Pub Date : 2024-08-09DOI: 10.12688/f1000research.151662.1
T. Cuisiniere, Manuela M Santos
Background Microbial communities are mainly composed of bacteria, archaea, viruses and fungi, and are present in the gut, mouth, nose, skin, lungs, vagina, and bladder, among other places. In recent years, research has highlighted the critical role that these highly complex communities play in health and disease. Advances in sequencing technology have resulted in the development of high-dimensional data, which are challenging to effectively analyze and visualize. In this context, traditional stacked bar-plot visualizations, while widely used, fall short of conveying the fundamental phylogenic relationships between community members and are thus difficult to interpret. Methods StackbarExtended is implemented in native R, required version (≥ 4.0), and is platform independent, with its source code available on GitHub and archived on Zenodo. Results StackbarExtended allows for the plotting of relative abundance at user-defined taxonomic levels while displaying phylogenetic information using color gradients. Additionally, StackbarExtended integrates differential abundance statistics directly into the visualization process and performs clustering of low-abundance taxa. Conclusions StackbarExtended offers researchers a user-friendly tool for rapid visualization, presentation, and analysis of the microbiota composition.
{"title":"StackbarExtended: a user-friendly stacked bar-plot representation incorporating phylogenetic information and microbiota differential abundance analysis","authors":"T. Cuisiniere, Manuela M Santos","doi":"10.12688/f1000research.151662.1","DOIUrl":"https://doi.org/10.12688/f1000research.151662.1","url":null,"abstract":"Background Microbial communities are mainly composed of bacteria, archaea, viruses and fungi, and are present in the gut, mouth, nose, skin, lungs, vagina, and bladder, among other places. In recent years, research has highlighted the critical role that these highly complex communities play in health and disease. Advances in sequencing technology have resulted in the development of high-dimensional data, which are challenging to effectively analyze and visualize. In this context, traditional stacked bar-plot visualizations, while widely used, fall short of conveying the fundamental phylogenic relationships between community members and are thus difficult to interpret. Methods StackbarExtended is implemented in native R, required version (≥ 4.0), and is platform independent, with its source code available on GitHub and archived on Zenodo. Results StackbarExtended allows for the plotting of relative abundance at user-defined taxonomic levels while displaying phylogenetic information using color gradients. Additionally, StackbarExtended integrates differential abundance statistics directly into the visualization process and performs clustering of low-abundance taxa. Conclusions StackbarExtended offers researchers a user-friendly tool for rapid visualization, presentation, and analysis of the microbiota composition.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.12688/f1000research.154400.1
Mohamed Mustaf Ahmed, Hodo Aideed Asowe, N. I. Dirie, Abdirahman Khalif Mohamud, Don Eliseo Lucero-Prisno, III, O. Okesanya, J. Ogaya, Shuaibu Saidu Musa, Muhammad Kabir Musa, Z. Othman, D. Shomuyiwa, Abdullateef Abdulsalam
Climate change poses a significant threat to Somalia’s food security and stability. This review examines the complex interplay between climate change impacts, food insecurity, and conflict in Somalia. Recent climate data and forecasts paint a concerning picture: the rainfall probabilistic forecast for April- June 2024 indicates a high likelihood of above-normal rainfall across much of Somalia, thus increasing the flood risks. Concurrently, temperature forecasts project above-normal temperatures, potentially exacerbating drought conditions between the rainy seasons. Historical climatology data reveal Somalia’s vulnerability, with average temperatures ranging from 25°C to 30°C and significant seasonal variations affecting agriculture and water resources. These climate trends, combined with ongoing political instability and weak governance, have created a storm of challenges. This perspective explores how recurrent droughts and floods disrupt agricultural production, decimate livestock, and displace vulnerable populations, particularly those affecting rural and nomadic communities. It also examines how environmental stress exacerbates poverty and conflict, thereby creating a vicious cycle of vulnerability. This analysis draws on recent data on poverty rates, food expenditure patterns, and climate-related displacement, to illustrate the multifaceted nature of the crisis. Finally, this perspective proposed recommendations for building climate resilience, enhancing food security, and promoting sustainable development in Somalia, emphasizing the need for integrated approaches that combine immediate humanitarian assistance with long-term adaptation strategies.
