F1000ResearchPub Date : 2025-07-21eCollection Date: 2025-01-01DOI: 10.12688/f1000research.165543.1
Charlotte Hutchings, Thomas Krueger, Oliver M Crook, Laurent Gatto, Kathryn S Lilley, Lisa M Breckels
{"title":"An updated Bioconductor workflow for correlation profiling subcellular proteomics.","authors":"Charlotte Hutchings, Thomas Krueger, Oliver M Crook, Laurent Gatto, Kathryn S Lilley, Lisa M Breckels","doi":"10.12688/f1000research.165543.1","DOIUrl":"10.12688/f1000research.165543.1","url":null,"abstract":"<p><strong>Background: </strong>Subcellular localisation is a determining factor of protein function. Mass spectrometry-based correlation profiling experiments facilitate the classification of protein subcellular localisation on a proteome-wide scale. In turn, static localisations can be compared across conditions to identify differential protein localisation events.</p><p><strong>Methods: </strong>Here, we provide a workflow for the processing and analysis of subcellular proteomics data derived from mass spectrometry-based correlation profiling experiments. This workflow utilises open-source R software packages from the Bioconductor project and provides extensive discussion of the key processing steps required to achieve high confidence protein localisation classifications and differential localisation predictions. The workflow is applicable to any correlation profiling data and supplementary code is provided to help users adapt the workflow to DDA and DIA data processed with different database softwares.</p><p><strong>Results: </strong>The workflow is divided into three sections. First we outline data processing using the QFeatures infrastructure to generate high quality protein correlation profiles. Next, protein subcellular localisation classification is carried out using machine learning. Finally, prediction of differential localisation events is covered for dynamic correlation profiling experiments.</p><p><strong>Conclusions: </strong>A comprehensive start-to-end workflow for correlation profiling subcellular proteomics experiments is presented. <b>R version</b>: R version 4.5.0 (2025-04-11) <b>Bioconductor version</b>: 3.21.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"714"},"PeriodicalIF":0.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12419147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F1000ResearchPub Date : 2025-07-18eCollection Date: 2023-01-01DOI: 10.12688/f1000research.143189.3
Makrem Soudani, Faical Farhat, Amine Ghram, Helmi Ben Saad, Mehdi Chlif
{"title":"Acute effects of virtual reality exercise bike games on psychophysiological outcomes in college North-African adolescents with cerebral palsy: A randomized clinical trial.","authors":"Makrem Soudani, Faical Farhat, Amine Ghram, Helmi Ben Saad, Mehdi Chlif","doi":"10.12688/f1000research.143189.3","DOIUrl":"10.12688/f1000research.143189.3","url":null,"abstract":"<p><strong>Background: </strong>Cerebral palsy (CP) is a neurological disorder that can affect motor skills and psychophysiological well-being. Virtual Reality Exercise (VRE) improves cognitive and physical outcomes in patients with CP. Therefore, this study aimed to investigate the effects of VRE on attention, vigor, and decision-making abilities in adolescents with CP.</p><p><strong>Methods: </strong>A randomized controlled trial was conducted. The intervention consisted of a single 40-minute session of VRE compared to TE conducted in a controlled laboratory environment.</p><p><strong>Results: </strong>Fourteen participants (42.9 % female) were included in this analysis. The results indicated that VRE had a statistically significant positive effect on attention and vigor compared to TE. While participants in the VRE group exhibited enhanced attention levels and reported elevated levels of vigor subsequent to the exercise sessions, the memory results did not reach statistical significance.</p><p><strong>Conclusions: </strong>The findings suggest that VRE is an effective intervention for improving attention and vigor in adolescents with CP.</p><p><strong>Registration: </strong>Pan African Clinical Trial Registry (PACTR202308598603482; 31/08/2023). The trial was reported in accordance with the CONSORT reporting guidelines.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"12 ","pages":"1597"},"PeriodicalIF":0.0,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11745216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F1000ResearchPub Date : 2025-07-18eCollection Date: 2025-01-01DOI: 10.12688/f1000research.164227.3
Guillaume Ngoie Mwamba, Michel Kabamba Nzaji, Oscar Luboya Numbi, Mala Ali Mapatano, Paul-Samson Lusamba Dikassa
