MethodsXPub Date : 2026-06-01Epub Date: 2025-12-11DOI: 10.1016/j.mex.2025.103761
Lu Tang , Yakup Yildirim , Ahmed H. Arnous , Ahmed Shaker Mahmood , Ibrahim Zeghaiton Chaloob , Anjan Biswas
{"title":"Bifurcation analysis and phase portraits for chiral solitons with bohm potential in quantum hall effect","authors":"Lu Tang , Yakup Yildirim , Ahmed H. Arnous , Ahmed Shaker Mahmood , Ibrahim Zeghaiton Chaloob , Anjan Biswas","doi":"10.1016/j.mex.2025.103761","DOIUrl":"10.1016/j.mex.2025.103761","url":null,"abstract":"<div><div>This paper presents a comprehensive bifurcation analysis and phase portrait investigation of chiral solitons governed by the chiral nonlinear Schrödinger equation with Bohm potential in the Quantum Hall Effect framework. The equation accounts for chirality, quantum corrections, and nonlinear interactions, making it a valuable model for soliton behavior in quantum fluids. We analyze the system’s dynamical properties, equilibrium points, and solution regimes using bifurcation theory, revealing stability transitions and structural changes in soliton solutions. Phase plane techniques visualize qualitative behaviors under varying parameters. Additionally, we derive exact optical soliton solutions, demonstrating the Bohm potential’s influence on soliton formation and evolution. These findings offer insights into nonlinear wave propagation in chiral quantum systems and have potential applications in condensed matter physics and optical fiber systems.</div><div>The paper analyzes chiral solitons using bifurcation theory and phase portraits to reveal stability transitions and dynamic behaviors.</div><div>Exact soliton solutions are derived, highlighting the effects of Bohm potential and chirality on soliton formation.</div><div>The results provide insights into nonlinear wave propagation in quantum fluids and optical fiber systems.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103761"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798170","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}
{"title":"AI-powered mental health application with data privacy preservation","authors":"Pooja Bagane , Anushree Dahiya , Shardul Kacheria , Ansh Sehgal , Shrishti Bajpai , Obsa Amenu Jebessa","doi":"10.1016/j.mex.2025.103756","DOIUrl":"10.1016/j.mex.2025.103756","url":null,"abstract":"<div><div>Anxiety disorders, emotional conditions, and stress are becoming an increasing tendency in modern society, which makes digital mental health technologies that provide support in these cases highly demanded. This paper focuses on proposing an AI-driven framework that combines Natural Language Processing (NLP) with privacy-protective systems to recognize emotions in the text of the user. The AES-256 encryption, Supabase authentication, and role-based access control are used to secure data security. It is presented as a multi-label problem of emotion classification, which is fine-tuned on the BERT-base-uncased and ModernBERT Large transformer. ModernBERT exhibited rapid convergence and enhanced situational sensitivity especially when it comes to sarcasm and mixed emotional states.</div><div>Key contributions include:<ul><li><span>•</span><span><div>Planning an emotion feedback loop offering contextual response and customized mindfulness teaching.</div></span></li><li><span>•</span><span><div>Performing a Class imbalance analysis of emotions and trade-offs in precision and recall.</div></span></li><li><span>•</span><span><div>Illustrating privacy-first architecture that is able to integrate with digital-therapy and clinician assisted decision software.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103756"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798169","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}
MethodsXPub Date : 2026-06-01Epub Date: 2026-06-03DOI: 10.1016/j.mex.2026.103988
Víctor Lecegui , Vincent E.J. Jassey , Aaron Pérez-Haase
