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Multi-pathway feature-level interpretability in MHC-i antigen presentation via concept-based modeling. 基于概念建模的MHC-i抗原呈递中的多途径特征水平可解释性。
IF 4.3 3区 生物学
Methods Pub Date : 2026-05-06 DOI: 10.1016/j.ymeth.2026.05.005
Piyush Borole, Denise Boulanger, Ajitha Rajan
{"title":"Multi-pathway feature-level interpretability in MHC-i antigen presentation via concept-based modeling.","authors":"Piyush Borole, Denise Boulanger, Ajitha Rajan","doi":"10.1016/j.ymeth.2026.05.005","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.05.005","url":null,"abstract":"<p><p>Accurate prediction of MHC-I antigen presentation is central to neoantigen discovery and immunotherapy development. Although recent deep-learning based predictors achieve high accuracy, most operate as black-box models, which limits interpretability, and consequently trustworthiness of these predictors. We present MHCCBM, a gray-box framework that decomposes antigen presentation into a set of pathway-level intermediate concepts. Each step, i.e. proteasomal cleavage, TAP transport, peptide-MHC binding affinity, and chaperone dependency is treated as an independent predictive module, allowing different computational or experimental estimators to be substituted without altering the overall model. This architecture naturally supports representational multimodality, permitting the integration of sequence-based, structure-informed, or empirical predictors. In our reference implementation, ESM-2-derived models estimate peptide processing and chaperone dependency, while peptide-MHC binding affinity is predicted using MHCflurry. The concept outputs are combined using logistic regression. Our accuracy is comparable to that of state-of-the-art accuracy while providing MHC-I pathway level interpretability consistent with known cellular mechanisms.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TEAMSTER: End-to-end pipeline for generation, processing, and automated quantitative image analysis of 3D tumour spheroids for nanobiology. TEAMSTER:端到端的管道,用于纳米生物学3D肿瘤球体的生成、处理和自动定量图像分析。
IF 4.3 3区 生物学
Methods Pub Date : 2026-05-06 DOI: 10.1016/j.ymeth.2026.04.015
Linda Barbieri, Andrea Banfi, Stefania Garbujo, Lucia Salvioni, Chiara Baioni, Giulia Tomaino, Maria Rita Chelazzi, Luisa Fiandra, Miriam Colombo, Davide Prosperi, Metello Innocenti
{"title":"TEAMSTER: End-to-end pipeline for generation, processing, and automated quantitative image analysis of 3D tumour spheroids for nanobiology.","authors":"Linda Barbieri, Andrea Banfi, Stefania Garbujo, Lucia Salvioni, Chiara Baioni, Giulia Tomaino, Maria Rita Chelazzi, Luisa Fiandra, Miriam Colombo, Davide Prosperi, Metello Innocenti","doi":"10.1016/j.ymeth.2026.04.015","DOIUrl":"https://doi.org/10.1016/j.ymeth.2026.04.015","url":null,"abstract":"<p><p>Three-dimensional (3D) tumour spheroids are widely used as physiologically relevant in vitro models to study tumour biology, therapeutic responses, and the distribution of drugs and nanomaterials. However, experimental workflows for spheroid-based studies remain highly heterogeneous, with limited standardization across spheroid generation, processing, and quantitative analysis, hindering reproducibility and accessibility. Here, we present TEAMSTER, an integrated, end-to-end pipeline for the generation, cryosectioning, immunostaining, and quantitative image analysis of tumour spheroids. The workflow combines optimized protocols for reproducible spheroid formation that minimize variability, a liquid nitrogen-free, colour-coded OCT embedding strategy improving spheroid localization during cryosectioning, standardized fixation and staining procedures compatible with multiplex fluorescence imaging, and a semi-automated, GUI-based CellProfiler pipeline enabling unbiased quantitative analysis without coding skills, machine learning, or dedicated computing hardware. TEAMSTER is experimentally validated in two distinct tumour spheroid models treated with fluorescently labelled nanoconjugates. Quantitative performance metrics for spheroid preparation (intraplate and interplate coefficients of variation) and image segmentation benchmarking (Dice and IoU coefficients) support the robustness of single-cell-resolved measurements across cryosectioned spheroid models and imaging conditions. By prioritizing experimental robustness, standardization, and usability, TEAMSTER provides a practical methodological resource for reproducible quantitative spheroid-based studies in cancer biology and nanomedicine.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147855697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Novel methods for the discovery of disease-associated T cell epitopes in autoimmunity 发现自身免疫疾病相关T细胞表位的新方法
