and snowball sampling may restrict the generalizability of the scale for hijra people across Bangladesh. Self-reporting in survey research may produce various biases, including social desirability bias. Additionally, participants may not accurately recall or report their experiences, feelings, or behaviors due to memory errors. Finally, the study did not include clinical samples, therefore, it was not possible to determine the norms. Future studies should establish norms with the inclusion of clinical samples.\n\n\nConclusions\n\nThe study is the first of its kind in Bangladesh that aimed to validate a suicidal ideation scale for the hijra population- a group of people that drew relatively little attention, especially for their suicidal ideation. The scale is easy to understand and takes only 5 minutes to administer. The scale can be used to measure the severity of suicidal ideation of hijra population. The scale is likely to produce more work into sexual orientation research. Finally, the scale can be used as an outcome measure in clinical settings.", "appendix": "Data availability\n\nDespite assuring the information would be kept confidential and anonymized, consent for sharing the data was not granted by the participants. Hijra people in general are subject to widespread negative attitudes in every aspect of their life that may have contributed to the higher levels of sensitivity when it comes to sharing information obtained from them. However, the authors endorse the scientific integrity by making the data publicly available. The dataset has been kept private and therefore, data will be made available upon request to the corresponding author (contact details are provided above). Access to data can be granted upon reasonable request to the corresponding author with proper document (e.g., IRB clearance copy, or institutional recommendation letter, etc.). We would provide access to data only to those researchers and organizations intending to utilize the data to advance transgender or LGBTQ research irrespective of their affiliation, institutions, and geographical location.\n\nFigshare: SIS materials. https://doi.org/10.6084/m9.figshare.22769708.v2 (Faruk et al., 2023).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to acknowledge the contribution of research assistants as well as the participants.\n\n\nReferences\n\nAkoglu H: User’s guide to correlation coefficients. Turk. J. Emerg. Med. 2018; 18: 91–93. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnderssen N, Sivertsen B, Lønning KJ, et al.: Life satisfaction and mental health among transgender students in Norway. BMC Public Health. 2020; 20: 138. 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Publisher Full Text\n\nGjersing L, Caplehorn JR, Clausen T: Cross-cultural adaptation of research instruments: language, setting, time and statistical considerations. BMC Med. Res. Methodol. 2010; 10: 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHair JF: Multivariate data analysis.2009.\n\nHau K-T, Wen Z, Cheng Z: Structural equation model and its applications. Beijing China Educ. Sci. 2004.\n\nHavron N: Why not both? Using multiple measures to improve reliability in infant studies. Infant Child Dev. 2022; 31: e2336.\n\nIbrahim M, Ibrahim N, Abdul Kadir NB, et al.: The Malay version of the Revised-Suicide Ideation Scale (R-SIS): An Examination of its Psychometric Properties. Int. J. Acad. Res. Psychol. 2021; 8: 10–21.\n\nIbrahim N, et al.: The role of social support and spiritual wellbeing in predicting suicidal ideation among marginalized adolescents in Malaysia. BMC Public Health. 2019; 19: 553. 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LGBT Health Res. 2008; 4: 127–141. PubMed Abstract \| Publisher Full Text\n\nLim S, Jahng S: Determining the number of factors using parallel analysis and its recent variants. Psychol. Methods. 2019; 24: 452–467. PubMed Abstract \| Publisher Full Text\n\nLin Y, et al.: The mental health of transgender and gender non-conforming people in China: a systematic review. Lancet Public Health. 2021; 6: e954–e969. PubMed Abstract \| Publisher Full Text\n\nLuxton DD, Rudd MD, Reger MA, et al.: A psychometric study of the Suicide Ideation Scale. Arch. Suicide Res. Off. J. Int. Acad. Suicide Res. 2011; 15: 250–258. Publisher Full Text\n\nMarsh HW, Hau K-T, Wen Z: In Search of Golden Rules: Comment on Hypothesis-Testing Approaches to Setting Cutoff Values for Fit Indexes and Dangers in Overgeneralizing Hu and Bentler’s (1999) Findings. Struct. Equ. Model. Multidiscip. J. 2004; 11: 320–341. Publisher Full Text\n\nMeyer IH: Prejudice, Social Stress, and Mental Health in Lesbian, Gay, and Bisexual Populations: Conceptual Issues and Research Evidence. Psychol. Bull. 2003; 129: 674–697. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorris CAW, Wester KL, Jones CT, et al.: School Counselors and Unified Educator–Counselor Identity: A Data-Informed Approach to Suicide Prevention. Prof. Sch. Couns. 2021; 24: 2156759X211011909.\n\nMozumder MK: Validation of Bengali perceived stress scale among LGBT population. BMC Psychiatry. 2017; 17: 314. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNarang P, Sarai SK, Aldrin S, et al.: Suicide Among Transgender and Gender-Nonconforming People. Prim. Care Companion CNS Disord. 2018; 20: 18nr02273.\n\nNassaji H: The importance of using multiple measures or data sources in L2 instructional research. Lang. Teach. Res. 2020; 24: 131–135. Publisher Full Text\n\nNkwuda FCN, Ifeagwazi CM, Nwonyi SK, et al.: Suicidal ideation among undergraduate students: Academic stress and self-esteem as predictive factors. Niger. J. Psychol. Res. 2020; 16.\n\nNunnally JC, Bernstein IH: Psychometric theory. McGraw-Hill; 1994.\n\nProctor CD, Groze VK: Risk factors for suicide among gay, lesbian, and bisexual youths. Soc. Work. 1994; 39: 504–513. Publisher Full Text\n\nRudd MD: The Prevalence of Suicidal Ideation among College Students. Suicide Life Threat. Behav. 1989; 19: 173–183. Publisher Full Text\n\nRussell ST, Fish JN: Mental Health in Lesbian, Gay, Bisexual, and Transgender (LGBT) Youth. Annu. Rev. Clin. Psychol. 2016; 12: 465–487. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRussell ST, Joyner K: Adolescent Sexual Orientation and Suicide Risk: Evidence From a National Study. Am. J. Public Health. 2001; 91: 1276–1281. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSartaj D, et al.: Mental illnesses and related vulnerabilities in the Hijra community: A cross-sectional study from India. Int. J. Soc. Psychiatry. 2021; 67: 290–297. PubMed Abstract \| Publisher Full Text\n\nSha Y, Marley G, Tang W: Need for transgender-specific data from Asia. Lancet HIV. 2021; 8: e318. PubMed Abstract \| Publisher Full Text\n\nSifat RI: The effect of COVID-19 on hijra (third gender) people in Bangladesh. Lancet Psychiatry. 2020; 7: 1015–1016. PubMed Abstract \| Publisher Full Text\n\nThoma BC, et al.: Suicidality Disparities Between Transgender and Cisgender Adolescents. Pediatrics. 2019; 144: e20191183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTopp CW, Østergaard SD, Søndergaard S, et al.: The WHO-5 Well-Being Index: a systematic review of the literature. Psychother. Psychosom. 2015; 84: 167–176. PubMed Abstract \| Publisher Full Text\n\nTourangeau R, Rips L, Rasinski K: The Psychology of Survey Response. Cambridge: Cambridge University Press; 2000. Publisher Full Text\n\nvan Prooijen J-W , van der Kloot WA : Confirmatory Analysis of Exploratively Obtained Factor Structures. Educ. Psychol. Meas. 2001; 61: 777–792. Publisher Full Text\n\nVirupaksha HG, Muralidhar D, Ramakrishna J: Suicide and Suicidal Behavior among Transgender Persons. Indian J. Psychol. Med. 2016; 38: 505–509. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZwickl S, et al.: Factors associated with suicide attempts among Australian transgender adults. BMC Psychiatry. 2021; 21: 81. Publisher Full Text" }	[ { "id": "232669", "date": "22 May 2024", "name": "Danish Suleman", "expertise": [ "Reviewer Expertise My area of expertise include gender studies", "feminism", "transgender studies." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is written in an organised manner. I appreciate the efforts of the authors in preparing this manuscript. The authors used the correct methods and analysis procedures to conduct this study. The analysis and discussion section is also correct. I don't have any corrections to make on this. The are no comments on corrections to be made from my side.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1148
https://f1000research.com/articles/12-1147/v1	13 Sep 23	{ "type": "Study Protocol", "title": "Assessment and comparison of the sensitivity and specificity of sickling and haemoglobin electrophoresis in haemolytic anaemia patients: A study protocol", "authors": [ "Pratiksha Raju Mungale", "Lokesh Singh Chauhan", "Miheer Jagtap", "Lokesh Singh Chauhan", "Miheer Jagtap" ], "abstract": "The present protocol will compare haemoglobin electrophoresis with sickling test, evaluating sensitivity, specificity, positive predicted value and negative predicted value of haemolytic anaemia patients. Haemoglobin electrophoresis is the confirmation test for sickle cell anaemia. Sickle cell anaemia is a type of haemolytic anaemia where red blood cells (RBC)’s biconcave form does not enable the best possible respiratory exchange. In haemolytic anaemia, EDTA is used to examine the peripheral smear stained with Giemsa stain. Peripheral smear shows polychromatic neutrophils, nucleated RBCs (Red blood cell) and fragmented RBCs. In haemolytic anaemia, patients have decreased haemoglobin (Hb) levels. In sickle cell disease (SCD), anaemia is brought about by a change in the DNA sequence of cells in the Hb beta-globin chain. Screening of the sickling test is done by using sodium metabisulfite to assess the shape of cells. Confirmation test of Hb electrophoresis on cellulose acetate paper uses band detection. This study will aim to evaluate the sensitivity and specificity of Hb electrophoresis with the sickling test utilizing quantifiable investigation. The effectiveness of sensitivity and specificity, positive and negative predicted values, and overall course of action for the two techniques, Hb electrophoresis and sickling test, will be collected. This research will also give an overview of existing haemolytic anaemia literature.", "keywords": [ "Hemolytic", "Anemia", "Electrophoresis", "Sickling", "Hemoglobin", "sensitivity", "specificity", "Sickle cell" ], "content": "Introduction\n\nHereditary causes of haemolytic anaemia include defects in haemoglobin (Hb) protein chains, leading to a reduced production rate of one or more of the beta-globin chain of Hb. Almost 200 million people, or 3% of the world’s population, are thought to be affected, in addition to the about 150,000 affected people born per year.1\n\nSickle cell anaemia caused due to mutation of Hb beta chains. These cells transform the typical biconcave disc shape to a crescent, holly wreath, and other forms when the oxygen pressure is reduced. This process is known as sickling.2\n\nThe pathophysiology of sickle cell disease (SCD) depends on haemoglobin sickle (HbS) polymerization, which is caused by a reduced oxygen affinity. The formation of permanently sickle cells results from repeated polymerization and sickling of cells. Haemolytic anaemia is the outcome of this, which accelerates cell death and shortens the lifespan of cells by greater than 75%.3\n\nThe heterogeneous presentation of sickle cell disease has been classified into trait (normal haemoglobin and reticulocytes, unconjugated bilirubin<1 mg/dL), mild (Hb>11 g/dL, reticulocytes 3–6%, unconjugated bilirubin 1–2 mg/dL), moderate (Hb 8–12 g/dL, reticulocytes 6–10%, unconjugated bilirubin>2 mg/dL) and severe (Hb>8 g/dL, reticulocytes>10%, unconjugated bilirubin>3 mg/dL). In such a case, iron deficiency is seen as uncommon, and clinical practice typically avoids prescribing iron supplements to these patients. Worldwide, anaemia due to primarily caused by iron deficiency, particularly in children and adult women.4\n\nIn the reticuloendothelial system, haemolysis may occur intravascularly or extravascularly, or both. Poor deformability, which leads to capture and phagocytosis, antibody-mediated destruction through phagocytosis, or direct complement activation, fragmentation caused by the microthrombi, physical injury, oxidation, or cellular apoptosis are a few mechanisms of haemolysis. Acute anaemia, jaundice, haematuria, dyspnoea, tiredness, tachycardia, and potentially hypotension are all possible symptoms of haemolysis in patients. Laboratory test results indicate haemolysis when reticulocytosis, increased lactate dehydrogenase (LDH), increased unconjugated bilirubin and decreased haptoglobin levels are present.5\n\nYouderian et al. noted that several proteins exist whose amino acid composition is entirely known, whose three-dimensional structure is known or determined by crystallography and for which a significant number of known amino acid substitutions are available for investigation. The vast amount of electrophoretic data currently available from surveys using the same electrophoretic approach may be calibrated using the findings.6\n\nPeripheral blood smear helps diagnose haemolytic anaemia. Peripheral smear cells show polychromatic neutrophils, micro spherocytes, high reticulocyte count, nucleated and fragmented RBC.7 Identifying “subclinical” haemolysis early is crucial since it can progress abruptly and quickly.8 The early effects in haemolytic anaemia patients are protein deficiency and dysfunction of the muscle skeleton of protein is seen in sickling tests.9 In a previous study, the sodium dithionite, sodium metabisulfite and moist seal methods were employed. The tests were repeated on specimens harmful to sickling.10\n\nWhen separating abnormal haemoglobins, cellulose acetate is a particularly good medium for routine use.11 The most prevalent haemolytic disorder includes HbS, foetal haemoglobin (HbF), and sickle cell trait (HbAS) which is not a haemolytic disorder but its carrier forms found via Hb electrophoresis; these are crucial for family counselling, which aims to address physiological support, behavioural and emotional issues associated with the condition.12 Hb electrophoresis is a special technique used to identify certain haemolytic anaemias due to thalassemia syndromes and abnormal structural HbS.13\n\nAli et al.,1 in 2011, conducted a study on Hb electrophoresis to diagnose hemoglobinopathies in hypochromic, microcytic, and sickle cell blood films. The study used Hb electrophoresis to analyse 80 blood samples from patients with suspected hemoglobinopathies. Seven participants (8.8%) had SCD (HbS), eight (10%) had sickle cell minor carrier status (HbAS), and 12 (15%) had sickle cell major (HbF) and thalassaemic significant (HbAF) types, respectively. Type 7 (8.8%) haemoglobin (HbA2) indicates mild thalassemia. However, 22 patients also had Hb electrophoresis results that were normal. Hb gel electrophoresis is an easy and suitable technique with alkaline pH (4.8 to 6.8) for the study of the inherited hemoglobinopathies.\n\nMaroufa et al.,13 in 2002, conducted research on hemoglobinopathies and Hb electrophoresis in Kuwait. The research comprised 2386 Hb electrophoresis tests performed on persons of various ages. The study found that 561 patients had abnormal Hb genes. Patients with haematological and clinical characteristics suggestive of hemoglobinopathies or those with a positive family history should be the only ones eligible for the test.\n\nKohn conducted a study on the HbS separate on cellulose acetate paper. The study applying a continuous current of 0-2 to 3 milli ampere/cm width established a bridge gap of 5 to 6 cm and a potential gradient of 200 to 240 V. Depending on the type of separation needed, the electrophoretic run time ranges from 30 to 90 minutes; for HbF, for example, it takes around 90 minutes. However, exploratory studies using marker HbS are the most effective way to determine the ideal circumstances. On standard laboratory equipment, “high voltage electrophoresis” conditions, such as 100 V/cm, can be easily reached by delivering 300 V over a 3 cm bridge gap. With this method, a completely adequate separation can be attained in eight to 15 minutes. The small opening prevents nearly all overheating, which results in an abundant supply of buffer, a relatively short running period, and these factors. Iterative electrophoresis is used to separate the applied samples until it is successful. The ideal way to monitor the electrophoretic run is to observe the movement of the heterozygous marker haemoglobins, such as AS or AC. The cellulose acetate paper is dried or fixed when the separation is finished, much like with regular protein electrophoresis.11\n\nHaemolytic anaemia often accompanies underlying causes of various hemoglobinopathies. One of India’s main health problems is the prevalence of quantitative and qualitative haemoglobin abnormalities. As a result, it has become a serious public health issue.14\n\nHaemolytic anaemia is characterized by excessive destruction of the RBCs in the central and peripheral circulation. The causes behind the excessive RBC destruction are attributed to either the extrinsic or the intrinsic defects that may be present in the RBC. Of all the screening tests used for screening cases of haemolytic anaemia, a sickling test is the most commonly used. However, this basic screening tests are plagued by a lot of disadvantages which may range from technical to human errors. On the other hand, Hb electrophoresis does not suffer from all these disadvantages and gives accurate results. The routine protocol followed in the diagnosis of haemolytic anaemia is to do a screening test first and then go for a confirmatory test, thus delaying the final diagnosis. The present protocol will aim to employ both these tests for the screening cases of haemolytic anaemia and compare their sensitivity and specificity with each other. Employing a definitive diagnostic test will greatly reduce delay in diagnosing cases of haemolytic anaemia.\n\n\nProtocol\n\n\n\n1. To evaluate the findings on peripheral blood smears that are suspicious for haemolytic anaemia.\n\n2. To screen for haemolytic anaemia by performing a sickling test.\n\n3. To determine the sickling test’s sensitivity, specificity, positive predictive value and negative predictive value.\n\n4. To screen for haemolytic anaemia by performing Hb electrophoresis.\n\n5. To calculate the sensitivity, specificity, and positive and negative predictive values of Hb electrophoresis and sickling test.\n\n6. To compare the sensitivity, specificity, positive and negative predictive values of haemoglobin electrophoresis and sickling test.\n\nStudy design\n\nThis will be a cross-sectional study.\n\nStudy settings\n\nThe following study is a cross-sectional investigative study that will be conducted in the haematology division of the Department of Pathology, Jawaharlal Nehru Medical College (JNMC), Sawangi (Meghe), Wardha, in collaboration with the Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi (Meghe), Wardha, from 2023. This investigation will take place after Institutional Ethics Committee approves it and the patients give their written consent. A total sample size of 80 blood specimens will be collected in EDTA (ethylenediaminetetra acetic acid) tubes and collected in phlebotomy section.\n\nMaterials\n\nThe following two methods will be used for this study.\n\nThe sickling test will be performed by inducing deoxygenation of the blood samples and observing the shape of the red blood cells under a microscope.15 The presence of sickle cells will be noted.\n\nThe steps for performing the sickling test are as follows:\n\nA small sample of blood will be collected from the patient’s fingertip or, in some cases, from a vein using a syringe. Clean and dry test tubes will be selected for the test. The tube should be free of any moisture, as water can interfere with the test results. A drop of blood will be placed on a glass slide or a clean, dry surface. Then, using a pipette or a capillary tube, a small amount of sodium metabisulfite solution will be added to the blood. The mixture will be gently stirred to ensure thorough mixing. After mixing, the sample will be allowed to stand undisturbed for a few minutes. During this time, the normal red blood cells will retain their round shape, while any red blood cells containing sickle hemoglobin will undergo a characteristic change in shape. The sickle cells will form a crescent or sickle-like shape, which gives the test its name. The test results will be observed under a microscope or by visual inspection. If the blood contains a significant number of sickle cells, it indicates the presence of sickle cell disease or sickle cell trait (heterozygous carrier of the sickle cell gene). If there are no sickle cells or only a small number present, the test is considered negative.\n\nSamples for Hb electrophoresis:\n\nHemolysate will be prepared from blood in EDTA citrate.\n\nFresh or refrigerated samples will be used.\n\nBuffer tank, cellulose acetate paper, micropipette or capillary.\n\nCellulose acetate strips will be soaked in a buffer solution, usually a Tris-glycine buffer, to prepare them for electrophoresis. This buffer establishes the pH and ionic conditions necessary for proper protein separation.\n\nA few microliters of the patient’s plasma or a hemolysate (RBC disrupted to release their contents) will be applied to the cellulose acetate strip near one end. Care will be taken to ensure that the sample is evenly distributed and doesn’t overlap.\n\nThe prepared cellulose acetate strip will be placed in an electrophoresis chamber, with the end containing the sample placed closer to the negative electrode. An electric current will be applied across the cellulose acetate paper, causing the charged haemoglobin molecules to migrate through the report based on their charge and size. As the electric current is applied, the different types of haemoglobin move at different rates and separate from each other along the length of the strip.\n\nSubjects of both sexes aged 5-45 will be included.\n\nFor minor/underage participants written informed consent will be taken.\n\nCases undergoing treatment for haemolytic anaemia, such as autoimmune management or splenectomy, along with supportive treatments like blood transfusions or iron supplementation.\n\nSubjects under the category of vulnerable personnel, patients in emergency conditions, ethnic minority groups, homeless people, nomads and refugees will be excluded.\n\nAll necessary measures to control bias at all levels will be taken. As it is an observational study, all the samples which are routinely received in the section of haematology will be taken into consideration for comparison between the Hb electrophoresis technique analogous to the routine sickling test. Institutional supply of EDTA samples and chemical constituents present in a buffer from different companies make minor modifications, an essential part of Hb electrophoresis protocol. Diagnostic search influences the finding of electrophoresis sickling band, i.e. the influence of content of result captions in response to a diagnosis of samples.\n\nCochran formula for sample size estimate\n\nFormula for determining sample size:\n\nX2 = the table value of chi square for 1 degree of freedom at the desired confidence level (3.841)\n\nPrevalence of disease (Prev) = 0.5\n\nEstimation error (d) = 0.5\n\nN = Total patient with haemolytic anemia = 100\n\nFormula reference: Krejcie and Morgan (1970).16\n\nStatistical analysis will be done by descriptive and inferential statistics using Chi square test, students’ unpaired t-test, regression analysis, one way analysis of variance (ANOVA) and multiple comparison Tukey test. The software used in the statistical analysis will be SPSS 27.0 version, Graph Pad Prism 6.0 and EPI INFO version 6.0.\n\nThe results will be published in an indexed journal.\n\nThe study is set to start in September 2023.\n\n\nResults\n\nAppropriate results will be obtained after the sensitivity, specificity, positive predictive value and negative predictive value of sickling test and haemoglobin electrophoresis are compared.\n\n\nDiscussion\n\nHaemolytic anaemia is the premature destruction of RBC while paroxysmal nocturnal haemoglobinuria (PNH) is chronic and life threatening. Most cases take place in less developed countries where there are no reliable testing campaigns available. Some of the risk factors include acquired immunodeficiency syndrome, acute anaemia, jaundice, hematuria, dyspnea, tiredness, tachycardia, and potentially hypotension. Physical examination of blood count and peripheral blood analyses will be carried out in all cases. Haemoglobin electrophoresis is a confirmative test of haemolytic anaemia and has higher sensitivity and specificity than screening test for sickling. According to the outcomes of randomized clinical research, blood transfusion and nutrition (calories, total fat, saturated fat, trans fat, cholesterol, sodium (salt), total carbohydrate) are considered standard care for haemolytic anaemia patients.\n\nIn 2020, Bee et al. researched iron deficiency anaemia, and found abnormal haemoglobin disorder was the most common cause of microcytic hypochromic anaemia. It is possible to make a differentiating diagnosis with a full hemogram and a peripheral smear. Still, other tests, such as a serum iron profile and Hb electrophoresis, are necessary to make the diagnosis. The structural and functional abnormalities of Hb, or hemoglobinopathies, are a significant global health issue. Thalassemia and sickle cell anaemia are examples of these single-gene, autosomal, recessive monogenic illnesses. Microcytic hypochromic anaemia is a symptom of hemoglobinopathies. Hemoglobinopathies, which do not require iron, are often misdiagnosed and treated as iron deficiency anaemia. The body becomes poisonous when exposed to excess iron that is not needed. Microcytic hypochromic anaemia can be divided into various subtypes using electrophoresis. Correct diagnosis is made with the aid of electrophoresis.17\n\nIn 2006, Huang et al. undertook research T-antigen activation to predict haemolytic anaemia and pneumococcus-induced haemolytic uremic syndrome. The outcome for positive TA initiation for P-HA was 57% explicit and 86% sensitive. Overall, 76% of expectations were exact. There was no intergroup struggle contrast in the pneumococcal serotype 14 that causes P-HUS most often (5/10) and is sensitive to anti-microbial. A total of 13 of the 36 patients needed packed RBC transfusions, three passed away, and two needed extracorporeal membrane oxygenation. Three of the patients also required transfusions. None experienced long-haul kidney impacts.18\n\nIn 2019, Garden observed the value of immune-mediated haemolytic anaemia diagnostic tests. The study compared saline and coombs test, which can be utilised to help to determine immune mediated haemolytic anaemia when examined.19\n\nIn 2016, Englum et al.’s results suggested that total splenectomy may require more serious consideration in children with the most severe haemolytic diseases. Future studies must look at these results in the context of the clinical advantages for children with various conditions. A total of 130 children were included in the analysis, and 81 of them (62.3%) had total splenectomy. All hematologic measurements in children with HS improved following TS, including an increase in Hb of 4.1 g/dl. Although the reaction was less strong, hematologic indicators similarly improved after peripheral smear (haemoglobin increase of 2.4 g/dL, p 0.001). In children with SCD, Hb levels were unchanged. Laparoscopy did not affect hematologic outcomes when compared to open surgery. Shorter lengths of stay were associated with total splenectomy and laparoscopy.20\n\nIn 2015, Sipol et al. conducted a study on the correlation among iterative labs for the distinguishing proof of paroxysmal nocturnal haemoglobinuria (PNH) copies utilizing high-responsiveness bloom cytometry in a Russian cohort. Seven PNH patients, five of whom were female and two of whom were male, had their copy sizes measured. Mean patient age was 37 years); three patients (one with aplastic weakness and two without it) had extreme haemolytic PNH and high plasma lactate dehydrogenase. Five of the patients had a history of aplastic frailty. PNH copy sizes at discovery ranged from 0.41 to 9.7% of granulocytes in patients with milder side effects, to 58 to almost 100% in patients with severe side effects. There were only negligible contrasts in the subsequent copy size estimation for every patient between the six research centres, especially in those with high qualities at determination.21\n\nInter-observer and intra-observer flexibility. Hb electrophoresis can detect and identify common abnormal haemoglobin variants such as HbS. Hb electrophoresis and sickling tests may produce false negative results in certain situations. In some cases, these tests can generate false positive results. This study can occur when certain conditions or factors, such as dehydration, fever, or recent blood transfusions, cause temporary changes in the shape of red blood cells and mimic the appearance of sickle cells. Hb electrophoresis and sickling tests focus on detecting abnormal Hb variants. While these tests are effective in detecting abnormal haemoglobin variants, they may not be suitable for assessing other aspects of sickle cell disease or thalassemia.\n\nHaemoglobin electrophoresis can identify different types of haemoglobin variants, aiding in the diagnosis of various haemoglobinopathies. Detection of sickling in the electrophoresis pattern suggests the presence of sickle cell disease or sickle cell trait, which can have significant clinical implications, but further confirmatory tests and clinical context are essential for accurate diagnosis and appropriate management.\n\nA review of literature revealed Hb electrophoresis generally exhibits higher sensitivity and specificity compared to the sickling method for diagnosing hemoglobin disorders in the general population.\n\nThis protocol was approved by the Institutional Ethics Committee of the Datta Meghe Institute of Higher Education and Research, Sawangi (M) Wardha, 4420001 Maharashtra, India (approval number DMIHER (DU)/IEC/2022/1206, dated 08/07/2022).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAli TH, Alamiry AA, Majeed MN: Detection of hemoglobinopathies in hypochromic, microcytic, and sickened cell blood films by haemoglobin electrophoresis. University of Thi-Qar Journal of Medicine. 2011; 5(1): 139–148.\n\nPauling L, Itano HA, Singer SJ, et al.: Sickle cell anaemia a molecular disease. Science. 1949 Nov 25; 110(2865): 543–548. Publisher Full Text\n\nArishi WA, Alhadrami HA, Zourob M: Techniques for the detection of sickle cell disease: a review. Micromachines. 2021 May 5; 12(5): 519. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKassim A, Thabet S, Al Kabban M, et al.: Iron deficiency in Yemeni patients with sickle-cell disease. East Mediterr. Health J. 2012; 18(3): 241–245. PubMed Abstract \| Publisher Full Text\n\nPhillips J, Henderson AC: HaemolyticAnaemia: evaluation and differential diagnosis. Am. Fam. Physician. 2018 Sep 15; 98(6): 354–361.\n\nMaloy S, Youderian P: Genetic analysis of DNA-protein interactions in vivo. Am. Biotechnol. Lab. 1996 Jan 1; 14: 14–18.\n\nEder AF: Acute Donath-Landsteiner haemolytic anaemia. Immunohematology. 2005 Jan 1; 21(2): 56–62. PubMed Abstract \| Publisher Full Text\n\nJacobs JW, Bastarache L, Thompson MA: Laboratory predictors of haemolyticAnaemia in patients with systemic loxoscelism. Am. J. Clin. Pathol. 2022 Apr; 157(4): 566–572. PubMed Abstract \| Publisher Full Text\n\nRavindranath Y, Johnson RM: Altered spectrin association and membrane fragility without abnormal spectrin heat sensitivity in a case of congenital haemolyticAnaemia. Am. J. Hematol. 1985 Sep; 20(1): 53–65. Publisher Full Text\n\nItano HA: A third is an abnormal haemoglobin associated with hereditary haemolyticAnaemia. Proc. Natl. Acad. Sci. 1951 Dec; 37(12): 775–784. Publisher Full Text\n\nKohn J: Separation of haemoglobins on cellulose acetate. J. Clin. Pathol. 1969 Jan; 22(1): 109–111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFredrick O, Mwanda W: Assessment of a Rapid Diagnostic Tool for Sickle Cell Hemoglobin S. Elixir Haematology. 2018; 116: 50095–50098.\n\nMarouf R, D’souza TM, Adekile AD: Haemoglobin electrophoresis and hemoglobinopathies in Kuwait. Med. Princ. Pract. 2002; 11(1): 38–41. PubMed Abstract \| Publisher Full Text\n\nKharche K, Bhake A: Hemoglobin Variants in Patients With Microcytic Hypochromic Anemia: A Review of Indian Studies. Cureus. 2023 Apr 30; 15(4). Publisher Full Text\n\nPauling L, Itano HA, Singer SJ, et al.: Sickle cell anemia, a molecular disease. Science. 1949 Nov 25; 110(2865): 543–548. Publisher Full Text\n\nKrejcie RV, Morgan DW: Determining sample size for research activities. Educ. Psychol. Meas. 1970 Sep; 30(3): 607–610. Publisher Full Text\n\nBee R, Srivastav AK: TO DETECT HEMOGLOBINOPATHIES BY DOING HEMOGLOBIN ELECTROPHORESIS IN MICROCYTIC HYPOCHROMIC ANAEMIA. Eur. J. Mol. Clin. Med. 2021; 7(09): 2020.\n\nHuang DT, Chi H, Lee HC, et al.: T-antigen activation for prediction of pneumococcus-induced haemolytic uremic syndrome and haemolyticAnaemia. Pediatr. Infect. Dis. J. 2006 Jul 1; 25(7): 608–610. PubMed Abstract \| Publisher Full Text\n\nGarden OA, Kidd L, Mexas AM, et al.: ACVIM consensus statement on the diagnosis of immune-mediated haemolyticAnaemia in dogs and cats. J. Vet. Intern. Med. 2019 Mar; 33(2): 313–334. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEnglum BR, Rothman J, Leonard S, et al.: Hematologic outcomes after total splenectomy and partial splenectomy for congenital haemolyticAnaemia. J. Pediatr. Surg. 2016 Jan 1; 51(1): 122–127. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSipol AA, Babenko EV, Borisov VI, et al.: An inter-laboratory comparison of PNH clone detection by high-sensitivity flow cytometry in a Russian cohort. Haematology. 2015 Jan 1; 20(1): 31–38. PubMed Abstract \| Publisher Full Text" }	[ { "id": "248773", "date": "23 Feb 2024", "name": "Asaad Mohammed Ahmed Babker", "expertise": [ "Reviewer Expertise Hematologic DiseasesClinical studies of hemostasis problems associated with recurrent pregnancy loss.Blood transfusion and immunohematology.Identification of hematological cells using image processing techniques." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Author's\n\nI have carefully reviewed your paper titled \"Assessment and comparison of the sensitivity and specificity of sickling and hemoglobin electrophoresis in hemolytic anemia patients: A study protocol\" and appreciate the effort and thought you've put into this work. The limitation part could be improved to enhance its quality and impact of the paper. I hope the following suggestions and feedback will be useful for you: - The sickling and hemoglobin electrophoresis tests, while valuable, also have limitations. Some of these limitations which you do not mention in your paper like: 1- The reliability of the sickling test and Hb Electrophoresis method may vary with the age of the individual being tested. 2- The accuracy of both methods is highly dependent on the technical expertise of the personnel performing the tests. 3- Improper sample collection, preparation, or interpretation can lead to inaccurate results. 4- Distinguishing between sickle cell trait (SCT) and SCD is essential, as individuals with SCT are carriers of the gene but typically do not experience symptoms or complications. Both screening methods may not always differentiate between SCT and SCD. 5- Additionally, these tests may not always detect minor hemoglobin variants or may be affected by external factors such as recent blood transfusions. -It's important to consider these limitations when interpreting the results of these tests.\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": "263854", "date": "14 May 2024", "name": "Ran An", "expertise": [ "Reviewer Expertise Sickle cell disease", "electrophoresis", "point of care testing" ], "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, Electrophoresis has been used as a standard for SCD testing. There are standard operation protocols for both laboratory based electrophoresis and point of care electrophoresis for SCD tests.\nThis is a poorly written manuscript. The authors did not clarify the relationship between sickle cell disease and anemia. While the intention of this manuscript is for testing sickle cell disease, it talked too much about anemia, which has nothing to do with their study design.\n\nBesides the content, the language and the manuscript structure are also poorly organized.\n\nFurthermore, there is also lack of key information. For example, what data analysis tool will be implemented?\nOverall, I would suggest the authors to resubmit this manuscript when they complete their study.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1147
https://f1000research.com/articles/11-878/v1	02 Aug 22	{ "type": "Research Article", "title": "The effect of coffee on contralateral suppression of transient evoked otoacoustic emissions", "authors": [ "Ishaan Srivastava", "Mohan Kumar Kalaiah", "Ritik Roushan", "Usha Shastri", "Kaushlendra Kumar", "Ishaan Srivastava", "Ritik Roushan", "Usha Shastri", "Kaushlendra Kumar" ], "abstract": "Background: Coffee is a popular non-alcoholic beverage consumed by humans across the world. It contains caffeine, which is a type of stimulant of the central nervous system. In the auditory system, it has a positive effect on auditory brainstem response and perception of speech in noise. Further, caffeine has an inhibitory effect in the cochlea, but studies have rarely investigated its effect on otoacoustic emissions (OAEs) in humans. OAEs are low-intensity sounds produced by the cochlea, which could be recorded in the ear canal. The present study was carried out to investigate the effect of coffee on transient evoked otoacoustic emission (TEOAE) and contralateral suppression of TEOAE. Method: A total of 52 young adults participated in the study. A cross-over study design was used for the present investigation. The TEOAE and contralateral suppression of TEOAE were recorded before and after consumption of coffee and milk. The contralateral suppression of TEOAE was measured by presenting white noise to the contralateral ear at 40, 50, and 60 dB sound pressure level (SPL). Results: The mean amplitude of TEOAE before and after consumption of coffee was similar in both ears. Further, the mean contralateral suppression of TEOAE was slightly larger after consumption of coffee in both ears. However, the mean difference was not significant in both the ears. Conclusions: Based on the findings of present study, coffee has no significant effect on the amplitude of TEOAE and contralateral suppression of TEOAE.", "keywords": [ "Otoacoustic emissions", "TEOAE", "Contralateral suppression", "Coffee", "Caffeine" ], "content": "Introduction\n\nCoffee is a non-alcoholic beverage which is widely consumed by humans across the world.1–3 It contains a variety of bioactive chemicals that have anti-oxidant, anti-inflammatory, and anti-cancer properties.1 It also contains caffeine which is a stimulating agent. Caffeine is also found in various other food items such as tea, cocoa beans, chocolate, energy drinks, among others.1,2 Further, the amount of caffeine in any food product is determined by the serving size, product type, and preparation method.4 Caffeine improves perception, increases the abilty to remain awake for longer periods, and reduces fatigue.5 The stimulatory effect of caffeine is due to the blocking of adenosine receptors, consequently regulating the neurotransmitter levels and activities in the central nervous system.3\n\nOtoacoustic emissions (OAEs) are very small amplitude sounds produced by the cochlea as a by-product of motile function of the outer hair cells (OHCs) (i.e. amplifier function of OHCs).6,7 The OAEs generated in the cochlea travel backwards through the middle ear to the external ear canal, and it can be recorded using a sensitive microphone from the external ear canal.6–8 In the cochlea, the OAEs are produced spontaneously and also in response to an external acoustic stimuli, referred as spontaneous OAEs and evoked OAEs respectively. Further, the OAEs elicited in response to short-duration stimuli such as clicks and tone-bursts are known as transient evoked OAEs (TEOAEs).8 The OAEs elicited in response to pure-tones are known as distortion product OAEs (DPOAEs) and stimulus frequency OAEs (SFOAEs).\n\nThe human auditory system comprises afferent and efferent auditory pathways. The efferent pathways have an inhibitory function in the auditory system. In the cochlea, the efferent fibres cause hyperpolarization of OHCs, subsequently reducing their motile function.9 The reduced motility of OHCs in the presence of efferent activity result in a reduction of the amplitude of OAEs.10 This reduction in the amplitude of OAE due to efferent activity is called suppression of OAE. In humans, the suppression of OAE can be measured by presenting noise to the test ear or non-test ear during the recording of OAEs. The suppression of OAE obtained by presenting noise to the non-test ear is known as the contralateral suppression of OAE.\n\nSeveral studies have investigated the effect of caffeine on the auditory system. Studies have been carried out to understand the effect of caffeine on auditory evoked potentials,11–20 speech perception,21,22 and otoacoustic emissions.23 Few studies have investigated the effect of caffeine on the auditory brainstem response (ABR). Findings from these investigations have showed significantly shorter latency and larger amplitude for ABR peaks following caffeine ingestion.11,12,16 Similarly, caffeine has been found to have an effect on the middle latency response and late latency response.12 In general, findings of the above studies suggest a positive effect of caffeine on the central auditory pathway. Very few studies have investigated the effect of caffeine on speech perception ability.21,22 Altin et al.21 investigated the effect of caffeine on speech identification score in noise. Results showed a significant improvement for speech identification score in noise after caffeine ingestion. Taghavi et al.22 investigated the short-term effect of caffeine on the acceptable noise level (ANL) in individuals with normal hearing. The results showed a significant reduction in the ANL after caffeine intake, suggesting that caffeine increases tolerance to noise, improving speech perception in noise. Based on findings from the above investigations, caffeine could be assumed to have a positive effect on the perception of speech in noise.\n\nStudies investigating the effect of caffeine on the OAEs in humans are scarce. Various studies investigating the effect of caffeine on the cochlea have reported, the caffeine causes hyperpolarization of OHCs in the cochlea which suppress the amplifier function of OHCs.24–26 Therefore, caffeine could be assumed to have a negative effect on the amplitude of OAEs. Recently, Drepath et al.23 reported no significant effect of coffee on the amplitude of DPOAE. In contrast, Bobbin27 reported an effect of caffeine on the amplitude of DPOAE in animal study. Therefore, although Drepath et al. 23 reported no effect of coffee on the amplitude of OAE in humans; similar investigations should be conducted before generalizing the results. Thus, the first objective of the present study was to investigate the effect of coffee on the amplitude of TEOAE. The second objective of the present study was to investigate the effect of coffee on the contralateral suppression of TEOAE, to understand the effect of caffeine on efferent activity in the auditory system. Studies investigating the effect of caffeine on the ABR have reported an improved transmission of neural activity in the auditory pathway. This improved transmission in the afferent pathways could also elicit stronger activity in the efferent pathways. However, none of the studies have investigated the effect of caffeine of the efferent activity. Further, studies investigating the effect of caffeine on the speech perception have reported a positive effect of caffeine on perception of speech in noise. The improvement in speech perception after caffeine ingestion could be a consequence of increased efferent activity in the auditory system. Studies investigating the role of efferent activity on perception of speech in noise have reported a significant relationship between the magnitude of efferent activity and speech perception in noise.28 Therefore, there is a need to understand the effect of caffeine on the efferent activity.\n\n\nMethod\n\nA total of 52 adults (nine males, 43 females) aged between 19 and 24 years (mean=21.65, standard deviation (SD)=1.36) participated in the study. All participants had hearing sensitivity within normal limits in both ears. The pure-tone threshold was less than 15 dB HL at octave frequencies from 250 Hz to 8000 Hz. Immittance evaluation showed ‘A’ type tympanogram with acoustic reflex present at normal levels in both ears. None of the participants had a history of otological problems, such as ear pain, ear discharge etc. None of the participants reported exposure to loud sounds or ototoxic medication. Individuals who agreed to participate in the study were randomly assigned into two groups (coffee-first group and milk-first group) using drawing lots method. The acoustic reflex threshold for white noise was greater than 70 dB SPL for all the participants. The study was approved by the institutional ethics committee of Kasturba Medical College, Mangalore (Protocol number: IEC KMC MLR 03-2021/89) and informed consent was obtained from all the participants.\n\nIndividuals who agreed to participate in the study were randomly assigned into two groups, namely the ‘coffee-first’ and ‘milk-first’ groups. The drawing lots method was used to assign the participants into two groups. The data collection was carried out in two phases. In phase I, the TEOAE and contralateral suppression of TEOAE were recorded before and after consumption of coffee (coffee-first group) or milk (milk-first group). In phase II, the TEOAE and contralateral suppression of TEOAE were recorded before and after consumption of milk (coffee-first group) or coffee (milk-first group). Phase II of the study was carried out after a gap of one week. Further, participants were informed to restrain from consuming caffeinated substances such as coffee, tea, energy drinks, or chocolate. for at least 12 hours prior to data collection. The procedure followed for data collection is shown in Figure 1.\n\nRecording of TEOAEs\n\nThe TEOAEs were recorded using the Otodynamics Echoport 292II otoacoustic emission analyzer. During the recording of TEOAEs, participants were made to sit comfortably on the reclining chair. They were instructed not to move throughout the duration of recording of TEOAEs. The OAE probe was fitted to the test ear and E-A-RTone 5A insert phone was fitted to the contralateral ear of participants. Initially, the TEOAE was recorded in non-linear mode. A total of 260 click-trains (1040 clicks) were presented at 80 dB SPL, and the responses were averaged. Following this, the TEOAEs were recorded in linear-mode. A total of four recordings were obtained with and without presenting noise to the contralateral ear of participants. In each recording, a total of 400 click-trains (1600 clicks) were presented at 60 dB SPL and the responses were averaged. The first recording of TEOAE was always obtained without presenting noise to the contralateral ear, and referred to as baseline TEOAE. The remaining three recordings were obtained by presenting white noise to the contralateral ear of participants at 60 dB SPL, 50 dB SPL, and 40 dB SPL. The order of noise level presented to the contralateral ear was randomized. All the recordings of TEOAE were obtained without disturbing the placement of OAE probe (i.e., single-fit condition). Further, the TEOAEs were recorded from both ears of the participants.\n\nThe TEOAEs were recorded in four sessions. The first two sessions were scheduled on day 1 and the remaining two sessions were scheduled after one week. In the first session, the TEOAEs were recorded in non-linear and linear modes and these recordings were referred to as ‘baseline measurements’. After completing the baseline measurements, coffee was given to participants in the ‘coffee-first’ group and milk was given to participants in the ‘milk-first’ group. After one hour, the second session of TEOAE recording was initiated. The TEOAEs obtained in the second session were similar to the first session and were referred as ‘follow-up measurements’. After one week, the baseline (session 3) and follow-up (session 4) measurements were repeated. After the third session milk was given to participants in the ‘coffee-first’ group and coffee was given to participants in the ‘milk-first’ group.\n\nCoffee preparation\n\nOne sachet of instant coffee powder (1.3 g – 70% coffee and 30% chicory) and two tablespoons of powdered milk were mixed in 150 mL of warm water and sugar was added to improve the flavour for each serving. Milk was prepared similarly without adding the coffee powder.\n\nThe global amplitude of TEOAE and noise-floor level was computed using EchoMaster software.29 The TEOAEs recorded in non-linear mode were considered to be present if the global signal-to-noise ratio (SNR) was at least 6 dB SNR. Further, the TEOAEs recorded in linear mode were considered to be present if the global SNR was at least 3 dB SNR. The magnitude of contralateral suppression of TEOAE was calculated by subtracting the global amplitude of TEOAE in various contralateral noise conditions (i.e., 60, 50 and 40 dB SPL) from the baseline condition.\n\n\nResults\n\nFigure 2 shows the mean global amplitude of TEOAE (recorded in non-linear mode at 80 dB SPL) for both ears before and after consumption of coffee and milk. The mean amplitudes were similar for both ears across the conditions (i.e., before and after consumption of coffee and milk). The Shapiro-Wilk test revealed that the amplitude of TEOAE of both ears across conditions was normally distributed. Thus, a repeated-measures ANOVA was carried out with ears (right and left), conditions (before and after consumption), and drink (coffee and milk) as repeated measures. Results showed no significant effect of ear [F(1,42)=0.505, p=0.481], condition [F(1,42)=0.162, p=0.689], and drink [F(1,42)=0.644, p=0.427] on the amplitude of TEOAE. Further, no significant interaction was found between ears and conditions [F(1,42)=2.016, p=0.163], drink and conditions [F(1,42)=0.644, p=0.427], ears and drink [F(1,42)=0.09, p=0.765], and ears, drink, and conditions [F(1,42)=0.135, p=0.751]. Bayesian repeated measures-ANOVA showed moderate evidence in favour of the null hypothesis for the effect of conditions [BF10=0.127] and drink [BF10= 0.156] on the amplitude of TEOAEs. Further, it showed anecdotal evidence in favour of the null hypothesis for the effect of ears [BF10=0.366] on the amplitude of TEOAE, which suggests more data need to be collected to draw a firm conclusion (Dienes, 2014).\n\nFigure 3 shows the mean global amplitude of TEOAE (recorded in linear mode at 60 dB SPL) for both ears before and after consumption of coffee and milk. The mean amplitude of TEOAE was larger in the right ear across the conditions (i.e., before and after consumption of coffee and milk). Further, the mean amplitudes of TEOAE before and after consumption of coffee or milk were similar for both ears. The Shapiro-Wilk test revealed that the amplitude of TEOAE of both ears across conditions was normally distributed. Repeated-measures ANOVA was carried out with ears (right and left), conditions (before and after consumption), and drink (coffee and milk) as repeated measures. Results showed no significant effect of ear [F(1,46)=2.851, p=0.1], condition [F(1,46)=0.604, p=0.441], and drink [F(1,46)=0.288, p=0.594] on the amplitude of TEOAE. Further, no significant interaction was found between ears and conditions [F(1,46)=1.267, p=0.266], drink and conditions [F(1,46)=0.752, p=0.39], ears and drink [F(1,46)=0.959, p=0.333], and ears, drink, and conditions [F(1,46)=0.146, p=0.704]. Bayesian repeated measures ANOVA showed extreme evidence in favour of the null hypothesis for the effect of conditions [BF10=0.002] and drink [BF10= 0.002] on the amplitude of TEOAEs. Further, it showed anecdotal evidence for the effect of ears [BF10=1] on the amplitude of TEOAE which suggests more data need to be collected to draw a firm conclusion (Dienes, 2014).\n\nFigures 4 and 5 show the mean contralateral suppression of TEOAE for both ears across the levels of noise before and after consumption of coffee and milk. Panel A and panel B of Figure 4 show the mean contralateral suppression of TEOAE across noise levels for baseline measurement. The mean contralateral suppression was slightly lower in the left ear compared to the right ear. Further, the mean contralateral suppression of TEOAE decreased with the reduction in the level of noise in the contralateral ear. Panels C and D of Figure 4 show the mean contralateral suppression of TEOAE before and after consumption of coffee and milk respectively for both ears. The results for the same are depicted in Figure 5 for better visualization. The mean contralateral suppression before and after consumption of milk was similar at each level of noise for both ears. In contrast, a slightly greater suppression was noted after consumption of coffee at each level of noise for both ears, except for the right ear at 40 dB noise.\n\nPanel A shows the mean contralateral suppression of TEOAE for both ears before consumption of coffee. Panel B shows the mean contralateral suppression of TEOAE for both ears before consumption of milk. Panel C shows the mean contralateral suppression of TEOAE for both ears before and after consumption of coffee. Panel D shows the mean contralateral suppression of TEOAE for both ears before and after consumption of milk.\n\nThe Shapiro-Wilk test revealed that the magnitude of contralateral suppression of TEOAE across conditions and levels of noise for both ears were not normally distributed. To investigate the effect of conditions (before and after consumption) and drink (coffee and milk) on the contralateral suppression of TEOAE, the Friedman test was carried out separately for each levels of noise (60 dB, 50 dB, and 40 dB) and ears (right and left). Results showed no significant difference for the magnitude of contralateral suppression of TEOAE before and after consumption of coffee and milk at each level of noise for right ear [60 dB (χ2(3)=4.021, p=0.259); 50 dB (χ2(3)=3.194, p=0.363); and 40 dB (χ2(3)=0.734, p=0.865)] and left ear [60 dB (χ2(3)=3.952, p=0.267); 50 dB (χ2(3)=1.54, p=0.673); and 40 dB (χ2(3)=4.625, p=0.201)]. Further, to investigate the effect of noise level on the contralateral suppression of TEOAE, the data obtained before consumption of coffee was subjected to the Friedman test separately for both ears. Results showed a significant effect of noise level on the contralateral suppression of TEOAE for both ears [right ear (χ2(2)=39.542, p<0.001); left ear (χ2(2)=39.872, p<0.001)]. Pairwise comparison using Wilcoxon signed ranks test showed the contralateral suppression of TEOAE was significantly different between noise levels 60 dB and 50 dB [right ear (Z=4.723, p<0.001); lef ear (Z=4.482, p<0.001)], 60 dB and 40 dB [right ear (Z=4.723, p<0.001); lef ear (Z=4.54, p<0.001)], and 50 dB and 40 dB [right ear (Z=3.377, p=0.001); left ear (Z=3.549, p<0.001)]. In addition, to investigate the effect of ear on the contralateral suppression of TEOAE, the data obtained before consumption of coffee were subjected to the Wilcoxon signed ranks test. It showed the contralateral suppression of TEOAE was not significantly different between ears at each level of noise [60 dB (Z=1.208, p=0.227); 50 dB (Z=0.688, p=0.492); 40 dB (Z=0.215, p=0.829)].\n\n\nDiscussion\n\nResults of the present study showed no significant effect of coffee on the amplitude of TEOAE. This finding is consistent with those of Drepath et al.23 which showed no effect of coffee on the amplitude of DPOAEs in humans. These findings suggests no effect of caffeine on the amplitude of OAEs in humans. But, in contrast to the findings of human studies, animal studies have reported an effect of caffeine on the amplitude of DPOAEs. Bobbin27 reported a stimulus level-dependent effect of caffeine on the amplitude of DPOAE. The amplitude of DPOAE was found to be reduced when elicited with lower-intensity stimuli and the amplitude was increased when elicited with higher-intensity stimuli. In addition, Bobbin27 also investigated the effect of caffeine on the compound action potentials (CAP), summating potential (SP), cochlear microphonics (CM) and latency of N1. The caffeine had a suppressive effect on the CAP, SP, and latency of N1. Bobbin27 attributed the reduction in the amplitude of DPOAE at low intensity to diminished amplifier function of OHCs in the cochlea, which is a consequence of caffeine. In the cochlea, caffeine causes activation of Ca2+-dependent K+ channels in the OHCs, which leads to hyperpolarization of the OHCs and subsequently suppresses the amplifier function of OHCs.24–26,30,31 Recently, Castellano-Muñoz et al.32 investigated the effect of caffeine on the electrical properties of OHCs and postsynaptic activity in auditory fibers. Results showed caffeine had no effect on the electrical properties of OHCs, but it had an effect on the postsynaptic activity in auditory fibers. The findings of the above study suggest that functioning of the OHCs may not be affected by caffeine, and thus the amplitude of OAE could be similar before and after consumption of caffeine.\n\nThe present study also investigated the effect of coffee on the contralateral suppression of TEOAE. The contralateral suppression of TEOAE was measured by presenting white noise to the contralateral ear at 40, 50, and 60 dB SPL. Results showed an increase in the magnitude of contralateral suppression of TEOAE with an increase in the level of noise in the contralateral ear. These findings are consistent with results of several investigations.33–36 The increase in contralateral suppression of TEOAE with noise level has been attributed to the strength of efferent activity. Further, results of the present study showed a slightly greater contralateral suppression after coffee consumption; however, the difference was not significant. As studies investigating the effect of caffeine on the contralateral suppression of TEOAE are not available in the literature, the results of the present study cannot be compared with other investigations. Further, although findings of the present study showed no significant effect of coffee or caffeine on the contralateral suppression of TEOAE, similar studies are essential before generalizing the findings.\n\nBased on the findings of the present study, we understand that consuming coffee before an audiological evaluation has no significant effect on the amplitude of TEOAE and contralateral suppression of TEOAE. However, there are few limitations to the present study. In the literature, studies investigating the effect of caffeine on the ABR have shown a dose-dependent effect of caffeine on the peaks of ABR.16 A similar a dose dependent effect of caffeine could be present on the amplitude of TEOAE and contralateral suppression of TEOAE. However, in the present study a fixed amount of coffee was provided to participants, thus currently it is not understood whether increasing the dose of caffeine would have any effect on the amplitude of TEOAE and contralateral suppression of TEOAEs. Further, the amount of caffeine present in coffee is dependent on the type of coffee (i.e., brewed, instant, or decaffeinated).37,38 In the present study instant coffee was given to participants, which contains lower amount of caffeine compared to brewed coffee. Therefore, if coffee has a dose-dependent effects of caffeine on the TEOAE and contralateral suppression of TEOAE, then findings of the present study cannot be generalized to all types of coffee.\n\nTo conclude, findings of the present study showed no effect of coffee on the findings of TEOAE. The procedure used for recording the non-linear TEOAE in the present research was similar to the protocol used in clinics for routine evaluation. Thus, based on findings of the present study, we understand that consuming coffee before an audiological evaluation may not have negative effects on the amplitude of TEOAE.\n\n\nData availability\n\nMendeley Data: The effect of coffee on TEOAE and contralateral suppression of TEOAE, https://doi.org/10.17632/p4pgd57zgd.139\n\nThis project contains the following underlying data:\n\n- CSTEOAE_linear.csv (contains data of contralateral suppression of TEOAE)\n\n- Read Me.txt (description to understand the variables in data files)\n\n- TEOAE_linear.csv (contains data of amplitude of TEOAE recorded in linear mode in baseline and contralateral conditions)\n\n- TEOAE_non-linear.csv (contains data of amplitude of TEOAE recorded in non-linear mode)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nLee S-Y, Jung G, Jang M, et al.: Association of coffee consumption with hearing and tinnitus based on a national population-based survey. Nutrients. 2018; 10(10): 1429. PubMed Abstract \| Publisher Full Text\n\nNawrot P, Jordan S, Eastwood J, et al.: Effects of caffeine on human health. Food Addit. Contam. 2003; 20(1): 1–30. Publisher Full Text\n\nVincent J, Giannetti NN: The effect of caffeine and choline combinations on short-term visual and auditory memory. Clin. Pharmacol. Biopharm. 2013; 02(2): 1000112. Publisher Full Text\n\nWolde T: Effects of caffeine on health and nutrition: A Review. Food Sci. Qual. Manag. 2014; 30: 59–65.\n\nFredholm BB, Bättig K, Holmén J, et al.: Actions of caffeine in the brain with special reference to factors that contribute to its widespread use. Pharmacol. Rev. 1999; 51(1): 83–133. PubMed Abstract\n\nSchrott A, Puel J-L, Rebillard G: Cochlear origin of distortion products assessed by using 2 types of mutant mice. Hear. Res. 1991; 52(1): 245–253. PubMed Abstract \| Publisher Full Text\n\nBrownell WE: Outer hair cell electromotility and otoacoustic emissions. Ear Hear. 1990; 11(2): 82–92. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKemp DT: Stimulated acoustic emissions from within the human auditory system. J. Acoust. Soc. Am. 1978; 64(5): 1386–1391. PubMed Abstract \| Publisher Full Text\n\nMurugasu E, Russell IJ: The effect of efferent stimulation on basilar membrane displacement in the basal turn of the guinea pig cochlea. J. Neurosci. 1996; 16(1): 325–332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuinan JJ: Cochlear efferent innervation and function. Curr. Opin. Otolaryngol. Head Neck Surg. 2010; 18(5): 447–453. PubMed Abstract \| Publisher Full Text\n\nTavanai E, Farahani S, Ghahraman MA, et al.: Effects of caffeine on auditory- and vestibular-evoked potentials in healthy individuals: A double-blind placebo-controlled study. J. Audiol. Otol. 2020; 24(1): 10–16. PubMed Abstract \| Publisher Full Text\n\nDixit A, Vaney N, Tandon OP: Effect of caffeine on central auditory pathways: An evoked potential study. Hear. Res. 2006; 220(1–2): 61–66. PubMed Abstract \| Publisher Full Text\n\nChen X, Zhang L, Yang D, et al.: Effects of caffeine on event-related potentials and neuropsychological indices after sleep deprivation. Front. Behav. Neurosci. 2020; 14: 108. PubMed Abstract \| Publisher Full Text\n\nDixit A, Vaney N, Tandon OP: Evaluation of cognitive brain functions in caffeine users: A P3 evoked potential study. Indian J. Physiol. Pharmacol. 2006; 50(2): 175–180. PubMed Abstract\n\nKawamura N, Maeda H, Nakamura J, et al.: Effects of caffeine on event-related potentials: Comparison of oddball with single-tone paradigms. Psychiatry Clin. Neurosci. 1996; 50(4): 217–221. PubMed Abstract \| Publisher Full Text\n\nSoleimanian S, Farahani S, Ghahraman MA, et al.: Effects of caffeine on auditory brainstem response. Audiology. 2008; 17: 45–52.\n\nBarry RJ, Johnstone SJ, Clarke AR, et al.: Caffeine effects on ERPs and performance in an auditory Go/NoGo task. Clin. Neurophysiol. 2007; 118(12): 2692–2699. PubMed Abstract \| Publisher Full Text\n\nBarry RJ, De Blasio FM, Cave AE: Caffeine effects on ERP components and performance in an equiprobable auditory Go/NoGo task. J. Caffeine Res. 2014; 4(3): 83–92. PubMed Abstract \| Publisher Full Text\n\nPan J, Takeshita T, Morimoto K: Acute caffeine effect on repeatedly measured P300. Environ. Health Prev. Med. 2000; 5(1): 13–17. PubMed Abstract \| Publisher Full Text\n\nDiukova A, Ware J, Smith JE, et al.: Separating neural and vascular effects of caffeine using simultaneous EEG–FMRI: Differential effects of caffeine on cognitive and sensorimotor brain responses. NeuroImage. 2012; 62(1): 239–249. PubMed Abstract \| Publisher Full Text\n\nAltin B, Cildir B, Yilmaz S: Effects of caffeine on speech in noise scores. J. Int. Adv. Otol. 2015; 11: 54–54.\n\nTaghavi SMR, Geshani A, Rouhbakhsh N, et al.: Effects of short-term caffeine consumption on speech and sound reception in individuals with normal hearing. Audit. Vestib. Res. 2018; 27(3): 150–156. Publisher Full Text\n\nDrepath KS, Rajan A, Nayak S, et al.: Effect of caffeine on otoacoustic emissions. Ann. Otol. Neurotol. 2021; Publisher Full Text\n\nYamamoto T, Kakehata S, Yamada T, et al.: Caffeine rapidly decreases potassium conductance of dissociated outer hair cells of guinea-pig cochlea. Brain Res. 1995; 677(1): 89–96. PubMed Abstract \| Publisher Full Text\n\nSlepecky N, Ulfendahl M, Flock Å: Effects of caffeine and tetracaine on outer hair cell shortening suggest intracellular calcium involvement. Hear. Res. 1988; 32(1): 11–21. PubMed Abstract \| Publisher Full Text\n\nSkellett RA, Crist JR, Fallon M, et al.: Caffeine-induced shortening of isolated outer hair cells: An osmotic mechanism of action. Hear. Res. 1995; 87(1–2): 41–48. PubMed Abstract \| Publisher Full Text\n\nBobbin RP: Caffeine and ryanodine demonstrate a role for the ryanodine receptor in the organ of Corti. Hear. Res. 2002; 174(1–2): 172–182. PubMed Abstract \| Publisher Full Text\n\nKumar UA, Vanaja CS: Functioning of olivocochlear bundle and speech perception in noise. Ear Hear. 2004; 25: 142–146. PubMed Abstract \| Publisher Full Text\n\nWen H, Berlin CI, Hood LJ, et al.: A program for quantification and analysis of transient evoked otoacoustic emissions. ARO Abstr. 1993; 16: 102.\n\nRobles L, Ruggero MA: Mechanics of the mammalian cochlea. Physiol. Rev. 2001; 81(3): 1305–1352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNenov AP, Norris C, Bobbin RP: Acetylcholine response in guinea pig outer hair cells. II. Activation of a small conductance Ca2+-activated K+ channel. Hear. Res. 1996; 101(1–2): 149–172. PubMed Abstract \| Publisher Full Text\n\nCastellano-Muñoz M, Schnee ME, Ricci AJ: Calcium-induced calcium release supports recruitment of synaptic vesicles in auditory hair cells. J. Neurophysiol. 2016; 115(1): 226–239. PubMed Abstract \| Publisher Full Text\n\nCollet L, Kemp DT, Veuillet E, et al.: Effect of contralateral auditory stimuli on active cochlear micro-mechanical properties in human subjects. Hear. Res. 1990; 43(2–3): 251–261. PubMed Abstract \| Publisher Full Text\n\nHood LJ, Berlin CI, Hurley A, et al.: Contralateral suppression of transient-evoked otoacoustic emissions in humans: intensity effects. Hear. Res. 1996; 101(1–2): 113–118. PubMed Abstract \| Publisher Full Text\n\nYashaswini L, Maruthy S: The influence of efferent inhibition on speech perception in noise: A revisit through its level-dependent function. Am. J. Audiol. 2019; 28(2S): 508–515. PubMed Abstract \| Publisher Full Text\n\nParthasarathy TK: Aging and contralateral suppression effects on transient evoked otoacoustic emissions. J. Am. Acad. Audiol. 2001; 12(2): 80–85. PubMed Abstract\n\nRogers PJ, Richardson NJ: Why do we like drinks that contain caffeine? Trends Food Sci. Technol. 1993; 4(4): 108–111. Publisher Full Text\n\nLudwig IA, Clifford MN, Lean MEJ, et al.: Coffee: Biochemistry and potential impact on health. Food Funct. 2014; 5(8): 1695–1717. PubMed Abstract \| Publisher Full Text\n\nSrivastava I, Kalaiah M: The effect of coffee on TEOAE and contralateral suppression of TEOAE. [dataset] Mendeley Data, V1. 2022. Publisher Full Text" }	[ { "id": "147805", "date": "09 Sep 2022", "name": "Wiktor Jedrzejczak", "expertise": [ "Reviewer Expertise neuroscience", "audiology", "signal processing", "otoacoustic emissions" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comments: The manuscript is related to effects of coffee on contralateral suppression of transient evoked otoacoustic emissions (OAEs). The strengths of the manuscript are large group of subjects and the design with repeated measurements. However there are also several weaknesses like lack of information of the caffeine content used for the experiments and lack of any other verification of caffeine influence on the subjects besides OAEs, no comparison with previous studies, old and wrong references to literature, very small references to OAE studies. My more specific comments are attached below.\nSpecific comments:\nIntroduction: Several sentences in the introduction should be backed up by references, e.g.:\n“In the cochlea, the OAEs are produced spontaneously and also in response to an external acoustic stimuli, referred as spontaneous OAEs and evoked OAEs respectively.”\n\n“The OAEs elicited in response to pure-tones are known as distortion product OAEs (DPOAEs) and stimulus frequency OAEs (SFOAEs).”\n\n“The suppression of OAE obtained by presenting noise to the non-test ear is known as the contralateral suppression of OAE.”\nThe authors refer to review by Guinan, but he uses term of inhibition not suppression and it is directly stated why in the referenced paper. This should be at least commented.\nMethod:\nHow much caffeine was in the coffee? Please provide information of the amount of caffeine used for the experiments.\n\nIt would be good if the authors evaluated effect of coffee by some other test, to show that coffee influenced the subject at all, e.g. in studies of effect of attention on OAEs the attention level is evaluated by counting of stimuli or by evoked potentials, and then OAE analyses are made.\n\nHow the authors evaluated the middle ear muscle reflex (MEMR)? Several studies point to MEMR interaction with experiments based on contralateral suppression of OAEs. The authors should check the MEMR influence or at least mention lack of it as the limitation of the study.\n\nWhy are OAE parameters calculated by some program, and not taken from the ILO system?\n\nProvide some rationale for using 3 dB SNR criterion while studies of reliability of OAE suppression recommend using at least 6 dB or even more.\nResults:\nPlease provide error bars on figures 4 and 5.\n\nMaybe the authors could select smaller dataset with OAEs of SNR > 6dB?\nDiscussion:\nStudy is based on TEOAEs so the comparisons to DPOAEs should be limited.\n\nPlease compare results with other studies of suppression on same equipment, especially recent studies of reliability/variability. Even if there are no studies of coffee on suppression of OAEs, there are some studies of reliability of TEOAEs measured by the same equipment. These are very good basis for comparison, and for reference what change in TEOAE suppression would show the significant effect.\nReferences:\nPlease add references of some OAE review studies.\n\nMost references are old. Please add references for papers from last 5 years.\n\nThere is in general too small number of references to OAE studies. There is plenty of OAE studies made on the same system with which the results could be compared.\n\nMistakes – references to papers in which there is no referenced information. For example: “Further, the OAEs elicited in response to short-duration stimuli such as clicks and tone-bursts are known as transient evoked OAEs (TEOAEs).” which cites Kemp 1978. At this time Kemp did not used the name of TEOAEs.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10149", "date": "13 Sep 2023", "name": "Mohan Kalaiah", "role": "Author Response", "response": "We thank you for peer reviewing the manuscript. Based on your recommendations, manuscript has been modified. See details below: Introduction: Reviewer comment: Several sentences in the introduction should be backed up by references, e.g.: “In the cochlea, the OAEs are produced spontaneously and also in response to an external acoustic stimuli, referred as spontaneous OAEs and evoked OAEs respectively.” “The OAEs elicited in response to pure-tones are known as distortion product OAEs (DPOAEs) and stimulus frequency OAEs (SFOAEs).” “The suppression of OAE obtained by presenting noise to the non-test ear is known as the contralateral suppression of OAE.” The authors refer to review by Guinan, but he uses term of inhibition not suppression and it is directly stated why in the referenced paper. This should be at least commented. Authors reply: Citations added to the manuscript Method: Reviewer comment: How much caffeine was in the coffee? Please provide information of the amount of caffeine used for the experiments. Authors reply: The caffeine content ranges from 2.2 to 3.1%. Thus, the amount of caffeine ranged from 27 to 40 mg per cup of coffee. Same information is added to the manuscript. Reviewer comment: It would be good if the authors evaluated effect of coffee by some other test, to show that coffee influenced the subject at all, e.g. in studies of effect of attention on OAEs the attention level is evaluated by counting of stimuli or by evoked potentials, and then OAE analyses are made. Authors reply: We agree with your recommendation, but other tests were not performed during the study. We acknowledge the same in discussion Reviewer comment: How the authors evaluated the middle ear muscle reflex (MEMR)? Several studies point to MEMR interaction with experiments based on contralateral suppression of OAEs. The authors should check the MEMR influence or at least mention lack of it as the limitation of the study. Authors reply: The middle ear muscle reflex was evaluated by measuring the acoustic reflex threshold for white noise. GSI Tympstar Pro immittance meter was used for measuring the reflex threshold for white noise. The lowest intensity at which a change in admittance was noted (referred as ‘reflex threshold’) was considered as an evidence of middle ear muscle reflex. In the present study the white noise was presented below the reflex threshold, during the measurement of contralateral suppression of TEOAE. Similar approach has been employed by several studies measuring the contralateral suppression of TEOAE. Reviewer comment: Why are OAE parameters calculated by some program, and not taken from the ILO system? Authors reply: During the study period, the computer used for recording and storing the OAE data failed. Data was not lost, as data files were copied to another computer. We could not find a way to load the data files back to ILO software platform for the purpose of data analysis. Thus, OAE parameters was calculated using EchoMaster software. Reviewer comment: Provide some rationale for using 3 dB SNR criterion while studies of reliability of OAE suppression recommend using at least 6 dB or even more. Authors reply: We have reanalyzed the data and presented results using 6 dB SNR criterion. Results: Reviewer comment: Please provide error bars on figures 4 and 5. Authors reply: Error bars (SD) added to figure 4. Data showed in figure 5 is same as figure 4. Reviewer comment: Maybe the authors could select smaller dataset with OAEs of SNR > 6dB? Authors reply: We have reanalyzed the data and presented results using 6 dB SNR criterion. Discussion: Reviewer comment: Study is based on TEOAEs so the comparisons to DPOAEs should be limited. Authors reply: As studies related to TEOAEs are not available in literature, DPOAEs are cited for the purpose of comparison. Please compare results with other studies of suppression on same equipment, especially recent studies of reliability/variability. Even if there are no studies of coffee on suppression of OAEs, there are some studies of reliability of TEOAEs measured by the same equipment. These are very good basis for comparison, and for reference what change in TEOAE suppression would show the significant effect. References: Reviewer comment: Mistakes – references to papers in which there is no referenced information. For example: “Further, the OAEs elicited in response to short-duration stimuli such as clicks and tone-bursts are known as transient evoked OAEs (TEOAEs).” which cites Kemp 1978. At this time Kemp did not used the name of TEOAEs. Authors reply: Citation changed and error corrected" } ] }, { "id": "153018", "date": "01 Dec 2022", "name": "Chhayakanta Patro", "expertise": [ "Reviewer Expertise Peripheral physiology", "speech perception", "and aging" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 results of an experiment that investigated the effects of caffeine intake on transient evoked otoacoustic emissions (TEOAEs) and contralateral suppression of TEOAEs, in a group of young listeners with normal hearing (N = 52). The results indicated that caffeine intake had no effects on absolute TEOAE amplitudes and had negligible effects on the contralateral suppression of TEOAEs. The following sections of general comments summarize my main comments and concerns. Specific comments (e.g., line-by-line editing) are not included as the line numbers are not available (to me).\nThe use of cross-over design is innovative. Some individuals may have a greater sensitivity to the effects of caffeine than others and by treating each participant as his/her own control, such individual differences were accounted for.\n\nAny general comments regarding the effects of caffeine on auditory/ speech perception could be removed from the introduction section since the experiment focused on physiological effects and not on the perceptual consequences of caffeine consumption.\n\nSome sections of the manuscript are questionable because of a lack of coherence, and under-developed arguments. For example, the authors should give a clearer motivation for the choice of stimuli and conditions. Why did the authors hypothesize that TEOAEs could be more sensitive to the effects of caffeine than the DPOAEs (since the DPOAEs have produced null results, as the authors rightly acknowledge)?\n\nThroughout the paper (including the discussion section), comparisons to DPOAEs should be limited.\n\n“Further, studies investigating the effect of caffeine on the speech perception have reported a positive effect of caffeine on the perception of speech in noise.” – citations are needed here. Were the “positive effects” mediated by improved efferent activity? If not, those results are not relevant here.\n\nAlthough the authors cite some of the classic studies on OAEs, more recent citations are needed.\n\nPrecisely how much caffeine was provided to the study participants?\n\nWere the acoustic reflexes present at all the test frequencies?\n\nDid the authors conduct an interview/ provide a questionnaire to determine whether the participants had a history of otological problems? Did the authors quantify the amount of noise exposure? This information is relevant because prolonged/repetitive exposure to loud sounds may lead to (subclinical) cochlear dysfunction and may obscure the observation of any potential relationship between caffeine consumption and cochlear function. At least, this needs to be addressed in the discussion section.\n\nInvolving a large group of participants is a major strength.\n\n“Further, the TEOAEs recorded in the linear mode were considered to be present if the global SNR was at least 3 dB SNR.” Citation(s) needed here. Was the +3 dB SNR criterion based on previous studies?\n\nDienes, 2014: numeric reference formatting need.\n\nThe statistical analyses did not reveal significant effects of caffeine consumption on contralateral suppression of TEOAEs. Still, the authors claim that “TEOAE was slightly larger after consumption of coffee in both ears” in the abstract, based on their qualitative judgment. Their observations may be highlighted in the discussion section, not in the abstract.\n\nWhat do the error bars in figures 2 and 3 depict?\n\nPlease provide error bars in figures 4 and 5.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10147", "date": "13 Sep 2023", "name": "Mohan Kalaiah", "role": "Author Response", "response": "We thank you for peer reviewing the manuscript. Based on your recommendation manuscript has been modified. See details below: Reviewer comment: Any general comments regarding the effects of caffeine on auditory/ speech perception could be removed from the introduction section since the experiment focused on physiological effects and not on the perceptual consequences of caffeine consumption. Authors reply: Agree. But no changes made to the manuscript. Reviewer comment: Some sections of the manuscript are questionable because of a lack of coherence, and under-developed arguments. For example, the authors should give a clearer motivation for the choice of stimuli and conditions. Why did the authors hypothesize that TEOAEs could be more sensitive to the effects of caffeine than the DPOAEs (since the DPOAEs have produced null results, as the authors rightly acknowledge)? Authors reply: Agree. We aimed to investigate the effect of coffee on the TEOAE. Reviewer comment: Throughout the paper (including the discussion section), comparisons to DPOAEs should be limited. Authors reply: DPOAE results are included as TEOAE results are not available in literature. Reviewer comment: “Further, studies investigating the effect of caffeine on the speech perception have reported a positive effect of caffeine on the perception of speech in noise.” – citations are needed here. Were the “positive effects” mediated by improved efferent activity? If not, those results are not relevant here. Authors reply: Studies have been cited. We do not know if positive effects are mediated by efferent activity. Reviewer comment: Although the authors cite some of the classic studies on OAEs, more recent citations are needed. Authors reply: References added Reviewer comment: Precisely how much caffeine was provided to the study participants? Authors reply: The amount of caffeine ranged from 27 to 40 mg per cup of coffee. Same information is added to the manuscript. Reviewer comment: Were the acoustic reflexes present at all the test frequencies? Authors reply: The acoustic reflex threshold was measured for puretones of frequency 500 Hz, 1000 Hz, 2000 Hz, and 4000 Hz and white noise. Reviewer comment: Did the authors conduct an interview/ provide a questionnaire to determine whether the participants had a history of otological problems? Did the authors quantify the amount of noise exposure? This information is relevant because prolonged/repetitive exposure to loud sounds may lead to (subclinical) cochlear dysfunction and may obscure the observation of any potential relationship between caffeine consumption and cochlear function. At least, this needs to be addressed in the discussion section. Authors reply: Yes, details were conducted through interview. Reviewer comment: Involving a large group of participants is a major strength. Reviewer comment: “Further, the TEOAEs recorded in the linear mode were considered to be present if the global SNR was at least 3 dB SNR.” Citation(s) needed here. Was the +3 dB SNR criterion based on previous studies? Authors reply: Earlier studies measuring contralateral suppression of OAE have used 3 dB SNR criterion. But, recent literature recommends 6 dB SNR or higher SNR for greater reliability. The data was reanalyzed with 6 dB SNR criterion and results are reported. Reviewer comment: Dienes, 2014: numeric reference formatting need. Authors reply: done Reviewer comment: The statistical analyses did not reveal significant effects of caffeine consumption on contralateral suppression of TEOAEs. Still, the authors claim that “TEOAE was slightly larger after consumption of coffee in both ears” in the abstract, based on their qualitative judgment. Their observations may be highlighted in the discussion section, not in the abstract. Authors reply: Abstract modified Reviewer comment: What do the error bars in figures 2 and 3 depict? Authors reply: error bars depict standard deviation. Added to description Reviewer comment: Please provide error bars in figures 4 and 5. Authors reply: Error bars (SD) added to figure 4. Data showed in figure 5 is same as figure 4." } ] }, { "id": "146365", "date": "13 Dec 2022", "name": "Sandeep Maruthy", "expertise": [ "Reviewer Expertise Audiology", "electrophysiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 compared the amplitude of OAEs and the magnitude of contralateral suppression of OAEs before and after consuming coffee. The results show no significant difference between the two conditions, which the authors interpret as ‘no effect of coffee on OAEs and contralateral suppression of OAEs.’ The authors have used a robust research design, an acceptable sample size and have made reasonable attempts to control the possible extraneous variables. Overall, I appreciate the authors for their work. It is a work worth indexing and of interest to the potential readers of this journal. However, the manuscript needs a significant revision before I can recommend this for indexing. Following are my section-wise comments (a few of them in the form of questions to the authors) which I suggest the authors consider while revising the manuscript.\nTitle The title reflects only the contralateral suppression of TEOAEs, and misses out on reflecting the amplitude of OAEs.\nAbstract The background should highlight the need for the study. Just stating that studies have rarely investigated its effect on OAEs may not be sufficient to justify the need for the current study. I suggest the authors to confine the reporting to the statistical test findings and not report the mean difference in the abstract. The abstract may have to be re-written after considering the comments of the other sections.\nIntroduction\nThe authors must explain in more detail the influence of caffeine on the biochemistry due to which they expect OAEs and contralateral suppression of OAEs (CSOAEs) to change. The last sentence of the first paragraph mentions it in brief. The authors can elaborate it in the context of OAEs and CSOAEs. Also, later in the Discussion section, the authors have explained it based on Castellano-Muñoz et al. and Bobbin’s studies, which needs mention in introduction.\n\nThe word ‘Further’ is not necessary in a couple of instances in the first two paragraphs and I suggest removing it.\n\nThe transition of thought from the second to the third paragraph could be smoother. I suggest the authors make the necessary change.\n\nThe abbreviation ‘OAEs’ once used, needs to be continued. For example, second line of the fourth paragraph has the full form.\n\nIn the second line of the fifth paragraph, the sentence should read as ‘caffeine on the cochlea have reported that’ instead of ‘caffeine on the cochlea have reported.’\n\nWhat is a positive effect? Needs clarity.\n\nEarlier studies have shown improvement in SPIN with caffeine intake; changes in SPIN are associated with changes in CSOAES; therefore, the authors expected caffeine intake to change the CSOAEs. However, the justification is not clearly narrated in the manuscript.\n\nDrepath et al. reported no significant effect of coffee on the amplitude of DPOAEs, but Bobbin found a significant effect. The presence of equivocal findings among previous studies alone cannot justify taking up a new study. I suggest that the authors critically analyze the method used in these studies and identify the reason for differences in the findings, to justify the study and the to support the method used here.\n\nThe earlier studies have used DPOAEs while in the current study the authors used TEOAEs. Why did the authors prefer TEOAEs over DPOAEs? Considering that the physiological mechanisms of these two types of OAEs are different, can we not expect different findings in the two? If so, is it reasonable to compare the current findings with that of the previous studies where a different type of OAE was used?\n\nThe statement ‘This improved transmission in the afferent pathways could also elicit stronger activity in the efferent pathway’ needs to be supported with a citation.\n\nIn the statement ‘However, none of the studies have investigated the effect of caffeine of the efferent activity’, I think the authors are referring to ‘efferent auditory activity’. Please specify.\n\nMany studies have shown an association between CSOAEs and SPIN. All of them need to be cited in the manuscript. For example, Maruthy et al. (2017). Also, not all the studies that probed this relationship have shown association between the two. Therefore, I prefer that the authors mention ‘some of the studies that probed ………….’\nMethod\nHow was the sample size determined? Give details.\n\nThe statement ‘The acoustic reflex threshold for white noise was greater than 70 dB SPL for all the participants’ can be moved to earlier in the paragraph\n\nThe first sentence in the procedure is a repetition of what is in the previous paragraph. Remove it from the procedure.\n\n‘Fitted to the ear test ear’ and ‘fitted to the contralateral ear’ can be changed to ‘inserted’\n\nWhat was the need to record contralateral suppression at 3 different noise levels? Did the authors expect differential effects of coffee across suppressor intensities? This needs a strong justification in the manuscript. Otherwise, I suggest that the authors present results of either 50dBSPL or 60dBSPL alone. If they wish to retain it as it is, intensity as a variable needs a mention and justification in the Introduction section.\n\nI have a similar comment for recording the effect in both ears of the subjects. Did the authors expect different effects in the two ears? If so, it needs to be justified.\n\nI suggest that the authors explain the significance of recording OAEs in both linear and nonlinear paradigms. Considering that contralateral suppression of OAEs is higher in the linear paradigm, the authors could have restricted it to only the linear paradigm.\n\nIt is stated that ‘All the recordings of TEOAE were obtained without disturbing the placement of OAE probe (i.e., single-fit condition)’. The authors need to specify what measures they took to ensure that probe did not move while drinking coffee or milk, and in the next 1 hour until the second recording of OAEs was made.\n\nAs I understood, the authors recorded CSOAEs after the baseline TEOAEs. I do not see a mention of that either in the text or in the Figure 1. Please make the necessary change.\n\nMention the rationale for 1-hour interval after coffee consumption.\n\nThe statement ‘The TEOAEs obtained in the second session were similar to the first session and were referred as ‘follow-up measurements’. Do authors mean that the procedure was the same?\n\nRather than calling them ‘baseline’ and ‘follow up’ measurements, I suggest ‘pre-drink’ and ‘post-drink’ measurements. This I think these terms will also compliment with the term given for this variable (drink) in the results section.\n\nCoffee preparation is one of the methods used in India. For example, coffee in USA is typically not prepared with milk or milk powder. I suggest the authors to mention that this is a method of coffee preparation followed in India.\n\nPlease explain the rationale for using 1.3g of coffee. How does it relate to the coffee dosage used in the earlier studies?\n\nAs mentioned earlier, Figure 1 does not reflect CSOAE measurements.\n\nProvide supporting reference to the 6 dB and 3dB criteria used.\n\nThe presence of 6dB in nonlinear mode and 3 dB in linear mode should have been a participant selection criterion.\n\nI suggest that the authors mention the target response measures in the method section.\nResults\nThe authors should talk about the normality test upfront and then describe the trend in the mean amplitude.\n\n‘conditions’ to be changed to ‘condition’\n\nIn Figure 2, I believe the unit is dB SPL. Please specify.\n\nComparing between ears and across intensities of suppressors needs to be stated in the objectives. Otherwise, I suggest the authors to remove it from the results section.\n\nIn the results of CSOAEs, the normality test revealed non-normal distribution of the data. Accordingly, Friedman test is used. In such a case, presenting median and IQR is more meaningful than mean and SD.\n\n‘both ears’ to be changed to ‘in the two ears’ in several places.\n\nError bars or the appropriate measure of variance is not reflected in Figure 4 and 5. Please include. I suggest to show median and IQR.\n\nThe Y-axis in Figure 4 and 5 should read as ‘magnitude of CSOAEs (dB)’.\n\nThe information in Figures 4 and 5 are the same but represented differently. I suggest retaining Figure 5 and removing Figure 4.\n\nDiscussion\n\nThe statement ‘The findings of the above study suggest that functioning of the OHCs may not be affected by caffeine, and thus the amplitude of OAE could be similar before and after consumption of caffeine’ is too profound for what authors can derive from their study. It should be read in the context of the dosage of coffee used in this study. I suggest that the authors tone down the inference drawn.\n\nThis study showed the absence of significant effect of coffee on CSOAEs in presence of improvement in SPIN (as shown by earlier studies). Does it reflect that improvements in SPIN observed by them is not efferent mediated? The authors can consider discussing this direction.\n\nThe results showed some effect, but that was not significant. Therefore, instead of concluding it as ‘findings of the present study showed no effect of coffee on the findings of TEOAE’ the authors can phrase it as ‘findings suggest no effect of coffee’.\n\nThe authors in the last statement of the manuscript state ‘may not have negative effects on the amplitude of TEOAE,’ but earlier in the manuscript, they expected positive effects. This is contradictory. I believe they meant that clinical measurement of TEOAEs and the inferences drawn from it don’t change with coffee consumption. Please make changes in the statement accordingly.\n\nTo summarize, one may find more criticisms in my peer-review report than appreciations. This does not take away the credit for the good work done by the authors and the significant contribution of their work to science. I suggest that they revise it based on the inputs provided and submit the revised manuscript for reconsideration.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10148", "date": "13 Sep 2023", "name": "Mohan Kalaiah", "role": "Author Response", "response": "We thank you for peer reviewing the manuscript. Based on your recommendations, manuscript has been modified. See details below: Title Reviewer comment: The title reflects only the contralateral suppression of TEOAEs, and misses out on reflecting the amplitude of OAEs. Authors reply: Title changed to “The effect of coffee on transient evoked otoacoustic emissions and contralateral suppression of transient evoked otoacoustic emissions” Abstract Reviewer comment: The background should highlight the need for the study. Just stating that studies have rarely investigated its effect on OAEs may not be sufficient to justify the need for the current study. I suggest the authors to confine the reporting to the statistical test findings and not report the mean difference in the abstract. The abstract may have to be re-written after considering the comments of the other sections. Authors reply: Statement on mean difference was removed from the abstract. Abstract modified Introduction Reviewer comment: The authors must explain in more detail the influence of caffeine on the biochemistry due to which they expect OAEs and contralateral suppression of OAEs (CSOAEs) to change. The last sentence of the first paragraph mentions it in brief. The authors can elaborate it in the context of OAEs and CSOAEs. Also, later in the Discussion section, the authors have explained it based on Castellano-Muñoz et al. and Bobbin’s studies, which needs mention in introduction. Authors reply: We agree with the recommendation Reviewer comment: The word ‘Further’ is not necessary in a couple of instances in the first two paragraphs and I suggest removing it. Authors reply: removed Reviewer comment: The transition of thought from the second to the third paragraph could be smoother. I suggest the authors make the necessary change. Authors reply: modified Reviewer comment: The abbreviation ‘OAEs’ once used, needs to be continued. For example, second line of the fourth paragraph has the full form. Authors reply: modified Reviewer comment: In the second line of the fifth paragraph, the sentence should read as ‘caffeine on the cochlea have reported that’ instead of ‘caffeine on the cochlea have reported.’ Authors reply: modified Reviewer comment: What is a positive effect? Needs clarity. Authors reply: Positive effect refer to improved neural transmission. Same has been added to the manuscript. Reviewer comment: The earlier studies have used DPOAEs while in the current study the authors used TEOAEs. Why did the authors prefer TEOAEs over DPOAEs? Considering that the physiological mechanisms of these two types of OAEs are different, can we not expect different findings in the two? If so, is it reasonable to compare the current findings with that of the previous studies where a different type of OAE was used? Authors reply: Yes, we agree that different findings are possible. TEOAEs were used in the present study as studies measuring the TEOAEs are not available in literature. Reviewer comment: The statement ‘This improved transmission in the afferent pathways could also elicit stronger activity in the efferent pathway’ needs to be supported with a citation. Authors reply: Statement modified to ‘This improved transmission in the afferent pathways could have an influence on the activity in the efferent pathway’ Reviewer comment: In the statement ‘However, none of the studies have investigated the effect of caffeine of the efferent activity’, I think the authors are referring to ‘efferent auditory activity’. Please specify. Authors reply: modified. ‘efferent activity’ changed to ‘efferent auditory activity’ Reviewer comment: Many studies have shown an association between CSOAEs and SPIN. All of them need to be cited in the manuscript. For example, Maruthy et al. (2017). Also, not all the studies that probed this relationship have shown association between the two. Therefore, I prefer that the authors mention ‘some of the studies that probed ………….’ Authors reply: references added. Method Reviewer comment: The statement ‘The acoustic reflex threshold for white noise was greater than 70 dB SPL for all the participants’ can be moved to earlier in the paragraph Authors reply: done Reviewer comment: The first sentence in the procedure is a repetition of what is in the previous paragraph. Remove it from the procedure. Authors reply: removed Reviewer comment: ‘Fitted to the ear test ear’ and ‘fitted to the contralateral ear’ can be changed to ‘inserted’ Authors reply: done Reviewer comment: What was the need to record contralateral suppression at 3 different noise levels? Did the authors expect differential effects of coffee across suppressor intensities? This needs a strong justification in the manuscript. Otherwise, I suggest that the authors present results of either 50dBSPL or 60dBSPL alone. If they wish to retain it as it is, intensity as a variable needs a mention and justification in the Introduction section. Authors reply: As the paper is already published we decided not to remove the data from the manuscript. However, for the purpose of statistical analysis only 60 dB noise was considered. Reviewer comment: I have a similar comment for recording the effect in both ears of the subjects. Did the authors expect different effects in the two ears? If so, it needs to be justified. Authors reply: Many studies have documented a higher contralateral suppression of OAE in the right, suggesting an asymmetry in the magnitude of suppression between ears. Thus, in the present investigation the effect of caffeine on the contralateral suppression of TEOAE was measured in both ears. Reviewer comment: I suggest that the authors explain the significance of recording OAEs in both linear and nonlinear paradigms. Considering that contralateral suppression of OAEs is higher in the linear paradigm, the authors could have restricted it to only the linear paradigm. Authors reply: Non-linear TEOAEs are commonly recorded for clinical applications. While linear TEOAEs are commonly used during measurement of contralateral suppression of TEOAE. As recommended, in the present study, the contralateral suppression of TEOAE was measured using linear TEOAE only. Reviewer comment: It is stated that ‘All the recordings of TEOAE were obtained without disturbing the placement of OAE probe (i.e., single-fit condition)’. The authors need to specify what measures they took to ensure that probe did not move while drinking coffee or milk, and in the next 1 hour until the second recording of OAEs was made. Authors reply: All the recordings in one session was obtained in single-fit condition. Two sessions were present in one day with a gap of 1 hour (before and after). Reviewer comment: As I understood, the authors recorded CSOAEs after the baseline TEOAEs. I do not see a mention of that either in the text or in the Figure 1. Please make the necessary change. Authors reply: Yes, initially ‘baseline’ TEOAE was recorded and after that the TEOAE was recorded by delivering noise to the contralateral ear. Reviewer comment: Mention the rationale for 1-hour interval after coffee consumption. Authors reply: The effects from caffeine reach peak levels after 30 to 45 minutes of consumption. Thus, 1-hour interval was used between sessions. Reviewer comment: The statement ‘The TEOAEs obtained in the second session were similar to the first session and were referred as ‘follow-up measurements’. Do authors mean that the procedure was the same? Authors reply: Yes Reviewer comment: Rather than calling them ‘baseline’ and ‘follow up’ measurements, I suggest ‘pre-drink’ and ‘post-drink’ measurements. This I think these terms will also compliment with the term given for this variable (drink) in the results section. Authors reply: done Reviewer comment: Coffee preparation is one of the methods used in India. For example, coffee in USA is typically not prepared with milk or milk powder. I suggest the authors to mention that this is a method of coffee preparation followed in India. Authors reply: Agreed and added to manuscript Reviewer comment: Please explain the rationale for using 1.3g of coffee. How does it relate to the coffee dosage used in the earlier studies? Authors reply: 1.3 g was the amount of coffee available in one sachet. It is typical serving size for one cup of coffee. Reviewer comment: As mentioned earlier, Figure 1 does not reflect CSOAE measurements. Authors reply: Details added to the legend of figure. Reviewer comment: The presence of 6dB in nonlinear mode and 3 dB in linear mode should have been a participant selection criterion. Authors reply: Agreed. We used 6 dB SNR in nonlinear mode as one of the criterion for participant selection in the present study. In linear mode, when the SNR was less than 6 dB OAE was considered as absent. Reviewer comment: I suggest that the authors mention the target response measures in the method section. Authors reply: We measured amplitude of TEOAE in non-linear and linear modes and magnitude of contralateral suppression of TEOAE. Same is mentioned in data analysis section. Results Reviewer comment: The authors should talk about the normality test upfront and then describe the trend in the mean amplitude. Authors reply: Results of normality tests are provided in the manuscript. Reviewer comment: ‘conditions’ to be changed to ‘condition’ Authors reply: done Reviewer comment: In Figure 2, I believe the unit is dB SPL. Please specify. Authors reply: SPL added Reviewer comment: Comparing between ears and across intensities of suppressors needs to be stated in the objectives. Otherwise, I suggest the authors to remove it from the results section. Authors reply: We prefer not to add the comparison across level of noise as an objective. Reviewer comment: ‘both ears’ to be changed to ‘in the two ears’ in several places. Authors reply: done Reviewer comment: The Y-axis in Figure 4 and 5 should read as ‘magnitude of CSOAEs (dB)’. Authors reply: Axis changed Reviewer comment: The information in Figures 4 and 5 are the same but represented differently. I suggest retaining Figure 5 and removing Figure 4. Authors reply: As manuscript is already published we prefer to retain both the figures. Discussion Reviewer comment: The statement ‘The findings of the above study suggest that functioning of the OHCs may not be affected by caffeine, and thus the amplitude of OAE could be similar before and after consumption of caffeine’ is too profound for what authors can derive from their study. It should be read in the context of the dosage of coffee used in this study. I suggest that the authors tone down the inference drawn. Authors reply: Modified Reviewer comment: This study showed the absence of significant effect of coffee on CSOAEs in presence of improvement in SPIN (as shown by earlier studies). Does it reflect that improvements in SPIN observed by them is not efferent mediated? The authors can consider discussing this direction. Authors reply: Could be mediated by efferent activity. Findings of Castellano-Muñoz et al. has revealed that caffeine resulted in changes in post-synaptic activity in auditory fibers in the absence of changes in OHCs. Thus, involvement of efferent activity may not be ruled out. Reviewer comment: The results showed some effect, but that was not significant. Therefore, instead of concluding it as ‘findings of the present study showed no effect of coffee on the findings of TEOAE’ the authors can phrase it as ‘findings suggest no effect of coffee’. Author reply: modified Reviewer comment: The authors in the last statement of the manuscript state ‘may not have negative effects on the amplitude of TEOAE,’ but earlier in the manuscript, they expected positive effects. This is contradictory. I believe they meant that clinical measurement of TEOAEs and the inferences drawn from it don’t change with coffee consumption. Please make changes in the statement accordingly. Author reply: Agreed Reviewer comment: To summarize, one may find more criticisms in my peer-review report than appreciations. This does not take away the credit for the good work done by the authors and the significant contribution of their work to science. I suggest that they revise it based on the inputs provided and submit the revised manuscript for reconsideration. Author reply: Thank you for agreeing to review the manuscript and providing recommendations." } ] } ]	1	https://f1000research.com/articles/11-878
https://f1000research.com/articles/11-1132/v1	04 Oct 22	{ "type": "Review", "title": "Pathomechanisms of non-coding RNAs and hub genes related to the oxidative stress in diabetic complications", "authors": [ "Fatemeh Hajibabaie", "Faranak Aali", "Navid Abedpoor", "Fatemeh Hajibabaie", "Faranak Aali" ], "abstract": "Cytokine storms, oxidative stress, and hyperglycemia can enhance the risk of type 2 diabetes (T2D). Moreover, T2D may change the functional and structural heart. However, some signaling pathways, such as insulin resistance, dyslipidemia, and hyperglycemia, can play in T2D, and various pathomechanics and pathophysiology involved in T2D are not understood. Moreover, it is well documented that the non-coding RNAs are potentially pivotal molecules in oxidative stress, inflammation, and cell death signaling pathways. Hence, long non-coding RNAs (lncRNAs) and microRNAs may have vital roles in oxidative stress, inflammation, metabolism, T2D, and cardiovascular systems. Non-coding RNAs can target hub gene networks and suppress or trigger various cascades. Furthermore, lifestyle is the other factor that may affect the prevalence of T2D. A sedentary lifestyle and excessive sitting can enhance inflammation, oxidative stress, and hyperglycemia. Here, we attempt to comprehend the role of hub genes, non-coding RNAs, and unhealthy lifestyles on the pathomechanics and pathophysiology of diabetic vascular complications.", "keywords": [ "Diabetes", "Cardiovascular diseases", "Oxidative stress", "Inflammation", "Non-coding RNAs", "Lifestyle" ], "content": "Abbreviations\n\n3′UTR: 3′ untranslated region\n\nAGEs: advanced glycation end products\n\nBAX: BCL2 Associated X\n\nBcl-2: B-cell lymphoma 2\n\nBCAAs: branched-chain amino acids\n\nCAT: catalase\n\nCycs: Cytochrome C\n\ncircRNAs: circular RNAs\n\nDAMPs: damage-associated molecular patterns\n\nDNA: deoxyribonucleic acid\n\nFas: Fas Cell Surface Death Receptor\n\nFNDC5: fibronectin type III domain containing 5\n\nGAS5: growth arrest-specific 5\n\nGPX: Glutathione peroxidase\n\nH2O2: hydrogen peroxide\n\nHOTAIR: HOX transcript antisense RNA\n\nIL-1: interleukin-1\n\nIL-6: interleukin-6\n\nIL-8: interleukin-8\n\nIL-18: interleukin-18\n\nlncRNAs: long non-coding RNAs\n\nMAPK: mitogen-activated protein kinase\n\nmPTP: mitochondrial permeability transition\n\nMEG3: maternally expressed 3\n\nNCCD: Nomenclature Committee on Cell Death\n\nNO: nitric oxide\n\nNCDs: non-communicable diseases\n\nNF-κB: nuclear factor kappa B\n\nNLRs: nucleotide binding and oligomerization domain\n\nO2-: superoxide\n\nOH: hydroxyl radical\n\nPKR: protein kinases R\n\nRIP3: receptor-interacting protein 3\n\nROS: reactive oxygen species\n\nSirt3: Sirtuin 3\n\nSODs: superoxide dismutase\n\nT2D: type 2 diabetes\n\nTNF-α: tumor necrosis factor-alpha\n\nTLR4: toll-like receptor 4\n\nTUG1: taurine up-regulated 1\n\nVDAC1: voltage-dependent anion channel 1\n\n\nIntroduction\n\nType 2 diabetes (T2D) has been classified as one of the four primary non-communicable diseases (NCDs), and it demands immediate medical attention to manage its prevalence and related problems.1 Growing evidence indicates that T2D could be a severe metabolic condition affecting more than 400 million individuals globally, and predicts that this number might surpass 600 million by 2040.2,3 Statistical evidence has demonstrated that T2D is a top 10 cause of death globally, killing over 1.5 million people worldwide.4 Moreover, T2D is the third most significant risk factor for worldwide premature mortality due to inflammation, hyperglycemia, and oxidative stress.5 Vascular complications, macrovascular and microvascular, are the leading causes of morbidity and mortality in people with diabetes, placing a significant economic burden on developed and developing nations due to disparities in healthcare spending and the inaccessibility of effective medicines.5,6 There is a well-established clinical connection between diabetes and atherosclerotic lesions.7 Foam cell production, fatty streak development, and plaque rupture are all proven to occur during atherosclerotic damage. In atherosclerotic lesions, vulnerable plaque development generates systemic inflammation that ultimately results in myocardial infarction.8\n\nT2D is recognized by β-cell dysfunction and hyperglycemia, which result in defective or inadequate insulin receptor activity, impaired function, and early destruction of insulin during its synthesis.9,10 Immense studies have indicated that T2D leads to severe chronic complications such as cardiovascular disease, peripheral nerve damage, neuropathy, retinopathy, and nephropathy.2,6,11 Impaired glucose tolerance in T2D is associated with insulin resistance, and insulin shortage impacts glucose consumption in the liver, adipose tissues, and skeletal muscle.12 Recent studies have revealed oxidative stress as a critical player in developing diabetes complications.13 Hyperglycemia causes increased oxidative stress, pro-inflammatory proteins, and infiltrating macrophages secreting inflammatory cytokines that impair the body's function.1 Moreover, It has been discovered that insulin resistance is associated with increased inflammation molecules such as tumor necrosis factor-alpha (TNF-α) production.14,15\n\nThe release of bioactive metabolites from adipocytes, such as lipids, free fatty acids, monocyte chemoattractant protein-1, and pro-inflammatory cytokines, have been associated with insulin resistance in obese people.16,17 On the other hand, evidence has indicated that the human body has an antioxidant defense mechanism that drastically lowers the rate at which oxidizing chemicals are oxidized.18 There are both enzymatic and non-enzymatic antioxidants in the human body. Glutathione peroxidase (GPX), catalase (CAT), and superoxide dismutase (SODs) are examples of enzymes that neutralize free radicals (Figure 1).19\n\nEven though many pathophysiological changes are produced by metabolic disorders such as insulin resistance, hyperglycemia, and dyslipidemia, oxidative stress may have a vital role in the physiological and pathological mechanisms of T2D.20 However, immense evidence has indicated that the vital role of oxidative stress in T2D, the molecular mechanism of oxidative stress is not elucidated. By generating ceramides, diacylglycerol, and reactive oxygen species (ROS), free fatty acids can accelerate oxidation and accumulate in the cytosol, resulting in lipotoxicity. Along with the development of cardiac glucotoxicity, hyperglycemia produces a rise in the concentration of ROS and the production of advanced glycation end products (AGEs). In addition, cell death is induced by ROS, which can have significant consequences that modulate pathogenic reactions in the rest of the cells, resulting in dysfunction and remodeling.21,22\n\nBesides, oxidative stress can trigger inflammation, cytokine storm, nitric oxide (NO) accumulation, mitochondrial dysfunction, and reduced mitochondrial biogenesis.10 Furthermore, epidemiology studies demonstrated that a sedentary lifestyle and excessive sitting caused dysmetabolic conditions.23 Furthermore, a lifestyle change, including being physically active, avoiding smoking and drinking, and eating healthy, could prevent many occurrences of T2D.24,25\n\nBased on the data mining, oxidative stress plays a key role in T2D, but the precise mechanism and essential factors related to oxidative stress are not comprehended. Hence, The main goal of this review article attempt to find out:\n\n• The cellular mechanisms relating oxidative stress and cell death in T2D.\n\n• The role of the non-coding RNAs and oxidative stress in managing T2D.\n\n• Finally, we will discuss how lifestyle can enhance oxidative stress in the body.\n\nFree radicals and other non-radical reactive derivatives are referred to as oxidants and are collectively referred to as ROS and reactive nitrogen species (RNS).26 Highly reactive molecules created during normal cellular metabolism react with a wide range of organic substrates, including lipids, deoxyribonucleic acid (DNA), and proteins.27 Oxidative radicals, including superoxide (O2−), hydroxyl radical (·OH), and hydrogen peroxide (H2O2), are produced at high concentrations in response to oxidative stress, leading to damaged cells and even cell death.28 Oxidative stress and cell death are hallmarks of diabetes and cardiovascular diseases, although managing these hallmarks may help postpone the development of diabetes and diabetic vascular complication.14\n\nIn silico and bioinformatics analysis have revealed that the hub genes involved in cell death, cytokine production, and oxidative stress pathways could be related to T2D (Figures 1–3). As a significant target in cardiac apoptosis, the cytochrome C (Cycs), sirtuin 3 (Sirt3), B-cell lymphoma 2 (Bcl-2), and Fas cell surface death receptor (Fas) network may be essential for preventing heart failure.29 BCl-2 protein may inhibit the cell death apoptosis pathway and can reduce cytochrome C activity in mitochondria, whereas apoptosis activators such as BAX (BCL2 Associated X) can increase cytochrome C secretion.30 Under certain pathological situations, the interaction between FAS and FAS ligands may also mediate the apoptotic death of cardiac cells. Thereby, hyperglycemia prompts the increased ROS, releasing cytochrome C, mitochondrial malfunction, and damage to heart tissue.31–33\n\nBased on the evidence, Sirt3 is identified as a coding gene that encodes class III histone deacetylases of the sirtuin family and is exclusively found in the mitochondrial matrix membrane. Consequently, this gene may function as a master regulator under various circumstances and induce apoptosis.29,34 In addition, Sirt3 has been discovered as a gene with far-reaching effects on energy metabolism, aging, apoptosis, diabetes, cardiovascular diseases, and neurological illnesses.35,36 Enhancement of ROS production causes oxidative stress, which triggers several cellular alterations.37 Increased ROS generation and apoptotic activation in β-cells are hallmarks of diabetes, whether the condition is acute or chronic.38 Tissue damage in the retina, heart, nervous system, and kidneys may lead to apoptosis and necroptosis, all of which play critical roles in developing diabetes complications.39,40 Growing evidence has indicated that apoptosis, autophagy, necroptosis, and ferroptosis are the categories of cellular death41–47 (Figure 3).\n\nIt should be noted that cell death mechanisms have a diversity of functions. The nomenclature committee on cell death (NCCD) has developed criteria for the morphological, biochemical, and functional classifications and descriptions of cell death.47 Type 1 cell death (apoptosis) occurs following cytoplasmic shrinkage, chromatin condensation (pyknosis), nuclear fragmentation (karyorrhexis), apoptotic bodies formation, phagocytic activity, and degradation within lysosomes by neighboring cells.48 Immense evidence has indicated that triggered Caspase is a crucial mechanism for inducing cell death.49 Multiple triggers operate on different cellular components in the intrinsic process of apoptosis, also called the mitochondrial pathway.50 As well as, after environmental damage, natural killer cells and macrophages release death molecules that, upon binding with death receptors (DRs) on the target extracellular membrane, trigger the extrinsic cascade of apoptosis by activating procaspase 8 to caspase 8. The DRs are a class of proteins that belong to the TNF (tumor necrosis factor) superfamily.51\n\nOn the other hand, saturated fatty acid lipid peroxidation is dramatically accelerated in the presence of iron, especially divalent iron. Cells generate ROS in addition to ATP during iron-dependent oxidative phosphorylation in the mitochondria.46 An oxidative stress response is triggered when the amounts of ROS in a cell are higher than its ability to neutralize them, and this can cause harm or death to the cell by directly or indirectly damaging significant molecular components, including proteins, nucleic acids, and lipids. Hence, increased levels of iron-dependent lipid peroxide cause ferroptosis cell death. Initiating ferroptosis requires reactive oxygen species production and iron availability.44,45\n\nMoreover, According to recent investigations, autophagy has emerged as a critical position in preventing insulin resistance and death generated by oxidative stress in pancreatic islet beta cells.42 Antioxidant-rich proteins and organelles are degraded and recycled by autophagy to preserve cellular homeostasis. ER stress, starvation, and growth factor deficiency can all trigger this process.41,52,53 Reducing aberrant protein build up, eliminating intracellular infections, and eliminating aberrant proteins can all be achieved by autophagy. This vital process directly influences cellular homeostasis and cell survival. According to growing research, autophagic dysfunction has been linked to numerous disorders, including tumors, neurodegenerative diseases, and inflammatory diseases. Autophagy may have a role in the pathophysiology of metabolic diseases like diabetes by redistributing resources away from inefficient activities and toward crucial ones essential for life.\n\nNecroptosis is the best-understood format of programmed necrosis death, exhibiting necrosis and apoptosis characteristics. TNF-1 (TNFR1) and Fas receptor ligands are involved in the cascade of necroptosis activation in response to high glucose stimulation.41 As well as necroptosis, damage-associated molecular patterns (DAMPs), nucleotide binding and oligomerization domain (NLRs), ripoptosome, and protein kinases R (PKR) complex are also involved. Apoptosis, necroptosis, or cell survival are all potential outcomes of TNFR1 binding to TNFs. Cell survival, apoptosis, or necroptosis are three distinct obligations that various signaling complexes can mediate following TNFR1 activation by TNFs binding. Based on the evidence, complex-I promotes survival, while complex IIa promotes apoptosis.41 Necroptosis occurs as a result of the development of complex IIb. Moreover, necroptosis is regulated by the receptor-interacting protein 3 (RIP3).41 In diabetes, RIP3 controls necroptosis by regulating RIP1 in a RIP-dependent way.54 RIP3 is triggered by self-phosphorylation to enhance MLKL phosphorylation after being recruited by RIP1 during high glucose exposure.46 This results in the cell membrane being permeable when MLKL oligomers translocate to the cell membrane, interacting with PIP2 lipids and cardiolipin. It has been discovered that CaMKII, a recently discovered RIP3 substrate, induces necroptosis. The myocardium contains a lot of CaMKII, which is usually inactive. RIP1 phosphorylation or Ca2+ phosphorylation of CaMKII is a necroptosis-inducing factor. High glucose raises ROS, oxidizing CaMKII and activating it.54,55\n\nTo sum up, these pathogenic alterations lead to necroptosis by activating the mitochondrial permeability transition (mPTP). Some evidence suggested that knocking down CypD, which increased the likelihood of mPTPs opening, could protect against RIP3-induced cardiomyocyte necrosis.56 Finally, the opening of the mPTP is brought about by the up-regulation of RIP3, which increases CypD phosphorylation and boosts PGAM5 expression. As the death signal was amplified, necroptosis occurred in the endothelial cells due to excessive mPTP opening.57\n\nOn the other hand, toll-like receptor 4 (TLR4) activation is another critical mechanism of ROS and hyperglycemia that can trigger apoptosis.58 A literature review revealed that the expression of the TLR4 is up-regulated in diabetic conditions, and TLR4 gene silencing may be able to regulate cardiac apoptosis in diabetes.58,59 Evidence has demonstrated an association between TLR4 and oxidative stress.60 As a result, the reduction of TLR4 leads to the dampening of stress responses, and caspase 3 in cardiomyocytes may be inhibited.61\n\nNotably, the inflammatory mediators of diabetes, such as lipoprotein-associated phospholipase A2, adiponectin, tumor necrosis factor-α (TNF-α), high mobility group box-1 (HMGB-1), advanced glycation end products (AGEs), and chemokines, interleukin-1 (IL-1), interleukin-6 (IL-6), interleukin-8 (IL-8), and interleukin-18 (IL-18). Upregulation of these inflammatory mediators might activate nuclear factor κB (NF-κB), which induces cytokine storm and angiogenic mediators. Hence, accumulation of the ROS molecule and inflammation agents leads to cell death and impairs the function of the cell.38,62\n\nNitric oxide (NO), a free radical component with pathophysiological effects, could induce inflammation.10,63 Overly, NO is an inflammatory and damaging component due to interactions with the intermediate factors of reactive oxygen species generally available in cells.64 Several diseases, including lung squamous cell carcinoma, colon cancer, depression, and diabetes, have been coupled to the NO/inflammation signaling cascade pathway.64–67 One category of nitric oxide synthase factors, endothelial nitric oxide synthase (eNOS), plays a significant role in managing NO function by stimulating NO synthesis.68\n\nIschemia/reperfusion-induced acute kidney injury, ischemia/reperfusion-induced liver injury, hypertension, and steatohepatitis have been highlighted as associated disorders with the PPAR/eNOS axis.69–72 Even though the PPAR/eNOS axis mediates the inflammatory status involved in T2DM pathogenesis, the mechanism and vital molecules remain controversial.\n\nOverall, based on the mentioned evidence, we could conclude that enhanced ROS molecules mediated the other pathomechanisms such as inflammation, apoptosis, autophagy, necroptosis, and ferroptosis. Furthermore, we found that oxidative stress correlated with inflammation and cell death based on the in silico analysis (Figure 2).\n\nNon-coding RNAs and oxidative stress in the management of type 2 diabetes\n\nThe pathogenetic state is established by interactions between genetic and epigenetic elements and may be affected by several regulatory elements.73 The length of non-coding RNAs is utilized for the recognition category of short non-coding RNAs and long non-coding RNAs (LncRNAs).73,74 MicroRNAs (miRNAs), one type of short non-coding RNA consisting of around 20–25 nucleotides, have a role in the biological processes by modifying the post-translational events of mRNAs.75 MiRNAs regulate gene expression through binding to specific seed sequences in the 3′ untranslated region (3′UTR) of target genes.75 Moreover, miRNAs are considered significant biomolecules involved in the beginning, development, prognosis, diagnosis, and therapy of different pathophysiological indications due to their role as fine tuners of gene expression, control of signaling, and molecular-cellular processes.8,75 Typically a nucleotide sequence of over 200 bp displaying as long noncoding RNAs (lncRNAs) influences gene expression by many mechanisms.76 Both the linear and the circular forms of lncRNAs are found in cells and the extracellular space.77 The RNAs that exist in a circular structure are referred to as circular RNAs (circRNAs). Furthermore, the annotated lncRNAs have been used to classify lncRNAs as the signal, decoy, guide, and scaffold molecules. Hence, non-coding RNAs are also interesting and attractive therapeutic targets since of their potential impact on various disease-related cellular processes.28\n\nGrowing evidence highlighted that lncRNAs have been recognized as significant transcripts involved in oxidative stress, inflammation, cell damage, apoptosis cell death, beta-cell function, insulin resistance/insulin secretion, metabolism, etc., and are now considered potential diagnostic biomarkers.78 Hence, lncRNAs are potentially pivotal molecules in oxidative stress, inflammation, and cell death studies. Only a significant portion of annotated lncRNAs have been shown to play critical roles in diseases associated with oxidative stress, such as those affecting the nervous, respiratory, metabolism, and cardiovascular systems.28 Based on the evidence, lncRNAs could be targeting ARE/Nrf2/Keap1 network and, through genetic interactions, are associated with the oxidation and antioxidation balance system.79 As major effective lncRNAs related to oxidative stress conditions could be pointed to the MALAT1, H19, SCAL1, NEAT1, gadd7, MACC1-AS1, ODRUL, LINC01619, LINC00963, FOXD3-AS1, and BDNF-AS.80 The previous review study briefly discussed lncRNAs Meg3, SNHG16, MALAT1, GAS5, HOTAIR, and CASC2's role in diabetic cardiovascular vascular damage through the oxidative stress response. Pei-Ming Chu et al. revealed that MEG3 targets miR-145/PDCD4 and HOTAIR by inhibiting miR-34a/SIRT1, miR-126/SIRT1, and PI3K/Akt could be regulated oxidative stress in diabetic cardiomyopathy complication status.28 Moreover, H19/miR-675 axis has been shown to modulate apoptosis cell death of cardiomyocytes by influencing voltage-dependent anion channel 1 (VDAC1), which is one of the several pathways involved in the progression of diabetic cardiomyopathy.81 Based on a systematic review and in-silico analysis, Cristine Dieter and colleagues revealed that lncRNAs Anril, Hotair, Malat1, Miat, and Kcnq1ot1 are up-regulated in diabetes Mellitus patients compared with control subjects, and MEG3 is down-regulated, consistently.82\n\nLifestyle and oxidative stress\n\nEpidemiological evidence has indicated that environmental risk factors such as alcohol, smoking, high-fat diet, and physical inactivity could contribute to oxidative stress. In addition, environmental factors may play a crucial role in the pathogenesis of heart failure and non-communicable diseases.83 Some studies have demonstrated that ROS might regulate the activity and mechanism of tissues, including muscle, liver, bone, intestinal, and brain.83–85 Most tissues, especially muscle and adipose tissue, continuously produce ROS at low-level exercise intensity.85 ROS production indirectly or directly influences muscle activity by several mechanisms (metabolism, calcium homeostasis, contractility, and excitability), which causes skeletal muscle exhaustion during intense exercise.19\n\nMoreover, long exercise training, overtraining syndrome, and exhausting exercises trigger oxidative stress pathways.86 In contrast, prolonged and low/moderate-intensity training ameliorates endogenous antioxidant status. Based on the evidence, physical activity could up-regulate mitogen-activated protein kinase (MAPK), and NF-κB induces several hub genes and proteins involved in the homeostasis, inflammation, and antioxidant/oxidative intracellular.87\n\nPhysical activity and dietary modifications are two of the most effective nonpharmacological strategies for many chronic conditions, especially cardiovascular conditions.85 In addition, ample evidence has revealed that exercise training and physical activity positively affect the cardiovascular system by improving oxidative stress, apoptosis, mitochondrial biogenesis, metabolism, and autophagy.88 Endurance training could up-regulate the expression level of the PPARγ/Pgc-1α/Fndc5 pathway in the heart and muscle mice. Evidence indicated that FNDC5 (fibronectin type III domain containing 5) and its cleavage type, irisin, might have an essential role to play in energy regulation and metabolism. Several studies demonstrated that PPARγ/Pgc-1α/Fndc5 could trigger by physical activity and exercise training, which induced the white adipose tissue's browning, and enhanced weight and energy expenditure.89\n\nMoreover, Abedpoor and colleagues revealed that the consumption of the branched-chain amino acids (BCAAs) and endurance training significantly regulated the expression of the PPARγ/Pgc-1α/Fndc5 and mitochondrial biogenesis genes such as Tfam, Cox4i1, ATP5a1, ATP5b, and Sirt1.89 Interestingly, Bahadorani et al. demonstrated that BCAAs and physical activity modified the percentage of sperm lipid peroxidation and sperm parameters.90 On the other hand, ample evidence indicated that a High-fat diet and diet enriched in advanced glycation end products (AGEs) could dysregulate the detoxification status and increase the oxidative stress in the cells.84,91 Besides, endurance exercise and leucine consumption modified the hub genes and lncRNAs involved in the brain-gut axis in mice with depression-like behaviors.76 In the current study, the authors found common genes, including Kdr/Vegfα/Pten/Bdnf, between the hippocampus region and ileum tissue. Moreover, some mediators such as lncRNAs such as MEG3 (maternally expressed 3), GAS5 (growth arrest-specific 5), TUG1 (taurine up-regulated 1), and HOTAIR (HOX transcript antisense RNA) could target the Kdr/Vegfα/Pten/Bdnf hub genes and modified by endurance exercise and leucine consumption.76\n\nIn addition, several evidence indicated that lifestyles such as physical activity and unhealthy diets could impact fertility and sperm function.92,93 High-fat diet and diet enriched advanced glycation end products dysregulated the function, parameters, and intracellular reactive oxygen species of sperm.92 Furthermore, the high-fat diet enriched AGEs enhanced the inflammation and apoptotic signaling pathway in the intestinal of the mice.91 Based on these data, consuming the high-fat diet enriched significantly increased the IL-6, AGER (advanced glycation end products receptor), ZO-1, P53, and NF-κB. In this study, the relative expression of the Sirt-1 and Ddost were decreased by consumption of the high-fat diet enriched. In the other study, a high-fat diet enriched with AGEs significantly increased the relative expression of the IL-1ß, which induced inflammatory bowel disease (IBD).91 Based on these data, we could conclude that physical inactivity and unhealthy food enhanced the inflammation and oxidative stress in the whole body.\n\nEpidemiology studies revealed that a sedentary lifestyle and ultra-processed foods such as AGEs-rich meals and high carbohydrates distributed the defense mechanisms against oxidative stress, including the Nrf2-Keap1 signaling pathway and downstream genes such as HO1, Nqo1, Txn, and Gpx1. These hub genes could regulate antioxidant response elements. AGEs rich meals and physical activity significantly dysregulated the expression level of the Nrf2 HO1, Nqo1, Txn, Gpx1, and antioxidant capacity of the liver in diabetic mice. Notably, physical activity and herbal medicine reversed these hub genes and improved the antioxidant capacity, insulin and glucose concentration, and liver damage in diabetic mice. Impaired muscle mitochondrial function and biogenesis could be the other side effect of the sedentary lifestyle and ultra-processed foods. Hence, the mitochondrial markers were significantly decreased in response to a high-fat diet and ultra-processed foods. These results show that the relative expressions of the Cpt2, Tfam, Pgc-1α, mt-Nd1, mt-Nd5, Ndufa2, Cox8b, Cox5a, mt-Co2, and mt-Co1 were dysregulated. Notably, exercise training and dietary phytochemicals modified and improved the relative expression of genes related to the muscle mitochondrial markers (function and biogenesis) and β-oxidation.\n\n\nConclusion\n\nOverall, based on these studies, we could conclude that environmental and exogenous factors have a substantial role in regulating oxidative stress of the cell. Moreover, environmental risk factors could raise ROS production due to oxidative stress, which induces several signaling pathways, including apoptosis, inflammation, autophagy, necroptosis, and ferroptosis.\n\n\nData availability\n\nThere are no underlying data associated with this article.\n\n\nDeclarations\n\nN/A\n\n\nAuthors' contributions\n\nFatemeh Hajibabaie and Navid Abedpoor conducted the study design. The data mining was evaluated by Fatemeh Hajibabaie, Navid Abedpoor, and Faranak Aali. The manuscript was written by Fatemeh Hajibabaie, Navid Abedpoor, and Faranak Aali and was approved by Navid Abedpoor. The authors declare that all data were generated in-house and that no paper mill was used.", "appendix": "Acknowledgments\n\nWe thank our colleagues for their association and helpful discussions in this study.\n\n\nReferences\n\nOguntibeju OO: Type 2 diabetes mellitus, oxidative stress and inflammation: examining the links. Int. J. Physiol. Pathophysiol. 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Publisher Full Text" }	[ { "id": "182417", "date": "13 Jul 2023", "name": "Gladys Ko", "expertise": [ "Reviewer Expertise diabetic retinopathy" ], "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 (MS) by Hajibabaie et al. is a review on oxidative stress in diabetes with a focus on type 2 diabetes. While this MS is an extensive review, there are major issues that need to be addressed.\nThe title of the MS is about non-coding RNAs and hub genes, but in the text, not much of non-coding RNAs was discussed. The title does not reflect the MS. Since the text focuses on type 2 diabetes, the title should reflect it.\n\nThe writing is inconsistent. Few paragraphs are well written, but most paragraphs are difficult to read.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? No\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "182434", "date": "27 Jul 2023", "name": "Yi Song", "expertise": [ "Reviewer Expertise Diabetes and 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 manuscript entitled “Pathomechanisms of non-coding RNAs and hub genes related to the oxidative stress in diabetic complications” Hajibabaie et al. summarized the role of hub genes, non-coding RNAs, and unhealthy lifestyles on the pathomechanics and pathophysiology of diabetic vascular complications. The authors concluded that environmental risk factors could raise ROS production due to oxidative stress, which induces several signaling pathways.\nI have listed my concerns below:\nThe authors narrated vast amounts of background in Hub genes and Non-coding RNAs, and the interaction between each other, also they explain how the Hub genes, Non-coding RNAs and Lifestyle link with oxidative stress. However, the content is much far away from diabetes, or those links are not under the diabetic background.\n\nThe title should state the outline of the whole article, so could be revised as “Pathomechanisms of non-coding RNAs, hub genes and Lifestyle related to the oxidative stress”, the authors may summarise the passages relative with diabetes in a single part.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? No", "responses": [] } ]	1	https://f1000research.com/articles/11-1132
https://f1000research.com/articles/11-463/v1	26 Apr 22	{ "type": "Research Article", "title": "Prevalence of Musculoskeletal, Neurological and Physical Disorder After COVID-19 in Saudi Arabia: A Cross Sectional Study", "authors": [ "Hayam Mahmoud", "Anwar Ebid", "Mohammed Alghamdi", "Abeer Ibrahim", "Ahmed Almoosa", "Hayam Mahmoud", "Mohammed Alghamdi", "Abeer Ibrahim", "Ahmed Almoosa" ], "abstract": "Background: The global pandemic of SARS-CoV-2, or COVID-19 continues to attack all human systems. Although COVID-19 is a respiratory disease, various extra-pulmonary manifestations, including musculoskeletal and neuropathies/myopathies was reported. This study aimed to investigates the long-term impacts of COVID-19 infection on physical health, capability of daily life activities, musculoskeletal and neurological functions in the Kingdom of Saudi Arabia (KSA). Methods: A total of 499 adults recovered from COVID-19 infection of both sexes, who resided in the KSA were recruited randomly and invited to participate in this cross-sectional web-based survey. A self-administered structured questionnaire was used as an instrument of data collection. All respondents returned the questionnaire. Their responses were recorded, stored into a Microsoft Excel sheet 2010 and analyzed with the Statistical Package for the Social Sciences (SPSS) version 24. Percentages were used to convey descriptive data. The percentages were presented with a 95% confidence interval (CI). For statistical significance, a 0.05 p-value was used. Results: The overall prevalence of neurological and musculoskeletal disorders as follows: headache (63.1%), muscle ache or weakness (62.3%), vertigo (25%), concentration problems (21.8%), breathing troubles (20.4%), loss of balance (19.4%), seizure (1%), and Guillain-Barre Syndrome (0.6%). The results also revealed a significant association between the influence of COVID-19 infection and daily activities, gender and respiratory disorders. Conclusion: The findings highlighted and concluded that COVID-19 infection had an impact on respiratory, nervous, musculoskeletal systems and affect daily activities.", "keywords": [ "COVID-19", "headache", "muscle weakness", "respiratory difficulties", "physical activities" ], "content": "Introduction\n\nThe global pandemic of coronavirus disease 2019, commonly known as COVID-19, continues to spread. The clinical presentations of COVID-19 varied from asymptomatic to severe critical condition. Although COVID-19 is a respiratory disease, numerous investigations documented extrapulmonary signs and symptoms. Musculoskeletal complaints, myopathies, and neuropathies are common post COVID-19 clinical presentations.1 Patients with multiple manifestations ranged from asymptomatic or moderate (70% of cases) to severe or possibly fatal (30% of cases).2 Although the severity of the symptoms varied with age and medical history of chronic diseases (comorbidity, such as chronic cardiac disease, lung disease, diabetes, chronic renal disease, and cancer). The most common symptoms included fever, cough, shortness of breath, fatigue, myalgia, and gastrointestinal symptoms. These symptoms may last for a long time even after recovery.3,4 Symptoms might linger for weeks or months, and some people never return to their previous level of health.4\n\nIn this regard, the emergence of COVID-19 has compelled governments worldwide to take different steps and decisions to prevent the pandemic from spreading quickly.5 Social distancing, capacity constraints in public venues and private houses, isolation, quarantine, and curfew enforcement were among the preventative measures employed.6 Saudi Arabia have been eager to apply social distancing and quarantine in order to avoid illness spread.\n\nAs a result, those preventative measures may have physical, emotional, and psychological impacts on people’s life. According to Mattioli et al., precautionary measures had a negative impact on individuals, the society, and the economy which resulted in (a) an increase of community anxiety and tension, (b) an economic decline, (c) decreased outdoor exercises and overall physical activity (PA), (d) and development of both stress and depression, which can lead to unhealthy dietary habits.5,7\n\nAlthough there are numerous examples of long-term problems after COVID-19 infection, there is lack of research to support. There was a loss in patients’ functional capacity, which was correlated to the reduction in numbers of health-related quality-of-life indices. There was also evidence of cognitive problems, such as confusion and memory loss. High blood pressure, obesity, and mental health disorders were identified as risk factors for the persistence of these symptoms.6 The importance of physical therapy in dealing with these issues should not be overstated. It is crucial to begin studying the long-term effects of COVID-19 infection.7 To our knowledge, there is a lack of information and no previous study on the correlation between the prevalence of neurological, musculoskeletal, and physical disorders and COVID-19 in KSA. So, we aimed in this study to determine the long-term impacts of COVID-19 on physical health, daily life activities, musculoskeletal and neurological functions in the KSA.\n\n\nMethods\n\nThis was an analytical cross-sectional survey study. The King Abdullah International Medical Research Center (KAIMRC) approved and considered this study ethically feasible (Approval study number: SP21J/015/02, E-CTS Ref. No. JED-21-427780-20935 and IBR NCBE Registration No.:H-01-R-005).\n\nA total number of 499 patients of both genders, aged from 20 to 60 years old who had issues following COIVD-19 and lived in Saudi Arabia were included in this study. All participants received full information and an explanation of the study’s objectives, advantages, and any potential hazards associated with participation. All participants signed an informed consent form indicating their willingness to participate in this study. A random sampling was performed based on city districts. This research was carried out between October 2020 and March 2021.\n\nThe required sample size was calculated using Raosoft sample size calculator (Raosoft, Inc., Seattle, WA, USA), with a confidence interval of 99%, a response rate of 70%, and a margin error of 5%. The sample size was 1200 participants. A two-stage sampling approach was employed to select participants, with a random sampling of participants from different district followed by a random selection of participants from those districts. During the first sampling stage, random selection was conducted on a list of patients in the hospital database and 520 patients returned the questionnaire. 21 respondents were excluded because of missing data. Finally, 499 respondents were included in this study (Figure 1).\n\nParticipants completed a structured self-administered questionnaire, which was subsequently uploaded to an online survey software (Google Forms), as well as an instant messaging application (WhatsApp). The objective of the study, consent information to assure voluntary participation, as well as participants’ anonymity and confidentiality, were all included in the introduction section of the questionnaire. The questionnaire was easily accessible to the participants. Their responses were exported and analyzed once collected. The 17-question questionnaire yielded the following results: (a) Demographic characteristics, (b) Work or occupation, (c) Exercises performed prior to COVID-19 infection (type, frequency and duration), (d) Daily habits and tasks, (e) Chronic disease complaints (high blood pressure, heart and lung diseases, diabetes, cancer), (f) Duration of COVID-19 infection, (g) Accompanied Symptoms during COVID-19 infection (whether the symptoms persisted after recovery, duration and the target symptoms persisted). All the questions were written in basic, brief, and straightforward language, and the responses were organized in a straightforward manner.\n\nThe responses were gathered using a Google form. The survey link was sent to potential participants via WhatsApp and email. To increase the response rate, two reminders were sent at three-days interval and the responses were organized in a Microsoft Excel sheet 2010.\n\nThe results were analyzed with SPSS version 24 (SPSS Inc, Chicago, Illinois, USA) (RRID:SCR_002865). Chi-squared test was performed to calculate the percentages and correlations between categorical variables in the descriptive analysis. Percentages with a 95% confidence interval were also computed. The significance level was established at a p-value of 0.05. ANOVA test was utilized to compare the disability scores among participants. Since the duration of long-term symptoms was skewed, the median and interquartile range (IQR) were chosen to summarize the data. For categorical and ordinal variables, proportion was used.\n\n\nResults\n\nA total of 499 responses were presented and analyzed. Duration of persistent symptoms was set from one month to three months. Females made up nearly 70% of the samples, with the majority aged under 45 years. Among the participants, 245 (49.1%) were employed, including 60 (24.9%) civilian workers, 38 (15.8%) military members, 37 (15.4%) medical workers, and 254 (50.9%) were unemployed. Out of 499 respondents, 275 (55.1%) of the participants reported that they had practice of exercising before COVID-19 infection (mostly walking, 67.6%), while 224 (44.9%) had not participated in any type of exercises before COVID-19 infection. 394 (69.9%) females were affected, while 150 (30.1%) men were affected. Most of them (420 = 84.2%) were under 45 years old, and 79 (15.8%) were over 45 years old. 405 (81.2%) of the participants came from the Western region of Saudi Arabia. About 118 (23.6%) of the participants had chronic diseases, including respiratory disease (42 = 8.4%), diabetes mellitus (DM) (41 = 8.2%), hypertension (HT) (26 = 5.2%), cancer (5 = 1.0%), and cardiac disorders (3 = 0.6%). 381 (76.4%) participants were free of chronic diseases (Table 1).\n\nIn this study, headache (63.1%) was the most reported symptom after COVID-19 infection, followed by muscle ache or weakness (62.3%), vertigo (25%), concentration problems (21.8%), breathing troubles (20.4%), and loss of balance (19.4%). On the other hand, five cases of seizure (1%, four cases of intermittent seizure and one case of continuous seizure), and three cases of Guillain-Barre Syndrome (0.6%) have been documented and were the least common symptoms. Many participants were suffering from more than one persistent symptoms after COVID-19 infection, so the percentages were more than 100 percent (Table 2).\n\nCertain symptoms, such as breathing problems and muscle discomfort or weakness persisted after COVID-19 infection had cleared up in a median duration of 30 days and an interquartile range of 45 days. Regarding muscle pain, back muscles were the most affected (122 = 24.4%), followed by lower limb muscles (77 = 15.4%), neck muscles (30 = 6.0%), pelvic muscles (19 = 3.8%), and upper limb muscles (17 = 3.4%) (Table 3).\n\nMany participants in this study showed a link between reported symptoms and certain physical activity performance after COVID-19 infection. Gender and physical activity performance were shown to have a significant relationship in 146 (29.3%) of participants (p = .001). There were 118 (80.8%) females and 28 (19.2%) males. There was a significant link between persistent symptoms’ impact on physical activity performance and respiratory disease (p = 0.017), with 330 (93.5) patients without respiratory diseases recording no persistent symptoms on physical performance and 127 (87.0) patients with respiratory diseases recording persistent symptoms on physical performance. No significant association were found between physical activity performance after COVID-19 infection and the habit of exercising before COVID-19 infection. 80 (54.8%) of the subjects had habit of exercising before the infection, whereas 66 (45.2%) had not. Furthermore, 195 (55.2%) had habit of exercising before the infection, which had no effect on their physical activity performances, while 158 (44.8%) had no habit of exercising before the infection and had no complaints of physical performance performances.\n\nA majority of 353 participants (70.7%) do not record any association between persistent symptoms and certain physical activity performance, 231(65.4%) were females and 122 (34.6%) were males. Patients without hypertension had the highest comorbidity value of 337 (95.5%), followed by those without respiratory diseases (330 = 93.5%), non-diabetic patients (323 = 91.5%), diabetic patients (30 = 8.5%), patients with respiratory diseases (23 = 6.3%), and patients with hypertension (16 = 4.5%) (Table 4).\n\nAdditionally, participants who recorded persistent symptoms were asked to specify the frequency of symptoms. However, significant association was found between gender and frequency of symptoms (from 58 participants who recorded symptoms to be always persisting); females (47 = 81%) recorded higher frequency than males (11 = 19%), as shown in Table 5. Another significant association was discovered between respiratory disorders before infection and the prevalence of persistent symptoms, (p < 0.001). The findings showed that 280 (98.2%) of those who had no respiratory disorders before COVID-19 infections had no symptoms after the infection, while 5 (1.8%) of those who had respiratory diseases before COVID-19 infection had no symptoms after the infection.\n\nTable 5 provided more information about the participants who reported the presence of symptoms occasionally while performing everyday activities, 133 (85.3%) without respiratory diseases and 23 (14.7%) with respiratory diseases. Other demographic data and comorbidities failed to reveal any statistically significant association between the impact and physical activity (age, practicing exercises before infection).\n\n\nDiscussion\n\nTo our knowledge, this is the first study to evaluate the prevalence of musculoskeletal, neurological and physical disorder after COVID-19 in the KSA adult population and their relationship with physical activities. The purpose of the current study is to determine the prevalence of musculoskeletal, neurological, and physical health problems after COVID-19 infection, as well as how it affects the capability of daily life activities. Overall, this study found that musculoskeletal, neurological, and physical activity were negatively affected after COVID-19 infection. This study involved 499 participants. According to demographic data, the percentage of women infected COVID-19 (349 = 69.9%) was higher than that of men (150 = 30.1%). This is different from a previous study in the KSA, in which the authors reported a higher prevalence among males than females. This is agreed with the percentage of total daily cases reported in the same study, in which male was decreased by 18.0%, compared to a 150% increase in females.8 Participants under 45 years old were also more impacted (420 = 84.2%) than those over 45 years old (79 = 15.8%), which matched the findings of a pervious study (Alyami et al., 2020) that COVID-19 was more prevalent in adults than in children and elderlies. Our findings revealed that 275 persons (55.1%) had practiced physical activities before COVID-19 infection, which is higher than that reported by the General Authority for Statistics in 2019.9 This could be due to the larger sample size and increased awareness of the health benefits of physical activity among the Saudi population.\n\nLow back pain was the most frequently recorded symptom among the participants after COVID-19 infection. The results are similar to those reported in a cross-sectional study conducted in Riyadh, Saudi Arabia with a sample of 463 participants. The reason for this is most likely owing to the detrimental impacts of quarantine for most nations during the Corona epidemic, as stated in a cross-sectional study done in Riyadh, Saudi Arabia with a sample size of 463 people. Sitting for long periods during quarantine may reduce lumbar muscle activity, which overloads the body’s passive tissues, such as intervertebral discs and ligaments.10 Furthermore, pain in the lower limb muscles was identified as the second most prevalent muscle pain in this study, which coincided with the previous study and could be due to the same reasons that produce low back pain.10 The presence of musculoskeletal manifestations in the current study findings could be explained by the fact that the Saudi Arabian government’s quarantine decree, as well as its strict implementation to ensure the preservation of public health for all people and the commitment of all people to it, which influenced the population’s lifestyle in terms of physical activity, dietary habits, and mental health. This phenomenon contributed to musculoskeletal problems, supported by multiple studies showing that physical activity rates were dramatically reduced, and food habits were negatively impacted following the lockdown.11 The high prevalence of muscle discomfort, particularly low back pain and other musculoskeletal complaints, may be explained by long hours of screen usage for work and education.\n\nIn this study, the impacts of COVID-19 on physical activity were recorded, and certain parameters such as gender and respiratory disease were found to be significantly related. The proportion of females who reported an impact on physical activity was 33.8%, compared to 18.67% of males (i.e., participants who declared that COVID-19 infection had a negative impact on their physical activity), like another finding, in which patient’s walking time was significantly reduced six months after the onset of persistent symptoms after COVID-19 infection.12 It could also be due to the muscle mass in male bodies and the fact that males, on average, engage in more physical exercise than females. Another viewpoint is that females are more likely to babysit and care for their children’s schooling, which has unquestionably altered substantially and become a bigger burden during COVID-19 pandemic, owing to quarantine and social isolation.\n\nCOVID-19 infection had a greater influence on physical activity among respondents with respiratory disease, which could lead to a negative impact on patients’ physical activity and cause further difficulties. However, more research is needed to confirm this link. Most people become sedentary as a result of the shift in lifestyle and the transformation of work and education to teleworking and tele-education. Impacts of COVID-19 was thoroughly documented in literature both locally and globally.11,12 Physical activity was found to be strongly affected by quarantine and course of disease in a systematic review of 15 publications.11 Furthermore, the reduction in physical activity after COVID-19 has a severe impact on people’s mental health and could lead to a variety of psychiatric problems.13\n\nDuring the COVID-19 pandemic, the prevalence of physical activity among participants was drastically reduced. Both active and inactive people became less active than they were before the lockdown.14,15 In Saudi Arabia, a survey-based study with 2,255 participants found comparable results, with more than half of respondents reporting a drop-in physical activity.10 However, the current study found a more significant link between COVID-19 infection and persistent symptoms in diabetic patients than non-diabetic patients, and in hypertension patients than patients without hypertension, which is supported by another study that found a higher prevalence of comorbidities with DM (68.3%), and hypertension (42.6%) after COVID-19 infection.16 As a result, patients with diabetes and chronic hypertension should be cautious about the long-term effects of COVID-19 infection on physical activity and muscular soreness after recovery.\n\n\nConclusion\n\nCOVID-19 had impacts on respiration, muscle strength, and daily activities. After COVID-19 infection, muscle ache and headache persisted in higher proportions than the other symptoms. Capability of daily activities was correlated to gender, respiratory diseases, diabetes, and hypertension.\n\nCohort studies with sufficient follow-up duration should be performed for more informative and precise results. Larger sample size will be needed in future studies for more generalized results.\n\n\nData availability\n\nFigshare: Underlying data for ‘Prevalence of Musculoskeletal, Neurological and Physical Disorder After COVID-19 in Saudi Arabia: A Cross Sectional Study\n\nThe project contains the following underlying data:\n\nFlow diagram of sample selection: 10.6084/m9.figshare.18585995\n\nTables: 10.6084/m9.figshare.18586016\n\nRaw data: 10.6084/m9.figshare.18586034\n\nSTROBE-checklist for observational study: 10.6084/m9.figshare.19161485\n\nThe project contains the following extended data:\n\nQuestionnaire:10.6084/m9.figshare.19161620\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication)", "appendix": "Acknowledgement\n\nThe authors would like to thank the Deanship of Scientific Research at Umm Al-Qura University for supporting this work by Grant Code: (22UQU4331100DSR01).\n\n\nReferences\n\nChan JF, Yuan S, Kok KH, et al.: A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020 Feb 15; 395(10223): 514–523. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTabish SA: Tackling SARS-CoV-2 Pandemic: The Way Forward. Health. September 25, 2020; 12(9): 1202–1216.Publisher Full Text\n\nAssiri A, Al-Tawfiq JA, Al-Rabeeah AA, et al.: Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study. The Lancet Infectious Diseases. 2013 Sep; 13(9): 752–761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinghal T: A Review of Coronavirus Disease-2019 (COVID-19). Indian Journal of Pediatrics. 2020 Apr; 87(4): 281–286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŠagát P, Bartík P, Prieto González P, et al.: Impact of COVID-19Quarantine on Low Back Pain Intensity, Prevalence, and Associated Risk Factors among Adult Citizens Residing in Riyadh (Saudi Arabia): A Cross-Sectional Study. International Journal of Environmental Research and Public Health. 2020 Oct 6; 17(19): 7302. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLong-term effects of COVID-19: 2020, September 11. Reference Source\n\nMarshall M: The lasting misery of coronavirus long-haulers. Nature. 2020, September 14; 585: 339–341. PubMed Abstract \| Publisher Full Text\n\nAlyami MH, Naser AY, Orabi MAA, et al.: Epidemiology of COVID-19 in the Kingdom of Saudi Arabia: An Ecological Study. Frontiers in Public Health. 2020 Sep 17; 8(8): 506. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHousehold Sports Practice Survey Bulletin 2019. General Authority for Statistics. 2019. Reference Source\n\nŠagát P, Bartík P, Prieto González P, et al.: Impact of COVID-19Quarantine on Low Back Pain Intensity, Prevalence, and Associated Risk Factors among Adult Citizens Residing in Riyadh (Saudi Arabia): A Cross-Sectional Study. International Journal of Environmental Research and Public Health. 2020 Oct 6; 17(19): 7302. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBakhsh MA, Khawandanah J, Naaman RK, et al.: The impact of COVID-19 quarantines on dietary habits and physical activity in Saudi Arabia: a cross-sectional study. BMC Public Health. 2021; 21: 1487. PubMed Abstract \| Publisher Full Text\n\nAbdullahi A, Candan SA, Abba MA, et al.: Neurological and Musculoskeletal Features of COVID-19: A Systematic Review and Meta-Analysis. Frontiers in Neurology. 2020 Jun 26; 11(11): 687. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoërtz YMJ, Van Herck M, Delbressine JM, et al.: Persistent symptoms 3 months after a SARS-CoV-2 infection: the post-COVID-19 syndrome?. ERJ Open Research. 2020 Oct 26; 6(4): 00542–02020. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nViolant-Holz V, Gallego-Jiménez MG, González-González CS, et al.: Psychological Health and Physical Activity Levels during the COVID-19 Pandemic: A Systematic Review. International Journal of Environmental Research and Public Health. 2020 Dec; 17(24). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu K, Wei X: Analysis of Psychological and Sleep Status and Exercise Rehabilitation of Front-Line Clinical Staff in the Fight Against COVID-19 in China. Medical Science Monitor Basic Research. 2020 May 11; 26: e924085. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlguwaihes AM, et al.: Diabetes and Covid-19 among hospitalized patients in Saudi Arabia: a single-centre retrospective study. Cardiovascular Diabetology, [s. l.]. 2020; 19(1): 205–212. PubMed Abstract \| Publisher Full Text" }	[ { "id": "143364", "date": "01 Aug 2022", "name": "Salah Abd Elmonem Sawan", "expertise": [ "Reviewer Expertise Physical therapy and movements disorders" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is valuable and it is clear, simple and with good sound but I have some questions and I need the answers from the authors:\n1. How could they assure that the link they sent for the patients was only for Saudi people? i.e., Is it possible to provide the reader with a simple explanation of how to send the query to Saudis only, that is, how can you ensure that the link sent was answered by Saudis only because you made this query for Saudis only?\n2. How was the query carried out, and how were the questions added? Have you hired a specialist to review the questions about the questionnaire? Was it approved and reviewed by a specialized authority? If you have, please add this to the paper in methodology section.\n3. Was the survey (Questionnaire) provided in Arabic language or in another language?\n4. Are there any further symptoms following COVID-19 were not mentioned at the paper?\n5. Were there another symptoms specific to people who have been vaccinated against the Corona virus at this work?\nThank you.\n\nDr Salah Sawan\n\nIs the work 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": "8628", "date": "06 Sep 2022", "name": "Anwar Ebid", "role": "Author Response", "response": "Dear Professor, Salah Sawan Thank you so much for your comments. The authors are grateful for the reviewers' voluntary contributions in the form of insightful comments that have assisted us in improving our manuscript. The authors have made every effort to revise the manuscript in response to your comments. In response to your suggestions, we have published an updated version of this article. Please consider these new versions to be the revised version of this article. Thank you very much. Regards, Authors The paper is valuable and it is clear, simple, and with good sound but I have some questions and I need the answers from the authors: 1. How could they assure that the link they sent for the patients was only for Saudi people? i.e., Is it possible to provide the reader with a simple explanation of how to send the query to Saudis only, that is, how can you ensure that the link sent was answered by Saudis only because you made this query for Saudis only? Reply: The King Abdullah International Medical Research Center (KAIMRC) was in responsible of selecting Saudi participants at random using a filing system and distributing the questionnaire via WhatsApp. 2. How was the query carried out, and how were the questions added? Have you hired a specialist to review the questions about the questionnaire? Was it approved and reviewed by a specialized authority? If you have, please add this to the paper in the methodology section. Reply: The research team first prepared the query, which was then sent to two different Arabic specialists to modify and correct any Arabic errors before being sent to a documented English translation office to prepare the final version of the questionnaire. It was reviewed by the ethical committee in The King Abdullah International Medical Research Center (KAIMRC). The questionnaire was submitted as a preliminary sample to see if there were any issues with it. The response was added to the methodology section. 3. Was the survey (Questionnaire) provided in Arabic language or in another language? Reply: Yes: The survey was provided in Arabic and English version after reviewing by specialists, also it was reviewed by the ethical committee in The King Abdullah International Medical Research Center (KAIMRC) 4. Are there any further symptoms following COVID-19 were not mentioned at the paper? Reply: All symptoms following COVID-19 mentioned with the respondent were reported in the paper 5. Were there another symptoms specific to people who have been vaccinated against the Coronavirus at this work? Reply No: There were no symptoms specific to people who had been vaccinated against the Coronavirus at this work. The questionnaire was only used to assess and collect symptoms after Covid-19, and we did not test for vaccine effect." } ] } ]	1	https://f1000research.com/articles/11-463
https://f1000research.com/articles/12-1139/v1	12 Sep 23	{ "type": "Study Protocol", "title": "Comparative evaluation of periapical healing in response to calcium hydroxide, polydimethyl siloxane and calcium silicate based endodontic sealers using radiograph", "authors": [ "Utkarsh Umre", "Shweta Sedani", "Pradnya Nikhade", "Akansha Vilas Bansod", "Abeer Mishra", "Shweta Sedani", "Pradnya Nikhade", "Akansha Vilas Bansod", "Abeer Mishra" ], "abstract": "Background: Success of root canal treatment depends upon 3-D seal obtained after obturation without any presence of post-operative symptoms. The focus of this investigation is on ability of a sealer to form 3D seal and to reduce periapical lesion. The study aims to evaluate periapical healing of teeth treated with calcium hydroxide, polydimethyl siloxane and calcium silicate based endodontic sealers using radiograph. The objectives of this study will be to evaluate periapical healing ability of root canal treated teeth with Sealapex, Nanoseal-S and Bio-ceramic sealers over the time period of 3, 6 and 9 months; and to compare the periapical healing ability of a root canal treated tooth. Methods: A total of 60 subjects having periapical radiolucencies will be divided into 3 groups of 20 subjects each; Group I- Calcium hydroxide based, Group II- Polydimethyl siloxane based and Group III- Calcium Silicate based sealers. Root canal procedure will be done. Patients will be recalled after 3, 6, 9 months for the evaluation of periapical healing and PAI score check-up using intraoral periapical radiograph. Expected results: It is expected that among the material used in the study Bio-Ceramic and Nanoseal-S sealer may give better results as compared to Sealapex used in routine practice due to its ability of anti-microbial properties, optimal biocompatibility and excellent sealing ability. Conclusion: Comparison amongst the three sealers would provide us with the information about the best material which offers better periapical healing to get the best outcome of the root canal treatment by clinician.", "keywords": [ "Periapical healing", "Calcium hydroxide", "Polydimethyl siloxane", "Calcium Silicate based endodontic sealers." ], "content": "Introduction\n\nThe ability to effectively obturate the prepared root canal space is one of the cornerstones to successful root canal therapy. Sealer and Gutta-percha can be used to effectively obturate the canal space.1 According to “Ingle and Bakland”, 60 percent of endodontic failures are caused by improper root canal obturation. Obturation’s main goal is to accomplish 3D hermetic sealing of the pulp chamber in order to form a fluid-tight seal and inhibit the invasion of the germs and toxins into the periapical tissues. Because of the complexity of the root canal system, a variety of procedures and sealers have been developed to ensure a perfect seal. The root canal sealer’s job is to create a link between the root dentine and core material, successfully preventing leaking.2\n\nSeveral sealers contain antibacterial or therapeutic substances like calcium hydroxide or corticosteroids, despite the fact that current endodontics prioritises sealing and biocompatibility characteristics of the materials. An endodontic sealer must strike a precise balance between cytotoxicity and antibacterial characteristics.3\n\nThrough the apical foramina and lateral canals, sealants placed in root canals can potentially inhibit the repair of periodontal tissue.4 Localized inflammation caused on by root canal obturation materials may lead to postoperative pain. It has been linked to a variety of treatment factors, including WL evaluation using an apex-locator hooked up to each of the file, the number of appointments, equipment selection, and selection of the root canal sealer.5 The severity of inflammatory reactions is determined by various elements, the most important of which is the sealer’s composition. Bio-ceramics are metal oxides or ceramic materials that have improved antibacterial and antifungal activity, improved sealing and also they are biocompatible, are used in dentistry and medicine.6 “NanoSeal-S” is a root canal sealer; polydimethyl siloxane-based that is cold flowable and contains nano silver in chemical form. It has great sealing properties as well as good radio-opacity. Silver is used as a preservative in chemical form. This study compares and evaluates the periapical healing response to calcium hydroxide, polydimethyl siloxane, and calcium silicate based endodontic sealers using radiographs.7\n\n\nProtocol\n\nThe study will be conducted in “Sharad Pawar Dental College, in Department of Conservative Dentistry and Endodontics.” The outpatient department will pick a total of 60 people requiring endodontic treatment with Periapical radiolucency of teeth ranging from 0.5 mm – 8 mm. Patient will be informed priorly about the procedure to be done and written consent will be taken. Detailed case history will be recorded to properly evaluate the symptoms of irreversible pulpitis and the teeth with periapical radiolucency. Sixty participants who met the inclusion criteria were asked to choose a paper chit from one of three sealer groups: group I consisted of participants who chose the sealer based on calcium hydroxide, group II consisted of participants who chose the sealer based on polydimethylsiloxane, and group III consisted of participants who chose the sealer based on calcium silicate, as shown in Table 1. In this way, random sampling of the participants was done by chit picking.\n\nSample size calculation: 60\n\nSample Size formula:\n\nWhere’s\n\nX2 is the chi square value at 5%. level of Significance for I degrees of freedom = 3.84\n\nP = 50%. proportion = 0.50\n\nN = No. of patients 64\n\nC = Confidence interval of one choice = 5% = 0.05\n\nn = 55 patients needed in the Study\n\nStatistical Method: Pearson’s Correlation Coefficient\n\nSoftware Used: SPSS 27-0 V, Graph Pad Prism 7.0v.\n\nFormula Reference: Prashanth D.7\n\nFor the ease of calculation and statistics sample size confirmed to 60 consisting of 20 subjects in each group.\n\nInclusion criteria:\n\n• Patients requiring endodontic treatment\n\n• Periapical radiolucency of teeth ranging from (0.5 mm – 8 mm)\n\nExclusion criteria:\n\n• Patients who are medically/systemically compromised (with systemic diseases, immunosuppressive disease or patients on medications)\n\n• Teeth wherein, there is inability to reach the full working length.\n\n\nMaterials\n\n\n\n1. Sealapex, Root canal Sealer: Compositions: Calcium hydroxide, barium sulfate, zinc oxide, titanium dioxide and zinc stearate. Manufacturer: SybronEndo, Glendora, CA, USA\n\n2. Nanoseal-S: Composition: Polydimethyl siloxane, Nano Silver powder, Silicone Oil, Platinum Catalyst, Zirconium Dioxide, Paraffin Liquid. Manufacturer: PrevestDenpro, USA\n\n3. Meta CeraSeal Calcium Silicate-based Bio-ceramic Root Canal Sealer: Composition: Calcium silicates, Zirconium oxide, calcium hydroxide, calcium phosphate, filler, and thickening agents. Manufacturer: Met biomed\n\nThe entire procedure will be performed under rubber dam isolation. Excavation of caries, and access-opening will be done using a round bur. Access will be refined with safe end bur. Pulp will be extirpated with suitable barbed broch. Working length will be established with apex locater and confirmed using IOPA. A glide path will be created using Path finder files. The “ProTaper Gold system” will be utilized to reshape the root canals. An “X-Smart endodontic motor” will operate every rotary file. To prevent over-instrumentation, the apex locator will evaluate the working length after each step. After each instrument, “2 mL 2% sodium hypochlorite (NaOCl)” will be used to irrigate the canals. Depending on the size of the apical foramen, the master file will range in size from F1-F5. Ending irrigation will be done using ultrasonic activation for a time period of 30 seconds with each solution “i.e., 2.0 mL NaOCl, 2.0 mL 17% EDTA, and 2.0 mL NaOCl per canal”. Canals will be dried using appropriate absorbent points till the canal is dry. Master cone fit will be checked clinically and radiographically. Sealer application will be performed using lentulo spiral and obturation will be done utilizing the appropriate GP point. Permanent restoration will be done with composite. Patient will be recalled after 3, 6, 9 months for the evaluation of periapical healing and PAI score check-up using Intraoral periapical radiograph.\n\nThe collected data will be compiled for additional statistical evaluation. Both descriptive and analytical statistical techniques will be used to analyse the data. The mean difference between measurements taken at intervals of three months, six months, and nine months will be examined for statistical significance. Statistical analysis of the collected data will be done using Statistical Package of Social Sciences V27-0 and Graph Pad Prism V7.0.\n\nAn ethical letter was issued from the Datta Meghe Institute of Higher Education and Research’s ethical committee for carrying out the study. IEC No.: DMIMS (DU)/IEC/2022/769.\n\n\nExpected results\n\nIt is expected that among the material used in the study Bio-Ceramic and Nanoseal-S sealer may give better results as compared to Sealapex used in routine practice due to its ability of anti-microbial properties, optimal biocompatibility and excellent sealing ability.\n\nIn this comparative study, the results expected are the superiority of one sealer over the other and hence, we could make better choice amongst the different sealers available in the market to produce successful outcome.\n\nConceptualization and piloting of study.\n\n\nDiscussion\n\nComparison among the endodontic sealers to evaluate its efficacy and clinical results have been performed by many authors. An author conducted the study where 3 sealers were used and evaluated. The materials investigated that included Proco-Sol, an epoxy resin, AH26, and Klorperka N0, a “resin-guttapercha-chloroform sealer,” which is based on zinc oxide and eugenol. Periapical lesions’ healing was observed for three years. Despite the fact that there were no statistically significant differences between the groups, the response to Kloroperka N0 seemed to be considerably lower than the responses to the other two groups.8\n\nAnother researcher evaluated the clinical and radiological results of three sealers, two of which contain calcium hydroxide. At the time of root filling, 204 teeth were assigned to one of three groups: PS group gutta-percha filled teeth and Procosol sealer; CR group, gutta-percha filled teeth and sealer CRCS; and SA group, gutta-percha filled teeth and Sealapex sealer. Overall, the treatment result were equivalent to, but slightly worse than, those previously reported from patients examined at the University of Oslo’s Dental School. The total effect of the sealer on the treatment outcome was found to be minor. Although root fillings with Ca (OH)2 may promote faster healing of the apical periodontitis or surgical damage, the subsequent results 3 to 4 years were comparable for zinc oxide-eugenol–based sealers with or without Ca (OH).9,10\n\nIn the other study, Colombo M et al. conducted a study on 810 roots to evaluate performance of endodontic sealers 810 roots were used to examine and evaluate the experimental clinical performance of endodontic sealers: Kloroperka N-0®, AH 26®, and ProcoSol®. Lateral condensation of gutta-percha and sealer by undergraduate students were done using a uniform technique. Prior to filling, the sealer was chosen at random. The patients were seen for a clinical and radiographic control assessment every year for four years, with the radiographs graded using the periapical index (PAI) grading system. Roots filled with or ProcoSol® or AH 26® had a better periapical state than roots filled with Kloroperka®. After one year, the change was considerable and lasted for the whole four-year observation period. The periapical index was found to be a good discriminatory tool for assessing treatment results in endodontics, outcome of endodontic treatment depends on the choice of sealer.11,12\n\nGeorge Taccio de Miranda’s investigation Canderio et al. investigated the physicochemical properties of Endosequence BC Sealer, a bio-ceramic root canal sealer.13 The results were compared to AH Plus cement in terms of radiopacity, pH, calcium ion release (Ca2+), and flow. ISO 6876/2001 criteria were used to assess radiopacity and flow. Metallic rings with a 10 mm diameter and a 1 mm in thickness were filled with cements for the investigation. The radiopacity was calculated using the radiographic density (mm Al). A flow-test was carried out using cement in 0.05 mL quantity on a glassslab. A weight of 120 grams was laid over cement with care. A computerised calliper was used to measure the greatest and smallest diameters of the discs created. With a spectrophotometer and a pH metre, the release of Ca2+ and pH were determined during a period of 3, 24, 72, 168, and 240 hours, respectively.14 The bio-ceramic endodontic cement has much lower radiopacity (3.84 mm Al) than AH Plus, according to their findings (6.90 mm Al). During the experimental periods, the pH and Calcium ions release of Endosequence BC Sealer was higher than those of AH Plus (P.05). AH Plus and BC Sealer had flow of 21.17 mm and 26.96 mm respectively, according to the flow test (P.05). According to ISO 6876/2001 recommendations, Endosequence BC Sealer demonstrated radiopacity and flow. The other physicochemical parameters investigated showed that a root canal sealer had favourable values.15\n\nIn our study we will be comparing the three endodontic sealers; it is expected that among the material used in the study Bio-Ceramic and Nanoseal-S sealer may give better results as compared to Sealapex used in routine practice due to its ability of anti-microbial properties, optimal biocompatibility and excellent sealing ability.\n\nThe study can provide us with the information about the best material which provide better periapical healing to get the best outcome of the root canal treatment by clinician. Further studies can be carried out using CBCT to get more accurate results over conventional intraoral periapical radiograph. Impossibility of controlling all variables such as varied healing time of patients may interfere with the results of the study.\n\nComparison amongst the three sealers would provide us with the information about the best material which offers better periapical healing to get the best outcome of the root canal treatment by clinician.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nEriksen HM, Brstavik D, Kerekes K: Healing of apical periodontitis after endodontic treatment using three different root canal sealers. Dent. Traumatol. 1988 Jun; 4(3): 114–117. PubMed Abstract \| Publisher Full Text\n\nWaltimo TM, Boiesen J, Eriksen HM, et al.: Clinical performance of 3 endodontic sealers. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2001 Jul 1; 92(1): 89–92. Publisher Full Text\n\nØrstavik D, Kerekes K, Eriksen HM: Clinical performance of three endodontic sealers. Dent. Traumatol. 1987 Aug; 3(4): 178–186. Publisher Full Text\n\nde Miranda Candeiro GT , Correia FC, Duarte MA, et al.: Evaluation of radiopacity, pH, release of calcium ions, and flow of a bioceramic root canal sealer. J. Endod. 2012 Jun 1; 38(6): 842–845. PubMed Abstract \| Publisher Full Text\n\nØrstavik D, Kerekes K, Eriksen HM: The periapical index: a scoring system for radiographic assessment of apical periodontitis. Dent. Traumatol. 1986 Feb; 2(1): 20–34. PubMed Abstract \| Publisher Full Text\n\nMishra P, Gupta S, Nikhil V, et al.: Root canal sealers: An review. IP Indian J. Conserv. Endod. 2020 Dec 15; 3(3): 69–74. Publisher Full Text\n\nPrashanth D: Recent advancements in medicated root canal sealers: An advanced step in creating bacteria free obturation. Int. J. Appl. Dent. Sci. 2017; 3(3): 37–41.\n\nAl-Haddad A, Che Ab Aziz ZA: Bioceramic-based root canal sealers: a review. Int. J. Biomater. 2016 May 3; 2016: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan MT, Moeen F, Safi SZ, et al.: The Structural, Physical, and in vitro Biological Performance of Freshly Mixed and Set Endodontic Sealers. Eur. Endod. J. 2021; 6(1): 98–109. PubMed Abstract \| Publisher Full Text\n\nSingh H, Markan S, Kaur M, et al.: Endodontic sealers: Current concepts and comparative analysis. Dent. Open J. 2015; 2(1): 32–37. Publisher Full Text\n\nColombo M, Poggio C, Dagna A, et al.: Biological and physico-chemical properties of new root canal sealers. J. Clin. Exp. Dent. 2018 Feb; 10(2): e120. Publisher Full Text\n\nTyagi S, Mishra P, Tyagi P: Evolution of root canal sealers: An insight story. Eur. J. Gen. Dent. 2013 Sep; 2(03): 199–218. Publisher Full Text\n\nde Miranda Candeiro GT , Correia FC, Duarte MA, et al.: Evaluation of radiopacity, pH, release of calcium ions, and flow of a bioceramic root canal sealer. J. Endod. 2012 Jun 1; 38(6): 842–845. PubMed Abstract \| Publisher Full Text\n\nRathi CH, Chandak M, Nikhade P, et al.: Functions of Root Canal Sealers-A Review. J. Evol. Med. Dent. Sci. 2020 Apr 27; 9(17): 1454–1458. Publisher Full Text\n\nBaras BH, Melo MA, Thumbigere-Math V, et al.: Novel bioactive and therapeutic root canal sealers with antibacterial and remineralization properties. Dent. Mater. 2020 Jan; 13(5): 1096. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "246901", "date": "14 Mar 2024", "name": "Olcay Özdemir", "expertise": [ "Reviewer Expertise Endodontics", "root canal sealers", "biocompatibility", "cytotoxicity", "nano materials." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor /Authors, I have carefully evaluated the submitted manuscript, entitled: Comparative evaluation of periapical healing in response to calcium hydroxide, polydimethyl siloxane and calcium silicate based endodontic sealers using radiograph.\nI have listed my comments below, appreciating the effort that the authors put into the study. Thank you very much. Reviewer comments\nAbstract section: 1. For the evaluated sealers the authors used commercial names in the introduction and results section, however in the material methods section the contents were used. In order to avoid confusion for the reader, it would be more appropriate to use standardized terms or to give content information in parentheses when using commercial names in the introduction section. 2. Kindly use 3-D or 3D. Use the chosen abbreviation in the same way in the rest of the article, in a standardized way.\nIntroduction:\n1. \"Several sealers contain antibacterial or therapeutic substances like calcium hydroxide or corticosteroids, despite the fact that current endodontics prioritizes sealing and biocompatibility characteristics of the materials. An endodontic sealer must strike a precise balance between cytotoxicity and antibacterial characteristics.3\"\nKindly check the article [6]. for current cytotoxicity any biocompatibility of the root canal sealers.\nLooking at the sentence, it seems as if these materials are widely used now. Although there are currently calcium hydroxide-containing materials, corticosteroid-containing root canal sealers are no longer in use, because the reference used is quite historical considering current material technology and developments.\n2. \"It has been linked to a variety of treatment factors, including WL evaluation using an apex-locator hooked up to each of the file, the number of appointments, equipment selection, and selection of the root canal sealer.5\" What is WL, explain first before the use of abbreviation.\n3. In my opinion, instead of dwelling on outdated information in the materials, emphasizing current innovations increases the impact of the article. For example, nano silver particles are very appropriate proposition in terms of materials and materials engineering for root canal sealers. It deserves a little more detail in the introduction section. And also, the calcium silicate containing are quite accepted for the clinical use and get attention, so nowadays they are widely used in clinical practice.\nKindly check the articles for your assistance [1],[2].\n\nMaterials and methods section:\n1. This is a clinical study, and for these types of the studies the standardization is a problem I understand but, the chosen patients are very variable 0.5- 8 mm ranging can cause statistical errors, especially Type II errors for a short period of time such as 9 months. What is your explanation for this situation? If this as a study protocol, treatment of teeth with more standardized PAI scores and follow-up for a longer period of time will provide much more clinically meaningful results.\n2. \" Working length will be established with apex locater and confirmed using IOPA.\" What is \"IOPA\"?\n3. Please kindly add brand and country information for used commercial materials and devices.\n\n4. There were a lot of abrevation, however there is no information about them. ( WL,IOPA, GP, PAI, etc...)\n5. Statistical analysis: Please add the set value of statistical significance.\n6. Irrigation activation techniques have been validated in increasing the success of current root canal treatment. Additionally, it increases paste penetration. I think it should be added to the protocol in a standardized way.[3]\n\nExpected Results:\n1. \"The study can provide us with the information about the best material which provide better periapical healing to get the best outcome of the root canal treatment by clinician.\"\n\nI think it would be a very wrong approach to use an expression such as \"the best material\" for a study that was evaluated over a period of only 9 months in terms of only 3 materials, some of which are not even current.\nPlease check these articles for your assistance [2].[4],[5]\nGeneral of report:\n1. In general, it may be better for the quality of the study to follow these guidelines when planning and reporting a study on endodontics. International Endodontic Journal (wiley.com)\nReferences:\n1. For such a clinical study that includes up-to-date materials, it is not enough to form the framework of the article based on 15 references, and in addition, the up-to-dateness of the articles is questionable.[1],[2],[3],[4],[5],[6]\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": [] }, { "id": "266144", "date": "03 Jun 2024", "name": "Mohamed Nagy", "expertise": [ "Reviewer Expertise 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\nThe article is a protocol for a clinical study comparing three endodontic sealers: Sealapex, Nanoseal-S, and Meta CeraSeal. Authors will evaluate periapical healing using Periapical index scores after 3, 6, and 9 months. The clinical relevance of the study is to find the best endodontic sealer among three tested sealers that leads to better clinical outcomes for patients undergoing root canal treatment. The protocol is well prepared, however I have some queries: Major points: 1. Inclusion of 0.5-8 mm lesion is very wide range. or sample size to be increased greatly 2. Please include the scoring system used for the Periapical Index (PAI) score to ensure consistent evaluation and cite the reference. Minor points: 1. Could you consider a more powerful randomization method like sealed envelopes or a computer-generated list to minimize selection bias?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "276984", "date": "06 Jun 2024", "name": "Wei Fan", "expertise": [ "Reviewer Expertise 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\nThis study aimed to compare the periapical healing response to different endodontic sealers, namely calcium hydroxide, polydimethyl siloxane, and calcium silicate-based sealers. I believe this article can be improved in the following aspects:\nStandardization\nStandardization is a key factor in ensuring the reliability and comparability of study results. The research design, although partly appropriate, could benefit from standardization improvements to enhance the study's validity.\n\n2. Standardization of Tooth type\nIt is not clinically reliable to compare periapical healing when there is a lack of homogeneity in the selection of teeth included in the analysis. Treating single-rooted teeth with a single canal in posterior teeth is recommended to enhance sample homogeneity. Efforts should be made during randomization to minimize the influence of factors like lesion extent, age, and gender on patient selection.\n\n3. Standardization of Treatment Procedures\nThe article lacks details on the number and timing of obturation visits, intracanal medicament, interim restoration, and obturation technique. So describing all treatment steps ensures consistent clinical protocols for all patients.\n\n4. Standardization of Size of the Periapical Lesion\nIncluding lesions ranging from 0.5 to 8 mm is a wide range and may lead to variability in the study results. So narrowing the lesion size range or increasing the sample size can enhance study validity.\n\n5. Outcome and Evaluation Methods\nAs mentioned in the abstract, success of root canal treatment depends upon the 3-D seal obtained after obturation without any presence of post-operative symptoms. To better reflect the purpose of the article, consider the following enhancements:\n\n6. Utilization of Cone-beam Computed Tomography\nIncorporate CBCT for long-term studies with strict evaluation criteria. CBCT provides detailed 3D imaging for better treatment outcome assessment.\n\n7. Comprehensive Outcome Analysis Include periapical healing assessment and other clinical symptoms (pain, sinus tract, mobility, and swelling) in outcome analysis.\n\n8. Evaluation of Residual Walls in Bone Defects Consider recognizing the number and size of residual walls in bone defects as a prognostic factor.\n\n9.The innovation of the study: Introduce more innovative types of sealers to expand the depth and breadth of the study.\nMinors comments\n\nIt is recommended to use the corresponding scientific and commercial names in the text to ensure readers have a clear understanding of the materials and products being used. Avoid using abbreviations directly when first introducing a term; use the full name instead. Avoid using non-standard abbreviations.\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": [] } ]	1	https://f1000research.com/articles/12-1139