{"title":"The Nexus of Climate Change, Food Insecurity, and Conflict in Somalia: A Comprehensive Analysis of Multifaceted Challenges and Resilience Strategies","authors":"Mohamed Mustaf Ahmed, Hodo Aideed Asowe, N. I. Dirie, Abdirahman Khalif Mohamud, Don Eliseo Lucero-Prisno, III, O. Okesanya, J. Ogaya, Shuaibu Saidu Musa, Muhammad Kabir Musa, Z. Othman, D. Shomuyiwa, Abdullateef Abdulsalam","doi":"10.12688/f1000research.154400.1","DOIUrl":"https://doi.org/10.12688/f1000research.154400.1","url":null,"abstract":"Climate change poses a significant threat to Somalia’s food security and stability. This review examines the complex interplay between climate change impacts, food insecurity, and conflict in Somalia. Recent climate data and forecasts paint a concerning picture: the rainfall probabilistic forecast for April- June 2024 indicates a high likelihood of above-normal rainfall across much of Somalia, thus increasing the flood risks. Concurrently, temperature forecasts project above-normal temperatures, potentially exacerbating drought conditions between the rainy seasons. Historical climatology data reveal Somalia’s vulnerability, with average temperatures ranging from 25°C to 30°C and significant seasonal variations affecting agriculture and water resources. These climate trends, combined with ongoing political instability and weak governance, have created a storm of challenges. This perspective explores how recurrent droughts and floods disrupt agricultural production, decimate livestock, and displace vulnerable populations, particularly those affecting rural and nomadic communities. It also examines how environmental stress exacerbates poverty and conflict, thereby creating a vicious cycle of vulnerability. This analysis draws on recent data on poverty rates, food expenditure patterns, and climate-related displacement, to illustrate the multifaceted nature of the crisis. Finally, this perspective proposed recommendations for building climate resilience, enhancing food security, and promoting sustainable development in Somalia, emphasizing the need for integrated approaches that combine immediate humanitarian assistance with long-term adaptation strategies.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141924767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.12688/f1000research.154408.1
Jeremy Y. Ng, Henry Liu, Mehvish Masood, Rubaina Farin, Mireille Messih, Amaya Perez, I. J. Aalbersberg, J. Alperin, Gregory L. Bryson, Qiuxia Chen, Alan Ehrlich, Alfonso Iorio, Wim J. N. Meester, John M. Willinsky, Agnes Grudniewicz, Erik Cobo, Imogen Cranston, Phaedra E Cress, Julia Gunn, R. Haynes, B. S. Keenoo, Ana Marušić, Eleanor-Rose Papas, Alan Purvis, João de Deus Barreto Segundo, P. R. Shankar, P. Stoev, Josephine Weisflog, Margaret Winker, K. Cobey, D. Moher
Background We propose the creation of a journal transparency tool (JTT), which will allow users to obtain information about a given scholarly journal’s operations and policies. We are obtaining preferences from different stakeholders to inform the development of this tool. This study aimed to identify the publishing community’s preferences for the JTT. Methods We conducted a modified three-round Delphi survey. Representatives from publishing houses and journal publishers were recruited through purposeful and snowball sampling. The first two Delphi rounds involved an online survey with items about JTT metrics and user features. During the third round, participants discussed and voted on JTT metric items that did not reach consensus after round 2 within a virtual consensus meeting. We defined consensus as 80% agreement to include or exclude an item in the JTT. Results Eighty-six participants completed the round 1 survey, and 43 participants (50% of round 1) completed the round 2 survey. In both rounds, respondents voted on JTT user feature and JTT metric item preferences and answered open-ended survey questions regarding the JTT. In round 3, a total of 21 participants discussed and voted on JTT metric items that did not reach consensus after round 2 during an online consensus group meeting. Fifteen out of 30 JTT metric items and none of the four JTT user feature items reached the 80% consensus threshold after all rounds of voting. Analysis of the round 3 online consensus group transcript resulted in two themes: ‘factors impacting support for JTT metrics’ and ‘suggestions for user clarity.’ Conclusions Participants suggested that the publishing community’s primary concerns for a JTT are to ensure that the tool is relevant, user-friendly, accessible, and equitable. The outcomes of this research will contribute to developing and refining the tool in accordance with publishing preferences.