{"title":"Standardizing food web reconstruction from metabarcoding data using iterative rarefaction and trait-based trophic inference model","authors":"Víctor Lecegui , Vincent E.J. Jassey , Aaron Pérez-Haase","doi":"10.1016/j.mex.2026.103988","DOIUrl":"10.1016/j.mex.2026.103988","url":null,"abstract":"<div><div>High-throughput metabarcoding combined with trait-based trophic inference models enables the reconstruction of food webs from community eDNA. However, uneven sequencing depth can bias inferred food web structure. Network metrics derived from unstandardized read counts may reflect sampling effort rather than ecological processes. Here, we present an objective and reproducible framework using iterative rarefaction with trait-based trophic inference to standardize food web metrics prior to ecological analysis.</div><div>Our approach links rarefaction depth to network-level properties by generating rarefaction curves based on food web metrics rather than taxonomic richness. An optimal rarefaction threshold is determined using a first derivative criterion, and rarefied networks are reconstructed repeatedly to obtain robust mean metric estimates.</div><div>We applied this method to soil protist communities assessed using 18S rRNA metabarcoding. The method reduced sequencing-depth bias and revealed environmental drivers that were masked in non-rarefied analyses.</div><div>This framework provides a standardized solution for comparing food webs derived from amplicon datasets across environmental gradients.</div><div>Integrates trait-based trophic inference with iterative rarefaction of metabarcoding communities.</div><div>Selects rarefaction thresholds using food web network properties rather than species accumulation curve.</div><div>Provides reliable estimates of food web structure independent of sequencing effort.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103988"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148184119","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}
MethodsXPub Date : 2026-06-01DOI: 10.1016/j.mex.2026.103979
Akihiro Maeta , Mamoru Tanaka , Kyoko Takahashi
{"title":"Development of an inexpensive, simple purification method for ω-5 gliadin from wheat flour","authors":"Akihiro Maeta , Mamoru Tanaka , Kyoko Takahashi","doi":"10.1016/j.mex.2026.103979","DOIUrl":"10.1016/j.mex.2026.103979","url":null,"abstract":"<div><div>ω-5 gliadin is a major causative allergen associated with various types of wheat allergy, including wheat-dependent exercise-induced anaphylaxis. Recently, ω-5 gliadin-deficient wheat has been developed. However, several wheat protein studies do not use standard ω-5 gliadin because its naturally derived form is expensive, and purifying it in-house is time-consuming. Therefore, we sought to develop an inexpensive, simple method for purifying ω-5 gliadin on a small scale.<ul><li><span>▪</span><span><div>We compared ω-5 gliadin-deficient wheat with normal wheat and screened for ω-5 gliadin bands using acid-polyacrylamide gel electrophoresis (A-PAGE) on a mini-slab electrophoresis apparatus.</div></span></li><li><span>▪</span><span><div>The ω-5 gliadin band was excised and sealed in dialysis tubing, and the protein was electroeluted using agarose gel electrophoresis. After electroelution, the eluted solution was filtered, dialyzed, and then freeze-dried.</div></span></li><li><span>▪</span><span><div>The main band of collected proteins migrated at approximately 55 kDa in SDS-PAGE, and the most intense band was identified as ω-5 gliadin using nano-LC-MS/MS.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103979"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148184243","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}
MethodsXPub Date : 2026-06-01Epub Date: 2026-06-02DOI: 10.1016/j.mex.2026.103983
Vinod Mulik , Vinod Patil
{"title":"Enhancing grape disease detection: A comparative analysis of hybrid CNN-LSTM and CNN methods","authors":"Vinod Mulik , Vinod Patil","doi":"10.1016/j.mex.2026.103983","DOIUrl":"10.1016/j.mex.2026.103983","url":null,"abstract":"<div><div>Crop disease detection is crucial for maintaining high agricultural productivity and minimizing the financial losses of farmers.<ul><li><span>•</span><span><div>This study compares the performance of a hybrid method based on integrating the Long Short-Term Memory algorithm (LSTM) and Convolutional Neural Network (CNN) with a standalone CNN method for grape crop disease detection and classification.</div></span></li><li><span>•</span><span><div>The proposed methods are trained and tested on a comprehensive balanced and imbalanced grape leaf dataset with 4000 and 4062 images, respectively. The imbalanced dataset has 423 images of the healthy class, 1383 of ESCA, 1076 of leaf blight, and 1180 images of the black rot class, while the balanced dataset has 1000 images in each class</div></span></li><li><span>•</span><span><div>The LSTM-CNN method achieved 100%, and the CNN method achieved 99.47% accuracy on the balanced dataset. Also, in the case of the imbalanced dataset, 100% and 97.89%, respectively.</div></span></li></ul>Among these two methods implemented, the proposed LSTM-CNN method has achieved excellent results in terms of performance metrics. This study presents a deep learning-based system for automated leaf disease classification. The model is designed for end-user deployment, where users can upload a leaf image and receive an immediate prediction of the disease without requiring model retraining or technical expertise.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103983"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148184244","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}