{"title":"Micronutrient and protein-energy supplementation enhance vaccine responses in undernourished children: Evidence from a systematic review.","authors":"Guillaume Ngoie Mwamba, Michel Kabamba Nzaji, Oscar Luboya Numbi, Mala Ali Mapatano, Paul-Samson Lusamba Dikassa","doi":"10.12688/f1000research.164227.3","DOIUrl":"10.12688/f1000research.164227.3","url":null,"abstract":"<p><strong>Background: </strong>Malnutrition impairs immune function and vaccine responses, particularly in low-income settings. This can lead to reduced seroconversion rates and compromised herd immunity in children. Nutritional interventions have been proposed to enhance vaccine immunogenicity, yet evidence remains scattered and context specific.</p><p><strong>Objective: </strong>This systematic review assesses the impact of nutritional interventions-especially vitamin A, zinc supplementation, and protein-energy rehabilitation-on serological responses to routine childhood vaccines among malnourished children in low- and middle-income countries.</p><p><strong>Methods: </strong>Following PRISMA guidelines, we searched PubMed, Embase, Cochrane Library, and WHO Global Health Library for studies published between 2000 and 2024. Eligible studies included randomized trials, cohort studies, and systematic reviews reporting on nutritional supplementation and vaccine seroconversion outcomes in malnourished children.</p><p><strong>Results: </strong>From 3,245 records, 42 studies met the inclusion criteria. Vitamin A supplementation improved measles vaccine seroconversion by 35%, especially among deficient children. Zinc enhanced responses to oral vaccines by 20%. Protein-energy rehabilitation significantly increased seroconversion rates for BCG and measles vaccines, particularly in children recovering from severe acute malnutrition.</p><p><strong>Conclusion: </strong>Nutritional interventions improve vaccine immunogenicity among malnourished children. Integrated strategies combining immunization and nutrition services should be prioritized to address immunity gaps in vulnerable populations.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"507"},"PeriodicalIF":0.0,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12334918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F1000ResearchPub Date : 2025-07-17eCollection Date: 2024-01-01DOI: 10.12688/f1000research.146982.2
Ni Made Renny Anggreni Rena, I Made Bakta, Ketut Suega
{"title":"High Levels of Soluble P-selectin, Neutrophil Extracellular Traps, and Myeloperoxidase as Risk Factor of Deep Vein Thrombosis in Malignancy Patients Receiving Platinum-Based Chemotherapy.","authors":"Ni Made Renny Anggreni Rena, I Made Bakta, Ketut Suega","doi":"10.12688/f1000research.146982.2","DOIUrl":"10.12688/f1000research.146982.2","url":null,"abstract":"<p><strong>Backgrounds: </strong>Venous Thromboembolism (VTE) is a disease entity comprising Deep Vein Thrombosis (DVT) and Pulmonary Embolism (PE). VTE events increase the mortality rate of patients with cancer receiving platinum-based chemotherapy. Soluble P-Selectin, Neutrophil Extracellular Traps (NET), and myeloperoxidase (MPO) are risk factors associated with DVT in malignancy patients receiving platinum-based chemotherapy. The purpose of this study was to determine the role of soluble P-selectin, NET, and MPO as risk factors for DVT in patients with malignancy receiving platinum-based chemotherapy.</p><p><strong>Patients and methods: </strong>This study used a case-control design (matched pair case-control study) based on age and gender. The case group consisted of subjects with DVT, whereas the control group consisted of subjects without DVT. The subjects were 31 in each case and control groups. Soluble P-selectin, NET, and MPO levels were measured in each group.</p><p><strong>Results: </strong>The mean age of case group was 50.26±12.15 years meanwhile in control group was 52.81±11.64 years. In the case group, 71% of the subjects were female, whereas 51.6% of the control group were male. Most subjects, either in the case group (71%) or the control group (71%), used carboplatin. In the case group, cervix malignancy was the most common malignancy (32.3%), whereas in the control group, it was nasopharyngeal malignancy (25.8%). High soluble P-selectin level was a risk factor for DVT (OR 3.38, CI 1.180 - 9.780, p=0.02). A high NET level was also a risk factor for DVT (OR 2.88, CI 1.026-8.074, p=0.04). The high MPO levels in this study could not be proven as a risk factor.</p><p><strong>Conclusions: </strong>Soluble P-selectin and NET are risk factors that play a role in the pathophysiology of DVT through the pathomechanism of immunothrombosis induced by endothelial injury and activation of monocytes and neutrophils due to the use of platinum-based chemotherapy.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"427"},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11729192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Progress and challenges for the application of machine learning for neglected tropical diseases.","authors":"ChungYuen Khew, Rahmad Akbar, Norfarhan Mohd-Assaad","doi":"10.12688/f1000research.129064.3","DOIUrl":"10.12688/f1000research.129064.3","url":null,"abstract":"<p><p>Neglected tropical diseases (NTDs) continue to affect the livelihood of individuals in countries in the Southeast Asia and Western Pacific region. These diseases have been long existing and have caused devastating health problems and economic decline to people in low- and middle-income (developing) countries. An estimated 1.7 billion of the world's population suffer one or more NTDs annually, this puts approximately one in five individuals at risk for NTDs. In addition to health and social impact, NTDs inflict significant financial burden to patients, close relatives, and are responsible for billions of dollars lost in revenue from reduced labor productivity in developing countries alone. There is an urgent need to better improve the control and eradication or elimination efforts towards NTDs. This can be achieved by utilizing machine learning tools to better the surveillance, prediction and detection program, and combat NTDs through the discovery of new therapeutics against these pathogens. This review surveys the current application of machine learning tools for NTDs and the challenges to elevate the state-of-the-art of NTDs surveillance, management, and treatment.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"12 ","pages":"287"},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12242132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F1000ResearchPub Date : 2025-07-16eCollection Date: 2025-01-01DOI: 10.12688/f1000research.161540.2