{"title":"Publisher preferences for a journal transparency tool: A modified three-round Delphi study","authors":"Jeremy Y. Ng, Henry Liu, Mehvish Masood, Rubaina Farin, Mireille Messih, Amaya Perez, I. J. Aalbersberg, J. Alperin, Gregory L. Bryson, Qiuxia Chen, Alan Ehrlich, Alfonso Iorio, Wim J. N. Meester, John M. Willinsky, Agnes Grudniewicz, Erik Cobo, Imogen Cranston, Phaedra E Cress, Julia Gunn, R. Haynes, B. S. Keenoo, Ana Marušić, Eleanor-Rose Papas, Alan Purvis, João de Deus Barreto Segundo, P. R. Shankar, P. Stoev, Josephine Weisflog, Margaret Winker, K. Cobey, D. Moher","doi":"10.12688/f1000research.154408.1","DOIUrl":"https://doi.org/10.12688/f1000research.154408.1","url":null,"abstract":"Background We propose the creation of a journal transparency tool (JTT), which will allow users to obtain information about a given scholarly journal’s operations and policies. We are obtaining preferences from different stakeholders to inform the development of this tool. This study aimed to identify the publishing community’s preferences for the JTT. Methods We conducted a modified three-round Delphi survey. Representatives from publishing houses and journal publishers were recruited through purposeful and snowball sampling. The first two Delphi rounds involved an online survey with items about JTT metrics and user features. During the third round, participants discussed and voted on JTT metric items that did not reach consensus after round 2 within a virtual consensus meeting. We defined consensus as 80% agreement to include or exclude an item in the JTT. Results Eighty-six participants completed the round 1 survey, and 43 participants (50% of round 1) completed the round 2 survey. In both rounds, respondents voted on JTT user feature and JTT metric item preferences and answered open-ended survey questions regarding the JTT. In round 3, a total of 21 participants discussed and voted on JTT metric items that did not reach consensus after round 2 during an online consensus group meeting. Fifteen out of 30 JTT metric items and none of the four JTT user feature items reached the 80% consensus threshold after all rounds of voting. Analysis of the round 3 online consensus group transcript resulted in two themes: ‘factors impacting support for JTT metrics’ and ‘suggestions for user clarity.’ Conclusions Participants suggested that the publishing community’s primary concerns for a JTT are to ensure that the tool is relevant, user-friendly, accessible, and equitable. The outcomes of this research will contribute to developing and refining the tool in accordance with publishing preferences.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.12688/f1000research.152917.1
Rasha Abdul Jabbar Najim, Batool Hassan Al Ghurabi
Background To evaluate the NETosis biomarkers citrullinated histone H3 (citH3), neutrophil elastase (ELA), calprotectin (CALPRO), and myeloperoxidase (MPO) as indicators of inflammation in the severe stages of periodontitis III and IV in both (smokers and nonsmokers) patients, and to determine the correlation between NETosis biomarkers and clinical periodontal parameters. Methods This study recruited male subjects with an age range of (20-60) years; 60 were stage III and stage IV periodontitis patients, 30 were cigarette smoker, and 30 were nonsmokers. After applying the inclusion and exclusion criteria to evaluate their eligibility for recruitment, 25 control subjects with a healthy periodontal status and good oral hygiene maintenance were included. Unstimulated saliva was obtained and evaluated using an enzyme-linked immunosorbent assay, and the following periodontal parameters were documented: [plaque index, bleeding on probing, periodontal pocket depth, and clinical attachment loss]. Results The mean levels of all salivary NETosis biomarkers citH3, ELA, CALPRO, and MPO were elevated in the periodontitis groups (smokers and nonsmokers) than in controls. Moreover, the mean NETosis biomarker‘s mean levels were significantly higher in smoker than in nonsmokers. In addition, the correlations were significant between CALPRO and CitH3 in smokers and between ELA and CitH3 in nonsmokers. Conclusions The results of this study showed that the chosen salivary biomarkers of NETosis revealed elevated clinical accuracy in differentiating the studied periodontitis groups (smokers and nonsmokers) from controls. In addition, cigarette smoking increases the risk of periodontitis, and neutrophils in smokers with periodontitis exhibited more susceptibility to form neutrophil extracellular traps when compared with nonsmokers.