https://f1000research.com/articles/12-1138/v1	12 Sep 23	{ "type": "Study Protocol", "title": "A Community-based cross-sectional study for assessment of the e-waste disposal practices amongst people living in Wardha district, India", "authors": [ "Fatima Hasan", "Abhishek Ingole", "Abhishek Ingole" ], "abstract": "Introduction: The disposal of e-waste, often known as waste from obsolete electrical and electronic equipment, is a serious issue that receives little attention. Electronic products are becoming more and more affordable, allowing consumers to use and discard them as they see fit. This has an immediate and long-term impact on our health and our environment. Bulks of e-waste are typically recycled in the informal sector (which are often unregulated), placing the recyclers—often women and children—at risk for dangerous exposure. The study’s objectives are to document the extent of knowledge consumers have related to their e-waste disposal; assessing their awareness and general practices associated with e-waste management. Methods: The study will focus on young adults who are electronics buyers aged 18 years old or above and electronic shopkeepers. To evaluate and obtain insight into their e-waste disposal processes, a pre-tested questionnaire will be used. Study implications: The goal of the study is to address any knowledge gaps regarding how important it is for people to recycle or correctly dispose their-waste. It is unhealthy, and the consequences will have a downward impact on both our health and our surroundings in a significant way.", "keywords": [ "e-waste", "e-waste disposal", "recycling", "heavy metals", "toxicity" ], "content": "Introduction\n\nThe electronics industry is currently among the most rapidly expanding and largest in the entire globe. It has seen amazing growth over the past 25 years, which has created a sharp rise in outmoded electronics and, in succession, a considerable increase in the production of electronic waste in developed nations. The production of e-waste is projected to rise to 74.7 million tons by 2030 which will impact our environment and our health wholly. Only about 40% of the 64.5 metric tons of e-waste produced worldwide each year are adequately handled.1 By 2025, it is anticipated that India, one of the world’s major buyers of electronic goods, will move up to the fifth spot from 12th place in the purchase of electronic goods. E-waste is generated in India in amounts of about 800,000 tons per year, with 50,000 tons imported annually from other nations.2 Because of the amenities supplied by IT and communication systems, the world feels small because of how filled it is now with everything related to electronics.3\n\n22% of all the e-waste produced comes from individual houses. Even while individual households do not make a significant contribution to the garbage produced by computers, they consume a lot of consumer durables and could be considered prospective waste producers.4 E-waste, such as outdated televisions, mobile phones, monitors, and fax machines, may be improperly dumped, which might cause lead and other toxins to leak into the soil. These toxins can damage soil and groundwater as well as potentially evaporate into the atmosphere. Remainders from burning metals, plastics, and other air pollutants adhere to surfaces like crops and commercial goods. In metropolitan regions with efficient waste management systems, e-waste is discarded in landfills alongside regular trash. E-waste disposal releases toxic materials that get into aquifers and drinking water systems.1 Soil contains 25% of the world’s biodiversity. Vertebrates, invertebrates, parasites, bacteria, and fungi all contribute to the planetary cycles that sustain all life in the ocean. These free natural interactions enhance water purification, animal and human health, food safety, and the prevention and adaptation to climate change.5 Around the world, the three leading causes of death in children under five years old are pneumonia, diarrhea, and hunger, because of water that is contaminated and causes disease in children and adults.6\n\nAccording to statistics, every day, 8500 mobile phones, 5500 televisions, and 3500 personal computers are disassembled.7 E-waste is uncommon since the components of it are hazardous, harmful, and not biodegradable.8 Human health may be impacted by harmful substances and metals such polychlorinated biphenyls (PCBs), cadmium, lead, and mercury. Lack of knowledge on how to treat waste can frequently have detrimental effects on public safety and have significant negative environmental impacts.9 Heavy metal pollution comes from industry’ widespread discharges of nickel, lead, chromium, zinc, copper, mercury, and cadmium, among others.10 According to research,1 people who have burnt e-waste had raised blood lead levels. Humans who have been exposed to hazardous substances may experience learning disabilities, genitourinary diseases, immune system suppression, pulmonary and cardiovascular disease, hormone imbalances, immune system abnormalities, genetic defects, and dementia in later life. Women who are exposed to heavy metals often succumb to anaemia, hormonal problems, irregular menstrual cycles, autoimmune illnesses, and cancer of the reproductive system. Lead and mercury exposure in the first trimester of pregnancy has been associated to birth defects, low birth weight, spontaneous abortion, and problems with neurobehavioral development. Additionally connected to infertility is the burning of e-waste in open pits.1\n\nProper e-waste management encompasses reuse, regulated recycling, recuperation of materials, burning, and landfilling.8 These items create health risks when they are burned or disposed of in landfills because they contain harmful materials.11 There is widespread agreement that a clean environment is necessary.12 Due to the quick development of new technology, electrical and electronic equipments (EEEs) have become obsolete quickly after purchase.13 India adopted laws under the Ministry of Environment and Forests (MoEF) that specifically address this issue. The e-waste (Management and Handling) Rules were passed by the Indian Federal Government through the MoEF in 2011 and went into effect in May 2012 as a result of intense advocacy and pressure from the civil society. The “Implementation of E-Waste Rules, 2011” bill, which was the first to specifically address the problem of e-waste, effectively mandated that producers, collecting facilities, dismantlers, and recyclers adhere to WEEE (Waste from Electrical and Electronic Equipments) policies. Additionally, these regulations offered recommendations for handling hazardous waste sustainably by both families and small enterprises. Understanding of this government policy and the risks of e-waste among the general people is essential for both vigorous involvement in management systems and the power to pressurize producers to comply.14\n\nTo safeguard, direct, and encourage safe e-waste management, India adopted a special electronic waste management policy, however plenty of its inhabitants have no comprehension of the regulations. As a result, there is a shockingly low degree of public awareness in India regarding the correct disposal of electronic devices and their adverse effects. Raising the general populace of the significance of e-waste reduction is the greatest way to fight the enormous rise in the sheer mass of e-waste in dumpsters and the harm it does to both the environment and human wellness by cause of the increasing market for electronic gadgets. Use of fewer toxic, readily recoverable, and recyclable materials needs to be paid more thought.1\n\nThe three Rs—Reduce, Reuse, and Recycle—are the guiding principles for all waste management practices.15 Similar to solid trash, proper management of e-waste necessitates active consumer participation, which results from their awareness of numerous e-waste-related issues. This would result in the proper accumulation and scrapping of e-waste at the point of usage. When district authorities develop appropriate disposal mechanisms and consumer knowledge, it is possible to handle e-waste in a formal, structured, and environmentally advantageous way. The goals of the current proposal were to evaluate consumer knowledge, awareness, and habits about numerous facets of managing e-waste and to identify the numerous socioeconomic factors connected to that knowledge.2\n\nIt is now difficult to survive without a cell phone or other electronic devices due to recent advances in science and technology. From institutional users to families, the usage of electrical and technological equipment has significantly expanded. Every person generates electronic waste because it is uncommon for a household to be without a television or other electronic appliances.\n\nBecause the government, health professionals and others constantly educating and informing the public about its effects, people are familiar with the term “biomedical waste,” yet the determinacy of e-waste and its ramifications remain a riddle. While some people are aware of the negative health effects of lead, a general understanding of how lead and mercury are mostly used in electronic equipment is still lacking.16 As a result, the study’s primary goal is to determine how well the general population understands e-waste and its effects.\n\nThose who carelessly dispose of their electronic waste will find this study to be helpful. This study is for everyone who are unaware of the fundamentals of e-waste and its enormous influence on people’s lives. By identifying the attitudes, knowledge, and perceptions surrounding e-waste and assessing how it affects peoples’ lives in the long run, the relevance of the study may be ascertained.\n\nThe study is required in order to:\n\n1. Identify knowledge gaps about the importance of appropriately managing our e-waste disposal.\n\n2. To ascertain the connection between e-waste knowledge and perception and independent variables including age, gender, occupation, education, and average income.\n\n3. To determine what impact e-waste has on our health.\n\n4. To assess community understanding of various e-waste topics.\n\nThe aim of this research is to document the level of awareness that consumers and owners of electronic stores have regarding the disposal of their e-waste while also evaluating their general awareness and e-waste management procedures.\n\nThe primary objective is to gauge the knowledge and awareness level of consumers and electronic shopkeepers about various aspects of e-waste and how is it crucial to dispose our electronic waste in a safe and standardized manner.\n\nThe secondary objectives are to determine the numerous aspects, such as socio-demographic parameters, which are related to awareness of e-waste disposal, and to assess whether levels of education impact the knowledge related to our general environment.\n\n\nMethods\n\nThe study is a community based cross sectional study among the consumers and electronic shopkeepers of electronic equipment (EE) in Wardha city, Maharashtra, India.\n\nThe study will be conducted to assess the e-waste practices of people living in Wardha district which is a part of central India. District Wardha is located in Maharashtra’s Vidarbha area. The districts of Amravati, Yavatmal, Chandrapur, and Nagpur are located on the west, north, south, and east, respectively, of the district. A total of 6310 square kilometers make up the district. It is home to 1,391,890 inhabitants. Exposure and data collection using the questionnaire will start from August 2023. The district was selected for both convenience and the fact that both authors live there.\n\nThe study participants will be young adults aged 18 or above who are consumers and electronic shopkeepers aged 20 to 50 years. This is because adults over the age of 18 frequently and vigorously use their phones and change them without thinking about where to dispose of them, and because electronic shop owners receive a significant amount of daily e-waste. We will be able to more properly understand their knowledge, attitude, and practices. The study will be conducted using simple random sampling. A total of five localities of Wardha will be randomly chosen. We shall travel to the locality’s centre or any nearby intersection after selecting those five localities. By spinning a pencil, a random direction from the neighborhood’s centre will be chosen. We will move in the first direction that the pencil’s tip points. For the study’s purposes, we are focusing on the four directions of north, south, east, and west. For the data collection, the first household will be selected randomly and six households from each of the four directions will be selected providing 24 samples from a single locality. This will be used with all the remaining localities giving us a sample of 120 households. The choice of the young adults was made for two reasons: first, younger generations use EE more frequently than older generations,2 and second, their expertise will influence how e-waste is disposed of in the near future. For the objective of learning more about their methods and knowledge about the disposal and management of e-waste, a sample of electronic shopkeepers, numbering roughly 15–18 participants, will be chosen by consecutive sampling.\n\nInclusion criteria\n\nAll e-consumers who are 18 years of age or above and electronic shopkeepers of age 20 to 50 years will be eligible for participation in the study. We defined “e-consumer” for the study as any individual who uses, repairs, or offers for sale electrical and electronic products such portable devices, cooling systems, televisions, fridges, mobile phones, computers, and other residential equipment.\n\nExclusion criteria\n\n1. Those participants who show non-willingness to participate even after explaining the research methods and aims will be excluded.\n\n2. Locked households where no one will be available to collect the data from will be excluded, since we are taking six side by side houses from all the four directions each.\n\n3. People without electronic devices at the time of data collection will be excluded.\n\nVariables\n\nThe study variables will include:\n\n1. Socio-demographics and background of the participants\n\n2. Percentage of people who are about the methods of disposing-waste\n\n3. Frequency for changing mobile phones\n\n4. The language of participants\n\nThe secondary goal of the study is to determine whether sociodemographic background has an impact on people’s awareness, attitudes, and practices. As such, the criteria for selecting the variable were based on this fact. Language has also been regarded as a significant factor because India is a country where people utilise a variety of languages in daily life.\n\nThe research tool consists of a structured, pre-tested, pre-designed online questionnaire for gathering quantitative data on e-waste awareness, perceptions, and practices to gather information on sociodemographic factors, as well as understanding of e-waste, its forms, disposal, and practices.20\n\nThe questionnaire20 will include three sections:\n\nSection A: Questionnaire pertaining to sociodemographic information about the e-consumer, such as age, gender, family type, marital status, occupation, socioeconomic status, and educational background (according to Kuppu swami categorization) features of the people.\n\nSection B: Questions on dealing with e-waste awareness and management, including e-waste information, health impacts, legal requirements, and usage/disposal options like hazards of improper e-waste disposal or methods for reducing the problem of e-waste.\n\nSection C: Questions on community-wide e-waste management practices for disposal and handling like ‘According to you (the participant), what is the best way to discard your old mobile phone batteries or have you ever heard of your neighbours taking their e-waste to a recycling facility?’\n\nTable 1 mentions the various data sources that will used.\n\n\n\n1. Age\n\n2. Caste\n\n3. Type of family\n\n4. Marital status\n\n5. Educational status\n\n6. Sociodemographic status\n\n\n\n1. Percentage of people aware about the methods of disposing off the e-waste, benefits of its disposal and the various hazards accompanying bad e-waste disposal practices.\n\n\n\n1. Best methods to dispose old mobile phones and related equipments\n\n2. Frequency for changing the mobile\n\nData analysis plan\n\nMicrosoft Excel (Version 2305) will be used to enter the data, and SPSS (Statistical Product and Service Solutions) (Version 22) will be used to analyse the responses. For categorical data, frequencies and percentages will be computed, while the mean and standard deviation will be presented for quantitative variables. The data analyzed will thus be presented in the form of tables and graphs. Figure 1 provides a flowchart depicting the plan of work.\n\nBias\n\nThe study might be subjected to participant bias or response bias. Since the study will choose 24 households from a single locality, and because of the close-proximity, respondents may occasionally misinterpret what an investigator is looking for, they may alter their responses or actions in different ways or ask around the neighborhood what the researcher is after which can lead to bias. To address the bias, we will provide them with multiple options, or we will ask one question at a time and do not confuse them.\n\nThe following equation was used to determine sample size2:\n\nZ(0.05) = 1.96\n\nn = required sample size\n\np (prevalence rate of disposal of e-waste) = 10%\n\nq = 100p = 90\n\nL = least permissible error (absolute precision) = 5%\n\nDesired confidence interval = 95%\n\nHence sample size\n\nIn order to gather information on sociodemographic factors and understanding of e-waste, its forms, disposal and practices, a sample size of 138 participants will be employed.\n\nA Microsoft Excel version 2305 file will contain the responses that were provided in response to the questionnaires used. The following step will involve encoding, entering, and processing the data using SPSS version 22 (RRID:SCR_002865). Descriptive data in the form of percentage and frequencies will be calculated.\n\nThere are certain ethical considerations that need to be taken into account. In the first instance, the institutional ethics committee (IEC) approval has been obtained from the Institutional Ethics Committee of Datta Meghe Institute of Higher Education, Wardha. Ethical approval of this study (DMIHER (DU)/IEC/2023/645) was provided on 11th February 2023. The participants will be treated with respect. A strategy of “verbal consent” will be adopted, with the aim and method of the research being made clear to all the participants before interviewing them. Along with the verbal consent, the participants will also receive two written informed consent forms—one in English and one in Marathi—that outline the study’s specifics and request their consent. Once they have signed, we’ll move on. The participants, since they are young, we will ensure that they feel comfortable. The data recorded will be confidential. There will not be any identifying features in the final presentation of our results. If our study proves fulfilling, the following anonymized information will be used to generalize the basic information and knowledge related to e-waste and its management.\n\nThrough our study, we expect to assess the following:\n\n1. Knowledge and awareness level of consumers and electronic shopkeepers about various aspects of e-waste and how are they disposing their e-waste.\n\n2. The different socio-demographic parameters connected to understanding of e-waste disposal procedures.\n\n3. Whether the participants’ level of education impacts their knowledge related to environmental safety.\n\nStudy is yet to be started. We expect to start it from August 2023.\n\n\nDiscussion\n\nE-waste differs chemically depending on the type and date of the objects that are disposed. To the contrary, the major bulk of e-waste comprises a mix of metals, especially copper, aluminum, and iron, affixed to, covered in, or coupled with various types of polymers and porcelain. A typical Cathode-ray tube (CRT)-equipped personal computer weighs 25 kilograms and is composed primarily of glass (15%), plastics (23.3%), metals (43.7%), and computer parts (17.3%). The majority-steel construction of Waste Electrical and Electronic Equipment (WEEE) items like refrigerators and washing machines may be less likely to contain contaminants than e-waste items that are lighter like laptops, tablets, which may have higher levels of heavy metals and flame retardants.17\n\nThe handling of e-waste is dangerous and difficult for numerous institutions. Concerns regarding the destiny of heavy metals and other compounds are also a driving force behind addressing the e-waste threat, in addition to the waste streams’ rapid growth. Regarding the effects of informal recycling, there is also much concern. Such waste management necessitates a comprehensive approach to policymaking that takes a close look at the local infrastructure in place. Recognizing the distinct interests of the many stakeholders, such as city authorities, producers, beneficiaries (consumers), collectors, and recyclers, is also necessary. The e-waste issue has been taken thoroughly both on the global and national levels by crafting recommendations, action networks, cooperation, and sponsored pilot projects with the goal to assist the nations in coming up with an achievable answer that should include both the official and informal sectors.18\n\nA surveillance system for diseases and the health effects of e-waste is necessary to estimate the amounts of e-waste and the precise scope of the issue in Indian cities. The collection and recycling mechanisms must be improved in order to ensure that e-waste methods of management are sustainable. Establishing public-private partnerships would be ideal when opening buy-back or drop-off locations. Another method for guaranteeing the sustainability of waste management is to charge upfront recycling fees. An ecologically sound, foreseeable development may depend on locating and successfully adopting the best e-waste management solutions everywhere. Many nations have implemented the Restriction of Hazardous Compounds (RoHS) regulations in a bid to reduce the consumption of potentially hazardous materials in electrical and electronic machinery and promote the adoption of their friendlier equivalents.16\n\nHuman scalp hair sample has been utilized as a substitute biological sample in biomonitoring exposures to various toxins in the workplace and in the environment, and is believed to be easier to obtain, quicker to store and transport, and less risky to deal with than urine and blood samples. Because of this, researchers have been able to pinpoint exposure rates that are rising. According to the length of the hair, the measured contamination levels can suggest exposure over a long period of time (weeks to years). Additionally, certain components may be found in high concentrations in hair strands, making a hair sample a useful assessment tool. This is comparable to blood and urine, which typically represent the most fresh exposures and may only contain traces of the substances of interest, making analysis a difficult task.19 Scalp hair has been used to measure exposure to heavy metals in large cohorts of people, calculate occupational exposure, and assess local exposure in contaminated areas. Additionally, by utilizing scalp hair, it has been demonstrated that residents of e-waste recycling zones and workers who disassemble equipment may be exposed to organic contaminants such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs). Due to the high concentration of some harmful trace elements and heavy metals present in electronic components, such as arsenic, cadmium, nickel, and lead.19\n\nIt is necessary to build a flexible e-waste management technology package that includes recovering valuable metals, reducing negative impact on the environment and human health, and demonstrating technology on a workable scale. E-waste is mostly treated on three levels of first level-treatment, second-level treatment and third-level treatment.20 The second stage receives the first stage’s output as an input. Three levels of environmentally friendly e-waste treatment are employed.\n\nThe present study will help in assessing the current awareness, knowledge about e-waste and its growing impact on our environment and the current e-waste disposal patterns of young consumers and shopkeepers. The study will assist the authors in figuring out how to properly dispose of our electronic garbage. It will be useful to learn more about the risks associated with inappropriate e-waste disposal to offer ways to lessen the issue of e-waste and determining the benefits of proper e-waste disposal.\n\nThe research might be subjected to participant bias or response bias which could be considered a crucial factor of limitation.\n\nThe results will be published in indexed journals or data will be disseminated through index conference.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: A Community-based cross-sectional study for assessment of the e-waste disposal practices amongst people living in Wardha district, India. https://doi.org/10.5281/zenodo.8143372. 20\n\nThis project contains the following extended data:\n\n- questionnaire zenodo.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nNisha B, Shajil S, Dutta R, et al.: Consumer awareness and perceptions about e-waste management in semi-urban area of northern Tamil Nadu: A mixed-method approach. J Fam Community Med. 2022 Aug; 29(2): 132. Publisher Full Text\n\n(PDF) A community based study on e-waste disposal in Srinagar, Uttarakhand: assessment of awareness and practices. ResearchGate.[cited 2022 Dec 1]. Reference Source\n\nNair A, Yadav N, Thawait D, et al.: Gadgets it’s use and stress on lifestyle. J Datta Meghe Inst Med Sci Univ. 2020; 15(2): 183. Publisher Full Text\n\nScrapping the hi-tech myth: computer waste in India\|Eldis.[cited 2022 Dec 7]. Reference Source\n\nAnurag L, Gaurav M, Sanjay D, et al.: Spectrum of IAEA standard with regard to radiation application. J Datta Meghe Inst Med Sci Univ. 2022; 17(2): 461. Publisher Full Text\n\nDevgade P, Patil M: Water, sanitation, and hygiene assessment at household level in the community: A narrative review. J Datta Meghe Inst Med Sci Univ. 2023; 18(1): 173. Publisher Full Text\n\nMaiya U: YOUTH PERCEPTION TOWARDS E-WASTE: A STUDY WITH REFERENCE TO UDUPI DISTRICT.2020 Oct 22.\n\nNuwematsiko R, Oporia F, Nabirye J, et al.: Knowledge, Perceptions, and Practices of Electronic Waste Management among Consumers in Kampala, Uganda. J Environ Public Health. 2021 Feb 12; 2021: 1–11. Publisher Full Text\n\nJoshi S, Waghmare R, Muntode P, et al.: Assessment of knowledge, attitude, and practices among the healthcare workers regarding biomedical waste management in a tertiary care hospital from Central India. J Datta Meghe Inst Med Sci Univ. 2020; 15(4): 551. Publisher Full Text\n\nSarkar A, Devi S: Health hazards of water contamination: An updated review among the COVID-19 pandemic. J Datta Meghe Inst Med Sci Univ. 2022; 17(4): 996. Publisher Full Text\n\nNeedhidasan S, Samuel M, Chidambaram R: Electronic waste – an emerging threat to the environment of urban India. J Environ Health Sci Eng. 2014 Jan 20; 12: 36. Publisher Full Text\n\nDelcea C, Crăciun L, Ioanăș C, et al.: Determinants of Individuals’ E-Waste Recycling Decision: A Case Study from Romania. Sustainability. 2020 Jan; 12(7): 2753. Publisher Full Text\n\nOrisakwe OE, Frazzoli C, Ilo CE, et al.: Public Health Burden of E-waste in Africa. J Health Pollut. 2019 Jun [cited 2022 Dec 7]; 9(22). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah A: An Assessment of Public Awareness Regarding E-Waste Hazards and Management Strategies. Indep Study Proj ISP Collect. 2014 Apr 1. Reference Source\n\nMishra S, Shamanna BR, Kannan S: Exploring the Awareness Regarding E-waste and its Health Hazards among the Informal Handlers in Musheerabad Area of Hyderabad. Indian J Occup Environ Med. 2017; 21(3): 143–148. PubMed Abstract \| Publisher Full Text\n\nMonika KJ: E-Waste Management: As a Challenge to Public Health in India. Indian J Community Med Off Publ Indian Assoc Prev Soc Med. 2010 Jul; 35(3): 382–385. Publisher Full Text\n\nRobinson BH: E-waste: An assessment of global production and environmental impacts. Sci Total Environ. 2009 Dec 20; 408(2): 183–191. PubMed Abstract \| Publisher Full Text\n\nBhat V, Patil Y: E-waste Consciousness and Disposal Practices among Residents of Pune City. Procedia Soc Behav Sci. 2014 May 1; 133: 491–498. Publisher Full Text\n\nWang T, Fu J, Wang Y, et al.: Use of scalp hair as indicator of human exposure to heavy metals in an electronic waste recycling area. Environ Pollut. 2009 Aug 1; 157(8): 2445–2451. PubMed Abstract \| Publisher Full Text\n\nHasan F: A Community-based cross-sectional study for assessment of the e-waste disposal practices amongst people living in Wardha district, India. [Dataset]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "212072", "date": "10 Oct 2023", "name": "Vusumuzi Maphosa", "expertise": [ "Reviewer Expertise Artificial intelligence", "information systems and technology", "ICT4D", "human-computer interaction." ], "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 strongly recommend that the article be Not Approved as it does not meet minimum scientific writing standards. It can only be indexed after thorough editing by a Language Editor and addressing these fundamental issues.\nThe introduction is poorly done and fails to summarise the work that will be done and articulate the aim and the objectives of the study.\nThe rationale of the study is weak. It does not show how the authors will add new knowledge or contribute literature to the subject area.\nThe literature review is poorly done and not organised into themes for easy flow and reading. It is disjointed and marred by grammatical and syntactic errors making it difficult to read.\nThe aims and objectives are not concise, but disjointed and make little or no sense at all.\n\nOver two dozen of the sentences are not referenced, yet they refer to actual figures. Where are the authors getting these from? The amount of global e-waste reported is incorrect. Over 30% of references in the reference list are incomplete, some mention two authors and use et al. for the rest. Over 40% of the references have no page numbers, while some have no author names and are written in capital letters.\nSPSS are described wrongly.\nThe study population and the participants keep on changing in the text and there is no rationale as to how the participants were selected.\nThe discussion is weak and an extension of the disorganised literature review.\nThe language used in this text is below academic writing and this article must be re-written. 60% of the text requires major English language revision. Authors use their own non-English words. This article cannot be indexed in this state.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] }, { "id": "269821", "date": "13 May 2024", "name": "Raghavendran Sivasubramanian", "expertise": [ "Reviewer Expertise Wastewater treatment", "Environmental Sustainability", "Linear Regression Statistics", "extracellular polymeric substances" ], "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\nVerdict: Rejected This article is setup to study the level of awareness that young adults have towards e-waste disposal management practices. The article needs to be rejected for the following reasons: 1.\n\nThe paper submitted has no results or analysis. A journal paper with no results is invalid unless it is a review paper. For the topic of interest, results in the form of data were very imperative and it was not presented. Rather, it was mentioned that the study would only be commenced after the submission of the paper. 2.\n\nAll the information presented in the Discussion and Limitations section are invalid and not connected without the results and analysis. Request to remove them completely. 3.\n\nA few minor points: a.\n\nPage 3 of 11\n\ni.\n\nRemove: “Because of the amenities supplied by IT and communication systems, the world feels small because of how filled it is now with everything related to electronics”\n\nii.\n\nRemove: “Due to the quick development of new technology, electrical and electronic equipment (EEEs) have become obsolete quickly after purchase.13 India adopted laws under the Ministry of Environment and Forests (MoEF) that specifically address this issue”\n\niii.\n\nPlease re-write the last paragraph. Reword the sentences completely. b.\n\nPage 4 of 11:\n\ni.\n\nWhy are the goals referenced? The goals and purpose of the paper should be individualistic and not referenced.\n\nii.\n\nRemove: “As a result, the study’s primary goal is to determine how well the\n\niii.\n\ngeneral population understands e-waste and its effects. Those who carelessly dispose of their electronic waste will find this study to be helpful. This study is for everyone who are unaware of the fundamentals of e-waste and its enormous influence on people’s lives. By identifying the attitudes, knowledge, and perceptions surrounding e-waste and assessing how it affects people’s lives in the long run, the relevance of the study may be ascertained.”\n\niv.\n\nRemove Aims and Objectives. They are already mentioned in the paragraphs before. c.\n\nPage 5 of 11:\n\ni.\n\nRemove Study settings/place.\n\nii.\n\nCompletely rewrite Participants. Wrong way of writing. The authors will prepare a questionnaire and deliver it to participants. The answers recorded in the questionnaire will then be analyzed.\n\niii.\n\nNo need for Inclusion and Exclusion criteria. 4. These surveys on people's perceptions have been conducted for a decade and no real progress has been made towards improving sustainability. Articles with meticulous views to improve and innovate sustainable practices are needed currently and there are enough surveys in the literature.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] }, { "id": "224657", "date": "30 Aug 2024", "name": "Victor Platon", "expertise": [ "Reviewer Expertise Waste management", "circular economy" ], "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 At page 2 we have the aim of the article: The aim of this research is to document the level of awareness that consumers and owners of electronic stores have regarding the disposal of their e-waste while also evaluating their general awareness and e-waste management procedures. The article has 12 pages, one diagram and one table. There are no figures, nor annexes. The main idea of the article is to perform a survey on a sample of youth people (more than 18 years old) and shopkeepers to see the situation of recycling e-waste. To do this the authors will select 24 houses (page 6) from 5 localities and administer a questionnaire. The questionnaire is not provided. Next, the data will be processed and interpreted. So far there are no data collected. The Section Discussions does provide for some rationale for e-waste recycling. E-waste has no a clear definition in this article. In the Section Dissemination, the authors expect to spread the results. It is not clear what results they want to spread. The article has no concrete result. The review Criteria Observations Is the work clearly and accurately presented and does it cite the current literature? The work is well presented but there is NO literature review mentioned Is the study design appropriate and does the work have academic merit? The design of the study is acceptable. The academic merit is low. Are sufficient details of methods and analysis provided to allow replication by others? There are common details that are used in many other survey studies. If applicable, is the statistical analysis and its interpretation appropriate? There are no data, nor statistical analysis. There is no interpretation. Are all the source data underlying the results available to ensure full reproducibility? The methodology is so simple and can be easily found on the internet. Own contribution is low. Are the conclusions drawn adequately supported by the results? There are no conclusions of the article.\nNOTE The paper analyzed is not a scientific article but a draft proposal for a future article that could be written after the questionnaire is drafted and answers received. The methodology is very common for surveys.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1138
https://f1000research.com/articles/12-750/v1	26 Jun 23	{ "type": "Research Article", "title": "Predicting multi-vascular diseases in patients with coronary artery disease", "authors": [ "Suko Adiarto", "Luthfian Aby Nurachman", "Raditya Dewangga", "Suci Indriani", "Taofan Taofan", "Amir Aziz Alkatiri", "Doni Firman", "Anwar Santoso", "Luthfian Aby Nurachman", "Raditya Dewangga", "Suci Indriani", "Taofan Taofan", "Amir Aziz Alkatiri", "Doni Firman", "Anwar Santoso" ], "abstract": "Background: Because of its systemic nature, the occurrence of atherosclerosis in the coronary arteries can also indicate a risk for other vascular diseases. However, screening program targeted for all patients with coronary artery disease (CAD) is highly ineffective and no studies have assessed the risk factors for developing multi-vascular diseases in general. This study constructed a predictive model and scoring system to enable targeted screening for multi-vascular diseases in CAD patients. Methods: This cross-sectional study includes patients with CAD, as diagnosed during coronary angiography or percutaneous coronary intervention from March 2021 to December 2021. Coronary artery stenosis (CAS) and abdominal aortic aneurysm (AAA) were diagnosed using Doppler ultrasound while peripheral artery disease (PAD) was diagnosed based on ABI score. Multivariate logistic regression was conducted to construct the predictive model and risk scores. Validation was conducted using ROC analysis and Hosmer-Lemeshow test. Results: Multivariate analysis showed that ages of >60 years (OR [95% CI] = 1.579 [1.153-2.164]), diabetes mellitus (OR = 1.412 [1.036-1.924]), cerebrovascular disease (OR = 3.656 [2.326-5.747]), and CAD3VD (OR = 1.960 [1.250-3.073]) increased the odds for multi-vascular disease. The model demonstrated good predictive capability (AUC = 0.659) and was well-calibrated (Hosmer-Lemeshow p = 0.379). Targeted screening for high-risk patients reduced the number needed to screen (NNS) from 6 in the general population to 3 and has a high specificity of 96.5% Conclusions: Targeted screening using clinical risk scores was able to decrease NNS with good predictive capability and high specificity", "keywords": [ "Coronary artery disease", "Peripheral artery disease", "Abdominal Aortic Aneurysm", "Carotid Artery Stenosis", "targeted screening", "predictive model", "clinical risk score" ], "content": "Introduction\n\nAtherosclerosis underlines some of the major cardiovascular diseases which are the leading cause of mortality worldwide. Due to its systemic nature, atherosclerosis in the coronary arteries may indicate occurrences in other arteries.1 Coronary arterial disease (CAD) is associated with peripheral artery disease (PAD), carotid artery stenosis, and abdominal aortic aneurysm (AAA). There is an increasing prevalence of vascular diseases in patients with a more severe CAD, especially high-risk CAD with metabolic syndromes and three-vessel disease.2–4 Therefore, the screening in patients with CAD is justifiable in assessing the risk of atherosclerosis occurrences in other arteries.\n\nCAD is one of the leading causes of mortality worldwide with a substantial incidence rate. According to the Centers for Disease Control and Prevention (CDC) in the United States, a total of 20.1 million adults aged 20 years old and older have CAD.5 Screening for PAD, carotid artery stenosis, and AAA enable early detection, risk stratification, and early cardiovascular treatment; all in favor of reducing morbidity and mortality.6,7 However, screening program targeting all CAD patients is highly ineffective, costly, and requires multiple resources such as specific instruments and trained technicians. On the other hand, screening for early detection of some vascular diseases, e.g., PAD, in patients with significant CAD was not shown to be more beneficial compared to a routine medical checkup.8 Therefore, targeted screening in patients with CAD requires careful consideration based on risk factors for atherosclerosis in other arteries.\n\nTargeted screening contributes to early detection while being more time and cost-effective than general screening; it can be beneficial for diseases previously deemed not necessary to screen. A study specifically assessed targeted screening for AAA was already done involving a small subset of indigenous people in Borneo.9 No research has been conducted to assess the predictors for developing multi-vascular diseases, including PAD, CAS, and AAA in patients with CAD. Furthermore, no studies assessed the number needed to screen (NNS) of screening for multi-vascular diseases in CAD patients and the impact of the clinical risk scoring system for said NNS. We hypothesize that a risk-scoring tool to measure the risk of other vascular diseases in CAD patients is feasible to construct and can be applied for targeted screening; in return, the risk-scoring tool can reduce the NNS for asymptomatic multi-vascular diseases. Therefore, this study aims to investigate factors predicting the occurrence of multi-vascular diseases in patients with CAD while constructing a predictive model and scoring system to enable targeted screening for future uses.\n\n\nMethods\n\nThis study was conducted based on the STROBE guideline for observational studies. The study protocol was approved by the National Cardiovascular Center Harapan Kita Hospital committee of ethics (ethics approval number: LB.02.01/VII/509/KEP005/2021). All patients gave written informed consent prior to the recruitment of the study and were free to decline participation.\n\nThis cross-sectional study was conducted at the National Cardiovascular Center of Harapan Kita Hospital from March 2021 to December 2021. All patients who underwent elective coronary angiography or percutaneous coronary intervention from March 2021 to December 2021 were initially included. Patients diagnosed with coronary artery disease (CAD) were eligible for inclusion in our study. We excluded patients with previously diagnosed CAD that were treated by medical therapy and revascularization therapy. We also excluded patients with connective tissue disorder. All included patients were concomitantly screened for vascular disease. The primary outcome of interest was vascular diseases in other vascular territories. For all patients, we examined the list of variables relating to sociodemographic characteristics, cardiovascular risk factors, and other related diseases.\n\nThe diagnosis of hypertension was based on documented medical history, the use of antihypertensive drugs, and the presence of elevated systolic and/or diastolic blood pressure according to European Society of Cardiology guidelines.10 Diabetes mellitus was diagnosed based on documented medical history through the use of hypoglycemic agents, and/or laboratory criteria according to the American Diabetes Association (ADA) 2021.11 Dyslipidemia was defined based on documented medical history and the use of lowering lipid agents or laboratory criteria according to the National Cholesterol Education Program’s Adult Treatment Panel III (NCEP-ATP III).12 Metabolic Syndrome was also defined according to the NCEP-ATP III. Information on the history of cerebrovascular disease (transient ischemic attack or stroke) was collected from the patient’s reports or medical records.12 CAD was diagnosed using angiography. The presence of coronary lesions was determined using visual estimation. Coronary artery lesions were considered as CAD if 1) at least one major epicardial artery or its major branches have significant stenosis (70% for left anterior descending artery, left circumflex artery, right coronary artery, or 50% for left main trunk) or 2) the patient was previously hospitalied for treatment of coronary artery lesions (balloon, stent, or coronary artery bypass grafting).\n\nLower extremity peripheral arterial disease (PAD) was defined with 1) ankle-brachial index of < 0.9 or 2) the patient was previously treated for PAD.13 Evaluation of carotid artery stenosis (CAS) and AAA was conducted using bedside ultrasound Affiniti 70 (Philips, Amsterdam, Netherlands) by a cardiovascular technician blinded to other data. Peak systolic velocity, end-diastolic velocity, and intima-media thickness of the common carotid artery and internal carotid artery were calculated to evaluate CAS. The degree of CAS was classified according to Grant et al.14 CAS was considered significant if 1) the presence of stenosis ≥50% from ultrasound examination or 2) the patient was previously treated for CAS (carotid stenting or carotid endarterectomy). AAA was defined as an enlargement of the abdominal aorta with a diameter of ≥3 cm or a previously treated AAA lesion (Endovascular aortic repair/EVAR or open surgical repair).15 The maximum and minimum abdominal aortic diameter (anteroposterior or transverse axis) were obtained.\n\nPotential bias for each diagnosis of vascular disease were minimized by involving third-party examiners who were not aware of the existence of this study.\n\nCategorical variables were expressed in the form of numbers and percentages, whereas continuous variables were expressed as their mean value±SD in data with normal distribution or their median (interquartile range) value in data without normal distribution. We compared categorical variables using Pearson’s chi-square or Fisher’s exact test while continuous variables were compared using the Student t-test or Mann-Whitney U test. We conducted multivariable stepwise logistic regression to generate prediction models with the primary endpoint of multivascular disease incorporating clinical variables. All variables with p value of <0.25 by univariate analysis were included in the multivariable model. The selection of variables for retention was based on p value of <0.05. We additionally performed the Hosmer-Lemeshow test to assess the goodness of fit of the model and plot the observed versus predicted data graph.\n\nFor each significant variable from multivariate analysis, a regression β coefficient was obtained, and a scoring system was created to predict the incidence of coexisting vascular diseases. Points for the scoring prediction rule were assigned by weighing each significant variable compared to the total β coefficient. Then, points were made using the weighted coefficients with rounding to the nearest whole number. We created the cutoff points to classify patients with low, moderate, and high-risk probability, respectively. To test the model discrimination, C-statistic was also conducted to calculate the area under the curve. We also conducted internal validation by bootstrap using the same amount of included samples. All statistical analyses were performed using SPSS version 23 (IBM, New York, USA) and STATA version 16 MP (StataCorp, Texas, USA).\n\n\nResults\n\nA total of 1314 patients with CAD were identified; 203 (15.4%) patients have vascular disease. All patients had complete medical record data and, therefore, no missing data in this study. Sociodemographic and clinical data are shown in Table 1. Amongst the variables in patient’s demographics, there was a significant difference in the proportion of patients with cerebrovascular disease, CAD three-vessel disease (CAD3VD), and CAD left main disease (CAD-LM). The prevalence of PAD, CAS, and AAA in patients with CAD were 143 (10.9%), 59 (4.5%), and 19 (1.4%), respectively. The overlap between vascular diseases is shown in Figure 1.\n\nThere is a difference in prevalence of vascular diseases in CAD patients with one, two, and three-vessel disease (Table 2).\n\nUnivariate analysis demonstrated individuals with older age, diabetes mellitus, cerebrovascular disease, CAD3VD, and left main disease were more likely to have multivascular disease (Table 3). After a multivariate analysis, four variables were retained to form the final clinical model: ages of ≥60 years (OR: 1.579; 95% CI: 1.153-2.164), diabetes mellitus (OR: 1.412; 95% CI: 1.036-1.924), cerebrovascular disease (OR: 3.656; 95% CI: 2.326-5.747), and CAD3VD (OR: 1.960; 95% CI: 1.250-3.073). All of the predictors remain significant after bootstrap internal validation (Table 3).\n\nThe area under the curve of the model was 0.659 (95% CI: 0.617-0.700) and was well calibrated (Hosmer-Lemeshow test p=0.379;). Using bootstrap validation, the optimism-corrected area under the curve was 0.653 (95% CI: 0.610-0.695), which represents the predictive ability of the model (Figure 2).\n\nThose four variables were assigned weighted points scores for the final clinical prediction of multi-vascular disease based on the magnitude of the β coefficient (Table 4). We designated a score of 0–2 as low probability (9% of chance), 3–5 as moderate probability (21%), and 6–8 as high probability (42%). The discriminatory ability of the scoring system was moderate (AUC: 0.649; 95% CI: 0.610-0.687).\n\nBased on our data, targeted screening for patients with moderate risk or higher decreases the number needed to screen (NNS) from six to five while targeted screening for patients with high risk reduces the NNS from six to three. Targeted screening for patients with moderate risk or higher had the most balanced results of diagnostic values with positive predictive value (PPV), negative predictive value (NPV), sensitivity, and specificity of 45,1%, 86,2%, 15,8%, and 96,5% respectively.\n\n\nDiscussion\n\nOur study reported factors associated with multi-vascular disease in patients with CAD. A total of three vascular diseases were identified in this study: PAD, CAS, and AAA. In this study, the prevalence of PAD, CAS, and AAA in patients with CAD were 143 (10.9%), 59 (4.5%), and 19 (1.4%), respectively. These numbers seem to be lower than other studies conducted elsewhere. For PAD, a study by Poredos et al (2007), exemplified that a total of 42% of patients with CAD had PAD based on screening using the ankle-brachial index (ABI).2 For CAS, a study by Tanimoto et al (2015), shows that the prevalence of CAS in CAD patients was between 7.0% to 36.0%.3 Prevalence of AAA in CAD patients was studied by Durieux et al (2014), which shows 2.5% to 14.4% of total CAD cases had asymptomatic AAA.4 The lower prevalence of PAD, CAS, and AAA in this sample study might be due to the younger mean age compared to studies conducted outside of Indonesia. It was known that the prevalence of PAD, CAS, and AAA increases with age.16–18 In this study, the mean age of CAD patients was 60 years old. Patients with multi-vascular diseases were significantly older than patients without any vascular disease (64 vs 59; p<0.001). This was in line with another study involving CAD patients in Indonesia. A study conducted at Dr. Soetomo regional hospital in Indonesia by Saputri et al (2020) demonstrated the prevalence of CAD peaked in patients between 51–60 years old which consists of 42.6% of all CAD cases. The prevalence of CAD in patients older than 60 years old was only 33.1%.19 Meanwhile, global data from 1990–2017 show that the peak prevalence of CAD happened in patients between 80 to 89 years old with a prevalence of 15,000–16,000 per 100,000 cases.20 This shift of peak prevalence towards younger patients in Indonesia might be caused by the higher prevalence of CAD risk factors in the younger generation. This statement is supported by data from the study of Hussain et al (2016), which show higher population attributable-risk proportion (PAR) percentages of smoking, hypertension, excess body weight, diabetes, and hypercholesterolemia in CAD patients less than 55 years old compared to older patients.21\n\nAnother factor that might influence the low prevalence of vascular disease in this study is the high rate of diabetes patients included. Our study data showed that 44.4% of patients had diabetes mellitus. Diabetes mellitus can decrease the rate of vascular disease in our study probably due to the protective effect of metformin medication on cardiovascular diseases. A randomized trial study called UK Prospective Diabetes Study (UKPDS) showed that in overweight patients newly diagnosed with diabetes mellitus type 2, metformin medication significantly decreases the relative risk of developing myocardial infarction, peripheral vascular disease, and microvascular disease.22,23 In mouse and human macrophage studies, metformin was known to directly inhibit atherosclerosis through the activation of AMPK-ATF1-M2-like pathway and suppression of PI3K/AKT/mTOR/autophagy pathway, which was associated with the aneurysmal wall of the abdominal aorta.24,25 Therefore the author concluded that the low prevalence of vascular disease especially AAA in this study might be caused by the high rate of diabetic patients included in this study.\n\nThere was a positive trend between the degree of CAD and the degree of atherosclerosis in another artery. The degree of fat deposit in coronary artery reflects the degree of atherosclerosis reflected on the increased serum level of interleukin-6 (IL-6) and leptin alongside the decreased serum level of adiponectin.26 In this study, heightened coronary fat deposits in multivessel CAD patients was associated with atherosclerosis in other arteries, as indirectly demonstrated by an increased prevalence of multi-vascular disease. This trend was observed for the prevalence of multi-vascular disease, PAD, and CAS, while no significant difference was observed in the prevalence of AAA. This trend was also observed in another study. Kim et al (2013) conducted the study with the Korean population, where they observed a higher prevalence for bilateral PAD in multivessel CAD patients compared to patients with univessel CAD (5.3% vs 1.9%; p<0.001). Moreover, patients with multivessel CAD were at a higher risk for a more severe PAD, indicated by low ankle-brachial index (ABI) score (<0.7) compared to univessel CAD patients (6.3% vs 2.2%; p=0.008).27 For carotid artery stenosis, Tanimoto et al (2005) reported an increase in prevalence of CAS in patients with zero, one, two, and three-vessel CAD with a prevalence of 7.0%, 14.5%, 21.4%, and 36.0% respectively (p<0.0001).3 This trend was also observed in AAA, where Durieux et al (2014) reported increasing prevalence of AAA in normal, one, two, and three-vessel CAD with a prevalence of 2.5%, 4.3%, 5.7%, and 14.4%, respectively.4 Our data showed no significant increase of AAA prevalence in relation to different CAD severities. This might be caused by small prevalence of AAA found in this study, which influenced the estimation of statistical significance. This study offered a broader view of the relationship between vascular disease and multivessel CAD. To date, this is the only study that includes various vascular diseases in one population to see each diseases trend in prevalence between different severity of CAD.\n\nThis study shows several risk factors associated with increased vascular disease in CAD patients. Multivariate analysis showed that patients with CAD, ages of ≥60 years old, diabetes mellitus, cerebrovascular disease, and CAD3VD have higher odds of having multi-vascular disease. Both age and diabetes mellitus are known risk factors for atherosclerosis. Hisayama reported that age (hazard ratio (HR) 1.08; 95% CI 1.07-1.10; p <0.001) and diabetes mellitus (HR 1.58; 95% CI 1.17-2.14; p=0.003) increase the 10-year risk for atherosclerotic cardiovascular disease in the Japanese population.28 The variable associated with the occurrence of another vascular disease somehow matched the factors associated with multivessel CAD. Predictive model made to predict high risk model based on data from PROMISE (Prospective Multicenter Imaging Study for Evaluation of Chest Pain) cohort shows that older age and diabetes mellitus increase the odds for multivessel CAD.29 On the other hand, multivessel CAD could be a predictor for other vascular diseases. In a targeted screening study by Saw et al (2020), multivessel CAD had a higher prevalence of asymptomatic AAA when compared to univessel CAD, where patients with asymptomatic AAA also had CAD3VD.9 Cerebrovascular disease, often manifested as stroke, is often a result of atherosclerosis. This study shows that the already manifested atherosclerosis in brain microvessel is a predictive factor for another atherosclerotic vascular disease in patients with CAD.\n\nAnalysis of risk factors significantly associated with the incidence of vascular disease in CAD patients resulted in a risk scoring system that enabled targeted screening. Risk scoring was made based from beta coefficient obtained from multivariate analysis. Goodness of fit test using Hosmer-Lemeshow test shows that the data fit the model. Predictive capability of risk score was shown to be moderately good with area under curve (AUC) of 65.9%. This predictive capability was comparable with another predictive model to predict PAD in patients with stable CAD made by Badheka et al (2011). In this study, ROC analysis of risk score that consists of history of hypertension, smoking, age, and history of diabetes showed AUC of 68.6%.30 In our study, it was shown that general screening of all CAD patients resulted in only 15.4% cases with other vascular diseases and number needed to screen (NNS) was 6. Meanwhile, targeted screening for patients only with high-risk based on our risk score decrease the NNS from 6 to 3 with 45% of patients had any other vascular disease. Our clinical risk score shows a very high number of specificity of 96.5%. This high specificity means that this tool is less likely to produce a false positive result. Thus, it is more suited for ruling in the possibilities of multivascular disease instead of ruling out. We conclude that this tool is more suited for tertiary care hospital and should be applied to patients with doubtful Doppler result for screening of multivascular diseases.\n\nThe main limitation of this study is the cross-sectional design, which does not study the potential for future vascular disease incidents and enabled bias. Potential bias in this study comes especially as a form of confirmatory bias by the assessor when diagnosing the incident of asymptomatic vascular disease. Although this confirmatory bias was minimized by involving third party examinators, this blinding was not properly controlled due to the number of patients involved in such short amount of time. Another limitation is the confirmation of the reduced NNS which used the same dataset with the one used to construct the risk scoring tool. External validation of our risk score using a different dataset is needed to confirm the generalizability of the study result.\n\n\nConclusion\n\nPatients who have diabetes mellitus, cerebrovascular disease, CAD3VD, and are above 60 years old are associated with increased odds of multi-vascular disease. By using risk scoring tool made from these risk factors, targeted screening in high-risk patients decrease the number needed to screen in half with high specificity.\n\n\nAuthor contributions\n\nSuko Adiarto: Conceptualization, Methodology, Writing – Original Draft, Writing – Review & Editing, Data Curation, Visualization. Luthfian Aby Nurachman: Formal Analysis, Writing – Original Draft. Raditya Dewangga: Formal Analysis, Investigation, Suci Indriani: Investigation, Methodology Taofan: Investigation, Methodology Amir Aziz Alkatiri: Investigation, Methodology Doni Firman: Investigation, Methodology Anwar Santoso: Conceptualization, Validation, Writing – Review & Editing, Supervision, Funding Acquisition All authors read and approved the final paper.", "appendix": "Data availability\n\nFigshare: Predicting Multi-Vascular Diseases_Dataset. DOI: http://doi.org/10.6084/m9.figshare.22881431. 31\n\nThis study contains the following underlying data: Predicting Multi-Vascular Diseases_Dataset.xlsx (data used for analysis).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nJebari-Benslaiman S, Galicia-García U, Larrea-Sebal A, et al.: Pathophysiology of Atherosclerosis. Int. J. Mol. Sci. 23: 23. Epub ahead of print March 2022. 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Publisher Full Text" }	[ { "id": "182362", "date": "10 Jul 2023", "name": "Marc Vuylsteke", "expertise": [ "Reviewer Expertise Vascular surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper contains an interesting cross-sectional study regarding the risk factors of developping multi-vascular diseases in patients with coronary artery disease. However I do have some comments:\nMajor comments\nMethods: Exclusion criteria: \"We excluded patients with previously diagnosed CAD\". But further you state: \"Coronary artery lesions were considered as CAD if 2) the patient was previously hospitalized for treatment of coronary artery lesions\". Isn’t that a contradiction?\n\nRisk factors: 'hypertension': how do you quantify hypertension. Some patients have only very mild hypertension, some severe hypertension. Similar regarding PAD, diabetes. Is it possible to distinguish the severity of these conditions?\n\nRisk-factors: ankle-brachial-index of >0.9: this is a very mild level of PAD. Most of those patients are asymptomatic and many of them will stay asymptomatic. Why not looking for the more severe form of PAD (ABI<0.4)? How do you assess ABI in patients with diabetes? As you know, this examination is not well reliable in diabetics given the presence of media sclerosis.\n\nFor assessing the risk of developing AAA, shouldn’t we look for a positive family history of AAA?\n\nTable 1: Patient’s baseline characteristics: Metabolic syndrome was found in 51.1 % of included patients, however only 14.7% were obese? How can you explain this?\n\nPlease shorten the discussion significantly. The literature overview is much too long.\nMinor corrections\nAbstract, methods: 'coronary artery stenosis (CAS)', should be Carotid artery stenosis.\n\nIntroduction : line 3: 'carotid artery stenosis', please add 'CAS';\n\nMethods: 'this study was conducted based on the STROBE guideline'. Please add reference.\n\nResults: \"A total of 1314 patients with CAD were identified; 203 patients have [multi vascular disease]\".\n\nIs the work 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": "10205", "date": "18 Sep 2023", "name": "Suko Adiarto", "role": "Author Response", "response": "Thank you very much for the review and the opportunity of revising the manuscript. Here is our comment by comment response: Major comments 1. Methods: Exclusion criteria: \"We excluded patients with previously diagnosed CAD\". But further you state: \"Coronary artery lesions were considered as CAD if 2) the patient was previously hospitalized for treatment of coronary artery lesions\". Isn’t that a contradiction? We have revised this the sentence in the first paragraph of patient selection: We excluded patients with previously diagnosed CAD that were treated by medical therapy and revascularization therapy into We excluded patients with previously diagnosed CAD that were hospitalized for other reason than elective coronary angiography or coronary angioplasty. 2. Risk factors: 'hypertension': how do you quantify hypertension? Some patients have only very mild hypertension, some severe hypertension. Similar regarding PAD, diabetes. Is it possible to distinguish the severity of these conditions? In this study, we did not quantify the severity of hypertension, PAD and diabetes. We just simply categorized the patients whether they have hypertension, PAD or diabetes according to ESC guidelines, the value of ankle brachial index and ADA guidelines respectively. 3. Risk-factors: ankle-brachial-index of >0.9: this is a very mild level of PAD. Most of those patients are asymptomatic and many of them will stay asymptomatic. Why not looking for the more severe form of PAD (ABI<0.4)? How do you assess ABI in patients with diabetes? As you know, this examination is not well reliable in diabetics given the presence of media sclerosis. The purpose of this study is to screen the presence of multi-vascular disease in patients with proven coronary disease and subsequently propose a risk score that enable targeted screening. Thus, the screening would be for those who are considered high risk but asymptomatic. Patients with ABI of <0.4 usually suffer from more severe PAD and would have already come for treatment. ABI is not a perfect diagnostic tool in the presence of media sclerosis; however it is still recommended for screening purposes by several professional organization through their guidelines (ESC, ACC/AHA, SVS, NICE) even in the presence of diabetes and chronic kidney disease. 4. For assessing the risk of developing AAA, shouldn’t we look for a positive family history of AAA? Very good point, unfortunately AAA is still underdiagnosed in our population. Thus the presence of family history might not be accurately identified. 5. Table 1: Patient’s baseline characteristics: Metabolic syndrome was found in 51.1 % of included patients, however only 14.7% were obese? How can you explain this? The criteria of metabolic syndrome was based on NCEP-ATP III Definition, in which 3 out of five criteria including waist circumference, blood pressure, LDL level, HDL Level and fasting glucose level. We re-analyzed metabolic syndrome using the definition, resulting in a prevalence of 37.7%. The difference between the 37.7% prevalence of metabolic syndrome and the 14.7% prevalence of obesity can be attributed to the presence of other criteria used to diagnose metabolic syndrome. 6. Please shorten the discussion significantly. The literature overview is much too long. We have shorten the discussion Minor corrections 1. Abstract, methods: 'coronary artery stenosis (CAS)', should be Carotid artery stenosis. Revised accordingly 2. Introduction : line 3: 'carotid artery stenosis', please add 'CAS'. Revised accordingly 3. Methods: 'this study was conducted based on the STROBE guideline'. Please add reference. We have added the reference 4. Results: \"A total of 1314 patients with CAD were identified; 203 patients have [multi vascular disease]\". Revised accordingly" } ] }, { "id": "182359", "date": "14 Jul 2023", "name": "Johanes Nugroho Ekoputranto", "expertise": [ "Reviewer Expertise Cardiology and vascular medicine" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article presents a study aimed at constructing a predictive model and scoring system to enable targeted screening for multi-vascular diseases in patients with coronary artery disease (CAD). Overall, the article provides valuable insights into improving screening programs for CAD patients.\nThe study methodology involves a cross-sectional design and the use of various diagnostic techniques. The inclusion and exclusion criteria are clearly defined, and the diagnostic techniques for various vascular diseases are explained. The article describes the statistical methods used, including univariate analysis, multivariable stepwise logistic regression, Hosmer-Lemeshow test, and the creation of a scoring system. The article also states that potential bias for each diagnosis of vascular disease was minimized by involving third-party examiners who were not aware of the existence of the study.\nThe results demonstrate the effectiveness of the predictive model in reducing the number needed to screen (NNS) and achieving high specificity. The area under the curve (AUC) of the model is reported as 0.659, indicating good predictive ability. However, it would be useful to provide the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the model at a chosen cutoff point. This information would further illustrate the diagnostic performance of the model. Overall, the discussion effectively acknowledges and discusses the study limitations. The discussion briefly mentions the need for external validation to confirm the generalizability of the risk scoring tool.\n\nIs the work 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": "10210", "date": "18 Sep 2023", "name": "Suko Adiarto", "role": "Author Response", "response": "Thank you for the suggestion. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the model at a chosen cutoff point were demonstrated in Table 5. Performance of risk score in detecting vascular disease in CAD patients. Because the cutoff point of our scoring system was two (three groups), we compared the at least moderate risk vs. low risk, and at least high risk vs. low risk." } ] } ]	1	https://f1000research.com/articles/12-750
https://f1000research.com/articles/11-1356/v1	21 Nov 22	{ "type": "Research Article", "title": "Criminalistic and criminological analysis of the Thomas Restobar case in Peru in the context of sanitary measures by COVID-19: A case study", "authors": [ "José Antonio Jauregui-Montero", "Oriana Rivera-Lozada", "Carlos Neyra-Rivera", "Cesar Antonio Bonilla-Asalde", "José Antonio Jauregui-Montero", "Carlos Neyra-Rivera" ], "abstract": "Background: The aim of this study was to collect and analyze the experiences in regard to the application of criminalistic and criminological protocols and procedures, which were used to carry out the intervention in the premises of Thomas Restobar in Peru, in the context of the declaration of sanitary measures to control COVID 19. This police intervention resulted in the death of 13 people. Methods: For the collection of information, we used the focus group technique, for which a script was designed and validated by five experts, considering six major subcategories: C1SC1: Joint investigation and prosecution work, C1SC2: Protocols and guidelines, C1SC3: Chain of custody (police, experts, and prosecutor), C1SC4: Quality of results; C2SC1: Participation of agents of Thomas Restobar and the municipality, C2SC2: Compliance with DIGESA-DIRIS health regulations. The study was approved by the Institutional Research Ethics Committee of the Universidad Norbert Wiener, with approval file N°864-2021. Results: From the criminological analysis it became evident that the deficiencies identified in the six structured subcategories have led to the tragic death of thirteen people from asphyxiation. The people who attended this bar did not comply with the sanitary norms, exposing the health and life of their relatives and other people. The security agents of the premises and of the Municipality of Los Olivos did not comply with the norms of supervision and control, which finally led to the unfortunate death of 13 people from asphyxiation, closely related to the case of Utopia, in 2002. Conclusions: When evaluated by the experts of the focus group, it has generated two emerging categories: creation of a School of Experts and the categorization of the experience, which would prevent cases like Utopia and Thomas Restobar from happening again.", "keywords": [ "Criminology", "Legislation", "Criminal law", "Social and economic law." ], "content": "Introduction\n\nOn August 22, 2020, approximately at nine o'clock at night, the main press, written, radio and television media in Peru, reported that an event took place in the Thomas Restobar discotheque in the city of Lima, capital of the country, with a massive attendance of people, where as a result of a police intervention in the context of the health emergency due to COVID-19, thirteen people died.\n\nIn Peru, the government established a compulsory curfew from 22:00 to 04:00, in addition to the prohibition of events involving crowds of people in order to avoid an increase in cases of COVID-19 in the country. However, the managers of “Thomas Restobar”, located in the district of Los Olivos, ignored the above provisions and organized a clandestine party. It resulted in the death of 13 people from asphyxiation as the more than 120 attendees tried to escape from the premises to avoid being arrested by the police (Gálvez, 2020). This information is consistent with what was published by the newspaper El Comercio (2020). According to their reports, it was the first major tragedy in the midst of the coronavirus pandemic, at least in Latin America, which was caused by the fact that people did not to follow the restrictions imposed. Thus, it was one of the aspects considered in this research as the cause of the tragedy. However, it was not the only festive activity in which the police intervened in the country, as in the northern city of Chiclayo, the day before the tragedy in Lima, the officers detained 40 people; and a week before, the police intervened with 90 people in another area of the city where people drank alcohol and danced in the premises of a transport company, without taking into consideration the sanitary control measures, although there were no deaths as was the particular case of Thomas Restobar.\n\nThree emblematic cases were analyzed: Case Utopia in Peru, Discotheque “Kiss” in Brazil, and clandestine premises in Spain.\n\nWe aim to examine the action protocols of the criminalistic and criminological investigation, identifying the relationship that was established between the institutions in charge of the investigative procedural function (Intitute of Legal Medicine, National Police of Peru [PNP], General Directorate of Environmental Health - Digesa and Municipality). Also, we describe the participation of the professional criminalistic experts in terms of compliance with the protocols and procedures, assessing the opinion that other professionals have regarding their compliance, and whether or not they were up to the circumstances. In addition, this research aims to identify the legislative, regulatory and operational factors that caused it; to make them known so that these unfortunate events, which have caused so much physical, psychological and health damage in the family and community environment, are not repeated.\n\nThe above mentioned, together with the new demands about the processes to guarantee the quality of the procedures, make it necessary to carry out a study to generate evidence about the role played by the compliance with norms, protocols, criminalistic and sanitary procedures, at the starting point of an emblematic case of media repercussion such as what happened in the present case of investigation.\n\nThis study will contribute to generate a perspective to be taken into account by the operators of the law, in regard to people’s actions with respect to the State, related to avoidable issues, which has to allow us to establish a change that should be based on the lessons learned, in order to ensure the protection of the fundamental rights of people.\n\nIt is too early to judge the impact of the COVID-19 pandemic in the country, in the context of the declaration of the emergency situation, however, even without further evidence, interesting lessons learned in the health, economic, social, political and legal fields can be identified, and this case is one of them.\n\nTherefore, the questions that arise are: why did the deaths of these people occur; were there deficiencies in the application of operational plans and action protocols, as well as irresponsibility and/or negligence on the part of the various actors involved; and were there deficiencies in the application of operational plans and action protocols? For this reason, the aim of the study is to investigate the perceptions of the actors regarding administrative and criminal responsibilities. The objective of the study is to analyze and interpret the experiences on the application of criminalistic and criminological protocols and procedures used in the investigation of the Thomas Restobar case in Peru in the context of the declaration of sanitary measures by COVID-19.\n\n\nLiterature review\n\nThe PNP’s mission is to: “…provide protection and assistance to individuals and the community, (…) investigate and combat crime (…) within the framework of a culture of peace and respect for human rights” (National Police of Peru, 2019, para. 1). To achieve this functional activity, the Directorate of Criminalistics of the National Police of Peru was created as a governing body of the Police Criminalistic System, with functional, administrative, regulatory, operational, technical, and scientific competence. It provides support to police units in the development of their functional activities by conducting technical and scientific tests, expressing opinions, issuing reports and other official documents at the request of the competent authorities as part of its functional activity established in the current legal regulations (Dirgen-PNP, 2018).\n\nIn compliance with this regulation, the first police officer who arrives at the scene is who, after verifying the existence of victims in order to help, will proceed to provide protection and isolate the scene, guaranteeing that nobody trespasses, using any suitable mechanism for their demarcation or cordoning (plastic tape, cords, etc.), adequately defining their limits and establishing the ways in and out of the isolated scene. If necessary, a double perimeter may be established (Minjus, 2014, p. 51).\n\nIn 2014, the New Code of Criminal Procedure was implemented, as well as the Regulations of the Chain of Custody. It aims to establish and unify basic procedures and responsibilities of the representatives of the Public Prosecutor's Office and officials, in order to ensure the authenticity and preservation of the material elements and evidence incorporated in any investigation of a punishable act, aided by forensic sciences, criminalistics, among other disciplines and techniques that serve the criminal investigation. In addition, it also aims to unify the general guidelines for the security and conservation of seized goods (MP-FN, 2006).\n\nThe culture of quality in the criminalistic function in Peru has not yet prospered because it is a voluntary procedure and due to its high implementation cost. Experiences such as the Quality Management Systems (QMS), in Argentina, in forensic laboratories are only known in the field of medicine, and only in specific cases, such as genetic analysis laboratories, […] the implementation of quality systems in forensic laboratories is increasingly in high demand, and constitutes a strategy for the continuous search for the quality of results, trying to minimize the margins of error (info-Lab Laboratory, 2020). In addition, we should note that the National Institute of Quality-Inacal, in Peru, aims to promote and ensure compliance with the National Policy for Quality in order to enhance the development and competitiveness of economic activities and consumer protection. Additionally, Inacal is the institution entrusted by the State to guarantee quality in such a way that companies obtain competitive advantages, by having laboratory services, certifications, and inspections based on integrity, efficiency and competence demonstrated with accreditation (Ministerio de la Producción, 2016).\n\nIn the congress organized by the Crime Laboratory Division in Peru, the work of the first respondent and the main challenges in a digital forensic laboratory was presented. Through this presentation, it was remarked that, today, police officers should be prepared and be able to collect evidence, as it is likely to find security cameras, mobile devices, computer servers, and they should work on and lift these devices, which are indications and recommendations that should not be alien to a superior. In regard to the Restobar case, it was indicated that it was not clear what had happened with the video files or their destination. Loyola (2021), Which was confirmed when the corresponding expert reports were made.\n\nJustice cannot be administered without the legal decisions determined by the Prosecutor and the Judge; therefore, we have taken into consideration the doctrines of Taruffo (2013) as this author mentioned that “Justice of the decision does not only presuppose its legality, that is, the derivation of a correct interpretation and application of the rules, but also truthfulness, this is, the inquiry of the truth about the relevant facts” (p. 98). In this regard, “The ultimate goal is to reach a stage in legal studies oriented by empirical research, in which it is possible to speak of evidence-based law” (Paez, 2015, p. 148). Thus, the determination of the facts is based on the reasons’ acceptability and validity criteria in order to consolidate the theory of evidence and not the subjective situation of the judge.\n\nFor this reason, it is necessary to include the legal regulations prior to the implementation of COVID-19 sanitary measures in the analysis; thus, Article 292 of the Penal Code typifies the crime of violation of sanitary measures as follows:\n\n“Whoever violates the measures imposed by law or by the authority for the introduction into the country or the spread of a disease or epidemic or an epizootic or plague, shall be punished with imprisonment of not less than six months nor more than three years and a ninety to one hundred and eighty days-fine” (Diario Oficial El Peruano, 2020).\n\nThe World Health Organization, on March 11, 2020, declared the SARS-CoV- 2 coronavirus outbreak (COVID-19) to be a pandemic. For this reason and in accordance with its constitutional competence, the Peruvian Government approved Article 1 of the Supreme Decree N.°020-2020-SA, which refers that: “The sanitary emergency declared by Supreme Decree N° 008-2020-SA is extended from June 10, 2020 for a period of ninety (90) calendar days” (Presidency of the Republic, 2020a).\n\nArticle 3 of the Supreme Decree N.°139-2020-PCM, norms about the limitation of the exercise of the right to freedom of transit of persons during the State of National Emergency, established the mandatory curfew of all people from 22:00 to 04:00 of the following day, from Monday to Saturday nationwide (Presidency of the Republic, 2020b).\n\nRegarding the functions of the municipalities during the sanitary emergency and with respect to their competence to control the freedom of transit of persons in the context of the Declaration of State of Emergency that imply the restriction of the exercise of constitutional rights related to personal freedom and security, inviolability of the home, and freedom of assembly and transit in the territory, as is the case of what is established in S.D. 008-2021-PCM (2021), the competent entities that are in charge of executing such measures are the PNP, with the support of the Armed Forces (FF.AA.). They ensure compliance with the provisions of the regulation of the state of emergency, for which purpose they can verify and intervene persons, goods, vehicles, premises, and establishments that are necessary to verify and, if necessary, prevent the carrying out of services and activities that are not allowed. They exercise control with respect to the limitation of the exercise of freedom of transit at the national level. The municipalities are obliged to collaborate with the PNP in this task.\n\nIn particular, S. D. 008-2021-PCM (2021) establishes that: “Local authorities have the duty to collaborate and not hinder the work of the police and military authorities in the exercise of their functions. In addition, local governments contribute (…), within the framework of their competences”. (Gob.pe, 2020a)\n\nIn regard to the functions of municipalities during the health emergency regarding public and private spaces in the case of activities or events that involve the concentration of people in indoor or outdoor spaces that offer great risks for the transmission of COVID-19, municipalities should contribute with the dissemination of information and sensitization of neighbors in order to avoid the organization or participation in activities that involve the agglomeration of people. In case of identifying places where these activities take place, municipalities should coordinate with the PNP to intervene, as the Ministry of the Interior (Mininter) is the competent entity to provide authorization for mass events. In addition, the entity itself should coordinate the measures of control of activities or events that involve the concentration of people in indoor and outdoor spaces that pose risks of COVID-19 transmissibility, and ensure that all commercial establishments and markets help in prevention efforts (Gob.pe, 2020b).\n\n\nMethods\n\nResearch with a qualitative approach was developed, with an intrinsic case study design, which presents its own specificities, “(…) aiming to achieve a better understanding of the specific case to be studied (…) the case is not chosen because it is representative of other cases, or because it illustrates a certain problem or feature, but because the case itself is of interest” (Stake, 2005, cited in Jiménez Chaves & Cornelio Comet, 2016, p. 7).\n\nThe primary sources of information used came from seven Peruvian professional experts, students of the Master's degree in Criminal Sciences of a Peruvian University, selected incidentally: a police crime scene expert, a biologist, a psychologist of the Ministry of Women, a lawyer Social Specialist of the Ministry of Women and Vulnerable Populations, two prosecutors of the Public Ministry, a lawyer of the Superior Court of Specialized Criminal Justice.\n\nThe authors did not have a previous relationship with the experts participating in the focus group. The experts were informed about the objectives of the study prior to their participation and the signing of the informed consent.\n\nFor the collection of information, the focus group technique was used, for which a script was designed and validated by five experts in law, for this purpose six open questions were applied, so that the experts could express themselves without limitations in their answers. For the development of the focus group, the sanitary provisions in force by COVID-19 were taken into consideration, being carried out virtually on the Microsoft Teams platform, being recorded in audio and video to be transcribed and evaluated.\n\nBefore the execution of the focus group, the researchers met three times to clarify the purposes of the activity and to review the content of the guide and to familiarize themselves with the open questions related to the objectives of the protocol. Additionally, it is important to mention that the researchers have experience in conducting qualitative research and the use of the focus group technique; the duration of the focus group session was two hours.\n\nThe transcripts were not given to the participating experts for their comments and/or corrections, they were only analyzed by the researchers.\n\nThe focus group participants have been coded as E1: police crime scene expert; E2: lawyer; E3: lawyer; E4: biologist; E5: prosecutor1; E6: prosecutor2; E7: psychologist and their responses RE1, RE2, RE3, RE4, RE5, RE6 and RE7.\n\nThe study was approved by the Institutional Research Ethics Committee of the Norbert Wiener University, with approval file No. 864-2021. The study participants gave their written informed consent and their identity was protected. The purpose of the research was to analyze from the perspective of important stakeholders – through their perception and opinion – to provide fundamental information about the object of study. Hence the usefulness of this approach for the study of what happened in Lima at Thomas Restobar in the context of the declaration of sanitary measures by COVID-19.\n\nIt was convenient to look at what happened from different angles to improve the perspective of the norms, protocols and procedures; as well as the conduct of the agents involved in this public event. In such sequence of ideas, the case study that was used in the to the criminalistic investigation (Jiménez and Comet, 2016, para. 6).\n\nFinally, in the triangulation, we proceeded to contrast and compare the focus group data, to identify coincidences and differences, incorporating symbolic interactionism, through a sociocultural interpretation, starting from the perception from the media point of view, which can influence the opinion of the actors involved in the study allowing to study in an economical, simple and undemanding way, the reality that surrounded about the methodological process of the study.\n\nIn Table 1 we can see the two categories: C1-Analysis of criminalistic procedures (1. Joint investigation and prosecution work, 2. Protocols and guidelines, 3. Chain of custody, 4. Quality of results); and C2-Criminological analysis and COVID-19 sanitary measures (1. Participation of Thomas Restobar agents and the municipality, 2. Compliance with DIGESA-DIRIS sanitary regulations), with four and two subcategories, respectively.\n\n\n\n1. Joint investigation and prosecution work\n\n2. Protocols and guidelines\n\n3. Chain of custody\n\n4. Quality of results\n\n\n\n1. Participation of Thomas Restobar agents and the municipality\n\n2. Compliance with DIGESA-DIRIS sanitary regulations\n\n\nResults\n\nThe results have been organized into two categories and six subcategories, with the additional identification of a meta-category called “Systematization and socialization of the experience” that synthesizes and groups the two categories: C1-Analysis of criminalistic procedures and C2-Criminological analysis and COVID-19 sanitary measures.\n\nThe main objective of the criminalistic procedures is to allow the formalization of the prosecutor's report, so that the criminal process can be supported by scientific and irrefutable evidence.\n\nQuestion: What are the advantages and disadvantages of the double participation of the national police and the Public Ministry in the criminalistic procedures and the issuance of expert reports, which will determine the formalization of the prosecutor's accusation?\n\nRE1, RE7 state that “…it is an advantage to have two institutions that look at the criminalistic aspect, because the police do not meet certain standards, and the Public Ministry does not have the number of personnel to deal with a crime scene……” This is shared by RE2.\n\nAccording to RE2 “… there should be an organization, an entity that can bring together the 2 entities of both the National Police and the Public Ministry to be in charge of the quality of the criminal investigation”.\n\nContinuing the analysis, RE3, RE5, RE6 state that given the administrative difficulties that exist between the National Police and the Public Ministry; perhaps it would be good to give this attribution to a private entity but the worrying thing is that it could generate a lot of suspicion, we have seen it with corruption issues, as an example the Odebrecht case and other institutions, in that same reasoning according to RE6 “it is necessary to create a school of experts, but the state has to control it, it may work…”\n\nDelimitation: The joint investigation and prosecution work is an advantage because they complement each other, it is a team effort. Weaknesses were identified such as: lack of personnel at the local and national level, hindering the formalization of the prosecution report; there is a lack of a State supervisory body to facilitate the work of both institutions.\n\nThe main objective of the protocols and guidelines is to ensure the integrity and quality of the processes.\n\nQuestion: What is your opinion regarding the Thomas Restobar case and the performance of the institutions involved in the timeliness, application, processing and chain of custody of the police, criminalistic and Public Ministry protocols?\n\nThe dialogue established during the development of the focus group has highlighted the experiences of the experts in the handling of the protocols and guidelines for the formalization of the public denunciation, which could be useful to understand their value in the analysis of what happened in Thomas Restobar Lima-Peru.\n\nRE1 explains “…we have seen that the first level of protection of the place of the facts was violated by the police officers, because they stole the DVR (Digital Video Recorder, the interpretation of the acronym is of the investigators), apparently with the content of the video images…”\n\nRE2, RE3, RE4 point out “…. yes there are these protocols of action to intervene in these investigations, but they are not easily accessible; there should be a portal to disseminate and publicize all these procedures, in a single portal. RE3 complements “…… should have acted with the corresponding police protocols, they were not organized correctly, despite the fact that the police intervened in the end there were several deaths and all this is related to the “utopia case”, there was no compliance with the use of protocols, they acted on impulse and did not measure the consequences of their police intervention”. RE4, RE5, RE6 consider that “…these criminalistic and operative manuals, protocols exist, however, they are not being applied, we are not prepared at the organizational level, they have not adopted the corresponding preventive measures since I can say a phrase “We have not learned from the mistakes of the past (…) only when the facts happen we reflect on it”.\n\nDelimitation: The police officers who intervened did not guarantee the intangibility of the scene; there are protocols, norms, guidelines, but they did not apply them correctly; they acted on impulse without measuring the consequences. They were not prepared; “We have not learned from past mistakes”; recalling the “Utopia” case where 23 people died.\n\nQuestion: What is your opinion regarding the Thomas Restobar case and the performance of the institutions involved in the timeliness, application, processing and chain of custody of the police, criminalistic and Public Ministry protocols?\n\nRegarding the analysis of the chain of custody, the disappearance of the DVR and therefore of the images recorded in this equipment was noted. In this regard, RE1 states “…it is assumed that the first interveners should have protected this scene, they are the guardians of the elements of evidence, if from there, the chain of custody has already been violated; protecting, isolating the crime scene or the scene of the crime is already a chain of custody (…) I consider that neither Public Ministry nor the experts were aware of this violation, until they arrived at the place where this DVR was missing and they did not know if it had been the people who were at the place or if it had been the police, there was a question: Who would have stolen this DVR? If it had been filmed or not, how did the events occur? I believe that the facts came to light through the press, who were the ones who disseminated the first images that showed that the DVRs were indeed taken from the scene. Then I consider that they have not acted adequately…”. RE2, RE3 and RE6, state that “…. the first thing to see is the police intervention and then the analysis of the cameras that was later disseminated, this allowed to see the contradictions that had been given in the first versions of the case, and this has allowed to determine above all that the police protocols had not been complied with”. RE4, RE6, RE7 consider that “…a lot of evidence was also lost due to the number of people, the family members who attended, the neighbors, the protocols came to nothing, and everything was chaotic that day”. Regarding the same, RE5 states “…… there was not a good communication between the police and the representative of the Public Ministry, but I understand that the police immediately reported the event, however the Public Ministry arrived a little late, even though being part of the Public Ministry, I cannot defend the indefensible, when a Prosecutor is on duty, he is on duty 24 hours a day. In conclusion, what I want to say is that this issue of the chain of custody was not respected at all; likewise, some basic criminalistic procedures were not taken into account, as I say and sometimes I also mention that the principles of Criminalistics were not taken into account, perhaps to adequately approach this type of investigation, there was an incorrect synergy between the police and the representative of the Public Ministry.\n\nDelimitation: There was an incorrect chain of custody procedure. There was an incorrect synergy between the police and the representative of the Public Ministry.\n\nQuestion: How are we prepared to guarantee the quality of the results of forensic procedures?\n\nInacal and other institutions refer to the importance of the culture of quality of the results to guarantee the effectiveness and efficiency of these in the processes in general that are also applied in the criminalistic processes. Thus, in RE1 it is mentioned: “….. I believe that there has not been a quality of the results, I consider that it would be feasible to use a private company, because as I said before, the laboratory of the National Police nor the Public Ministry, do not have an ISO quality certification nor quality standards, so they could be questioned; in the analysis of the opinion of RE2 it is found that ”…. the quality of the procedures is related to training, infrastructure, implementation of the departments, investment in technology; there should be a unit to verify the procedures and really contribute to improve the work of the investigators; Inacal should intervene to ensure that these procedures are correct, thus RE4, RE7 agree with what was stated; thus RE5 also adds the high rotation of investigators, absence of a standardized format of expert reports, lack of a school of experts, more experts (….) all these aspects, since they are not taken into account become factors that weaken the quality of the results.”\n\nRE3 states: “…it is required to be an expert to have enough experience in the matter (…) then in this case Thomás Restobar apparently has not been carried out correctly, it has been wanted to act properly; becoming evident that we are not prepared to guarantee the quality of the results, even though there are standard procedures these are not carried out\"; within this same line of reasoning in RE6 also highlights that “…. … most of these experts have been trained by the National Police in different trainings, and their expertise makes them better, we need a National School of Experts as in other countries of the world”.\n\nDelimitation: The National Police and the Public Ministry do not have ISO quality certification and quality standards. Inacal should intervene in order to improve the processes or a private institution that performs this function. Additionally, a national school of experts should be created.\n\nQuestion: What is your opinion of the Thomas Restobar case and the actions of the Municipality of Los Olivos, the Directorate of Integrated Health Networks Lima Norte-Diris and the Ministry of Health's General Directorate of Environmental Health-Digesa?\n\nRegarding the participation of the key social players of Thomas Restobar and the municipality, interviewees RE1, RE2, RE3, RE4, RE7 told us “……. that the preventive part is neglected, that they are responsible, that if we are in a state of emergency, the municipality is in charge of enforcing it, because that place should have been closed, why was it open at that time? They should have fulfilled their task of control and supervision of these businesses, it seems that a license had already been previously denied, so this place already had problems, it was a place that should have received more attention”; Finally, RE7 stated that “… we were in a state of emergency, what were these people doing at that time in this place, concentrated, not respecting the social distance”.\n\nRE3 reports that “…it did not have the conditions for a restobar, for example, it had only one entrance and exit staircase, if an inspection had been carried out previously, which was not done, if the corresponding fine had been imposed to fix that aspect, I believe that so many victims would have been avoided, at the time the police entered. In addition, in RE5 he also reminds us that ”…… we are always going to relive the case of Utopia (discotheque where a fire occurred in 2002 and 13 people died - this explanation is from the investigators), the tragedy of that time could have been avoided, the municipality can establish sanctions, fines, temporary or permanent closure, but nothing was done”. Thus in RE6 he reminds us: “…… the mayor justifies his actions by indicating to the press that he did not have enough economic resources to hire more personnel, so I believe that here there are responsibilities on the part of the municipal authorities, well it is assumed that the death of any person produces in the first place serious consequences of sentimental order, patrimonial, he considered that it is necessary to foresee and prevent.\n\nDelimitation: It is very strange that the officials of the municipality did not realize that it did not have the optimal conditions for its operation. The mayor justifies his actions by indicating that he does not have the economic resources to hire more inspectors. The death of any person has serious psychological and financial consequences.\n\nQuestion: What is your opinion of the Thomas Restobar case and the actions of the Municipality of Los Olivos, the Directorate of Integrated Health Networks Lima Norte-Diris and the Ministry of Health's General Directorate of Environmental Health-Digesa?\n\nFrom the focus group analysis, RE1, RE2 and RE3 say that: “… the rapid tests were done, the handling of these bodies generated contagion both to the intervening personnel and the prosecutor; they could have been infected; they do not know if there was any follow-up to determine if the quarantine was complied with.\n\nRE4 adds: “… evaluations should have been made not only to the participants of these parties, but also to those who lived around them. Also RE5 and RE7 refer that people should have been aware that, beyond exposing their lives, they were also exposing their relatives, because when going to this center, to the discotheque, the mandatory social distance was not respected, they were in contact, even people who had Covid-19 were identified, this is also a responsibility on their part, without any doubt, responsibility on the part of these institutions for not exercising greater control. RE6 states: “… well I am not going to repeat what my colleagues have already pointed out, the only thing I am going to say is that the Public Ministry has opened proceedings for three crimes: Culpable homicide, culpable injuries, failure to comply with sanitary measures. I consider that the preventive function has been carried out by both the Directorate of the Integrated Health Networks of Lima Norte and the General Directorate of Environmental Health, it was seen in the videos that all the people were being analyzed with the tests and it was precisely there that almost all of them were infected, because they had all been without social distancing.\n\nDelimitation: The rapid tests were performed on the police officers and people who were detained; others left without taking the rapid tests. It is not known if they complied with the corresponding quarantine, they would have spread the contagion to other local people and family members.\n\nFinally, a closing question was posed; from their perception:\n\nQuestion: What changes do you consider or should be implemented to improve criminalistic work, for example, training of criminal profilers, dynamic retrospective, forensic planimetric, or others?\n\nIn this regard, RE7 said that “…investigation is limited by non-optimized investigation capabilities, for various reasons such as: lack of technology, accreditation, optimization, therefore there should be an area of interinstitutional coordination of criminal investigation, interdisciplinary. RE2 “… … above all, it is necessary to systematize the experience, standardize procedures at the level of all instances, many of these people have years doing specialized investigations, but they have not been able to organize, systematize, create a magazine where all experts can publish the cases they have carried out”.\n\nRE1 “… … The crime scene expert is the one who directs, organizes, plans and the forensic photographer is part of his team, of course, I think there should be protocols for everything”.\n\nDelimitation: Strengthening of criminalistics. Their experiences are not shared. Creation of a school of experts. Creation of an interinstitutional coordination area for interdisciplinary criminal investigation. It has generated a meta-category called “Systematization and socialization of the experience”.\n\n\nDiscussion\n\nIn Peru, the government established mandatory social immobilization from 22:00 to 04:00 hours, in addition to the prohibition of events involving crowds of people in order to avoid an increase in cases of Covid-19 in the country. However, the managers of the local “Thomas Restobar” located in the district of Los Olivos ignored the above provisions and organized a clandestine party that resulted in the death of 13 people by asphyxiation, as the more than 120 attendees tried to escape from the establishment to avoid being arrested by the police (Gálvez, 2020); This information is consistent with the information provided by the newspaper El Comercio (2020) that it is the first major tragedy in the midst of the coronavirus pandemic, at least in Latin America, due to the decision of the people not to follow the restrictions imposed; it will be one of the aspects to be considered in this research as the cause of the tragedy. However, it was not the only festive activity in which the police intervened in the country, in the northern city of Chiclayo the day before what happened in Lima, the agents arrested 40 people. A week before, the police intervened 90 people in another area of Lima where they drank liquor and danced in the premises of a transport company, without taking into consideration the sanitary control measures; although there were no human losses to regret; as was the particular case of the study.\n\nThree emblematic cases will be taken to analyze: Utopia case in Peru, Discotheque “Kiss” in Brazil and a clandestine premises in Spain.\n\nA fire in the discotheque Utopia-Peru occurred on July 20, 2002; it had a tragic end with 28 dead and 57 injured. This place had no operating license because it did not comply with the minimum standards of civil defense. People tried to flee, but it was difficult for them to leave, because there were no signs indicating the emergency doors (EnfoqueDerecho.com, 2022). Also on January 23, 2013, in a fire at the Kiss nightclub in southern Brazil, 242 people died; there was only one exit and there were scenes of panic as people tried to get out (BBC, 2013). In both cases the unfortunate end was due to having only one escape door and security deficiencies.\n\nIn the case reported by the newspaper La Vanguardia (2020) where the Barcelona Police intervened 58 people in a clandestine party without masks in an event in the context of the COVID-19 pandemic, no deaths were recorded; note that in this case and other irregular events that occurred in other places in Peru did not result in deaths to regret; we believe that the concurrence of deficiencies that we will find in this research did not occur.\n\nThe following, based on the experiences of these emblematic cases, we will analyze the categories identified in the light of the findings of this study, from the perspective of the experts interviewed.\n\nThe category of joint work between the National Police and the Public Ministry is regulated and established to exercise interinstitutional coordination functions protected by the Political Constitution of Peru, its organic laws, the Code of Criminal Procedures, protocols of the Ministry of Justice and other provisions, in order to achieve an efficient function. The Ombudsman (2020) in a letter sent to the President of the Republic, asks the Government, together with local authorities, coordination with neighbors and the National Police of Peru, to contribute to the surveillance and prevention of mass gatherings of people during the COVID-19 pandemic. The experts have perceived deficiencies in the intervention process, which could be associated to the death of the 13 people by asphyxiation; evidenced through the videos spread by the press and those recorded by the security cameras of the premises.\n\nThe category of protocols and procedures of action, allows standardizing and ensuring the efficiency and effectiveness of the procedures; in our country the Supreme Decree 010-2018-JUS (2018) establishes that the first police officer who arrives at the scene must proceed to its protection and isolation guaranteeing its intangibility; adequately defining its limits and establishing the routes of entry and exit of the isolated scene; we have been able to evidence that there are; for example the Protocol of interinstitutional action for the protection and investigation of the crime scene, the Protocol of specific interinstitutional action for the protection and investigation of the crime scene. In this regard Taruffo (2013) and Paez (2015) agree that the determination of facts is based on criteria of acceptability and validity of reasons in order to consolidate the theory of evidence, guided by empirical research, in which it is possible to speak of evidence-based law. In the opinion of the experts, the manner in which the police approached the only entrance and exit door, closing it, caused the people trying to leave to crowd the stairs, which was evidenced in the video images disseminated by the press and the security cameras of the premises. This made it possible to determine that an operational plan of intervention, approach and processing of the place of investigation was not applied, in spite of having the respective regulations and protocols in place.\n\nThe Chain of Custody category starts with the participation of the first police intervener; it is fully regulated in the Code of Criminal Procedure; the Guide of Criminalistic Procedures of the National Police of Peru (PNP), the Manual of Criminalistic Expert Procedures; Loyola (2020) warns that a superior cannot be unaware that it is very likely that mobile devices, security cameras, servers, computers are found; regarding the case, he believes that more than six thousand video files were recovered or wanted to be deleted; it would have to be seen if these files were deleted on the day or at the moment when the agent was intervening. In the opinion of the experts, the chain of custody procedure was incorrect because there was an inadequate synergy between the police and the representative of the Public Ministry, this process was also flawed; this was also seen preliminarily in the video images disseminated by various media and later corroborated by the forensic experts when processing the scene, finding that the video recording equipment - DVR - was not in place. Therefore, it is evident that not only the chain of custody was not complied with, but also that an attempt was made to hide evidence, whose purpose is of probative value in the investigation.\n\nThe category quality of the results seeks the truth of the facts, which in the theory of evidence is about the criteria of acceptability and validity of the reasons, not the subjective situation of the Judge. In this context, the Ministry of Production counts on the National Institute of Quality (Inacal) to guarantee that the processes are executed in compliance with the protocols. Info-Lab Laboratory (2020) states that the implementation of quality systems in forensic laboratories is increasingly demanded, and constitutes a strategy for the continuous search of the quality of the results, trying to minimize the margins of error. The results obtained showed that there was no quality, that the laboratories of the National Police and the Public Ministry do not have an ISO 17025 quality certification, and recommended that it would be feasible to use a private company or that Inacal would have to intervene to ensure that these procedures are correct and above all that there is uniformity of procedures, as well as to promote the development and awareness of the institutional “culture of quality”.\n\nRegarding the category participation of players of Thomas Restobar and the municipality, the Organic Law of the municipalities establishes its supervisory role, granting licenses and sanctions, it should contribute with the dissemination and sensitization of neighbors in order to prevent them from organizing and participating in activities that involve the agglomeration of people; Agencia Andina (2020) also agrees that it should prohibit social gatherings in bars and nightclubs during the health emergency, taking into consideration that the civil defense certificate of the premises would have expired in January 2020. Cahuana (2020) agrees with the Ombudsman Office (2020) on the participation of the organizer of the event before an administrative responsibility, for organizing this type of events in a place that was not adequate. The experts are of the opinion that it is evident that the municipality has not fulfilled its supervisory role, as well as the preventive work that it is responsible for, considering also co-responsibility with the owner and the administrators of the premises; emphasizing also that the death of any person produces in the first place serious consequences of psychological and patrimonial order.\n\nRegarding the category of compliance with DIGESA-DIRIS sanitary regulations, article 292 of the Penal Code typifies the crime of violation of sanitary measures, article 3 of the Supreme Decree No. 139-2020-PCM (2020) provides for the mandatory social immobilization of all persons in their homes from 22:00 hours to 04: Pacheco (2020) confirms that necropsies were performed on the 13 bodies and that rapid tests were applied to the police officers who intervened, but it is not known if the people who tested positive have complied with the respective quarantine; In the opinion of the experts, the Digesa-Diris would have complied with the preventive function by disseminating the sanitary dispositions; however, many people withdrew without being tested and all those who tested positive were not informed of their compliance with the quarantine, which may have determined that the contagions occurred to the family members and their environment.\n\n\nConclusions\n\nThe need to investigate and reflect on the advantages and difficulties involved in complying with the rules and protocols under the perspective of justice operators in sanitary conditions, as in the COVID-19 pandemic; has allowed the identification of six subcategories: Joint investigative and prosecutorial work; the protocols and action guides; the chain of custody; the quality of the results; the participation of the Thomas Restobar actors in charge of organizing the event and the municipality; compliance with DIGESA-DIRIS sanitary regulations; in all of them deficiencies have been established. As a result of the theorization delimitations and contrasts, a new emerging meta-category called “Systematization and socialization of the experience” was generated. Society is exposed to various events, due to its own irresponsibility or negligence on the part of the State, which can lead to tragic endings such as the case studied. In this sense, the judicial and health systems face challenges in order to correct and develop theoretical, methodological and attitudinal capacities, which allow the planning of actions and coordinated work, as quality instruments; in order to avoid physical, psychological and social damage in the family and community environment.", "appendix": "Data availability\n\nZenodo: Criminalistic and criminological analysis of the Thomas restobar case in Peru in the context of sanitary measures by covid 19: case study, https://doi.org/10.5281/zenodo.7030306 (Cesar Antonio bonilla-Asalde, Oriana Rivera-Lozada, José Jauregui-Montero, & Carlos Neyra-Rivera, 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAgencia andina: Defensoría: Municipios deben fiscalizar que se cumpla prohibición de reuniones sociales [Ombudsman Office: Municipalities must monitor compliance with ban on social gatherings]. Empresa Peruana de Servicios Editoriales S. A. 23 August 2020.\n\nBBC: Brasil: Tragedia en discoteca deja 233 muertos [Brazil: Nightclub tragedy leaves 233 dead]. BBC News World;27 January 2013. Congreso de la República [Congress of the Republic] (23 May 2003). Proyecto de Ley N° 27972. Ley Orgánica de Municipalidades [Draft Bill No. 27972. Organic Law of Municipalities]. El peruano Gazette.Reference Source\n\nCcahuana Castillo HD: El caso Thomas Restobar: ¿homicidio doloso u homicidio culposo? [The Thomas Restobar case: intentional homicide or manslaughter?] LP.11 September 2020.\n\nDefensoría del Pueblo [Ombudsman Office] : Defensoría del Pueblo emite comunicado por hechos ocurridos en Los Olivos [Ombudsman Office issues statement on events in Los Olivos]. Defensoría del Pueblo - Perú [Ombudsman Office - Peru]. 23 August 2020.\n\nGazette EPO: Código Penal: Normas legales actualizadas [Penal Code: Updated legal norms]. Editora Perú;2020.\n\nLoyola: Seminario Internacional Virtual “La evidencia digital y su relación con las Ciencias Forenses de la Criminalística, para combatir la criminalidad organizada y delitos comunes” [International Virtual Seminar “Digital evidence and its relationship with the Forensic Sciences of Criminalistics, to combat organized crime and common crimes”]. Divlacri Digital Forensic Laboratory Department;1 March 2021; 1. : 02: 40.\n\nDirgen-PNP: Normas, procedimientos y criterios que regulan las actividades en el sistema criminalístico policial a cargo de la Dirección de Criminalística de la Policía Nacional del Perú [Norms, procedures and criteria that regulate the activities in the police criminalistic system in charge of the Directorate of Criminalistics of the National Police of Peru]. StuDocu;2018.\n\nEl Comercio: Discoteca en Los Olivos: Las peores tragedias en discotecas en América Latina y el mundo [Discotheque in Los Olivos: Las peores tragedias en discotecas en América Latina y el mundo] [Empresa Editora El Comercio]. Elcomercio.pe. Grupo El Comercio.28 August 2020.\n\nEnfoqueDerecho.com: Caso Emblemático\|Utopía [Emblematic Case\|Utopia]. Enfoque Derecho\|El Portal de Actualidad Jurídica de THĒMIS [The Legal News Portal of THĒMIS]. 30 January 2022.\n\nGálvez S: Fiesta en cuarentena: Tragedia en discoteca «Thomas Restobar» y recordando el caso de la discoteca «Utopía» [El portal jurídico IUS ET VERITAS] [Party in quarantine: Tragedy in discotheque “Thomas Restobar” and remembering the case of the discotheque “Utopia” [The legal portal IUS ET VERITAS]]. IUS. 25 August 2020; 360.\n\nGob.pe: Gestión Municipal: Funciones de las municipalidades durante la emergencia sanitaria [Municipal Management: Functions of the municipalities during the sanitary emergency]. Peruvian Government Unique Digital Platform. 2020a.\n\nGob.pe: Gestión Municipal: Funciones de las municipalidades durante la emergencia sanitaria [Municipal Management: Functions of the municipalities during the sanitary emergency]. Peruvian Government Unique Digital Platform. 2020b.\n\nJiménez V, Comet C: Los estudios de casos como enfoque metodológico [Case studies as a methodological approach]. ACADEMO Journal of Research in Social Sciences and Humanities. December 2016; 3(2): 7.\n\nInfo-lab Laboratory: Metodología de Implementación de un Sistema de Gestión de la Calidad en un Laboratorio Informático Forense [Methodology for the Implementation of a Quality Management System in a Computer Forensic Laboratory]. Laccei. 2020; 2020.\n\nLa Vanguardia: Identificadas decenas de personas en una fiesta sin mascarillas en Barcelona bajo el lema “hoy se lía” [Dozens of people identified at a party without masks in Barcelona under the slogan “It gets messy today”]. La Vanguardia;23 August 2020.\n\nMinisterio de la Producción [Ministry of Production] : Instituto Nacional de Calidad: Presentación [National Institute of Quality: Introduction]. Consulted 4 November 2021.2016.\n\nMinisterio de Justicia y Derechos Humanos, [Minjus] [Ministry of Justice and Human Rights] : Protocolos de Actuación Interinstitucional Específicos para la Aplicación del Código Procesal Penal Peruano [Specific Interinstitutional Action Protocols for the Implementation of the Peruvian Code of Criminal Procedure]. Decreto Supremo 010-2018-JUS Comisión Especial de Implementación del CPP [Special Commission for the Implementation of the CPP]. 2018.\n\nMinjus: Supreme Decree 003-2014-JUS. Protocolos de trabajo conjunto entre el ministerio público y policía [Protocols for joint work between the Public Ministry and the Police]. Comisión Especial de Implementación del CPP [Special Commission for the Implementation of the CPP]. 2014.\n\nMP-FN: Reglamento de la Cadena de Custodia de Elementos Materiales, Evidencias y Administración de Bienes Incautados (12512doc_5.pdf) [Regulations for the Chain of Custody of Material Elements, Evidence and Administration of Seized Goods]. Instituto de Medicina Legal y Ciencias Forenses [Institute of Legal Medicine and Forensic Sciences]. 15 June 2006.\n\nPacheco D: Caso discoteca Thomas: PJ dicta prisión preventiva contra Luque Ayala [Thomas discotheque case: The Judiciary orders remand in custody against Luque Ayala]. [video]. LPderecho.28 August 2020.\n\nPáez A: Hechos, evidencia y estándares de prueba: ensayos de epistemología jurídica [Facts, evidence and standards of proof: essays in legal epistemology]. First ed.Bogota, D.C., Colombia:Universidad de Los Andes, School of Law;2015. 978-958-774-216-9.\n\nPeruvian Government Unique Digital Platform for Citizen Orientation: Gestión Municipal: Funciones de las municipalidades durante la emergencia sanitaria [Municipal Management: Functions of the municipalities during the sanitary emergency]. Peruvian Government Unique Digital Platform;Gob.pe, 2020.\n\nNational Police of Peru [PNP]: Misión [Mission]. Consulted 20 May 2022.2019.\n\nPresidencia de la República [Presidency of the Republic]: Supreme Decree No. 010-2018-JUS. Aprueban protocolo de actuación Interinstitucional de carácter sistémico y transversal para la aplicación del Código Procesal Penal. Official Gazette. Publicado 25 de agosto 2018.23 Agous 2018. www.elperuano.es.pga\n\nPresidencia de la República [Presidency of the Republic] : Supreme Decree No. 020-2020-SA. Decreto Supremo que prorroga la Emergencia Sanitaria declarada por Decreto Supremo N° 008-2020-SA [Supreme Decree that extends the Sanitary Emergency declared by Supreme Decree N° 008-2020-SA]. Official Gazette.3 June 2020a. www.elperuano.es.pga\n\nPresidencia de la República [Presidency of the Republic] : Supreme Decree No. 139-2020-PCM. Decreto Supremo que modifica el Decreto Supremo N° 116-2020-PCM [Supreme Decree that modifies Supreme Decree N° 116-2020-PCM]. Decreto Supremo que establece las medidas que debe observar la ciudadanía en la nueva convivencia social y prorroga el Estado de Emergencia Nacional por las graves circunstancias que afectan la vida de la Nación a consecuencia de COVID-19, modificado por los Decretos Supremos N° 129-2020-PCM y N° 135-2020-PCM [Supreme Decree that establishes the measures to be observed by the citizens in the new social coexistence and extends the National State of Emergency due to the serious circumstances affecting the life of the Nation as a result of COVID-19, modified by Supreme Decrees No. 129-2020-PCM and No. 135-2020-PCM]. Official Gazette.12 August 2020b. www.elperuano.es.pga\n\nTaruffo M: Verdad, prueba y motivación en la decisión sobre los hechos. México, DF:Tribunal Electoral del Poder Judicial de la Federación;2013. 978-607-708-179-1." }	[ { "id": "177574", "date": "22 Jun 2023", "name": "Effi Lambropoulou", "expertise": [ "Reviewer Expertise Criminology", "Sociology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 contains new information to justify publication.\n\nThe title is adequate.\n\nThe Abstract/Summary and the material are suitable.\n\nIn general, the study is clearly and accurately presented. The text is written in good English and is easily understood.\n\nThe used literature is technical and there is no theoretical context in the article; I don’t think that the authors had an intension of theorising.\n\nI cannot answer if adequate reference is made to other work in the field for the reasons mentioned above (technical).\n\nThe details of methods are sufficient. The replication is difficult because the researchers have used focus groups and the same groups cannot be recreated.\n\nThe study is appropriate for indexing after some changes: I could not find the analysis of the three other cases the authors say they compare (Case Utopia in Peru, Discotheque “Kiss” in Brazil, and clandestine premises in Spain). The cases are only referred twice, pp. 3 and 10.\n\nAll the source data underlying the results are available to ensure full reproducibility.\n\nNone of the material can be deleted without detriment.\n\nThe conclusions drawn are adequately supported but not sufficiently.\n\nIs the work 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": [] } ]	1	https://f1000research.com/articles/11-1356
https://f1000research.com/articles/12-728/v1	22 Jun 23	{ "type": "Research Article", "title": "Reduction of hydrocarbon pollutants by hyacinth plants (Eichhornia crassipes)", "authors": [ "Syahril Nedi", "Irwan Effendi", "Afrizal Tanjung", "Elizal Elizal", "Irwan Effendi", "Afrizal Tanjung", "Elizal Elizal" ], "abstract": "Background: The application of phytoremediation by utilizing plants has been used to control oil pollution in waters. One of the plants that can act as a phytoremediator is the hyacinth because this plant can reduce various pollutants including petroleum hydrocarbons. This study aims to study the reduction ability of petroleum hydrocarbons at different concentrations including improving water quality. Methods: This study consisted of one treatment (petroleum hydrocarbon) consisting of five factors with three replicates. The treatments consisted of 10 ppm (E1), 30 ppm (E2), 50 ppm (E3), 70 ppm (E4), 90 ppm (E5), and (E0) without aquatic plants as controls. The treatments were observed daily and measured from the first day (D-1), the seventh day (D-7), and the 14th day (D-14). The water quality in each treatment was also measured, such as water temperature, pH, and dissolved oxygen. Results: The results showed that the hyacinth plant was able to reduce hydrocarbon in terms of total petroleum hydrocarbon (TPH) by 79% while it was only between 17–27% naturally without the hyacinth. The reduction of TPH in the water was in line with the decrease of chlorophyll in the leaves of hyacinths, and it was followed by the increase of dissolved oxygen in the water media. Conclusions: In conclusion, hyacinths can reduce petroleum hydrocarbons and they can improve the water quality as well.", "keywords": [ "Hydrocarbon pollutants", "Hyacinths", "Phytoremediation", "TPH", "Chlorophyll" ], "content": "Introduction\n\nOil pollution is a common problem in coastal waters; such as oil slicks or spills. Most of the oil contains toxic hydrocarbon compounds that are vulnerable to habitats and biota. Common ways to encounter this pollution are through the oil boom, skimmer, dispersant, and bioremediation.1–3 Bioremediation is a way to clean up contaminants in an environment by living organisms; for example, the use of bacteria and water plants. Research on hyacinth as a phytoremediator has been conducted by several researchers before; for example, for radioactive waste4–6 and using biogas hyacinth as a phytoremediator of industrial waste.7,8 Besides, the use of water plants for phytoremediators is cost-effective and eco-friendly and well-documented.9,10 Based on this circumstance, the author is interested in testing the ability of the hyacinth plant to reduce hydrocarbon pollutants in saline water.\n\n\nMethod\n\nThis research was conducted in June 2022 at the Lagio Laboratory, Pekanbaru. The test plant, hyacinth, was taken from the reservoir of Binawidya Campus, Faculty of Fisheries and Marine, Universitas Riau. Meanwhile, the hydrocarbon pollutants used come from Pertamina DEX Solar from Pekanbaru gas stations. The seawater was taken from the coastal waters of Dumai and composted fertilizer was also used for the test plants. The plants were grown in 20 L plastic washbasins.\n\nIn this experiment, petroleum hydrocarbon was added to the water of growing plants as a pollutant with different concentrations (Table 1). Each treatment consisted of three replicates. The reductions of the petroleum hydrocarbon in the treatments were measured in terms of total petroleum hydrocarbon (TPH); they were measured once a week, starting from the 1st day (D-1), the 7th day (D-7), and the 14th day (D-14).\n\nAcclimatization to salinity\n\nThe container used was a black tub with a volume of 10 L of 15 units. The research was started by acclimatizing hyacinth plants to different salinities, namely 1, 3, 5, 7, and 9 ppt. In each container, 200 g of hyacinth was added and its growth was observed for seven days. Plant growth was seen based on changes in leaf color, root condition, and number of leaves. The acclimatization results showed that the test medium with a salinity of 3 ppt was suitable for plants to grow in coastal areas, some plants at salinity 5,7, and 9 died after being given salinity treatment.\n\nPetroleum hydrocarbon observations\n\nAfter determining the suitable salinity for the test plants, they were then planted in petroleum hydrocarbon pollutant solutions with different concentrations, namely 10, 30, 50, 70, and 90 ppm, and without plants (control). The first step was a black tub with a volume of 20 L of 15 units filled with 10 L of water with a salinity of 3 ppt. Then 50 g of fertilizer was added to each container and 200 g of test plants were added. After that, petroleum hydrocarbons were added according to the concentration determined and observed for 14 days.11,12 The parameters observed were total petroleum hydrocarbons, water quality (temperature, pH, DO, and salinity), and plant conditions (leaf color, root condition, and stem shape). To maintain the salinity in the test container, fresh water was added according to a predetermined volume limit, i.e. 10 L. Each container was marked, to determine the level of water whose volume is 10 L.\n\nLeaf chlorophyll measurement\n\nThe chlorophyll value of water hyacinth leaves was read using a chlorophyll meter (Konica Minolta Spad 502 Plus). Observation of chlorophyll content in the leaves was carried out randomly by placing the leaves in the sensor area and waiting for the value to be displayed on the screen. Leaf chlorophyll measurements were carried out in situ between 10.00 AM–03.00 PM.\n\nData on TPH concentration and chlorophyll were tabulated and analyzed using SPSS version 23. Data were analyzed using a One Way ANOVA and continued by a Student Newman Keuls (SNK) test if necessary.\n\n\nResult\n\nThe phytoremediators (hyacinths) could grow well in the tested media; with 3 ppt of saline water at 10–20 cm in height after acclimation. The content of hydrocarbon pollutants can naturally decrease, this also occurs in the treatment without the addition of plants; this is thought to be due to evaporation (E0). The concentrations of TPH in all treatments at the time of observations can be seen in Table 2.\n\nTable 2 showed that the TPH in all treatments reduced after the seventh day (D-7) and the 14th day (D-14) of observations. The reductions were higher on the seventh day in comparison to the 14th day of observation. These reductions ranged from 6.3–47.3 ppm and from 1.6–9 ppm consecutively. However, the total reductions ranged from 7.9–56.3 after the 14th day of observations. This means that the longer the observation time the higher the TPH reductions. The affectivity of the plant to reduce TPH showed the same pattern due to the time constraint of observations (Figure 1).\n\nThe treatment without a phytoremediator (E0) can only reduce the TPH by as much as 17.78% after the 7th day (D-7) and 27.78% after the 14th day (D-14). In contrast, it ranged between 41.67% and 63% reduction using a phytoremediator. The highest effectivity of reductions was found at the treatment E10 (79%) with 10 ppm of petroleum hydrocarbon because the reduction process will be optimum at lower concentrations of pollutants. In addition, there was a significant effect of hydrocarbon concentrations on the plant’s ability to reduce TPH, based on ANOVA analysis that p<0.05.\n\nChlorophyll is also an indication of the productivity of green plants and is one of the important elements in the process of photosynthesis. The results showed that the amount of chlorophyll in the leaves of the test plant (hyacinth) decreased in line with the increase in hydrocarbon pollutants and the length of observation time (Figure 2). In the treatment without hydrocarbons (E0), the amount of chlorophyll on the leaves of hyacinths was 48.3 units on the first day (D-1), then increased to 50.8 and 51.2 units on the 7th day and the 14th day (D-7 and D-14). In treating hydrocarbon pollutants (e.g. E5), the amount of chlorophyll encountered was 17.9 units on the seventh day and 13.9 on the 14th day.\n\nDifferences in pollutant concentration treatment influence the chlorophyll content in hyacinth leaves (p<0.05). Another parameter of water quality is dissolved oxygen (DO). In control media (without plants), the average DO on the first day (D-1) was 3.0 ppm; it increased to 3.3 ppm and 3.5 ppm after seven and 14 days consecutively. It indicated that the DO naturally increased with the pollutant hydrocarbon. However, the increases of DO were higher in the treatments with hyacinth phytoremediators; it was up to 20% compared to the treatments without the phytoremediator plants (Figure 3).\n\nVariations in the concentration of hydrocarbon pollutants affect the dissolved oxygen of the test medium. The higher the concentration of hydrocarbon pollutants given, the higher the decrease in DO content in the test media water (Figure 4).\n\nHowever, the DO figures were slightly higher based on the days of observations and concentrations; D-14>D-7>D1. Temperature plays an important role in plant life and growth. A good temperature for the plant to grow is known as the optimum limit of temperature. At this limit, plants can grow well both in terms of morphology and physiology. Temperature conditions at the treatment with 10 ppm hydrocarbon without phytoremediator’s plant (E0) were seen to decrease in line with the observation time ((D-1, D-2, and D-3); see Figure 4).\n\nFigure 5 shows that the presence of hydrocarbon pollutants affected the temperature of the water test medium. On the seventh and 14th days, the same concentration of hydrocarbon pollutants occurs with a decrease in temperature by 0.2–0.3°C.\n\nThe temperature in the treatment medium with different concentrations of hydrocarbon pollutants and phytoremediators (E1–E5) can be seen in Figure 6.\n\nBased on this figure, it can be seen that the temperature of the media increases in line with the increase in pollutant concentration and the length of time of observation. The increase in temperature may be closely related to the hydrocarbon reduction process that releases heat by phytoremediators when carrying out water purification.\n\nThe degree of acidity (pH) is the concentration of hydrogen ions in the water. The pH of the growing water of treatments tended to decrease along with the higher concentration of pollutants; it might be due to the phytoremediator process and pollutant degradation. The decrease was 0.4–0.7 between D-1 and D-14 (Figure 7).\n\n\nDiscussion\n\nWater hyacinth is a native freshwater plant from South America.13–15 The results showed that this plant grows well at a salinity of 3 ppt; Ting et al., 201816 also reported that this plant can adapt and grow at a salinity of <5 ppt. In addition, this plant can act as a phytoremediator against toxic pollutants derived from petroleum hydrocarbons. The effectiveness of TPH reduction depends on the concentration and length of time of observation (Table 2 and Figure 1). Meanwhile, optimum reduction efficiency is found in treatments with low concentrations (10 ppm); i.e. 63% on D-7 and 79% on D-14. The process of reducing TPH by this plant is inseparable from its root system which acts as an absorbent and then spreads to all parts of the plant.17–19 Some of the organic content contained in hydrocarbon pollutants is used as nutrients for plants; Oke et al., 202020 reported that the highest absorption of hydrocarbons by 100 g of hyacinth is 72%. The presence of biodegradable bacteria in the water hyacinth root system may also play a role in the process of reducing TPH in the test media, according to Xia & Ma (2006)21 the presence of bacteria in roots can degrade pollutants by 12%. Thus, these plants can purify water contaminated by hydrocarbon pollutants.\n\nAlthough water hyacinths can reduce TPH and purify water, it has an impact on the growth of the test plants. This condition was indicated by a decrease in the amount of chlorophyll in each treatment along with an increase in concentration and length of observation time (Figure 2).\n\nThe decrease in the amount of chlorophyll on the leaves is inseparable from the disruption of metabolic processes in plants so that their productivity is disturbed. Plants exposed to pollutants for a certain time will experience chlorosis due to inhibition of the chlorophyll synthesis.22 Of course, a decrease in the amount of chlorophyll affects the process of photosynthesis and enrichment of DO in waters.\n\nIn the control treatment without hyacinths (E0), it was seen that DO increased in line with the observation time (Figure 5). The amount of DO in the treatment with hyacinths was higher than without plants or controls. The increase in DO may come from the diffusion of oxygen from the air as well as the photosynthetic activity of phytoplankton and test plants. Nevertheless, DO conditions decreased with increasing concentrations of hydrocarbons and the length of time of observation (Figure 6). The same condition is also shown by the temperature and pH of the water test plant (Figure 7). The decrease could be due to the reduction of chemical processes and the decomposition of TPH. Where in these processes, in addition to requiring oxygen, there is also absorption and release of heat, including the use of hydrogen ions which affect the pH of water.\n\n\nConclusion\n\nHyacinth plants can reduce hydrocarbon pollutants. The effectiveness of the reduction of hydrocarbon pollutants by hyacinths can reach 79% at a hydrocarbon pollutant concentration of 10 mg/L. The presence of hydrocarbon pollutants has led to a decrease in chlorophyll in the leaves of hyacinths. Hyacinths can absorb organic matter without using oxygen for the decomposition process. Differences in pollutant concentration treatment influence the chlorophyll content in hyacinth leaves (p<0.05). Watered hydrocarbon pollutants are tolerated by hyacinth plants and can prevent water quality degradation.", "appendix": "Data availability\n\nZenodo: Reduction of Hydrocarbon Pollutants by Hyacinth Plants (Eichhornia crassipes), https://doi.org/10.5281/zenodo.7659979. 23\n\nThis project contains the following underlying data:\n\n• EXCEL KONFILASI DATA ECENG GONDOK (1).xlsx (Effectiveness Hyacinth, water quality and Chlorophyll)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to thank the Laboratory of Fisheries Universitas Riau.\n\n\nReferences\n\nNedi S, Pramudya B, Riani E, et al.: Karakteristik Lingkungan Perairan Selat Rupat. J. Environ. Sci. 2010; 4(1): 25–35.\n\nSayed K, Baloo L, Sharma NK: Bioremediation of total petroleum hydrocarbons (TPH) by bioaugmentation and biostimulation in water with floating oil spill containment booms as bioreactor basin. Int. J. Environ. Res. Public Health. 2021; 18(5): 2226). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva IA, Almeida FCG, Souza TC, et al.: Oil spills: impacts and perspectives of treatment technologies with focus on the use of green surfactants. Environ. Monit. Assess. 2022; 194(143): 143. PubMed Abstract \| Publisher Full Text\n\nNag S, Biswas S: Bioremediation — the natural solution. Development in Wastewater Treatment Research and Processes. 2022. Publisher Full Text\n\nSaleh HM: Water hyacinth for phytoremediation of radioactive waste simulate contaminated with cesium and cobalt radionuclides. Nucl. Eng. Des. 2012; 242: 425–432. Publisher Full Text\n\nSaleh HM: Biological Remediation of Hazardous Pollutants Using Water Hyacinth- A Review. J. Biotechnol. Res. 2016; 2(11).\n\nChaithra KS, Lokeshappa B, Gabriel KP: Water Hyacinth-A potential Phytoremediator and Biofertilizer. Int. Res. J. Eng. Technol. 2016; 3(8).\n\nSaha P, Shinde O, Sarkar S: Phytoremediation of industrial mines wastewater using water hyacinth. Int. J. Phytoremediation. 2017; 19(1). Publisher Full Text\n\nHakeem KR, Sabir M, Öztürk M, et al.: Phytoremediation: An Eco-Friendly Green Technology for Pollution Prevention, Control and Remediation. Soil Remediation and Plants. 2015.\n\nNewete SW, Byrne MJ: The capacity of aquatic macrophytes for phytoremediation and their disposal with specific reference to water hyacinth. Environ. Sci. Pollut. Res. 2016; 23(11): 10630–10643. Publisher Full Text\n\nZhang Z, Hou Z, Yang C, et al.: Degradation of n-alkanes and polycyclic aromatic hydrocarbons in petroleum by a newly isolated Pseudonomas aeruginosa DQ8. Bioresour. Technol. 2011; 102(5): 4111–4116. Publisher Full Text\n\nParida P, Satapathy KB, Mohapatra A: Phytoremediation potential of aquatic macrophyte Azolla pinnata R.BR and Salvinia molesta Mitchell to remove chromium from waste water. Plant Arch. 2020; 20(1): 2560–2595.\n\nDe Carvalho LB, Junior CWR: Control of water hyacinth: a short review. Commun. Plant Sci. 2019; 9(1). Publisher Full Text\n\nMunjeri K, Ziuku S, Maganga H, et al.: On the potential of water hyacinth as a biomass briquette for heating applications. Int. J. Energy Environ. Eng. 2016; 7(1): 37–43. Publisher Full Text\n\nPatoka J, Bláha M, Kalous L, et al.: Potential pest transfer mediated by international ornamental plant trade. Sci. Rep. 2016; 6: 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTing WHT, Tan IAW, Salleh SF, et al.: Application of water hyacinth (Eichhornia crassipes) for phytoremediation of ammoniacal nitrogen: A review. J. Water Process. Eng. 2018; 22: 239–249. Publisher Full Text\n\nWagiono W, Atmono A, Wulandari D: Pengaruh Variasi Waktu Terhadap Penurunan Total Petroleum Hydrocarbon (TPH) pada Proses Bioremediasi Limbah Oli dengan Metode Biostimulasi. Jurnal Lingkungan Dan Sumberdaya Alam (JURNALIS). 2022; 5(2): 109–120. Publisher Full Text\n\nKalsum U, Napoleon A, Yudono B: Efektivitas Eceng Gondok (Eichhornia crassipes), hydrilla (Hydrilla verticillata), dan rumput paying (Cyperus alternifolius) dalam pengolahan limbah grey water. J. Penelit. Sains. 2015; 17(1): 20–25. Publisher Full Text\n\nAhmad H, Adiningsih R: Efektivitas Metode Fitoremediasi Menggunakan Tanaman Eceng Gondok dan Kangkung Air dalam Menurunkan Kadar BOD dan TSS pada Limbah Cair Industri Tahu. J. Farmasetis. 2019; 8(2): 31–38. Publisher Full Text\n\nOke FM, Ndiribe CC, Musa SI: Bioremediation of diesel polluted soils with Eichhornia crassipes (water hyacinth). Not. Bot. Horti. Agrobot. Cluj Napoca. 2020; 12(4): 920–928. Publisher Full Text\n\nXia H, Ma X: Phytoremediation of ethion by water hyacinth (Eichhornia crassipes) from water. Bioresour. Technol. 2006; 97(8): 1050–1054. PubMed Abstract \| Publisher Full Text\n\nCaroline J, Moa GA: Fitoremediasi Logam Timbal (Pb) Menggunakan Tanaman Melati Air (Echinodorus palaefolius) pada Limbah Industri Peleburan Tembaga dan Kuningan. Seminar Nasional Sains Dan Teknologi Terapan III. 2015.\n\nNedi S, Effendi I, Tanjung A, et al.: Reduction of Hydrocarbon Pollutants by Hyacinth Plants (Eichhornia crassipes). [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "192190", "date": "21 Aug 2023", "name": "Anithadevi Kenday Sivaram", "expertise": [ "Reviewer Expertise Phytoremediation", "Ecotoxicology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, the author applied phytoremediation using water hyacinth to remove the total petroleum hydrocarbons from the water. The work is presented with current literature. However, there are issues with the experimental techniques and methods. Firstly, the method section lacks information on how the TPH concentration in water is measured after spiking, the QA/QC procedure for TPH analysis and spiking recovery (%). Secondly, the procedure for other parameters (DO, Salinity) were missing. Finally, it is important to include bioaccumulation in the hyacinth by measuring the concentration of TPH in the hyacinth.\nSpecific comments:\nAbstract:\nPlease rewrite the last three sentences in the background.\n\nPlease give the details on the treatments and control clearly for better understanding. As per the results, there are 2 controls i) one without plant grown in 90 ppm TPH and ii) another with plant and without TPH concentration for biochemical and TPH analysis.\n\nIt is good to change the concentration expression to mg/L rather than expressing it as ppm. Also, measured TPH concentration can be provided rather than the nominal concentration.\nIntroduction: Too short. It would be better to add about the i) toxic properties of TPH; ii) remediation methods followed; iii) Significance of phytoremediation; iv) why water hyacinth and previous reports to support your plant and TPH selection.\nMaterials and Methods:\nPlease mention the controls used for the experiment.\n\nIt is recommended to include the measured concentrations and the basis for choosing different TPH concentrations.\n\nPlease add a section on the TPH analysis procedure in water and plants and QA/QC procedure.\n\nPlease add on the pH, DO and salinity experiment procedure.\nResult:\nTable 2. It is better to provide the results in terms of removal percentage by merging the results in Fig.1 to Table 2 for better clarity.\n\nFig.2 can be removed.\n\nIt is suggested to include standard deviation (SD) in all the figures.\n\nFigure 7. Is the E0 with TPH conc?\n\nOverall, the explanation of the results can be improved.\nDiscussion: The discussion part focused more on results. Needs comprehensive discussion.\nConclusion: Explains only results and also repeats the contents present in the abstract and result section. Please revise.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "196910", "date": "29 Aug 2023", "name": "Hemen Deka", "expertise": [ "Reviewer Expertise Bioremediation and phytoremediation of hydrocarbons and heavy metals" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 comments:\nThe authors of the manuscript conducted research on “Reduction of hydrocarbon pollutants by hyacinth plants (Eichhornia crassipes)’—however, the authors must make it more evident in their paper to outline the design of the study and methods. The manuscript's writing and discussion are not up to mark, requiring thorough improvements across all sections. In addition to addressing scientific shortcomings, the entire paper necessitates careful editing and enhancement. Make sure that your manuscript has been thoroughly edited for proper use of the English language and accurate technical terminology.\nAuthors should have a strong justification for choosing only hyacinth plants (Eichhornia crassipes). Why not other aquatic plants? It should be mentioned more elaborately in the introduction part itself.\nCertain errors in spelling are also noticeable. Please correct these mistakes.\nSpecific comments:\nAbstract:\nRequires modifications. Please incorporate more numerical date into the abstract.\nIntroduction:\nIntroduction part is very poor. It should be expanded.\n\nThis section lacks clear cut objective of the study. Also highlight the significance of the topic, identify research gaps, and explain how this paper will contribute theoretically, empirically, and methodologically.\nResearch methods:\nHow was petroleum hydrocarbon was added to the water? Isn’t it non-polar? Write the detail procedure.\nPetroleum hydrocarbon observations\nWhat is the concentration of total petroleum hydrocarbons in control without plants?\n\nHow do you calculate total petroleum hydrocarbons, pH, DO etc.? Give standard protocol.\n\nTable 1: concentration of petroleum hydrocarbon in E0=?\nData analysis\nIn which significance level data were analyzed?\nResult:\n\nPlease rewrite the section so that it becomes readable for readers.\nTotal petroleum hydrocarbon concentration\n\"This is thought to be due to evaporation (E0)\" - you should mention this line in ‘Discussion’.\n\n3rd para: What is E10?\n\nTable 2, 2nd column-last row: Is Con. of E0=90? I can’t understand. Why do you keep only one concentration for total petroleum hydrocarbons in E0? Why not other concentrations like 10, 30, 50 and 70 ppm as mentioned in the treatments with phytoremediator?\n\nThe figures and tables can't communicate on their own. Instead, the authors should explain the insights revealed by the findings. In Figure 2, 5 and 6, check the Y-axis title and give proper units\n\nYou have taken three replicas, right? Then why didn’t you mention about standard deviations in any of the figures. Also, In each figure, instead of putting values above the line or bar, you should give a clear cut idea about significant variations in the values.\nChlorophyll content and water quality\nIn the treatment without hydrocarbons (E0): What is E0? Previously, in Table 2 you mentioned E0 as without phytoremediator? Here you have mentioned E0 as without hydrocarbons. Please give a detail information about the treatments with proper notation.\n\n\"Temperature conditions at the treatment with 10 ppm hydrocarbon without phytoremediator’s plant (E0) were seen to decrease in line with the observation time ((D-1, D-2, and D-3)\" - Isn’t it D-1, D-7, D14?\n\nIn Figure 3 red line indicates ‘with plant’- What is the notation for this treatment? Please give in details.\n\n\"Based on this figure, it can be seen that the temperature of the media increases in line with the increase in pollutant concentration and the length of time of observation.\" - The figure is not indicating itself the findings.\n\n\"The increase in temperature may be closely related to the hydrocarbon reduction process that releases heat by phytoremediators when carrying out water purification\" & \"ii) it might be due to the phytoremediator process and pollutant degradation.\" - these two sentences should be written in discussion part.\n\n\"The pH of the growing water of treatments...\" - What is 'growing water'?\n\nI recommend for revising the discussion to better address the theoretical, empirical, policy, and methodological issues presented in the paper. Also, more recent literature in the introduction and discussion section is of required. For better representation your MS, you may add new references and work; the following are suggested references: Chakravarty & Deka (2021)1; Chakravarty et al. (2022)2; Kalita et al. (2022)3; Boruah et al. (2020)4; Chakravarty et al. (2023)5.\nConclusion:\n\nThe concluding section is quite brief. Kindly present the specifics of your work concisely, making it easily accessible to everyone.\nReferences:\nAll references according to the journal format.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-728
https://f1000research.com/articles/12-1136/v1	11 Sep 23	{ "type": "Research Article", "title": "SWAT 137: A 2x2 randomised factorial SWAT of the use of a pen and brief information leaflet to improve recruitment in a randomised controlled trial of a community-based clinic for patients with persistent physical symptoms", "authors": [ "David White", "Laura Sutton", "Cara Mooney", "Jeremy Dawson", "Chris Burton", "PROMETHEUS Group", "Laura Sutton", "Cara Mooney", "Jeremy Dawson", "Chris Burton" ], "abstract": "Background Many strategies are used by trialists to improve recruitment, but few have been tested. We aimed to evaluate two interventions: 1) a study branded pen and 2) brief participant information leaflet, included within invitation packs for the Multiple Symptoms Study 3 (MSS3) trial. Methods A 2x2 factorial ‘study within a trial’ (SWAT) embedded into MSS3 – a randomised trial of a community-based clinic for patients with persistent, medically unexplained, physical symptoms. Potential MSS3 participants received postal invitations sent via GP practices, along with a MSS3 branded pen and/or brief participant information leaflet (PIL) or neither. The primary outcome was randomisation rate. Secondary outcomes were return rate, time to return, reasons for non-randomised returns and cost-effectiveness. Results 108 GP practices posted 6946 invitations, from which 318 participants (4.6%) were randomised to the host trial. Between those sent a brief PIL (n=3467) and not sent a brief PIL (n=3479) there was no significant difference in randomisation rates (166 (4.8%) vs 152 (4.4%); OR 1.10, 95% CI 0.88-1.38). Response rates were significantly higher in those sent the brief PIL (573 (16.5%) vs 513 (14.7%); OR 1.14, 95% CI 1.01-1.30). Between those sent the pen (n=3464) and not sent the pen (n=3482) there was no evidence of increased randomisation (145 (4.2%) vs 173 (5.0%); OR 0.84, 95% CI 0.67-1.05) and the difference in response rates was not statistically significant (563 (16.3%) vs 523 (15.0%); OR 1.10, 95% CI 0.96-1.25). For both SWAT interventions, time to response was comparable between groups. Conclusion There was no significant evidence of effectiveness of the brief PIL intervention or the pen intervention on recruitment to the host study. There was evidence of increased response rates to the initial invitation in the brief PIL group, compared to those not receiving a brief PIL in their invitation pack.", "keywords": [ "study within a trial", "pen", "participant information", "brief information leaflet", "recruitment", "factorial", "randomised controlled trial", "persistent physical symptoms" ], "content": "Introduction\n\nDespite substantial funds being invested in the UK and internationally, many randomised controlled trials (RCT) in healthcare fail to recruit on time and to budget.1 Many strategies are used by trialists to improve recruitment; however few such interventions have been rigorously evaluated.2,3 Trials embedded in real-life ‘host’ trials (also known as ‘Studies within A Trial’ [SWATs]) are the most robust way of evaluating such interventions.\n\nThere is some evidence that using a pen as a nonmonetary incentive increases response rates and time to response for trial follow-up questionnaires.3,4 The primary theory underlying the use of pen incentives is that of reciprocation.5–8 In the context of trial recruitment, offering a potential participant a gift such as a pen may make the person more likely to take up the trial invitation to enrol. It is also possible that the convenience of having a pen to hand upon receipt of the invitation may increase the likelihood of the forms being completed, or the timeliness of return. One U.S. trial embedded in an observational study showed that including a pen with the study logo to a questionnaire mailed to women who had previously not responded, significantly improved recruitment rates.9 However, a SWAT embedded into a RCT testing yoga for older adults with multimorbidity found no improvement in randomisation or response rates with the inclusion of a pen incentive within postal recruitment packs.10\n\nA common method of recruiting participants from general practices and other registries into trials is to send letters to potentially eligible patients inviting them to participate, along with the trial Participant Information Sheet (PIS). PISs are lengthy and increasingly complex11 and being asked to read such a large document may act as a deterrent to potential participants. A shorter PIS (or participant information leaflet (PIL)) may be more appealing initially, as it is likely to provide a more manageable volume of information.12 A Cochrane review of recruitment interventions identified two trials that have evaluated a brief PIL compared with a full PIS,2,12,13 and found the brief PIL makes little or no difference to recruitment compared with a full PIS. RD = 0% (95% CI = -2% to 2%); GRADE: moderate. However, this needs replicating in different populations.\n\nIn this study we aimed to evaluate the effectiveness and cost effectiveness of a brief PIL (provided in addition to a standard length PIS) and a trial logo branded pen on recruitment and response rates in the Multiple Symptoms Study 3 (MSS3) host trial. The SWAT was part of the PROMETHEUS programme (MRC MR/R013748/1) designed to identify effective and cost-effective methods to improve recruitment to and retention in trials, and to identify if it is possible to routinely embed SWATs within trials.\n\n\nMethods\n\nThe MSS3 SWAT was approved alongside the host MSS3 trial by the North West – Greater Manchester Central Research Ethics Committee (18/NW/0422). In line with that approval, patients were not informed about the SWAT and therefore, informed consent was not obtained. The MSS3 protocol was registered on ISRCTN (57050216) and has been published.14 The SWAT was registered with the Northern Ireland Network for Trials Methodology Research SWAT repository (SWAT137). The paper is reported in line with the Trial Forge Guidance: template for reporting the results of randomised Studies Within A Trial.15\n\nWe undertook a 2×2 factorial randomised SWAT. Potential MSS3 participants were identified by GP practices through computer searches and record screening. Practices were located in Yorkshire and the Humber, Greater Manchester, Newcastle and Gateshead, and Northwest London. All identified individuals that were to be invited to participate in MSS3 were randomised to one of four arms, determining how they would be invited to participate:\n\n- Standard invitation\n\n- Standard invitation + brief PIL\n\n- Standard invitation + trial-branded pen\n\n- Standard invitation + brief PIL + pen\n\nThe pen was branded with the MSS3 logo and colours (Figure 1). The brief PIL consisted of an A4 sized sheet printed on high quality paper in colour and folded into three, in a leaflet style (Figure 2). It was designed to provide a more succinct and easy to read summary of the MSS3 trial than the standard PIL. The information and format were reviewed by the patient representative on the MSS3 Trial Management Group. It was provided alongside the standard PIL in the recruitment pack. The invitation letter explained that the brief PIL provides a summary of the research in order for the potential participant to decide if they might be interested in the study and that the standard PIL provides more details should they wish to read this before returning the form, but that they will have the opportunity to discuss the study with a member of the research team and ask questions later.\n\nThe primary outcome was the recruitment rate, being the proportions of participants in each SWAT intervention group who were randomised into the host trial. Secondary outcomes were the proportion of patients who returned an expression of interest form, the proportion of patients who returned an expression of interest form but were not randomised due to a) ineligibility or b) non-consent, the time taken to respond to an invitation, and the cost-effectiveness of the interventions. The characteristics of participants returning an expression of interest and of those randomised into the host study were also collected. Data on sex were self-reported.\n\nWe did not undertake a formal power calculation to determine the sample size, since this was constrained by the number of patients being approached in the MSS3 host trial. However, based on response rates achieved in two preliminary studies we estimated we would need to invite 4888 patients in order to recruit 376 to the trial, representing a recruitment rate of about 8%. This would provide 80% power to identify a 3% absolute difference between the groups in recruitment rate if one existed. A simple multiple comparison adjustment was applied, using a significance level of 2.5%, which would allow us to test both interventions.\n\nIndividual-level randomisation using randomly-permuted blocks of length four or eight, equal allocation ratio and stratification by GP centre was used to allocate participants to receive one of the four packs. The allocation lists were generated by a CTRU statistician and shared only with the CTRU staff preparing the invitation packs, who were independent of the CTRU staff who processed the invitation responses.\n\nAll recruitment materials were placed in pre-stamped envelopes. The packs were placed in order of the random allocation list and then numbered sequentially before being sent to the practice. Practice staff were informed to label the recruitment packs with patient addresses in the sequential order that the researcher had prepared them. Patients did not know that they were part of a trial testing recruitment interventions so were blind to the SWAT hypothesis. CTRU staff undertaking MSS3 trial recruitment were blind to the SWAT group to which patients were allocated. It was not possible to entirely blind practice staff to the interventions as it will have been clear that some packs contained pens.\n\nAnalyses were conducted on an intent-to-treat basis, including all participants in the intervention group to which they were randomised. Participants entering the recruitment process following a reminder invitation were not included in the SWAT analysis.\n\nFactorial analysis ‘in the margins’ was used to investigate the main effects of the brief PIL intervention and the pen intervention. The assumption of no interaction between factors was tested by fitting multivariable regression models including interaction terms. There were no other covariates included in the models.\n\nThe primary outcome of randomisation into the host trial was assessed using binary logistic regression. Results for each intervention are presented as odds ratios with 95% confidence intervals. The main model included fixed effects only; sensitivity analysis was conducted using random centre effects.\n\nCost-effectiveness was determined by calculating the number needed to treat (the inverse of the absolute difference in proportions with successful outcome between intervention and control) and multiplying it by the additional cost of the intervention compared with the standard invitation pack.\n\nThe time taken to respond to the initial invitation was determined by calculating the days between the date an invitation was posted and the date a response was received. Partial postage dates were imputed using the first day of the month. Negative or zero date differences were set to missing. Non-responders were censored at the date the study closed to recruitment. Median response times were calculated for participants returning an expression of interest. Data were assessed visually using Kaplan-Meier plots, and between-group comparisons made using Cox regression. Hazard ratios are reported for each intervention with corresponding 95% confidence intervals.\n\nSummary statistics are reported for each of the four arms to which participants were randomised. Categorical variables are summarised by counts and percentages, and continuous variables using mean (SD) and median (range). Missing data are quantified. Inferential statistics are reported by way of main effects for each of the two interventions. Odds ratios and hazard ratios greater than one favour the intervention group; ratios of one are indicative of no between-group difference; ratios less than one favour the respective control group. For each outcome the brief PIL-pen interaction term is also reported. Analyses were conducted in R version 4.1.2.\n\n\nResults\n\nParticipant flow from the initial postal invitation to randomisation in the MSS3 trial is detailed in Figure 3. Recruitment took place between October 2018 to December 2021. A total of 108 GP practices participated in the recruitment process, with 6978 patients initially identified as potentially eligible for invitation to the MSS3 host trial. There were 32 patients whose eligibility status changed between initial GP search and the point at which invitations were posted, so a total of 6946 invitations were sent, of which 318 (4.6%) were randomised following an initial invitation. The SWAT analysis excludes participants who responded to a reminder invitation - there were 2530 reminders sent over the course of the recruitment period and a further 36 participants randomised. The total proportion recruited to the MSS3 host study following both initial and reminder invitations was 354/6946 (5.1%).\n\nPIL= brief participant information leaflet.\n\nParticipant numbers for factorial analysis ‘in the margins’ to determine average brief PIL and pen effects are presented in Table 1.\n\nThe proportion randomised per intervention group is shown in Table 2.\n\nInterval estimates for both interventions include the null value, consistent with the hypothesis of no effect on recruitment to the host trial. Sensitivity analysis was conducted using random GP practice effects. The intra-class correlation coefficient was 0.074 and the fixed-effect estimates were consistent with the primary model.\n\nOf the 6946 invited participants, 1086 (15.6%) returned an expression of interest form. Proportions expressing interest in participating in the MSS3 host trial are shown by intervention group in Table 3.\n\nThere was evidence of a higher rate of return in the brief PIL group, with estimated odds of return 14% greater than participants not receiving a brief PIL.\n\nThe additional cost of including a brief PIL in the invitation pack was £0.50. Given the 0.4% increase in participants randomised (shown in Table 2), 239 brief PIL invitations would need to be sent at a cost of £119.50 to recruit one additional participant to MSS3. The additional cost of including a pen in the invitation pack was £0.41. Cost-effectiveness was not calculated for the pen intervention, given the lower proportion randomised compared to the group of participants not receiving a pen.\n\nThere were 768 SWAT participants (70.7%) who returned an expression of interest form but did not go on to be randomised to the main trial. Reasons for non-randomisation are provided in Table 4, by arm and overall.\n\n* Following return of expression of interest.\n\n At telephone screening.\n\n* At baseline.\n\nMore than half the participants expressing interest but not going on to be randomised to the host study were found to be ineligible at one of the screening assessments. Of the 65 participants who completed the full screening process but did not consent to be randomised, 16 (24.6%) stated they were no longer interested in participating. The remaining reasons were listed as “other” or missing; free text notes implied the majority occurred due to participant non-attendance.\n\nFor participants who returned an expression of interest, the median return time was 16 days. Eight GP centres had partial postage dates imputed with the first day of the month. Five observations were excluded due to missing time-to-event data. Kaplan-Meier plots are presented in Figure 4.\n\nPIL = participant information leaflet.\n\nFor those who responded, the time to response was comparable between groups, but a higher proportion responded in the brief PIL and pen groups compared to their respective control groups. Hazard ratios are presented in Table 5. There was evidence of greater response rate (estimated 13% improvement) at any given time in the brief PIL group compared to no brief PIL.\n\nCharacteristics of participants returning an expression of interest form are provided in Table 6.\n\nDemographic information for the group of participants successfully randomised is presented in Table 7. Age and sex distributions are comparable to the larger ‘expression of interest’ group.\n\n\nDiscussion\n\nWe observed no significant evidence of a difference in the proportion of participants randomised to the MSS3 trial, in those receiving either a pen or brief PIL compared to control. We did observe a significantly higher response rate in those receiving the brief PIL compared to control, but this did not result in an increased randomisation rate in this group. Response rates for those receiving the pen were also higher than the control group, but this was not statistically significant. Response rates were overall lower than had been anticipated when designing the MSS3 trial. There was no difference in time to response between the groups. We did not observe any differences in the characteristics of those expressing an interest versus those randomised, although very little data were available for this comparison.\n\nIt is interesting that inclusion of the brief PIL resulted in better response rates but not randomisation rates. One previous SWAT of a brief PIL12 reported a similar difference in response rates between the brief PIL and control group, however this was not statistically significant. In our study, those returning an expression of interest in the SWAT intervention groups were more likely than those in the control group to not proceed at baseline due to no longer being interested or non-attendance at the appointment. It is possible that receipt of the pen and/or brief PIL may make return of the form more likely as a result of the hypothesised minor incentive, ease of form return or digestion of the study information – resulting in higher expression of interest rates – but that this does not then translate to randomisation when the requirements of participation are fully considered and understood. It is also possible that the brief PIL resulted in a small improvement in randomisation rate that we were not powered to detect, but that would nonetheless have been meaningful.\n\nAlthough we did not observe evidence of statistically significantly higher randomisation rates, the SWAT interventions were low cost. It should be noted that improved recruitment rates may not be the only rationale for including similar interventions in future trials. For example, the provision of shorter, simplified recruitment materials may aid the representativeness of RCTs by reaching underserved populations.\n\nIdeally, we would have collected demographic data on all participants who were sent an MSS3 invitation, in order to explore whether the SWAT interventions were of benefit to particular groups of participants - however this was not possible. Additionally, only limited data were collected on those returning an expression of interest form. We did not collect any qualitative data from participants with regards the SWAT interventions. This may have enabled us to explore the views of those receiving the interventions. If such data were collected, these would ideally include those who did not go on to participate in the host trial as well as those that did – although this would have been logistically challenging. The host MSS3 RCT was conducted both prior to and during the COVID-19 pandemic, with 59% of MSS3 invitations sent during the pandemic (post March 2020) – however, the number of participants in the SWAT arms were approximately equal pre-pandemic and during pandemic, so this is unlikely to have had an impact on the findings.\n\nIn conclusion, there was no significant evidence of effectiveness of the brief PIL intervention or the pen intervention on recruitment to the MSS3 study, but there was evidence of increased response rates to the initial invitation in the brief PIL group. The results of this SWAT should be combined with those from randomised SWATs testing the same interventions, in order to determine definitively whether they are an effective tool to improve recruitment rates.\n\n\nAuthor roles\n\nWhite D: Funding acquisition, Methodology, Writing – original draft preparation, Writing – review & editing; Sutton L: Formal analysis, Visualisation, Writing – original draft preparation, Writing – review & editing; Mooney C: Funding acquisition, Methodology, Project Administration, Writing – review & editing; Dawson J: Funding acquisition, Methodology, Validation, Writing – review & editing; Burton C: Funding acquisition, supervision, writing – review & editing.", "appendix": "Data availability\n\nPer our info governance team, raw data are not able to be provided publicly due to the risk of identification. Readers and reviewers can apply for private access to the data via the following link: https://doi.org/10.15131/shef.data.22795418.\n\nData access (raw data file and dictionary) will be granted once users have provided a written proposal and consented to a data sharing agreement. Requests can be submitted to multiple.symptoms.study3@sheffield.ac.uk.\n\nAggregate data are available via the following:\n\nfigshare: MSS3 aggregate SWAT data, https://doi.org/10.15131/shef.data.23791731.v1. 16\n\nThis project contains the aggregate data file and dictionary.\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 PROMETHEUS group: Catherine Arundel, Laura Clark, Adwoa Parker, Elizabeth Coleman, Catherine Hewitt, David Torgerson, Laura Doherty.\n\n\nReferences\n\nWalters SJ, Bonacho I, Bortolami O, et al.: Recruitment and retention of participants in randomised controlled trials: a review of trials funded and published by the United Kingdom Health Technology Assessment Programme. BMJ Open. 2017; 7: e015276–e015210. Publisher Full Text\n\nTreweek S, Pitkethly M, Cook J, et al.: Strategies to improve recruitment to randomised trials. Cochrane Database Syst. Rev. 2018; 2018: MR000013. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrueton VC, Tierney JF, Stenning S, et al.: Strategies to improve retention in randomised trials: a Cochrane systematic review and meta-analysis. BMJ Open. 2014; 4(2): e003821. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nBell K, Clark L, Fairhurst C, et al.: Enclosing a pen reduced time to response to questionnaire mailings. J. Clin. Epidemiol. 2016; 74: 144–150. Publisher Full Text\n\nGouldner AW: The Norm of Reciprocity: A Preliminary Statement. Am. Sociol. Rev. 1960; 25(2): 161. Publisher Full Text Reference Source\n\nCialdini RB, et al.: Reciprocal concessions procedure for inducing compliance: The door-in-the-face technique. J. Pers. Soc. Psychol. 1975; 31(2): 206–215. Publisher Full Text\n\nRegan DT: Effects of a favor and liking on compliance. J. Exp. Soc. Psychol. 1971; 7(6): 627–639. Publisher Full Text\n\nFalk A, Fischbacher U: A theory of reciprocity. Games Econ. Behav. 2006; 54(2): 293–315. Publisher Full Text\n\nWhite E, Carney PA, Kolar AS: Increasing response to mailed questionnaires by including a pencil/pen. Am. J. Epidemiol. 2005; 162(3): 261–266. PubMed Abstract \| Publisher Full Text\n\nFairhurst C, Roche J, Bissell L, et al.: A 2x2 randomised factorial SWAT of the use of a pen and small, financial incentive to improve recruitment in a randomised controlled trial of yoga for older adults with multimorbidity [version 2; peer review: 2 approved]. F1000Res. 2022; 10: 326. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNational Research Ethics Service: Information sheets and consent forms: guidance for researchers and reviewers.2018.\n\nBrierley G, Richardson R, Torgerson DJ: Using short information leaflets as recruitment tools did not improve recruitment: A randomized controlled trial. J. Clin. Epidemiol. 2012; 65(2): 147–154. Publisher Full Text Reference Source\n\nChen F, Rahimi K, Haynes R, et al.: Investigating strategies to improve attendance at screening visits in a randomized trial. Trials. 2011; 12(Suppl 1): A111. Publisher Full Text\n\nMooney C, White DA, Dawson J, et al.: Study protocol for the Multiple Symptoms Study 3: a pragmatic, randomised controlled trial of a clinic for patients with persistent (medically unexplained) physical symptoms. BMJ Open. 2022; 12: e066511. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTrial Forge Guidance: template for reporting the results of randomised Studies Within A Trial. http\n\nWhite D, Sutton L, Mooney C, et al.: MSS3 aggregate SWAT data. The University of Sheffield. [Dataset]. 2023. Publisher Full Text" }	[ { "id": "208019", "date": "04 Oct 2023", "name": "Peter Knapp", "expertise": [ "Reviewer Expertise Patient information. SWATs." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 is a clear rationale for the study that has been reported and the SWAT design is appropriate. Using a 2x2 factorial design for the SWAT is innovative and efficient.\nThe paper is clearly structured and written.\nIt would be helpful to include more details on the standard invitation, for example, how long was that PIL and how was it presented? Trial PILs vary greatly in their length, presentation, writing style, the inclusion of a summary section, etc, which would impact on the degree of difference between it and the brief PIL, which could impact on people's response to it.\nThe abstract, which is otherwise clear, would also benefit from a few more words on the inclusion of the standard PIL, to clarify that in that aspect of the SWAT people were randomised to standard PIL + brief PIL, or standard PIL only.\nTesting the effects of providing a brief PIL is a valid and important question but the requirement to always provide a standard PIL makes this SWAT design problematic in my view. I wonder what some people must think when they receive a postal invitation to take part in research and find they have been given two versions of the written information - one short and one full-length. It seems somewhat artificial and lacking in external validity. (I understand that RECs may require that standard PILs are always provided but it does inhibit the conduct of SWATs with real world applicability).\n\nIs the work 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": "208018", "date": "25 Oct 2023", "name": "Michelle E Kho", "expertise": [ "Reviewer Expertise Research methodology", "trial design and reporting" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this SWAT. The authors conducted a 2x2 factorial study to evaluate the effect of adding a trial logo branded pen or a brief patient information leaflet on the recruitment to a parent study of a community-based clinic for patients with persistent physical symptoms (Multiple Symptoms Study 3). Patients were randomized to one of four conditions, all including the standard invitation: pen only, brief patient information sheet only, pen and brief patient information sheet, and standard invitation alone. The primary outcome was recruitment, and secondary outcomes included return of expression of interest, time to respond to the invitation, and cost-effectiveness. Recruitment occurred between Oct 2018 and Dec 2021. There was no difference in randomization between groups for either condition.\nI commend the authors for persisting with this SWAT during the pandemic. The trial has several strengths, including rigorous design, and collection of respondent information by sex. There are a few items that would improve readers’ understanding of the SWAT:\n\nThe authors planned to invite 4888 potential participants to recruit 376 patients, but ultimately invited 6946 and enrolled 318. Can the authors further explain the discrepancy in patients approached for the parent trial and the impact on the SWAT?\n\nInvestigators excluded patients from the SWAT if they were sent a reminder invitation for the parent trial. Can the authors help the readers understand why this occurred in the parent trial, and any impact on selection bias for the SWAT?\n\nRecruitment occurred between Oct 2018 and Dec 2021.\nCan the authors comment on how the pandemic affected the SWAT?\n\nCan the authors also add information about any effects of the pandemic on the SWAT using the CONSERVE statement (JAMA. doi:10.1001/jama.2021.9941)\n\nThe authors’ primary outcome was recruitment, which was not different among groups. However, those who received the brief patient information leaflet made faster decisions than those who did not.\nCan the authors comment on the future use of a brief patient information leaflet to help triallists identify those not interested in participating in the trial, more quickly, and potentially save costs in reminders?\n\nWhy is “in the margins” reported in quotes?\n\nIn the introduction, the authors reported this study as part of the PROMETHEUS research programme, to evaluate effective methods to improve recruitment and retention to clinical trials. Can the authors share any information on the effect of their SWAT on retention?\n\nThe reference 15 link (Trial Forge Guidance: template for reporting the results of randomised Studies Within A Trial) was broken when I attempted to review it. Can the authors please update to a permanent link?\n\nIs the work 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1136