Saeid Motevalli, Rogayah A Razak, Richard Peter Bailey, Amalia B Madihie, Katayoun Mehdinezhadnouri, Yifei Pan
{"title":"Parents' Sharenting Behaviours: A Systematic Review of Motivations, Attitudes, Perceptions, and Impression Management Perspectives.","authors":"Saeid Motevalli, Rogayah A Razak, Richard Peter Bailey, Amalia B Madihie, Katayoun Mehdinezhadnouri, Yifei Pan","doi":"10.12688/f1000research.161540.2","DOIUrl":"10.12688/f1000research.161540.2","url":null,"abstract":"<p><strong>Introduction: </strong>Sharenting involves parents sharing photos, videos, or other information about their children on their social media profiles via online platforms. Research indicated the rising prevalence of parental sharenting behaviour among various countries.</p><p><strong>Objective: </strong>The main aim of this article was to explore the role of motivations, perceptions, attitudes, and impression management on parental sharenting behaviours.</p><p><strong>Methods: </strong>A systematic review examined empirical studies published from 2019 to 2024 regarding parental motivations, attitudes, perceptions, and impression management associated with sharenting. Relevant studies were identified via Scopus and manual reference searches, with data extraction concentrating on study characteristics, demographics, objectives, design, and principal findings.</p><p><strong>Findings: </strong>Parental sharenting is motivated by intrinsic desires, social validation, and impression management, as parents curate content to improve their social image. While children value favourable representations, many object to sharing without consent. Notwithstanding privacy concerns, parents frequently prioritise advantages, raising ethical enquiries regarding children's autonomy, privacy, and digital identity in digital self-representation.</p><p><strong>Conclusion: </strong>Parental sharenting, motivated by emotional satisfaction, social validation, and impression management, frequently neglects privacy risks and ethical considerations. Such practices may compromise children's autonomy, privacy, and digital identity, resulting in conflicts with their rights. Children's varied responses underscore these dilemmas, highlighting the necessity of reconciling parental intentions with safeguarding children's digital futures and overall well-being.</p><p><strong>Recommendation: </strong>Parents should engage in mindful sharenting, policymakers must safeguard children's digital rights, professionals should enhance awareness, and researchers should investigate methods to reconcile parental desires with children's welfare.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"448"},"PeriodicalIF":0.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12344405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144845072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dual tasking as a predictor of falls in post-stroke: A cross-sectional analysis comparing Walking While Talking versus Stops Walking While Talking.","authors":"Disha Lamba, Abraham M Joshua, Vijaya Kumar K, Akshatha Nayak, Prasanna Mithra, Rohit Pai, Shivananda Pai, Shyam Krishnan K, Vijayakumar Palaniswamy","doi":"10.12688/f1000research.158764.3","DOIUrl":"10.12688/f1000research.158764.3","url":null,"abstract":"<p><strong>Background: </strong>Dual-task assessments, including Walking While Talking (WWT) and Stops Walking While Talking (SWWT) tests, predict fall risk in stroke survivors. However, their effectiveness relative to established predictors, such as the Berg Balance Scale (BBS) and Falls Efficacy Scale (FES), remains unclear. This study evaluated the comparative predictive value of WWT and SWWT tests alongside BBS and FES among stroke survivors.</p><p><strong>Methods: </strong>This cross-sectional study included 68 stroke survivors who completed WWT-Simple (WWT-S), WWT-Complex (WWT-C), and SWWT, as well as the BBS and FES. Spearman correlations assessed relationships between balance, fear of falling, and dual-task performance. Logistic regression identified fall risk predictors, and Receiver Operating Characteristic (ROC) analysis evaluated predictive accuracy. The study adhered to STROBE guidelines.</p><p><strong>Results: </strong>BBS scores were strongly negatively correlated with WWT-S (r = -0.734, p < 0.0001) and WWT-C (r = -0.737, p < 0.0001), indicating poorer balance with slower dual-task completion. Positive correlations were found between WWT-S and FES (r = 0.668, p < 0.0001) and WWT-C and FES (r = 0.610, p < 0.0001), linking slower completion times with higher fear of falling. SWWT was significantly negatively correlated with BBS (r = -0.625, p < 0.0001). WWT tests had higher sensitivity (97.8%) and specificity (99%) than SWWT (sensitivity = 68.9%; specificity = 91.3%). Logistic regression identified SWWT (Positive) as a significant predictor of fall risk (p = 0.009), and ROC analysis showed an AUC of 0.911, indicating excellent predictive power.