背景 目的 评估作为炎症指标的NETosis生物标志物瓜氨酸组蛋白H3（citH3）、中性粒细胞弹性蛋白酶（ELA）、钙蛋白（CALPRO）和髓过氧化物酶（MPO）在严重牙周炎III期和IV期患者（吸烟者和非吸烟者）中的作用，并确定NETosis生物标志物与临床牙周参数之间的相关性。方法 本研究招募了年龄在（20-60）岁之间的男性受试者，其中 60 人为 III 期和 IV 期牙周炎患者，30 人为吸烟者，30 人为不吸烟者。在采用纳入和排除标准评估受试者的招募资格后，还纳入了 25 名牙周健康、口腔卫生保持良好的对照组受试者。采用酶联免疫吸附测定法采集和评估未经刺激的唾液，并记录以下牙周参数：[牙菌斑指数、探诊出血、牙周袋深度和临床附着丧失]。结果 牙周炎组（吸烟者和非吸烟者）所有唾液NETosis生物标志物citH3、ELA、CALPRO和MPO的平均水平均高于对照组。此外，吸烟者的NETosis生物标志物平均水平明显高于非吸烟者。此外，吸烟者的 CALPRO 与 CitH3 之间以及非吸烟者的 ELA 与 CitH3 之间存在显著相关性。结论 本研究结果表明，所选的唾液生物标志物在区分所研究的牙周炎组（吸烟者和非吸烟者）与对照组方面具有较高的临床准确性。此外，吸烟会增加罹患牙周炎的风险，与非吸烟者相比，患有牙周炎的吸烟者体内的中性粒细胞更容易形成中性粒细胞胞外陷阱。
{"title":"Evaluation of NETosis (Neutrophil Extracellular Traps) biomarkers in smokers and nonsmokers periodontitis patientsÂ","authors":"Rasha Abdul Jabbar Najim, Batool Hassan Al Ghurabi","doi":"10.12688/f1000research.152917.1","DOIUrl":"https://doi.org/10.12688/f1000research.152917.1","url":null,"abstract":"Background To evaluate the NETosis biomarkers citrullinated histone H3 (citH3), neutrophil elastase (ELA), calprotectin (CALPRO), and myeloperoxidase (MPO) as indicators of inflammation in the severe stages of periodontitis III and IV in both (smokers and nonsmokers) patients, and to determine the correlation between NETosis biomarkers and clinical periodontal parameters. Methods This study recruited male subjects with an age range of (20-60) years; 60 were stage III and stage IV periodontitis patients, 30 were cigarette smoker, and 30 were nonsmokers. After applying the inclusion and exclusion criteria to evaluate their eligibility for recruitment, 25 control subjects with a healthy periodontal status and good oral hygiene maintenance were included. Unstimulated saliva was obtained and evaluated using an enzyme-linked immunosorbent assay, and the following periodontal parameters were documented: [plaque index, bleeding on probing, periodontal pocket depth, and clinical attachment loss]. Results The mean levels of all salivary NETosis biomarkers citH3, ELA, CALPRO, and MPO were elevated in the periodontitis groups (smokers and nonsmokers) than in controls. Moreover, the mean NETosis biomarker‘s mean levels were significantly higher in smoker than in nonsmokers. In addition, the correlations were significant between CALPRO and CitH3 in smokers and between ELA and CitH3 in nonsmokers. Conclusions The results of this study showed that the chosen salivary biomarkers of NETosis revealed elevated clinical accuracy in differentiating the studied periodontitis groups (smokers and nonsmokers) from controls. In addition, cigarette smoking increases the risk of periodontitis, and neutrophils in smokers with periodontitis exhibited more susceptibility to form neutrophil extracellular traps when compared with nonsmokers.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.12688/f1000research.154704.1
Faizul Hasan, Hendrik Setia Budi, Lia Taurussia Yuliana, Mokh. Sujarwadi
Background Dental caries is a common chronic oral disease, posing a serious public health issue. By analyzing large datasets, machine learning shows potential in addressing this problem. This study employs bibliometric analysis to explore emerging topics, collaborations, key authors, and research trends in Southeast Asia related to the application of machine learning in dental caries management. Methods A comprehensive selection using the Scopus database to obtain relevant research, covering publications from inception to July 2024 was done. We employed the Bibliometric approaches, including co-authorship networks, yearly publishing trends, institutional and national partnerships, keyword co-occurrence analysis, and citation analysis, for the collected data. To explore the visualization and network analysis, we employed the tools such as VOSviewer and Bibliometrix in R package. Results The final bibliometric analysis included 246 papers. We found that Malaysia became the top contributor with 59 publications, followed by Indonesia (37) and Thailand (29). Malaysia had the highest Multiple Country Publications (MCP) ratio at 0.407. Top institutions including the Universiti Sains Malaysia led with 39 articles, followed by Chiang Mai University (36) and the National University of Singapore (30) became the leader. Co-authorship analysis using VOSviewer revealed six distinct clusters. A total of 1220 scholars contributed to these publications. The top 10 keywords, including ‘human’ and ‘dental caries,’ indicated research hotspots. Conclusion We found growing evidence of machine learning applications to address dental caries in Southeast Asia. The bibliometric analysis highlights key authors, collaborative networks, and emerging topics, revealing research trends since 2014. This study underscores the importance of bibliometric analysis in tackling this public health issue.