https://f1000research.com/articles/12-1135/v1	11 Sep 23	{ "type": "Study Protocol", "title": "Comparative analysis and assessment of radiological investigation reports for abdomen and pelvic computed tomography scans", "authors": [ "Shreya Naik", "Gaurav V Mishra", "Suhas Tiwaskar", "Anurag Luharia", "Gaurav V Mishra", "Suhas Tiwaskar", "Anurag Luharia" ], "abstract": "Background: Medical imaging modalities have significantly improved the accuracy and timeliness of diagnoses over the years; they also present a risk of diagnostic errors due to various factors. One of the primary issues is the variation in findings between preliminary and final reports, specifically for current imaging technologies such as magnetic resonance imaging, and computed tomography (CT) among others. Although several studies have investigated variations between preliminary and final reports in different contexts, research specific to the radiology department is limited. Through this study protocol, we aim not only to help provide a comprehensive evaluation of the variation in findings between preliminary and final diagnostic reports in radiology but also aid in improving the accuracy and quality of patient care and contribute to developing effective strategies to minimize diagnostic errors. Methods: A total of 128 male and female patients presenting to the radiology diagnosis department for abdomen and pelvic CT scans would be considered for the study. The radiological investigation reports for the scans would be interpreted by junior residents and radiologists. The reports will be manually compared to check for similarities, new findings, and exclusions. The degree and frequency of variability will be statistically assessed and reported in tabulations and graphs under the patient's age and gender. Discussion: This study seeks to investigate the differences in interpretations between resident and radiologist reports, consistent with previous research. The results of this study will provide insights into the variations in interpretations, highlighting the importance of continuous training. Examining the findings of a report as a whole can also deliver valuable knowledge into the potential impact on patient care. This can lead to enhancements in radiology reports and overall patient management. The implications involve improving the education of residents, optimising clinical decision-making processes, and promoting positive patient outcomes.", "keywords": [ "radiology reports", "abdo-pelvic CT scans", "variations", "reporting", "resident", "radiodiagnosis", "provisional report", "final report" ], "content": "Introduction\n\nIn recent years, diagnostic imaging investigations have advanced and been amplified. It has spurred the necessity for thorough, accurate reporting. Well-crafted reports reflect the judgement of the radiologists serving as a standard of reference for radiology trainees, thus acting as a channel of communication with physicians, guiding the decision-making, management, and long-term follow-up. Also, it works as a legal document when malpractice is asserted.1\n\nThe reporting services provided by many radio-diagnostic imaging facilities of large hospitals have progressed so much over the years that the facilities can provide quick support to the attending residents in order to produce reports promptly. Contrarily, this rapidity of report generation has also increased the likelihood of variations between the preliminary and final attending reports, as reflected in numerous studies; however, there is a dearth of research about it, specific to the radiology department and its practices.2–5 Radiology residents at healthcare facilities routinely provide preliminary imaging study interpretations within hours, and their skill and accuracy are vital to the treatment of patients.6 Therefore, all radiologists must seek to acquire, improve, and update the skills needed to generate optimal reports from the very outset of their training. Towards this goal, a radiologist’s formative training or residency years should incorporate a method to generate an adequate report.7\n\nQuantifying the frequency and types of variations in the standard, abnormal, additional findings and interpretations between the junior residents’ and the radiologists practising in the same hospital system can be a valuable tool for directing general education and systematic quality improvement. This topic has been the subject of numerous past research but was often limited to particular or short periods.2–5 Thus, an attempt has been made in this study to examine provisional and final computed tomography (CT) scan reports of the abdo-pelvic region prepared by junior residents in radiology and radiologists to prepare a study protocol.8 The reports have been collected and analysed for a comprehensive study. Findings and variances have been assessed in provisional and final reports based on the examinations performed and their interpretations.9\n\nTo identify appropriate indicators of resident performance effectiveness and competence that are equally consistent with patient care, reading the provisional and finalized report findings can serve as a potential criterion for finding better interpretation possibilities and eliminating contradictions. Additionally, it can serve as a valuable source of research to demonstrate and strengthen the fact that radiology residents’ reporting is genuinely on par with the radiologists’, contributing to residents’ credibility and elevating their overall self-confidence in reporting.\n\n\nProtocol\n\nThe Institutional Ethics Committee at Datta Meghe Institute of Higher Education and Research (Deemed to be University), Nagpur, approved the study (Date: 02/02/2023, Ref.No. DMIHER (DU)/IEC/2023/589). Written informed consent will be requested from all patients having C.T. scans of the abdomen and pelvis.\n\nThe study is a prospective observational study.\n\nThe duration of the study will extend from October 1st, 2022, to October 1st, 2024, covering a period of 24 months. During this time period, data will be gathered from several residents and radiologists, who are actively engaged in the process of generating preliminary and final reports. Every month, a total of three residents and two radiologists will contribute to the reports, guaranteeing a wide variety of interpretations.\n\nThe selection criteria for the reports will encompass individuals of both genders, aged 18 years and older, with a specific emphasis on radiological examinations conducted within the abdominal and pelvic regions.\n\nParticipants must meet the following criteria in order to be included:\n\n• Patients who came to seek treatment at the Acharya Vinoba Bhave Rural Hospital, Datta Meghe Institute of Higher Education & Research, Sawangi Meghe, Wardha, radio-diagnosis department for abdo-pelvic CT examinations.\n\n• A single anatomical region at a time examination.\n\n• Patients requiring follow-up examinations.\n\n• Patients aged 18 years old or above.\n\nParticipants meeting the following criteria will be excluded:\n\n• Patients who do not wish to participate.\n\n• Patients aged below 18 years old.\n\n• Repeat imaging procedure examinations.\n\n• Multi-region examinations.\n\nThe purpose of this study is multi-pronged. It will assess the findings and variations between preliminary and final attending reports. Also, it will assist in determining precise performance standards for radiology residents. Together these findings will help leverage the patient care paradigm.\n\nTo assess and analyse the findings in provisional and final radiology reports by the junior resident and radiologist for abdo-pelvic CT scan examinations.\n\n\n\n• To identify the findings by junior radiology resident interpretations of diverse diagnostic imaging investigations for the abdo-pelvic region.\n\n• To identify the findings by senior radiologist interpretations of diverse diagnostic imaging investigations for the abdo-pelvic region.\n\n• To identify the variations between interpretations made by junior residents and radiologists for diverse diagnostic imaging investigations of the abdo-pelvic region.\n\nIs there any significant difference between the findings in provisional and final abdo-pelvic CT scan reports, and can they be used to determine the precise performance standards for radiology residents?\n\nA total of 128 male and female participants will be included in this study presenting to the radio-diagnosis department for abdo-pelvic CT scans.\n\nThe following formula will be used to determine the sample:\n\nWhere n = desired sample size\n\nZα = 1.96 (95% confidence level)\n\nZβ = 0.84 (statistical power of 80%)\n\np1 = 26.5 % = 0.265 (proportion of outcome in an exposed group)\n\np2 = 12.8 % = 0.128 (proportion of outcome in an unexposed group)\n\nThis study, referencing Harari et al., utilizes the Chi-Square test and Kappa test as statistical methods, with data analysis performed using SPSS version 27.0 software.10\n\n\nMethods\n\nInitially, the reports will be reviewed for findings such as under-reading, fulfilment of search, flawed reasoning, irregularities outside the scope of interest, fulfilment of report, neglecting to refer to prior imaging studies, inaccurate or insufficient clinical history, report not reaching referring clinician accurately, flawed measurements and so on during the two-year research period to assess their clinical impact on the hospital system and patient care.\n\nSecondly, the database will encompass a total of 128 abdo-pelvic CT imaging studies that were first evaluated by a junior resident and then reviewed by the radiologist.\n\nUnder the supervision of an experienced senior radiologist, a comparison of the preliminary reports by the resident and the final reports by the attending radiologist will then be conducted. Finally, patterns of “similar,” “additional,” and “not carried forward” findings will be noted and tabulations, graphs will be used to quantify the degree and frequency of variation between the two report interpretations. Utilizing a standardized proforma considering the age and sex of the patient, a thorough investigation of the radiological reports for abdominal and pelvic CT scans will be done.11 This method of approach seeks to help document and evaluate the factors contributing to the variations between preliminary and final reports.\n\nThe principal objectives to be assessed in this investigation involve the divergences noted in radiology observations among trainees, with a specific emphasis on the disparities between the initial assessments conducted by residents and the ultimate evaluations conducted by attending radiologists. The study aims to precisely quantify and meticulously analyse these intriguing variations in order to thoroughly comprehend their frequency and ascertain their potential impact on the provision of optimal patient care.\n\nRegarding secondary outcomes, the study seeks to assess the impact of these variations on patients and examine educational opportunities for residents. Furthermore, this investigation aims to augment the assurance and reporting proficiencies of residents, ultimately resulting in enhanced patient care. The results are anticipated to make a significant contribution to the overall enhancement of radiology services rendered to patients, potentially leading to advancements in diagnosis and treatment planning.\n\nStatistical investigations will be performed using IBM SPSS Statistics software version 27.0, with a significance level of 0.05. Statistical methods employed for analysing the data will be Chi-square and Kappa tests. Descriptive analysis will be performed to identify variations in reporting. Independent sample tests would also be performed to look for differences between provisional and final radiology reports.\n\nThe study’s findings will be disseminated through scientific conferences and published in peer reviewed indexed journals.\n\nThe study is ongoing. It is expected to complete before October 2024.\n\n\nDiscussion\n\nRadiology reports serve an essential role in medical diagnosis and treatment; therefore, the consistency and quality of these reports are vital in guiding clinical decision-making and providing optimal patient care. The variation rates in radiological reports have been the subject of numerous studies, with various degrees of success. According to a study by Ruutiainen et al. (2011), there were differences in the rates of key findings in reports depending on the residents themselves, the modalities they used, and their training levels.4 Mellnick et al. (2016), on the other hand, discovered a reasonably low incidence of variance for radiology residents interpreting examinations after hours, with a very low rate of critical variations.12 According to a 2016 study by Harari et al., 31% of reports were confirmed as unaltered, with no appreciable differences between junior and senior residents.10 However, according to an earlier study by Cooper et al. (2008), a slight increase in accuracy was noticed as the resident year progressed.13 However, Dinh et al. (2020) suggested that despite advancements in technology and training, variances can still happen.14 In relation to our research, these studies offer insightful information about the variables, such as resident training level, modality, and reporting quality, that affect variability in radiology reports. They highlight the significance of quality assurance processes, training opportunities, and adopting benchmark criteria for variation rates and response times to ensure high-quality patient care. Despite advancements in technology and training, variations can persist; thus, it is essential to inquire into their potential causes and find efficient strategies to mitigate them, providing patients with the best possible care.15\n\n\nConclusions\n\nIn conclusion, reviewing and analyzing the results of abdominopelvic CT scans for patients of different age groups and genders is a viable way to assess the clinical outcomes and can serve as a roadmap for educational and training programs for residents. The results of this study will help emphasize how crucial precise and accurate reporting is in medical practice. Furthermore, this kind of research encourages residents’ confidence in their reporting skills, resulting in high-quality patient care. Overall, this research holds significant implications for improving patient care and the profession of medical imaging.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Proforma for the assessment of radiological investigation reports of abdomen and pelvic computed tomography scans based on age and sex of the patient, https://doi.org/10.5281/zenodo.8159058. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nCastillo C, Steffens T, Sim L, et al.: The effect of clinical information on radiology reporting: a systematic review. J. Med. Radiat. Sci. 2021 Mar; 68(1): 60–74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrady AP: Error and discrepancy in radiology: inevitable or avoidable? Insights Imaging. 2017 Feb; 8: 171–182. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrickland NH: Quality assurance in radiology: peer review and peer feedback. Clin. Radiol. 2015 Nov 1; 70(11): 1158–1164. Publisher Full Text\n\nRuutiainen AT, Scanlon MH, Itri JN: Identifying benchmarks for discrepancy rates in preliminary interpretations provided by radiology trainees at an academic institution. J. Am. Coll. Radiol. 2011 Sep 1; 8(9): 644–648. PubMed Abstract \| Publisher Full Text\n\nLauritzen PM, Andersen JG, Stokke MV, et al.: Radiologist-initiated double reading of abdominal CT: retrospective analysis of the clinical importance of changes to radiology reports. BMJ Qual. Saf. 2016 Aug 1; 25(8): 595–603. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBruno MA, Duncan JR, Bierhals AJ, et al.: Overnight resident versus 24-hour attending radiologist coverage in academic medical centers. Radiology. 2018 Dec; 289(3): 809–813. PubMed Abstract \| Publisher Full Text\n\nRuchman RB, Jaeger J, Wiggins EF III, et al.: Preliminary radiology resident interpretations versus final attending radiologist interpretations and the impact on patient care in a community hospital. Am. J. Roentgenol. 2007 Sep; 189(3): 523–526. PubMed Abstract \| Publisher Full Text\n\nWallis A, McCoubrie P: The radiology report—are we getting the message across? Clin. Radiol. 2011 Nov 1; 66(11): 1015–1022. PubMed Abstract \| Publisher Full Text\n\nWalls J, Hunter N, Brasher PM, et al.: The DePICTORS Study: discrepancies in preliminary interpretation of CT scans between on-call residents and staff. Emerg. Radiol. 2009 Jul; 16: 303–308. PubMed Abstract \| Publisher Full Text\n\nHarari AA, Conti MB, Bokhari SJ, et al.: The role of report comparison, analysis, and discrepancy categorization in resident education. Am. J. Roentgenol. 2016 Dec; 207(6): 1223–1231. PubMed Abstract \| Publisher Full Text\n\nNaik S: Proforma for the assessment of radiological investigation reports of abdomen and pelvic computed tomography scans based on age and sex of the patient (Version v1). [Dataset]. Zenodo. 2023. Publisher Full Text\n\nMellnick V, Raptis C, McWilliams S, et al.: On-call radiology resident discrepancies: categorization by patient location and severity. J. Am. Coll. Radiol. 2016 Oct 1; 13(10): 1233–1238. PubMed Abstract \| Publisher Full Text\n\nCooper VF, Goodhartz LA, Nemcek AA Jr, et al.: Radiology resident interpretations of on-call imaging studies: the incidence of major discrepancies. Acad. Radiol. 2008 Sep 1; 15(9): 1198–1204. Publisher Full Text\n\nDinh ML, Yazdani R, Godiyal N, et al.: Overnight radiology resident discrepancies at a large pediatric hospital: categorization by year of training, program, imaging modality, and report type. Acta Radiol. 2022 Jan; 63(1): 122–126. PubMed Abstract \| Publisher Full Text\n\nSchweikhart SA, Dembe AE: The applicability of Lean and Six Sigma techniques to clinical and translational research. J. Investig. Med. 2009 Oct; 57(7): 748–755. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "208022", "date": "25 Sep 2023", "name": "Simin Mouodi", "expertise": [ "Reviewer Expertise Research in Clinical Sciences" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study protocol aims to compare similarities, new findings, and exclusions between preliminary and final reports for abdomen and pelvic CT-scans. In recent years, some studies assessed different factors impacting abdominal and pelvic CT exam reporting. Multicenter study will increase the value of the research.\nSome characteristics are recommended to include in this research; for example:\nIs this research carried out in a single center or multicenter?\n\nWhere the reports are dictated (in-house or remotely or ….)?\n\nThe patients (outpatient or inpatient) and (emergent or non-emergent)?\n\nThe number of organs which should be searched in imaging process\n\nThe radiologist and resident years of experience\n\nThe use of structured templates for reporting?\nThe \"Keywords\" should be revised according to main heading terms of the MeSH.\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? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1135
https://f1000research.com/articles/12-1134/v1	11 Sep 23	{ "type": "Research Article", "title": "The relationship of perceived discrimination in healthcare and future falls among community-dwelling older persons from an English longitudinal cohort", "authors": [ "Felipe Alfonso Sandoval Garrido", "Timothy Bolt", "Yuta Taniguchi", "Peter Lloyd-Sherlock", "Timothy Bolt", "Yuta Taniguchi", "Peter Lloyd-Sherlock" ], "abstract": "Background: The objective of this study is to examine the relation between the perceived discrimination suffered by older adults aged 60 and over during a healthcare encounter and its effects on the likelihood of falling 4 and 8 years later.\n\nMethods: To identify discrimination, we used the English Longitudinal Study of Ageing (ELSA) data collected in 2010-2011 (wave 5) that asked respondents about feeling discriminated against by doctors or at hospitals in the past year. Falls were assessed by the question: “Have you fallen down in the last two years?” in subsequent waves. We performed longitudinal analyses using the 2014-2015 (wave 7) and 2018-2019 (wave 9) follow-ups. Multivariable logistic regression was used to estimate the odds ratios of falling. Results: At baseline, 707 (15.1%) of all respondents experienced healthcare discrimination. Those suffering from discrimination in health care had 64% higher chances of falling 4 years later (odds ratio: 1.637, 95% confidence interval: 1.131-2.368) compared to those who did not, adjusting for age, sex, marital status, wealth, ethnicity, education levels, self-perceived health, depressive symptoms, and difficulties with basic and/or instrumental activities of daily living (ADL/IADL) and difficulties with walking. After 8 years, the effect was not statistically significant. Older age was the only significant detrimental factor at both 4 and 8 years.\n\nConclusions: Understanding discrimination in health care is important to enable safe and welcoming environments for the timely future use of services. These results remind us of the physical risk and the complex panorama of bio-psychosocial determinants involved in tackling discrimination over time.", "keywords": [ "perceived discrimination", "health services", "falls", "older persons", "England" ], "content": "Introduction\n\nAs people age, they experience psychological, physical, and societal transformations that greatly affect their overall health and well-being.1 Among these changes, falls emerge as a public health concern for older individuals.\n\nThe number of fatal falls that occur yearly is estimated to be 684,000, making falls the second greatest cause of unintentional injury-related fatalities behind traffic accidents.2 In addition to mortality, falls contribute significantly to disability in older adults. Approximately 37.3 million falls yearly are severe enough to require medical attention worldwide.2 Injuries resulting from falls, such as fractures or traumatic brain injuries, often lead to long-term disabilities.3 In the world, around 172 million persons suffer from either short or long-term disabilities after falling.2\n\nThe 2019 and latest Cochrane Review on falls, with data from over 25 countries, shows that one-third of community-dwelling older persons aged 65 and over fall each year.4 In the United States, evidence shows that 10% of falls result in major injuries and 30% to 50% in minor ones.5 Hip fractures occurred in around 1% of all falls, but 95% of hip fractures were caused by falls.5 In the United Kingdom, the Public Health Outcomes Framework reports that between 2017-2018 falls led to approximately 220,160 hospital admissions for individuals aged 65 and over. Around two-thirds of these cases (146,665 cases) were patients aged 80 and above.6 In the 2021/2022 period, the number of hospital admissions due to falls in people aged 65 and over had risen to 223,101 cases (about 2,100 per 100,000 persons). Among these, nearly 147,000 involved individuals were aged over 80.6\n\nApart from the harm they can cause, falls also have consequences that negatively affect the well-being of older individuals. One common psychological response among those who have experienced a fall or are at risk is the fear of falling.7 Following a fall, this fear leads to decreased independence and self-imposed limitations on activities and isolation from interactions. All these factors contribute to declining quality of life.8\n\nUnderstanding the reasons behind falls in adults is crucial in order to develop strategies for preventing them.4 As individuals age, various physiological changes occur, including decreased bone density, muscle mass and strength. These changes can compromise balance, gait and overall physical stability, making older adults more susceptible to falling.9 Diminished cardiovascular performance and degenerative neurological changes in older adults also contribute to this risk, leading to dizziness, fainting spells, slower reaction times, and impaired coordination.10 Moreover, age-associated vision and hearing impairments negatively affect balance and spatial orientation, further increasing fall risk.11\n\nWhile these physiological factors leading to falls have traditionally been the focus, the importance of psychosocial factors cannot be overlooked.12 Perceived discrimination in healthcare has emerged as a significant concern for older adults. Discrimination based on age, sex, race, or socioeconomic status can erode trust in healthcare providers, lead to avoidance of healthcare, and result in increased stress levels and poorer overall health outcomes13,14 and thus contributing to the risk of falling.\n\nA previous study explored the relationship of discrimination and falling using a representative national sample in Colombia.15 Based on their previous research, the rationale is that traumatic events have an effect in the possibility of falling,16 but there were no studies linking discrimination and falls, unlike other adverse events with a more direct connection. From a life course perspective, the argument is that severe stressors that continue overtime or are repeated could lead to other secondary stressors, following the stress proliferation theory.17 In line with this, the physical and mental damage caused by feeling discriminated will have an indirect and future effect on falls. The idea of exploring the indirect effects of perceived discrimination has been reviewed before suggesting pathways to negative health outcomes.14\n\nHowever, besides the work of Reyes et al.,15 the role of perceived discrimination as a potential risk factor for falls remains largely unexplored, particularly in England where discrimination among older populations remains understudied.18 The aim of the study is to grasp the relationship between feeling discriminated and the likelihood of falling in 2 subsequent points, measured at 4-year intervals.\n\nUnderstanding the potential long-term effects of perceived discrimination on the risk of falling can help one develop multifaceted intervention strategies that incorporate physical and psychosocial components, enabling a more comprehensive approach to fall prevention and addressing the need for more inclusive, respectful, and patient-centred healthcare environments.\n\n\nMethods\n\nThis study used a longitudinal design to examine the relationship between perceived discrimination during healthcare encounters and subsequent fall risks in older adults. The longitudinal nature of this research design allowed us to investigate changes in individuals’ risk of falls over a period following experiences of discrimination, providing insights into the temporal dynamics of this association.\n\nThe data used in this research was obtained from the English Longitudinal Study of Ageing (ELSA) which is a study that follows adults aged 50 and older living in England. ELSA aims to gather data over time on different fields such as mental health, disabilities, biological indicators of diseases, economic situation, social engagement, wellbeing and more.19 Participants provided consent at the start of the longitudinal study as part of the Health Survey for England (HSE). Later, at the end of each ELSA wave, they are asked again to confirm or amend their consent.\n\nThis study focused on ELSA participants during the 2010-2011 wave of data collection (wave 5). Wave 5 is the only time where questions about discriminations have been included, as of early 2023. We also used the data from periods 2014-2015 (wave 7) and 2018-2019 (wave 9) to detect falls in these two subsequent periods.\n\nThe flow of participants through the study is depicted in Figure 1, illustrating the inclusion and exclusion criteria for the sample. In wave 5, a total of 10,274 participants were initially enrolled.\n\nDue to the subjective nature of feeling discriminated, which takes into account unique perceptions, feelings, and experiences, proxy respondents were excluded from the study. Thus, 537 participants (5.2%) were dropped from the research because they needed a proxy respondent to reply to the questions. This means that 9737 individuals, or 94.8%, were able to answer the questions on their own. Additionally, 904 individuals (9.3% of the remaining sample) were subsequently eliminated as a result of lacking information about healthcare discrimination. This led to a sample size of 8,833 individuals who provided valid responses regarding healthcare discrimination. An additional exclusion criterion was applied to individuals who reported falling in the past year before the baseline (excluding 1803 participants) or provided invalid answers to this question (2347 excluded participants), leaving a total of 4,673 participants who confirmed not experiencing a fall in the year prior to the baseline assessment.\n\nOverall, the study included 4,673 participants who did not fall in the past year, had valid responses regarding healthcare discrimination, and provided self-reported answers to the study questions.\n\nPerceived discrimination\n\nPerceived discrimination was identified using responses to questions in the ELSA 2010-2011 period (wave 5) about participants’ experiences of feeling discriminated by doctors or at hospitals in the past year by asking the frequency as follows:\n\nIn your day-to-day life, how often have any of the following things happened to you?\n\nYou receive poorer service or treatment than other people from doctors or hospitals.\n\n1. Almost every day\n\n2. At least once a week\n\n3. A few times a month\n\n4. A few times a year\n\n5. Less than once a year\n\n6. Never\n\nAs described in Figure 1, most participants answered that they have never felt discriminated. Due to this skewness, for our preliminary descriptive statistics we decided on a dichotomous variable that will separate the observations into those who never felt discriminated and those who felt discriminated at least once (options 1-5 vs 6). Later, based on our sensitivity analyses, for the multivariable analysis we created a dichotomous variable that separates the participants into those who experienced healthcare discrimination more frequently (options 1 to 4), against those who experience it less frequently (options 5 and 6).\n\nExperience of falling\n\nFalls were assessed using responses to the question, “Since we last talked to you on [date of last interview] have you fallen down in the last two years (for any reason)?” Possible answers were yes or no. This question, at baseline wave 5, was used as an exclusion criterion, to focus on the participants who had not fallen in the past two years, to isolate the effect of discrimination and minimize possible bias in dealing with a recurrent faller. In subsequent waves 7 and 9, this question was used as the main outcome variable.\n\nCovariates\n\nWe controlled for several covariates that were organized into a demographic, socioeconomic, and health factors.\n\nDemographic factors included age and sex. Age was categorized into four groups: less than 60 years, 60-69 years, 70-79 years, and over 80 years. Sex was categorized as male or female. Lastly, ethnicity was grouped as either ‘White’ or ‘Non-white’.\n\nThe determination of socioeconomic status was done based on two metrics: the wealth of the household and the educational background. Wealth was assessed without taking pensions into account, segmented into five distinct categories - the first meaning the least wealthy and the fifth being the wealthiest. Education level was categorized as low (no educational qualifications or incomplete lower level), middle (NVQ1/CSE and NVQ2/GCE O level or equivalent to primary and secondary school), and high (NVQ3/GCE A level, higher education below a degree or NVQ4/NVQ5 degree or equivalent to the last 2 years or secondary -vocational- or tertiary education). We also controlled for current working status which was categorized as ‘working’ or ‘not working’. Marital status representing those ‘in a partnership’ (either married or cohabiting) and those ‘not in a partnership’.\n\nWe also adjusted for health variables. These included self-perceived physical health answering to the question “Would you say your health is…”. The options were “1 excellent, 2 very good, 3 good, 4 fair, or 5 poor?” dividing those who consider their health to be fair or poor against the rest. We also assessed walking difficulties, a strong predictor falls, by whether individuals reported difficulty walking a quarter of a mile (400 metres) (‘Yes’ or ‘No’), and mental health status, determined using the Center for Epidemiologic Studies Depression (CES-D) scale. This scale classified participants into those with ‘No depressive symptoms’ (score less than 4) and those with ‘Depressive symptoms’ (score of 4 or more). Finally, we also included an indicator of lost independence in the form of difficulties with ADL/IADL.\n\nThis study used data collected in the 2010-2011 period (wave 5) of ELSA for identifying perceived discrimination and the 2014-2015 (wave 7) and 2018-2019 (wave 9) waves for fall incidents. These waves were chosen to allow for a lag period of 4 and 8 years between the reported experiences of discrimination and fall incidents, providing adequate temporal distance to observe potential long-term impacts. As of early 2023, wave 5 remains the only wave to include questions on discrimination. Ethical clearance was obtained from the University of Tsukuba on October 14, 2022, notification number 1817.\n\nBivariate analyses were conducted to examine the associations between the variables at baseline using chi-square analyses with 95% confidence intervals. A p-value of less than 0.05 was considered statistically significant.\n\nMultivariate logistic regression models were used to estimate the odds ratios of falling 4 and 8 years after experiencing discrimination. Models were adjusted for potential confounding variables including age, marital status, self-perceived health, depressive symptoms, wealth, ethnicity, education levels, and difficulties walking, and with Activities of Daily Living (ADL) and Instrumental Activities of Daily Living (IADL). This approach allowed us to isolate the effect of perceived discrimination on the likelihood of falls while accounting for known demographic, health, and socioeconomic factors leading to falling. Statistical significance was set at p < 0.05. All analyses were performed using SPSS statistical software, version 29.0.1.0.\n\n\nResults\n\nIn this study of 4673 individuals, the baseline sociodemographic characteristics, as well as economic and health factors, were analysed in relation to perceived age discrimination in healthcare settings. The results shown in Table 1 revealed that, out of the 4673 individuals, 707 perceived to be discriminated. Associations between perceived age discrimination and sociodemographic items were explored using the Pearson’s Chi-square statistic, with significance set at a p-value less than 0.05 (95% confidence interval). The variables are discussed in the following categories: sociodemographic, economic, and health factors.\n\nAge and education level emerged as significant sociodemographic factors associated with perceived discrimination (p=0.023 and p=0.001, respectively). Younger participants (60-69) reported more discrimination than their older counterparts. Similarly, individuals with higher educational qualifications were more likely to report discrimination than those with middle or low levels of education. However, gender and marital status did not show significant associations with perceived discrimination (p=0.603 and p=0.161, respectively). Similarly, no significant difference was observed in the perceived discrimination reports between non-white and white participants (p=0.201).\n\nIn terms of economic factors, wealth quintiles based on non-pension wealth were not significantly associated with perceived discrimination (p=0.776). This indicates that the level of wealth does not significantly influence the perception of age discrimination in healthcare settings in this sample.\n\nThe health-related factors were the most significantly associated with perceived discrimination. Perceived health status, depressive symptoms as measured by the CES-D scale, difficulties with ADL/IADLs, and the ability to walk a quarter mile (400 metres) unaided were all significantly associated with perceived discrimination (p<0.001, p<0.001, p<0.001, and p=0.025, respectively). This means that participants who rated their health as fair or poor, those who exhibited depressive symptoms, those with difficulties in ADL/IADLs, and those who had difficulty walking unaided reported higher levels of discrimination. These findings indicate that individuals with poorer health status or limitations in functional ability perceive higher levels of age discrimination in healthcare settings. Full details can be found in Table 1 below.\n\nIn Table 2, we present the relation between the frequency of perceived healthcare discrimination and falling events in wave 7 of the study to observe the bivariate association of the main exposure (frequency of healthcare discrimination) and our main outcome variable (subsequent fall). The chi-square test was employed to assess the association between the variables in the table. A significance level of p < 0.05 was used to determine statistical significance. With a total sample size of 3,674, the frequency of perceived healthcare discrimination is broken down into six ordinal categories that are based on participant responses, ranging from “Almost every day” to “Never.”\n\nOverall, these results suggest a potential trend towards a higher prevalence of falling events among those who reported perceived healthcare discrimination less frequently. It must be noted that the p-value is marginally not significant. This is not surprising due to the small number of observations in some of the cells and the non-parametric distribution of the responses. This Chi-square test is not meant to verify the statistical significance but the distribution and trend. A non-parametric Mann-Whitney U test was used to compare the distribution of ranks for small number of samples (table not included) just to detect the significant ordinal connection (p=0.007). This trend supports that this skewed distribution may need a transformation of the explanatory variable for analysis. Table 2 shows that two of the categories with a lower percentage of falls were number 5: “less than once a year”; and number 6 “never”. However, to ascertain the explanatory power of our cutoff point sensitivity analyses were used.\n\nThe sensitivity analyses were conducted to confirm the impact of different cutoff points for measuring perceived healthcare discrimination on prospective falls in Waves 7 and 9. We used the Pearson’s Chi-square statistic, with significance set at a p-value less than 0.05 (95% Confidence Interval). The results are summarized in Table 3.\n\nOur first cutoff point is at the lowest frequency of perceived discrimination (never) against all other lower frequencies. This is also the closest we could be to the mean of the measure as possible given the skewed distribution. For falls at wave 7, a significant association was observed between perceived healthcare discrimination and falls (p = 0.011). Among participants who reported “No” discrimination (never), 79.1% did not experience falls, while 20.9% experienced falls. Conversely, among those who reported “Yes” discrimination (almost every day, at least once a week, a few times a month, a few times a year, or less than once a year), 74.3% did not experience falls, and 25.7% experienced falls.\n\nHowever, for falls at wave 9, no significant association was observed between discrimination and falls (p = 0.636). Among participants who reported “No” discrimination, 74.9% did not experience falls, and 25.1% experienced falls. Similarly, among those who reported “Yes” discrimination, 76.9% did not experience falls, and 23.1% experienced falls.\n\nWe used a different cutoff point for perceived healthcare discrimination to divide infrequent events (never and less than once a year), against more frequent events (almost every day, at least once a week, a few times a month and a few times a year). The results indicated a significant association with falls at wave 7 (p = 0.004). Among participants who reported “No” discrimination (never or less than once a year), 78.7% did not experience falls, and 21.3% experienced falls. Among those who reported “Yes” discrimination (almost every day, at least once a week, a few times a month, or a few times a year), 68.8% did not experience falls, and 31.2% experienced falls.\n\nIn terms of falls at wave 9, no significant association was found between perceived healthcare discrimination and falls (p = 0.837). Among participants who reported “No” discrimination (never or less than once a year), 74.9% did not experience falls, and 25.1% experienced falls. Similarly, among those who reported “Yes” discrimination (almost every day, at least once a week, a few times a month, or a few times a year), 75.3% did not experience falls, and 24.7% experienced falls.\n\nThis sensitivity analysis provides insights into the relationship between perceived healthcare discrimination and prospective falls. While both cutoff points are significant, the more significant influence is when the exposure group perceives discrimination more frequently. However, this common significance is only true for the relationship four years later, at wave 7. No significant relationship was observed at wave 9 for neither cutoff point.\n\nMultivariable association between perceived discrimination and future falls\n\nThe multivariable logistic regression analysis in Table 4 shows that for wave 7, participants who reported frequent perceived discrimination in health care were 64% more likely to have fallen compared to those who reported less frequent discrimination (OR=1.637, 95% CI: 1.131-2.368, p=.009). Age was also a significant factor, with individuals aged 70-79 and over 80 having higher odds of falling compared to those aged 60-69 (OR=1.263, 95% CI: 1.053-1.515, p=0.012 and OR=1.59, 95% CI: 1.186-2.131, p=0.002, respectively). Females were 26% more likely to fall than males (OR=1.26, 95% CI: 1.058-1.5, p=0.01).\n\nMarital status had an impact as well, with individuals who were married or cohabiting having 20% lower odds of falling compared to those who were divorced, separated, or widowed (OR=0.806, 95% CI: 0.664-0.979, p=.03). Lastly, participants with difficulties walking a quarter of a mile (400 metres) were 26% more likely to have fallen compared to those without difficulties (OR=1.263, 95% CI: 1.007-1.583, p=0.043).\n\nOther variables such as household wealth quintiles, education level, ethnicity, physical health, mental health, and ADL/IADL difficulties did not show significant associations with the occurrence of falls at wave 7.\n\nFor wave 9, the analysis revealed age and ADL/IADL difficulties as the significant predictors. Age remained a strong predictor, with individuals aged 70-79 and over 80 having higher odds of falling compared to those aged 60-69 (OR=1.492, 95% CI: 1.229-1.810, p<0.001 and OR=2.525, 95% CI: 1.734-3.678, p<0.001, respectively). ADL/IADL difficulties were also associated with a higher likelihood of falling (OR=1.311, 95% CI: 1.022-1.682, p=0.033).\n\nVariables such as perceived discrimination in healthcare, sex, household wealth quintiles, education level, marital status, ethnicity, physical health, mental health, and walking difficulties did not significantly predict falls at wave 9.\n\n\nDiscussion\n\nOur study found that older adults who perceived discrimination in healthcare settings were significantly more likely to experience falls, adjusting for potential confounders. This observation aligns with a prior study that suggests the negative psychological and physiological impact of perceived discrimination may manifest in an increased risk of falls. This study by Reyes et al.15 is to our knowledge the first and only study on the association of perceived discrimination and falls. They argue that that discrimination represents cumulative stress and chronic psychological trauma that add risk factors for falling.15 Our results are in line with their findings on the detrimental effects of discrimination on falls.\n\nDiscrimination, according to Pascoe and Richman, is a sort of social stressor that can cause both psychological anguish and physical health issues.14 In this situation, prejudice in healthcare settings may exacerbate stress and anxiety, which may in turn have an influence on physical abilities including balance and physical coordination, raising the risk of falls. According to Du Mont and Forte,20 perceived prejudice was linked to worsening physical health conditions, which may be risk factors for falls or its predecessors.\n\nThe body’s stress reaction, which results in the production of stress hormones that over time can severely affect numerous bodily systems, including the musculoskeletal and neurological systems, may be directly responsible for this indirect association between perceived discrimination and falls.21 This may lead to diminished muscular tone and coordination, increased frailty, and worse balance in older persons, all of which raise the risk of falls.9 Previous research that has emphasised the influence of unpleasant social experiences on physical health outcomes support the stress response implicated in the link between perceived discrimination in healthcare and falls.\n\nA conceivable mechanism that can support our findings in addition to the stress response theory is the deterioration of confidence in healthcare practitioners, which might be a result of perceived discrimination. Perceived discrimination is associated with decreased levels of confidence in healthcare practitioners, according to previous studies.22,23 Lower trust can therefore lead to a person avoiding medical care, which could limit the early detection and management of fall risk factors. For instance, a person who refuses to get routine checkups because they feel discriminated against may pass up chances for eye screening, medication reviews, or balance evaluations, all of which can help prevent falls.9\n\nThe experience of perceived discrimination among older adults in healthcare settings may extend beyond personal distress and mistrust; it can also manifest as disparities in the quality of healthcare provided. Discrimination can inadvertently lead to older adults being ignored, misdiagnosed, or suggested inappropriate treatments by medical staff, further exacerbating health disparities and adverse health outcomes, including increased fall risk.\n\nResearch has shown that healthcare professionals, like all individuals, can harbour implicit biases that may influence their behaviour and clinical decision-making.24 These biases can subtly affect the interaction between healthcare providers and patients, leading to differential treatment and lower quality of care.24 For instance, older adults who are perceived as less important due to institutional ageist biases may find their symptoms are ignored or dismissed as part of ‘normal’ aging.25\n\nMisdiagnosis is another significant concern. Studies have suggested that perceived discrimination can negatively impact patient-provider communication,26 which is a crucial element in accurate diagnosis. Older persons may be less likely to completely report their symptoms or medical history if they feel discriminated against, which might result in missed diagnoses or improper treatment regimens. Perceived discrimination might potentially result in medical negligence in some severe situations. Some patients may experience lower-quality care as a result of discrimination, including the recommendation of needless or unsuitable therapies. These differences in treatment may increase the likelihood of falls among people who encounter frequent discrimination and have a direct influence on the health of older persons.\n\nIt is crucial to remember that perceived discrimination and overt abuse reflect opposite sides of the spectrum in terms of prejudice. While our study concentrated on perceived discrimination, further research is required to examine the systemic or overt types of prejudice that older persons experience in hospital settings and how these affect their risk of falling. These measurements would need to go from being perceived to being observed, becoming objective.\n\nIn line with the recognised risk factors for falls in older persons,9 age and gender also had a substantial impact on the chance of falls in our research. Women and older people were more likely to fall than males and younger people. Women’s increased likelihood may be due to variables including a higher incidence of osteoporosis, which increases the risk of fractures and the fear of falling, both of which may result in less physical activity and a corresponding loss of strength and balance.21 Particularly on age, since it was the only factor significant on both waves, unlike our main exposure, discrimination, that was significant only in wave 7 but not wave 9, may mean that there are latent factors linked to chronological ageing itself that may confound the effect at longer intervals.\n\nOur research’s findings conclude that perceived discrimination in healthcare settings may increase the incidence of falls among older people. This emphasises the need of encouraging courteous, non-discriminatory healthcare environments as a potential way to lower older individuals’ risk of falling. The effectiveness of treatments aiming at reducing perceived prejudice in hospital settings, as well as potential mediating variables, should be investigated further in future studies. The lack of significance of perceived discrimination 8 years after feeling discriminated also hints to need of more detailed longitudinal studies that could try to fully grasp the conditions of older persons and discrimination continuously. Despite being a long-standing panel data, ELSA only included questions on perceived discrimination in wave 5, not allowing to see if the discriminatory acts were persistent or not. With the future inclusion of discrimination question in the upcoming wave 10 (2022-2023) we can only look forward to studies trying to cover this gap.\n\nLimitations\n\nOur study offers important new understandings into the connection between older persons’ falls and felt discrimination in healthcare settings. However, these results need to be evaluated in the context of a number of factors. First off, due to its observational methodology, our study, while identifying connections, does not demonstrate causal linkages.27 The possibility of residual confounding caused by unmeasured factors cannot be totally removed even after accounting for a number of possible confounders, which means we might not be able to identify the full causal mechanism.27 In this regard, it is important to emphasise that due to data limits, it was not possible to control for recognised risk factors for falls, such as impaired eyesight, the use of psychiatric medications, and polypharmacy.\n\nAdditionally, a key variable in our study, the evaluation of perceived discrimination, was assessed by self-report, which may have introduced reporting bias.28 Similar to this, the occurrence of falls was self-reported, a technique that, particularly among older persons, might be subject to under-reporting and recollection bias.29\n\nWhile we have speculated about possible psychological and physiological pathways linking perceived discrimination to falls, the actual mechanisms were not tested directly in our study. Further research incorporating mediation analysis would be beneficial to explore these mechanisms more comprehensively.30\n\nDue to the fact that our study only included older persons (aged 60 and above), it is possible that its findings are not applicable to all population groups. Despite our best attempts to control for these ideas, factors including frailty and comorbidities that are widespread in this age group might alter both perceived discrimination and fall risk,31 influencing the generalizability of our findings.\n\nConfounding by indication is another potential concern. Those with worse health status, who are more likely to interact frequently with healthcare providers and thus may perceive more discrimination, could be at a higher risk of falls due to their underlying health status.32 Furthermore, the temporal sequence of perceived discrimination and subsequent falls is not entirely clear given the design of our study. The questions for falls cover two years prior to the data collection in each wave, but there are 4 periods for the design used. Since wave 5 is the only one that asked about being discriminated, we do not know if previous or subsequent perceptions of discrimination are actually driving the falls 4 and 8 years later more strongly than our measurement at baseline.\n\n\nConclusion\n\nOur study, in the context of existing literature, underscores the potential influence of perceived discrimination in healthcare settings on the likelihood of falls among older adults. Our findings suggest that chronic psychological stress induced by discrimination could physiologically manifest in ways that increase the risk of falls, through both the erosion of trust in healthcare providers and potential disparities in healthcare quality. Additionally, the role of age and gender as significant factors in fall risk aligns with known determinants, hinting at an intricate interplay of demographic, social, and psychological factors shaping fall risks.\n\nOur work serves as a starting point for further investigation into this region, which is mostly uncharted. First, research that employs methods that can demonstrate causal links and more thoroughly rule out possible confounders is required. Future studies should take into account these elements for more thorough assessments due to the possible influence that factors like impaired vision, the use of psychiatric medications, and polypharmacy may have on fall risk.\n\nSecondly, more nuanced approaches to measuring perceived discrimination, perhaps through the combination of self-reports with observer-rated measures, may minimize the potential for reporting bias. This could also involve broadening the scope beyond perceived discrimination to include overt forms of discrimination, aiming to create a more complete picture of the role of discrimination in healthcare settings.\n\nFinally, the actual physiological and psychological mechanisms linking perceived discrimination to falls need further exploration. Studies employing mediation analysis could provide more insights into the underlying pathways between discrimination and fall risk.\n\nThe preliminary findings of this study do suggest potential areas of intervention. As perceived discrimination in healthcare settings emerges as a potential risk factor for falls in older adults, promoting respectful and non-discriminatory environments should be considered a priority. This includes efforts to address potential implicit biases among healthcare professionals, and institutional policies promoting equality and respect for all patients.\n\nFurthermore, strategies to improve patient-provider communication may help counter the adverse effects of perceived discrimination on diagnostic accuracy. Greater attention to the symptoms of older adults, regardless of any bias, could lead to more accurate diagnoses and appropriate treatments, potentially reducing fall risk.\n\nUltimately, while the relationship between perceived discrimination in healthcare settings and fall risk among older adults needs further elucidation, the findings of this study emphasize the need to ensure equality and respect in healthcare interactions, not only for their inherent ethical value but also for their potential impact on patients’ health outcomes.\n\nThe Multicentre Research and Ethics Committee received ethical clearance for ELSA Wave 1 data collection (Reference number MREC/01/2/91) on February 7, 2002.33\n\nThe University of Tsukuba granted ethical approval for our secondary analysis (October 14, 2022, n. 1817). The present study was carried out following the Helsinki Declaration and the Ethical Guidelines for Medical and Biological Research Involving Human Subjects.", "appendix": "Data availability\n\nEnglish Longitudinal Study of Ageing (ELSA) http://doi.org/10.5255/UKDA-Series-200011. 34 This study contains the underlying data from 3 distinct waves:\n\n• Wave 5\n\n• Wave 7\n\n• Wave 9\n\nThe data and relevant documentation from waves 5, 7, and 9 have been obtained and are readily available via the archive provided by the Economic and Social Data Service, which is an F1000Research-approved repository. Except for the categories of data that are considered confidential or sensitive in nature, such as linked administrative files, geographically identifiable items or genetic material information. On their website, data-archive.ac.uk, further details can be obtained via the registered DOI: 10.5255/UKDA-Series-200011. 34 Users just need to consent to the repository data sharing policy to have access to the data, which is publicly available.\n\n\nReferences\n\nBeard JR, Bloom DE: Towards a comprehensive public health response to population ageing. Lancet. 2015; 385(9968): 658–661. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOrganization, W.H: Step safely: strategies for preventing and managing falls across the life-course.2021.\n\nBurns ER, Stevens JA, Lee R: The direct costs of fatal and non-fatal falls among older adults - United States. J. Saf. Res. 2016; 58: 99–103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSherrington C, et al.: Exercise for preventing falls in older people living in the community. Cochrane Database Syst. Rev. 2019; 2019. Publisher Full Text\n\nMasud T, Morris RO: Epidemiology of falls. Age Ageing. 2001; 30 Suppl 4: 3–7. PubMed Abstract \| Publisher Full Text\n\nFramework, P.H.O: Public health profiles. Office for Health Improvement and Disparities. Public health profiles. 2023© Crown copyright 2023, Office for Health Improvement and Disparities.Reference Source\n\nZijlstra GA, et al.: Prevalence and correlates of fear of falling, and associated avoidance of activity in the general population of community-living older people. Age Ageing. 2007; 36(3): 304–309. PubMed Abstract \| Publisher Full Text\n\nLachman ME, et al.: Fear of falling and activity restriction: the survey of activities and fear of falling in the elderly (SAFE). J. Gerontol. B Psychol. Sci. Soc. Sci. 1998; 53(1): P43–P50. PubMed Abstract \| Publisher Full Text\n\nRubenstein LZ: Falls in older people: epidemiology, risk factors and strategies for prevention. Age Ageing. 2006; 35: ii37. Publisher Full Text\n\nRutan GH, et al.: Orthostatic hypotension in older adults. The Cardiovascular Health Study. CHS Collaborative Research Group. Hypertension. 1992; 19(6 Pt 1): 508–519. PubMed Abstract \| Publisher Full Text\n\nLord SR, Dayhew J: Visual risk factors for falls in older people. J. Am. Geriatr. Soc. 2001; 49(5): 508–515. Publisher Full Text\n\nAmbrose AF, Paul G, Hausdorff JM: Risk factors for falls among older adults: a review of the literature. Maturitas. 2013; 75(1): 51–61. Publisher Full Text\n\nBurgess DJ, et al.: The association between perceived discrimination and underutilization of needed medical and mental health care in a multi-ethnic community sample. J. Health Care Poor Underserved. 2008; 19(3): 894–911. Publisher Full Text\n\nPascoe EA, Smart Richman L: Perceived discrimination and health: a meta-analytic review. Psychol. Bull. 2009; 135(4): 531–554. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReyes-Ortiz CA, et al.: The Association Between Discrimination and Falling. A National Sample of Older Adults. J. Aging Health. 2022; 34(4-5): 614–625. PubMed Abstract \| Publisher Full Text\n\nReyes-Ortiz CA, et al.: Association Between History of Abuse and Falling in Older Adults. J. Am. Geriatr. Soc. 2018; 66(8): 1603–1607. PubMed Abstract \| Publisher Full Text\n\nPearlin LI, et al.: Stress, health, and the life course: some conceptual perspectives. J. Health Soc. Behav. 2005; 46(2): 205–219. Publisher Full Text\n\nRippon I, et al.: Perceived age discrimination in older adults. Age Ageing. 2014; 43(3): 379–386. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSteptoe A, et al.: Cohort Profile: The English Longitudinal Study of Ageing. Int. J. Epidemiol. 2012; 42(6): 1640–1648. PubMed Abstract \| Publisher Full Text\n\nDu Mont J, Forte T: Perceived discrimination and self-rated health in Canada: an exploratory study. BMC Public Health. 2016; 16(1): 742. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchneiderman N, Ironson G, Siegel SD: Stress and health: psychological, behavioral, and biological determinants. Annu. Rev. Clin. Psychol. 2005; 1: 607–628. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaywood C Jr, et al.: Perceived discrimination, patient trust, and adherence to medical recommendations among persons with sickle cell disease. J. Gen. Intern. Med. 2014; 29(12): 1657–1662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHong HC, et al.: Factors affecting trust in healthcare among middle-aged to older Korean American women. BMC Womens Health. 2018; 18(1): 109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFitzGerald C, Hurst S: Implicit bias in healthcare professionals: a systematic review. BMC Med. Ethics. 2017; 18(1): 19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLloyd-Sherlock PG, et al.: Institutional ageism in global health policy.2016; 354.\n\nBalsa AI, et al.: Clinical uncertainty and healthcare disparities. Am. J. Law Med. 2003; 29(2-3): 203–219. Publisher Full Text\n\nRothman KJ, Greenland S, Lash TL: Modern epidemiology. Wolters Kluwer Health/Lippincott Williams & Wilkins Philadelphia; 2008; vol. 3. .\n\nFadnes LT, Taube A, Tylleskär T: How to identify information bias due to self-reporting in epidemiological research. The Internet Journal of Epidemiology. 2009; 7(2): 28–38. Publisher Full Text\n\nGanz DA, Higashi T, Rubenstein LZ: Monitoring falls in cohort studies of community-dwelling older people: effect of the recall interval. J. Am. Geriatr. Soc. 2005; 53(12): 2190–2194. PubMed Abstract \| Publisher Full Text\n\nVanderWeele TJ: Mediation analysis: a practitioner’s guide. Annu. Rev. Public Health. 2016; 37: 17–32. PubMed Abstract \| Publisher Full Text\n\nFried LP, et al.: Frailty in older adults: evidence for a phenotype. J. Gerontol. A Biol. Sci. Med. Sci. 2001; 56(3): M146–M157. Publisher Full Text\n\nPsaty BM, et al.: Assessment and control for confounding by indication in observational studies. J. Am. Geriatr. Soc. 1999; 47(6): 749–754. Publisher Full Text\n\nBanks J, et al.: English longitudinal study of ageing: waves 0-9, 1998-2019.2022.\n\nResearch, N.S., U.C. London, and I.f.F. Studies: English Longitudinal Study of Ageing. UK Data Service; 2023." }	[ { "id": "235617", "date": "07 Feb 2024", "name": "Tszshan Ma", "expertise": [ "Reviewer Expertise Epidemiologist" ], "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 thorough and clear description of an analysis of the relation of perceived healthcare discrimination and risk of falls among older adults. Overall, an excellent presentation of analyses and results, and the conclusions are supported by the data. The paper is well-written and well-discussed. Some issue of clarification has been noted below.\nComments: 1. This study looks at the “perceived discrimination in health care settings” as the main exposure. Based on the framing of the question, the perceived discrimination is not specifically related to age. In the manuscript, there are 4 places mentioned “perceived age discrimination” as exposure. Please correct or clarify if the discrimination is related to age. Page 6, Results – Demographic characteristics section Page 6, Results – Economic factors section Page 6, Results – Health factors section\n2. Please explain why age is categorized into 10-year bins in the regression model instead of treating it as a continuous variable.\n3. Among adjusted confounders, age, difficulties walking, perceived physical health, and ADL/IADL difficulties are both significantly/marginally significantly associated with exposure and outcome. It is suggested to perform additional effect modification analyses to assess whether these characteristics could modify the relation between exposure and outcome. This could provide potential insights in identifying subgroups of persons who are more susceptible to the effect of perceived discrimination on risk of falls, hence delineating potential pathways linking perceived discrimination to falls.\n\nIs the work 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": "259206", "date": "05 Apr 2024", "name": "Christine Waszynski", "expertise": [ "Reviewer Expertise Delirium", "Gerontology" ], "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 addresses two very important topics, falls and discrimination, each of which can have a profound impact upon the life of older adults .Exploring the relationship between these 2 experiences has the potential for the development of preventative and intervention strategies to improve quality of life.\nThis paper uses available data from a large, longitudinal study in England known as ELSA. Self reported responses on perceived discrimination and fall episodes were analyzed and found to be associated, with those experiencing discrimination more likely to experience a fall within 4 years.\nThis paper found the participants of younger age and higher educational status reported more perceived discrimination than those who were older or less educated. A discussion of this would be helpful in the article.as well as including this in a future study. . This paper paves the way for future work that could be structured to obtain more details surrounding the population studied and their experience of discrimination. The following limitations of this study were due to the database (ELSA) utilized:\nELSA followed individuals for many years. This paper reported on discrimination scores collected in 2010-2011 (wave 5 ) and linked the response to falls data collected 2014-2015 (wave 7 ) and 2018-2019 (wave 9) . There was no information shared about the participants' living situation (community vs facility) at the time of the discrimination report or at the time of the fall report. This variable could have influence on both measures.\nThe question regarding perceived discrimination gave choices that may not be applicable to many participants. For example, participants who could potentially report that they experience discrimination from a doctor or hospital \"every day\"\n\nwould need to either be hospitalized or in a care facility where they encounter a doctor every day. A better measure to use in a future study may be to ask the participant to rate the % of times they have encountered discrimination from a doctor or hospital.\nStructuring the discrimination question to describe behavior they found discriminatory rather than how often they experienced discrimination would be more informative.\nOne of the discussion points in this paper was that perceived discrimination could lead to a hesitancy to seek preventative care or treatment for symptoms, therefore leading to falls. It would be useful to gather data on the frequency of healthcare visits for those who fell vs those who did not..\nIn summary, this paper reported on available data to describe the relationship between perceived discrimination and falls. It also generated opportunities for future study of these relationships.\n\nIs the work 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/12-1134
https://f1000research.com/articles/12-1133/v1	11 Sep 23	{ "type": "Systematic Review", "title": "The cognitive remediation of attention in HIV-associated neurocognitive disorders (HAND): A meta-analysis and systematic review", "authors": [ "Sizwe Zondo" ], "abstract": "Background: Despite medical advances in Highly Active Antiretroviral Therapy (HAART), patients living with HIV continue to be at risk for developing HIV-associated neurocognitive disorders (HAND). The optimization of non-HAART interventions, including cognitive rehabilitation therapy (CRT), shows promise in reversing the impact of HAND. No data exist indicating the efficacy of CRT in remediating attention skills following neuroHIV. This paper presents a meta-analysis of randomised and non-randomised controlled trials (RCTs) to remediate attention skills following HIV CRT. Methods: The database search included literature from Google Scholar, ERIC, Cochrane Library, ISI Web of Knowledge, PubMed, PsycINFO, and grey literature published between 2013 and 2022. Inclusion criteria included studies with participants living with HIV who had undergone CRT intervention to remediate attention skills following neuroHIV. Exclusion criteria included case studies, non-human studies, and literature reviews. To assess study quality, including, randomisation, allocation concealment, participant and personnel blinding, the Cochrane Collaboration ratings system was applied. Results: A total of 14 studies met the inclusion criteria (n = 532). There were significant pre- to post-intervention between-group benefits due to CRT in the experimental group relative to control conditions for the remediation of attention skills following HIV acquisition (Hedges g = 0.251, 95% CI = 0.005 to 0.497; p < 0.05). No significant effects (p > 0.05) were demonstrated for subgroup analysis. Conclusions: To the author's knowledge, this is the first meta-analysis that exclusively analyses the remediation of attention skills in the era of HAART and neuroHIV, where all studies included participants diagnosed with HIV. The overall meta-analysis effect indicates the efficacy of CRT in remediating attention skills in HIV and HAND. It is recommended that future cognitive rehabilitation protocols to remediate attention skills should be context and population-specific and that they be supplemented by objective biomarkers indicating the efficacy of the CRT. Registration: Protocols.io (01/03/2023).", "keywords": [ "HIV", "HAND", "Attention Rehabilitation", "Neuroplasticity", "meta-analysis", "meta-regression" ], "content": "Introduction\n\nThe Human Immunodeficiency Virus (HIV) continues to be a significant global pandemic with no known cure. Latest figures from UNAIDS (2021) indicate that by the end of 2021, approximately 38.4 million people were living with the virus, with 1.5 million newly reported cases in 2021 alone. Virologically, HIV is a ribonucleic acid (RNA), single-stranded retrovirus (Poltronieri et al., 2015) that targets cells in the immune system. Through pathobiology yet to be understood, following transmission to the host, HIV permeates the blood-brain barrier (BBB), where it leads to the differentiation of monocytes into macrophages. This differentiation leads to the infection of cells in the CNS, namely microglia and astrocytes (Filipowicz et al., 2016; Sillman et al., 2018). In breaching the BBB, HIV is thought to dysregulate the brain’s intrinsic nerve cell architecture, leading to aberrant neural transmission, including excess glutamate levels and decreased dopaminergic transmission (Elbirt et al., 2015; Nolan & Gaskill, 2019). Markedly, HIV’s viral penetrance and persistence in the CNS is implicated in neuronal apoptosis, leading to a milieu of neurocognitive impairments associated with HIV (Das et al., 2016; Smail & Brew, 2018).\n\nNeurocognitive impairments resulting from HIV are well-documented and include HIV Dementia (Hussain et al., 2022; Mattson et al., 2005), HIV-associated neurocognitive disorder (HAND) (Elbirt et al., 2015; Smail & Brew, 2018), and HIV encephalitis (Morgello, 2018). Specific to HAND1, although no reliable worldwide estimates exist, the prevalence rates are estimated to range from 25% to 59% of HIV cases (Bonnet et al., 2013; Elbirt et al., 2015; Kinai et al., 2017). According to updated criteria, HAND is diagnosed if a patient performs more than one standard deviation (SD) below his or her normative mean, on standardized neuropsychological measures, in two or more cognitive domains (e.g., attention, speed of processing, verbal memory, executive functioning) (Antinori et al., 2007; Brew, 2018; Chan et al., 2019; Chan & Wong, 2013; Saloner & Cysique, 2017).\n\nPharmacological interventions, namely Highly Active Antiretrovirals (HAART), have improved cognitive outcomes in HIV (Benki-Nugent & Boivin, 2019; Jantarabenjakul et al., 2019). However, to date, their efficacy in treating or reducing the impact of HAND remains variable (Alford & Vera, 2018; Lanman et al., 2019; Yuan & Kaul, 2019). For example, Underwood et al. (2015) found that prolonged treatment with efavirenz (a non-nucleoside reverse transcriptase inhibitor) (NNRTI) and raltegravir (integrase inhibitor) may play a role in HIV-associated cognitive decline and poorer cognitive function in children living with HIV. A cognate study by Hammond et al. (2019) found that children in a South African study showed no cognitive gains after receiving efavirenz. The study hypothesised that efavirenz, due to its pharmacokinetic profile (genetically slow metabolites), may be a risk factor for neurotoxicity, leading to the poor neurocognitive outcomes associated with HAND.\n\nCorrespondingly, Crowell et al. (2015), in their study involving 396 children living with HIV, found an association between early viral suppression and improved neurocognitive outcome; however, they found no association between a high CNS Penetration-Effectiveness score (CPE)2 and neurocognitive improvement in the children. These findings are similar to those reported by Ellis et al. (2014), who found no association between high CPE and gains in neurocognition in a longitudinal study conducted among adults living with HIV. Similarly, Puthanakit et al. (2013), found no improvement in neurocognitive outcomes amongst 139 Thai and Cambodian children living with HIV after a three-year initiation of cARTs. Other studies (Das et al., 2016; Iglesias-Ussel & Romerio, 2011; Kumar et al., 2018) indicate that when antiretrovirals (ARVs) act upon the brain HIV viral reservoir, they are indicated to significantly cause neurotoxicity, leading to further neurocognitive and psychiatric impairments (Alford & Vera, 2018; Das et al., 2016; Lanman et al., 2019; Vázquez-Santiago et al., 2014; Wilmshurst et al., 2018).\n\nGiven the pharmacological limitations associated with ARVs, including limitations in viral reservoir penetration in the brain and neurotoxicity, studies have begun investigating the efficacy of alternative non-pharmaceutical therapies, namely cognitive rehabilitation therapy (CRT)3, to reverse HAND. The principles of CRT are based on neuroplasticity. Neural brain plasticity posits that the human cortex is malleable and has the inherent capacity to undergo structural and functional change (Bach-y-Rita, 2003; Wilson et al., n.d.). Within the mammalian cortex, structural and functional change is attendant to continued and repeated exposure to cognitively demanding brain training exercises, purposed to rewire and improve neuronal connectivity, increase blood supply and improve brain function (Hebb, 1949; Luria, 1948; Merzenich, 2013). Luria (1970), particularly notes that brain plasticity and cognitive training allow for axonal and synaptic connections reintegrating. Accordingly, through dendritic outflow, synaptic connections are thought to stimulate neuronal density and cortical enrichment in near and distant neuronal networks responsible for disparate cortical functions.\n\nGiven the promise of positive neuroplasticity to harness neurocortical networks and ameliorate brain function, the extant literature has documented the efficacy of brain training exercises to reduce the risk of cognitive impairment sequent HAND. For example, data indicate improvements in cognitive domains such as executive functions (Boivin et al., 2016; Frain & Chen, 2018), attention (Basterfield, & Zondo, 2022; Boivin et al., 2010; Towe et al., 2017), processing speed (Cody et al., 2020; Vance et al., 2012), and working memory (Fraser & Cockcroft, 2020; Towe et al., 2017), following intensive brain training exercise in neuroHIV.\n\nDespite the above early promising findings, contradictory findings have been reported. For example, Vance et al. (2012) used a computerized CRT program (InSight) to investigate processing speed in adults. Although the experimental group showed significant baseline-to-post-test improvements in speed processing, speed processing deficits are not prevalent in the post-cART era (Heaton et al., 2011). In another study, Pope et al. (2018) found that a computerised program (Posit Science: BrainHQ) could improve abstraction and executive functions, whereas Fazeli et al. (2019), reported that the same software enhanced other cognitive domains, such as attention, working memory, and information processing in the experimental group. Moreover, some studies returned insignificant findings (e.g., Vance et al., 2018; Fazeli et al. 2019) when comparing the effect of the cognitive rehabilitation on the experimental group, compared to the control, despite utilizing brain training programs and techniques that have proven to improve cognition in HIV.\n\nGiven contradictory findings within the literature, Vance et al. (2019), conducted a systematic review of 13 computerised cognitive rehabilitation (CCT) studies investigating the efficacy of cognitive rehabilitation to reverse HAND. The review by Vance et al. (2019) found that, for the most part, CRT in HIV was associated with improved cognitive outcomes that translated to improvements in quality of life. Nonetheless, although the systematic review provides summary data on the effect of CRT on working memory, processing speed, and ageing, it does not provide effect size data for each of the reviewed cognitive domains. Most importantly, it does not provide information on the cognitive rehabilitation of attention skills, although deficits in attention are the foremost and common consequence of HIV (Posada et al., 2012; Wang et al., 2017). Moreover, since the review did not provide effect size data, it did not provide data detailing the effect of moderator variables or subgroup meta-analytic data on HIV cognitive rehabilitation outcomes. Given these limitations, the current study aimed to conduct a meta-analysis investigating the efficacy of CRT in remediating attention skills among people living with HIV. Significantly, the study aimed to (1) provide effect size data detailing pre- and post-intervention improvement in attention due to CRT among people living with HIV. Secondly, the study sought to (2) investigate the effect of moderator variables by conducting subgroup analyses of the effect size (if significant). Lastly, the study aimed to provide clinical suggestions for implementing HIV CRT interventions in low-to medium-income countries with a high number of HIV cases.\n\n\nMethods\n\nThis study was registered on Protocols.io (dx.doi.org/10.17504/protocols.io.5jyl8jqm7g2w/v1; 01/03/2023). Although the study was not registered in PROSPERO the review protocol can be found as Extended data (Zondo, 2023). The study followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guidelines for meta-analyses (Moher et al., 2009).\n\nThe units of analysis were chosen from published literature containing medical subject headings (MeSH) and text words related to: ‘HIV and attention rehabilitation’ or ‘HIV and cognitive rehabilitation’, ‘HIV and/or attention’, ‘HIV and attention remediation’, ‘HIV and executive attention remediation’. These were combined with terms related to outcome research such as: ‘effect’, ‘efficacy’ ‘evaluation’, or ‘outcome’. To identify relevant studies, journal articles, books, dissertations, and electronic databases were searched. Electronic database searches included Google Scholar (RRID:SCR_008878), ERIC (RRID:SCR_007644), Cochrane Library (RRID:SCR_013000), ISI Web of Knowledge, PubMed (RRID:SCR_004846), and PsycINFO (RRID:SCR_014799). Grey literature and unpublished papers were searched based on indices of conference proceedings and dissertation abstracts to minimise publication bias (Higgins & Green, 2008). A complete breakdown and description of the search strategies are available as Extended data (Zondo, 2023).\n\nThe inclusion criteria for studies included in the meta-analysis were included based on the PICOS criteria. The population and condition of interest were patients diagnosed with HIV, receiving cognitive rehabilitation to remediate attention. Participants in the experimental group should have undergone an intervention to remediate attention skills following neuroHIV. Studies should have included a comparison between the experimental group and at least one control group (passive control group, or active control group). Studies should also have reported outcome data in the form of pre-and post-intervention attention scores using validated neuropsychological measures of attention4. Lastly, studies were included if they used random and non-random control trial study designs. In addition to the PICOS criteria, studies should have reported sample sizes to enable effect size weighting (Borenstein et al., 2021).\n\nThe above inclusion criteria were combined with the 27-item PRISMA checklist to produce a four-phase PRISMA flow diagram as suggested by Moher et al. (2009). The complete PICOS criteria accompanied by the PRISMA checklist can be found as Extended data (Zondo, 2023). The PRISMA flow diagram is indicated below in Figure 1. All duplicate studies for the meta-analysis were removed using Mendeley Data (RRID:SCR_002750) Software, Version 1. The author (S.Z) and two researcher assistants (K.S and T.C), independently assessed the titles and abstracts retrieved from literature searches for relevance. After the initial assessment, the same reviewers determined the eligibility of all full-text relevant for the meta-analysis. Any disagreements (three articles) were resolved by a third research assistant (N.M) with expertise in meta-analytic research. Relevant but excluded studies from the reviewed literature are indicated in the Extended data (Zondo, 2023).\n\nData extraction was done by the author and cross-checked (by K.S. and T. C.) using an Excel spreadsheet (Microsoft Corporation) (RRID:SCR_016137). The relevant summary statistics to investigate attention outcomes due to cognitive rehabilitation included individual data points linked to: (a) The number of participants in each of the groups, (b) relevant statistical data such as means, and standard deviations, for both the experimental and control groups (active or passive control) on the attention measures, pre and post the intervention (Field & Gillett, 2010; Lee, 2018).\n\nThe extraction of attention outcomes (dependent variable) for each of the studies used in the meta-analysis are available as Extended data (Zondo, 2023). Other key moderator data extracted from each of the studies included in the meta-analysis included data related to: (a) the duration of the cognitive training exercises (<10 sessions; 10 sessions; >10 sessions in each study; (b) the type of cognitive training received (computerised; pencil and paper, mixed); (c) the setting of the cognitive training (individualised training; group intervention); (d) the type of research design employed (random control trial vs. non-random control); (e) the socio-economic setting of the study (High vs. Low); (f) the data quality of the study (Low, Medium, High); (g) the type of sample (paediatric HIV vs. geriatric HIV); (h) the type of control group utilised (active, passive, both) and (g) whether participants were blind or aware to their condition (experimental or control). The above variables were included in the subgroup meta-analysis to investigate the influence of pertinent moderator variables on the overall effect size of the cognitive rehabilitation.\n\nThe meta-analysis was performed using Stata 17 (StataCorp. 2021. Stata Statistical Software: Release 17. College Station, TX. StataCorp, LLC) (RRID:SCR_012763) (free alternative, RStudio). The overall effect size was determined by measuring attention scores pre-and-post the CRT to investigate the effectiveness of the attention intervention. Given the heterogeneity across all studies, the random effect model was used to estimate the pooled effect (Borenstein et al., 2009). Effect sizes were calculated based on the standardised mean difference (SMD) sizes for the individual studies, weighted according to the relevant sample size. Briefly, when using SMD, effect is calculated as the mean change in pre-intervention scores compared to post-intervention scores in the intervention group minus the mean change from pre-intervention to post-intervention scores in the control group, divided by the combined pre-intervention standard deviation scores (Borenstein et al., 2009; Field & Gillett, 2010).\n\nFollowing suggestions from Borenstein et al. (2021), the inverse variance method was used to interpolate the SMDs of each study. As suggested by Borenstein et al. (2021), since the SMD model also corrects for the use of different outcome measures (i.e., different neuropsychological outcomes used to assess attention), it, however, fails to account for differences in the direction of the participants’ behavioural performance (neuropsychological performance) within the various outcome measures used in the meta-analysis (neuropsychological assessments). Stated differently in certain assessments, an increase in mean scores may represent a decline in disease severity, whereas, in some neuropsychological assessments, a decrease in mean scores represents a decline in disease severity (Borenstein et al., 2009). To correct these differences, mean scores from studies in which a decrease in mean scores represents a decline in disease severity were multiplied by -1, ensuring conformity of direction for all the scales used in the meta-analysis calculation (Borenstein et al., 2009). Based on the above recommendations, the mean scores for both the control and experimental group from the following studies Fazeli et al. (2019), Zondo and Mulder (2015) were corrected by multiplication of -1.\n\nThe H2 and I2 statistic (based on the Q statistic) was used to assess the proportional significance of heterogeneity (Borenstein et al., 2009). The author tested for publication bias using a funnel plot, which is a type of scatterplot with treatment effect size (Cohen’s D) plotted on the x-axis, and the standard error (variance) plotted on the y-axis (Borenstein et al., 2009). Statistical significance for all analyses was set at a threshold of p < 0.05.\n\n\nResults\n\nSince the inclusion criteria of the studies are detailed in the methods section, a PRISMA flow chart indicating the decision process and study selection is described in Figure 1. In summary, the study included a total of 1,225 records; after removing duplicates (489), 736 records were screened. A further 527 records were excluded based on title searches, abstracts, and methodological considerations (i.e., case studies and qualitative designs). A total of 15 studies were deemed relevant but were excluded from the analysis due to reasons provided as Extended data (Zondo, 2023). In total, 29 studies were assessed for eligibility with the final selection including 11 randomised control studies (Basterfield, & Zondo, 2022; Boivin et al., 2010; Casaletto et al., 2016; Cody et al., 2020; Fazeli et al., 2019; Frain & Chen, 2018; Fraser & Cockcroft, 2020; Livelli et al., 2015; Ownby & Acevedo, 2016; Pope et al., 2018; Vance et al., 2012) and three non-randomised studies (Cody et al., 2015; Ezeamama et al., 2020; Zondo & Mulder, 2015).\n\nThe characteristics of all studies included in the meta-analysis are detailed in Table 1. The analysis included data from South Africa (Basterfield, & Zondo, 2022; Fraser & Cockcroft, 2020; Zondo & Mulder, 2015), Uganda (Boivin et al., 2010; Ezeamama et al., 2020), Italy (Livelli et al., 2015), and the US (Casaletto et al., 2016; Cody et al., 2015, 2020; Fazeli et al., 2019; Frain & Chen, 2018; Ownby & Acevedo, 2016; Pope et al., 2018; Vance et al., 2012). In total, the study comprised 532 participants (255 participants in the intervention group and 277 participants in the control group).\n\nCRT, cognitive rehabilitation therapy; HIV, Human Immunodeficiency Virus; HAART, Highly Active Antiretroviral Therapy; ARV, antiretroviral; HAND, HIV-associated neurocognitive disorders.\n\na The definition ‘child’, is based on age guidelines from the UN Convention of the Rights of the Child that describe the child/paediatric age as ranging from birth to adolescence (16-19 years) (UN Convention Assembly, 1989).\n\nb In most studies (e.g., Fraser & Cockcroft, 2020), a session lasted for a period of 30-45 mins.\n\nAs indicated in Table 1, participant ages for adults ranged from a mean of 47.5 years (Livelli et al., 2015) to 59.7 years (Ezeamama et al., 2020) in the intervention group; and 50.0 years (Livelli et al., 2015) to 62.12 years (Cody et al., 2020) in the control group. Participant ages in the paediatric HIV groups ranged from a mean of 10.34 years (Boivin et al., 2010) to 12.0 years (Fraser & Cockcroft, 2020) in the intervention group and 9.36 years (Boivin et al., 2010) to 12.41 years (Fraser & Cockcroft, 2020) in the control group. The proportion of female participants ranged from 0% (Frain & Chen, 2018) to 66% (Boivin et al., 2010) in the intervention group and 0% (Zondo & Mulder, 2015) to 90% (Boivin et al., 2010) in the control group.\n\nThe ‘types’ of attention intervention implemented varied extensively and included selective attention training (Basterfield, & Zondo, 2022), divided attention training (Casaletto et al., 2016), selective and divided attention training (Fazeli et al., 2019), selective, divided, and sustained attention training (Fraser & Cockcroft, 2020; Livelli et al., 2015), visual attention (Frain & Chen, 2018; Vance et al., 2012), and simple attention training (Ezeamama et al., 2020; Ownby & Acevedo, 2016). Nine of the studies (Boivin et al., 2010; Casaletto et al., 2016; Ezeamama et al., 2020; Fazeli et al., 2019; Frain & Chen, 2018; Livelli et al., 2015; Ownby & Acevedo, 2016; Pope et al., 2018; Vance et al., 2012) reported participant biomarker data, in the form of CD4+ T-cell count, pre-and post-the intervention. CD4+ T-cell counts in the treatment group ranged from 552 cells/μL (Casaletto et al., 2016) to 833 cells/μL (Fazeli et al., 2019). None of the studies reported biomarker data in the form of neuroimaging data (i.e., MRI, EEG, fNIRS) detailing the effects of the intervention from baseline to post-intervention changes.\n\nThe total number of rehabilitation sessions ranged from 1 (Casaletto et al., 2016) to 36 sessions (Livelli et al., 2015). There was much variability within the studies regarding the duration of each rehabilitation session, with some sessions, ranging from 10-15 minutes per session (Casaletto et al., 2016) to others ranging from 30-45 minutes per session (Fraser & Cockcroft, 2020). Training frequency within studies ranged from two sessions per week (Boivin et al., 2010) to four sessions per week (Fraser & Cockcroft, 2020; Pope et al., 2018). For most studies, the control conditions were divided into one of two control types: either active controls (six studies: Basterfield & Zondo, 2022; Casaletto et al., 2016; Cody et al., 2020; Ezeamama et al., 2020; Fazeli et al., 2019; Fraser & Cockcroft, 2020; Livelli et al., 2015), or passive controls (five studies: Boivin et al., 2010; Cody et al., 2015; Frain & Chen, 2018; Vance et al., 2012; Zondo & Mulder, 2015). None of the reviewed studies included both active and passive controls, to assess the impact of the active ingredient (cognitive rehabilitation), compared to the influence of a sham activity (active control) and/or passive interaction (passive control).\n\nOverall, 10 of the studies implemented computerised cognitive rehabilitation (CCT) protocols (Boivin et al., 2010; Cody et al., 2015, 2020; Ezeamama et al., 2020; Fazeli et al., 2019; Frain & Chen, 2018; Fraser & Cockcroft, 2020; Ownby & Acevedo, 2016; Pope et al., 2018; Vance et al., 2012, 2018); two utilised pencil and paper protocols (Basterfield & Zondo, 2022; Zondo & Mulder, 2015), whereas one study employed a mixture of computer and paper-pencil protocols (Livelli et al., 2015), whilst another used a mixture of Goal Management and individualised metacognition training (Casaletto et al., 2016). Of the 10 studies that implemented computerised CRT, two (Cody et al., 2020; Fazeli et al., 2019) coupled computerised training with transcranial deep brain stimulation (tDCS). Moreover, of the studies that utilised computerised interventions, six used the PositScience-BrainHQ system (Cody et al., 2015, 2020; Fazeli et al., 2019; Frain & Chen, 2018; Pope et al., 2018; Vance et al., 2012), whereas two employed the Captain’s Log (Boivin et al., 2010; Ezeamama et al., 2020), which trains multiple cognitive domains including working memory and executive skills, and one made use of Jungle-Memory (Fraser & Cockcroft, 2020), which trains working memory.\n\nThe analysis was carried out using the standardized mean difference as the outcome effect measure. As indicated in Figure 2, a random-effects model was fitted to the data. The amount of heterogeneity (tau2) was estimated using the restricted maximum-likelihood estimator (Viechtbauer, 2010). In addition to the estimate of tau2, the Q-test for heterogeneity and the I2 statistic was conducted on a total of 14 studies included in the analysis. The observed standardized mean differences ranged from -1.129 to 1.115, with the majority of estimates being positive (71%). The estimated average standardized mean difference based on the random-effects model was Hedges, g = 0.251 (95% CI: 0.005 to 0.4977).\n\nNote: The overall standardized mean difference was estimated using the restricted maximum-likelihood estimate (REML).\n\nThe average outcome for attention rehabilitation differed significantly from zero (z = 2.00, p = 0.045). According to the Q-test, the true outcome of the effect size appears to be heterogeneous (Q (13) = 24.70, p = 0.025, tau2 = 0.097, I2 = 44.89%). A 95% prediction interval for the true outcomes of the intervention ranged from - 0.3901 to 0.8579. Although the average outcome for the rehabilitation was estimated to be positive (Hedges g = 0.251, p = 0.045), the data indicate that in some studies the true outcome of the rehabilitation may in fact be negative. Further examination of the studentized residuals revealed that none of the studies had a value larger than ± 2.9137. Hence, there was no indication of outliers in the context of this model. As further indicated by the Forest Plot (Figure 3), there was greater variability in the 95% CIs in studies with smaller sample sizes and larger weights in studies with post-intervention follow-ups and larger sample sizes.\n\nNote: The overall effect of the cognitive rehabilitation to remediate attention skills following neuroHIV was significant, z = 2.00, p < 0.05.\n\nSubgroup analyses are presented in Table 2. These were conducted to investigate the effect of key moderator variables, namely (a) the duration of the intervention (<10 sessions, 10 sessions, >10 sessions), (b) the type of rehabilitation (computerized, pencil and paper, mixed), (c) the setting of the rehabilitation (individualized or group), (d) the type of research design employed (randomized, non-randomised), (e) data quality rating (Low median, high), (f) the population of the study (paediatric HIV or geriatric HIV), (g) the type of control group in the study (active control, passive control), and (h) the blinding of subjects (aware or blind). No significant subgroup differences were found on any of the moderator variables. Further meta-regression analysis could not be conducted on the data, despite the significant outcomes of the cognitive rehabilitation (Hedges g = 0.25, p < 0.05).\n\nHIV, Human Immunodeficiency Virus.\n\na Heterogeneity measures for the each of the group analysis.\n\nStudy quality assessment ratings were conducted on all studies based on criteria established by the Cochrane Collaboration (Cumpston et al., 2019; Higgins & Green, 2008). The criteria for quality assessment were as follows: (1) adequate randomization concealment of participants to either the treatment or control group (by the Primary Investigator (s); (2) Blinding of participants to either the treatment or control condition(s)5; (3) Baseline comparability, detailing whether the experimental and control group(s) were comparable on all outcome measures from baseline to post-intervention; (4) Power analysis: Did the study have adequate power and/or at least 15 participants per group for comparative analysis (experimental vs. control)? (5) Completeness of follow-up data: Was there adequate follow-up of at least three months post the intervention, with clear attrition analysis of data? (6) Handling of missing data: Were multiple imputation analysis and/or maximum likelihood analysis (or other advanced statistical techniques) applied to account for missing data and high attrition rates? Each of the above criteria was rated as 0 (the study does not meet criterion) or 1 (the study meets criterion). In summary, all studies were rated as Low (score 1 or 2), Medium (score 3 or 4), and High (Score 5 or 6) following suggested guidelines by Cochrane collaboration.\n\nBased on the above criteria, five studies (Boivin et al., 2010; Casaletto et al., 2016; Fazeli et al., 2019; Fraser & Cockcroft, 2020; Livelli et al., 2015) had high-quality evidence. Six studies (Cody et al., 2020; Ezeamama et al., 2020; Frain & Chen, 2018; Ownby & Acevedo, 2016; Pope et al., 2018; Vance et al., 2012) had moderate-quality evidence, and three studies (Basterfield & Zondo, 2022; Cody et al., 2015; Zondo & Mulder, 2015) had low-quality evidence. Summary data for the quality assessment of each study are available as Extended Data (Zondo, 2023). The studies with low-quality ratings primarily presented with small sample sizes and had no follow-ups of at least three months post-intervention and presented large 95% CIs (e.g., Basterfield & Zondo, 2022; Zondo & Mulder, 2015). Expectedly, the studies with high-quality ratings implemented randomisation, including blinding research participants to group allocation, and had adequate follow-up assessments of at least three months post-intervention. Further indication for study quality and publication bias based on Cook's distances indicated that one study (Ezeamama et al., 2020) could be overly influential on the meta-analysis effect. Nonetheless, in terms of publication bias, neither the rank correlation nor the regression test indicated any funnel plot asymmetry (p = 0.6265 and p = 0.3459, respectively), but one study was identified with publication bias as indicated in Figure 4.\n\nNote: According to the funnel plot, only one study could indicate publication bias.\n\n\nDiscussion\n\nTo the author’s knowledge, this is the first meta-analysis to specifically investigate the efficacy of cognitive rehabilitation therapy as it pertains to brain training to remediate attention in neuroHIV. The nascent brain plasticity literature indicates intrinsic functional connectivity, particularly within the frontoparietal brain network, following attention and working memory cognitive rehabilitation training (Astle et al., 2015; Marek & Dosenbach, 2022; Spreng et al., 2010, 2013). Based on the scalability of attention and working memory cognitive training, the current meta-analysis found a small but significant effect (Hedges g = 0.25, p < 0.05) for the cognitive rehabilitation of attention following HIV acquisition, pre- and post-the rehabilitation.\n\nFindings from this meta-analysis are consistent with previous studies indicating the efficacy of cognitive rehabilitation to train and remediate attention skills in patients with attention deficit-hyperactivity disorder (ADHD) (Bikic et al., 2018; Wexler et al., 2021), autism (Spaniol et al., 2018), as well as children (Astle et al., 2015; Schrieff-Elson et al., 2017), and adults (Rosenbaum et al., 2018; Spreng et al., 2010) without ADHD. Nonetheless, despite the significant findings indicated in the overall meta-analysis regarding the efficacy of attention remediation in HIV, insignificant effects were noted on key sub-group moderator effects contrary to expectation.\n\nNoteworthy research (e.g., Azouvi, 2015; Shawn Green et al., 2019; Shoulson et al., 2012; Simons et al., 2016) indicate that multiple moderator effects, including methodological standards, such as the type(s) of the control group employed, randomization and blinding of subjects, and other contextual factors (the social environment of the rehabilitation), including the setting of intervention (group vs. individual rehabilitation) (das Nair et al., 2016; Lincoln et al., 2020), influence cognitive rehabilitation outcomes in brain training protocols.\n\nWithin the current meta-analysis, presumably, the null effect observed at the subgroup level may be a result of (a) the limited number of studies and the small number of participants in some of the studies, which might have resulted in insignificant findings being noted at the subgroup level. Secondary to the above, given the variegated nature of ‘attention types’ remediated in the various studies (i.e., sustained, selective, divided, and simple attention) may have led to a lack of uniformity in the analysis, despite controlling for, and applying the standardised mean difference (SMD) as suggested in the meta-analysis literature (Borenstein et al., 2009).\n\nThere continues to be a dearth of research investigating the efficacy of cognitive rehabilitation therapy in neuroHIV, and as such, there were limitations on the number of studies that could be included in the analysis. It is thus possible that the strict inclusion criteria (data points reporting ‘attention’ rehabilitation), permitted a weak interpretation of the treatment effect of the cognitive rehabilitation in the current study. The above observation is particularly significant, given that most studies investigating cognitive rehabilitation in the current era of neuroHIV have tended to focus on re-establishing cognitive functions related to ‘executive functions’, ‘working memory’, ‘processing speed’, and ‘aging’ (Vance et al., 2019). As such, in some studies (e.g., Ezeamama et al., 2020; Fraser & Cockcroft, 2020), the cognitive rehabilitation of attention was a secondary consideration to the study's main objectives (e.g., to remediate executive functions’ or working memory in neuroHIV).\n\nMoreover, considering the somewhat limited evidence base for the cognitive rehabilitation of attention in neuroHIV, the current study included data from both paediatric and geriatric HIV populations. Resultantly, the age-heterogeneous nature of participants may have affected the results as indicated by high 95% confidence intervals of some paediatric studies (e.g., Basterfield & Zondo, 2022). To this end, although research indicates that younger brains have a greater susceptibility to cognitive training compared to adult brains (Luria, 1970), conducting a meta-analysis on a composite ‘group’ (paediatric and geriatric) at different levels of brain plasticity may have resulted in different magnitudes of observed effects within the analysis. Additionally, as noted within the brain science literature (e.g., Boot et al., 2013; Simons et al., 2016), there continues to be a preponderance of cognitive rehabilitation studies to compare the effects of the cognitive intervention to passive, inactive controls. As noted by Boot et al. (2013), although this approach is expedient, it limits the vigorous interpretation of the ‘active ingredient’ within the rehabilitation and fails to control for the placebo effect that may be present within the intervention group. Significantly, the inclusion of ‘active control groups’, in brain research serves the dual purpose of mitigating the placebo effect and subsequently aids in matching perceived expectations of the cognitive rehabilitation within the treatment group. Unfortunately, none of the studies included in the meta-analysis had active control groups in order to match ‘the active ingredient’ within the intervention group in order to establish causal inference and treatment potency resulting from the intervention, resulting in a major limitation in the current meta-analysis.\n\n\nConclusions\n\nBased on the current body of literature, coupled with findings from the current meta-analysis, there appears to be reasonable evidence to suggest the efficacy of cognitive rehabilitation to remediate attention dysfunction in neuroHIV. Nonetheless, more studies are required to confirm these nascent findings, especially in contexts such as Sub-Saharan Africa, where the high incidence of HIV/AIDS continues to be a significant risk factor for HAND. Following a review of the HIV literature, the suggestions below should be considered when designing cognitive rehabilitation protocols in Sub-Saharan Africa (SSA) and other low-to medium-income countries with a high number of HIV cases.\n\nAlthough the reviewed literature indicates that random control trial studies incorporating individualized interventions coupled with intensive intervention protocols (i.e., 30 sessions of 30-45 minutes per session) (e.g., Frain & Chen, 2018; Fraser & Cockcroft, 2020) generate larger effect sizes, the nature of brain training intervention research tends to be taxing, time-consuming, and resource heavy, and tends to be associated with high attrition rates (Ballieux et al., 2016; Salkind, 2015; Schrieff-Elson et al., 2017).\n\nIt is thus suggested that future studies could benefit from adopting the Single Case Experimental Designs (SCED) to study the efficacy of CRT as it pertains to neuroHIV in SSA. The benefits of the SCED approach include in-depth rehabilitation sessions (30–45 min) with a limited number of participants (6-8) for prolonged periods of intervention. Their adoption could help mitigate high attrition rates often observed with paediatric intervention research, further improving the internal validity of neuroHIV rehabilitation studies.\n\nClosely linked to the above, due to the limited number of participants required in SCEDs, the adoption of SCEDs could help address research design limitations within the rehabilitation literature by enabling the incorporation of both active and passive control groups in the same analysis in so doing, enabling the evaluation of the ‘active ingredient’ within the treatment arm (Evans et al., 2014; Krasny-Pacini & Evans, 2018). Additionally, due to SCED’s individualised and meta-cognitive nature, these designs have the added benefit of incorporating shorter intervention sessions (15 minutes), interspaced with longer sessions (30-45 mins), thereby allowing for regular follow-up of shorter periods (two weeks), juxtaposed with longer follow-ups (four to eight weeks) (Evans et al., 2014; Krasny-Pacini & Evans, 2018; Manolov & Moeyaert, 2016) to evaluate the efficacy of neuro-rehabilitation protocols.\n\nThe reviewed literature further indicates that a limited number of studies report biological marker data, such as patient viral loads, before and after cognitive rehabilitation intervention. To this end, previous studies (e.g., Benki-Nugent & Boivin, 2019) have found that (a) people living with HIV with CD4+ T-cell counts lower than 500 cells/μL are more likely to indicate HAND. Conversely, data suggests that (b) participants with lower viral loads and higher CD4+ T-cell counts may experience significant benefits from cognitive rehabilitation therapy (Brahmbhatt et al., 2017). It is therefore recommended that future studies conducting cognitive rehabilitation in the era of neuroHIV, report objective bio-marker data, such as viral load data, to complement neuropsychological measures indicating changes due to the cognitive rehabilitation. In line with the above observation, it is recommended that cognitive rehabilitation studies further supplement post-rehabilitation findings with objective brain imaging techniques such as functional near-infrared spectrometry (fNIRS), EEGs or other affordable neuroimaging markers to ascertain the efficacy of brain training protocols.\n\nLastly, several of the reviewed studies highlight the evolving nature of HIV/AIDS, especially the fact that the neuropsychological and neurobiological sequelae of HIV differ from population to population (Brahmbhatt et al., 2017; Brew & Garber, 2018). Consequently, it is recommended that cognitive interventions implement context-specific population norms, paired with specific cognitive rehabilitation protocols, supplemented with specific objective biomarker evaluations (e.g., fNIRS or CD4 viral load data). These context-specific norms could form the blueprint for cognitive rehabilitation studies regarding expected trajectories or outcomes related to the implementation of cognitive rehabilitation protocols within the specific context of interest, for example, in SSA or other low to middle-income settings with a heavy burden of neuroHIV.", "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: The cognitive remediation of attention in HIV Associated Cognitive Disorder: A Meta-Analysis and Systematic Review, https://doi.org/10.6084/m9.figshare.22196833 (Zondo, 2023).\n\nThis project contains the following extended data:\n\n• Study Protocol.doc\n\n• Prisma Flow Diagram.pdf\n\n• Study Prisma Checklist.docx\n\n• Supplementary Materials.docx (Full Search Strategy, Relevant but Excluded Studies, Attention Outcome Measures, Study Quality Assessment)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe author acknowledges the assistance of three research assistants (Ms. Kate Solomons, Ms. Tatenda Chivuku, and Ms Nike Mes) in cross-checking all studies included in the meta-analysis. 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Reference Source\n\n\nFootnotes\n\n1 Within the extant literature, the terms ‘HAND’ and ‘neuroHIV’ are used concurrently to indicate cognitive impairment following HIV (Saloner & Cysique, 2017).\n\n2 CPE ranks all ARVs on four categories (a) physicochemical properties, (b) concentrations achieved in the CSF, (c) efficacy based on CSF virologic suppression, and (d) neurocognitive improvement (Letendre et al., 2008).\n\n3 Within the extant literature, the terms ‘cognitive rehabilitation therapy’, ‘cognitive-training intervention’, and ‘brain training’, are used interchangeably (Shawn Green et al., 2019; Simons et al., 2016), and this sequence will be equally applied in the manuscript.\n\n4 Valid measures of attention were cross checked and validated based on (Lezak et al., 2004; Strauss et al., 2006).\n\n5 Following personal correspondence with multiple authors, the blinding of assessors to the experimental condition was not possible in most cases due to (a) resource constrains, (b) limited time frames to conduct research, and (c) the pilot nature of most studies in the field." }	[ { "id": "272767", "date": "10 May 2024", "name": "David E Vance", "expertise": [ "Reviewer Expertise I am a psychologist who studies cognitive aging with HIV and conduct cognitive interventions in those with HIV." ], "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 appreciate the opportunity to review this well-written and thoughtful systematic review and meta-analysis on cognitive interventions to improve attention in people with HIV-associated neurocognitive disorder. The rationale for, and objectives of, the systematic review and meta-analysis are clearly stated. In the Introduction, the author clearly provided a compelling opening in the first paragraph and summarized the literature of how HIV impacts brain health leading to cognitive impairments in some individuals. I do think it is important to state however that most people with HIV do not experience such cognitive problems; sometimes when reading literature like this, it is important to provide this balance as the lay population may just assume this occurs in everyone and catastrophizes the scope of the problem. The author provides a succinct explanation of why non-pharmaceutical approaches to addressing cognitive impairment in people with HIV; this leads logically to the focus on cognitive rehabilitation (i.e., cognitive training) approaches as a burgeoning solution. Sufficient details of the methods and analysis are provided to allow replication by others. This systemic review and meta-analysis provide the accepted step-by-step methodology in which the studies were chosen, evaluated, and data analyzed. The cognitive rehabilitation studies had to examine some type of cognitive intervention (i.e., computer based, pencil and paper, hybrid) to determine if it was effective in producing meaningful change in attention scores in pre-post assessment. Diligence was applied to the selection of articles. Several search terms were used across databases (i.e., ERIC, Google Scholar, etc.) to locate potential articles that met eligibility criteria. The eligibility criteria (i.e., inclusion criteria) for selecting the articles was logical as it addressed the purpose of the research question. From this, 16 studies were included in the qualitative synthesis and 14 studies were included in the meta-analysis/quantitative analysis. Standard PRISMA and PICO rubrics were applied. It was not registered with PROSPERO, but it was registered on Protocols.io. I was not familiar with Protocols.io but this appears to be a way to share one’s more detailed methodology and have it publicly available. As I’ve worked with PROSPERO, it can very difficult and arcane to register studies and be rejected for unknown reasons; so, I am fine with this not being registered with PROSPERO as it is not always straightforward in knowing how or why it will take some registration of studies and not others as feedback is not provided. But I digress. A unique and laudable aspect of this meta-analysis is that it considered several key moderators into the meta-analysis. This is so desperately needed in the cognitive rehabilitation field already, but it was expertly applied in this article. In Table 2, such moderators included duration of training (<10 sessions; 10 sessions; >10 sessions), type of samples (paediatric HIV vs geriatric HIV), type of control group, and so forth. These moderation variables were all excellent, yet there might be some that are missing. For example, instead of duration of training measured in sessions, I would find it better to include hours of training instead of number of sessions. Yet, in the Discussion, this author argues, and I agree, that shorter sessions interspersed with longer sessions may be efficacious. I would argue further that the length of sessions should be self-directed by the participant who can better monitor his/her engagement, fatigue, and interest level; and thus, self-directed training of variable time periods may be more optimal for therapeutic benefit. Again, I digress. Other moderator variables that I would have liked to see include in person lab training vs at home training. I recognized that some of these studies might have required people to do the training in the lab while others were conducted at home or in community settings such as a library. Location of training may provide different benefits. In the lab setting, there is certainly less distraction from extraneous noise and daily interruptions which may allow one to focus more on the cognitive rehabilitation tasks, yet this is an artificial environment. Likewise, in the lab setting, one can usually reach out to research staff who can easily trouble shoot any technical difficulties that arise, especially with the computerized cognitive rehabilitation approaches. Yet, at home training may provide more flexibility and is a more ecologically valid place in which we as cognitive researchers want the rehabilitation to occur, that is to be put in the community and in the hands of those who need and would benefit from the intervention. It is not clear if these studies were conducted in the lab setting or if some were done in the community or more preferably for participants, at home. After the COVID-19 pandemic, globally we have grown accustomed to doing more things in the comfort of our homes as technology has expanded to accommodate this new reality; examining such cognitive interventions in the home environment would be a logical next step. Even if the studies in this review were not occurring in a home setting, providing such a discussion is warranted. There are three areas that I’m less clear after reading the methods, and that concerns: 1) HAND diagnosis, 2) type of attention training, and 3) type of attention performance measure. First, concerning HAND, the title states that these studies look at cognitive rehabilitation in those with HAND. There are a variety of methods to measure HAND, and studies have shown that different types yield different prevalence rates of HAND in the same sample. There is not much we can do about that, but in Table 1, or elsewhere, it may be helpful to say how HAND was measured in each of the studies as these obviously vary from study to study. Second, concerning type of attention training, I was uncertain if it was being argued that the cognitive rehabilitation studies were using interventions specifically designed to improve attention or were the studies targeting a specific cognitive ability (i.e., speed of processing) but the researchers happened to measure attention before and after the training that may or may not have been focused on improving attention specifically. I think it is fine either way, but perhaps it should be stated in Table 1 or elsewhere (supplemental file) what was being done in each study. And finally, it is not clear how attention is being measured in each study; it would be helpful to name the specific cognitive performance test for each study in which attention is measured. As neuropsychologists, sometimes we agree and often disagree on what we consider a specific cognitive performance test is measuring. I will not dive into splitting those hairs, but again, I think it should be reported in Table 1 or elsewhere. The statistical analysis and its interpretation are appropriate. These are typical approaches for conducting meta-analyses (i.e., forest plot, mean differences, funnel plot). With the funnel plot, I’ve not seen this done and I don’t do this with my meta-analytic studies but I might, but perhaps we can identify the dots to the particular study (although not necessary, just a thought). The subgroup analyses were certainly an added bonus of this meta-analysis; something I don’t see often. Kudos! The conclusions drawn are adequately supported by the results. There were no surprises; this made sense. I agree with the comments that braining training interventions can be fatiguing, time consuming, and prone to high attrition rates. As such, it does make me question whether attrition rates and completion rates of the intervention should be considered in Table 2 as one of the moderators. Otherwise, I whole heartedly agree that more research should be invested in this approach especially concerning examining its mechanistic properties using brain imaging; I would also suggest examining whether it changes neurochemical levels (i.e., BDNF, NfL) in the brain and periphery. Overall, this article is a welcome addition to the scientific literature on cognitive rehabilitation in neuroHIV. This article provides new methodological insights and considerations for future research.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Partly", "responses": [] }, { "id": "272773", "date": "21 May 2024", "name": "Antonio Lentoor", "expertise": [ "Reviewer Expertise NeuroHIV", "Cognition", "CNCD and Cognition", "Neuropsychology" ], "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 describes a systematic review and meta-analysis of published studies on an important topic relevant to the efficacy of cognitive rehabilitation intervention for attention remediation of HIV-associated cognitive disorders in the era of HAART.\nSimilarities and contrasts between the selected studies were found via the narrative synthesis. The results of the meta-analysis demonstrate the effectiveness of cognitive rehabilitation as an intervention for improving attention in HIV-associated cognitive disorders (HANDS). In the context of HAART, this is pertinent and helpful for the study of HIV and brain health, particularly in Africa. There is currently little systematic clinical suggestion or consensus regarding the interventions most suitable for this population in the African environment. As this study fills a vacuum in rigorous research evaluating the effectiveness of cognitive rehabilitation intervention, it further emphasizes the significance of cognitive rehabilitation interventions for this population and environment. The results point to crucial areas for more study, especially in the African context.\nGenerally, the study is conducted per the Cochrane Handbook guidelines, while the article is well-written in compliance with the standard reporting guidelines- PRISMA. The number of electronic database searches carried out was sufficient. Appropriate PICOS inclusion criteria were adhered to and in keeping with addressing the research aim. The results section answers the research question reliably and adequately. This is supported and presented in tables, and figures. The author considered several important moderating factors in the subgroup analysis (duration, type, setting of the rehabilitation), study design, data quality, population, and type of study group to establish the effect size of interventions. The study also measured for heterogeneity (with a graphical forest plot illustration) of the intervention based on the Q statistic in the meta-analysis. A total of 14 studies were included for analysis. Quality assessments of these studies were also conducted, reflected in narrative text. In addition, a funnel plot with a symmetrical visual illustration is suggestive of minimal detected bias.\nI do not find any major concern in the article; I believe it is worth the approval. No further changes are required from my point of view.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1133
https://f1000research.com/articles/12-1129/v1	11 Sep 23	{ "type": "Case Report", "title": "Case Report: Acute peritonitis inaugurating Crohn's disease with spontaneous perforation in the peritoneal cavity", "authors": [ "Anis Belhadj", "Fahd Khefacha", "Ahmed OMRY", "Med Dheker Touati", "Ahmed Saidani", "Faouzi Chebbi", "Anis Belhadj", "Ahmed OMRY", "Med Dheker Touati", "Ahmed Saidani", "Faouzi Chebbi" ], "abstract": "Background: Crohn's Disease is a chronic, idiopathic, and transmural inflammatory condition that mainly affects the distal ileum. It is characterized by intricate pathophysiology and numerous complications, some of which can be fatal. In this report, we present a case study of acute generalized peritonitis resulting from the perforation of a distal ileal loop, inaugurating the diagnosis of Crohn's disease. Case presentation: A 43-year-old patient presented with a clinical presentation of acute peritonitis. He had a one-year history of intermittent abdominal pain and diarrhea. As the maximum pain was in the right iliac fossa, an acute appendicitis complicated with peritonitis was considered and the patient underwent laparoscopic exploration, without morphologic exploration. Peroperative observation found an inflamed conglomerate of small bowel loops associated with sclerolipomatosis, and purulent peritonitis by perforation of a distal ileal loop, 40 cm from the ileocaecal valve. A peritoneal toilet, ileocaecal resection, and ileo-colostomy were performed. The postoperative course was uneventful.\nDiscussion: Various complications may arise during the evolution of Crohn’s disease. However, fatal complication such as generalized peritonitis leading to the diagnosis is rare. The underlying pathophysiology of free perforation remains unknown. The most common site affected is the terminal ileum. The surgical treatment is based on a limited resection of the affected bowel segment, followed by a temporary stoma. A primary anastomosis can be performed in selected patients. Conclusion: Perforative peritonitis as an initial presentation of Crohn's disease is challenging. Surgery is obviously required for acute peritonitis, with limited resection with or without anastomosis.", "keywords": [ "Crohn", "Emergency", "Surgery", "Laparoscopy", "Inaugural", "Small bowel", "Peritonitis", "Appendicitis" ], "content": "Introduction\n\nCrohn’s disease (CD) is a chronic transmural inflammation that can affect the gastrointestinal tract from the mouth to the anal margin.1 Inaugural spontaneous perforation with generalized peritonitis is infrequent and potentially life-threatening occurrence.2 Herein, we present a case study of acute generalized peritonitis caused by the perforation of a distal ileal loop, leading to the diagnosis of Crohn's disease.\n\n\nCase presentation\n\nA 43-year old man presented to the emergency department with a one-day history of abdominal pain and vomiting. There were no signs of bowel obstruction or fever. The patient had no medical or surgical history, and was a non-smoker. He reports paroxysmal abdominal pain and diarrhea for the last year.\n\nOn examination, his temperature was 37.4 °C and generalized abdominal tenderness were noticed. The maximum pain was at the level of the right iliac fossa. Hemodynamic state remained stable, and the respiratory rate was normal.\n\nLaboratory data showed elevated white blood cell count (18500/mm3) and C-reactive protein level (140 mg/l). The results of the serum electrolyte and kidney function tests were normal.\n\nAcute appendicitis complicated with peritonitis were considered and the patient underwent urgent laparoscopic exploration, without morphologic exploration.\n\nThe peroperative exploration of the abdominal cavity found a free purulent fluid caused by a perforation in the anti-mesenteric border at the distal ileum (Figure 1), 40 cm from the ileocecal valve. Furthermore, we observed the presence of an inflammatory-looking conglomerate of small bowel loops associated with sclerolipomatosis (Figure 2 and 3). Terminal ileal loop, caecum and appendix were grossly normal. Due to poor exposure conditions, we decided to convert to a midline procedure.\n\na: Specimen after resection, (the yellow asterisk shows the sclerolipomatosis), b: Appearance of the perforation before resection.\n\nAn abundant peritoneal toilet with serum salin and ileocaecal resection carrying out 50 cm of bowel were performed. Remaining bowel length was estimated at 4.5 meter. An ileo-colostomy in the right iliac fossa was performed.\n\nThe post-operative course was uneventful. First oral intake was allowed since the first post-operative day. The patient was discharged on the fifth postoperative day.\n\nThe histopathological analysis of the specimen revealed a chronic granulomatous ileitis lesions, which are indicative of Crohn's disease.\n\n\nDiscussion\n\nCrohn's disease is a chronic inflammatory disease of unknown origin that has the potential to impact the entire gastrointestinal tract from the mouth to the anus.2 Although, the terminal ileum and colon are the most frequently involved areas.3 The transmural characteristic of Crohn's disease (CD) can lead to localized perforation, which has the potential to progress rapidly into generalized peritonitis.1 Free perforation of the small intestine in the peritoneal cavity is a rare and serious complication in Crohn's disease (CD).4\n\nThe originality of our case lies in the fact that peritonitis secondary to ileal perforation was inaugural, leading to the diagnosis of Crohn's disease.\n\nThe diagnosis of acute peritonitis can be considered on physical examination.4 However, the challenge of conducting etiological investigations is particularly pronounced, especially given the absence of supportive findings in the medical history for Crohn's disease.5 In our case, paroxysmal abdominal pain and diarrhea suggest Crohn's disease and a CT scan could be performed to better support the diagnosis. However, the surgery was obviously required, regardless of the scan features. For this reason, the patient underwent a laparoscopic exploration without any morphological investigations.\n\nPerforative peritonitis as a primary manifestation of Crohn's disease is very rare, and occurs in 1 to 3 % in general population.2,4 However, The CONNECT retrospective cohort Korean study reported a higher incidence of 6,5% which is similar to a Japanese meta-analysis result.2,3,6\n\nAmong the reported cases of perforation in various literature, the most frequently site affected is ileum, particularly the terminal ileum (80%).2,4 Less frequently involved locations consist of other segments of the ileum, the colon, and the jejunum.2,4\n\nThe precise mechanism behind the occurrence of free perforation in Crohn's disease remains unidentified. However, many risk factors may be incriminated such as anti TNF therapy or significant distension upstream of a stenosis.3,4\n\nSurgical treatment involves performing a limited resection of the affected segment of the bowel, followed by either a primary anastomosis or a temporary stoma.3 In this particular case, considering the peritoneal contamination, an ileocecal resection with a stoma was performed.\n\n\nConclusion\n\nAlthough Crohn’s free perforation in the peritoneal cavity is infrequent, it should be kept in mind especially in front of suggestive features.4 Timely diagnosis and prompt treatment significantly enhance the prognosis.5 Surgery is obviously required for acute peritonitis, with limited resection with or without anastomosis.\n\n\nConsent\n\nWritten informed consent to publish this case and associated images was obtained from the patient.", "appendix": "Data availability statement\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare. CARE checklist. DOI: 10.6084/m9.figshare.23904546.\n\n\nReferences\n\nFreeman HJ: Spontaneous free perforation of the small intestine in adults. WJG. 2014; 20(29): 9990–9997. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDoh YS, Kim YS, Bae SI, et al.: The clinical characteristics of patients with free perforation in Korean Crohn’s disease: results from the CONNECT study. BMC Gastroenterol. 2015; 15(1): 31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChirantan B, Niladri S, Madhumita M, et al.: Crohn’s Perforation: Not so Uncommon in the Indian Population. Indian J. Surg. 2013; 75(1): 28–30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaddad A, Ben Mahmoud A, Chaker Y, et al.: Presentation with perforation of the terminal ileum and acute limb ischemia in Crohn’s disease: A case report. Int. J. Surg. Case Rep. 2021; 80: 105626. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu B, Lin C, Yang Y, et al.: Spontaneous Perforation in Crohn’s Disease: A Report of Two Cases. Inflamm. Bowel Dis. 2022; 28(3): e40–e42. PubMed Abstract \| Publisher Full Text\n\nIkeuchi H, Yamamura T: Free perforation in Crohn’s disease: review of the Japanese literature. J. Gastroenterol. 2002; 37(12): 1020–1027. PubMed Abstract \| Publisher Full Text" }	[ { "id": "263820", "date": "11 Apr 2024", "name": "Muhammad Z. Ali", "expertise": [ "Reviewer Expertise Colorectal 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\nThank you very much for giving me opportunity to do peer review of this case report titled “Case Report: Acute peritonitis inaugurating Crohn's disease with spontaneous perforation in the peritoneal cavity”. Young patient presented first time with free ileal perforation and turned out to be Crohn's disease. It’s a good effort however I have following comments.\n\nSpontaneous perforation is rare although but no novelty in this case. Even I have question in title.(title should be revised)\ncase Hx is not available in detail. Spontaneous perforation always happened when background disease becomes really symptomatic. No detailed lab work especially renal penal, electrolytes and albumin available. X ray abdomen erect is mandatory whenever any acute abdomen is suspected supported by CT abdomen. Decision of diagnostic laparoscopy should always be after complete morphological investigations when clinician failed to find any road map. How the patient and family was counseled? before surgery.\n\nHow much was quantity of purulent fluid in peritoneal cavity, was there any stricture in the small bowel. If there is perforation there must be some stricture and upstream dilatation. Why surgery not completed laparoscopically. Need to add picture of histopathology to support diagnosis of crohn disease.\n\nDiscussion is not focusing how many times and ways spontaneous crohn perforation presented first time without any background disease symptoms. What author think reasons to justy his claim of spontaneous perforation as first presentation in this case without prior background Hx of abdominal symptoms. Need to add relevant references.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] }, { "id": "285058", "date": "21 Jun 2024", "name": "Ved Prakash", "expertise": [ "Reviewer Expertise GI surgery", "Laparoscopic Surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a good report of uncommon and serious presentation of a common condition. However, few details are required to make it more useful for readers.\n1. The condition of terminal ileum (which seems to be disease free) is not mentioned in detail. The disease free length of TI from ileocaecal valve is important to preserve as much functional bowel as possible in view of the suspected diagnosis i.e. Crohn's. This would have implication of making a safer anastomosis ( if adequate and good quality bowel is available ) compared to an Ileo-colic anastomosis. 2. Although a hindsight comment, we do check the remaining bowel ( and document) for any external features of disease to guide future therapy based on extent of involvement and suggestion to our Gastro-enterology colleagues. 3.Since being performed in contaminated field, mention of method of anastomosis is paramount ( hand sewn, how many layers, suture used or stapled anastomosis) 4. few typographical errors need to be amended - last 3 paragraphs needs revision and spell check 5. A passing mention of value of pre- operative CT imaging can be made if deemed helpful. However, given relatively younger age and male patient it may not entirely be required.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1129
https://f1000research.com/articles/12-1128/v1	11 Sep 23	{ "type": "Research Article", "title": "The discourse of organizational resilience before and after the global pandemic", "authors": [ "Budi Harsanto", "Egi Arvian Firmansyah", "Egi Arvian Firmansyah" ], "abstract": "Background: Over the past decade, there has been a surge in public and academic discussions about organizational resilience, particularly in the wake of the coronavirus disease (COVID-19) pandemic. It is essential to understand the changes in the discourse of organizational resilience before and after the pandemic. This study aims to understand how the concept of organizational resilience evolved before and after the pandemic. Methods: This study is qualitative in nature, employing discourse analysis techniques on scholarly documents on organizational resilience. Our analysis considers the global context of organizational resilience discussions and highlights the most frequently discussed industries, such as tourism and hospitality, manufacturing, and healthcare. The documents were searched on Scopus academic databases with the key search term of organizational AND resilience. Results: Our findings indicate that themes related to \"response to external threats\" and \"supply chain vulnerabilities and disruptions\" have gained significant attention post-pandemic. Meanwhile, discussions around \"preparedness and organizational reliability\" and \"coping with occupational and job demands\" have remained consistent before and after the pandemic. Conclusions: This study contributes to the academic understanding and practical application of organizational resilience evolution by discourse before and after the pandemic. It highlights the significance of being prepared for external threats and managing supply chain disruptions while recognizing the importance of preparedness and organizational reliability.", "keywords": [ "discourse analysis", "organizational resilience", "pre and post-pandemic" ], "content": "Introduction\n\nThe coronavirus disease (COVID-19) pandemic has profoundly impacted business activities and organizations worldwide (Setiawan et al., 2023). Many researchers in business and management fields have also documented various findings related to COVID-19, as presented in a study by Harsanto and Firmansyah (2023a). Furthermore, the concept of resilience, or the ability to endure adverse circumstances, has gained increased recognition and attention in the management field, particularly in the context of crisis management. The term resilience was first commonly used in reference to how well society can respond to and recover from natural disasters (Bohensky & Leitch, 2014). Despite this increased attention, in the context of organizational resilience, the definition and understanding remain evolving and inconsistent, with different authors emphasizing different aspects such as capacity, capability, or outcomes (Duchek, 2014; Hillmann & Guenther, 2021).\n\nOrganizational resilience is crucial in facing disruptions and challenges, as leaders must respond effectively to maintain and grow their businesses (Denyer, 2017). The pandemic represents a severe test of a firm’s ability to adapt and become stronger in adverse situations. Firms need to quickly learn and adapt to seize opportunities, intending to bounce back effectively and avoid prolonged downturns, even if they experience short-term setbacks (Teo et al., 2017).\n\nThe concept of organizational resilience has gained more attention recently, particularly after the outbreak of the COVID-19 pandemic in 2020. However, there has been a lack of research comparing the development of the concept before and after the pandemic. The pandemic, an extraordinary event considered one of the worst global events since World War II, has significantly impacted organizations and their ability to adapt and bounce back in the face of adversity. Understanding how the discourse of organizational resilience has evolved before and after the pandemic would be valuable for academics and practitioners in the field. It would provide insights into how organizations have responded to the unprecedented challenges posed by the pandemic and how they have worked to enhance their resilience.\n\nTherefore, this study aims to understand how the concept of organizational resilience evolved before and after the pandemic. The study seeks to answer the following research questions: (1) In which industries was the concept of organizational resilience used before and after the pandemic? (2) What themes in organizational resilience have received increased attention before and after the pandemic? (3) How has the discourse surrounding each theme changed before and after the pandemic?\n\nThe contribution of this study lies in its ability to provide an understanding of how the discourse of organizational resilience has evolved before and after the global pandemic. In addition, by examining the industries in which the concept was used and the themes that received increased attention, this study offers insights into how organizations have responded to the unprecedented challenges posed by the pandemic.\n\nThe implications of this study are significant for both academics and practitioners in the field of organizational resilience. For academics, the findings of this study can serve as a basis for further research and development of the concept. For practitioners, the insights from this study can be applied in practical settings to enhance their organization resilience and ability to respond to future disruptions. The results of this study can also inform public policy decisions aimed at improving the resilience of organizations in the wake of future pandemics or other disruptive events.\n\nThis paper is structured as follows: the next section describes the methodology used to search for datasets and the analytical techniques used. The study results are presented in the third section, followed by a discussion in the fourth section. The last section is implications and further directions.\n\n\nMethods\n\nThis study is qualitative in nature, employing discourse analysis techniques on scholarly documents of organizational resilience (Leitch & Bohensky, 2014). Discourse analysis is one technique of literature review. Data in this study are academic documents published by publishing slots, such as journals, conference proceedings, and book chapters. The search for documents for this study’s dataset was conducted on July 5, 2022. The scholarly dataset in this study was obtained from the Scopus (RRID:SCR_022559) database. Scopus and Web of Science are two comprehensive academic databases that are currently market leaders. In this study, we utilized Scopus due to its comprehensive coverage, which is more extensive than other databases (Harsanto, 2020; Harzing & Alakangas, 2016). Scopus is widely recognized as the world’s largest abstract citation database of scholarly literature (Schotten et al., 2017).\n\nDuring our search, we used the search term “Organizational AND Resilience” so that both terms were inseparable. In the initial search using: “TITLE (organizational AND resilience),” 584 documents were retrieved. The TITLE was used to obtain articles relevant to the topic under investigation straightforwardly. Further refinement was performed using “TITLE (organizational AND resilience) AND (LIMIT-TO (SUBJAREA, “BUSI”) OR LIMIT-TO (SUBJAREA, “ECON”)),” which meant we focused only on the subject areas of Business and Economics, resulting in 273 documents (Harsanto & Firmansyah, 2023b). Finally, after selecting only articles written in English, the search yielded 262 documents. Therefore, the inclusion criteria in this study were as follows:\n\n• Articles mentioning the phrase ‘organizational resilience’ in the title.\n\n• Articles included in business and economics areas.\n\n• Articles in the English language.\n\nOther articles not meeting those three criteria were excluded from this study. The overall methodological process is similar to previous studies (Harsanto & Firmansyah, 2021; Jan et al., 2022). The process is shown in Figure 1.\n\nWe manually read the article title and abstract to ensure that all documents were related to organizational resilience. Furthermore, limiting to business or economics subject areas was expected to provide better relevancy by resulting in only the documents discussing organizational resilience in business and economics settings. Omitting documents in other areas, such as engineering, medicine, and computer science, provided relevant documents in business and economics contexts. The obtained dataset (CSV format) was then converted and processed in an Excel spreadsheet for data cleaning and coding to produce research findings.\n\nThe data of this study were analyzed in three different ways: descriptive statistical analysis, discourse analysis, and comparison analysis. First, descriptive statistics were used to understand two things: the industry context in which organizational resilience is applied (Table 1) and document types (Table 2). We used Microsoft Excel (RRID:SCR_016137) in Microsoft Office 365 software to produce these descriptive statistics, allowing us to tabulate each category. Abstract reading was performed to categorize the industry type, while Scopus data were used to categorize the document type of the selected documents.\n\nIn the second analysis, a discourse analysis, similar to Leitch and Bohensky, was used to examine the term “organizational resilience” in 262 documents. Discourse analysis is appropriate to select because it allows us to see the shift in organizational resilience studies before and after the pandemic. Specifically, discourse analysis provides information on how the term ‘organizational resilience’ is used in those two different points in time.\n\nIn the third analysis, which is the development of the second analysis, we mapped and compared the selected documents before and after the pandemic (Leitch & Bohensky, 2014). We considered publications before 2020 to be before the pandemic, and 2020 onwards were after the pandemic. In particular, the analysis of the selected documents focuses on seven key themes of organizational resilience identified in Denyer’s report (Denyer, 2017). We further produced a framework depicting the shift in the organizational resilience studies available in the literature between before and after the pandemic.\n\n\nResults\n\nThe term “organizational resilience” is used in different industries. As shown in Table 1 (Harsanto & Firmansyah, 2023b), most of its use in previous studies was in mixed-industry analysis (51.15%), which involved more than one industry in one study. The three industries that individually receive the highest attention in studies on organizational resilience are tourism and hospitality (9.54%), manufacturing (6.115%), and healthcare (5.34%). The industry that experienced a rapid increase in academic attention when the pandemic hit was tourism and hospitality, which was indeed one of the industries that experienced the worst impact due to the imposition of restrictions on mobility and restrictions on activities involving many people.\n\nThere have been diverse document types published in organizational resilience documents, as shown in Table 2. This study did not limit to only one or two types of documents because we expected to obtain heterogeneous information about organizational resilience from various publication types, thus enhancing the findings of this study. Furthermore, this study revealed that organizational resilience was primarily found in journal articles, with more than 75%. This percentage was higher than other types of research documents, such as conference papers (6.11%), books (2.67%), and book chapters (8.02%). It also indicated that organizational resilience had been documented in high-quality document types because journals require a peer-review process to filter the documents before publication.\n\nTable 3 shows the percentage of publications on organizational resilience before and after the pandemic. The themes in the table were adopted from Denyer’s report on organizational resilience (Denyer, 2017). From the analysis, it can be seen that both before and after the pandemic, the theme that received the highest attention was “preparedness and organizational reliability”, followed by “coping with occupational and job demands”. By contrast, the theme that received the least attention was “Ensuring IT/IS/cybersecurity”. It indicates that some studies are more general on organizational resilience or the impact on work in various areas of the organization instead of focusing on specific areas of IT with specific threats such as cyberattacks.\n\nWhen comparing before and after the pandemic, the highest percentage increase was on the theme “Response to external threats,” followed by “Supply chain vulnerabilities and disruptions.” This is understandable because the pandemic, which was a great shock to organizations, made organizations worldwide struggle, and they were looking for the best response to these unexpected and highly impactful events. That makes publications regarding organizational responses to external threats has the highest percentage because these publications allow for observations of immediate impacts to be carried out directly. Among those severely shaken by the COVID-19 pandemic were supply chains due to lockdown policies, mobility restrictions, and other policies, especially at the beginning of the pandemic, which was full of uncertainty. The summary of organizational resilience discourse before and after the pandemic is shown in Table 4.\n\nCOVID-19, coronavirus disease.\n\n\nDiscussion\n\nThe study results show how organizational resilience was discussed before and after the pandemic in diverse industries. The themes discussed in the literature have also been shown in various publications, grouped into seven main themes, which are then identified as the discourse that occurs in each theme, as shown in Table 4. The discourse in each of these themes is then discussed in more detail in the following subsections.\n\nThe number of studies on organizational resilience in response to external threats has increased since the COVID-19 pandemic. Before 2020, studies on organizational resilience in this theme were limited to one main sub-theme: organizational response to nature-based exposure and disasters. For instance, some studies focused on natural disasters, including climate change and extreme weather (Tisch & Galbreath, 2018), and floods (Bang et al., 2019). Nature-based exposure deals with climate change, which is considered a severe issue for companies, for it affects how a business entity will determine products and approach its customers. Mitigating natural disruptions can be aided by using a decision support system to help minimize the impacts (Gumbira & Harsanto, 2019).\n\nMoving forward in 2020 and beyond, numerous organizational resilience studies relate to the COVID-19 pandemic. This sub-theme is dominant and found in more than ten papers of our dataset. For instance, a study by Herrero and Kraemer (2022) examines how non-profit fundraisers dealt with a sudden decline in financial revenue during the pandemic by creating strategic ways of raising money. Furthermore, during the pandemic, Țiclău et al. (2021) interviewed ten female leaders from the non-profit and private sectors, revealing that government regulation, support, and financial pressures have been the major organizational challenges regardless of the sector. By contrast, the organizational dimension seems to impact the ability to adapt and respond to adversity. One study further discovered that organizational resilience and leadership skills play a crucial role in how well private higher education institutions succeed, even in times of crisis like the COVID-19 outbreak (Zahari et al., 2022). Based on our review of this theme, it can be implied that COVID-19 has even attracted more researchers to study organizational resilience, thus contributing to this literature using profit- and non-profit-oriented entities.\n\nPreparedness and organizational reliability\n\nThis study’s results reveal that the theme of preparedness and organizational reliability contributes most to the dataset. Furthermore, the proportion of this theme before and after the pandemic is relatively balanced. The studies conducted before the pandemic deal with various topics related to the preparedness and organizational reliability theme, such as the significance of emergency planning for enhancing business resilience (Crichton et al., 2009), employee stock ownership and employee governance involvement for boosting resilience (Lampel et al., 2014), and building organizational resilience train through balancing organizational structures (Andersson et al., 2019). We also found studies with an emphasis on corporate social responsibility (CSR) embeddedness (Lamprinakis, 2019) and strategic human resource management (Al-Ayed, 2019), which contribute to organizational resilience.\n\nIn 2020 and beyond, studies on this theme have incorporated the COVID-19 pandemic as one of the research settings. For instance, in a study by Yang et al. (2021) employing the retail industry in China, it was uncovered that various factors, such as supply chain, digital construction, improvisational capability, and CSR had a positive role in responding to the COVID-19 outbreak. Meanwhile, Orth and Schuldis (2021) put forward organizational learning by implementing an open system culture to enable employees to withstand adversity, such as the COVID-19 pandemic. Furthermore, Rai et al. (2021) emphasize the essence of having the capability to predict the crisis and build robustness and recoverability since they positively affect the social and economic aspects of firm sustainability. In addition, an organization’s reliability during a crisis is also affected by its business network and social capital (Chowdhury et al., 2019; Ozanne et al., 2022).\n\nThe theme of ‘coping with occupational and job demands’ shows a balanced proportion between before and after 2020. Studies on this theme before 2020 are dominant on the general topics related to the role of conducive organizational culture (Ahiauzu & Ololube, 2017) and sound psychological condition (Cho et al., 2017) in fostering firm resilience. Other topics related to the relationship of various factors with organizational resilience are also present, such as citizenship behavior (Paul et al., 2019), organizational learning (Abu-Tineh, 2011), and human resource practices (Bustinza et al., 2019).\n\nLike the previous themes, in 2020 onwards, the studies on ‘coping with occupational and job demands’ also mix with the COVID-19 context. For example, a study by Fathy El Dessouky and Al-Ghareeb (2020) proposes that an organization must support its workforce to be resilient in a dynamic environment such as an outbreak. Furthermore, using a case study of Geneve airport in Switzerland, a study by Romig (2021) emphasizes the importance of assessing the current contingency plans and devising fresh strategies to lessen the enormous operational and financial effects of the unheard-of circumstance, such as COVID-19 pandemic. In the context of the hotel industry, a study by Prasongthan (2022) revealed that organizational resilience positively affects employee engagement in the company, even during the outbreak, which implies that companies must explore various ways to enhance their employees’ resilience.\n\nThis theme relates to various efforts made by organizations to recover themselves from unwanted circumstances, such as crises. Our dataset on this theme also shows a balanced proportion before and after the pandemic. Before 2020, the studies on this theme primarily discussed various efforts made by organizations to build resilience through the implementation of business reputation continuity (Koronis & Ponis, 2012), information and technology optimization (Chewning et al., 2012; Mazini, 2014), dynamic capabilities (Jiang et al., 2019), the implementation of strategic human resource management (Bouaziz & Smaoui Hachicha, 2018), relational leadership (Teo et al., 2017), and affect and team leadership (Sommer et al., 2016).\n\nThe theme in 2020 and beyond certainly captures the COVID-19 outbreak because it has altered how organizations view their current strategies to stay competitive. A dominant topic on this theme relates to the essence of organizational learning. For instance, a study by Zhou and Sun (2020) focuses on a red teaming strategy to encourage organizational learning and resilience. Using Huawei company as a case study, they argued that the red teaming strategy helps Huawei learn from its industry counterparts and ensures that the company operates robustly in the face of a challenging external environment. Furthermore, a study on the primary care sector conducted by Schuttner et al. (2021) reveals that developing organizational learning and firm resilience may be a helpful step in implementing continuous quality improvement agenda within a company. Besides, a brief paper by independent authors reports that focusing on organizational learning at the individual, group, and collective levels can help a company become more resilient in the face of adversity and turn potentially destructive situations into beneficial sources of opportunity (“How Organizational Learning Increases Organizational Resilience: Build Multi-Stakeholder Networks to Strengthen the Effect,” 2020). Future discussions on renewal and strategic ability can connect resilience and sustainability or its specific aspects, such as sustainability innovation. Organizations can strategically build a strong foundation for long-term success, reduce risk exposure, and enhance their ability to adapt to change (Harsanto et al., 2018; Harsanto & Permana, 2021).\n\nThis theme experienced an increase before and after the COVID-19 pandemic compared to other themes. The supply chain is one of the areas that has been severely disrupted and has produced many publications that examine the impact of the pandemic on the supply chain, predictions of future disruptions, and various steps to build supply chain resilience for organizations (Nikolopoulos et al., 2021). The discourse that occurred on this theme before and after the pandemic was the focus of general pre-pandemic investigations on natural disasters with topics related to safety performance indicators (Rigaud & Martin, 2014), the influence of culture and resilience on supplier risk levels (Borekci et al., 2014; Mandal, 2017), resilience to the buyer-supplier relationship (Yilmaz Borekci et al., 2015), vulnerabilities as a consequence of the currently developing global supply chain (Stafford & Bouwens, 2016), as well as the influence of supply chain agility and resilience towards performance (Altay et al., 2018). Regarding supply chain vulnerabilities due to global operations, Stafford and Bouwens (2016), for example, investigate how the flood in the case of Intel in Thailand or the fire in New Mexico significantly impacted the company’s supply chain globally.\n\nWhile after the pandemic, the focus of this theme is on vulnerabilities and disruptions due to the COVID-19 pandemic in diverse industrial contexts, such as healthcare (Hundal et al., 2021) and Small and Medium Enterprises (SMEs) (Banerjee et al., 2022). The challenges of the pandemic have encouraged the birth of publications that contribute to building a culture of resilience within organizations, such as stakeholder partnerships, systematic sharing, and rapid responses, including the Strategic Management of Organizational Resilience (SMOR). Classic techniques such as Lean Six Sigma can also be used to build resilience (Hundal et al., 2021). Apart from that, organizational ambidexterity, which is concerned with balancing exploitation and exploration along with solid collaboration, is also an effort to build supply chain resilience and agility in the long term (Küffner et al., 2022).\n\nThis theme was discussed in the literature before and after the pandemic with relatively the same intensity and tended to decrease slightly (-0.95%). Before the pandemic, the discussion in the publications was about building resilience, especially in the area of information systems in dealing with the risk of cyberattacks to the organizations that invest in hardware and software in their information systems, by identifying various potential sources for IS vulnerabilities at various levels, starting from individual to organizational. Various tools and strategies were developed to increase organizational resilience in various cyber-attack phases, including recovery, access gain, escalating privileges, system browsing, and installing additional tools (Bouwens & Stafford, 2019). This topic is also related to industry 4.0, marked by the cyber-physical environment (Nica, 2019).\n\nAfter the pandemic, this discourse theme is still about resilience in dealing with cyberattacks, with the possibility of bigger cyberattacks equivalent to the challenges of the COVID-19 pandemic. The direction of the discussion is regarding globalization characterized by super-high connectivity, making IT and company operations efficient and vulnerable simultaneously. Here, enterprise security risk management (ESRM) as a security management approach emphasizing collaboration between business and security professionals becomes essential in mitigating existing risks (Marquez-Tejon et al., 2022). In organizations, the need for resilience is also considered by standardization institutions such as ISO, which is reflected in ISO 22316, defining organizational resilience with the keywords absorb and custom in changing environments. Resilient organizations can anticipate and respond appropriately, including allocating the right resources to various internal and external threats (Bennett & Lemoine, 2014).\n\nThis theme did not experience an increase during the pandemic compared to before the pandemic. Of course, in terms of the period, it is not comparable between before the pandemic (before 2020) and after the pandemic (2020 onwards). However, several other themes in a short time (2021-2022) reveal that publications can exceed what happened in the past or before the pandemic. In line with other themes, the discourse on this theme before the pandemic was more directed toward efforts to build resilience in dealing with disruptions from the natural environment. This conceptualization is carried out from various perspectives, for example, from the organization’s capacity, which includes cognitive behavioral and contextual (Lengnick-Hall et al., 2011), business model innovation (Müller et al., 2018), and layers of micro, meso, macro (Luo & Shi, 2011) in various natural disasters such as floods, hurricanes or heat waves (Linnenluecke et al., 2012). This conceptualization is necessary because the needs for resilience in each organization are different. Resilience is highly imperative for high-reliability organizations (HROs) such as hospital or fire department units (Ishak & Williams, 2018). The proposed concept, for example, is the Resilience Architecture Framework (RAF), which consists of ambidexterity, dynamic capabilities, rigidity (Limnios et al., 2014), or three dimensions of resilience, including anticipation, coping, and learning (Duchek, 2014), or the three aspects or organization resilience including power structure, actions, language (Witmer, 2019). Resilience conceptualization is also carried out with other related concepts such as adaptation, change, networks, systems, social capital, or vulnerability (Hall et al., 2017).\n\nAfter the pandemic, the definition and conceptualization of resilience continued with a discourse emphasis on the need for severe disruption due to COVID-19. The proposed framework, for example, includes the mindset and action elements needed to build resilience in one of the sectors worst affected by the pandemic: tourism and hospitality (Ho et al., 2022). This sector is also sensitive during the pandemic to disruptions originating from natural disasters (Chowdhury et al., 2019; Prayag et al., 2020). With the right mindset and action, it is expected that the organization will be able to bounce back and undergo a fast recovery. Indeed, this is a difficult challenge because of the different shock intensities in volume, velocity, or variety (Cruickshank, 2020). Resilience is considered a meta-capability consisting of various individual constructs that go through various stages of crisis (Duchek, 2020). Among the interesting conceptualizations is the effort to measure resilience using quantitative measures involving time windows and counter-factuality (Ilseven & Puranam, 2021).\n\nFigure 2 illustrates the discourse summary before and after the pandemic. Among the seven analyzed themes, each has distinct discourse but with a common theme of pre-pandemic focus on resilience to natural disasters, while post-pandemic discourse has shifted to the challenges posed by the COVID-19 pandemic.\n\nCOVID-19, coronavirus disease.\n\n\nImplications and future directions\n\nThis study is of interest to both academics and practitioners. Academically, this study advances knowledge of organizational resilience by providing a discourse analysis before and after the pandemic. Before the pandemic, researchers focused primarily on natural disasters such as floods or fires, with pandemics receiving little attention. However, the pandemic has since garnered significant attention, substantially impacting the global socio-economic landscape. Practitioners and policymakers can direct efforts to build organizational resilience in the face of diverse types of disruptions, including huge ones like pandemics.\n\nThis study has several limitations that open up avenues for future research. First, the study finds that the main focus of attention in this area is on a few sectors and suggests that future research should pay more attention to other sectors, such as retail, construction, or textile, which have not yet received much attention. Second, technically, the academic document search in this study was limited to the Scopus database, which may result in some academic documents being overlooked. Future studies could complement the Scopus database with other academic databases. Third, since this current study only employs a search strategy on the title field, future studies may use a broader search strategy by adding abstract and keyword fields.\n\nFurther, future discourse studies can build upon the themes discussed in this study by exploring each of these themes in greater depth. For example, future research can focus on the evolution of resilience conceptualization before and after the pandemic and beyond. Besides, quantitative studies employing statistical analysis may also be conducted in future studies to gain insight into organizational resilience.", "appendix": "Data availability\n\nFigshare: 273 document results Organizational Resilience.csv., https://doi.org/10.6084/m9.figshare.23567103 (Harsanto & Firmansyah, 2023b).\n\nThis project contains the following underlying data:\n\n- 273 document results Organizational Resilience.csv (The dataset contains 273 list of documents indexed in Scopus mentioning “organizational resilience” in either title, keyword, or abstract. The dataset is specific on business and economics fields only.)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbu-Tineh AM: Exploring the relationship between organizational learning and career resilience among faculty members at Qatar University. Int. J. Educ. Manag. 2011; 25(6): 635–650. 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Publisher Full Text" }	[ { "id": "227892", "date": "15 Dec 2023", "name": "Naglaa Fathy El Dessouky", "expertise": [ "Reviewer Expertise Public Policy Analysis and Evaluation", "Management Sciences", "Organizational studies", "Sustainability", "Virtual Organizations." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general, the article tackled an important up to date topic. The paper succeeded in presenting a thorough literature review about the topic. The paper employed an adequate research methodology. However, it was not very reliable that the authors search for documents for the study’s dataset in only one day stated on July 5, 2022. Moreover, the authors’ search in Scopus focused only on Business and Economics without providing detailed arguments about the reason of selection while other dataset can be an asset for the study such as Management and Public Policy. The study succeeded in presenting the results and discussion in a systematic way. The author may improve the implications of the study by providing a concrete action plan for the public policy makers and the management of organizations.\n\nIs the work 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": "247507", "date": "20 Mar 2024", "name": "Diego Polanco-Lahoz", "expertise": [ "Reviewer Expertise Organizational Resilience in Higher 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\nSummarized, the paper analyzes using thematic analysis the change in trends and how was understood Organizational Resilience in the media and other sources, before and after the COVID-19 pandemic. The thematic analysis shows that most vulnerabilities are related to the supply chain and that preparedness is an important topic to consider. This helps the literature by giving value and a time-lapse to the changes in understanding of Organizational Resilience. I think the paper is good. It does not offer a breakthrough of new ideas or concepts, but papers such as those analyzing the change of conceptualization and how people understand topics are also important. The methodology used is precisely good. Thematic analyses are needed when the data to be analyzed is qualitative, and in this case, this was the vast majority. The only enhancement I could see is the motivation behind it. When studies talk about COVID-19 is clear where the motivation comes through, but also many of those types of drafts do not state explicitly why the proposal study is important. As a researcher in the field, I get it, but not all readers are researchers with years of reading in the field. Besides that, detail, and some formatting issues, the paper is good for approval. I hope the authors are proud of the work done! Shown in detail, the introduction shows a great starting point for an Organizational Resilience (OR) standpoint just before COVID-19. The awareness grew even higher when the pandemic was at its peak. The major point to consider in this section is the origin of the concept. Future papers trying to go beyond the literature and explore the origin of OR should be aware of initial management theories as well as the ecological perspective of resilience. The methodology section is good, and I have used similar phrases when looking for the data. The only detail that readers should be aware of is the software tool to analyze data. When researchers find thousands of words and results, a better approach could be using NVivo with its internal tool of thematic analysis. The results are shown perfectly in detail, I cannot include anything in this section that has not been shown. The tables presented help to understand the idea of each paragraph. In the discussion, all sections are very well presented, the only major point is related to the definition of OR. It seems logical that the discussion needs to present information derived from the methodology results, but the topic of OR conceptualization goes beyond 2022 which is the last study specified. If we consider the literature there are multiple ways to conceptualize OR: as a process (Duchek, 2020), as a static capability (Chen et al., 2021), or as an outcome (Ilseven and Puranam, 2021). These three perspectives are currently my primary focus of research related to OR. Future literature will converge when the phenomena of OR understanding can be classified more clearly, and that will be the time to consider which approach is better depending on the context that is being seen. Things such as the stated before are needed for the reader to consider if OR is part of their research goal. Again, going over the details of definitions and obvious phenomena derived from understanding OR in all its extensions, the paper is very good and helps literature with the understanding before and after COVID-19. Very good job!\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1128
