MethodsX最新文献

{"title":"Machine learning and Fuzzy logic fusion approach for osteoporosis risk prediction","authors":"Rabia Khushal,&nbsp;Dr. Ubaida Fatima","doi":"10.1016/j.mex.2024.103152","DOIUrl":"10.1016/j.mex.2024.103152","url":null,"abstract":"<div><div>The metabolic disorder osteoporosis has affected a humongous number of individuals globally. Its progression can be slowed down by modifying lifestyle risk factors and by following appropriate treatment. In this research work, modifiable risk factors of osteoporosis have been considered. All these variables are binary thus providing incomplete information. Machine learning implementation on these factors took a large computation time and has shown poor accuracy. Thus fuzzy concept has been introduced leading to the development of a fusion of machine learning and fuzzy logic approach. Three binary variables of the considered dataset have been compared thus fuzzy input is produced which also considers the uncertainty of these binary variables and since three input variables are transformed into one the number of features has also been reduced leading to optimization of computation time and accuracy. Moreover, it guides the individual to modify lifestyle factors to slow down the disease progression or reduce the risk of osteoporosis. The proposed model is validated on the diabetes risk prediction dataset.<ul><li><span>•</span><span><div>The study examines modifiable binary risk factors for osteoporosis, such as diet, smoking, and exercise etc.</div></span></li><li><span>•</span><span><div>A fusion of machine learning and fuzzy logic is introduced to improve accuracy and reduce computation time.</div></span></li><li><span>•</span><span><div>The model, which condenses three binary inputs into one, is validated using a diabetes risk prediction dataset.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103152"},"PeriodicalIF":1.6,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11764049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046333","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":"The effectiveness of non-invasive brain stimulation in enhancing lower extremity function in children with spastic cerebral palsy: Protocol for a systematic review and meta-analysis","authors":"Clàudia Arumí-Trujillo ,&nbsp;Francisco José Verdejo-Amengual ,&nbsp;Oriol Martínez-Navarro ,&nbsp;Jord J.T. Vink ,&nbsp;Fran Valenzuela-Pascual","doi":"10.1016/j.mex.2024.103141","DOIUrl":"10.1016/j.mex.2024.103141","url":null,"abstract":"<div><div>Non-invasive brain stimulation (NIBS<span><span>¹</span></span>) techniques have emerged as a promising non-pharmacological adjunct to neurorehabilitation. Children with Cerebral Palsy (CP<span><span>²</span></span>) exhibit altered cortical excitability, and while CP remains incurable, physiotherapy combined with other interventions is essential for managing motor dysfunction. Although some studies have examined NIBS using various stimulation parameters, there is limited evidence regarding its effects on the lower extremities and optimal administration protocols. This review aims to evaluate the effectiveness of NIBS techniques, such as transcranial direct current stimulation (tDCS<span><span>³</span></span>) and repetitive transcranial magnetic stimulation (rTMS<span><span>⁴</span></span>), for the treatment of motor function in spastic cerebral palsy, specifically in the lower extremity. A systematic search will be conducted in databases including MEDLINE, CINAHL Plus, EMBASE, Scopus, ISI Web of Science, and the Cochrane Central Register of Controlled Trials. The search strategy will follow the PICO framework (Participants, Intervention, Comparison, Outcomes), focusing on randomized controlled trials (RCTs). Two independent reviewers will manage screening, selection, data extraction, risk of bias assessment, and grading of evidence. This review will provide key insights into the effectiveness of NIBS for lower-extremity function in children with spastic CP, guiding future research and clinical applications.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103141"},"PeriodicalIF":1.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11755019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028869","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":"Technique for improving concrete characteristics with bacillus: Insights on strength and durability","authors":"Sayali Sandbhor,&nbsp;Sayali Apte,&nbsp;Shubham Puranik,&nbsp;Mansi Asati,&nbsp;Samyak Rai","doi":"10.1016/j.mex.2024.103151","DOIUrl":"10.1016/j.mex.2024.103151","url":null,"abstract":"<div><div>Numerous problems, including weathering, cracks, leaks, and bending, among others, appear in concrete after construction. The optimum procedure for treating concrete cracks is the subject of this study. The research goal is to find potential crack treatment materials and analyze the effect on the properties of concrete caused by the addition of bacterial solution to the concrete mix along with a particular method of preparation of bacterial solution. The principal results of the experimental testing showcased a successive growth in the compressive strength when the concrete cubes were casted with the bacterial addition from Bacillus family with a significant change in the quality of concrete. Following are the primary research outcomes of the method:<ul><li><span>•</span><span><div>Use of Bacillus bacterial with direct addition in concrete improves concrete's performance.