MethodsX最新文献

{"title":"A blockchain-enabled healthcare system for cervical cancer risk prediction using enhanced metaheuristic optimised graph convolutional attention based GRU","authors":"Anusha R,&nbsp;Srinivas Prasad","doi":"10.1016/j.mex.2025.103564","DOIUrl":"10.1016/j.mex.2025.103564","url":null,"abstract":"<div><div>Cervical cancer is a serious health concern that entails high risks for individuals due to delayed detection and treatment worldwide. Formal screening for the condition is challenging in developing countries due to several factors, including medical costs, access to healthcare facilities, and delayed symptom manifestation. A blockchain-enabled healthcare system for cervical cancer risk prediction ensures data security, privacy, and accurate risk assessment. This system uses blockchain to provide decentralised, tamper-proof storage and access control over sensitive patient data, ensuring that only authorized entities can interact with the information. An improved spotted hyena optimization algorithm is employed for cervical cancer risk prediction, fine-tuning a Graph Convolutional Network (GCN) integrated with an Attention Mechanism and a Gated Recurrent Unit (GRU). The GCN captures complex relationships between medical attributes and patients, while the attention mechanism dynamically assigns weights to features based on relevance, improving predictive accuracy. The GRU processes sequential data, such as medical history, to model temporal dependencies in the risk factors. The metaheuristic optimization further enhances the model by finding the optimal parameters, boosting performance</div><div>Introduces a blockchain-enabled system for secure and decentralized medical data management</div><div>Applies an intelligent model for predicting cervical cancer risk using patient health records</div><div>Demonstrates improved accuracy, privacy, and reliability over traditional diagnostic methods</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103564"},"PeriodicalIF":1.9,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896174","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":"Rapid one-step CRISPR-cas vector assembly by isothermal spacer removal linearization and sequence-ligation independent cloning (ISRL-SLIC)","authors":"Claus Krogh Madsen ,&nbsp;Tobias Hanak ,&nbsp;Henrik Aronsson ,&nbsp;Henrik Brinch-Pedersen","doi":"10.1016/j.mex.2025.103567","DOIUrl":"10.1016/j.mex.2025.103567","url":null,"abstract":"<div><div>CRISPR-Cas genome editing is a powerful tool in various fields, but current cloning methods can be time-consuming due to the frequent use of intermediate entry vectors and multiple steps involving restriction enzymes and ligases. These multiple steps can create a bottleneck in CRISPR-Cas experiments. In response to this challenge, we propose a highly efficient streamlined approach, which enables simultaneous linearization of the acceptor plasmid and protospacer cloning in a single isothermal reaction. This eliminates the need for entry vectors, pre-linearization of vectors, and <em>in vitro</em> ligation, thus significantly simplifying the cloning process. The method can be applied to clone short synthetic oligos for single protospacer constructs or multiple amplicons for multiplex genome editing designs. Either way, researchers can proceed directly to <em>Escherichia coli</em> transformation after a one-hour isothermal reaction and recover the final construct within two days. By combining the advantages of sequence-ligation independent cloning (SLIC) cloning with a streamlined workflow, our approach facilitates rapid and efficient construction of CRISPR-Cas vectors and holds the promise of accelerating research and development in genome editing and related fields.</div><div>To expedite the cloning of constructs, we propose a rapid one-step CRISPR-Cas vector assembly method that combines isothermal spacer removal with a sequence-ligation-independent cloning reaction.</div><div>We could show that <strong>I</strong>sothermal <strong>S</strong>pacer <strong>R</strong>emoval <strong>L</strong>inearization and <strong>S</strong>equence-<strong>L</strong>igation <strong>I</strong>ndependent <strong>C</strong>loning (ISRL-SLIC) can create single, double and triple protospacer constructs in one reaction with scalability.</div><div>The ISRL-SLIC reaction delivers clones under a broad range of oligo concentration making it a robust and time saving alternative to other methods for constructing CRISPR-Cas vectors.