https://f1000research.com/articles/12-1124/v1	11 Sep 23	{ "type": "Study Protocol", "title": "Evaluating the reliability of the sickling test and peripheral blood film method for screening of sickle cell disease: a study protocol", "authors": [ "Tejaswini Bawane", "Sahitya Vodithala", "Sahitya Vodithala" ], "abstract": "Background: Mutations in beta-globin are the cause of a widespread condition known as sickle cell disease (SCD). Sickle cells cause organ damage, hemolysis of blood cells, weakness, and sometimes even death. SCD can be effectively managed and mortality can be reduced through early detection. This protocol’s study aims to evaluate the sensitivity and specificity of the sickling test, peripheral blood smear, and hemoglobin electrophoresis for SCD screening. Methods: In this study,75 cases of SCD will be selected. 5ml blood will be drawn into a dipotassium ethylenediaminetetraacetic acid tube for testing of SCD. Testing will involve: the sickling test, where an equal volume of K2EDTA blood will be mixed with 2% sodium metabisulfite; the peripheral blood smear, where Leishman’s stain will be placed on a thin film of blood for 2 minutes; and Hb electrophoresis, where equal parts of distilled water and packed cells will be combined and then the mixture will be centrifuged. Results: We will be comparing between the sickling test and the peripheral blood film method, and we will conclude depending upon the results as to which test is better. Conclusions: Using peripheral blood smear images, SCD can be quickly diagnosed. A peripheral smear-based differential diagnosis may be possible but requires special tests such as hemoglobin electrophoresis to confirm the diagnosis. Therefore, early diagnosis can help initiate transfusion therapy and create a better prognosis.", "keywords": [ "Sickle cell disease (SCD)", "Anemia", "Sickling test", "Peripheral blood smear", "Hemoglobin electrophoresis." ], "content": "Introduction\n\nRed blood cells contain a pigment called hemoglobin, which carries oxygen to the tissue.1 Defective hemoglobin structure is the cause of the hereditary blood disorder known as sickle cell disease (SCD).2 In the year 1910 Herrick first described the sickle shaped red blood cell (RBC).3 A multisystem disease termed sickle cell anemia (SCA) is associated with acute illness and progressive organ damage.4\n\nPoint mutations cause SCA. In codon 6 of the HBB gene, which encodes a subunit, adenine is switched out for thymine (GAG > GTG). Nucleotide substitution has occurred. Hemoglobin S (Hgb S) is produced as a result of an amino acid change in which valine takes the place of glutamic acid. Sickle cells become rigid and less soluble when Hgb S polymerizes in anoxic conditions.4,5 Hemolyticanemia is the result of this, which hastens cell death and reduces cell life by about 75%.6\n\nAnaemia is not a diagnosis, but a finding that needs additional investigation. Anaemia is defined as a reduction in hemoglobin concentration below the lower limit of normal with regard to age and gender. In addition to low hemoglobin levels, a few other parameters should be taken as well when researching anemia. The initial investigations for these individuals begin with red cell indices, red cell count, and morphological evaluation of peripheral blood film.7\n\nThis disease is common in the tribal population of central India including Andhra and Telangana. The frequency of the sickle cell gene in the Indian population varies from 2-3.5 %.8\n\nThough hemoglobin electrophoresis is the gold standard for diagnosis of SCD, peripheral smear examination remains an invaluable tool in preliminary diagnosis in unsuspected cases and those in sickle crisis.9 Early diagnosis, complete treatment, and general medical care have increased the life expectancy of patients with SCD in developed countries. Early detection, therefore, helps in effective disease management.10\n\nSickle cell disease is a hemoglobinopathy caused by a point mutation in the ß globin gene that leads to the production of hemoglobin S, which polymerizes under deoxygenated conditions and causes red blood cells (RBCs) to form a sickle shape.11–13 Sickle RBCs result in hemolysis, vaso-occlusive pain crises, acute chest syndrome, post-operative infections, congestive heart failure, cerebrovascular accident and endothelial damage.14 Of all the screening tests used for screening cases of SCD, the sickling test is the most commonly used. However, these basic screening tests are plagued by a lot of disadvantages which may range from technical to human errors. The changes in the edge, location, shape, and size of the cells make blood film analysis extremely difficult. A computerized approach has been created as a result to provide a simple technique for identifying the type of anemia. The peripheral blood smear is an imperfect test, It is a formative hematological test that depends on the pathologist’s skills, and there aren’t many skilled pathologists to choose from. Haemoglobin electrophoresis, on the other hand, does not suffer from all these disadvantages and gives accurate results. Hemoglobin electrophoresis is the gold standard for the diagnosis of SCD. The routine protocol followed in the diagnosis of SCD is to do a screening test first and then go for a confirmatory test thus delaying the final diagnosis. The present study aims to employ both these tests for the screening cases of SCD and reliability with each other. Employing a superior diagnostic test will greatly reduce delays in diagnosing cases of SCD to a considerable extent.15\n\nRecently, many studies have been done on techniques for the detection of SCD. Wjdan A. Arish et al.in (2021) studied the various prospective approaches that could be used to aid in the early identification of SCD, as well as the present and new methods for sickle cell disease detection.16\n\nEmmanuel Gbenga Dada et al.’s (2022) study reported that traditional methods for diagnosing SCD are expensive, error-prone, time-consuming, and necessitate the help of medical professionals. The development of affordable and controllable methods for the early identification and diagnosis of SCD is thus required immediately.17\n\n\nProtocol\n\nTo evaluate the reliability of the sickling test and peripheral blood film method for screening of sickle cell disease.\n\n\n\n1. To evaluate the sensitivity and specificity of the sickling test, peripheral blood smear, and hemoglobin electrophoresis for SCD screening.\n\n2. To diagnose SCD on peripheral blood smear examination.\n\n3. To screen for SCD of sickling.\n\nThis will be a descriptive, laboratory-based, observational and comparable study.\n\nEthical approval for the study was obtained from the institutional ethics committee of Datta Meghe Institute of Higher Education and Research (Deemed to be University) (ref. No: DMIHER (DU)/IEC/2023/24), date of approval: 21/07/2023. A written participant information sheet will be given regarding the details of the study, and it will be explained to participants before enrolment in the study. Their involvement benefits and harms will be explained to the participants. Written informed consent from the participants will be obtained before involving them in the study.\n\nThe following study will be conducted in the Department of Pathology (Central Clinical Laboratory), AVB Rural Hospital, Sawangi Meghe (Wardha), India.\n\nInclusion criteria\n\n1. Patients aged 6 months – 60 years who present with anemia.\n\n2. Patients willing to participate in the study.\n\nExclusion criteria\n\n1. Patients aged <6 months ad >60 years.\n\n2. Patients with multiple blood transfusions within three months of screening for SCD.\n\n3. Patients who are not willing to participate in the study.\n\nPotential participants will be selected on the basis of their chief complaints such as clinical anemia, any bone pain, family history along with complete blood count report and peripheral blood examinations suggesting hemolytic anemia. After that, we will do the sickling test and the correlation with peripheral blood examination will be done. If the sickling test is positive, then we will do Hb electrophoresis which will confirm type of hemolytic anemia on the basis of presence of abnormal hemoglobin such as HbS. This will further confirm the type of hemolytic anemia as sickle cell anemia (SCA). Informed consent will be obtained prior to participation in the study. The patient will be comfortably seated and a blood sample will be taken under aseptic precautions. 5ml blood will be drawn into a dipotassium ethylenediaminetetraacetic acid (K2EDTA) tube through a standard central cubital vein, for testing of SCD.\n\nAll patients will be examined further for\n\n1. Sickling test\n\n2. Peripheral Blood smear\n\n3. Hemoglobin electrophoresis\n\nSickling test\n\nThe sickling test’s basic method depends on microscopic observations of red blood cells (RBC) that are exposed to low oxygen tension or start to swell. An equal volume of EDTA blood will be mixed with 2% sodium metabisulfite. A drop of blood and a mixture of reagents will be taken on a glass slide. A cover slip will be placed over it, and the four corners will be sealed with wax and the slide will be observed under a microscope for presence of any sickle shaped red blood cells if any (40x) after 2, 4, and 24 hrs.\n\nPeripheral blood smear\n\nThe peripheral blood smear (PBF) examines the blood cell’s morphology and evaluates any microscopic alterations, which can offer useful information that helps in the diagnosis of SCD.\n\nThe method is as follows: the smear will form a thin film of blood. Allow it to air dry, and then place it in a staining rack. Leishman’s stain will be placed dropwise on the slide and left for 2 minutes. This allows the determination of PBF in methyl alcohol. Add a double volume of buffered water dropwise to the slide and let stand for 8 minutes and then rinse in water for 1 to 2 minutes. Air dry and examine under the oil immersion lens of a microscope.\n\nHemoglobin electrophoresis\n\nEqual parts of distilled water and packed cells will be combined and then the mixture will be centrifuged. As a sample, this hemolysate will be used. Medium 2% agarose gel pH 8.6 with Tris/EDTA/borate (TEB) buffer will be used. The basic idea behind this method is based on the fact that proteins can be positively or negatively charged based on the amino acids that are normally charged.\n\nThe positively charged proteins will move to the cathode when an electric field is applied to a solution containing protein molecules, and vice versa. Different hemoglobin will separate and migrate at different rates depending on their charges, size, and shape. Following this, bands are stained and their color concentration is scanned in comparison to known controls.\n\nAll necessary measures to control bias at all levels will be taken. As it is an observational study, all the samples which are routinely received in the section of hematology will be taken into consideration for comparison between the Hb electrophoresis technique analogous to the routine sickling test. Institutional supply of EDTA samples and chemical constituents present in a buffer from different companies make minor modifications, essential part of Hb electrophoresis protocol. Diagnostic search influences the finding of electrophoresis sickling band.\n\nDaniel’s formula for sample size\n\nWhere,\n\nZ∝2 statistics for a level of confidence (for the level of confidence of 95%, which is conventional, the Z value is 1.96) = 1.960\n\np = prevalence of sickle cell anemia = 5 % = 0.05\n\nD = desired error of margin = 6% = 0.06\n\nn is the no. of patients is 72.99\n\nn=72.99\n\n=75patients needed in the study.\n\nFormula reference: Daniel et al. (1977).18\n\nPrimary outcomes\n\nWe will observe any sickle shaped red blood cells under the microscope which can be easily seen in case of sickle cell disease (SCD) patients, but gold standard for diagnosis of SCD is always hemoglobin electrophoresis which shows the percentage of HbS hemoglobin on its report.\n\nExpected outcome\n\nTo evaluate the sensitivity and specificity of the sickling test, peripheral blood smear, and hemoglobin electrophoresis for SCD screening.\n\nSPSS version 23.0 will be used to conduct the statistical analysis. A p value of 0.05 will be regarded as significant. The mean distribution of inhibition zones will be documented as part of the descriptive analysis. Patient and repeated measures will be analysed using ANOVA.\n\nThe results will be published in an indexed journal.\n\nThe study is set to start in September 2023.\n\n\nResults\n\nThe results will inform healthcare professionals and policymakers about the effectiveness of these methods and contribute to improved screening strategies for early detection and management of sickle cell disease.\n\n\nDiscussion\n\nThe screening techniques include the sickling and peripheral blood film examination. We will collect the blood samples and we will evaluate these for validity of the sickling test and peripheral blood film. Clinical anemia is present in patients ranging from age 6 months to 60 years till now.\n\nSickle cell disease is the most common a single-gene disorder correlated with recurrent episodes of intense ailment and myeloproliferative. Herrick originally recognised SCD in a Chicago-based West Indian patient with anemia and heart disturbances in 1910.3 After he published his paper describing the sickle-shaped haemocyte, Pauling determined the deformity of hemoglobin in SCD and invented the term “molecular disease” in 1949.19\n\nIndia forms a major part of all worldwide cases of sickle cell anemia (SCA).1\n\nA study conducted by A. L. Okwietal (2010),‘The Reliability of Sickling and Solubility Tests and Peripheral Blood Film Methods for Sickle Cell Disease Screening at District Health Centers in Uganda’, reported that sensitivity estimations for the tests of solubility and sickling were 65.0% and 45.0%, respectively, while the peripheral film had a 35.0% sensitivity. There were 95.6%, 90.0%, and 96.7% specificities for sickling, solubility, and peripheral film, respectively. Sickling received a diagnosis of 92.5% accuracy, 85.5% solubility, and 90.5% of peripheral film. Cohen’s Kappa for sickling was 0.6, solubility was 0.3, and peripheral film was 0.4. Turnaround time for the sickling test was 38 minutes, solubility was 70 minutes, and peripheral was 44 minutes.15\n\nFalse-positive results occur when the test indicates the presence of SCD when it is not actually present, leading to unnecessary concern and follow-up testing. False-negative results occur when the test fails to identify individuals with SCD, delaying necessary interventions and treatment.\n\nThe reliability of the sickling test and peripheral blood film method may vary with the age of the individual being tested. Some infants with SCD may not show symptoms or positive test results immediately after birth, leading to potential delays in diagnosis. The accuracy of both methods is highly dependent on the technical expertise of the personnel performing the tests. Improper sample collection, preparation, or interpretation can lead to inaccurate results. Distinguishing between sickle cell trait (SCT) and SCD is essential, as individuals with SCT are carriers of the gene but typically do not experience symptoms or complications. Both screening methods may not always differentiate between SCT and SCD.\n\nThe quality of the blood sample used for testing can impact the accuracy of the results. Factors such as hemolysis or contamination can affect the reliability of the tests.\n\nSickling method confirms abnormal hemoglobin presence, while peripheral blood smear reveals sickle-shaped red blood cells, aiding the diagnosis of sickle cell disease and assessing disease severity.\n\nPeripheral smear and sickling evaluation offer a reliable and widely applicable method for diagnosing hemoglobin disorders in the general population.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: STROBE checklist for ‘Evaluating the reliability of the sickling test and peripheral blood film method for screening of sickle cell disease: a study protocol’. https://doi.org/10.5281/zenodo.8199129\n\n\nAcknowledgments\n\nWe would like to thank our institute and colleagues. We acknowledge the support of Sonali Jakkulwar in the conceptualisation and preparation of this manuscript.\n\n\nReferences\n\nGorakshakar AC: Epidemiology of sickle hemoglobin in India. In Proceeding of the National Symposium on Tribal Health 2006 Oct 19. (pp. 103–108).\n\nDisorders of hemoglobin structures and synthesis. de Gruchy’sClinicalHaematology in Medical Practice. 5th edition.Oxford University Press; 1990; 171–87.\n\nHerrick JB: Peculiar elongated and sickle-shaped red blood corpuscles in a case of severe anemia. 1910. Yale J. Biol. Med. 2001 May; 74(3): 179–184. PubMed Abstract\n\nKato GJ, Piel FB, Reid CD, et al.: Sickle cell disease. Nat. Rev. Dis. Primers. 2018 Mar 15; 4(1): 1–22. Publisher Full Text\n\nNagel RL, Johnson J, Bookchin RM, et al.: Β-Chain contact sites in the hemoglobin S polymer. Nature. 1980 Feb 28; 283(5750): 832–834. PubMed Abstract \| Publisher Full Text\n\nBenesch RE, Kwong S, Benesch R: The effects of α chain mutations cis and trans to the β 6 mutation on the polymerization of sickle cell hemoglobin. Nature. 1982 Sep 16; 299(5880): 231–234. PubMed Abstract \| Publisher Full Text\n\nBee R, Srivastav AK: TO DETECT HEMOGLOBINOPATHIES BY DOING HEMOGLOBIN ELECTROPHORESIS IN MICROCYTIC HYPOCHROMIC ANEMIA. European Journal of Molecular & Clinical Medicine. 2021; 7(09): 2020.\n\nPomburg T, Ha SSJ, Wells IL: Sickle Cell Anemia, a Molecular Disease. Science. 1949; 110: 543–548. Publisher Full Text\n\nKrishna OR, Bapanpally N, Fatima SS, et al.: Quantification of Sickle Cells in the Peripheral Smear as a Marker of Disease Severity in Sickle Cell Disease in Paediatric Patients. J. Med. Sci. 2023 Jan; 9(1): 104–109. Publisher Full Text\n\nLubeck D, Agodoa I, Bhakta N, et al.: Estimated life expectancy and income of patients with sickle cell disease compared with those without sickle cell disease. JAMA Netw. Open. 2019 Nov 1; 2(11): e1915374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJadhav U, Babu R, Ghewade B, et al.: Acute chest syndrome, a distinctive manifestation in sickle cell disease–A case study. J. Datta Meghe Inst. Med. Sci. Univ. 2020 Jul 1; 15(3): 492–494. Publisher Full Text\n\nVarma A, Vagha J, Agrawal A, et al.: Sociodemographic determinants in prevalence of anemia in adolescents of rural area of Maharashtra. J. Datta Meghe Inst. Med. Sci. Univ. 2020 Apr 1; 15(2): 209–214. Publisher Full Text\n\nMithra P, Khatib MN, Sinha AP, et al.: Interventions for addressing anemia among children and adolescents: an overview of systematic reviews. Front. Pediatr. 2021 Feb 16; 8: 549549. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgrawal S, Deshmukh P, Deshmukh P, et al.: Anesthetic Management of Patients with Sickle Cell Disease Posted for Bipolar Prosthesis. Indian. J. Forensic Med. Toxicol. 2020 Oct 1; 14(4).\n\nOkwi AL, Byarugaba W, Parkes A, et al.: The reliability of sickling and solubility tests and peripheral blood film method for sickle cell disease screening at district health centers in Uganda. Clinics in Mother and Child Health. 2010 Oct 6; 7(1): 1–5. Publisher Full Text\n\nArishi WA, Alhadrami HA, Zourob M: Techniques for the detection of sickle cell disease: a review. Micromachines. 2021 May 5; 12(5): 519. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDada EG, Oyewola DO, Joseph SB: Deep convolutional neural network model for detection of sickle cell anemia in peripheral blood images. Communication in Physical Sciences. 2022 Mar 8; 8(1).\n\nDaniel et al. (1977).\n\nPauling L, Itano HA, Singer SJ, et al.: Sickle cell anemia, a molecular disease. Science. 1949; 110(1): 543–548. Publisher Full Text" }	[ { "id": "242309", "date": "13 May 2024", "name": "Brian D. Adkins", "expertise": [ "Reviewer Expertise Clinical transfusion medicine", "blood banking", "academic pathology", "DEI", "hematopathology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 protocol describing Hemoglobin S screening. There are several points which require attention. Please see detailed explanation below.\nIntroduction: Please focus content of introduction on what is being investigated in this study. Please remove general paragraph about anemia, as the specialized audience will be aware of the described information. Line 1 – please refer to hemoglobin as an oxygen containing molecule that gives RBCs their red color. Calling hemoglobin, a pigment is too reductive. Also please use a PubMed indexed reference. Rationale Line 1 – this repeats the information contained in paragraph 2 of introduction. Please incorporate most of this data into the introduction and focus this section on the rationale. Third sentence first paragraph: please include examples of false positives/negatives from package insert. “There aren’t many skilled pathologists to choose from” too colloquial, remove/reword please. Finally, would point out that some countries, such as the USA have routine newborn screening for SCD and other hemoglobinopathies. Discussion “Clinical anemia is present in patients ranging from age 6 months to 60 years till now” not true, please remove. Generalizability We don’t know if these tests are generalizable because the study has not been completed. Please reword to reflect that.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/12-1124
https://f1000research.com/articles/12-1123/v1	11 Sep 23	{ "type": "Research Article", "title": "Quantum data communication protection with the quantum permutation pad block cipher in counter mode and Clifford operators", "authors": [ "Michel Barbeau" ], "abstract": "Background: This article integrates two cryptographic schemes for quantum data protection. The result achieves authentification, confidentiality, integrity, and replay protection. The authentication, integrity, and replay aspects leverage quantum Clifford operators. Confidentiality of quantum messages is achieved using the quantum permutation pad (QPP) cryptographic scheme. Methods: Clifford operators and the QPP are combined into a block cipher in counter mode. A shared secret is used to seed a random number generator for the arbitrary selection of Clifford operators and quantum permutations to produce a signature field and perform encryption. An encryption and signature algorithm and a decryption and authentication algorithm are specified to protect quantum messages. Results: A symmetric key block cipher with authentication is described. The plain text is signed with a sequence of randomly selected Clifford operators. The signed plaintext is encrypted with a sequence of randomly selected permutations. The algorithms are analyzed. As a function of the values selected for the security parameters, there is an unavoidable risk of collision. The probability of block collision is modelled versus the number of blocks encrypted, for block sizes two, three, four, and five qubits. Conclusions: The scheme is practical but does not achieve perfect indistinguishability because of the risk of message collision. This is normal and unavoidable when fixed-size fields are assumed to make a scheme practical. The model can be used to determine the values of the security parameters and the lifetime of session keys to mitigate the risk of information leakage according to the needs of the scheme’s users. The session key can be renewed when a tolerable maximum number of messages has been sent.", "keywords": [ "Clifford operator", "quantum permutation pad", "quantum communication", "quantum network", "security", "confidentiality", "encryption." ], "content": "Introduction\n\nClassical communications and networks, such as sonars, cellular networks, and the Internet, use the macroscopic properties of acoustic, electromagnetic, or light waves. In contrast, quantum communications use the microscopic properties of light. For instance, using an appropriate encoding, the quanta of light, called a photon, is used for quantum data communications. Each photon represents a quantum value. Applications of quantum communications include secret communications, quantum networking, and distributed quantum computing. Quantum networks are envisioned for quantum communications across long distances. A quantum network comprises links, repeaters, routers, and terminals. Nodes combine classical memory and quantum bit (qubit) memory. They have classical and quantum computing capabilities. Links are the communication channels, which may be classical or quantum. Applications of quantum networks encompass communications and computation. Quantum communications and networking enable the transfer of quantum states from one location to another. They permit pooling quantum computation resources to solve complex and distributed computing issues.\n\nAs with classical data, quantum data is vulnerable to various attacks.1–6 Quantum data needs to be protected. Fundamental properties are authenticity, confidentiality, integrity, and replay protection.7–9 We focus on the authenticity, confidentiality, integrity, and replay protection of quantum messages. An authenticity attack deceives the destination about the trustworthy source of a message.7,9 Mitigating the authenticity attack requires a proof of the source identity in a message. Confidentiality protection mitigates the risk of disclosing or leaking information contained in messages. Confidentiality protection is achieved by ciphering plaintext messages. An integrity attack modifies the content of a message. In the quantum setting, this modification on a quantum state \|ϕ⟩ takes the form of a unitary transformation U. The state \|ϕ⟩ is modified by U. Mitigating this attack requires a modification detection mechanism. In the quantum setting, a replay attack in the classical sense is not possible because of its non-cloning property. However, an adversary can delay the delivery of a message or, when it knows how, can recreate the state. Mitigating this attack requires a mechanism to ensure that a message is new. Classical computing uses a digital signature to address authenticity, integrity, and replay attacks, possibly combined with a nonce field or a timestamp. This signature mechanism cannot be used in the quantum world in the classical sense.7 Indeed, generating a digital signature in the classical sense requires reading the message content and generating a corresponding signature value using, for instance, a one-way hash function. Reading the content of a quantum state, i.e., measuring, is destructive. However, in the following, we use the signature concept with the understanding that it is not obtained by calculating a value that involves measuring the content of a quantum message.\n\nThe article includes one main result. It presents a quantum data protection scheme that achieves all these properties, acknowledging that, at least in the short term, qubit bandwidth is narrow. Such protection schemes need to be lightweight (few additional qubits are required to implement a security scheme). The solution integrates two existing cryptographic schemes: Clifford-operator based authentication9 and quantum permutation pad (QPP).10 In this context, lightweight means that few additional qubits are required to implement a security scheme. Confidentiality is achieved using quantum permutations while authenticity, integrity, and replay protection are obtained using quantum Clifford operators. While this new protection scheme benefits from the security analyses developed for the two cryptographic schemes that it uses, the article takes the investigation further by combining a collision probability analysis, Clifford-operator-based authentication, the QPP symmetric-key encryption, and the block counter mode to create a quantum data protection scheme.\n\nWe review related work and introduce relevant quantum information background. We present and analyze the original quantum data block cipher and authentication scheme.\n\n\nRelated work\n\nThe work presented in this article is about protecting quantum data using quantum resources. It is a topic that has received attention in the research literature, as discussed in this section. Work can be categorized into two groups: authentication and confidentiality.\n\nBarnum et al. introduced an authentication scheme for quantum data, considering their specific nature, and defined the concepts of completeness and soundness in this context.7 Foundations for cryptographic schemes for authentication have been proposed by Aharonov et al.11 and Broadbent and Wainewright,12,13 building on quantum Clifford operators. This work has been used to build an authenticity, integrity, and replay protection scheme for quantum messages by Barbeau et al.,14,15 with demonstrated soundness and completeness, and to analyze attack probability. Other quantum data authentication efforts include the work of Das and Siopsis,16 building on a position authentication protocol, and Satoh et al.,17 building on the concept of quantum state tomography.\n\nFor confidentiality, asymmetric and symmetric encryption schemes have been proposed by Alagic et al.18 and St-Jules,19 using Clifford operators. Efforts have been devoted to adapting the Advanced Encryption Standard (AES)20 to the quantum environment.21–23 A challenge is the amount of required quantum resources. In the short term, the available quantum computers have low quantities of memory and high error probabilities in comparison to classical computers. New lighter-weight quantum encryption schemes requiring fewer quantum resources have been proposed.24–26 Kuang and Barbeau introduced a universal symmetric encryption scheme called QPP.10 The scheme can be used in several ways in classical and quantum environments.\n\nIn this article, we propose and analyze a symmetric key encryption scheme for blocks of quantum data. Building on our previous research,9,10 a general symmetric-key cipher is developed building on QPP in counter mode. Conditions are identified to achieve perfect indistinguishability. Use cases are also identified where perfect indistinguishability is not achieved, but where the probability of collision is low. As emphasized in,10 the QPP scheme can be considered for both classical data and quantum data. In companion papers, we developed a QPP block cipher scheme in counter mode for classical data adapted specifically for the underwater environment.14,15 For the encryption aspect, this article parallels this work for quantum data for a general quantum networking environment. More related work is cited in the following sections.\n\n\nQuantum information background\n\nIn the quantum computing model, the unit of information is called the quantum bit (qubit). Mathematically, using the Dirac ket notation \|⟩, the Boolean values zero and one are represented, with the matrix-form equivalent, as\n\nKet zero, i.e., \|0⟩, and ket one, i.e., \|1⟩, are the standard computational basis states. A qubit can be in both states \|0⟩ and \|1⟩ at the same time. A qubit is in a continuum of intermediate states. These intermediate states are called a superposition. A superposition is represented as a unit vector in a complex vector space. Let α and β be two complex numbers, with the constraint that [1]\n\nThe term \|ψ⟩ reads as ket ψ. The factors α and β are the probability amplitudes associated with each state, i.e., \|0⟩ and \|1⟩. In other words, we do not know in which state a qubit is. According to the probabilistic model of Equation (3), however, the actual measurement of a qubit yields \|0⟩, i.e., Boolean value zero, with probability α2 and \|1⟩, i.e., Boolean value one, with probability β2. The matrix format is a convenient alternative equivalent representation of the linear superposition of a qubit:\n\nThe two coefficients α and β are organized in a one-column, two-row vector. A qubit state that can be written in the form of Equation (4), that is, in the column-vector form, is called a pure state. A qubit is a two-dimensional entity. Using probability amplitude α, the first dimension defines the 0 information component. Using probability amplitude β, the second dimension defines the 1 information component.\n\nQubits can be composed together. For instance, a two-qubit register consists of a superposition of the four states \|00⟩, \|01⟩, \|10⟩, and \|11⟩, i.e., the four possible two-bit binary values. Together with the corresponding probability amplitudes α, β, γ, and δ, the two-qubit linear superposition is\n\nAll α, β, γ, and δ are complex numbers with the constraint that α2+β2+γ2+δ2 is equal to one.\n\nIn general, a n-qubit quantum register is a 2n-term expression of the following form\n\nThe computational basis is the orthogonal basis\n\nA n-qubit quantum register is a 2n-dimensional entity. The ith dimension, using probability amplitude ψi, defines the ith information component, with i=0,1,2,…,2n−1. Both the summation form and equivalent column-vector form are shown. In the summation form, the plus sign is conjunctive, rather than disjunctive. In the quantum-superposition model, all terms in the summation exist simultaneously. One can also appreciate the memory complexity of simulating the quantum computing model with a classical one. A n-qubit register requires the storage of 2n probability amplitudes. For instance, the memory complexity of a 10-qubit register is in the order of kilobytes, a 20-qubit register is in the order of megabytes, and a 30-qubit register is in the order of gigabytes.\n\nThe 2n probability amplitudes are organized in a one-column, 2n-row vector in the column-vector form. The ket notation \|⟩ reflects the vectorial nature of a qubit or a quantum register. The term ket ψ can be interpreted as a mapping to a column vector of the corresponding probability amplitudes:\n\n\nQuantum data block cipher and authentication scheme\n\nWe first briefly review the highlights of Clifford-operator-based authentication, QPP encryption, and the block counter mode. Then, we define original source and destination algorithms for authenticated and confidential quantum data communications.\n\nThe following four matrices constitute the Pauli operators:\n\nOver the n-qubit quantum states, the Pauli matrices Pn are the set of all 2n by 2n matrices resulting from tensor products like P1⊗P2⊗…⊗Pn, where P1,P2,…,Pn are Pauli operators. The set Pn has 22n. Pauli matrices form a group. Hence, they can be interpreted as operators mapping Pauli matrices to Pauli matrices.\n\nThe set Pn∗ contains all the Pauli matrices in Pn excluding the identity matrix I⊗n. The set U1 represents the set of all complex numbers modulo one. That is, U1 is equal to ejθ:θ∈ℝ, with j equal to −1. The set U2n represents all the 2n by 2n unitary matrices. Given a unitary C, its conjugate transpose C†, and a Pauli matrix P, the expression CPC† is the conjugation of matrix P by unitary C.\n\nOver the n-qubit quantum states, the set of Clifford operators is defined as\n\nA Clifford operator is a bijection mapping Pauli matrices in Pn∗ to Pauli matrices in Pn∗, through the action of conjugation. The suffix /U1 implies that two Clifford operators, different solely because of a factor in U1, are considered equivalent. The set Cn has 2n2+2n∏i=1n4i−1 elements. In the following, we refer to it as \|Cn\|.\n\nLet us consider the n-qubit orthonormal computational basis defined in Equation (6). Let V be the vector space where every element of it can be expressed as a linear combination of members of this basis. The elements of the symmetric group S2n are permutations over the set V. The degree of the group S2n is 2n. It is of order 2n!. This means that there are 2n! permutation operators. In the following, we refer to them as \|S2n\|. Each of them can be represented by a 2n by 2n matrix Pi, where i=1,…,2n!. Note that every permutation Pi is a bijective function from the set V to itself. Furthermore, the inverse of Pi, denoted as Pi−1, is also contained in the symmetric group S2n.\n\nA plaintext M is made of m vectors v0,v1,…,vm−1 in V. QPP encryption of plaintext M uses a sequence π of m randomly selected permutations corresponding to the list P0,P1,…,Pm−1, all selected in group S2n. The sequence π is the encryption key of message M. The encryption of plaintext message M with key π is denoted as EπM. It corresponds to the sequence W of vectors w0,w1,…,wm−1 where w0=P0v0,w1=P1v1,…,wm−1=Pm−1vm−1. Conversely, the decryption of W, encrypted with key π, is denoted as DπW. It corresponds to the sequence of vectors P0−1w0, P1−1w1,…,Pm−1−1wm−1.\n\n(Shannon perfect secrecy). For any pair of plaintexts M1 and M2, when ciphertext W is equally likely to be the encryption of M1 or M2, the corresponding cryptographic scheme is perfectly secure.\n\nThe QPP cryptographic scheme is perfectly secure.\n\nProofs can be found in Refs. 10 and 14. The proofs establish that the probabilities are identical for all messages. The statement of Theorem 1 is theoretical because it requires very long keys. In the following, we use the QPP practically. This property is not maintained.\n\nThe implementation of QPP for quantum data has been investigated by Kuang and Perepechaenko.27–29 They proposed solutions to several quantum implementation issues, while the open problem of dispatching quantum permutations - that is, the selection of the applied permutations in a quantum circuit - is highlighted. The security of block sizes (n) two, three, four, and five is analyzed for the number of different permutations in a session required to achieve 256-bit of entropy, to mitigate the risk of breaking keys by the Grover’s algorithm.30–32 It is highlighted that a 256-bit size yields a brute force search space of 2256 keys. In the sequel, we take the security analysis one step further. As highlighted by Bellare and Rogaway, making the plaintext hard to recover from ciphertext is not enough to declare a cryptographic scheme secure.33 Indeed, information may leak just by observing patterns in traffic. In the next section, we analyze the probability of collisions, which is a cause of information leakage.\n\nThe concept of block counter mode has been examined in detail by Bellare and Rogaway.33 We summarize the main facts.\n\nThere are four main block modes, namely the electronic code book (ECB), cipher-block chaining (CBC) with a random initialization vector (IV), counter-based version of CBC (CBCC), and counter (CTR). The block modes are compared in Table 1. An important criterion is the risk of information leakage, which is significant for both the ECB and CBC with random IV modes. We use the CTR mode because of the low risk of information leakage.\n\nThe symmetric key block cipher with authentication is described hereafter. Let m and n be non-null positive integers. A quantum plaintext message consists of m quantum blocks w0,w1,…,wm−1. Each block consists of n qubits. An additional ℓ qubits are added to every block for a signature field; ℓ is a non-null positive integer.\n\nThere are two participants: a message source and a message destination. They share the following security parameters: i) block size (n), ii) number of blocks in a message (m), iii) length of the signature field (ℓ), iv) a set C of d1 Clifford operators randomly selected in Cn+ℓ, and v) a set P of d2 permutations randomly selected in S2n+ℓ. d1 and d2 are non-null positive integers. The source and destination share two secret arbitrary long sequences of random numbers s, modulo d1, and r, modulo d2. The sequence s and set C, and the sequence r and set P can be interpreted as the session authentication and encryption keys shared between the source and destination.\n\nBefore transmission, the source signs and encrypts each message. On the source side, there is a static variable i. It is initialized to zero. After the completion of the encryption of a message, the new value of the static variable i is incremented by m units.\n\nThe plaintext is signed with a sequence of m randomly selected Clifford operators:\n\nAll operators are in the set C. The selection of Clifford operators is determined by the sequence of random numbers s. The message signing key is the sequence of Clifford operators π.\n\nFollowing the signature procedure, the signed plaintext is encrypted with a sequence of m randomly selected permutations:\n\nAll permutations are in the set P. The selection of permutations is determined by the sequence of random numbers r. The message encryption key is the sequence of permutations ρ.\n\nThe expression\n\nThe quantum ciphertext C and the value of classical variable i are sent together to the destination.\n\nNote that the term signature is used but not in the classical sense. A classical message signature is calculated by reading the payload of a message. For quantum data, reading the payload to calculate a signature is not feasible because the measurement of the payload qubits would destroy their states.\n\nIt is assumed that the plaintext is random and unbiased. A diffusion phase before encryption, on the source side, and an assembly phase after decryption, on the destination side, can be added to remove statistical bias in ciphertext. See Ref. 27 for a circuit design which does that using CNOT gates.\n\nBuilding the set C of Clifford operators involves the random selection of d1 integers in the range one to \|Cn+ℓ\| and mapping these integers to Clifford operators. Koenig and Smolin have published a On3 algorithm for doing this mapping while van den Berg34 proposed a On2 algorithm. Barbeau et al.9 investigated this aspect for message key purposes.\n\nThe destination receives a quantum ciphertext C and a classical value i. For the purposes of replay protection, the destination ensures that the value of i is new. The ciphertext C consists of m blocks of n+ℓ qubits ωj, j=i,…,i+m−1. The decryption of a block with index j consists of the following product:\n\nCsj† is the conjugate transpose of Clifford operator Csj. The product Csj†Csj is an identity. Prj−1 is the inverse permutation of Prj. The product Prj−1Prj is also an identity. Assuming that a received message is intact, we have:\n\nThe original content is restored. To confirm that a verification is performed, measuring the qubits from positions n to n+ℓ−1 of every block, testing equality with the corresponding block number j, and taking the logical conjunction of the results:\n\nThe result is the Boolean value v. When it evaluates to one, the message is accepted and the resulting plaintext is\n\nOtherwise, the ciphertext C is rejected.\n\nThe message verification key is the sequence of conjugate transposes Csi†,Csi+1†,…,Csi+m−1†, which can easily be derived given π. Verification of the condition of Equation (16) is interpreted as a proof of ownership of the authentication key π by the message source and a validation of integrity. The value of the signature suffix aims to make every message unique, for replay protection. However, there is a risk of collision according to the selected security parameters. The collision probability is further investigated in the next section. The message decryption key is the sequence of inverse permutations Pri−1,Pri+1−1,…,Pri+m−1−1, also easily derived given ρ. It is a symmetric key that both the source and destination must share.\n\n\nCollision probability\n\nAs a function of the values selected for the security parameters, d1, d2, ℓ, m, and n, there is a risk of collision, i.e., a repeated message value is signed and encrypted the same way.\n\n(Collision). A collision arises when a reoccurring message consisting of m quantum blocks, each of them representing a n-qubit state, is re-numbered with the same sequence of integers i,i+1,…,i+m−1, modulo ℓ, re-resigned with the same sequence of Clifford operators C0,C1,…,Cm−1, chosen in the group Cn+ℓ, and re-encrypted with the same sequence of permutations P0,P1,…,Pm−1, chosen in the symmetric group S2n+ℓ. The same numbering, Clifford operators, and permutations are picked twice to sign and encrypt a repeating message content.\n\nThe smaller the collision probability, the better, because collisions leak information. They make it possible to identify traffic patterns, which can eventually lead to breaking encryption schemes. For the analysis, let us assume that a quantum block state is a single member of the orthonormal basis, i.e., no superposition. A message consists of m column vectors in the basis Bn. It is assumed that all members of the basis are equally probable. It is also assumed that, for a message, all block numbering sequences of m integers module ℓ are equally probable. These assumptions are reasonable, particularly when diffusion before encryption and assembly after decryption are done.\n\nThere are 2mn+ℓd1md2m unique combinations consisting of a message of m blocks of n qubits, a numbering sequence of ℓ-bit integers, a sequence of m Clifford operators chosen among a set of d1 available operators, and a sequence of m permutations chosen among a set of d2 available permutations. When over 2mn+ℓd1md2m messages are authenticated and encrypted with the same session key, at least one collision has occurred. We calculate the collision probability when less than 2mn+ℓd1md2m messages have been encrypted with the same session key. Note that collisions are unavoidable with finite-length fields, determined in this case by the security parameters.\n\nLet i be the number of messages consisting of m quantum states in Bn authenticated using m Clifford operators, chosen in subset C, included in Cn+ℓ, of d1 Clifford operators, and encrypted with m permutations, chosen in subset P, included in S2n+ℓ, of d2 permutations. ℓ is the number of signature qubits allocated for each block. Let i be greater than zero and less than equal to imax=2mn+ℓd1md2m. When i messages have been encrypted, the probability that at least one collision has occurred, denoted as Kd1d2ℓmni, is at least cmin=0.6⋅ii−12mn+ℓ+1d1md2m but not greater than cmax=ii−12mn+ℓ+1d1md2m.\n\nLet us assume that all messages are equally probable, that the choice of Clifford operators and permutations is uniform, and that probabilities are independent across messages.\n\nLower bound. The absence of collision after encrypting i messages is represented as the event ei. The event corresponds to a condition where i messages have been authenticated and encrypted. When no collision has occurred after the authentication and encryption of i messages, it means that among the available 2mn+ℓd1md2m combinations of message value, numbering sequence, Clifford operator sequence, and permutation sequence, solely 2mn+ℓd1md2m−i combinations have not been used. Therefore, the probability of no collision when the i+1-th message is signed and encrypted is\n\nIt follows that the probability of the absence of collision after the completion of the signature and encryption of i messages is\n\nLeveraging the inequality 1−x≤e−x≤x, with 0≤x≤1, the fact 0≤k2mn+ℓd1md2m≤1, and the equality ∑k=1i−1k=ii−12, the product of Equation (18) is less than equal to\n\nLeveraging the inequality 1−ex≥1−1/ex, Equation (20) is greater than\n\nHence, we obtain that\n\nUpper bound. Let the event fi denote a collision resulting from the ith block encryption. The probability of fi is\n\nDue to the existence of 2mn+ℓd1md2m of unique triples comprising a message, a Clifford operator, and a permutation, we obtain that\n\n□\n\nThe collision probability approaches the value of one-half by growing the block size (n) and number of blocks in a message (m). It is upper bounded by the value one-half because the weight of the subtrahend one is progressively diminishing, in the numerator ii−1, with i reaching imax.\n\nFigure 1 plots the collision probability Kd1d2ℓ1ni (y-axis) versus the number of transmitted messages i (x-axis), from one to imax. The message size (m) is one. There are curves for two-, three-, four-, and five-qubit QPP (n). The corresponding numbers of gates are 56, 17, six, and three. As mentioned in Remark 1, in the analysis, the maximum collision probability is one-half (or 10−0.3 on the logarithmic y-axis) when the number of encrypted blocks i is equal to imax. Of course, when i is greater than equal to 2mn+ℓd1md2m, the probability is one. From this perspective, i.e., from the block-key point of view, the collision probability is noticeably high for a low number of encrypted blocks.\n\nFigure 2 presents the message-key point of view. The x-axis corresponds to the block size (n), while the y-axis represents the value of imax as a function of the number of blocks in a message (m) and the block size (n). Again, as noted in Remark 1, in the analysis, the collision probability approaches value one-half as the number of blocks in a message (m) and the block size (n) grow and i approaches imax. Figure 2 plots values for imax (Theorem 2) for block sizes two, three, four, and five and message sizes one, two, four, and eight. imax is a parameter to consider when conducting a risk assessment and determining the maximum number of messages that can be sent before renewing a session key.\n\nSecurity parameters d1 and d2, selected according to the block size, are as suggested by Kuang and Perepechaenko.27 ℓ is equal to two.\n\n\nConclusion\n\nAn authentication and encryption scheme for quantum messages consisting of blocks of qubits has been presented. The scheme is simple and considers the scarcity of qubits for the upcoming first-generation quantum Internet. The authentication and verification key consists of a sequence of quantum Clifford operators. The encryption and decryption key is made of a sequence of quantum permutations. The scheme uses the block counter mode. Integrity and replay protection are also provided. For authentication, the source provides proof of ownership of the authentication key to the destination. Validation of integrity and replay protection rely on testing the consistency of the signature field of every block. The scheme is practical but does not achieve perfect indistinguishability because of the risk of message collision. This is normal and unavoidable when fixed-size fields are assumed to make a scheme practical. The message collision probability has been analytically determined. The model can be used to determine the values of the security parameters and the lifetime of session keys to mitigate the risk of information leakage according to the needs of the scheme’s users.", "appendix": "Data and software availability\n\nZenodo. Quantum Data Communication Protection with the Quantum Permutation Pad Block Cipher in Counter Mode and Clifford Operators https://doi.org/10.5281/zenodo.8246914.\n\nThis project contains the following underlying data:\n\n• QPPCTRC.mlx (The data and Matlab scripts used to produce the plots presented in this article\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nNational Security Agency - Central Security Service: Quantum Key Distribution (QKD) and Quantum Cryptography (QC). accessed: August 26, 2023. Reference Source\n\nVakhitov A, Makarov V, Hjelme DR: Large pulse attack as a method of conventional optical eavesdropping in quantum cryptography. J. Mod. Opt. 2001; 48(13): 2023–2038. Publisher Full Text\n\nMakarov V, Hjelme DR: Faked states attack on quantum cryptosystems. J. Mod. Opt. 2005; 52(5): 691–705. Publisher Full Text\n\nFerenczi A, Grangier P, Grosshans F: Calibration attack and defense in continuous variable quantum key distribution. International Quantum Electronics Conference. Optica Publishing Group; 2007; page IC_13.\n\nZhao Y, Fung C-HF, Qi B, et al.: Quantum hacking: Experimental demonstration of time-shift attack against practical quantum-key-distribution systems. Phys. Rev. A. 2008; 78(4): 042333. Publisher Full Text\n\nScarani V, Kurtsiefer C: The black paper of quantum cryptography: real implementation problems. Theor. Comput. Sci. 2014; 560: 27–32. Publisher Full Text\n\nBarnum H, Crépeau C, Gottesman D, et al.: Authentication of quantum messages. The 43rd Annual IEEE Symposium on Foundations of Computer Science, 2002. Proceedings. IEEE; 2002; pp. 449–458.\n\nSchuknecht C: Quantum Private Broadcasting. Université d’Ottawa/University of Ottawa; 2021. PhD thesis.\n\nBarbeau M, Kranakis E, Perez N: Authenticity, Integrity, and Replay Protection in Quantum Data Communications and Networking. ACM Transactions on Quantum Computing. 2022; 3(2): 1–22. Publisher Full Text\n\nKuang R, Barbeau M: Quantum Permutation Pad for Universal Quantum-Safe Cryptography. Quantum Inf. Process. 2022; 21(6): 211. Publisher Full Text\n\nAharonov D, Ben-Or M, Eban UME: Interactive proofs for quantum computations. Proceedings of Innovations of Computer Science. New York, NY: ACM; 2010; pp. 453–469.\n\nWainewright E: Efficient simulation for quantum message authentication. Ottawa, ON, Canada: Faculty of Graduate and Postdoctoral Studies, University of Ottawa; 2016. Master’s thesis.\n\nBroadbent A, Wainewright E: Efficient simulation for quantum message authentication. International Conference on Information Theoretic Security. Heidelberg: Springer; 2016; pp. 72–91.\n\nBarbeau M: Cryptographic Schemes for Secret Long-Distance Underwater Communications. J. Commun. 2023. to appear. Publisher Full Text\n\nBarbeau M: Confidential Underwater Communications Using Quantum Permutation Pad in Counter Mode. Proceedings of 12th International Conference on Communications, Circuits, and Systems (ICCCAS), Singapore. 2023.\n\nDas S, Siopsis G: Practically secure quantum position verification. New J. Phys. June 2021; 23(6): 063069. 1367-2630. Publisher Full Text\n\nSatoh T, Nagayama S, Oka T, et al.: The network impact of hijacking a quantum repeater. Quantum Science and Technology. 2018; 3(3): 034008. Publisher Full Text\n\nAlagic G, Broadbent A, Fefferman B, et al.: Computational security of quantum encryption. International Conference on Information Theoretic Security. Heidelberg: Springer; 2016; pp. 47–71.\n\nSt-Jules M: Secure quantum encryption. Ottawa, ON, Canada: School of Graduate Studies and Research, University of Ottawa; November 2016. Master’s thesis.\n\nNational Institute of Standards and Technology: Advanced Encryption Standard (AES). accessed: June 23, 2023. Reference Source\n\nLangenberg B, Pham H, Steinwandt R: Reducing the cost of implementing the advanced encryption standard as a quantum circuit. IEEE Transactions on Quantum Engineering. 2020; 1: 1–12. Publisher Full Text\n\nWang Z-G, Wei S-J, Long G-L: A quantum circuit design of AES requiring fewer quantum qubits and gate operations. Front. Phys. 2022; 17(4): 41501. Publisher Full Text\n\nZou J, Wei Z, Sun S, et al.: Quantum circuit implementations of AES with fewer qubits. Advances in Cryptology–ASIACRYPT 2020: 26th International Conference on the Theory and Application of Cryptology and Information Security, Daejeon, South Korea, December 7–11, 2020, Proceedings, Part II 26. Springer; 2020; pp. 697–726.\n\nJang K, Song G, Kim H, et al.: Efficient implementation of PRESENT and GIFT on quantum computers. Appl. Sci. 2021; 11(11): 4776. Publisher Full Text\n\nBaksi A, Jang K, Song G, et al.: Quantum implementation and resource estimates for RECTANGLE and KNOT. Quantum Inf. Process. 2021; 20: 1–24. Publisher Full Text\n\nZixuan H, Kais S: A quantum encryption design featuring confusion, diffusion, and mode of operation. Sci. Rep. 2021; 11(1): 23774. Publisher Full Text\n\nKuang R, Perepechaenko M: Quantum encryption with quantum permutation pad in IBMQ systems. EPJ Quantum Technol. 2022; 9(1): 26. Publisher Full Text\n\nKuang R, Perepechaenko M: Quantum encryption and decryption in IBMQ systems using quantum permutation pad. J. Commun. 2022; 17(12): 972–978. Publisher Full Text\n\nPerepechaenko M, Kuang R: Quantum encryption of superposition states with quantum permutation pad in IBM quantum computers. EPJ Quantum Technol. 2023; 10(1): 7. Publisher Full Text\n\nGrover LK: A fast quantum mechanical algorithm for database search. Proceedings of the Twenty-eighth Annual ACM Symposium on Theory of Computing. 1996; pp. 212–219.\n\nMashatan A, Heintzman D: The complex path to quantum resistance. Commun. ACM. 2021; 64(9): 46–53. Publisher Full Text\n\nBernstein DJ, Lange T: Post-quantum cryptography. Nature. 2017; 549(7671): 188–194. Publisher Full Text\n\nBellare M, Rogaway P: Introduction to modern cryptography. accessed: June 23, 2023. Reference Source\n\nVan Den E: A simple method for sampling random Clifford operators. 2021 IEEE International Conference on Quantum Computing and Engineering (QCE). IEEE; 2021; pp. 54–59.\n\n\nFootnotes\n\n1 Let α=x+jy be a complex number, \|α\| yields the absolute value (also called modulus or magnitude) of the complex number, that is, x2+y2 ." }	[ { "id": "230252", "date": "23 Jan 2024", "name": "Cherry Mangla", "expertise": [ "Reviewer Expertise Quantum communication and cybersecuirty schemes" ], "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 plays a crucial role in the world of cybersecurity and quantum computing, and I fully agree with what the author is saying. The author points out that because of some problems with quantum mechanics, many cybersecurity plans hit roadblocks or never get off the ground. I agree that we need more research like this to push forward in both quantum computing and cybersecurity.\nHowever, I think the author could explain the proposed plan in more detail. It seems like the author has a background in this area, so a bit more explanation would help. A deeper dive into the plan's ins and outs, including how it works, what it found, and what it could mean, would make the research more thorough. This would not only make the research more trustworthy but also contribute more to what we already know in this field.\nIn simple terms, the connection between quantum computing and cybersecurity is important, and this article is a part of that connection. By calling for more attention and refinement of the proposed plan, we create a space for continued growth and new ideas in both these fields.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10949", "date": "22 Mar 2024", "name": "Michel Barbeau", "role": "Author Response", "response": "Thanks for your report! I will address your feedback." } ] } ]	1	https://f1000research.com/articles/12-1123
https://f1000research.com/articles/12-404/v1	14 Apr 23	{ "type": "Case Report", "title": "Case Report: Tracheal infiltration with wheezing revealing Hodgkin's disease", "authors": [ "Selsabil Daboussi", "Asma Saidane", "Samira Mhamdi", "Nouha boubaker", "Chaabane Mariem", "Chiraz Aichaouia", "Ghedira Hela", "Fehmi Msadek", "Moetemri Zied", "Asma Saidane", "Samira Mhamdi", "Nouha boubaker", "Chaabane Mariem", "Chiraz Aichaouia", "Ghedira Hela", "Fehmi Msadek", "Moetemri Zied" ], "abstract": "Hodgkin's disease with an initial tracheobronchial involvement is extremely rare. The symptoms might be misleading, resulting in a diagnosis delay. We report the case of a 38-year-old woman with a one-month history of wheezing and a non-productive cough. The physical examination revealed a good general state of health, bilateral diffuse wheezing and supra-clavicular lymphadenopathy. The adenopathy biopsy's histopathology revealed Hodgkin's disease. The whole body FDG-PET scan was an important tool to assess the diagnosis as well as for the staging. The patient was treated with chemotherapy. Another unusual aspect is the tracheobronchial metastasis confirmed by a bronchial biopsy. Thus, our patient was put on a second-line chemotherapy. She died one year after the initial diagnosis. To conclude, it is a rare case of an Hodgkin lymphoma with a tracheobronchial relapse. It should be considered in the differential diagnosis of a tracheal tumor.", "keywords": [ "Hodgkin’s disease", "wheezing", "trachea", "chemotherapy" ], "content": "Background\n\nHodgkin's disease cases with tracheobronchial involvement are rare.1 The symptoms are not specific and may mimic many other diseases like asthma or chronic obstructive pulmonary disease (COPD), which delays the lymphoma diagnosis as well as the treatment.1,2 It is now recognised as a treatable neoplasia. Thus, it is worth mentioning this entity for clinicians especially after the recent therapeutic progress We report the case of a 38-year-old woman with a one-month history of wheezing and a non-productive cough unresponsive to bronchodilators revealing Hodgkin's disease.\n\n\nCase presentation\n\nA 38-year-old female presented to our department with a one-month history of dry cough and wheezing. She has never smoked. She has not any comorbidities or allergies. She is a stay-at-home spouse and is white. She has visited the emergency room several times in the last month for chest wheezing. She received beta2-mimetics nebulizations, without any improvement. The physical examination at admission revealed a good general state. Respiratory auscultation revealed bilateral diffuse wheezing. Oxygen saturation was (98 %) on room air. The examination of the ganglionar areas detected peripheral bilateral fixed supra-clavicular lymphadenopathy measuring about (2cm of diameter). There was no hepatosplenomegaly. The neurological examination was normal.\n\nThe chest x-ray showed a retractile opacity in the right chest with a hilar enlargement (Figure 1).\n\nThe body computed tomography (CT) scans revealed a bulky mediastino-hilar tumor in the right chest, measuring (90 x 85 x 71 mm), invading the right main bronchus, extending to the vena cava and infiltrating the pericardium with a subpleural right node (Figures 2 and 3). Bronchoscopy showed a polypoid mass located in the carina, involving the right main bronchus. Cytology revealed malignant cells. Histopathology of the bronchial biopsy did not show any malignant lesions. In addition, we performed a biopsy of the supra-clavicular adenopathy. Histopathology revealed an intense staining for CD15 and CD30 with large multinuclear reed Sternberg cells. Therefore, the diagnosis of an Hodgkin lymphoma was confirmed.\n\nThe 18-fluorodeoxyglucose-positron emission tomography (FDG-PET) showed many sites of activity of the disease, with a high metabolic fixation of the FDG in the lymph node stations (1L,3,5,6,7,8,9,10,11R) as well as subphrenic adenopathy. Besides, it revealed an intense endotracheal metabolic fixation (Figures 4, 5). Moreover, the bone marrow biopsy was negative.\n\nThe patient received 4 courses of an escalated BEACOPP chemotherapy protocol (Bleomycin, Etoposide, Adriamycin, Cyclophosphamide, Vincristine, Procarbazine, Prednisone) as detailed below (Table 1).\n\nShe was readmitted in our department 2 months after for acute respiratory failure with wheezing. Bronchoscopy revealed a bulky stenosing polypoid mass, measuring about 3 cm of diameter, rising from the carina extending to the trachea and to the main bronchus that remains partially patent. Histopathology revealed large cells associated with an inflammatory granuloma of (lymphocytes, eosinophils, neutrophils) and a positive staining for CD 15 and CD 30. Therefore, we concluded to a tumoral progression with an endotracheobronchial relapse.\n\nThe decision of the multidisciplinary medical team was to put the patient under a second-line chemotherapy: IGEV Regimen as a salvage therapy (ifosfamide, gemcitabine, vinorelbine and methylprednisolone). Moreover, injected Chest CT scans revealed a segmental pulmonary embolism. So, she received a curative anticoagulant treatment. She died one year after the initial diagnosis.\n\n\nDiscussion\n\nIt is well known that Hodgkin lymphoma usually involves the mediastinum. However, pulmonary involvement is less common and can be observed in the lymph nodes, parenchyma, and tracheobronchial tree.1\n\nIt is worth mentioning that Hodgkin lymphoma with a tracheobronchial involvement remains extremely rare.1 Patients usually present with respiratory symptoms (such as dyspnea, wheezing and cough), fever, and weight loss.2 The diagnosis may be challenging because the symptoms are not specific. About (30%) of the patients have more than 6-months diagnosis delay.3 We should consider a tracheobronchial tumor in the differential diagnosis when the patient presents to our department with asthma symptoms without any improvement after bronchodilators. In our case, the patient complained of a dry cough and chest wheezing mimicking an asthma attack. She received Beta2-mimetics without any improvement.\n\nAtelectasis is the most frequent radiological finding, occurring in (2/3) of patients. Besides, the chest CT scan may reveal a solitary hilar mass or an obstructive emphysema. Mediastinal or hilar lymphadenopathy are often present.4\n\nEndoscopy may show ulceration, mucosal infiltrate, or a polypoid mass.1 Our patient had a polypoid mass rising from the trachea extended to the main bronchus.\n\nHistopathology shows typically large Sternberg cells with positive staining for CD15 and CD30.3 The diagnosis was made thanks to a biopsy of the supra-clavicular adenopathy in this case. Recent studies suggest that endobronchial ultrasound (EBUS) may be useful in the diagnosis and staging of Hodgkin lymphoma with endobronchial involvement to avoid mediastinoscopy.5\n\nIt is worth mentioning that the PET scan is a reliable imaging tool for the diagnosis as well as for the staging of lymphoma especially in this case because mediastinal adenopathy may be due to infectious or inflammatory diseases.6,7 In our case, this exam showed an intense metabolic fixation FDG in many ganglionar areas as well as an endotracheobronchial fixation. It is also very interesting for the follow-up.\n\nTreatment is commonly based on chemotherapy with or without radiotherapy. It depends strongly on the extent of the disease, the general state and the comorbidities.8 Complete resection of the stenotic tracheal tumor may be performed in patients with critical airway obstruction thanks to interventional procedures such as rigid bronchoscopy with a stent placement, photodynamic laser therapy, laser therapy with a neodymium: yttrium-aluminum-garnet laser (Nd-YAG) and photodynamic laser therapy.9,10\n\nRelapsed Hodgkin lymphoma is another challenging problem for clinicians especially when it affects the tracheobronchial tree as seen in our case. Prognostic Factors associated to the relapse of the disease have been recently identified including: a poor performance status (PS), an age greater than 50 years old, failure to achieve remission after an initial therapy, anemia and an advanced lymphoma with a clinical staging (III or IV).11\n\n\nConclusion\n\nTo conclude, we report a very rare case of lymphoma with an endobronchial involvement. We do underline the importance of considering Hodgkin lymphoma in the differential diagnosis of asthma symptoms without any improvement after bronchodilators or in the case of a tracheal tumor. Further studies are required in order to highlight the prognostic factors in order to improve the outcomes.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the family of the patient.", "appendix": "References\n\nTrilok C, Avdhesh B, Harsh D, et al.: Endotracheobronchiallymphoma: Twounusual case reports and review of article. Lung India. 2016; 33: 653–656. Publisher Full Text\n\nKiani B, Magro C, Ross P: Endobronchial Presentation of Hodgkin Lymphoma: A Review of the Literature. Ann. Thorac. Surg. 2003; 76: 967–972. PubMed Abstract \| Publisher Full Text\n\nKaseb H, Babiker HM: Hodgkin Lymphoma. Last Update: July 10, 2022. Hodgkin Lymphoma - StatPearls - NCBI Bookshelf. Reference Source\n\nMsaad S, Yangui I, Ketata W, et al.: Atteinte trachéale révélatrice d’une maladie de Hodgkin. Rev. Pneumol. Clin. 2007; 63(5): 323–325. PubMed Abstract \| Publisher Full Text\n\nFurukawa B, Bernstein M, Siddiqi N, et al.: Diagnosing Hodgkin Lymphoma From an Endobronchial Ultrasound Core Needle Biopsy. J. Bronchol. Interv. Pulmonol. 2016; 23(4): 336–339. PubMed Abstract \| Publisher Full Text\n\nFriedberg JW, Chengazi V: PET scans in the staging of lymphoma: current status. Oncologist. 2003; 8(5): 438–447. Publisher Full Text\n\nThanarajasingam G, Bennani-Baiti N, Thompson C: PET-CT in Staging, Response Evaluation, and Surveillance of Lymphoma.CurrTreat Options. Oncologia. 2016 May; 17(5): 1–9. Publisher Full Text\n\nLymphoma Research Foundation: Hodgkin Lymphoma: Treatment Options.Reference Source\n\nMemorial Sloan Kettering Cancer Center: Treatment of Tracheal & Bronchial Tumors.2023. Reference Source\n\nRibechini A, Bottici V, Chella A, et al.: Interventional bronchoscopy in the treatment of tracheal obstruction secondary to advanced thyroid cancer. J. Endocrinol. Investig. 2006; 29: 131–135. PubMed Abstract \| Publisher Full Text\n\nKuruvilla J, Keating A, Crump M: How I treatrelapsed and refractory Hodgkin lymphoma. Blood. 2011; 117(16): 4208–4217. PubMed Abstract \| Publisher Full Text" }	[ { "id": "171452", "date": "10 May 2023", "name": "Ruwaida Ben Musa", "expertise": [ "Reviewer Expertise My area of expertise in research is the neuronal control of the Cardiorespiratory system during exposure to hypoxia by using the transgenic animals model." ], "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’s an interesting case report that addressed the importance of considering a tracheal tumor in the differential diagnosis of bronchial asthma when the patient presents with asthma symptoms without any improvement after bronchodilators. Although Hodgkin lymphoma with a tracheobronchial involvement remains extremely rare, the clinician should be aware of that and consider it in the differential diagnosis in order to diagnose the tumor in the early stage of the disease and save the patient's life.\n\nI have a number of comments that the authors may find useful:\nThe background of the case’s history was very short, I encourage the authors to give more details about Hodgkin's disease. As well as more details about the patient's history in the (case presentation) would be helpful such as nationality, if she is married, occupation/environment, history of passive smoking, alcohol, family history, and other risk factors. Also, if the patient presented with any other symptoms such as unexplained fever or weight loss, fatigue, night sweating, and chest pain?\n\nThe authors state that the patient visited the emergency room several times, I am wondering if the ER doctor performed a complete physical examination including the lymph node examination in order to discover the supra-clavicular lymphadenopathy. I am also wondering if the patient does not improve by the Beta agonist treatment, why the ER doctor does not order the chest X-ray during that time to exclude any other diseases?\n\nDuring respiratory auscultation usually, we used the term bilateral diffuse rhonchi instead of wheezing. Also, I suggest the authors include more details on the physical examination, such as the vital signs during the time of admission, and the general physical examination if the patient was conscious, oriented, dyspneic, tachypneic, anemic, any cyanosis and lower limb edema?\n\nOn page #3, the authors mentioned (PET) scan that showed many sites of activity of the disease, with a high metabolic fixation of the FDG in the lymph node stations (1L,3,5,6,7,8,9,10,11R). Are the authors using the International Association for the Study of Lung Cancer (IASLC) to define the stations? Could you explain it in the paper if this is the case? Also, the patient was at which stage when Hodgkin's lymphoma was diagnosed?\n\nFor Fig #3; to be more clear, I think it's better to use the arrow to show the site of the bulky tumor which invades the carina. The same thing with Fig #4, the CT mediastinal section, please add more description in the legend that would be helpful.\n\nFor Fig #4, looks like a blurry image and is not clear to me with little description in the legend. I encourage the authors to mention more details in each figure and use arrows and landmarks to be easier to understand the regions that are involved with tumors.\n\nI am wondering as I did not see any blood test results or requested such CBC, ESR, CRP, Blood film, etc.? Have physicians requested? I think it’s worth mentioning it in the case report by making a table of the blood test results even if it is normal.\n\nI think more details on the BEACOPP chemotherapy protocols would be helpful such as regimens, dosage, and for how long the patient received it. Additionally, if there was any follow-up CT or PET scan done after the patient received chemotherapy. Does the patient receive any radiotherapy or immunotherapy?\n\nIt appears the patient does not have regular follow-ups with her doctor after receiving the chemotherapy as she developed acute respiratory failure as a result of bulky stenosing polypoid mass which was diagnosed by bronchoscopy and unfortunately she also developed segmental pulmonary embolism. I encourage the authors to address if the patients were on regular follow-ups in the case presentation section or not.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "190574", "date": "16 Aug 2023", "name": "Jeffrey W Craig", "expertise": [ "Reviewer Expertise Diagnostic hematopathology", "lymphoma biology" ], "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 reports a single case of classic Hodgkin lymphoma in a young adult female presenting with one month of dry cough, wheezing and palpable supraclavicular lymphadenopathy. Initial imaging revealed extensive mediastinal disease (up to 90 mm) with infiltration of the pericardium and right mainstem bronchus, the latter of which was also visualized bronchoscopically as a polypoid carinal mass. Diagnosis was based on histopathology of an involved lymph node. PET scan showed extensive foci of hypermetabolism, including the tracheal lesion and lymph nodes above and below the diaphragm. The patient was treated with front-line BEACOPP therapy; however, primary refractory disease was confirmed just two months later. A salvage IGEV regimen was then employed, but the patient expired roughly one year after the initial diagnosis.\nI have the following general comments/criticisms of the manuscript.\nI think it’s very misleading to describe or compare this case to primary endobronchial Hodgkin lymphoma, as this patient presented with palpable lymphadenopathy and more widespread disease on imaging. Lung/airway involvement by Hodgkin lymphoma is not particularly uncommon, especially in young adult patients with bulky intrathoracic disease. The clinical presentation did include airway symptoms, but the diagnosis was readily obtained via conventional lymph node biopsy.\n\nThe current WHO & ICC nomenclature for this entity is classic Hodgkin lymphoma, not Hodgkin’s disease (antiquated terminology). I strongly recommend the addition of a hematopathologist to the authorship list, with the goal of improving the descriptions of the histopathologic findings. Further, the manuscript would likely benefit from having a microscopic image in support of this diagnosis, as well as formal staging information (presumably stage IIIA/IVA).\n\nThe manuscript could use another round of proofreading for language, grammar and punctuation.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [ { "c_id": "10103", "date": "11 Sep 2023", "name": "DABOUSSI SELSABIL", "role": "Author Response", "response": "Dear Dr. Craig, Thanks a lot for your interest! We have included two specialists in clinical Hematology and a specialist in anatomopathology in order to improve the description of the lesions. Moreover, our therapeutic protocol was made according to the recent guidelines. Extranodal lymphoma is not rare itsself. However, a primary clinical presentation of an extranodal lymphoma with an associated tracheobronchial involvement is so rare in antemortem series. It is often diagnosed in patients followed up for lymphoma during the follow up or in autopsy series. In fact,the diagnosis is so challenging given that the symptoms may mimic a wide spectrum of diseases like asthma or COPD as shown in our case report. Indeed, the bronchial biopsy is often negative. Thus, we aimed to highlight the importance of interventional endoscopy procedures in the initial diagnosis and during the follow up. Moreover, the tracheobronchial relapse is unusual. As you know, the Hodgkin lymphoma invades typically the lymph nodes. Finally, we aimed to highlight the atypical manifestations of lymphoma in order to increase the awareness of clinicians and improve the prognosis. Since an early diagnosis implies an early treament, it would alleviate the burden of the disease. Besides, we really hope to share this case with other experts in order to find out better therapeutic stratgies. Our patient died despite a combined chemotherapy and a strict follow-up. The treatment of an advanced stage lymphoma is usually aggrssive with a poor prognosis. The median survival does not exceed some months in our developing countries. It would encourage experts to carry on new researchers in this field. Kind regards Saidane Asma Military hospital" } ] } ]	1	https://f1000research.com/articles/12-404
https://f1000research.com/articles/12-140/v1	07 Feb 23	{ "type": "Research Article", "title": "Effect of feed enriched by products formulated from coconut water, palm sap sugar, and mushroom on the chemical composition of feed and carcass, growth performance, body indices, and gut micromorphology of giant gourami, Osphronemus goramy (Lacepède, 1801), juveniles", "authors": [ "Azrita Undefined", "Hafrijal Syandri", "Netti Aryani", "Ainul Mardiah", "Hafrijal Syandri", "Netti Aryani", "Ainul Mardiah" ], "abstract": "Background: Giant gourami, Osphronemus goramy (Lacepède, 1801) is the most important freshwater fish species produced by aquaculture in Indonesia. This study seeks to determine the effects of various newly formulated products on the amino acid composition of the diet and whole-body carcass, and to analyse the growth coefficient, body indices, and gut micromorphology. Methods: 100 g of palm sap sugar was cooked in 1.1 litre of fresh water for fifteen minutes, to create 1 litre of 11% palm sap sugar solution (after some of it had been boiled off). 2 litres of coconut water were then mixed with the litre of palm sugar solution. 1 litre of this product was added in turn to 2 g of Aspergillus niger (CP2), 2 g of Rhizopus oligosporus (CP3), and 2 g of Saccharomyces cerevisiae (CP4), while freshwater was used as a control (labeled CP1). Aquafeed was added to CP1, CP2, CP3, and CP4, to make diets labeled KP1, KP2, KP3, and KP4. The dosage was 150 ml/kg of feed. Juvenile giant gourami (initial weight 50±0.25 g and length 13.2±0.07 cm) were reared in triplicate net frames (2×1×1 m; water volume 1.5 m3) in a freshwater concrete pond with a stocking density of 30 juveniles/net. Results: The results supported our hypothesis that different product formulations have a significant effect (P < 0.05) on aquafeed nutrition and the whole-body carcass, growth coefficient, feed utilization, body indices, and gut micromorphology of giant gourami juveniles. The thermal growth coefficient strongly correlated with the daily growth coefficient (r2 = 91%). The KP3 diet contains a higher concentration of amino acids, which increased the growth coefficient, feed utilization, and carcass quality more than the other diets we tested. Conclusions: Diet KP3 contains higher total amino acids in diets and carcasses and leads to better growth for giant gourami.", "keywords": [ "Giant gourami", "amino acid profile", "growth performance", "palm sap sugar", "coconut water", "gut micromorphology" ], "content": "Introduction\n\nIn this decade, the production of capture fisheries has decreased; meanwhile, the demand for fish products for human consumption is increasing. Therefore, according to the Food and Agriculture Organisation, 60% of fisheries production in the future will come from aquaculture activities and this figure will continue to rise.1 The utilization of a variety of fish for aquaculture has now increased the need for commercial feed.2–5 At the same time, for aquaculture operations, the cost of aquafeed is still a significant challenge.2,6–8 On the other hand, commercial feed produced by factories still does not contain complete nutrition for fish growth, while being acknowledged for its positive effects on food safety.9–11 In this context, enriching fish feed with cost-effective natural ingredient resources is key to increasing feed nutrient quality and feed efficiency in commercial fish farming and ensuring the sustainability of aquaculture operations.2,12,13\n\nThe target is fish feed that is wealthy in many important nutrients, including protein, fat, vitamins, and minerals that cultured fish can utilize to increase their growth rate and survival and that is beneficial for human health.4,14–16 Therefore, novel approaches have been developed by scientists to improve the nutrition of fish feeds, such as feed supplemented with EPA and DHA,17 iodine and selenium,10 methionine,18 fish oil,11,19 and soybean oil.20 In addition, supplementing probiotics into the diet21 and supplemental glycine, prebiotics, and nucleotides in a soybean meal-based diet have been studied.22\n\nThe progress of aquaculture biotechnology has stimulated the interest of scientists in improving aquatic animal production, for example, to increase giant gourami production. One of the experimental techniques is to increase feed nutrition used for this purpose, such as, the use of fish meal and Azolla flour as a feed ingredient for giant gourami,23 and the utilization of new products formulated from water coconut, palm sap sugar, and fungus for the enrichment of commercial feed.9 Additional research has involved a diet supplemented using glutamine,24 feed supplemented with a growth hormone,25 and substitute fish meal incorporating chicken feather.26 Whether using coconut water and palm sap sugar fermented with mushrooms affects the amino acid composition of the diet, body carcass, growth coefficient, and body indices is still not understood.\n\nCoconut water has extraordinary nutritional value and contains supplements for health like minerals, amino acids, fatty acids, vitamins, enzymes, organic acids, and several phenolic compositions.27–30 Palm sap sugar also has health benefits due to its essential nutrient content, such as a low glycaemic index, and it contains antioxidants, vitamins, and minerals.31–34 Meanwhile, mushrooms have been widely used in fermentation due to their ability to degrade antigenic proteins in fish feed ingredients.7,35,36 Additionally, coconut water is a functional food that can protect the lens from diabetic cataract development in rats.37 Coconut water is also a treatment for burning pain during urination, dysuria, gastritis, increasing semen, and indigestion.38\n\nOn the other hand, Azrita et al.9 have reported using new formulations of products containing coconut water and palm sap sugar that are fermented with various mushrooms involving a dosage of 300 ml/kg feed. Their newly formulated products can increase fatty acid levels in the diet and whole body carcasses. Besides that, they also improve giant gourami's growth performance and feed efficiency.\n\nHowever, the effect of these new formulation products at a dosage of 150 ml/kg feed on the diet amino acid composition, and body meat's amino acid composition has not yet been analyzed. In line with that, the relationships between thermal growth coefficient and condition factor, daily growth coefficient, and feed utilization coefficient, including body indices parameters, as well as the gut micromorphology of giant gourami, have not yet been analyzed.\n\nWe hypothesized that commercial aquafeed combined with different newly formulated products at the dosage of 150 ml/kg feed could improve the amino acids compositions of the aquafeed and whole body carcass, body indices, and gut micromorphology. Hence, this investigation's first purpose was to analyze the effect of various newly formulated products on the diet's proximate compositions, amino acid composition, and whole-body carcass. The second aim was to analyze the impact of newly formulated products on the growth coefficient and relation to thermal growth coefficient, body indices, and gut micromorphology in giant gourami juveniles.\n\n\nMethods\n\nThe Research and Community Service Ethics Committee at Universitas Bung Hatta, West Sumatera, Indonesia approved this research (89/LPPM/Hatta/III-2022) which followed the ARRIVE guidelines. The Ministry of Education, Culture, Research and Technology of the Republic of Indonesia funded the research under grant No. 076/E5/PG.02.00 PT/2022 on March 16, 2022. Approval was given by the ethics committee to collect and rear juvenile gurami sago in the aquaculture laboratory, Faculty of Fisheries and Marine Science at Universitas Bung Hatta. All efforts were made to relieve the suffering of experimental animals. Therefore, the animal did not suffer for this study, and they were still in good condition when returned to the pond after research was completed. Where some fish were euthanized, this was carried out by piercing part of the fish’s brain. Gurami sago fish are not classified as a protected animal according to Indonesian legislation.\n\nWe prepared 100 g of palm sap sugar by traditional production and cooked it in 1.1 litre of fresh water for fifteen minutes at 600 C, and only got 1 litre of palm sap sugar solution due to some of it being boiled off. Then, this was cooled in an open space for twenty minutes. Furthermore, we also prepared 2.0 litres of mature coconut water (Cocos nucifera L.) and mixed it with the 1.0 litre of palm sap sugar solution. The product was stored for ten minutes in a cool air-conditioned room. A total of 3.0 litres of the formulated product was divided into three parts of 1.0 litre each. We added 2 g of Aspergillus niger (labeled as CP2 product) to the first part of the formulated product solution, 2 g of Rhizopus oligosporus (labeled as CP3 product) to the second part, and 2 g of Saccharomyces cerevisiae (labeled as CP4 product) to the third portion. The CP2, CP3, and CP4 products were fermented for 48 hrs in a jerry can (2.0 litres) using an Aerasi PUJIMAC, MAC-40 K 40 L/min. The products of CP2, CP3, and CP4 were used to enrich the nutrition of commercial aquafeed (781-2, PT. Japfa Comfeed Indonesia, Tbk) and labeled as the KP2, KP3, and KP4 diets. The aquafeed was supplemented with freshwater (labeled as the KP1 diet; placebo).\n\nGiant gourami juveniles were adapted for one month to standard feed, namely floating commercial aquafeed 781-2 (pellet size 2 mm), which contained 10.66% water content, 30.10% crude protein, 4.09% crude fat, 45.35% total carbohydrates, 2.5% ash, and 9.18% crude fibre. The minerals in the commercial feed were 280.08 mg/100 g Na, 1415.02 mg/100 g Ca, 1358.07 mg/100 g K, 1200.31 mg/100 g P, 292.03 mg/100 g Mg, 18.14 mg/100 g Fe, and 13.83 mg/100 g Zn. The aquafeed was added to freshwater to create the KP1 diet as observed, and the formulated CP2, CP3, and CP4 products were added to the aquafeed at a dosage of 150 ml/kg of feed to create the enriched fish diets. The formulated product added to the aquafeed was mixed manually with it for three minutes to obtain maximum homogenization and then the blend was dried in the open air for thirty minutes. Thereafter, it was given to the trial animal.\n\nIn the present study, we measured fish weight using AD-600i scales with 0.001 g accuracy (ACIS model number AD-600i, China). At the same time, a meter ruler with 1 mm accuracy was used to estimate the body length. A total of 360 sago strain juveniles of giant gourami were counted; the initial mean weight was 50 ± 0.25 g, and the initial length was 13.2±0.07 cm. For rearing juveniles, twelve nets framed with 2 m3 (2 × 1 × 1 m) PVC pipe (water volume of 1.5 m3) were placed inside two freshwater concrete ponds with a size of 18 m3 (6 × 2 × 1.5 m). This experiment consisted of four treatments and three replications, and each frame net was stocked with 30 juveniles. The giant gourami were fed the KP1, KP2, KP3, and KP4 diets three times a day (08:00, 12:00, and 17:00 hrs) during the 90-day feeding trial. Juveniles of giant gourami were fed at a 3% body weight rate per day based on the percentage of stored biomass. Fish samples were collected every 30 days for body weight and length measurements. Ten fish per net frame were collected and anesthetized orally using clove oil. Then, their lengths and weights were measured. Prior to sampling, the fish fasted for 24 hrs to empty their intestinal contents.\n\nThe diet samples and proximate carcass composition were analyzed using standard AOAC methods.39 The matter was dried to a constant weight at 105°C. We used the standard Kjeldahl method to analyse crude protein (N × 6.25). We used the Soxhlet method with ether extraction to analyse crude lipids; the ash was incinerated at 550°C for 16 hrs, whereas gross energy was measured in a bomb calorimeter. The amino acid composition was determined by using a high-performance liquid chromatography (HPLC) system consisting of a water 1525 binary HPLC pump, 717 autosamplers (water®), and water 2475 multi λ fluorescence detector optics (wavelengths: 250 nm for excitation and 395 nm for emission). It was hydrolysed in triplicate with 6 N hydrochloric acid for 24 hrs at 11°C.40\n\nThe growth coefficients in the fish experiments were measured by using the thermal growth coefficient (TGC), daily growth coefficient (DGC), total feed intake (FI), and protein efficiency ratio (PER) of giant gourami, assessed using the following formulae:\n\nThree fish from each net frame were sacrificed and dissected immediately to determine the Condition factor (CF), Viscerosomatic index (GSI%), Hepatosomatic index (HSI%), Visceral fat-somatic indexes (VFSI%), and Bilesomatic index (BSI) as given below:\n\nFor histological analyses, each gut specimen of the animal was cut into the foregut, midgut, and hindgut. Moreover, the cells were cleaned in saline solution and fixed in Bouin's fixative solution for 24 hrs. After sequential dehydration steps in alcohol, the gut samples were embedded in paraffin. The implanted tissue blocks were sectioned at 5 μm, and sections were consistently stained with Haematoxylin-eosin and observed under a light microscope (Olympus IX71) equipped with Image-Pro Plus 7.0 software. The digitalized analysis measures the micrometer length of various enteric structures of gut images. We determined the average fold height (hF), fold width (wF), and enterocyte height (hMV) of the gut per slice (5 fields per individual sample) according to procedures described by Li et al.18 The specific measurement method of gut samples is shown in Figure 1.\n\n(A) Fold height and fold width were analyzed in a lower magnification of objective lens of microscope (magnification × 100), (B) Enterocytes height and microvilli height were analyzed using a higher magnification of an objective lens microscope (magnification × 200). hF = fold height, wF = fold width, hE = enterocyte height, hMV = microvillus height (hematoxylin and eosin).\n\nThe water quality values of the freshwater concrete ponds that were used to rear the giant gourami juveniles were recorded weekly. The water samples were collected at 10:00 am at a depth of 20 cm from each concrete pond to determine the water temperature, dissolved oxygen, and pH value. In addition, we also measured the total alkalinity, hardness, and nitrates of the water in the pond experiments. A thermometer (Celsius scale) was used to measure water temperature. To measure water dissolved oxygen (O2; mg L-1), we used an oxygen meter (YSI Model 52, Yellow Instrument Co, Yellow Spring, OH USA). A digital pH meter (Mini 0–14 pH IQ, Scientific Cemo Science, Thailand) was used to determine the pH values of water in the experiments. The level of nitrate-nitrogen (NO3-N; mg L-1), alkalinity (mg L-1), and hardness (mg L-1) were measured according to standard procedures.41\n\nThe data from this study were reported in the form of the mean ± standard deviation for each treatment. Data were analysed using the SPSS 16.0 software package (SPSS; Chicago, IL). Normality was tested using the Kolmogorov–Smirnov statistic. Homogeneity was checked using absolute residuals according to Levine's test. One-way ANOVA was used to determine the treatment effect, followed by a post-hoc Duncan's multiple range test.42 To create the figures, Microsoft Office Professional Plus 2019 was used.\n\n\nResults\n\nCommercial feed supplemented with different formulated products with the dosage of 150 ml/kg of feed significantly affects the proximate composition of diets. One-way ANOVA results showed a marginal interaction among treatments in the case of protein content (F(3,8) = 1.522, P = 0.282), fat (F(3,8) = 5.663, P = 0.022), carbohydrates (F(3,8) = 1.862, P = 0.214), crude fibre (F(3,8) = 1.445, P = 0.300), and ash (F(3,8) = 0.272, P = 0.844), and the total energy content (F(3,8) =1.112, P = 0.400) differed considerably (P < 0.05) among the four diets (Table 1). Duncan's Post-hoc test revealed that the protein content (21.6967 ± 0.17%) was significantly higher (P < 0.05) in the KP3 diet than in the other treatments, while the carbohydrate (31.19 ± 0.38%), crude fibre (2.82 ± 0.06%), and ash (6.57 ± 0.04%) contents were significantly higher (P < 0.05) in the KP3 diet than in the other diets. Conversely, the total energy content was 240.88 ± 0.74 (kg calories/100 g), which was significantly higher (P < 0.05) in the KP3 diets than in the KP1, KP2, and KP4 diets (Table 1).\n\nMean ± SD.\n\n Values represent the means of triplicate samples.\n\nThe levels of free amino acids in the diets supplemented with different formulated products with a dosage of 150 ml/kg of feed are presented in Table 1. All types of amino acids in the diets of KP1, KP2, KP3, and KP4 were significantly different (P < 0.05), except for tryptophan, and there was no significant difference (P > 0.05) between KP2, KP3, and KP4. Among the essential amino acids, leucine and arginine were found in the highest amounts in the KP1, KP2, KP3, and KP4 diets. There was no significant difference (P > 0.05) in the alanine content between KP2 and KP3 diets and the cystine level in KP1 and KP3 diets. Of the nonessential amino acids, glutamic and aspartic acid represented a significant portion of all four diets.\n\nThe present study found significant differences in the overall free essential and nonessential amino acid pools in the KP1, KP2, KP3, and KP4 diets (Table 1). One-way ANOVA results exhibited a marginally significant interaction between experimental diets in terms of essential amino acids (F(3,8) = 11.371, P = 0.003), nonessential amino acids (F(3,8) = 0.407, P = 0.752), and overall amino acid pools (essential plus nonessential) (F(3,8) = 7.355, P = 0.011). Duncan's Post-hoc test revealed that the free essential amino acids (9.03 ± 0.003%), nonessential amino acids (8.88 ± 0.004%), and overall amino acid pools (17.91%) were significantly higher (P < 0.05) in feed supplemented with CP3 products, followed by CP2, CP4, and CP1 products (Table 1).\n\nCommercial feed combined with a new formulation product significantly affected the proximate carcass composition of juvenile giant gourami. One-way ANOVA results showed a marginal interaction among group treatments in the case of protein contents (F(3,8) = 1.522, P = 0.282), fat (F(3,8) = 5.663, P = 0.022), carbohydrates (F(3,8) = 1.862, P = 0.214), and crude fibre (F(3,8) = 1.445, P = 0.300). Duncan's Post-hoc test revealed that the protein content (28.85 ± 0.45%), fat (2.67 ± 0.04%), carbohydrates (1.97 ± 0.09%), and crude fibre (0.83 ± 0.02%) were significantly higher (P < 0.05) in the KP3 diet than in the other treatments. Meanwhile, the carcass protein content of fish fed KP1, KP2, and KP4 was not significantly different (P > 0.05) between treatments. For the energy total, KP3 was significantly higher (P < 0.05) than the other treatments (Table 2). However, the moisture content of the carcass did not show any significant variation among the KP1, KP2, KP3, and KP4 diets.\n\nMean ± SD.\n\n Values represent the means of triplicate samples.\n\nThe mean quantities of total amino acids in the carcasses of O. goramy fed different diets are given in Table 2. Lysine and leucine represented a significant portion of the essential amino acids of the whole body carcass, and methionine was present in small quantities in all of the whole-body meat. Of the nonessential amino acids, glutamic acid, aspartic acid, and alanine were the highest, and cystine was the lowest for all whole-body carcasses of giant gourami fed different diets. The levels of glutamic acid were significantly higher in carcasses of fish fed the KP3 diet than in those provided the KP1, KP2, and KP4 diets.\n\nWhen the overall quantities of total essential and nonessential amino acids were compared, the whole-body carcass amino acid content was significantly lower (P < 0.05) in fish fed the KP1 diet than in those fed the KP2, KP3, and KP4 diets (Table 2). The number of amino acids (essential plus nonessential) in the carcasses of fish fed the KP3 diet was significantly higher than that in fish fed the KP1, KP2, and KP4 diets.\n\nThe growth coefficient and feed utilization of the giant gourami juveniles displayed significant differences among the diets. One-way ANOVA results exhibited a marginally significant difference between experimental diets in the case of the thermal unit growth coefficient (F(3,8) = 153.99, P = 0.458), and daily growth coefficient (F(3,8) = 59.88, P = 0.288), while total feed intake (% BW day-1) (F(3,8) = 14.938, P = 0.56), and protein efficiency ratio (F(3,8) = 15.78, P = 0.29) also showed significant differences (P < 0.05) among the treatment diets (Figure 2).\n\n(A) Thermal growth coefficient (TGC), (B) daily growth coefficient (DGC), (C) feed intake (FI), and (D) protein efficiency ratio (PER). The mean value and standard deviation (mean ± SD) are presented for giant gourami (n = 3). Different superscripts in the bar diagram of the giant gourami juvenile TGC, DGC, FI, and PER indicate significant differences among other diets (P < 0.05, One-way ANOVA Duncan Post-Hoc).\n\nFurthermore, the thermal growth coefficient (TGC) has often been used to predict growth performance and production performance of aquaculture using water temperature at the fish-rearing location. This study presents the relationship between thermal growth coefficient and condition factor, daily growth coefficient, and protein efficiency ratio (Figure 3). The thermal growth coefficient had strong relationships with the condition factor (r2 = 0.777, Figure 3A), daily growth coefficient (r2 = 0.920, Figure 3B), and protein efficiency ratio (r2 = 0.749, Figure 3D), while the thermal growth coefficient had a moderate relationship with the feed intake (r2 = 0.698, Figure 3C).\n\nThe condition factor was significantly different between diets (F(3,8) = 19.98, P = 0.566) in the present study; while the GSI, HIS, and VFSI displayed marginally significant differences between diets. The HIS was significantly (F(3,8) = 5.389, P = 0.500) higher in the KP3 diet, but KP1, KP2, and KP4 diets had no significant differences among them (Table 3). The GSI value of giant gourami was significantly (F(3,8) = 10.492, P = 0.243) different between diets, and the GSI of giant gourami fed KP3 rations was higher than if fed KP1, KP2, or KP4 diets. The VFSI was not considerably different among the KP1, KP2, and KP4 diets. The Duncan's post-hoc test revealed that the HIS (1.30 ± 0.13%), GSI (4.15 ± 0.36%), and VFSI (2.75 ± 0.34%) were significantly higher (P < 0.05) in the KP3 diet than in the other diets. Meanwhile, BSI showed no significant difference (P > 0.05) among the treatment diets (Table 3).\n\nThe gut morphometric measurements of giant gourami juveniles are presented in Table 4. Fish gut micromorphology was significantly affected by different feeds. One-way ANOVA results showed a significant effect of feed differences between groups in terms of foregut fold height (F(3.8) = 816.70, P = 0.135), foregut fold width (F(3.8) = 129.34, P = 0.974), height of the foregut (F(3.8) = 169,80, P = 0.882), and microvillus height of the foregut (F(3.8) = 56,01, P = 0.285). The Duncan's post-hoc test demonstrated that the foregut fold height (434.13 ± 1.76 μm), fold width (53.23 ± 0.88 μm), enterocyte height (27.42 ± 0.42 μm), and microvillus height (2.79 ± 0.45 μm) were significantly higher (P < 0.05) in fish fed the KP3 diet than those fed the other diets. For the midgut, one-way ANOVA results showed a significant interaction among treatments in the case of fold height (F(3,8) = 5602.628, P = 0.055), fold width (F(3,8) = 129.341, P = 0.974), enterocyte height (F(3,8) = 169.809, P = 0.882), and microvillus height (F(3,8) = 56.016, P = 0.285). The Duncan's post-hoc test showed that the fold height of the midgut (324.96 ± 1.43 μm), fold width (61.50 ± 1.02 μm), and enterocytes (32.82 ± 0.54 μm) were significantly higher (P < 0.05) in fish fed the KP3 diet, whereas microvillus height was significantly higher in fish fed the KP2 diet (Table 4). Fish fed the KP3 diet showed a higher fold height of the hindgut (F(3,8) = 5459.01, P = 0.066), fold width (F(3,8) = 271.94, P = 0.865), enterocyte height (F(3,8) = 299.180, P = 0.821), and microvillus height (F(3,8) = 253.57, P = 0.316).\n\na hF = fold height.\n\nb wF = fold width.\n\nc hE = enterocyte height.\n\nd hMV = microvillus height.\n\nThe pond water quality values of the giant gourami juvenile rearing freshwater concrete pond were recorded; water temperatures, dissolved oxygen (DO), total alkalinity, hardness, pH, and nitrates were in the range of typical values as given by WHO/FAO, as shown in Table 5.\n\n\nDiscussion\n\nThe chemical analysis of fish feed is essential because it provides valuable information to aquafeed nutritionists concerned with readily available sources of proximate and amino acid compositions, including minerals and vitamins. This study investigated the nutritional quality of fish feed enriched with three different formulation products and one as a placebo. Dietary protein levels for giant gourami ranged from 19.68 to 21.70%. Overall, the crude protein content in the feed of this study was within the ranges observed by other authors.47–49 The giant gourami belongs to the trophic level of herbivorous fish.50 Generally, herbivorous fish require a lower dietary protein level than carnivorous fish.51,49 Reducing the protein content of aquafeed is one method to increase continuous fish farming, by diminishing feed costs and reducing the impact on the aquatic environment.2,52 The fat content of the feed ranged from 3.41 to 3.67%, which is similar to the feed fat content for juvenile grass carp, Ctenopharyngodon idella,53 and lower than the feed fat content for the herbivorous fish Ancistrus cirrhosis48 and for rearing rohu, Labeo rohita.54 At the same time, the carbohydrate content of all feed treatments ranged from 26.37 to 31.19%, and the energy total (kg calorie/100 g) was between 234.41 and 240.87. Although protein content as an energy source for the maintenance and growth of giant gourami is relatively low, energy can be acquired from either protein or nonprotein sources, i.e., fat and carbohydrates.\n\nIn the present study, the commercial fish feed was enriched with natural sources, i.e., formulated products of mature coconut water and palm sap sugar fermented with various fungi (Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae). In the recent past, the dose used was 300 ml/kg of feed. This method is a new approach that has been developed by Azrita et al.9 to improve feed nutrition and whole-body carcasses, covering fatty acids, the atherogenic index and thrombogenic, feed efficiency, and growth performance of giant gourami. Here, we continued the investigation by reducing the feed dose to 150 ml/kg. This study's results found that supplementing feed with newly formulated products can increase feed nutrition, covering amino acids in diet and body meat, and the growth coefficient of giant gourami. Several authors have reported increasing feed nutrition and maximizing the digestive enzyme activity of aquacultured fish by providing feed supplemented with EPA and DHA,17 iodine and selenium,10 methionine,12 fish oil,19,11 and soybean oil.20 In addition, the provision of feed has been supplemented with probiotics,21 glycine, and prebiotics.22 In this study, mature coconut water and palm sap sugar solution fermented with various fungi were used to supplement fish feed. In addition to coconut water and palm sugar, mushrooms also play a role in increasing feed nutrition. However, it's better to use Rhizopus oligosporus. As in the present study, Varzakas55 and Vong et al.56 showed that Rhizopus oligosporus can produce various extracellular enzymes. Aspergillus niger. has a high capacity to degrade antigenic proteins, including carbohydrases, proteases, lipases, and phosphatases, when used for fermenting plant-sourced fish feed ingredients.12,57 Saccharomyces cerevisiae is one of the most acclaimed microorganisms. Its effectiveness is due to its useful composition, such as “β-glucans, nucleic acids, mannan oligosaccharides and chitin,” which are used for fermented ingredients.7,58\n\nThe amino acid composition can be used to assess feed quality. Leucine, arginine, and glutamic acid were the most abundant free amino acids in the KP1, KP2, KP3, and KP4 diets. Similarly, in other studies on fish feed, such as feed for largemouth bass, Micropterus salmoides, the feeds were supplemented with glycine, prebiotics, and nucleotides in a soybean meal-based diet.22 Feed for pacu, Piaractus mesopotamicus, was supplemented with an essential amino acid,59 and feed for snubnose pompano, Trachinotus blochii, was supplemented with different levels of protein.60 Apparently, supplementing feed with different ingredients is common, and in other species, leucine, arginine, and glutamic acid were the most abundant FAAs. Conversely, methionine levels were low in all experimental feeds. Methionine is one amino acid that must be available in fish feed because methionine is needed to protect body cells from stress. For optimal growth of juvenile hybrid grouper, 1.89% methionine is required in the feed.18 The experimental feed contained 0.18–0.30% methionine, but whether this amount is sufficient for the needs of giant gourami is poorly understood.\n\nIn the current study, the nonessential amino acid compositions were slightly higher than the essential amino acid compositions in all the experimental diets. It was higher in the KP3 diet than the other diets. In contrast, the essential amino acids of fish feed for snubnose pompano were slightly higher than the nonessential amino acids content.60 This difference may be caused by differences between freshwater fish and marine fish. As in the present study, Prabu et al.60 reported that different dietary protein levels also caused different pools of FAAs, including limiting essential amino acid types in the diet59 and supplemental glycine, prebiotic, and nucleotide levels in the soybean meal-based diet.22 In the present study, this difference in FAA content is caused by various mushrooms used in the formulated products.\n\nGiant gourami juveniles fed the KP3 diet showed higher levels of glutamic acid, aspartic acid, leucine, and lysine and lower levels of tyrosine, methionine, histidine, tryptophan, and cystine in their carcasses than those fed other diets. The carcasses of giant gourami fed the KP3 diet showed the highest sum of FAAs compared to cultured fish fed the KP1, KP2, and KP4. The differences in the FAA profile in the whole-body carcasses of giant gourami could be related to the fungus type used in the formulated products for enriched feed. Each type of mushroom has a different function depending on the fermented fish feed ingredients and is correlated with the whole-body carcass amino acids.12,57 The FAA profile differences could be related to different aspects, such as diet composition,61 dietary protein level,62 and methionine levels in the diet,18 including the water quality of the ponds.63 This study does not analyse the relationship between growth performance and FAA profile or pond water quality. Several authors have reported that the physiological parameters of water quality and animal body composition are usually interrelated.64,60 The present study did not examine whether the difference in FAAs in the whole-body carcass is correlated to pond water quality.\n\nThe lower weight gain of fish fed the KP1 diet compared to fish fed the KP2, KP3, and KP4 diets shows that a deficiency of either fungus in the formulated product for the enriched diet could lower the protein content and related sum amino acids, leading to the inhibition of giant gourami growth. In addition, it also affects feed intake and feed conversion ratios. The low protein efficiency ratio and daily growth coefficient in fish provided the insufficient KP1 diet were perhaps due to an amino acid imbalance. The amino acid content of the KP2, KP3, and KP4 diets increased, ranging from 16.88% to 17.91% after fermentation. The increase may be due in part to the increased protein content in the KP2, KP3, and KP4 diets, which was in line with the results of Jannatullah et al.57 and Li et al.,12 who found that Aspergillus niger and Aspergillus awamori fermentation increased the amino acid content of soybean meal by 2.56% and 15.56%, respectively. In addition, Dawood et al.36 stated that the essential amino acid profile was changed after fermentation by Saccharomyces cerevisiae. This might result from the different fungi used having different utilization patterns for amino acids in this study. It influences the growth performance and nutrient utilization of giant gourami juveniles. We found that the methionine proportion was lower in the diets in the current study. In addition, methionine is an essential amino acid that plays a unique role in protein structure and metabolism.18 It is possible that Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae fermentation promoted the conversion of specific amino acids to methionine. However, the exact mechanisms need to be studied further.\n\nIn the present study, the thermal growth coefficient (TGC) strongly correlated with the daily growth coefficient (DGC). Because faster daily fish growth requires a quality diet and constant water temperature during the rearing period, in this study, water temperature ranged from 27 to 30°C, and dissolved oxygen was between 5.8 and 6.2 mg/L. According to Besson et al.,65 higher daily energy availability in the diet can lead to faster-growing fish, which is supported by constant water temperature and higher daily oxygen levels. The thermal growth coefficient had an essential change in environmental value.66 Therefore, it was very important to keep the water temperature and dissolved oxygen constant in the aquaculture locations. At the same time, 78% of TGC values were determined by the condition factor connected to whole body weight and the total fish length. TGC of Atlantic cod, Gadus morhua, is influenced by body size and condition factors.67\n\nIn this study, a higher value of TGC was detected in fish fed KP3; the effect is that the daily growth coefficient, and the protein efficiency ratio is better. Conversely, decreasing TGC has two effects, i.e., a slow fish growth and lowered daily feed intake. Many scientists state that in aquaculture operations, net yield (kg/m3) depends upon TGC fluctuation, feed intake, and daily oxygen consumption.65,68,69\n\nIn the present study, feed enrichment with different formulated products did not affect HIS or VFSI except in the KP3 diet. Whereas GSI is influenced by differences in diet, it did not affect BSI. The condition factor of largemouth bass, Micropterus salmoides (1.49–1.52%), fed enriched 1–2% EPA + DHA17 was different from the value (0.68) reported by Arriaga-Hernandez et al.70 for white snook (Centropomus viridis) juveniles fed a 15% replacement of fish meal with soybean meal. Moreover, Hassan et al.71 reported condition factor values ranging from 1.52 to 2.95 and an HSI between 1.4 and 1.5 for Lates calcarifer under different feeding rates (3–9% body weight d-1). Barbosa et al.72 reported VSI and LSI values of 2.24 and 3.86, respectively, for Centropomus parallelus fed a commercial diet. On the other hand, Syed et al.64 also reported HSI and VSI values of 3.41 and 4.90, respectively, for Oreochromis niloticus at different levels of aloe vera extract as feed additives. In our study, the VSI of O. goramy ranged from 3.17 to 4.15, and the LSIs were between 1.74 and 2.75, both higher than those recorded at different stocking densities of O. goramy.44 The high content of visceral fat observed in fish fed the KP3 diet might be explained by the diet having fat contents that exceed the needs of giant gourami juveniles and by the reduced energy expenditure of fish that are confined to rearing frame nets. Therefore, further analysis is necessary to determine the optimum dosage of the formulated product for the enrichment of feed to improve the growth performance of O. goramy.\n\nFor fish, the gut plays a significant role in absorbing nutrients, which is closely related to feed utilization.18,73 Rossi et al.22 demonstrated that the development of enterocytes affected the nutrient-absorbing efficiency of the gut of Micropterus salmoides. Feeding Lates calcarifer juveniles with the same basal diet supplemented with 1% probiotic yeast, Saccharomyces cerevisiae, and lactic acid bacteria, Lactobacillus casei, revealed a higher number of gut mucosal goblet cells and increased microvillous length.74 In contrast, substituting as much as 12.5–25% soya protein concentrates with lupin (Lupinus albus) meal in carp (Cyprinus carpio) diets does not significantly affect the villi length and villi width of the gut.75 In the current study, enriched feed with products supplemented from coconut water, palm sap sugar, and fungus significantly affected the micromorphology and gut size. The fold height, fold width, enterocyte height, and microvilli of fish fed the KP3 diet were higher than those of fish fed the KP1, KP2, and KP4 diets. The KP3 diet is a relevant formulated product to enrich commercial feed to promote the development of the gut in animal experiments, which may somewhat describe the significant growth performance and feed efficiency used in this study.\n\nFurthermore, the micromorphology gut size of giant gourami is smaller than that of juvenile hybrid grouper,18 turbot, Scophthalmus maximus,12 largemouth bass, Micropterus salmoides,22 and common carp, Cyprinus carpio.75 The trophic food habits of fish may also affect the gut's hF, wF, hE, and hMV size because these habits are correlated with the digestibility coefficient. Under natural conditions, giant gourami is an herbivorous fish, while grouper, largemouth bass, and turbot are predatory fish, and common carp are omnivorous. Whether giving fish from different trophic levels the same diet affects the size of gut hF, wF, hE, and hMV is poorly understood.\n\n\nConclusions\n\nThe present investigation observed that feed enriched with newly formulated products made from mature coconut water and palm sap sugar, and fermented with various mushrooms, given to fish in a dose of 150 ml/kg substantially affected the amino acid composition of the diet and whole-body carcass of giant gourami juveniles. It also affected the growth coefficient, feed utilization, body indices, and gut micromorphology size. The thermal growth coefficient had a strong relationship with the daily growth coefficient (r2 = 91%) and a moderate relationship with the feed intake (r2 = 69%). The CP3 formulation was optimal for feed quality, and the KP3 diet was optimal for body carcass, growth coefficient, body indices, and the ability of the intestines for feed absorption. Thus, our study also informs fish farmers about culturing good quality giant gourami and fulfilling nutrition requirements for food security.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Effect of feed enriched by products formulated from coconut water, palm sap sugar, and mushroom on the chemical composition of feed and carcass, growth performance, body indices, and gut micromorphology of giant gourami, Osphronemus goramy (Lacepède, 1801), juveniles’. https://doi.org/10.6084/m9.figshare.20407647. 76\n\nThis project contains the following underlying data:\n\n- Table 1. Raw data of the experimental diets’ proximate composition\n\n- Table 2. Raw data of amino acid of feed experimental\n\n- Table 3. Raw data of whole body carcass proximate composition\n\n- Table 4. Raw data of amino acid of whole-body carcass\n\n- Table 5. Daily growth coefficient, feed utilization and body indices of giant gourami after 90 days of feeding.\n\n- Table 6. Raw data gut micromorphology of giant gourami juveniles fed different diets for 90 days\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 are grateful to the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia for funding this research. We would also like to thank the students and fish farmers who helped with data collection in the field and in the laboratory.\n\n\nReferences\n\nFood and Agriculture Organization (FAO): The state of world fisheries and aquaculture: Opportunities and challenges. Food and Aqriculture Organization of the United Nations;2018; 209.\n\nHua K, Cobcroft JM, Cole A, et al.: The future of aquatic protein: Implications for protein sources in aquaculture diets. One Earth. 2019; 1(3): 316–329. 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Publisher Full Text\n\nAndriani J, Setiawati M, Sunarno MTJ: Diet digestibility and growth performance of giant gourami juvenile, Osphronemus goramy fed on a diet supplemented using glutamine. Jurnal Iktiologi Indonesia. 2019; 19(1): 1–11. Publisher Full Text\n\nBudi DS: Alimuddin, Suprayudi MA: Growth response and feed utilization of giant gourami (Osphronemus goramy) juvenile feeding different protein levels of the diets supplemented with recombinant growth hormone. HAYATI J. Biosci. 2015; 22(1): 12–19. Publisher Full Text\n\nWibowo WP, Sumidjan I, Rachmawati D: Analysis of relative growth rate, feed efficiency and survival of giant gourami, Osphronemus goramy juvenile through substituting chicken feather flour silage in artificial feed. J. Aquac. Manag. Technol. 2017; 6(2): 51–58.\n\nSegura-Badilla O, Lazcano-Hernández M, Kammar-García A, et al.: Use of coconut water (Cocus nucifera L) for the development of a symbiotic functional drink. Heliyon. 2020; 6(3): e03653. 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Publisher Full Text\n\nProkoso VA, Pouil S, Chahyanti W, et al.: Fluctuating temperature regime impairs growth in giant gourami (Osphronemus goramy) larvae. Aquaculture. 539: 736606. Publisher Full Text\n\nSyandri H, Mardiah A, Azrita, et al.: Effect of stocking density on the performance of juvenile gurami sago (Osphronemus goramy) in the synthetic sheet pond. Pak. J. Zool. 2020; 52(2): 717–726.\n\nBoyd CE, Tucker CS, Somridhivej B: Alkalinity and hardness: Critical but elusive concepts in aquaculture. J. World Aquacult. Soc. 2016; 47(1): 6–41. Publisher Full Text\n\nBoyd CE, Tucker CS: Pond aquaculture water quality management. Boston:Kluwer Academic Publishers;1988.\n\nTimalsina P, Yadav CNR, Lamsal GP, et al.: Effect of stocking density and source of animal protein on growth and survival of rainbow trout fingerling in flow-through system at Nuwakot Nepal. Aquac. Rep. 2017; 8: 58–64. Publisher Full Text\n\nVucko MJ, Cole AJ, Moorhead J, et al.: The freshwater macroalga Oedogonium intermedium can meet the nutritional requirements of the herbivorous fish Ancistrus cirrhosis. Algal. Res. 2017; 27: 21–31. Publisher Full Text\n\nYu H, Liang H, Ren M, et al.: A study to explore the effects of low dietary protein levels on the growth performance and nutritional metabolism of grass carp (Ctenopharigodon idella) fry. Aquaculture. 2022; 546: 737324.\n\nSyandri H, Azrita, Sumiarsih E, et al.: Nutrient loading and farm characteristics of giant gourami fish aquaculture systems in Lake Maninjau, Indonesia: Basic knowledge of production performance. F1000 Res. 2021; 10: 378. Publisher Full Text\n\nOmasaki SK, Janssen K, Besson M, et al.: Economic values of growth rate, feed intake, feed conversion ratio, mortality and uniformity for Nile tilapia. Aquaculture. 2017; 481: 124–132. Publisher Full Text\n\nArenas M, Alvarez-Gonzalez A, Barreto A, et al.: Effect of dietary carbohydrates on growth performance, feed efficiency and glucose metabolism in common snook (Centropomus undecimalis) and yellowtail snapper (Ocyurus chrysurus) juveniles. Aquaculture. 2021; 543: 736958. Publisher Full Text\n\nTian J, Li Y, Zhang K, et al.: Dietary Pennisetum sinese Roxb meal reduces lipid accumulation and alleviates enteritis in juvenile grass carp, Ctenopharingodon Idella. Aquac. Rep. 2021; 21: 1000915.\n\nAli S, Kaviraj A: Aquatic weed Ipomoea aquatica as a feed ingredient for rearing Rohu, Labeo rohita (Hamilton). Egypt. J. Aquat. Res. 2018; 44(4): 321–325. Publisher Full Text\n\nVarzakas T: Rhizopus oligosporus mycelial penetration and enzyme diffusion in soya bean tempee. Process Biochem. 1998; 33(7): 741–747. Publisher Full Text\n\nVong WC, Hua XY, Liu SQ: Solis-state fermentation with Rhizopus oligosporus and Yarrowia lipolytia improved nutritional and flavor properties of okara. LWT. 2018; 90: 316–322. Publisher Full Text\n\nJannathulla R, Dayal JS, Ambasankar K, et al.: Effect of Aspergillus niger fermented soybean meal and sunflower oil cake on growth carcass composition and hemolymph indices in Peneus vannamei Boone, 1931. Aquaculture. 2018; 486: 1–8. Publisher Full Text\n\nHuang L, Ran CHS, Ren P, et al.: Effects of dietary Saccharomyces cerevisae culture or live cells with Bacillus amyloliquefaciens spores on growth performance, gut mucosal morphology, hsp70 gene expression, and disease resistance of juvenile common carp (Cyprinus carpio). Aquaculture. 2015; 438: 33–38. Publisher Full Text\n\nOliveira TS, Khan KU, Boarartt AZ, et al.: Evaluation of the optimum dietary essential amino acid pattern for adult pacu (Piarachus mesopotamicus). Aquaculture. 2021; 540: 736686. Publisher Full Text\n\nPrabu DL, Ebeneezar S, Chandrasekar S, et al.: Influence of graded level of dietary protein with equated level of limiting amino acids on growth, feed utilization, body indices and nutritive profile of snubnose pompano, Trachinotus blochii (Lacepede, 1801) reared in low saline water. Anim. Feed Sci. Technol. 2020; 269: 114685. Publisher Full Text\n\nHua K, Bureau D: Estimating changes in essential amino acid requirements of rainbow trout and Atlantic salmon as a function of body weight or diet composition using a novel factorial requirement model. Aquaculture. 2019; 513: 734440. Publisher Full Text\n\nLu X, Peng D, Chen X, et al.: Effect of dietary protein levels on growth, muscle composition, digestive enzymes activities, hemolymph biochemical indices and ovary development of pre-adult red swamp crayfish (Procombarus clarkia). Aqua. Rep. 2020; 18: 100542. Publisher Full Text\n\nFatima S, Komal W, Manzoor F, et al.: Analysis of the growth performance, stress, profile of fatty acids and amino acids and cortisol in Tilapia (Oreochromis niloticus), cultured at high stocking density using in-pond raceway system. Saudi J. Biol. Sci. 2021; 28(12): 7422–7431. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSyed R, Masood Z, Hasan HU, et al.: Growth performance, heamatological assessment and chemical composition of Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) fed different levels of Aloe vera extract as feed additives in a closed aquaculture system. Saudi J. Biol. Sci. 2022; 29: 296–303. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBesson M, Vandeputte M, van Arendonk JAM , et al.: Influence of water temperature on the economics of growth in fish farming: The case of sea bass (Dicentrarchus labrax) cage farming in the Mediterranean. Aquaculture. 2016; 462: 47–55. Publisher Full Text\n\nBesson M, Aubin J, Komen H, et al.: Environmental impacts of genetic improvement of growth rate and feed conversion ratio in fish farming under rearing density and nitrogen output limitations. J. Clean. Prod. 2015; 116(10): 100–109.\n\nJobling M: The thermal growth coefficient (TGC) model of fish growth: A cautionary note. Short Communication. Aquac. Res. 2003; 34: 581–584. Publisher Full Text\n\nZhou X, Wang J, Huang L, et al.: Modelling and controlling dissolved oxygen in recirculating aquaculture systems based on mechanism analysis and an adaptive PID controller. Comput. Electron. Agric. 2022; 192: 106583. Publisher Full Text\n\nSun M, Hassan SG, Li D: Models for estimating feed intake in aquaculture: A review. Comput. Electron. Agric. 2016; 127: 425–438. Publisher Full Text\n\nArriaga-Hernandez D, Hernandez C, Martinez-Montano E, et al.: Fish meal replacement by soybean products in aquaculture feeds for white snook, Centropomus viridis: Effect on growth, diet digestibility, and digestive capacity. Aquaculture. 2021; 530: 735823. Publisher Full Text\n\nHassan HU, Ali QM, Ahmad N, et al.: Assessment of growth characteristics, the survival rate and body composition of Asian sea Lates calcarifer (Bloch, 1790) under different feeding rates in closed aquaculture system. Saudi J. Biol. Sci. 2021; 28: 1324–1330. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarbosa MC, Jatoba A, Vieira FN, et al.: Cultivation of Juvenile Fat Snook (Centropomus parallelus, Poey, 1860) Fed Probiotic in Laboratory Conditions. Braz. Arch. Biol. Technol. 2011; 54(4): 795–801. Publisher Full Text\n\nMohammadi M, Imani A, Farhangi M, et al.: Replacement of fishmeal with processed canola meal in diets for juvenile Nile tilapia (Oreochromis niloticus): Growth performance, mucosal innate immunity, hepatic oxidative status, liver and intestine histology. Aquaculture. 2019; 518: 734824. Publisher Full Text\n\nSiddik MAB, Foysal MJ, Fotedar R, et al.: Probiotic yeast Saccharomycs cerevisiae coupled with Lactobacillus casei modulates physiological performance and promotes gut microbiota in juvenile barramundi. Lates calcarifer. Aquaculture. 2022; 546: 737346. Publisher Full Text\n\nAnwar A, Wan AH, Omar S, et al.: The potential of a solid-state fermentation supplement to augment white lupin (Lupinus albuas) meal incorporation in diets for farmed common carp (Cyprinus carpio). Aqua. Rep. 2020; 17: 100348. Publisher Full Text\n\nAzrita A, Syandri H, Aryani N, et al.: Underlying data for ‘Effect of feed enriched by products formulated from coconut water, palm sap sugar, and mushroom on the chemical composition of feed and carcass, growth performance, body indices, and gut micromorphology of giant gourami, Osphronemus goramy (Lacepède, 1801), juveniles’. At Figshare. 2022. Publisher Full Text" }	[ { "id": "163500", "date": "28 Feb 2023", "name": "Fatimah Hashim", "expertise": [ "Reviewer Expertise Cytotoxicity", "microscopy techniques", "protozoology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, thank you for your paper and we appreciate the effort and contribution that you have made to the field.\nHowever, we noticed that your paper lacks results for the micromorphology part, which makes it difficult to fully understand the conclusions of your study. Specifically, we're unable to fully assess the morphological characteristics of the samples and how they relate to the overall findings. Therefore, we suggest that you consider adding some additional data/results where necessary. Additionally:\nSome scientific names were not italicised.\n\nThe number at the beginning of the sentence must be spelt out.\n\nSome literature in the introduction compares the use of coconut water on terrestrial animal or human levels. It is better to compare with aquatic organisms that are more related to the gourami.\n\nThe author should provide all morphology results on gut micromorphology (in the form of images/ figures), not only the data measurement (Table 4.)\n\nAdditional comments from Fatimah Hashim attached here.\nAdditional comments from Nor Omaima Harun attached here.\n\nIs the work 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": "9578", "date": "11 Sep 2023", "name": "Azrita Azrita", "role": "Author Response", "response": "Reviewer Report by Fatimah Hashim, Universiti Malaysia Terengganu, Terengganu, Malaysia Nor Omaima Harun, Universiti Malaysia Terengganu, Terengganu, Malaysia Author Respond: We agree that several scientific names should be italicized as in the Abstract: Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae. Author response: We agree that when a number appears at the beginning of a sentence, the number must be spelled out with letters, just like the example in the Abstract where the number 100 is changed to One hundred, the number 2 liters is changed to Two litres, and 1 litres changed to One litres. Author's Response: Previously, we stated in the introduction that animals or humans have used coconut water on land. However, no literature has been found testing the use of coconut water on aquatic animals, including gourami. Therefore, this study focuses on the novelty of using new product formulas for coconut water, palm sugar, and mushroom in aquatic animals, especially giant gourami. Author response: Olympus Model IX71, HBO 100W, Phase Contrast Microscopy, Fluorite Lenses, Inverted Cell Culture, Fluorescence Microscope, Country: Japan. Author response: We have prepared gut micromorphology images and are willing to display Figure 4 in the article if the editorial team approves the addition (Please open this link)." } ] }, { "id": "196596", "date": "25 Aug 2023", "name": "Qadar Hasani", "expertise": [ "Reviewer Expertise Plant Botany and Ecology", "Pollution", "and Environmental Chemistry", "The Dynamics of the Plankton Community", "fish biology", "and fish nutrition." ], "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\nBackground: Please add the sentence \"of juvenile giant gourami\" to the end of the sentence.\n\nMethods: Scientific names of Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae \"please write in italic\"\n\nResults: Please add include the regression values (r2) for the condition factor, feed intake, and protein efficiency ratio.\n\nConclusion: Please add a sentence for the condition factor and body indices to the end of the sentence.\nIntroduction\nPlease include the scientific name of the Azolla plant.\n\nPlease maintain consistency with the term \"whole-body carcass\".\n\nPlease enhance the third paragraph by introducing or used fermented mushrooms (specifically Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae).\n\nPlease incorporate into the seventh paragraph the second objective of the research, which focuses on analyzing the condition factor and feed intake of giant gourami juveniles, along with their correlation to thermal growth coefficient, body index, and gut micromorphology.\nMethods:\n\nEthical approval part; Please explain, namely \"Gurami sago\" whether it is a new species or strain.\n\nExperimental procedures part and sampling; Please ensure consistency with the term \"gurami sago.\" or changed to \"giant gourami\"\n\nPlease add state the manufacturing country of the light microscope (Olympus IX71) equipped with Image-Pro Plus 7.0 software.\nResults:\nThe authors have displayed data concerning intestinal micromorphology (Table 4). It is recommended that the authors present all morphological findings related to intestinal micromorphology in the form of images/figures.\nDiscussion:\n\nPlease be consistent with the name used for example giant gourami.\nConclusions:\nPlease include regression values for each parameter, such as the condition factor (r2 = 0.77) and protein efficiency ratio (r2 = 0.74).\n\nPlease maintain consistency with the term \"whole-body carcass\".\n\nIs the work 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": "10117", "date": "29 Aug 2023", "name": "Azrita Azrita", "role": "Author Response", "response": "Reviewer Report response by Qadar Hasani, Aquatic Resources Study Program, Faculty of Agriculture, Lampung University, Bandar Lampung, Lampung, Indonesia. Abstract Background: We agree to add the sentence \"of juvenile giant gourami\" at the end of the sentence. These suggestions will be fixed in a new revised version. Methods: We have agreed that some scientific names should be italicized as shown in the abstract, for example Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae. These suggestions will be fixed in a new revised version. Results: We will add the regression value (r2) for each parameter if the abstract does not exceed 300 words. Conclusion: We will add the condition factor and body indices if the abstract does not exceed 300 words. Introduction We will add scientific name of Azolla plant (Azolla pinnata) in new revised version. In the new revised version, we will consistently use the phrase \"whole-body carcass\" We have mutually decided to include the scientific names of three specific species: Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae, in the upcoming revised version. The seventh paragraph of the new revised version will encompass the second research objective. This objective entails investigating the condition factor concerning the feeding of giant gourami fingerlings and its correlation with the thermal growth coefficient, body index, and gut micromorphology. Methods Ethical Approval Section: The Sago gourami represents one of the giant gourami strains, and we will include it in the new revised version. We will consistently write \"Giant gourami\" in the revised version of the article. We will append a newly revised version of the article with the information that Japan is the nation where light microscopes (Olympus IX71) equipped with Image-Pro Plus 7.0 software are manufactured. In order to enhance the data presented in Table 4, we will incorporate images or figures depicting intestinal micromorphology within the new version of the revision. Discussion In the revised version, we will consistently use the name \"Giant gourami\". Conclusions: In the new revised version, we agreed to include the coefficient of determination (r2) in the conclusion section, for the condition factor (r2 = 0.77) and the protein efficiency ratio (r2 = 0.74)." } ] } ]	1	https://f1000research.com/articles/12-140
https://f1000research.com/articles/12-811/v1	11 Jul 23	{ "type": "Research Article", "title": "Investigating the link between frontal sinus morphology and craniofacial characteristics with sex: A 3D CBCT study on the South Indian population", "authors": [ "Ceena Denny", "Mohana Bhoraskar", "Sabiha Abdul Aziz Shaikh", "Bastian T S", "Nanditha Sujir", "Srikant Natarajan", "Ceena Denny", "Mohana Bhoraskar", "Sabiha Abdul Aziz Shaikh", "Bastian T S", "Nanditha Sujir" ], "abstract": "Background: Measurement of craniofacial parameters plays an important role in sex determination in forensic science. The present study was done using cone beam computed tomography (CBCT) scans to evaluate the morphologic structure of the frontal sinuses and compare it with the width of nasal, cranial, maxillary and mandibular width which might help us in sex determination. Methods: A cross-sectional retrospective study was conducted using 142 full field of view (FOV) scans of patients archived from the department. The width of the nose, cranium, maxilla, and mandibular width was measured and compared with the frontal sinus between the two sexes. Results: A paired t-test was done to compare the linear measurements for both sexes' right and left frontal sinuses. The measurements were higher in males when compared to females. There was a statistically significant asymmetry (larger dimension on the left side) of the anterioposterior (p-value of 0.012) and superior-inferior dimensions in males (p-value of 0.135). Spearman's correlation showed that frontal sinus correlated with other craniofacial parameters like nasal, cranial, maxillary and mandibular width among both sexes. The frontal sinus, nasal, cranial, maxillary and mandibular widths were higher in males when compared to females (independent t-test). Discriminant function scores showed 66-68% accuracy to discriminate sex, using the anteroposterior dimension and mandibular width. Conclusions: The measurement of craniofacial parameters using CBCT can aid in determining the sex of unidentified and decomposed bodies.", "keywords": [ "Frontal sinus", "Craniofacial parameters", "Forensic science", "Cone Beam Computed Tomography", "Sex determination" ], "content": "Introduction\n\nDetermining the identity of human remains through visual assessment of craniofacial parameters using linear measurements is a common practice in forensic science. Unfortunately, accidents, natural disasters, and fires can cause severe decomposition or damage to the body, making identification difficult. In these cases, anthropological knowledge is crucial in identifying the remains. The skull, being the most complex and stable part of the human body, can withstand force and assist in forensic investigations.1\n\nThe frontal sinus is a crucial component of the human skull, located in the pneumatized cavity of the frontal bone. While typically paired, these sinuses are seldom symmetrical and can vary in size. Radiographically visible by the 2nd or 3rd year of life, the frontal sinus completes its growth by the age of 20. Interestingly, these sinuses are unique to each individual, even when compared in monozygotic twins.2 By analyzing the shape and size of the frontal sinus, we can gain valuable insights into an individual's craniofacial parameters. This information can be used to diagnose and treat various medical conditions, including sinusitis and facial trauma. It is important to note that the morphology of the frontal sinus can vary significantly between individuals, making it a valuable tool in personalized medicine.\n\nRadiographs are crucial in identifying anthropological structures when DNA samples and soft tissues are not accessible. Radiology plays a significant role in determining these structures, particularly when considering morphological parameters.3 Cone beam computed tomography (CBCT) is a cutting-edge diagnostic imaging technique that provides a three-dimensional view of a specific region in the head and neck. This technology allows for the visualization of anatomical structures from different angles, without any superimposition, distortion, or magnification. The accuracy of measurements obtained through CBCT makes it a superior imaging modality compared to traditional two-dimensional imaging.4 One of the most significant advantages of CBCT is its cost-effectiveness, as well as its ability to expose individuals to less radiation. This makes it a safer and more accessible option for patients. While CBCT has been widely used in the field of anthropology, it has recently gained more attention in the field of forensic identification.5\n\nNumerous studies have been conducted in the past using radiographs to assess the importance of the frontal sinus in determining an individual's characteristics. However, very few studies have been conducted using CBCT in the South Indian population. Our study aims to fill this gap by focusing on the South Indian population, which has distinct craniofacial features compared to other populations. Through this research, we hope to enhance the understanding of the relationship between frontal sinus morphology and craniofacial parameters in this specific population.\n\nThe purpose of this study is to evaluate the morphological structure of the frontal sinuses and compare it with the nasal, maxillary, cranial and the mandible widths. This information can be useful in identifying and determining human characteristics.\n\n\nMethods\n\nEthical approval was obtained from the Manipal College of Dental Sciences' Institutional Ethics Committee (protocol ref no: 21056, dated 20/9/21). As part of the dental treatment, participants were asked to provide written consent for the use of their anonymized data in future research and publications.\n\nA cross-sectional retrospective study was conducted after obtaining ethical clearance. 142 full field of view (FOV) scans of patients were archived from the Oral Medicine and Radiology department. The images selected were those of South-Indian population which included a subset of residents of the Dakshina Kannada district catering to the West coast of India.\n\nBased on the article “Association between frontal sinus morphology and craniofacial parameters: A forensic view published in the Journal of Forensic Legal Medicine by authors S.K. Buyuk et al. in the year 2017,6 the correlation coefficient derived/reported was 0.231. With an alpha error of 5% and a power of 80%, the Z values of the given alpha and beta values are 1.95996398454005 and 0.841621233572915. With the correlation coefficient and using the above formula the required sample size was 142.\n\nThe frontal sinuses were evaluated in patients who were above 20 years with no history of trauma, cranial anomalies, associated pathologies in the sinus, skull/orthognathic surgery, and endocrine disorders. 66 scans were of the male sex and 77 scans were of the female sex in the age range of 20-54 years old.\n\nThe cone beam computed tomographic (CBCT) scans were acquired using the Promax 3DMid (Planmeca Oy., Helsinki, Finland) CBCT unit. The large FOV, low dose images that allowed complete visualization above the frontal sinuses were taken with the exposure parameters being 90 kVp, 5.6 mA, and exposure time of 18 seconds (DAP-925 mGycm2, CTDI-3.7 mGy). A slice thickness of 0.400 mm was used to assess the sections. The exposure parameters according to the standard default values were based on the FOV. The images were reconstructed using the Romexis software version 4.6.2.R (ITK-SNAP 4.0 I can be used as an alternative).\n\nThe linear measurements were done on the reconstructed image in the following way (Figure 1):\n\n• Frontal sinus - For assessment of maximum supero-inferior measurements, the coronal section was utilized and measurement was taken between the highest and lowest point of both the right and left frontal sinus, while the axial section was used to measure the maximum antero-posterior and mesiodistal width of the left and right frontal sinus.\n\n• Cranium - For the measurement of the maximum width of the cranium, the axial section was adjusted to the level of the superior border of the orbit (while looking at the coronal view), and at this level, measurement was taken from the inner cortical plate on one side to the inner cortical plate on the contralateral side.\n\n• Nasal - The maximal nasal width was taken in the axial section after adjusting it at the level of the zygomatic arch.\n\n• Maxilla - Axial section was skimmed till the maximal width of the maxilla was observed and in this section, measurement was taken.\n\n• Mandibular width at antegonial notch - The maximum width of the mandible was taken at the level of the antegonial notch. For this purpose, first, the axial view was angulated so that in the sagittal section, the gonial and antegonial notch were observed. The axial view was then adjusted to the level of the antegonial notch and in this section, the maximal mandibular width was taken.\n\nData were analyzed using Statistical Product and Service Solutions (SPSS, version 20.0 (SPSS Inc, Chicago IL). Asymmetry between the dimensions measured was compared using paired t-test. The correlation of the anthropometric variables with the sinus morphometry was done using Spearman's correlation. The difference in the dimensions between the sexes was explored using an independent t-test and the precision of classification was calculated using discriminant function analysis.\n\n\nResults\n\nThere was asymmetry detected of the frontal sinus in all the patients in terms of the mesiodistal, anteroposterior and superoinferior dimensions with the majority showing the left side larger than the right side.24 However, only the anteroposterior dimension was significantly more on the left side in males (p-value 0.012, paired-test) (Table 1).\n\nMandibular parameter correlates moderately with anteroposterior dimension on the left and right side in males but not in females. The anteroposterior dimension of the left side and the mesiodistal dimension of the left side correlate significantly (r=0.357, p=0.003) in males but not in females. On the other hand, the anteroposterior dimension of the right side correlates with the mesiodistal dimension of the right side in both females and males. The cranial parameter shows a moderate negative correlation with the anteroposterior dimension of the left side (r value of-0.235, p-value of 0.039) and nasal dimension (r value of -0.248, p-value of 0.03) in females but not in males. Maxillary dimension showed a significant positive correlation with mandible (r value of 0.326 and p value of 0.004) in females and not in males. Nasal dimensions correlated with superoinferior dimensions on the right side in females (0.233 and p-value of 0.041) but not in males. Superoinferior dimensions correlated positively with mesiodistal as well as anteroposterior dimensions in males and females (p<0.05, r ranges from 0.248 to 0.461) (Table 2).\n\n Significant with p value <0.05.\n\n** Significant with p value <0.001.\n\nAn independent t-test was done to compare the measurements between the two sexes and it was found that there was a statistically significant difference between them. The frontal sinus, nasal, cranial, maxillary and mandibular widths were higher in males when compared to the females and this was statistically significant except for the nasal width, cranial and mesiodistal measurements of the frontal sinus (Table 3).\n\nComparing the discriminant function scores we found that the male values are consistently higher than the female values in all the cases. The discriminant function equations and the demarcation points are given in Table 4. The highest accuracy was seen with the mandibular width with 68.3% accuracy, followed by anteroposterior left dimensions with 66.90%. Both the mandible and the left anterior-posterior dimensions were more accurate in females than in males. The other variables like the superio-inferior and mesio-distal measurements of frontal sinus and nasal dimensions were below 60% accuracy. The discriminant function equations can be used with sectioning points of roughly zero to demarcate the sex.\n\n\nDiscussion\n\nSex, age and stature are crucial factors in identifying unknown individuals through skeletal remains, especially when the body is decomposed or fragmented beyond recognition. Radiographs are often used to aid in this process, as the anatomic structures and their variations are unique to each individual.7 In forensic dentistry, craniometric parameters also play a significant role in both postmortem and antemortem evaluations of bodies. Cranial dimensions vary among different populations, and measuring the cranium can help determine racial differences.8 Zuckerkandl reported in 1895 that the morphology of the frontal sinus is unique to each individual and can be used for identification purposes.9 Our study was a retrospective cone beam computed tomographic study, utilizing archived images from the South-Indian population, specifically a subset of the Dakshina Kannada district on the West coast of India. This research aims to establish specific anthropometric patterns for different populations, highlighting the importance of considering regional variations in forensic investigations.\n\nThe frontal sinus is a structure that becomes visible on radiographs at around 5-6 years of age and stops growing around 20 years.7 It is intriguing to note that no two individuals have the same frontal sinus.10 Research has shown that the frontal sinus is larger in males than in females,11–13 which is consistent with our own findings. Moreover, when comparing the size of the frontal sinus on each side, we observed that the left side was larger than the right side. This finding is in line with previous studies conducted by Rubira-Bullen IR et al. (2010), Kanat A et al. (2015), Soman BA et al. (2016), and Denny C et al. (2018),12–16 but not with the study by Camargo et al. 2007.11 The difference in size could be attributed to the independent development of the sinuses, resulting in varying sizes even among individuals of the same age.14 Kanat et al. (2015)15 suggested that handedness and footedness may play a role in predicting cerebral dominance, with right-handed individuals exhibiting left hemispheric dominance and vice versa for left-handed individuals.\n\nIn summary, the frontal sinus is a distinctive anatomical structure that exhibits variations in size and shape among individuals. Our study corroborates previous research indicating that males tend to have larger frontal sinuses than females, and that the left side is typically larger than the right. These differences may be attributed to independent development and handedness/footedness, which could potentially impact cerebral dominance.\n\nOur study found that the maximal cranial width measurement was comparable to the research conducted by Ulcay T and Kamaşak B (2021).17 Additionally, we discovered that cranial width was significantly greater in males than in females.18,19 This dimorphism in the male skull is attributed to pubertal changes that result in increased muscular attachments, while the female skull retains juvenile features.20\n\nAccording to a study conducted by Buyuk SK (2017), it was discovered that males have a greater maxillary width than females.6 Dr. G Venkat Rao and G Kiran (2016), stated in their article that dental arch width is indicative of the size of the basal bone. As the basal bone of the jaws is larger in males, this explains why males have a larger maxillary arch.21\n\nThe width of the mandible was found to be greater in males, which is consistent with the findings of previous studies conducted by Sreelekha D et al. (2020)22 and Albalawi AS et al. (2019).3\n\nThe present study investigated nasal width in both males and females and determined that there were no significant differences between the two groups. This finding is consistent with previous research conducted by Buyuk SK (2017) and M. I. Marini et al. (2020).6,23\n\nSpearman's correlation analysis reveals that there is a significant correlation between the right side anterolateral and mesiodistal/superior inferior dimensions in both males and females. Additionally, mandibular dimensions show a significant correlation with anteroposterior dimensions in males, while cranial dimensions exhibit a negative correlation with anteroposterior and nasal dimensions in females. Furthermore, maxillary dimensions display a significant correlation with anteroposterior and mandibular dimensions in females.\n\nThese observations can provide valuable insights for future research by comparing findings across different ethnicities and nationalities. However, to ensure a more accurate representation of the population, it is necessary to conduct further studies with larger sample sizes.\n\n\nConclusions\n\nCone beam computed tomography has revolutionized the way we approach diagnostic imaging, providing a more comprehensive and accurate view of the head and neck region. Its benefits extend beyond the medical field, making it an essential tool for forensic investigations. With its increasing popularity, CBCT is sure to continue to play a vital role in the future of diagnostic imaging.\n\nThis study has the potential to offer valuable insights to medical professionals and researchers in the field of craniofacial medicine. By leveraging advanced imaging technology and focusing on a specific population, we can gain a deeper understanding of the intricate relationship between the frontal sinus and craniofacial parameters.", "appendix": "Data availability\n\nfigshare: Investigating the Link between Frontal Sinus Morphology and Craniofacial Characteristics with Sex: A 3D CBCT study on the South Indian Population. https://doi.org/10.6084/m9.figshare.23559849.v1. 24\n\nThis project contains the underlying measurement data (please note code 1 represents male, and 2 represents female in the sex column).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHarshitha K, Mohamed S, et al.: Evaluation and Correlation of Tooth Morphometrics in the Maxillary Arch for Sex Identification. Oral Maxillofac. Patho. J. 2019; 10(2): 57–60.\n\nSuman JL, Jaisanghar N, et al.: Configuration of frontal sinuses: A forensic perspective. J. Pharm. Bioallied Sci. 2016; Oct; 8(Suppl 1): S90–S95. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlbalawi AS, Alam MK, Vundavalli S, et al.: Mandible: An Indicator for Sex Determination - A Three-dimensional Cone-Beam Computed Tomography Study. Contemp. Clin. Dent. 2019; 10(1): 69–73. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBotticelli S, Verna C, Cattaneo PM, et al.: Two- versus three-dimensional imaging in subjects with unerupted maxillary canines. Eur. J. Orthod. 2011; 33(4): 344–349. PubMed Abstract \| Publisher Full Text\n\nChoi IGG, Duailibi-Neto EF, Beaini TL, et al.: The Frontal Sinus Cavity Exhibits Sexual Dimorphism in 3D Cone-beam CT Images and can be Used for Sex Determination. J. Forensic Sci. 2018; 63(3): 692–698. PubMed Abstract \| Publisher Full Text\n\nBuyuk SK, Karaman A, Yasa Y: Association between frontal sinus morphology and craniofacial parameters: A forensic view. J. Forensic Legal Med. 2017; 49: 20–23. PubMed Abstract \| Publisher Full Text\n\nRao KA, Doppalapudi R, Al-Shammari NT, et al.: Evaluation of frontal sinus index in establishing sex dimorphism using three-dimensional cone beam computed tomography in Northern Saudi Arabian population. J. Forensic Sci. Med. 2022; 8: 1–5. Publisher Full Text\n\nViloria A, Pineda OB, Romero L: Predicting the anthropometric properties of cranial structures using big data. Procedia Comput. Sci. 2020; Jan 1; 170: 905–910. Publisher Full Text\n\nda Silva RF , Pinto RN, Ferreira GM, et al.: Importance of frontal sinus radiographs for human identification. Braz. J. Otorhinolaryngol. 2008; 74(5): 798. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuckland-Wright JC: A radiographic examination of frontal sinuses in early British populations. Man. 1970; 5: 512–517. Publisher Full Text\n\nCamargo JR, Daruge E, Prado FB, et al.: The frontal sinus morphology in radiographs of Brazilian subjects: Its forensic importance. Braz. J. Morphol. Sci. 2007; 24: 239–243.\n\nDenny C, Jacob AS, Ahmed J, et al.: Frontal Sinus as an aid in Gender Identification in Forensic Dentistry: A Retrospective Study using Cone Beam Computed Tomography. World J. Dent. 2018; 9(1): 34–37. Publisher Full Text\n\nBelaldavar C, Kotrashetti VS, Hallikerimath SR, et al.: Assessment of frontal sinus dimensions to determine sexual dimorphism among Indian adults. J. Forensic Dent. Sci. 2014; 6(1): 25–30. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRubira-Bullen IR, Rubira CM, Sarmento VA, et al.: Frontal sinus size on facial plain radiographs. J. Morphol. Sci. 2010; 27(2): 77–81.\n\nKanat A, Yazar U, Ozdemir B, et al.: Frontal sinus asymmetry: Is it an effect of cranial asymmetry? X-ray analysis of 469 normal adult human frontal sinus. J. Neurosci. Rural Pract. 2015; Oct-Dec; 06(4): 511–514. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoman BA, Sujatha GP, Lingappa A: Morphometric evaluation of the frontal sinus in relation to age and gender in subjects residing in Davangere, Karnataka. J. Forensic Dent. Sci. 2016 Jan-Apr; 8(1): 57. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUlcay T, Kamaşak B: Evaluation of craniometric measurements in human skulls. J. Health Sci. Med. 2021; 4(1): 38–44. Publisher Full Text\n\nIlayperuma I: On the Prediction of Personal Stature from Cranial Dimensions. Int. J. Morphol. 2010; 28(4):1135–1140. Publisher Full Text\n\nKhan MA, Chaudhry MN, Altaf FMN: Cranial measurements; estimation of stature from cranial measurements. Professional Med. J. 2015; 22(8): 1034–1038. Publisher Full Text\n\nScheuer L: Application of osteology to forensic medicine. Clin. Anat. 2002; 15(4): 297–312. Publisher Full Text\n\nVenkat DG, Rao GK: Sex Determination by means of Inter-Canine and Inter-Molar Width- A Study in Telangana population. APJHS. 2016 Dec 30 [cited 2023 Apr 4]; 3(4): 171–175. Publisher Full Text Reference Source\n\nSreelekha D, Madhavi D, Jothi SS, et al.: Study on mandibular parameters of forensic significance. J. Anat. Soc. India. 2020; 68: 21–24.\n\nMarini MI, Angrosidy H, Kurniawan A, et al.: The anthropological analysis of the nasal morphology of Dayak Kenyah population in Indonesia as a basic data for forensic identification. Transl. Res. Anat. 2020 Jun; 19: 100064. Publisher Full Text\n\nDenny C: Investigating the Link between Frontal Sinus Morphology and Craniofacial Characteristics with Sex: A 3D CBCT study on the South Indian Population. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "186254", "date": "19 Jul 2023", "name": "Sudeendra Prabhu", "expertise": [ "Reviewer Expertise oral pathology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGood study and well-written manuscript.\n\nBut the discussion and conclusion is incomplete. Kindly mention about the importance of parameters taken for sexual dimporphism and its correlation with sex in the CBCT.\n\nHighlight the important parameter having good co-relation co-efficient.\n\nKindly quote a few more studies using CBCT for sex dimorphism.\n\nThis manuscript can be accepted for indexing with minor modifications.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "186253", "date": "27 Jul 2023", "name": "Arvind Babu Rajendra Santosh", "expertise": [ "Reviewer Expertise Primary focus is on oral disease", "and secondary attention is given towards forensic dentistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe researchers undertook an investigation into the essential areas of forensic dental sciences, particularly focusing on the morphometric characterization of the frontal sinus with respect to gender.\nThe title of the study clearly highlights this specific area of interest. However, in the last two paragraphs of the introduction, it would be advisable for the researchers to provide a more comprehensive justification for studying the morphometric characterization of the frontal sinus with consideration of gender.\n\nThe study's methodology was well-structured and comprehensive, facilitating reliable data collection. However, for the data analysis section, I recommend seeking input from a statistician. Did the study use age-gender matching in their sampling strategy?\n\nThe most highlighting and promising results of the study should be emphasized in the initial section of discussion.\n\nAdd a statement that directly reflects striking findings of your study in the conclusion that answer your hypothesis.\n\nOverall, this study is a valuable contribution to the literature, and we commend the authors for their excellent work. I endorse the manuscript for indexing with minor 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?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-811
https://f1000research.com/articles/11-166/v1	10 Feb 22	{ "type": "Data Note", "title": "Curating maternal, neonatal and child health (MNCH) datasets for spatiotemporal data analytics", "authors": [ "Moses Effiong Ekpenyong", "Patience Usoro Usip", "Kommomo Jacob Usang", "Nnamso Michael Umoh", "Samuel Bisong Oyong", "Chukwudi Obinna Nwokoro", "Aminu Alhaji Suleiman", "Kingsley Attai", "Anietie Emmanuel John", "Inyang Abraham Clement", "Ekemini Anietie Johnson", "Temitope Joel Fakiyesi", "Patience Usoro Usip", "Kommomo Jacob Usang", "Nnamso Michael Umoh", "Samuel Bisong Oyong", "Chukwudi Obinna Nwokoro", "Aminu Alhaji Suleiman", "Kingsley Attai", "Anietie Emmanuel John", "Inyang Abraham Clement", "Ekemini Anietie Johnson", "Temitope Joel Fakiyesi" ], "abstract": "We provide in this Data Note the details of maternal, neonatal and child health (MNCH) datasets curated directly from patients’ medical records; comprising 538 maternal, 720 neonatal and 425 child records, captured at St Luke’s General Hospital, Anua, Uyo, Nigeria, from 2014 to 2019. Variables included in the datasets are gender, age, class of patient (mother/infant/child), LGA (local government area), diagnosis, symptoms, prescription, blood pressure (mm Hg), temperature (degree centigrade), and weight (Kg). The purpose of this publication is to describe the datasets for researchers who may be interested in its reuse (for analysis, research, quality assurance, policy formulation/decision, patient safety, and more). The curated datasets also involved the capturing of location information (GPS: global positioning system data) from the study area, to aid spatiotemporal and informed demographic analysis. We detail the methods used to curate the datasets and describe the protocol of variables selection and processing. For reasons of data privacy, some patients’ personal information such as names were replaced with patient numbers (a sequence generated using Microsoft Excel). Furthermore, the addresses/locations of the patients, date of visit, latitude, longitude, elevation, and GPS accuracy are restricted. Restricted data can be made available to readers after a formal request to the corresponding author (see data restriction statement). The curated datasets are available at the Open Science Framework.", "keywords": [ "context-aware system", "robust decision support", "GeoAI", "healthcare indicator", "location-based information", "MNCH data" ], "content": "Introduction\n\nAccess to health services is essential for promoting health equity and quality of life (dos Anjos Luis & Cabral, 2016). Hence, knowledge of health facilities is crucial for providing informed health planning decisions. Furthermore, available health datasets such as the one presented in this publication show that some patients travel long distances to access health facilities, with the urban areas holding very high concentration of patients’ population per facility. Oleribe et al. (2019) identified financial barrier, poor governance and limited infrastructure, as major factors mitigating access to quality healthcare, typical of sub-Saharan Africa. Situating these factors to the patients’ domain in a country such as Nigeria, reveals the following mitigating factors: finance (poor living condition), increased security threat, type and nature of ailment, geography of residence, race and ethnicity, gender, age, language, and disability. These factors significantly determine the degree at which medical/healthcare services – including availability, timeliness, convenience, and affordability, are utilised (Babalola & Fatusi, 2009). Adoption of modern technology has however simplified healthcare services through the implementation of automated systems. For instance, the integration of electronic health records and predictive intelligence (e.g., smart technology) into healthcare services have achieved efficient, accurate storage and retrieval of patients’ records, as well as intelligent data-driven analysis, prediction, and visualisation (Tian et al., 2019).\n\nUnlike developed nations, health facilities in low- and medium-income countries such as the sub-Sahara African region are overly stressed, generating a large pool of manually unstructured and inconsistent data that defies real-time, patient-centred care. Furthermore, the reduced health budget has decreased government’s efforts in establishing new healthcare centres to equate the present population growth, hence, increasing the establishment of privately owned healthcare centres, premised on business and which services are not conducive to patients in terms of cost. Even though availability of health facilities is often prioritised over accessibility by decision makers (Tuba et al., 2010), Mishra et al. (2019) maintained that geographic accessibility and availability of healthcare facilities are essential parameters in determining the quality of care received, as analysis of both parameters could reveal useful patterns and trends for providing a more robust health system that derives patient-centred care. Patient-centred care (Epstein & Street, 2011) empowers patients to actively participate in their care with physicians and other healthcare providers connecting with patients to effectively address patients’ needs. In providing such a service, location-based information, and details of every parameter within the health system should be available in real-time. Also, collaboration between the necessary stakeholders (physicians and other healthcare providers, government, patients) is necessary and can be enabled using geospatial artificial intelligence (GeoAI) (VoPham et al., 2018; Boulos et al., 2020). GeoAI combines spatial science methods such as GIS (geographic information system), data mining, and high-performance computing to extract meaningful knowledge from spatial big data (VoPham et al., 2018; Janowicz et al., 2020). By integrating machine learning into ArcGIS, GeoAI offers intelligent context-aware models for accurate location-allocation (e.g., assignment of healthcare facilities) and robust healthcare decisions modelling.\n\nWe demonstrate in this publication the importance of unstructured data processing to achieve semi-structured maternal, neonatal and child health (MNCH) datasets curated directly from patients’ medical file/records, to support intelligent health data mining, informed policy planning and robust decision support system design.\n\nThe following constitute our expected hypotheses on the applications of our datasets:\n\nMNCH datasets would encourage the development of resources for the sub-Saharan African region and advance future research progress in the medical/healthcare system of Nigeria.\n\nMNCH datasets would drive integrated GeoAI applications for robust spatiotemporal data analysis.\n\nMNCH datasets would support decision systems with suitable ontologies or knowledge representations, to drive intelligent data analytics.\n\nA study using the MNCH datasets is Usip et al. (2021), which developed a preposition-enabled parser that extracts prepositions from clinical notes to visualise unstructured patients’ data using generated location items such as noun phrase, geolocation, and place name.\n\n\nMaterials and methods\n\nEthical clearance was granted by the University of Uyo Health Research Ethics Committee (UNIUYO-HREC) – Ref. number: UU/CHS/IHREC/VOL.I/017 with the acceptance that the study did not require direct contact with patients.\n\nThe source of the datasets is patients’ medical records/files retrieved from the St Luke’s General Hospital, Anua, Uyo, Akwa Ibom State, Nigeria (the healthcare facility), between 2014 and 2019. The study subjects were randomly selected through physical inspection of the patients’ records (or file bundles) manually stored in the hospital’s file cabinets or archives. To facilitate this exercise, informed consent was processed through the Chief Medical Director of the hospital, to retrieve the required data. This permission was granted, and logistics were put in place to commence the exercise. The investigators did not have access to the records room or (patients’ population) archive. Only files selected by the responsible officers assigned by the Chief Medical Director of the hospital were presented to the investigators. Before giving the files to the investigators for attributes capture, the officers glossed through the files to ensure that the primary attributes of the study (see Table 1) are satisfied.\n\nTo capture the primary attributes for maternal, neonatal and child health, a data template (a table with attributes of the study), was designed with ethical considerations in mind. No sensitive information such as patient’s name was captured. Furthermore, patient’s location/address was truncated by removing street number, to avoid privacy and security implication. Maternal health data template had the following attributes (Date of visit, Gender, Class of patient [mother/infant/child], Address, Symptom, Diagnosis, Prescription, Blood pressure, Temperature, Weight). Neonatal health data template had the following attributes (Date of visit, Gender, Age, Class of patient, Address, Symptom, Condition, Height, Weight). Child health data template had the following attributes (Date of visit, Gender, Age, Class of patient, Address, Diagnosis, Health history, temperature, Weight). The description of these attributes is tabulated on Table 1.\n\nThe total sample of data retrieved (before processing) included maternal (1063), neonatal (1367) and child patients (826), covering the 3 senatorial districts of Akwa Ibom State namely Uyo, Ikot Ekpene and Eket, and the 31 local government areas (LGAs) as presented on Table 2.\n\nLGA=local government area.\n\nTo enable the support of GeoAI services, additional attributes were collected by visiting the respective study locations. The visited locations were those associated with the collected data. The UTM Geo Map, a simple android application for coordinates capture, GIS, and Spatial analysis was deployed for this purpose. The UTM Geo Map app can be downloaded from the Google play store, and has several modules, but the Map Coordinates module, which maps coordinates in real-time was used to capture the respective location coordinates. The process for obtaining the location coordinates (latitude and longitude) using the UTM Geo Map app are summarised as follows:\n\nStep 1: Launch the UTM Geo Map app when in the vicinity of patient address\n\nStep 2: Select Map Coordinates\n\nStep 3: Select Goto GPS Location (this step gives the real-time location of the mobile device with GPS accuracy in meters appearing on the screen. Ensure that the GPS accuracy is within an acceptable range).\n\nStep 4: Select Mark. A request to enter the Point Name will pop up. Enter the point name or address of the patient\n\nStep 5: Select Save. Each saved point is stored on the mobile device. To transfer the measured data to an external file, there is an Export tool, which supports different file formats such as KML, CSV, GPX, DXF, TXT, GeoJSON.\n\nStep 6: Select Export/Import, Export to CSV, type in a filename with “.csv” extension.\n\nStep 7: Select Save.\n\nThe exported file format used in this publication is the CSV format, and the columns (attributes) extracted are described in Table 3. A GPS accuracy range of 1 – 9.65 metres (i.e., how close the device’s calculated position is from the truth, expressed as a radius), was used as an acceptable accuracy range for this publication. A lower GPS accuracy defines the precision of the patient location. The coordinates capturing was carried out by doctoral students, using different mobile devices. Where the GPS accuracy was too high, such location was recaptured and tuned to the acceptable accuracy range. Due to ethical reasons, we are only interested in the vicinity of the patient, hence the defined accuracy range.\n\nTo clearly mark the location boundaries of patients and geographically localise them within a local government unit, the address column was further split to form an additional attribute, called the LGA. Location attributes documented as part of the datasets include Latitude, Longitude, Elevation, Date recorded, and GPS accuracy. For this publication, we were only able to provide location data for patients within the Uyo metropolis, hence, resulting in a total of 1683 MNCH records and distributed as follows: maternal=538, neonatal=720, child=425. We hope to cover other senatorial districts as soon as future funding is available.\n\nAt the end of the data capturing exercise, the data template was converted into electronic format using Microsoft Excel, and manually merged with the geolocation records (exported CSV file) from the field (or study locations visited). The first 10 samples of the maternal, neonatal and child health datasets are given in Figure 1, Figure 2, and Figure 3, respectively. The dataset can be found as Underlying data (Ekpenyong et al., 2021).\n\nLGA=local government area.\n\nLGA=local government area.\n\nLGA=local government area.\n\n\nData availability\n\nOpen Science Framework: Maternal, Neonatal and Child Health Datasets for Spatiotemporal Data Analytics. https://doi.org/10.17605/OSF.IO/J9ZH8 (Ekpenyong et al., 2021).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAccess to restricted data (GPS data) will be made available to readers after a formal request to the corresponding author (mosesekpenyong@uniuyo.edu.ng) and on the condition that data will be used strictly for research purposes.", "appendix": "Acknowledgements\n\nWe extend our gratitude for staff of the St Luke’s General Hospital, Anua, and participating doctoral students, for enabling a smooth data capture of the MNCH datasets.\n\n\nReferences\n\nBabalola S, Fatusi A: Determinants of use of maternal health services in Nigeria--looking beyond individual and household factors. BMC Pregnancy Childbirth. 2009; 9(1): 43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoulos MN, Peng G, VoPham T: An overview of GeoAI applications in health and healthcare. Int J Health Geogr. 2019; 18(1): 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\ndos Anjos Luis A, Cabral P: Geographic accessibility to primary healthcare centers in Mozambique. Int J Equity Health. 2016; 15(1): 173. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEpstein RM, Street RL Jr: The values and value of patient-centered care. Ann Fam Med. 2011; 9(2): 100–103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEkpenyong ME, Usip PU, Umoh NM, et al.: Maternal, Neonatal and Child Health (MNCH) Datasets for Spatiotemporal Data Analytics. Open Science Framework. 2021. http://www.doi.org/10.17605/OSF.IO/J9ZH8\n\nFinster M, Wood M, Raja SN, et al.: The Apgar score has survived the test of time. Anesthesiology. 2005; 102(4): 855–857. PubMed Abstract \| Publisher Full Text\n\nJanowicz K, Gao S, McKenzie G, et al.: GeoAI: spatially explicit artificial intelligence techniques for geographic knowledge discovery and beyond. Int J Geogr Inf Sci. 2020; 34(4): 625–636. Publisher Full Text\n\nMishra S, Sahu PK, Sarkar AK, et al.: Geo-spatial site suitability analysis for development of health care units in rural India: Effects on habitation accessibility, facility utilization and zonal equity in facility distribution. J Transp Geogr. 2019; 78: 135–149. Publisher Full Text\n\nOleribe OO, Momoh J, Uzochukwu BS, et al.: Identifying key challenges facing healthcare systems in Africa and potential solutions. Int J Gen Med. 2019; 12: 395–403. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTian S, Yang W, Le Grange JM, et al.: Smart healthcare: making medical care more intelligent. Global Health Journal. 2019; 3(3): 62–65. Publisher Full Text\n\nTuba M, Sandoy IF, Bloch P, et al.: Fairness and legitimacy of decisions during delivery of malaria services and ITN interventions in Zambia. Malar J. 2010; 9(1): 309. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUsip PU, Ekpenyong ME, Ijebu FF, et al.: PeNLP Parser: An Extraction and Visualization Tool for Precise Maternal, Neonatal and Child Healthcare Geo-locations from Unstructured Data. Deep Learning in Biomedical and Health Informatics. CRC Press, 2021; 157–181. Reference Source\n\nVoPham T, Hart JE, Laden F, et al.: Emerging trends in geospatial artificial intelligence (geoAI): potential applications for environmental epidemiology. Environ Health. 2018; 17(1): 40. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "157440", "date": "19 Dec 2022", "name": "Peter M. Macharia", "expertise": [ "Reviewer Expertise Geospatial health/spatial 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\nSharing such datasets is key for research. It facilitates reproducibility, generation of new research questions to improve the health of community or develop new research approaches. More important, when these datasets have linked location details, additional insights linked to space can be harnessed. I have a few thoughts which I welcome the authors to consider:\nA location map showing the approximate hospital catchment for which the datasets are available. You could also show other facilities in the vicinity, useful for context.\n\nIn addition to the map, provide general details/characteristics of the study area for researchers/potential users of the data but not familiar with Nigeria and the region.\n\nThe introduction has mainly concentrated on health care access aspects of health facilities. However, not much has been said in relation to other key attributes of the data provided. That is, the data provides attributes that spans beyond a discourse of health care access only.\n\nArcGIS should be given as an example of a geospatial software among others but not as the only option. Please paraphrase the sentence.\n\nIn the abstract, you state, “The curated datasets also involved the capturing of location information from the study area, to aid spatiotemporal and informed demographic analysis”. Should it not be aid in spatial and spatio-temporal analysis?\n\nAs these datasets were refer to between 2014 and 2019, and one envisioned application will be spatio-temporal analysis, a date attribute should be availed on the main database. You can truncate it monthly or quarterly in each year to align with confidentiality guidelines.\n\nI wonder whether the tittle could be edited to Maternal, neonatal and child health (MNCH) datasets from a hospital’s catchment area in Nigeria between 2014 and 2019?\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "10175", "date": "29 Nov 2023", "name": "Moses Ekpenyong", "role": "Author Response", "response": "Comment 1: Sharing such datasets is key for research. It facilitates reproducibility, generation of new research questions to improve the health of community or develop new research approaches. More important, when these datasets have linked location details, additional insights linked to space can be harnessed. I have a few thoughts which I welcome the authors to consider: A location map showing the approximate hospital catchment for which the datasets are available. You could also show other facilities in the vicinity, useful for context. Response 1: Reviewer's comment is addressed and captured as Fig. 1. Comment 2: In addition to the map, provide general details/characteristics of the study area for researchers/potential users of the data but not familiar with Nigeria and the region. Response 2: Reviewer's comment addressed. general details/characteristics of the study area provided as follows: St Luke’s General Hospital, Anua is one of the foremost Missionary Hospitals in the South-South and South-East Nigeria. The hospital is located along Nwaniba Road in Uyo Metropolis of Akwa Ibom State, Nigeria, West Africa. A location map showing the approximate hospital catchment for which the datasets are available is presented in Fig. 1. Comment 3: The introduction has mainly concentrated on health care access aspects of health facilities. However, not much has been said in relation to other key attributes of the data provided. That is, the data provides attributes that spans beyond a discourse of health care access only. Response 3: Other key attributes of the data as provided in Tables 1 and 2 and are well documented and explained in the OSF, as prescribed by the F1000Research. Comment 4: ArcGIS should be given as an example of a geospatial software among others but not as the only option. Please paraphrase the sentence. Response 4: Sentence paraphrased and enriched as follows: Geospatial software tools for managing and visualizing MNCH datasets are discussed below: ArcGIS: Developed by Esri (Environmental Systems Research Institute) is a comprehensive and widely used GIS software suite, designed for managing, analyzing, visualizing, and sharing geospatial data and information. QGIS (Quantum GIS): An open-source and user-friendly GIS software that provides powerful mapping and data analysis capabilities. GRASS GIS (Geographic Resources Analysis Support System): An open-source GIS software that focuses on geospatial data management, analysis, and visualization. R with Spatial Packages: The R programming language, coupled with specialized spatial packages like \"sp,\" \"sf,\" and \"raster,\" can be used for geospatial data analysis and visualization. GeoDa: A free software program designed for exploratory spatial data analysis, spatial statistics, and spatial econometrics. SAGA GIS: An open-source geographic information system with a wide range of geospatial analysis and modeling tools. Mapbox: A cloud-based platform for designing and publishing custom maps, providing tools for geospatial data visualization and analysis. OpenStreetMap (OSM) Tools: Tools and APIs for working with OpenStreetMap data, which can be useful for incorporating community-contributed geographic data. Google Earth Engine: A cloud-based platform for analyzing and visualizing Earth observation data, which can be valuable for spatiotemporal analysis. The choice of geospatial software however depends on factors such as, data requirements, project goals, budget, and end-users’ familiarity. Each of these software options offers unique features and capabilities for working with geospatial data. Comment 5: In the abstract, you state, “The curated datasets also involved the capturing of location information from the study area, to aid spatiotemporal and informed demographic analysis. Should it not be aid in spatial and spatio-temporal analysis? Response 5: Yes, statement rephrased to '...facilitating spatiotemporal analysis' Comment 6: As these datasets were refer to between 2014 and 2019, and one envisioned application will be spatio-temporal analysis, a date attribute should be availed on the main database. You can truncate it monthly or quarterly in each year to align with confidentiality guidelines. Response 6: The date attribute is revealed in the OSF platform. Comment 7: I wonder whether the tittle could be edited to Maternal, neonatal and child health (MNCH) datasets from a hospital’s catchment area in Nigeria between 2014 and 2019? Response 7: We agree with reviewer's comment. Appears very informative. Hence, we have modified the title to: \"Curating Maternal, neonatal and child health (MNCH) datasets from a hospital’s catchment area in Nigeria between 2014 and 2019\"." } ] }, { "id": "173253", "date": "31 May 2023", "name": "Liberty Makacha", "expertise": [ "Reviewer Expertise Geographic Information Systems", "Health Geography or Spatial 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\nThe objective of this study is to create a publicly available geographically precise dataset for a data poor setting that will enable driving location sensitive decision making. The authors collected patient data and linked it to participants precise locations (home address). The article would benefit more if the authors seek grammar review from experts in the the field. Whilst the manuscript presence an important argument for data poor settings, this did not come out elaborate in the current phrasing of a bigger part of the current version of the manuscript.\n\n........ Hence, knowledge of health facilities is crucial for providing informed health planning decisions. The statement may need to be qualified. What knowledge of health facilities are the authors referring to here?\n\n.......with the urban areas holding very high concentration of patients’ population per facility. .....as major factors mitigating access to quality healthcare I would use technical terms like patient to provider ratio to describe the same.\n\nmitigating factors: finance (poor living condition), increased security threat, type and nature of ailment, geography of residence, race and ethnicity, gender, age, language, and disability. These factors significantly determine the degree at which medical/healthcare services – including availability, timeliness, convenience, and affordability, are utilised What are mitigating factors?\n\nAdoption of modern technology has however simplified healthcare services through the implementation of automated systems. What do the authors mean by this statement? Consider rephrasing for clarity.\n\n.....that defies real-time, patient-centred care. Again this statement may require clarification. How does unstructured data defy patient-centred care?\n\n.....and details of every parameter within the health system should be available in real-time. In my opinion this statement may need to be qualified as its overly ambitious in implication for technology driven systems that aim to improve the utility of healthcare delivery systems. Most have only tended to target a subset of the core architectures that drive the same.\n\nWe demonstrate in this publication the importance of unstructured data processing to achieve semi-structured maternal, neonatal and child health (MNCH) datasets curated directly from patients’ medical file/records, to support intelligent health data mining, informed policy planning and robust decision support system design. The idea behind this statement in the introduction section of the manuscript is to present the study objectives. In my opinion this objective is not elaborately presented in the current wording of the statement. Consider rephrasing.\n\n.......expected hypotheses on the applications of our datasets What does this mean?\n\nMNCH datasets would encourage the development of resources for the sub-Saharan African region What do the authors mean by this statement? Which resources are in discussion. Consider rephrasing.\n\nMNCH datasets would drive integrated GeoAI applications for robust spatiotemporal data analysis. If this hypothesis is true, why has MNCH datasets failed to achieve the same all along? Consider rephrasing. Do the authors still mean maternal, neonatal and child health by MNCH? If so, in my opinion I think the three hypothesis statements must be revised. MNCH datasets have ever been there both in developed and developing communities. The new argument which I thought the authors would bring is the utility of technology driven/AI powered MNCH datasets.\n\nData source, sample size and capturing procedure Would the description presented here still not amount to person level data capture. SEE ---Ethical clearance was granted by the University of Uyo Health Research Ethics Committee (UNIUYO-HREC) – Ref. number: UU/CHS/IHREC/VOL.I/017 with the acceptance that the study did not require direct contact with patients.\nWhile the investigators would not know the the physical person behind each hospital record. It is possible that being a local community there is bound to be a level of familiarity with each other at community level. What protocols were put in place to blind the same since not individual patient consent was sought?\n\nFurthermore, patient’s location/address was truncated by removing street number, to avoid privacy and security implication. Whilst this is OK from an ethics point of view, I am of the opinion that the approach will compromise the geo-mapping utilities required by the investigators. What did the investigators do make sure that mapping was still possible using information captured in this dataset after dropping off this field. Would that amount to going back to the parent records after patient profile data capture to achieve precise location establishment at field data capture?\n\nDue to ethical reasons, we are only interested in the vicinity of the patient, hence the defined accuracy range. 1 - 9.65 metres amounts to a precise location especially in less populated communities. What is the average household to household distance in the study area?\n\nIs the rationale for creating the dataset(s) clearly described? No\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "10176", "date": "29 Nov 2023", "name": "Moses Ekpenyong", "role": "Author Response", "response": "Comment 1: ........ Hence, knowledge of health facilities is crucial for providing informed health planning decisions. The statement may need to be qualified. What knowledge of health facilities are the authors referring to here? Response 1: We are referring to facilities offering MNCH services. statement is rephrased to \"...Hence, knowledge of available MNCH facilities\" Comment 2: .......with the urban areas holding very high concentration of patients’ population per facility. .....as major factors mitigating access to quality healthcare I would use technical terms like patient to provider ratio to describe the same. Response 2: The statement hase been rephrased to \"...In urban areas, there is a notable imbalance in the patient-to-provider ratio, with a significant concentration of the patient population per healthcare facility\" Comment 3: mitigating factors: finance (poor living condition), increased security threat, type and nature of ailment, geography of residence, race and ethnicity, gender, age, language, and disability. These factors significantly determine the degree at which medical/healthcare services – including availability, timeliness, convenience, and affordability, are utilised What are mitigating factors? Response 3: Mitigating factors are factors hindering access to quality healthcare. Hence the paragraph has been rephrased as: Oleribe et al. (2019) identified major factors hindering access to quality healthcare in sub-Saharan Africa, including financial barriers, poor governance, and limited infrastructure. In Nigeria identified hidering factors include, financial constraints due to poor living conditions, heightened security threats affecting healthcare access, the type and nature of ailments influencing healthcare choices, geographic residence impacting access, racial and ethnic disparities affecting healthcare outcomes, gender-related disparities, age-related healthcare considerations, language barriers affecting communication, and disability-related healthcare challenges. These factors significantly influence the utilization of medical and healthcare services in terms of availability, timeliness, convenience, and affordability (Babalola & Fatusi, 2009). Comment 4: Adoption of modern technology has however simplified healthcare services through the implementation of automated systems. What do the authors mean by this statement? Consider rephrasing for clarity. Response 4: Statement rephrased as \"The integration of modern technology into the health sector has simplified healthcare services\" Comment 5: .....that defies real-time, patient-centred care. Again this statement may require clarification. How does unstructured data defy patient-centred care? Response 5: The statement has been rephrased to \"...defying efforts to extract meaningful insights, hinder accurate decision-making, and impede the creation of reliable healthcare solutions and strategies\" Comment 6: .....and details of every parameter within the health system should be available in real-time. In my opinion this statement may need to be qualified as its overly ambitious in implication for technology driven systems that aim to improve the utility of healthcare delivery systems. Most have only tended to target a subset of the core architectures that drive the same. Response 6: The sentence has been rephrased as: \"To achieve this, it's essential that technology-driven systems, aiming to enhance the utility of healthcare delivery systems, prioritize the availability of real-time location-based information and comprehensive details of the healthcare system\" Comment 7: We demonstrate in this publication the importance of unstructured data processing to achieve semi-structured maternal, neonatal and child health (MNCH) datasets curated directly from patients’ medical file/records, to support intelligent health data mining, informed policy planning and robust decision support system design. The idea behind this statement in the introduction section of the manuscript is to present the study objectives. In my opinion this objective is not elaborately presented in the current wording of the statement. Consider rephrasing. Response 7: The statement is rephrased to distinguish the overall ojective and specific objectives: This publication creates a maternal, neonatal, and child health (MNCH) datasets directly sourced from patients' medical records for a data poor setting. The curated datasets are instrumental in facilitating driving location sensitive decision making, intelligent health data mining, informed policy planning, and robust decision support systems design. The specific objectives of the researh therefore include: To gather and compile detailed MNCH data from various sources to create a comprehensive dataset. To develop a standardized MNCH data and structure format. To convert unstructured healthcare data into a semi-structured format, making it suitable for analysis. To integrate location-based information into the MNCH dataset for facilitating spatiotemporal analysis and visualization. Comment 8: .......expected hypotheses on the applications of our datasets What does this mean? Response 8: It means the study/research hypothesis Comment 9: MNCH datasets would encourage the development of resources for the sub-Saharan African region What do the authors mean by this statement? Which resources are in discussion. Consider rephrasing. Response 9: Statement deleted and rephrased to address the next reviewer's comment Comment 10: MNCH datasets would drive integrated GeoAI applications for robust spatiotemporal data analysis. If this hypothesis is true, why has MNCH datasets failed to achieve the same all along? Consider rephrasing. Do the authors still mean maternal, neonatal and child health by MNCH? If so, in my opinion I think the three hypothesis statements must be revised. MNCH datasets have ever been there both in developed and developing communities. The new argument which I thought the authors would bring is the utility of technology driven/AI powered MNCH datasets. Response 10: We agree with the reviewer's suggestion on change of hypothesis. The hypothesis are therefore restated as follows: 1) Technology driven data curation practices improves MNCH outcome predictions 2) Integration of location-based data into MNCH datasets leads to more informed policy insights and recommendations for MNCH. 3) Geo-referenced features of MNCH datasets enables real-time demographic/spatiotemporal analysis Comment 11: Data source, sample size and capturing procedure Would the description presented here still not amount to person level data capture. SEE ---Ethical clearance was granted by the University of Uyo Health Research Ethics Committee (UNIUYO-HREC) – Ref. number: UU/CHS/IHREC/VOL.I/017 with the acceptance that the study did not require direct contact with patients. Response 11: The paragraphs in this section have been rephrased to clear this misconception as follows: The datasets used in this study originated from patients' medical records/files retrieved from St Luke's General Hospital in Anua, Uyo, Akwa Ibom State, Nigeria, which is the healthcare facility under consideration. These records cover the period from 2014 to 2019. The process of selecting properly documented files involved physically inspecting the patients' records, which were manually stored in the hospital's file cabinets or archives. To initiate this procedure, we sought informed consent through the Chief Medical Director of the hospital to obtain the necessary data. After obtaining permission, the necessary arrangements were made to commence the exercise. It's important to note that the investigators did not have direct access to the records room or the patient archives. Only files preselected by the designated officers assigned by the Chief Medical Director of the hospital were made available for the investigators' use. Before handing over these files for the capture of attributes, the assigned officers reviewed them to ensure compliance with the primary attributes of the study, as outlined in Table 1. ... Comment 12: While the investigators would not know the physical person behind each hospital record. It is possible that being a local community there is bound to be a level of familiarity with each other at community level. What protocols were put in place to blind the same since not individual patient consent was sought? Response 12: Protocols established to maintain the confidentiality and anonymity of patients' health records and to mitigate the risk of inadvertently identifying specific individuals within the local community include: Data De-Identification: Personal identifiers, such as names, were systematically removed or replaced with codes or pseudonyms to prevent any association between the data and specific individuals. Location Privacy Measures: Specific location/address details, including street numbers, were redacted or generalized to a broader geographic level to minimize the risk of identifying individual patients based on their addresses. Aggregated Data Analysis: Instead of analyzing individual-level data, the analysis was conducted at an aggregated or group level whenever possible. This approach ensures that results and insights do not pertain to any single person but are generalized across a broader population. Access Control: Access to the dataset and any related information was restricted to authorized personnel only, and strict confidentiality agreements were in place to prevent any unauthorized disclosure of patient identities. Ethical Review and Compliance: The study and its data-handling procedures were subject to ethical review and compliance with relevant privacy and data protection regulations and guidelines to ensure patient anonymity. Comment 13: Furthermore, patient’s location/address was truncated by removing street number, to avoid privacy and security implication. Whilst this is OK from an ethics point of view, I am of the opinion that the approach will compromise the geo-mapping utilities required by the investigators. What did the investigators do make sure that mapping was still possible using information captured in this dataset after dropping off this field. Would that amount to going back to the parent records after patient profile data capture to achieve precise location establishment at field data capture? Response 13: We have rephrased this in the protocol. The location (Lat and Long) records are available at OSF. Comment 14: Due to ethical reasons, we are only interested in the vicinity of the patient, hence the defined accuracy range. 1 - 9.65 metres amounts to a precise location especially in less populated communities. What is the average household to household distance in the study area? Response 14: Please see above. Statement deleted. Average household to household distance not established. May be useful for future works." } ] } ]	1	https://f1000research.com/articles/11-166
