Pub Date : 2025-11-28eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103736
Parisa Khaleghi, Duygu Cakir, Ali Hamidoğlu, Omer Melih Gul, Seifedine Kadry
Depression affects over 280 million people worldwide, with neurological patients particularly prone to medication-induced episodes. Conventional diagnostic approaches rely on subjective evaluations, limiting reproducibility and consistency in clinical settings. This study proposes an interpretable deep learning framework for objective depression detection using EEG signals. We hypothesize that combining EEG-based features with explainable artificial intelligence can provide both high accuracy and transparency in diagnosis. The model was trained on EEG data from 232 neurological patients, achieving 98 % classification accuracy. Interpretability was enhanced through SHAP (SHapley Additive exPlanations) analysis, which identified clinically meaningful EEG biomarkers such as the delta/alpha ratio and theta band power. This paper highlights the following contributions: Integration of EEG features with a lightweight deep learning model for depression detection High diagnostic accuracy achieved while maintaining interpretability for clinicians An objective tool that is compatible with existing EEG infrastructure, supporting clinical adoption These results show that our framework bridges predictive performance with interpretability, offering a transparent and scalable EEG-based diagnostic tool. We conclude that this approach can complement clinical decision-making, reducing dependence on subjective evaluation and enabling more consistent, data-driven mental health care.
{"title":"Interpretable deep learning for depression detection in neurological patients using EEG signals.","authors":"Parisa Khaleghi, Duygu Cakir, Ali Hamidoğlu, Omer Melih Gul, Seifedine Kadry","doi":"10.1016/j.mex.2025.103736","DOIUrl":"10.1016/j.mex.2025.103736","url":null,"abstract":"<p><p>Depression affects over 280 million people worldwide, with neurological patients particularly prone to medication-induced episodes. Conventional diagnostic approaches rely on subjective evaluations, limiting reproducibility and consistency in clinical settings. This study proposes an interpretable deep learning framework for objective depression detection using EEG signals. We hypothesize that combining EEG-based features with explainable artificial intelligence can provide both high accuracy and transparency in diagnosis. The model was trained on EEG data from 232 neurological patients, achieving 98 % classification accuracy. Interpretability was enhanced through SHAP (SHapley Additive exPlanations) analysis, which identified clinically meaningful EEG biomarkers such as the delta/alpha ratio and theta band power. This paper highlights the following contributions: Integration of EEG features with a lightweight deep learning model for depression detection High diagnostic accuracy achieved while maintaining interpretability for clinicians An objective tool that is compatible with existing EEG infrastructure, supporting clinical adoption These results show that our framework bridges predictive performance with interpretability, offering a transparent and scalable EEG-based diagnostic tool. We conclude that this approach can complement clinical decision-making, reducing dependence on subjective evaluation and enabling more consistent, data-driven mental health care.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103736"},"PeriodicalIF":1.9,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12720302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820068","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}
Image Captioning is a crucial task that enables systems to generate descriptive sentences for visual content. Though image captioning systems bloom at the intersection of Computer Vision and Natural Language Processing, these models act mostly as black boxes offering little or no insight into how captions are derived. We present a novel explainable image captioning framework that integrates a Convolutional Neural Network encoder with a Transformer decoder. Attention-based heatmaps are used to explain the visuals offering transparency in the decision making process. The method evaluates captioning quality and interpretability on the MS COCO dataset using BLEU, METEOR, CIDER and SPICE. The method enhances the trustworthiness and transparency, making it reliable for applications like healthcare, education, security, surveillance and forecasting. A reproducible method for integrating visual explainability into image captioning exploring transformer decoder attention maps. The method contributes to the growing body of eXplainable AI (XAI) by addressing the transparency gap in vision-language models Balance performance with interpretability paving the way for more transparent and trustworthy AI systems.