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103567"},"PeriodicalIF":1.9,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144867451","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":"Validation and application of a visual LAMP assay for Mpox diagnosis — Insights from clinical samples in Thailand","authors":"Wansadaj Jaroenram ,&nbsp;Yada Ongchanchai ,&nbsp;Ravee Nitiyanontakij ,&nbsp;Pawita Suwanwatthana ,&nbsp;Ratchana Ponang ,&nbsp;Wansika Kiatpathomchai","doi":"10.1016/j.mex.2025.103568","DOIUrl":"10.1016/j.mex.2025.103568","url":null,"abstract":"<div><div>Despite numerous recent advances in infectious disease diagnostic technologies including quantitative (q) polymerase chain reaction (PCR) and antigen test kit (ATK), there remains a need to develop more efficient point-of-care assays for large-scale operations. In an effort towards such a screening test for low-resource settings, we have established a colorimetric loop-mediated isothermal amplification assay and detected the amplified DNA via naked-eye observation to maximize assay simplicity using monkeypox (Mpox) as a model. The assay is cheap, highly sensitive and specific to Mpox with the potential for translation into broader applications.<ul><li><span>•</span><span><div>Our protocol offers a simpler, faster, and cheaper test for Mpox than the current gold-standard qPCR, with 100% accuracy.</div></span></li><li><span>•</span><span><div>assay enables decentralized screening and provides visually interpretable results immediately after incubation</div></span></li><li><span>•</span><span><div>The versatility of this protocol allows for easy adaptation to detecting new or re-emerging diseases, utilizing a visual readout for maximum simplicity.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103568"},"PeriodicalIF":1.9,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144887081","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":"Bacterial concrete: the future of self-healing and sustainable infrastructure","authors":"Anumol Sukumaran ,&nbsp;V Johnpaul ,&nbsp;N Balasundaram ,&nbsp;S Senthil Kumar","doi":"10.1016/j.mex.2025.103569","DOIUrl":"10.1016/j.mex.2025.103569","url":null,"abstract":"<div><div>This study investigates the durability enhancement of bacterial concrete incorporating microbial strains (Bacillus Licheniformis, Bacillus Flexus, Pseudomonas stutzeri, Escherichia coli, and Bacillus subtilis) through microbial-induced calcium carbonate precipitation (MICP). Various durability tests, including water absorption, RCPT, sulphate resistance, hydrochloric acid strength loss, sorptivity, and energy-dispersive X-ray analysis (EDAX), were conducted to evaluate the effectiveness of bacterial concrete. Bacterial concrete significantly reduces water absorption and chloride ion penetration, with Bacillus subtilis (M16) and Bacillus Flexus (M7) demonstrating the highest impermeability. Sulphate resistance analysis confirmed reduced weight loss before and after healing, highlighting microbial self-healing capabilities. Hydrochloric acid strength loss and sorptivity tests further validated improved acid resistance and reduced capillary absorption. EDAX analysis confirmed the formation of calcium carbonate, contributing to matrix densification and enhanced durability. Overall, microbial concrete exhibited superior resistance to environmental degradation, with Bacillus subtilis, Bacillus Flexus, and Bacillus Licheniformis at higher concentrations (10⁶ cells/ml) providing the most significant improvements.</div><div>Bacterial concrete showed increased workability and notable compressive, flexural, and split tensile strengths with Bacillus subtilis and Bacillus licheniformis at 10⁶ cells/mL,</div><div>Bacterial concrete provide the best self-healing and strength recovery capability; SEM and XRD data revealed higher density and effective crack healing.</div><div>Bacterial concrete is a sustainable material since it provides long-term durability by means of inherent self-healing systems.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103569"},"PeriodicalIF":1.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144867452","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":"Method for fetal ultrasound image classification using pseudo-labelling with PCA-KMeans and an attention-augmented MobileNet-LSTM model","authors":"Aniket K. Shahade ,&nbsp;Priyanka V. Deshmukh ,&nbsp;Pritam H. Gohatre ,&nbsp;Kanchan S. Tidke ,&nbsp;Rohan Ingle","doi":"10.1016/j.mex.2025.103563","DOIUrl":"10.1016/j.mex.2025.103563","url":null,"abstract":"<div><div>Accurate classification of fetal ultrasound images is critical for early diagnosis, yet remains challenging due to limited labeled data and high inter-class variability. This study presents a robust deep learning framework that combines a MobileNet backbone with multi-head self-attention and LSTM layers to enhance feature learning and temporal context. To address data scarcity and imbalance, unsupervised clustering was employed using Principal Component Analysis (PCA) for dimensionality reduction and K-means (k=4) for pseudo-label generation. These pseudo-labeled clusters were then balanced using oversampling techniques. The proposed model was trained using transfer learning on the augmented dataset and achieved a test accuracy of approximately 98 % with a macro-F1 score of 0.98, indicating highly reliable classification performance.<ul><li><span>•</span><span><div>Employed PCA (100 components) and K-means (k=4) for effective pseudo-labeling and class balancing.