https://f1000research.com/articles/12-1122/v1	08 Sep 23	{ "type": "Systematic Review", "title": "Efficacy of modafinil compared to γ-hydroxybutyrate in the treatment of narcolepsy", "authors": [ "Aaron L. Kennedy", "Andrew J. Boileau", "Andrew J. Boileau" ], "abstract": "Hypothesis: γ-hydroxybutyrate is more efficacious than modafinil in the treatment of patients with narcolepsy. Methods: A total of four research papers were reviewed and analyzed to assess the validity of the hypothesis. Studies compared the effects of each of the drugs on narcolepsy symptoms. Results of both subjective and objective tests were considered by these studies to complete the analysis. These tests were Epworth Sleepiness Scale, Maintenance of Sleep Test, measures of sleep attacks and inadvertent naps, Pittsburgh Sleep Quality Index, and polysomnography. Results: Each of the reviewed studies showed significant evidence of improved narcolepsy symptoms (efficacy) with the use of both γ-hydroxybutyrate and modafinil. There was also a positive correlation between dosage and efficacy for γ-hydroxybutyrate. Some studies showed additive interaction between modafinil and γ-hydroxybutyrate when used in combination. Overall, it is suggested that the efficacy of γ-hydroxybutyrate is potentially superior to that of modafinil, but greatest improvements occur when these drugs are used in combination. Conclusions: While both γ-hydroxybutyrate and modafinil both significantly improve the symptoms of narcolepsy, the difference between these drugs’ maximal magnitude of efficacy remains unclear. While most findings did support the hypothesis, additional research is required.", "keywords": [ "Narcolepsy" ], "content": "Introduction\n\nNarcolepsy is a chronic disease state which causes overwhelming daytime sleepiness, regardless of the circumstances or settings, and sometimes cataplexy. Cataplexy is the sudden loss of muscle tone, often precipitated by a strong emotion. Narcolepsy Type 1 (NT1) is defined as presenting with cataplexy, while narcolepsy without cataplexy is termed Narcolepsy Type 2 (NT2). Other common manifestations include sudden sleep attacks, insomnia episodes (inability to achieve or maintain sleep during normal sleeping hours), hypnagogic and hypnopompic hallucinations, and altered sleep stage architecture, specifically Rapid Eye Movement (REM) sleep. Narcolepsy is often debilitating, but typically does not pose a direct threat to one’s life. Rather, daily routines (i.e., driving, being productive at work, etc.), normal functioning and mental health are often greatly impacted (Thorpy and Dauvilliers, 2015).\n\nMany co-morbidities have been strongly associated with both NT1 and NT2, such as obesity, type 2 diabetes mellitus, mood/psychiatric disorders, eating disorders, and attention deficit hyperactivity disorder. Additionally, associations also exist with other sleep and sleep-related disorders, such as restless-leg syndrome and REM parasomnias (Barateau and Dauvilliers, 2019). In a meta-analytic study of more than eight-million subjects, Scheer et al. (2019) found that 0.079% of the general United States public met criteria for narcolepsy, while incidence rates for NT2 are generally several-fold less than that of NT1. Additionally, females are more likely to be affected than males at a ratio of 3:2 (Scheer et al., 2019).\n\nAlthough the specific etiology of narcolepsy is largely unknown, the literature clearly asserts that narcolepsy is characterized by specific physiological changes. Of these changes, the reduced levels of hypocretin (also known as orexin) in the lateral hypothalamus is the most understood and studied association (Takenoshita et al., 2018). Hypocretin is a peptide hormone that is involved with wakefulness regulation and REM sleep stages. Cerebrospinal fluid levels of < 110 pg/ml are consistent with a diagnosis of narcolepsy (Stephansen et al., 2018). It has been hypothesized that loss of hypocretin-producing cells could be due to autoimmune phenomena (Latorre et al., 2018), genetics (Ollila et al., 2015), human leukocyte antigen (HLA) haplotypes (Stephansen et al., 2018), modern pharmacological therapies such as influenzae vaccines (Miller et al., 2013), or the influenza virus itself (Bonvalet et al., 2017).\n\nMany treatment strategies have been developed for this chronic disease state with some promising results, although further research is required to identify the most robust ‘gold standard’ of therapy. Currently, it is generally accepted that lifestyle changes (diet, regular sleep schedule, avoiding sleep deprivation, etc.) and pharmacological therapies are the most promising means for providing relief to patients with both NT1 and NT2 (Barateau and Dauvilliers, 2019). Examples of therapies for this purpose include γ-hydroxybutyrate (GHB, also known as sodium oxybate), modafinil (or its R-enantiomer, armodafinil), amphetamines (increases dopamine/norepinephrine in the CNS), methylphenidate (increases dopamine/norepinephrine in the CNS), pitolisant (selective histamine agonist at H3 receptors), orexin agonists, immune-based therapies, and more (Barateau and Dauvilliers, 2019).\n\nModafinil is the current standard for treatment of excessive daytime sleepiness in narcolepsy (Sahni et al., 2019), although its mechanism is complex and largely unknown. The leading theory suggests that modafinil blocks the dopamine reuptake transporter (DAT) at the presynaptic neuron, providing amplified dopaminergic stimulation (Karabacak et al., 2015). Other theories include flux alterations of neurotransmitter exocytosis into the synaptic cleft (Ranjbari et al., 2021), and norepinephrine and/or serotonin reuptake inhibition at the presynaptic neuron (Murillo-Rodríguez et al., 2018). Since modafinil is a stimulant, it is typically taken in the morning and/or early afternoon.\n\nOn the other hand, GHB is an oral medication that is typically taken once before bedtime, and once 2.5 to 4 hours after upon briefly waking up. The total sum of the two doses typically ranges from 6 to 9 grams (Ohayon et al., 2019). It is also noteworthy to mention that GHB is often combined with modafinil for the treatment of narcolepsy (Erman et al., 2017), and that GHB is currently the only FDA-approved drug for the treatment of cataplexy associated with narcolepsy (Thorpy and Bogan, 2020). This drug agonizes both the Gamma-hydroxybutyric Acid B (GABAB) receptor and the GHB-specific receptor (Trombley et al., 2020). Since stimulation of the GABAB receptor causes cellular hyperpolarization in the CNS (through G-protein-mediated opening of inward rectifying potassium channels), GHB has a depressive/sedative effect on the brain. Conversely, when the GHB-specific receptor is stimulated (e.g., by GHB), excitatory effects are elicited, as seen in an animal-model study by Trombley et al. (2020), which found increased extracellular glutamate following selective stimulation of these receptors in neural tissue. Although GHB is more well-known for its depressive and sedative effects (e.g., at high concentrations through GABAB stimulation), concentration-dependent differences in receptor affinity allow GHB to cause excitatory effects at lower concentrations through GHB-specific receptor stimulation (Trombley et al., 2020). Similar to modafinil, the current understanding of GHB’s complex mechanism of specifically treating narcolepsy is unknown. It has previously been hypothesized that GHB consolidates sleep by reducing fragmentation of the sleep stages (Roth et al., 2017).\n\nOne area of interest is the effect of pharmacotherapy on the sleep architecture and sleep staging. Before a patient falls asleep, they will be exhibiting β-waves on the electroencephalogram (EEG) portion of the PSG. When the patient dozes off (eyes shut, but still awake), this is termed N1, and the brain exhibits α-waves on EEG. N2 consists of theta-waves and contains sleep spindles and K-complexes (Latreille et al., 2020), while N3 (also called deep sleep, stage 3 sleep, slow-wave sleep) presents with larger 𝛿-waves (Hasan et al., 2015). Stephansen et al. (2018) explains that patients with narcolepsy often present with sleep architectural changes such as a shortened sleep latency, poor sleep consolidation and rapid/frequent shifts into REM sleep (Stephansen et al., 2018). Patients may also experience “sleep-wake dissociation,” in which the patient is partially awake and partially in REM sleep, which may be related to certain comorbidities. Examples include sleep paralysis and cataplexy (REM muscle paralysis in the setting of wakefulness). Dreaming while awake is another example, which has been termed hypnogogic/hypnopompic hallucinations (Stephansen et al., 2018).\n\nThis is an important area of research because refinement of treatment is paramount to the well-being and quality of life for patients with NT1/NT2. This review of the literature attempts to identify and compare efficacies of GHB and modafinil. As such, it is hypothesized that GHB provides greater functional efficacy than modafinil in the treatment of narcolepsy. It is also important to consider the adverse effects of these drugs, because if a patient stops using any given drug, there is no chance for the drug to be functionally efficacious. Hopefully, clarifying this knowledge will encourage physicians to prescribe the most appropriate medications to patients with narcolepsy, while minimizing adverse effects and reactions.\n\nKey Terms: narcolepsy (NT1/NT2), γ-hydroxybutyrate (GHB) (also known as sodium oxybate, Xyrem), modafinil, REM sleep, N2, N3, N4, sleep latency, cataplexy, Epworth Sleepiness Scale (ESS), Maintenance of Wakefulness Test (MWT), Polysomnography (PSG), Pittsburgh Sleep Quality Index (PSQI)).\n\n\nMethods\n\nDatabase used: PubMed\n\nSearch stem: (oxybate OR GHB) AND modafinil\n\nThe initial search yielded 122 results. After removing one duplicate, 121 articles remained. Certain study designs, such as reviews, systematic reviews, case reviews, clinical reviews and meta-analyses (n = 77) were excluded, leaving 44 articles. Non-human studies (n = 3) were excluded, leaving 41 articles. No date ranges were set, in attempt to collect all journal entries making the direct comparison between the two drugs of interest. Thus, it follows that studies were only included if they directly compared both GHB and modafinil in the treatment of narcolepsy. Studies (n = 36) not fitting this criterion were excluded. This final intended parameter left five remaining articles, which were to be used for this review. One of the five papers was excluded upon further examination because of insufficient data reporting of the study’s modafinil statistics (Husain et al., 2020). To clarify, modafinil was given to the various applicable study groups, but authors failed to present sufficient numerical data, analysis, and discussion in their entry. For this reason, this journal entry was also excluded, leaving a grand total of four articles to be incorporated in the review.\n\nThe Epworth Sleepiness Scale (ESS) is a standardized questionnaire, based on the patient’s own perceived likelihood of nodding-off (falling asleep) in eight specific situations (i.e., watching TV, or sitting quietly after a meal, etc.). Each circumstance is self-graded on a scale, from zero-to-three points. A higher score predicts more severe symptoms (Johns, 1991).\n\nThe Maintenance of Wakefulness Test (MWT) is used to objectively determine sleepiness. The MWT measures patients’ abilities to stay awake in a dark, comfortable, quiet room during the daytime hours. Generally, four trials are done, with two-hour wash-out periods in-between. An average of < 8 minutes for sleep induction indicates an abnormal result (Mitler et al., 1982), while a score of > 8 minutes typically points away from a narcolepsy diagnosis. This test is often used to assess treatment efficacy, as will be discussed in this paper.\n\nPolysomnography (PSG) is a testing procedure in which patients sleep one night in a lab. Probes placed on various points of the body can detect sleep architecture (awake, N1/2/3, REM, etc.), bruxism, leg movements, eye movements and more during the patient’s night of sleep (Rundo ad Downey, 2019).\n\nThe Pittsburgh Sleep Quality Index (PSQI) is a series of nineteen self-reported questions, which retrospectively assesses patients’ subjective quality of sleep. Each of the questions falls under one of seven categories (i.e., sleep duration, medication use, disturbances, etc.). For example, question #6 of the PSQI poses the following question: “During the past month, how do you rate your sleep quality overall?” Responses could range from 0 (very good) to 3 (very bad). (Manzar et al., 2018).\n\n\nResults\n\nOf the papers included in this review, two were retrospective placebo-controlled RCTs (Black et al., 2016 & Dauvilliers et al., 2017), one was a double-blinded placebo-controlled RCT (Black et al., 2009), and one was a double-blinded multicenter RCT design (Black and Houghton, 2006). Table 1 describes the study design of the four papers selected for this review of the literature.\n\nBlack and Houghton (2006) conducted a double-blind, placebo-controlled multicenter RCT to assess the effects of GHB, modafinil and the combination of both drugs on patients with narcolepsy. Multiple sites (n = 44) across the globe were involved, including the United States, Canada, France, Germany, Czech Republic, the Netherlands, Switzerland, and the United Kingdom. To be included, each subject (n = 270) was previously diagnosed with narcolepsy and treatment with modafinil was present for purposes of baseline assessments. Pre-intervention modafinil dosage ranged from 200 mg to 600 mg per day (Black and Houghton, 2006).\n\nPatients in the Black and Houghton (2006) study were divided into one of four groups: [1] GHB alone (GHB group), [2] modafinil alone (modafinil group), [3] GHB and modafinil together (GHB plus modafinil group), or [4] double-placebo group (placebo group). Before the eight-week intervention phase occurred, there was a two-week baseline period, during which patients continued to take their previously prescribed dosages of modafinil. During this phase, MWT, ESS and PSG data were collected for baseline analysis. At the beginning of the intervention phase, 6 grams of GHB was given to each subject in the GHB or GHB plus modafinil groups, for a total of four weeks. During weeks six through ten, the dosage was elevated to 9 grams of GHB per night. The principal outcome measures were the MWT, ESS, and sleep diaries to assess inadvertent naps and sleep attacks (Black and Houghton, 2006).\n\nCompared to the mean baseline modafinil MWT (daytime sleep latency) score (and standard deviation) of 9.74 ± 6.57 minutes, the placebo group scores significantly decreased (worsened) to 6.87 ± 6.14 minutes at the end of the eight-week intervention (p < 0.001). This is likely due to the removal of modafinil during the intervention. However, the GHB group showed no decrease in sleep latency compared to its baseline score. For the GHB plus modafinil group, an additive effect was found, such that daytime sleep latency increased (improved) from a baseline of 10.43 ± 6.77 minutes to 13.15 ± 6.91 minutes (p < 0.001). It is noted that majority of change occurred during the first four weeks of intervention (Black and Houghton, 2006). Compared to baseline, ESS scores were significantly decreased (improved) at the end of week eight, for only the GHB group, 15 to 12 (p < 0.001), and the GHB plus modafinil group, 15 to 11 (p < 0.001). Standard deviation or standard error data was not provided for the remainder of this study’s applicable results.\n\nThese authors also found that at week eight, compared to placebo and modafinil groups, the GHB group and the GHB plus modafinil group presented with significantly lower instances of sleep attacks. The GHB group scored 10.05 sleep attacks per week at baseline, but only 7.10 at the conclusion of the intervention, while the GHB plus modafinil group scored 11.82 and 5.55, respectively. These differences were both significant (for both, p < 0.001) (Black and Houghton, 2006). The placebo group and the modafinil group remained unchanged for this parameter.\n\nBlack et al. (2009) investigated the effects of modafinil and GHB on nocturnal sleep cycle disruption, thus directly affecting and predicting the presence and strength of narcolepsy symptoms. This double-blinded, placebo-controlled study included 278 test subjects, each of whom had previously been taking modafinil due to a narcolepsy diagnosis. Pre-intervention modafinil dosages ranged from 200 – 400 mg per day. To prevent pregnancy and its potentially confounding complications, female patients were only accepted if they agreed to using birth-control, were surgically sterile, or held post-menopausal status. Patients were excluded if they had used GHB within the past month (e.g., for another clinical trial), had a diagnosis of sleep apnea (or positive screening at baseline testing in the current study), substance abuse disorder, seizures, or other neurological reasons (Black et al., 2009).\n\nFollowing a two-week baseline period, each patient was randomized into one of four possible groups for the interventional period of eight total weeks. These groups’ drug regimen included [1] GHB placebo and modafinil placebo (placebo group), [2] GHB only (GHB group), [3] modafinil only (modafinil group), or [4] both GHB and modafinil (GHB plus modafinil group). Patients randomized into the modafinil group or the GHB plus modafinil group did not change their personalized dose of modafinil throughout the study, while patients in the placebo group and the GHB group were not prescribed any modafinil throughout the entire interventional phase. In the GHB group and GHB plus modafinil group, 6 grams of GHB was given nightly for the first four weeks of intervention, while nine grams were administered during each night of the final four weeks. This study used the MWT, PSG, sleep diaries and ESS for assessment of narcolepsy symptoms. Specifically, the MWT and PSG data were collected at three points: once at the conclusion of the baseline (pre-interventional) phase, once after week four and once following week eight of the interventional phase (Black et al., 2009).\n\nPSG results at weeks four and eight showed no change in total sleep time in any of the test groups. At week eight, compared to baseline, two of the study groups showed greater proportions of N3 sleep, rather than lighter stages of sleep. More specifically, both the GHB group and the GHB plus modafinil group had an increased median of 43.5 minutes (p < 0.001) and 24.25 minutes (p < 0.001) of N3 sleep, respectively. Standard error and standard deviation data were not reported for this study’s results. By virtue of more N3 sleep, both groups showed a decrease of total time spent in N1 and REM sleep. At baseline, the GHB group spent 16 (p < 0.001) and 38.5 (p < 0.001) more minutes per night in N1 and REM, respectively, than week eight. At baseline, the GHB plus modafinil group spent 17 (p = 0.004) and 26.5 (p < 0.001) more minutes in N1 and REM, respectively, than week eight. No significant sleep architectural differences were found when the placebo group or the modafinil group were compared to their respective baseline scores (Black et al., 2009).\n\nResults for the MWT after eight weeks of intervention also showed certain significant results. It was found that compared to baseline, when the placebo group patients started the intervention (modafinil was removed altogether), there was significant decrease in sleep latency. Numerical data was not provided, except for a p-value of < 0.001. Conversely, as compared to their baseline, the GHB plus modafinil group had a significantly elevated median sleep latency period. Numerical data was not provided, except for a p-value of < 0.001. Patients assigned to either the modafinil group or the GHB group failed to demonstrate any significant change in MWT sleep latency, compared to baseline therapy (Black et al., 2009).\n\nPertaining to the ESS, results showed that the placebo group’s week eight scores were significantly worse than baseline modafinil treatment scores. Exact numerical data was not presented, except for a p-value of 0.011. Lastly, after week eight, there were significant improvements for the GHB group and the GHB plus modafinil group, compared to their baseline. Exact numerical data was not presented, except for p-values of < 0.001 and < 0.001, respectively. There were no significant results for the modafinil group for the ESS (Black et al., 2009).\n\nIn a separate study, Black et al. (2016) conducted a retrospective analysis of a Phase-III RCT, which investigated efficacy of: [1] GHB alone (GHB group), [2] modafinil alone (modafinil group), [3] a combination of GHB and modafinil (GHB plus modafinil group), and [4] double-placebo (placebo group). Furthermore, the modafinil group received a GHB placebo, and the GHB group received a modafinil placebo (instead of the pre-interventional ‘authentic’ modafinil). The placebo group received both GHB placebo and modafinil placebo. The study followed a double-dummy protocol, allowing for proper blinding of the treatment regimes. Inclusion criteria consisted of adult age and a diagnosis of narcolepsy as defined by the criterion set by the International Classification of Sleep Disorders, 2nd Edition (Thorpy, 2012). Patients with both NT1 (n=95) and NT2 (n=127) were included but studied separately. Additionally, each patient took a stable dose of modafinil prior to the onset of the pharmacological intervention (range: 200-600 mg/day). Subjects were GHB-naïve (Black et al., 2016).\n\nEach subject took their respective medication regimen for a total of 56 days. Patients who were assigned to take modafinil (modafinil group and GHB plus modafinil group) remained with their respective personal doses of modafinil, although patients assigned to take GHB (GHB group & GHB plus modafinil group) followed a graded dosage scheme throughout the study. For the first 28 days, a total dosage of six grams per night were ingested. For the following 28 days, a total of 9 grams per night were taken. All administration of GHB (and GHB placebo) was given in two equal doses: the first dose was given at bedtime, and the second dose was administered 2.5-4 hours later. For example, on the 35th day, each patient received two separate doses of 4.5 grams of GHB (or GHB placebo). This study measured changes over time in narcolepsy symptoms, by administering the ESS and MWT at various times throughout the study. These tests occurred at the beginning of week one (baseline) and at the end of weeks four and eight (Black et al., 2016).\n\nComparing to baseline ESS to week 8 ESS, Black et al. (2016) found significant change for the GHB plus modafinil group for both NT1, -3.8 (p = 0.002) and NT2, -2.8 (p = 0.015). Standard errors were provided graphically, but numerical values were not reported in this study. In patients with NT2, there were also significant improvements for the GHB group compared to baseline, -3.0 (p = 0.021). After eight weeks, average placebo group ESS scores for both NT1 and NT2 were +0.8 and +0.8, respectively. Compared to this placebo, NT1 patients scored significantly less for both the GHB group, -2.9 (p = 0.011), and the GHB plus modafinil group, -3.8 (p = 0.002). Similarly, for NT2 patients, significant reductions in score were -3.0 (p = 0.021), and -2.8 (p = 0.015), respectively. The modafinil group did not yield statistically significant results whilst being compared to the placebo group for either NT1 patients or NT2 patients (Black et al., 2016).\n\nFor NT1 and NT2 patients in the placebo group, MWT results showed that mean sleep latencies were 2.58 (p < 0.05) and 2.90 minutes (p < 0.05) less at week eight than at baseline. Relative to the placebo results, the GHB plus modafinil groups stayed awake for 3.34 (p < 0.05) and 2.16 minutes (p < 0.001) longer at week eight than at baseline. The NT2 GHB group also reported longer mean wakefulness periods of 0.45 minutes (p = 0.007), under these same comparison parameters (Black et al., 2016).\n\nIn another study, Dauvilliers et al. (2017) reported similar findings to those of Black et al. (2016). The purpose of this study was to investigate the effects of the same three narcolepsy treatment modalities (and placebo) on sleep stage shifts and disrupted nighttime sleep (DNS). Both parameters directly relate to subjective feelings of sleepiness during the daytime hours. Selection of patients (n= 222) and study group allocation were identical to the Black et al. (2016) study. However, PSG results were analyzed for sleep architecture, rather than ESS or MWT. Specifically, the number of shifts from N2/N3/REM to N1/awake, REM to N1/awake, and N1/awake to REM were measured. Additionally, question #6 of the PSQI was used to grade individual sleep quality, both preceding (baseline) and during (weeks four and eight) the intervention (Dauvilliers et al., 2017).\n\nResults were reported as least-square mean change (LSMC). At week eight, this study found a significant decline, from baseline, in the number of shifts from N2/N3/REM to N1/awake in both the GHB group, -16.5 (p < 0.001), and GHB plus modafinil group, -13.7 (p < 0.001). Again, standard errors were provided graphically, but numerical values were not reported for any results of interest for this study. Furthermore, both changes were greater than those demonstrated by the placebo group, with an insignificant LSMC of -0.6. There were no significant results for this shift in the modafinil group at week eight compared to baseline, or when compared to the placebo group. There was also a significant decline in the number of transitions from REM to N1/awake for the GHB group and GHB plus modafinil group when compared to baseline. LSMC score changes were -6.0 (p < 0.001), and -6.8 (p < 0.001), respectively. The modafinil group, -0.5, did not differ significantly from the placebo group, -0.6. Finally, from baseline to week eight, among the patients who had shifts from N1/awake to REM, both the GHB group, -2.5 (p = 0.083) and GHB plus modafinil group, -2.2 (p = 0.002), showed significantly less frequent shifts per hour compared to placebo, +0.2 (Dauvilliers et al., 2017).\n\nThese authors found that quality of sleep, as measured by the PSQI, improved significantly among the GHB group, -0.52 (p < 0.001 from baseline, p < 0.05 from placebo), and the GHB plus modafinil group, -0.49 (p < 0.001 from baseline, p < 0.05 from placebo), but not with modafinil alone, -0.04. For comparison, placebo LSMC at week eight was -0.07 (Dauvilliers et al., 2017).\n\n\nDiscussion\n\nThe purpose of this literature review was to explore and compare the efficacy of modafinil and GHB for the treatment of NT1 and NT2. The four previously mentioned journal articles will now be discussed and analyzed in depth to determine supporting and/or refuting evidence for the hypothesis. Additionally, weaknesses and limitations will be considered for each study, as well as areas for potential further research.\n\nBlack and colleagues (2006), help prove the hypothesis in certain ways. For example, these authors found that compared to modafinil baseline therapy, the placebo group MWT scores were significantly lower (worse) at week eight, suggesting that the modafinil was providing beneficial effects before it was stripped away. In comparison, for the GHB group, significant score reductions at week eight were not found. Since modafinil was also stripped from this group, it is suggested that GHB can ‘replace’ the missing effects of modafinil.\n\nAdditionally, GHB was the only drug that showed efficacy in preventing sleep attacks (cataplexy) and inadvertent daytime naps. This is because both groups which contained GHB treatment showed markedly reduced frequencies of these symptoms when compared to their respective baseline. Neither the modafinil group nor the placebo group showed signs of reductions. This finding is completely consistent with the hypothesis because while GHB shows at-least some efficacy, modafinil fails to show any efficacy for preventing these specific symptoms of narcolepsy.\n\nThese authors found that “As determined by MWT measures, sodium oxybate (GHB) alone was as effective as modafinil for the treatment of EDS and significantly more efficacious, as measured by ESS and the number of weekly inadvertent naps or sleep attacks …” (Black and Houghton, 2006). Further, specifically for the MWT, the strongest positive results among any group were for the GHB plus modafinil group. This group received GHB in addition to the existing modafinil regimen, suggesting an additive effect of the two drugs. Sleep attack assessment results also point towards an additive effect. In contrast, additive effects were not found for the ESS tests.\n\nSince this research took place in multiple centers, including 44 states in the USA and an additional seven countries across the globe, this study design allowed for great generalizability for different races, cultures, and climates. However, using multiple international study centers carries its own limitation; each finding was not simply measured, interpreted, and analyzed by one sole researcher, potentially resulting in communication complications (e.g., language barriers). Further, lack of equipment standardization among the different international sites could lead to measurement precision issues (rather than accuracy) of the results.\n\nThe study by Black et al. (2009) also evaluated the efficacy of GHB, modafinil and the two drugs in combination for the treatment of narcolepsy. Both groups who took GHB presented with improved amount of time spent in deeper stages of sleep, while modafinil did not change, or seemed to hinder the amount of time spent in deeper stages of sleep.\n\nMWT results for the placebo group point towards modafinil’s positive effects on daytime wakefulness. By removing modafinil, patients unfortunately fell asleep faster during the MWT. At week eight, compared to modafinil-only baseline, the GHB plus modafinil group showed significant improvements in the MWT, while the modafinil alone and GHB alone did not produce significant results. Results from this study are partially in line with the hypothesis. This study would suggest that the most efficacious outcomes are yielded when both GHB and modafinil are used together. Overall, while modafinil has strong effects on wakefulness, it seems that GHB’s sleep architectural-altering properties provide the strongest efficacy.\n\nA limitation of this study is that it does not discern between the different doses of GHB. During the first four weeks of the intervention, patients took 6 g of GHB, while during weeks five through eight, patients took 9 g. This limitation also holds true among each of the four studies in this review. Future studies could investigate differences among doses of GHB (and modafinil) to further refine the search for a better standard of treatment. Black et al. (2009) also speculate that nocturnal EEG changes in the GHB groups (PSG) could truly not be secondary to genuine sleep architecture alterations, but potentially to anaesthetic-like properties of the drug or something different all-together. One final limitation of the study design is that pregnant women or women who did not accept taking birth control were not permitted to participate in this study, limiting the generalizability of the results. Further research is clearly needed to understand the complete mechanism of GHB on sleep architecture.\n\nAt the beginning (baseline) of the Black et al. (2016) study, it was also found that subjects with NT1 scored more poorly on the ESS and MWT, as compared to NT2 scores. These differences are important because it helps us recognize the spectrum of disease state presented by a narcolepsy diagnosis. However, once the drugs were added, many results for both NT1 and NT2 yielded very similar results, suggesting that GHB and modafinil have similar effects across this spectrum of narcolepsy symptoms. The authors effectively displayed and discussed how GHB and modafinil effect the ESS and the MWT. GHB alone, and GHB in combination with modafinil resulted in improvements in excessive daytime sleepiness (ESS and MWT) relative to the placebo. Modafinil on its own however did not yield any significant results in this parameter. Also, the fact that the GHB plus modafinil group showed the strongest improvement suggests that these drugs have an additive effect. Overall, these findings are consistent with the hypothesis of this review, and consistent with findings of the other reviewed articles. This study earns merit, as discussed above, because it objectively stratifies for presence of cataplexy, allowing for greater generalizability of results across the narcolepsy spectrum. However, certain limitations of this study also exist. The authors explain that differences in narcolepsy diagnosis measures among patients could have led to misclassification of patients with NT1, into the NT2 group, and vice-versa. It is explained that different methods of diagnosing NT1 versus NT2 (e.g., sleep-onset REM periods on PSG, hypocretin levels, HLA-DQB1*06:02 positivity, etc.) can lead to this misclassification. The authors do however acknowledge that this is an unlikely phenomenon. If misclassification did occur, it is also unlikely to majorly affect the findings since the sample size (n = 222) is relatively high.\n\nIn the paper written by Dauvilliers et al. (2017), various sleep architectural changes were measured using PSG. It was found that GHB (with and without modafinil combination) created more condensed and efficient sleep for patients in this study arm. For the N2/N3/REM to N1/awake shift, patients taking GHB alone demonstrated the strongest decline of incidence. In the group who took GHB and modafinil, significant reductions were also found, but to a lesser degree. This would make one think that these results are consistent with the hypothesis. Although this is likely true, it must be considered that modafinil is a wakefulness promoting drug, and it does not produce any sedative effects. It is most likely that the addition of modafinil to a GHB regimen creates stimulation during the day but has a somewhat detrimental residual effect on sleep architecture during the night. Although GHB and modafinil have opposing mechanisms, the summation of their gross effects (with proper circadian rhythmic timing) is to reduce the severity of narcolepsy symptoms during the day. It is also important to consider that higher concentrations of GHB stimulate the GABAB receptors, creating an overall neuro-depressive effect, while lower concentrations will stimulate the GHB-specific receptors, causing an excitatory effect. One should understand that since GHB possesses multiple concentration-dependent mechanisms, it is possible that alterations in the equilibrium of this system could be an important player in future research moving forward.\n\nThe authors effectively combined these objective measures (PSG) and subjective measures (PSQI) allowing for the reader to speculate that the sleep architectural changes translate into the subjective feelings of a good night’s rest. By manipulating the sleep architectural changes, we are potentially presented with an exciting way to improve sleep quality in patients with narcolepsy.\n\nAs seen with each of the other three studies in this review, Dauvilliers et al. (2017) study length was too short to generalize results beyond a period of two months. Future studies should evaluate whether these promising effects remain robust throughout a period of one year (or more). In general, a large proportion of drugs display phenomena such as tolerance or sensitization and pharmacodynamic changes, so this is a crucial topic to investigate regarding GHB and modafinil. Unlike the study done by Black et al. (2016), this study was limited in that it did not focus on the presence of cataplexy as a stratification parameter. In future studies, it would be important to assess the differences of sleep architecture in patients with NT1 and NT2.\n\nIn general, these four studies exhibit certain similar limitations due to similar study designs, since all came from related laboratory groups with overlapping authors, therefore weakening any clear scientific conclusion. For example, the results for modafinil may have been overrepresented due to a selection bias. Since pre-trial modafinil therapy was required as a selection criterion for each of the studies, it is likely that more patients who respond positively to modafinil were included as study subjects. This is because prospective patients who had previously failed to experience the benefits of modafinil had simply stopped taking the drug altogether before they could have been considered for inclusion. It is also possible that results for modafinil were underrepresented, as discussed by Black and Houghton (2006), because patients having previously taken modafinil before the start of the trial. Extending this idea, there is a possibility of some patients not being sufficiently medicated with modafinil before the commencement of the trial. This potential under-dosing could spill over into the RCTs and under-represent any positive findings for the modafinil group. The root of this problem is the patients themselves (or their third-party physicians) deciding the “proper” dose of modafinil (varying from 200-600 mg/day). Ideally, researchers of the reviewed journals would have assessed the modafinil dosages for each patient to correct any obscurities/incongruencies before the commencement of the trials. Future extensions could also explore additional drug combinations (i.e., pitolisant, methylphenidate, etc.) and dosage timelines.\n\n\nConclusion\n\nThis review of the literature uncovered four primary journal articles to assess efficacy of GHB and modafinil. Through the conglomeration and analysis of the subjective and objective findings, modafinil and GHB both proved effective for treating excessive daytime sleepiness associated with narcolepsy. While GHB seems to alter the sleep architecture, creating less disruption and more sleep-stage consolidation, modafinil works as a stimulant to augment arousal during the day. Collectively, these four studies suggest that combinations of these drugs may create the best possible treatment for patients with excessive daytime sleepiness due to narcolepsy. It is also somewhat suggested that GHB monotherapy is superior to that of modafinil, although more research is needed to confirm that conclusion.", "appendix": "Data availability\n\nZenodo: Data for “Efficacy of modafinil compared to γ-hydroxybutyrate in the treatment of narcolepsy”. DOI: https://doi.org/10.5281/zenodo.8259918.\n\nThis project contains the following underlying data:\n\n- Data file 1.doc (All data for current paper).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: PRISMA flow chart for ‘Efficacy of modafinil compared to γ-hydroxybutyrate in the treatment of narcolepsy’. DOI: https://doi.org/10.5281/zenodo.8259794.\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\nBarateau L, Dauvilliers Y: Recent advances in treatment for narcolepsy. Ther. Adv. Neurol. Disord. 2019; 12: 175628641987562–175628641987512. Publisher Full Text\n\nBlack J, Houghton WC: Sodium oxybate improves excessive daytime sleepiness in narcolepsy. Sleep. 2006; 29(7): 939–946. Publisher Full Text\n\nBlack J, Pardi D, Hornfeldt CS, et al.: The nightly administration of sodium oxybate results in significant reduction in the nocturnal sleep disruption of patients with narcolepsy. Sleep Med. 2009; 10(8): 829–835. PubMed Abstract \| Publisher Full Text\n\nBlack J, Swick T, Bogan R, et al.: Impact of sodium oxybate, modafinil, and combination treatment on excessive daytime sleepiness in patients who have narcolepsy with or without cataplexy. Sleep Med. 2016; 24: 57–62. Publisher Full Text\n\nBonvalet M, Ollila HM, Ambati A, et al.: Autoimmunity in narcolepsy. Curr. Opin. Pulm. Med. 2017; 23(6): 522–529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDauvilliers Y, Roth T, Guinta D, et al.: Effect of sodium oxybate, modafinil, and their combination on disrupted nighttime sleep in narcolepsy. Sleep Med. 2017; 40: 53–57. PubMed Abstract \| Publisher Full Text\n\nErman M, Emsellem H, Black J, et al.: Correlation between the Epworth Sleepiness Scale and the Maintenance of Wakefulness Test in patients with narcolepsy participating in two clinical trials of sodium oxybate. Sleep Med. 2017; 38: 92–95. PubMed Abstract \| Publisher Full Text\n\nHasan YM, Heyat MBB, Siddiqui MM, et al.: An overview of sleep and stages of sleep. Sleep. 2015; 4(12): 505–507.\n\nHusain AM, Bujanover S, Ryan R, et al.: Incidence and duration of common, early-onset adverse events occurring during 2 randomized, placebo-controlled, phase 3 studies of sodium oxybate in participants with narcolepsy. J. Clin. Sleep Med. 2020; 16(9): 1469–1474. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohns MW: A new method for measuring daytime sleepiness: the Epworth sleepiness scale. Sleep. 1991; 14(6): 540–545. Publisher Full Text\n\nKarabacak Y, Sase S, Aher YD, et al.: The effect of modafinil on the rat dopamine transporter and dopamine receptors D1–D3 paralleling cognitive enhancement in the radial arm maze. Front. Behav. Neurosci. 2015; 9: 215. Publisher Full Text\n\nLatorre D, Kallweit U, Armentani E, et al.: T cells in patients with narcolepsy target self-antigens of hypocretin neurons. Nature. 2018; 562(7725): 63–68. PubMed Abstract \| Publisher Full Text\n\nLatreille V, von Ellenrieder N , Peter-Derex L, et al.: The human K-complex: insights from combined scalp-intracranial EEG recordings. NeuroImage. 2020; 213: 116748. PubMed Abstract \| Publisher Full Text\n\nManzar MD, BaHammam AS, Hameed UA, et al.: Dimensionality of the Pittsburgh Sleep Quality Index: a systematic review. Health Qual. Life Outcomes. 2018; 16(1): 1–22. Publisher Full Text\n\nMiller E, Andrews N, Stellitano L, et al.: Risk of narcolepsy in children and young people receiving AS03 adjuvanted pandemic A/H1N1 2009 influenza vaccine: retrospective analysis. BMJ. 2013; 346. Publisher Full Text\n\nMitler MM, Gujavarty KS, Browman CP: Maintenance of wakefulness test: a polysomnographic technique for evaluating treatment efficacy in patients with excessive somnolence. Electroencephalogr. Clin. Neurophysiol. 1982; 53(6): 658–661. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMurillo-Rodríguez E, Barciela Veras A, Barbosa Rocha N, et al.: An overview of the clinical uses, pharmacology, and safety of modafinil. ACS Chem. Neurosci. 2018; 9(2): 151–158. Publisher Full Text\n\nOhayon MM, Thorpy MJ, Short SA, et al.: 0605 Sodium Oxybate Dosing Utilization Patterns in the Nexus Narcolepsy Registry. Sleep. 2019; 42(1): A241. Publisher Full Text\n\nOllila HM, Ravel JM, Han F, et al.: HLA-DPB1 and HLA class I confer risk of and protection from narcolepsy. Am. J. Hum. Genet. 2015; 96(1): 136–146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRanjbari E, Philipsen MH, Wang Z, et al.: Combined electrochemistry and mass spectrometry imaging to interrogate the mechanism of action of modafinil, a cognition-enhancing drug, at the cellular and sub-cellular level. QRB Discovery. 2021; 2: e6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoth T, Dauvilliers Y, Guinta D, et al.: Effect of sodium oxybate on disrupted nighttime sleep in patients with narcolepsy. J. Sleep Res. 2017; 26(4): 407–414. PubMed Abstract \| Publisher Full Text\n\nRundo JV, Downey R III: Polysomnography. Handb. Clin. Neurol. 2019; 160: 381–392. Publisher Full Text\n\nSahni AS, Carlucci M, Malik M, et al.: Management of excessive sleepiness in patients with narcolepsy and OSA: current challenges and future prospects. Nat. Sci. Sleep. 2019; 11: 241–252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScheer D, Schwartz SW, Parr M, et al.: Prevalence and incidence of narcolepsy in a US health care claims database, 2008–2010. Sleep. 2019; 42(7): 91. Publisher Full Text\n\nStephansen JB, Olesen AN, Olsen M, et al.: Neural network analysis of sleep stages enables efficient diagnosis of narcolepsy. Nat. Commun. 2018; 9(1): 1–15. Publisher Full Text\n\nTakenoshita S, Sakai N, Chiba Y, et al.: An overview of hypocretin based therapy in narcolepsy. Expert Opin. Investig. Drugs. 2018; 27(4): 389–406. PubMed Abstract \| Publisher Full Text\n\nThorpy MJ: Classification of sleep disorders. Neurotherapeutics. 2012; 9(4): 687–701. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThorpy MJ, Dauvilliers Y: Clinical and practical considerations in the pharmacologic management of narcolepsy. Sleep Med. 2015; 16(1): 9–18. PubMed Abstract \| Publisher Full Text\n\nThorpy MJ, Bogan RK: Update on the pharmacologic management of narcolepsy: mechanisms of action and clinical implications. Sleep Med. 2020; 68: 97–109. PubMed Abstract \| Publisher Full Text\n\nTrombley TA, Capstick RA, Lindsley CW: DARK Classics in Chemical Neuroscience: Gamma-Hydroxybutyrate (GHB). ACS Chem. Neurosci. 2020; 11(23): 3850–3859. PubMed Abstract \| Publisher Full Text" }	[ { "id": "208036", "date": "16 Oct 2023", "name": "Shuqin Zhan", "expertise": [ "Reviewer Expertise Narcolepsy and Sleep medicine" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. Initial search results and potential biases:\nThe initial search of this manuscript yielded 122 clinical study results related to modafinil and GHB. After eliminating duplicates, systematic reviews, meta-analyses, and non-human studies, only four articles directly comparing the treatment of narcolepsy with GHB and modafinil were included. The aim was to explore and compare the effects of modafinil and GHB in the treatment of NT1 and NT2.\nBias concerns:\nPotential missed information: Excluding 77 reviews and meta-analyses may mean that some valuable conclusions and perspectives were not considered, such as insights about the two drugs in other contexts or compared to other treatments.\nNarrow selection criteria: Due to strict inclusion criteria, a large number of preliminary search results were excluded, potentially leading to result bias. Selection bias: Narrowing down from 122 articles to 4 could result in significant studies being overlooked, especially those that might not align with the current review's conclusions.\n2. Limitations of the study:\nThe manuscript seems to merely organize and describe existing research, without adopting new statistical analysis methods or drawing conclusions significantly different from previous studies. Such literature is commonly referred to as a \"narrative review\" or \"descriptive review.\"\nValue and limitations: The value of a narrative review is that it can provide readers with a comprehensive overview of a specific topic, especially for those unfamiliar with the field. However, since it doesn't use systematic methods or conduct new statistical analyses, its conclusions might be influenced by the original authors' biases, lacking clear evidence to support them.\nCompared to systematic reviews: Compared to systematic reviews or meta-analyses, narrative reviews might not be considered as authoritative in academia. Systematic reviews and meta-analyses typically involve strict study selection, quality assessment, and may involve new statistical analyses, leading to more reliable conclusions.\n3. Issues with novelty:\n\nThe conclusions of this review don't offer new perspectives or findings compared to previous research results. Although the manuscript provides a narrative review of the efficacy of modafinil and GHB in treating narcolepsy, it lacks originality and novelty. The manuscript doesn't employ new statistical analysis methods and doesn't present conclusions that differ significantly from prior studies.\nThe value of this manuscript lies in providing readers with a comprehensive overview of the topic, it's necessary to add some new analyses, discussions, or insights, or to explicitly highlight the differences between this review and the existing literature\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1122
https://f1000research.com/articles/12-1121/v1	08 Sep 23	{ "type": "Case Report", "title": "Case Report: A rare presentation of wandering spleen with rare cardiac anomalies and hepatomegaly in a young woman", "authors": [ "Isha Sahai", "Benumadhab Ghosh", "Gajendra Agrawal", "Isha Sahai", "Benumadhab Ghosh" ], "abstract": "The presence of a wandering spleen with hepatomegaly causing acute abdominal symptoms is an extremely rare clinical entity. The combination of this condition with cardiac anomalies like ostium primum and VSD (ventricular septal defect) has been a cause for the severe growth abnormalities and clinical features like early satiety, blood in vomit and palpitations. Here we report the case of an early 20s woman who presented with decreased appetite, hematemesis, syncopal attacks, palpitations, irregular menstrual cycle, pallor, cyanosis and with a known case of ventricular septal defect. This report focuses on a rare association of wandering spleen with ostium primum and hepatomegaly and ovarian cyst. The significance of this case is heightened because if the patient had received an earlier diagnosis, it could have prevented the onset of these clinical conditions, leading to a better quality of life for the patient.", "keywords": [ "Wandering spleen", "Hepatomegaly", "VSD", "Ovarian cyst." ], "content": "Introduction\n\nWandering spleen with torsion is a very uncommon condition, with a reported incidence rate of less than 0.2%, and accounting for only 0.002% of splenectomies.1 There can be associated hepatic complications. Liver dysfunction is one of the major non-cardiac complications associated with congenital heart disease (CHD) and has been reported in 6% of deceased patients with CHD.2 The development of hepatic complications may result from persistent chronic passive venous congestion or reduced cardiac output, either due to the underlying cardiac disease or as a consequence of palliative cardiac surgery.2\n\nWith respect to the recent data of epidemiology of atrial septal defects (ASDs), there is a prevalence of 1.6 per 1000 cases.3 Among these ASDs, the third most common type is ostium primum. This occurs when the septum primum fails to fuse with the endocardial cushions, leading to atrio-ventricular complications.4 In most of the cases of ASDs, lengths smaller than 5 mm undergo spontaneous closure in their first year of birth. However, defects larger than 1 cm require medical or surgical procedures to help in the closure of the defect.5\n\nThis case report describes a rare presentation of a female patient having wandering spleen with ostium primum type of atrial defect along with an enlarged liver. The patient was undiagnosed till she was of this age before she visited the Cardiology department of the Shalinitai Meghe Superspeciality Centre, Wardha, India. This is a rare presentation involving several clinical conditions and organ systems which makes the treatment more challenging.\n\n\nCase report\n\nA female patient in her early 20s, who is a resident of Wardha and is a student, came to the outpatient department, in a conscious state with chief complaint of decreased appetite for one month. This was associated with weight loss of 5kg within two months. There is an associated history of hematemesis, syncopal attacks lasting for a few seconds and continuous palpitations and irregular menstrual cycles with passage of clots and hot flashes. Patient is a known case of ventricular septal defect (diagnosed at the age of 16 years). In a routine health checkup, the physician heard an ejection systolic murmur due to septal defects. The clinician referred the patient to the Cardiology department of Acharya Vinoba Bhave Rural Hospital which comes under Shalinitai Meghe Super Specialty Center, where the patient was immediately advised to undergo routine investigations, chest x-ray, electrocardiography (ECG), ultrasonography (USG), computed tomography (CT) of the abdomen and pelvis, 2-dimensional echocardiography and CT abdominal angiogram. There was no significant family history.\n\nOn general examination, the patient was conscious and well oriented with time, place and person. The patient seemed afebrile, pulse rate was around 76/min, respiratory rate was recorded at 18/min, and blood pressure was measured and was found to be lower than normal (100/70 mm of Hg). Estimated weight was 40kg, height was 138 cm and body mass index (BMI) was 21. The patient’s oxygen saturation was 79% (SpO2) on admission. On further examination, pallor and cyanosis were seen. There were no other significant findings in the general examination.\n\nA clinical examination revealed normal findings of the central nervous system (as per Glasgow coma score and reflex examinations), respiratory system (air entry bilaterally equal) and renal system. Cardiovascular system and gastrointestinal system showed abnormalities; the examination is detailed below.\n\nOn cardiovascular assessment, apex impulse was visible, whereas no precordial bulge, dilated veins, scars, and sinuses were visible. On palpation, the presence of a thrill was heard on the apex beat over the 5th intercostal space and anterior axillary line. On auscultation, S1 and S2 were heard best at the mitral area along with the ejection systolic murmur {grade 4 (loud and associated with a palpable thrill)} radiating to the anterior axillary line. Loud P2 was heard with a wide variable split. Abdominal assessment showed a soft abdomen. There was mild tenderness over the epigastric region without any distension. Liver was palpable and the spleen was not palpable.\n\nLab findings showed normal sodium levels (134 mEq/dl), normal potassium (4.5 mEq/dl) and low serum creatinine (0.6 mg/dl). Hematological findings showed normal hemoglobin levels (13.4g%) and normocytic normochromic red blood cells with few microcytes. However, the platelet count was reduced on smear with giant platelets. The absolute platelet count is 40000 cells per cubic millimeter. No haemoparasites were seen.\n\nOn recording ECG, there were biphasic waves seen in V2 V3, right axis deviation (right ventricular hypertrophy) along with the presence of inverted P wave in lead 2, 3, as shown in Figure 1. On chest x-ray, plethora of lungs, cardiomegaly (increased CT ratio), and scoliosis of the spine were found, as shown in Figure 2. A 2D echo was performed, which showed ostium primum type of ASD. The observations are shown in Figure 3.\n\nCT: cardiothoracic.\n\nUpon CT abdomen and pelvis plane, it was observed that there was a large central liver, simple right ovarian cyst, mild bulky pancreas and the spleen could not be visualized at its normal position. A wandering spleen was seen. There was a cystic mass of 5.1 by 4.1 centimeters in the right ovary. Left ovaries appeared normal. Cardiomegaly was also noted from the CT. Renal system was normal. Observations are shown in Figure 4a and 4b.\n\nAbdomen angiography was also done which suggested the presence of approximately 46 by 5 mm well defined homogeneously enhancing splenunculi -like structure noted in the right lumbar region with splenic vessels which directed us to the possibility of wandering spleen. The accessory splenic artery directly arises from abdominal aorta at T 11 level and measures 1.8 mm at origin. Early opacification of inferior vena cava and hepatic vein noted in arterial phase.\n\nSurgery was not performed in this patient as the patient did not consent to the surgery. Deranged coagulation profile and low platelet count also contributed towards the fact that surgery could not be performed. Surgeries which this patient needs to undergo are for ostium primum, and the percutaneous closure of VSD. Patient was discharged with advice to continue drugs which were prescribed to her like sildenafil 25mg (thrice day dose), spironolactone 20mg (once daily), and Met XL 25mg (once daily). The medications were prescribed till the next follow up visit at 3 months.\n\nWandering spleen with torsion and splenic infarction causing acute abdomen is an extremely rare clinical entity. Patient was advised to attend regular follow-ups and the practitioner explained to her the potential for pregnancy related complications. CECT is the preferred diagnostic modality for the wandering spleen. Surgery was not performed in the patient as the patient did not consent to the surgery. The patient’s platelet count was much lower than normal levels which would have made surgery difficult. Surgery could be performed for ostium primum, and the percutaneous closure of VSD could also be done in the patient. The spleen did not cause any symptomatic difficulties, so it was not indicated for surgery. The cardiac anomalies along with hepatomegaly have been the cause of the severe growth abnormalities and clinical conditions like early satiety, abdominal fullness, and lethargy. The case becomes more important because if the patient had been diagnosed earlier, these clinical conditions could have been averted, and the patient could have had a better quality of life.\n\n\nDiscussion\n\nWhile there is no gender difference in cases under the age of ten, after the first decade, the prevalence of wandering spleen is higher in females than in males, with a ratio of 7:1.1 Wandering spleen can present in various ways, ranging from no symptoms to acute abdominal pain caused by torsion and infarction. In our patient, there was no complaint of abdominal pain. Wandering spleen is a condition where the spleen exhibits abnormal mobility and moves from its usual position in the left hypochondrium. This displacement is attributed to the absence of proper fixation and an elongated splenic pedicle. Normally, the spleen is held in position by gastrosplenic and lienorenal ligaments. It is a congenital condition or an acquired one. Congenital cases are due to the failure of ligament development, resulting in long splenic mesentery. Some acquired cases like prune belly syndrome and hypermobile colon can be associated with the condition.6 Splenic torsion can be acute, mimicking other abdominal conditions like appendicitis, peritonitis, or bowel obstruction.7\n\nDifferent imaging techniques such as ultrasonography, Doppler ultrasound, plain radiography, contrast enhanced computed tomography (CECT), magnetic resonance imaging (MRI), scintigraphy, and angiography are diagnostic imaging techniques commonly used to identify wandering or ectopic spleen. These imaging modalities, along with a thorough physical examination, play a crucial role in accurately diagnosing the condition.1 Additional imaging examinations such as abdominal ultrasonography, Doppler and CECT abdomen are particularly important for a comprehensive diagnosis.\n\nWith respect to treatment modalities, surgical intervention is mostly favored for wandering spleen. There are two surgical options present depending on the condition of the spleen: splenopexy and splenectomy.8 The preferred method among these interventions is decided by the specific properties and requirements with respect to cases of patients. Laparoscopic or open splenopexy methods can be used to treat patients having uncomplicated cases of wandering spleen (WS).8 However, in the case of our patient with a significantly low platelet count, alternative considerations may be necessary. This can lead to complications, such as splenic infarction, rupture, hemorrhage, abscess, splenomegaly with mass effect, or signs of hypersplenism, for which the preferred treatment option is a splenectomy. This procedure can be performed using either an open or laparoscopic approach, depending on the specific circumstances and requirements of the patient.8\n\nDuring the fourth week of gestation,9 atrial septation begins in the fourth gestational week9 as the primary atrial septum (septum primum). It extends from the roof of the primitive atrium to the endocardial cushions. The embryonic endocardium (the mesenchymal cap) is the source from which the mesenchymal cells are derived which enclose the caudal end of the septum primum. The septum primum extends and connects to the atrioventricular endocardial cushions, eventually closing and eliminating the ostium primum, which is the space between the mesenchymal cap and the atrioventricular cushions. In our patient, there is an ostium primum resulting in the formation of a single atrium.\n\nLiver congestion caused by heart failure is a common problem that can lead to cardiac fibrosis and cirrhosis. To understand how venous congestion causes disease, it’s important to know about the unique blood supply of the liver. The liver has two vessel systems: the hepatic artery and the portal vein. About 70% of the blood supply to the liver comes from the portal vein. From the portal triads, both the portal venous system and the hepatic artery enter the acinus of the liver. Blood flows from both systems through the liver’s capillary system and toward the central vein, where it drains into the inferior caval vein. Hepatocytes near the portal triad receive oxygen- and nutrient-rich blood, while those near the central vein receive blood with fewer nutrients and less oxygen. There are defined metabolic zones in the liver that correspond to these differences in nutrient and oxygen supply. On histopathological evaluation, there were signs of venous congestion, such as sinusoidal dilation, hemorrhagic necrosis, and fibrosis, which are predominantly in the pericentral zone III.10 A typical pattern of fibrosis is seen in liver congestion, bridging the central veins.\n\nLiver dysfunction in CHD is not solely caused by venous congestion, as various factors related to CHD can also affect the oxygen supply to the liver. These factors may include low cardiac output, cyanosis, or impaired oxygenation due to lung problems associated with CHD. Liver diseases in CHD can occur for reasons beyond just hemodynamic alterations. This is partly due to the fact that survival rates for CHD patients have significantly improved in recent decades, resulting in a growing population of CHD patients over the age of 65.11\n\nThe beneficial and functional management of this condition should consist of a team of a cardiologist, cardiovascular surgeon, gastroenterologist, and interventional radiologist. The cardiovascular surgeons and interventional cardiologists could not perform the surgery as the patient did not consent for an open and percutaneous approach of intervention. Thus, the patient was discharged with medical advice.\n\nThe patient provided written informed consent for the publication of this manuscript with her clinical details and 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 thank Anuj Chaturvedi for assisting the authors in writing, editing and reviewing the case report.\n\n\nReferences\n\nMemari M, Nikzad M, Nikzad H, et al.: Wandering spleen in an adult man associated with the horseshoe kidney. Arch. Trauma. Res. 2013; 2: 129–132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEngelings CC, Helm PC, Abdul-Khaliq H, et al.: Cause of death in adults with congenital heart disease - An analysis of the German National Register for Congenital Heart Defects. Int. J. Cardiol. 2016; 211: 31–36. PubMed Abstract \| Publisher Full Text\n\nChelu RG, Horowitz M, Sucha D, et al.: Evaluation of atrial septal defects with 4D flow MRI-multilevel and inter-reader reproducibility for quantification of shunt severity. MAGMA. 2019; 32: 269–279. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNaqvi N, McCarthy KP, Ho SY: Anatomy of the atrial septum and interatrial communications. J. Thorac. Dis. 2018; 10: S2837–S2847. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBehjati-Ardakani M, Golshan M, Akhavan-Karbasi S, et al.: The Clinical Course of Patients With Atrial Septal Defects. Iran. J. Pediatr. 2016; 26: e4649. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSatyadas T, Nasir N, Bradpiece HA: Wandering spleen: case report and literature review. J. R. Coll. Surg. Edinb. 2002; 47: 512–514. PubMed Abstract\n\nDawson JH, Roberts NG: Management of the wandering spleen. Aust. N. Z. J. Surg. 1994; 64: 441–444. Publisher Full Text\n\nNastiti NA, Niam MS, Khoo PJ: Emergency laparoscopic splenectomy for torsion of wandering spleen in a geriatric patient: A case report. Int. J. Surg. Case Rep. 2019; 61: 91–95. Publisher Full Text\n\nKloesel B, DiNardo JA, Body SC: Cardiac Embryology and Molecular Mechanisms of Congenital Heart Disease: A Primer for Anesthesiologists. Anesth. Analg. 2016; 123: 551–569. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMyers RP, Cerini R, Sayegh R, et al.: Cardiac hepatopathy: clinical, hemodynamic, and histologic characteristics and correlations. Hepatology. 2003; 37: 393–400. Publisher Full Text\n\nAfilalo J, Therrien J, Pilote L, et al.: Geriatric congenital heart disease: burden of disease and predictors of mortality. J. Am. Coll. Cardiol. 2011; 58: 1509–1515. Publisher Full Text" }	[ { "id": "264707", "date": "09 May 2024", "name": "Ilse Castro-Aragon", "expertise": [ "Reviewer Expertise pediatric radiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 understand that surgical treatment was not possible since patient did not consent and platelets were low. There is a list of medications prescribed but no explanation about the thought process behind that decision. In addition they refer to: discharged with medical advice, but they don't expand on that concept and don't give any other followup parameters which they consider important to consider in the future. In addition, once medical management is optimized there may be reasons to consider surgical or more urgent treatment which could also 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? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1121
https://f1000research.com/articles/12-1120/v1	08 Sep 23	{ "type": "Research Article", "title": "Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPAR-γ signaling pathways in lipopolysaccharide-induced RAW 264.7 cell line", "authors": [ "Nada S. Shaker", "Hayder B. Sahib", "Zeena A. Hussein", "Nibras J. Tahseen", "Hayder B. Sahib", "Zeena A. Hussein", "Nibras J. Tahseen" ], "abstract": "Background: Cytokine storm syndrome (CSS) is a leading cause of morbidity and mortality in patients with late-stage coronavirus disease 2019 (COVID-19), causing multiple organ failure and death. According to prior research, fraxin, and quercetin have anti-inflammatory, antioxidant, antimicrobial, and antiviral properties. Therefore, this study aimed to investigate the anti-cytokine storm activity of fraxin and quercetin, their combination, and the molecular mechanism behind this activity in Lipopolysaccharide (LPS)-induced RAW 264.7 cells. Methods: LPS-induced macrophage cells were treated with fraxin, quercetin, or their combinations at various doses for cytotoxicity, anti-cytokine assays, and gene expression analyses. An enzyme-linked immunosorbent assay was used to quantify the levels of proinflammatory cytokines, interleukin 1 beta (IL1β), interleukin 6 (IL-6), and tumor necrosis factor-α (TNF-α), and RT-PCR was used to measure the gene expression of PPAR-γ and Toll-like receptor 4 (TLR-4) concerning GAPDH as a reference gene. Results: The results revealed a slight decrease in cell viability only when higher concentrations were applied to the cells. Fraxin, quercetin, and their combination reduced the generation of proinflammatory cytokines. The combination (fraxin + quercetin (FQ)) reduced the levels of IL-1β, IL-6, and TNF-α by 56.2%, 58.5%, and 70.6% respectively, compared to the LPS-only control; pretreatment of cells with farxin, quercetin, and their combination resulted in significant inhibition of TLR-4 gene expression by 89%, 82%, and 93% respectively, compared to the control (P˂ 0.05); FQ upregulated PPAR-γ expression up to 60-fold compared to the control, while fraxin and quercetin increased PPAR-γ by 17.6 and 8.6-folds, respectively. Conclusions: Based on these findings, fraxin, quercetin and their combination might be considered anti-cytokine storm agents, which could lay the groundwork for future research into other combinations of fraxin and quercetin, as well as the pathways involved in the molecular mechanisms underlying the synergistic anti-cytokine-storm-activity.", "keywords": [ "Fraxin", "Quercetin", "Anti-Cytokine Storm", "RAW 264.7 Murine Macrophage Cell Line", "Lipopolysaccharide", "Proinflammatory Cytokines", "PPAR Γ", "TLR-4", "Tnfα", "IL1β", "IL6", "Synergistic Combination", "MTT Assay" ], "content": "Introduction\n\nA cytokine storm is a condition of uncontrolled systemic hyperinflammation caused by excess cytokines, leading to multiorgan failure.1 Cytokine storms may occur for many reasons, including malignancy, rheumatoid arthritis, and sepsis. Recently, cytokine storms were found to be related to mortality and morbidity in many cases of coronavirus disease 2019 (COVID-19).2 Since coronavirus disease is characterized by hyperinflammation and an excessive immune response, the need to develop anti-cytokine drugs has increased.3 Lipopolysaccharide (LPS), a component of the outer membrane of gram-negative bacteria, signals toll-like receptor 4 (TLR 4) to activate macrophages, which stimulates several intracellular signaling pathways, including those for nuclear transcription factor kappa-B (NF-B) and mitogen-activated protein kinases (MAPKs). Interleukin IL-6, IL-1, and tumor necrosis factor (TNF-α) are proinflammatory cytokines activated macrophages release.4\n\nFraxin, a coumarin derived from the plant Fraxinus and Cortex fraxin, is referred to as 7,8-Dihydroxy-6-methoxy coumarin, 8-D glucopyranoside.5 Fraxin possesses different pharmacological activities, including as an anticancer, antiviral, anti-inflammatory, and antioxidant.6 For this vast potential, fraxin is a target for further immunomodulating studies.\n\nQuercetin is a bioflavonoid widely distributed in apples, berries, grapes, and onions. Quercetin was reported in previous studies as having a wide range of biological actions, such as anti-inflammatory properties due to the inhibition of inflammation-related enzymes, cyclooxygenase (COX), and lipoxygenase (LOX).7 RAW 264.7, a standard monocyte/macrophage cell line, is mainly used to study the anti-inflammatory activity of plant-derived extracts and their active constituents by evaluating the reduction in the production of inflammatory mediators, cytokines, and chemokines in LPS-stimulated RAW 264.7 cells (RAW 264.7 a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus).8\n\nPeroxisome proliferator-activated receptor γ (PPAR-γ) is a nuclear hormone receptor and a ligand-activated transcription factor family member. Increasing evidence indicates promising anti-inflammatory properties of cancer cells exerted by activating PPARγ by synthetic ligands.9\n\nPPAR-γ agonists have been thought to inhibit the production of monocyte inflammatory cytokines and the expression of inducible nitric oxide synthase (iNOS), which has been observed in response to synthetic anti-diabetic thiazolidinedione drugs (such as BRL 49653 and ciglitizone), and negatively regulates the expression of proinflammatory genes and suppresses tumor cell growth.10\n\nDrug combinations have been previously used as a new approach for treating many diseases. Their beneficial effects appear to be enhancing pharmacological activity and minimizing the dose to avoid any unwanted side effects of drugs without compromising their efficacy.11 Furthermore, previous literature mentioned that both fraxin and quercetin possess some antioxidant and anti-inflammatory activity in different disease models. In this research, we aim to investigate fraxin and quercetin anti-cytokine storm effects through suppression of the production of proinflammatory cytokines from the LPS-induced murine macrophage RAW 264.7 cell line, the possible mechanism underlying it, through changes in expression of TLR4 and PPAR-γ signaling pathways, and if there is a potential synergy between them when combined using isobolographic analysis, based on the median effect principle.12\n\n\nMethods\n\nThe investigations followed the guidelines established by the Ethics Committee of Al-Nahrain University, College of Medicine (approval number Nah. Co). Pha.12 on 27 June 2022.\n\nQuercetin hydrated 2-(3,4-dihydroxy phenyl)-3,5,7-trihydroxy-4Hchromenen-4-one dihydrate (purity ≥ 96%), fraxin (7,8-Dihydroxy-6-methoxy coumarin-8-beta-D-glucoside) (purity ≥ 98%), dexamethasone (purity ≥ 98%), and lipopolysaccharide (LPS) (Escherichia coli, 055: B5) were purchased from Hangzhou-Hyper Chem. Limited/China, dimethyl sulfoxide (DMSO) from Thomas Baker/India, Mouse Interleukin1β (IL-1β), (IL-6), and (TNF-α) enzyme-linked immunosorbent assay (ELISA) kits were purchased from MyBiosource, USA, RAW 264.7, (TIB-71) murine macrophage cell line (ATCC® TIB-71™), and Dulbecco’s modified Eagle’s medium (DMEM) from American Type Culture Collection (ATCC, USA), fetal bovine serum (10% FBS), Trypsin- EDTA, penicillin/streptomycin solution from Capricorn Scientific/Germany, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) kit from MyBioSource, USA; TRIazol® reagent (Invitrogen); RT-PCR primers: glyceraldehyde 3-phosphate dehydrogenase (GAPDH), PPAR-γ, and TLR-4 from OriGene/USA, LightCycler® FastStart™ SYBR® Green master kit/Roche, Germany, Revert AidTM first strand Complementary Deoxyribonucleic acid (cDNA) synthesis kit/Thermo Scientific, USA (Tables 1 and 2).\n\nCell culture\n\nThe RAW264.7 TIB-71 murine macrophage cell line was maintained in Dulbecco’s Modified Eagle Medium (Capricorn Scientific) with 10% fetal bovine serum (FBS) 1% penicillin-streptomycin and then kept in an incubator at 37°C with 5% carbon dioxide until confluent. Trypsin-EDTA was used to clean and harvest cells.13\n\nMethod of trypsinization, cell harvesting using trypsin-EDTA\n\nThe trypsinization procedure was performed in a laminar flow hood using proper aseptic technique. Trypsin, media, and phosphate buffer solution (PBS) were warmed in a 36°C water bath for at least 20 minutes prior to the procedure. All growth media was aspirated from the cell culture flask, washed once with PBS, and gently shaken with the PBS around the flask and aspirated. Half of the culture volume of trypsin was ejected directly onto cells, which was enough to cover the cells. The cells were incubated for 5 minutes at 37°C. cells were quite adherent to the flask. Cell lifter was needed at this point, trypsin was neutralized with serum containing medium (half of culture volume + 0.5 mL); warm media was directly ejected onto cells and a cell lifter was used gently to scrape cells off the flask. The cell suspension was collected from the flask and centrifuged for 4 minutes at 2500 rpm, after which the trypsin-containing supernatant was then discarded, and the cell pellet was resuspended with fresh medium, and counted or cultured as desired.13\n\nCell viability in RAW264.7 was evaluated using the MTT assay after treatment with quercetin, fraxin, and fraxin + quercetin (FQ). RAW264.7 cells were plated at a density of 1 × 104 cells/well in a 96-well plate and allowed to grow for 24 h. before the medium was removed. Then the cells were treated with fraxin, quercetin, and FQ in a ratio of 1:1 in serial dilutions (200, 100, 50, 25, 12.5, and 6.25 μg/ml), each concentration in tri-replicate, for 2 h. from the treatment. First, LPS (1 μg/ml) was added to each well and incubated for 24 h. Next, 20 μL of MTT (5 mg/mL) was added to each well, followed by incubation for 4 h at 37°C with 5% CO2. After removing the media, 150 μL of dimethyl sulfoxide (DMSO) was added to each well to dissolve the insoluble formazan crystals in viable cells. The ELISA plate reader read an absorbance of 540 nm. Cell viability was calculated relative to the untreated control cells, which were considered to have 100% viability. The following formula was used to determine cell viability:\n\nExperiments were performed in triplicate, and the data are presented as mean ± standard error of the mean.\n\nQuercetin hydrated 2-(3,4-dihydroxy phenyl)-3,5,7-trihydroxy-4Hchromenen-4-one dihydrate (purity ˃ 96%), Fraxin (7,8-Dihydroxy-6-methoxy coumarin-8-beta-D-glucoside) (purity ˃ 98%), and LPS (lipopolysaccharide) (Escherichia coli, 055: B5) were all purchased from Hangzhou-Hyper Chem. Limited/China. Both quercetin and fraxin were dissolved using DMSO (Dimethyl sulfoxide, from Thomas Baker/India), and LPS was dissolved and diluted in PBS for preparation of 1 μg/ml solution. Each agent (quercetin and fraxin) was dissolved in DMSO and then diluted to final volume with (Mg2+, Ca2+)-free PBS buffers at pH 7.4 to prepare a stock solution of 1 mg/ml for each fraxin and quercetin. Serial dilutions were freshly prepared at the same day of the experiment from the stock solution. Agents were tested at concentrations of 200, 100, 50, 25, 12.5, and 6.25 μg/ml and for FQ (half the concentration was tested for each agent in the same well), cells were supplemented with 200 μl of fresh medium along with the tested agent. The concentration of DMSO used (<0.1%) did not influence the performed assays.\n\nThe results of the MTT assay were analyzed using the isobologram equation for the median effect/combination index (CI) by Chou (2006) and Chou and Talalay (1984). A dose-response curve can be generated by experimenting with different concentrations of each drug and its combination. For example, D is the dose, and Dm is the dose for a 50% effect; in this case, it is equal to IC50%. The parameters of the dose-effect curves were calculated with the help of a computer program (Compusyn), which then determines the CI values using the general combination index equation, from which we can infer that synergism, additive effects, and antagonism are present if the CI value is less than one, equal to one, or more than one, respectively.12\n\nIn comparison with dexamethasone as a positive control drug, the anti-cytokine storm activity of fraxin, quercetin, and FQ was evaluated by measuring levels of proinflammatory cytokines IL-1β, IL-6, and TNF-α in RAW 264.7 cells induced with (1 μg/ml) LPS. A 96-well plate was seeded with RAW264.7 cells at a density of 1 × 104 cells/well and incubated for 24 h. Cells were pretreated with fraxin (concentration 25 μg/ml), quercetin (concentration 12.5 μg/ml), and FQ (concentration 6.25 μg/ml). These concentrations were selected according to the MTT assay results, and dexamethasone (5 μg/ml) was used as a positive control drug. All treatments were performed in triplicate; untreated cells were considered a negative control. After 2 hours adding treatment, LPS was added to all wells in the plate and incubated for 24 h at 37 °C in a humidified CO2 5% incubator. After that the medium was collected and centrifuged at 2000xg for 10 min. Culture supernatants were collected to quantify proinflammatory cytokines by enzyme-linked immunosorbent assay (ELISA) kits for the targeted cytokines IL-1β, IL-6, and TNF-α. All reagents, and dilutions were prepared on instructions provided by the manufacturer (My BioSource, USA). From each, 100 μl of dilution of standards, blank, and the collected samples were added to each well in a 96-well plate then covered, gently shaken, and incubated at 37°C for 60 minutes. The liquid was removed from each well, without washing. A volume of. 100 μl of detection reagent A was added to each well and incubated at 37°C for 60 minutes. The washing was repeated three times, 100 μl detection reagent B was added to each well, and was incubated for 30 minutes at 37°C. The washing was repeated five times, 90 μl substrate Solution was added to each well and incubated for 10–20 minutes at 37°C. Away from light, the liquid turned blue, 50 μl stop Solution was added and the liquid turned yellow. Under 450 nm wavelength, the optical density (OD) was calculated. The linear regression equation of the standard curve was computed based on concentrations of standards and related OD values. Then the concentration of the corresponding sample was calculated, and the levels of IL-1β, IL-6, and TNF-α in cell culture supernatants were expressed as pg/ml. The OD was calculated at a wavelength of 450 nm. The linear regression equation of the standard curve was computed based on the concentrations of the standards and corresponding OD values. Then the attention of the corresponding sample was calculated, and the levels of IL-1β, IL-6, and TNF-α in cell culture supernatants were expressed as pg/ml.\n\nEach well of a 6-well plate was inoculated with 1 × 106 cells and incubated for 24 hours. Fraxin (25 μg/ml), quercetin (12.5 μg/ml), and FQ (6.25 μg/ml) were applied to cells in triplicate (1 μg/ml). After Two hours,cells were treated with fraxin, quercetin, and FQ, LPS was added. The cells were then incubated at 37°C for 24 hours in a humidified CO2 5% incubator. Prior to harvesting, the cells were rinsed three times with PBS. The cells were pre-treated with fraxin (25 μg/ml), quercetin (12.5 μg/ml), and FQ (6.25 μg/ml) all in triplicate, (1μg/ml) LPS was added after 2 h. Subsequently, cells were incubated for 24 h at 37 °C in a humidified CO2 5% incubator. The cells were washed three times with PBS before being harvested. The growth media was then removed. To lyse the cells, 1 mL of TRIzol™ Reagent was added directly. The lysate was pipetted up and down several times to homogenize, then incubated for 5 minutes at room temperature before 0.2 mL of chloroform was added, then thoroughly mixed by shaking and incubated for 2–3 minutes at room temperature. The sample was centrifuged at 12,000 × g at 4°C for 15 minutes. The mixture separated into a lower red phenol-chloroform, an interphase, and a colorless upper aqueous phase. By angling the tube at 45° and pipetting the solution out, the aqueous phase containing the RNA was transferred to a new tube. After 0.5 mL of isopropanol was added to the aqueous phase, it was incubated for 10 minutes at 4°C before being centrifuged for 10 minutes at 12,000 × g at 4°C. The total RNA precipitated formed a white gel-like pellet at the bottom of the tube, and the supernatant was discarded with a micro pipettor. The pellet was resuspended in 1 mL of 75% ethanol, briefly vortexed then centrifuged for 5 minutes at 7500 × g at 4°C. The supernatant was discarded with a micro pipettor, and the RNA pellet was vacuumed or air dried for 5–10 minutes. By pipetting up and down, the pellet was resuspended in 20–50 μL of RNase-free water, 0.1 mM EDTA, or 0.5% SDS solution, incubated in a water bath at 55–60°C for 10–15 minutes, then proceeded to downstream applications, or stored the RNA at -70°C. Total RNA was extracted from stimulated cells using TRIzol® reagent, and the first strand of cDNA was produced using a commercial kit according to the manufacturer’s instructions, the detailed steps were as the following: after thawing, the kit’s components were mixed and briefly centrifuged. The following reagents were added to an ice-cold sterile, nuclease-free tube in the following order:\n\na - Template RNA (total RNA) 0.1 ng – 5 μg\n\nb - Primer (Random Hexamer primer) 1 μL\n\nc - Water, nuclease-free added to make the total volume of 12 μL\n\n- Total volume 12 μL\n\nThis was gently mixed, briefly centrifuged and incubated at 65°C for 5 min then placed on ice for 1 min. The following components were added in the indicated order:\n\n• 5× Reaction Buffer 4 μL\n\n• RiboLock RNase Inhibitor (20 U/μL) 1 μL\n\n• 10 mM dNTP Mix 2 μL\n\n• Revert Aid M-MuLV RT (200 U/μL) 1 μL\n\nTotal volume 20 μL\n\nThis was gently mixed, and centrifuged briefly, incubated for 5 min at 25°C followed by 60 min at 42°C. The reaction was terminated by heating at 70°C for 5 min.\n\nTotal nucleic acid content is determined by 260 nm absorbance, while sample purity is determined by 280 nm absorbance. Because free nucleotides, RNA, ssDNA, and dsDNS absorb at 260 nm, they all contribute to the sample’s total absorbance. Using the NanoDropTM spectrophotometer, RNA samples can be quantified by absorbance without prior dilution. In the reaction tube, 18 μl of SYBR Green PCR mix containing nuclease-free water, reverse and forward primers, SYBR Green I dye, 1U Taq DNA polymerase, 1.25 mM MgCl2, PCR buffer, and 100 μM Deoxynucleotide triphosphate (dNTP) was added to 2 μl cDNA template to accomplish PCR in 20 μl of the reaction mixture. Primers were used for amplification, and their sequences (5′–3′) are listed in Table 3.\n\nThe amplification conditions were as follows: the RT-PCR reaction began with one cycle at 95°C for 3 min, followed by one process at 95°C for 25 s, 55°C for 25 s, and 40 cycles at 95 °C for 25 s each to prevent the amplification of non-specific products. A melting curve assay was performed from 60 to 94°C at a transition rate of 1°C/s. The relative expression ratio of each target gene in the experimental group relative to the control group was computed using the 2−△△Ct method and normalized against GAPDH, which was used as an internal reference gene. The results are expressed as fold-changes compared to the control.\n\nAll tests were performed in triplicate, and the results are presented as mean ± standard error of the mean (SEM), analyzed by one-way ANOVA-Tukey post hoc test for multiple comparisons. SPSS (RRID: SCR_013726) version 25 was used for statistical analysis; P < 0.05, was considered significant.\n\n\nResults\n\nThe MTT assay determined the cell viability of RAW 264.7 cells35; Figure 1 illustrates the effects of fraxin, quercetin, and FQ on cell viability (expressed as a percentage compared to the control-untreated cells-considered 100% cell viability) in the presence of LPS. A reduction in cell viability was noticeable with higher concentrations of both fraxin and quercetin. While FQ exhibited the highest cytotoxicity among all three treatment groups, the viability of cells was decreased in a dose-dependent manner.\n\nCell viability was determined using an MTT assay. The lower red line indicates that cells were subjected to different concentrations of all treatment groups with the presence of lipopolysaccharide (LPS) (1 μg/ml), and the upper red line represents 70% cell viability in all treatments. Cell viability was expressed as a percentage compared with the control, which was considered 100% cell viability, and data are presented as mean ± SEM.\n\nHalf-maximal inhibitory concentration (IC50) values were 248, 54, and 26.5 for fraxin, quercetin, and FQ, respectively. Based on these results, the threshold for cell viability was set at 70% or higher for the anti-cytokine storm assay,8 and the concentrations (25, 12.5, 6.25 μg/ml) for fraxin, quercetin, and FQ were selected, respectively, for the cytokine storm assay following assay.\n\nThe combination index (CI) for FQ in a 1:1 ratio was calculated using CompuSyn based on the MTT results. Dose-effect and median-effect curves were plotted for each drug and its combination. The Results showed that FQ in a 1:1 ratio exhibited synergism, with CI values of 0.297 at IC50 and CI values of 0.409, 0.333, 0.332, 0.267, 0.265, and 0.276 at the following concentrations FQ (200, 100, 50, 25, 12,5, 6.25 g/ml).\n\nFraxin, quercetin, and FQ in concentrations of 25, 12.5, 6.25 μg/ml, respectively, significantly suppressed the production of IL-1β, IL-6, and TNF-α (P ˂ 0.01) in a dose-dependent manner when compared to control (cells treated with LPS only). LPS significantly upregulated production of proinflammatory cytokines compared to the control group (P ˂ 0.05). The highest inhibition activity was recorded with dexamethasone (5 μg/ml) (positive, treated group) which significantly (P ˂ 0.05) suppressed IL-1β, IL-6, and TNF-α by 75.7%, 69%, and 79% respectively compared with the LPS treated control. In the case of the combination, FQ, the levels of IL-1β, IL-6, and TNF-α reduced by 56.2%, 58.5%, and 70.6% respectively, suggesting it is more effective in inactivating cytokine production than each drug alone. The results are shown in Figure 2A, B, and C).\n\nWhen compared to the control, pretreatment of RAW 264.7 cells with farxin (25 μg/ml), quercetin (12.5 μg/ml), and FQ (6.25 μg/ml) for 2 hours before LPS (1 μg/ml) resulted in significant (P ˂ 0.05) suppression of TLR-4 gene upregulation by (89%, 82%, and 93%, respectively). Treatment with LPS activated the TLR-4 pathway, as shown in Figure 3A, and treatment with fraxin, quercetin, and FQ successfully counteracted the stimulatory impact of LPS on RAW 264.7 cells. Furthermore, compared to either treatment alone, the combination synergistically reversed the impact of LPS on cells.\n\nWhile Figure 3B reveals that there is a considerable stimulatory impact on the PPAR-γ pathway, this effect is shown as enhanced gene expression. FQ increased up to 60-fold relative to the control, whereas fraxin and quercetin (17.6, 8.6-folds, respectively) decreased proinflammatory cytokines (Figure 3B), indicating a mechanism by which fraxin, quercetin, and their combination reduce proinflammatory cytokines.\n\n\nDiscussion\n\nThe devastating epidemic caused by SARS-CoV-2 in 2019 prompted researchers to make a considerable effort to search for a possible solution to limit infection. Following the demonstration of the pathological role of the “cytokine storm”, evidence for a cytokine release syndrome can be seen in increased proinflammatory cytokines in late-stage COVID-19. As seen in previous epidemics caused by SARS-CoV and MERS-CoV, dysregulated cytokine production and an influx of inflammatory myeloid cells can cause lung infiltration, septic shock, respiratory failure, acute respiratory distress syndrome (ARDS), multiorgan failure, and death.14,15 Gram-negative bacteria’s outer membrane lipopolysaccharide (LPS) is used in inducing a cytokine storm model both in vivo and in in vitro studies. The stimulation of macrophages with LPS can cause the excessive release of proinflammatory cytokines by activating the nuclear factor κB (NF- κB) and mitogen-activated protein kinase (MAPK) signaling pathways, increasing (COX-2) and (iNOS).16 RAW 264.7 cells induced by LPS is the most widely used model for evaluating anti-cytokines in vitro. For centuries, plants have been used as a natural remedy for numerous illnesses. Hong et al. (2012) reported a dose-dependent reduction in cell spreading and pseudopodia production after treatment with an ethanol extract of Fraxinus rhynchophylla bark on LPS-stimulated macrophages.17 Whang et al. (2005) suggested in their study that fraxin and fraxin-related chemicals improved cell survival rate in human umbilical vein endothelial cells (HUVECs) when exposed to hydrogen peroxide (H2O2) mediated oxidative stress; other previous studies discussed the effect of quercetin on cell migration, which plays a vital role in the development of cancer.18 Quercetin strongly inhibited LPS-induced macrophage adhesion and migration in a dose-dependent manner.19 Previous research has highlighted the various biological activities of fraxin and quercetin, including anti-inflammatory and antioxidant effects, raising the need for additional investigation into their role in cytokine storms. Our study observed that fraxin, quercetin, and fraxin + quercetin exerted low cytotoxic activity on RAW 264.7, and only when cells were exposed to higher concentrations of fraxin and quercetin, which was in agreement with a study by Cui et al. that suggested that only the highest concentration of quercetin reduced macrophage viability when administered together with LPS (1 μg/mL).19 Other previous studies compatible with our study support that the cell viability of RAW 264.7 was not compromised by the presence or absence of LPS.17,20\n\nLi et al. (2019) concluded that fraxin confers protection against LPS-induced lung injury and the inflammatory response in A549 cells.20 In an approach to modulate virus hyperinflammation such as chronic systemic symptoms, the anti-inflammatory effects of quercetin were investigated in mouse macrophage cells exposed to polyinosinic-polycytidylic acid (poly (I:C) as an experimental model for viral inflammation by Kim YJ and Park W. (2016). They found that quercetin might suppress poly (I:C)-induced inflammation by reducing the levels of inflammatory mediators.\n\nOur findings support previous research that found that both fraxin and quercetin were effective at suppressing the release of proinflammatory mediators from LPS-induced RAW 264.7, the mechanism underlying which may be related to interference with various inflammatory signaling pathways, including the TLR signaling system. Following their activation, proinflammatory molecules (such as IL-1, IL-6, and TNF-α) are abundantly generated, and NF-κB phosphorylation, nuclear translocation, and upregulated transcription of proinflammatory factors are all results of TLR-4 activation.16,21\n\nIn numerous macrophage models, PPAR-γ has been shown to exert anti-inflammatory effects by suppressing the expression of multiple proinflammatory genes, such as IL-6, TNF-α, and IL-12.22 From earlier studies, fraxin, isolated from the roots of Ulmus macrocarpa Hance, significantly suppressed the expression of iNOS and COX-2, increased PPAR-γ expression, activated the nuclear factor erythroid 2-related factor 2/heme oxygenase-1 (HO-1) (Nrf2/HO-1) pathway, and inhibited NF-κB and ERK1/2 in a dose-dependent manner The neuroprotective and anti-inflammatory effects of fraxin were also diminished by treatment with GW9662 which is a PPAR-γ antagonist.23,24\n\nIn LPS-induced ARDS in mice, fraxin reduced the production of TNF-α, IL-1β, IL-6, Reactive oxygen species (ROS), and Malondialdehyde (MDA), increased Super oxide dismutases (SOD), and suppressed NF-κB and MAPK signaling.25\n\nLi et al., 2019 discovered that pretreatment with fraxin decreased protein expressions of NF-κB and nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) activated in response to lipopolysaccharide (LPS).26 Aesculin, a hydroxycoumarin, is the 6-O-beta-D-glucoside of esculetin, another organic compound isolated from Cortex fraxini that is structurally related to fraxin. Furthermore, studies in the peritoneum and macrophages demonstrated that aesculin inhibits the production of inflammatory mediators such as iNOS, IL-1, and TNF-α via the PPAR-γ/NF-κB pathway.27\n\nWhile quercetin inhibits liver inflammation mainly through NF-κB/TLR/NLRP3, it also inhibits LPS-stimulated NO increase by suppressing iNOS.28,29 In addition, in differentiated human acute monocyte leukemia cell line (THP-1), quercetin might lower cholesterol levels in macrophages with elevated PPAR-γ expression. Quercetin metabolites, such as quercetin-3-glucuronide (Q3G) and quercetin-3′-sulfate, also upregulated PPAR-γ in A549 lung cancer cells.30,31\n\nFlavonoids, such as quercetin and kaempferol, increase PPAR-γ-mediated gene expression through a mechanism distinct from conventional PPAR-γ agonists.32\n\nDihydroquercetin activates AMPK/Nrf2/HO-1 signaling in macrophages, which mediates its anti-inflammatory effects.33\n\nOur results were consistent with previous studies supporting that fraxin and quercetin upregulated PPAR-γ expression and downregulated TLR-4, stimulated by LPS treatment in macrophage RAW 264.7 cells.\n\nFraxin + quercetin showed synergistic activity when combined, which may be due to multiple targets involved when coming to their anti-inflammatory mechanism, resulting in suppression of proinflammatory mediators IL-1, IL-6, TNF-α and suppression of other pathways like iNOS, COX-2, Nrf2/HO-1, NF-κB, NLRP3, TLR-4, and upregulation of PPAR-γ,\n\nA study described the synergistic combination of two bioflavonoids: quercetin and catechin; this combination caused inhibition of the LPS-activated upregulation of iNOS and COX-2.20 Previous studies have shown that drug combinations, especially in phytopharmaceuticals, may activate entirely different sets of genes than those started by each drug alone.34 This may provide another theoretical explanation for the synergistic activity between fraxin and quercetin, despite the differences in their chemical structures.\n\n\nConclusions\n\nOur study showed that fraxin, quercetin, and their combination exert anti-cytokine storm activity on LPS-induced RAW246.7 cells by targeting multiple signaling pathways and suppressing TLR-mediated NF-κB. Upregulation of PPAR-γ mediated gene expression (Figure 3A and B) may serve as a foundation for future research into other combinations of fraxin and quercetin and pathways involved in their molecular mechanisms explaining the synergistic anti-cytokine storm activity.", "appendix": "Data availability\n\nZenodo: Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data https://doi.org/10.5281/zenodo.7822393. 35\n\nThis project contains the following underlying data:\n\n• Article data.xlsx (Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRabaan AA, Al-Ahmed SH, Muhammad J, et al.: Role of inflammatory cytokines in COVID-19 patients: A review on molecular mechanisms, immune functions, immunopathology and immunomodulatory drugs to counter cytokine storm. 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Publisher Full Text\n\nWhang WK, Park HS, Ham I, et al.: Natural compounds, fraxin and chemicals structurally related to fraxin protect cells from oxidative stress. Exp. Mol. Med. 2005; 37(5): 436–446. Publisher Full Text\n\nCui S, Wu Q, Wang J, et al.: Quercetin inhibits LPS-induced macrophage migration by suppressing the iNOS/FAK/paxillin pathway and modulating the cytoskeleton. Cell Adhes. Migr. 2019; 13(1): 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi T, Li F, Liu X, et al.: Synergistic anti-inflammatory effects of quercetin and catechin via inhibiting activation of TLR4–MyD88-mediated NF-κB and MAPK signaling pathways. Phytother. Res. 2019; 33(3): 756–767. Publisher Full Text\n\nShi H, Hua X, Kong D, et al.: Role of Toll-like receptor mediated signaling in traumatic brain injury. Neuropharmacology. 2019; 145: 259–267. PubMed Abstract \| Publisher Full Text\n\nHuang C, Yang Y, Li WX, et al.: Hyperin attenuates inflammation by activating PPAR-γ in mice with acute liver injury (ALI) and LPS-induced RAW264.7 cells. Int. Immunopharmacol. 2015; 29(2): 440–447. Publisher Full Text\n\nKwon J-H, Kim S-B, Park K-H, et al.: Antioxidative and anti-inflammatory effects of phenolic compounds from the roots of Ulmus macrocarpa. Arch. Pharm. Res. 2011; 34: 1459–1466. PubMed Abstract \| Publisher Full Text\n\nYao H, Zhao J, Song X: Protective effects of fraxin on cerebral ischemia-reperfusion injury by mediating neuroinflammation and oxidative stress through PPAR-γ/NF-ΚB pathway. Brain Res. Bull. 2022; 187: 49–62. PubMed Abstract \| Publisher Full Text\n\nMa X, Liu X, Feng J, et al.: Fraxin alleviates LPS-induced ARDS by downregulating inflammatory responses and oxidative damages and reducing pulmonary vascular permeability. Inflammation. 2019; 42: 1901–1912. PubMed Abstract \| Publisher Full Text\n\nLi W, Li W, Zang L, et al.: Fraxin ameliorates lipopolysaccharide-induced acute lung injury in mice by inhibiting the NF-κB and NLRP3 signalling pathways. Int. Immunopharmacol. 2019; 67: 1–12. Publisher Full Text\n\nTian X, Peng Z, Luo S, et al.: Aesculin protects against DSS-Induced colitis though activating PPARγ and inhibiting NF-кB pathway. Eur. J. Pharmacol. 2019; 857: 172453. PubMed Abstract \| Publisher Full Text\n\nZhao X, Wang J, Deng Y, et al.: Quercetin as a protective agent for liver diseases: A comprehensive descriptive review of the molecular mechanism. Phytother. Res. 2021; 35(9): 4727–4747. PubMed Abstract \| Publisher Full Text\n\nChen J-C, Ho F-M, Chao P-DL, et al.: Inhibition of iNOS gene expression by quercetin is mediated by the inhibition of IκB kinase, nuclear factor-kappa B and STAT1, and depends on heme oxygenase-1 induction in mouse BV-2 microglia. Eur. J. Pharmacol. 2005; 521(1-3): 9–20. PubMed Abstract \| Publisher Full Text\n\nLee S-M, Moon J, Cho Y, et al.: Quercetin up-regulates expressions of peroxisome proliferator-activated receptor γ, liver X receptor α, and ATP binding cassette transporter A1 genes and increases cholesterol efflux in human macrophage cell line. Nutr. Res. 2013; 33(2): 136–143. PubMed Abstract \| Publisher Full Text\n\nChuang C-H, Yeh C-L, Yeh S-L, et al.: Quercetin metabolites inhibit MMP-2 expression in A549 lung cancer cells by PPAR-γ associated mechanisms. J. Nutr. Biochem. 2016; 33: 45–53. PubMed Abstract \| Publisher Full Text\n\nBeekmann K, Rubió L, de Haan LHJ , et al.: The effect of quercetin and kaempferol aglycones and glucuronides on peroxisome proliferator-activated receptor-gamma (PPAR-γ). Food Funct. 2015; 6(4): 1098–1107. PubMed Abstract \| Publisher Full Text\n\nLei L, Chai Y, Lin H, et al.: Dihydroquercetin activates AMPK/Nrf2/HO-1 signaling in macrophages and attenuates inflammation in LPS-induced endotoxemic mice. Front. Pharmacol. 2020; 11: 662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUlrich-Merzenich G, Panek D, Zeitler H, et al.: Drug development from natural products: exploiting synergistic effects.2010.\n\nShaker NS: Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data. [Dataset]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "257418", "date": "29 Jun 2024", "name": "Dr. Amany Ghazy", "expertise": [ "Reviewer Expertise Micobiology and Immunology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors The current manuscript presents a good point for further research and is presented well. However, I have a few comments: - Authors link the cytokine storm to COVID-19 only but it can be generalized particularly, it is not a big problem now. -The study design is unclear, it can be presented by diagram to show groups of the study and the chronological order of analysis. Some parts of the methods include cell viability, gene expression, and cytokine levels without cited references. -What do you mean by anti-cytokine storm assay (misleading), it could be Determination of anti-cytokine storm markers not Anti-cytokine storm assay -ÃÂÃÂ The methodology is too long and needs to be shortened.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1120
https://f1000research.com/articles/12-660/v1	13 Jun 23	{ "type": "Research Article", "title": "Effect of green tea extract antioxidant on dentin shear bond strength and resin-tag penetration depth after non-vital bleaching", "authors": [ "Darin Safinaz", "Paramita Widyandari", "Ratna Meidyawati", "Citra Kusumasari", "Dewa Ayu Nyoman Putri Artiningsih", "Darin Safinaz", "Paramita Widyandari", "Citra Kusumasari", "Dewa Ayu Nyoman Putri Artiningsih" ], "abstract": "Background: 35% Hydrogen peroxide (H2O2) as an active material for internal bleaching can produce free radicals that can affect resin tag penetration into the dentinal tubules. Application of 10% and 35% green tea (GT) extract as an antioxidant after 2 minutes are expected to remove free radical residues and increase dentin shear bond strength and resin tags penetration depth after non-vital bleaching. Methods: 30 extracted healthy human premolars were cut horizontally 2 mm from the Cemento Enamel Junction margin to the crown part, then cut in a mesio-distal direction into two parts. The specimens were divided into five groups: normal dentin, post bleaching dentin, delayed 2 weeks, 10% GT, and 35% GT group. Non-vital walking bleach with 35% H2O2 gel was done to all groups except control group. Soon after, 10% and 35% GT extract gel were applied on dentin for 2 minutes, then the specimens were rinsed-off with aquabidest for 2 minutes and dried. All specimens were etched and bonded with an etch-and-rinse adhesive system and filled with resin composite. The shear bond strength assessment was carried out using a Universal Testing Machine (UTM) with a cross-head speed of 0.5 mm/minute. Confocal laser scanning microscopy (CLSM) with a wavelength of 560 nm and a lens magnification of 40x was used to analyze the resin tag penetration. Data were analyzed by one way ANOVA and t-test. Results: There was a significant difference in resin tag penetration depth and shear bond strength between applying 10% and 35% GT extract (p < 0.05). The 35% GT extract group resulted in a significantly longer resin tag penetration than the 10% GT extract group. Conclusions: The application of 35% GT extract is more effective than 10% GT extract as an antioxidant for increasing the shear bond strength of composite resin after internal bleaching.", "keywords": [ "Tooth bleaching", "green tea extract", "antioxidant" ], "content": "Introduction\n\n35% hydrogen peroxide (H2O2) is commonly used as an active material for non-vital bleaching; however, it can produce radical oxygen species (ROS).1,2 These ROS can form bubbles trapped inside the dentinal tubules interfering with resin tag penetration into the dentinal tubules.3 Moreover, they can also inhibit the polymerization process due to the disrupting of the vinyl radical group propagation process in the composite resin. So, the termination process occurs earlier in the formation of polymer chains.4\n\nThe inhibition of the resin tag penetration and polymerization process can reduce physical properties such as the bond strength of adhesive material to dentin, and increase the microleakage of composite resin restorations.4 Previous studies have stated that naturally, free radicals in the dentinal tubules take one to three weeks to disappear.5 However, delayed restoration can lead to a higher risk of crown fracture and loss of temporary restorations, leading to re-discoloration. Free radicals from the bleaching process can be eliminated by applying antioxidants.6,7 Recently, natural antioxidants from green tea extracts are being developed to eliminate free radicals after bleaching.8 The concentration and time of application of antioxidant agents have major roles in enhancing their antioxidant effects.9\n\nApplying of 10% green tea (10% GT) extract for 10 minutes effectively increased shear bond strength and reduced microleakage formation, which is closely related to the ability of the resin tag penetration which can affect the retention of the composite resin restoration to dentin.10–12 The concentration of antioxidants must be proportional to the concentration of hydrogen peroxide, and the application of 35% sodium ascorbate for 2 minutes has been proven to remove free radicals after the application of 35% H2O2.13 Therefore, 35% green tea (35% GT) extract was used in this study, and it was expected that it could remove free radical residue and increase the resin tag penetration depth.13 The application of 35% sodium ascorbate for 2 minutes has previously been shown to be effective in removing residual free radicals after application of 35% H2O2.14\n\nBased on our knowledge, there is no study that has investigated the effects of application of 2 minutes 35% GT extract on the shear bond strength and penetration of resin tags on dentin after non-vital bleaching with 35% H2O2. Thus, this study aims to evaluate the effect of green tea extract application on the shear bond strength and penetration of resin tags on dentin after non-vital bleaching. The null hypothesis was that there would be no difference on the shear bond strength and penetration of resin tags on dentin after non-vital bleaching.\n\n\nMethods\n\nThis study was held on March - April 2022. Due to there being two components of the study (sheer bond strength and resin tag penetration), two ethics applications were submitted. The study was approved by the Ethics Committee of Universitas Indonesia (10/Ethical Approval/FKGUI/III/2022 approved on March 9th 2022) and deemed exempt by the Ethics Committee of Universitas Indonesia (09/EthicalExempted/FKGUI/IV/2022, on March 11th 2022). It was conducted in accordance with the Declaration of Helsinki. 30 maxilla premolars, previously extracted for orthodontic reasons, which were free of caries, fractures, and defects were included in this study. The teeth were soaked in a thymol solution (0.1%; pH 7.0) for 1 week post extraction. Then, after 1 week the teeth were placed in 4oC distilled water, and have to be used within 1 month post extraction.15 The root portion of each tooth was removed 2 mm below the cement-enamel junction with a double side disc diamond bur (Buehler, Lake Bluff, IL, USA). The coronal portion was sectioned mesiodistally, and the buccal and palatal portions were used. Each portion is considered to be one specimen (n=60). 55 were used in total during this research.\n\nThe dentin surfaces of the specimens were flattened using 600- and 1200-grit sandpaper and polished with felt discs (Arotec, Cotia, SP, Brazil) impregnated with alumina paste (0.5 μm). The specimens were washed ultrasonically in distilled water for 5 minutes to eliminate any residue. For the shear bond strength test the specimens were fixed in self-cure acrylic 20 mm, and for the resin tag penetration test the specimens were fixed in plasticine 1×1 mm. A mould with a diameter of 2 mm was glued over the specimen in the pulp chamber using plasticine.\n\nThe specimens were randomly divided into 5 groups (for resin tag penetration test n=6, for shear bond strength test n=5). Group 1: Non-bleached without green tea extract (normal dentin/negative control group). Group 2: Bleached without green tea extract (post bleaching dentin/positive control group). Group 3: Bleached without green tea extract and delay for 2 weeks before being restored (delay 2 weeks). Group 4: Bleached+10% Green tea extract for 2 min (10% GT), Group 5: Bleached+35% Green tea extract for 2 min (35% GT).\n\nGreen tea extract with a concentration of 10% and 35% was made by grinding 1 kilogram of pure green tea leaves (Tea Heaven, Indonesia) into a powder. The green tea powder was then soaked in 3 litres of ethanol and left for 24 hours. The mixture was then concentrated using an evaporator. To change the consistency into a 35% gel, 35 grams of extract were added to 65 grams of water and mixed with 2.5 grams of carboxymethyl cellulose (CMC). To change the consistency into a 10% gel, 10 grams of green tea extract were added to 90 grams of water, then mixed with 2.5 grams of CMC. Then the 10 % and 35 % extracts were neutralized by adding triethanolamine drop by drop until the gel reached a pH of 7. This was determined by using a laboratory digital pH meter (Transinstrument BP3001). The extract was placed in a clean container and the probe was dipped into the container. The pH meter started to calculate the pH; once the pH number on the screen remained steady, that was the pH number. The probe was then removed and cleaned and added back, as more triethanolamine was gradually added and the process was repeated until a pH of 7 was reached. Green tea extract was tested by spectrophotometry before and after mixing the gelling ingredients, to determine the flavonoid levels did not change.\n\nThe walking bleach procedure was carried out on specimens of groups 2, 3, 4, and 5 by applying 1 mm thick of 35% H2O2 gel bleaching agents (Opalescence Endo, Ultradent, USA) into the mould that has been placed on the pulp chamber. The moulds were covered with plastic wrap and then the specimens were stored in an incubator for 5 days at 37oC and 100% relative humidity. The cavity was cleaned with distilled water for 1 minute, then dried with a three-way syringe. At the end of each day of treatment, the bleaching gel was rinsed with distilled water for 1 minutes.\n\nThe 10% green tea extract gel was applied in the mould for 2 minutes for group 4, and 35% GT extract gel was applied in the mould for 2 minutes for group 5. Then, the cavity was cleaned with distilled water for 2 minutes and dried using a three-way syringe. Meanwhile, in groups 1, 2, and 3, no antioxidants were given.\n\nAll specimens in all test groups were etched with 37% phosphoric acid (Scotchbond, 3M ESPE) for 10 seconds and then rinsed and partially dried to moist conditions and to prevent collagen collapse. After that, for the resin tag penetration test the adhesive was mixed with 0.1% rhodamine B isothiacyanate (RITC) fluorescent dye (Aldrich Chem. Co., Milwaukee, WI, USA) and for shear bond strength test the adhesive was not mixed with anything. Then, the adhesive (Adper Single Bond 2, 3M ESPE, USA) was applied using a micro brush to the specimen and allowed to stand for 20 seconds, then air-dried using a three-way syringe for 5 seconds and light cured with a light curing unit (DBA, Guilin Woodpecker Medical Instrument Co., China, wave length 440-490 nm, dan light intensity 1200 mW/cm2) for 10 seconds. For the shear bond strength test, the specimen was restored with composite resin (Filtek Z350XT, 3M ESPE, USA).\n\nThe resin tag penetration in the specimen can be seen from the luminescence of rhodamine B through CLSM (LSM 700, Carl Zeiss Microscopy, Germany) with a wavelength of 560 nm and a lens magnification of 40x. The depth of penetration of the resin tag into the dentinal tubules was observed by two experienced observers at the same time and the mean fluorescence intensity (MFI) was calculated using the ZEN 2010 software (Carl Zeiss Microscopy GmbH, Jena, Germany).\n\nThe shear bond strength assessment was carried out using a Universal Testing Machine (AG 5000E, Shimadzu) with a cross head speed of 0.5 mm/minute. The load applied when restoration detached from specimen is recorded. The value of shear bond strength was calculated and presented in megapascal (MPa).15\n\nThe data was analyzed using one-way ANOVA, followed by post-hoc Tamhane test for resin tag penetration and post-hoc Bonferroni test for shear bond strength test (IBM SPSS Statistics 24 version program, IBM Corp., Armonk, NY, USA).\n\n\nResults\n\nTable 1 shows that the longest penetration of resin tag is in the 35% GT group with a mean value of 190.1 (SD 33.6) μm. Meanwhile, the post-bleaching dentin group showed the shortest resin tag penetration with a mean value of 87.4 (SD 6.9) μm.30 The results of the one-way ANOVA test showed a value of 0.001 (p<0.05), which means that there was a significant difference in the depth of penetration of the resin tags from the five groups.\n\n* One-way ANOVA test with p<0.05.\n\nMeanwhile, to determine the difference in depth of resin tag penetration between treatment groups with one another, the post-hoc Tamhane test was conducted (Table 1). The results of the post-hoc test in Table 1 show that there was a significant difference in the resin tag penetration between the 10% GT group and the 35% GT group (p=0.008). The 35% GT group showed a longer depth of resin tag penetration compared to the 10% GT group. There was also a significant difference of resin tag penetration between the 10% GT group and the normal dentin group. The 10% GT group showed a shorter depth of resin tag penetration than the normal dentin. There was no significant difference of resin tag penetration between the 35% GT group and the normal dentin group.\n\nThe results of CLSM imaging of the resin tag penetration for each group can be seen in Figure 1A, B, C, D, and E.29 From the picture, it can be seen that the longest resin tag penetration is in the 35% GT group. In addition to being longer, the resin tags formed in the 35% GT group seemed more abundant, thicker, and continuous than the other group. The results of the shear bond strength test between groups are described in Table 2. The data obtained showed that the value of shear bond strength in the 35% GT group had the highest mean value, which was 10.84 (SD 2.68) MPa. The lowest shear bond strength value was in the post bleaching dentin group, which was 3.52 (SD 0.22) MPa. The results of the one-way ANOVA test showed significantly different values from each treatment group, as seen from the p-value of 0.001 with p<0.05.\n\nTo determine the difference in shear bond strength between treatment groups, the results of the post-hoc Bonferroni test are displayed in Table 2. The results show a significant difference in the shear bond strength between the 10% GT group and the 35% GT group (p=0.001). The 35% GT group showed the higher shear bond strength compared to 10% GT group. These results show that the application of 35% GT extract can increase the post-bleaching shear bond strength more than the application of 10% GT. The 10% GT group showed lower shear bond strength than normal dentin. There was no significant difference of shear bond strength between the 35% GT group and the normal dentin group.\n\n\nDiscussion\n\nH2O2 is a strong oxidizer that has a faster reaction and is effective in whitening teeth. These reactive molecules break the long chains of the chromophore molecules, making them diffuse more and become colourless.16 However, the active ingredient of bleaching H2O2 will release large amounts of free radicals, so it can produce a negative effect in the form of reducing the bonding of the resin material with dentin and enamel. The oxygen formed can interfere with the penetration of the adhesive material so that the resin tag becomes sparse, short, not well-defined, and structurally incomplete, and in some areas the resin tag is not formed at all.17 This situation results in decreased bond strength due to disturbances in the polymerization process, and changes in the chemical structure of enamel and dentin.18–20\n\nTo eliminate the negative effects of these free radicals, Torres et al. (2006) and Ismail et al. (2017) stated that the antioxidant agents are oxidation inhibitors. They can neutralize free radicals by binding free radicals through hydrogen atom donation or electron transfer so that free radicals become more stable, less reactive, and less dangerous. Thus, restoration procedures can be done immediately after the bleaching procedure.21,22 This study uses green tea as an antioxidant agent because it is a natural antioxidant agent and biocompatible. The toxicity of natural ingredients is not always linearly proportional to their concentration so an increase in the concentration of a substance does not always increase its toxicity.8\n\nThe content of flavonoids contained in green tea is influenced by weather, climate, tea varieties, geographical location, soil conditions, leaf age, and the way of picking.23 The green tea used in this research had an unfermented processing process where there is inactivation of the polyphenol oxidase enzyme present in the fresh tea shoots, so that it is not oxidized much and the content of polyphenols or catechins, especially EGCG, is higher with the main nutrients being maintained.23 El-Hack et al. (2020) stated that EGCG in green tea is 100 times more effective in eliminating free radicals than vitamin C and 25 times more effective than vitamin E.24\n\nThe results of this study showed that the longest penetration of resin tags and the highest number of shear bond strength was in the 35% GT group (Tables 1 and 2). From the post-hoc test, it appears that there is a significant difference in the resin tag penetration and shear bond strength between the 35% GT group and the post-bleaching dentin group (p<0.05). In the 35% GT group, there was a longer resin tag formation (Figure 1B & E) and higher shear bond strength compared to the post-bleaching dentin group. These results are in line with research conducted by Briso et al. (2012) which reported that the use of antioxidants immediately after bleaching can reduce the presence of reactive oxygen in post-bleaching tooth tissue.25 One theory is that hydrogen peroxide can split into water and oxygen in the collagen matrix and dentinal tubules. Release of oxygen can interfere with resin penetration into dentin which has been etched.26 Gündoğdu and Yılmaz (2020) stated that the strong antioxidant activity of green tea has been attributed to its high content of catechins and flavanols, which can neutralize free radicals by donating hydrogen from the hydroxyl group in its structure.11\n\nThere was no significant difference in resin tag penetration and shear bond strength between the 35% GT group, the normal dentin group, and the two-week delayed group (p>0.05) (Tables 1 and 2). These results are in line with the findings of a study conducted by Freire et al. (2009) who state that the concentration of antioxidants must be directly proportional to the concentration of hydrogen peroxide.13 In other words, the concentration of 35% green tea extract is effective in eliminating 35% H2O2 free radicals. However, the average penetration value of the resin tag in the 35% GT group was longer than the normal dentin group; this might be because, after the internal bleaching procedure with 35% acidic H2O2 (pH 5), there was a change in the organic and inorganic components of dentin which causes an increase in the diameter of the dentinal tubules.8\n\nAlthough the administration of 35% GT extract antioxidants can induce cross-linking of dentin collagen molecules, induce the remineralization process, and inhibit matrix metalloproteinase (MMP) activity, only 2 minutes of application may not be able to form collagen and minerals perfectly as in normal dentin, so that tubule diameter will still be larger than normal dentin. Dentinal permeability is closely related to the functional diameter of the dentinal tubules, so the larger the functional diameter, the higher the flow rate of liquid that can penetrate to the dentinal tubule. This liquid can be assumed as a bonding material; the bonding used is Adper Single Bond 2 (3M, USA) which contains spherical silica filler particles with a diameter of five nanometers. The small size causes Adper Single Bond 2 to have a better ability to penetrate into dentinal tubules, as its small particles are stable in the form of a colloidal suspension, which means that they do not combine with one another and do not agglomerate. This allows the Adper Single Bond 2 to have the ability to penetrate into deep dentinal tubules.8\n\nIn addition, the results of the post-hoc test also showed that there was a significant difference in the penetration depth of the resin tag and shear bond strength between the 10% GT group and the 35% GT group (p<0.05) (Tables 1 and 2). The 35% GT group showed significantly longer resin tag formation than the 10% GT group (Figure 1D & E). Similarly, the value of shear bond strength in the 35% GT group was significantly higher compared to the 10% GT. The result is in line with research conducted by Freire et al. (2009) who revealed that the concentration of antioxidants had a greater effect than the exposure time on the rate of free radical reduction.13 In addition, Hamid et al. (2010) showed that when higher concentrations of antioxidants were used, the time required to eliminate all free radical residues was reduced.27\n\nAlthough previous studies have stated that the use of 10% GT extract for 10 minutes is effective as an antioxidant agent after bleaching, its use for only two minutes appears to be less effective in eliminating free radicals. It can be seen from the results of the post-hoc test that there was no significant difference in the depth of penetration of the resin tag and shear bond strength between the 10% GT group and the post-bleaching dentin group (p<0.05) (Tables 1 and 2). However, there was a significant difference between the 10% GT group and the normal dentin group (p>0.05).\n\nIn this study, we only use one type of adhesive where the particle size of the adhesive material affected the penetration ability of the resin tag into the dentinal tubules. So further research is needed by comparing the penetration of resin tags from several types of adhesives. The results of the CLSM analysis could not see whether the residual oxygen in the dentinal tubules after internal bleaching had been eliminated after the application of green tea antioxidants, so further research using SEM is needed to be able to see visually whether the oxygen bubbles have completely disappeared in the dentin after internal bleaching after the application of green tea antioxidants. Therefore, the null hypothesis which stated that there was no difference in the effect of the application of green tea extract antioxidant with different concentrations for 2 minutes on dentin shear bond strength and resin-tag penetration depth after internal bleaching was rejected.\n\n\nConclusion\n\nThe application of 35% GT extract antioxidant for 2 minutes increased the shear bond strength and resin tag penetration, compared to the application of 10% GT extract for 2 minutes on dentin after internal bleaching using 35% H2O2.", "appendix": "Data availability\n\nfigshare: Resin tag and shear bond strength data, https://doi.org/10.6084/m9.figshare.22568338.v1. 28\n\nThis project contains the following underlying data:\n\n- Shear bond strength dataset\n\n- Resin tag penetration data\n\n- Figures for the manuscript\n\n- Figure data\n\nfigshare: Resin Tag Microscopic images, https://doi.org/10.6084/m9.figshare.22761662.v1. 29\n\nThis project contains the original microscopy images.\n\nfigshare: Effect of Green Tea Extract Antioxidant on Dentin Shear Bond Strength and Resin-Tag Penetration Depth after Non-vital Bleaching, https://doi.org/10.6084/m9.figshare.22568581.v3. 30\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nKwon SR, Wertz PW: Review of the mechanism of tooth whitening. 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PubMed Abstract \| Publisher Full Text\n\nAl-Hassani AA, Al-Shamma A: Effect of delayed bonding and different antioxidants on composite restoration microleakage of internally bleached teeth. Adv. Dent. Oral Health. 2018; 9: 001–006. Publisher Full Text\n\nGündoğdu S, Yılmaz NA: The Antioxidant Effect of Green Tea, Rosemary, and Their Combination on Resin Bond Strength to Bleached Tooth Structures. Meand. Med. Dent. J. 2020; 21(3): 204–214. Publisher Full Text\n\nSharafeddin F, Motamedi M, Modiri S: Effect of immediate application of pomegranate peel, grape seed and green tea extracts on composite shear bond strength of in-office bleached enamel. Res. J. Biol. Sci. 2013; 8: 83–87.\n\nFreire A, Souza EM, de Menezes Caldas DB , et al.: Reaction kinetics of sodium ascorbate and dental bleaching gel. J. Dent. 2009; 37(12): 932–936. PubMed Abstract \| Publisher Full Text\n\nFreire A, Durski MT, Ingberman M, et al.: Assessing the use of 35 percent sodium ascorbate for removal of residual hydrogen peroxide after in-office tooth bleaching. J. Am. Dent. Assoc. 2011; 142(7): 836–841. Publisher Full Text\n\nKadiyala A, Saladi HK, Bollu IP, et al.: Effect of different anti-oxidants on shear bond strength of composite resins to bleached human enamel. J. Clin. Diagn. Res. 2015; 9(11): ZC40–ZC43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOzkocak I, Hekim M, Gokturk H, et al.: The assessment of different bleaching agents’ efficiency on discoloured teeth using image-processing methods. Photodiagn. Photodyn. Ther. 2020; 31: 101901. PubMed Abstract \| Publisher Full Text\n\nSundfeld RH, Briso ALF, De Sá PM, et al.: Effect of time interval between bleaching and bonding on tag formation. Bull. Tokyo Dent. Coll. 2005; 46(1+ 2): 1–6. PubMed Abstract \| Publisher Full Text\n\nIshwarya G, Vidhya S, Mahalaxmi S: Marginal integrity of aesthetic restorations following intracoronal bleaching with sweet potato extract as an additive: An SEM study. Heliyon. 2020; 6(2): e03424. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaradas M, Demirbuga S: Influence of a short-time antioxidant application on the dentin bond strength after intracoronal bleaching. Microsc. Res. Tech. 2019; 82(10): 1720–1727. PubMed Abstract \| Publisher Full Text\n\nKhan AA, Zafar MS, Ghubayri AAA, et al.: Polymerisation of restorative dental composites: influence on physical, mechanical and chemical properties at various setting depths. Mater. Technol. 2022; 37(12): 2056–2062.\n\nTorres CRG, Koga AFK, Borges AB: The effects of anti-oxidant agents as neutralizers of bleaching agents on enamel bond strength. Brazilian J. Oral Sci. 2006; 4(14): 783–786.\n\nIsmail EH, Kilinc E, Hardigan PC, et al.: Effect of two-minute application of 35% sodium ascorbate on composite bond strength following bleaching. J. Contemp. Dent. Pract. 2017; 18(10): 874–880. PubMed Abstract \| Publisher Full Text\n\nAnjarsari I: Indonesia tea catechin: Prospect and benefits. J. Kult. 2016; 15: 99–106.\n\nEl-Hack ME, Elnesr S, Alagawany M, et al.: Impact of green tea (Camellia sinensis) and epigallocatechin gallate on poultry. Worlds Poult. Sci. J. 2020; 76: 49–63. Publisher Full Text\n\nBriso A, Toseto RM, Rahal V, et al.: Effect of sodium ascorbate on tag formation in bleached enamel. J. Adhes. Dent. 2012; 14(1): 19–23. PubMed Abstract \| Publisher Full Text\n\nVieira C, Silva-Sousa YTC, Pessarello NM, et al.: Effect of high-concentrated bleaching agents on the bond strength at dentin/resin interface and flexural strength of dentin. Braz. Dent. J. 2012; 23: 28–35. PubMed Abstract \| Publisher Full Text\n\nHamid A, Aiyelaagbe O, Usman L, et al.: Antioxidants: Its medicinal and pharmacological applications. Afr. J. Pure Appl. Chem. 2010; 4(8): 142–151.\n\nWidyandari P, Meidyawati R, Kusumasari C, et al.: Resin tag and shear bond strength data. [Dataset]. figshare. 2023. Publisher Full Text\n\nWidyandari P, Safinaz D, Meidyawati R, et al.: Resin Tag Microscopic Images. [Dataset]. figshare. 2023. Publisher Full Text\n\nWidyandari P, Meidyawati R, Kusumasari C, et al.: Effect of Green Tea Extract Antioxidant on Dentin Shear Bond Strength and Resin-Tag Penetration Depth after Non-vital Bleaching. figshare. Journal Contribution. 2023. Publisher Full Text" }	[ { "id": "179218", "date": "03 Jul 2023", "name": "Myrna Zakaria", "expertise": [ "Reviewer Expertise Endodontics", "oral microbiology", "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\nThe study highlights the effect of anti oxidants (green tea extract) in improving bond strength of adhesives after external bleaching. The study evaluated the bond strength supported by CLSM evaluation to observe the penetration depth of the adhesive. However, I personally think that the CLSM images is unclear, therefore interpretation is rather dubious, particularly to being asses quantitatively.\n\nIn details, here are my concern to be addressed:\nAbstract:\nPlease mention the aim of the study in the abstract.\n\nPlease specify the method in abstract section including the statistics. What was the post hoc analysis following the ANOVA and what was the t test for? (there was no t test mention in the script)?\n\nPlease change 'aquabidest' to 'distilled water'.\n\nResults is unclear, it seemed that author only explained comparison between 2 groups (leads to assumption the result of t test, but then it was not in the methods and results of the manuscript).\n\nPlease specify the results of shear bond strength of the 5 groups, then mention the significance. Since author is not only comparing 10% and 35% GT extract, how was the results for the other groups tested (highest? Lowest?)? Was there any host hoc analysis done?\nIntroduction:\nWhat was the rationale in using 10 and 35% extract? Generalizing the results from 35% sodium ascorbate to this study is irrelevant. GT extract differs from sodium ascorbate, therefore it cannot be used as a standard for concentration.\n\nIntroduction paragraph 3:\n“The concentration of antioxidants must be proportional to the concentration of hydrogen peroxide, and the application of 35% sodium ascorbate for 2 minutes has been proven to remove free radicals after the application of 35% H2O2.13 Therefore, 35% green tea (35% GT) extract was used in this study, and it was expected that it could remove free radical residue and increase the resin tag penetration depth.13 The application of 35% sodium ascorbate for 2 minutes has previously been shown to be effective in removing residual free radicals after application of 35% H2O2.14” - Even though they have different citations, the two phrases have the same meaning. Avoid overwriting it.\n\nWhat was the colour of the green tea extract? Isn’t there a chance of staining to the tooth compromising the bleaching results?\nMethods:\n\"The dentin surfaces of the specimens were flattened using 600- and 1200-grit sandpaper and polished with felt discs (Arotec, Cotia, SP, Brazil) impregnated with alumina paste (0.5 μm).\" - what was the final specimen dimension?\n\n\"The specimens were washed ultrasonically in distilled water for 5 minutes to eliminate any residue. For the shear bond strength test the specimens were fixed in self-cure acrylic 20 mm, and for the resin tag penetration test the specimens were fixed in plasticine 1×1 mm. A mould with a diameter of 2 mm was glued over the specimen in the pulp chamber using plasticine.\" - What was the exact size? 20mm is the length? Please clarify?\n\nSpecify more details on the specimen preparation particularly for the CLSM, the specimen should be different than for the shear bond test.\n\nThe statistical method written in the abstract is different than in the method section, was there any t test performed (as stated in abstract)?\nResults\n\"Table 1 shows that the longest penetration of resin tag is in the 35% GT group with a mean value of 190.1 (SD 33.6) μm. Meanwhile, the post-bleaching dentin group showed the shortest resin tag penetration with a mean value of 87.4 (SD 6.9) μm.30 The results of the one-way ANOVA test showed a value of 0.001 (p<0.05), which means that there was a significant difference in the depth of penetration of the resin tags from the five groups.\" - What does the citation for 30 mean? No citations should be included in the results section.\n\nPlease change the writing in Table 1 to a more suitable scientific table. Since all sample numbers for the resin penetration are the same in each group (n=6) and also for the shear bond strength (n=5), there is no need to include a column sample number. Instead, mention the measurement's unit (m) and clarify in the Figure legend what the x ,y, z, superscript mean?\n\nHow was the CLSM quantitatively evaluated, and how did the author determine the mean value of each specimen's penetration depth?\n\nThe image of CLSM is unclear, there is no significant adhesive penetration seen, and the image of CLSM is vague. Some adhesive fragments from the dentin cuttings might be mistakenly interpret as adhesive penetration. There is no continuous adhesive penetration from the interface to the tubules seen, therefore it might not be reliable to quantitative measurement. How thick were the samples, in case the specimen was too thick?\n\nImages needs to be improved, and clearly state the what the star, rectangle, red and blue colour represent.\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": "10109", "date": "08 Sep 2023", "name": "Paramita Widyandari", "role": "Author Response", "response": "We would like to thank the reviewers for their thoughtful comments on our manuscript. We have carefully considered their suggestions in revising our manuscript, and we believe that the revised manuscript is improved and suitable for publication. Detailed responses to the comments are presented in this document. Abstract 1. Please mention the aim of the study in the abstract. Response: We have revised the manuscript and you can find the aim of the study in background section in abstract line 3-5 “The aim of this study is to evaluate the effect of 10% and 35% GT extract after 2 minutes of application on dentin shear bond strength and resin tags penetration depth after non-vital bleaching” 2. Please specify the method in abstract section including the statistics. What was the post hoc analysis following the ANOVA and what was the t test for? (there was no t-test mention in the script). Response: The data was analyzed using one-way ANOVA followed by post-hoc Tamhane test for resin tag penetration. Then, we used post-hoc Bonferroni test for shear bond strength test. However, there is no t-test we did, which was accidentally mistaken in the original manuscript. We revise it as mention in paragraph 10 line 1-3 “The data was analyzed using one-way ANOVA, followed by post-hoc Tamhane test for resin tag penetration and post-hoc Bonferroni test for shear bond strength test (IBM SPSS Statistics 24 version program, IBM Corp., Armonk, NY, USA).” 3. Please change 'aquabidest' to 'distilled water'. Response: This issue has already been addressed in the abstract part of the original manuscript: “Soon after, 10% and 35% GT extract gel were applied on dentin for 2 minutes, then the specimens were rinsed-off with distilled water for 2 minutes and dried.” 4. Results is unclear, it seemed that author only explained comparison between 2 groups (leads to assumption the result of t test, but then it was not in the methods and results of the manuscript). Response: We agree with the reviewer. However, due to our focus is on the effect of green tea extract antioxidant application on dentin shear bond strength and resin tag penetration depth after non-vital bleaching dentin, therefore, our conclusion is focusing on the antioxidant materials only. The other groups are positive and negative control groups which were already mentioned in discussion section, paragraph 4 line 2-4. “From the post-hoc test, it appears that there is a significant difference in the resin tag penetration and shear bond strength between the 35% GT group and the post-bleaching dentin group (p<0.05).” 5. Please specify the results of shear bond strength of the 5 groups, then mention the significance. Since author is not only comparing 10% and 35% GT extract, how was the results for the other groups tested (highest? Lowest?)? Was there any host hoc analysis done? Response: Thank you for the question and we agree with the reviewer. Unfortunately, due to the limitation number of the words in the abstract it cannot be written in the abstract. Therefore, we mentioned it on the results part, paragraph 4, line 2-7. “The results show a significant difference in the shear bond strength between the 10% GT group and the 35% GT group (p=0.001). The 35% GT group showed the higher shear bond strength compared to 10% GT group. These results show that the application of 35% GT extract can increase the post-bleaching shear bond strength more than the application of 10% GT. The 10% GT group showed lower shear bond strength than normal dentin. There was no significant difference of shear bond strength between the 35% GT group and the normal dentin group.” Introduction 1. What was the rationale in using 10 and 35% extract? Generalizing the results from 35% sodium ascorbate to this study is irrelevant. GT extract differs from sodium ascorbate; therefore, it cannot be used as a standard for concentration. Response: The rationale in using 10% GT extract has been conducted by Alhasani et al. (Al-Hassani AA, Al-Shamma A: Effect of delayed bonding and different antioxidants on composite restoration microleakage of internally bleached teeth. Adv. Dent. Oral Health. 2018;9:001–006. 10.19080/ADOH.2018.09.555762) and we it was mentioned in the reference section number 10. Moreover, the background in using 10% GT extract already written in the original manuscript, paragraph 3 line 1-4. “Applying of 10% green tea (10% GT) extract for 10 minutes effectively increased shear bond strength and reduced microleakage formation, which is closely related to the ability of the resin tag penetration which can affect the retention of the composite resin restoration to dentin”. The rationale in using 35% GT was based on the statement that the concentration of antioxidants must be proportional to the concentration of hydrogen peroxide (The concentration of antioxidants must be proportional to the concentration of hydrogen peroxide, and the application of 35% sodium ascorbate for 2 minutes has been proven to remove free radicals after the application of 35% H 2O 2., Reference number 13: Freire A, Souza EM, de Menezes Caldas DB , et al.: Reaction kinetics of sodium ascorbate and dental bleaching gel. J. Dent. 2009;37(12):932–936. 19660514 10.1016/j.jdent.2009.07.008). As we used 35% hydrogen peroxide in this study, thus, the authors choosing 35% green tea extract for other group. 2. Introduction paragraph 3:“The concentration of antioxidants must be proportional to the concentration of hydrogen peroxide, and the application of 35% sodium ascorbate for 2 minutes has been proven to remove free radicals after the application of 35% H2O2.13 Therefore, 35% green tea (35% GT) extract was used in this study, and it was expected that it could remove free radical residue and increase the resin tag penetration depth.13 The application of 35% sodium ascorbate for 2 minutes has previously been shown to be effective in removing residual free radicals after application of 35% H2O2.14” - Even though they have different citations, the two phrases have the same meaning. Avoid overwriting it. Response: Thank you for your comment. This issue has already been addressed in the introduction part in the paragraph 3 line 3-5. “Applying of 10% green tea (10% GT) extract for 10 minutes effectively increased shear bond strength and reduced microleakage formation, which is closely related to the ability of the resin tag penetration which can affect the retention of the composite resin restoration to dentin. 10 – 12 The concentration of antioxidants must be proportional to the concentration of hydrogen peroxide, and the application of 35% sodium ascorbate for 2 minutes has been proven to remove free radicals after the application of 35% H 2O 2. 13[PW1] Therefore, 35% green tea (35% GT) extract was used in this study, and it was expected that it could remove free radical residue and increase the resin tag penetration depth. 13” 3. What was the colour of the green tea extract? Isn’t there a chance of staining to the tooth compromising the bleaching results? Response: The color of the green tea extract is dark green using colorimetry test, below are the results and no significant discoloration were found. Result of Colorimetri test Number of samples Before application of 35% GT for 2 minutes After Application of 35% GT for 2 minutes 1 65.835 67.336 2 60.672 61.419 3 54.489 58.709 T-Test [DataSet3] Methods 1. \"The dentin surfaces of the specimens were flattened using 600- and 1200-grit sandpaper and polished with felt discs (Arotec, Cotia, SP, Brazil) impregnated with alumina paste (0.5 μm).\" - what was the final specimen dimension? Response: We checked the dimension of the samples after the polishing step, and the final specimen thickness is 3 mm and if the final thickness is decreased more than 0.5 mm, specimens will discarded and replaced. 2. \"The specimens were washed ultrasonically in distilled water for 5 minutes to eliminate any residue. For the shear bond strength test the specimens were fixed in self-cure acrylic 20 mm, and for the resin tag penetration test the specimens were fixed in plasticine 1×1 mm. A mould with a diameter of 2 mm was glued over the specimen in the pulp chamber using plasticine.\" - What was the exact size? 20mm is the length? Please clarify? Response: The dimensions of the self-cure acrylic for the placement of the specimen were both 20 mm in diameter (cylindrical form) and in the length. 3. Specify more details on the specimen preparation particularly for the CLSM, the specimen should be different than for the shear bond test. Response: The specimen preparation procedures are same for CLSM and shear bond test. Additionally, there is only one difference in the specimen placement media (CLSM is using plasticine and shear bond strength is using self-curing acrylic). The procedures detailed and written in the manuscript in methods section, paragraph 2, line 1-6. “The dentin surfaces of the specimens were flattened using 600- and 1200-grit sandpaper and polished with felt discs (Arotec, Cotia, SP, Brazil) impregnated with alumina paste (0.5 μm). The specimens were washed ultrasonically in distilled water for 5 minutes to eliminate any residue. For the shear bond strength test the specimens were fixed in self-cure acrylic 20 mm, and for the resin tag penetration test the specimens were fixed in plasticine 1×1 mm. A mould with a diameter of 2 mm was glued over the specimen in the pulp chamber using plasticine. ” 4. The statistical method written in the abstract is different than in the method section, was there any t-test performed (as stated in abstract)? Response: Thank you for the comment, and we apologize for the accidentally mistaken. We did not use t-test in this study and we wrote it in methods section (paragraph 10 line 1-3). “The data was analyzed using one-way ANOVA, followed by post-hoc Tamhane test for resin tag penetration and post-hoc Bonferroni test for shear bond strength test (IBM SPSS Statistics 24 version program, IBM Corp., Armonk, NY, USA).” Results 1. \"Table 1 shows that the longest penetration of resin tag is in the 35% GT group with a mean value of 190.1 (SD 33.6) μm. Meanwhile, the post-bleaching dentin group showed the shortest resin tag penetration with a mean value of 87.4 (SD 6.9) μm.30 The results of the one-way ANOVA test showed a value of 0.001 (p<0.05), which means that there was a significant difference in the depth of penetration of the resin tags from the five groups.\" - What does the citation for 30 mean? No citations should be included in the results section. Response: Thank you for the comment, and we apologize for the accidentally mistaken. We revised it. “Table 1 shows that the longest penetration of resin tag is in the 35% GT group with a mean value of 190.1 (SD 33.6) μm. Meanwhile, the post-bleaching dentin group showed the shortest resin tag penetration with a mean value of 87.4 (SD 6.9) μm.” 2. Please change the writing in Table 1 to a more suitable scientific table. Since all sample numbers for the resin penetration are the same in each group (n=6) and also for the shear bond strength (n=5), there is no need to include a column sample number. Instead, mention the measurement's unit (m) and clarify in the Figure legend what the x ,y, z, superscript mean? Response: Thank you for your comment. We revise it as detailed in the manuscript page 6-7 Table 1. Mean, standard deviation, and significancy between group of resin tag penetration (µm) Treatment Number of specimens Mean (SD) p-value Normal dentin 6 146.9 (10.1)x 0.001* Post-bleaching dentin 6 87.4 (6.9)y Delay 2 weeks 6 134.4 (9.5) 10% GT 6 107.2 (18.9)x,z 35% GT 6 190.1(33.6)y,z GT = Green Tea; x= significance difference normal dentin with 10% GT; y= significance difference post bleaching dentin with 35% GT; z = significance difference 10%GT with 35% GT * One-way ANOVA test with p<0.05 Table 2. Mean, standard deviation, and significancy between group of shear bond strength (MPa) Treament group Number of specimens Mean (SD) p-value* Normal dentin 5 10.14 (1.85)a 0.001* Post-bleaching dentin 5 3.52 (0.22)b Delay 2 weeks 5 8.65 (2.09) 10% GT 5 5.42 (0.54)a,c 35% GT 5 2.68)b,c GT = Green Tea; a= significance difference normal dentin with 10% GT; b= sigficance difference post bleaching dentin with 35% GT ; c= significance difference 10% GT with 35% GT *One-way Anova test with p<0.05 3. How was the CLSM quantitatively evaluated, and how did the author determine the mean value of each specimen's penetration depth? Response: We measure the continuous and longest penetration depth from each specimen based on the previous studies “ The SEM observation of resin inltration samples showed resin-inltrated tags. InIIa, the deepest depths of inltration were determined to range from 245 to 317 µm and the mean depth was 284 µm”(Effect of Resin Inltration on Bleached Enamel: An In Vitro Evaluation of Micromorphology, Resin Penetration and Microhardness, Zhen Wei, et al , GuangzhouInstitute of Oral Disease). Table 3 4. The image of CLSM is unclear, there is no significant adhesive penetration seen, and the image of CLSM is vague. Some adhesive fragments from the dentin cuttings might be mistakenly interpret as adhesive penetration. There is no continuous adhesive penetration from the interface to the tubules seen, therefore it might not be reliable to quantitative measurement. How thick were the samples, in case the specimen was too thick? Response: We revise it and please find it in the results section, page 6 and here. Regarding the thickness of the samples, it written on the manuscript methods section, page 3, paragraph 2 line 1-3 “The dentin surfaces of the specimens were flattened using 600- and 1200-grit sandpaper and polished with felt discs (Arotec, Cotia, SP, Brazil) impregnated with alumina paste (0.5 μm) until a specimen thickness of 3 mm was obtained” 5. Images needs to be improved, and clearly state the what the star, rectangle, red and blue colour represent. Response: Thank you for your comment. We revise it as detailed in the manuscript results section, page 7. Figure 1. The red arrow indicates the depth of penetration of the resin tag on (A) Normal dentin group, (B) Post bleaching group, (C) Delay 2 weeks group, (D) 10% GT group, (E) 35% GT group. Rectangle indicates the adhesive; star indicates the hybrid layer; blue area means there is no adhesive penetration/no fluorescence, red area means the thickest fluorescence." } ] } ]	1	https://f1000research.com/articles/12-660