{"title":"Trends of machine learning for dental caries research in Southeast Asia: insights from a bibliometric analysis","authors":"Faizul Hasan, Hendrik Setia Budi, Lia Taurussia Yuliana, Mokh. Sujarwadi","doi":"10.12688/f1000research.154704.1","DOIUrl":"https://doi.org/10.12688/f1000research.154704.1","url":null,"abstract":"Background Dental caries is a common chronic oral disease, posing a serious public health issue. By analyzing large datasets, machine learning shows potential in addressing this problem. This study employs bibliometric analysis to explore emerging topics, collaborations, key authors, and research trends in Southeast Asia related to the application of machine learning in dental caries management. Methods A comprehensive selection using the Scopus database to obtain relevant research, covering publications from inception to July 2024 was done. We employed the Bibliometric approaches, including co-authorship networks, yearly publishing trends, institutional and national partnerships, keyword co-occurrence analysis, and citation analysis, for the collected data. To explore the visualization and network analysis, we employed the tools such as VOSviewer and Bibliometrix in R package. Results The final bibliometric analysis included 246 papers. We found that Malaysia became the top contributor with 59 publications, followed by Indonesia (37) and Thailand (29). Malaysia had the highest Multiple Country Publications (MCP) ratio at 0.407. Top institutions including the Universiti Sains Malaysia led with 39 articles, followed by Chiang Mai University (36) and the National University of Singapore (30) became the leader. Co-authorship analysis using VOSviewer revealed six distinct clusters. A total of 1220 scholars contributed to these publications. The top 10 keywords, including ‘human’ and ‘dental caries,’ indicated research hotspots. Conclusion We found growing evidence of machine learning applications to address dental caries in Southeast Asia. The bibliometric analysis highlights key authors, collaborative networks, and emerging topics, revealing research trends since 2014. This study underscores the importance of bibliometric analysis in tackling this public health issue.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.12688/f1000research.153399.1
S. Sayhi, Houssem Abida, Yosr Boukhobza, A. Khallouli, A. Maalej, Nadia Ben Abdelhafidh
Introduction Antiphospholipids syndrome is a rare autoimmune whose Clinical manifestations are very wide and different. Vaso-occlusive manifestations are the most frequent ones. Vessels of all organs can be involved. Ocular involvement is among the rarest. We report a case of retinal arterial thrombosis in the context of APS. Case report A 46-year-old patient with no previous medical history was admitted to the ophthalmology department for visual field amputation of the right eye without other associated signs. On the fundus, the left side was without abnormality and the right side was the site of a mixed arterial and superior temporal venous occlusion. Retinal angiography revealed a retinal focus in the superior temporal region with mixed occlusion of arterial and venous branches with ischemia of the superior temporal quadrant on the right and a retinal focus in the superficial inferior temporal region without occlusion on the left. Optical coherence tomography revealed ischemia of the superficial layers with alteration of the macular microvascularization in the right superior temporal quadrant. Immunological work-up showed antinuclear antibodies to be positive at 160 and anti-bgp1 positive with an IgG level of 118 IgM higher than 118 IgA at 101. The patient was put on effective anticoagulation with good clinical evolution. Conclusion Ocular involvement is rare in APS and associated with poor prognosis, it seems to be difficult to diagnose but also to manage. Larger studies are required to establish guidelines on how and when to screen asymptomatic APS patients for ocular damage, but also on how to prevent and treat it.
{"title":"Case Report: Localized retinal ischemia revealing an antiphospholipids syndrome: A case report and review of the literature","authors":"S. Sayhi, Houssem Abida, Yosr Boukhobza, A. Khallouli, A. Maalej, Nadia Ben Abdelhafidh","doi":"10.12688/f1000research.153399.1","DOIUrl":"https://doi.org/10.12688/f1000research.153399.1","url":null,"abstract":"Introduction Antiphospholipids syndrome is a rare autoimmune whose Clinical manifestations are very wide and different. Vaso-occlusive manifestations are the most frequent ones. Vessels of all organs can be involved. Ocular involvement is among the rarest. We report a case of retinal arterial thrombosis in the context of APS. Case report A 46-year-old patient with no previous medical history was admitted to the ophthalmology department for visual field amputation of the right eye without other associated signs. On the fundus, the left side was without abnormality and the right side was the site of a mixed arterial and superior temporal venous occlusion. Retinal angiography revealed a retinal focus in the superior temporal region with mixed occlusion of arterial and venous branches with ischemia of the superior temporal quadrant on the right and a retinal focus in the superficial inferior temporal region without occlusion on the left. Optical coherence tomography revealed ischemia of the superficial layers with alteration of the macular microvascularization in the right superior temporal quadrant. Immunological work-up showed antinuclear antibodies to be positive at 160 and anti-bgp1 positive with an IgG level of 118 IgM higher than 118 IgA at 101. The patient was put on effective anticoagulation with good clinical evolution. Conclusion Ocular involvement is rare in APS and associated with poor prognosis, it seems to be difficult to diagnose but also to manage. Larger studies are required to establish guidelines on how and when to screen asymptomatic APS patients for ocular damage, but also on how to prevent and treat it.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.12688/f1000research.153447.1
Justin Pulford, M. N. Mutua, Imelda Bates, N. Tagoe
‘Research capacity strengthening’ (RCS) is an umbrella term that can be used to describe a wide variety of activities conducted in support of diverse objectives premised upon distinct, potentially opposing, views. Despite this, the ultimate objective of RCS activities is rarely made explicit which can be problematic when diverse objectives are possible. By ‘ultimate’ objective we are referring to the overarching (often long-term) goal an RCS initiative is intended to contribute towards (e.g. better population health) as opposed to the more immediate ‘proximate’ (often short-term) objectives of any such activity (e.g. improved capacity to undertake infectious disease research). We argue a need for those funding, designing and implementing RCS initiatives to make clear statements as to the ultimate objective that they foresee their respective initiative contributing towards as well as the proposed pathway and associated assumptions that underlie their approach. Examples of distinct ultimate objectives for RCS initiatives are presented alongside fictitious examples of how they may be transparently reported from both a funder and implementor perspective. Such transparency should be routine within the scope of funding calls for RCS activities (even when such activities are only a minor component of the call), subsequent applications to those calls and any description of an applied RCS activity/ies and/or the associated outcomes thereof. The process of determining one’s ultimate objective will further cause funders and actors to think through their respective initiatives more thoroughly and make informed choices and better designed RCS projects. Doing so would reduce any ambiguity associated with the use of the term ‘research capacity strengthening’ and would provide a stronger foundation for robust programme evaluation.