</div></span></li><li><span>•</span><span><div>Designed a hybrid deep learning architecture using MobileNet, multi-head attention, and LSTM.</div></span></li><li><span>•</span><span><div>Achieved ∼98 % test accuracy and 0.98 macro-F1 score, demonstrating strong model generalization.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103563"},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144860399","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":"Detailed examination of a double-dividend case in a recent two-engine growth model","authors":"Kei Hosoya","doi":"10.1016/j.mex.2025.103562","DOIUrl":"10.1016/j.mex.2025.103562","url":null,"abstract":"<div><div>An important recent achievement in environmental macroeconomics is that reported by Cheng et al. [J. Macroecon. 81, 103614 (2024)]. Their model implements multiple growth engines and realizes the double dividend of economic growth and environmental improvements. However, regarding the environmental aspect, the situation could change drastically in general cases, and so a detailed understanding of the mechanisms in such cases is important for future similar studies. This paper presents additional numerical results that complement the analysis by Cheng et al. (2024), clarifies the underlying mechanisms, and makes some policy comments.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103562"},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004058","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":"The state of the art in Blue Amazon biodiversity: Protocol for a systematic review","authors":"G.B. Farias ,&nbsp;M. Bassoi ,&nbsp;J.B. Vasconcelos ,&nbsp;Y. Costa ,&nbsp;J.N. Freire ,&nbsp;J. Lucatelli ,&nbsp;M. Arangüena-Proaño ,&nbsp;A.J. Silva ,&nbsp;M. Previero ,&nbsp;L.H. Bordin ,&nbsp;B.P. Ferreira ,&nbsp;L.C. Lopes ,&nbsp;E.R. Secchi","doi":"10.1016/j.mex.2025.103561","DOIUrl":"10.1016/j.mex.2025.103561","url":null,"abstract":"<div><div>Brazil holds approximately 40 % of its territory in the sea, an area known as the \"Blue Amazon\" due to its dimension, and strategic, economic and biological significance. Despite this importance, much of Brazil’s marine biodiversity remains poorly mapped and quantified. Therefore, the National Institute of Science and Technology for the Blue Amazon Biodiversity (INCT-BAA) was established to expand knowledge on this region. One of INCT-BAA's primary objectives is to develop an integrated database that combines historical and contemporary information on marine biodiversity. To support this objective, a state-of-the-art systematic literature review was conducted to synthesize existing knowledge on species occurrence, spatial and temporal distribution, natural and anthropogenic threats, ecological scope of studies, and knowledge gaps and trends. Given the broad scope of the review, a specific protocol was developed, requiring adaptations to traditional systematic review methodologies (e.g., elaboration of a robust glossary of categories and methods to extract species locations from papers), which are detailed in this document. The review was conducted over one year using 1,034 search strings across Web of Science, ScienceDirect, and Google Scholar and retrieving over 200,000 species occurrences from 7,687 studies, covering more than 27,000 species from 1917 to 2023.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103561"},"PeriodicalIF":1.9,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852841","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":"Design and performance of two stages square cut rectangular multiband microstrip fractal antenna","authors":"Sudhir Kadam ,&nbsp;Kamalakar Ravindra Desai ,&nbsp;Payal kadam ,&nbsp;Aarti Prasad Pawar ,&nbsp;Sonali Pawar ,&nbsp;Prof. Anuradha Nigade","doi":"10.1016/j.mex.2025.103559","DOIUrl":"10.1016/j.mex.2025.103559","url":null,"abstract":"<div><div>Modern wireless systems require compact, low-profile, and multiband antennas. The designs offer high performance without structural complications. The classic, traditional single-band antenna mostly does not fit the bandwidth of applications. This study represented the challenges by introducing a two-stage square-cut fractal microstrip antenna design. This antenna integrated the two fractal geometries with one feed line and used periodical edge etching along with internal slotting to increase the electrical length and improve radiation efficiency without enlarging the size of the antenna. Through FEM-based simulation, the antenna dual-band characteristics for S-band (2.4263–3.2018 GHz) and C-band (5.3789–7.2308 GHz), giving a total bandwidth of approximately 3.7 GHz. The gain value remains stable about 6 dB in the S-band and 7.5 dB in the C-band, while return loss stays below –10 dB and VSWR under 2. These results offer a scalable platform for further research in reconfigurable and flexible antenna systems.