{"title":"A vision explainability method for image captioning using transformer decoder attention maps.","authors":"Meena Kowshalya, Suchitra, Rajesh Kumar Dhanaraj, Dragan Pamucar","doi":"10.1016/j.mex.2025.103744","DOIUrl":"10.1016/j.mex.2025.103744","url":null,"abstract":"<p><p>Image Captioning is a crucial task that enables systems to generate descriptive sentences for visual content. Though image captioning systems bloom at the intersection of Computer Vision and Natural Language Processing, these models act mostly as black boxes offering little or no insight into how captions are derived. We present a novel explainable image captioning framework that integrates a Convolutional Neural Network encoder with a Transformer decoder. Attention-based heatmaps are used to explain the visuals offering transparency in the decision making process. The method evaluates captioning quality and interpretability on the MS COCO dataset using BLEU, METEOR, CIDER and SPICE. The method enhances the trustworthiness and transparency, making it reliable for applications like healthcare, education, security, surveillance and forecasting. A reproducible method for integrating visual explainability into image captioning exploring transformer decoder attention maps. The method contributes to the growing body of eXplainable AI (XAI) by addressing the transparency gap in vision-language models Balance performance with interpretability paving the way for more transparent and trustworthy AI systems.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103744"},"PeriodicalIF":1.9,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12719966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820019","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}
Pub Date : 2025-11-27DOI: 10.1016/j.mex.2025.103733
Rene Welch Schwartz , Cindy L. Zuleger , Michael A. Newton , David M. Vail , Mark R. Albertini , Irene M. Ong
Motivation
Profiling the T cell receptor (TCR) repertoire using next-generation sequencing (NGS) to quantify adaptive immune responses has become common in human and animal research. Companion dogs with spontaneous tumors have similarities with humans who have cancer. T cells undergo clonal expansion when they recognize specific antigens via surface TCRs. TCR counts from NGS data provide a way to quantify T cell response to vaccines, cancer, or infectious diseases for preclinical and clinical health studies. One complication is that the power and accuracy of TCR experiments depend substantially on the TCR sequencing depth, therefore it is important to determine the optimal read depth of an experiment to verify whether a subject’s repertoire is correctly represented.
Results
The optimal TCR sequencing depth for future experiments can be determined by randomly sampling lower TCR sequencing depths from a sequencing experiment, assembling the TCR clonotypes, and determining where the saturation of power and accuracy occurs. Moreover, one can determine whether an existing experiment has sufficient sequencing depth to justify its conclusions. We provide guidelines to determine whether the sequencing depth is adequate and a computational pipeline that:
Samples pairs of sequences and assembles clonotypes
{"title":"SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine","authors":"Rene Welch Schwartz , Cindy L. Zuleger , Michael A. Newton , David M. Vail , Mark R. Albertini , Irene M. Ong","doi":"10.1016/j.mex.2025.103733","DOIUrl":"10.1016/j.mex.2025.103733","url":null,"abstract":"<div><h3>Motivation</h3><div>Profiling the T cell receptor (TCR) repertoire using next-generation sequencing (NGS) to quantify adaptive immune responses has become common in human and animal research. Companion dogs with spontaneous tumors have similarities with humans who have cancer. T cells undergo clonal expansion when they recognize specific antigens via surface TCRs. TCR counts from NGS data provide a way to quantify T cell response to vaccines, cancer, or infectious diseases for preclinical and clinical health studies. One complication is that the power and accuracy of TCR experiments depend substantially on the TCR sequencing depth, therefore it is important to determine the optimal read depth of an experiment to verify whether a subject’s repertoire is correctly represented.</div></div><div><h3>Results</h3><div>The optimal TCR sequencing depth for future experiments can be determined by randomly sampling lower TCR sequencing depths from a sequencing experiment, assembling the TCR clonotypes, and determining where the saturation of power and accuracy occurs. Moreover, one can determine whether an existing experiment has sufficient sequencing depth to justify its conclusions. We provide guidelines to determine whether the sequencing depth is adequate and a computational pipeline that:</div><div>Samples pairs of sequences and assembles clonotypes</div><div>Summarizes the results in a parametrized report</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103733"},"PeriodicalIF":1.9,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749536","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 : 2025-11-26eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103737