{"title":"Articulating the ultimate objectives of research capacity strengthening programmes: Why this is important and how we might achieve it.","authors":"Justin Pulford, M. N. Mutua, Imelda Bates, N. Tagoe","doi":"10.12688/f1000research.153447.1","DOIUrl":"https://doi.org/10.12688/f1000research.153447.1","url":null,"abstract":"‘Research capacity strengthening’ (RCS) is an umbrella term that can be used to describe a wide variety of activities conducted in support of diverse objectives premised upon distinct, potentially opposing, views. Despite this, the ultimate objective of RCS activities is rarely made explicit which can be problematic when diverse objectives are possible. By ‘ultimate’ objective we are referring to the overarching (often long-term) goal an RCS initiative is intended to contribute towards (e.g. better population health) as opposed to the more immediate ‘proximate’ (often short-term) objectives of any such activity (e.g. improved capacity to undertake infectious disease research). We argue a need for those funding, designing and implementing RCS initiatives to make clear statements as to the ultimate objective that they foresee their respective initiative contributing towards as well as the proposed pathway and associated assumptions that underlie their approach. Examples of distinct ultimate objectives for RCS initiatives are presented alongside fictitious examples of how they may be transparently reported from both a funder and implementor perspective. Such transparency should be routine within the scope of funding calls for RCS activities (even when such activities are only a minor component of the call), subsequent applications to those calls and any description of an applied RCS activity/ies and/or the associated outcomes thereof. The process of determining one’s ultimate objective will further cause funders and actors to think through their respective initiatives more thoroughly and make informed choices and better designed RCS projects. Doing so would reduce any ambiguity associated with the use of the term ‘research capacity strengthening’ and would provide a stronger foundation for robust programme evaluation.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-26DOI: 10.12688/f1000research.148453.1
Yada Thadanatthaphak, J. Kanpittaya, Wittawat Takong, Sutin Chanaboon, Kukiat Tudpor
Background Renal blood flow (RBF) is regulated by an autonomic nervous system and is reduced in older adults. Massage has been previously found to increase blood flow. Objective This two-armed double-blind, randomized controlled trial aimed to investigate the immediate effects of Thai foot massage (TFM) on RBF, psychological stress, and heart rate variability (HRV) in older adult persons. Material and Methods The 26 healthy older adult volunteers were recruited and randomly assigned to the TFM group (13 persons) and the control group (13 persons). The TFM group received a 15-minute Thai foot massage, and the control group received a 15-minute bed rest. Primary outcomes – RBF parameters [peak systolic velocity (PSV), end-diastolic velocity (EDV), resistive index (RI), volumetric arterial blood flow (VF)] and secondary outcomes – HRV parameters [standard deviation of the normal-to-normal intervals (SDNN), root mean square of successive differences (RMSSD), high frequency (HF), low frequency (LF), and low frequency per high frequency (LF/HF)] were measured after each intervention. Results Results showed that the VF significantly increased after TFM (P < 0.05) but not in control. Meanwhile, the stress index significantly reduced after TFM (P < 0.05). SDNN and RMSSD, the proxies of parasympathetic activity, also significantly increased in the TFM group (p < 0.05). Only RMSSD was significantly enhanced in the control group. No side effects were observed. Conclusion The TFM could increase RBF and alleviate psychological stress through parasympathetic activity actuation. Therefore, this intervention might improve RBF and relieve stress in the older population. Further study should be carried out on a larger population.