</div></span></li><li><span>•</span><span><div>The proposed method of concrete mix with Bacillus Sphaericus Solution in 30 ml concentration, replacing partial water cement ratio, yields maximum compressive strength on 28th day curing. For expediting setting time with high compressive strength, adding Bacillus Sphaericus solution in 45 ml concentration is recommended.</div></span></li><li><span>•</span><span><div>For achieving a homogenous mix with lesser cracks on 28th day, Bacillus Subtilis Spores in 30 ml concentration can be added to concrete with partial replacement of the water requirement.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103151"},"PeriodicalIF":1.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046581","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":"Development and validation of a species-specific environmental DNA (eDNA) primer for endangered Asian arowana, Scleropages formosus (Teleostei: Osteoglossidae) for law enforcement and wild population monitoring","authors":"Nurul Affiqah Edora Mohd-Azhar ,&nbsp;Haslawati Baharuddin ,&nbsp;Mohamad-Sufiyan Salmi ,&nbsp;Noor Faizah Ismail ,&nbsp;Amatul-Samahah Md. Ali ,&nbsp;Syazwan Saidin ,&nbsp;Adibah Abu-Bakar","doi":"10.1016/j.mex.2024.103133","DOIUrl":"10.1016/j.mex.2024.103133","url":null,"abstract":"<div><div>The Asian Arowana, <em>Scleropages formosus</em> (Müller and Schlegel, 1844) is a large majestic freshwater teleost, crowned as the king of aquariums with its bright charismatic appearance and magnificent swimming performance. The most expensive Asian arowana is the Golden Blue-based Malayan Arowana which is endemic to the Bukit Merah Lake and Kerian River Basin, Perak, Malaysia. <em>S. formosus</em> has been listed as endangered by the IUCN (International Union for Conservation of Nature), regulated under Appendix 1 of the Convention of International Trade on Endangered Species (CITES) for commercial trade. Environmental DNA (eDNA) analysis has become widely accepted in biodiversity monitoring for the detection of rare and endangered species without harming any ecosystem or threatened species. Hence, the application of eDNA as wild population monitoring of <em>S. formosus</em> is possible for conservation and CITES enforcement program.<ul><li><span>•</span><span><div>The species-specific primer of <em>S. formosus</em> was designed based on selected sequences obtained from GenBank</div></span></li><li><span>•</span><span><div>This report presents the potential application of eDNA in the management of the Malaysian 686 CITES Act for conservation monitoring of the Asian Arowana</div></span></li><li><span>•</span><span><div>The detection and wild population monitoring is possible through the eDNA method as complementary tools</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103133"},"PeriodicalIF":1.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11757771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047239","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":"MBCdeg4: A modified clustering-based method for identifying differentially expressed genes from RNA-seq data","authors":"Chiharu Ichikawa ,&nbsp;Koji Kadota","doi":"10.1016/j.mex.2024.103149","DOIUrl":"10.1016/j.mex.2024.103149","url":null,"abstract":"<div><div>RNA-seq is a commonly employed methodology for the measurement of transcriptomes, particularly for the identification of differentially expressed genes (DEGs) between different conditions or groups. In a previous report, we described a clustering-based method for identifying DEGs, designated MBCdeg1 and MBCdeg2. and a modified version, MBCdeg3. This study presents a further improved version, designated MBCdeg4. The four versions of MBCdeg employ an R package, designated MBCluster.Seq, internally. The sole distinction between them is the manner of data normalization. MBCdeg4 employs normalization factors derived from a robust normalization algorithm, designated as DEGES. Seven competing methods were compared: the four versions of MBCdeg and three conventional R packages (edgeR, DESeq2, and TCC). MBCdeg4 demonstrated superior performance in a multitude of simulation scenarios involving RNA-seq count data. Therefore, MBCdeg4 is recommended for use in preference to the earlier versions, MBCdeg1–3.<ul><li><span>•</span><span><div>MBCdeg4 is a method for both identification and classification of DEGs from RNA-seq count data.</div></span></li><li><span>•</span><span><div>MBCdeg4 is available as an R function and performs well in a wide variety of simulation scenarios.