https://f1000research.com/articles/12-1119/v1	08 Sep 23	{ "type": "Research Article", "title": "A mixed-methods evaluation of capacity strengthening within an international conservation agriculture research consortium", "authors": [ "Kirsten Duda", "Alessia D’Artibale", "Miyanda Moombe", "R.Murray Lark", "Justin Pulford", "Kirsten Duda", "Alessia D’Artibale", "Miyanda Moombe", "R.Murray Lark" ], "abstract": "Background: The Strengthening Capacity in Environmental Physics, Hydrogeology and Statistics for conservation agriculture research (CEPHaS) consortium sought to to strengthen research capacity among a network of African and UK researchers, and their respective institutions, to fill knowledge gaps on the impacts of conservation agriculture practices on the water cycle in cultivated soils.\n\nWe examined experiences of consortium membership and, drawing on this information, determined key recommendations for future programmes with similar objectives. Methods: A mixed methods study encompassing an online survey (N=40) and semi-structured interviews (N=19) completed between June 2021 and February 2022 with CEPHaS consortium members from Malawi, UK, Zambia and Zimbabwe. Survey and interview data were analysed separately, using univariate statistics and framework synthesis respectively Results: Survey and interview findings were generally aligned, with both revealing a wide range of reported capacity strengthening gains resulting from CEPHaS engagement at both an individual and institutional level. Participants consistently expressed their CEPHaS involvement in positive terms with praise for the applied ‘learn by doing’ approach underpinning many of the activities as well as the engaging and highly inclusive leadership.\n\nThere was evidence that the various trainings and resources provided through CEPHaS were valued, frequently utilised, and often transferred beyond the immediate CEPHaS membership for wider benefit. Resource provision and staff training were seen as foundational for long-term institutional benefits. Some challenges and suggested areas for improvement were reported by participants as were potential opportunities to facilitate greater impact.\nConclusion: Our findings suggest that the basic ‘template’ of the CEPHaS consortium provided a strong basis for research capacity strengthening in Conservation Agriculture, especially at the level of individual researchers, and that this template could be further enhanced in any future iteration of the same or similar programme. Recommendations for replicating and enhancing CEPHaS programme strengths are presented.", "keywords": [ "Conservation agriculture", "capacity strengthening", "consortium", "evaluation", "Africa" ], "content": "Introduction\n\nConservation Agriculture (CA) is a set of practices which aim to improve the sustainability of crop production and which are widely advocated in sub Saharan Africa and elsewhere as a ‘climate-smart’ strategy.1 CA entails the use of zero-till, or minimum till to reduce the disturbance of soil architecture by cultivation, the use of mulches, typically crop residues, to protect the soil and enhance its organic content and biological activity, and the employment of crop rotation or intercropping to diversify the system.1 Increasing global population and subsequent demand for food, combined with the pressures of climate change necessitates the adoption of sustainable agricultural practices.1 With increased promotion of CA practices in Africa, both by NGOs and through government policy, there is a need to develop institutions and networks across the continent to assess its impacts on environmental systems and not just on crop yield.2,3 This includes the development of interdisciplinary research capacity as an integrated assessment is needed of how CA affects soil physical properties, nutrient cycling and the water cycle.4\n\nResearch capacity strengthening has been defined as “the ongoing process of empowering individuals, institutions, organisations and nations to: define and prioritise problems systematically; develop and scientifically evaluate appropriate solutions and share and apply the knowledge generated”.5 As indicated by this definition, strengthening research capacity is a multi-faceted and layered endeavor that involves a comprehensive assessment and understanding of individuals and collective entities within the research environment.6 In multinational research, often historic power dynamics dictate continued capacity imbalances to the detriment of sustained research capacity in low-income and middle-income countries.7 To facilitate sustained research capacitation, research gaps should be identified, and the needs of all partners supported to address those gaps.6\n\nAlthough some research has been conducted to identify key aspects that may support multi-sectoral collaboration in CA, the same has not been done for international CA consortia.2,8 There is an identified need for building stronger partnerships in CA research, but there is limited information on what is contextually beneficial or challenging for CA consortia partners.2–4,8,9 Unlike the field of global health, multi-national consortia within the field of CA are less common, with research consortia primarily existing at the national level. Developing multi-disciplinary research consortia offers an opportunity for enhancing and diversifying CA knowledge and facilitating knowledge transfer across disciplines. Likewise, as food security and supporting sustainable practices have global effects, pooling knowledge internationally to develop a comprehensive and adaptive understanding of CA across geographic locations via international research consortia could provide a more nuanced and iterative understanding of CA concepts and practices.\n\nIn this paper we present findings from a mixed methods investigation of capacity strengthening experiences and outcomes as reported by members of a multi-national CA research consortium; namely, Strengthening Capacity in Environmental Physics, Hydrogeology and Statistics for conservation agriculture research (CEPHaS). The CEPHaS consortium was designed to allow for CA research to occur in parallel with capacity strengthening activities, inclusive of training and resource provision, to support individuals and institutes conducting CA in the UK and sub-Saharan Africa. We sought to identify the perceived benefits of CEPHaS participation to both research and research support staff belonging to the consortium as well as perceived benefits to their respective institutions. Challenges faced by CEPHaS consortium members were also explored with the overall aim of distilling key recommendations that may inform the implementation of similar initiatives in the future. Findings in this paper expand on a preliminary report from the same study presented elsewhere.10\n\n\nMethods\n\nEthical approval for this study was obtained from Liverpool School of Tropical Medicine’s Research Ethics Committee (REC), UK under approval number (LSTM REC 18-038). All interview participants provided written informed consent. No incentives were provided for participation.\n\nA mixed methods study consisting of an online survey and semi-structured interviews (SSI), both conducted with CEPHaS consortium members from all partner countries in the final six months of the programme.\n\nThe CEPHaS consortium sought to strengthen research capacity among a network of African and UK researchers, and their respective institutions, to fill knowledge gaps on the impacts of CA practices on the water cycle in cultivated soils. The consortium brought together a cross-national, multidisciplinary network of researchers who worked together at sites where African partners have long-established CA trials. These included the University of Zambia’s Liempe Farm, Chitedze Research Station in Malawi and Domboshava, Zimbabwe. Through collaborative planning, installing, monitoring and data interpreting at each site, consortium members were expected to develop 1) their understanding of cross-discipline contributions to problem-solving; 2) their research skills in cutting-edge methodologies; and 3) their generic research skills (e.g., in project design or academic writing). CEPHaS delivered a wide range of training across diverse subject areas to researchers and research support staff across the CEPHaS network and supplied specialist field and laboratory equipment to consortium partners. A learning-centred structure of the demonstration studies was utilised to enable participants to take the lead in establishing similar studies or experiments both during and beyond the CEPHaS project lifetime. Further information about the CEPHaS consortium can be found at: https://www2.bgs.ac.uk/CEPHaS/.\n\nThe sampling frame for the survey included anyone who had been invited to attend and/or delivered a CEPHaS training between January 2018 and June 2021 and for whom an email address was held by CEPHaS project management (N=60). Survey participants were asked to indicate whether they would also be willing to participate in an SSI and, if yes, to provide their name and email address. Interview participants were purposively selected from this sample, with the objective of achieving representation across the final interview sample in terms of CEPHaS partner country, career stage, gender and position. An additional 12 CEPHaS co-investigators and staff at partner institutions, who had not been included in the survey sample, were also invited to participate in the SSIs, with the objective of ensuring representation from across CEPHaS leadership and from across a range of positions including scientific, managerial and technical. These individuals were nominated by CEPHaS project management and email addresses supplied.\n\nThe survey was developed by the research team and piloted with African early career researchers not belonging to the sample frame to test face and content validity of the stated questions. Minor changes to wording and survey lay out were subsequently made. The revised survey was administered via the ‘Online Surveys’ platform (https://www.onlinesurveys.ac.uk/) and took approximately 10-15 minutes to complete. Participation was both anonymous and voluntary. Participants provided consent by selecting the ‘I consent to the survey’ option in order to access the rest of the survey. An information sheet was included with the initial survey invitation, which was sent via email with a link to the survey form. Two ‘reminder’ messages were sent, also via email. The survey remained ‘live’ online for a six-week period between June-August, 2021. Participants were able to complete the survey at any time during this period. The online survey consisted of four sections: 1) demographic and professional information; 2) investigation of uptake, utilisation and transfer of any training provided by CEPHaS as well as potential barriers and enablers to training utilisation and transfer; 3) examination of the use of any resources provided by CEPHaS as well as enablers and barriers to the use of these resources; and 4) broader exploration of participant experiences of CEPHaS participation. Survey structure consisted primarily of closed response questions with one or multiple answer options.\n\nProspective interviewees were invited to participate by email and, if they accepted, a suitable date and time for an interview was agreed. All SSIs were completed remotely, via a recorded Zoom call, between September 2021 and February 2022. Participation was voluntary in all cases, with each interview taking between 30-80 minutes to complete. Semi-structured interviews were informed by a topic guide which covered the same four sections as included in the survey, albeit in an open-ended format. Both the survey and interview guide were designed to elicit information pertaining to both the individual participant as well as their respective university or research institution. The two methods were considered complementary as they afforded breadth (survey) and depth (SSI) to the subsequent data analysis and allowed for data triangulation to improve reliability. All design and evaluation activities of this study were conducted by the lead author (KAD) and supported by a senior colleague (JP), based in the UK at LSTM, and both were completely independent of project activities. Survey design was reviewed by CEPHaS members (MM, AD) to inform contextual understanding and inclusion of key project areas for evaluation.\n\nSurvey data were exported from online surveys into Stata/SE V.14.1 (https://www.stata.com/) for analysis. RStudio, (https://posit.co/products/open-source/rstudio/) a freely accessible alternative, is capable of the same analysis used in this study. Univariate analysis was performed to describe characteristics of the sample and for calculating frequencies and percentages across key focal areas of training, including knowledge/skill gain and transfer, resource use, and CEPHaS activities experienced and perceived value. All interviews were audio recorded and transcribed in full. Transcripts were entered into NVIVO 12 (https://lumivero.com/products/nvivo/) for coding and thematically analysed using a framework synthesis approach,11 informed by the interview guide. Taguette (https://www.taguette.org/), a freely accessible alternative, is capable of the same analysis used in this study. Key themes were identified and systematically reviewed. Key themes within and across consortium dynamics were examined in a series of discussions by two investigators (KAD, JP) at key intervals within the coding cycle. Preliminary findings were presented at the CEPHaS Conference in December 2021 to help interpret the findings in the context of the programme. Survey findings have been aggregated to further protect participant anonymity. Interview excerpts presented below have been labelled with relevant participant characteristics, including profession/career stage, location and gender, to aid interpretation yet maintain anonymity. Unique participant codes, ranging from P1-P19, are also presented against interview excerpts to indicate where the same participant has been quoted more than once.\n\n\nResults\n\nA total of 40 respondents completed the online survey (response rate of 67%) and 19 participants completed a semi-structured interview. As shown in Table 1, survey and interview participants were predominantly male (77.5% and 78.9%, respectively), aged between 25-44 years (65% and 68%, respectively) and graduate or early career researchers (60% and 63%, respectively). Participants were relatively evenly spread between the four CEPHaS partner countries.\n\nOf the survey participants, 72.5% (29/40) reported attending two or more training events provided by CEPHaS, 12.5% (5/40) attended one training, and 15% (6/40) did not attend a training event (i.e., they were invited, but did not attend). The 34 participants who reported attending at least one CEPHaS training were asked to report the frequency with which they used this training and how they had applied the training. Participants who attended more than one training were asked to respond based on the training they used the most. As shown in Table 2, 50% of these 34 participants reported using their training at least monthly and 29% at least weekly. The most frequent applications of the training received were in support of the participants’ own research (68%), supporting others research (50%) or teaching within their respective institutions (38%). ‘Other’ responses included consultancy work (n=1) or application within CEPHaS (n=2).\n\n* Participants could select more than one response option.\n\nWhen asked ‘apart from teaching, have you transferred this training in any other way?’, 24 out of these 34 participants responded ‘yes’. Table 3 presents the various ways in which these 24 participants reported transferring knowledge/skills gained from a CEPHaS training. As shown, knowledge/skills transfer primarily took place in the context of student supervision or supporting/supervising institutional colleagues.\n\n* Participants could select more than one response option.\n\nAll participants who reported attending or transferring a training were asked to identify, from a list of specified response options, enablers or barriers to utilising or transferring CEPHaS training. As shown in Table 4, the most frequently reported enablers to utilising and transferring training were ‘training was applicable to my work’, (74% and 75%, respectively), ‘having the applicable knowledge/skillset’ (62% and 71%, respectively) and ‘sufficient training’ and ‘sufficient mentorship/support’ (both 53% and 54%, respectively). The most frequently reported barriers included ‘insufficient time’ (30% and 24%, respectively) and ‘insufficient access to equipment’ (15% and 9%, respectively). However, over 50% of respondents reported ‘no barriers’ to either the use or transfer of training.\n\n* Only participants who reported transferring CEPHaS training were asked to report enablers.\n\nAll survey participants were presented with a list of resources supplied by CEPHaS and were asked to identify those to which: A) they had access to; B) had used; and C) had used most often (when more than one resource had been used). As shown in Table 5, most participants had access to, and had used, training materials, equipment and software supplied by CEPHaS; however, the resource used most often by 60% of participants was supplied equipment.\n\nParticipants were asked how frequently they used the resources supplied by CEPHaS and for what purpose. For participants who reported using more than one resource, they were asked to respond based on the resource that they utilised the most. As shown in Table 2, almost all participants used the stated resource at least once a month or more (92.5%) most often in support of their own research (77.5%) or teaching within their own institution (47.5%). ‘Other’ responses included for practice (n=1) or were undefined (n=2).\n\nAll participants were asked to identify, from a list of specified response options, enablers or barriers to utilising CEPHaS provided resources. As shown in Table 4, the most frequently reported enablers to resource use were ‘resource was applicable to my work’ (65%), and ‘having the applicable knowledge/skillset’ (57.5%). The most frequently reported barriers included ‘insufficient time’ (20%) and ‘insufficient training’ (10%). However, 67.5% of respondents reported ‘no barriers’ to resource use.\n\nAll survey participants were presented with a list of research-related activities and asked to identify which, if any, they had experienced during CEPHaS participation; they had experienced for the first time during CEPHaS participation; and had been most useful to them and their respective institution. As shown in Table 6, ‘data analysis’ (85%) and ‘field work’ (82.5%) were the most widely reported activities, with the former also the activity most often experienced for the first time (20%) and the activity considered most useful for the individual (27.5%) and their respective institution (25%).\n\n* n=20 (50%) participants did not experience any of these for the first time.\n\nParticipants described a wide range of benefits from CEPHaS membership at both an individual and institutional level. Table 7 presents a summary of these stated benefits as attributed to training provided by CEPHaS, resources provided by CEPHaS or the broader experience of CEPHaS membership.\n\nInterview participants reported a range of challenges that to some extent impacted on their, or their institution’s, ability to make optimal use of (some) opportunities made available through CEPHaS membership. Challenges identified included Covid pandemic travel limitations within and between countries and the subsequent loss of face-to-face interactions; misalignment of procedures amongst institutes, and between institutes and the funders, resulting in delays in project activities; and differing partner working and communication dynamics across institutes and time-zones.\n\n“I think I know there is always a difference between virtual meetings versus physical meetings. Because that physical relationship normally at times is important in establishing networks, that’s how I look at it … You meet, you discuss, and then you are sat somewhere on a bench, you are talking and physically you can touch this person. Yeah, it’s different from a virtual, yeah, that’s…even when you are doing all sorts of training. I think sometimes that physical one adds a bit of value than a virtual one.”\n\n- P16, Senior Researcher, Zambia, Male\n\nFour primary themes that positively influenced the consortium experience for consortia members emerged from the interview data, including: resource provision, strategic integration, the partnership network, and inclusivity. We discuss each theme in turn below alongside selected illustrative quotes in support of some points.\n\nResource provision\n\nThe CEPHaS project provided a multitude of resources to consortium partner institutes, including funding, equipment, software, training materials, and procedural guidelines. African institutes were the primary beneficiaries of the equipment which they could retain indefinitely. Institutes received both field and laboratory geophysics and soil science equipment that were used to rebuild and in one instance, establish a new soil science laboratory unit. The receipt of this equipment was seen as both individually and institutionally beneficial across consortium partners. Individually, members benefitted from equipment that reduced the work and time required to complete research tasks. The new equipment mechanically completed tasks that previously would have been meticulously done by hand, easing the workload of researchers and providing time to complete additional tasks.\n\n“I used to see most of the time they had a lot of samples in the lab that needed drying then they would just remain somewhere on the benches. But now this is not the case. If you want to dry something they have bigger capacities so they can be able to do that, and much more efficiently. So, I would say generally it has really made work easier. And for most of us it has also given us that opportunity to be able to do research which maybe in most cases would be a little bit difficult.”\n\n- P11, Mid-career researcher, Zambia, Male\n\nConsortium members had utilized the equipment not just to conduct research for CEPHaS but research areas outside of the scope of CEPHaS, and where this had not already begun, members felt that this new equipment would enable them to expand the scope of their research and explore new areas. Likewise, having the equipment to explore new research areas was seen as a long-term benefit to the member institutes as it had the potential to expand its research portfolio. Northern consortia members, who did not receive this equipment, also saw this as beneficial to their personal research and research institutes as it meant that there were now institutes in other geographical locations that have well equipped laboratories for future collaborations and new research.\n\nThe receiving institutes were also utilizing the new equipment to support student research in individual research projects as well as existing formal courses. Consortia members at receiving institutes felt that the new equipment increased the institutes’ prestige by increasing student satisfaction, by attracting prospective students and by making them appealing to other institutes and funders as a potential research partner. Students could now have hands on experience applying the theories they learned in class, and where conducting research, students would no longer need to pay for samples to be processed at other institutions.\n\n“Our students are also going to benefit a lot in terms of doing their practicals, to test some things in the lab … Prior to the project, our labs were not functioning well. For instance, I can mention the pressure plates. The pressure plates we use to measure the capacity of the soil to retain water were no longer functional. Thanks to the project, we managed to get those equipment that are very, very important. Especially for those students who are doing soil science and those who are doing agronomy. Because at some point, they would want to understand how the soil would be able to retain water after some amendments to it … so it’s very important for us as an institute.”\n\n- P8, Early career researcher, Zimbabwe, Male\n\nIn some instances, this was also seen as an opportunity that could provide additional revenue streams through the provision of for-profit laboratory services which in turn would support local organizations and farmers that may benefit from these types of tests.\n\nStrategic integration\n\nThe CEPHaS project was designed to capacitate institutes and individuals within the consortium and consciously incorporated complementary, integrated components into program delivery to facilitate this. Resources were provided with accompanying formal and informal training. Training started at the basics, facilitating a common scientific language across a multidisciplinary team and ensuring inclusion across demographics. Resource provision was intentionally multi-purpose. Equipment and software were provided not just to complete CEPHaS research activities, but also to establish laboratory facilities and field sites that could function as key CA research facilities in the region and provide institutes with equipment that could support revenue building services. The project framework was responsive to the context of the environment and the individuals and institutes. For example, in the initial phase of the project, it became apparent that the consortium partner institutes had different research management processes. Having aligned practices was required for the smooth transfer of funds and meeting funder requirements. The project was responsive to these needs, allocating time, resources and staff to support the training of institute staff not directly employed in CEPHaS to support project activities.\n\n“But I think in terms of preparing the financial reports, I think people in our accounts system have benefitted. They are able to generate reports in accordance with the department or the funder. I think that experience is helpful for them when they implement other activities within the university but also even for any future or present projects in the institute.”\n\n- P16, Senior Researcher, Zambia, Male\n\nStaff included on the project were both permanent institute employees and employees hired specifically for CEPHaS, with the rationale to provide for the present needs of the project and capacitate sustainability beyond the end of the project life. Including permanent institute employees meant that the skills and knowledge obtained by project staff would be retained at the university and that teaching staff at teaching institutes would be able to facilitate knowledge transfer within the existing institute framework beyond the project life. Permanent institute employees also have other institute responsibilities and have time allocated across non-CEPHaS activities which could restrict availability. Employing staff outside of the institute allowed the CEPHaS project to have full time staff, while also capacitating recent institute graduates from the departments engaged in CEPHaS and other local organisations, allowing the project’s activities to support not just the consortium partners but other individuals and institutes within the local areas.\n\n“Looking at our lab technicians, some of my colleagues where they’re academics people, they have been trained. That is a long-lasting knowledge that will be used for uplifting some of the issues that we do for our institution. For me also being trained in terms of the geophysics, it means I’m capable to say if somebody else brings in the issue of geophysics, I should be able to address and the institution will benefit or maybe they can be able to collaborate in another project.”\n\n- P2, Senior Researcher, Malawi, Male\n\nThe project design included partners from the global north and the global south with the view to allow mutual learning across cultures and geographical context. The partners included multidisciplinary staff within the field of CA to allow for knowledge transfer across sub disciplines and allow specialists to see potential connections and develop a holistic understanding of the field. The partnerships included early-, mid- and senior career researchers. Within the project framework, staff were organized into distinct units called ‘Working Groups’ that allowed the incorporation of individuals from each of these demographics to support the inclusion of a multitude of perspectives and facilitate the creation of networks across institutes.\n\nPartnership network\n\nThe partnership network created by the CEPHaS project was noted across participant members. The inclusivity, structure and duration of the project were key factors in supporting the network development. In addition to the diversity within the working groups, regular project workshops and trainings throughout the duration of the project and a range of communication mediums allowed for continuous formal and informal engagement between partners regardless of institute or geographic location. Members felt comfortable reaching out to other members through email with queries or requests for support and WhatsApp groups that allowed for both informal and formal communication. Members felt the network that was created through CEPHaS was something beneficial during the project and that it would continue beyond the life of the project, allowing for further development and research opportunities. Members felt comfortable that if queries or opportunities arose after the project, the CEPHaS members who supported them during the project would be willing to continue that engagement. These networks were seen as particularly important to early career researchers (ECRs) who could utilize this new network at a pivotal point in their career.\n\n“And some of the contacts which I have, I think they are really important for the development of my career, which is crucial at this point as a junior researcher, I can say. I think I have long-term benefits participating in the CEPHaS … I can say some of the guys, I don’t hesitate to talk to them when I need any assistance or anything … But the network and the interaction include the whole CEPHaS team, which at times if I need anything, I can communicate with anyone without hesitation, of course.”\n\n- P9, Early career researcher, Zimbabwe, Male\n\nMembers attributed this to trust that was developed throughout the project due to the continuous engagement between members, the length of the CEPHaS project, and the inclusivity that was generated through the project facilitation and leadership style (see below). Being a part of a project as long as CEPHaS was seen as a rare opportunity, and this allowed members to get to know working and communication styles as well as areas of expertise of other members. Additionally, although the CEPHaS project did not include PhD studentships, in at least two instances CEPHaS network membership led indirectly to scholarship opportunities for early career researchers.\n\n“But I’d say even the scientists have learnt a lot from each other. Because as I say, the soil scientist is now appreciating the hydrogeologist, or the hydrogeologist and the shallow geophysicist are working together. They’ve instrumented a borehole and they’re both getting results from that borehole.”\n\n- P3, Research support staff, UK, Female\n\nNetworks were facilitated across countries and supported mutual learning opportunities to develop cross-cultural professionalism and a cultural exchange of ideas to understand CA in different geographical environments.\n\nInclusivity\n\nInclusivity was a key feature of the CEPHaS project for consortia members. CEPHaS included both African and European institutes and individuals from a range of specialties and career levels. At the inception of the project, a workshop was held that was specifically designed to engage each member in the formation of the project plan and identify needs. Highly engaging project brainstorming activities around project deliverables were utilized. Perspectives and participation were encouraged by the project leads, facilitating a sense of value and respect amongst members regardless of position. Having this type of respect and seat at the table, from the beginning and throughout, was valuable to members and fueled their continued engagement.\n\n“From the beginning, every member of the project was involved. We didn’t have a top-down thing. Rather, it was like, together, let’s achieve this. That was a great experience for me, how to arrange a large project of this nature, interdisciplinary or maybe cross-cultural, many countries, how to arrange it so that we could be able to work together and deliver.”\n\n- P14, Mid-career researcher, Zambia, Female\n\nThe sense of inclusion that was generated throughout the project was attributed in part to the project leadership. The leader of the project, working groups, and the administrative staff provided verbal encouragement and support to allow members of the consortium to feel empowered, regardless of age, position or nationality. This leadership style further inspired members to want to develop a similar leadership style and incorporate elements of this approach within their own project management and teaching.\n\n“I think it was not like a forcing, it was an encouraging. It was flexible, motivating, allowing for people to think freely, like your ideas are welcome. That was important. Even when you bring an idea, you see your idea is being debated further and sometimes even taken up. Even trainings, people were allowed, can you suggest which are the trainings you would like to attend. So, people suggest a number of trainings.”\n\n- P14, Mid-career researcher, Zambia, Female\n\nAnother aspect that facilitated inclusivity and collaboration between members was the way members were grouped within the consortium. Small interactive working groups that reported within a defined consortia structure allowed everyone to participate. Division of tasks across demographics within working groups facilitated ongoing communication and meant all members were included and participating in the research and outputs.\n\nThis inclusive environment afforded opportunities to travel and engage in activities and discussions that were considered rare for ECRs.\n\n\nDiscussion\n\nThe survey and interview findings revealed a wide range of reported capacity strengthening gains resulting from CEPHaS engagement at both an individual and institutional level. Participants consistently expressed their CEPHaS involvement in positive terms with praise for the applied ‘learn by doing’ approach underpinning many of the activities as well as the engaging and highly inclusive leadership. There was evidence that the various trainings and resources provided through CEPHaS were valued, frequently utilised, and often transferred beyond the immediate CEPHaS membership for wider benefit. Resource provision and staff training were seen as foundational for long-term institutional benefits. Some challenges and suggested areas for improvement were reported by participants as were potential opportunities to facilitate greater impact.\n\nPerceptions highlighted in the survey and interview data were primarily aligned, with the overarching theme that the strategic integration of applicable training and resources were supportive components to participant experiences and allowed for research to be understood and conducted holistically. Provision of resources in complement with timely associated trainings and project research activities allowed for a cohesive learning experience and ensured that project activities were interconnected and consistently supported. Data analysis skills and fieldwork experiences were highly valued in both survey and interview data, with the survey data further highlighting that this was experienced by many participants for the first time. CEPHaS was viewed as a particularly valuable opportunity for ECRs to have access to hands-on multidisciplinary learning, resources, networks, and a collaborative working environment at this pivotal career point.\n\nA primary motivating factor for participants was a supportive environment. Leadership and programme structure that facilitated inclusion were two of the key components noted by participants that fuelled personal engagement and inspiration. The inclusion of participant perspectives from the outset by the project leads, regardless of participant position, engendered respect and trust. Providing an environment and a forum in which all partners could shape the research priorities provided equity that is often lacking in North-South research environments.7,12,13 Regardless of programme type, leaders setting an example of inclusion supports engagement and empowerment of its members, inspires and motivates.14,15 Likewise, aligning partner interests with the goals of a project from the outset are more likely to allow for the success of a project and supports a positive learning culture.15–18\n\nNetworking and collaboration opportunities were considered one of the most useful aspects of CEPHaS participation at both individual and institutional levels and participant responses suggested a high demand for additional networking opportunities over and above what was already provided. Bringing together specialists from within CA across geographies and demographics to form a multi-disciplinary team was a key benefit to CEPHaS participants. However, the initial need to train non-CEPHaS research management staff, the absence of structured knowledge transfer into institute teaching curriculum and potential for institutionally led incorporation of CEPHaS resources for revenue building activities, signify the potential value of a broader multi-disciplinary team that included additional research management and regulatory staff. Structured investment in research management staff within institutes and project structure can further allow for cohesive integration and sustained project benefits.15,19 Although CEPHaS had the flexibility in project structure to allow for unforeseen financial management training, further inclusion of a strategically focussed research management working group and additional research management training may have provided insight into how potential revenue streams could have been further advanced during the project lifespan. Greater cohesion of research management functionality and staff across institutes may also have further advanced additional future funding opportunities. Structured investment in research management staff would also provide the opportunity to bridge and formalise benefits from the individuals and departments involved in CEPHaS to the wider institution.\n\nInsufficient time was noted as a barrier within both the survey and interviews, as the quantity of information to be absorbed and utilised within the project was seen as a challenge. A recent study exploring the experiences of African postdoctoral fellows belonging to a vector borne disease research capacity strengthening consortium also identified the need to allow for additional time when a programme has both research and capacity strengthening objectives.20 The lack of face-to-face interactions, primarily caused by the Covid-19 pandemic, was predominantly seen as a limitation by participants. Although virtual engagement had the benefit of recordings and scheduling flexibility, face-to-face interactions were seen as valuable opportunities to gain deeper connections with partners. The reported value of face-to-face interaction, in terms of both learning and networking, is important to consider given the recent growth and normalisation of virtual meeting and teaching delivery.21\n\nAlthough CEPHaS was focussed on capacity strengthening in CA research, key benefits identified by participants are consistent with benefits reported from research capacity strengthening programmes in other fields. A supportive environment, networking opportunities, and a strategically integrated approach, inclusive of methodological skills and resource provision, is important to capacity strengthening programmes regardless of topic area.14,16,22–24 A supportive environment with trust and respect and inclusive decision making facilitates successful partner interactions, particularly in North-South partnerships.14,16,18,22–24 Additionally, having mutual interest in the subject matter supports consortia success.22,24 Although there are commonalities in capacity strengthening enablers across disciplines, many of these were reported as new and enlightening experiences within CEPHaS that shifted perspectives. As global consortia in conservation agriculture are less common than health-focused global research capacity strengthening consortia (from which much of the aforementioned evidence was drawn), our findings corroborate widely reported experiences within a new context.\n\nWhilst a primary focus of CEPHaS was to enhance CA research capacity within the network of Southern institutes, the CEPHaS consortium was a mutually beneficial experience for both Northern and Southern institutes, evolving from intentions of capacity strengthening to actualised capacity sharing. In aspects of professionalism, networking, scientific research, and training, participants felt they benefitted regardless of geographic location. Frequently, North-South collaborations/consortia are heavily weighted to provide monetary and educational benefits to Southern institutes with Northern institutes directing activities.7 Although resources were provided to southern institutes, and the training was provided to facilitate the use of these resources, partners from both the UK and African institutions were active participants in the application of this training and use of the equipment in the field setting, providing new insights into geographical differences. Northern partners gained valuable knowledge of the dynamics of their field and equipment beyond geographic boundaries, providing new areas of investigation. Mutual training and benefits to career regardless of institute are beneficial to research partnerships.16 Likewise, cross-disciplinary and cross-cultural knowledge exchange was mutually beneficial in broadening perspectives and challenging operational assumptions. A consortium and research project as large as CEPHaS was seen as a rare opportunity for both institutes and individuals across locations, and for many, it was their first time being involved in a project of this size. Northern partners reported internal institutional and cross-departmental recognition of the project as a model for international consortia. Both Northern and Southern participants felt that their institutional staff had gained skills that would support future grants and project operations. The CEPHaS consortium was inclusive of elements that enabled a North-South knowledge exchange that was mutually beneficial, professionally and scientifically, and could provide a template/model supportive of capacity sharing and increased equity within global consortia, divergent from helicopter research.7,16,18\n\nThe study was not without limitations, including the small sample populations (survey N=40; interviews N=19) across four countries and five research institutes. However, the mixed-methods study design did allow for some triangulation of data, allowing for greater depth and breadth than either quantitative or qualitative method would have allowed on its own and aiding confidence in the reported findings. Additionally, the study was conducted while participants were still employed by the study, and therefore, their shared perceptions may have been influenced by their ongoing engagement with the project. The study was also limited to a single CA consortium.\n\n\nConclusion\n\nOur findings suggest that the basic ‘template’ of the CEPHaS partnership provided a strong basis for research capacity strengthening in Conservation Agriculture, especially at the level of individual researchers, and that this template could be further enhanced in any future iteration of the same or similar programme. Key recommendations include:\n\n• Provide inclusive leadership practices that facilitate capacity sharing;\n\n• Strategically integrate training and resource provision within research project structure;\n\n• Strengthen networking and collaboration opportunities, specifically for ECRs;\n\n• Integrate research management training to develop sustainable operating structures internally and across institutes;\n\n• Include multi-disciplinary and multi-cultural partnerships within consortia;\n\n• Provide means for formalised inclusion of institutional level benefits to support sustainability, e.g., curricula development or commercial service provision.\n\n\nAuthor contributions\n\nConceptualisation: Justin Pulford, R. Murray Lark\n\nFormal analysis: Kirsten Duda, Justin Pulford\n\nFunding acquisition: Justin Pulford, R. Murray Lark\n\nInvestigation: Kirsten Duda\n\nMethodology: Justin Pulford, Kirsten Duda, Alessia D’Artibale, Miyanda Moombe\n\nProject administration: Kirsten Duda, Justin Pulford, Alessia D’Artibale\n\nSupervision: Justin Pulford\n\nWriting – original draft: Kirsten Duda, Justin Pulford\n\nWriting – review & editing: Kirsten Duda, Justin Pulford, R. Murray Lark, Alessia D’Artibale, Miyanda Moombe", "appendix": "Data availability\n\nInterview transcripts have not been made available as a data set because they cannot be readily de-identified without compromising anonymity. Requests for access to the interview transcripts, along with a statement as to the intended use, can be made to the corresponding author and will be considered on a case-by-case basis.\n\nHarvard Dataverse: Capacity Research, Centre for, 2023, “Data, instruments and checklists in support of publication titled: A mixed methods evaluation of capacity strengthening within an international conservation agriculture research consortium”, https://doi.org/10.7910/DVN/ANCIWR. 25\n\nThe project contains the following underlying data:\n\n• Online survey dataset.xlsx. (Anonymised responses to online survey).\n\nHarvard Dataverse:Capacity Research, Centre for, 2023, “Data, instruments and checklists in support of publication titled: A mixed methods evaluation of capacity strengthening within an international conservation agriculture research consortium”, https://doi.org/10.7910/DVN/ANCIWR. 25\n\nThis project contains the following extended data:\n\n• Survey instrument.pdf (Blank copy of the online survey tool).\n\n• Interview guide.pdf (Blank copy of the interview guide).\n\nHarvard Dataverse: SRQR checklist for ‘A mixed methods evaluation of capacity strengthening within an international conservation agriculture research consortium’, https://doi.org/10.7910/DVN/ANCIWR. 25\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe are grateful to all participants who agreed to take part in this study. We would also like to thank Imelda Bates, of the Centre for Capacity Research, Liverpool School of Tropical Medicine, for her contributions towards study implementation and for reviewing the final manuscript.\n\n\nReferences\n\nMitchell J, et al.: Conservation agriculture systems. CABI Reviews. 2019; 2019: 1–25. Publisher Full Text\n\nMkomwa S, et al.: Centres of Excellence in Conservation Agriculture: Developing African Institutions for Sustainable Agricultural Development. Conservation Agriculture in Africa: Climate Smart Agricultural Development. CABI GB; 2022; pp. 402–415.\n\nChinseu EL, Dougill AJ, Stringer LC: Strengthening Conservation Agriculture innovation systems in sub-Saharan Africa: Lessons from a stakeholder analysis. Int. J. Agric. Sustain. 2022; 20(1): 17–30. Publisher Full Text\n\nHermans TD, et al.: Bridging the disciplinary gap in conservation agriculture research, in Malawi. A review. Agron. Sustain. Dev. 2020; 40: 1–15.\n\nLansang MA, Dennis R: Building capacity in health research in the developing world. Bull. World Health Organ. 2004; 82(10): 764–770. PubMed Abstract\n\nMirzoev T, et al.: Conceptual framework for systemic capacity strengthening for health policy and systems research. BMJ Glob. Health. 2022; 7(8): e009764. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar M, et al.: What should equity in global health research look like? Lancet. 2022; 400(10347): 145–147. PubMed Abstract \| Publisher Full Text\n\nKienzle J, Sims B, Mutai W: Sustainable Agricultural Mechanization and Commercialization for Widespread Adoption of Conservation Agriculture Systems in Africa. Conservation Agriculture in Africa: Climate Smart Agricultural Development. CABI GB; 2022; pp. 382–401.\n\nOgega OM, et al.: Strengthening climate research capacity in Africa: lessons from the ‘Climate impact research capacity leadership enhancement’ project. Reg. Environ. Chang. 2022; 22(4): 1–5. Publisher Full Text\n\nDuda K, Pulford J, Bates I: Analysis of capacity strengthening within the CEPHaS project. Liverpool, UK: Liverpool School of Tropical Medicine; 2022.\n\nDixon-Woods M: Using framework-based synthesis for conducting reviews of qualitative studies. BMC Med. 2011; 9(1): 1–2. Publisher Full Text\n\nHodson DZ, et al.: Striving towards true equity in global health: A checklist for bilateral research partnerships. PLoS Global Public Health. 2023; 3(1): e0001418. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlamondon KM, Bisung E: The CCGHR Principles for Global Health Research: Centering equity in research, knowledge translation, and practice. Soc. Sci. Med. 2019; 239: 112530. PubMed Abstract \| Publisher Full Text\n\nAiyenigba A, et al.: Enabling research capacity strengthening within a consortium context: a qualitative study. BMJ Glob. Health. 2022; 7(6): e008763. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDing Y, Pulford J, Bates I: Practical actions for fostering cross-disciplinary global health research: lessons from a narrative literature review. BMJ Glob. Health. 2020; 5(4): e002293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohn CC, Ayodo G, Musoke P: Successful Global Health Research Partnerships: What Makes Them Work? Am. J. Trop. Med. Hyg. 2016; 94(1): 5–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTran TBH, Choi SB: Effects of inclusive leadership on organizational citizenship behavior: The mediating roles of organizational justice and learning culture. J. Pac. Rim Psychol. 2019; 13: e17. Publisher Full Text\n\nFranzen SR, Chandler C, Lang T: Health research capacity development in low and middle income countries: reality or rhetoric? A systematic meta-narrative review of the qualitative literature. BMJ Open. 2017; 7(1): e012332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEl Hajj T, et al.: Strengthening capacity for natural sciences research: a qualitative assessment to identify good practices, capacity gaps and investment priorities in African research institutions. PLoS One. 2020; 15(1): e0228261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAmegee J, Valea I, Bates I, et al.: Factors affecting African postdoctoral researcher capacity development within ‘learn-by-doing’ international research partnerships: Findings from the ‘Partnership for Increasing the Impact of Vector Control (PIIVeC)’. BMJ Glob. Health. 2023. (Under review).\n\nGuppy N, et al.: The post-COVID-19 future of digital learning in higher education: Views from educators, students, and other professionals in six countries. Br. J. Educ. Technol. 2022; 53(6): 1750–1765. Publisher Full Text\n\nTagoe N, et al.: Managing health research capacity strengthening consortia: a systematised review of the published literature. BMJ Glob. Health. 2019; 4(2): e001318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMayhew SH, Doherty J, Pitayarangsarit S: Developing health systems research capacities through north-south partnership: an evaluation of collaboration with South Africa and Thailand. Health Res. Policy Syst. 2008; 6: 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaric J, et al.: Leveraging research partnerships to achieve the 2030 Agenda: Experiences from North-South cooperation. GAIA - Ecological Perspectives for Science and Society. 2019; 28(2): 143–150. Publisher Full Text\n\nCapacity Research, Centre for: Data, instruments and checklists in support of publication titled: A mixed methods evaluation of capacity strengthening within an international conservation agriculture research consortium. Dataset. Harvard Dataverse. 2023; V2. Publisher Full Text" }	[ { "id": "207166", "date": "26 Sep 2023", "name": "Bruce Currie-Alder", "expertise": [ "Reviewer Expertise Climate adaptation and resilience", "research-for-development", "science policy", "international development", "research 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\nA very clear article that adds to the evidence on capacity strengthening efforts. The insights on capacity 'sharing' and how both southern and northern participants benefited are particularly welcome. A few minor addition could potentially enhance the article's usefulness for those involved in designing such efforts:\n\nPlease provide more detail on the content (subjects, skills, competencies) covered by the training provided. This would provide context priori to delving into survey results.\n\nProvide an estimate on the size of effort under the consortium, for example, the overall financial value involved, total number/variety of training, and number of participants (while the article mentions 40+19 participants in the evaluation, this reviewer did not readily see the total number of people would participated in training).\n\nConsider reordering the rows on tables 4, 5 and 6 to present the entries from most-to-least frequently cited.\n\nConsider elaborating upon the bullet list of conclusions. As written these do not yet provide a level of detail for future programme designers. An additional sentence or two for each conclusion could describe advice on what to do in future efforts and 'how to' act on these insights.\n\nTwo additional references to consider in situating the article are Chadwick et al (2022) 'Research capacity strengthening lessons from UK funded research UKCDR, and http://hdl.handle.net/10625/58680.\nFinally, Table 7 is hard to digest as drafted, and could be presented with training/resource/experience on the vertical axis and individual/institutional on the horizontal.\n\nIs the work 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": [] }, { "id": "216406", "date": "20 Nov 2023", "name": "Ashim Datta", "expertise": [ "Reviewer Expertise Soil carbon sequestration", "GHGs dynamics", "salt affected soils managment", "conservation agriculture and bioenergy crops" ], "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\nExcellent article on capacity development and its strengthening approaches under conservation agriculture research consortia. This article provides evidence of the importance of these kind of consortia between global north and south. There are few minor corrections:\n\nIn abstract under \"Background\" section in 3rd line \"to\" is repeated. It should be \"sought to strengthen...\"\n\nIn Introduction, first paragraph 4th line, it can be written as \"enhance its organic carbon content and biological activity....\"\nRest is fine. I have a few suggestions:\nThe interview replies of the participants may be avoided. There are many.\n\nThe conclusion part may be revised instead of writing bullet points with way forward and implications.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1119
https://f1000research.com/articles/12-1118/v1	08 Sep 23	{ "type": "Case Report", "title": "Case Report: Breaking barriers - Pregnancy achieved by intracytoplasmic sperm injection of a zona-free oocyte", "authors": [ "Jarul Shrivastava", "Akash More", "Virul Shrivastava", "Namrata Anjankar", "Virul Shrivastava", "Namrata Anjankar" ], "abstract": "The zona pellucida is a protective layer surrounding the oocytes and early-stage embryos. It is said to be essential for the process of fertilisation and protecting the pre-implantation embryo. Absence of zona pellucida can pose great problems during in vitro fertilisation (IVF), like impaired fertilisation, polyspermy and hindered embryo development, thus leading to a low implantation rate and unsuccessful pregnancy outcome. This case report demonstrates the successful treatment of primary infertility in a 35-year-old female with significantly low anti-Mullerian hormone (AMH) levels and limited ovarian reserve. Her husband (41 years) had oligoasthenozoospermia. The couple had been trying to conceive for two years before seeking medical assistance. Following an unsuccessful intrauterine insemination (IUI) attempt, the decision was made to pursue IVF with ovarian stimulation. Two oocytes were retrieved after ovum pickup, one of which was at the germinal vesicle (GV) stage and later degenerated, while the other was without the zona pellucida. In this case, the intracytoplasmic sperm injection (ICSI) of zona-free oocyte was chosen to prevent polyspermy, resulting in successful fertilization. The embryo progressed to the eight-cell stage and was transferred on day three. A positive beta-human chorionic gonadotropin (β-hCG) test confirmed pregnancy fourteen days later. In assisted reproductive techniques (ART), zona-free oocytes are a common occurrence, but fertilizing those oocytes is not common; they are usually considered to be of no use and rejected. In the present case, we realized that zona-free gametes are not only capable of getting fertilized and developing into good-quality embryos, but also give successful pregnancy outcomes.", "keywords": [ "Primary infertility", "zona-free oocyte", "low AMH", "In- vitro fertilization", "intracytoplasmic sperm injection", "a successful outcome" ], "content": "Introduction\n\nThe zona pellucida is a thick acellular layer surrounding mammalian eggs and pre-implantation embryos.1 The zona contributes to oocyte growth and the development of follicles. It plays a crucial role during fertilisation and has many other important functions in pre-implantation embryos like protecting it from infections, preventing its premature adherence, and also prevents premature implantation.2 It contains certain glycoproteins including ZP1, ZP, and ZP3, that help in sperm binding and recognition, which in turn facilitates sperm penetration by acrosomal reaction; it also creates a barrier which prevents polyspermy by zona reaction.1,3 In addition, after fertilisation, it protects the growing embryo before implantation by preventing aggregation of embryos and its premature adherence to the oviduct wall.4 It also hampers chimera formation and protects embryos against bacterial and viral infections. These functions make the zona essential for the fertilisation and development of the oocyte and embryo.5,6\n\nAbsence of zona pellucida can be due to genetic, immunological or mechanical factors. Genetic and immunological factors can impair the zona production or cause defects in ZP1 expression, while mechanical factors cause trauma to zona pellucida, such as a fracture which can occur during the ovum pick-up procedure. Sometimes, the zona is removed intentionally.6 Absence of a zona makes oocytes very fragile.7,8 It is said that composition, thickness, or shape of zona pellucida may affect optimal function and pregnancy outcome might be reduced.9\n\nZona-free oocytes are usually seen in the assisted reproductive laboratory, but are mostly considered unsuitable for fertilisation. There are not many studies and reports showing successful pregnancy outcomes with zona-free oocytes.8 This case report shows that zona-free oocytes can be successfully fertilised and lead to a positive outcome.\n\nUsing conventional in vitro fertilisation (IVF) on zona-free oocytes can increase the chances of polyspermy; thus, we used intracytoplasmic sperm injection (ICSI). Sometimes, the zona pellucida is damaged during denudation or ICSI. Those zona-free oocytes are mostly rejected. It is said that most of these oocytes are degenerated. However, it is possible that a few of them are still healthy and can be successfully fertilised. Those can be fertilized using ICSI and give successful pregnancy outcome.7\n\n\nCase presentation\n\nA 35-year-old female visited our centre with her husband (41 years) with an issue of infertility after three years of marriage. They had been trying to conceive for two years. Due to taboo around IVF, they consulted a doctor after two years. The female patient is a teacher in a government school and her husband is a businessman.\n\nThere was no significant medical history. This was the first-time couple was seeking treatment for infertility.\n\nThe woman’s BMI was 21 and husband’s was 24, which were normal. There were no relevant findings relating to infertility.\n\nBoth underwent comprehensive infertility workup to find out the cause of infertility.\n\nHusband’s semen analysis revealed oligoasthenozoospermia, which is low sperm count of 15 million/mL with reduced (10%) progressive motility. The husband’s hormonal evaluation including testosterone, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and prolactin levels, showed no abnormalities.\n\nThe female partner underwent a transvaginal ultrasound to assess her ovarian reserve and check for any structural abnormalities. Three follicles were seen on the right side and zero on the left ovary. Her hormonal profile showed low AMH levels at 0.3 ng/dL and high FSH. To assess the tubal patency, a hysterosalpingography (HSG) was performed. The Fallopian tubes were open and normal, suggesting no tubal factors were causing infertility.\n\nThis was a case of primary infertility. The probable cause of infertility was low AMH with low ovarian reserve of the woman and oligoasthenozoospermia of her husband.\n\nFirstly, intrauterine insemination was done using the husband’s semen but sadly the results were unsuccessful. Then IVF was chosen as a treatment.\n\nThe female patient underwent controlled ovarian stimulation to increase the number of available eggs for fertilization. She received a GnRH antagonist to suppress natural ovulation. After that, we began ovarian stimulation using gonadotropins. The ovarian response was monitored by ultrasound scans and serum oestradiol measurements. The trigger was given when follicles reached the desired size of 18 mm and above. After thirty six hours of trigger, oocytes retrieval procedure was carried out.\n\nDuring the oocyte retrieval procedure, two oocytes were retrieved, but one of them was a germinal vesicle (GV) and the other one lacked a visible zona pellucida, which is the outer protective layer surrounding the oocyte. The absence of the zona pellucida was confirmed through careful examination under high magnification after denudation (Figure 1).\n\nGiven this unique situation, the couple was informed about the possibility of performing ICSI with a zona-free oocyte, as it was their only chance for fertilization in this particular cycle. After analysing potential outcomes, the couple decided to proceed with the ICSI procedure using the zona-free oocyte.\n\nThe ICSI procedure of the zona-free oocyte was performed (Figure 2). The zona-free oocyte was held in place using a holding pipette, while a single motile spermatozoon was aspirated into a needle. The sperm was then injected directly into the oocyte. Following ICSI, the injected oocyte was cultured in a suitable culture medium and assessed for fertilization after 16-17 hours.\n\nThe embryo progressed from the four-celled to eight-celled embryo stage (Figure 3).\n\nOn day three, fresh embryo transfer was carried out. Fourteen days after embryo transfer, a βhCG test was done and it was positive.\n\nThe couple was delighted with the successful outcome of the treatment and expressed gratitude. They were counselled on the importance of regular care during gestation and the need for appropriate follow-up post-delivery.\n\nFirstly, Follow-up was done after embryo transfer. Oestrogen and progesterone tablets were prescribed to support the uterus. During these follow-ups, endometrium thickness was evaluated. On the fourteenth day, the pregnancy test came back positive. After that, during antenatal care, the woman was advised regular check-ups and was prescribed vitamins. Her health and the growth of the foetus were monitored routinely. Presently, at time of writing, she is at 21 weeks of gestation with normal foetal growth and movements.\n\n\nDiscussion\n\nOur report discusses the rare situation where not only successful fertilization occurred in a zona-free oocyte using ICSI, but also where this fertilized egg cleaved, implanted and led to a positive pregnancy outcome. As mentioned above, the zona pellucida is a highly important component of the oocytes and has multiple functions during fertilization, oocyte growth, follicles and preimplantation development. Despite these important purposes, our study demonstrates that an embryo can still survive without zona pellucida and pregnancy is very much possible. There are very few reports regarding this. Although zona-free oocytes have been shown to have fertilized after ICSI, cleavage and blastocyst formation is always challenging. ICSI is usually preferred when infertility is due to male factors, but when zona-free oocytes are encountered, then ICSI should be chosen because in the absence of zona, multiple sperms can enter the oocyte during conventional IVF.\n\nIn a report by Ebner et al, zona-free oocytes were successfully fertilised and cleaved, but pregnancy could not be achieved with zona-free embryos.9 Similarly, a study by Ding et al. reported two cases where oocytes without zona were fertilised and developed into blastocyst but implantation could not occur.7 Finally, Stranger et al. demonstrated ICSI of zona-free oocytes and successful pregnancy was achieved.10 Hu and Trolice presented the first case using repetitive autologous zona-free oocytes that underwent ICSI and fertilisation. When these reached at blastocyst stage, fresh embryo transfer was conducted, which resulted in a positive pregnancy and later, led to the live birth of twins.11\n\nIn the future, zona-free culture have a potential to become a feasible alternative to the conventional approach in ART.6 Similarly, another case study by Watson et al. reported a live birth using zona-free oocytes. They used detailed protocols with time-lapse footage of blastocyst development and demonstrated that a careful improved approach to ovarian stimulation, oocyte pick-up, and culture of embryo may encourage successful blastocyst development and healthy live birth in patients with failed/impaired zona production.8 Lately, it has been observed that the absence of zona pellucida does not necessarily affect he normal development of preimplantation embryos. Zona-free embryo culture systems in animals also showed improvement in overall efficiency. Further studies are required to confirm this.4 Some even claim that zona-free embryos give better pregnancy outcome. Monsour et al. intentionally removed the zona pellucida. Their study compared the transfer of day 3 zona-free embryos and day 3 zona-intact embryos in two groups. Results showed improved pregnancy rates in a selected group of poor-prognosis women undergoing ICSI. There was no negative effect of removing zona on the pregnancy rate in either of the groups studied.12\n\n\nConclusions\n\nOne in five couples suffers from infertility. It can be either primary or secondary infertility. In this case report, the couple had primary infertility. Here, the probable causes of infertility were low AMH, poor ovarian reserve, the poor-quality oocytes of the female and oligoasthenozoospermia of the male patient.\n\nThe absence of zona in the oocyte could be due to various causes like genetic, immunological or physical damage during denudation. Since the zona pellucida is said to be essential for the fertilisation and early-stage embryo, zona-free are usually being considered ‘unusable’ in ART labs. Thus, this report illustrates that zona-free oocytes are equally advantageous as zona intact oocytes. Also, using ICSI for such oocytes is the most favourable choice, because it can be assured that only one sperm is fertilising the egg. ICSI should be carried out attentively and carefully. As rare as it is considered, zona-free oocytes can be successfully fertilised and implanted, giving a positive pregnancy outcome. This case report is significant in highlighting this major breakthrough in ART. ICSI in zona-free oocytes can pioneer advancement, paves the way for future research and offers a new hope for individuals seeking infertility treatment.\n\n\nConsent\n\nWritten informed consent of the couple was taken for publishing their clinical details.", "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\nBleil JD, Wassarman PM: Structure and function of the zona pellucida: Identification and characterization of the proteins of the mouse oocyte’s zona pellucida. Dev. Biol. 1980; 76(1): 185–202. PubMed Abstract \| Publisher Full Text\n\nHerrler A, Beier HM: Early embryonic coats: Morphology, function, practical applications. An overview. Cells Tissues Organs. 2000; 166(2): 233–246. PubMed Abstract \| Publisher Full Text\n\nSinowatz F, Töpfer-Petersen E, Kölle S, et al.: Functional morphology of the zona pellucida. Anat. Histol. Embryol. 2001; 30(5): 257–263. Publisher Full Text\n\nMadani S, MacHaty Z, Vajta G: An Alternative Way to Improve Mammalian Embryo Development “yes” In Vitro: Culture of Zona Pellucida-Free Embryos. Cell. Reprogram. 2022; 24(3): 111–117. PubMed Abstract \| Publisher Full Text\n\nVan Soom A, Wrathall AE, Herrler A, et al.: Is the zona pellucida an efficient barrier to viral infection? Reprod. Fertil. Dev. 2010; 22(1): 21–31. PubMed Abstract \| Publisher Full Text\n\nVajta G, Rienzi L, Bavister BD: Zona-free embryo culture: Is it a viable option to improve pregnancy rates? Reprod. Biomed. Online. 2010; 21(1): 17–25. PubMed Abstract \| Publisher Full Text\n\nDing J, Rana N, Dmowski WP: Intracytoplasmic sperm injection into zona-free human oocytes results in normal fertilization and blastocyst development. Hum. Reprod. 1999; 14(2): 476–478. PubMed Abstract \| Publisher Full Text\n\nWatson K, Korman I, Liu Y, et al.: Live birth in a complete zona-free patient: a case report. J. Assist. Reprod. Genet. 2021; 38(5): 1109–1113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEbner T, Moser M, Tews G: Intracytoplasmic Sperm Injection in Zona-free Oocytes.2004; 5(23): 294–298.\n\nStanger JD, Stevenson K, Lakmaker A, et al.: Pregnancy following fertilization of zona-free, coronal cell intact human ova. Hum. Reprod. 2001; 16(1): 164–167. PubMed Abstract \| Publisher Full Text\n\nHu Y, Trolice MP: Live birth of twins derived from zona-free oocytes. Fertil. Steril. 2016; 105(5): 1232–1235. PubMed Abstract \| Publisher Full Text\n\nMansour RT, Rhodes CA, Aboulghar MA, et al.: Transfer of zona-free embryos improves outcome in poor prognosis patients: A prospective randomized controlled study. Hum. Reprod. 2000; 15(5): 1061–1064. PubMed Abstract \| Publisher Full Text" }	[ { "id": "298754", "date": "16 Sep 2024", "name": "Anca Huniadi", "expertise": [ "Reviewer Expertise Human reproduction specialist" ], "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\nFirstly I would like to congratulate you for the work that you have done. I would like you to answer some questions: - If the patient is 35 years old and has a AMH 0.3 explain why did you try an IUI? - Why did you choose day 3 embryo transfer in this case specifically? - What was the relevance of the couples jobs? - You have to use medical terminology such as AFC = antra follicle count when you refer to it - How high the FSH of the patient? - How long was the stimulation protocol? - Why did you evaluate the endometrium after the embryo transfer and you did not mention about it before? What's the relevance? - Please formulate the conclusion.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1118
https://f1000research.com/articles/12-1117/v1	08 Sep 23	{ "type": "Research Article", "title": "Impact of estrogen and progesterone hormone receptors on the progression of interferon-γ sensitized breast cancer cells", "authors": [ "Israa Shihab", "Amal Bouzid", "Burcu Yener", "Alaa Altaie", "Poorna Manasa Bhamidimarri", "Mouza Al Ameri", "Riyad Bendardaf", "Mawieh Hamad", "Rifat Hamoudi", "Israa Shihab", "Amal Bouzid", "Burcu Yener", "Alaa Altaie", "Poorna Manasa Bhamidimarri", "Mouza Al Ameri", "Riyad Bendardaf", "Mawieh Hamad" ], "abstract": "Background: Breast cancer is a chronic complex disease. Its progression depends partly on the interaction between tumor and immune cells. Whilst immunotherapy is the new promising treatment, many patients with breast cancer acquire resistance. Interferon gamma (IFN-γ) is a pleiotropic cytokine that is primarily released by T cells and natural killer (NK) cells and has always been praised for its antitumor activities. However, IFN-γ may induce different modulations in breast cancer cells that are expressing or not expressing the hormone receptors estrogen and progesterone. Methods: In this study, to examine the effect of IFN-γ on the subtypes of breast cancer in relation to the expression of estrogen and progesterone genes, we performed RNA-sequencing on the triple negative cells MDA-MB231 and ER/PR transfected MDA-MB231 cells (untreated or treated with 100 ng/ml IFN-γ). Various bioinformatics analyses were performed to investigate the affected functional pathways, and immune genes related to the different types of breast cancer cells. Results: The set of differentially expressed genes (DEGs) that are regulated by IFN-γ were unique, and specific to each breast cancer subtype. These unique DEG patterns in hormone-positive cells (GBP3, HLA-DPA1, HLA-DRB1, HLA-E, IL6) and triple negative cells (IFI6, ISG15, CCL5) showed significant but distinct effects on patients’ overall survival as well as noticeable differences in immune modulation and regulation. Conclusions: IFN-γ signaling can differentially affect the pattern of gene expression in breast cancer cells in an estrogen receptor (ER) / progesterone receptor (PR)-dependent manner. IFN-γ treatment of ER+/PR+ breast cancer cells upregulated the expression of genes related to immune cells and showed improved patient prognosis, while TNBC showed negative regulation of the expression of genes related to immune cells and worse patient prognosis.", "keywords": [ "Breast cancer", "IFN-γ", "Hormonal", "ER", "PR", "Triple negative", "Immune cells" ], "content": "Introduction\n\nCancer is still the second leading cause of death in the world despite advances in cancer therapy and the emerging relevance of genomics in cancer treatment and precision medicine.1,2 Among all types of cancer, breast cancer (BC) is the most frequent type in women worldwide. According to the World Health Organization, each year, this malignancy affects more than two million women globally and is the primary cause of cancer-related death in women.3,4 Disease heterogeneity in BC increases its resistance to targeted treatment. BC can be molecularly classified into luminal A, luminal B, human epidermal growth factor receptor 2 (HER2) positive, and basal-like, with respect to the biomarkers status of estrogen receptor (ER), progesterone receptor (PR), and HER2.5,6 Particularly, the triple negative BC subtype is considered to be the most aggressive subtype and has poor outcomes due to limited options for effective treatment.7 However, there is a better overall survival (OS) rate for patients with ER+ or PR+ tumors, in part because of the intrinsic characteristics of these tumors and in part because of the improved treatments targeting these tumors.8 Approximately, 60% of diagnosed BC cases are ER+/PR+, while those expressing HER2 account for 15-20% of cases.9 In addition, the tumor microenvironment (TME) has a crucial role in tumor development and immune modulation. The TME may induce immune cells such as natural killer (NK) and T cells to release molecules that favor tumor progression and immune inhibition.10,11 However, the modulatory interactions between the tumor and the immune system remain poorly understood.\n\nAs is well known, immune cells get activated when encountering altered self cells including transformed and tumor cells. Activated immune cells secrete cytokines and chemokines, such as IL-12, IL-15 and interferon gamma (IFN-γ), to activate the immune cells besides its direct effect on the transformed cells.12,13 Recent data showed that IFN-γ is also involved in promoting the progression of different tumors with immunosuppression phenotype, which may be the reason for some patients showing resistance to immunotherapy.14 Furthermore, IFN-γ autocrine signaling has been detected in BC cells, affecting their behavior and sensitivity to treatment, besides suppressing tumor immune cells.15,16 Therefore, understanding the role of IFN-γ in defining tumor heterogeneity may advance our knowledge of TME and allow for more effective personalized immunotherapeutic approaches in BC.\n\n\nMethods\n\nThis study was performed on the triple negative human BC cell lines (TNBC) MDA-MB-231(ER-, PR-, HER2-) (RRID:CVCL_0062) and transformed hormone receptor-positive MDA-MB-231 (ER+, PR+). Triple negative and ER- and PR-positive cells were then treated with IFN-γ, followed by sequencing and analysis using different bioinformatics tools. Figure 1 summarizes the experimental methods and software analyses used in this study.\n\nCreated with BioRender.com. IFN-γ, interferon gamma; ER, estrogen receptor; PR, progesterone receptor.\n\nHuman BC cells MDA-MB-231(ER-, PR-, HER2-) were obtained from American Type Culture Collection (Manassas, VA, USA). Cells were cultured in RPMI-1640 media (Sigma-Aldrich, Cat # R8758, Germany) supplemented with 10% fetal bovine serum (Sigma-Aldrich, Cat # F9665, Germany) and 1% penicillin-streptomycin (Sigma-Aldrich, St. Louis, MO, USA) and incubated at 37°C and 5% CO2 in a humidified incubator.\n\nMDA-MB-231 cells were seeded one day before the transfection experiment as 2×105 cells in 2 ml per well of a 6-well plate. On the day of transfection, MDA-MB-231 cells were co-transfected with 1 μg pcDNA-PR (RRID:Addgene_89130) and pEGFP-CI-ER alpha (RRID:Addgene_28230) expression plasmid construct for PR and ER, respectively, using ViaFect™ Transfection reagent (Promega; E4982). Briefly, the plasmids were diluted and mixed in 200 μl serum-free Opti-MEM™ medium (Gibco, Cat# 31985-070), then 6 μl ViaFect™ Transfection reagent was added with the ratio of plasmid DNA in μg to ViaFect Reagent in μl was 1:3. The ViaFect™ Transfection complex (Reagent:DNA mixture) was incubated for 10 minutes at room temperature and added to the well of a 6-well plate containing 2 ml of cells in growth medium drop by drop. Two biological replicates were done. Negative control cells were treated with ViaFect reagents only without adding any plasmids. After 24 hours, transfected and non-transfected cells were collected by trypsinization for measuring transfection efficiency.\n\nRNA was extracted from cell pellets using RNA extraction kit (Norgen Biotek Corp, Cat# 47700, Thorold, Canada). Briefly, 300 μL lysis buffer was added to the pellet to lyse cells, then 300 μL of 70% ethanol was added and mixed by pipetting for 15 seconds, total lysates were transferred onto a separating column and centrifuged for 2 minutes at 3,500 x g, 400 μL wash solution was added to the column and centrifuged at 3,500 x g for 1 minutes, then wash solution was added again and centrifuged for another 2 minutes. Lastly, 50 μL Elution solution was added to elute the RNA and centrifuged for 2 minutes at 200 x g for 1 minute. cDNA was synthesized from total RNA using a High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Cat # 4368813). A total volume of 20 μL is synthesized from 1,000 ng of total RNA template. RNA samples were mixed with Nuclease-free H2O for up to 10 μL (containing 1,000 ng), the component of the cDNA kit were added together for up to 10 μL, then mixed with the RNA for a total 20 μL and loaded into thermal cycler Eppendorf™ Mastercycler® nexus gradient (Eppendorf, Cat #6331000041, RRID:SCR_023266) with thermal conditions as following: 10 minutes at 25°C, 120 minutes at 37°C, and 5 minutes at 85°C.\n\nQuantitative PCR analysis was carried out to quantify the mRNA levels of different genes, and expression of these candidate genes was normalized against the internal control GAPDH of the same sample. For mRNA quantification, the relative expression of these genes was obtained using the 2-ΔΔCt method.17 All primers were reconstituted with Tris-EDTA (TE) buffer to a concentration of 100 μM. Then, forward and reverse primers were diluted at 1:10 in nuclease free water at the time of the experiment, and 500 ng/μL cDNA was prepared by mixing cDNA sample with nuclease free water for a total volume of 20 μL. Maxima SYBR Green/ROX qPCR Master Mix (Thermo Fisher Scientific, Cat # K0223) was used for qPCR set up, 9.5 μL of the mixture was mixed with 0.5 μL cDNA for a total volume of 10 μL. The reaction tubes were loaded into the QuantStudio 5 Real-Time PCR (Applied Biosystems, Cat # A28567, RRID:SCR_020240). Thermal cycling conditions were as follows: Optimal UDG pre-treatment one cycle for 2 minutes at 50°C, then initial denaturation for one cycle for 10 minutes at 95°C, followed by 40 cycles of denaturation at 95°C for 15 seconds, annealing for 30 seconds at 60°C, then extension at 72°C for 30 seconds. The primer sequences for PR, ER, and GAPDH were as follows: PR Forward: CACAAAACCTGACACCTCCA, Reverse: TTCGAAAACCTGGCAATGAT; ESR1 Forward: GTGCCTGGCTAGAGATCCTG, Reverse: ATTTTCCCTGGTTCCTGTCC; GAPDH Forward: CCAGGTGGTCTCCTCTGACT, Reverse: ACATACCAGGAAATGAGCTT. Results were analyzed with GraphPad Prism 9 (RRID:SCR_002798). The statistical tests can be carried out using freely available alternative software such as the R programming language and JAMOVI.\n\nAfter 24 hours transfection, the cells were collected and disrupted by sonication (at 40% amplitude for 10 seconds) in M-PER Mammalian protein extraction reagent (Thermo Scientific, Cat #78501) containing 1% protease inhibitor cocktail (Sigma-Aldrich Cat # P2714) and 1 mM DTT (Sigma-Aldrich Cat # 43815), which were added prior to use. Protein concentrations were determined by the Bio-Rad Protein Assay Dye Reagent Concentrate (Bio-Rad Cat # 5000006, USA). Proteins were mixed with NuPAGE LDS Sample Buffer (2x) (Life Technologies Cat # NP0008) at a 1:1 ratio and heated for 5 minutes at 95°C. Equal amounts of proteins were loaded (60 μg) then separated by 10% SDS-polyacrylamide gel and transferred to a nitrocellulose membrane (Bio-Rad, Cat # 1620112, Germany). Membranes were blocked with 5% non-fat milk for 1 hour at room temperature, then incubated with primary antibodies overnight at 4°C. The next day, membranes were washed three times with TBST, and secondary antibodies were added for 1 hour at room temperature. The blots were developed using Clarity Western ECL substrate (Bio-Rad, Cat # 170-5061, USA). The Bio Rad ChemiDoc™ MP Imaging System (Bio-Rad, Cat # 12003154, RRID:SCR_019037) was used for chemiluminescence imaging, and images were analyzed with Image Lab software (version 6.1, Bio-Rad, RRID:SCR_014210). Western blotting images were cropped to separate between PR or ER transfection, and to remove unused wells. The antibodies used in the study were: Anti-ERα (Cell Signaling Technology, Rabbit monoclonal, Cat # 8644S, RRID:AB_2617128, dilution 1:1,000), Anti-PR A/B (Cell Signaling Technology, rabbit monoclonal, Cat # 8757S, RRID:AB_2797144, dilution 1:1,000), Anti-β-actin (Sigma-Aldrich, mouse monoclonal, Cat # A5441, RRID:AB_476744, dilution 1:3,000), Anti-rabbit IgG, HRP-linked (Cell Signaling Technology, goat anti-rabbit, Cat # 7074S, RRID:AB_2099233, dilution 1:2,000) and anti-mouse IgG, HRP-linked (Cell Signaling Technology, horse anti-mouse, Cat # 7076S, RRID:AB_330924, dilution 1:2,000).\n\nThe triple negative MDA-MB-231 cells and the transfected MDA-MB-231 cells were seeded at a density of 3x105. At 80% confluency, the cells were washed with PBS (Sigma-Aldrich, Cat # D8537, Germany) and cultured with recombinant human IFN-γ (R&D Systems, Cat # 285-IF-100, Minneapolis, MN, USA) at a concentration of 100 ng/ml. The cells were then incubated at 37°C and 5% CO2 in NuAire incubator NU-5700 (RRID:SCR_023278) for 24 hours.\n\nGenomic DNA removal was ensured by treating the RNA (from duplicate samples of IFN-γ treated and untreated hormone-positive and TNBC MDA-MB-231 cells) with Turbo DNase (Thermo Fisher Scientific, Cat # AM1907, USA). Next, whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq™ whole transcriptome human gene expression kit (Thermo Fisher Scientific, Cat # A26325, Massachusetts, USA). Briefly, cDNA was synthesized using a SuperScript™ VILO™ cDNA Synthesis kit (Thermo Fisher Scientific, Cat # 11754050, USA) and amplified using Ion AmpliSeq gene expression core panel primers. Amplified products were proceeded for enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads (Beckman Coulter, Cat # A63881, Indianapolis, USA), quantified using an Ion Library TaqMan™ Quantitation Kit (Applied Biosystems, Cat # 4468802, Waltham, USA), further diluted to 100 pM, pooled equally, and amplified using emulsion PCR on Ion OneTouch™ 2 instrument (OT2) (Thermo Fisher, RRID:SCR_023289, Cat # 4474778, USA) and the enrichment was performed on Ion OneTouch™ ES (Thermo Fisher, Cat # 4469495, RRID:SCR_023290, USA).18 Finally, RNA-sequencing was performed on the Ion S5 XL Semiconductor sequencer using the Ion 540-Chip (Life Technologies, Cat # A27765, California, USA).\n\nRNA-Seq data were extracted and proceeded using an in-house pipeline.19 The raw sequencing reads were aligned to the GRCh37/hg19 Human reference genome. The differentially expressed genes (DEGs) were identified between IFN-γ treated and IFN-γ untreated ER-PR transfected and un-transfected MDA-MB-231 cells using the DESeq R/Bioconductor package (Version 4.1.0, RRID:SCR_006442).20 The DEGs were selected based on a log2 fold change ≥ 2 or ≤ -2 and p < 0.05. Shared and unshared DEGs were determined using Venn diagram plots.21 Volcano plots were generated using Enhanced Volcano package in R.22 Biorender (RRID:SCR_018361) was used to put volcano plots and Venn diagrams together, and to show the flowchart summary, Chemix is a freely available alternative software that can be used instead of Biorender.\n\nFunctional enrichment analysis was performed for each DEGs list using Gene Ontology (GO) (RRID:SCR_002811)23,24 and Kyoto Encyclopedia of Genes and Genomes (KEGG) (RRID:SCR_012773) databases.25–27 GO and KEGG terms with a p < 0.05 were mapped as significantly enriched in the DEGs list. The functional clustering and pathways for the identified genes were performed using the Metascape tool (version v3.5.20230101, RRID:SCR_016620).28 In addition, a digital cytometry CIBERSORT (RRID:SCR_016955)29 was applied to the upregulated DEGs genes in IFN-γ treated compared to untreated cells in order to estimate immune cell type abundance in each MDA-MB-231 cell group. The in-silico cell fraction prediction was performed using LM22 reference gene lists for BC.30\n\nThe prognostic impact of top candidate genes was assessed in patients with BC using the Kaplan-Meier Plotter (RRID:SCR_018753),31 which is an online database that can assess the effect of gene expression on the overall survival (OS) of a large cohort of patients with BC.32 Overall, 1,880 cases of patients with BC were used in the Kaplan-Meier plotter analysis from Gene Expression Omnibus (GEO) (RRID:SCR_005012),33 European Genome phenome Archive (EGA) (RRID:SCR_004944),34 and The Cancer Genome Atlas (TCGA) (RRID:SCR_003193).35 The Expression Analysis module of the Gene Expression Profiling Interactive Analysis, version 2 (GEPIA2) (RRID:SCR_018294)36 web server was used to obtain the expression differences of IL-6 and CCL5 tumors and adjacent normal tissues with p-value cutoff = 0.01, log2FC (fold change) cutoff = 1.\n\nThe Kaplan-Meier survival plots with number at risk, hazard ratio (HR), 95% confidence intervals (CI) and log-rank P-values were obtained using the Kaplan-Meier plotter website. For validation, statistical differences between two groups were analyzed using unpaired Student’s t-test. p < 0.05 was considered to be statistically significant.\n\n\nResults\n\nThe differential gene expression analysis showed different transcriptional profiling between hormone receptor-positive and TNBC MDA-MB-231 cells after treatment with IFN-γ. Following transcriptomic data normalization and filtering, a total of 191 and 512 genes were differentially expressed (FC > 2 and p < 0.05) in ER- and PR-positive BC cells after treatment with IFN-γ cytokine compared with untreated cells and in the TNBC cells after treatment with IFN-γ cytokine compared with untreated cells, respectively (Table 1).37\n\nBC, breast cancer; DEGs, differentially expressed genes; ER, estrogen receptor; PR, progesterone receptor.\n\nDEGs were investigated with regard to the expression of the hormone receptor genes (ER and PR). Most genes were found to be unique to the cell type when treated with IFN-γ. Only 29 genes were found to be commonly differentially expressed in both types of cells (Figure 2).\n\nCreated with BioRender.com. IFN-γ, interferon gamma; ER, estrogen receptor; PR, progesterone receptor; DEGs, differentially expressed genes.\n\nFunctional enrichment pathways indicate enhancement of some pathways shared between both types of BC cells regardless of the ER and PR expression. Among these pathways are “hsa04612: antigen processing and presenting”, “GO:0006954: inflammatory response”, “GO:0042157: lipoprotein metabolic process”, and “GO:0031347: regulation of defense response” pathways (Figure 3).\n\nIFN-γ, interferon gamma; DEGs, differentially expressed genes.\n\nIFN-γ induces a modulation of 162 unique DEGs in ER- and PR-positive cells, among them, 130 genes were upregulated, and 32 genes were downregulated. While in the TNBC cells, 483 unique DEGs were identified including 117 upregulated genes and 366 downregulated genes (Figure 2).\n\nFunctional clustering and pathways analysis of the upregulated genes in the hormone-positive and TNBC MDA-MB-231 cells after treatment with IFN-γ revealed differences in genes expression in both types of cells. Both cell types showed a response to IFN-γ by upregulating some functional pathways. These pathways are: “R-HAS-877300: Interferon gamma signaling”, and “R-HAS-1280218: Adaptive immune system” were among the enriched pathways upregulated in ER and PR positive cells. Similarly, the pathways “GO:0071346: cellular response to interferon-gamma”, and “GO:0045824: negative regulation of innate immune response” were among the pathways enriched in TNBC cells (Figure 4).\n\nIFN-γ, interferon gamma.\n\nNotably, the genes involved in the immune system pathway are different between the two cell types, as shown in Table 2. The ER and PR positive cells showed upregulated genes that are involved in the “R-HSA-1280218: adaptive immune system” pathway, including B2M, CD74, CTSS, HLA-B, HLA-DPA1, HLA-DRB1, HLA-E, ICAM1, PPP2R1A, PSMB8, PSMB10, PSME2, TRIM21, ERAP1, SPSB1 and ZNRF1 (Figure 4A, Table 3). While the TNBC cells showed that upregulated genes including CEACAM1, LGALS9, NMI, ISG15, TRAFD1, and SLAMF8 modulate the “GO:0045824: negative regulation of innate immune response” (Figure 4B, Table 3).\n\nBC, breast cancer.\n\nTNBC, triple negative breast cancer; GO, Gene Ontology.\n\nBased on the functional clustering and pathways analysis of the upregulated genes, the ER- and PR-positive cells showed the activation of B2M, GBP3, HLA-B, HLA-DPA1, HLA-DRB1, HLA-E, ICAM1, OAS3, PML, TRIM21, and STAT1 as significantly related genes to “R-HSA-877300: IFN-γ signaling”. The survival analysis using gene expression data on patients with BC was used to verify the prognostic relationship between the aforementioned genes and BC. All genes involved were investigated for OS in BC (Extended data37). Only the genes that showed a significant association with BC prognosis were reported (p-value < 0.05; Figure 5A-D). The highly expressed genes like GBP3 (HR, 0.52; 95% CI, 0.39–0.69; P= 3.0e-6; Figure 5A), HLA-DPA1 (HR, 0.74; 95% CI, 0.61–0.9; P= 0.0024; Figure 5B), HLA-DRB1 (HR, 0.76; 95% CI, 0.63–0.92; P=0.0049; Figure 5C), and HLA-E (HR, 0.75; 95% CI, 0.62–0.91; P=0.0041; Figure 5D) were significantly associated with improved OS in patients with BC.\n\nLikewise, the TNBC cells showed the significant activation of the following genes CCL8, IFI6, ISG15, LGALS9, SP100, CLDN1, and NMI in the”GO:0071346: cellular response to IFN-γ”. Importantly, Kaplan-Meier curve analysis of these genes and the BC patients’ survival analysis showed that the highly expressed genes of IFI6 (HR, 1.29; 95% CI, 1.06–1.56; P= 0.0096; Figure 6A) and ISG15 (HR, 1.23; 95% CI, 1.02-1.49; P= 0.034; Figure 6B) were significantly associated with poor OS in patients with BC. The remaining genes were not significantly associated with the prognosis of BC.\n\nTo understand the role of the genes involved in functional pathways, we explored the genes that most frequently appear in functional pathways. The top five genes of each cell type were selected, IL-6, HLA-DRB1, HLA-E, PSMB10, B2M most frequently appeared in hormone receptor-positive cells pathways, and CCL5, JAK2, LGALS9, TLR3, CEBPB most frequently appeared in TNBC cells pathways. IL-6 was shown to be involved in 160 functional pathways in the hormone receptor-positive cells. CCL5 was shown to be involved in 135 functional pathways of the TNBC cells (Figure 7A and B). These top frequently appearing genes were further assessed across various cancer types. The GEPIA2 database explored IL-6 and CCL5 expression in various cancer types, and BC showed significant differential expression between normal and tumor tissues. IL-6 showed high expression in normal tissue (n= 291) compared with adjacent breast tumor tissue (n= 1,085), while CCL5 gene showed higher expression in breast tumor tissue (n= 1,085) compared with adjacent normal tissues (n= 291) (Figure 7C-F).\n\nNext, we investigated the downregulated genes in both cell types. The downregulated genes of hormone receptor-positive cells were only associated with the “GO:0043414: macromolecule methylation” and “GO:0006091: generation of precursor metabolites and energy” pathways (Figure 8A). While the downregulated genes in TNBC cells were mainly enriched to cell organization and synthesis, including “GO:0000278: mitotic cell cycle”, “R-HSA-1852241: organelle biogenesis and maintenance”, and “GO:0007005: mitochondrion organization” pathways (Figure 8B).\n\nIFN-γ, interferon gamma.\n\nSince BC cells treated with IFN-γ showed differences in functional clustering pathways, we wanted to explore the effect of this cytokine on the abundance of related immune cells. An in-silico analysis of the differential expressed genes of each cell type was performed using CIBERSORT to find the expected abundance of the immune cells. As expected, immune related gene expression in hormone receptor-positive cells was significantly different from that in TNBC cells (Figure 9). In hormone receptor-positive cells, a distinct increase was detected in the adaptive immune gene expression of CD4 naïve T cell (19.5%) and B cells (3.7%), in addition to an increase in neutrophils (32.5%), NK cells (15.2%), M2 (13.4%) eosinophils (10.5%), and an obvious activation on monocytes (4.8%) (Figure 9). However, TNBC cell lines showed an increase mainly in M1 (21.5%), and M2 (28.8%) (Figure 9). Moreover, the TNBC cells do not show the major innate immune cells related genes e.g., dendritic cells (DCs), eosinophils, neutrophils, NK cells, TCR-γδ+ T cells, activated mast cells, and M0 (Figure 9).\n\nDEGs, differentially expressed genes.\n\n\nDiscussion\n\nIFN-γ is known to be highly released from different types of cells, such as the innate immune cells NK cells, and cells of the adaptive immune response, such as CD8+ and CD4+ T cells.38,39 Previously, IFN-γ was believed to have antitumor activity by modulating immune cells in the TME besides its direct pro-apoptotic effect on cancer cells.40 However, recent studies have shown that IFN-γ is a cytokine that has both protumor and antitumor activities.41 It may contribute to tumor progression and metastasis in different ways such as increasing PD-L1 expression on the tumor cell surface leading to tumor escape immune detection.42,43\n\nThe presence or absence of ER/PR is critical to BC cells and forms the basis for its classification.44 MDA-MB231 cells transfected with ER/PR, provide an alternative in vitro model to the MCF7 ER/PR cell line. This transfection allows us to evaluate the specific effect of PR and ER without interference with other biological components.45,46\n\nIn the present study, IFN-γ induced a significant change between the transcriptome of hormone receptor-positive and TNBC MDA-MB-231 cells. It has been reported that the cytokine network, such as IL-6, IL-8, IL-10, IL-17, IL-1β, TNF-α, IFN-γ, and MCP-1, has distinctive functional features on the status of the immune system, and the patient’s prognosis depends on the BC subtype.47,48\n\nIFN-γ induced upregulation in DEGs and enhanced the IFN-γ signaling pathway and adaptive immune system pathway in ER- and PR-positive cells. Our study revealed the upregulation of the adaptive immune pathways, which have a crucial role in normal tissue development and breast tumor suppression. The adaptive immune cells, mainly T lymphocytes, are reduced in number in BC and have been correlated with tumor rejecting capacity.49,50 Immune cells within TME communicate with each other and with tumor cells in order to control tumor growth,51 and an increase in immune cell infiltration is associated with a favorable prognosis of BC.10 This explores the role of IFN-γ in the induction and regulation of adaptive immune responses, which may implicate tumor regression and death in the ER/PR-positive BC cells.\n\nBy contrast, the functional clustering and pathway of the TNBC cells showed a negative regulation of the innate immune response in the IFN-γ treated BC cells. Immunosurveillance is a term referring to innate immune cells’ recognition and rejection of cancer cells at an early stage of tumor initiation. The innate immune cells, mainly NK cells, control the abnormal growth of cancer cells by secreting various cytokines such as IFN-γ.52,53 Our finding indicates that IFN-γ treated TNBC cells attained an immune regulatory phenotype in which negative regulation of the innate immune system was highly enhanced, and this might further promote tumor progression and survival in this type of cell.\n\nThe IFN-γ signaling pathway is highly associated with the OS of patients with BC. The upregulation in GBP3, HLA-DPA1, HLA-DRB1, HLA-E transcriptome predicted a good prognosis. GBP3 participates in host defense against pathogens and transformed cells, and induces apoptosis in cancer cells other than normal cells.54 The expression of HLA, composed of an α chain (DRA) and a β chain (DRB), is highly associated with the activation of antitumor immunity through interactions with T lymphocyte receptors and produces an active antitumor immune response thereby improving the survival and prognosis of patients with cancer.55,56 In various healthy tissues, expression of nonclassical HLA class I molecules (HLA-E and HLA-G), play an essential role in immune surveillance by NK cells.56 Elevated levels of these genes is associated with good prognosis in patients with cancer. Upregulation of these genes by IFN-γ treatment may have a protective role in ER- and PR-positive cells by inducing tumor cell death and activating immune defense.\n\nThe TNBC cell-associated genes with IFN-γ pathway (IFI6, ISG15) showed a negative association with the OS of patients with BC. IFI6, also known as ISG 6-16, is one of the IFN-γ-induced genes that has been reported to have antiapoptotic effects on some types of cancer, including BC.57 ISG15 protein conjugates with many different cellular proteins involved in regulation of protein turnover that might also be associated with tumorigenesis in cancers originating from other tissue types.58,59 Our findings suggest that upregulating these genes in TNBC cells by IFN-γ treatment, may exacerbate tumor progression by upregulating oncogenic genes. We suggest that the role of IFN-γ in patients with TNBC should be considered when customizing treatments. Our analysis of the top frequently appearing genes in functional pathways revealed that IL-6 and CCL5 mostly appeared in hormone-positive and TNBC cells, respectively. IL-6 is a cytokine that is known to be involved in the regulation of tissue repair besides its antitumor cell immune response in TME.60,61 The chemokine CCL5, also called Regulated upon Activation, Normal T Cell Expressed and Presumably Secreted (RANTES), has been associated with cell proliferation, migration, angiogenesis, metastasis, and survival.62,63 Showing IL-6 gene expression in hormonal receptor positive cells, and CCL5 gene expression in TNBC cells may further confirm the opposing role of IFN-γ on hormone receptor and TNBC cells.\n\nIn the present study, IFN-γ induced a significant modulation in immune cell related genes of both BC cell types. The increase in neutrophils, eosinophils, T cell, NK cells, monocyte, and B cells suggest that hormone receptor-positive cells enhance their immune defense against tumor cells when treated with IFN-γ. M1 macrophages display the polarized state that characterizes the antitumor activity, while M2 macrophage display the state that directs to tumor promotion.64,65 M1/M2 ratio defines the survival outcome and destiny of the tumor cells.65,66 By comparison, our results for the TNBC cells showed higher increases in M2 than in M1. The M1/M2 ratio indicates immune suppression and poor tumor prognosis. In addition, the missing gene expression of the important innate immune cells, DC, eosinophils, neutrophils, NK cells, T cell γδ, and activated mast cells contributes to immune escape and tumor progression of this type of cancer, and these results support our earlier findings of the negative regulation of the innate immune pathway.\n\n\nConclusions\n\nIn this study, we applied several bioinformatics analyses on whole transcriptomics data on triple negative and hormone receptor-positive cell lines and validated it using patient data obtained from publicly available sources to explore the effect of ER and PR on tumor progression in the presence of IFN-γ. The results showed that genes upregulated in hormone receptor-positive cells (GBP3, HLA-DPA1, HLA-DRB1, HLA-E, IL6) and TNBC cells (IFI6, ISG15, CCL5) had roles in immune modulation and tumor progression as well as patient prognosis. Upregulated genes in IFN-γ treated hormone receptor-positive BC push tumor cells toward immune activation and patients’ survival, while upregulated genes in IFN-γ treated TNBC induce negative immune responses and thus decrease patients’ overall survival. These results may provide novel insights into the IFN-γ molecular mechanism in BC with respect to the ER/PR/HER2 status and may form the basis to improve personalized therapy for patients with BC with better results and minimal side effects.", "appendix": "Data availability\n\nFigshare: Impact of estrogen and progesterone hormone receptors on the progression of interferon-γ sensitized breast cancer cells. https://doi.org/10.6084/m9.figshare.21814527. 37\n\nThis project contains the following underlying data:\n\n• Data file 1 RawData Transcriptome IFNγ BC (1).xlsx (Whole transcriptomic raw for ER/PR transfected and un-transfected MDA-MB-231 cell line treated with 100 ng/ml IFN-γ)\n\n• Data file 2 Processed IFNγ BC data (1).xlsx (ER/PR transfected and un-transfected MDA-MB-231 cell line treated with 100 ng/ml IFN-γ)\n\n• Data file 4 ER-PR raw data PCR results.xlsx\n\n• Data file 5 ER-PR raw data western blots.docx\n\n• Data file 6 ER-PR raw data western blots.zip\n\nThis project contains the following extended data:\n\n• Data file 3 Extended data.docx (Validation of transfection, overall survival in breast cancer patients, CIBERSORT table).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors would like to thank staff at the University of Sharjah Tissue Bank for their support.\n\n\nReferences\n\nBray F, Ferlay J, Soerjomataram I, et al.: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. 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PubMed Abstract \| Publisher Full Text\n\nDatta J, Fracol M, McMillan MT, et al.: Association of Depressed Anti-HER2 T-Helper Type 1 Response With Recurrence in Patients With Completely Treated HER2-Positive Breast Cancer: Role for Immune Monitoring. JAMA Oncol. 2016; 2(2): 242–246. PubMed Abstract \| Publisher Full Text\n\nGrivennikov SI, Greten FR, Karin M: Immunity, inflammation, and cancer. Cell. 2010; 140(6): 883–899. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDunn GP, Bruce AT, Ikeda H, et al.: Cancer immunoediting: from immunosurveillance to tumor escape. Nat. Immunol. 2002; 3(11): 991–998. PubMed Abstract\n\nMalmberg KJ, Carlsten M, Bjorklund A, et al.: Natural killer cell-mediated immunosurveillance of human cancer. Semin. Immunol. 2017; 31: 20–29. Publisher Full Text\n\nLuo Y, Jin H, Kim JH, et al.: Guanylate-binding proteins induce apoptosis of leukemia cells by regulating MCL-1 and BAK. Oncogenesis. 2021; 10(7): 54. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "204914", "date": "05 Oct 2023", "name": "Aamir Ahmed", "expertise": [ "Reviewer Expertise Cancer", "Signaling pathways in cancer", "Biomarker discovery in epithelial cancers" ], "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 identifies putative differentially expressed genes (DEGs) and aims to associate these with sub-types of breast cancer (BC) overall survival rates (e.g. GBP3,HLA-DPA1, HLA-DRB1, HLA-E, IL6 for hormone-positive and IFI6, ISG15 and CCL5 for triple negative cells). These genes are identified initially from in vitro experiments in breast cancer cell lines (± estrogen or progesterone receptors) treated with interferon gamma (IFN- γ). The pathways and genes thus identified were mined in various publicly available resources (such as GEPIA2 and Kaplan-Meier plotter) to extract survival specific gene signatures for sub-types of BC. The outcomes described in this manuscript are important, apposite and timely. The standard bioinformatic analyses are conducted thoroughly.\nThe paper requires some revision, mostly in the methods and discussion sections. My concerns, stated below, relate to the design of the in vitro assays that precede and serves as a semaphore for in silico analysis to identify the BC sub-type DEGs (steps 8-11 of the experimental methods).\nMajor points:\nA major concern is the design of in vitro experiments. IFN- γ levels in normal individuals in peripheral blood mono-nuclear cells (PBMC) is measured at 0.0154ng/ml (Caldas,A et al BMC Infectious Diseases 5:113, 2005); during disease (e.g. acute visceral leishmaniasis infection) IFN- γ levels increase to about 0.47ng/ml. The serum concentration of IFN- γ in patients with psoriasis is reported to be 0.00191 ng/ml (compared to control group with 0.00091 ng/ml, Kurtovic, NO, Med Arch 72: 410, 2018). The authors use IFN- γ at 100ng/ml to treat MDA-MB-231 cell lines for 24 hours prior to RNA isolation for their sequencing experiments. 100ng/ml is multiple orders of magnitude greater than the reported in vivo IFN- γ values reported in the literature. It will be unrealistic to request a re-run of in vitro experiments, at physiological concentrations, considering that these are only used to provide a starting point for DEGs eventually identified from publicly available human tissue databases. I suggest that the authors acknowledge this vast discrepancy in the physiological IFN- γ levels and those used in their in vitro experiments in the discussion (or alternatively provide a cogent rationale for this in the introduction).\n\nAn evident strength of the manuscript is the identification of gene signature and associating these to overall survival in hormone positive and triple negative cancer from the Kaplan-Meier Plotter resource. The descriptive nature of writing, however, dilutes the impact of this manuscript. For example, there is little to no discussion regarding possible mechanisms through which e.g. GBP3, HLA-DPA1, ISG15 or IFI6 may impact overall survival. This needs to be addressed in the discussion.\n\nMinor concerns:\nThe Bioinformatics analysis section needs to be beefed up and not just rely on reference 19.\n\nFigure legends are non-existent. Each figure must have a detailed legend rather than just a figure heading.\n\nA number of terms require explanation in the context of this study (e.g. Figure 9 In silico deconvolution). The authors should also discuss the results from Figure 9 in detail as these are germane to the proposed aims of this study.\nExplanation for questions in the peer review form:\nIs the study design appropriate and is the work technically sound?\nPartly: The work is technically sound, however, the use of supra-physiological in vitro IFN- γ concentration is a concern. Please see point 1 above.\n\nAre sufficient details of methods and analysis provided to allow replication by others? Please see ‘minor concerns’ 1 and 2 for this response.\n\nAre all the source data underlying the results available to ensure full reproducibility? It is not clear if your journal requires all raw data for sequencing experiments to be deposited into a repository or if the authors have made such a deposit?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "253103", "date": "16 Apr 2024", "name": "Wenbin Zhou", "expertise": [ "Reviewer Expertise sc RNA-seq" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 RNA sequencing analysis of human triple-negative breast cancer (TNBC) and ER+PR+ breast cancer cell lines before and after stimulation with IFN-γ. The authors observed differential gene expression in TNBC and ER/PR-positive breast cancer cells following IFN-γ stimulation, with enrichment in distinct immune-related pathways. Additionally, the authors suggest that some of the differentially expressed genes induced by IFN-γ stimulation may be associated with patient prognosis. 1. Figure 2 illustrates common differentially expressed genes in the two cell lines. It is recommended to clarify whether there are differences in the direction and magnitude of changes in these common differentially expressed genes. Furthermore, it is advisable to explain the significance of the enrichment pathways shared by these genes. 2. It is suggested that the cell lines corresponding to Figures A and B should be clearly labeled in Figure 4 3. The immune-related pathways enriched in the two cell lines are not identical, indicating differences in the genes along these pathways. Is Table 2 intended to demonstrate the different immune-related differentially expressed genes induced by IFN stimulation in the two cell lines? Given that this study only sequenced tumor cells, the authors are encouraged to explain the role of immune-related differentially expressed genes in tumor cells. 4. Tumor cells are cultured in vitro and cannot form a tumor microenvironment. CIBERSORT can not account for the degree of immune infiltration in the cell line.\n\nIs the work 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": [] }, { "id": "258753", "date": "17 Apr 2024", "name": "Claudia Lanari", "expertise": [ "Reviewer Expertise Expertise: breast cancer models", "hormone receptors. Not an expert in the bioinformatic 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\nIn this study, the authors modify the MDA-MB-231 triple-negative breast cancer cells to express ERalpha and PR isoform B and compare the transcriptomics of these cells incubated with interferon ϒ as compared to wt cells in similar experimental conditions. The authors aim to explain why interferon ϒ is on certain occasions protumor genic, and in others anti tumorigenic.\nComments: 1) Progesterone receptor-positive cells express mainly two PR isoforms, PRA and PRB; the former of 95 kDa and the latter 115 KDa in human tissues. In the WB only one isoform of 105 KDa is shown. According to the paper cited in the data sheet, Plasmid #89130 corresponds to PRB, and a band at 115 kDa should have been observed. Why the band has a MW of 105Kda? The biology of cells expressing PRB or PRA differs, so the authors must mention this in their study. They are working with PRB+ cells, not with PR-positive cells. Human breast cancers usually have an excess of one isoform for the other. 2) The addition of hormone receptors to a triple negative cell line does not convert the cell line into a luminal cell line, is just a model. To increase the robustness of the data the authors should use a luminal cell line and silence ER and PR expression and compare as a proof of principle if there is agreement with their data, or at least use more than one triple negative cell line. 3)No comparisons are made between untreated cells. Since cells expressing hormone receptors usually grow more slowly than those lacking receptors, many genes differentially expressed by both cell types might be masking differences observed in interferon-treated cells. This should be included/ discussed. 4) In the introduction the concept that most breast cancers are cold tumors should be emphasized. 5)Why are empty vector plasmids not used as controls? 6) Fig 2: The Figure Legend should clarify and explain all graphs shown, i.e. Top left: Volcano plot showing…. This applies to other Figures 7) Is Table 1 necessary? Is the information in Table 1 included in Figure 2? 8) Table 2, has the same info as the text. 9) To predict the immune microenvironment by studying individual gene expression in this model seems ambitious considering that CIBERSORT is regarded as “An alternative approach is to acquire aggregative high dimensional data from cellular mixtures and to subsequently infer the cellular components computationally. We recently described CIBERSORT, a versatile computational method for quantifying cell fractions from bulk tissue gene expression profiles (GEPs).\" The authors mention in the discussion “In the present study, IFN-γ induced a significant modulation in immune cell-related genes of both BC cell types. The increase in neutrophils, eosinophils, T cells, NK cells, monocytes, and B cells suggest that hormone receptor-positive cells enhance their immune defense against tumor cells when treated with IFN-γ”. They did not show this. They are inferring this which is completely different. 10) Did the authors use Graphpad or the alternative programs mentioned in the text. 11) Did the authors use Biorender of the free alternative mentioned in the text? 12) In Kaplan graphs, authors evaluated the genes separately, why they did not analyze signatures? In addition, the genes in the \"hormone receptor positive cells\" are analyzed using the whole database. Why not using only the luminal cases?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1117
https://f1000research.com/articles/12-1116/v1	08 Sep 23	{ "type": "Review", "title": "Biodesulfurization of Fossil Fuels: Analysis and Prospective", "authors": [ "Wisam Mohammed Kareem Al-Khazaali", "Seyed Ahmad Ataei", "Saeed Khesareh", "Seyed Ahmad Ataei", "Saeed Khesareh" ], "abstract": "Biodesulfurization (BDS) of fossil fuels is a promising method for treating the high content of sulfur in crude oils and their derivatives in the future, attributed to its environmental-friendly nature and the technical efficient ability to desulfurize the organosulfur compounds recalcitrant on other techniques. It was found that the bioreaction rate depends on the treated fluid, targeting sulfur compounds, and the microorganism applied. Also, many studies investigated the operation conditions, specificity, and biocatalysts modification to develop BDS efficiency. Furthermore, mathematical kinetics models were formulated to represent the process. In this review, the previous studies are analyzed and discussed. This review article is characterized by a clear picture of all BDS's experimental, industrial, procedural, theoretical, and hypothetical points.", "keywords": [ "Biodesulfurization", "aerobic", "anaerobic", "recalcitrant organosulfur compounds." ], "content": "1. Introduction\n\nFossil fuel (FF) is a crucial source of energy and power in numerous industries and aspects of daily life. However, to ensure Health, Safety, and Environmental (HSE) protection, it must adhere to relevant standards before use, including the treatment of sulfur compounds. Fossil fuels come in various forms, such as coal, crude oil, tar, petroleum fractions, shale oil, and sands. Regulations for HSE, quantity assurance, and quality control (QQHSSE) are based on specific criteria, including:\n\n• The technical quality of crude oil is determined by its specifications, including the American Petroleum Institute (API) density, viscosity, and combustion heat value. These specifications can be influenced by the presence of organic sulfur compounds in refineries, as highlighted by various studies (Adlakha et al., 2016; Bergh, 2012; Sadare et al., 2017; Alves et al., 2015).\n\n• The sustainable quantity of crude oil is indirectly influenced by the presence of sulfur, which can limit or reduce its marketability due to its negative impact on QQHSSE criteria. As a result, many efforts are being made towards clean energy, which has led to a commitment to meeting quality standards in various regions.\n\n• The health impact of sulfur is significant, as sulfur dioxide emissions can lead to safety hazards, corrosion, and environmental leaks that can cause heart disease, asthma, and respiratory ailments, as evidenced by various studies (Sadare et al., 2017; Srivastava, 2012). Hydrogen sulfide (H2S) is another hazardous sulfur compound that can cause acute toxicity, leading to fatalities in natural settings and workplaces. Exposure to H2S can also result in loss of consciousness, paralysis, nervous system disorders, cardiovascular disorders, ocular disorders, gastrointestinal disorders, and even death, as highlighted by Rashidi et al. (2015).\n\n• The safety implications of sulfur compounds are significant, as their release into the environment can lead to pollution, acid rain, and damage to buildings and forests, as noted by Sadare et al. (2017). Additionally, sulfur compounds can poison the catalytic converters in automotive engines, leading to premature failure and reduced efficiency, as highlighted by Sadare et al. (2017) and Bergh (2012). The presence of sulfur in liquid fuels can also harm vehicles and lower the efficiency of catalytic converters, as noted by Sadare et al. (2017) and Srivastava (2012). Furthermore, sulfur can cause corrosion of pipelines, pumps, fittings, and refining equipment, as noted by Adlakha et al. (2016). The poisoning or deactivation of catalysts used in refining is another concern, as higher levels of sulfur in petroleum distillates can lead to the deactivation of catalysts by poisoning the fluid catalytic cracking (FCC) and hydrocracking processes that convert heavy distillates to lighter ones, as highlighted by Sadare et al. (2017).\n\n• Environment: The combustion of fossil fuels can result in the release of harmful components such as SOx, NOx, CO2, and H2S, which can have serious environmental consequences. These emissions can cause acid rain, acid deposition, and severe air pollution, which can be detrimental to agriculture, human health, and wildlife (Chen et al., 2019a; Sadare et al., 2017; Srivastava, 2012; Ansari, 2017; Pacheco et al., 2019).\n\n• As a result of these concerns and in order to implement risk control measures, the Clean Air Act of 1964 was introduced, with subsequent amendments in 1990 and 1999. These laws were strengthened with even more stringent requirements aimed at further reducing the quantity of sulfur released into the air. Currently, the U.S. Environmental Protection Agency (EPA) has revised the sulfur standards to the following levels:\n\n• The current standard of 500 ppmw for diesel fuel was replaced with a stricter requirement of 15 ppmw, which became effective in mid-2006.\n\n• The standard for reformulated gasoline has been revised to lower the limit from 300 ppmw to 80 ppmw, with a yearly average not exceeding 10 ppm, effective from January 1, 2004.\n\nSimilarly, the EU has also implemented similar modifications by setting a sulfur limit of 10 ppmw for diesel fuels and gasoline in 2005 to address these adverse effects. In order to mitigate these effects, environmental agencies in various countries around the world have imposed more stringent legislative provisions on the total sulfur content of oil (Chen et al., 2018, 2019a, 2019b).\n\nThis review provides a more comprehensive analysis of modern chemicals and biotechnology compared to previous review papers. Additionally, the study offers a significant insight into the modeling and optimization of biodesulfurization.\n\n\n2. Desulfurization methods\n\nThere exist various treatment methods that can be classified into three categories: physical, chemical, or biological. These methods include lab or industrial techniques, such as adsorptive desulfurization (ADS) (Akhmadullin et al., 2012; Al-Otaibi., 2013; Dantas et al., 2014; Mujahid et al., 2020; Sadare et al., 2017), alkylation-based desulfurization, microbial or bacterial desulfurization (BDS) (Chen et al., 2019), catalytic reaction treatment (Akhmadullin et al., 2012; Jarullah, 2012), sodium metal reaction (Chavan et al., 2012), Caustic Washing Method for demercaptanization and H2S removal, Chlorinolysis-based desulfurization, Extraction (desulfurization by extraction, EDS) (Heidari et al., 2013; Qader et al., 2021), dry gas desulfurization, hydrodesulfurization (HDS), oxidative desulfurization (ODS) (Sadare et al., 2017), and supercritical water-based desulfurization (SWD) (Siddiqui and Ahmed, 2016).\n\nCompared to other methods that are not yet commercialized, BDS is capable of removing refractory heterocyclic compounds in crude oil to achieve ultra-low sulfur diesel (ULSD) with high efficiency and at an ultra-low cost (Malani et al., 2021). Undoubtedly, BDS is suitable for desulfurizing heavy oils, such as shale oils, which have higher concentrations of thiophene (Mohebali and Ball, 2016; Pacheco et al., 2019), making it a promising method for commercialization. Moreover, it is more efficient and cost-effective than HDS.\n\nHarsh reaction conditions are required for the hydrodesulfurization (HDS) process to remove certain recalcitrant sulfur-containing compounds like alkylated dibenzothiophenes (DBTs), which can lead to fuel degradation and reduced quality. In contrast, bacterial desulfurization (BDS) has shown high efficiency and low cost for ultra-low sulfur diesel (ULSD) production and is a promising alternative to HDS. Therefore, several studies have been conducted to facilitate the industrial application of BDS due to its advantages over HDS (Chen et al., 2019b; Mohebali and Ball, 2016; Sadare et al., 2017).\n\nSome examples of combined desulfurization methods are BDS-ODS-EDS (Duissenov, 2013), EDS-HDT (Hamad et al., 2013), OEDS (oxidation extraction desulfurization) (Awad, 2015; Jiang et al., 2018; Sadare et al., 2017), and the microwave catalytic hydrogenation process (Duissenov, 2013; El-Gendy et al., 2014).\n\n\n3. Susceptibility of treated oils and biodesulfurizers\n\nBDS is capable of treating various pretreated crude oils and its derivatives, including LPG, gasoline, jet fuel, kerosene, fuel oil, and gas oil. HCS may be present in these fractions or the entire crude oil, including alkyl sulfides (thioesters), carbon bisulfide, disulfides, hydro thiophene, mercaptans (thiol “alkyl hydrosulphide” and thiophenol), thiophenes, thiophane, thiolates, sulfides (non-cyclic sulfides, cyclic sulfides), sulfoxides, sulfones, and sulfonic acid.\n\nFew studies and patents have been conducted on the application of Aspergillus flavus, Achromobacter Spp., Leptospirillum Spp., Pseudomonas Spp., Sulfolobus Spp., Thiobacillus Spp., Rhodococcus Spp., Sphingomonas subarctica, Bacillus Spp., Desulfovibrio desulfuricans, Pyrococcus Spp., Desulfomicrobium scambium, Desulfovibrio longreachii, or Pantoea agglomerans for the desulfurization of whole crude oil under aerobic or anaerobic conditions (Adegunlola et al., 2012; Gunam et al., 2013; Yang et al., 2016). The advantage of BDS for the desulfurization of whole crude oil is that it can reduce the cost of the desulfurization treatment in refineries (El-Gendy and Nassar, 2018; Al-Jailawi et al., 2015).\n\nIn addition, microorganisms such as Mycobacterium goodii, Pseudomonas Spp., Gordonia Spp., Rhodococcus Spp., Mycobacterium phlei, Paenibacillus Spp., Rhodococcus globerulus, and Nocardia Spp. have also been used for BDS treatment of gas oil, gasoline, petro-diesel fuels, petroleum wastes, fuel oil, and cracked stocks (El-Gendy and Nassar, 2018; Li and Jiang, 2013; Murarka and Srivastava, 2020; Nassar et al., 2021a).\n\nIn addition, model compounds representing the recalcitrant HCS in fossil fuels can be used to study the efficiency of BDS. These compounds can be in the form of pure or mixture solutions such as B.T., DBT, DBTO2, M DBTSO2, MgSO4, BNT, DBS, 2,8 DMDBT, 2,6 DNDBT, DMDBT, thianthrene, and dibenzyl sulfide (Alejandro et al., 2014; Boshagh et al., 2014; Bordoloi et al., 2014; Jiang et al., 2014; Kawaguchi et al., 2012; Nassar et al., 2013; Sohrabi et al., 2012; Zhang et al., 2013). It is worth noting that microorganisms used for BDS on water or coal could also be effective for crude oil applications (Feng et al., 2018). A recent study conducted in 2022 by Al-Kazaali (Al-Kazaali and Ataei, 2022) investigated the BDS of heavy sour crude oil using various microorganisms and media. Table 1 summarizes the recent research on BDS application on various fractions of crude oil using different microorganisms.\n\nDesulfurizing microorganisms can be classified based on their air requirement (Raheb, 2016) into the following categories:\n\n• Aerobic conditions\n\n• Anaerobic conditions\n\n• Favored anaerobic\n\nThe reaction mixture for biodesulfurization contains the fluid to be treated, which could be crude oil, one of its derivatives, or model compounds of the recalcitrant HCS such as benzothiophene (BT) or DBT. This fluid is mixed with the main nutrient medium, trace element solution, and vitamin solution. The microorganism is then added to this reaction mixture. The equipment used for BDS can be either a simple incubator or an airlift reactor.\n\nRhodococcus strains have been widely used in BDS to desulfurize various fractions, including pure DBT and its alkylated derivatives such as 4,6-DB-DBT and 4-HDBT, as well as light gas oil by Sphingomonas subarctica T7b (Mohamed et al., 2015). Other microorganisms that have been applied in BDS for real fluids and model compounds include Bacillus strains such as subtilis DSMZ 3256, Gordonia strains such as IITR 100 and D. alkanivorans strain 1B, Klebsiella sp. 13T, Mycobacterium goodii X7B, Pseudomonas strains such as P. delafieldii R-8, P. aeruginosa, and P. putida CECT5279, Paenibacillus validus strain PD2, and Stachybotrys sp. (AL-Faraas et al., 2015; Boshagh et al., 2014; Bhatia and Sharma, 2012; Chauhan et al., 2015; Derikvand and Etemadifar, 2015). Moreover, the BDS of TH, BTH, or DBT by sulfur-reducing bacteria (SRB) has been studied, as well as coal and pyrite by Theobacillus ferroxidans and Ascidians Spp. Brierley (Rossi, 2014).\n\nAnaerobic BDS has been reported for crude oil and its distillates using microorganisms such as Desulfovibrio desulfuricans M6 and extreme thermophile Pyrococcus furiosus. In addition, BDS of thiophene, benzothiophene, and benzothiophene were detected in anaerobic mixed microbial communities of SRB from three Russian oilfields. These communities used reducing processes and produced sulfide-containing hydrogen, lactate, and ethanol as potential electron donors. The conversion of DBT to biphenyl was observed, but HC products from BTH and TH desulfurization remained undetected. Further enrichment of thiophene as the only electron acceptor led to the disappearance of conversion activity, and homo-acetogenic bacteria were abundantly present. Attempts were made to isolate sulfide-producing bacteria to attain stable conversions of THs, but the activity remained low, and homo-acetogenesis was dominant. However, the rate of anaerobic BDS is low, which prevents commercialization.\n\nMany aerobic microorganisms have been studied for crude oil BDS, including Pantoea agglomerans D23W3 and Klebsiella sp. 13T. Additionally, biotreatment can be classified based on the temperature conditions into thermophilic and mesophilic microorganisms.\n\n\n4. Biodesulfurization performance\n\nThere are many factors that can affect the efficiency of BDS treatment. Physical factors include operation conditions, such as pressure, temperature, time, and mixing rate. Chemical factors include the medium used to create an appropriate environment for the microorganisms. Biological factors are represented by the presence and concentration of the added microorganisms, which can be either thermophilic or mesophilic, such as Paenibacillus Spp. and Rhodococcus erythropolis, respectively. Microorganisms can also be used under either aerobic or anaerobic conditions, such as Gordonia IITR 100 and Desulfovibrio desulfuricans M6, respectively. Moreover, microorganisms can be used in different forms, including pure or single microorganisms, multiple bacterial bio-mixtures with known presence ratios, and isolated colonies. It is important to note that certain bacterial isolates, such as Rhodococcus Spp., have shown a particular ability to attack heterocyclic HCSs and desulfurize derivatives of thiophene found in petroleum.\n\nGiven this objective, and given that the physical and chemical factors serve to support the biological factors, the biological factors can be considered as the primary treatment agents, and the process is referred to as biotreatment, or BDS. As a result, the BDS treatment is carried out under the influence of biotreaters.\n\nAnother important factor to consider in BDS treatment is aeration. Aerobic microorganisms depend on the presence of oxygen for their growth and metabolism, such as Arthrobacter simplex, Acidithiobacillus Spp., and Rhodococcus Spp., while anaerobic microorganisms can survive in the absence of oxygen, such as SRB and Desulfovibrio desulfuricans M6.\n\nThe efficiency of BDS is affected by various factors such as the type of microorganism used, the level of biopurity (septic, semi-septic, or aseptic), and the environmental conditions (quantity and types of nutrients available). The differences in the ratio of sources of carbon (C), nitrogen (N), and phosphorus (P) can significantly impact the efficiency of crude oil desulfurization as they affect the growth and treatment of microorganisms. The optimal ratio of carbohydrates/nitrates/phosphates in the microorganism strain and cell volume should be considered to maximize the desulfurization efficiency.\n\nThe efficiency of BDS varies depending on the microorganism used, the biopurity status, and the environmental status. The efficiency can also be affected by the specificity of microorganisms towards different types of HCS present in fossil fuels, as well as the competition for available sources of sulfur compounds. Multiple substrates can also decrease efficiency compared to a single substrate. Microorganisms have different efficiencies for desulfurizing crude oil and its derivatives due to the presence of various HCS in different fractions. However, the pure rate of BDS is generally low. To increase the bioreaction rate, electrokinetic or sonochemical fields can be used (Awadh et al., 2020; Chauhan et al., 2015; Gunam et al., 2021b; Ismail et al., 2016; Shahaby and Essam-El-din, 2017; Boshagh et al., 2014).\n\n\n5. Isolation and identification of microorganisms\n\nMicroorganisms can be prepared and identified using various techniques. They can be isolated from soil contaminated with hydrocarbon fuel, the fuel itself, or through the cultivation of pure microorganisms obtained from culture collections such as ATCC and PTCC. Fermentation processes can then be used to cultivate the microorganisms.\n\nThe microorganisms were isolated by inoculating the samples onto suitable culture media and incubated under appropriate conditions in a shaker incubator. For the bacterial mixture, a suitable medium containing distilled water, microorganism seeds, a source of carbon and energy, and sulfur for adaptation was used. The growth environment for each isolate typically includes sources of energy such as carbon or iron sources, nitrogen, metals, and vitamins. Rhodococcus strains, such as R. erythropolis, have been isolated from contaminated soil using basal salts or sulfur-free medium (Jarullah, 2012). Other isolates, such as Gordonia sp., Noocaria sp., Pantoea agglomerans, Pseudomonas delafieldii, Pseudomonas aeruginosa, SRB, and Sphingomonas subarctica, have also been prepared and studied (Chen et al., 2019a, 2019b; Gunam et al., 2021a, 2021b; Saeed et al., 2022).\n\nThere are various methods available for the identification of microorganisms based on their physiological, chemotaxonomical, chemical, and biochemical properties. Gram staining is one such method that distinguishes between gram-negative and gram-positive bacteria, while other characteristics such as metabolic types, oxygen requirements, and motility can also be used for classification. For instance, Rhodococcus Spp. can be identified based on their mycolic acid, DAP acid, and cell wall sugar composition, as well as their menaquinone profile. Other methods such as fatty acid analysis, 16S rRNA gene sequencing, and PCR amplification can also be employed for microbial identification, as exemplified by studies on Rhodococcus erythropolis and Gordonia Spp. (Morales and Le Borgne, 2017; Bergey’s manual of systematic bacteriology).\n\nOther resources for microbial identification include the Deutsche Sammlung von Microorganismen und Zellkulturen GmbH (DSMZ). In some cases, techniques such as electroporation can be used to improve the genetic manipulation of microorganisms, such as the genus Gordonia.\n\n\n6. Experimental developments technics\n\nThe studies aimed to target the treatment of whole crude oil by modeling various compounds as single or mixtures of hydrocarbons (HC) and heterocyclic sulfur compounds (HCS) to represent the required treatment crude and target, especially to treat the recalcitrant HCS on hydrodesulfurization (HDS) and oxidative desulfurization (ODS).\n\nStudies have focused on using biocatalysts or biotreaters as a means of treating crude oil, with a particular emphasis on targeting the recalcitrant HCS on HDS and ODS. Various improvements have been reported, including the use of recombinant strains, DNA (primers, operons, enzymes, and promoters), non-cell biocatalysts (monooxygenases, oxidases, and peroxidases), thermophilic enzymes, increasing the expression of key enzymes, expression of desulfurization enzymes in heterologous hosts, alternate cells for the expression of dsz genes, coexpression of dsz genes (dsz, tds, mds, sox), increasing the number of desulfurization genes present, changes in the dsz operon’s gene order, the addition of flavin reductase, modifications to the dsz operon’s promoter, rearrangements of the dsz gene cluster, alterations to translational sequences, and the use of multiple strains or wild strains of some microorganisms. These changes have been reported in various studies (Boniek et al., 2015; Calzada et al., 2011; Chauhan et al., 2015; El-Gendy and Nassar, 2018; Kawaguchi et al., 2012; Kilbane and Star, 2016; Li et al., 2019; Malani et al., 2021; Mohebali and Ball, 2016; Nazari et al., 2017; Yaqoub, 2013; Martinez et al., 2016).\n\nModifying the expression of enzymes or the genes involved in the process can lead to biostability, which can increase the likelihood of commercialization (Nazari et al., 2017). Modifying the enzymes involved in the pathway can also lead to the development of a more efficient and effective treatment process (Raheb et al., 2011).\n\nThe efficiency of BDS can be affected by the reactor type, such as a stirred tank reactor, airlift reactor, or bubble column bioreactor, as well as the reactor size and geometry, which can be related to the flask or bioreactor. Several studies have reported on these factors, including Chen et al. (2018), Malani et al. (2021), Martínez et al. (2016), Prasoulas et al. (2021), and Zhang et al. (2013). Amin et al. (2013) designed two vertical rotating immobilized cell reactors (VRICR) and applied Bacillus subtilis BDCC-USA-3 and Rhodococcus erythropolis ATCC 53868 with bio-emulsifier in BDS of DBT.\n\nProcess design and scale-up are crucial aspects of BDS. The process package typically involves a microorganism generator or fermenter for the vegetation step, a bioreactor for the multi-stage or series process, separation of O/W/microorganism and precipitation of sulfates using lime or salts, biocatalyst recycling, and residual oil purification units (Mohebali and Ball, 2016; Nazari et al., 2017; Speight and El-Gendy, 2017). BDS can be intensified by using various physical, chemical, and biochemical methods, such as ultrasonic irradiation (sonication) as a stirrer (Tang et al., 2013), the application of electricity (Malani et al., 2021; Yi et al., 2019), and a combination of units, such as microwave-catalytic hydrogenation, BDS-ODS-RA, and Ads-BDS (Duissenov, 2013; Mohebali and Ball, 2016). Additionally, coupling BDS with other treatment methods, such as bio-hydrotreater or adsorption, can lead to better efficiency.\n\nEnvironmental factors play an important role in biodesulfurization (BDS). The selection of an appropriate medium composition is crucial, with water being the most commonly used basis for microorganism growth. The medium should be tailored to the specific requirements of the microorganism, with sources of carbon, energy, and sulfur chosen based on their metabolic needs (Duissenov, 2013; Pacheco et al., 2019). One way to enhance BDS is by controlling mass transfer limitation of oxygen and hydrogen sulfide (Mohebali and Ball, 2016), as well as reaction rate and pathways through the use of emulsifiers (Duissenov, 2013; Li and Jiang, 2013; Karimi et al., 2017; Jiang et al., 2014; Malani et al., 2021; Mohebali and Ball, 2016; Martínez et al., 2016; Martinez et al., 2015; Rocha e Silva et al., 2017). Immobilization techniques, such as using alginate beads or lignin nanoparticles, can also improve BDS efficiency (Amin, 2011; Capecchi et al., 2020; Gunam et al., 2013; Gunam et al., 2021a, 2021b; Nassar et al., 2021a, 2021b; Silva et al., 2020). Chemical catalysts and host improvers have also been used to enhance BDS (Malani et al., 2021; Silva et al., 2020; Nazari et al., 2017; Sousa et al., 2016). In addition, diagnostic GFP fusions can be employed to improve pathway efficiency.\n\nOptimization studies in BDS often focus on identifying the best pre-treatment methods, such as isolation techniques or desulfurization conditions. For mixtures, optimization involves determining the operating conditions of BDS to achieve the desired selectivity, while for pure substrates or lumped mixtures, the aim is to determine the availability or specificity of the microorganism. Intensification can also be optimized by defining a suitable range. Several studies have investigated optimization in BDS, including Awadh et al. (2020), Boniek et al. (2015), Chen et al. (2019b), Chen et al. (2021), and Chauhan et al. (2015).\n\nOne of the main objectives in biodesulfurization research is to understand the preferential attraction of each microorganism to the different types of HCS, both under aerobic and anaerobic conditions (Awadh et al., 2020; Mohebali and Ball, 2016). This information can be used to optimize the selection of microorganisms for specific HCS desulfurization processes. Table 2 provides an overview of the most significant biotechnology techniques for desulfurization of hydrocarbon fuel fractions.\n\n\n7. Theoretical development methods\n\nTheoretical development involves both mathematical modeling and statistical optimization of the process to simulate the treatment phenomena and achieve higher quality and lower costs, respectively.\n\nMicroorganisms have various pathways for oxidative or reductive cleavage of C-S or C-C bonds, as shown in Table 3. However, it is advisable to selectively remove the sulfur atom from the hydrocarbon (HC) structure (such as DBT) through the 4S-pathway while retaining its HC skeleton and fuel value. This produces non-toxic or less toxic compounds such as 2-HBP, 2,2′-bihydroxybiphenyl, 2-methoxybiphenyl, and 2,2′-dimethoxy-1,1′-biphenyl, which are divided into the H.C. phase (i.e., the fuel) while the sulfur is eliminated as inorganic sulfate in the aqueous phase containing the biocatalyst (Bhatia and Sharma, 2012; Bordoloi et al., 2014; El-Gendy and Nassar, 2018; Hirschler et al., 2021; Kilbane and Star, 2016; Malani et al., 2021; Mohebali and Ball, 2016).\n\nVan Afferden demonstrated the differences between BDS and biodegradation (BDG) (Van Afferden et al., 1990). The Konami kinetic model’s biodegradation mechanism can be compared to BDS, as illustrated in Figure 1. Some strains can be used in BDS, while others in BDG of oils (Bahmani et al., 2018; Hamidi et al., 2021a,b).\n\nThe 4S pathway for biodesulfurization can be represented by the following set of equations:\n\n1- DibenzothiopheneDBT+ATP+H2O→DBTmonooxygenase→DBTsulfone+AMP+PPi\n\n2- DBTsulfone→desulfinase→2‐hydroxybiphenylHBP+SO42−\n\n3- HBP+NADH+H+→HBPdioxygenase→2′‐hydroxybiphenyl‐2‐sulfinateHBPS\n\n4- HBPS+H2O→HBPS sulfatase→biphenyl‐2‐sulfinateBPS+HSO4−\n\nOn the other hand, the Kodama pathway for biodegradation can be represented by the following set of equations:\n\n1- DibenzothiopheneDBT+O2→DBTdioxygenase→DBTsulfone\n\n2- DBTsulfone→desulfinase→2‐hydroxybiphenylHBP+SO42−\n\n3- HBP+O2→HBPdioxygenase‐2‐hydroxy‐2′‐oxobiphenyl‐3‐sulfonateHOBS\n\n4- HOBS+H2O→HOBS sulfatase→2‐hydroxy‐2′‐oxobiphenyl‐3‐sulfonate lactoneHOBL+HSO4−\n\n5- HOBL+H2O→HOBL hydrolase‐2‐hydroxy‐2′‐oxobiphenyl‐3‐carboxylateHOCB\n\n6- HOCB+O2→HOCB dioxygenase‐2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoateHOPDA+CO2\n\n7- HOPDA+H2O→HOPDA hydrolase‐2‐hydroxy‐6‐oxo‐6‐phenylhexa‐2,4‐dienoic acidHOPDA acid\n\nLimited efforts have been made to engineer BDS due to the lack of commercialization (Malani et al., 2021). Various models have been developed to understand the BDS phenomenon, which can be classified based on the pretreated fluid (single or multiple substrates) or the system or phenomena design-based models (Abin-Fuentes et al., 2014; Maass et al., 2015; Zhang et al., 2013). Metabolism-based models (Bhatia and Sharma, 2012; Calzada et al., 2012) can also be used when considering a single substrate. Gross mathematical models, such as Monod, Haldane, or similar models, are commonly used for preliminary evaluations and to compare microbial cultures’ desulfurization efficiencies. These models need to be improved to consider the interaction between competition and inhibition (Dejaloud et al., 2019; Irani et al., 2011). A study by Kareem in 2013 modeled the BDS of real kerosene in a batch reactor (Kareem et al., 2013).\n\n\n8. Qualification for industrialization and commercialization applicability\n\nEfforts to engineer BDS have been limited, as it has not yet been commercialized (Malani et al., 2021). To achieve the required desulfurization rate and efficiency without side effects, both experimental and theoretical development are needed. This includes rapid isolation and bio-identification characterization, as well as reaching high efficiency and rate in thermotolerant conditions using available chemicals such as solvents, and reducing product toxicity. Additionally, reusability and stability of the biocatalyst are important criteria (Alkhalili et al., 2017; El-Gendy and Nassar, 2018). The reaction rate needs to be increased by 500-fold (Malani et al., 2021; Nassar et al., 2016), and minimizing OWR is crucial to reduce separation difficulties. Mathematical models such as Monod, Haldan, or similar models are useful for preliminary evaluation and comparing microbial cultures’ desulfurization efficiencies. However, these models need to consider the interaction between competence and inhibition (Dejaloud et al., 2019; Irani et al., 2011). Kareem (2013) studied the modeling of BDS of real kerosene in a batch reactor.\n\n\n9. Summary of main points\n\n\n\n• Fossil fuels’ sulfur content poses a significant challenge in meeting quality, health, safety, and environmental regulations.\n\n• BDS is a desulfurization process used for removing sulfur from fuels and crude oil.\n\n• The development of microorganism-based bioreactors is crucial for BDS.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbin-Fuentes A, Leung JC, Mohamed MES, et al.: Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system. Biotechnol. Bioeng. 2014; 111(5): 876–884. 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PubMed Abstract \| Publisher Full Text\n\nDerikvand P, Etemadifar Z: Sulfur removal from dibenzothiophene by newly isolated Paenibacillus validus strain PD2 and process optimization in aqueous and biphasic (model-oil) systems. Pol. J. Microbiol. 2015; 64(1): 47–54. Publisher Full Text\n\nDuissenov D: Production and processing of sour crude and natural gas-challenges due to increasing stringent regulations (Master’s thesis, Institutt for petroleumsteknologi og anvendt geofysikk).2013.\n\nEl-Gendy NS, Nassar HMN: Biodesulfurization in petroleum refining. John Wiley & Sons; 2018. Publisher Full Text\n\nEl-Gendy NS, Nassar HN, Abu Amr SS: Factorial design and response surface optimization for enhancing a biodesulfurization process. Pet. Sci. Technol. 2014; 32(14): 1669–1679. Publisher Full Text\n\nFeng S, Lin X, Tong Y, et al.: Biodesulfurization of sulfide wastewater for elemental sulfur recovery by isolated Halothiobacillus neapolitanus in an internal airlift loop reactor. Bioresour. Technol. 2018; 264: 244–252. PubMed Abstract \| Publisher Full Text\n\nGunam IBW, Sitepu A, Antara NS, et al.: Bacterial desulfurization of dibenzothiophene by Pseudomonas sp. strain KWN5 immobilized in alginate beads. Jurnal Teknologi. 2021a; 83(2): 107–115. Publisher Full Text\n\nGunam IBW, Sone T, Asano K: Biodesulfurization of the mixture of dibenzothiophene and its alkylated derivatives by Sphingomonas subarctica T7b. Indian J. Biotechnol. 2021b; 26(3): 122–127. Publisher Full Text\n\nGunam IBW, Yamamura K, Sujaya IN, et al.: Biodesulfurization of dibenzothiophene and its derivatives using resting and immobilized cells of Sphingomonas subarctica T7b. J. Microbiol. Biotechnol. 2013; 23(4): 473–482. PubMed Abstract \| Publisher Full Text\n\nHamad EZ, Al-Shafei EN, Al-Qahtani AS: Desulfurization of whole crude oil by solvent extraction and hydrotreating. 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Publisher Full Text\n\nIrani ZA, Mehrnia MR, Yazdian F, et al.: Analysis of petroleum biodesulfurization in an airlift bioreactor using response surface methodology. Bioresour. Technol. 2011; 102(22): 10585–10591. PubMed Abstract \| Publisher Full Text\n\nIsmail W, El-Sayed WS, Abdul Raheem AS, et al.: Biocatalytic desulfurization capabilities of a mixed culture during non-destructive utilization of recalcitrant organosulfur compounds. Front. Microbiol. 2016; 7: 266. Publisher Full Text\n\nJarullah AT: Kinetic Modelling Simulation and Optimal Operation of Trickle Bed Reactor for Hydrotreating of Crude Oil. 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International Journal of Engineering Science Invention. 2013; 2(4): 61–66.\n\nKarimi E, Jeffryes C, Yazdian F, et al.: DBT desulfurization by decorating Rhodococcus erythropolis IGTS8 using magnetic Fe3O4 nanoparticles in a bioreactor. Eng. Life Sci. 2017; 17(5): 528–535. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKawaguchi H, Kobayashi H, Sato K: Metabolic engineering of hydrophobic Rhodococcus opacus for biodesulfurization in oil–water biphasic reaction mixtures. J. Biosci. Bioeng. 2012; 113(3): 360–366. PubMed Abstract \| Publisher Full Text\n\nKilbane JJ, Star B: Biodesulfurization: A model system for microbial physiology research. World J. Microbiol. Biotechnol. 2016; 32(8): 137. Publisher Full Text\n\nLi L, Liao Y, Luo Y, et al.: Improved efficiency of the desulfurization of oil sulfur compounds in Escherichia coli using a combination of desensitization engineering and DszC overexpression. ACS Synth. Biol. 2019; 8(6): 1441–1451. 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Publisher Full Text\n\nMorales M, Le Borgne S: Protocols for the isolation and preliminary characterization of bacteria for biodesulfurization and biodenitrogenation of petroleum-derived fuels. Hydrocarbon and Lipid Microbiology Protocols: Bioproducts, Biofuels, Biocatalysts and Facilitating Tools. 2017; 201–218. Publisher Full Text\n\nMujahid A, Maryam A, Afzal A, et al.: Molecularly imprinted poly (methyl methacrylate)-nickel sulfide hybrid membranes for adsorptive desulfurization of dibenzothiophene. Sep. Purif. Technol. 2020; 237: 116453. Publisher Full Text\n\nMurarka P, Srivastava P: Biodesulfurization of petroleum wastes. Biovalorisation of Wastes to Renewable Chemicals and Biofuels. Elsevier; 2020; (pp. 165–187).\n\nNassar HN, Abu Amr SS, El-Gendy NS: Biodesulfurization of refractory sulfur compounds in petro-diesel by a novel hydrocarbon tolerable strain Paenibacillus glucanolyticus HN4. Environ. Sci. Pollut. Res. 2021a; 28: 8102–8116. PubMed Abstract \| Publisher Full Text\n\nNassar HN, Ali HR, El-Gendy NS: Waste prosperity: Mandarin (Citrus reticulata) peels inspired SPION for enhancing diesel oil biodesulfurization efficiency by Rhodococcus erythropolis HN2. Fuel. 2021b; 294: 120534. Publisher Full Text\n\nNassar HN, Deriase SF, El-Gendy NS: Modeling the relationship between microbial biomass and total viable count for a new bacterial isolate used in biodesulfurization of petroleum and its fractions. Pet. Sci. Technol. 2016; 34(11-12): 980–985. Publisher Full Text\n\nNassar HN, El-Gendy NS, Mostafa YM, et al.: Desulfurization of dibenzothiophene by a novel strain Brevibacillus invocatus C19 isolated from Egyptian coke. Biosci. Biotechnol. Res. Asia. 2013; 10(1): 29–46. Publisher Full Text\n\nNazari F, Kefayati ME, Raheb J: The study of biological technologies for the removal of sulfur compounds. J. Sci. Islam. Repub. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "205148", "date": "09 Oct 2023", "name": "Shuiquan Chen", "expertise": [ "Reviewer Expertise Biodesulfurization", "bioremediation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article summarizes the main advantages and challenges of BDS, as well as the future research directions. The article points out that BDS is an environmentally friendly, low-cost, and high-efficiency method that can achieve ultra-low sulfur diesel (ULSD) standards, but it still needs to improve the reaction rate, biocatalyst stability and reusability, and engineering and commercialization efforts. I recommend accepting it with the following major changes that can complement the text content:\nSome details need to be modified, such as “B.T., DBT, DBTO2, M DBTSO2, MgSO4, BNT, DBS, 2,8 DMDBT, 2,6 DNDBT, DMDBT, thianthrene, and dibenzyl sulfide ” in page 4.\n\nSome abbreviations are not defined in the article: e.g.: BNT, 4,6-DB-DBT, 4-HDBT, etc. please check and correct them throughout the text.\n\nIt has been more than thirty years since the first biodesulfurization bacterium was discovered, but the biodesulfurization technology has not been industrialized yet. Please summarize the existing problems in detail.\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": "10365", "date": "10 Oct 2023", "name": "Wisam Al-Khazaali", "role": "Author Response", "response": "Thank you for important notes. I am doing the note." }, { "c_id": "11131", "date": "13 Apr 2024", "name": "Wisam Al-Khazaali", "role": "Author Response", "response": "I confirm that I finish these suggestions from reviewer. Thank you for your cooperation." } ] }, { "id": "252874", "date": "21 Mar 2024", "name": "Iqrash Shafiq", "expertise": [ "Reviewer Expertise Desulfurization", "Photocatalysis" ], "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 provided text appears to be an in-depth review article on biodesulfurization (BDS) of fossil fuels. Here's a summary of the key points covered in each section:\nAbstract: The abstract provides an overview of BDS as a promising method for treating sulfur in fossil fuels, highlighting its environmental benefits and technical efficiency. Introduction: This section introduces the importance of fossil fuels, the need for sulfur treatment due to health, safety, and environmental concerns, and the regulations surrounding sulfur content in fuels. Desulfurization methods: Various methods of desulfurization are discussed, including physical, chemical, and biological methods. BDS is emphasized for its efficiency and cost-effectiveness compared to other methods like hydrodesulfurization (HDS). Susceptibility of treated oils and biodesulfurizers: Different microorganisms and their applications in BDS for treating various fractions of crude oil and model compounds are discussed. Biodesulfurization performance: Factors affecting BDS efficiency, such as physical, chemical, and biological factors, are explored. The role of microorganisms, environmental conditions, and biocatalysts in BDS efficiency is highlighted. Experimental developments techniques: This section covers experimental techniques and developments in BDS, including biocatalysts, reactor systems, environmental factors, and optimization studies. Theoretical development methods: Mathematical modeling and theoretical aspects of BDS are discussed, including kinetic mechanisms, metabolic pathways of microorganisms, and mathematical models for simulating the BDS process.\nOverall, the article provides a comprehensive overview of BDS, covering its methods, performance, experimental developments, and theoretical aspects. It highlights the importance of BDS as a promising method for reducing sulfur content in fossil fuels, addressing environmental concerns and regulatory requirements.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "227751", "date": "25 Mar 2024", "name": "Talib M. Albayati", "expertise": [ "Reviewer Expertise Chemical Engineering" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. I have not found comparative study with other studies in this field. 2. Re-write the introduction part so as to give more details and mention the sulfur effect on environment. 3. In introduction give more emphasis to the fact that most of the previous research refers to petroleum products rather than crude oil. 4. The aims of the present work must be more cleared at the end of the introduction part. 5. What is the mechanism of Ionic Liquids aqueous solution for sulfur removal from actual crude oil. 6. The Ionic Liquids aqueous solution surface area is very important. The author must be discussing this point in detail because the surface area is very important factor increasing the removal rate. 7. What is the role of Ionic Liquids aqueous solution? Is it extraction solution or catalytic solution? How we can guess which one is the working? 8. What about the properties of Fuel desulfurization after treatment or removal sulfur? 9. I hope from the author to draw figure explain the relationship between the actual and predict values (Residual plots for the desulfurization). 10. What is the main conclusion from this study? The conclusion must be reduced. 11. Clarify the term \"Sulfur wt %\" (I assume it is the percentage of sulfur in the product oil). 12. I hope from the author of this paper to give more details about optimization method with 3D figure for the result of this 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? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] }, { "id": "241257", "date": "28 Mar 2024", "name": "Jaykumar Bhasarkar", "expertise": [ "Reviewer Expertise Nanomaterials", "Desulfruization of liquid fuels", "sonochemistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 \"Biodesulfurization of Fossil Fuels: Analysis and Prospective\"provide the insight into the biodesulfurization of fossil fuel, however, some modification can improve the quality of the paper. 1. In introduction part, it is recommended to give more information about the overall desulfruization process such as conventional process (hydrodesulfruization). Also it required to give brief about all thee other alternative methods for the desulfurization of fossil fuels. 2.In present manuscript, authors have not mention about the metabolic pathways followed by microorganisms. Therefore, it is essential to provide the metabolic pathway such as 4C pathway and Kodoma pathway with their merits and demerits. 3.Some more literature needs to be added to the present manuscript : [Ref 1,2,3,4] 4.In modeling section, authors are requested to provide more details about the kinetic model and inhibition models of the cell growth and substrate consumption. [refer : Ref 1]. The manuscript is mainly focused on a detailed review on bio desulfurization process. The present manuscript cover good-quality information on biodesulfurization process but it requires to provide merits and demerits of the other desulfurization processes.Therefore, some more alternative technologies need to be addressed in the present manuscript. It is essential to cite more references on alternative methodologies adopted for efficient desulfurization. It is also requested to provide the comparative table for the biodesulfurization process.\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": [] }, { "id": "252876", "date": "08 May 2024", "name": "Jasim I. Humadi", "expertise": [ "Reviewer Expertise Chemical 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\nThe topic of this paper interested. It is observed goodly. However, It should incorporate the following corrections: 1) The abstract must be written more clear about the important highlights in bio desulfurization technology 2) In the introduction, the authors mentioned that the lest ppmw of sulfur is 15 in diesel fuel. What is the reference. The update level for sulfur content based on EPA in zero. 3)The benefits of bio desulfurization over other technologies should be provided in separated section 4)The essential bio catalysts for this technology must be observed clearly 5) The language must be enhanced 6) Add suggested mechanism as a figure based on the previous works 7) The conclusion must be improved. Mention more highlights about the technology\nEnhancement of Desulfurization Process for Light Gas Oil Using New Zinc Oxide Loaded Over Alumina Nanocatalyst\nMathematical model, simulation and scale up of batch reactor used in oxidative desulfurization of kerosene[6],[7],[8].\nF, Mohammed, et.al., 2022(Ref 9) I, Jasim, et.al., 2023 (Ref 10)\nI only recommend the authors to enhance the paper by more new related references. I don't say \"must be\" but I say \"can\".\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? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1116
https://f1000research.com/articles/12-266/v2	26 Jun 23	{ "type": "Research Article", "title": "Seroepidemiology of Hepatitis E virus among the voluntary blood donors in the coastal region of Karnataka, India", "authors": [ "Sangthang S", "Shamee Shastry", "Sudheesh N", "Kiran Chawla", "Mridula Madiyal", "Dhivya Kandasamy", "Sangthang S", "Sudheesh N", "Kiran Chawla", "Mridula Madiyal", "Dhivya Kandasamy" ], "abstract": "Background: Hepatitis E is a fecal orally transmitted disease and an emerging transfusion transmissible infection with potential transfusion safety implications. Hepatitis E Virus screening among blood donors is not routinely done despite the fact that it is endemic in India. As there are very few reports and evidence, the justification for mandating HEV screening among blood donors is still only marginally convincing. Therefore, the present study was carried out to determine the incidence and prevalence of HEV infection among blood donors in Coastal Karnataka, India. Methods: This cross-sectional study was conducted in a tertiary care hospital in Udupi district of Karnataka, India. A total of 1939 blood donors were randomly selected between June 2020 to June 2022 to participate in the study, where anti-HEV IgM antibody screening was performed using HEV IgM ELISA test kit (DiaPro, Italy). Further, a randomly selected 588 and 1620 pooled donor samples were screened for anti-HEV IgG antibodies and HEV RNA, respectively. Results: The overall prevalence of HEV IgM antibodies among study population is found to be 1.39%, with a statistically significant difference between males and females (n=20, 1.18% vs. n=7, 3.07 %; p=0.027). The prevalence of HEV IgG antibodies was 11.39%. Exposure to agriculture, animal husbandry, and poor hand hygiene were significant risk factors for HEV IgG reactivity. Conclusions: Given the high prevalence of HEV viral markers in the study population, routine screening of blood donors for risk factors and implementation of serologic testing in endemic areas may be considered.", "keywords": [ "Transfusion-transmitted infections", "epidemiology", "Hepatitis E virus", "Blood donors", "India" ], "content": "Introduction\n\nHepatitis E virus (HEV) is the most common causative agent of acute viral hepatitis and is self-limiting in most cases. The World Health Organization (WHO) estimates that, every year there are an estimated 20 million HEV infections worldwide, leading to an estimated 3.3 million symptomatic cases of hepatitis E.1 Four reported genotypes of HEV are known to infect humans, of which genotype-1 (HEV1) and genotype-2 (HEV2) infect only humans, whereas genotype-3 (HEV3) and genotype-4 (HEV4) are zoonotic and are transmitted particularly by swine populations and their related meat products.2 To date, HEV1 is the only genotype known to infect humans in India.3 HEV is considered highly endemic in various parts of India and neighbouring countries.4 And, it has caused several outbreaks and epidemics of viral hepatitis in India.5,6 HEV is also one of the emerging infectious diseases associated with blood transfusions. In 2004, the first case of transfusion-transmitted HEV (TT-HEV) infection was reported from Japan, HEV RNA from the recipient and donor were genotype-matched to confirm the transmission of the infection through blood transfusion in this case.7\n\nThe prevalence of HEV in different populations varies, and in recent times, there has been an increasing report of HEV infection among blood donors in developing countries.8–10 Although HEV is endemic in India, there are only a few reports on the prevalence of HEV among blood donors and none from south India. Currently, there are no policies or guidelines for screening for HEV among blood donors in the country. Therefore, it is essential to investigate the burden of the disease and the extent of the threat to blood safety through healthy asymptomatic blood donors, particularly in India.\n\nImportant characteristics that have been reported in developed countries include serological and molecular evidence of TT-HEV, prevalence and risk factors among blood donors, and severity of the infection among immunocompromised patients.11 However, there is little, or no information related to TT-HEV and possible risk factors, common genotype of HEV that is prevalent among healthy blood donors from India.\n\nTherefore, this prospective cross-sectional study was carried out to determine the prevalence of HEV in healthy voluntary blood donors and the potential risk factors for a silent infection. To the best of our knowledge, this is the first study of its kind to examine the incremental risk of exposure to asymptomatic HEV infection among healthy volunteer blood donors in India.\n\n\nMethods\n\nA cross-sectional study was conducted between July 2020 and June 2022 in a blood center of a tertiary care hospital in the coastal belt of Karnataka, India. The center has a yearly collection of approximately 15,000 blood donations, and participants were recruited from this healthy volunteer blood donor pool who were residents of Udupi district, Karnataka. The blood donor participants were from an in-house blood center collection and voluntary blood donation camps held within the district. The study was conducted following the principles of the Helsinki Declaration 2013,12 and approval was obtained from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee (IEC no: 06/2020). Blood donors’ registration numbers were systematically randomized, and every fifth donor number was the pre-determined participant included in the study. However, if the 5th donor did not meet the study's inclusion criteria, the next donor in line was considered for recruitment. Only donors who were eligible for blood donation according to the criteria of the National Blood Transfusion Council (NBTC) and the Drug and Cosmetic Act 1940 of the Government of India were recruited for the study.13,14 Written informed consent was obtained from each participant after counseling, and a pre-validated questionnaire was given to the participants to gather information about the risk of exposure. The questionnaire included details regarding exposure to a high-risk work environment, dietary choices, the source of drinking water, travel history, floods in the locality, and the type of sanitation used by the donor.\n\nScreening for Transfusion Transmitted Infections (TTIs) was done on the samples collected in 4 mL and 6 mL vacutainers from the diversion pouch of the blood collection bag. The samples were centrifuged at 3500 rpm for 5 minutes. An automated Enzyme Linked Immunosorbent Assay instrument (EVOLIS, BioRad, USA) was used for screening the viral markers. The ELISA based test kit for viral markers includes the fourth-generation test kit Genscreen™ Ultra HIV Ag-Ab, Catalogue no. 72388 (Biorad, France), Monolisa™ HBsAg Ultra, Catalogue no. 72348 (Biorad, France) and Monolisa™ Anti-HCV Plus Version 3, Catalogue no. 72341 (Biorad, France) for screening of HIV, HBV, and HCV markers, respectively. Qualisa™ Malaria, Catalogue no. 405010096 (Qualpro Diagnostic, Goa, India) and Carbogen Rapid Plasma Reagin, Catalogue no. 10514100 (RPR) card test (Tulip Diagnostics Pvt Ltd, India) were also routinely used in our blood centre according to the manufacturer's protocol for screening of Malarial parasites and syphilis. Further, the 6 ml vacutainer samples were subjected to a mini pool nucleic acid amplification test (NAT) for TTIs screening with the Roche Cobas® TaqScreen MPX test kit in Roche Cobas® s201 instrument. This NAT test kit can simultaneously detect HIV-1 (group M and O), HIV-2, HBV, and HCV nucleic acid. About 500 μL of plasma was aliquoted from these pilot tubes into 1.5 mL cryotubes for screening HEV.\n\nWe have screened the samples of the study subjects for anti-HEV IgM antibodies to determine the prevalence of HEV among blood donors. Anti-HEV IgM antibodies were screened at the same time as other TTIs. Anti-HEV IgM antibodies were screened as per the manufacturer's instructions for the screening kit used (DiaPro HEV IgM ELISA kit, Diagnostic Bioprobe SRL, Milano, Italy). The manufacturer’s manual claims a diagnostic sensitivity and specificity of greater than 98%. A sample to cut-off ratio (S/CO) above 1 is considered to be reactive. All the samples that were reactive or in the grey zone (S/CO between 0.9 and 1) were repeated in duplicate in the subsequent run for confirmation (as per the standard operating procedure of the deparmtent).\n\nScreening for anti-HEV IgG antibodies was performed to determine the seroprevalence and exposure to HEV in recent or past infections. A total of 571 samples were estimated as the minimum number of samples required to determine the prevalence of HEV IgG with a reference from the previous study and the current study population, with a confidence level of 96% and a 4% margin of error.15 To detect HEV IgG antibodies, we used a DiaPro HEV IgG ELISA test kit (Diagnostic Bioprobe Srl, Milan, Italy). The test kit is CE marked and has 100% sensitivity and specificity as per the manufacturer's manual.\n\nSamples that tested negative for anti-HEV IgM antibodies were randomly selected and grouped into six sample pools. Nucleic acid was manually extracted from the pooled samples with the FavorPrep Viral Nucleic Acid Mini Kit (Favorgen Biotech Corporation, Taiwan) following the manufacturer's protocol. The extracted nucleic acid was screened for the presence of HEV RNA with RT-PCR using the RealStar™ HEV RT-PCR test kit 2.0 (Altona Diagnostic, Hamburg, Germany) in a QuantStudio™ 5 platform (Applied Biosystem, USA) as per manufacturer guidelines.\n\nAll data were primarily documented and stored in a spreadsheet in Microsoft Excel, and they were analyzed using SPSS 20.0 software (IBM, US). Quantitative and qualitative descriptive variables were presented with the mean, median, mode, and frequency of nominal variables. The factors influencing HEV seropositivity were examined using a chi-square test and logistic regression analysis (95% confidence range).\n\n\nResults\n\nA total of 1939 voluntary blood donors were recruited for the study and among them, 1711 (88.2%) were males and 228 (11.8%) were females, with a male-to-female ratio of 7.5:1. Participants include 871 (44.9%) first-time donors and 1068 (55.1%) repeat blood donors. The mean age of donors was 29.6 years (SD ±9.3 years) within a range of 18 to 64 years, and the predominant participants were (53%) between 18 and 28 years old. Table 1 provides an overview of the demographic characteristics of the participants and the results of serological screening for HEV. On routine serological screening tests for TTIs, 7(0.36%), 8(0.41%), 3(0.15%), and 2(0.10%) participants were reactive to HIV, HBV, HCV, and syphilis, respectively. None were reactive on NAT screening, and for malarial antigen.\n\n* Statistically significant, SSLC; senior secondary school, PUC; Pre-University College.\n\nA total of 27 participants were reactive to anti-HEV IgM antibodies, including 20 males and seven females, representing a prevalence of 1.39% in our study population. The prevalence of HEV IgM antibodies in different age groups is shown in Table 1. Except for one donor who was reactive for syphilis in the RPR test, none of the HEV IgM reactive donors were reactive to the other TTI markers.\n\nIrrespective of the anti-HEV IgM status, anti-HEV IgG antibody screening was performed on 588 randomly selected samples, and a total of 67(11.39%) samples were reactive to IgG antibodies. Of the anti-HEV IgG reactive samples, 7 (10.4%) of them were reactive for IgM antibodies as well. In this group, the coexisting HCV and HIV infection was seen in 2 and 4 donors, respectively.\n\nNone of the 270 pools, which included 1620 samples, showed HEV viral RNA.\n\nA pre-validated questionnaire was used to assess epidemiological risk factors among blood donors. The epidemiological features and risk factors are shown in Table 2. None of the participants had a jaundice-like illness in the past year, and there was no statistically significant correlation between any of the risk factors assessed and reactive status for anti-HEV IgM antibodies. A significantly higher number of participants reactive to anti-HEV IgG antibodies were exposed to agricultural or veterinary settings (p<0.05). The positivity of IgG antibodies was significantly higher among participants who did not follow regular handwashing with soap and water before eating food.\n\n\nDiscussion\n\nThe prevalence of anti-HEV IgM and IgG antibodies among blood donors in the study population was 1.39% and 11.39%, respectively. Seven donors were reactive to both anti-IgM and anti IgG HEV antibodies, which may represent the late icteric phase of infection. The prevalence of anti-HEV IgM antibodies is significantly higher in females than in males (1.16% vs. 3.16%; p<0.05). However, there was no significant difference in the prevalence of anti-HEV IgG antibodies between male (54 of 512) and female (13 of 76) participants, this result is in consistent with the study by Tripathy et al., in Pune, India.16\n\nIn India, particularly in south India, there is a paucity of data pertaining to risk factors and HEV infections among the healthy population. As per our knowledge, the present study is the first of its kind on this subject. The prevalence of anti-HEV IgM antibodies in our study (1.39%) is comparatively lower than that mentioned in the study by Gajjar et al., from Gujarat (4.78%) and Shrestha et al., from Nepal (3.0%) but higher than that of the study by Tripathy et al., from Pune, Mumbai (0.20%). The HEV seroprevalence report varies across the Indian subcontinent, although the disease is considered endemic in the region (in Table 3 and Table 4). The anti-HEV IgM prevalence of our study is in accordance with the reports from Poland (1.27%), however, few other international studies report a lower prevalence of anti-HEV IgM (Table 4). None of the pooled samples screened were positive, for HEV RNA and our finding is line with those of Katiyar et al., from Lucknow, India, Al Dossary et al., from Al Khobar, Saudi Arabia and Fu et al., from Yunnan Provinces of China.15,17,18 Additionally, it was noted that none of the countries on the Indian subcontinent had any guidelines for HEV screening blood donors.\n\nNevertheless, Tendulkar et al., (2015, Mumbai) reported a case in which a blood donor self-reported developing jaundice a day after the donation and eventually he was diagnosed to have HEV infection However, the transmission of HEV viremia to the blood recipient was not confirmed.19 Blood donors reactive to HEV must postpone blood donation for 12 months, as per the blood donor selection and deferrals guidelines in India (published in 2017).13 The high endemicity of HEV in the area and the high prevalence of anti-HEV antibodies among blood donors may be the key criteria in deciding the necessity for HEV screening in India.20–22\n\nThe majority of HEV-infected people experience asymptomatic, self-limiting infections or a brief sickness without signs of liver damage. The typical infection has an incubation period of up to 2 to 6 weeks, with a prodrome phase and viremia peaking in the fourth week.23Anti-HEV IgM antibodies begin to increase in the late incubation stage and reach their peak in the middle of the icteric phase, its concentration declines later with the raise in anti-HEV IgG antibodies.24 The presence of anti-HEV IgG antibodies among the anti-HEV IgM positive participants could be an indication of late icteric phase stage of infection.25 Anti-HEV IgG antibodies are detectable for a longer period of time. In our study, there were 61 participants reactive solely to anti-HEV IgG antibodies which indicates either the past infection, or they are in convalescent phase.\n\nThere is a chance of iatrogenic HEV transmission throughout the incubation phase and the prodrome stage since HEV viremia is evident even before an anti-HEV antibody response and lasts for about three weeks.26 HEV viremia, however, might be regarded as blood transfusion transmissible at any stage.\n\nIn the current study, the participants were mainly students (1031/1939) and the majority of them were between 18 and 28 years of age. The majority (34.6%) of participants were undergraduate students with the highest degree of education, either Pre-University (PUC) or Higher secondary education. Our results are in line with a longitudinal research conducted in rural Bangladesh among healthy individuals, which found no statistically significant association between anti-HEV IgM antibody reactivity and demographic variables including age and educational qualification.27 The analysis of the different demographic variables and prevalence of anti HEV antibodies (IgM and IgG) is shown in Table 1.\n\nSince eating with the hands is preferred in India, maintaining good hand cleanliness is crucial in preventing the transmission of HEV infection. Among participants who regularly wash their hands with soap before eating food, the prevalence of HEV IgG was significantly lower (p<0.05) than in other group. Therefore, hand washing with soap could be essential in preventing the transmission of fecal-orally transmitted diseases such as HEV. The anti HEV IgM antibody reactivity rate among donors who wash hands before eating and who did not wash were 1.3% and 2.3% respectively.\n\nThere is an increased report of autochthonous HEV cases in developed countries, where HEV is primarily transmitted zoonotically, and it may also be associated with travel. Thus, for a traveller in HEV endemic countries food sources and dietary choice are risk factors for exposure, hence, it is also referred to as a travel-associated disease. However, travel to other districts, states, or other countries, length of stay, and dietary habits were not significant risk factors in the present study. Exposure to agricultural work or animal husbandry was a significant (p < 0.05) risk factor associated with anti-HEV IgG reactivity (OR 2.016; 95% CI 1.149, 3.525) but not with anti-HEV IgM reactivity in the study population, which is consistent with the results from Nigeria.28 This implies that agricultural and livestock exposures, particularly the swine population, pose a significant occupational risk for HEV infection, which has been noted in several epidemiological studies.29 The zoonotically transmitted HEV4 and HEV3 genotype has been reported to cause chronic diseases in immunocompromised patients, and HEV4 has been detected among pigs in India.30\n\nChronic HEV infections due to HEV3 and HEV4 is well known in developed countries. The sporadic cases of HEV were due to the consumption of undercooked pork and wild boar meat, However, given that outbreaks and epidemics caused by HEV1 are frequently recorded in India, this is an unlikely risk factor for exposure to HEV infection there.6 A chronic HEV-1 is an emerging infection in immunocompromised patients and was documented by Singh et al., in 2018.31 Therefore, a critical analysis to perform selective HEV screening in blood donation for high-risk groups such as pregnant women and immunocompromised patients might be helpful.\n\n\nConclusion\n\nThe present study shows that the prevalence of anti-HEV antibodies among blood donors is found to be high and it appears to be a hidden threat to blood safety. This study emphasizes the importance of a larger multicentric study to estimate the actual burden the disease. The development of policies on universal or selective screening of blood donors for HEV infections will benefit from a review of the cost-effectiveness of HEV testing.", "appendix": "Data availability\n\nMendeley Data: Seroepidemiology of hepatitis E virus among the voluntary blood donors in the coastal region of Karnataka, India, https://doi.org/10.17632/kr27p3kv9p.2. 49\n\nThis project contains the following underlying data:\n\n• Hepatitis_E_Virus data.sav\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe author (SS) would like to acknowledge the Ministry of Tribal Affairs, Government of India, for awarding the Fellowship for his Ph.D. research work.\n\n\nReferences\n\nWorld Health Organization: Hepatitis E. Accessed on 30/07/2021. Reference Source\n\nDevhare P, Madiyal M, Mukhopadhyay C, et al.: Interplay between Hepatitis E Virus and Host Cell Pattern Recognition Receptors. Int. J. Mol. 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Publisher Full Text" }	[ { "id": "196289", "date": "29 Aug 2023", "name": "Ibrahim M Sayed", "expertise": [ "Reviewer Expertise HEV" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the authors assessed HEV markers in blood donors in India. None of the enrolled subjects were positive for HEV RNA, but 1.39% of tested cohort were anti-HEV IgM positive.\nMajor points\nIRB and ethical approval should be mentioned.\n\nSince none of the subjects were HEV RNA positive, the authors need to mention the sensitivity and specificity of the assay used. Also which target of HEV genome is the qPCR amplified.\n\nWhat about HEV Ag?\n\nPlease provide liver function profiles in IgM positive cases and compared with IgG positive cases and other.\n\nHEV genotype 1 is common circulating isolate in India, and this genotype does not infect animal. So how animal contact could be risk factor for HEV infection?\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": "10211", "date": "26 Sep 2023", "name": "shamee shastry", "role": "Author Response", "response": "Dear Reviewer, Thank you for your comments Major points IRB and ethical approval should be mentioned. Reply: The study was approved by Doctoral Advisory Committee for Ph.D. which was further approved in the Institutional Ethical Committee meeting (IEC: 06/2020) Since none of the subjects were HEV RNA positive, the authors need to mention the sensitivity and specificity of the assay used. Also which target of HEV genome is the qPCR amplified. Reply: The analytical sensitivity of the test kit is 0.20 IU/µL What about HEV Ag? Reply: Screening of HEV Ag in the sample was not opted for the study as WHO mentioned that the definitive diagnosis of HEV infection is usually based on the detection of anti-HEV IgM antibodies Please provide liver function profiles in IgM positive cases and compared with IgG positive cases and other. Reply: he participants in the research were healthy, voluntary blood donors. During the pre-donation stage, they were examined by the medical officer for any symptoms or signs of hepatitis to rule it out. Consequently, liver function tests weren't carried out. However, the data would have supported the study's findings, as the reviewer had indicated. HEV genotype 1 is common circulating isolate in India, and this genotype does not infect animal. So how animal contact could be risk factor for HEV infection? reply: HEV1 is the genotype known to produce outbreaks and epidemics in India. However, there is still a paucity of data on HEV3 and HEV4, the zoonotic-born HEV genotypes among Indians that have caused sporadic cases in developed nations, which requires consideration." } ] } ]	2	https://f1000research.com/articles/12-266
https://f1000research.com/articles/12-1115/v1	07 Sep 23	{ "type": "Study Protocol", "title": "Efficacy of lung boost device on pulmonary function and chest expansion in pleural effusion patient: a randomized control trial protocol", "authors": [ "Saurabh Zunzunwala", "Dr Vishnu Vardhan", "Dr Vishnu Vardhan" ], "abstract": "Background: The respiratory system is consisting of alveoli, bronchioles, pleura etc. The pleura is the name for the layer of tissue that is thin covers every lung and folds to the back side and creates border of the cavity of chest. Pleural effusion medically is termed for an accumulation of fluid above the required amount in the pleural space. Firstly, while evaluating the subjects with effusion of pleura is to determine if it is an exudate or a transudate. The factors that are pathophysiological may be clinically significant and play role in differentiating trait of effusion of pleura -transudate vs. exudates-include oncotic pressure that is low, increase in pressure of pulmonary capillary, increased permeability, obstruction of lymphatic system, and lowered pressure between pleura. Aim: To find the efficacy of the lung boost device on pulmonary functions and chest expansion in pleural effusion patient. Methods: A total of 70 of participants with pleural effusion would be taken in the study and they are separated in two groups 35 participants in single group. Group A would be having lung boost device and group B would be treated with Conventional Physiotherapy program which will be included in both the groups. Treatment will last for two weeks with six sessions a week. Pre- and post-intervention pulmonary function test and chest expansion would be found out and would be sent for the analysis. Expected results: The results of the study are expected to prove lung boost device is more effective than conventional physiotherapy. So that it can help in increasing expansion of chest and function of pulmonary system of patients with effusion of pleura.", "keywords": [ "Pleural effusion", "lung boost device", "Pulmonary function test", "chest expansion", "conventional chest physiotherapy." ], "content": "Introduction\n\nThe pleura is the tissues that name as thin layer that covers single lung and turn up backwards to create the border of the cavity of chest. Pleural effusion is a medical term for an collection of fluid more than normal in the spaces of pleura. It may be difficult for the treating physician to diagnose because it is related to systemic disorders, pleural diseases, and lung diseases. first step in examine the patients with a effusion of pleura is to decide whether it’s an exudates or a transudate.1\n\nThe causes are highly varied, differ from effusion which are benign related with pleuritis caused due to viral infection that are critically decisive in terms of prognosis because of congestive heart failure or malignancy. One-year death rates for people with non-malignant pleural effusions range from 25% to 57%. The average rate of the hydrostatic and oncotic pressure differential between the systemic and pulmonary circulation and the pleural space, as well as their generation and absorption. This equilibrium has been disturbed in pleural effusion, likely as a result both have production which is excessive and resorption which is decreased. Factors that are pathological and effective to contribute to significance that is clinically correlated and characteristics that distinguish effusion of transudate of pleura vs. exudates-include pressure that is low oncotically, elevated pressure of pulmonary capillary, elevated permeability, obstruction of lymphatic system, and diminished negative pressure between the pleura.2\n\nPleural effusion, a frequent symptom of the critically ill, is frequently thought by clinicians to be intrinsically lung-restrictive, worsening overall respiratory system complaisance as it stiffens wall of the chest and compresses the lung. Studies accomplished on individuals who were breathing on their show that intrapleural liquid may reduce lung capacity by only a small portion of the total liquid volume when effusions separate the quantity of the lung and chest wall.3 In contrast, there is no usefulness in using B-mode ultrasound as an imaging modality to determine whether a PE is malignant. Computed tomography (CT) is a common method of overview imaging for this use.4 On the other hand, determining the malignancy of a PE using B-mode ultrasonography as an imaging tool is useless. For this function, computed tomography (CT) is a popular overview imaging technique.5\n\nShivering, increase in heart rate, dyspnoea, pain in chest, retained sputum, auscultatory alterations, and changes in radiological findings are all symptoms of the postoperative chest. According to recent research, the illness is caused by muscle spasms, abdominal pain, and other reactions that limit the movement of the diaphragm wall of the chest. In patients with postoperative discomfort, the continuous constriction they experience keeps the lungs' size from expanding during normal tidal breathing, which lowers FRC. Studies have shown that airways, particularly dependent on regions of lung, may close for part or the entirety of the respiratory cycle. As a possible adaptive reaction to the worsening pressure-volume relationships brought on by atelectasis, tidal volume falls and respiratory rate rises.6\n\nAt the ground level of lungs, the breath sounds are heard unilaterally or bilaterally that are reduced or non-existent, and the percussion is indistinct at the base. If the effusion is significant, tachypnoea might be present. When a par pneumonic effusion is first begins, a pleural rub may be audible. Large quantity of fluid in pleural effusions inspire space in the chest that pulmonary parenchyma typically fills, resulting in a reduced in total lung capacities.2 Pleural effusion may cause in the decrease in expansion of chest and it leads to atelectasis of the lung, because capacity of the lung in the thorax is limited and extra fluid leads to collapse to the lungs. Hypoventilation does occur in certain areas in the lungs because of the pain and muscle guarding after surgery, atelectasis and pleural effusion.7\n\nThe space of pleura is often a space which is that is present in middle of the mesothelium of the parietal and visceral pleura, with the measurement of 10 to 20 millimetres wide. It may hold a little amount of lubricating fluid (0.3 mL/kg body mass) with a minor amount of protein (around 1 g/dL).8 The inward recoiling of the lung and the outward recoiling of the chest wall are typically balanced at the FRC, and there is a contemporaneous negative pleural pressure.9\n\nAccording to some series, lung cancer accounts for roughly half of all occurrences of benevolent pleural effusion. In all Up to 15% of lung cancer patients may have an MPE when they first arrive, and up to 50% may develop one throughout the course of the illness.10 MPE can be develop directly from invasion at tumour or spread that is heterogenous to the pleura that is parietally located, but the most common causes are direct or hematogenous dissemination of benevolent cells to the visceral pleura with secondary seeding to the parietal pleura.11 A pleural effusion can also be brought on by malignancy without any involvement of the pleura. This disorder, known as a Para malignant effusion, can result from a number of different processes, including superior vena cava syndrome, obstructive pneumopathy, pulmonary embolism, lymphatic mediastinal blockage, and pulmonary embolism.12 Muscle guarding at the ICD site brought on by this pain results in hypoventilation. Therefore, it's crucial to emphasise the reduction of discomfort and expansion. Total number of 266,000 Medicare managed care patients were evaluated in 2010 and 2012 for this large cohort study, and discovered that pain with dyspnoea frequently co-occurred, developed, and resolved simultaneously.13 An important method for enhancing lung function is respiratory physiotherapy. Dyspnoea, localised pain at ICD, improper breathing sign, poor briefing, decreased lung expansion, activity intolerance, and anxiety are some of the most prevalent impairments associated with pleural effusion.14 Chest physiotherapy mainly reduced the duration of hospital stay and improved recovery are the effects of combining respiratory physiotherapy, which includes breathing exercises, posture corrections exercises and mobilisations, sputum clearance exercises, and patient education, with medical treatment and drainage for effusion of pleura. This combination therapy causes intrathoracic pressure changes that improve drainage and hence improve expansion.15\n\nThis study's objective is to assess and evaluate the effectiveness of lung boost device in patients who underwent post icd removal of pleural effusion in a two-arm parallel superiority/equivalence based randomized control trial (RCT). The end point results will be compared on a marginal basis to determine effectiveness.\n\n\nAim and objectives\n\n\n\n➢ To assess and evaluate the subjects underwent pleural effusion for the change in pulmonary function parameters (FEV1, FVC AND FEV1/FVC ratio) treated with lung boost device and with conservative physiotherapy management, if it can improve pulmonary functioning in the entire populace.\n\n➢ To assess and evaluate the subjects underwent pleural effusion for the change in chest expansion treated with lung boost device and with conservative physiotherapy management, if it can improve pulmonary functioning in the entire populace.\n\n➢ To analyse the efficacy over the treatment of lung boost device along with conventional physiotherapy management and along with conventional physiotherapy management for bringing on change in pulmonary function and chest expansion for the population underwent post icd pleural effusion.\n\nTrail design – single centric, two arm parallel randomized controlled trial.\n\nMethodology: This study will be conducted with written informed consent from all participants. Participants will be chosen from inpatient and outpatients from respiratory medicine department at AVBRH Sawangi Meghe, Wardha, Maharashtra, following acceptance from the institutional ethics committee of DMIHER. Participants in the study will be split into two groups. Group-A (conservative physiotherapy management) & Group-B (lung boost devices and conservative physiotherapy management) allotted randomly with 1:1 allocation with intent to treat purpose. All The participants whoever participating will be screened for the study as per inclusion and exclusion criteria, and then followed by randomization by using a computer-generated list. Allocation will be done by sequentially numbered opaque sealed envelopes Allocation and participant enrolment will be done by primary investigator. Selection for the will be based on the cut-off values at baseline parameters when engaging participants through inclusion and exclusion criteria. Throughout the six-month recruitment phase, a second source of recruitment will be used if more study participants are needed. We will ensure that the patients adhere well to the recommended treatment through regular treatment sessions. If needed, patients will be counselled or contacted telephonically for a reminder about the therapy sessions. To compare improvements in pulmonary function capacity and chest expansion at the end point, the interventional group will receive lung boost device and conservative physiotherapy management (Table 1), and the control group will receive conservative physiotherapy management (Table 1). The total number of participants will be enrolled and evaluated with the several intervals, including their first visit and second visit for subject enrolment and the screening will be done on baseline and two weeks respectively, after treatment the follow-up are taken, where the primary and secondary parameters will be assessed. The study design is depicted in Figure 1.\n\n\n\n1. Patients with pleural effusion.\n\n2. Patient with Age from 18-45 years.\n\n3. Patients underwent ICD in pleural effusion\n\n\n\n1. Patients with ICD.\n\n2. Patients with any obstructive complications\n\n3. Patients with any cardiac problems such as (MI, Unstable Angina, or arrhythmia).\n\nAll the patients enrolled into the study are required to complete the whole two weeks of rehabilitation protocol after enrolment in the study. The assessment will be performed at initial and at the end of the session. Follow up will be taken after one week.\n\nGroup A- Group A will receive conservative physiotherapy management which will start from POD-3. At the beginning of the training, the patient will give with thoracic expansion, deep breathing exercise, incentive spirometry, postural correction. The session of treatment will be given for two sets of 15 repetitions for six days/week daily for two weeks. Table 1 explains the conventional treatment that will be administered to the patients.\n\nGroup B- Group B will receive lung boost device along with conservative physiotherapy management which will start from POD-3. At the beginning of the postoperative training, the patient has started with the stage one settings with the patient and the difficulty level will be increasing till five stages after that a small valve is applied that will apply resistance which will lead to start again from level 1. Participants will be instructed to take breathe deeply and forcefully for 2-3 seconds, slight pause, then exhale forcefully for 2-3 seconds for 15 repetition two sets. The treatment will be taken for 6 days in a week for two weeks twice a day. The time period for each session will be approx. about 15-20 minutes in which the rest period is also includes. Table 2 explains the treatment protocol of interventional group that will be administered to the patients.\n\nSafety outcomes: Adverse events are reported at each time.\n\nPrimary outcome measures: -\n\n\n\n1. Pulmonary function test.\n\nThis is the specific measurement was computed by an instrument called Spirometry (RMS HELIOS401). Following are the parameters:\n\nForced Vital Capacity (FVC) - Forced Vital Capacity (FVC) it is the maximum volume of gas that can be expired when the patient exhales as forcefully and rapidly as possible after a maximal inspiration. This procedure often referred to as the FVC maneuver.\n\nNormal value- FVC and VC (vital capacity) should be within 200 ml of each other.\n\nForced Expiratory Volume in One Second (FEV1)-FEV 1 measures the volume expired over the first second of an FVC maneuver.\n\nNormal values: Forced expiratory volume in persons with normal respiratory functions is as follows:\n\nFEV 1 = 75%-85% of total vital capacity.\n\nFEV 1/FVC Ratio - The ratios may be derived by dividing predicted FEV1 by predicted FVC.\n\nPeak expiratory flow rate (PEFR) - PEFR is the maximum flow attained during an FVC maneuver. It is expressed in liter per second.\n\nNormal range for adults- 100-850 L/min\n\n2. Chest expansion.\n\nThe changes between Maximum inspiration and maximum expiration is known to be chest expansion. Chest expansion will be measured with the help of tape method at different stages of the chest which measures symmetry and extent of expansion. It will perform at three levels, for three different lobes of the lungs from top to bottom. This method is active for measuring chest expansion in unilateral lung disease. The levels of measurements are at sternal notch and at xiphiod process.\n\n\n\n1. Posture examination\n\nAs because of pain over the suture site the patient was not able to maintain the proper posture. So, after the treatment the patient was analyse with the good and bad posture and had given the exercises for the good posture.\n\nSample size calculation resulted at 5% level of significance considering both the sides at 5% error probability with total 10 % for Z(1-α) value =1.64 & (1- β) at power of 80 % = 0.84 measuring the mean difference (effect size) of δ= 0.34 & standard deviation (σ) = 0.102\n\nFormula Using Mean difference\n\nPrimary Variable (Forced vital capacity)\n\nMean ± SD. (Pre) result on forced vital capacity for conventional chest therapy (Control group) = 1.25 ± 0.28.\n\nMean ± SD. (Post) result on forced vital capacity for conventional chest therapy (Control group) = 1.59 ± 0.38.\n\nDifference. = 0.34 ± 0.16. (As per ref.article)\n\nClinically relevant superiority = 30 % = (0.3430)/100 = 0.102.\n\nAs per reference articles.\n\nTotal samples required = 31 per Group.\n\nConsidering 10% drop out = 4\n\nTotal sample size required = 35 per group\n\nNotations: -\n\nRef Article: - Gunjan SB, Shinde NK, Kazi AH et. al. Effectiveness of deep breathing versus segmental breathing exercises on chest expansion in pleural effusion. Int J Health Sci Res. 2015; 5(7):234-240\n\nAll the results will be calculated using R software version 4.3. Descriptive statistics over the categorial variable will be tabulated & presented with frequency & percentage. For the quantitative assessment over the continuous variable will be expressed & presented with Mean±SD, maximum and minimum. For inferential statistics. The outcome assessment variable over continuous scale (quantitative) will be tested following normal distribution using Shapiro- Wilk test. If data comes under non normal distribution will be transformed into normal distribution using mathematical algorithms. For finding significance over mean parametric test will be used as paired t-test for intra assessment & independent t-test will be used for inter-group assessment. Alternative Wilcoxon Test as a non-parametric test will be used if the data persist with non- normal distribution. Similarly, for unpaired-t test Mann Whitney test will be using as an alternative test. Association analysis for finding significance of cofounding parameters will be evaluated by using Chi-squared test or Fisher’s exact test or by using multi-variant analysis. Sensitivity and specificity of the device will be tested over primary outcome (MIP). AUC (area under curve) will be calculated based on observational values for finding accuracy of the device.\n\nDissemination- Planning for presenting my study in conference preceding.\n\nStudy status- The study is yet to be started.\n\n\nDiscussion\n\nThe study is going to be done in comparison with the pulmonary functions and the chest expansion in the control as well as in the experimental group. Mainly we are doing the study to find out the effective result in both the group. Another study which is done as taking the experimental group in abdominal surgery has got the significant change in pulmonary functions and in the chest expansion. As we are doing by taking the experimental group just for evaluating in pleural effusion and finding the results from it. The experimental group is expected to show more effective results and as the device is useful to treat the patient in the short duration of time period as compared to control group. Tiwari et al studied about Physical Therapy Rehabilitation for a Chronic Alcoholic Patient with Loculated Pleural Effusion. In this study the author has studied about the effects of pursed lip breathing along with the thoracic expansion exercise in patient with pleural effusion. The study concluded that there is a significant improvement in chest expansion in pleural effusion patient.1 Amisha. A. Alande et al studied the effect of lung boost device on inspiratory muscle strength in abdominal surgery patients. 30 subjects with abdominal surgeries were enrolled in the study and were divided into two groups. the study concluded that g lung boost device showed significant improvement in inspiratory muscle strength and in 6 minute walk distance.16\n\n\nConsent\n\nThe principal investigators of the study will obtain the written informed consent from the participant on a printed form (local language) with the signatures and give the proof of confidentiality.\n\n\nEthical considerations\n\nIEC no. – DMIHER (DU)/IEC/2023/810\n\nIEC approval date – 21/03/23\n\nCTRI no. – CTRI/2023/05/053024\n\nCTRI registration date – 22/05/23", "appendix": "Data Availability\n\nNot applicable as this is only a study protocol.\n\nFigshare. SPIRIT checklist. DOI: 10.6084/m9.figshare.23798676\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).\n\n\nAcknowledgement\n\nI would like to acknowledge Mr. Manoj Patil and Mr. Laxmikant Umate who had helped me in sample size calculation and data analysis planning.\n\n\nReferences\n\nTiwari N, Kumbhare R, Walke RR: Physical Therapy Rehabilitation for a Chronic Alcoholic Patient With Loculated Pleural Effusion. Cureus. 14(10): e30368.\n\nJany B, Welte T: Pleural Effusion in Adults—Etiology, Diagnosis, and Treatment. Dtsch. Ärztebl. Int. 2019 May; 116(21): 377–386. PubMed Abstract \| Publisher Full Text\n\nGraf J, Formenti P, Santos A, et al.: Pleural effusion complicates monitoring of respiratory mechanics. Crit. Care Med. 2011 Oct; 39(10): 2294–2299. PubMed Abstract \| Publisher Full Text\n\nSafai Zadeh E, Görg C, Dietrich CF, et al.: Contrast-Enhanced Ultrasound for Evaluation of Pleural Effusion. J. Ultrasound Med. 2022; 41(2): 485–503. PubMed Abstract \| Publisher Full Text\n\nKalantri S, Joshi R, Lokhande T, et al.: Accuracy and reliability of physical signs in the diagnosis of pleural effusion. Respir. Med. 2007 Mar; 101(3): 431–438. Publisher Full Text\n\nDesai PM: PAIN MANAGEMENT AND PULMONARY DYSFUNCTION. Crit. Care Clin. 1999 Jan; 15(1): 151–166. Publisher Full Text\n\nGunjal SB, Shinde NK, Kazi AH, et al.: Effectiveness of Deep Breathing versus Segmental Breathing Exercises on Chest Expansion in Pleural Effusion. Int. J. Health Sci. 2015; 7.\n\nLight RW: Anatomy of the pleura.Light RW, editor. Pleural Diseases. Philadelphia: Lippincott Williams & Wilkins; 2001; Volume 1. ; 1–7.\n\nMitrouska I, Klimathianaki M, Siafakas NM: Effects of pleural effusion on respiratory function. Can. Respir. J. 2004 Oct; 11(7): 499–503. PubMed Abstract \| Publisher Full Text\n\nNaito T, Satoh H, Ishikawa H, et al.: Pleural effusion as a significant prognostic factor in nonsmall cell lung cancer. Anticancer Res. 1997; 17: 4743–4746. PubMed Abstract\n\nHeffner J, Klein J: Recent advances in the diagnosis and management of malignant pleural effusions. Mayo Clin. Proc. 2008; 83: 235–250. Publisher Full Text\n\nRodríguez-Panadero F, Borderas Naranjo F, et al.: Benign pleural effusions in cancer patients. Frequency and etiopathogenic mechanism in a series of autopsy cases. Rev. Clin. Esp. 1988; 183: 311–312. PubMed Abstract\n\nClark N, Fan VS, Slatore CG, et al.: Dyspnea and pain frequently co-occur among Medicare managed care recipients. Ann. Am. Thorac. Soc. 2014 Jul; 11(6): 890–897. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBott J, Blumenthal S, Buxton M, et al.: Guidelines for the physiotherapy management of the adult, medical, spontaneously breathing patient. Thorax. 2009 May 1; 64(Suppl 1): i1–i52. PubMed Abstract \| Publisher Full Text\n\nValenza-Demet G, Valenza MC, CabreraMartos I, et al.: The effects of a physiotherapy programme on patients with a pleural effusion: a randomized controlled trial. Clin. Rehabil. 2014 Nov; 28(11): 1087–1095. PubMed Abstract \| Publisher Full Text\n\nAlande A, Vardhan V: Effect of lung boost device on inspiratory muscle strength in abdominal surgery patients. Int. J. Physiother. Res. 2021 Apr 11; 9: 3793–3799. Publisher Full Text" }	[ { "id": "249746", "date": "04 Mar 2024", "name": "Gopal Nambi", "expertise": [ "Reviewer Expertise Rehabilitation" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract:\nPlease include some information about the condition of the study in the background. Mention about lung boost device. Mention the character of the study participants. Mention the study design, study setting and study duration. The outcome measures used in the study are not clear. Mention the statistical tests used for the study.\nManuscript:\nPlease elaborate the introduction part as it is not scientifically written. Provide a reference for lung boost device in pleural effusion patients. Mention the application procedure, merits, and demerits of lung boost device in pleural effusion patients. The need for the study is not mentioned clearly in recent references. Mention the gaps monitored by the researcher in the previous studies. Include the clinical significance of the study for the researchers, clinicians and patients. The article is presented like a research proposal. Mention the study design, study duration and study setting. Include the ethical approval and clinical trial registration number. Follow the CONSORT guidelines to present the study. Mention the randomization and allocation procedure in clear. Mention the blinding procedure in detail. Include the diagnostic criteria of the disease and its ICD classification. Mention who will diagnose the participants and their qualifications and experience. Mention the outcome variables with their reliability and validity. Mention the intervention parameters of study interventions. Include the sample size calculation with a suitable reference. The samples included in the study are not sufficient to generalize the results. The statistical tests included are not apt for this study. Mention how the covariables will be controlled and how the homogeneity is measured.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1115