<ul><li><span>•</span><span><div>The antenna is beneficial for 2.4263–3.2018 GHz bandwidth of approximately 1.53 GHz and 5.3789–7.2308 GHz bandwidth of approximately 1.53 GHz respectively with minimal power reflection within bands.</div></span></li><li><span>•</span><span><div>Smith chart maintained at less than 51Ω. A few deviations occurred due to manual errors duringfabrication, soldering and testing antenna.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103559"},"PeriodicalIF":1.9,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144840948","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":"A novel hybrid approach for thyroid disease detection: Integrating cuttlefish algorithm and simulated annealing for optimal feature selection","authors":"Kapil Shrivastava ,&nbsp;Saroj Pandey ,&nbsp;Rishav Dubey ,&nbsp;Mayank Namdev ,&nbsp;Vipin Tiwari ,&nbsp;Aditi Sharma","doi":"10.1016/j.mex.2025.103558","DOIUrl":"10.1016/j.mex.2025.103558","url":null,"abstract":"<div><div>Effective treatment relies on a timely diagnosis, which is critical in the case of thyroid disorder—one of the chronic endocrine disorders alongside diabetes and obesity—with profound health concerns. Thyroid disorders occur due to the malfunctioning of the thyroid gland, which may result in an imbalanced metabolic rate due to inappropriate hormone levels synthesis. An overactive gland results in hyperthyroidism, whereas an underactive or sluggish thyroid lead to hypothyroidism. Both disorders, if not detected and managed timely, can lead to severe health complications. Early identification is crucial to delay or avoid debilitating complications and achieve a better quality of life through the right medical interventions and precise hormonal readjustments. The proposed hybrid algorithm method finds the best features for finding thyroid disease uses performance measures such as accuracy, F1-score, precision, and recall. The research demonstrates promising results with an accuracy of 98.91 % and an F1-score of 94.83, showcasing the robustness of the proposed algorithms on a benchmark dataset. The findings hold potential to improve clinical decision-making processes. This study advances medical diagnostics by combining machine learning algorithms with nature-inspired optimization techniques to detect thyroid illnesses in their early stages.<ul><li><span>•</span><span><div>This article proposes a novel hybrid algorithm that combines the Cuttlefish Optimization Algorithm (CFA) and Simulated Annealing (SA) to find the best features for finding thyroid disease.</div></span></li><li><span>•</span><span><div>The study uses machine-learning models for classification.</div></span></li><li><span>•</span><span><div>The integration of machine learning and nature-inspired optimization significantly enhances the diagnostic capabilities of healthcare systems, enabling prompt diagnosis and treatment planning for thyroid disorders.</div></span></li></ul></div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103558"},"PeriodicalIF":1.9,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144830149","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":"Landfill site suitability analysis for sustainable solid waste management using AHP and GIS in Burdur Lake Basin, Türkiye","authors":"İbrahim İskender Soyaslan","doi":"10.1016/j.mex.2025.103555","DOIUrl":"10.1016/j.mex.2025.103555","url":null,"abstract":"<div><div>A critical challenge confronting cities today is the disposal or storage of generated waste. Municipal solid waste landfill site appraisal is essential for sustainable and ecologically responsible solid waste management. In this study, a suitability analysis for municipal solid waste disposal sites in the Burdur Lake Basin was conducted using multi-criteria decision-making tools, specifically the Analytic Hierarchy Process and Geographic Information System. AHP established a hierarchy structure that facilitated the determination of the significance levels of the parameter and sub-parameter through the assignment of weights. A landfill suitability map was created using these parameter weights in a GIS analysis. The study region is categorized into four landfill suitability classes: inappropriate (35.72 %), low suitability (23.75 %), suitable (18.14 %) and high suitability (22.38 %). Thus, it has been determined that the conditions of the existing landfill site in Burdur province are met, and two alternative landfill sites have been identified for future use.</div><div>The study offers valuable insights for decision-makers engaged in sustainable solid waste management in Türkiye and comparable regions.</div><div>– How to find an environmental landfill to achieve sustainable development</div><div>- What regional characteristics and parameters are considered in the selection of the landfill site.</div></div>","PeriodicalId":18446,"journal":{"name":"MethodsX","volume":"15 ","pages":"Article 103555"},"PeriodicalIF":1.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144826501","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}