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-11 DOI: 10.1016/j.ymeth.2026.02.004
Eline Mertens , Barbara Willekens , Judith Derdelinckx , Nathalie Cools
{"title":"Novel methods for the discovery of disease-associated T cell epitopes in autoimmunity","authors":"Eline Mertens ,&nbsp;Barbara Willekens ,&nbsp;Judith Derdelinckx ,&nbsp;Nathalie Cools","doi":"10.1016/j.ymeth.2026.02.004","DOIUrl":"10.1016/j.ymeth.2026.02.004","url":null,"abstract":"<div><div>A detailed understanding of the pathology of autoimmune diseases hinges on the identification of self-antigens and epitopes targeted by the immune system. While the characterization of autoantibodies is now well-established, facilitating both mechanistic insights and clinical biomarker applications, the identification of autoreactive T cell epitopes remains considerably more challenging. This complexity is amplified by the presence of autoreactive T cells in healthy individuals, necessitating highly sensitive and specific methods to allow for the detection of subtle differences between the autoreactive T cell population in healthy controls and in patients. Fortunately, T cell epitope discovery is a rapidly advancing field, with new methods continually emerging to improve sensitivity, throughput, and resolution. In this review, we will provide a structured overview of the key methods used to identify T cell epitopes, spanning both foundational techniques that<!--> <!-->have been instrumental in the early discovery of self-epitopes involved in autoimmunity as well as recent high throughput approaches that offer enhanced precision and scalability. In the second part, we give an overview of the techniques used in the validation of the role of self-peptides in the autoimmune disorder. We conclude by discussing future directions in the field, emphasizing the critical role of T cell epitope discovery in driving the development of targeted, antigen-specific therapies for autoimmune disorders. This review aims to provide a practical and conceptual framework for T cell epitope discovery in autoimmune diseases, integrating established experimental approaches with emerging computational and high-throughput methodologies to guide informed method selection in contemporary research.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 64-82"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146187063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ultra-sensitive diagnostic platform utilizing gold nanoparticle integrated in a freestanding hydrogel matrix 利用金纳米颗粒集成在独立水凝胶基质中的超灵敏诊断平台。
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-02 DOI: 10.1016/j.ymeth.2026.02.002
Omar M. Rahman , Shengxi Lan , Andrea M.A. Pizano , Woosuk Chung , Younghun Kim , Dae Kun Hwang
{"title":"Ultra-sensitive diagnostic platform utilizing gold nanoparticle integrated in a freestanding hydrogel matrix","authors":"Omar M. Rahman ,&nbsp;Shengxi Lan ,&nbsp;Andrea M.A. Pizano ,&nbsp;Woosuk Chung ,&nbsp;Younghun Kim ,&nbsp;Dae Kun Hwang","doi":"10.1016/j.ymeth.2026.02.002","DOIUrl":"10.1016/j.ymeth.2026.02.002","url":null,"abstract":"<div><div>Fluorescence-based analysis for protein detection has been widely adopted; however, they fall short in achieving ultra-sensitive detection because of their inherently low signal-to-noise ratio at sub-picomolar concentrations. To overcome this limitation, signal amplifying materials such as gold nanoparticles (AuNPs) have been integrated into various detection platforms to enhance fluorescence signals. However, fabrication of such AuNP integrated platforms remains complex, often requiring