https://f1000research.com/articles/10-623/v1	21 Jul 21	{ "type": "Research Article", "title": "Evaluation of clinical, histology, TNF-α, and collagen expressions on oral ulcer in rats after treatment with areca nut and chrysanthemum oral gel", "authors": [ "Liza Meutia Sari", "Zaki Mubarak", "Dina Keumala Sari", "Zaki Mubarak", "Dina Keumala Sari" ], "abstract": "Background: Areca nut (Areca catechu Linn.) is the seed of the fruit of the oriental palm that is commonly used among Southeast Asian communities. Chrysanthemum (Dendrathema grandiflora) is a flowering plant originating from East Asia and dominantly grows in China. Both of these plants have strong antioxidant activities. To investigate the mechanism of their wound healing activities, we prepared areca nut and chrysanthemum polyethylene oral gel and performed several in vivo assays using Sprague–Dawley rats. Methods: Sprague–Dawley rats were divided into five groups: Negative control group (rats with base gel treatment), positive control group (rats treated with triamcinolone acetonide), F1 (treatment with 20% areca nut:80% chrysanthemum), F2 (treatment with 50% areca nut:50% chrysanthemum), and F3 (treatment with 80% areca nut:20% chrysanthemum). Traumatic ulcers were performed on the buccal mucosa of all experimental animals that received topical oral gel and triamcinolone acetonide twice a day for seven days. The clinical and histological characteristics were analyzed and scored. Results: During the six days, the ulcerated area receded linearly over time and was completely cicatrized in F2 and positive control group (Dependent t-test, p<0.05). There were significant increases in body weight in F2 and positive control groups. There were no significant differences between groups in histology examination (Kruskal Wallis test, p<0.05). The moderate score of TNF-α levels was seen in F2 and positive control groups (ANOVA/Tukey test). Similar results were seen in the collagenases assay. Conclusions: A balanced combination of areca nut and chrysanthemum extract in the oral gel can optimize the healing of traumatic oral ulcers in rats through the increase of TNF-α and collagen deposition.", "keywords": [ "Oral ulcer", "Areca nut", "Chrysanthemum", "TNF-α", "Collagen" ], "content": "Introduction\n\nOral ulceration is the most common presentation in the oral cavity caused by many etiologic factors.1 Most of the etiologies of ulcerative lesions on the oral mucosa are divided into four categories; namely, infectious (bacterial and virus infection), immune-related (autoimmune and allergic), traumatic (mechanical trauma), and neoplastic (oral squamous cell carcinoma).2 Traumatic ulcers are injuries to the oral mucosa caused by mechanical or physical trauma such as sharp food, accidental biting during mastication, biting while speaking, punctured by sharp objects, fractured, malformed, carious, or malposed teeth on the superficial epithelial layer or underlying connective tissue or may involve both.3\n\nCurrently, increasing the resolution of wound healing is one of the main priorities in the medical field to accelerate the healing of chronic wounds and traumatic injuries.4 The process of tissue regeneration and repair occurs immediately after lesion onset. The linear tissue repair and regeneration involves growth factors that induce cell proliferation, especially parenchymal cells, followed by dynamic changes in soluble mediators, blood cells, and the extracellular matrix.5 The unique oral cavity environment shows advantages in accelerating wound healing compared with skin repair. This is due to differences in the response to inflammation, differentiation and proliferative programs, modulation of stem cells, collagen synthesis, the role of macrophages, and epithelial remodeling.6,7 Collagen synthesis and tumor necrosis factor-α (TNF-α) are important components during acute inflammation and responsible for a diverse range of signaling events within cells in the wound-healing process. TNF-α is one of inflammatory cytokine and regulates the immune system.8\n\nAreca nut is the seed of the areca palm (Areca catechu Linn.), which grows thrive in tropical Pacific region, South and South East Asia, including Indonesia where it is known as “Pinang”. It has been consumed by people worldwide as part of ancient tradition, custom, or ritual for a long time. Several studies have been conducted to prove the healing ability of areca nut, including that the alkaloid and polyphenols content in areca nut could enhance the healing of burn wounds, leg ulcers, and skin graft surgery.9,10 Chrysanthemum or chrysanth (Dendrathema grandiflora) is a flowering plant originating from East Asia and dominantly grows in China. The flowers are generally consumed in herbal teas and as a supplement. Previous studies reported the effect of increasing keratinocyte proliferation and skin regeneration derived from Chrysanthemum boreale.11 Chrysanthemums are usually used for treating allergies, anxiety, hypertension, inflammation, headache, cold, sore throat, and tinnitus by certain communities.12\n\nHowever, scientific research has not been conducted related to the healing process on the oral mucosa by oral application of these herbal plants. This study aimed to evaluate the potential of the combination of areca nut and chrysanthemum oral gel on oral mucosa using the Sprague–Dawley rat model.\n\n\nMethods\n\nThis study was approved by the Ethics Committee for Animal Research of Tropical Biopharmaceutical Research Center (Trop BRC), Bogor Agricultural University, West Java, Indonesia, with number 042-2020-KEH TROP BRC.\n\nAreca nuts were obtained from the Pinang plant from Aceh Besar, Indonesia. 2 kg of areca nuts (gross weight) were cleansed of dirt and dried in the open air and sunlight. Further drying was done using an oven set at a temperature of 50°C. The nuts were crushed using a blender and then strained with a 20-mesh sieve. The maceration process was conducted using 96% ethanol diluent solvent for 7 days before being subsequently filtered and evaporated using a vacuum rotary evaporator at 30–40°C and then reconcentrated using a water bath until a solid dry powder extract was obtained. Chrysanthemum polyethylene (P.E.) (Product No. 1237X17911) was provided by Javaplant Company, Indonesia.\n\nThe extract was formulated into four gel dosage forms with various concentrations of the extract combination, namely F1 (20% of areca nut:80% of chrysanthemum), F2 (50% of areca nut:50% of chrysanthemum), F3 (80% of areca nut:20% of chrysanthemum), and base gel (gel without areca nut and chrysanthemum). Preparation of the extract oral gel began with making two mixtures. The first mixture consisted of a carbamoyl and extract combination of areca nut and chrysanthemum and mixed with 10 mL of water at 70°C. The second mixture consisted of methylparaben dissolved in a little water and then mixed with a mixture of glycerin and propylene glycol. This mixture was then combined and stirred with water so that it is mixed homogeneously.\n\nA total of 25 adult male Sprague–Dawley rats weighing 200–240 g were provided by the animal laboratory at Tropical Biopharmaceutical Research Center (Trop BRC), Bogor Agricultural University. The rats were kept for adaptation at 25°C in the well-ventilated laboratory for 14 days under a 12/12 h light/dark cycle and fed with a standard pellet diet and tap water ad libitum before being entered into the experiment. All the animals were given an initial examination for systemic health conditions and stored in boxes with sawdust.\n\nUlcer induction was performed after the animals were anesthetized by intraperitoneal injection of 33 mg/kg of ketamine and 13 mg/kg of xylazine (2%). The left buccal mucosa was smeared with 10% povidone–iodine on cotton pellets. An abrasion was made with 5 mm diameter, 1 mm depth, and was limited to the mucosa without muscular involvement. The ulceration was performed by using a number 15 scalpel blade. The standardization area was marked with an 8-mm diameter demarcator. The surgical and technique was standardized for animals and performed by the same operator.13 The ulceration was not performed in the normal group. The formation of the ulcers could be observed after 24 hours.\n\nThe animals were randomly divided into five groups with 12 animals each: negative control group (rats with base gel treatment), positive control group (rats treated with triamcinolone acetonide), F1 (treatment with 20% areca nut:80% chrysanthemum), F2 (treatment with 50% areca nut:50% chrysanthemum), and F3 (treatment with 80% areca nut:20% chrysanthemum). A normal group (without ulcer and treatment) was added for the microscopic evaluation. All the groups were treated every 12 hours for seven days with topical application. The application of the oral gel was performed by using the individual sterile and disposable dental micro brush (SDent, USA). Each group was sacrificed gradually through the end of the seventh-day study period. After the animals were sacrificed, a section of buccal mucosa containing the ulcer of each rat was collected. Histopathology, immunohistochemistry, and collagenases evaluation were analyzed in Primate Research Center, Bogor Agricultural University, Indonesia.\n\nThe animal body weights and diameter of the ulcers were measured before and after treatment on the second and seventh days. The diameter of the ulcers were measured with the naked eyes using a digital stainless vernier caliper which is capable of measuring diameter in 0.05 mm increments.14,15 All measurements were performed by the same operator.\n\nThe collected fragments of ulcers were identified and immersed in 10% formol for 24 hours. After fixation in formol, the specimens were macroscopically analyzed, subjected to dehydration in crescent alcoholic series, diaphanized in xylol, impregnated in paraffin, and melted at 60°C. The fragments were packed in paraffin-forming blocks at room temperature. The fragments were sectioned to 5 μm in thickness through the use of microtome and histology using routine coloration by hematoxylin-eosin (HE) was performed. The histopathological parameters were determined and scored from 0 to 4 according to previously published criteria (Table 1).16\n\nThe selected tissue sections of the ulcers (2.5 μm) were deparaffinized and rehydrated with distilled water. Blocking endogen peroxidase activity was done using 3% hydrogen peroxide solution for 15 minutes, followed by washing with phosphate-buffered saline (PBS) three times every 5 minutes. After protein blocking, the dripping of Biocare’s Background Sniper was performed and the specimens were incubated for 15 minutes at 37°C. The dripping of normal serum was performed and incubated for 60 minutes at 37°C. The specimens were washed with PBS and anti-TNF-α antibody (TNFA/1172) (ab220210Abcam), was diluted at 1:100, and then dripped and incubated at 4°C for two days. After washing with PBS, the secondary antibody goat anti-rabbit IgG H&L horseradish peroxidase (HRP) (RRID: AB_955447; ab6721-Abcam) was given for 30 minutes at 25°C and followed by Betazoid DAB chromogen solution (BDB2004H-Biocare Medicare LLC). It was used for increasing stability and staining intensity for HRP detection in the specimens. The specimens were washed with distilled water and checked with the microscope. After counterstaining with hematoxylin for 30 seconds, the specimens were rinsed in tap water, dehydrated, purified, and mounted. The percentage of nuclear and cytoplasmic expression in the connective tissue was divided into four scores, namely: 0: no positive cells; 1 (mild): 1–33% of positive cells; 2 (moderate): 34–66% of positive cells; 3 (intense): 67–100% of positive cells. Two observers analyzed the same scores until they were considered as the final scores.17\n\nThe same fragments were sectioned to a thickness of 3 μm, de-wax, hydrate paraffin section, and stained using picrosirius red (solution A) for one hour. After washing in acidified water (solution B), the specimens were dehydrated and mounted for observation under polarized light microscopy. The collagen bundles shown in red in the image were then calculated using Adobe Photoshop CC 2017 (RRID:SCR_014199; GNU Image Manipulation Program (RRID:SCR_003182) is an open-access alternative) and ImageJ (v1.50i) (RRID:SCR_003070) software. The percentage of collagen was derived from collagen area pixel divided by tissue pixel and multiply by 100%. The mean of three percentages was used as a sample unit.18\n\nAll experiments were carried out in triplicate and the data were expressed as mean ± standard deviation (SD). Statistical analysis was performed by using the SPSS 20 software (SPSS Inc., Chicago, USA) (RRID:SCR_019096); JASP (RRID:SCR_015823) is an open-access alternative. Clinical evaluation in changes of the area of ulcer and body weight of rats analyzed by the dependent t-test. Differences among samples in histopathological and immunohistochemistry analysis were evaluated by using the Kruskal–Wallis test. Collagenesis analysis was evaluated by using analysis of variance (ANOVA/Tukey test). A significant difference was assumed at p < 0.05.\n\n\nResults\n\nThe change comparison of ulcer size analysis in the buccal mucosa of rats showed a significant decrease in ulcer size in F1, F2, F3, and positive control groups (Figure 1A–J, Table 2). This observation was carried out on the second day after the ulcer was formed and at the end of the experiment. The most significant decrease in ulcer area was seen in positive control (triamcinolone acetonide orabase) and F2 treatment groups. Notably, the average ulcer size in positive control and F2 treatment on the second day was 10.10 ± 0.17 and 10.08 ± 0.16 mm2. On the seventh day, it was seen that the size of the ulcer had almost closed, namely 0.03 ± 0.01 and 0.11 ± 0.07 mm2. These data analyses showed that treatment with areca nut and chrysanthemum oral gel caused significantly (p < 0.05) ulcer healing in a dose-dependent manner. Analysis of changes in body weight showed a significant increase in the F2 and positive control groups, while a significant decrease in body weight occurred in the F1 and F3 treatment groups (Table 2). Meanwhile, in the negative control group, there was a decrease in body weight, but it was not significant.\n\nNegative control: base gel treatment group (A and B); Positive control: triamcinolone acetonide treatment (C and D); F1 treatment: 20% areca nut:80% chrysanthemum (E and F); F2 treatment: 50% areca nut:50% chrysanthemum (G and H); F3 treatment: 80% areca nut:20% chrysanthemum (I and J).\n\nTo verify the mechanism of ulcer healing by areca nut and chrysanthemum oral gel, the ulcers were subjected to histological examination. As seen in Table 3, the mean of histological scores on the seventh day showed that positive control, F1, and F3 groups indicated that there were no ulcers in the epithelial layer, presence of fibrosis, and slight chronic inflammation in the conjunctive tissue. The score 0 indicating no ulcers and remodeling in the conjunctive tissue was seen in the negative control, F2, and normal groups, but significant differences between groups were not detected in histology examination. Analysis of photomicrograph of ulceration showed loss of ulcer with remodeled connective tissue and accompanied by a slight inflammatory infiltrate in Figure 2B, 2C, and 2E (score 1). There were no visible inflammations in Figure 2A, 2D, and 2F (score 0).\n\n(A) Negative control: base gel; (B) Positive control: triamcinolone acetonide in orabase; (C) F1: 20% areca nut:80% chrysanthemum; (D) F2: 50% areca nut:50% chrysanthemum; (E) F3: 80% areca nut:20% chrysanthemum; (F) Normal group: without ulcer and treatment (Hematoxylin and eosin, 40×).\n\nThe immunostaining for TNF-α aims to show changes in TNF-α expression released by connective tissue cells in the cytoplasm during the healing process (Figure 3). The increase in the expressions with a mean score of 2 (moderate) was showed by positive control (2.67 ± 0.58) and F2 groups (2.33 ± 0.58) (Table 3). The lower scores (1-mild) were seen in the negative control, F1, F3, and normal groups. This study showed significant differences between the six groups with changes in TNF-α expression. These results were in line with the pictures that revealed brown diffuse granular-like staining pattern of the connective tissue and epidermis in the Figure 3B and 3D, while the other groups did not show dominant TNF-α expressions except in the F3 group, the immunostaining of TNF-α was prominently found in the basal cell layer (Figure 3E).\n\n(A) Negative control: base gel; (B) Positive control: triamcinolone acetonide in orabase; (C) F1: 20% areca nut:80% and chrysanthemum; (D) F2: 50% areca nut:50% chrysanthemum; (E) F3: 80% areca nut:20% chrysanthemum; (F) Normal group: without ulcer and treatment (TNF-α immunostaining, 40×)\n\nThe results of red picrosirius staining on the last experimental day showed the highest collagen deposition in the F2 group with a mean of 25.4 ± 2.12, while the lowest collagen deposition while collagen deposition in low level was seen in the F3 group (5.63 ± 2.28) (Table 3). Figure 4B (Positive control) and 4D (F2 group) showed regular, dense, and thick collagen, whereas, in the negative control (Figure 4F), collagen deposition showed thin, irregular, and many empty gaps. The ANOVA analysis showed significant differences (p < 0.05) in collagen expression between groups (Table 3). The Tukey test demonstrated significant differences between F2 and F3 groups. Other significant differences were evaluated between F1, F2, F3, and negative control groups.\n\n(A) Negative control: base gel; (B) Positive control: triamcinolone acetonide in orabase; (C) F1: 20% areca nut:80% chrysanthemum; (D) F2: 50% areca nut:50% chrysanthemum; (E) F3: 80% areca nut:20% chrysanthemum; (F) Normal group: without ulcer and treatment (Picosirius red staining, 40×). Yellow arrow: Disintact collagen bundles. Blue arrow: Intact collagen bundles.\n\n\nDiscussion\n\nIn the present study, we demonstrated that application of the oral gel to ulcerated lesions for 6 days showed significant lesion healing in the composition of the oral gel containing balanced areca nut and chrysanthemum (50%:50%). This significant wound healing was based on the clinical appearance such as ulcer size reduction, reepithelization over the ulcer base, and formulation of granulation tissue around the ulceration. This result has the same clinical appearance as the positive control group that using triamcinolone acetonide. Areca nut, as one of the main ingredients, contains phenolic and flavonoids which function as antioxidants.19 Catechin is a component of flavonoids present in areca nut that acts as an antioxidant by chelating the ions and scavenging the free radicals particularly, superoxide (O2–), peroxyl, hydroxyl radicals (·OH), and hence inhibit both DNA damage and lipid peroxidation, which can cause membrane damage.20 Catechin can reduce the expression of interleukin-6 (IL-6) and IL-8 which function to overcome inflammation and increase the wound healing process by chemotactic for fibroblasts, accelerates their migration and stimulates deposition of tenascin, fibronectin, and collagen I during wound healing in vivo.21–24 The success of using areca nut in oral gel to heal the ulcers is in line with a previous study using ointment with 2% ethanolic extract on burns on the skin.10 This study also used a combination with chrysanthemum. Previous studies have shown that chrysanthemum has antioxidant, antiproliferative, antimicrobial, acetylcholine esterase inhibition, antitimelanogenic, and antiviral activities, especially Chrysanthemum morifolium, Chrysanthemum indicum, and Chrysanthemum coronarium. The active phytochemistry content of chrysanthemum is apigenin-7-O-glucoside.25\n\nThis present study observed the body weight of rats before and after application. There are similarities between ulcer repair and weight gain. A significant increase in body weight in the F2 and positive control showed faster healing of ulcers, making it easier for rats to consume more food. The use of healthy rats aims to evaluate the effect of ulcers in the oral cavity purely based on the ability of rats to gain healing process without being affected by systemic diseases that can affect rat’s body weight. Areca nut is capable of repressing prostaglandin E2 (PGE2) and arachidonic acid-induced inflammation, thereby helping to accelerate ulcer healing.26 The analgesic or antinociceptive activity of the areca nut is originated by inhibition of prostaglandin synthesis. The oral gel form was chosen to facilitate absorption in the oral mucosa and it has a rapid cool soothing effect, although the drawback is that the gel is easily soluble in saliva. Application twice a day in the morning and evening regularly showed a fairly good cicatrization process in both groups (F2 and positive control). The increase in body weight in the rat showed that in the last few days the diet was not disturbed by the size of the ulcer.\n\nHistological examination with HE staining on day seven showed no significant difference between all treatment groups, normal, positive, and negative control groups. The oral gel containing a balanced composition of areca nut and chrysanthemum, negative control, and normal groups did not show any ulcers and the epithelial tissue had been completely remodeled. Meanwhile, the other group still showed fibrosis and inflammation without ulcers. Fibrosis, persistent neutrophil infiltration, and poor angiogenesis in the ulcer base are factors involved in the underlying mechanism of delayed healing ulcers.27 The ulcer healing mechanism begins with ulcer base contraction which includes contraction of the ulcerated area, re-epithelization over the ulcer base, and formation of granulation tissue. The next step is epithelial regeneration and mucus secretion. This epidermal repair is regulated by a key growth factor (KGF) that is expressed at very high levels within 24 h of injury on dermal skin.28 The buccal mucosa is a non-keratinocyte layer, so it is probably the most involved in the re-epithelization process in the oral mucosa is salivary mucin. Mucin is the primary gel-forming component of mucus that provide a critical layer of protection on the wet epithelial surface including gastrointestinal, female genital, and respiratory tracts.29 Angiogenesis is the next step of ulcer healing. It allows the supply of nutrients and oxygen to the ulcerated area thereby giving the collagen in connective tissue and epithelium an opportunity to recover. Matrix formation is the last step of ulcer repair. This remodeling formation is regulated by the temporospatial expression of the fibrillar and basement membrane collagen (types I, III, IV), and matrix metalloproteinase-2 (MMP-2). Fibronectin is important for cell proliferation, adhesion, differentiation, and matrix formation.\n\nIn the present study, the analysis of TNF-α showed that the increase in the moderate expressions was showed by positive control and F2 groups. This is in line with research by Kobayashi et al. which showed that the water-soluble component in dried chrysanthemum has antioxidant ability to increase TNF-α. This activity was observed within 3 hours after ulcer formation.8 TNF-α is a cytokine produced primarily by immune cells such as monocytes/macrophages, but several cell types, such as T and B lymphocytes, natural killer cells, neutrophils, fibroblasts, and osteoclasts can also secrete TNF-α in smaller quantities. 30 TNF-α levels which had the same score between F2 and positive control on the seventh day showed that the amount of this cytokine was still high detected in the local connective tissue. Prolonged or remaining elevated expression of TNF-α may occur for up to the third to the fifth day following the traumatic injury.31 Prolonged increase in TNF-α especially in delayed healing reflects their augmented blood TNF-α, suggesting an association between impaired healing and hard work TNF-α in the inflammatory response so that wound healing is achieved.32 In this study, we did not examine the level of TNF-α in the blood so that the role of areca nut-chrysanthemum oral gel to accelerate wound healing systemically cannot be explored.\n\nTriamcinolone acetonide was chosen as a positive control because this preparation has efficacy as a synthetic corticosteroid that has anti-inflammatory, antipruritic, and anti-allergic effects. This preparation has the advantage of being an emollient dental paste that can attach the drug to the oral mucosal tissue so that it is not easily soluble in saliva. An important role of steroids in triamcinolone acetonide is to alter the localization of high junction proteins thereby increasing the adhesion density between epithelial cells.33 A tight epithelial protective barrier can be achieved through tight cell adhesion. Contacts between adjacent cells are made up of tight junctions, adherens junctions, and desmosomes which help in preserving tissue homeostasis. This study showed that with the use of triamcinolone acetonide and F2 group on the seventh day, the ulcers had closed tightly without any inflammation. These results prove that there might be a possibility of areca nut–chrysanthemum oral gel also can close the adhesion bonds between epithelial cells so that the level of wound closure density which is similar to that of the group positive control (triamcinolone acetonide).\n\nCollagenesis analysis showed a lot of collagen deposition in the F2 group. The results of this study are in line with the fact that the alkaloids in areca nut are potent inducers to increase the amount of collagen. Previous research has shown that a series of synthetic arecaidine esters by oral mucosa fibroblast was closely correlated with the extent of collagen synthesis.34 Alkaloids in the areca nut in a long term play a major role in the accumulation of collagen in oral submucous fibrosis (OSF). Collagen is a key component of the extracellular matrix that plays a critical role in the regulation of the phases of wound healing. Collagen exposure due to injury in the inflammatory phase will activate the clotting cascade, resulting in a fibrin clot that stops the initial bleeding. It also acts as potent chemoattractants for neutrophils, enhancing phagocytosis and immune response and modulating gene expressions. Collagen promotes anti-inflammatory, proangiogenic wound macrophage phenotype via microRNA signaling. In the angiogenesis phase, collagen stimulates angiogenesis in vitro and in vivo through the engagement of specific integrin receptors. The C-propeptide fragment of collagen I recruit endothelial cells, potentially triggering angiogenesis in the healing wound.35\n\nThe results of the evaluation of collagen deposition after treatment, with picrosirius red staining, showed a picture of collagen with thicker density, large fiber size, and lots of collagen fibrils in the oral gel with a balanced composition of areca nut and chrysanthemum and a positive control group. This shows the good work of collagen to repair wounds. What's interesting from this observation is that, although there were groups that received treatment with a higher composition of areca nut in oral gel, this was not able to induce collagen as in a balanced composition of areca nut and chrysanthemum. This explains that the ulcer healing rate in this study was not dose dependent but more dependent on the peak efficacy of each phytochemistry composition of an extract\n\n\nConclusion\n\nThe present study provides the activity of the healing effect of combination areca nut and chrysanthemum. This oral gel can improve ulcer wound healing through the role of TNF-α and collagen with the same results as topical steroid therapy.\n\n\nData availability\n\nDryad: Underlying data for ‘Evaluation of clinical, histology, TNF-α, and collagen expressions on oral ulcer in rats after treatment with areca nut and chrysanthemum oral gel’. https://doi.org/10.5061/dryad.8w9ghx3mw.\n\nThe project contains the following underlying data: body weight, oral ulcer’s size, histology and tnf-α score, collagen percentage.", "appendix": "References\n\nSeyyedi SA, Sanatkhani M, Pakfetrat A, et al.: The therapeutic effects of chamomilla tincture mouthwash on oral aphthae: A Randomized Clinical Trial. 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Bioeng. 2021; 8(63): 1–15." }	[ { "id": "91931", "date": "16 Aug 2021", "name": "Gunawan Indrayanto", "expertise": [ "Reviewer Expertise Analytical Method Development and its Validation", "Natural Product Chemistry", "Herbal Drugs" ], "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\nSome important methods and data were not reported:\nScientific identification of the plant was missing.\n\nStability evaluation of the extract was missing.\n\nNo validation data of the biological assays were reported, without any validation, the validity of the data cannot be confirmed (Z factors, Selective Index, etc.)\n\nNo need to report the significance statistic evaluations, data should be presented ad Mean +/- Confidence interval; p values cannot be trusted.\n\nAdd Gandevia et al. (20211) and related references.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "7131", "date": "10 Sep 2021", "name": "Liza Sari", "role": "Author Response", "response": "Scientific identification of the plant was missing. Response: This research is a series of research on the benefits of areca nut seeds that has been started in 2012. We have published several publications since 2016 using areca nut extract from the same source (Aceh Besar). We apologize for the negligence or forgetting to re-enter the scientific identification that has been done. We have re-entered the plant identification in the “Extract preparation” section in “Methods”. Thank you for your accuracy in reviewing. Stability evaluation of the extract was missing. Response: We have added the stability evaluation in the manuscript. No validation data of the biological assays were reported, without any validation, the validity of the data cannot be confirmed (Z factors, Selective Index, etc.) Response: We have included the validation data in the manuscript especially the selectivity index of areca nut and chrysanthemum. The studies of areca nut on oral squamous cell carcinoma cell lines (HSC-2 dan HSC-3 cell lines) and human dermal keratinocytes (HaCat cell lines) have been published in 2 previous journals: Sari LM, Subita GP, Auerkari EI. Potential antioxidant and cytotoxic activities of areca nut (Areca catechu Linn.) extract in human oral squamous cell carcinoma and keratinocyte cells. Asian J Pharm Clin Res 2017;10(10):286-91. Sari LM, Subita GP, Auerkari EI. (2019). Areca nut extract demonstrated the apoptosis-inducing mechanism by increased caspase-3 activities on oral squamous cell carcinoma F1000 Res, 7(723), 1-34. No need to report the significance statistic evaluations, data should be presented ad Mean +/- Confidence interval; p values cannot be trusted. Response: Data have been changed to “Mean ± SD, 95% CI, p-value”. Several statements in “Discussion” dan “Results” has undergone changes regarding data interpretations. Add Gandevia et al. (2021) and related references. Response: We have added: Gandevia S. Replication: Do not trust your p-value, be it small or large. J Physiol 2021;599(11):2989-90." } ] }, { "id": "90097", "date": "24 Sep 2021", "name": "Nurrul Shaqinah Nasaruddin", "expertise": [ "Reviewer Expertise pathology", "histology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe major concern of this manuscript is the technique of treatment process. While the rats are fully awake, it is very difficult to apply the topical on the ulcerated buccal mucosa. The rats will chew the probe and it is very difficult to visualize the lesions for monitoring. Since the mucosal epithelium is highly dividing cells, how sure are you the healing occur due to treatment given?\n\nAmong all inflammatory cytokines, why TNF-alpha was chosen?\n\nThe contrast color for special staining picrosirius red should be yellow and red, and the red indicates positive for collagen. However, the pictures were lacked with the contrast and all the tissues appear homogenously red.\n\nThe author should briefly explain the histology findings in the figure legend.\n\nThe clinical evaluation results were contradicted with histology evidence, whereby the author mentioned that the ulcer is almost healed. but histologically, it showed complete healing with thick stratified epithelium.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "7235", "date": "08 Oct 2021", "name": "Liza Sari", "role": "Author Response", "response": "Dear Reviewer, I would like to respond to the comment's report: 1. The major concern of this manuscript is the technique of the treatment process. While the rats are fully awake, it is very difficult to apply the topical on the ulcerated buccal mucosa. The rats will chew the probe and it is very difficult to visualize the lesions for monitoring. Since the mucosal epithelium is highly dividing cells, how sure are you the healing occur due to treatment given? Answer: In this study, we performed oral gel application on the buccal mucosa of the rat twice a day at 8 am and 8 pm. This application is by holding the rats, opening his mouth gently and slowly, then applying to the wound and holding it for about 20-30 seconds. After that, the mice were isolated briefly for 1 hour to avoid eating and drinking. We try our best to make the gel last well even if it's only for a few minutes, considering that this gel dissolves easily in saliva. We have acknowledged that this is one of the limitations of this study. We hope that with further research, we can make a formulation of topical oral gel in orabase so that it can last longer in the mouth. However, despite the brief application of the buccal mucosa, cellular changes can be seen differently on immunohistochemistry examination and collagenase assay after seven days of treatment. The extent of absorption of materials through the skin or oral mucosa depends on the surface area over which the substance is applied, the concentration of the substance administered, the lipid solubility of the material or vehicle, whether the skin surface is intact, the skin thickness at the site of application, the length of time that the material is in contact with the skin surface, and the degree of skin hydration and surface occlusion, in that covered and well-hydrated skin absorbs substances faster than does uncover or dry skin. The surface of the buccal mucosa is covered by non-keratinized stratified squamous epithelium. Keratinized mucosa is less permeable to the drugs as compared to the non-keratinized mucosa. This causes the buccal mucosa to more easily absorb the drug than the gingiva and palate. The turnover of the buccal epithelium which is due to differentiation and desquamation of the epithelium also accelerates the wound healing process happens faster. The turnover time for the buccal epithelium has been estimated at 14 days. Oral mucosa is well-hydrated skin that can absorb substances faster than dry skin. We have added this explanation in the “Discussion” section. 2. Among all inflammatory cytokines, why TNF-alpha was chosen? Answer: This research was initiated with lesions originating from simple injuries. We hope that the development of the results of this study can help the development of herbal extracts to accelerate the healing of oral diseases such as mucositis, RAS, and traumatic ulcers. The reason why we choose TNF-α is that TNF-α is a central regulator of inflammation. TNF-α is also a crucial cytokine in the establishment and maintenance of inflammation in multiple autoimmune diseases. Although its precise role in wound healing is not fully understood, however, Ritsu et al. (Ritsu M, Kawakami K, Kanno E, et al. Critical role of tumor necrosis factor-α in the early process of wound healing in skin. J. Dermatol. Dermatol. Surg. 2017. Vol 21(1). 14-19) reported that TNF-α is involved in the early process of wound healing. It is quickly released and initiates inflammation at wound tissues. The wound healing was accelerated on day 3 when mice were treated with bioactive TNF-α. Another previous study reported that impaired healing in animal models and age-related delayed healing of acute human wounds exhibit raised local and systemic levels of TNF-α that may parallel the pro-inflammatory phenotype. Despite previous studies showed varying results, there is an interest in observing the effect of TNF-α levels in ulcer healing after application of an oral topical gel. 3. The contrast color for special staining picrosirius red should be yellow and red, and the red indicates positive for collagen. However, the pictures lacked contrast and all the tissues appear homogenously red. The resulting photos consist of two types; polarized and non-polarized light microscopy. The polarized colors of Picosirius red staining depend only on fiber thickness and packing, not on the composition of the specific collagen type within collagen bundles. Under polarized light, the oral mucosa sections seem to show collagen type 1 which showed thicker and denser fibers on the seventh day. We don't know why the red color was very generalized in the oral mucosa section although the Picosirius staining was done according to the standard procedure (as you can see in Figures 1a and b, the section was taken from one of the photos of positive control). We searched the reason from another source (Kiernan JA. Sirius red for collagen staining protocol. The University of Western Ontario, Canada). It was said that if we used the polarized light, sometimes we will lose \"the yellow background\" of picric acid staining. The loss of the yellow cytoplasmic background is probably caused by the dehydrating process. Figure 1.a. Polarized light microscopy (Positive control) Figure 1. b. Non-polarized light microscopy (Positive control) 4. The author should briefly explain the histology findings in the figure legend. Thank you for the advice given. We have added the histology findings in the figure legend. 5. The clinical evaluation results were contradicted histology evidence, whereby the author mentioned that the ulcer is almost healed. but histologically, it showed complete healing with thick stratified epithelium. All measurements were performed by the same operator. We analyzed the ulcers directly and through photos. Histological examination results were analyzed several weeks after the visual examination was performed. At that time, some lesions showed the tip of the wound still have a light and thin ulcer while the other end had healed completely. The clinical examination data are the actual data based on our observations before seeing the histological results. The histological score showed that the group F1, F3, and positive control (Figure 2) had a score of 1. The normal, negative control and F2 showed a score of 0. We decided to perform the first data just the way they were without adjusting with the histological assessment." } ] } ]	1	https://f1000research.com/articles/10-623
https://f1000research.com/articles/12-188/v1	16 Feb 23	{ "type": "Systematic Review", "title": "Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis", "authors": [ "Valeska Candrawinata", "Ricarhdo Hanafi", "Bernard Agung Baskoro", "Andry Irawan", "Christofani Ekapatria", "Natalia Maria Christina", "Heru Sutanto Koerniawan", "Freda Halim", "Ricarhdo Hanafi", "Bernard Agung Baskoro", "Andry Irawan", "Christofani Ekapatria", "Natalia Maria Christina", "Heru Sutanto Koerniawan", "Freda Halim" ], "abstract": "Introduction: Acute appendicitis is the most common surgical emergency in pregnant women. There has been a wide variance in clinical practice worldwide, with some favoring an antibiotic-only approach while others prefer surgery as the first-line management. Therefore, we designed the current analysis to synthesize the available evidence on the efficacy and safety of antibiotics versus surgery management. Methods: We searched PubMed, Scopus, EuropePMC, and Cochrane Central from March 4, 1904 until November 25, 2022, to look for studies comparing antibiotics and surgery in pregnant patients with acute appendicitis. We only included studies that provided a comparison between the two treatments. We included preterm delivery, fetal loss, maternal death, and complications as outcomes. The results were compared using an odds ratio and 95% confidence interval. We also performed a sensitivity analysis by excluding studies with a serious risk of bias. Results: We included five non-randomized studies for the analysis. We found that patients in the antibiotic group had a lower risk of preterm labor (OR 0.63 [95% CI 0.43–0.92]; p 0.02) but a higher risk of complications (OR 1.79 [95% CI 1.19–2.69]; p 0.005). We did not find any difference in the other outcomes. Conclusion: The increased risk of complications should caution clinicians about using antibiotics as the first-line management. More studies are required to identify patients who would benefit the most before antibiotics could be adopted as a treatment for acute appendicitis in pregnant patients.", "keywords": [ "Antibiotic", "Surgery", "Acute Appendicitis", "Pregnant" ], "content": "Introduction\n\nThe prevalence of acute appendicitis in pregnancy is quite high, making it one of the most common surgical emergencies in the pregnant population. Its prevalence ranges from 1 in 700 to 1500 live births.1–3 Although not as common as other non-surgical emergencies, acute appendicitis has dire consequences both for the mother and her fetus. Acute appendicitis correlates with placental abruption, preterm labor, fetal loss, and even maternal death.\n\nAcute appendicitis in pregnancy could be treated with surgery, either open or laparoscopic appendectomy, or with antibiotics alone. The 2020 update of the World Society of Emergency Surgery (WSES) Jerusalem guidelines gave a low-strength recommendation against treating acute appendicitis non-operatively during pregnancy and recommended using laparoscopic appendectomy.4 One of the reasons for this recommendation was the lack of high-level evidence, where they only considered three studies, of which two were case reports. As a result, clinical practices regarding the treatment of acute appendicitis in pregnancy worldwide continued to vary from one region to another. In Korea, 25% of pregnancy affected by acute appendicitis was treated conservatively,5 compared to 63% in China,6 67% in Japan,7 and 45% in the United States of America.8 This wide variance and high usage of conservative strategy could mean that not all clinicians adopted the existing guideline.\n\nSome considerations for treating acute appendicitis conservatively were the lack of surgical resources, patient’s preference, and uncomplicated type of appendicitis. There has also been controversy regarding the type of appendectomy, with one systematic review reporting a higher proportion of fetal loss in patients treated with laparoscopic appendectomy.9 Moreover, two meta-analyses have reported that antibiotics treatment alone for uncomplicated appendicitis in the general population had a lower rate of complications, with an acceptable, albeit lower, rate of success.10,11 Therefore, seeing the lack of strong evidence and variance in clinical practice, we planned the current review to identify the efficacy and safety of conservative treatment in the treatment of acute appendicitis in pregnancy.\n\n\nMethods\n\nWe searched PubMed, Scopus, EuropePMC, and Cochrane Central from the March 4, 1904 until November 25, 2022, using the following keywords: [“acute appendicitis” or “appendicitis” and “pregnancy” and “conservative” or “antibiotic” or “antibiotics”]. We also reviewed the bibliographies of relevant studies to identify any other studies. We only included English-language literature. The initial search and screening were done by two independent authors. Any discrepancies were resolved by discussion with a third author.\n\nThe inclusion criteria were: 1) types of patients: pregnant patients with uncomplicated and complicated acute appendicitis; 2) types of intervention: conservative management with antibiotics alone; 3) types of comparison: open or laparoscopic appendectomy; 4) analyzed outcomes: preterm delivery, fetal loss, maternal death, and complications; and 5) types of studies: prospective and retrospective studies. We defined complications as those arising from the pathological processes or treatment, including, but not limited to, sepsis or septic shock, pneumonia, venous thromboembolism (VTE), and surgical site infection. Studies that did not provide the aforementioned variables as outcomes were excluded. We excluded review articles, editorials, case reports, and case series. This analysis was started in July 31, 2022 and finished in November 9, 2022.\n\nAfter the studies were selected, two authors independently extracted the data on study authors, publication year, study design, patients’ characteristics, treatment characteristics, and outcomes using a standardized form. Patients were then dichotomized according to the treatment they received.\n\nWe inputted patients’ data in a 2-by-2 contingency table according to the analyzed outcomes. We compared each outcome between conservative and surgical groups using odds ratios (OR) and 95% confidence intervals (CI). Heterogeneity among studies was evaluated using the I2 statistic and Cochrane Q-statistic test. An I2 value higher than 40% or a P value higher than 0.10 indicated a significant presence of heterogeneity. However, a random-effect model was used regardless of heterogeneity because we expected the studies to have significant differences in the choice of antibiotics. We also planned a subgroup analysis according to whether the studies’ participants had uncomplicated or complicated appendicitis. As performing a randomized controlled trial on a pregnant population is ethically difficult, we expected most studies to be non-randomized. Therefore, we also planned a sensitivity analysis by excluding studies with a serious risk of bias.\n\nWe assessed the risk of bias using the Cochrane risk-of-bias tool (The Cochrane Collaboration) for randomized studies and the Risk of Bias in Non-randomized Studies - of Intervention tool (ROBINS-I) for non-randomized studies. We used a funnel plot analysis to assess publication bias. We graded the strength of evidence for each outcome using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. We used the Review Manager version 5.4 (The Cochrane Collaboration) (https://training.cochrane.org/online-learning/core-software/revman/revman-5-download) program for all statistical analysis. We conducted this study according to the 2015 PRISMA guidelines for a systematic review. This review has been registered at The International Prospective Register of Systematic Reviews (PROSPERO) under the registration number CRD42022371119.\n\n\nResults\n\nOur initial search resulted in 3,275 records. After duplicate removal, 2,165 titles and abstracts were screened. This initial screening resulted in 92 studies being sought for retrieval. All studies were retrieved, and we assessed their full texts for eligibility. We excluded 87 studies because they did not provide a comparison between antibiotics and surgery and did not provide data on the outcomes we planned to analyze. Finally, five studies were included for final analysis (Figure 1).6,7,12–14\n\nThe characteristics of the included studies are presented in Table 1. All of the studies were non-randomized and mostly retrospective. Patients were mostly 25 to 35 years old and in their second trimester. Liu et al. included only uncomplicated appendicitis case6 while Abbasi et al., Nakashima et al., and Vasileiou et al. included both complicated and uncomplicated appendicitis case.7,13 However, Yang et al. did not report the severity of appendicitis in their samples.14 Four studies reported their antibiotic use.6,7,12,14 Third-generation cephalosporin was the main choice. Five studies reported surgery type, and all used either open or laparoscopic appendectomy.6,7,12,14\n\n* Mean.\n\n† Median.\n\nWe used the ROBINS-I tool to assess the risk of bias, and the results are presented in Table 2. We judged the study by Nakashima et al. to have a serious risk of bias because there was a significantly higher rate of complicated appendicitis in the surgery group. We assessed the remaining study to be of moderate risk of bias because confounding had been sufficiently controlled. However, the possibility of unmeasured confounding variables inherent in the design of non-randomized studies gave a moderate risk of confounding bias. We judged bias from the outcome measurement to be low because although no blinding was used, the outcomes were fairly objective. We did not perform analysis for publication bias because funnel plot analysis or other statistical methods did not have enough power to detect bias in a small number of studies.\n\nTwo studies with a total of 10,325 patients assessed the occurrence of preterm labor. Overall, patients in the antibiotic group had a significantly lower risk of preterm delivery (OR 0.63 [95% CI 0.43–0.92]; p 0.02) (Figure 2).\n\nThree studies with a total of 10,494 patients assessed the occurrence of fetal loss. Overall, there were no significant differences in fetal loss between the two groups (OR 1.02 [95% CI 0.84–1.24]; p 0.81) (Figure 3).\n\nFrom the two studies with a total of 223 patients, there was no report of maternal death either in the antibiotic or the surgery group. Therefore, a meta-analysis could not be performed.\n\nFour studies with a total of 7,378 patients assessed complications. Abbasi et al. included sepsis, septic shock, peritonitis, and VTE as complications. Liu et al. reported one grid iron complication in the surgery group. Nakashima et al. included surgical site infection, VTE, and pneumonia as complications. Lastly, Vasileiou et al. used Clavien-Dindo complications. Overall, there was a lower risk of complications in the antibiotic group, but it was not statistically significant (OR 0.72 [95% CI 0.16–3.32]; p 0.68) (Figure 4). However, only Abbasi et al. reported peritonitis, and they found that patients in the antibiotic group significantly had a higher rate of peritonitis (28.8% vs. 19.8%; p < 0.001).\n\nWe excluded the study by Nakashima et al. in our sensitivity analysis. Regarding fetal loss, the result did not differ from our primary analysis. However, regarding the outcome, we found that patients in the antibiotic group significantly had a higher rate of complications (OR 1.79 [95% CI 1.19–2.69]; p 0.005) (Figure 5).\n\nThe certainty of the evidence was very low to low (Table 3). Evidence regarding fetal loss and complication had a serious risk of bias and inconsistency, so we judged them to be of very low quality. Evidence regarding fetal loss did not have serious concerns, but we assessed them to be of low quality due to the observational design of studies. Table 3 gives a summary of the assessment.\n\n* One study rated as having a serious risk of bias. Downgraded by one point.\n\n† 95% CI overlaps no effect. Downgraded by one point.\n\n‡ I2 > 40%. Downgraded by one point.\n\n\nDiscussion\n\nOur analysis showed that conservative management of acute appendicitis in pregnant patients resulted in a lower risk of preterm labor (OR 0.63 [95% CI 0.43–0.92]; p 0.02). The rate of complications in our primary analysis was also comparable between the two groups. However, after excluding the study by Nakashima et al. in our sensitivity analysis, we found that antibiotic treatment resulted in a significantly higher risk of complications (OR 1.79 [95% CI 1.19–2.69]; p 0.005). The result of this analysis mainly came from the study by Abbasi et al., which had the highest number of participants. Abbasi et al. was also the only one that reported the occurrence of sepsis and peritonitis.12 Several newer studies have suggested that conservative management is a safe option in treating acute appendicitis in the pregnant population.6,7,13 Interestingly, none of those studies found any occurrence of sepsis and peritonitis. We suspected those studies did not have adequate statistical power to detect those complications. Immunological changes during pregnancy are one of the possible reasons for an increase in infectious complication, such as peritonitis and sepsis. Immune response in patients with acute appendicitis includes increased neutrophil and C-reactive Protein (CRP).15 During pregnancy, there is evidence of increased neutrophil activation, but its activity and phagocytosis function are limited.16 In conclusion, decreased activities of activated neutrophils in pregnancy may explain higher rates of infectious complications, such as sepsis, in the pregnant population.\n\nAnother concern is the difference in the number of patients with complicated appendicitis. Abbasi et al. in their study, had 20.3% of the study population diagnosed with complicated appendicitis,12 Vasileiou et al. had 25%,13 while Liu et al. only included patients with uncomplicated appendicitis.6 Liu et al. in their study, expectedly did not report a higher complication rate in the antibiotic group.6 However, Vasileiou et al., comparable with the study by Abbasi et al. in terms of patients with complicated appendicitis also reported a lower rate of complication.13 This made it difficult to arrive at a definite conclusion on whether patients with complicated appendicitis could benefit from conservative management.\n\nDespite a higher risk of complications, we found that conservative management reduced the risk of preterm labor. Therefore, the potential benefits of conservative management should not be crossed out just yet. Two meta-analyses on non-pregnant patients also concluded that conservative management is a viable option.10,11 Aside from the studies included in the analysis, there were two studies that also supported the use of antibiotic for acute appendicitis in the pregnant population. However, we excluded those two studies because they did not provide a comparison with a control group.5,17 Rather than focusing solely on comparing the efficacy and safety between conservative and surgical approaches, more attention should be given to tailoring a strategy for each patient. Several studies have identified predictors for the failure of conservative management in non-pregnant patients, such as high serum C-reactive protein, presence of appendicolith, diabetes, longer duration of symptoms, higher temperature, higher Alvarado score, and larger appendiceal diameter.18–20 However, those studies only studied patients with uncomplicated appendicitis.\n\nDiagnosis of acute appendicitis in pregnancy also has its consideration. Negative appendectomy in the pregnant population ranges from 25 to 50%, higher than those in the general population, which only ranges from 15 to 35%.21 To reduce unneeded surgery, radiographical imaging is usually ordered to supplement the diagnosis. As computed tomography (CT) scan is often contraindicated in pregnant patients, ultrasonography and magnetic resonance imaging (MRI) are the main radiographical modalities for diagnosing appendicitis. As ultrasonography has a low sensitivity and specificity, MRI is often warranted in patients with a negative ultrasonography finding.22,23 However, MRI is not widely available, especially in low to middle-income settings. Therefore, in those settings, it can be expected that a significant number of pregnant patients with suspected appendicitis would receive a misdiagnosis. In a pregnant patient with a doubtful clinical presentation of acute appendicitis and a negative ultrasonography finding, a conservative approach might be appropriate as first-line management. However, a surgical approach should always be preferred for a patient with a set of specific and characteristic symptoms of acute appendicitis.\n\nWe listed comparison as surgical treatment, either open or laparoscopic based on insufficient evidence of suspected association between laparoscopic appendectomy and miscarriage. This association needs further research which results in no recommendation of one method superior of the other. Furthermore, resources needed to carry out laparoscopic procedures in developing countries are still limited - hence open appendectomy remains a viable and equal option.23\n\nOne limitation of the available studies on this subject is the lack of information on whether appendicitis recurred or not after conservative management. Vasileiou et al. reported that patients in the antibiotic and surgery group had a comparable emergency department (ED) return rate after 30 days.13 However, they did not specify the reason for the ED visit. One meta-analysis by Sallinen et al. found that 8.5% of patients in the antibiotic group required an appendectomy within one month.10 Future studies intending to study conservative management for acute appendicitis in pregnant patients should include recurrence as one of the outcomes.\n\nAdditionally, the use of tocolytic agents was not mentioned in any of the journals included in this review. Although there had been some evidence in the past regarding the function of tocolytic agents administration for pregnant women undergoing surgery, latest systematic review and recommendation do not recommend its use because it has not been shown to improve outcomes.24 Lastly, the studies did not provide information regarding complications in accordance with each trimester. There has been evidence in the past regarding lower risk of acute appendicitis in the third trimester of pregnancy, therefore, future studies should evaluate any complication in accordance with the patients’ trimester.25\n\nOur analysis has several limitations. One limitation is the small number of studies and the non-randomized design. It is indeed difficult to perform a clinical trial on pregnant patients. Therefore, future cohorts should be carefully designed as they are the main modality to address this issue. Another limitation is the potential risk of confounding bias. We addressed this issue by performing a sensitivity analysis. However, unmeasured confounding inherent in the design of cohort studies remained a problem.\n\n\nConclusion\n\nPatients in the antibiotic group had a significantly lower risk of preterm labor but a higher risk of complications. Seeing the result and the available evidence, we suggested that conservative management should not be given indiscriminately to pregnant patients until it is found which patients could benefit the most from such a strategy. Conservative management must also be given with close and routine monitoring to prevent life-threatening complications, such as sepsis and peritonitis. Nevertheless, the potential benefit should warrant future studies addressing the identified concerns, namely patient selection and recurrence.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis, https://doi.org/10.5281/zenodo.7538790. 26\n\nThis project contains the following extended data:\n\n- Database and Literature Search\n\n- Fig 1. PRISMA flow diagram.\n\n- Fig 2. Forest plot showing preterm delivery between antibiotic and surgery group.\n\n- Fig 3. Forest plot showing fetal loss between antibiotic and surgery group.\n\n- Fig 4. Forest plot showing complications between antibiotic and surgery group.\n\n- Fig 5. Forest plot showing the sensitivity analysis for fetal loss (A) and complications (B) between antibiotic and surgery group.\n\n- Table 1. Characteristics of Included Studies.\n\n- Table 2. Risk of bias assessment The Risk of Bias in Non-Randomized Studies – of Interventions (ROBINS-I) tool.\n\n- Table 3. Certainty of evidence.\n\nZenodo: PRISMA checklist for ‘Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis’, https://doi.org/10.5281/zenodo.7538790. 26\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbbasi N, Patenaude V, Abenhaim HA: Evaluation of obstetrical and fetal outcomes in pregnancies complicated by acute appendicitis. Arch. Gynecol. Obstet. 2014; 290(4): 661–667. PubMed Abstract \| Publisher Full Text\n\nAndersen B, Nielsen TF: Appendicitis in pregnancy, Diagnosis, management and complications. Acta Obstet. Gynecol. Scand. 1999; 78(9): 758–762. Publisher Full Text\n\nMourad J, Elliott JP, Erickson L, et al.: Appendicitis in pregnancy: New information that contradicts long-held clinical beliefs. Am. J. Obstet. Gynecol. 2000; 182(5): 1027–1029. PubMed Abstract \| Publisher Full Text\n\nDi Saverio S, Podda M, De Simone B, et al.: Diagnosis and treatment of acute appendicitis: 2020 update of the WSES Jerusalem guidelines. World J. Emerg. Surg. 2020; 15(1): 27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIl JJ, Park HC, Kim MJ, et al.: Outcomes of Antibiotic Therapy for Uncomplicated Appendicitis in Pregnancy. Am. J. Med. 2017; 130(12): 1467–1469. PubMed Abstract \| Publisher Full Text\n\nLiu J, Ahmad M, Wu J, et al.: Antibiotic is a safe and feasible option for uncomplicated appendicitis in pregnancy - A retrospective cohort study. Asian J. Endosc. Surg. 2021; 14(2): 207–212. PubMed Abstract \| Publisher Full Text\n\nNakashima M, Takeuchi M, Kawakami K: Clinical Outcomes of Acute Appendicitis During Pregnancy: Conservative Management and Appendectomy. World J. Surg. 2021; 45(6): 1717–1724. PubMed Abstract \| Publisher Full Text\n\nAshbrook M, Cheng V, Sandhu K, et al.: Management of Complicated Appendicitis during Pregnancy in the US. JAMA Netw. Open. 2022; 5(4): E227555. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChakraborty J, Kong JC, Su WK, et al.: Safety of laparoscopic appendicectomy during pregnancy: a systematic review and meta-analysis. ANZ J. Surg. 2019; 89(11): 1373–1378. PubMed Abstract \| Publisher Full Text\n\nSallinen V, Akl EA, You JJ, et al.: Meta-analysis of antibiotics versus appendicectomy for non-perforated acute appendicitis. Br. J. Surg. 2016; 103(6): 656–667. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPoprom N, Numthavaj P, Wilasrusmee C, et al.: The efficacy of antibiotic treatment versus surgical treatment of uncomplicated acute appendicitis: Systematic review and network meta-analysis of randomized controlled trial. Am. J. Surg. 2019; 218(1): 192–200. PubMed Abstract \| Publisher Full Text\n\nAbbasi N, Patenaude V, Abenhaim HA: Management and outcomes of acute appendicitis in pregnancy - Population-based study of over 7000 cases. BJOG Int. J. Obstet. Gynaecol. 2014; 121(12): 1509–1514. PubMed Abstract \| Publisher Full Text\n\nVasileiou G, Eid AI, Qian S, et al.: Appendicitis in Pregnancy: A post-hoc analysis of an EAST multicenter study. Surg. Infect. 2020; 21(3): 205–211. PubMed Abstract \| Publisher Full Text\n\nYang J, Wen SW, Krewski D, et al.: Association of treatments for acute appendicitis with pregnancy outcomes in the United States from 2000 to 2016: Results from a multi-level analysis. PLoS One. 2021; 16(12 December): e0260991. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeeters T, Martens S, D’Onofrio V, et al.: An observational study of innate immune responses in patients with acute appendicitis. Sci. Rep. 2020; 10(1): 17352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbu-Raya B, Michalski C, Sadarangani M, et al.: Maternal Immunological Adaptation During Normal Pregnancy. Front. Immunol. 2020; 11: 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarstens AK, Fensby L, Penninga L: Nonoperative Treatment of Appendicitis during Pregnancy in a Remote Area. Am. J. Perinatol. Rep. 2018; 08(01): e37–e38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoftus TJ, Brakenridge SC, Croft CA, et al.: Successful nonoperative management of uncomplicated appendicitis: predictors and outcomes. J. Surg. Res. 2018; 222: 212–218.e2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShindoh J, Niwa H, Kawai K, et al.: Predictive factors for negative outcomes in initial non-operative management of suspected appendicitis. J. Gastrointest. Surg. 2010; 14(2): 309–314. PubMed Abstract \| Publisher Full Text\n\nTsai MC, Lin HC, Lee CZ: Diabetes increases the risk of an appendectomy in patients with antibiotic treatment of noncomplicated appendicitis. Am. J. Surg. 2017; 214(1): 24–28. PubMed Abstract \| Publisher Full Text\n\nKave M, Parooie F, Salarzaei M: Pregnancy and appendicitis: A systematic review and meta-analysis on the clinical use of MRI in diagnosis of appendicitis in pregnant women. World J. Emerg. Surg. 2019; 14(1): 37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaruch Y, Canetti M, Blecher Y, et al.: The diagnostic accuracy of ultrasound in the diagnosis of acute appendicitis in pregnancy. J. Matern. Neonatal Med. 2020; 33(23): 3929–3934. PubMed Abstract \| Publisher Full Text\n\nKonrad J, Grand D, Lourenco A: MRI: first-line imaging modality for pregnant patients with suspected appendicitis. Abdom. Imaging. 2015; 40(8): 3359–3364. PubMed Abstract \| Publisher Full Text\n\nBall E, Waters N, Cooper N, et al.: Evidence-Based Guideline on Laparoscopy in Pregnancy: Commissioned by the British Society for Gynaecological Endoscopy (BSGE) Endorsed by the Royal College of Obstetricians & Gynaecologists (RCOG). Facts, Views Vis. ObGyn. 2019; 11(1): 5–25. PubMed Abstract Reference Source\n\nZingone F, Sultan AA, Humes DJ, et al.: Risk of acute appendicitis in and around pregnancy a population-based cohort study from england. Ann. Surg. 2015; 261(2): 332–337. PubMed Abstract \| Publisher Full Text\n\nCandrawinata VS, Hanafi RV, Baskoro BA, et al.:Antibiotic versus surgery in the treatment of acute appendicitis in the pregnant population: A systematic review and meta-analysis. [Dataset]. Zenodo. 2022. Publisher Full Text" }	[ { "id": "195177", "date": "01 Sep 2023", "name": "Rıfat Peksöz", "expertise": [ "Reviewer Expertise My areas of expertise are general surgery", "especially acute appendicitis. Surgery interest: (General surgery", "Gastrointestinal diseases): Emergencies in general surgery", "ERCP", "Endoscopy-colonoscopy", "endoscopic interventions", "colo-rectal diseases (colorectal cancers", "diverticülitis)", "stomach diseaes (gastric cancer)", "gastrointestinal cancers", "open or laparoscopic hernias (groin hernias", "incisional", "umbilical)", "anorectal diseases (pilonidal sinüs", "hemorrhoid", "anal fissure", "perianal fistüla...)", "gallbladder surgery", "spleen surgery", "bariatric surgery (morbid obesity)", "nissen fundoplication." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors aimed to investigate the current review to identify the efficacy and safety of conservative treatment in the treatment of acute appendicitis in pregnancy in this study.\nAcute appendicitis is the most frequently seen surgical emergency in pregnant women and the most frequently encountered cause of non-obstetric acute abdomen. Due to the physiological and anatomical changes that occur during pregnancy and the limited use of radiological methods, it is difficult to diagnose AA during pregnancy. These conditions increase the risk of morbidity and mortality. Studies on acute appendicitis in pregnant women will provide a better understanding of this issue. In this regard, this study is very important in terms of contributing to the literature. Howewer, some issues should be raised from my point of view. I hope my comments contribute to your article, good luck to the authors.\nPlagiarism rate: didn’t evaluate because of this paper’s pre-review form published on the F1000 research page.\nComments to the author(s):\nIn the Abstract section, the complications which are seen more in the results section should be mentioned a little bit. This can be difficult to do, but when researchers read the articles, they read the abstract first. It is important to provide this information in order for the study to be more effective.\n\nKeywords should be rewritten, comments; Add 'antibiotic therapy' instead of 'Antibiotic'. Add 'Pregnancy' instead of 'pregnant', and, add outcomes or complications words.\n\nIn your article, it was emphasized that the treatment of acute appendicitis in pregnant women is controversial, but in the introduction section, only the superiority of antibiotic therapy was emphasized, and the study highlighting surgery was not emphasized. I recommend that this study with good surgical results be emphasized in this section.\n\nDiscussion section: ‘’Immunological changes during pregnancy are one of the possible reasons for an increase in infectious complication, such as peritonitis and sepsis. Immune response in patients with acute appendicitis includes increased neutrophil and C-reactive Protein (CRP)’’.(15, doi: 10.1111/ans.17443) I suggest adding an additional reference at the end of this sentence. Our work on this subject is up-to-date and has received many references in a short time (Peksöz et al., 20221).\n\nDiscussion section: \"We listed comparison as surgical treatment, either open or laparoscopic based on insufficient evidence of suspected association between laparoscopic appendectomy and miscarriage. This association needs further research which results in no recommendation of one method superior of the other. Furthermore, resources needed to carry out laparoscopic procedures in developing countries are still limited - hence open appendectomy remains a viable and equal option.23\"\n\nDisadvantages of LA were mentioned in your article, but Laparascopic appendectomy has been routinely applied in pregnant women today. Although the subject of your study is antibiotic treatment or surgical treatment, this current information should be renewed and reviewed. An important study demonstrated the superiority of LA. ‘’Compared with OA, LA was associated with lower wound infection rates and shorter LOS. Based on our results and recent literatures, we suggest that LA shows non-inferior safety with respect to pregnancy outcomes but superior with regard to surgical outcomes compared with OA in pregnant women with suspected appendicitis’’ (Lee et al., 20192).\n\nEvaluation report: Congratulations to the authors for good work, this study well written. Introduction, materials and methods, results and discussion sections of the article have enough scientific knowledge. I think it is acceptable for indexing after minör revisions.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [ { "c_id": "10153", "date": "06 Oct 2023", "name": "Valeska Candrawinata", "role": "Author Response", "response": "Dear Reviewer, we thank you for your kind review and insightful notes. We have revised the manuscript accordingly. In the Abstract section, the complications which are seen more in the results section should be mentioned a little bit. This can be difficult to do, but when researchers read the articles, they read the abstract first. It is important to provide this information in order for the study to be more effective. Response: We have revised the abstract accordingly and added more information about the complications in the abstract. Keywords should be rewritten, comments; Add 'antibiotic therapy' instead of 'Antibiotic'. Add 'Pregnancy' instead of 'pregnant', and, add outcomes or complications words. Response: We have revised the keywords accordingly. In your article, it was emphasized that the treatment of acute appendicitis in pregnant women is controversial, but in the introduction section, only the superiority of antibiotic therapy was emphasized, and the study highlighting surgery was not emphasized. I recommend that this study with good surgical results be emphasized in this section. Response: We have revised this section accordingly and added them. Discussion section: ‘’Immunological changes during pregnancy are one of the possible reasons for an increase in infectious complication, such as peritonitis and sepsis. Immune response in patients with acute appendicitis includes increased neutrophil and C-reactive Protein (CRP)’’.(15, doi: 10.1111/ans.17443) I suggest adding an additional reference at the end of this sentence. Our work on this subject is up-to-date and has received many references in a short time (Peksöz et al., 20221). Response: We have added the reference. Discussion section: \"We listed comparison as surgical treatment, either open or laparoscopic based on insufficient evidence of suspected association between laparoscopic appendectomy and miscarriage. This association needs further research which results in no recommendation of one method superior of the other. Furthermore, resources needed to carry out laparoscopic procedures in developing countries are still limited - hence open appendectomy remains a viable and equal option.23\" Response: We have revised the article accordingly. Disadvantages of LA were mentioned in your article, but Laparascopic appendectomy has been routinely applied in pregnant women today. Although the subject of your study is antibiotic treatment or surgical treatment, this current information should be renewed and reviewed. An important study demonstrated the superiority of LA. ‘’Compared with OA, LA was associated with lower wound infection rates and shorter LOS. Based on our results and recent literatures, we suggest that LA shows non-inferior safety with respect to pregnancy outcomes but superior with regard to surgical outcomes compared with OA in pregnant women with suspected appendicitis’’ (Lee et al., 20192). Response: We have revised the article accordingly." } ] } ]	1	https://f1000research.com/articles/12-188
https://f1000research.com/articles/11-1575/v1	23 Dec 22	{ "type": "Research Article", "title": "CHARACTERIZATION OF BY-PRODUCTS WITH HIGH FAT CONTENT DERIVED FROM THE PRODUCTION OF BOVINE GELATIN", "authors": [ "Victor Alonso Garcia Londoño", "Natalia Marín González", "Diego Fernando Roa-Acosta", "Lina Marcela Agudelo Laverde", "Laura Botero", "Liliana Maria Lellesch", "Natalia Marín González", "Diego Fernando Roa-Acosta", "Lina Marcela Agudelo Laverde", "Laura Botero", "Liliana Maria Lellesch" ], "abstract": "Background: Gelatin is a protein obtained by partial hydrolysis of collagen contained in skins, connective tissue and/or animal bones, which are by-products of the meat industry. The main raw material to produce bovine gelatin is the dermis of the skin, but there is a variation in fat and moisture content depending on the bovine skin origin. As a contribution to the circular economy and sustainability, these by-products with high fat content and the fat released from them during the gelatin production process can be managed for food industries, mainly in the development or formulation of animal feed. Methods: For the initial physicochemical characterization, moisture, fat, protein and ashes content were determined. Once the by-products with high fat content were identified, alteration parameters such as acidity, peroxide and saponification indexes were evaluated. Additionally, thermal, rheological and fatty acid composition characterization was carried out in order to study the possible applications of the by-products. Results and Discussion: The results showed that some of the by-products presented fat content values lower than 15.0%, so the viability of their use is limited. On the other hand, some by-products have more than 30% fat content, however, they can only be removed manually, and the efficiency of this process is low. By-products removed from the supernatant in the extractors presented 99.9 and 98.9% of fat, and there is the possibility of conditioning a mechanical method for their extraction. The determination of alteration and oxidation parameters, thermal and rheological characterization, fatty acid profile and solid fat content were carried out only on these by-products. According to the characterization, these by-products could be valued and used in the formulation of animal feed, however, they present some limitations for some applications such as biodiesel production or food industry.", "keywords": [ "fats", "gelatin", "by-products", "characterization", "circular economy" ], "content": "Introduction\n\nThe gelatin production process consists of three main steps: preparation, processing and mixing. One of the raw materials used is the dermis of bovine leather, which is a by-product of the meat industry. The dermis contains collagen (molecule of interest in the gelatin production process) within its native structure. The preparation step aims to prepare the raw material so that it can be later processed in the production area. It begins with the reception of the cattle hides, which are subjected to basic and acid treatments that favor the extraction of the collagen. During the processing step, the extraction and concentration of the collagen are carried out. The concentrated liquor goes through a high temperature treatment (sterilization) to eliminate any possible microorganisms present. The sterile liquor is then chilled and extruded (in cold) as noodles, and the gelled material is deposited as a bed onto an endless, open weave, stainless steel belt, and is subsequently dehydrated in a drying tunnel. Finally, the dried gelatin is crushed and ground. In the mixing step, the ground gelatin is physiochemically analyzed and mixed according to the requirements of each client. In the gelatin production process, five different bovine raw materials can be used: dry, whole, leather, selvedge and trimmings (the one with the highest percentage of fat). The trimmings correspond to different parts of the animal which include udders, gonads, prepuces, and faces. They can be of national origin (CPFC) or imported (PPSL).\n\nIn particular, the production of gelatin takes advantage of by-products generated in the leather and meat industry. In the literature review, no studies were found on the use of by-products generated in the gelatin production process. The non-use or under-use of by-products not only leads to the loss of potential income, but also represents an increase in the cost of elimination or disposal of this waste.1 Traditional uses for protein-rich byproducts include food, pet food, livestock feed, and fertilizers. Regarding fatty by-products of animal origin, in recent years, different alternatives have been proposed for their use and recovery: chemical transformation into soaps (derived from fatty acids), formulation of products for the food industry or reincorporation into the food chain as balanced feed for animals, after physical and chemical treatment.2\n\nIn recent years, new alternative uses of fat as energy/fuel sources have been developed, such as the production of biodiesel.3 Any raw material that contains triacyl glycerides can be used to produce biofuels: sunflower oil, rapeseed oil, soybean oil, used frying oils, lard, beef tallow. Although in some countries, the production of biofuels comes mainly from oils extracted from oilseeds, especially sunflower (in Spain and Italy) and rapeseed (in Central European countries), the use of waste from used vegetable oils and animal fats has been popularized.4–6 Different products have been formulated from beef fat for the food industry, among which are substitutes for cocoa butter,7 fat base for the production of margarine with plastic characteristics,8 shortenings9 and products for baking industry.6 In some cases, the fatty acid composition of the by-product is similar to the original product, but in other cases, great variability can be found. These differences can extend to other factors or properties that have incidence on nutritional value, stability or general quality.10\n\nThe characterization of the by-products is fundamental since, based on certain results, it is possible to predict, for example, the fat behavior during its processing to obtain a biofuel or its possible applications in the food industry. Among the parameters commonly evaluated are the acidity, iodine and saponification indexes, humidity, fatty acid profile and triacyl glycerides content.5 Another important aspect when characterizing these by-products is to evaluate possible alterations. A typical alteration reaction is the autoxidation of lipids, which is one of the main causes of the deterioration of foods rich in fat, giving rise to the appearance of unpleasant odors and flavors. This reaction occurs primarily with unsaturated fatty acids through a series of free radical chain reactions. Another deterioration reaction that occurs is lipolysis, which is produced from the hydrolysis of lipid ester bonds (enzymatic by the action of lipases or by heat in the presence of water). In animal fats, lipolysis releases fatty acids, some of which (short-chain ones) are responsible for off-flavors and off-odors. Some of the most frequently used chemical indices to determine the development of oxidation are the peroxide index (PI), which measures the amount of peroxides formed; the thiobarbituric acid reactive substances (TBARS), which quantify the secondary products of lipid oxidation; and the acidity index that determines the degree of hydrolysis of an oil or fat.10\n\nUnderstanding the functions and properties of fats and oil bases is essential for the design of possible applications and uses, or to obtain food products with the desired final attributes. The satisfactory performance of a fat depends on important elements that determine its applicability: the stability during the post-processing period, the total compatibility of the fat with the product for which it is intended and its physical and functional characteristics, such as plasticity and spreadability.11 Therefore, an application study should be based primarily on understanding the relationships among parameters such as fatty acid and triacylglyceride composition, melting point, solid fat content, thermal behavior, crystallization, microstructure and rheological properties.12\n\nThe objectives of the present study were to carry out the physicochemical characterization of the by-products generated in the gelatin production process, to analyze oxidation and alteration parameters, thermal behavior, rheological profile, fatty acid profile and solid fat content of the potentially usable fatty by-products.\n\n\nMethods\n\nThe sampling of the by-products was carried out in the preparation, processing and wastewater treatment plant (WTP) areas. A total of 10 points were sampled, differentiating by raw material in those points where CFPC and PPSL were treated independently (basification, alkaline wash, and extraction). Figure 1 shows the flow chart and the sampling points.\n\nSampling was carried out for three consecutive days (29/08/2022 to 31/08/2022) and each sample was analyzed in triplicate in all tests.\n\nMoisture content determination\n\nMoisture content was determined by the indirect method AOAC (Association of Official Analytical Chemists) 964.22, where 5±0.005 g of sample was weighed and dried at 110°C in a forced air oven until constant weight. Constant weight was achieved after approximately 16 h of drying. Weight loss was considered as moisture content and dry residue was considered as dry matter. The results were expressed as a percentage.\n\nFat content determination\n\nFat content was determined by the direct organic solvent extraction method, AOAC, 960.39. Due to the high moisture content of the by-products, the measurement was made on the dry matter obtained from the moisture determination. The dehydrated material was quantitatively transferred to a cellulose cartridge, covered with cotton and placed in the Soxhlet extractor. Extraction was carried out with anhydrous ethyl ether for 4 h, heating at a condensation rate of 5 or 6 drops per second. The extract was then quantitatively transferred to an Erlenmeyer flask and the remained solvent was evaporated in a water bath and dried at 100°C for 30 min. Finally, it was cooled and weighed. The results were expressed as percentage of fat on wet basis.\n\nProtein content determination\n\nProtein determination was performed by the Kjeldahl-Arnold-Gunning method (AOAC, 928.08), by digesting 0.8±0.01 g of sample in a Kjeldahl digestion tube with 6 g of Na2SO4, 0.3 g of CuSO4 and 12 ml of concentrated H2SO4. The digestion was carried out in a Selecta digester (PRO-NITRO M) under the following conditions: 125°C – 15 minutes; 300°C – 15 minutes; 400°C – 90 minutes. The distillation was carried out in a Selecta automatic Kjeldahl Distiller (Pro-nitro). The digested sample was alkalized and distilled by steam addition. The distillate was collected in 50 ml of saturated boric acid solution with combined indicator. Nitrogen content was determined by titration with 0.1N HCl. Results were expressed as protein percentage using a conversion factor of 6.25.\n\nAsh content determination\n\nBased on AOAC 923.03 method, 5±0.01 g of sample was placed in a porcelain capsule of 6 cm of diameter. The sample was first incinerated with a Bunsen burner until complete carbonization and then in a high-temperature muffle furnace at 500°—550°C until constant weight. Finally, it was cooled in a desiccator and weighed. Results were expressed as ash percentage.\n\nSaponification index (SI)\n\nAccording to the CTS (Colombian Technical Standard) 335, 2±0.005 g of sample was weighed in an Erlenmeyer flask and 25 mL of ethanolic solution of potassium hydroxide were added together with boiling aids. The reflux condenser was connected to the flask and the solution was allowed to boil slightly, while stirring sporadically. After 60 min of boiling, the condenser was removed and 0.5 mL of phenolphthalein solution was added to the hot solution. It was then titrated with 0.1 N HCl. A reagent blank was analyzed in the same way. The results were expressed as the number of milligrams of KOH required to saponify 1 g of fat.\n\nAcidity index (AI)\n\nThe acidity index was performed following the procedure established in the CTS 218. A sample of 2.5±0.005 g was weighed in a flask. In a second flask, 50 mL of ethanol containing 0.5 mL of phenolphthalein was heated to boiling. While the temperature was above 70°C, it was neutralized with a 0.1 N KOH solution. The neutralized ethanol was added to the flask with the sample and they were mixed and boiled. Finally, it was titrated with 0.1 N KOH solution. The results were expressed as the number of milligrams of KOH required to neutralize free fatty acids in 1 g of sample.\n\nPeroxide index (PI)\n\nAccording to the Colombian Technical Standard 236, 5.0±0.1 g of sample was weighed and 30 mL of acetic/chloroform solution (3:2) was added. The sample was dissolved by shaking and 0.5 ml of KI solution was added. The flask was covered and stirred. It was kept at rest for 60 s and then 30 mL of water were added. The released iodine was immediately titrated with 0.01 N sodium thiosulfate solution until the solution turned pale-yellow color. Then, 0.5 mL of starch solution was added and the titration was continued until colorless. A reagent blank was also analyzed. The results were expressed in milliequivalents of active oxygen per kg of sample.\n\nDetermination of fatty acid methyl esters (FAMEs)\n\nFor the determination of fatty acid methyl esters, the weighed sample (0.7 g) was placed in a 50 mL three-necked flask with 6 mL of a 0.5 M NaOH solution. This flask was placed at reflux, controlling the temperature (maximum of 60°C), until the sample was completely dissolved. 20 minutes were counted from that moment. Then, the sample was derivatized with 5 mL of BF3 at 14% in MeOH and the reaction was continued for another 20 minutes. Finally, 3 mL of n-heptane was added. After cooling, the derivatized sample was taken to a test tube and 15 mL of saturated NaCl solution was added. An aliquot of 1.5 mL was taken of the organic phase and placed in a vial.\n\nA gas chromatography equipment coupled to a Shimadzu GC-MS QP-2010 mass spectrometer, a system equipped with an AOC-20i autoinjector and an AOC-20s autosampler were used. Chromatographic conditions were: Zebron ZB-5 column 30 m × 0.25 mm I. D, 0.25 μm, temperature ramp programmed from 100°C to 300°C (2 min of heating at 100°C, then the temperature was increased from 7°C/min up to 300°C and held for 5 min). The temperature at the injection port was 250°C, the injection was in split mode (1:20), the column flow was 1.00 ml/min, the total flow was 24.0 ml/min, the temperature at the ion source and at the interface was 290°C. The total analysis time was 36 min.\n\nAn AR 1500 rheometer (TA Instruments, New Castel, USA) equipped with a Peltier temperature control system in the lower plate and an upper plate of 40 mm diameter and 0° was used. An opening of 1.5 mm was set between the lower and upper plates. The sample was conditioned for 2 min at the measurement temperature before running. A shear stress (Pa) scan was performed as a function of time (5 min) at a shear rate of 50 (s-1). The data were modeled by the Weltman equation, where the parameter A is the instantaneous effort necessary to start the structure de-structuring process during shearing and parameter B indicates the rate of de-structuring of fats.13 The rheological profile was performed at 25°C and 35°C.\n\nThermal behavior was determined by differential scanning calorimetry (DSC) with a Netzsch polyma 214 calorimeter. A gaseous N2 flow at 50 mL/min was used as carrier gas to avoid humidity in the measurement cell. About 9 mg of each sample was weighed into hermetically sealed 40 μL aluminum pans. The samples were melted at 80°C (heating speed of 10°C/min) for 15 min. Subsequently, cooling to 0°C was carried out at 10°C/min, keeping this temperature for 30 min. Then, the samples were heated up to 20°C (10°C/min) for 30 min and finally, melted at 80°C (heating rate of 5°C/min) for 2 min.\n\nSolid fat content (SFC) of the samples at equilibrium was determined with a Bruker mq 20 Minispec equipment that has a cell with temperature control and a magnetic field of 0.47 Tesla, which operates at a frequency of 20 MHz. A 10 mm diameter glass tube specific for NMR with approximately 6 mL of sample was used. Solid fat content (SFC) was studied following the methodology described in the American Oil Chemists' Society (AOCS Cd 16b 93 for confectionery fats). The samples were prepared in triplicate and the results were expressed by the average of three values and their standard deviation. The experimental protocol was: the sample was melted at 100°C and kept isothermally for 15 min in order to erase its thermal history, then it was cooled to 60°C for 5 min, followed by further cooling to 0°C for 90 min. Tempering was carried out at 26°C for 40±0.5 h. Cooling at 0°C was repeated for 90 min and finally, it was kept for 60 min at each of the selected crystallization temperatures (CT) for the determination of the SFC of the fat from extractors (CFPC and PPSL): 10, 15, 20, 25, 30, 35 and 40°C.\n\n\nResults\n\nThe physicochemical parameters of the identified fatty by-products are shown in Table 1.\n\nThe results showed that some of the by-products (B1, B2, D1, D2, E1 and E2) presented fat content values lower than 15.0%, so the viability of their use is limited. On the other hand, by-products A1 and A2 have more than 30% fat content, however, they can only be removed manually and the efficiency of this process is low. By-products C1 and C2 presented 99.9 and 98.9% of fat, respectively, and a very low ash content. These fatty by-products are removed from the supernatant in the extractors and there is the possibility of conditioning a mechanical method for their extraction. Given the above, the determination of alteration and oxidation parameters, thermal and rheological characterization, fatty acid profile and solid fat content as a function of temperature were carried out only on C1 and C2 by-products.\n\nTable 2 shows the saponification, acidity and peroxide indices obtained for the potentially usable fat by-products.\n\nResolution 2154 of 2012 of the Ministry of Health and Social Protection of the Republic of Colombia (chapter X) establishes the physicochemical requirements for food tallow, defined as the product obtained by the fusion of fatty, clean and healthy tissues, including fat from trimmings and related muscles and bones, from bovine (Bos taurus) and/or sheep (Ovis aries) animals. C1 and C2 saponification index values were within the parameters established in the mentioned resolution (SI between 190 and 202 mg KOH/g), but neither of the two by-products complied with the acidity parameters (AI < 2.5 mg of KOH/g). The peroxide value for C1 was within the established limit (<10 meq active oxygen/kg), while C2 was just within the established limit. The difference in the oxidation and alteration parameters between the fatty by-products obtained from the two raw materials, CFPC (C1) and PPSL (C2), was mainly due to the chemical treatments and transport times to which they are subjected before being received at the gelatin factory. CFPC is unhaired in local tanneries where sulfides are generally used. Normally, this material arrives at the gelatin factory between 2 and 4 days after being processed in the tannery. PPSL is a raw material imported principally from Argentina and the United States, and for its conservation during maritime transport, salt or brines are added. Moreover, the minimum time between its obtention and its arrival to the gelatin factory in Colombia is 15 days, time enough to cause oxidation and alteration processes. Although neither of the two by-products complied with the parameters of the resolution 2154, there are some strategies for the reduction of free fatty acids14,15 that could be evaluated in the future.\n\nTable 3 shows the percentage of fatty acids for C1, C2 and a commercial refined beef tallow.\n\nThe fatty acid profile obtained for C1 and C2 was similar to that of beef tallow, however, it was shown that C2 had a lower percentage of unsaturated fatty acids, possibly due to autoxidation or rancidity processes generated by the previous treatment in tanneries and to the time and conditions of storage and transport. Beef tallow is a raw material normally used in the biodiesel industry, but it has unfavorable properties because of the presence of a high concentration of saturated fatty esters (stearic and palmitic). In fact, it is normally mixed with other raw materials with higher content of unsaturated fatty acids.16 Taking into account that C2 has about 9% more saturated fatty acids than standard beef tallow and a high content of free fatty acids, this by-product is not attractive for the biodiesel industry. Some alternatives for the use of these by-products are to obtain fractions with different properties through thermal fractionation17 or chemical or enzymatic esterification.18\n\nFigures 2A and 2B show the decrease of the shear stress of C1 and C2 with time. This type of behavior is characteristic of thixotropy and the shear stress tends to become constant with time until reaching an equilibrium shear stress (σe). The byproduct C1 (CFPC) showed σe greater than 150 Pa, while the σe of C2 was less than 100 Pa. The parameter B of C1 was greater than that of C2. This could indicate that C1 destructures faster when it applied a shear stress, so it can slide over a surface more easily than C2. It is important to note that this ease of sliding on a surface does not change significantly with an increase of 10°C of temperature. Otherwise, parameter B of C2 is affected by the temperature change (Figure 2C). It is also observed that the initial resistance factor (parameter A) was higher in C1 and this did not depend significantly on the temperature.\n\n(A) shows the shear stress behavior for C2 subjected to a shear rate of 50 s-1 for 5 minutes at 25°C and 35°C. (B) shows the shear stress behavior for C1 subjected to a shear rate of 50 s-1 for 5 minutes at 25°C and 35°C. (C) shows the rate of de-structuring (parameter B) for C1 and C2 at 25°C and 35°C. (D) shows the initial resistance (parameter A) for C1 and C2 at 25°C and 35°C.\n\nThis behavior is influenced by the relationship between saturated and unsaturated fatty acids in each of the samples. By-product C1 could be included in the preparation of puff pastry-type bakery products, in which fats that are easily mixed with flour are needed.\n\nFigures 3A and 3C showed an exothermic peak, attributed to the phenomenon of fat crystallization. In the C2 by-product, this phenomenon started at slightly lower temperatures, however, there were no significant differences between the crystallization temperature of the two by-products. Figures 3B and 3D showed two endothermic peaks for each of the by-products analyzed, attributed to the fat melting phenomenon. There was a peak at 35°C in both by-products thermograms, however, in the thermogram of C2, there was a peak at 28°C absent in that of C1. On the other hand, C1 showed a peak at 43°C that was not evidenced in C2 thermogram. These results were correlated with the behavior in the solid fat percentage profiles as a function of temperature. The application of a thermal fractionation to the by-product C1 would allow obtaining two fractions with different ranges of applicability, which would enhance its value.\n\n(A) Shows the crystallization peak of C1. (B) Shows the melting peaks of C1. (C) Shows the crystallization peak at 20°C of C2. (D) Shows the melting peaks of C2.\n\nFigure 4 shows the solid fat content as a function of temperature for by-products C1 and C2, and a sample of refined commercial beef tallow.\n\nThe solid fat content profile as a function of the temperature of the two by-products evaluated varied significantly with respect to a commercial beef tallow. The SFC of C1 and C2 were lower in the entire temperature range evaluated. If the SFC is analyzed together with the fatty acid profile obtained for C1 and C2, a higher percentage would be expected for C2, since it had a higher proportion of saturated fatty acids with a higher melting point. However, this by-product had a free acidity value three times higher than C1, which indicates that a greater proportion of these fatty acids were not forming a triacylglyceride. In general, beef tallow has a poor plastic range and is too firm at room temperature to meet the requirements of a “shortening”. In fact, it is usually mixed with vegetable oils or soft fats.19 When analyzing the SFC profile of the C1 and C2 fatty by-products, these had a broader plastic range than beef fat, possibly due to spontaneous interesterification processes catalyzed by chemical agents, such as sodium sulfide, potassium hydroxide and lime, used in the process of tanning, unhairing, conservation and preparation. The SFC profile obtained for C1 and C2 was similar to some reported in the literature for hard and fluid “shortenings”.20 However, the peroxide index values for both by-products exceed the typical values, 2 mEq O2/kg, for this type of products obtained by interesterification.21\n\n\nConclusion\n\nThe by-products obtained from the gelatin production process were analyzed, two of them obtained in the extraction stage were identified as potentially usable due to their high fat content. Once identified and analyzed, it was determined that they did not comply with at least one of the parameters established in resolution 2154 that states the physicochemical requirements for food tallow. The rheological and thermal characteristics, the fatty acid profile and the solid fat content showed that the previous treatments and those carried out in the preparation stages affect the properties with respect to a commercial beef fat. The solid fat content as a function of the temperature of the by-products showed a wider plastic range than commercial beef fat, however, the peroxide and acidity index limit its spectrum of applicability. These by-products could be valued and used in the formulation of animal feed, however, for applications such as biodiesel production or the food industry, they present some limitations. Then, it is important to evaluate some alternatives such as thermal fractionation to obtain fractions with a broader potential application or the reduction of free fatty acids for their potential use for biodiesel production.\n\n\nEthics statement\n\nNot required.", "appendix": "Data availability\n\nFigshare: https://doi.org/10.6084/m9.figshare.21603474. 22\n\nThis project contains the following underlying data:\n\nTable 1. Raw data - Physicochemical parameters.\n\nTable 2. Raw data - Alteration and oxidation parameters\n\nTable 3. Raw data - Sample C1 (CFPC) FAMEs CG MS\n\nTable 3. Raw data - Sample C2 (PPSL) - FAMEs CG MS\n\nTable 4 and Figure 3. Raw data - Thermal behavior DSC C1 and C2\n\nFigure 2. Raw data - Rheological profile C1 (CFPC) and C2 (PPSL)\n\nFigure 4. Raw data - RMN Solid Fat Content\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nThe authors acknowledge the collaboration of the University of Buenos Aires (Argentina), the University of Quindío, the University of Caldas and the University of Cauca.\n\n\nReferences\n\nJayathilakan K, Sultana K, Radhakrishna K, et al.: Utilization of byproducts and waste materials from meat, poultry and fish processing industries: a review. J. Food Sci. Technol. 2012; 49(3): 278–293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCastañeda Fea MA: Methods of processing agricultural by-products to raise their nutritional value. Chapingo, México:Livestock Centre, Postgraduate College;2010. 978-607-715-083.\n\nWoodgate S, Veen JVD: The role of fat processing and rendering in the European Union animal production industry. Biotechnol. Agron. Soc. Environ. 2004; 8: 283–294.\n\nNelson RG, Schrock MD: Energetic and economic feasibility associated with the production, processing, and conversion of beef tallow to a substitute diesel fuel. Biomass Bioenergy. 2006; 30(6): 584–591. Publisher Full Text\n\nRamírez N: Evaluation of the physicochemical properties of potential residual oils and fats for biofuel production. Querétaro:CIDETEQ;2018.\n\nZhang Z, Shim YY, Ma X, et al.: Solid fat content and bakery characteristics of interesterified beef tallow-palm mid fraction based margarines. RSC Adv. 2018; 8(22): 12390–12399. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOsborn HT, Akoh CC: Enzymatically Modified Beef Tallow as a Substitute for Cocoa Butter. J. Food Sci. 2002; 67(7): 2480–2485. Publisher Full Text\n\nRiquelme Coloma IAR: Interesterificación Química de Grasa Animal y Aceite de Nuez. Universidad de Chile;2006.\n\nRodríguez A, Castro E, Salinas MC, et al.: Interesterification of tallow and sunflower oil. J. Am. Oil Chem. Soc. 2001; 78(4): 431–436. Publisher Full Text\n\nNuchi C, Guardiola F, Bou R, et al.: Assessment of the Levels of Degradation in Fat Co- and Byproducts for Feed Uses and Their Relationships with Some Lipid Composition Parameters. J. Agric. Food Chem. 2009; 57(5): 1952–1959. PubMed Abstract \| Publisher Full Text\n\nRibeiro APB, Basso RC, Grimaldi R, et al.: Instrumental Methods for the Evaluation of Interesterified Fats. Food Anal. Methods. 2009; 2(4): 282–302. Publisher Full Text\n\nBrien R, Timms R: Fats and oils-formulating and processing for applications. Eur. J. Lipid Sci. Technol. 2004; 106(7): 451.\n\nJuszczak L, Oczadły Z, Gałkowska D: Effect of Modified Starches on Rheological Properties of Ketchup. Food Bioprocess Technol. 2013; 6(5): 1251–1260. Publisher Full Text\n\nMartins PF, Ito VM, Batistella CB, et al.: Free fatty acid separation from vegetable oil deodorizer distillate using molecular distillation process. Sep. Purif. Technol. 2006; 48(1): 78–84. Publisher Full Text\n\nMićić R, Tomić M, Martinović F, et al.: Reduction of free fatty acids in waste oil for biodiesel production by glycerolysis: investigation and optimization of process parameters. Green Process. Synth. 2019; 8(1): 15–23. Publisher Full Text\n\nTeixeira LSG, Couto MB, Souza GS, et al.: Characterization of beef tallow biodiesel and their mixtures with soybean biodiesel and mineral diesel fuel. Biomass Bioenergy. 2010; 34(4): 438–441.\n\nRezaei F, Gharachorloo M, Azizinejad R: Fraction of Iranian Beef Tallow – Chemical and Physical Evaluations of the fractions. J. Food Biosci. Technol. 2013; 3(3).\n\nMarulanda-Buitrago P-A, Marulanda-Cardona V-F: Supercritical Transesterification of Beef Tallow for biodiesel production in a batch reactor. CT&F - Ciencia, Tecnología y Futuro. 2015; 6: 57–68. Publisher Full Text\n\nMorris SG, Magidman P, Luddy FE, et al.: Beef tallow in shortening preparations. J. Am. Oil Chem. Soc. 1956; 33(8): 353–355. Publisher Full Text\n\nIsmail NH, Sahri MM, Abd HR: Influence of palm-based fluid shortening on the physical and textural properties of biscuits. J. Oil Palm Res. 2018; 30(2): 299–305. Publisher Full Text\n\nTourchi Rudsari M, Najafian L, Shahidi SA: Effect of chemical interesterification on the physicochemical characteristics of bakery shortening produced from palm stearin and Ardeh oil (Sesamum indicum) blends. J. Food Process. Preserv. 2019; 43(10): e14101.\n\nGarcia Londoño VA, Gonzalez NM, Roa DF, et al.: CHARACTERIZATION OF BY-PRODUCTS WITH HIGH FAT CONTENT DERIVED FROM THE PRODUCTION OF BOVINE GELATIN. figshare.2022. Publisher Full Text" }	[ { "id": "159201", "date": "19 Jan 2023", "name": "Julián Andres Gómez Salazar", "expertise": [ "Reviewer Expertise food processing and preservation", "meat technology", "meat science", "food 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\nGeneral comment: The authors studied the physicochemical characterization of by-products derived from the production of bovine gelatin. They determined chemical (moisture, fat, protein, ashes, fatty acid) and physical parameters (thermal and rheological). This work shows the possible applications of the by-products obtained in the stages of the gelatin production process.\nThe manuscript is well written and organized. The topic is interesting and has potential applications for the food and pharmaceutical industry. I suggest indexing after a minor revision. Suggestions and requirements to improve the manuscript are mentioned below:\nIndicate, what is the reason that by-products with less than 1.5% fat have low viability? (page 6). Add reference please (page 6).\n\nComment on the results of the other physicochemical parameters obtained (protein, moisture, ash) (table 1) and compare them with other studies.\n\nAdd resolution 2154 of 2012 in references (page 7).\n\nPlease, describe the determination of the fatty acid profile of beef tallow in the methodology and add the reference. Likewise for the determination of the fat solids content in beef tallow.\n\nCompare the rheological results and thermal behavior with other studies carried out on similar by-products.\n\nInclude linear correlations between fat solids content and temperature.\n\nIndicate the meaning of the letters in table 4. Describe the statistical analysis used.\n\nIs the work 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": "10047", "date": "05 Sep 2023", "name": "Victor Alonso Garcia Londoño", "role": "Author Response", "response": "Comments to Reviewer 1: Indicate, what is the reason that by-products with less than 1.5% fat have low viability? (page 6). Add reference please (page 6). Fatty by-products below 15% correspond to the alkaline wash (B1, B2), polymer waste tanks (D1 and D2), acid water sieve (E1), and alkaline water sieve (E2). Although a fat content was detected in all cases, extracting this fat would necessitate a secondary operation due to its emulsified or mixed state with protein, fiber residue, and inorganic substances like salts or minerals. This secondary operation would incur additional energy and labor costs. For this specific analysis, no reference is provided as it pertains exclusively to the evaluated process. Comment on the results of the other physicochemical parameters obtained (protein, moisture, ash) (table 1) and compare them with other studies. This study represents the first-ever physical-chemical characterization conducted on by-products from the gelatin production industry. It is important to note that the primary focus of this investigation is on by-products with high fat content. However, it is worth mentioning that residues A1, A2, B1, B2, D1, and D2 hold potential usability due to their protein content. These residues could find applications in areas such as animal feed, provided the fat is separated beforehand. The following text was added to the manuscript: “Although the primary focus of this investigation is on by-products with high fat content, it is worth mentioning that residues A1, A2, B1, B2, D1, and D2 hold potential usability due to their protein content. These residues could find applications in areas such as animal feed, provided the fat is separated beforehand.” Add resolution 2154 of 2012 in references (page 7). Reference added. Please, describe the determination of the fatty acid profile of beef tallow in the methodology and add the reference. Likewise for the determination of the fat solids content in beef tallow. The fatty acid profile method is described on page 5 (heading: “Determination of fatty acid methyl esters (FAMEs)”) and the solid fat content procedure is described on page 6 (heading: “Solid fat content as a function of temperature”). Compare the rheological results and thermal behavior with other studies carried out on similar by-products. Rheological and thermal results were compared with other studies. Nevertheless, it is important to consider that no papers were found on fatty by-products in the gelatin industry. Include linear correlations between fat solids content and temperature. Linear correlations were added. Indicate the meaning of the letters in table 4. Describe the statistical analysis used. The statistical analysis method used was added in the section Materials and Methods: “Analysis of variance (ANOVA) was performed using the statistical program Statgraphics Centurion version XVI (Statistical graphics Corporation, USA), comparing the means by the least significant difference test of Fisher (LSD) with a confidence level of 95%.” The following text was added to the table foot (Table 4): “Results are mean of three determinations ± standard deviation. The means with different letters in the superscript are significantly different (p <0.05).” A new version of the revised manuscript was submitted." } ] }, { "id": "173259", "date": "26 May 2023", "name": "Xugang Dang", "expertise": [ "Reviewer Expertise Natural biomass and biopolymers" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract and throughout the manuscript: the authors should present more tangible data (values, %, etc.).\n\nThe introduction section should be reasonably organized, highlighting key innovations and discoveries. Partial paragraphs should be merged.\n\nThe references should be updated to recent years.\n\nThe authors mentioned that the gelatin has a wide range of applications because of their excellent properties. The related references should be cited: Zhang et al. (20211) and Dang et al. (20222).\n\nThe results and discussion section should add the related references to compare and discuss the key innovations and discoveries of the research.\n\nThe English of the whole manuscript should be improved.\n\nThe results section should be revised to results and discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "10048", "date": "05 Sep 2023", "name": "Victor Alonso Garcia Londoño", "role": "Author Response", "response": "Comments to Reviewer 2: Abstract and throughout the manuscript: the authors should present more tangible data (values, %, etc.). Abstract was written according the journal author guide. More data was throughout the manuscript. The introduction section should be reasonably organized, highlighting key innovations and discoveries. Partial paragraphs should be merged. Introduction section was improved: English writing was revised; partial paragraphs were merged and some cites were added. The references should be updated to recent years. Some updated references were added throughout the manuscript. Nevertheless, it is important to consider that no papers were found on fatty by-products in the gelatin industry. The authors mentioned that the gelatin has a wide range of applications because of their excellent properties. The related references should be cited: Zhang et al. (20211) and Dang et al. (20222). The following paragraph has been added to the introduction, where both suggested references were added: “It is worth mentioning, in order to achieve the recovery of gelatin extracted from solid leather waste and contribute to the circular economy, innovative applications have been developed where gelatin can be used, for example, as a starch-based biomass adsorbent for treating discharged wastewater1 or as part of hydrogel films for antibacterial wound dressing2.” The results and discussion section should add the related references to compare and discuss the key innovations and discoveries of the research. Some related references were added throughout the Results and Discussion section. However, it is important to consider that no papers were found on fatty by-products in the gelatin industry. The English of the whole manuscript should be improved. The manuscript has been subject to revision and improvement in its English writing. The results section should be revised to results and discussion. The discussion was included in the Results section. Anyway, the title of the section was changed to “Results and discussion”. A new version of the revised manuscript was submitted." } ] } ]	1	https://f1000research.com/articles/11-1575
https://f1000research.com/articles/10-1096/v1	28 Oct 21	{ "type": "Research Article", "title": "P2P Lending platforms in Malaysia: the awareness among young adults", "authors": [ "Lan Thi Phuong Nguyen", "Saravanan Muthaiyah", "Malick Ousmane Sy", "Saravanan Muthaiyah", "Malick Ousmane Sy" ], "abstract": "Background - Since 2016, the Securities Commission (SC) in Malaysia has given licenses to only eleven P2P lending platforms. Such lending platforms are expected to disrupt the lending services of traditional lenders in the coming years. However, being still in their infant stages, it is essential to know the extent to which such platforms are made known to potential investors out there. This study examines the extent to which young adults are aware of Malaysia's eleven P2P lending platforms.\n\nMethods - A sample of 65 undergraduate students majoring in finance and accounting was used for this pilot study. An online questionnaire was designed with three main parts: demographic, financial literacy, and P2P lending awareness.\n\nResults - Findings show that more than half of respondents in the sample are not aware of P2P lending platforms in Malaysia. Most of the respondents are financially literate to certain degrees. Those aware of their presence underestimated the potentially high level of their default rates and misunderstood that investor would be fully protected by such platforms when a loan default.\n\nConclusions -The study's findings have shed light on the current awareness of P2P lending platforms among Malaysian young adults, potential investors of such platforms in the coming years.", "keywords": [ "P2P lending platforms", "financial literacy", "Malaysian young adults", "awareness", "FinTech", "investors" ], "content": "Introduction\n\nStarting from North America and Europe, P2P lending has grown aggressively in many Asian countries since 2014, taking up its market share even faster than in developed countries (Stern, Makinen, and Qian, 2017). The availability of the internet and the everyday use of mobile phones in Asia in recent years has open doors for various types of FinTechs platforms, including P2P lending, to come into a country. For instance, China has the most significant number of P2P lending platforms, estimated at 2000 in 2017, according to Stern et al. (2017). There are only eleven P2P lending platforms licensed by the Securities Commission (SC) in Malaysia now. Therefore, these platforms need to follow guidelines issued by SC, from which all of them must be incorporated under the Companies Act 1965 with a minimum paid-up capital of RM5 million. In addition, P2P lending platforms cannot place funds received from lenders into their accounts instead of in a third-party account. Furthermore, directors of those P2P lending platforms must prove themselves fit and proper to manage the business. All these requirements help to prevent future fraud caused by these platforms.\n\nTo apply for a loan in each P2P lending platform, a borrower needs to apply via its online platform, where information such as payslip, phone number, and other social media profiles are required. Based on such given information, the borrower's risk profile will be analyzed and categorized. Once the borrower's application is accepted, it is open to investors to invest. Unlike the traditional banks, P2P lending platforms do not bear any credit risk of their loans; however, their investors do. Given the standardized set of information (business plan, financial performance, social network status, etc.) required from borrowers, different credit scoring methodologies, different loan disbursement and collection mechanisms at different P2P lending platforms, many questions regarding issues such as security, creditability, and trust of P2P lending platforms, need clear answers to investors, borrowers, and regulators.\n\nFurthermore, the collapse of hundreds of P2P lending platforms in China since 2013 (Bloomberg Businessweek, October 3, 2018) due to frauds may signal potential risks possessed by P2P lending platforms to investors. In Malaysia, the first P2P lending platform defaulted in August 2018. According to Funding Society Malaysia, this default is mainly because of its SMEs' business slowdown that led to its default payments to the platform (the Edge, September 21, 2018).\n\nAlthough the default rate for P2P lending platforms remains at 1% and below, as reported by the CEO of Funding Society Malaysia, we do not want to see more P2P lending platforms default in Malaysia soon. Like most Fintech platforms, P2P lending is expected to attract more young adults who are technology savvy and financially literate. This pilot study aims to examine the extent to which the presence of the eleven P2P lending platforms is known to financially literate young adults.\n\nThe rest of the paper is organized as follows: Section 2 describes the data sample, study period, and method of analysis used for this study; Section 3 discusses empirical findings and implications of this study; the final section presents main conclusions.\n\n\nMethods\n\nBased on the study's objective, an online survey was carried out between January and September 2020. This online survey was approved by the Director of Technology Transfer Office (TTO) and Secretariat of the Research Ethics Committee of Multimedia University. All respondents are MMU university students who were informed with a clear explanation on the questionnaire about the objective of the data collection. Respondents' participation is entirely voluntarily.\n\nUndergraduate students taking finance and accounting courses at Multimedia University, Malaysia, were approached for this pilot study. There are several reasons for this choice of sample selection. First, young adults are more technology savvy and thus are expected to be more aware of the emergence of Fintech, including P2P lending, compared to older people. Secondly, students with finance and accounting knowledge are expected to be more aware of P2P lending than young people with little and no financial knowledge. Thus, results obtained from students with finance and accounting knowledge will provide a somewhat picture of the overall awareness of P2P lending among young people in Malaysia in general. A selected sample of 70 university students majoring in Finance and Accounting answered an online questionnaire consisting of three main parts: demographic, financial literacy, and P2P lending awareness. The first section is the respondents' demographic information, including gender, marital status, age, race, place of residence, and educational background. To measure the financial knowledge of respondents, three big financial literacy questions, created by Global Financial Literacy Excellence Center (GFLEC), are asked in the second section of the questionnaire. These three questions have been used in more than 20 countries around the world to test the level of financial literacy of individuals in three essential areas of knowledge in finance: (1) the effect of compounding interest, (2) the effect of the inflation rate, and (3) the benefit of diversification. The third section of the questionnaire is to collect data on the awareness of the eleven P2P lending platforms. Questions related to the main characteristics of P2P lending given in Shi, Wu, and Hollingsworth (2019) are used to test the awareness of P2P lending platforms in Malaysia. After filtering and validating the collected data, answers from only 65 respondents are used for the analysis. Cross-tabulation analysis and descriptive statistics were employed to analyze the collected data for this pilot study.\n\nAmong the selected 65 undergraduate students, 61.5% are females, and 38.5% are males. In terms of ethnicity, most respondents are Chinese (41%) and Malay (43%), while the remaining are Indian and foreign citizens (see Figure 1). All respondents are from generation Y and are all single. Also, they are all under the age of 50 and are undergraduate students majoring in finance and accounting.\n\nBased on the three answers provided by the respondents, 35.38% of respondents answer all three questions correctly, while 27.69% have two correct answers, and 24.62% have one correct answer. Moreover, 12.31% of them have all three wrong answers (see Figure 2). In short, 87.69% of respondents are all financially literate from low to high degrees. This finding could be because all respondents are undergraduate students taking either finance or accounting degree courses.\n\nWhen asked whether P2P lending is a direct lending from lenders to borrowers (see Figure 3), almost half (49.23%) of respondents, among which about 44.62% are financially literate, said they have no idea. However, more (36.92%) people agree and strongly agree with the statement than those (13.84%) who disagree and strongly disagree.\n\nWhen asked if obtaining loans from banks is much easier than from P2P lending platforms (see Figure 4), 58.46% of respondents, among which 47.69% are financially literate, have no idea. However, more respondents (29.23%) disagree and strongly disagree than those (12.31%) who agree with the statement.\n\nWhen asked if lending money to banks is safer than lending money to P2P lending platforms (see Figure 5), 49.23% of respondents, from which 43.08% are financially literate, have no idea. However, more respondents (43.07%) agree and strongly agree than those (7.7%) who disagree and strongly disagree with the statement.\n\nWhen asked if lenders are protected by P2P lending platforms (see Figure 6), 55.38% of respondents have no idea, from which 47.69% are financially literate. However, fewer respondents (7.69%) disagree and strongly disagree than those (36.92%) who agree and strongly agree with the statement. This finding implies that most respondents are not aware of the straightforward fact that P2P lending platforms do not recover loans for their investors if a loan defaults.\n\nWhen asked if default risk at P2P lending platforms is perceived as low and manageable (see Figure 7), 50.77% of respondents, from which 46.15% are financially literate, have no idea. However, fewer respondents (18.38%) disagree and strongly disagree than those (30.77%) who agree with the statement. Again, this suggests that most respondents underestimate a possible high default rate that can occur at P2P lending platforms.\n\nWhen asked if P2P lending platforms offer higher returns to investors than what banks offer (see Figure 8), 43.08% of respondents, from which 36.92% are financially literate, have no idea. However, more respondents (43.07%) agree with the statement, while only a smaller number (13.88%) of respondents do not.\n\nWhen asked if fewer documents are needed to get a loan from P2P platforms than banks (see Figure 9), 45.24% of respondents have no idea, among which 33.33% are financially literate. However, more respondents (45.24%) think that P2P lending platforms may be much more lenient to borrowers in terms of their loan procedures than those (9.52%) who did not think so.\n\nBased on the seven questions used to test the awareness of P2P lending platforms, scores of awareness are computed, where a 100% score is given to respondents who can give all correct answers for the seven questions. Figure 10 shows only percentages of respondents who have above the average level of awareness, ranging between 60% and 91%, about P2P lending platforms in Malaysia from respondents with low (1), medium (2) and high financial literacy (3). Only 3.5% of respondents have the highest level of awareness, ranging from 80% to 91%. Most respondents (75%), whose scores are from 60% to 77%, are somewhat aware of the presence of P2P lending platforms.\n\n\nConclusion\n\nWith the presence of the eleven P2P lending platforms in Malaysia, the lending services of traditional lenders are expected to be disrupted in the coming years. Thus, this study examined the extent to which potential investors in Malaysia know such platforms. Using the non-probability sampling method, a sample of 65 finance and accounting students at Multimedia University, Malaysia, participated in an online questionnaire survey. Most respondents are financially literate at different levels. However, more than half of them had no idea about the presence of P2P lending platforms in Malaysia. Clearly, half of the respondents often could not express their view on the common characteristics of P2P lending platforms. Based on answers related to P2P lending platforms, results show that from 50% to 90% of respondents could answer correctly about some, but not all the main characteristics of P2P lending platforms, i.e., the direct lending function from lenders to borrowers, more straightforward loan assessment, lesser security, lesser document requirement, and higher returns, as compared to banks. However, in terms of loan recovery and default risk at P2P lending platforms, many are not aware of the high potential default rate and the potential zero loan recovery when a loan default occurs at those platforms. As most respondents in the sample are financially literate, lesser awareness about P2P lending platforms in Malaysia may be expected for young adults with lower financial literacy. The overall computed score of financial literacy is relatively low, where only a tiny number of respondents showed their high level of awareness. At the same time, the majority are somewhat aware of the presence of P2P lending platforms. The obtained results shed light on the current awareness of P2P lending platforms in Malaysia among young adults, potential investors of such platforms in the coming years.\n\n\nAuthor contributions\n\nLiterature review, research framework, questionnaire design, hypothesis testing and data analysis have been discussed and carried out by all authors of this paper.\n\n\nData availability\n\nFigshare. Data source_P2P Lending Platforms in Malaysia - The Awareness Among Young Adults.xlsx. DOI: https://doi.org/10.6084/m9.figshare.14877381.v1 (Nguyen, 2021).\n\nThis project contains the following data:\n\n- Since 2016, the Securities Commission (SC) in Malaysia has given licenses to only 11 P2P lending platforms. Such lending platforms are expected to disrupt lending services of traditional lenders in the coming years. However, being still in their infant stages, it is important to know the extent to which such platforms are made known to potential investors out there. This study aims to examine the extent to which young investors are aware of the presence of the 11 P2P lending platforms in Malaysia. Using non-probability sampling method, a pilot study was carried out with a sample of 65 undergraduate students, majoring in Finance and Accounting. An online questionnaire was designed with three main parts: demographic, financial literacy, and P2P lending awareness. Findings show that more than half of respondents in the sample are not aware of the existence of P2P lending platforms in Malaysia. Most of respondents are are financially literate at certain degrees. Those who are aware of their presence, underestimated the potential high level of their default rates, and misunderstood that investors would be fully protected by such platforms when a loan is default. Findings of the study shred lights on the current awareness of P2P lending platforms in Malaysia among young adults, who are potential investors of such platforms in the coming years.", "appendix": "Acknowledgement\n\nWe are grateful for the idea and advice are given by Malick Sy, who is also a Corporate Constancy and Risk Management Strategist and a Corporate Trainer at Aventis Learning Group, Singapore. We also acknowledge the ongoing collaboration between researchers from MMU with RMIT (Australia) that brought the idea for this research to be launched. We also acknowledge all respondents who provided their valuable views and answers to our questionnaire survey. Without them, this research would not be possible.\n\n\nReferences\n\nBloomberg News: How China’s Peer-to-Peer Lending Crash Is Destroying Lives.2018.Reference Source\n\nChen X, Chong Z, Giudici P, et al.:Networking with Peers: Evidence from a P2P Lending Platform.Asian Development Bank Institute;2020. Working Paper No.1080, February 2020.\n\nGibilara L, Mattarocci G: Peer-to-Peer Lending and Real Estate Mortgages: Evidence from the United Kingdom. J. Euro. Real Estate Res. 2018; 11(3): 319–334. Publisher Full Text\n\nGonsalez L: Blockchain, herding and trust in peer-to-peer lending. Manag. Financ. 2019; 46: 815–831. Publisher Full Text\n\nHidajat T: Unethical practices peer-to-peer lending in Indonesia. J. Financial Crime. 2020; 27(1): 274–282. Publisher Full Text\n\nHe Q, Li X: The Failure of Chinese Peer-to-Peer Lending Platforms: Finance and Politics. J. Corp. Finan. 2021; 66: 101852. Publisher Full Text\n\nKim D: Bounded rationality in a P2P lending market. Rev. Behav.Finan. 2020; 13: 184–201. Publisher Full Text\n\nLi Q: The Mechanism and Effectiveness of Credit Scoring of P2P Lending Platform: Evidence from Renrendai.com. China Finance Review International. 2018; 8(3): 256–274. Publisher Full Text\n\nLusardi A, Mitchell OS: Planning and Financial Literacy: How Do Women Fare?. Am. Econ. Rev. 2008; 98: 413–417. Publisher Full Text\n\nNemoto N, Storey D, Huang B:Optimal Regulation of P2P Lending for Small and Medium-Sized Enterprises.Asian Development Bank Institute;2019. Working Paper No.912.\n\nSan-Jose L, Retolaza JL: Crowdlending as a Socially Innovative Corporate Financial Instrument. International Perspectives on Crowdfunding. 2017; 129–149.\n\nShi X, Wu J, Hollingsworth J: How does P2P Lending Platform Reputation Affect Lenders ‘Decision in China?. Int. J. Bank Mark. 2019; 37(7): 1566–1589. Publisher Full Text\n\nStern C, Makinen M, Qian Z: FinTechs in China – With a Special Focus on Peer-to-Peer Lending. J.Chinese Economic and Foreign Trade Studies. 2017; 10(3): 215–228. Publisher Full Text\n\nRosavina M, Rahadi RA, Kitri ML, et al.: P2P Lending Adoption by SMEs in Indonesia. Qualitative Research in Financial Markets. 2019; 11(2): 260–279. Publisher Full Text\n\nTrönnberg CC, Hemlin S: Lending Decision Making in Banks: A Critical Incident Study of Loan Officers. Eur. Manag. J. 2014; 32(2): 362–372. Publisher Full Text\n\nThe World Bank Group: the Little Data Book on Financial Inclusion. The Global Findex database.Reference Source\n\nNguyen TPL: Data source_P2P Lending Platforms in Malaysia The Awareness Among Young Adults.xlsx. figshare. Dataset. 2021. Publisher Full Text" }	[ { "id": "98215", "date": "10 Nov 2021", "name": "Hassanudin Mohd Thas Thaker", "expertise": [ "Reviewer Expertise I did research on crowdfunding and p2p lending as well." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study on P2P lending platforms which explores the topic in an area in which the literature is limited by focusing on Malaysia. However, there are some major issues that need to be resolved.\nIssues:\nIt is unclear what drives the research motivation: what was the goal of the article, what is the state of debate pertaining to this research?\nLiterature review: not included. Why is a literature review reported in the paper?\nMethods: how did the authors determine the sample of 65 students? How are they representative of Malaysia’s youngsters? Please provide a justification for why these ones were chosen in particular.\nFurthermore, the authors report information, but I would suggest the authors include analysis. What is your hypothesis about platform awareness? What are the factors that drive awareness of these platforms? Where are your research gaps? What are the current debates pertaining to your topic in the literature?\nConclusion: at present, it appears to just be a summary of your results. What do the authors think their managerial/theoretical implications are, and what should we take away from those 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? 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": "8225", "date": "31 May 2022", "name": "Thi Phuong Lan Nguyen", "role": "Author Response", "response": "The authors' response to the reviewer can be found here: https://f1000researchdata.s3.amazonaws.com/linked/421363.Resposes_to_Reviewer%232.docx" } ] }, { "id": "124173", "date": "08 Apr 2022", "name": "Raden Aswin Rahadi", "expertise": [ "Reviewer Expertise Financial Technology", "P2P Lending" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAs the data involved in this study is quite limited, the results and analysis from the work is also limited and prone to judgment error. I would suggest to enrich the data to reach 100 at least, following the guidelines of Israel (1992) for minimum number of respondents.1 If the authors can get more data, then the result would be much better\nResults - Findings show that more than half of respondents in the sample are not aware of P2P lending platforms in Malaysia. Most of the respondents are financially literate to certain degrees. Those aware of their presence underestimated the potentially high level of their default rates and misunderstood that investor would be fully protected by such platforms when a loan default. This can happen because of the limited data.\nOnly descriptive analysis is presented in this work. A heavy revamping of the paper has to be done, to present the analysis result in a more scientific way.\nConclusions should be written as follows: RQ answers, implications (theoretical, practical, managerial), implementation plan, recommendations, limitations and future research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "8224", "date": "31 May 2022", "name": "Thi Phuong Lan Nguyen", "role": "Author Response", "response": "The authors' response to the reviewer can be found here: https://f1000researchdata.s3.amazonaws.com/linked/421364.Resposes_to_Reviewer%231.docx" } ] } ]	1	https://f1000research.com/articles/10-1096
https://f1000research.com/articles/12-1109/v1	05 Sep 23	{ "type": "Study Protocol", "title": "Therapeutic effectiveness of virtual reality-based exercise through Oculus Quest 2 on balance, dizziness, nystagmus, and quality of life in patients with posterior canal benign paroxysmal positional vertigo - a randomized control trial protocol", "authors": [ "Shrushti Jachak", "Raghumahanti Raghuveer", "Raghumahanti Raghuveer" ], "abstract": "BPPV (benign paroxysmal positional vertigo) is one of the most prevalent causes of vertigo.The clinical features include nausea, imbalance, nystagmus, light-headedness, dizziness, fear of fall. Various exercises and maneuvers have been proved to be beneficial till date. Many technologies had also contributed in the physical rehabilitation. Virtual rehabilitation using virtual reality (VR) is a novel innovation in therapy. Virtual reality is widely used in treating the patients and adding to get back to their day-to-day life. Occulus quest 2 is a VR device. Depending on the patient's motions, Oculus Quest enables you to interact genuinely while immersing yourself in a virtual reality. BPPV is a very common condition and Posterior canal BPPV (PC-BPPV) is commonest of all. Most of the available literature targets conventional treatment including Exercises for repositioning and adaptation of otoconia. Comparative studies between the conventional rehabilitation protocols have also been done. There is paucity of research on virtual rehabilitation in PC-BPPV. VR utilizing Oculus Quest 2, a device designed to incorporate VR environment can be used to mobilize the patients head position there by repositioning the otoconia. Lack of evidence related to Virtual rehabilitation and specifically Oculus Quest 2 emphasises the need to study its effects on BPPV outcomes like balance, dizziness, quality of life and nystagmus. In this study, an attempt is made to use the oculus quest 2 for BPPV rehabilitation in addition to standard treatment. Patients will be divided into 2 groups control and experimental. Control group will receive Brandt-droff exercise on the other hand experimental will receive occulus quest 2 game “Coaster combat” in adjunct to the conventional. Berg balance scale, nystagmus time quality of life, dizziness handicap index and vertigo symptom scale are the outcomes. Outcomes will be assed at baseline and after 4 weeks.", "keywords": [ "Benign Paroxysmal Positional Vertigo", "Virtual reality", "Physiotherapy", "Occulus quest", "Rehabilitation", "Vestibular rehabilitation." ], "content": "Introduction\n\nBenign paroxysmal positional vertigo (BPPV), the abrupt sensation that you are spinning or that the interior of your head is whirling, is one of the most frequent causes of vertigo. Mild to severe vertigo can briefly be caused by BPPV. The most frequent inner ear ailment that causes vertigo or dizziness is BPPV.1 The most typical kind of vertigo in modern culture is BPPV. The posterior canal is the most typical of them.2 Moderate symptoms of positional assaults include frequent occurrences and an imbalance. BPPV reportedly afflicted every third person who had vestibular vertigo, making it likely the most common vestibular disease. 10.7 to 140 out of every 100,000 persons have BPPV. Idiopathic cases often afflict persons between the ages of 50 and 55, while children are very seldom affected. It is more commonly seen in older age groups due to the degradation of statoconia caused by demineralization, which has been established in histological examinations.3 The signs may come on abruptly or gradually over a period of days, weeks, months, or years.4 BPPV almost often happens when the head position changes. Some people may have symptoms whether laying down or sitting up in bed. Others may be able to see symptoms when they lean forward or back or towards the side. These symptoms usually deteriorate with time due to ordinary ear structural wear and tear.5 It is possible to treat BPPV. Physical therapy and conventional medicine are used to treat it. In its treatment, physical therapy plays a significant part. Numerous workout routines and techniques continue to be effective. BPPV may be treated with physical therapy, a common clinical vertigo problem.5 The Brandt-Daroff method (B-D) is another treatment option for BPPV sufferers, however it is not always feasible due to their movement issues. BPPV sufferers are subjected to many gaze stabilisation exercises.6 Balance training for patients aids in the improvement of balance in people affected by BPPV.7 Recent developments indicate that additional progress in physical recovery is expected. Virtual rehabilitation using virtual reality is a novel innovation in therapy.\n\nWith the aid of technological devices such special goggles with screens or gloves with sensors, a person may interact with an imagined three-dimensional environment in virtual reality (VR). The simulation model built by virtual reality gaming systems enables players engage with the computer-generated interactive environment while giving them the sense that they are in the actual world. An interactive environment created by computers is present in these systems. Such programmes enable the adoption of task-based learning strategies by giving participants an exciting and motivating experience.8 Using the virtual reality instrument Oculus Quest, patients may explore a digital setting. Depending on the patient’s motions, Oculus Quest enables you to interact genuinely while immersing yourself in a virtual reality.9 In this study, an effort is made to augment conventional treatments for BPPV patients with the use of the Oculus Quest 2. BPPV is a very common condition and PC-BPPV is commonest of all. Most of the available literature targets conventional treatment including Exercises for repositioning and adaptation of otoconia. Comparative studies between the conventional rehabilitation protocols have also been done. There is paucity of research on virtual rehabilitation in PC-BPPV. VR protocols utilizing Oculus Quest 2, a device designed to incorporate VR environment can be used to mobilize the patients head position there by repositioning the otoconia. The lack of evidence related to Virtual rehabilitation and specifically Oculus Quest 2 emphasises the need to study its effects on BPPV outcomes like balance, dizziness, quality of life and nystagmus.\n\nThe study’s goal is to assess the therapeutic benefit of oculus quest 2 guided physical therapy in patients with Posterior canal Benign Paroxysmal Positional Vertigo (PC-BPPV) in addition to conventional therapy on balance, dizziness, nystagmus, and quality of life.\n\n1. To study the effect of virtual reality-based exercise through oculus quest 2 on balance in patients with PC-Benign Paroxysmal Positional Vertigo.\n\n2. To study the effect of virtual reality-based exercise through oculus quest 2 on dizziness in patients with PC-Benign Paroxysmal Positional Vertigo.\n\n3. To study the effect of virtual reality-based exercise through oculus quest 2 on quality of life in patients with PC-Benign Paroxysmal Positional Vertigo.\n\n4. To study the effect of virtual reality-based exercise through oculus quest 2 on nystagmus time in patients with PC-Benign Paroxysmal Positional Vertigo.\n\n5. To compare the effect of virtual reality-based exercise through oculus quest 2 in adjunct to conventional therapy in patients with PC-Benign Paroxysmal Positional Vertigo.\n\nSingle Centric, two arm parallel open label superiority randomized controlled trial.\n\nParticipants would be recruited from the OPD of Neuro-Physiotherapy, Aachrya Vinobha Bhave Rural Hospital, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, Maharashtra, India for this hospital-based study.\n\nThis study will be carried out at the department of Neuro-physiotherapy at Ravi Nair Physiotherapy College, Sawangi (Meghe), Wardha, India, after approval from the institutional ethics committee of Datta Meghe Institute of Higher Education and Research, deemed to be University. A screening method will be used to choose the subjects. For subject allocation, a randomization procedure employing a computer-generated list will be used. Participants in the study will be split into two arms. With the goal to treat, Arm-A (conventional therapy) and Arm -B (conventional therapy with VR exercise using Oculus Quest 2) were randomly assigned for comparison. The trial will be open-label, and cut-off values at baseline parameters will be used to select participants while taking into account inclusion and exclusion criteria. If the study needs more participants, a second source of recruiting will be used. The active group will get VR-based exercise through Oculus Quest 2 in addition to traditional treatment, while the control group will receive Brandt-droff. Exercises to assess their effectiveness regarding balance, nystagmus, dizziness, and general quality of life. Participants will be included and evaluated during a variety of time periods, including visits 1 and 2 for subject enrolment and participant screening, baseline, and the four weeks during which primary and secondary parameters will be examined. Figure 1 depicts the study’s design.\n\n\n\n1. Both Males and Females between 20 to 50 years, diagnosed will positive Loaded Dix-Hallpike test (as the gender has no role in the pathophysiology of BPPV and on the outcomes).\n\n2. Patients with Dizziness Handicap Inventory score ≤ 52.\n\n3. Patients who are willing to participate in the study.\n\n\n\n1. Patients with Central vestibular dysfunction, Cerebellar dysfunction, Cognitive impairments, and migraines.\n\n2. Patients with Dizziness Handicap Inventory score ≥ 52.\n\n3. Patients with inner ear infections and auditory dysfunctions.\n\n4. Patients under medications.\n\n5. Enrolment in another clinical trial involving physiotherapy or an investigational drug.\n\nControl group\n\nSubjects will get 20 minutes of traditional rehabilitation training per day, 12 sessions per week, three days a week for four weeks. The patient will be given the Bandt-Droff exercise, which consists of 10 repetitions with a rest after each cycle of five sets. This traditional rehabilitation is provided by a hospital therapist. To imitate the abilities necessary in the immersive VR group, conventional therapy will be built with equal intensity and complexity. For the Brandt-daroff exercise, the patient will begin in a sitting position and swivel the head 45 degrees to one side (left), then immediately lie down on the other shoulder (right). The patient should be told to hold this posture for 30 seconds or until the vertigo disappears. The patient then gradually returns to the beginning position, keeping the hear rotation (left) until seated upright. The patient next turns his head in the other direction (right) and lies down on the opposite shoulder (left), following the same 30 second time constraints. To ensure the quality of the training, researchers in the investigation will observe and encourage all participants to actively engage in the programme.\n\nExperimental group\n\nA therapist at the hospital will provide subjects with 20 minutes of traditional rehabilitation and 20 minutes of virtual reality rehabilitation training each day, 12 sessions, three days a week for four weeks. The patient will begin the standard therapy in a sitting position, move their head 45 degrees to one side (to the left in this case), and then rapidly lie down on the opposing shoulder (to the right). The patient should be told to hold this posture for 30 seconds or until the dizziness passes. The patient then gently assumes the beginning posture while continuing to rotate their head to the left until they are sitting up straight. Then, while still adhering to the same 30 second time limits, the patient turns their head in the other direction (to the right) and lies down on the opposite shoulder (to the left). Subjects in the experimental group will have to finish the “Coaster Combat” game on a back-supported chair in a virtual setting during the daily 20-min VR therapy. The patient will be requested to play two sets of this game, which has a 10-minute time limit. When utilising the Oculus Quest 2, the patient may swivel their head a small amount to gaze around. This offers a very high degree of immersion and comes very near to being a genuine experience. A virtual environment provided by a VR game will eventually increase a patient’s level of interest and commitment to rehabilitation.\n\nPre and post intervention measures\n\nPrimary outcomes\n\n1. Berg Balance Scale (BBS)\n\nThe scale was created specially to evaluate older people’s balance. It is 0.97 percent reliable. It received a total score of 56. It consists of 14 total elements, each of which has a maximum score of 4. The outcome will be reported pre-treatment and after four weeks following the treatment.\n\n2. Dizziness Handicap Inventory (DHI).\n\n3. The DHI items that make up the F3 (positional) subscale produced the highest scoring in the BPPV group when compared to Dix-Hallpike tests, with 75% sensitivity and 92% negative predictive value (NPV).10 The test-retest reliability of DHI is outstanding (r=0.97) and it has a great internal consistency reliability (r=0.89). The outcome will be reported pre-treatment and after four weeks following the treatment.\n\n4. Quality of Life Scale (QOLS)\n\nIt has 16 questions; the minimum score is 16 and the maximum score is 112.\n\nThe outcome will be reported pre-treatment and after four weeks following the treatment.\n\n5. Nystagmus time\n\nNystagmus time will be calculated when the patient elicits the nystagmus and when the nystagmus subsides. The outcome will be reported pre-treatment and after four weeks following the treatment.\n\nSecondary outcome\n\n1. Vertigo Symptom Scale Short Form\n\nThe VSS, VDI-symptom scale, and VDI-health-related quality of life scale have all demonstrated high levels of internal consistency in the Turkish translation, with corresponding Cronbach’s alpha values of 0.91, 0.85, and 0.93. Significant intraclass correlation coefficients (ICCs) of 0.83, 0.90, and 0.89, respectively, were discovered for the VSS, the VDI-symptom scale, and the VDI-health related quality of life scale over the two time periods.11 The outcome will be reported pre-treatment and after four weeks following the treatment.\n\nSample size calculation\n\nSample size - 74\n\nFormula Using Mean difference\n\nVariable (Vestibular symptom scale)\n\nMean ± SD. (Pre) result on (Vestibular symptom scale) = 15.10 ± 4.89.\n\nClinically relevant superiority 20% in virtual reality group = (15.10 *20)/100 = 3.02.\n\nDifference. = 0.34 ± 0.16. (As per ref. article)\n\nAs per reference articles.\n\nTotal samples required = 33 per Group.\n\nConsidering 10% drop out = 4\n\nTotal sample size required = 37 per group\n\nNotations:\n\nRef Article: Virtual Reality Vestibular Rehabilitation in 20 Patients with Vertigo Due to Peripheral Vestibular Dysfunction.12\n\n\nDiscussion\n\nBPPV is commonest disease which hampers the activity of daily living as it causes nystagmus, dizziness, light headedness, loss of balance and fear of fall. The goal of the study is to assess the therapeutic effectiveness of standard treatment for patients with posterior canal benign paroxysmal positional vertigo (PC-BPPV) on balance, vertigo, nystagmus, and quality of life. Virtual reality and physical therapy have both been extensively studied as potential treatments for BPPV. The Vestibular Activities and Participation Measure (VAP) score at post-intervention and the Fall Efficacy Scale (FES) score across the groups were significantly different, according to research by Jaffar et al. from 2023. The findings of the within-group analysis were significant (p=0.01).13 In line with this we are also using the Brandt-droff as a gold standard in this protocol. Xie et al. (2021) in the systematic review declared that virtual reality-based vestibular rehabilitation is very beneficial. However, the studies limition stated further research to be done on same. We are aiming to use VR to see its potential benefits in patients with same population.14 VeR is a successful treatment strategy that is backed by research, according to Matsumura and Murofushi’s assessment from 2021. BVP has a significant balance issue that might cause a fall and perhaps result in death. While VeR has obvious advantages for UVP, it only provides marginal advantages for BVP. However, VR, which has lately been used for VeR, is a promising technique.15 In this study we are also trying to find out the benefit of oculus quest 2. The impact of balancing vestibular rehabilitation treatment on elderly patients with benign paroxysmal positional vertigo was investigated by Ribeiro et al. (2017). Over the course of the 13 weeks, there were no between-group differences in dizziness, quality of life, or standing balance. Through examinations, significant variations in dynamic balance measures across groups were found (p 0.05 for most tests). Both groups improved across the board in the intragroup analysis, with the exception of the majority of the dynamic balance tests in the control group, which showed no change.16 We are also using the outcomes for balance as it is highly impaired in BPPV.\n\nData over the outcome variables will be tested for normal distribution for the mean and standard deviation (SD), and median statistics will be positioned for finding skewed distributions and interquartile range (IQR). Results over the outcome variables will be tabulated and described using descriptive statistics. For descriptive statistics, frequency and percentages for binary and categorical variables will be tallied. All statistical analysis will be done using the free version of R programme. The inferential statistics will be examined in accordance with the following explanation.\n\nInferential statistics will be used for comparing the two groups for measurement score resulted for their mean change in primary variable (Berg balance scale, dizziness handicap inventory, quality of life, nystagmus time) and secondary variables (vertigo symptom scale) between baseline and end visits.\n\nBaseline variables will be tested for finding significance in mean using Anova or Kruskal wallis test for more than 2 assessment period. Post-hoc (Tuckey’s or Dunccan) test will be used to find the significance difference between two group for pair-wise comparison.\n\nOutcome variables will be tested for intra difference in measurement at pre- and postvisits using paired t-test for finding the significance in mean. While for inter group difference unpaired t-test for comparison of two group & Anova for comparison of three groups will be used. Generalized models for repeated measures will be tested for different visit periods (within the group) & for comparison of three groups (between the group) to find fixed & random effects.\n\nFor non-normal distribution Mathematical algorithms will be used for conversion of the data to normal distribution. If Data over primary variable still follows the non-normal distribution, then we will use alternate nonparametric test (Chi square, Mann Whitney, Wilcoxon test, Kruskal wallis, Friedmann test).\n\nChi square analysis will be performed for categorial evaluation between two groups control against experimental for statistical evidence of finding significance at 5% l.o.s. (P ≤ 0.05).\n\nT-test unpaired or alternative nonparametric test will be used for finding significance at 5% l.o.s. (P ≤ 0.05) between groups control against experimental.\n\nEffect size over mean change difference on primary variable will be measured with corresponding 95% confidence interval (CI) & will be presented for finding the significance at 5% level.\n\nPlanning to publish in indexed journal and present the study in National Conference Proceedings.\n\nRecruitment of participants is yet to be started.\n\nInstitutional Ethical Clearance has been obtained on 21/03/2023. Written informed consent will be obtained from the study participants.\n\nIEC No – DMIHER (DU)/IEC/2023/811\n\nCTRI Registration was obtained 24/05/2023", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: SPIRIT checklist for protocol Therapeutic effectiveness of virtual reality-based exercise through Oculus Quest 2 on balance, dizziness, nystagmus and quality of life in patients with posterior canal benign paroxysmal positional vertigo -A randomized control trial, DOI: 10.5281/zenodo.8162236. 17\n\n\nAcknowledgements\n\nI would like to thank Mr. Laxmikant Umate for his assistance in designing the data analysis and calculating the sample size.\n\n\nReferences\n\nParnes LS, Agrawal SK, Atlas J: Diagnosis and management of benign paroxysmal positional vertigo (BPPV). CMAJ Can Med Assoc J. 2003 Sep 30; 169(7): 681–693.\n\nCalifano L, Salafia F, Mazzone S, et al.: Anterior canal BPPV and apogeotropic posterior canal BPPV: two rare forms of vertical canalolithiasis. Acta Otorhinolaryngol Ital Organo Uff Della Soc Ital Otorinolaringol E Chir Cerv-facc. 2014 Jun; 34(3): 189–197.\n\nHornibrook J: Benign Paroxysmal Positional Vertigo (BPPV): History, Pathophysiology, Office Treatment and Future Directions. Int J Otolaryngol. 2011; 2011: 1–13. Publisher Full Text\n\nKatsarkas A: Benign paroxysmal positional vertigo (BPPV): idiopathic versus post-traumatic. Acta Otolaryngol (Stockh). 1999; 119(7): 745–749. Publisher Full Text\n\nSingh PM: BENIGN PAROXYSMAL POSITIONAL VERTIGO: OUR EXPERIENCE AT A TERTIARY CARE CENTRE OF CENTRAL INDIA. Int J Sci Res. 2020 Sep 1; 1–3. Publisher Full Text\n\nMandalà M, Pepponi E, Santoro GP, et al.: Double-blind randomized trial on the efficacy of the Gufoni maneuver for treatment of lateral canal BPPV. Laryngoscope. 2013 Jul; 123(7): 1782–1786. Publisher Full Text\n\nvon Brevern M , Radtke A, Lezius F, et al.: Epidemiology of benign paroxysmal positional vertigo: a population based study. J. Neurol. Neurosurg. Psychiatry. 2007 Jul; 78(7): 710–715. Publisher Full Text\n\nIkbali Afsar S, Mirzayev I, Umit Yemisci O, et al.: Virtual Reality in Upper Extremity Rehabilitation of Stroke Patients: A Randomized Controlled Trial. J Stroke Cerebrovasc Dis Off J Natl Stroke Assoc. 2018 Dec; 27(12): 3473–3478. Publisher Full Text\n\nShum LC, Valdés BA, der Loos HMV : Determining the Accuracy of Oculus Touch Controllers for Motor Rehabilitation Applications Using Quantifiable Upper Limb Kinematics: Validation Study. JMIR Biomed Eng. 2019 Jun 6; 4(1): e12291. Publisher Full Text\n\nZamyslowska-Szmytke E, Politanski P, Jozefowicz-Korczynska M: Dizziness Handicap Inventory in Clinical Evaluation of Dizzy Patients. Int J Environ Res Public Health. 2021 Feb 24; 18(5): 2210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYanik B, Külcü DG, Kurtais Y, et al.: The reliability and validity of the Vertigo Symptom Scale and the Vertigo Dizziness Imbalance Questionnaires in a Turkish patient population with benign paroxysmal positional vertigo. J Vestib Res Equilib Orientat. 2008; 18(2–3): 159–170. Publisher Full Text\n\nStankiewicz T, Gujski M, Niedzielski A, et al.: Virtual Reality Vestibular Rehabilitation in 20 Patients with Vertigo Due to Peripheral Vestibular Dysfunction. Med Sci Monit Int Med J Exp Clin Res. 2020 Dec 31; 26: e930182. Publisher Full Text\n\nJaffar M, Ghous M, Ayaz M, et al.: Effects of Half-Somersault and Brandt-Daroff exercise on dizziness, fear of fall and quality of life in patients with posterior canal benign paroxysmal positional vertigo: A randomised control trial. JPMA J Pak Med Assoc. 2023 Jan; 73(1): 139–142.\n\nXie M, Zhou K, Patro N, et al.: Virtual Reality for Vestibular Rehabilitation: A Systematic Review. Otol Neurotol Off Publ Am Otol Soc Am Neurotol Soc Eur Acad Otol Neurotol. 2021 Aug 1; Publish Ahead of Print(7): 967–977. Publisher Full Text\n\nMatsumura M, Murofushi T: Vestibular Rehabilitation after Vestibulopathy Focusing on the Application of Virtual Reality. J Otorhinolaryngol Hear Balance Med. 2021 Jun; 2(2): 5. Publisher Full Text\n\nRibeiro KMOB d F, Freitas RV d M, Ferreira LM d BM, et al.: Effects of balance Vestibular Rehabilitation Therapy in elderly with Benign Paroxysmal Positional Vertigo: a randomized controlled trial. Disabil Rehabil. 2017 Jun; 39(12): 1198–1206. PubMed Abstract \| Publisher Full Text\n\nJachak S, Raghuveer R: Therapeutic effectiveness of virtual reality-based exercise through Oculus Quest 2 on balance, dizziness, nystagmus and quality of life in patients with posterior canal benign paroxysmal positional vertigo -A randomized control trial. (Version v1). Zenodo. 2023. Publisher Full Text" }	[ { "id": "235035", "date": "16 Jan 2024", "name": "Oskar Rosiak", "expertise": [ "Reviewer Expertise Neurootology", "Virtual reality in vestibular research" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a proposition for a clinical trial protocol on the effectiveness of VR-aided rehabilitation in Posterior Canal BPPV patients.\n\nThe general aim of the project is well described and the proposed methodology is valid, the two-arm randomized approach with both groups receiving standardized Brand-Daroff Exercises and study group receiving additional VR therapy is a good approach.\nThe rationale for this study is convincing, as similar studies were conducted using VR in other vestibular disorders and with good outcomes, while well-designed randomized trials are scarce.\n\nI have some minor comments:\nFigure 1 - box with VR has a second line that is illegible.\nInclusion criteria: 1. What is the rationale behind the cutoff at 50 y.o? 2. Be more specific as to the Dix-Hallpike maneuver test. Will only geotropic rotational horizontal nystagmus be accepted? or any evoked nystagmus? Will additional maneuvers be performed to account for multi-canal BBPV? 3. Instrumental measures could be useful to establish baseline vestibular function such as the vHIT\nExclusion criteria 4. Any medication? I suppose the authors should list the groups of medication.\nFollowing abbreviations are not explained: VeR - ??? UVP - ??? BVP- ???\nEnglish language needs major correction.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "204278", "date": "12 Jun 2024", "name": "Nicolas Perez-Fernandez", "expertise": [ "Reviewer Expertise Neurotology" ], "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 rationale of the study is well set. The main issue is that the main issue with which the authors are performing their study is against spontaneous resolution. As no repositioning maneuver is done (Epley or Semont) Brandt Daroff exercises are showing adaptation. But there is adaptation ion daily living as well spontaneous recovery. So a third arm should be needed or this has to be taken into consideration.\nThe inclusion criteria must be more clear. How do you classify the PSC-BPPV. Loaded Dix-Hallpike? clarify what is that\nData on the patients must be more precise: age, sex, disease duration, time since first day of vertigo, first episode ever or recurring, clinical history of concomitant disease (BP, diabetes, etc, low vitamin D, migraine, etc)\nThe specific protocol for virtual rehabilitation must be better explained. Why sitting? Head restrained?\n\nThe english is very poor and the academic style too.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1109
https://f1000research.com/articles/12-337/v1	27 Mar 23	{ "type": "Case Report", "title": "Case Report: Mepolizumab in the treatment of idiopathic chronic eosinophilic pneumonia", "authors": [ "Selsabil Daboussi", "Samia Essebaa", "Samira Mhamdi", "Chiraz Aichaouia", "Ghedira Hela", "Aida Ayadi", "Moetemri Zied", "Samia Essebaa", "Samira Mhamdi", "Chiraz Aichaouia", "Ghedira Hela", "Aida Ayadi", "Moetemri Zied" ], "abstract": "Idiopathic chronic eosinophilic pneumonia (ICEP) is a rare interstitial lung disease of unknown cause. It usually responds well to systemic corticosteroid therapy, but relapses are frequent. We describe two cases of 21- and 27-year-old patients, presenting with dyspnea. The diagnosis of steroid-relapsing and steroid-dependent ICEP was made respectively. Mepolizumab was prescribed to both patients. This treatment resulted in successful long-term disease management with much fewer side effects than a traditional corticosteroid therapy.", "keywords": [ "Mepolizumab", "Idiopathic chronic eosinophilic pneumonia", "Corticosteroid", "Treatment" ], "content": "Introduction\n\nIdiopathic chronic eosinophilic pneumonia (ICEP) is a rare interstitial lung disease of unknown origin, associated with abnormal eosinophilic lung infiltration.1–3 Clinical presentation is non-specific. It is traditionally diagnosed based on the chronic onset of respiratory symptoms, pulmonary peripheral infiltrates, blood and/or alveolar eosinophilia, and exclusion of other eosinophilic disorders.2–5 Systemic corticosteroids are the first line recommended treatment. They are efficient, but relapses are frequent. Relapses may occur when the treatment is stopped or when the dose is reduced.2\n\nMepolizumab is a humanized monoclonal antibody that specifically targets interleukin 5 (IL-5) and neutralizes its effect. Two cases of successfully treated ICEP with mepolizumab are presented. The study was approved by the Ethics Committee Of The Military Hospital In Tunis. Written informed consent was collected from the patients. Anonymity was respected during data treatment.\n\n\nCase report 1\n\nA 21-year-old patient, high-level athlete, was admitted for dry cough and progressively worsening dyspnea for a month. He also reported 10 kg weight loss during this period. He did not have high fever or wheezing. He was a never smoker and he had no previous medical history. Laboratory findings showed an elevated leukocyte count with a high level of eosinophilia (4.57 G/L, 34.7%). Liver and kidney function tests were normal. Chest computed tomography (CT) showed bilateral and peripheral infiltrative shadows, essentially on the right side (Figure 1). Bronchoalveolar lavage fluid (BALF) showed an elevated eosinophil percentage (26%). Antineutrophil cytoplasmic antibodies (ANCA) were negative. FIP1L1-PDGFRA and JAK2 V617F mutations were absent. Video-assisted thoracoscopic lung biopsy showed pulmonary eosinophilia with appearances of organizing pneumonia (Figure 2). The diagnosis of ICEP was established. The patient was managed with high-dose of corticosteroids (20 mg dexamethasone for three days, then 1 mg/kg/day of prednisolone which was tapered over six months). Clinical, biological and radiological improvements were noted. However, the patient relapsed three days after the treatment was stopped. He responded again to steroids. But because of the side effects he experienced from chronic steroid use (muscle wasting, tendon rupture and depression), the decision to initiate an off-label anti-IL5 treatment was made. A monthly 100mg of subcutaneous mepolizumab was started and oral corticosteroids were gradually stopped. With 12 months of hindsight, he was asymptomatic, the eosinophil counts dropped to normal range (Figure 3) with a complete radiological clearance. No adverse reaction to the therapy was noted.\n\n\nCase report 2\n\nOur second case is a-27-year-old man, active military, admitted for increasing dyspnea, cough and wheezing for a few weeks. He had been diagnosed with asthma one year earlier. He was an ex-smoker of two-five packs per year. Tests showed blood eosinophilia (2G/L, 15%). The C-reactive protein level was 10 mg/L. Chest CT reveled peripheral and diffuse ground glass opacities. The serum Immunoglobulin E level was 502 IU/mL. The BALF showed a marked percentage of eosinophils of 31%. Further investigations were unrevealing for parasitic or fungus infections, vasculitis, and hematologic disorders. Hence, the diagnosis of ICEP was made. Systemic corticosteroids were prescribed (4 days of 20 mg of dexamethasone, then 1 mg/kg/day of prednisone, which was tapered over 3 months). His asthma was treated with daily inhaled budesonide and formoterol. The patient responded well to the therapy: a rapid resolution of symptoms was noted, the eosinophils blood count dropped to normal range, and the pulmonary infiltrates completely disappeared. However, attempts at tapering the corticosteroids below 35 mg were met with three relapses in 16 months, which were associated with clinical worsening, reascension of eosinophil count, recurrence of pulmonary lesions and multiple hospital admissions. A high glucose level due to the chronic steroid use was noted. Subcutaneous mepolizumab 100 mg monthly was initiated. A gradual decrease of oral steroids was well tolerated (Figure 3). The patient is currently at four months of overlap of anti-IL5 and tapering doses of corticosteroids. With a current dose of 20 mg of prednisone, no relapse has occurred.\n\n\nDiscussion\n\nEosinophils play a major role in the pathogenesis of ICEP. The IL-5 is a cytokine involved in the production, maturation and release of eosinophils from the bone marrow. Therefore, using a therapy that specifically targets eosinophil activity and proliferation could help treating ICEP.1,3\n\nMany reports support the use of anti-IL5/5R agents - such as mepolizumab, reslizumab or benralizumab – for the treatment of relapsing and/or corticosteroid dependent/intolerant ICEP.2,4–7 These agents have been clinically proven to be effective for eosinophilic asthma, eosinophilic granulomatosis with polyangiitis (EGPA), and FIP1L1-PDGFRA-negative hypereosinophilic syndrome (HES).4\n\nTargeting IL-5 cytokin in patients with ICEP was firstly done by To and al. in 2018. The suppression of local levels of IL-5 and infiltration of eosinophils with mepolizumab resulted in the resolution of CT findings and decreased symptoms.5 In a recent study conducted by Delcros et al. - which is the largest cohort of ICEP patients treated with anti-IL5/5R-, no relapses were reported with a median follow up of 13 months. In that study, median annual rate of severe asthma exacerbations decreased from 0.15 to 0, median blood eosinophil count dropped to normal range and a complete disappearance of pulmonary infiltrates was noted in 71% of patients.4\n\nIn our patients, the search for alternative therapies was due to an attempt to minimize corticosteroid use. Mepolizumab was chosen due to its availability and the body of evidence to support its use. We prescribed mepolizumab at a monthly dose of 100 mg subcutaneously, which is the dosage used to treat eosinophilic asthma. This dose is three times lower than that used for EGPA and HES.2,8 Both our patients had a rapid decrease of the blood eosinophil count along a significant clinical and radiologic improvement. Corticosteroid tapering without relapse was also allowed. In the study of Brenard et al., the median daily corticosteroid dose dropped from 5 mg prednisone (range 0–10) at baseline to 0 (range 0–5) after three months of mepolizumab use.7\n\nThe overall safety profile of long-term use of mepolizumab has been reported by numerous studies.4,7,9 This medication has far fewer toxicities than systemic corticosteroids and can possibly be used in the long term to prevent relapses of ICEP.\n\n\nConclusion\n\nMepolizumab and other anti-IL5/5R agents seems to be a both safe and effective option as a primary steroid-sparing therapy for corticosteroid dependent or relapsing ICEP. Further investigations and clinical trials are necessary to establish recommendations and clear protocols.\n\n\nConsent for publication\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patients.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare. CARE flow diagram and CARE checklist. DOI: https://doi.org/10.6084/m9.figshare.22236772.v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).\n\n\nAcknowledgments\n\nCEREO – Reference center for hypereosinophilic syndromes Affiliated to the MaRIH immuno-haematological rare diseases healthcare sector.\n\n\nReferences\n\nSato H, Miyata Y, Inoue H, et al.: Efficacy of Mepolizumab Extended Interval Dosing for 2 Asthmatic Patients With Chronic Eosinophilic Pneumonia. J Investig Allergol Clin Immunol. 2021 Oct 22; 31(5): 459–460. PubMed Abstract \| Publisher Full Text\n\nSarkis E, Patel S, Burns K, et al.: Anti-interleukin (IL)-5 as a steroid-sparing agent in chronic eosinophilic pneumonia. J Asthma. 2018 Nov 16; 57(1): 82–86. PubMed Abstract \| Publisher Full Text\n\nKisling A, Jones J, Hixson C, et al.: Mepolizumab: an alternative therapy for idiopathic chronic eosinophilic pneumonia with glucocorticoid intolerance. Drugs Context. 2020 Aug 18; 9: 1–7. Publisher Full Text\n\nDelcros Q, Taillé C, Vallée A, et al.: Targeting IL-5/5R for the treatment of idiopathic chronic eosinophilic pneumonia. J Allergy Clin Immunol Pract. 2022 Dec. S2213219822013356. PubMed Abstract \| Publisher Full Text\n\nTo M, Kono Y, Yamawaki S, et al.: A case of chronic eosinophilic pneumonia successfully treated with mepolizumab. J Allergy Clin Immunol Pract. 2018 Sep; 6(5): 1746–1748.e1. PubMed Abstract \| Publisher Full Text\n\nRicketti PA, Ricketti AJ: Relapsing chronic eosinophilic pneumonia treated successfully with benralizumab. Ann Allergy Asthma Immunol. 2021 Jun; 126(6): 726–727. PubMed Abstract \| Publisher Full Text\n\nBrenard E, Pilette C, Dahlqvist C, et al.: Real-Life Study of Mepolizumab in Idiopathic Chronic Eosinophilic Pneumonia. Lung. 2020 Apr 1; 198(2): 355–360. PubMed Abstract \| Publisher Full Text\n\nLin RY, Santiago TP, Patel NM: Favorable response to asthma-dosed subcutaneous mepolizumab in eosinophilic pneumonia. J Asthma. 2019 Nov; 56(11): 1193–1197. PubMed Abstract \| Publisher Full Text\n\nKhatri S, Moore W, Gibson PG, et al.: Assessment of the long-term safety of mepolizumab and durability of clinical response in patients with severe eosinophilic asthma. J Allergy Clin Immunol. 2019 May; 143(5): 1742–1751.e7. PubMed Abstract \| Publisher Full Text" }	[ { "id": "168068", "date": "04 Apr 2023", "name": "Sevim Bavbek", "expertise": [ "Reviewer Expertise Asthma", "severe asthma", "biologicals", "drug allergy", "desensitization to drugs" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI would like to thank you for the opportunity to review this article.\nIdiopathic chronic eosinophilic pneumonia (ICEP) is a rare interstitial lung disease of unknown cause and responds well to systemic corticosteroid therapy, although frequent relapses are reported. Here two cases of CEP patients have been reported.\nThe paper might have potential to be indexed but the point below needs to be clarified:\nCases with CEP in the case report, have been well evaluated and presented but for case 2, presence of EGPA may be an alternative diagnosis. In this case, there is not data about ANCA but anyway ANCA may be negative in cases with eosinophilic dominant without presence of vasculitis yet. This possibility should be discussed. Mepolizumab has also been approved in EGPA\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [ { "c_id": "9678", "date": "30 Jun 2023", "name": "DABOUSSI SELSABIL", "role": "Author Response", "response": "We would like to thank you for reviewing this article and for providing pertinent comments. For the case 2, the ANCA were negative. Indeed, ANCA-negative EGPA is an alternative diagnosis for this patient. But he did not present with paranasal abnormalities, cutaneous, neurological, gastrointestinal or cardiovascular symptoms, and did not meet the ACR criteria for the disease. Therefore, we retained the diagnosis of ICEP. This possibility will be discussed in the revised version of the article." } ] } ]	1	https://f1000research.com/articles/12-337