Katiusca E Gonzales-Rivera, Jessica I Nieto-Juárez
Antiepileptic drugs are considered contaminants of emerging concern in water and are resistant to conventional wastewater treatment processes. Therefore, their presence has been detected in surface waters, and their elimination/degradation requires effective treatment methods. In this research, ultrasound-based methods (e.g., sonolysis, sono-Fenton, and sono-photo-Fenton) were addressed in the degradation of antiepileptic drug primidone at laboratory scale. A high-frequency ultrasound (at 578 kHz and 20.4 W) was applied. Then, Fe2+ ions (5 mg l-1) and a UVA lamp (4 W) were added to the sonochemical reactor. After 75 min of treatment, the sono-photo-Fenton method showed better degradation efficiency (93 %) than the sono-Fenton (83 %) and sonolysis (62 %) methods. Finally, the effectiveness of the degradation method by sono-photo-Fenton was tested in simulated pharmaceutical wastewater, degrading 72 % of primidone at 75 min of treatment, indicating matrix effect plays a role in the degradation (which could be a potential application of ultrasound hybridized with the photo-Fenton process).•Three ultrasound-based treatment methods were applied to degrade primidone in water.•The sono-photo-Fenton method degraded 93 % of primidone during 75 min of treatment.•The matrix influence on primidone degradation by sono-photo-Fenton was evaluated.
{"title":"Degradation method for the antiepileptic drug primidone in water using a hybrid high-frequency ultrasound and photo-Fenton process.","authors":"Katiusca E Gonzales-Rivera, Jessica I Nieto-Juárez","doi":"10.1016/j.mex.2025.103737","DOIUrl":"10.1016/j.mex.2025.103737","url":null,"abstract":"<p><p>Antiepileptic drugs are considered contaminants of emerging concern in water and are resistant to conventional wastewater treatment processes. Therefore, their presence has been detected in surface waters, and their elimination/degradation requires effective treatment methods. In this research, ultrasound-based methods (e.g., sonolysis, sono-Fenton, and sono-photo-Fenton) were addressed in the degradation of antiepileptic drug primidone at laboratory scale. A high-frequency ultrasound (at 578 kHz and 20.4 W) was applied. Then, Fe<sup>2+</sup> ions (5 mg l<sup>-1</sup>) and a UVA lamp (4 W) were added to the sonochemical reactor. After 75 min of treatment, the sono-photo-Fenton method showed better degradation efficiency (93 %) than the sono-Fenton (83 %) and sonolysis (62 %) methods. Finally, the effectiveness of the degradation method by sono-photo-Fenton was tested in simulated pharmaceutical wastewater, degrading 72 % of primidone at 75 min of treatment, indicating matrix effect plays a role in the degradation (which could be a potential application of ultrasound hybridized with the photo-Fenton process).•Three ultrasound-based treatment methods were applied to degrade primidone in water.•The sono-photo-Fenton method degraded 93 % of primidone during 75 min of treatment.•The matrix influence on primidone degradation by sono-photo-Fenton was evaluated.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103737"},"PeriodicalIF":1.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12720135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145820038","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}
Pub Date : 2025-11-26DOI: 10.1016/j.mex.2025.103738
Ioannis Kamas , Stephen K. Suryasentana , Harvey J. Burd , Byron W. Byrne
Monopiles are a widely-used foundation system for offshore wind turbine support structures. In current practice, design calculations typically employ one-dimensional (1D) models in which the monopile is represented as an embedded beam. The current study presents a data-driven 1D design model for the analysis of offshore monopiles subjected to monotonic lateral load and moment loading. The method is based on the PISA design model framework; enhancements are incorporated in the model to improve its accuracy, scalability and to facilitate applications to a wide range of geotechnical conditions. The data-driven model incorporates a spline-based parametrisation of the soil reaction curves combined with machine learning techniques. The model is calibrated using a database of previously-published three-dimensional finite element calibration analyses. The method described in the current paper is concerned with:
•
Modifications to the PISA design model framework to develop a data-driven 1D design model.