sophisticated fabrication steps, yet none approach the ultra-sensitive detection range of 10<sup>0</sup> fg mL<sup>−1</sup>. In this study, we enabled analysis of captured protein/antibody at 10<sup>0</sup> fg mL<sup>−1</sup> concentrations through fluorescence signals utilizing freestanding gold nanoparticle integrated freestanding hydrogel platforms. The platform is fabricated by integrating AuNPs into the hydrogel matrix using a single-step photolithographic technique. The integrated AuNPs significantly enhanced the fluorescence signals compared to controls. Notably, at fg mL<sup>−1</sup> levels of fluorophore, the AuNP integrated hydrogels produced a robust optical signal in contrast to negligible responses observed in controls. The platform’s versatility was validated using tumor necrosis factor-alpha antibody (TNF-α Ab), achieving detection at 10<sup>0</sup> fg mL<sup>−1</sup>. By synergizing the hydrogels’ porous structure with AuNPs’ signal amplification, this platform successfully achieves fluorescence-based ultra-sensitive protein/antibody detection.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 43-52"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146117321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Disentangling the events that constitute the main phase transition of predominantly neutral lipid bilayers containing anionic lipids by measuring their macroscopic properties 通过测量阴离子脂质的宏观性质,解开构成主要中性脂质双分子层主要相变的事件。
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-08 DOI: 10.1016/j.ymeth.2026.02.005
Ramona Petko , Ivan Marić , Barbara Pem , Danijela Bakarić
{"title":"Disentangling the events that constitute the main phase transition of predominantly neutral lipid bilayers containing anionic lipids by measuring their macroscopic properties","authors":"Ramona Petko ,&nbsp;Ivan Marić ,&nbsp;Barbara Pem ,&nbsp;Danijela Bakarić","doi":"10.1016/j.ymeth.2026.02.005","DOIUrl":"10.1016/j.ymeth.2026.02.005","url":null,"abstract":"<div><div>The thinning of lipid bilayers during their main phase transition, as the outcome of the weakening of van der Waals interactions between their hydrocarbon chains and the hydration of the polar headgroup region, displays a peak at the specific temperature (<em>T</em><sub>m</sub>). The most common technique used for <em>T</em><sub>m</sub> determination is differential scanning calorimetry (DSC), which provides the required information straightforwardly and rapidly, but it cannot provide any details on the molecular-level events that underlie the main phase transition. To uncouple the impact of hydrogen bonding and (de)protonation in the polar headgroup region on the measured <em>T</em><sub>m</sub>, in this work, we determined the latter of anionic lipid-containing predominantly neutral bilayers (10:90% molar ratio) in Britton-Robinson buffers with pH values 4, 7, and 9 using macroscopic techniques. Specifically, the temperature-dependent UV–Vis spectra combined with the measurement of refractive indices allowed the modeling of the bilayer thickness (<em>d</em>) change during the main phase transition. Significantly, the alteration in the hydrogen bonding pattern affected the change in <em>d</em>, unlike the deprotonation of anionic lipids. A molecular polarizability displayed an abrupt decrease upon the main phase transition, but its magnitude and associated uncertainty level were found to be acceptable only for a lipid mixture in which anionic lipid does not exchange protons with aqueous milieu, i.e., a pH-dependent (de)protonation obscures more precise determination of <em>T</em><sub>m</sub>. Besides the determination of <em>T</em><sub>m</sub> values, this new methodology enabled us to rank the contributions to <em>T</em><sub>m</sub> value: van der Waals interactions &gt; hydrogen bonding &gt; (de)protonation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 53-63"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An optimized method for establishing experimental rat periodontitis using “double-ligature” technique 采用“双结扎”技术建立实验性大鼠牙周炎的优化方法。
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-03 DOI: 10.1016/j.ymeth.2026.01.010
Cheng Hu , Haixia Wang , Yuwei Liao , Xiaoli Hu