https://f1000research.com/articles/12-662/v1	13 Jun 23	{ "type": "Research Article", "title": "Mapping movie genre evolution (1994 – 2019) using the role of cultural and temporal shifts: a thematic analysis", "authors": [ "Anshuman Mohanty", "Aditi Mudgal", "Shirshendu Ganguli", "Aditi Mudgal", "Shirshendu Ganguli" ], "abstract": "Background: The gratification each person seeks through a movie is different. Sometimes a person would seek information through movies or use them for educational purposes, and some might watch movies to escape into a world of fantasy or humour. Keeping in mind the diverse and ever-changing needs of the audience, the primary objective of this study is to observe the evolution of movie genre and content preference in India, which is one of the largest and culturally intriguing movies producing nation across the globe.\nMethods: To attain the objective, the researchers have thematically analysed the top five revenue grossing movie genres over a span of 26 years (1994 to 2019) in Bollywood. More than 100 storylines have been analysed to develop genre trend graphs and the results indicate a sharp decline in the popularity of romantic and family dramas, whereas comedy and action movies have witnessed an overall growth with romantic comedies (romcoms), being the most stable amongst the top five.\nResults: Several societal factors like the changing family structure, education level, access to dating applications and even terrorism have been considered to elucidate the evolving psyche of the audience. The theoretical understanding of the result is derived from the uses and gratification theory, cross culture communication theory, and Bandura’s social cognitive theory.\n\nConclusions: This study would provide film-makers with a guide to understanding the changing movie genre preferences in India, which in turn would help them to produce economically profitable movies in future.", "keywords": [ "Movie Genres", "Thematic Analysis", "Cross Culture Communication Theory", "Social Cognitive Theory", "and India." ], "content": "Introduction\n\nMovies have been the cornerstone of social and cultural surroundings over the past 100 years. They have not only entertained the viewers but also, they have been a driving force in taking forward political ideologies across generations. Academically, they have enabled us to understand the “society, history and culture” of a country in a lucid way (Kerrigan, 2017). UNESCO has also recommended preserving movies as they reflect the “cultural identity of people” and as they act as an integral part of the “nation’s cultural heritage” (Kerrigan, 2017). As movies are consistently mentioned in television, internet and newspapers, they are a common topic for consumer conversations and thus, they have always been instrumental in creating cultural ideologies. This is especially true in India, where the affinity towards movies has always surpassed other entertainment avenues (Poddar, 2014). The researchers thus focus on the Indian motion picture industry that garnered over $2.1 billion in 2016 and is deemed to be one of the largest movies producing nations in the entire world (MPAA, 2016).\n\nHowever, most of the movies released in India are not always profitable. Despite promising numbers, trade reports suggest that around 85% of the movies were not able to recover their investment and labelled as flops in 2016 (Box office India, 2017). While scrutinizing the top 50 revenue grossers in Bollywood, it was found that the number of profit-making movies reduced from 30 in 2012 to 18 in 2016 and on top of that only 22% of the movies contributed 96% of the overall box office collections. This skewed revenue distribution, along with the short life cycle of movies, coupled by the downward trend in the theatrical sales, poses a serious concern for movie makers and the distributors (Moon et al., 2016). Furthermore, the decline in revenue generation is also attributed to several factors like the increasing rate of piracy, influx of Hollywood movies, shutting down of single screen theatres and so on. However, trade analysts suggest that the most important point of concern for the movie makers is the lack of quality themes and seamless storyline in a movie (E&Y, 2012). Although marketers and researchers have pondered upon numerous variables like budget, stars, reviews etc. impacting the commercial success of a movie, ‘genre’ is the only element that hints about the probable theme and the storyline (Zufryden, 1996). As the movie genre captures the audience’s imagination from the word go, it becomes the most decisive factor impacting the success of a movie.\n\nThroughout history there has always been a segregation between commercial movies (genre movies) and art movies (anti-genre1 movies). It is conceded that the major chunk cinemas released in the market are typically genre movies which are “formulaic, conservative and repetitive” in nature (Jancovich, 2010). Movie genre researcher Barry Keith Grant stated that “…genre movies are those commercial feature films which, through repetition and variation, tell familiar stories with familiar characters in familiar situations” (Grant, 1995). As genre encapsulates the collective belief of the audience, it is one of the most dominant variables that impacts the box office performance (Jancovich, 2010; Lee, 2006). Through pre-release buzz and trailers, genre becomes the initial point of contact with the audience, and it inculcates various expectations within them before they select to watch a movie (Stam and Miller, 2000). As the focus of this study is on the economic aspect of movie making, the researchers have emphasized on the commercial movies released in India.\n\nCommercial movies have always been a dominant force in the Indian market. These movies are popular for its portrayal of musical and well-choreographed dance numbers along with it’s over the top and melodramatic storylines across different genres (Bouman et al., 2010; Mooij, 2006). Although this stereotypical perception of Bollywood holds true for several movies till date, it is also an undeniable fact that genres have continuously reformed their storytelling style over the period of time (Matusitz and Payano, 2011). Despite the growing importance of movie genres in media studies, scant research has been made on the genre preferences in Bollywood. This absence of literature motivated the researchers to find out are there any evolutionary changes that movie genres and content have gone through in Bollywood over the last two decades?\n\nThus, the objective of this study is divided into two parts: firstly, the researchers attempt to track the evolution of Bollywood’s most preferred movie genres from 1994 to 2019. Secondly, the researchers investigate the change in the storytelling practices of the most preferred genres over the last 26 years. From a managerial point of view, this research might provide important cues to movie makers in understanding the consumer’s preference and the evolution of movie genres in a better way, guiding them in producing economically profitable movies. As movie watching is deemed to be a cultural phenomenon, the study draws its theoretical standing from the likes of uses & gratification theory (Weiyan, 2015), cross culture communication theory (Tannen, 1983), and Bandura’s social cognitive theory (Bandura, 2005). The theories used in this research, provide a reasoning to comprehend the audience’s behaviour pre, post and during the exposure to movies. The uses & gratification theory (UGT) (Weiyan, 2015) helps in understanding the mechanism of choosing one genre over the other, which further motivates the content creators to serve the ‘popular’ or ‘in-demand’ content. It is a cyclical process wherein a genre becomes a popular choice among the audience, which brings in commercial success, hence the creators incline towards building stories in and around that genre commonly. The cross-communication theory (Tannen, 1983) helps one understand the repackaging and adoption of content from other parts of the world and serving them according to the Indian context. The content is flavoured according to the taste preferences of the Indian audiences. The social cognitive theory of Bandura explicates the ongoing evolution of content, i.e., the genre reshaping according to the push and pull of temporal and cultural levers of Indian society. So, a movie reflects and mirrors its society, the storyline brings in the characteristics of the society. It is a two-way process of learning and evolving in forms of sociological and cultural changes which take place continuously. The content reflects the undercurrents a society is going through at a particular time. It becomes a two-way responsibility for both the moviemakers and society to bring fresh ideas, evolve through them and adopt them by making them a part of their life.\n\n\nLiterature review\n\nThe literature review of this study is divided into two parts. Firstly, we throw light on the literature of genre evolution, where we understand that the changes in the kind of movie genres presented can be validated through social cognitive theory and behaviour of choosing a genre over the other, hence making it a popular choice is aligned with Uses and Gratification Theory (Zia et al., 2017). The second section emphasizes on portraying the fact that although several researchers have conducted numerous studies, there is no uniformity in the preference of movie genres across the world. This motivated the researchers to conduct a study focusing on the preference of movie genres in India, which is one of the largest movies producing nations in the world.\n\nThe temporal fluid nature of the movie genre is the function of the social and cultural taste an audience undergoes over a time frame (Booth, 2012). This is a gradual change which takes place over the time, an example would be the way consumer behaviour and preferences changes over the due course of time which is mapped in the social cognitive theory (Schunk, 2012). A movie has the ability to depict a cultural confluence and enact a social change in its storyline. This makes a movie a powerful tool to generate an idea of change in the society and behaviour of the audience (Gross, 1985). The taste and time are linked and blending both these components help in creating the content for the audience to which they relate and resonate with their real world. The addition of subcultural developments, contextuality, and topical themes of content can be usefully understood as a component of an audience's tastes while choosing a particular genre (Bourdieu, 1984).\n\nThe cultural milieu of societies and the growing globalisation in a cyber era transcends time, distance, and place broadens the scope of cross-cultural amalgamation. The individual choices operate on beliefs, efficacy, sociocentric focus and influence (Bandura, 1997). These are influenced by the type of futures they seek to achieve collectively as a society. Socio-centric forces interact to re-shape the nature of cultural life, through rapid cultural and technological evolution in their beliefs, morals, social roles, and styles of behaviour. The nature of adaptability and learnability (Dobzhansky, 1972) helps the human species to remarkably evolve. The humans learn by observing, acquiring knowledge, attitudes, values, emotional proclivities, and competences through the rich fund of information conveyed by actual and symbolic modelling of behaviour in the movies (Bandura, 1986). The cultures develop and replicate themselves in the form of language, customs, and social practices. In a larger view, one can project the cultural patterns a society has gone through over time.\n\nThis agentic capacity rooted in beliefs of personal and collective efficacy to produce effects by one’s actions in a society influence the representation in genre of movies. Cultures are diverse and dynamic social systems which are not static and so is their influence on the current undercurrents integrated with content and influence on genre of movies.\n\nFigure 1 helps us in understanding the evolving nature of genres over time. The genre of the movie is dependent on the kind of content satisfying the gratification needs of the audience and the gradual change in the nature and kind of content over the time influenced by subcultural developments taking place in the society. The content is levelled up from time to time to seep in the form of new storylines, genres and plots.\n\nThe choice of exposing oneself to a genre of content is personal to everyone. As stated, previous gratification studies conducted in the area of media listed quite a few moderating variables affecting choice. The choice of content is highly dependent on the personal gratification sought by the individual. The repeat behaviour or binge watching a certain kind of content is associated with fulfilment of cognitive and affective gratification needs. The objective of this study is to focus on understanding the evolution of movie genre preferences in India. This study will enable movie makers to identify popular genres that provides the highest gratification to the audience. The theoretical underpinning that supports the process of learning and unlearning behaviour is derived from the social cognitive theory, which explains that a movie genre is temporal and contextual in nature. Movie genres blend in the social and cultural undercurrents to design fresh content for the audience (Memory, 2008). Thus, movie genres are tweaked according to the changing human behaviour practiced at a particular point of time.\n\nTraditional motion picture researchers have always tried to generate a proper definition for the movie genre. However, with the passage of time, the idealist thought of defining a genre was discarded away and the overall collective belief of the audience was used to signify the genre for a movie (Tudor, 1986). Despite Tudor’s thought on genre being widely accepted in the movie literature, a handful of theorists such as Altman (1999) have described that as a movie genre is perceived differently by several user groups, it becomes fairly difficult to come up with a consensus that identifies the true definition of a movie genre. However, Altman’s theory shows very little interest in the consumption process of movie genres. His research on the consumption pattern of a movie genre remained highly abstract and was concerned with several “hypothetical spectators” rather than focusing on the actual behaviour of the society and the market (Jancovich, 2010). As researchers found it very difficult to find a collectively acceptable definition of genre, several theorists have tried to simplify the situation by distinguishing between the mainstream (genre) versus art (anti-genre) movies. Genre movies are defined as “commercial feature films which, through repetition and variation, tell familiar stories with familiar characters in familiar situations' (Keith, 1995). On the other hand, anti-genre movies are deemed to be free from the formulaic and repetitive storytelling style which is evident in the mainstream movies. As the focus of our research is based on the consumption pattern of top revenue grossing Bollywood movies in India, we focus on the mainstream definition of movie genre.\n\nThe relevance of understanding genre preference has been discussed by several researchers in the media literature. The most important aspect of the genre is that it helps the audience in anticipating the prospective storyline of a movie through trailers (Zufryden, 1996). In the first instance itself, the audiences consider watching or skipping the movie based on their genre preferences. Thus, it becomes very important for the producers to make movies that hits the sweet spot among the audience. This has motivated numerous researchers to conduct studies to comprehend the preference of movie genres in their country. For example, in the USA Brewer et al. (2009) analysed the top 100 revenue grossers released between 1997-2001. They reported that although a variety of genres were successful at the box office, violent and adrenaline genres such as horror and action were found to be having more attention seeking power. Meanwhile, Gazley et al. (2011) conducted a primary survey in New Zealand and comedies and dramas had more impact on the box office when compared to sci-fi or action movies. In 2012, Walls & McKenzie conducted a study to check whether Hollywood movies portraying American culture dominated the world movie market or whether Hollywood produced movies as per the demand of the world audience. They found out that compared to other genres only Hollywood action movies had a better collection throughout the world. They also pointed out that a successful run in the U.S. market does not guarantee profitable box office returns throughout the world due to cultural disparity. On similar lines Lauren et al. (2015) conducted a study on several undergraduates in the U.S. and found that as young Americans had fanciful expectations about romantic relationships, they were more inclined towards romantic drama movies when compared to other genres.\n\nIn China, Ye and Starkey (2018) were involved in a study in which they had to ascertain the diversity in genre preference between East Asian nations and countries belonging to Central Eastern Europe. Their study reported that the Asian nations were more inclined towards action-adventure movies compared to the European nations who displayed a higher preference for romantic and comedy genres. Simon et al., (2019) conducted a similar study to analyze the relationship between adolescents and their movie watching preferences in eight different countries in Europe. They reported that comedy and adventure were the most popular genres and the preference for suspense, sci-fi and romance varied across countries. Nagaraj et al. (2019) analysed the Malaysian audience to determine the reason behind the degrading demand of Malaysian movies when compared to Hollywood. Their results depicted that the Malaysian audience had a higher preference for Hollywood because of their affinity towards action and horror genre movies. As Malaysian movies were not able to cater their needs, the audience shifted towards Hollywood movies. Jam et al. (2020) surveyed 400 respondents to study the preference of movie genres in Pakistan. Interestingly they reported that around 80% of the audiences were inclined towards patriotic movies as they were proud of their armed forces and such movies ignited a sense of eternal love for their country.\n\n\nMethods\n\nFor the first objective, the researchers collected secondary data consisting of the top five revenue grossing movies released between 1994 to 2019. The data was collected from boxofficeindia.com, as it is regarded to be one of the most important data repositories of Bollywood movies in India. The researchers opted for the top five leading revenue grossers as they indicate the highest number of footfalls the movie attracted in a particular year. The researchers generated a comprehensive list of 130 movies divided into twelve genres (Alien, Superhero, Action, Comedy, Dance, Family Drama, Horror, Mythology, Rom – Com, Romantic Drama, Sports Drama and Thriller). However, for the analysis the researchers opted to select only the top 5 recurring genres in the list (Action, Comedy, Romantic Comedy, Family Drama and Romantic Drama) which consisted of 105 (81%) out of the 130 movies (see Table 1). The remaining 25 movies were not included in the analysis as they were not sufficient to form a trend line for the analysis. For the second objective, that is to comprehend the evolution of Bollywood’s most preferred movie genres the researchers have adopted the approach by Longart et al., (2018) of generating themes by conducting thematic analysis (TA) of the storyline of 105 movies. Braun and Clarke (2012) defined TA as “A method for systematically identifying, organizing and offering insight into patterns of meaning (themes) across a dataset”. TA helps the researcher to come up with meaningful and sensible patterns from an available set of texts. The history of TA in media and advertising literature dates back to the 1970s (Barcus,1980). In recent years, Nelson and Salawu (2016) implemented TA to analyse the impact of covert product placements in Spiderman movies. Similarly in Britain, Cranwell et al. (2017) conducted TA to study the impact of alcohol abuse and sexual objectification in YouTube videos.\n\nTo address the first objective of the study the researchers have considered analysing the trend of the top five revenue grossing genres between 1994 to 2019. A total of 105 movies are spread across the five genres. The genre with the highest frequency of movies is Romantic Dramas followed by Action, Family Drama, Comedy and Romantic Comedies. Figure 2 displays the trend of Romantic Dramas in Bollywood.\n\nFrom Figure 2 it can be comprehended that the frequency of romantic dramas being commercially successful has drastically reduced after the early 2000s as compared to Action movies (see Figure 3), which has seen a steady growth after the early 2000s.\n\nAs depicted in Figure 4, it can be interpreted that the audiences have also started to lose interest in family dramas post 2010. Although the graph displays a huge spike in 2015, one should notice that only two mainstream family drama movies have managed to hit the top five spots over the last eight years.\n\nWhen compared to the remaining genres, comedy films have managed to hold a steady graph after 2004 (see Figure 5). Except for the years 2013 and 2016, they have always secured a spot among the top five revenue grossers.\n\nThe final genre on the list is romantic comedies. It is deemed to be a hybrid genre as it is an amalgamation of comedy and romance. Romantic comedies are typically light-hearted, humorous stories which revolves around romantic ideals such as ‘true love’ (Filmbug, 2021). From Figure 6 it can be seen that although not as steady as comedy movies, romantic comedies have managed to pull off a balanced run over the last few years.\n\nFor addressing the second objective, the researchers extracted the storyline (in text format) of 105 movies from boxofficeindia.comand imdb.com to conduct the TA. The data corpus consisted of 27,572 words, divided into five different genres. To recognize a specific pattern the researchers conducted TA on the textual data and generated several codes to understand them. The analysis follows the six- phase approach of TA (see Figure 7).\n\nThe first phase of the TA was to familiarize the researcher with the dataset. The researchers went through the dataset more than twice in order to highlight important points in the text for future analysis. Once the researchers were familiarized with the dataset, they manually coded the data in alignment with the research objectives. One should take into account that codes are not fully written up explanations, rather they are compact and small descriptions of the underlying text. The researchers followed a deductive method of coding. The deductive method of coding is used when the researcher is investigating a specific question and is anticipating a detailed and explicit description for only one specific aspect of the data (Boyatzis, 1998). To check the stability of the codes the researchers coded the transcriptions more than once. However, to improve the reproducibility of the codes, two external coders (having prior coding experience and keen interest in Bollywood films) were selected for the process. To avoid any misinterpretation, the coders were provided with instructions which clearly mentioned the objective and scope of the study along with the sampling procedure which helped the coder to set boundaries while coding. Finally, a total of 24 codes and 10 themes were extracted from the dataset which was spread across the five genres (see Table 2).\n\nBased on the storyline of the movies, the researchers divided the overarching theme of romantic dramas into two broad domains. Firstly, ‘Restricted access to romantic relationships which was prevalent during the early 90s’ and secondly ‘Realistic portrayal of romantic relationships after 2000’. Similarly, the two overarching themes for family dramas were ‘addressing emotional conflicts during the 90s and early 2000s’ which gradually shifted their focus towards ‘addressing societal problems after the early 2000s’. Action movies were classified into three themes. Predominantly, ‘family revenge stories were common during the early 90s and early 2000s’ which slowly transformed towards addressing ‘national security threats after early 2000s’. Another theme that emerged with the on-set of the millennium was more focus on ‘female empowerment’ and strong female characters in action movies. While analysing comedy movies, the researchers found that the popularity of ‘slapstick comedies’ surged during the 2000s and is still going strong till date. And finally, the researchers attributed two broad themes with romantic comedies. Although there were a few hit romantic comedies in the early 90s, the major change was visible with the dawn of the twenty-first century. The two primary themes attributed with romantic comedies were their focus on ‘liberated lifestyle’ and ‘individual aspirations’ after the early 2000s.\n\n\nDiscussion\n\nTheme 1: Restricted access to romantic relationships (early 1990s)\n\nCulturally, India has been a country which is associated with arranged marriages. Although the Indian literature and scriptures reported the importance of love and romance in abundance, yet romantic relationships have not been a decisive factor in prospective marital alliance (Gupta 1976). The prospect of a romantic relationship attracted social embarrassment and thus, despite their displeasure young individuals in India abstained from getting involved and expressing their love romantically (Bhalerao, 2018). Thus, the researchers theorize that most of the young individuals were deprived of romantic relationships, and they imagined themselves in the shoes of the main character and momentarily escaped reality by seeking out emotional closure from romantic movies. This made romantic dramas extremely popular in India. However, there was a drop in the popularity of romantic dramas over the last two decades as the Indian population started opening up about romantic relationships explicitly. With access to the internet and Hollywood content during the early 2000s, the Indian population was highly influenced by the liberal and independent lifestyle of the West.\n\nOne of the most evident features of the western civilization was the access to unrestricted “partner selection and relationship maintenance” (Bejanyan, 2015). As the modern Indian population was exposed to the western culture, the concept of dating evolved in the country which resulted in the growth of dating applications and love marriages (Gogaga, 2018). The process of selecting a life partner underwent a change in India. The decision of choosing their life-partners also became more of a personal choice than a family discussion (Sarkar and Rizzi, 2020). Thus, the researchers point out that, as the younger population found romantic closure through online dating and unobtrusive matchmaking in their workplace, they gradually distanced themselves from the highly redundant and melodramatic content of romantic movies (Gittel, 2017). This social change was reflected in the way the number of family dramas and romantic drama movies was reduced. The romantic movies were shifting to exposure and inclusion of liberal values and excluding family storylines out of them, making them unfit for family movie night affairs.\n\nTheme 2: Realistic storylines (after 2000s)\n\nMost of the Bollywood romantic movies in the 90s like Dilwale dulhaniya le jaenge (1995), Pardes (1997), Pyaar to hona hi tha (1998) etc. ended on a happy note, where the male and the female lead would get married and live happily ever after. However, with the decline in the popularity of such romantic movies during the early 2000s, the movie makers sought to reformulate the over-the-top melodramatic content of romantic movies by incorporating realistic storylines (Chakraborty, 2018). They started reflecting on the post marital disagreements between couples, which is a very common occurrence in India (TOI, 2018). Culture and communication go hand in hand, the cross-culture communication theory (Tannen, 1983) helps us in understanding the phenomenon where the Indian audience shifted from positive stories to realistic stories and chased a practical slice of life content. This kind of content enables them to resonate more with their own life struggles, where each day might not end on a happy note. Thus, the young population of India have shown an inclination towards accepting realistic love stories which tends to capture the bitter and sweet aspects of a modern-day relationship (Filmfare, 2021). As people were becoming more aware of the societal problems in India, romantic movies like Hamara Dil Aapke Paas Hai (2000) and Toilet – Ek Prem Katha (2017) also became very popular as they addressed societal problems like rape and the importance of hygiene in the purview of a romantic backdrop (Jhunjhunwala, 2020). Thus, to keep the romance genre alive the movie makers transformed the content of Bollywood romantic dramas making them more realistic and relevant for the audience.\n\nTheme 1: Emotional Conflicts (1990s – early 2000)\n\nThis theme categorizes family movies that focus on the ego clash between the rich and the poor, intra family conflicts and moral dilemmas. These storytelling attributes were common till the early 2000s. The presence of a joint family was very common in all these movies. The primary content of these movies focused on the clash between diverse economic backgrounds, suppression of the female lead and demonstrating strong Indian family values. However, the popularity of family dramas saw a drastic fall after the early 2000s and their story telling style also transformed. The most visible change was in portrayal of an Indian family structure in a movie during the early 2000s. Researchers have pointed out that the traditional Indian family structure was predominantly based on the joint family culture for centuries (Sinha, 1984). However, urbanization and rapid industrialization impacted the society drastically by altering the employment scenario in the country. As most of the Indian population was slowly shifting from the joint family structure to a nuclear family structure, their taste in the family dramas also transformed over time. Opening up of Indian society in terms of family structure from joint to nuclear family structure brought in the concept of individual decision making. These changes were captured in the family drama movies as well. For example, most of the successful family drama movies released during the 90s and early 2000s such as Hum aapke hain kaun (1994), Hum saath saath hain (1999) and Kabhi khusi kabhi gham (2001) depicted the conflicts faced within a joint family. However, with time Bollywood family dramas like Taare zameen par (2008) and My name is Khan (2010) started portraying the problems confronted in a nuclear family.\n\nTheme 2: Addressing Societal Problems: (After early 2000)\n\nWith time, the family drama movies not only shifted their focus from joint to nuclear families, but they also started addressing societal and sensitive problems like child education, religious harmony and illegitimate childbirth. Movies like My name is Khan (2010), Kya Kehna (2000) and Taare Zameen Par (2008) touched upon sensitive topics with a strong focus on nuclear family values. The audience found themselves more connected to stories which focused on the problems faced by a nuclear family due to the change in the overall family structure in the country (Jhambekar, 2015). Taking a lesson from the past, the movie-makers intentionally brought in the element of our contemporary culture with an amalgamation of social message to serve different needs of the society (Tannen, 1983). This reflected the changes the Indian society underwent at different times and contexts. The movies preach and bring the culture of acceptance of new reformative steps the society witnessed as a part of entertainment with fresh genres of movies and sometimes mixing two genres together.\n\nTheme 1: Family revenge stories (1990s – early 2000s)\n\nMost of the popular blockbusters released in the 90s and 2000s like Karan Arjun (1995), Ghatak (1996) Soldier (1998) and Gadar (2001) were typically family revenge stories. However, with time this trend slowly changed, and family/romance driven revenge stories took a back seat after the early 2000s. The moviemakers realized that the audiences were not interested in watching family driven action stories and thus, they reformulated their story-telling style. Furthermore, after the growth of the internet and influx of English movie channels via cable television during the early 2000s, the Indian audience was exposed to several Hollywood movies which also had an impact on their movie watching preference. As explained in the previous section, the taste of the audience was slowly shifting from family driven movies during the 2000s which had a spill over effect on the Action genre as well. This movie genre was completely influenced by western standards of sci-fi and action movies. The west was a step ahead in introducing this genre. The exposure to such content increased the motivation of movie makers and seekers both. Hence, we see a change in preference of audiences shifting movies towards action, thrillers and scientific thinking.\n\nTheme 2: Addressing national threats (Late 2000s)\n\nThe most popular Bollywood action blockbusters released in early 2000s like Dhoom (2004), Dhoom 2 (2007) and Ghajini (2008) were heavily inspired by Hollywood flicks. However, there was a drastic change in the content of Bollywood action movies after the 26/11 Taj Attack at Mumbai. A similar type of paradigm shift was also visible in Hollywood after the 9/11 World Trade Centre attack in New York. The world saw a rise of superhero movies being released in Hollywood, starting with Spiderman in May 2002. As America was grappling with immense grief, Hollywood’s response to this unjust tragedy was felt by the continuous release of superhero movies which instilled a sense of hope and reassurance among them (Hsiao, 2016). Based on the existing literature, the researchers of this study theorize that a similar course of events unfolded in Bollywood after the 26/11 attack in Taj at Mumbai. As the entire population was feeling insecure about the safety conditions in the country, Bollywood’s response to this scenario was to produce movies which presented the heroics of the Mumbai Police and the Indian Army. Movies like Wanted (2009), Dabangg (2010), Singham (2011), Ek Tha Tiger (2012), Tiger Zinda Hai (2017), Simmba (2018), URI (2019) and many others were released, where the main protagonists worked for the police or the army and fought against terrorist organizations, corrupt officers, drug abuse, human trafficking etc. Like many other developing nations, India also faced several threats and Bollywood’s response was to produce movies which instil a sense of faith and confidence in the Indian security forces. Thus, this study theorizes that as most of these action flicks tend to develop stories showcasing real national threats, it evokes a sense of patriotism and valour among the audience and hence they tend to feel more connected with them.\n\nTheme 3: Female empowerment (Late 2000s)\n\nOne of the most crucial and visible transformations was the changing role of the female characters in Bollywood action movies. In most of the action blockbusters like Karan Arjun (1995), Jeet (1996), Soldier (1998) or Gadar (2001), the leading lady was portrayed as a damsel in distress who was ultimately saved by the male lead. However, the stereotypical portrayal of women in Bollywood saw a drastic change during the late 2000s. Action flicks like Ek Tha Tiger (2012), Singham Returns (2014), War (2019) and URI (2019) portrayed strong and self-reliant female characters, which was a rare occurrence in Bollywood action movies released during the 90s and early 2000s. Historically, women in India led a suppressed life and they were confined to taking care of their family only. However, India has been witnessing cultural and societal changes that promotes equality of opportunities to women in various domains of the society (Krishnan, 2019). This study primarily attributes these changes to the rising education level in India. Government schemes like the Ujjwala Scheme (2007) and Beti Bachao Beti Padhao Abhyan (2015) also helped to raise the awareness of the importance of the human rights of the female population in the country. These positive changes are also reflected in most of the contemporary Bollywood movies where the role of the female lead is not just confined to being a source of solace for her male counterpart.\n\nThe increasing literacy rate, reduction in number of female infanticides, participation of women in workforce, female-friendly labour laws and workplaces, and emergence of entrepreneurial ventures from women leaders, have changed the power structure of society (Nishi, 2021; Kaur, 2022; Hindrise 2022). Today equality is just not an abstract concept in India. It is a reality experienced by both males and females in the country which is aptly represented in movies like Ki&Ka (2016), English Vinglish (2012) and many more. The social cognitive theory of learning and unlearning (Schunk, 2012) of certain behaviours can be utilized here as the justification of the evolving nature of society, movie genres and audience taste preferences time and again.\n\nTheme 1: Rise of mainstream slapstick comedies.\n\nThe researchers found that the mainstream comedy movies became a consistent part of the top revenue grossers only after 2005. Prior to 2005, there were only two mainstream comedy movies that made it to the top five list. Post 2005, comedy films made it to the top five grossers more frequently. Interestingly, it was found that most of the popular comedies like Welcome (2007), Ready (2011), Housefull 2 (2012), Housefull 4 (2019) etc. were slapstick in nature where broad comedy, confusion and absurd situations were their prominent feature. The researchers attribute the growing popularity of slapstick comedies with the escapist mentality of the Indian audience. Escapism has been mostly associated with those individuals who seek retreat from their monotonous life (Katz and Foulkes, 1962). The authors point out that India as a country has been gradually going down in the happiness index list. India ranks 136 among the 146 surveyed countries and its average happiness score has dropped drastically from 4.77 in 2013 to 3.82 in 2022. More than 89% of the Indian population suffer from mental stress which makes India one of the most depressed countries in the world (India Today, 2019). The change in lifestyle of the younger generation, increasing working hours and no time for physical activities and hobbies has shifted people to seek enjoyment and fulfilment through movies. Which has shown an increased indulgence towards light-hearted happy movies. Thus, the researchers assume that because of a hectic and stressful lifestyle people are drawn towards slapstick comedies in order to relieve their mental tension. Hence, Bollywood has witnessed a sharp rise in the popularity of slapstick comedies.\n\nTheme 1: Liberated lifestyle (after early 2000s)\n\nOn one hand, when melodramatic romantic movies saw a dip in its popularity during the early 2000s, the popularity of comedy movies was on a rise. This is when several movie makers kickstarted the era of romantic comedies in India (Ajaz, 2019). This amalgamation of love and humour brought forward a tectonic change in the portrayal of romantic characters in Bollywood. When compared to the older romantic movies, the principal characters in rom coms like Salaam Namaste (2005), Garam Masala (2005) and Love Aaj Kal (2009) had a much more liberated view of life and romance when compared to the stereotyped Bollywood movies. The portrayal of western ideologies like live in relationships, casual dating and polyamorous relationships was popularized by rom coms. As discussed in the earlier section (see Romantic dramas), the influence of western culture was vividly visible in India. Cross-cultural communication theory explains the need of adopting western culture concepts with an Indianized blend of values. The exposure the younger generation has been through the movies, going and living abroad and social media trickles down the effect in their behaviour and choices. The younger generation found themselves more connected with the bold and liberated idea of relationships and romance which was portrayed in the contemporary rom coms.\n\nTheme 2: Individual aspirations (after early 2000s)\n\nThis theme captures another important aspect of romantic comedies i.e., the urge of young individuals to pursue their dreams and passion instead of following the usual societal norms of pursuing a regular nine-to-five job. Several rom coms like Love Aaj Kal (2009), Ajab Prem Ki Ghazab Kahani (2009) and Yeh Jawani Hai Deewani (2013) portrayed beliefs of a progressive Indian society where every individual was ready to quit their monotonous jobs to follow their passion without any compromises. As ‘follow your passion’ became the buzz phrase of the twenty-first century (Reneau, 2021), Bollywood movie makers also started portraying characters who were independent, optimistic, and open to an alternative form of lifestyle. The researchers attribute this phenomenon with the social cognitive theory (Tyron, 2013), which provides an understanding about how people shape their behaviour and lifestyle through observational learning. It was found that the young population in India also started displaying similar attributes as they were increasingly seeking employment opportunities that aligns with their individual aspirations (World Economic Forum, 2018). Moreover, the emergence of the entrepreneurial culture in India, gave rise to more than hundred unicorns2 which provided a platform for young individuals to achieve their dreams (Invest India, 2021). Thus, the researchers theorize that as India as a country was going through an entrepreneurial wave, the audience felt more connected in watching movie characters who were willing to take risks in order to follow their passion.\n\n\nConclusion\n\nAfter thematically analysing each of the genres separately, this study proposed ten themes. However, the most interesting outcome of the study was found when the researchers looked into all the themes in conjunction. It was found that the change in the Indian audience’s preference can be broadly classified into three overarching themes which encapsulated the type of content the audiences preferred across genres for twenty-six years (see Table 3). It should be noted that the overarching theme trends depicted in Table 3 are time specific and not genre specific. They holistically capture the overall shift of the content preferred trend from 1994 – 2019 irrespective of the type of movies.\n\nIt was between the 1990s and early 2000s when the Indian audience had immense affinity for watching family movies. However, with the change in the Indian family structure, the desire to watch family dramas also saw a significant dip. Not only in family dramas, but the same attribute was seen across all the genres and very rarely did movie makers focus their stories on joint families. Similarly, with the growth of the internet and rise in the awareness level of the audience, movie makers started focusing on realistic storylines and sensitive issues across several genres during the early 2000s. Social issues like drugs overdoses, rape and sexual assault, struggling education systems etc. were addressed by the movie makers. And simultaneously, it was also during the same period when the growth of self-expression among the Indian audience was strikingly evident, as they preferred watching movies which induced a sense of individuality among them. We argue that although the change in the genre preference was a gradual process and nothing changed overnight, the transformations were extremely clear and profound. The overall impact of the overarching themes was visible across all the genres. The drastic changes in the Indian society had a systematic impact on the culture of the audience which resulted in their change in preference of movie genres. Movies are nothing but a synthesized version of larger culture with respect to time and context they are developed in. It has the ability to carry strong messages to a wider audience.\n\nFrom a business perspective, this study would help movie makers to understand the changing preference for movie genres in India over the last two decades and assist them in producing commercially successful movies. For example, as one can clearly observe the growth in the popularity of comedy movies, movie makers can green light more comedy scripts to tap in substantial economic benefits. They can also develop a hybrid (like romcoms) to revive a declining genre like family drama. But most importantly, the results should entice them to keep a close eye on all the major events (social, political, and cultural) that take place in India, as well as globally, to understand what excites the audience in order to produce relevant content for them. Other entertainment avenues like video games, soap operas, advertisements etc. can also pick up important cues to come up with alluring content. And although this study is focused only on the Indian subcontinent, academicians throughout the world can benefit by investigating the impact of society and culture on entertainment.\n\nThis study takes the support of three theories to explain the behaviours of the audience and creators. Traditionally, genres or storylines rest on a linear sense of temporality and contemporary cultural context (Booth, 2012). The development of movie storylines by creators is influenced by the topical undercurrents of society, hereby revalidating the social cognitive theory of learning and unlearning, of certain behaviours in a particular timeframe. The process of making a choice by the audience, seeking certain kinds of gratification in the form of entertainment value or informational value is supported by Uses & Gratification Theory. Hence, from a theoretical perspective, this study reaffirms the relevance of the theories in the context of the Indian entertainment (movie) industry (Bandura, 2005; Weiyan, 2015; Gross, 1985).\n\nOne of the major limitations of the study is that it excluded 25 out of the 130 selected movies. Those movies were spread across seven additional genres. As those 25 movies were inadequate to develop an adequate trend line for the analysis, they had to be dropped from the study. This resulted in the exclusion of genres like biopics, sports dramas and suspense thrillers which have become extremely popular in the recent past. For future studies, we suggest including a larger pool of movies to generate better results. Lastly, although the context of the study was limited to movies, future researchers might also make an effort to comprehend the evolutionary changes of other entertainment avenues like gaming, music, advertisement etc.", "appendix": "Data availability\n\nZenodo: Top 5 Bollywood grossers from 1994-2019_Zenodo, https://doi.org/10.5281/zenodo.7154229 (Mohanty et al., 2022).\n\nThis project contains the following underlying data:\n\n• Top 5 Bollywood grossers from 1994-2019_Zenodo (1)\n\nData are available under the terms of the Creative Commons Attribution 1.0 Generic (CC-BY 1.0)\n\n\nReferences\n\nAjaz M:2019Masala.accessed on 22/10/2022.Reference Source\n\nAltman R: Film/Genre. London: BFIAnnie Reneau 2021, We Need To Rethink Encouraging Our Teens To “Follow Your Passion”, Grown & Flown.1999. accessed on 02.02.2022.Reference Source\n\nAnshuman M, Mudgal A, Ganguli S:Top 5 Bollywood grossers from 1994-2019_Zenodo. [Data set]. Zenodo. 2022. 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Res. 1996; 36(4): 29–41.\n\n\nFootnotes\n\n1 Anti-genre: ‘A cinema which is either free from genre or else subverts the genres of mainstream culture’ (Jancovich, 2010).\n\n2 Unicorns: a privately held startup company with a value of over $1 billion." }	[ { "id": "178632", "date": "28 Jun 2023", "name": "Parichay Patra", "expertise": [ "Reviewer Expertise Film history", "film aesthetics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article has its promises, primarily because of its interdisciplinary appeal. Here a number of management scholars are using a fairly large dataset and statistical methods to offer their comments on an apparently specific trend of cinema-going and film business in India. While their interest in this mode of industrial research with cinema as their site of inquiry seems rewarding, it should also be noted that the understanding and interpretation of genre requires more careful consideration of existing literature.\n\nAllow me to elaborate on this. How to identify a genre? In the context of the global north, there are semantic and syntactic methods for that (please refer to Rick Altman’s iconic essay). In the global south, it’s not that easy. Indian cinema scholars have often argued that the identification of genres in the context of South Asia/India is a challenge as, unlike Hollywood, Bombay popular cinema does not have clearly demarcating genres. The presence of the ‘social’ as an all-encompassing super-genre in Bombay cinema has been theorized by M. Madhava Prasad, who also went on to suggest that genre-mixing works as ‘creative fabrication’ across several Indian cine-industries.\n\nThe article does not refer to such context-specific theorizations and methods. Instead, despite its methodological promises, it often resorts to generalizations without considering the temporal and ideological differences between films. For instance, it groups Hamara Dil Aapke Paas Hai (2000) and Toilet: Ek Prem Katha (2017) under the same section, contextualizing them in a similar way, ignoring the enormous temporal gap between them.\n\nMoreover, the ideological transitions have not been taken into account. Films such as Toilet: Ek Prem Katha and Uri: The Surgical Strike (2019) belong unquestionably to the ‘new India’ of the Narendra Modi regime and its cine-politics, with the Prime Minister praising the former for its ‘message’ and the latter playing a significant role in the pre-2019 election Indian public sphere. Uri’s success led to the making of a series of propaganda films favored actively by the present regime, many of them becoming major hits through their controversies.\n\nThe article needs major revision, references to existing literature should be made, and several generalizations might be avoided.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10100", "date": "04 Sep 2023", "name": "Anshuman Mohanty", "role": "Author Response", "response": "Dear Dr. Patra, Thank you for giving us the opportunity to revise and resubmit our manuscript. By keeping your insightful suggestions in mind, we have resubmitted the revised version of the paper titled, ‘Mapping movie genre evolution (1994–2019) using the role of cultural and temporal shifts: a thematic analysis’ for publication. We have aspired to address most of the suggestions given by you in our manuscript. Below is the summary of the changes (along with the line numbers) that we made in the manuscript. All page numbers refer to the revised manuscript file with tracked changes. Comment 1: The first suggestion was to explore context specific theorizations on movie genres laid down by well-known researchers like Rick Altman and M. Madhava Prasad to comprehend the interpretation of genre in the global north and global south. It was also suggested to look into the presence of the ‘all-encompassing social genre’ and ‘genre mixing’ in India. Response to comment number 1: As suggested, we have included Rick Altman’s iconic essay on semantic and syntactic genre in the literature review section of our manuscript (line number 95-114). Then we have focused on M. Madhava Prasad’s (2011) paper, where he has mentioned about the presence of the all-encompassing social genre in India post the independence era (line number 115-132). However, we have also cross referred to Ravi Vasudevan’s book ‘The melodramatic public’ to emphasize the rise of the ‘self-conscious genre cinema’ in India (line number 133-177). Referring to Vasudevan’s work, Prasad (2011) has also acknowledged the emergence of the self-conscious genre in India from the 1990s. In his book, Vasudevan has explained how movie making was revolutionised after the economic liberalisation in the 1990s which gave rise to a contemporary film making style in India. He also attributes this change to the corporatisation of the film industry which supported several small players (film institute graduates and theatre professionals) to produce movies which was inspired by Hollywood genres in terms of narrative integration. Thus, although we acknowledge the presence of the ‘social’ genre as explained by Prasad, we cannot overlook the rise of the self-conscious genres in India during 1990s. And as we have analysed movies released after 1994, a phase which witnessed the growth of the self-conscious genres, we have interpreted movies based on specific genres rather than identifying them as ‘socials’ which was regarded as a ‘superficial’ label as it did not do justice to most of the movies to which it was applied to (Prasad 2011 and Vasudevan, 2011). Secondly, although we acknowledge the phenomenon of ‘genre mixing’ as explained by Prasad, we have resorted to categorise movie genres based on the core-content (theme) of their storyline (line number 177-199). In the revised manuscript we have stated that although majority of the popular cinemas in India are typically hybrids (inspired from several genres), the story line revolves around a specific theme/topic. Thus, we have interpreted movie genres based on the core-content portrayed in their narratives. Comment 2: The second suggestion was to avoid generalizations while citing examples of movies that does not consider the temporal differences between films. Response to comment 2: As rightly suggested by you, we have tried to avoid several generalizations while citing movie examples in the manuscript. For example, we have removed the grouping of certain films like Humara Dil Apke Paas Hai (line number 452), Kabhi Khusi Kabhi Gham (line number 477), Kya Kehna (line number 485) and Wanted and Dabanng (line number 538). We have attempted to cite examples of movies which have certain commonalities between them without tampering the temporal gap. Comment 3: The third suggestion was to consider the ideological transitions in cine politics that has impacted the way in which movies are being made in the present time. We were told to explore how the present government’s ideology of ‘new India’ has been embedded in the narratives of several movies. Response to comment 3: We have included specific examples of movies under the explanation of ‘Romantic Drama’ (line number 445-450) and ‘Action’ (line number 547-558) genre in our analysis that highlights the overt appreciation of the present government’s ideology of the ‘new India’ which has been focusing a lot on the importance of health and hygiene, make in India products etc. We have also touched upon the present government’s affinity for pro-nationalistic themes in their narratives. We have aspired to convey that movies supporting the present regime’s ideology gets active political support from the government which ultimately boosts their popularity. However, I would like to point out that although several movies like The Kashmir Files (2022), The Kerala Story (2023) etc. gained immense success owing to their pro-nationalistic themes and controversial storylines, they have not been taken into consideration as they were released after 2019 which is beyond the scope of our analysis. We would like to thank you for your time and effort in reviewing our manuscript. The feedback has been invaluable in improving the content and presentation of the paper. We look forward to hearing from you. Thanks. Regards." } ] }, { "id": "178633", "date": "04 Jul 2023", "name": "Rebecca Bell-Metereau", "expertise": [ "Reviewer Expertise Film and media studies", "genre research", "memory and film", "gender and film", "depictions of autism in film", "international film", "philosophy and feminism", "auteur theory", "thematic studies such as conspiracy films", "environmental films", "body studies", "disability in film", "acting", "modernity in film" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAssuming that profitability is the most important factor ignores the importance of artistic or intellectual value, which does not always correlate with a film's popularity or box office success. The author should consider the critique of Judith Hess (see “Genre films and the Status Quo,” Judith Hess, Jump Cut, no. 1, 1974, pp.1, 16, 18 copyright, Jump Cut: A Review of Contemporary Media, 1974, 2004)1.\nCorrect possessive in line 1, Par. 4. change \"its\" and \"it's\" to \"their\"\nCorrect in line 4, Pr. 4. \"till date\" change to \"to date\"\nThis essay does not seem to address the influence of capitalism on film, since it is a money-making and expensive medium, and it is in the interest of filmmakers to use formulaic plots and genre conventions because they are easier to produce quickly and efficiently.\n\nIt is also important to include consideration of the climax and resolution of films since the impression viewers have at the end of the film is an important factor in a film's success and profitability.\nThe author should consider why action films are more successful, particularly for international films, because they do not rely on language for their interest and success.\n\nThe analysis of themes needs more sophisticated analysis. How do films encourage viewers to accept the social status quo? What about films that encourage rebellion or individualism?\n\nThe discussion of romantic films in conjunction with the practice of arranged marriages is fertile ground, since it dovetails with the economic aspect of the arranged marriage to maintain the practice of marrying within one's social class or improving one's social class by marrying a partner with higher status.\nIn general, this is a good analysis in terms of descriptive factors. I would like to see more speculation and perhaps inclusion of discussion of those outlier films that gained international success and recognitions, to see how and why these films broke the mold and rose above the category of genre to represent original art.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10101", "date": "04 Sep 2023", "name": "Anshuman Mohanty", "role": "Author Response", "response": "Dear Dr. Metereau, Thank you for giving us the opportunity to revise and resubmit our manuscript titled, ‘Mapping movie genre evolution (1994–2019) using the role of cultural and temporal shifts: a thematic analysis’ for publication. By keeping your insightful suggestions in mind, we have resubmitted the revised version of the paper. We have aspired to address most of the suggestions given by you in our manuscript. Below is the summary of the changes (along with the line numbers) that we made in the manuscript. All page numbers refer to the revised manuscript file with tracked changes. Comment 1: The first suggestion was to explore the critique of ‘Judith Hess Wright, Genre films and the Status Quo, Jump Cut (1974)’ to consider the fact that assuming profitability is the most important factor, it ignores the importance of artistic or intellectual value, which does not always correlate with a film's popularity or box office success. Response to comment 1: As suggested, we have gone through and included the aforementioned critique by Judith Hess Wright in our manuscript (line number 690-699). We have articulated that despite lacking artistic and intellectual value, genre films have always managed to achieve popularity and commercial success as they tend to provide easy comfort and solace to the audience by temporarily relieving them from real world problems. Kindly note that we have cited Judith Hess Wright’s article that was published in Film Genre reader IV in 2012 (Edited by Barry Keith Grant). Comment 2: The second suggestion was to address grammatical errors in the manuscript. a. Correct possessive in line 1, Par. 4. change \"its\" and \"it's\" to \"their\". b. Correct in line 4, Pr. 4. \"till date\" change to \"to date\". Response to comment 2: The specific changes have been addressed in line number 47, 48 and 50. Comment 3: It was suggested to address the impact of capitalism on the filmmaking process which ultimately influences filmmakers to use formulaic plots and genre conventions as they are easier to produce quickly and efficiently. Response to comment 3: To address this comment, we have included a specific segment in our manuscript (line number 719-739) that highlights the impact of capitalism on the filmmaking process. We have pondered upon the fact that as the financial risk associated in the movie making business is growing exponentially, filmmakers are inclined to play safe by adopting formulaic plots that have a higher probability of success. We have also highlighted the adoption of the ‘ritualistic approach’ (Altman, 1984) by filmmakers to cater the needs of the audience. Comment 4: It was suggested to consider the climax and resolution of films since the impression viewers have at the end of the film is an important factor in a film's success and profitability. Response to comment 4: We have referred to Thomas Sobchack’s essay on ‘Genre Film: A Classical Experience, Literature/Film Quarterly (1975)’ to address this comment (line number 685-690). We have highlighted that popular genre films have a tendency to resolve all the conflicts and ambiguities in their storyline by providing a congenial resolution at the end, which provides the audience with a feeling of catharsis that helps in boosting the popularity of the movie – hence, the commercial success. Similarly, we have also highlighted about the proclivity of Bollywood filmmakers to provide an ending that instils a sense of satisfaction and harmony among the audience (line number 699-711). Kindly note that we have cited Thomas Sobchack’s article that was published in Film Genre reader IV in 2012 (Edited by Barry Keith Grant). Comment 5: It was suggested to highlight why international Action films have become more successful despite not relying on language for success. Response to comment 5: We have used the concept of ‘cultural discount’ in order to explain the global acceptance of international action films (line number 510-520). This concept states that a cultural product (movie) rooted in one culture will have a diminished appeal elsewhere as viewers might find it difficult to identify with the values and beliefs of the foreign culture. However, as action films rely more on graphic violence, they have a universalistic appeal and are resistant to cultural discount when compared to other genres like comedy or drama which are more culturally specific. Comment 6: The sixth comment was divided into two parts. a. It was suggested to highlight how movies encourage viewers to accept social status quo. b. And it was also suggested to analyze movies those have encouraged a sense of individualism and rebellion among the audience. Response to comment 6a: In order to address this comment, we have referred to Judith Hess Wright’s essay on ‘Genre films and the Status Quo’. In our write-up we have highlighted that popular genre films helps to maintain social status quo as these films helps the audience to temporarily transport to an imaginative narrative where all problems have simplistic solutions (line number 693-696). The explanation is in line with the prevalence of a congenial climax/resolution that satisfies the audience at the end of the movie. Response to comment 6b: We have considered Bellah et al.’s (1996) proposition of ‘expressive individualism’ to highlight movies that encouraged an individualistic and rebellious way of life (line number 638-650). We have explained how several characters in romantic comedies portrayed an eccentric lifestyle that aligned with the contemporary individualistic ideology of the west. Comment 7: It was suggested to include the discussion of outlier movies that gained international success and recognitions, to see how and why these films broke the mold and rose above the category of genre to represent original art. Response to comment 7: As suggested, we have attempted to discuss about original art movies (parallel cinema) in our manuscript that does not follow the narrative conventions of a popular genre film (line number 768-796). We have cited examples of several internationally acclaimed Bollywood art films that touched upon sensitive topics with high level of realism in their storylines. We have speculated that despite receiving international recognition, art movies are not commercially successful in the domestic market as they do not provide a congenial resolution that helps in maintaining social status quo among the audience. However, we would like to point out that our analysis has focused only on the popular genre movies in India and thus, we have suggested that an in-depth analysis of art cinemas in future can provide detailed insights on the socio-political state of the country. We would like to thank you for your time and effort in reviewing our manuscript. The feedback has been invaluable in improving the content and presentation of the paper. We look forward to hearing from you. Thanks. Regards." } ] } ]	1	https://f1000research.com/articles/12-662
https://f1000research.com/articles/12-1103/v1	04 Sep 23	{ "type": "Research Article", "title": "Controlled seeding of contact cracks in test pieces for the evaluation and validation of non-destructive testing systems", "authors": [ "Daniel Preston", "Daniel Rodriguez Sanmartin", "James Watts", "Julian Wright", "Daniel Preston", "Daniel Rodriguez Sanmartin", "James Watts" ], "abstract": "Background: A major inhibitor in the development and certification of non-destructive test equipment is the lack of access to statistically appropriate numbers of test pieces which contain relevant flaws. Methods of introducing these flaws in a controllable and repeatable manner are always in demand. Methods: This paper discusses the development and evaluation of a method for seeding contact cracks in ASTM F519-18 Type 1a.1 notched tensile coupons. Contact cracks of controlled dimensions are successfully introduced into a set of these specimens by closely monitoring the resonance frequency and peak splitting due to anisotropy. Results: Results are confirmed using Scanning Electron Microscopy, carried out on a selection of the coupons. The least exposed coupon was shown to have a crack propagating inwards from the notch with a length of approximately 50 microns. More heavily exposed samples had longer cracks spanning nearly the entire notch with a crack width of 1.3 microns. Conclusions: The correlation between crack growth and the frequency monitoring proves that this technique could be further developed for the controlled creation of contact cracks for NDT validation or other applications.", "keywords": [ "Resonance", "Flaw seeding", "Cracks", "Contact cracks" ], "content": "Introduction\n\nThe field of non-destructive testing (NDT) is critical to many industries, with several new techniques emerging. These offer new and commercially relevant solutions for flaw detection, but require validation on controlled specimens. For these emerging techniques and other established methods, there is a need for options which quickly and reproducibly create multiple test pieces with embedded flaws.\n\nEmbedding flaws into test pieces can be achieved using methods such as thermal cycling, mechanical fatigue, or chemical processes. Localised thermal fatigue is one method which uses repeated heating and cooling cycles on a small area to generate thermal fatigue cracks,1 which may be particularly representative of flaws in high temperature environments such as power stations.2 More common are mechanical techniques such as notching, where crack-like flaws are machined, or fatigue cracking, where a cyclic load initiates crack mechanisms at a fraction of the ultimate tensile strength. These two methods may achieve similar results for some NDT techniques; however, notches are often not representative of real-life flaws and conventional fatigue processes require a large number of cycles to complete.3 Other methods use chemical processes such as hydrogen induced cracking, where hydrogen diffuses into the metallic structure causing weakness and internal pressure, resulting in internal cracking.4,5 All of these processes generally give rise to flaws of uncontrolled dimensions.\n\nThe recent additive manufacturing (AM) standard ISO/ASTM/TR 52906:20226 notes that “there is currently no proven method for controlled and replicable seeding of intimate disbonds (sometimes known as “kissing bonds”) – where two surfaces are in intimate or close contact, but with compromised adhesion”. This holds true for conventional manufacturing methods in addition to AM. These intimate disbonds are also known as “contact cracks”, or “stealth flaws”, because they are difficult to detect using established NDT techniques. Figure 1 shows such features formed by hydrogen embrittlement.\n\nThis paper describes a system which rapidly introduces contact cracks of controlled dimensions into metallic coupons using a combination of static and dynamic loading. After the flaws were created their presence was confirmed destructively, using Scanning Electron Microscopy (SEM) on a representative selection.\n\n\nMethods\n\nASTM F519-18 Type1a.1 tensile coupons7 were chosen as the host test pieces. The coupons were procured from Green Specialty (Green Specialty Service Inc, Joshua, Texas, US) and provide a standardised geometry with an incorporated stress-raising notch in the centre (Figure 2).\n\nThe key to successful implementation is to approach the local ultimate tensile strength of the material, in order to initiate the fatigue cracking process. By exploiting resonance in the coupon, strain profiles are more readily controlled and amplified: targeting different resonance modes will place the stress maxima in different locations. However, for the chosen coupon the first natural frequency occurs at approximately 6.6 kHz, where displacements (and hence strain energies) will be low. In order to accentuate the excitation energies, it is necessary to mass-load the coupon to reduce the natural frequencies significantly. Under these conditions the first flexural mode offers a low complexity, low frequency vibration. This mode maximises stress in the notch by imposing high strain due to the high displacement associated with low frequency modes (Figure 3).\n\nThe threaded ends of the coupons allow for convenient attachment of additional masses to control the resonance behaviour of the assembly. The F519 testpiece is mass-loaded at each end with a 2.35 kg cylindrical bob (Figure 4), designed such that the first flexural eigenfrequency of the specimen is significantly reduced, to 105 Hz, while also ensuring that the frequency of vibration is within the operating bandwidth of the excitation system. The change in resonance frequency, displacement and velocity that accompanies the addition of the bobs is illustrated by the markers in Figure 3. By tailoring the bob properties, it can be ensured that crack formation will occur over an appropriate time: if the period is too short, crack formation will be uncontrolled and if the period is too long, the experiment will consume too much resource.\n\nA laser vibrometer is used to measure system resonance.\n\nEach bob is female-threaded such that it can be readily attached to the testpiece. Initial trials were made with brass bobs; however, the threads deteriorated rapidly under dynamic loading. For this reason, the next iteration was fabricated using EN1A steel, which is easily machined and of sufficient density to permit a compact design.\n\nThe excitation system is a Hottinger Brüel & Kjær LDS V406 Permanent magnet shaker (Hottinger Bruel & Kjaer UK Ltd, Royston, UK), attached to a threaded steel stinger. The stinger is attached at the other end, via a thread and a locking nut, to the upper bob (Figure 4). A Polytec PDV 100 laser vibrometer (Polytec Ltd, Coventry, UK) was used to measure the velocity of the resonating system. Due to the stiff coupling, the resonance mode involves the vibration of the two bobs and the coupon as one combined part. Laser measurement is taken from the upper bob in a position which is known to have a high velocity (an antinode). A Fast Fourier Transform was used to determine the precise resonance frequency. The entire setup is represented by the block diagram in Figure 5.\n\nIt is very important to ensure that there is no relative motion between the bobs and the coupon: if this occurs, there can be rapid and uncontrolled fast fracture. For this reason, the contact was reinforced using a locking nut, adjusted to a torque of 10Nm (Figure 6). The entire assembly was then suspended under gravity using four aramid wires (Figure 4), chosen for their resistance to wear and fracture in comparison to conventional fibres/polymers.\n\nIn order to understand the stress distribution in the assembly, and the frequencies of specific modes, Finite Element Analysis (FEA) was carried out on a defeatured CAD model (Figure 7) using the CalculiX finite element solver version 1.0.0, with ParaView version 5.10.0 for visualisation of the modes. The first flexural mode was predicted to be at 99.7 Hz, the exaggerated displacement profile of which is illustrated in Figure 8.\n\nIt can be seen from the Y-plane sectioned view (Figure 8a) and the stress line plot across the thickness (Figure 8b) that the stress is concentrated at the notch. The model suggests that the crack initiation and propagation will occur primarily in the stress raising notch, parallel to the excitation source (parallel to plane Z in Figure 2).\n\nAlternative resonance modes could be selected to induce stress differently in the cylindrical section; Figure 9 shows, for comparison, a Z-plane sectioned view of the flexural mode stress distribution and the first torsional mode, which has stress more symmetrically distributed across the Z-plane. The flexural mode is more suitable in this case, due to experimental simplicity and the desire for crack initiation at the circumference of the notch and in a controlled direction.\n\nColourmap shows relative values of stress distribution.\n\nTwenty coupons were tested to destruction, in order to determine the fracture point threshold under experimental conditions and the optimum setup parameters required for stable crack growth.\n\nA broadband sinusoidal sweep was first conducted, to establish the frequency of the first flexural mode of the assembly. Figure 10 illustrates a typical output, showing a first resonance at 105 Hz. This peak corresponds adequately with the FEA model.\n\nNext, in order to concentrate the excitation energy around the selected resonance mode, a high-resolution narrowband sweep (±10 Hz) was conducted around this frequency (Figure 11).\n\nThe dynamic stresses during the sweep cause crack formation in the specimen, located at the notch. This leads to a reduction in structural stiffness and a consequent measurable reduction in resonance frequency. The new frequency was located, and a second narrowband sweep was conducted, centred upon this new frequency. This process was iterated until the specimen failed. The value of the change in resonance frequency, Δf, was recorded. Several specimens were thus tested, in order to ascertain the range of Δf values at which failure occurs, ΔF. Figure 12 illustrates the change in frequency up to failure for four coupons that were tested to destruction. It can be seen that there is some variation in ΔF values; this is probably due to micro/mesoscale material flaws that affect the crack propagation and rate of growth.8 In the early stages of the process, the reproducibility is much closer, because the crack is more stable.\n\nHaving established a ΔF threshold, it should now be possible to run a controlled set of experiments to seed cracks. These can be created with a range of severity, by setting the control software to stop the test at various values of Δf prior to reaching ΔF. Figure 13 shows three different examples of this, with Δf values of 5, 15 and 20 Hz. Each sweep corresponds to a single point on the graph, and takes approximately 30 seconds. Some variation in gradient is inevitable, given that the initial conditions of the specimens are likely to vary.\n\nA range of Δf stopping points was used for the coupons with the aim to obtain different crack sizes (Table 1).\n\nDuring crack formation, the resonance peak is likely to exhibit “splitting”.9 The testpieces are exposed to dynamic loading in one axis with stress concentrations from the flexural mode parallel to this axis. The resulting crack initiation and propagation is therefore preferentially in one direction (Figure 14), giving rise to an anisotropic stiffness profile in the Z-plane and, therefore, degenerate modes manifesting as split peaks.\n\nFigure 15 shows the flexural mode response; the left peak is parallel to the excitation, which has a reduced stiffness due to cracking, whereas the right peak is the orthogonal flexural mode. Figure 16 shows the measured difference in frequency between the split peaks in each of the coupons. It can be seen that all but the controls exhibit this effect. These measurements were taken after the exposure process, with bobs removed.\n\nAs the cracks propagate through the test piece, the left peak will move towards lower frequencies and the peak separation (i.e. the difference in frequency between the split peaks) can therefore be used as an indicator of crack propagation. The sensitivity of the peak splitting metric will depend on the Quality Factor and the position of the crack initiation points: it will not be possible to distinguish two closely-spaced peaks if the Quality Factor is not sufficiently high. The crack initiation points are unpredictable and are likely to depend on pre-existing material inhomogeneity.8 Anisotropy will be less affected by initiation points that are, for example, 45 degrees off-axis from the shaker excitation and will be more affected when they are parallel to the excitation direction, the latter creating the greatest difference between the two split peaks. This is because a crack initiated at 45 degrees will affect the stiffness of both of the degenerate modes equally.\n\nSpecimens RD20, RD25 and RD30 represent different crack propagation stages (5 Hz, 15 Hz, 20 Hz frequency shift respectively), and so were selected for destructive imaging. They were sectioned close to the Y plane and then carefully polished to remove the remaining material in order to expose the plane fully. This provided images in the areas of high stress concentrations. The imaging was then conducted using a JSM-IT800 Schottky Field Emission Scanning Electron Microscope.\n\n\nResults\n\nSEM images were gathered from a selection of the exposed coupons, chosen as representing a wide range of exposure conditions. In RD20, the coupon which exhibited the lowest frequency shift of 5 Hz, a small crack ranging from 0.5 microns to 5 microns in width was discovered at the edge of the notched section (Figure 17). The length of the crack is approximately 50 microns, suggesting that it is in the early stages of propagation.\n\nRD25 and RD30 are shown in Figure 18 and Figure 19 respectively. The two outer images show the extent of propagation from the right-hand edge of the notch (the ‘excitation side’) and the central image shows a magnified view of a central portion of the crack. These coupons have much more extensive cracking, which propagates over a significant proportion of the diameter. RD25 and RD30 have similar propagation lengths; however, RD30, which exhibited the highest frequency shift, has a maximum crack width at approximately 2 microns. RD25 has a smaller width at approximately 1 micron. It is believed that both of these coupons were close to failure due to the propagation length of the cracks. The coupons display increasing crack propagation with increased exposure to the technique, proving that contact cracks can be rapidly and controllably seeded in these metallic test coupons. This builds on the capability of the other techniques identified in the introduction by creating a flaw more representative of fatigue type cracking without requiring the large number of cycles. Due to constraints on the project, only three coupons were selected for the SEM validation stage. In future developments, it would be desirable to select more coupons from earlier stages of propagation so that the correlation between crack dimensions and exposure level can be more closely established.\n\n\nConclusions\n\nThis paper reports the development of a rapid, controlled method for seeding contact cracks in ASTM coupons, which could be adapted for other geometries. The technique involves an electromagnetic shaker, laser vibrometer and two steel bobs attached to ASTM F519-18 Type 1a.1 tensile coupons. This has been trialled on a selection of twelve coupons with an additional three retained as controls.\n\nWhen a coupon is exposed to a combination of a static tensile load and a dynamic cyclic load, very small contact cracks of varying severity can be created at stress riser locations. The dynamic loading exploits the first flexural resonance of a system consisting of the coupon and two mass-loading bobs. This is important, as it will maximise the excitation energy at the desired flaw locations. The crack size can be controlled by precisely measuring the resonance frequency of the system and stopping the exposure process upon reaching predetermined thresholds.\n\nThe crack-seeding process was validated using scanning electron microscopy. The SEM images clearly identified the cracks that were responsible for the measured changes in resonance frequency. They indicate that the cracks are much more advanced in coupons RD25 and RD30 when compared to RD20, suggesting that the rate of change of resonance frequency closely correlates with rate of crack growth. The extent to which the cracks have propagated through the RD25, RD30 coupons suggests that they are likely to be very close to fracture, whereas the crack in RD20 had only just initiated and has a much lower propagation length of approximately 50 microns.", "appendix": "Data availability\n\nFigshare. Controlled Seeding of Contact Cracks in Testpieces for the Evaluation and Validation of Non-Destructive Testing Systems. https://doi.org/10.6084/m9.figshare.23391566.v1\n\nThis project contains the following underlying data:\n\n• Data for F1000.xls (Co-ordinate data for all graphs)\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 gratefully acknowledge the help of Francesca Willcocks and Thomas O’Hanlon from the Plymouth Electron Microscopy Centre, University of Plymouth for making the SEM images of the sectioned coupons, and Peter Woolliams and Maria Lodeiro at the National Physical Laboratory for providing Figure 1.\n\n\nReferences\n\nKemppainen M, Virkkunen I, Pitkänen J, et al.: Advanced flaw production method for in-service inspection qualification mock-ups. Nucl. Eng. Des. 2003; 224(1): 105–117. Publisher Full Text\n\nElfvin K, Hanninen H, Kemppainen M, et al.: inventors, Method for Producing Defects and Tensile Residual Stresses. Finland patent US 6,723,185 B1.2004.\n\nNenadic NG, Wodenscheck JA, Thurston MG: Seeding Cracks Using a Fatigue Tester for Accelerated Gear Tooth Breaking. Rotating Machinery, Structural Health Monitoring, Shock and Vibration. Conf. Proc. Soc. Exp. Mech. 2011; 5: 349–57.\n\nChakraborty G, Rejeesh R, Albert SK: Study on hydrogen assisted cracking susceptibility of HSLA steel by implant test. Def. Technol. 2016; 12: 490–495. Publisher Full Text\n\nHaneefa TK, Chakrabortya G, Rejeeshb R, et al.: Characterisation of hydrogen assisted cracking in modified 9Cr-1Mo steel welds using acoustic emission non destructive technique. Nondestructive Testing and Evaluation. 2021; 36(6): 692–708. Publisher Full Text\n\nISO/ASTM/TR 52906:2022 Additive manufacturing — Non-destructive testing — Intentionally seeding flaws in metallic parts. Introduction.\n\nASTM F: F519-18: Standard Test Method for Mechanical Hydrogen Embrittlement Evaluation of Plating/Coating Processes and Service Environments. American Society for Testing and Materials; 2018.\n\nGross D, Seelig T: Micro and macro phenomena of fracture.Ling FF, editor. Fracture Mechanics With an Introduction to Micromechanics. New York: Springer; 2006; pp. 49–57.\n\nMigliori A, Sarrao JL: Resonant Ultrasound Spectroscopy: Applications to Physics, Material Measurements and Nondestructive Evaluation. Wiley VCH; 1997." }	[ { "id": "228759", "date": "31 Jan 2024", "name": "Sena Tayfur", "expertise": [], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study focuses on the evaluation of a method for seeding contact cracks in ASTM F519-18 Type 1a.1 notched tensile coupons. The subject of the study is attractive, proposing a development and evaluation to the existing standard. The method has been evaluated through the experimental and finite element analysis. The reviewer recommends providing more details as the existing literature and explanations of the possible practical implications of the study to better interest the reader. This will make the paper more compatible with the applications. Additionally, please provide more technical details about the procedure of the evaluation method that the authors have made. I believe that the results are sufficient but they should be discussed more. Finally, the conclusion should not merely summarize the findings. It should be revised considering the effects of this evaluation on recommendations for the standard and its application and the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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": "241460", "date": "05 Feb 2024", "name": "Alaa Abdulhady Jaber", "expertise": [ "Reviewer Expertise Fault diagnosis", "Condition monitoring", "Vibration analysis", "Machine learning" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper discusses a method for introducing small, controlled cracks called \"contact cracks\" into metal test samples. The method uses vibration to initiate and grow the cracks in a notch in the sample. The presence and size of the cracks are confirmed using scanning electron microscopy images. The paper’s objective has been reached systematically; however, there are areas where the authors could improve before being accepted, such as:\n1. The introduction could be expanded with more comprehensive coverage of relevant prior work on flaw seeding techniques. Only a few methods are mentioned.\n\n2. More information could be provided on the number of test samples and the rationale for selecting certain samples for SEM imaging.\n3. Details are lacking on quantitative uncertainty estimates or statistical analysis of the results.\n4. The criteria for selecting the exposure levels (frequency shift values) for controlled seeding could be clarified.\n5. More information could help interpret the variability in frequency shifts between different samples shown in Figure 12.\n6. The resolution and settings for the SEM imaging should be reported.\n7. There is limited discussion of the relationship between crack dimensions and resonance frequency shifts.\n8. Effects of sample orientation and position on the repeatability of flaw seeding are not evaluated.\n\n9. Discussion of the peak splitting phenomenon is unclear and requires more explanation or context.\n10. The conclusions emphasize applications in NDT evaluation, but practical implementation details for this are not provided.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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/12-1103
https://f1000research.com/articles/11-1358/v1	21 Nov 22	{ "type": "Genome Note", "title": "Characterization of the Complete Chloroplast Genome of Gaultheria nummularioides D.Don 1825 (Ericaceae)", "authors": [ "Xiao-Juan Cheng", "Yan-Ling Xu", "Catherine M. Bush", "Yan-Jun Lin", "Xin-Yu Du", "Lu Lu", "Xiao-Juan Cheng", "Yan-Ling Xu", "Catherine M. Bush", "Yan-Jun Lin", "Xin-Yu Du" ], "abstract": "Gaultheria nummularioides D.Don 1825 (Ericaceae) is a traditional Chinese medicinal plant used to treat rheumatoid arthritis. The complete chloroplast genome of G. nummularioides has been sequenced and assembled. The genome is 176,207 bp in total with one large single copy (LSC: 107,726 bp), one small single copy (SSC: 3,389 bp), and two inverted repeat regions (IRa and IRb; each 32,546 bp). The chloroplast genome encoded a total of 110 unique genes; the GC content of these genes is 36.6%. The results based on phylogenetic analysis confirmed that G. nummularioides diverged later than G. praticola, and the sister-group relationship between G. nummularioides and the clade comprising G. fragrantissima Wall. 1820 and G. hookeri C.B.Clarke 1882 was strongly supported, revealing the phylogenetic position of G. nummularioides. This work provides additional information for studying the genetic diversity of G. nummularioides and its closely related taxa, as well as further exploration of chloroplast genomes in the Ericaceae family.", "keywords": [ "Ericaceae", "Gaultheria nummularioides", "plastid genome", "phylogeny" ], "content": "Introduction\n\nAs a traditional medicinal plant, Gaultheria nummularioides D. Don 1825 is often used to treat rheumatoid arthritis (Luo et al. 2018). This species is a small shrub predominantly distributed in alpine meadows from 1300 to 4600 m in China (mainly in the Himalaya-Hengduan Mountains region (HHM) in Yunnan, Sichuan, and Tibet), as well as in other regions in Southeast Asia (Fritsch et al. 2008). It is morphologically distinct from most other species from the HHM region based on characteristics such as growth habit and leaf and corolla indumentum (Middleton 1991). Middleton (1991) therefore placed G. nummularioides into a separate section, i.e., sect. Monoanthemona Middleton from ser. Leucothoides (Airy-Shaw) Middleton of sect. Brossaea (L.) Middleton. Although G. nummularioides did fall within the Leucothoides clade within Gaultherieae, it is not a monophyletic species, as its evolution may have involved gene introgression or gene capture based on four cpDNA genic regions (matK, rpl16, trnL-trnF, and trnS-trnG) indicated one sample of G. nummularioides from Bhutan diverged earlier but other five samples from China later than those of G. praticola C.Y. Wu 1981 (Lu et al. 2010). Chloroplast DNA is mostly maternally inherited and is characterized by a relatively small genome and slow mutation rate, which make it extremely useful in inferring phylogeny (Palmer et al. 1988). Therefore, the complete chloroplast genome is of great value for understanding the phylogenetic relationships and maternal inheritance within the species and closely related taxa (Jung et al. 2014; Xu et al. 2021). However, the sequence and characteristics of G. nummularioides had not been identified. This current study presents the complete chloroplast genome of G. nummularioides and its resulting phylogenetic relationship.\n\n\nMethods\n\nThe sample was collected from Duoxiongla in Motuo County, Tibet, China (29°30′37″N, 94°51′25″E). The voucher specimen was deposited at the herbarium of the Kunming Institute of Botany (collection number: LL-07304; contact person: Lu Lu, lulukmu@163.com; https://www.cvh.ac.cn/spms/detail.php?id=ea952b43) under the voucher number 1248321. The plants were collected and studied in accordance with the regulations of the author's institution and national or international regulations; no specific permits were required.\n\nGenomic DNA was extracted from leaves dried with silica gel using the CTAB method (Doyle and Doyle 1987). The raw reads were obtained by next-generation sequencing, conducted on the Illumina Solexa platform (Illumina, New England Biolabs). The clean reads were de novo assembled (a assemble method for constructing genomes without a reference sequence) using GetOrganelle v1.7.5.0 (Jin et al. 2020). Bandage v0.8.1 (Wick et al. 2015) was used for visualization of the assembly results. Annotation of the genome was conducted and then manually modified by Geneious v8.0.2 (Biomatters Ltd., Auckland, New Zealand). OrganellarGenomeDRAW v1.3.1 (Greiner et al. 2019) was used to draw the chloroplast genome map. The complete chloroplast genome of G. nummularioides and 11 complete chloroplast genomes of related species from the genus Gaultheria, in addition to those of four samples as outgroup from the Vaccinieae tribe of Ericaceae were aligned using HomBlocks v1.0 (Bi et al. 2018). A maximum likelihood phylogenetic tree was reconstructed by RAxML v8.2.X (Stamatakis 2014) with GTRGAMMA substitution model and 1000 rapid bootstrap replicates.\n\n\nResults\n\nThe complete chloroplast genome of G. nummularioides (GenBank accession no. OL944386) is a typical quadripartite structure with 176,207 bp in total length, and is composed of a large single-copy (LSC: 107,726 bp) region, a small single-copy (SSC: 3,389 bp) region, and a pair of inverted repeats (IRs: 32,546 bp). The GC content in the chloroplast genome is 36.6%. This chloroplast genome encoded a total of 110 unique genes, of which 25 were duplicated once in the IR regions. Three genes were characterized by their multiple duplicates: rpl23 and rps14 have three duplicates and trnfM has four duplicates in both LSC and IR regions. Out of the 110 genes, there were 76 protein-coding, 30 tRNA, and 4 rRNA genes. The results based on maximum likelihood analysis confirmed that G. nummularioides diverged later than G. praticola, the sister-group relationship between G. nummularioides and the clade comprising G. fragrantissima Wall. 1820 and G. hookeri C.B.Clarke 1882 was strongly supported (Figure 1). The four taxa comprise the Leucothoides clade.\n\nGenBank accession numbers are listed beside the Latin name. The bootstrap support values based on 1000 replicates are shown next to the nodes. Gaultheria nummularioides is marked in bold and with an asterisk.", "appendix": "Data availability\n\nGenBank: Gaultheria nummularioides chloroplast, complete genome, Accession number OL944386: https://identifiers.org/ncbi/insdc:OL944386.\n\nBioProject: Gaultheria nummularioides Raw sequence reads, Accession number PRJNA744357: https://identifiers.org/NCBI/bioproject:PRJNA744357.\n\nSRA: The complete chloroplast genome: Gaultheria nummularioides, Accession number SRX11377412: https://www.ncbi.nlm.nih.gov/sra/?term=SRX11377412.\n\nBio-Sample: Plant sample from Gaultheria nummularioides, Accession number SAMN20088414: https://identifiers.org/biosample:SAMN20088414.\n\n\nReferences\n\nBi GQ, Mao YX, Xing QK, et al.: HomBlocks: a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics. 2018; 110(1): 18–22. PubMed Abstract \| Publisher Full Text\n\nDoyle JJ, Doyle JL: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987; 19: 11–15.\n\nFritsch PW, Zhou LH, Lu L, et al.: The Flowering Plant Genus Gaultheria (Ericaceae) in the Gaoligong Shan, along the Border Region of China and Myanmar. Proc. Natl. Acad. Sci. 2008; 59(6): 147–214.\n\nGreiner S, Lehwark P, Bock R: OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47: W59–W64. PubMed Abstract \| Publisher Full Text\n\nJin JJ, Yu WB, Yang JB, et al.: GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020; 21(1): 241. PubMed Abstract \| Publisher Full Text\n\nJung J, Kim KH, Yang K, et al.: Practical application of DNA markers for high-throughput authentication of Panax ginseng and Panax quinquefolius from commercial ginseng products. J. Ginseng Re. 2014; 38(2): 123–129. PubMed Abstract \| Publisher Full Text\n\nLu L, Fritsch PW, Cruz BC, et al.: Reticulate evolution, cryptic species, and character convergence in the core East Asian clade of Gaultheria (Ericaceae). Mol. Phylogenet. Evol. 2010; 57(1): 364–379. Publisher Full Text\n\nLuo BS, Gu RH, Kennelly EJ, et al.: Gaultheria ethnobotany and bioactivity: Blueberry relatives with anti-inflammatory, antioxidant, and anticancer constituents. Curr. Med. Chem. 2018; 25(38): 5168–5176. PubMed Abstract \| Publisher Full Text\n\nMiddleton DJ: Infrageneric classification of the genus Gaultheria L. (Ericaceae). Bot. J. Linn. Soc. 1991; 106(3): 229–258. Publisher Full Text\n\nPalmer JD, Jansen RK, Michaels HJ, et al.: Chloroplast DNA Variation and Plant Phylogeny. Ann. Mo. Bot. Gard. 1988; 75(4): 1180–1206. Publisher Full Text\n\nStamatakis A: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9): 1312–1313. PubMed Abstract \| Publisher Full Text\n\nWick RR, Schultz MB, Zobel J, et al.: Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015; 31(20): 3350–3352. Publisher Full Text\n\nXu YL, Du XY, Li YR, et al.: The complete chloroplast genome of Gaultheria fragrantissima Wall. (Ericaceae) from Yunnan, China, an aromatic medicinal plant in the wintergreens. Mitochondrial DNA B: Resour. 2021; 6(6): 1761–1762." }	[ { "id": "160447", "date": "23 Jan 2023", "name": "Xing Huang", "expertise": [ "Reviewer Expertise Genetics and molecular biology of plants" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 has assembled and characterized the chloroplast genome of Gaultheria nummularioides, which is meaningful to Ericaceae family. However, several major concerns should be addressed:\nIn methods part, how was the dried leaves processed for DNA isolation by CTAB method? Which should be described.\n\nThe Illumina Solexa platform was used according to the methods, which is different from the SRA information. The authors should thoroughly check it.\n\nHow were the clean reads generated? Raw reads were directly generated by the sequencing machine.\n\nIn methods part, ‘OrganellarGenomeDRAW v1.3.1 (Greiner et al. 2019) was used to draw the chloroplast genome map’. And where is the map presented in the manuscript?\n\nThe sequence of Gaultheria griffithiana (NC_057623.1) should be added in phylogenetic analysis.\n\nThe details of sequencing data should be described in results part.\n\nThe tRNA and rRNA couldn’t be considered as unique gene.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes", "responses": [ { "c_id": "10112", "date": "04 Sep 2023", "name": "Xiaojuan Cheng", "role": "Author Response", "response": "Question 1: In methods part, how was the dried leaves processed for DNA isolation by CTAB method? Which should be described. Response: After collecting fresh leaves in the field, they were dried using silica gel with discoloration. Subsequently, genomic DNA was extracted using the CTAB method (Doyle and Doyle, 1987). Specifically, 1000 μL of 4× CTAB solution, preheated at 65°C and containing a small amount of mercaptoethanol, was added to leaf grinding. Question 2: The Illumina Solexa platform was used according to the methods, which is different from the SRA information. The authors should thoroughly check it. Response: Upon further review, the sequencing methodology utilizes the Illumina HiSeq 2000 platform and has been rectified. Question 3: How were the clean reads generated? Raw reads were directly generated by the sequencing machine. Response: Raw data obtained from sequencing contains some low-quality data or data with connectors. In order to ensure the quality of subsequent information analysis, it is necessary to remove these low-quality data or paired reads with connectors, i.e., to filter the raw data. The specific characteristics of the data to be filtered and removed are as follows: (1) the N content in single- end sequencing reads exceeds 10% of the length of the reads; (2) the number of low-quality (Q≤5) bases in single-end sequencing reads exceeds 50% of the length of the reads. The filtered data are called clean data and are used for subsequent analyses. Question 4: In methods part, ‘OrganellarGenomeDRAW v1.3.1 (Greiner et al. 2019) was used to draw the chloroplast genome map’. And where is the map presented in the manuscript? Response: Thank you for the reminder! We add the map in the latest version. Question 5: The sequence of Gaultheria griffithiana (NC_057623.1) should be added in phylogenetic analysis. Response: This manuscript focuses on reporting the chloroplast genome structure of a single species within the genus Gaultheria. We have another manuscript for displaying the plastid phylogenomic relationships of the whole clade (ca. 60 species) within Gaultheria at species level (unpublished data). Add one more species cannot help on resolving the phylogenetic position of this species in such a large clade. Question 6: The details of sequencing data should be described in results part. Response: we reference to the similar description of the other articles and revise it accordingly. Question 7: The tRNA and rRNA couldn’t be considered as unique gene. Response: We know each of tRNA gene or rRNA gene has two copies in the IR region. The “unique gene” we used in our study means that tRNA and rRNA have not appeared in any other place but in the IR region. We described this in the way following the literature such as Henriquez et al. (2020) and (Gao et al., 2023). We revised this accordingly. (a) The genomes contain 114 unique genes, including four rRNA genes, 80 protein-coding genes, and 30 tRNA genes (Henriquez et al., 2020). (b) The chloroplast genomes of R. rubiginosa, R. hybrida, and R. acicularis were conserved and contained 115 unique genes, of which 80 were protein-coding genes, 31 were transfer RNA (tRNA) genes, and 4 were ribosomal RNA (rRNA) genes (Gao et al., 2023). Reference: Henriquez, C. L., Abdullah, Ahmed, I., Carlsen, M. M., et al. 2020. Molecular evolution of chloroplast genomes in Monsteroideae (Araceae). Planta, 251, 1–16. Gao, C., Li, T., Zhao, X., et al. 2023. Comparative analysis of the chloroplast genomes of Rosa species and RNA editing analysis. BMC Plant Biology, 23(1), 318." } ] }, { "id": "167786", "date": "29 Mar 2023", "name": "Hoang Dang Khoa Do", "expertise": [ "Reviewer Expertise Genomics", "Phylogeny" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you very much for studying on chloroplast genome of Gaultheria nummularioides which provides new information about genomic data of Gaultheria as well as the Ericaceae family. The content of the manuscript is suitable for a Genome Note of F1000Research.\nI have some comments as the following:\nPlease ask an English editing service for checking the writing of the manuscript. Some sentences are very long.\n\nPlease provide more details of the sequencing process (i.e., single-end or paired-reads, size of reads 150 bp, 250 bp or 300 bp).\n\nPlease provide details on the step of filtering raw reads to get clean reads for de novo assembly.\n\nPlease use italic font for species names in the Data availability part.\nThank you.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Partly\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": "10113", "date": "04 Sep 2023", "name": "Xiaojuan Cheng", "role": "Author Response", "response": "Question 1: Please ask an English editing service for checking the writing of the manuscript. Some sentences are very long. Response: One of our co-author, Catherine M. Bush is a native speaker of English from USA and published many papers in English. English has been polished by her. Question 2: Please provide more details of the sequencing process (i.e., single-end or paired-reads, size of reads 150 bp, 250 bp or 300 bp). Response: Sequencing was carried out on the Illumina HiSeq 2000 platform, generating 2-3 Gb of paired-end reads with a length of 150 bp for each sample. Question 3: Please provide details on the step of filtering raw reads to get clean reads for de novo assembly. Response: The raw data obtained from sequencing may contain low-quality data or data with connectors. To ensure the quality of subsequent information analysis, it is necessary to eliminate these low-quality data or paired reads with connectors, referred to as filtering the raw data. The specific characteristics of the data to be filtered and removed are as follows: (1) Single-end sequencing reads with an N content exceeding 10% of the read length. (2) Single-end sequencing reads with a number of low-quality bases (Q≤5) exceeding 50% of the read length. The resulting filtered data is referred to as clean data and is used for subsequent analyses. Question 4: Please use italic font for species names in the Data availability part. Response: We correct that in the latest version." } ] } ]	1	https://f1000research.com/articles/11-1358
https://f1000research.com/articles/12-1100/v1	01 Sep 23	{ "type": "Study Protocol", "title": "Study on awareness of health insurance among the adult population of rural areas in the Wardha district of Maharashtra: a protocol", "authors": [ "Sudha Rani Bhoi", "Nikhilesh Nagtode", "Nikhilesh Nagtode" ], "abstract": "Introduction: Globally, the foundation of health insurance is substantial. However, the Indian health insurance sector lags. Only 14.1% of the rural population is covered by health insurance. That is, 85.9% of individuals in rural India still lack any form of health expenditure coverage and are unaware and thus are uninsured. Despite all the efforts made by the health system to assist the Indian population with supporting their healthcare finances, the public is unable to use these services simply because they are unaware of them. Individuals without health insurance will experience impoverishment due to health-related problems. Increased health insurance awareness can also be an indicator of universal health coverage. The objective is to study rural community individuals' awareness, perception, and utilisation of health insurance and to determine the association between sociodemographic variables and awareness of health insurance. Methods: The study will be a community based cross-sectional and observational study design in the Wardha district of Maharashtra from September 2023. Individuals within the region who are over 18 and at home during the visit will be included in the study. Individuals under the age requirement, and any empty households during the visits will be excluded. A pre-designed and semi structured questionnaire will be used. House-to-house visits will be done and information will be obtained by interviews. SPSS 24.0 software will be used for the data analysis. Variables included are name, age, sex, type of family, occupation, and knowledge of health insurance. Conclusions: The results of this study will involve an assessment of the participant’s awareness, perception, and utilisation of health insurance, and the association between socio demographic variables and awareness of health insurance. Descriptive statistics like frequency and percentages will be calculated. Chi-square test will be used for association between variables.", "keywords": [ "Health insurance awareness", "Rural", "Health insurance coverage", "Health insurance", "awareness" ], "content": "Introduction\n\nGlobally, the foundation of health insurance is substantial. However, the Indian health insurance sector lags. Every year, a substantial number of Indians, primarily women and children, die due to a shortage of healthcare facilities, particularly in rural areas which are home to the majority of Indians. Most of these rural residents live below the poverty line and cannot afford medical expenditures. Obtaining health insurance is a difficult task for these people.1\n\nAn individual or group can pre-pay for healthcare with the help of health insurance by paying a premium. For the rural poor, health insurance provides a rapidly progressing social security strategy, whose ability to make an income is seriously threatened by chronic health issues brought on by the prevalence of diseases and lack of access to affordable healthcare.2,3 But according to the 75th round of the National Sample Survey (NSS), only 14.1% of the rural population is covered by health insurance in its report “Key Indicators of Social Consumption in India: Health” (July 2017 – June 2018).4 Therefore 85.9% of individuals in rural India still lack health expenditure coverage and thus are uninsured. These findings reflect that a more significant proportion of the rural population is unaware of health insurance and its associated benefits.5\n\nThe predominant causes of morbidity, particularly in rural regions, are infectious, communicable, and waterborne illnesses, respiratory infections, pneumonia, and genital tract infections. Cancer, blindness, mental health issues, high blood pressure, diabetes, HIV/AIDS, accidents, and injuries are among the non-communicable diseases on the rise.6 Rural communities are especially vulnerable to distressing health financing due to their distinctive socioeconomic situations, like the inability to afford healthcare expenditures at an unforeseen time.7 For the same reason, it is necessary to give low-income families financial protection. Health insurance may be a means to lower expenditure and make it more accessible to high-quality healthcare.8,9 Even if a population uses either private or public health systems, the policymakers want to provide health insurance to them to reduce their out-of-pocket expenditures and assist them in achieving the majority of universal health coverage.10\n\nIn India, the state and central governments offer numerous health insurance programs. Through the process of comprehensive coverage along with affordable premiums, these programs aim to offer health insurance to all Indians. The Mahatma Jyoti Rao Phule Jan Arogya Yojana (MJPJAY) (https://www.jeevandayee.gov.in/), Ayushman Bharat-Pradhan Mantri Jan Arogya Yojana (AB-PMJAY) (https://nha.gov.in/PM-JAY), and Central Government Health Scheme (CGHS) (https://cghs.nic.in/) are a few of the government-sponsored health insurance plans. On April 1, 2020, the MJPJAY and ABPMJAY were introduced in the state of Maharashtra.11 Health insurance is provided to beneficiaries in the insurance mode by United India Insurance Company Limited and in the assurance mode by the State Health Assurance Society. On behalf of the eligible households, the State Health Assurance Society pays an insurance premium of Rs.797/- per family annually to the insurance firm in quarterly instalments.12\n\nThe ultimate sustainable development goal (SDG) Target 3.8 is to achieve universal health coverage (UHC) including financial risk protection and affordable quality health care services and medicine for all. These efforts are strategies to promote health equity by reducing disparities among individuals across the globe. Hence rural individuals must be aware of and use the abovementioned health insurance programs.\n\nDespite all the efforts made by the health system to assist the Indian population with supporting their healthcare finances, the public is unable to use these services simply because they are unaware of them. Additionally, due to poverty and a lack of education, most rural population needs to gain first-hand knowledge about health services compared to their urban counterparts. The idea that healthy people don’t need health insurance is one of the most widespread misconceptions about acquiring it.\n\nIndia’s rural population needs to be informed that health insurance can assist them in managing their finances when using healthcare services. A robust health insurance plan will be most beneficial for reducing the burden of health care expenses in an emergency. However, this will only be achievable if the rural Indian population is aware of these advantages, enabling them to use services like health insurance to lower their out-of-pocket health expenses and solve health-associated poverty.\n\nThe aim of this study will be to assess the level of awareness about health insurance among the adult population in rural areas in Wardha district of Maharashtra.\n\nThe objectives are:\n\n1) To study rural community individuals’ awareness, perception, and utilisation of health insurance\n\n2) To determine the association between socio demographic variables and awareness of health insurance\n\n\nMethods\n\nThis research proposal has been approved by the Institutional Ethics Committee of the Datta Meghe Institute of Higher Education and Research (Deemed to be University) (Ref. No. DMIHER (DU)/IEC/2023/648). We will obtain written informed consent from all the participants before beginning the data collection procedure, which includes the study’s objective. We will give them a thorough explanation of the survey so they understand it is being done only for research purposes. Anonymity and confidentiality of participant responses and data will be maintained. We will ensure that the interviewee has privacy and feel comfortable throughout the interview.\n\nThe present study will be a community based cross-sectional observational study design. The proposed study would take place in the Wardha district of Maharashtra, in the rural field practice area under the Department of Community Medicine, at Jawaharlal Nehru Medical College (JNMC), Datta Meghe Institute of Higher Education and Research (DMIHER).\n\nThe selection of villages for this study will be based on the convenience sampling method. The inclusion criteria will be those individuals within the region who are above the age of 18 and were at home during the house-to-house visit. The Adhaar card, a government issued proof of identify document, will be used as identification of study participants. The exclusion criteria will be individuals who do not give consent to take part in the study, those individuals who did not meet the age requirement, and any empty households during the visits.\n\nThis study will examine both socio-demographic factors and the level of knowledge regarding health insurance amongst the population. These will include:\n\n1. Socio demographic variables\n\n• Name, age groups (in years), gender, type of the family, religion, occupation, education, marital status, and socioeconomic status of the participants.\n\n2. Health insurance awareness among participants\n\n• Percentage of participants aware about health insurance,\n\n• Source of information regarding health insurance,\n\n• Preferences on the type of health insurance,\n\n• Reasons to take up health insurance; and\n\n• Reasons for not enrolling in health insurance.\n\nA pre-designed and semi structured questionnaire will be used. The questionnaire has been developed by the authors and has not been piloted yet. It will be piloted before start of the study and will be in both English and the regional language i.e., Marathi/Hindi. It has two sections: section A includes questions about the participant’s socio-demographic characteristics, whereas section B includes questions about the participant’s awareness of health insurance.\n\nHouse-to-house visits will be done within the selected region and information will be obtained by interview. The interview will be held in either Marathi or Hindi and the consent of the participants will be recorded in a signed consent form. The KoboToolbox software will be used for data collection during interview.\n\nTo maintain anonymity, we will use numbers for participants on all the research records and documents. The data will be entered in Microsoft Excel 365 and analysed by SPSS 24.0 Software. Descriptive statistics such as frequency and percentages will be calculated. Association between variables will be calculated using Chi-Square Test including the sociodemographic variable and health insurance awareness. The data thus analysed will be presented in tables, graphs, and charts.\n\nA participant may be unable to recollect details about his or her usual health expenditures leading to recall bias. In order to avoid this bias, we can ask participants to look at their recent medical bills for references.\n\nDuring participant responses to various study variables, information bias may emerge. So, if any questions are unclear to participants, we will clarify them throughout the interview.\n\nConsidering ‘p’ as 0.81 from a previous study conducted by Gowda et al.,13 the sample size is calculated using following formula outlined in equation 1. This study in particular, was selected as a reference for sample size calculation because of the similar study setting, which comprises a rural field practice area of an attached medical institution.\n\nAlpha (α) = 0.05\n\nEstimated proportion (p) = 0.81\n\nEstimated error (d) = 0.05\n\nSample size = 237\n\nThe results of this study will involve an assessment of the participant’s awareness, perception, and utilisation of health insurance. These results will be calculated in frequency and percentage using descriptive statistics and the association between socio demographic variables and awareness of health insurance will be calculated using chi-square test.\n\n\nDiscussion\n\nGowda et al., did a study named ‘Awareness about health insurance in rural population of South India’ in 2014.13 The study objective was to evaluate the sociodemographic features of respondents and to assess the level of health insurance awareness among rural residents. 81% of the participants in this survey knew about health insurance, as per the results of this study. But this study also came to the conclusion that among them, utilization of health insurance was low and the respondents needed to be educated on behaviour change.\n\nIn 2013, Bansal et al., carried out another study with the title ‘A community-based study to assess the awareness of health insurance among rural Northern Indian population’.2 The setting for this study was rural Uttar Pradesh. The study’s main objective was to determine how much rural individuals in Northern India knew about health insurance. Study outcomes suggested that 55.5% of study participants had never heard of health insurance, compared to 44.5% who were generally aware of it. Conclusions from the research revealed that among the study subjects, health insurance awareness was currently not widely prevalent.\n\nA community-based study entitled ‘Awareness and perception of health insurance among rural population in Kancheepuram district, Tamil Nadu’ was conducted in 2019 by Raja T. K. et al.14 This study’s objective was to evaluate rural residents’ knowledge, use, and attitudes toward health insurance. Study results showed that, health insurance awareness was seen in 51% of participants, with television being the most primary source of information.\n\nIn 2015, Indumathi K et al., conducted a study entitled ‘Awareness of health insurance in a rural population of Bangalore, India’.8 Analysis of the study population’s awareness of health insurance as well as the study of its socioeconomic and demographic features was among the study’s primary objectives. The study’s findings indicated that while 24.3% of participants were unaware of health insurance, 75.7% of the participants had some knowledge of it. This study concluded that, it is necessary to start effective Information, Education, and Communication (IEC) programs to raise awareness of the importance of health insurance.\n\nThis cross-sectional study will be conducted only in selected villages of Wardha district of Maharashtra. Thus, the findings of the study may not be compared to results related to a geographical area with a larger population and external validity of this research would be limited.\n\n\nConclusions\n\nLack of health insurance in rural areas is one of the barriers to healthcare access. Individuals without health insurance will experience impoverishment due to health-related problems. Increased health insurance awareness can also be an indicator of universal health coverage. The awareness, perception, and utilization of health insurance among people in rural communities will be evaluated in this study. With the help of this study, we can gain an understanding of this aspect in rural areas.", "appendix": "Data availability\n\nNo data associated with this article.\n\n\nReferences\n\nSafi O: HEALTH INSURANCE FOR RURAL AND POOR PEOPLE IN INDIA.2015; 3(1): 4.\n\nBansal A, Goel S, Singh A, et al.: A community-based study to assess the awareness of health insurance among rural Northern Indian population.2015 Jan 1; 3.\n\nNinave S, Lohana V, Ninave S, et al.: Knowledge and Practices regarding the Health insurances and Out-Of-Pocket Payments (OOPs) in Patients Suffering Cardiovascular Disease (CVD) and Cerebrovascular Accident (CVA) in Tertiary Health Centers of Central India. J. Indian Acad. Forensic Med. 2022 Dec 14 [cited 2023 May 18]; 44(4): 43–45. Publisher Full Text Reference Source\n\n7a3541a5-a490-8f9e-e83b-dd097eb871c5.pdf.[cited 2022 Dec 5]. Reference Source\n\nSamal J, Dehury RK: A Critical Appraisal on the State of the Health Workforce During the COVID Pandemic in India. J. Datta Meghe Inst. Med. Sci. Univ. 2022 Aug [cited 2023 May 18]; 17(Suppl 1): 151. Publisher Full Text Reference Source\n\nMadhukumar S, Sudeepa D, Gaikwad V: Awareness and perception regarding health insurance in Bangalore rural population. Int. J. Med. Public Health. 2012 May 10 [cited 2022 Dec 4]; 2(2): 18–22. Publisher Full Text Reference Source\n\nJoshi A: A Study to Assess Health Profile, Morbidities and Health Insurance Coverage amongst Class IV Contractual Employees of DMIMS. J. Res. Med. Dent. Sci. 2022; 10(10).\n\nIndumathi K, Hajira Saba I, Gopi A, et al.: Awareness of health insurance in a rural population of Bangalore, India. Int. J. Med. Sci. Public Health. 2016 [cited 2022 Dec 4]; 5(10): 2162. Publisher Full Text Reference Source\n\nKhanam N, Meshram GD, Athavale AV, et al.: A Cross Sectional Study on Pattern of Health Care Seeking Behavior and Out-Of-Pocket Household Expenditure on Curative Medical Care in Rural Central India. Natl. J. Community Med. 2013 Mar 31 [cited 2023 May 20]; 4(01): 70–75. Reference Source\n\nGoyal: Health insurance coverage and its sociodemographic determinants among urban and rural residents of Haryana.[cited 2022 Dec 4]. Reference Source\n\nAmbekar SM, Quazi SZ, Gaidhane A, et al.: Steps towards Universal Health Coverage through Health and Wellness Center under Ayushman Bharat Programme Delivering Comprehensive Primary Health Care in Bhandara District. J. Pharm. Res. Int. 2021 Jun 30 [cited 2023 May 20];34–38. Publisher Full Text Reference Source\n\nMJPJAY: [cited 2022 Dec 28]. Reference Source\n\nGowda S, Manjunath C, Krishna D: Awareness about health insurance in rural population of South India. Int. J. Community Med. Public Health. 2017 Feb 6 [cited 2022 Dec 4]; 2(4): 648–650. Publisher Full Text Reference Source\n\nRaja TK, Buvnesh Kumar M, Muthukumar T, et al.: Awareness and perception of health insurance among rural population in Kancheepuram district, Tamil Nadu. Int. J. Community Med. Public Health. 2019 Aug 27 [cited 2022 Dec 4]; 6(9): 3808–3812. Publisher Full Text Reference Source" }	[ { "id": "222438", "date": "27 Nov 2023", "name": "Sabu Karakka Mandapam", "expertise": [ "Reviewer Expertise Health Information 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 study is similar to studies conducted elsewhere covering various populations in India across different time periods. The study's only merit is that it focuses on the rural population of a particular district in Maharashtra. An overview of the selected district in the introduction and a justification for selecting this particular district for the study could be added.\nThe overall study methodology is appropriate; however, the methodology needs more clarity on the following aspects.\n\nThe study design mentioned is a \"community-based cross-sectional observational study.\" Is the cross-sectional study itself a type of observational study design? Why were both terms included in the study design?\n\nMore clarification is needed on the selection criteria of houses in chosen villages to cover the sample size.\n\nThis particular district has eight taluks. Is the sample going to represent villages of all these eight taluks?\n\nQuestionnaire validation methodology must be clearly explained.\n\nIt is indicated that \" who are above the age of 18 and were at home during the house-to-house visit will be included in the study. If more than one member aged above 18 years was present in a house during the survey, who will be included in the survey?\n\nThis study will provide more insights into health insurance utilization among a specific rural population. It also provides an understanding of their awareness, factors affecting awareness, and perception of health insurance. The study's outcomes may be useful for policymakers to strengthen the health insurance drive across the rural populations in India, especially in the context of the progress of Ayushman Bharat's health insurance scheme across the country.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "222451", "date": "27 Nov 2023", "name": "Risky Kusuma Hartono", "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\nAbstract:\nThe introduction is robust, highlighting only 14% of the urban population covered by health insurance. However, the overall introduction needs simplification. The method used is a survey but lacks information on the ability to pay, willingness to pay, and the need factor of the community. Additionally, the method does not detail the data analysis process. The abstract lacks research conclusions.\nIntroduction:\nWhile the introduction addresses the issue broadly, it fails to describe healthcare expenses incurred by the poor and rural communities. It should include a portrayal of catastrophic conditions, not just listing disease types without percentages. The introduction does not present the impact of the problem and should express amounts in dollars. The research questions are unclear.\nMethods:\nConvenience sampling for respondents poses problems, especially regarding population representation. The choice of study variables lacks clarification on the theoretical approach. The bivariate chi-square analysis is weak in predicting public awareness. The questionnaire link is not provided.\nDiscussion:\nThe discussion, akin to a literature review, could aid in variable selection for the method. The study's strengths are not highlighted.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1100
https://f1000research.com/articles/12-1099/v1	01 Sep 23	{ "type": "Study Protocol", "title": "3D comparative evaluation and correlation of condylar morphology in bruxers and non-bruxers", "authors": [ "Aakanksha Tiwari", "Suwarna Dangore-Khasbage" ], "abstract": "Parafunctional habits like bruxism may have a deleterious effect on the temporomandibular joint. It can lead to the alteration of condylar morphology which can further lead to temporomandibular joint disorders. The early three-dimensional evaluation may help detect morphological changes in the condyle and reduce the risk of developing temporomandibular disorders. It will also help to make patients aware of the condition and encourage prompt treatment of parafunctional habits. To do a 3-Dimensional comparative evaluation and correlation of condylar morphology in bruxers and non-bruxers. 90 patients with parafunctional habits will be evaluated on cone beam computed tomography in two groups (control group, study group) of 45 each, for alteration in condylar morphology based on the suggested classification. Results will be formulated based on the classification of condylar morphology. Evaluation of condylar morphology will be done on cone beam computed Tomography based on the amount of variation in condylar morphology in bruxers as compared to non-bruxers. Thorough clinical examination and early evaluation of condylar morphology on cone beam computed tomography will help early detection of changes in the morphology of condyle and prompt treatment to reduce the risk of development of temporomandibular disorders.", "keywords": [ "Temporomandibular joint", "TMJ", "Bruxers", "CBCT", "Condyle", "Condylar morphology" ], "content": "Introduction\n\nThe Temporomandibular joint (TMJ) is a unique joint in our body that allows movement of the mandible in different direction.1 The functional balance of the TMJ is maintained by mastication pattern i.e. the ideal bilateral mastication pattern is important in maintaining the functionality of TMJ.1 Different forces that are exerted on the craniomandibular joint have an effect on the morphology of the bony components. This may lead to changes in the shape and thickness of these components.1\n\nOne of the important bony components to the TMJ is the mandibular condyle. The condyle articulates with the glenoid fossa and brings about the movement of mandible.2 The shape and morphology of condyle may be altered due to various reasons. One common reason being tooth loss.2 Tooth loss, due to any reason, causes inappropriate distribution of masticatory forces leading to structural alterations in condyle.2\n\nClinical examination alone is not satisfactory to evaluate structural changes in the condyle.1 Due to the complex anatomy of maxillofacial region, adjacent structures may be superimposed, and it becomes tough to carry out accurate radiographic examination of the TMJ. Numerous radiographic techniques are being used to evaluate the TMJ like orthopantomograms, reverse Townes, lateral oblique, transcranial, transorbital, transpharyngeal etc.2 These radiographic images are two dimensional and show superimposition of surrounding structures. Cone beam computed tomography (CBCT) has been indicated as an accurate and efficient imaging technique for determining structures in maxillofacial region by various studies performed previously.3\n\nCBCT is a three dimensional imaging technique which gives accurate details of the structure without superimposition and deformity.2 Clinical examination of the TMJ can lead to the diagnosis of TMJ disorders, but it is recommendable to use clinical and radiographic evaluation in combination to reach an accurate diagnosis.1 A number of studies have been done to evaluate the morphological changes in condyle due to loss of teeth. Eda Didem Yalcin et al.4 in 2019 conducted a study to evaluate condylar morphology in relation with age, sex and edentulism using CBCT. Another study was performed by Dr. Saraswathi Gopal et al.5 which showed that evaluation of condylar morphology helps in detection of the temporomandibular joint disorders in early stages. But on searching existing literature, there was a lack of studies which depict comparative changes in condylar morphology in bruxers and non-bruxers with the use of CBCT. Taking into account the lack of enough studies on condylar morphological changes with CBCT imaging in bruxers and non-bruxers, the purpose of this study is to correlate the morphological changes of condyle in bruxers and non-bruxers using CBCT.\n\n\nAim and objectives\n\nDimensional comparative evaluation and correlation of condylar morphology in bruxers and non-bruxers\n\n\n\n• 3D evaluation and correlation of condylar morphology in non-bruxers\n\n• 3D evaluation and correlation of condylar morphology in bruxers\n\n• Comparison and correlation of condylar morphology in Bruxers and non-bruxers using CBCT\n\nTrial design\n\n• Clinical Trial, Comparative, Parallel group study.6\n\n\nMethods\n\nStudy setting\n\nAcademic Hospital, Sharad Pawar Dental College and Hospital, Sawangi Meghe, Wardha 442001\n\nThe study will be performed in India.\n\nThe study has been approved by “INSTITUTIONAL ETHICS COMMITTEE (IEC)” of Datta Meghe Institute of Higher Education And Research (Deemed to be University), Sawangi (Meghe), Wardha. This prospective study will be conducted in Oral Medicine and Radiology Department at Sharad Pawar Dental College.\n\nPatient between age group of 40-60 years will be included in the study. Those patients with a complete set of dentition (except third molars) and give history of bruxism for a duration of more than a year, and complaining of orofacial pain, which on clinical examination will reveal severe attrition leading to reduced vertical height will be included in the study group. The control group will be formed by the patients with complete set of dentition (except third molar) with no complaint of orofacial pain, no history of bruxism, no evidence of attrition or reduced vertical height will be included in control group.\n\nThese criteria will be evaluated by the post graduate student performing the study and will be confirmed by the senior master of dental surgery (MDS) staff in the Department of Oral Medicine and Radiology.\n\nPatients who will give history of surgery, fracture, congenital anomalies of TMJ, history of trauma from occlusion, any systemic disease affecting the bones, history of consumption of medications affecting the bone, presence of pathologic lesions of jaws, and patients giving history of adverse habits like betel nut or kharra chewing and patients with developmental tooth anomalies will be excluded from the study.\n\nEligibility criteria for Center will be availability of CBCT machine, Planmeca Romexis viewer will be used for analysis of the three-dimensional reconstructed images.\n\nThe intervention will be performed by the Post Graduate student under the supervision of radiologist.\n\nThe patient reporting to the Department of Oral Medicine and Radiology, Sharad Pawar Dental College and Hospital, Sawangi Meghe, Wardha, 442001 and willing to participate in the study will be taken for the study.\n\nDetailed history and thorough clinical examination of each patient will be performed after taking informed written consent from each patient. Detailed history of the patient will be used to rule out systemic disease affecting joints, history of medications affecting the joint anatomy, history of trauma to the temporomandibular joint or surgical intervention for temporomandibular joint.\n\nExamination of the TMJ will be done to rule out any TMJ disorder. This will be performed by Post Graduate Student (the author) and will be confirmed by MDS faculty. Inspection of joint movement on opening and closing of mouth (restricted mouth opening, pain on opening jaw, deviation or deflection while opening jaw).\n\nThis will be performed by Post Graduate Student (the author). The patient will be asked to slowly open and close the mouth. The movements on the mandible will be closely inspected for any restriction in opening mouth, pain and tenderness while opening the mouth will be inferred by the patient’s facial expressions, any deviation or deflection in the path of closure will be inspected closely. Palpation of joint will be used to evaluate any clicking sound, crepitus, and tenderness while opening and closing of jaws. Palpation of the TMJ will be done by post graduate student and will be cross checked by MDS faculty. Patient will be positioned upright in the dental chair. Palpation of TMJ will be done by extra auricular or intra auricular methods. Palpation will be done by standing on 10 or 11’o clock position i.e. in front of the patient. Intra auricular palpation will be done using little finger. By placing little finger in both the ears, the posterior pole of condylar head can be palpated with pulp of little finger, during mandibular movements. Extra auricular palpation is done by placing index finger in pre-auricular region about 1.5 cm medial to tragus of ear. The lateral pole of condyle is accessible during this examination.\n\nExamination of muscles of mastication\n\nPalpation of masseter, temporalis, lateral and medial pterygoid muscles will be done for any tenderness if present. Thorough intraoral examination will be done to evaluate the patient with reduced vertical height due to bruxism. Clinical examination will be done by the post graduate student via thorough intra-oral inspection by correlating with the Tooth Wear Index. The findings will be confirmed by the Master of Dental Surgery faculty. Temporalis and masseter muscle will be palpated through entire length and breadth with clenched teeth with help of index and middle finger from 12’o clock position. Lateral pterygoid muscle will be palpated by placing index finger or little finger lateral to maxillary tuberosity and medial to coronoid process. Medial pterygoid muscle will be palpated by placing finger at a 45° angle in floor of mouth near base of relaxed tongue. The opposite hand will be used to extra orally to palpate posterior and inferior portion of insertion. The body of muscle will be palpated by rotating index finger upwards against the muscle to near its origin on tuberosity.\n\nIntervention will be performed using the 3-dimensional x-radiation technique, CBCT. Evaluation of condylar morphology will be done in coronal, sagittal and axial planes as suggested in figures below (Figures 1–3).\n\nThe figure is available under the CC-BY-4.0 license from Ref. 7.\n\nThe figure is available under the CC-BY-4.0 license from Ref. 7.\n\nThe figure is available under the CC-BY-4.0 license from Ref. 7.\n\nModification\n\nIn case of over radiation exposure, if patient is already subjected to radiation previously for multiple times as in conditions where patients have been subjected to radiographic evaluation multiple times or in condition where patients have been taking radiotherapy, there is risk of worsening the disease due to radiation exposure the patient will be excluded from the study. A patient will also be excluded if they don’t give consent for the radiation exposure\n\nAdherence\n\nIntervention will be monitored (i.e. X radiation in the form of CBCT exposure, its exposure parameters monitoring) by the post graduate student and the radiologist for adherence.\n\nThe primary outcome expected is that there will be change in condylar morphology i.e. flattening, osteophyte, sclerosis, surface erosion in patients with habit of bruxism. We also expect that the use of CBCT could be beneficial for making patients aware of the condition and need prompt intervention at that particular time so that the condition does not progress to temporo-mandibular disorders. The intervention will be done after the confirmation of habit of bruxism for duration of at not less than 1 year.\n\nThe patients after reporting to the Department of Oral Medicine and Radiology will be screened to meet the eligibility criteria to be included in the study by thorough clinical examination during first visit and patient will be allocated in study and control group in the same visit based on the findings of clinical examination. Informed written consent will be taken from the patient. After getting the consent, patient will be subjected to CBCT exposure for evaluation. Assessment will be done and variables will be observed and evaluated by the post graduate student and masters of dental surgery faculty (as seen in Table 6).\n\n\n\nAlpha (α): 0.05\n\nBeta (β): 0.2\n\nProportion in group 1: 0.758\n\nProportion in group 2: 0.458\n\nProportion of condylar morphological change i.e. proportion of surface erosion in group 1 (control group: non-bruxers) = 75.8% (% of surface erosion of mandibular condyle) and group 2 (study group: bruxers) = 48.5% (% of surface erosion of mandibular condyle).\n\n\n\n(1-β) Power of the test = 100-20 = 80%, considering 20% as Type II error = 0.84\n\nr = Ratio = 1:1\n\nTotal sample size = 49 each group.\n\nStudy reference: Ref. 1.\n\nEach and every patient reporting in the OPD in Oral Medicine and Radiology department will be examined for habit of bruxism. We will also have some collaboration with the Department of Orthodontics for patients with bruxism and they will recommend patients for us.\n\nAllocation: sequence generation\n\nComputer generated random numbers method will be used for generation of the sequence of the study participants. The list of the study participants will be fed as raw data in the computer and it will be randomly shuffled. The numbers allotted to the participants will be computer generated random numbers and participants will be selected randomly and the arranged in sequence as needed.\n\nAllocation concealment mechanism\n\nAllocation concealment mechanism will be sequentially numbered.\n\nBlinding will be done while evaluating the CBCT images of group 1 and group 2 subjects by post graduate student and two radiologists (who will be blinded).\n\nData collection plan\n\nThe patients reporting to the Department of Oral Medicine and Radiology, will be evaluated for habit of bruxism using a questionnaire.8,9\n\nAfter diagnosing the patients, written consent will be given by them and the procedure of intervention will be explained thoroughly.\n\nFollowing collection of consent the bruxers and non-bruxers will be evaluated prospectively using CBCT. This will form two separate groups as follows:\n\n- Bruxers: 49 patients (based on the questionnaire given to the patient and thorough clinical examination)\n\n- Non-Bruxers: 49 patients (control group) (based on the questionnaire given to the patient and thorough clinical examination)\n\nNo blinding will be applied while selecting the groups. Evaluation of condylar morphology will be done based on the following classifications:\n\nA) Classification of Condylar Morphology on Coronal section of TMJ on CBCT10\n\nB) Classification of Condylar Morphology on Sagittal section of TMJ on CBCT10\n\nC) Classification of condylar Morphology on Axial section of TMJ in CBCT7\n\nThe patients diagnosed with bruxism based on the questionnaire will be thoroughly examined clinically for the wearing of teeth, using a “Tooth Wear Index”. The tooth wear index distributed from score 0-4 will be used.9,11\n\nAfter diagnosing the patients, written consent will be given by them and the procedure of intervention will be explained thoroughly.\n\nRetention\n\nThe participation of the patients in the study will be increased by proper counselling regarding the condition. As the patients will not be aware of the situation because of no signs and symptoms of the disease, proper guidance and counselling will be helpful in making them aware of the consequences of the same.\n\nData management\n\nThe data of CBCT images of the bruxers and non-bruxers will be entered in a mastersheet with percentage of changes in condylar morphology in both the groups (Tables 1–4).\n\nAll statistical analysis will be completed using r software version 4.3 (RRID:SCR_001905).\n\nDescriptive statistics for the qualitative variable will be reported in count and percentage.\n\nQuantitative analysis\n\nQuantitative analysis over continuous data (defect in the tooth in mm due to loss of enamel, exposure of dentin) will be reported in mean, standard deviation, median, maximum and minimum.\n\nUnpaired t test or alternative Wilcoxon test will be used to find out significant difference in condylar morphology between group 1 (Bruxers) and group 2 (non-Bruxers).\n\nData for the Quantitative outcome variables i.e. the defect in teeth in mm due to loss of enamel, exposure of dentin, will be tested for the normality using Kolmogorov Smirnov test.\n\nNon-normal data will be transformed into normal data by using mathematical algorithms. If data persists with non-normal distribution, then alternative test (Wilkoxon) will be used for Unpaired t test.\n\nWearing of teeth will be quantitatively measured using Tooth Wear Index Table 5.12\n\nQuantitative variables: Defect in the tooth in mm due to loss of enamel, exposure of dentin.\n\nQualitative variables: Condylar morphological changes in coronal, sagittal and axial sections on CBCT.\n\nInferential statistics will be performed on finding the significant difference among bruxers and non bruxers.\n\nQualitative analysis\n\nThe outcome variables flattening, osteophyte, sclerosis, surface erosion i.e. will be categorized for frequency distribution and will be tested for significant association among bruxers and non bruxers using the Chi square test.\n\nThe outcome variables flattening, osteophyte, sclerosis and surface erosion for tooth wear index distributed from score 0-4 will be categorized for frequency distribution and will be tested for significant association among bruxers and non bruxers using Chi square test.\n\nFormal committee\n\nNo specific data monitoring committee will be used for this study. The collected data will be monitored by the post graduate student, the MDS faculty and the radiologists. As this study will be performed by post graduate student only, there is no need of the specific committee for data monitoring.\n\nInterim analysis\n\nThe data can be accessed by the post graduate student performing the study and by the MDS faculty who is monitoring the study. Final decision to terminate the trial will be with post graduate student and MDS faculty.\n\nHarms\n\nPatients will be closely monitored for any harmful effect of radiation after being exposed and if observed any, the intervention will be stopped immediately and patient will be excluded from the study.\n\nAuditing\n\nNo such procedure is applied yet and is not planned.\n\n\nEthics and dissemination\n\nThe study was applied for ethical approval on 02/02/2023 and has been approved by the Institutional Ethics Committee of Sharad Pawar Dental College and Hospital, Wardha on 06/02/2023.\n\n- Ethical approval number – DMIHER (DU)/IEC/2023/567\n\n\n\n- Post graduate student and MDS faculty can be contacted for any modification in protocol\n\n\n\n- Consent will be taken by post graduate student\n\nThe written informed consent statement that will be used is available from Zenodo.\n\nDOI - 10.5281/zenodo.7975639\n\nIMAGE URL - https://zenodo.org/badge/DOI/10.5281/zenodo.7975639.svg\n\nTARGET URL - https://doi.org/10.5281/zenodo.7975639\n\nDetails will shared only with the MDS faculty\n\nDissemination\n\nThis study protocol will be published in PubMed, Web of Science and Scopus Indexed Journal. When the study is completed it is expected that a manuscript detailing the results and all analysis will also be published in an indexed journal.\n\nStudy status\n\nThe study is not yet started. It is expected to be started by 12/06/2023 and expected to end before completion of MDS curriculum i.e. before October 2025.\n\n\nDiscussion\n\nIt is expected that there will be a significant alteration in condylar morphology in bruxers as compared to non-bruxers as observed on CBCT.\n\nKazuhiro Yamada et al. (2001)2 conducted a study to evaluate condylar morphology in subjects with self-reported parafunctional habits. This study included 94 female patients diagnosed with temporomandibular disorders based on the questionnaire and clinical examination. The results revealed condylar bony changes in 53 females out of 94 (56.4%). They concluded that subjects with bruxism and clenching showed significant condylar bony changes. Parafunctional habits revealed relationship condylar bony changes.\n\nOzlem Isnam et al. (2020)13 conducted a study to evaluate the density, mineralization, and morphology of bone in patients with sleep bruxism. The study included 120 patients (60 bruxers and 60 non-bruxers) in which cortical width at different locations was evaluated using panoramic radiography. The results showed significant changes in bone density, morphology and mineralisation in bruxers. They concluded that there were defects in endosteal margins of cortex and cortical bone thickening in mental foramen region in bruxers.\n\nBenedikt Sagl et al. (2022)14 performed a study to evaluate the effect of grinding direction of teeth, morphological parameters of teeth, on TMJ. In Silico computer model of masticatory region of a male volunteer was made. The result of this study stated that bruxism increases load on TMJ. This study proposed an innovative, forward dynamic approach to study the effect of bruxism on TMJ loading.\n\nJuan Zhang et al. (2022)15 conducted a study to evaluate TMJ morphology in definite sleep bruxers using magnetic resonance imaging (MRI) and CBCT. 38 subjects were studied (19 definite sleep bruxers, 20 asymptomatic patients). The results showed higher prevalence of disc deformity and disc displacement and condylar bony changes in sleep bruxers.\n\nAghitsna Aulia Aufa et al. (2022)16 conducted a cross sectional study to evaluate mandibular morphological changes in bruxers and non-bruxers using panoramic radiography. Samples of 30 patients were studied. The results were drawn based on the Levandoski’s basic reference lines. The conclusion stated that there was a significant relationship between mandibular morphological changes in bruxers.\n\nEarly detection of alteration in condylar morphology in bruxers as observed on CBCT will help prompt treatment and will reduce the risk of developing temporomandibular disorders. As it is a 3D imaging technique, it will best reveal slightest of change in condylar morphology which will help in making the patient aware of the condition and offering accurate treatment.", "appendix": "Data availability\n\nZenodo: Tooth wear index, https://doi.org/10.5281/zenodo.7955094 12\n\nThis project contains the following extended data:\n\n- Tooth wear index.docx\n\nZenodo: Questionnaire for bruxism, https://doi.org/10.5281/zenodo.7955064. 9\n\nThis project contains the following extended data:\n\n- Questionnaire for bruxism.docx\n\nZenodo: 3D comparative evaluation and correlation of condylar morphology in bruxers and non-bruxers, https://doi.org/10.5281/zenodo.7954711. 6\n\n- SPIRIT_checklist.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nDean SPDC Dr. Manoj Chandak sir for his support and guidance.\n\nStatistician Mr. Laxmikant Umate sir for sample size evaluation.\n\nMr.Manoj Patil sir for guidance in framing the format of protocol.\n\n\nReferences\n\nKumar S: Assessment Of Condylar Osseous Changes in Patients with Bruxism Using Cone-Beam Computed Tomography-A Cross Sectional Observational Study. J. Posit. Sch. Psychol. 2022 Mar 23; 6(3): 1189–1203.\n\nYamada K, Hanada K, Fukui T, et al.: Condylar bony change and self-reported parafunctional habits in prospective orthognathic surgery patients with temporomandibular disorders. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2001 Sep 1; 92(3): 265–271. PubMed Abstract \| Publisher Full Text\n\nLarheim TA, Abrahamsson AK, Kristensen ML, et al.: Temporomandibular joint diagnostics using CBCT. Dentomaxillofac. Radiol. 2015 Jan; 44(1): 20140235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYalcin ED, Ararat E: Cone-beam computed tomography study of mandibular condylar morphology. J. Craniofac. Surg. 2019 Nov 1; 30(8): 2621–2624. Publisher Full Text\n\nGopal S, Vardhan BG, Kumar M, et al.: Clinical experience with cone beam CT: a report of incidental findings in 60 cases. Int. J. Biol. Med. Res. 2015; 6(3): 5065–5067.\n\nTiwari A, Khasbage SD: 3D comparative evaluation and correlation of condylar morphology in bruxers and non-bruxers. Zenodo. 2023. Publisher Full Text\n\nDaneshmehr S, Razi T, Razi S: Relationship between the condyle morphology and clinical findings in terms of gender, age, and remaining teeth on cone beam computed tomography images. Braz. J. Oral Sci. 2022 Sep 19; 21. Publisher Full Text\n\nShinkaic RSA: Concordance analysis between two questionnaires of self-reported bruxism.2018.\n\nTiwari A, Khasbage SD: Questionnaire for bruxism. [Data]. Zenodo. 2023. Publisher Full Text\n\nShubhasini AR, Birur P, Shubha G, et al.: Study of three dimensional morphology of mandibular condyle using cone beam computed tomography. MJDS. 2016 Apr; 1: 7–12.\n\nLópez-Frías FJ, Castellanos-Cosano L, Martín-González J, et al.: Clinical measurement of tooth wear: Tooth wear indices. J. Clin. Exp. Dent. 2012 Feb; 4(1): e48–e53. Publisher Full Text\n\nTiwari A, Khasbage SD: Tooth wear index. [Data]. Zenodo. 2023. Publisher Full Text\n\nIsman O: Evaluation of jaw bone density and morphology in bruxers using panoramic radiography. J. Dent. Sci. 2021 Mar 1; 16(2): 676–681. Publisher Full Text\n\nSagl B, Schmid-Schwap M, Piehslinger E, et al.: The effect of tooth cusp morphology and grinding direction on TMJ loading during bruxism. Front. Physiol. 2022; 13: 964930. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Yu W, Wang J, et al.: An observational study of temporomandibular joints in adults with definite sleep bruxism on magnetic resonance imaging and cone beam computer tomography images.\n\nAufa AA, Rikmasari R, Wulansari D: Differences in mandibular morphology between bruxism and non-bruxism patients based on the Levandoski analysis. Majalah Kedokteran Gigi Indonesia. 2023; 8(3): 161–168. Publisher Full Text" }	[ { "id": "286834", "date": "25 Jun 2024", "name": "Jing Guo", "expertise": [ "Reviewer Expertise 1.Dental maxillofacial malformation associated with the airway physiology mechanism. 2.Associated mechanism of occlusion and temporomandibular joint function." ], "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 used CBCT to compare the condylar morphological characteristics of patients with and without bruxism. The results not only confirmed the damage of the anatomical morphology of the temporomandibular joint in the progression of bruxism, but also provided some evidence for the understanding of its patho-physiological mechanism in the process of clinical diagnosis. In addition, the study also involved the comparison of tooth attrition index between the two groups, which provided clinical support for early intervention of bruxism to reduce dental tissue damages. The objectives of this study were clearly described.The formulation of scientific questions, the consistency of research subjects and the design of sample size were consistent with the methodology of clinical research.\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": "11912", "date": "29 Jun 2024", "name": "Aakanksha Tiwari", "role": "Author Response", "response": "Respected sir, I extend my heartfelt thanks to you for taking out your valuable time to review and approve my protocol and to provide your valuable views on my topic." }, { "c_id": "11960", "date": "04 Jul 2024", "name": "Aakanksha Tiwari", "role": "Author Response", "response": "Thank you for your valuable reviews." } ] }, { "id": "257842", "date": "11 Sep 2024", "name": "Dr. Garima Yeluri", "expertise": [ "Reviewer Expertise Temporomandibular joint disorders", "Premalignant lesions and conditions", "Orofacial 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\nThe Title of the study justifies the study design. Aims & Objectives are clearly mentioned. The study design is apt with inclusion and exclusion criterias along with the Statistical analysis design. The condylar morphology to be evaluated in in coronal, saggital and axial sections are completely explained in the methodology. The datasets designed are very clear. Overall the rationalle of the study is scientifically sound.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [ { "c_id": "12416", "date": "12 Sep 2024", "name": "Aakanksha Tiwari", "role": "Author Response", "response": "Dear Madam, Thank you so much for taking out your valuable time to review my study protocol and for approving it." } ] } ]	1	https://f1000research.com/articles/12-1099
https://f1000research.com/articles/12-1097/v1	01 Sep 23	{ "type": "Research Article", "title": "Matrix mismatch and its estimation in single-lab studies", "authors": [ "Steffen Uhlig", "Bertrand Colson", "Kirstin Frost", "Petra Gowik", "Bertrand Colson", "Kirstin Frost", "Petra Gowik" ], "abstract": "Background: Matrix mismatch arises when the matrix of the test sample differs from the calibration or standard matrix. Matrix mismatch often accounts for a large part of between-laboratory variation. Notwithstanding, it is seldom characterized in method validation studies. Methods: Matrix-mismatch manifests itself as the variation of bias across matrices and has two components: the variation of method bias and the variation of laboratory bias across matrices. The laboratory bias component of matrix mismatch can be considered to constitute a component of precision. In the case of horizontal methods, a comprehensive characterization of method performance should thus include matrix mismatch. The different precision and matrix-mismatch components can be estimated by means of mixed linear models. Results: A relatively simple single-lab design with spiked sample material is presented here, allowing an estimate of matrix mismatch via ANOVA calculations. Conclusions: In the statistical model for precision experiments described in ISO 5725-2, there is no matrix mismatch term. Indeed, a characterization of matrix mismatch is not possible if only one matrix is represented in the collaborative study, or if the samples sent to the laboratories do not reflect the properties of the matrices of “true” samples. If matrix mismatch was not estimated in the validation study, a subsequent single-lab study can be conducted. A relatively simple design was described, but more sophisticated designs may present various advantages.", "keywords": [ "Method validation", "collaborative study", "single-lab study", "precision", "reproducibility", "repeatability", "bias", "matrix mismatch" ], "content": "Introduction\n\nLaboratory bias can vary considerably – even among laboratories using one and the same standardized analytical method. This variation can be explained by differences with respect to reagents, staff competence, equipment, etc., see Section 0.3 in ISO 5725-3.1 One important source of between-laboratory variation is matrix mismatch. From the chemical analyst’s point of view, matrix mismatch arises when the matrix of the test sample (the substance or material in which the analyte of interest is present) differs from the calibration or standard matrix.2–4 Such differences may result in chemical or physical interferences that affect the measurement. In particular: if the calibration standards do not adequately represent the sample matrix, the calibration curve may not accurately capture the relationship between the analyte concentration and the instrument response, resulting in a bias.5 In the literature, matrix mismatch is also referred to by other terms such as matrix effects.\n\nFigure 1 illustrates how matrix mismatch arises in connection with calibration curves. The underlying data were generated with spreadsheet software for the purpose of illustration.17 Three calibration curves are shown for the determination of a given analyte via mass spectrometry. The top calibration curve (black) corresponds to results obtained from a standard solution. The second curve (blue) corresponds to results obtained from spiked samples for a given matrix (matrix 1). Finally, the lowest curve (green) corresponds to results obtained for another given matrix (matrix 2). As can be seen, while the calibration curve for matrix 1 lies very close to the standard solution curve, there are considerable suppression effects for the second matrix, resulting in a considerable negative bias. For instance, if the standard solution calibration curve is used for the determination of analyte concentration in a sample with matrix 2 and a peak intensity of 6,000,000 is obtained, analyte concentration will be determined to be 52.7 ng/ml, whereas the correct concentration should be 100 ng/ml.\n\nThree calibration curves are shown: one obtained on the basis of standard solutions (black curve), and two “matrix calibration” curves (blue and green). If the standard solution calibration curve is used to measure analyte concentration in a sample with matrix 2, measurement results will display a considerable negative bias.\n\nSome analytical methods have a scope which includes many different matrices (such methods are sometimes referred to as “horizontal” methods). For instance, a cold vapor atomic fluorescence spectrometry method for the determination of mercury content in foodstuffs will be applied to matrices such as carrots, broccoli, spinach, etc. see method BVL L00.00-19-7 in the official collection of methods of analysis according to § 64 of the German Food and Feed Act.6 For such methods, a complete characterization of method performance should include a measure of matrix mismatch.\n\nIn this paper, the focus is on the quantification of matrix mismatch effects and their contribution to between-laboratory variation by means of the statistical evaluation of data from method validation studies. In such data sets, matrix mismatch manifests itself as the variation of bias across matrices, and this will serve as a metrological definition of matrix mismatch in the following.\n\nBias is the difference between the mean value (across test results) and the “true value”. Strictly speaking, bias is a measure of systematic error, see definition 3.3.2 in ISO 3534-2.7 However, calculating individual bias values – e.g. for a given laboratory and a given matrix – often offers little practical use. Rather, the aim is to determine the degree to which bias varies across the matrices lying within the method’s scope. In other words, the aim is to characterize matrix mismatch as a random effect.\n\nWhile matrix-mismatch effects may be observed between different “types of matrices” such as beef or pork, they may also be observed within one type of matrix, e.g. between different types of beef. Depending on the method and its scope, it may be expedient to divide the population of different matrices in different matrix groups, whereby all the matrices in a given group can be expected to interact in a similar manner with the analyte. Matrix mismatch can then be characterized in terms of the variation of bias across matrix groups, see Jülicher et al. (1998).8,9\n\nApproaches for the characterization of matrix mismatch were described in the European Union CD 657 (2002)10 – revised and published in 2021 as CIR 808.11 As far as authors are aware, a characterization of matrix mismatch is not required in any other method validation standard or guideline. The alternative approach described in the CD 657 and CIR 808 is implemented in InterVAL.12\n\nIn the following, the relationship between matrix mismatch and precision will be discussed and a relatively simple approach for the estimation of matrix mismatch by means of a single-lab study will be presented.\n\n\nMatrix mismatch and precision\n\nMatrix mismatch, considered as variation of bias across matrices, has two different components: variation of laboratory bias and variation of method bias. These two components have a different relation to precision, as will now be discussed.\n\nPrecision is defined in terms of the degree of agreement between test results obtained under given conditions on the basis of identical samples, see ISO 3534-2.7 Thus, in theory, it seems reasonable to conclude that matrix mismatch – considered as variation of bias across matrices, i.e. across different types of samples – is not a component of precision. Notwithstanding, in practice, matrix mismatch and precision are often conflated. The reason is the following.\n\nThe basic design for interlaboratory method validation studies – often referred to as collaborative studies – conducted in order to estimate method precision is described in ISO 5725-213 and allows the estimation of two effects: laboratory bias and repeatability. If only one matrix is represented in the collaborative study – as is typically the case, albeit at different concentrations levels – the variation of bias from matrix to matrix cannot be characterized. If part of the observed between-laboratory variation is caused by matrix mismatch – for instance, if the calibration procedure interacts differently with the matrix under consideration in each laboratory – then matrix-mismatch effects will be included in the estimate of the reproducibility standard deviation. In summary: if the basic design from ISO 5725-2 is applied, there is no way to extricate the matrix-mismatch component from the reproducibility estimate, and matrix mismatch and precision are thus conflated.\n\nFor this reason, it is proposed to take a pragmatic approach and to include matrix mismatch (to be specific: the variation of laboratory bias across matrices) among the components of precision.\n\nIn order to shed further light on the relation between precision and matrix mismatch, the following scenario is considered:\n\n• A collaborative study is conducted with 10 participating laboratories\n\n• Each laboratory receives 3 samples, corresponding to 3 different matrices\n\n• The sample material was spiked, so that it is possible to calculate recovery values\n\n• For each sample and laboratory, 2 duplicate test results are obtained\n\nTable 1 shows recovery values (generated with spreadsheet software for the purpose of illustration17) corresponding to the above scenario.\n\nPerfect recovery is 100%.\n\nAs can be seen in Table 1, laboratory bias depends on the matrix. For instance, Lab 2 displays a positive bias for Matrix A, but a negative bias for Matrix C. Conversely, Lab 9 displays a negative bias for Matrix A but a positive bias for Matrix C. Even when a consistently positive or negative bias across matrices is observed (e.g. consistent positive bias for Lab 1), variation of bias across matrices is nonetheless present (the bias for Matrix A is larger than for Matrix B). The variation of laboratory bias across matrices can be modelled as a random effect for the interaction of laboratory and matrix. The corresponding standard deviation is denoted smatrix,lab.\n\nThe mean recovery values across laboratories [1] are provided in Table 2.\n\nPerfect recovery is 100 %.\n\nThese mean recovery values allow a characterization of the variation of method bias across matrices. This component of matrix mismatch is a measure of the dispersion of the matrix-specific mean values (with due consideration of the mean values’ statistical uncertainty). The corresponding standard deviation is denoted smatrix,method. Unlike the laboratory bias component of matrix mismatch, smatrix,method cannot be calculated if only one matrix is represented in the collaborative study. It is straightforward to distinguish precision components from smatrix,method.\n\nIn summary, in this scenario, the following precision and matrix-mismatch parameters can be calculated:\n\n• Repeatability standard deviation sr (random differences between the duplicates for a given sample within a given laboratory)\n\n• Reproducibility standard deviation sR (total variation, including repeatability and between-laboratory effects)\n\n• Matrix-mismatch standard deviation smatrix,lab corresponding to the variation of laboratory bias across matrices (random term for laboratory-matrix interaction)\n\n• Matrix-mismatch standard deviation smatrix,method corresponding to the variation of method bias across matrices (dispersion of matrix-specific means values)\n\nThese different variance components are best estimated by means of a linear model such as the following:\n\nyijk denotes The test result for matrix i, laboratory j and replicate k\n\nμi denotes The mean value (across laboratories) for matrix i\n\naj denotes The laboratory effect for lab j, modelled as a random effect with standard deviation (SD) sL (in the absence of matrix mismatch, we have sR2=sL2+sr2)\n\nbij denotes The interaction effect for matrix i and lab j, modelled as a random effect with SD smatrix,lab\n\neijk denotes The repeatability effect for matrix i, lab j and replicate k, modelled as a random effect with SD sr\n\nFor further information regarding mixed linear models, the reader is referred to Searke SR et al.14\n\nFigure 2 illustrates the relationship between matrix mismatch and precision.\n\nThe following notation is used: sR denotes the reproducibility standard deviation, sr denotes repeatability standard deviation, sL denotes the between-laboratory standard deviation, sL,nonmatrix denotes the component of between-laboratory variation consisting of sources of laboratory bias other than matrix mismatch, smatrix denotes the matrix-mismatch standard deviation consisting of (a) the variation of lab bias across matrices smatrix,lab and (b) the variation of method bias across matrices smatrix,method. The latter is not a component of sR.\n\nIf the samples sent to the laboratories in the collaborative study are not “true” samples, the various estimates of precision and matrix mismatch may be affected. In particular, if sample material is (a) homogenous (b) sent to the laboratories in the form of test portions requiring no further sample preparation steps, then the reproducibility standard deviation may be underestimated in the sense that observed variation during testing with “true” samples may be much larger.\n\nIt should be noted that while sample heterogeneity [2] will impact repeatability, it does not impact laboratory bias. Thus, while sample heterogeneity may cause differences in the repeatability standard deviations for different matrices, it will have no effect on the between-laboratory standard deviation.\n\nBy contrast, sample preparation can impact both repeatability and lab bias. Indeed, since the sample preparation steps must be performed separately for each replicate, it is clear they will contribute to repeatability. Moreover, there may be differences between the sample preparation procedures from laboratory to laboratory, resulting in a contribution to lab bias, and inflating the between-laboratory standard deviation. Finally, if there are interactions between the different sample preparation procedures and the matrices, sample preparation effects can also contribute to the variation of laboratory bias across matrices, i.e. to matrix mismatch.\n\n\nEstimation of matrix mismatch by means of a single-lab study\n\nA simple design for the evaluation of matrix mismatch in an in-house validation study will now be described. This design can be applied for the estimation of the variation of a given laboratory’s bias across matrices. It is only applicable if spiking is possible. Accordingly, in this design, the materials from which the different samples are collected must not contain the analyte. This will ensure that, upon spiking, the different samples can be considered to have identical analyte concentration levels.\n\nIn this design, test results are obtained on the basis of 12 samples – representing 12 different matrices. For each sample, duplicate measurements are performed. In this manner, variation between the samples (matrix mismatch) can be distinguished from variation within each matrix (repeatability). As explained above, matrix mismatch is modelled as a random effect, and the result is a standard deviation characterizing variation across all the samples consistent with the specification of the measurand.\n\nTable 3 provides an example of data which could be obtained in such a single-lab experiment. These data were generated using spreadsheet software for the purpose of illustration.17\n\nValues for the matrix-mismatch standard deviation smatrix and the repeatability standard deviation sr are calculated by means of one-way analysis of variance (ANOVA). For an introduction to ANOVA, the reader is referred to Sahai H et al.15\n\nThe following notation is introduced: the samples are indexed i=1,…,m (in this example, m=12); the replicates within each sample are indexed j=1,n (in this example, n=2); and the individual measurement results are denoted xij.\n\nFirst, compute the overall mean value x¯, and the sample-specific mean values x¯i. Then compute the between-sample sum of squares:\n\nThe repeatability standard deviation sr is then obtained as\n\n(If the value under the square root sign is negative, then smatrix=0.)\n\nTable 4 and Table 5 illustrate the ANOVA calculations by applying equations 2-3 to the data in Table 3.\n\nUsing the above equations, the following precision estimates are obtained:\n\nIn this example, matrix-mismatch effects can thus be considered non-negligible.\n\nMore sophisticated single-lab designs are described in Jülicher et al. (1998)8,9 and ISO TS 23471.16\n\n\nConclusions\n\nIn method validation studies, one of the aims is a characterization of method performance, often in terms of trueness and precision. For horizontal methods – or any method whose scope includes several types of matrices – this should involve obtaining an estimate of matrix mismatch. Considered as a source of metrological variation, matrix mismatch consists of two components: variation of laboratory bias and variation of method bias – whereby the term variation is meant here as variation across matrices. Each component will typically be expressed as a standard deviation: smatrix,lab and smatrix,method. In the statistical model for precision experiments described in ISO 5725-2, there is no matrix mismatch term. Indeed, a characterization of matrix mismatch is not possible if only one matrix is represented in the collaborative study, or if the samples sent to the laboratories do not reflect the properties of the matrices of “true” samples. If matrix mismatch was not estimated in the validation study, a subsequent single-lab study can be conducted. A relatively simple design was described, but more sophisticated designs may present various advantages. If spiking is not possible, the laboratory bias component of matrix mismatch smatrix,lab can be estimated by means of a collaborative study with “real” samples (i.e. samples representing the matrices in the method’s scope). For the estimation of the method bias component of matrix mismatch smatrix,method, a collaborative study with “real” samples and (certified) reference values is required. It should be noted that proper estimation of the latter term may require due consideration of the statistical uncertainty of the matrix-specific mean values (across laboratories). The estimation of matrix mismatch by means of collaborative studies will be discussed in a subsequent article.", "appendix": "Data availability\n\nZenodo. Data for article: Matrix mismatch and its estimation in single-lab studies. DOI: 10.5281/zenodo.8246900 17\n\nThis project contains the following underlying data:\n\n• Matrix mismach Table 1.ods\n\n• Matrix mismatch Figure 1.ods\n\n• Matrix mismach Table 3.ods\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nISO 5725-3: Accuracy (trueness and precision) of measurement methods and results — Part 3: Intermediate measures of the precision of a standard measurement method. (A new revision is currently being prepared for publication.).1994.\n\nSteiner D, Krska R, Malachová A, et al.: Evaluation of Matrix Effects and Extraction Efficiencies of LC–MS/MS Methods as the Essential Part for Proper Validation of Multiclass Contaminants in Complex Feed. J. Agric. Food Chem. 2020; 68(12): 3868–3880. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatuszewski BK, Constanzer ML, Chavez-Eng CM: Matrix effect in quantitative LC/MS/MS analyses of biological fluids: a method for determination of finasteride in human plasma at picogram per milliliter concentrations. Anal. Chem. 1998 Mar 1; 70(5): 882–889. PubMed Abstract \| Publisher Full Text\n\nZhou W, Yang S, Wang PG: Matrix effects and application of matrix effect factor. Bioanalysis. 2017 Dec; 9(23): 1839–1844. Epub 2017 Nov 24. PubMed Abstract \| Publisher Full Text\n\nNoegrohati S, Hernadi E, Asviastuti S: Matrix Effect Evaluation and Method Validation of Azoxystrobin and Difenoconazole Residues in Red Flesh Dragon Fruit (Hylocereus polyrhizus) Matrices Using QuEChERS Sample Preparation Methods Followed by LC-MS/MS Determination. Bull. Environ. Contam. Toxicol. 2018 Jun; 100(6): 821–826. PubMed Abstract \| Publisher Full Text\n\nAmtliche Sammlung von Untersuchungsverfahren – Official collection of methods of analysis according to § 64 of the German Food and Feed Act. Reference Source\n\nISO 3534-2: Statistics — Vocabulary and symbols — Part 2: Applied statistics.2006.\n\nJülicher B, Gowik P, Uhlig S: Assessment of detection methods in trace analysis by means of a statistically based in-house validation concept. Analyst. 1998; 123: 173–179. Publisher Full Text\n\nJülicher B, Gowik P, Uhlig S: A top-down in-house validation based approach for the investigation of the measurement uncertainty using fractional factorial experiments. Analyst. 1998; 124: 537–545. Publisher Full Text\n\nCommission Decision 2002/657/EC. Reference Source\n\nCommission Implementing Regulation (EU) 2021/808. Reference Source\n\nInterVAL Plus®, Software for In-house Validation. QuoData GmbH, Version 3.5.0.0.2022.\n\nISO 5725-2: Accuracy (trueness and precision) of measurement methods and results — Part 2: Basic method for the determination of repeatability and reproducibility of a standard measurement method.2019.\n\nSearle SR, Casella G, McCulloch CE: Variance Components. John Wiley & Sons; 1992.\n\nSahai H, Ageel M: The Analysis of Variance. Birkhäuser Boston; 2000.\n\nISO TS 23471: Experimental designs for the evaluation of uncertainty – Use of factorial designs for determining uncertainty functions.2022.\n\nUhlig S, Colson B, Frost K, et al.: Data for article: Matrix mismatch and its estimation in single-lab studies. [Data set]. Zenodo. 2023. Publisher Full Text\n\n\nFootnotes\n\n1 These can be easily reproduced by taking the arithmetic mean of the values in Table 1, separately for each matrix.\n\n2 In Section 8 of ISO 5725-3, 8 the basic design from ISO 5725-2 is extended to allow the estimation of the variability between subsamples in the case of “heterogeneous material”. In this extended design, a minimum of two samples per level are analyzed in duplicate in each participating laboratory." }	[ { "id": "311570", "date": "15 Aug 2024", "name": "Andrej Razumić", "expertise": [ "Reviewer Expertise Dimensional Metrology", "Statistical Modeling", "Quality Management", "Quality Assurance", "Quality Control" ], "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 addresses the application of the ISO 5725-2 standard in chemical analysis. The authors describe matrix mismatch arises when the matrix of the test sample differs from the calibration or standard matrix. In accordance with ISO 5725-2, an analysis of the repeatability and reproducibility of measurement results was conducted. The paper introduces the concept of matrices and employs analysis of variance for calculations. The calculations presented in the tables and expressions are accurate.\nThe following corrections are necessary: - The arithmetic means of the matrices should not be separated from Table 1. It is suggested to add a row in Table 1 containing the values of the arithmetic means. - In Table 4, the columns labeled \"differences\" have identical headings but opposite numerical values. The expression in the 6th column needs to be changed. Instead of \"xij – xi-bar,\" it should be \"xi-bar – xij.\"\nIn the future, it is recommended that collaborative studies be performed using measurement uncertainty according to the Guide to the expression of uncertainty in measurement (GUM) and Degree of Equivalence (DoE). The impact of matrices would then be included in the evaluation of measurement uncertainty, and other factors influencing the result could also be considered.\nThe paper is accepted 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? 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/12-1097
https://f1000research.com/articles/12-1096/v1	01 Sep 23	{ "type": "Study Protocol", "title": "Protocol for the evaluation of cyclin D1 expression in tumor tissue and surgical margins in oral squamous cell carcinoma – a retrospective study", "authors": [ "ANKITA CHAVHAN", "Swati Patil", "Madhuri Gawande", "Alka Hande", "Archana Sonone", "Aayushi Pakhale" ], "abstract": "Oral squamous cell carcinoma (OSCC) is a malignant epithelial tumor with poor prognosis. There is an increase in the proliferation of epithelial cells in OSCC which is control by cell cycle regulators like Cyclin D1. Cyclin D1 is linked to a poor prognosis for patients, including aggressive malignancies, recurrence, protracted remission, etc. To evaluate Cyclin D1 immunoexpression in different grades and surgical margins in OSCC. All tissue sections will be processed for Cyclin D1 IHC. After that light microscopic evaluation of Cyclin D1 expression was classified as weak (scoring 1-4), moderate (score 5-8), or strong based on a final expression score that was obtained by multiplying the labelling index score by the intensity score (score 9–12). The present study will find the immunohistochemical expression of Cyclin D1 in OSCC. There will be variation in the immunoexpression of Cyclin D1 among different grades of OSCC its surgical margin and normal oral mucosa. We hypothesize that: As the disease condition goes towards poor grade, intensity of cyclin D1 expression immunohistochemically may increase. Hence, the intensity can be used as a prognostic marker.", "keywords": [ "Cyclin d1", "Cell proliferation", "Oral potential malignant disorder", "Oral squamous cell carcinoma", "Immunohistochemistry" ], "content": "Introduction\n\nOral squamous cell carcinoma (OSCC) is a malignant epithelial tumor with poor prognosis. OSCC is one of the top causes of death in India and Southeast Asia.1 Oral squamous cell carcinoma caused due to chewing tobacco, such as panmasala, gutkha, gudakhu, khaini, and other products composed of tobacco.2,3 Patients with middle-aged to older ages typically affected by OSCC.4 OSCC have a high rate of proliferation of malignant epithelial cells. The prognosis of OSCC depends on recommended surgical margin.\n\nIn the surgical margin, the epithelial cells may be altered by field cancerization. There is an increase in the proliferation of epithelial cells in OSCC which is control by cell cycle regulators like Cyclin D1.5\n\nCyclin control the orderly phases of the cells through the G1, S, G2, and M phases of the cell cycle.6,7 It plays a role in cell cycle induction, transcriptional control, and DNA damage-induced death.2 (CCND1) Cyclin D1, 11q13 location of chromosomes, carries the cell cycle from the G1 to the S phase by encoding a vital cell cycle regulating protein.8‐10 The control of the cell cycle is facilitated by Cyclin D1, proto-oncogenes and an enzyme known as Cylin-dependent kinase 4 (CDK4). It also interacts with other transcriptional factor (TFs) and controls the activity of transcriptional cofactors.4 Lack of regulation of the cell cycle mechanism is an essential phase in the carcinogenic change. Cyclin D1 is linked to a poor prognosis for patients, including aggressive malignancies, recurrence, protracted remission, etc.3\n\n\nObjectives\n\n\n\n1) To evaluate the Cyclin D1 immuno-expression in –\n\n• Normal oral mucosa.\n\n• Different grades of OSCC.\n\n• Surgical margin of OSCC.\n\n2) To compare Cyclin D1 immuno-expressions in –\n\n• Normal oral mucosa.\n\n• Different grades of OSCC.\n\n• Surgical margin of OSCC.\n\nTRIAL DESIGN: Retrospective study.\n\n\nMethods\n\nThis study will be conducted in the Department of Oral Pathology and Microbiology, Sharad Pawar Dental College in collaboration with Central Research Laboratory, Datta Meghe Institute of Higher Education & Reasearch, Sawangi (Meghe) Wardha.\n\nInclusion criteria\n\n• Paraffin embedded tissue sections of well differentiated squamous cell carcinoma (WDSCC), moderately differentiated squamous cell carcinoma (MDSCC), poorly differentiated squamous cell carcinoma (PDSCC) histopathologically, their surgical margins and normal oral mucosa (NOM) will be retrieved from archival of department.\n\n• 80 surgically treated patients who have been clinically and histopathologically diagnosed with OSCC.\n\n• Recorded demographic data of clinical presentation, habits and its duration, histopathological findings, operative details will be noted in detail from department.\n\n• Follow-up data for 2-3 years of disease-free survival.\n\nExclusion criteria\n\n• Patients who have a history of pre-malignant lesion, recurrent or distant metastasis and pre-operative chemotherapy, radiation therapy and the patients previously having undergone surgery for recurrence (except biopsy).\n\n\nIntervention\n\nAll tissue sections will be proceeded for Cyclin D1 IHC. After that, a light microscopic evaluation of Cyclin D1 expression was classified as weak (scoring 1-4), moderate (score 5-8), or strong based on a final expression score that was obtained by multiplying the labelling an index score by the intensity score (score 9–12).\n\n\nOutcomes\n\nThe present study will find the immunohistochemical expression of cyclin D1 tumor tissue and surgical margins of OSCC, in order to evaluate the prognosis of OSCC.\n\nThere will be a variation in the immunoexpression of Cyclin D1 among different grades of oral squamous cell carcinoma, its surgical margin and normal oral mucosa.\n\nConsidering the prevalence of OSCC as 70.7% in the outpatient department of Oral Pathology and Microbiology, using a single proportion formula, the sample size is calculated via the expression below.11\n\nWhere,\n\nZ21-α/2 - The level of significance at 5 %\n\ni.e. 95 % confidence interval =1.96\n\np - Sample demonstrating +ve Cycline D1 expressions in tiny groups of cells in the basal layer of the\n\nepithelium = 70.7% = 0.707\n\nE - Errors of margins = 10 % = 0.10\n\nn = 1.962x 0.707 x (1-0.707) /0.102\n\nn = 80\n\nFormula reference - Angadi PV, Krishnapillai R. Cyclin D1 expression in OSCC and verrucous carcinoma: correlation with histological differentiation. OS, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontology. 2007 Mar 1;103(3):e30-5\n\nA paraffin block having suitable mass of tumor and acceptable amount of normal tissue is selected. On Poly-L-Lysinecoated slides, sections of having thickness of three micrometers are cut & placed. For De-paraffinization, sections are placed in the xylene solution. Sections are rehydrated by subjecting them to descending concentrations of alcohol (70-100%). In order to wash sections, tap water is used. Washing time for sections in distilled water is 60 seconds. After washing all the sections are transferred to Coplin’s jar containing the retrieval buffer solution. The solution which is used for Antigen retrieval is composed of 30 ml of retrieval solution in 1500 mili-liters of distilled water for fifteen to twenty minutes in the pressure cooker. Cooling is done at room temperature.\n\nSections are dipped once in distilled water. Sections are washed with Tris buffer solution for at least 5 minutes at room temperature. This step is repeated thrice. For peroxidase blocking a mixture of “3,5 Hydrogen Peroxide and Methanol” is used for thirty minutes. Tris buffer solution is used for washing the sections 3 times for 5 minutes each. Primary antibody cyclin D1 is applied at room temperature for 1 hour. Envision technique is performed by utilizing a labelled polymer for 30 minutes at room temperature. For washing the sections tris buffer solution is used thrice for five minutes.\n\nThe application of “DAB (3,3’-diaminobenzidine)” substrate is done for fifty to twenty minutes. The working DAB solution is comprised of following –one millilitre of DAB buffer & twenty five microliters of “DAB concentrate”. This time, washing of sections is done by Tris buffer, for 15-20 minutes. Sections are cleaned in distilled water. For counter staining Mayer’s hematoxylin is used, which is done for five minutes. Again, the washing of sections is done under tap water and then dried. Once the sections are dried; mounte in DPX. After that a microscopic examination is done. Calculations will be made to determine the median percentage per slide (labelling index) and the proportion of IHC positive tumour cells per hot spot. Labelling indices of 1-35%, 36-70%, and 71-100%, respectively, each received a score of 1, 2, or 3. According to their microscopic appearance, Cyclin D1 immunostaining intensity will be assigning each a score of 0, 1, 2, or 3 will indicate whether it is weak, intermediate, or strong. Cyclin D1 expression was classified as weak (scoring 1-4), moderate (score 5-8), or strong based on a final expression score that was obtained by multiplying the labelling index score by the intensity score (score 9–12). We will tabulate and do the necessary statistical analysis on all relevant clinical, histopathological, and immunohistochemical information that we will gather.\n\nWill be published in an indexed journal.\n\nNot started yet.\n\n\nDiscussion\n\nKing Y. Lam at el., (2000) examined how Cyclin D1 relates to the clinical and pathological characteristics of OSCC. They found that Cyclin D1 expressions were present in 63% of OSCC; that was typically modest but more commonly positive in high-grade lesions. Radiation therapy had no effect on either Cyclin D1's expression. Expression was unrelated to patient age, gender, survival, tumour stage, or patient demographics. Patients with the floor of the mouth, gingiva, oropharynx, and palate squamous cell carcinomas had overexpressed Cyclin D1. The researchers came to the conclusion that Cyclin D1 was often expressed in OSCC, connected to the high grade of tumours, and was not similar in different regions of the oral cavity, indicating diverse tumour biology of carcinoma from theis area.\n\nR Miyamoto et al., in 2003 showed that the relationship among Cyclin D1 (CCND1) extension and over expressions in OSCCs were examined, and the predictive validity of Fluorescence in-situ Hybridization (FISH) on Cyclin D1 (CCND1) amplification with immunohistochemical over expression in fine-needle aspiration (FNA) samples was established. In every instance where CCND1 was amplified, they noticed CCND1 overexpression. While 14 of the 28 instances 50.0% that did not show such intensification showed CCND1 overexpression. They noticed insignificant The statistical correspondence among CCND1 over-expression and reduced endurance as well as the independent prognostic significance of CCND1 amplification and nodal status. They came to the conclusion that there is a need to look into the additional routes besides CCND1 amplification that control CCND1 expression. They also came to the conclusion that in OSCCs, CCND1 intensification is a more accurate analytical predictor than CCND1 over expression.\n\nS Saawarn et al., in Cyclin D1's immunohistochemistry reactivity and expression, as well as their relationships to the location, clinically staged, and histological discrimination of OSCC, were examined in 2011. (OSCC). 45% of people showed expression of cyclin D1 of Oral SCC cases, although it was unrelated to the site or clinical stage. Moreover, they find a statistical significance link among the highest expression being detected in well-differentiated squamous cell carcinomas, followed by MDSCC and PDSCC. They came to the conclusion that as differentiation rises, Cyclin D1 expression does as well.\n\nY OHNISHI et al., in 2014 immunohistochemically examined the relationship among cyclin D1 expression and ki-67 expressions in oral Squamous CC and connected their expression among cells segregation, cells abundance, and metastasis. They discovered the expression of Cyclin D1 and Ki-67 in the nucleus of all 35 Squamous CC tissue, although they did not discover a connection between oral SCC differentiation and Cyclin D1 protein expression. Also, they discovered that 90% of metastatic foci had significant Cyclin D1 expression, in contrast to metastatic foci treated with preoperative adjuvant therapy, which had poor expression. Moreover, Cyclin D1 and Ki-67 were found in the basal to suprabasal cell layer of the WD oral SCC, while the highly-differentiated region also contained cyclin D1-positive and Ki-67-negative cells. Also, they proposed that in WD oral SCC, Cyclin D1 protein expression is essential for the growth and differentiation of cells.\n\nEthical approval received from Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha.\n\nIEC reference number- DMIHER (DU)/IEC/2023/842.\n\nInformed written consent was obtained from the patient before surgery and before the before the write-up of the protocol as per the data requirement of this study.", "appendix": "Data availability\n\nNo data associated with this study.\n\nZenodo, STROBE checklist for cross sectional study.\n\nDOI - 10.5281/zenodo.7874225.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nI would like to thank my institute and my colleagues.\n\n\nReferences\n\nSherkheli MA, Gisselmann G, Hatt H: Supercooling agent icilin blocks a warmth-sensing ion channel TRPV3. Sci. World J. 2012 Jan 1; 2012: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOhnishi Y, Watanabe M, Wato M, et al.: Cyclin D1 expression is correlated with cell differentiation and cell proliferation in oral squamous cell carcinomas. Oncol. Lett. 2014 Apr 1; 7(4): 1123–1127. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMishra R, Das BR: Cyclin D1 expression and its possible regulation in chewing tobacco mediated oral squamous cell carcinoma progression. Arch. Oral Biol. 2009 Oct 1; 54(10): 917–923. PubMed Abstract \| Publisher Full Text\n\nMoharil RB, Khandekar S, Dive A, et al.: Cyclin D1 in oral premalignant lesions and oral squamous cell carcinoma: An immunohistochemical study. Journal of Oral and Maxillofacial Pathology: JOMFP. 2020 May; 24(2): 397. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLam KY, Ng IO, Yuen AP, et al.: Cyclin D1 expression in oral squamous cell carcinomas: clinicopathological relevance and correlation with p53 expression. J. Oral Pathol. Med. 2000 Apr; 29(4): 167–172. PubMed Abstract \| Publisher Full Text\n\nBasnaker M, Srikala SP, Satish BN: Cyclin d1 gene expression in oral mucosa of tobacco chewers–an immunohistochemical study. J. Clin. Diagn. Res. 2014 May; 8(5): ZC70–ZC75. PubMed Abstract \| Publisher Full Text\n\nLaco J, Mottl R, Höbling W, et al.: Cyclin D1 expression in ectomesenchymal chondromyxoid tumor of the anterior tongue. Int. J. Surg. Pathol. 2016 Oct; 24(7): 586–594. PubMed Abstract \| Publisher Full Text\n\nMiyamoto R, Uzawa N, Nagaoka S, et al.: Prognostic significance of cyclin D1 amplification and overexpression in oral squamous cell carcinomas. Oral Oncol. 2003 Sep 1; 39(6): 610–618. PubMed Abstract \| Publisher Full Text\n\nRamos-García P, González-Moles MÁ, Ayén Á, et al.: Asymmetrical proliferative pattern loss linked to cyclin D1 overexpression in adjacent non-tumour epithelium in oral squamous cell carcinoma. Arch. Oral Biol. 2019 Jan 1; 97: 12–17. PubMed Abstract \| Publisher Full Text\n\nBova RJ, Quinn DI, Nankervis JS, et al.: Cyclin D1 and p16INK4A expression predict reduced survival in carcinoma of the anterior tongue. Clin. Cancer Res. 1999 Oct; 5(10): 2810–2819. PubMed Abstract\n\nAngadi PV, Krishnapillai R: Cyclin D1 expression in oral squamous cell carcinoma and verrucous carcinoma: correlation with histological differentiation. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2007 Mar 1; 103(3): e30–e35. PubMed Abstract \| Publisher Full Text" }	[ { "id": "253012", "date": "07 May 2024", "name": "KIRAN JADHAV", "expertise": [ "Reviewer Expertise Oral and Maxillofacial Pathology", "Oral Cancer", "Lymph node metastasis in Oral cancer", "micro RNA in Saliva", "Oral exfoliative cytology" ], "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 major issues with article are as follows:\nIf it is a protocol then the aim and objectives, and material methodology should be written in future tense.\n\nIn the introduction the authors should address the gap of knowledge in the literature so that the rationale of the study will be clear.\n\nDiscussion should not be just a literature review, the authors should justify results with reference to previously published literature.\n\nMinor points:\nThe title of article is misleading and it does not match with the objectives of study.\n\nThe abstract can be rewritten to highlight the importance of the study, describing a succinct summary of the study.\n\nThe sample calculation references are not necessary to include in the manuscript text.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1096

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