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103149"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046500","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":"The game of language learning and rewiring biocognitive receptors","authors":"Sri Takshara K ,&nbsp;Bhuvaneswari G ,&nbsp;T.S. Pradeep Kumar","doi":"10.1016/j.mex.2024.103143","DOIUrl":"10.1016/j.mex.2024.103143","url":null,"abstract":"<div><div>This study introduces a framework that integrates AI-driven Game-Based Language Teaching (GBLT) with advanced neuroscience to transform language education for visually impaired learners. Built on the principles of neuroplasticity and epigenetics, the approach leverages educational psychology with the help of adaptive AI to deliver personalized, gamified learning experiences that reshape neural pathways, improve memory retention, and strengthen emotional resilience. By fostering low-stress, immersive environments, it triggers positive epigenetic changes, enhancing long-term cognitive flexibility. This method article presents an interdisciplinary inclusive scientific framework that unites gamification, technology, epigenetics, and neuroscience, empowering learners and promoting sustainable well-being, while laying the groundwork for intergenerational academic and personal growth.<ul><li><span>•</span><span><div>To propose a teaching methodology that aims to bridge gaps in traditional and game based language teaching by integrating neuroscience and epigenetics, creating an inclusive framework tailored to meet the unique needs of visually impaired learners.</div></span></li><li><span>•</span><span><div>The method emphasizes creating stress-free, rewarding educational environments that induce neural and epigenetic changes. These changes optimize gene expression to improve retention, emotional resilience, and cognitive flexibility, ensuring both immediate academic success and lifelong developmental benefits for diverse learners.</div></span></li><li><span>•</span><span><div>This framework promotes cognitive, emotional, social and biological development alongside language acquisition giving a holistic mode of growth.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103143"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143024091","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":"A multi-dimensional student performance prediction model (MSPP): An advanced framework for accurate academic classification and analysis","authors":"V. Balachandar,&nbsp;K. Venkatesh","doi":"10.1016/j.mex.2024.103148","DOIUrl":"10.1016/j.mex.2024.103148","url":null,"abstract":"<div><div>Forecasting student performance with precision in the educational space is paramount for creating tailor-made interventions capable to boost learning effectiveness. It means most of the traditional student performance prediction models have difficulty in dealing with multi-dimensional academic data, can cause sub-optimal classification and generate a simple generalized insight. To address these challenges of the existing system, in this research we propose a new model Multi-dimensional Student Performance Prediction Model (MSPP) that is inspired by advanced data preprocessing and feature engineering techniques using deep learning. We developed a method that targets the common issues associated with educational datasets over imbalanced and temporal settings which is also explainable through AI features. Moreover, through adaptive hyper-parameter tuning and advanced graph neural network layers in the MSPP model allow to make output more dense representation for predictions resulting more accurate classification. The experiments results show that MSPP outperforms the other EAI&amp;ML, MTSDA, XAI, DGNN and DLM with high accuracy 76 %, precision score of 0.79 and macro F1-score of 0.73. The model also helps to bring down the False Positive Rate (FPR) substantially at a 0.15 level, which ensures more reliable predictions for student classification.<ul><li><span>•</span><span><div>The model of the MSPP includes contextual information and multi-layered analysis in order to improve prediction accuracy, placing a sound basis for predicting students in different performance categories such as distinction, pass, fail or withdrawn.</div></span></li><li><span>•</span><span><div>Our approach is obviously to generalize and extract those sparse, heterogeneous academic data in the form of structured training record using domain specific preprocessing integrating with multi-class classification mechanisms that improves on precision-recall across multiple categories.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103148"},"PeriodicalIF":1.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143047236","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":"Uniform hyperscanning paradigm to study cooperation and competition","authors":"Pablo A. Nogueira-Islas ,&nbsp;Paola V. Olguín-Rodríguez ,&nbsp;Hugo Tlahuext-Aca ,&nbsp;Markus F. Müller","doi":"10.1016/j.mex.2024.103139","DOIUrl":"10.1016/j.mex.2024.103139","url":null,"abstract":"<div><div>It is assumed that social interaction like cooperation or competition takes place via synchronized interbrain activity, measurable via hyperscanning experiments. However, interbrain synchronization might also be due to common external stimuli without any genuine inter-personal interaction. In addition, a consistent experimental paradigm is required to distinguish between different modalities such as cooperation or competition. To facilitate retrospective analysis, it would also be desirable for the task that the participants have to perform not to be divided into short time intervals, but to be continuous over a longer period of time. Here we present an experimental protocol that allows<ul><li><span>•</span><span><div>The same paradigm for different modalities</div></span></li><li><span>•</span><span><div>Tasks demands a continuous interaction during a period of minutes</div></span></li><li><span>•</span><span><div>Contains two different control conditions to differentiate between inter-brain synchronization provoked by genuine interpersonal interactions and accidental synchronization via common external stimuli.