•
Calibration of the data-driven 1D model for ground conditions comprising: (i) offshore glacial tills with varying strength–stiffness properties, and (ii) sands with a wide range of relative densities.
•
Validation of the proposed method by comparing 1D model predictions for monopiles in homogeneous and layered soils with detailed 3D finite element analyses.
{"title":"Data-driven 1D design model for monotonic lateral loading of monopile foundations","authors":"Ioannis Kamas , Stephen K. Suryasentana , Harvey J. Burd , Byron W. Byrne","doi":"10.1016/j.mex.2025.103738","DOIUrl":"10.1016/j.mex.2025.103738","url":null,"abstract":"<div><div>Monopiles are a widely-used foundation system for offshore wind turbine support structures. In current practice, design calculations typically employ one-dimensional (1D) models in which the monopile is represented as an embedded beam. The current study presents a data-driven 1D design model for the analysis of offshore monopiles subjected to monotonic lateral load and moment loading. The method is based on the PISA design model framework; enhancements are incorporated in the model to improve its accuracy, scalability and to facilitate applications to a wide range of geotechnical conditions. The data-driven model incorporates a spline-based parametrisation of the soil reaction curves combined with machine learning techniques. The model is calibrated using a database of previously-published three-dimensional finite element calibration analyses. The method described in the current paper is concerned with:<ul><li><span>•</span><span><div>Modifications to the PISA design model framework to develop a data-driven 1D design model.</div></span></li><li><span>•</span><span><div>Calibration of the data-driven 1D model for ground conditions comprising: (i) offshore glacial tills with varying strength–stiffness properties, and (ii) sands with a wide range of relative densities.</div></span></li><li><span>•</span><span><div>Validation of the proposed method by comparing 1D model predictions for monopiles in homogeneous and layered soils with detailed 3D finite element analyses.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103738"},"PeriodicalIF":1.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749541","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 : 2025-11-26eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103739
Rizal Bakri, Eva Boj Del Val, Basri Bado, Ansari Saleh Ahmar
This article presents the development of LOSARI, a novel R-based statistical software designed to facilitate students' self-regulated learning (SRL) in statistics courses. LOSARI can be accessed online without installation and allows students to perform statistical analyses through a point-and-click interface without coding. It integrates several innovative features: interactive video tutorials embedded in the analysis environment, real-time error notifications that guide students in correcting mistakes, and automatic interpretation of results to support independent learning. The software was validated through a student satisfaction survey using the End-User Computing Satisfaction (EUCS) model, which indicated that most users had positive perceptions of LOSARI and found it effective for learning statistics outside the classroom. Possible extensions and enhancements are also discussed.•A structured process for developing LOSARI as an R-based statistical learning tool.•Introduction of key features, including interactive video tutorials, real-time error notifications, and automatic interpretation.•Validation method through student satisfaction measurement and comparison with manual statistical coding.