{"title":"An optimized method for establishing experimental rat periodontitis using “double-ligature” technique","authors":"Cheng Hu ,&nbsp;Haixia Wang ,&nbsp;Yuwei Liao ,&nbsp;Xiaoli Hu","doi":"10.1016/j.ymeth.2026.01.010","DOIUrl":"10.1016/j.ymeth.2026.01.010","url":null,"abstract":"<div><div>Establishing stable and dependable animal models of experimental periodontitis is critical in advancing our understanding of the etiology, clinical diagnosis, and treatment of periodontitis. However, conventional silk ligation methods for inducing periodontitis in rats have limitations, with silk thread detachment being a major concern. In this study, we established a reliable rat periodontitis model using a novel “double-ligature” technique combining silk sutures with orthodontic wires, augmented by a high-sugar diet. Thirty rats were randomized into five groups: control, wire-only, silk-only, wire+silk, and wire+silk+sugar. After 2 weeks, the wire+silk+sugar group demonstrated significantly elevated clinical indices (sulcus bleeding index, probing depth, plaque index) versus controls (*p* &lt; 0.05), alongside severe alveolar bone resorption quantified by micro-CT. Molecular analyses revealed upregulated inflammatory gene expression (e.g., TNF-α, IL-1β) in double-ligature groups. Histology confirmed extensive immune infiltration and periodontal ligament disruption. The combined approach induced robust periodontitis with 103% greater CEJ-ABC distance versus controls, while TRAP staining revealed 5-fold increased osteoclast activity. By this “double-ligature” technique, the pathogenesis of periodontitis can be studied on the one hand, and the therapeutic effect of biomaterials on the alveolar bone defects caused by periodontitis can be verified on the other hand. This reproducible method overcomes traditional silk ligature limitations (e.g., thread detachment) and provides a foundation for translational periodontitis research.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 20-29"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146123306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing dna调控的金属纳米材料结构工程:一种先进的光学生物传感策略
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-03 DOI: 10.1016/j.ymeth.2026.02.001
Junyao Li , Ling Cai , Peiming Liu , Rui Zhang , Wenrong Cai , Datong Wu , Laidi Xu , Yong Kong
{"title":"DNA-regulated structural engineering of metal nanomaterials: A strategy for advanced optical biosensing","authors":"Junyao Li ,&nbsp;Ling Cai ,&nbsp;Peiming Liu ,&nbsp;Rui Zhang ,&nbsp;Wenrong Cai ,&nbsp;Datong Wu ,&nbsp;Laidi Xu ,&nbsp;Yong Kong","doi":"10.1016/j.ymeth.2026.02.001","DOIUrl":"10.1016/j.ymeth.2026.02.001","url":null,"abstract":"<div><div>The development of highly sensitive optical biosensors has emerged as a focal point in chemical research, exerting a profound influence on numerous fields related to the national economy and public welfare. Owing to their dual nanostructural and metallic properties, metal nanomaterials exhibit certain distinctive optical properties. Among them, localized surface plasmon resonance (LSPR), surface-enhanced Raman scattering (SERS), and fluorescence emission are particularly prominent. Therefore, metal nanomaterials possess significant potential to enhance the analytical performance of optical biosensors. Compared to peptides and proteins, DNA demonstrates remarkable superiority in terms of the diversity of length, sequence, backbone structure, and modification groups. Integrating DNA with metal nanomaterials provides a prerequisite for accurately identifying targets and precisely regulating metal nanomaterials. Effectively combining the superior properties of DNA and metal nanomaterials represents a critical scientific challenge in facilitating the development of highly sensitive optical analytical approaches. Exploring novel strategies to regulate the optical properties of metal nanomaterials can provide more opportunities for developing high-performance optical biosensors. In this review, the regulation modes of DNA with metal nanomaterials can be summarized into three parts <em>i.e.</em>: the morphological evolution of DNA-guided metal nanomaterials, the assembly of DNA with metal nanomaterials, and the formation of DNA-templated metal nanomaterials. For each part, typical applications have been displayed based on regulating the optical properties of metal nanomaterials via DNA. Furthermore, perspectives and challenges are also discussed at the end of the review.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 1-19"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