MethodsXPub Date : 2026-06-01Epub Date: 2025-12-04DOI: 10.1016/j.mex.2025.103748
Muhammad Furqan , Fahim Raees , Muhammad Khalid
{"title":"Artificial neural network based predictive modeling of viscosity of an oil based hybrid nanofluid","authors":"Muhammad Furqan , Fahim Raees , Muhammad Khalid","doi":"10.1016/j.mex.2025.103748","DOIUrl":"10.1016/j.mex.2025.103748","url":null,"abstract":"<div><div>In many industries like micro-electronics, mechanical engines, transportation, manufacturing and nuclear reactors cooling characteristics which is a crucial challenge can optimize using nanofluid. Nanofluids are also used for better energy transfer and storage in many devices. In the current study the viscosity variation studied by the impact of input variables solid volume fraction and temperature. Sol-gel auto-combustion was used to prepare nickel ferrite (NiFe<sub>2</sub>O<sub>4</sub>) nano-particles. The structure of the NiFe<sub>2</sub>O<sub>4</sub> was obtained using an X-ray diffraction method. The Fourier transform infrared spectrum provided evidence of NiFe<sub>2</sub>O<sub>4</sub> presence. In order to better understand the surface morphology of nickel ferrite nano-particles, scanning electron microscopy (SEM) was employed. AT the various concentrations of nanofluid 0, 0.25, 0.50, 0.75, and 1 % were prepared. The viscosity was calculated at temperatures ranges 40 to 80 °C. The experimental results showed that the viscosity of nanofluid (µ<sub>nf</sub>) falls as the volume fraction(φ) increases and as the temperature rises. RSM and ANN predicted data have R<sup>2</sup> values of 0.9987 and 0.9999 respectively.. ANN accuracy can also be seen by MSE value. ANN shows less MSE value (0.00001) as compare to RSM that has MSE 0.0002. Which shows the ANN accuracy over RSM.</div><div>Predictive modelling for viscosity of Oil-Based Hybrid Nanofluid.</div><div>Artificial Neural Network and Response surface methodology methods were used for correlation.</div><div>Results were correlated with experimental data.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103748"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749537","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}
MethodsXPub Date : 2026-06-01Epub Date: 2025-11-26DOI: 10.1016/j.mex.2025.103738
Ioannis Kamas , Stephen K. Suryasentana , Harvey J. Burd , Byron W. Byrne
{"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":"2026-06-01","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}
{"title":"Health policies in long-term care facilities for older adults: A systematic review of textual evidence","authors":"Florbela Bia , Matheus Kirton dos Anjos , Zaida Charepe , Cristina Marques-Vieira","doi":"10.1016/j.mex.2026.103798","DOIUrl":"10.1016/j.mex.2026.103798","url":null,"abstract":"<div><h3>Background</h3><div>Health polices in residential care settings for older adults are essential to align housing and care provision with the needs of ageing populations, ensuring safety, participation, and quality of life. Despite their importance, evidence regarding policy implementation in long-term care (LTC) facilities remains fragmented and inconsistent.</div></div><div><h3>Objective</h3><div>This protocol describes an original method for synthesizing health policy documents using the Joanna Briggs Institute (JBI) framework for textual evidence. It aims to identify, analyze, and integrate policy evidence related to LTC facilities for older adults.</div></div><div><h3>Methods</h3><div>Following JBI methodological guidance for systematic reviews of text and opinion, this protocol employs the PICo framework to define inclusion criteria and a three-step search strategy. Searches will be conducted in MEDLINE, CINAHL Complete®, and the Virtual Health Library (BVS). Eligible documents include laws, regulations, policy frameworks, and technical guidelines addressing long-term care within publicly regulated systems. Data extraction and quality appraisal will be independently performed by two reviewers using JBI instruments.</div></div><div><h3>Expected Results</h3><div>The review will synthesize existing polices, highlighting their characteristics, implementation strategies, and outcomes. By applying a transparent and replicable JBI-based method, this protocol supports the production of high-quality evidence to inform equitable and effective governance in LTC facilities</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103798"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146034287","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}