{"title":"LOSARI: A novel R-based statistical software to facilitate students' self-regulated learning in statistics courses.","authors":"Rizal Bakri, Eva Boj Del Val, Basri Bado, Ansari Saleh Ahmar","doi":"10.1016/j.mex.2025.103739","DOIUrl":"10.1016/j.mex.2025.103739","url":null,"abstract":"<p><p>This article presents the development of LOSARI, a novel R-based statistical software designed to facilitate students' self-regulated learning (SRL) in statistics courses. LOSARI can be accessed online without installation and allows students to perform statistical analyses through a point-and-click interface without coding. It integrates several innovative features: interactive video tutorials embedded in the analysis environment, real-time error notifications that guide students in correcting mistakes, and automatic interpretation of results to support independent learning. The software was validated through a student satisfaction survey using the End-User Computing Satisfaction (EUCS) model, which indicated that most users had positive perceptions of LOSARI and found it effective for learning statistics outside the classroom. Possible extensions and enhancements are also discussed.•A structured process for developing LOSARI as an R-based statistical learning tool.•Introduction of key features, including interactive video tutorials, real-time error notifications, and automatic interpretation.•Validation method through student satisfaction measurement and comparison with manual statistical coding.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103739"},"PeriodicalIF":1.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12718211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145810119","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}
Whole gut transit time (WGTT) provides essential insights into gastrointestinal health, but traditional measurement methods are often expensive or invasive. This study optimizes and validates the "blue dye method," an affordable and minimally invasive approach to WGTT measurement. Using "Hollinger Farbpulver Blau" (containing food colors E131 and E132), dye concentrations ranging from 30 mg to 241 mg were tested across four modes of delivery: capsule with liquid, gummy bear, muffin, and capsule with rice crackers and liquid. Each presented limitations: capsules taken with liquid led to inconsistent transit times, gummy bears caused staining, and muffins were perishable. Measured WGTTs varied between 18 and 29 h depending on the mode of delivery and dye concentration. Optimal protocol was a capsule containing 60 mg of dye taken with two rice crackers and liquid, ensuring accurate detection without practical inconveniences. The standardized and optimized blue dye method provides valid WGTT measurements, making it well suited for large-scale population studies and clinical applications.
Uses a simple blue dye as a marker for gut transit.
Tested several modes of delivery and concentrations to find the most practical option.
Established a standardized protocol for reliable and reproducible measurement.
{"title":"Optimizing blue poo: A validated, cost-effective method for measuring whole gut transit time","authors":"Cyra Schmandt , Julia Trunz , Claudio Perret , Anneke Hertig-Godeschalk , Zeno Stanga , Jivko Stoyanov","doi":"10.1016/j.mex.2025.103741","DOIUrl":"10.1016/j.mex.2025.103741","url":null,"abstract":"<div><div>Whole gut transit time (WGTT) provides essential insights into gastrointestinal health, but traditional measurement methods are often expensive or invasive. This study optimizes and validates the \"blue dye method,\" an affordable and minimally invasive approach to WGTT measurement. Using \"Hollinger Farbpulver Blau\" (containing food colors E131 and E132), dye concentrations ranging from 30 mg to 241 mg were tested across four modes of delivery: capsule with liquid, gummy bear, muffin, and capsule with rice crackers and liquid. Each presented limitations: capsules taken with liquid led to inconsistent transit times, gummy bears caused staining, and muffins were perishable. Measured WGTTs varied between 18 and 29 h depending on the mode of delivery and dye concentration. Optimal protocol was a capsule containing 60 mg of dye taken with two rice crackers and liquid, ensuring accurate detection without practical inconveniences. The standardized and optimized blue dye method provides valid WGTT measurements, making it well suited for large-scale population studies and clinical applications.</div><div>Uses a simple blue dye as a marker for gut transit.</div><div>Tested several modes of delivery and concentrations to find the most practical option.</div><div>Established a standardized protocol for reliable and reproducible measurement.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103741"},"PeriodicalIF":1.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145692906","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 : 2025-11-25eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103734
Luís Valença Pinto, Miguel Inácio, Fernando Santos-Martín, Benjamin Burkhard, Paulo Pereira
Ecosystem condition can be understood as the quality of an ecosystem in terms of its abiotic, biotic, and landscape characteristics. It is a measure of structural integrity, functional capacity, and resilience of any given ecological system. Its assessment is essential to support environmental objectives (e.g., nature restoration or sustainable use). Spatially explicit assessment of ecosystem condition requires integrating diverse geospatial data. Here, we present the EcoCondition Toolset, a QGIS plugin implementing a user-friendly GIS weighted-sum methodology for ecosystem condition assessments. It simplifies data preparation and analysis through five sequential toolsets: i) layer alignment and resampling; ii) no-data handling; iii) multicollinearity testing; iv) indicator normalisation and inversion; and v) condition assessment. The plugin calculates six specific ecosystem attribute - or state - composites (Physical, Chemical, Compositional, Structural, Functional, Landscape) from user-selected variables (in raster format), according to the System of Environmental-Economic Accounting. After data preparation and verification, the tool displays default equal weights for each composite and related variables, which users can adjust (e.g., to reflect stakeholder preferences). The toolset automates best-practice multicollinearity screening, normalisation, and flexible weighting for ecosystem condition assessment and monitoring. The resulting index preserves true severity and variation among ecosystem states. The results can support robust policy instruments and land-use decision-making, prioritising conservation and restoration actions.