</p><p><strong>Conclusions: </strong>Findings highlight the superior predictive value of WWT tests over SWWT in assessing fall risk among stroke survivors. Incorporating dual-task measures into clinical practice may enhance fall risk evaluation, supporting targeted stroke rehabilitation.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"1395"},"PeriodicalIF":0.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12317310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144774982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F1000ResearchPub Date : 2025-07-16eCollection Date: 2025-01-01DOI: 10.12688/f1000research.162436.2
Jhilik Chakraborty, Arpita Goswami
{"title":"Women and nature: Ecofeminist study in social media.","authors":"Jhilik Chakraborty, Arpita Goswami","doi":"10.12688/f1000research.162436.2","DOIUrl":"https://doi.org/10.12688/f1000research.162436.2","url":null,"abstract":"<p><strong>Background: </strong>This research examines how ecofeminist themes are presented and shared on digital platforms. It focuses on three widely used social media networks, namely YouTube, Instagram, and Facebook to explore how their features, such as videos, reels, posts, and images, convey ecofeminist ideas and principles in online spaces.</p><p><strong>Methods: </strong>We have adopted a purposive, qualitative, and thematic analysis method. Data have been manually collected from the selected social media platforms using keywords like \"ecofeminism\" and \"women and nature.\" Content has been selected based on thematic relevance. Only publicly available materials have been used.</p><p><strong>Results: </strong>Instagram, YouTube, and Facebook each contributes uniquely to the ecofeminist discourse by offering visually engaging reels and images, academic and artistic content, and select group and page-based advocacy, respectively. Through various digital entities such as groups, pages, reels, videos, and pictures, many social media accounts vividly demonstrate the close relationship between women and nature, the exploitation they face from patriarchal society and how they can be protected. Despite this vivid portrayal, the content across platforms remains scattered and inconsistent.</p><p><strong>Conclusion: </strong>The study highlights both the potential and the limitations of social media in presenting ecofeminist narrative. It emphasizes the need for consistent and dedicated efforts to promote ecofeminist values online. The study adds to the fields of ecofeminism and media studies by showing how online content can reflect, support, and shape ecofeminist thinking today.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"455"},"PeriodicalIF":0.0,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12381554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144948202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prevalence, satisfaction and preference of tooth shades and their correlation with age, gender and skin color : A cross sectional study.","authors":"Prashanth Bajantri, Tanay Chawda, Srikant Natarajan, Alisha Ono, Thilak Shetty, Shobha Rodrigues, Umesh Pai, Mahesh M, Sharon Saldanha, Puneeth Hegde, Sandipan Mukherjee, Ann Sales, Vignesh Kamath","doi":"10.12688/f1000research.146428.3","DOIUrl":"10.12688/f1000research.146428.3","url":null,"abstract":"<p><p>Shade selection is a crucial factor influencing patient satisfaction with dental prostheses and the overall success of treatment. Conventional visual methods of shade selection are inherently subjective, regardless of the availability of dental records or photographs. This study aims to assess the prevalence, satisfaction, and preference of tooth shades in a cross-section of the local Indian population and to evaluate their correlation with age, gender, and skin color in a diverse sample of 120 participants visiting the outpatient department of this Institution.</p><p><strong>Methods: </strong>A total of 120 participants, comprising 60 males and 60 females across four age groups (20-30, 30-40, 40-50, and 50-60 years), were visually evaluated using the VITA 3D Master shade guide. Participants also indicated their satisfaction with their current tooth shade and their preferred shade.</p><p><strong>Results: </strong>Value 2 was the most prevalent existing shade (52.5%) and the most preferred across all groups, especially among individuals aged 41-50 years (p < 0.001). Satisfaction was highest among males aged 41-50 years. No significant association was found between skin color and tooth shade preference or satisfaction.</p><p><strong>Conclusions: </strong>The results suggest that shades in the Value 2 category are universally preferred, offering a useful reference for shade selection in clinical practice.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"1076"},"PeriodicalIF":0.0,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144527101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}