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103139"},"PeriodicalIF":1.6,"publicationDate":"2024-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11755012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028991","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":"Exploring computational thinking, executive functions, visuospatial skills and experiences with toys in early childhood: Protocol for a controlled trial","authors":"Carolina Robledo-Castro ,&nbsp;Camilo Vieira Mejía ,&nbsp;Jennifer Chiu","doi":"10.1016/j.mex.2024.103145","DOIUrl":"10.1016/j.mex.2024.103145","url":null,"abstract":"<div><div>The research aims to evaluate the effect of a robotics-based computational thinking program on executive functions and visuospatial skills in preschool children. Additionally, the study will explore the relationship between these three variables and early experiences with toys. The study will be a cluster-randomized controlled trial with pre- and post-intervention measures. Participants will be preschool children aged 5 to 6 years from both public and private institutions. The intervention will involve a new educational robotics device called ROVERSA and will consist of eight sessions distributed over four weeks, with the experimental group placed on a waitlist. To assess executive functions and visuospatial skills, standardized and validated neuropsychological measures will be used, including the Flanker task, the NIH Toolbox Card Sorting Test, the Corsi Block Test, the NEPSY-II Mental Rotation Test, the Pyramid of Mexico from the ENI-2 battery, and the Computational Thinking Test (CTt). Data analysis will begin with a hypothesis tested through ANOVA-MR, and linear regressions will be implemented to assess the relationship between variables. It is expected that the results will contribute to the discussion on teaching computational thinking and educational robotics as early learning experiences and their impact on the cognitive development of children.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103145"},"PeriodicalIF":1.6,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11764239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143045928","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":"Methodological study on coal-based microbial modification of mineral black clay to overcome plant growth challenges on open-pit mine dumps in cold regions","authors":"María Laura Gigena ,&nbsp;Dong Xiao ,&nbsp;Fangzhou Li ,&nbsp;Chengyu Wu ,&nbsp;Yuhong Zhang","doi":"10.1016/j.mex.2024.103138","DOIUrl":"10.1016/j.mex.2024.103138","url":null,"abstract":"<div><div>A critical challenge in ecological restoration of open-pit mine dumps in cold regions with limited topsoil resources is how to rapidly mitigate the plant growth-inhibitory effects of mineral black clay, thereby converting it into arable soil. Leveraging the high degradation capacity of coal seam-associated microorganisms on fossil carbon materials, combined with soil conditioning techniques, this study developed a microbial-based approach for modifying black clay. Seed germination experiments informed both laboratory and field trial designs. This approach focused on removing germination-inhibiting compounds, establishing a plant-compatible soil ecological environment, and employing composite strategies to reduce soil viscosity. Field experiments demonstrated that in-situ microbial modification of black clay effectively supports ecological restoration, enhances plant growth. To refine and implement this microbial-based bioremediation strategy in practical ecological restoration efforts, two key technical methods were employed:<ul><li><span>•</span><span><div>A comprehensive experimental protocol was established for black clay bioremediation, covering both laboratory-scale and field test procedures, ensuring the approach can be readily adapted to diverse environmental conditions.</div></span></li><li><span>•</span><span><div>By incorporating the characteristics of local species, employing representative seed germination tests to assess plant compatibility can facilitate a rapid evaluation of the bioconversion of mineral substrates into arable soils.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"14 ","pages":"Article 103138"},"PeriodicalIF":1.6,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046526","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}