{"title":"EcoCondition Toolset - A QGIS plugin for ecosystem condition assessments.","authors":"Luís Valença Pinto, Miguel Inácio, Fernando Santos-Martín, Benjamin Burkhard, Paulo Pereira","doi":"10.1016/j.mex.2025.103734","DOIUrl":"10.1016/j.mex.2025.103734","url":null,"abstract":"<p><p>Ecosystem condition can be understood as the quality of an ecosystem in terms of its abiotic, biotic, and landscape characteristics. It is a measure of structural integrity, functional capacity, and resilience of any given ecological system. Its assessment is essential to support environmental objectives (e.g., nature restoration or sustainable use). Spatially explicit assessment of ecosystem condition requires integrating diverse geospatial data. Here, we present the EcoCondition Toolset, a QGIS plugin implementing a user-friendly GIS weighted-sum methodology for ecosystem condition assessments. It simplifies data preparation and analysis through five sequential toolsets: i) layer alignment and resampling; ii) no-data handling; iii) multicollinearity testing; iv) indicator normalisation and inversion; and v) condition assessment. The plugin calculates six specific ecosystem attribute - or state - composites (Physical, Chemical, Compositional, Structural, Functional, Landscape) from user-selected variables (in raster format), according to the System of Environmental-Economic Accounting. After data preparation and verification, the tool displays default equal weights for each composite and related variables, which users can adjust (e.g., to reflect stakeholder preferences). The toolset automates best-practice multicollinearity screening, normalisation, and flexible weighting for ecosystem condition assessment and monitoring. The resulting index preserves true severity and variation among ecosystem states. The results can support robust policy instruments and land-use decision-making, prioritising conservation and restoration actions.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103734"},"PeriodicalIF":1.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145763029","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}
Pub Date : 2025-11-22eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103732
Shejal A Rao, Koushik Sau, Shovan Saha, Vani R Lakshmi, Ashwath M Acharya
Hand injuries are among the most common musculoskeletal injuries and can significantly impair an individual's ability to perform activities of daily living (ADL), thereby impacting quality of life. Self-efficacy plays a vital role in influencing daily performance and recovery following injury. This cross-sectional study aims to explore the relationship between ADL performance and self-efficacy among clients with hand injuries within the Indian context. Secondary objectives of this study include assessing self-efficacy levels and evaluating ADL performance in this population. • A self-administered, closed-ended, structured questionnaire comprising performance-based and self-efficacy measures will be used for data collection. Participants will include adults aged 18 years and above who have sustained fractures of the hand or wrist, including digits, and have undergone surgical treatment. • Clients will be recruited from the Occupational Therapy department. • The findings aim to highlight the importance of considering both objective and subjective measures in occupational therapy assessment and to emphasize the role of self-efficacy in ADL performance following hand injuries, potentially informing culturally sensitive rehabilitation interventions.