From wrinkles to malignancy: small-molecule-mediated stem cell approaches in skin aging 从皱纹到恶性肿瘤:小分子介导的干细胞在皮肤衰老中的应用。
IF 4.3 3区 生物学
Methods Pub Date : 2026-04-01 Epub Date: 2026-02-06 DOI: 10.1016/j.ymeth.2026.02.003
Abdullah Alkhammash, Ghallab Alotaibi
{"title":"From wrinkles to malignancy: small-molecule-mediated stem cell approaches in skin aging","authors":"Abdullah Alkhammash,&nbsp;Ghallab Alotaibi","doi":"10.1016/j.ymeth.2026.02.003","DOIUrl":"10.1016/j.ymeth.2026.02.003","url":null,"abstract":"<div><div>Skin aging is driven by the progressive exhaustion of stem cell niches, epigenetic drift, and accumulation of senescent cells, which together promote both aesthetic decline and a pro-tumorigenic microenvironment. This review focuses on the emerging methodological theme of small-molecule-mediated reprogramming as a strategy to restore skin homeostasis. We evaluated the shift from traditional regenerative medicine toward targeted chemical modulation, focusing on the use of small-molecule cocktails to induce partial reprogramming and rejuvenate aged stem cell populations without erasing cellular identity. Central to this theme is the integration of high-throughput virtual screening and AI-driven predictive modeling to identify potent modulators of Wnt, Notch, and TGF-β pathways. We further bridge the gap between preclinical innovation and clinical application by analyzing “serious clinical studies” with proven efficacy, including randomized controlled trials of stem cell-derived secretomes and clinically validated small molecules, such as tretinoin and firming peptides. By contextualizing advanced delivery systems, including microneedles and stimuli-responsive nanoparticles, within this reprogramming framework, we demonstrate how spatially controlled interventions can optimize clinical outcomes. This review provides a unified perspective on how the intersection of computational drug discovery and niche-targeted pharmacology is moving small-molecule skin rejuvenation from theoretical potential to widespread clinical translation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"248 ","pages":"Pages 30-42"},"PeriodicalIF":4.3,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146140679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Korean longitudinal study on digitally optimized mental healthcare: a cohort profile 韩国对数字优化精神保健的纵向研究:队列概况。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2025-12-25 DOI: 10.1016/j.ymeth.2025.12.011
Ok Kim , Kyung-Hwa Choi , Tae Hui Kim , Sungmin Son , Jonghun Lee , Kyungmin Kim , Un Sun Chung , Eun-Jin Cheon , Ilju Lee , Hyunwoo Jung , Ho-Jang Kwon , Xue Han , Jonghyuk Choi , Jung Won Kim , Ah Lahm Shin , Jung Jae Lee
{"title":"Korean longitudinal study on digitally optimized mental healthcare: a cohort profile","authors":"Ok Kim ,&nbsp;Kyung-Hwa Choi ,&nbsp;Tae Hui Kim ,&nbsp;Sungmin Son ,&nbsp;Jonghun Lee ,&nbsp;Kyungmin Kim ,&nbsp;Un Sun Chung ,&nbsp;Eun-Jin Cheon ,&nbsp;Ilju Lee ,&nbsp;Hyunwoo Jung ,&nbsp;Ho-Jang Kwon ,&nbsp;Xue Han ,&nbsp;Jonghyuk Choi ,&nbsp;Jung Won Kim ,&nbsp;Ah Lahm Shin ,&nbsp;Jung Jae Lee","doi":"10.1016/j.ymeth.2025.12.011","DOIUrl":"10.1016/j.ymeth.2025.12.011","url":null,"abstract":"<div><div>The Korean Longitudinal Study on Digitally Optimized Mental Healthcare is an innovative multicenter trial-ready cohort study. It aims to develop a digitally integrated mental healthcare platform that integrates robots, artificial intelligence, and local community services. A total of 3,100 participants, including 1,000 from the previous Chungnam Province cohort and 700 each from Chungnam, Gangwon, and Daegu, will be recruited between December 2024 and the end of 2027. Sociodemographic factors and physical health data