{"title":"Immediate effects of Thai foot massage on renal blood flow, psychological stress, and heart rate variability in community-dwelling older adults: a randomized controlled trial","authors":"Yada Thadanatthaphak, J. Kanpittaya, Wittawat Takong, Sutin Chanaboon, Kukiat Tudpor","doi":"10.12688/f1000research.148453.1","DOIUrl":"https://doi.org/10.12688/f1000research.148453.1","url":null,"abstract":"Background Renal blood flow (RBF) is regulated by an autonomic nervous system and is reduced in older adults. Massage has been previously found to increase blood flow. Objective This two-armed double-blind, randomized controlled trial aimed to investigate the immediate effects of Thai foot massage (TFM) on RBF, psychological stress, and heart rate variability (HRV) in older adult persons. Material and Methods The 26 healthy older adult volunteers were recruited and randomly assigned to the TFM group (13 persons) and the control group (13 persons). The TFM group received a 15-minute Thai foot massage, and the control group received a 15-minute bed rest. Primary outcomes – RBF parameters [peak systolic velocity (PSV), end-diastolic velocity (EDV), resistive index (RI), volumetric arterial blood flow (VF)] and secondary outcomes – HRV parameters [standard deviation of the normal-to-normal intervals (SDNN), root mean square of successive differences (RMSSD), high frequency (HF), low frequency (LF), and low frequency per high frequency (LF/HF)] were measured after each intervention. Results Results showed that the VF significantly increased after TFM (P < 0.05) but not in control. Meanwhile, the stress index significantly reduced after TFM (P < 0.05). SDNN and RMSSD, the proxies of parasympathetic activity, also significantly increased in the TFM group (p < 0.05). Only RMSSD was significantly enhanced in the control group. No side effects were observed. Conclusion The TFM could increase RBF and alleviate psychological stress through parasympathetic activity actuation. Therefore, this intervention might improve RBF and relieve stress in the older population. Further study should be carried out on a larger population.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141798640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-26DOI: 10.12688/f1000research.151896.1
Daniela Montoya-Urrego, J. M. Vanegas, J. N. Jiménez, Difariney González-Gómez
Background Hemodialysis patients are frequently colonized by Staphylococcus aureus, leading to severe infections with high mortality rates. However, little is known about transition from non-colonization to colonization or bacteremia over time. The aim was to analyze the behavior of S. aureus colonization, identifying the probability of transition from non-colonized to colonized state or bacteremia, and the influence of some covariates. Methods The study was conducted in a dialysis unit associated with a high complexity hospital in Medellín between October 2017 and October 2019. An initial measurement was taken to evaluate S. aureus colonization, and follow-up measurements were performed 2 and 6 months later. Bacteremia evolution was monitored for 12 months. A two-state recurrent continuous-time Markov model was constructed to model transition dynamics from non-colonization to S. aureus colonization in hemodialysis patients. Subsequently, the model was applied to a third state of bacteremia. Results Of 178 patients on hemodialysis, 30.3% were colonized by S. aureus. Transition intensity from non-colonization to colonization was three times higher (0.21; CI: 0.14-0.29) than from colonization to non-colonization (0.07; CI: 0.05-0.11). The colonization risk increased in patients with previous infections (HR: 2.28; CI: 0.78-6.68), hospitalization (HR: 1.29; CI: 0.56-2.99) and antibiotics consumption (HR: 1.17; CI: 0.53-2.58). Mean non-colonized state duration was 10.9 months, while in the colonized state was 5.2 months. In the 3-state model, it was found that patients colonized were more likely to develop S. aureus infection (13.9%). Conclusion A more likely transition from non-colonization to colonization was found, which increases with factors such as previous infection. In addition, the development of bacteremia was more likely in colonized than in non-colonized patients. These results underline the importance of surveillance and proper management of S. aureus colonization to prevent serious complications, such as bacteremia, and improve prognosis in this vulnerable population.