{"title":"The relationship between activities of daily living performance and self-efficacy among clients with hand injury in Indian context- A cross-sectional study protocol.","authors":"Shejal A Rao, Koushik Sau, Shovan Saha, Vani R Lakshmi, Ashwath M Acharya","doi":"10.1016/j.mex.2025.103732","DOIUrl":"10.1016/j.mex.2025.103732","url":null,"abstract":"<p><p>Hand injuries are among the most common musculoskeletal injuries and can significantly impair an individual's ability to perform activities of daily living (ADL), thereby impacting quality of life. Self-efficacy plays a vital role in influencing daily performance and recovery following injury. This cross-sectional study aims to explore the relationship between ADL performance and self-efficacy among clients with hand injuries within the Indian context. Secondary objectives of this study include assessing self-efficacy levels and evaluating ADL performance in this population. • A self-administered, closed-ended, structured questionnaire comprising performance-based and self-efficacy measures will be used for data collection. Participants will include adults aged 18 years and above who have sustained fractures of the hand or wrist, including digits, and have undergone surgical treatment. • Clients will be recruited from the Occupational Therapy department. • The findings aim to highlight the importance of considering both objective and subjective measures in occupational therapy assessment and to emphasize the role of self-efficacy in ADL performance following hand injuries, potentially informing culturally sensitive rehabilitation interventions.</p>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"103732"},"PeriodicalIF":1.9,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145763090","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}
Pub Date : 2025-11-21eCollection Date: 2025-12-01DOI: 10.1016/j.mex.2025.103727
Sifriyani, I Nyoman Budiantara, Krishna Purnawan Candra, Syaripuddin, Syatirah Jalaluddin, Mariani Rasjid, Ruslan
This study proposes an advanced spatio-temporal framework to forecast strategic food commodity prices in Indonesia using Geographically and Temporally Weighted Spline Regression (GTWSR), a nonparametric extension of GTWR designed to capture nonlinear spatio temporal effects. Monthly data from the Strategic Food Price Information Center (SFPIC) and Statistics Indonesia (BPS), covering eight key commodities and the Farmer Price Index across 34 provinces (January 2022-August 2024), were analyzed through spatial distance measurement, bandwidth optimization, local parameter estimation, and statistical validation. The GTWSR model demonstrated strong predictive performance (overall accuracy: R² = 91.61 %, RMSE = 1.22, MAE = 0.94, MAPE = 3.7 %), with rice and garlic achieving the highest accuracy, while red and cayenne chili showed greater errors due to price volatility. Spatial disparities were evident, as eastern provinces such as Papua, Maluku, and East Nusa Tenggara consistently faced higher prices compared to western regions. These findings underscore the need for region-specific interventions to strengthen logistics and stabilize horticultural supply chains. Limitations include reliance on monthly aggregated data, the temporal scope ending in 2024, and dependence on secondary datasets, which may affect replication and long-term applicability.
本研究提出了一个先进的时空框架,利用地理和时间加权样条回归(GTWSR)预测印度尼西亚的战略粮食商品价格,GTWSR是GTWR的非参数扩展,旨在捕捉非线性时空效应。通过空间距离测量、带宽优化、局部参数估计和统计验证,对来自战略食品价格信息中心(SFPIC)和印度尼西亚统计局(BPS)的月度数据进行了分析,涵盖了8种关键商品和34个省份的农民价格指数(2022年1月至2024年8月)。GTWSR模型显示出较强的预测性能(总体准确率:R²= 91.61%,RMSE = 1.22, MAE = 0.94, MAPE = 3.7%),其中大米和大蒜的预测准确率最高,而红辣椒和辣椒由于价格波动的影响,预测误差较大。空间差异很明显,东部省份如巴布亚省、马鲁古省和东努沙登加拉省的价格一直高于西部地区。这些发现强调需要采取针对特定区域的干预措施,以加强物流和稳定园艺供应链。限制包括依赖每月汇总数据,时间范围截止于2024年,以及依赖辅助数据集,这可能会影响复制和长期适用性。
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