are collected at enrollment using questionnaires. Every four months, formal tools are used to conduct psychiatric diagnoses and determine participants’ mental health condition, such as depressive symptoms, anxiety symptoms, suicidality, stress, insomnia, loneliness, quality of life, and disability. We assessed smartphone overdependence at regular intervals. Passive data on phone usage, life patterns, and health monitoring from a smart band are collected in real time. Weekly ecological momentary assessments monitor daily life and mood and detect risk situations early. A subset of 500 participants engages in a Living Lab, collecting multi-modal data through robots and sleep radar sensors while evaluating the usability of and satisfaction with these devices. This study will show how tailored digital applications and web-based platforms can facilitate personalized self-help interventions, enhance expert–user interaction, and promote active user engagement. This approach can potentially reduce stigma and improve public awareness of mental healthcare by shifting from a treatment-centered model to a community-based prevention framework.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 41-49"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of a novel microsampling device to standardize the analysis of intranasal inflammatory biomarkers 一种新型微采样装置的开发,以标准化鼻内炎症生物标志物的分析。
IF 4.3 3区 生物学
Methods Pub Date : 2026-03-01 Epub Date: 2025-12-18 DOI: 10.1016/j.ymeth.2025.12.006
Tanya Lupancu , Jonathan Limpah , Esrin Aydin , Timothy Fan , Vanessa Wong , Joanne Rimmer , Brian S. Wang , David M. Yen , Eldin Rostom , Adam M. Damry
{"title":"Development of a novel microsampling device to standardize the analysis of intranasal inflammatory biomarkers","authors":"Tanya Lupancu ,&nbsp;Jonathan Limpah ,&nbsp;Esrin Aydin ,&nbsp;Timothy Fan ,&nbsp;Vanessa Wong ,&nbsp;Joanne Rimmer ,&nbsp;Brian S. Wang ,&nbsp;David M. Yen ,&nbsp;Eldin Rostom ,&nbsp;Adam M. Damry","doi":"10.1016/j.ymeth.2025.12.006","DOIUrl":"10.1016/j.ymeth.2025.12.006","url":null,"abstract":"<div><div>Nasal fluid biomarker analysis is an emerging technique for studying sinonasal pathophysiology, monitoring therapeutic efficacy, and discovering novel drug targets. Variability in biomarker results can be contributed to non-standardized collection methodology. To address this, a novel microsampler was developed, designed to enable precise site-specific sampling, consistent volume collection, and high analyte recovery. This study aims to evaluate the performance of this new microsampler device compared to commonly utilized flocked swab, and other absorbent materials. To do so, fixed volumes of a synthetic nasal fluid mimic were deposited onto the anterior region of the inferior turbinate of a 3D-printed sinus model to assess volumetric and collection site accuracy of the nasal microsampler, in comparison to a flocked swab. Additionally, protein biomarker recovery properties of the device’s absorption membrane, Leukosorb<sup>TM</sup>, versus experimental proprietary absorbent materials, were assessed using ELISA. The microsampler, contrasting the flocked swab, demonstrated statistically significant lower coefficient of variation for collected nasal fluid volume and greater sampling site precision. The spike and recovery study indicated that the proprietary materials had statistically significant higher biomarker recovery rates than Leukosorb<sup>TM</sup>. Overall, the novel nasal microsampler offers significantly improved volumetric control and site-specific collection against flocked swab. All experimental proprietary absorbent materials displayed significantly higher protein recovery rates, comparing to widely accepted and utilized Leukosorb<sup>TM</sup>. Consistent use of the novel nasal microsampler device has the potential to standardize protein recovery processes and minimize variability across studies, leading to enhanced reliability and comparability of future findings.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"247 ","pages":"Pages 25-33"},"PeriodicalIF":4.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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