{"title":"Analysis of the dynamics of transition from non-colonization to colonization and Staphylococcus aureus bacteremia in hemodialysis patients using Markov models.","authors":"Daniela Montoya-Urrego, J. M. Vanegas, J. N. Jiménez, Difariney González-Gómez","doi":"10.12688/f1000research.151896.1","DOIUrl":"https://doi.org/10.12688/f1000research.151896.1","url":null,"abstract":"Background Hemodialysis patients are frequently colonized by Staphylococcus aureus, leading to severe infections with high mortality rates. However, little is known about transition from non-colonization to colonization or bacteremia over time. The aim was to analyze the behavior of S. aureus colonization, identifying the probability of transition from non-colonized to colonized state or bacteremia, and the influence of some covariates. Methods The study was conducted in a dialysis unit associated with a high complexity hospital in Medellín between October 2017 and October 2019. An initial measurement was taken to evaluate S. aureus colonization, and follow-up measurements were performed 2 and 6 months later. Bacteremia evolution was monitored for 12 months. A two-state recurrent continuous-time Markov model was constructed to model transition dynamics from non-colonization to S. aureus colonization in hemodialysis patients. Subsequently, the model was applied to a third state of bacteremia. Results Of 178 patients on hemodialysis, 30.3% were colonized by S. aureus. Transition intensity from non-colonization to colonization was three times higher (0.21; CI: 0.14-0.29) than from colonization to non-colonization (0.07; CI: 0.05-0.11). The colonization risk increased in patients with previous infections (HR: 2.28; CI: 0.78-6.68), hospitalization (HR: 1.29; CI: 0.56-2.99) and antibiotics consumption (HR: 1.17; CI: 0.53-2.58). Mean non-colonized state duration was 10.9 months, while in the colonized state was 5.2 months. In the 3-state model, it was found that patients colonized were more likely to develop S. aureus infection (13.9%). Conclusion A more likely transition from non-colonization to colonization was found, which increases with factors such as previous infection. In addition, the development of bacteremia was more likely in colonized than in non-colonized patients. These results underline the importance of surveillance and proper management of S. aureus colonization to prevent serious complications, such as bacteremia, and improve prognosis in this vulnerable population.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141800814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-26DOI: 10.12688/f1000research.143777.1
Eva María Ventura Hernández, Marco Antonio Nolasco-Mamani, Domingo Hernández Celis, Julian Monrroy Aime, Efraín Jaime Guardia Huamani
Background The micro, small and medium-sized enterprises (SMEs) play a pivotal role in the Latin America economy, creating jobs, boosting local economic activity and contribute to the socio-economic development of the region. The purpose is to reflect on the current costs management prices, the common challenges faced by SMEs in the region, and effective strategies to improve the profitability and sustainability of these companies. Methods it is addressed as a review study of type reflective, which used the dialectic as a method for the construction of the speech, based on techniques of triangulation of information. Result in order to obtain the results, these study topics were pre-selected: (a) determinants of the costs of production in the SMES, b) strategies for the reduction and control of production costs, and c) impact of production costs on the profitability of SMES. Conclusion the present research article delves into the pivotal factors influencing production costs within microenterprises and small businesses situated in the Latin American context. This study posits that the determinants underpinning these costs encompass a spectrum of elements including but not limited to labor, raw materials and supplies, energy and utilities, infrastructure and logistics, regulatory frameworks, and administrative intricacies. Furthermore, the intricate interplay of technology adoption and innovative capabilities is also recognized as a crucial facet in this cost determination paradigm. The overarching understanding underscores the direct and substantial influence of these multifaceted determinants on the operational expenditure of microenterprises and small businesses.
{"title":"Production costs and their effect on the profitability of the SMES in Latin America","authors":"Eva María Ventura Hernández, Marco Antonio Nolasco-Mamani, Domingo Hernández Celis, Julian Monrroy Aime, Efraín Jaime Guardia Huamani","doi":"10.12688/f1000research.143777.1","DOIUrl":"https://doi.org/10.12688/f1000research.143777.1","url":null,"abstract":"Background The micro, small and medium-sized enterprises (SMEs) play a pivotal role in the Latin America economy, creating jobs, boosting local economic activity and contribute to the socio-economic development of the region. The purpose is to reflect on the current costs management prices, the common challenges faced by SMEs in the region, and effective strategies to improve the profitability and sustainability of these companies. Methods it is addressed as a review study of type reflective, which used the dialectic as a method for the construction of the speech, based on techniques of triangulation of information. Result in order to obtain the results, these study topics were pre-selected: (a) determinants of the costs of production in the SMES, b) strategies for the reduction and control of production costs, and c) impact of production costs on the profitability of SMES. Conclusion the present research article delves into the pivotal factors influencing production costs within microenterprises and small businesses situated in the Latin American context. This study posits that the determinants underpinning these costs encompass a spectrum of elements including but not limited to labor, raw materials and supplies, energy and utilities, infrastructure and logistics, regulatory frameworks, and administrative intricacies. Furthermore, the intricate interplay of technology adoption and innovative capabilities is also recognized as a crucial facet in this cost determination paradigm. The overarching understanding underscores the direct and substantial influence of these multifaceted determinants on the operational expenditure of microenterprises and small businesses.","PeriodicalId":504605,"journal":{"name":"F1000Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141799374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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