MethodsXPub Date : 2026-06-01Epub Date: 2025-12-11DOI: 10.1016/j.mex.2025.103758
M. Burak Erturan
{"title":"Reconciled multiplicative relational two-stage network data envelopment analysis","authors":"M. Burak Erturan","doi":"10.1016/j.mex.2025.103758","DOIUrl":"10.1016/j.mex.2025.103758","url":null,"abstract":"<div><div>Relational two-stage network DEA (data envelopment analysis) is an approach for two-stage systems, where all input, output and the intermediate products have same weights regardless of which process they are related. One of the main approaches to relational model is the multiplicative relational approach where main process efficiency is the product of two sub-process efficiencies. A shortcoming of the relational model is that the solution of the sub-process efficiencies may not be unique. Researchers have developed some models to overcome this problem, like prioritizing one sub-process to the other or assessing the sub-process efficiencies first and then the main process efficiency. In this study, a novel methodology is presented for a fairer efficiency assessment, where none of the processes is prioritized.<ul><li><span>•</span><span><div>Reconciled Multiplicative Relational (RMR) model presented in this study uses data reconciliation method to determine maximum efficiency values for all processes simultaneously within the relational constraints.</div></span></li><li><span>•</span><span><div>RMR model has unique efficiency assessment solution, which solves the non-uniqueness problem and useful where none of the DMUs are preferred to another or there is no previous information in that matter.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103758"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798162","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}
MethodsXPub Date : 2026-06-01Epub Date: 2025-12-13DOI: 10.1016/j.mex.2025.103765
Steven A Flanagan , Zachary J. Robbins , Mac A. Callaham Jr , J. Kevin Hiers , Brian R. Miranda , Joseph J. O’Brien , Robert M. Scheller , E. Louise Loudermilk
{"title":"The Rapid Initial Community Builder (RICB) V1.1 for LANDIS-II","authors":"Steven A Flanagan , Zachary J. Robbins , Mac A. Callaham Jr , J. Kevin Hiers , Brian R. Miranda , Joseph J. O’Brien , Robert M. Scheller , E. Louise Loudermilk","doi":"10.1016/j.mex.2025.103765","DOIUrl":"10.1016/j.mex.2025.103765","url":null,"abstract":"<div><div>Forest succession, or ecosystem process models, can aid in many land management decisions as they inherently incorporate ecological processes to predict how disturbances impact the resilience of the forest and its potential future structure. The landscape class of ecosystem process models are often ideal for management goals as they simulate individual tree species interactions through time at the landscape scale and offer a robust assortment of disturbance extensions. However, broad implementation and adoption are often limited as users must rebuild the landscape models for every new site of interest. Creation of the initial forest communities that all model simulations depend on, can be particularly time consuming. To address this issue, we created the Rapid Initial Community Builder (RICB) that:<ul><li><span>•</span><span><div>Starts with high resolution CONtinental United States (CONUS) forest coverage and type data.</div></span></li><li><span>•</span><span><div>Makes modifications to the data for use in the landscape class ecosystem process model LANDIS-II.</div></span></li><li><span>•</span><span><div>Packages everything in an executable file that eliminates coding language or version barriers.</div></span></li></ul>Thus, greatly reducing the initialization time often associated with the intensive data assimilation techniques commonly used to generate initial communities.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"16 ","pages":"Article 103765"},"PeriodicalIF":1.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798164","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}