Methods最新文献 - Book学术

Bio-impedance spectroscopy-based classification of mental acuity in university students via machine-learning and deep-learning approaches 基于生物阻抗谱的大学生心理敏锐度机器学习和深度学习分类

IF 4.2 3区生物学

Methods Pub Date : 2025-07-24 DOI: 10.1016/j.ymeth.2025.07.009

Kusum Tara , Sadman Sakib , Md Hasibul Islam , Shadhon Chandra Mohonta , Md.Shamim Anower , Takenao Sugi

{"title":"Bio-impedance spectroscopy-based classification of mental acuity in university students via machine-learning and deep-learning approaches","authors":"Kusum Tara , Sadman Sakib , Md Hasibul Islam , Shadhon Chandra Mohonta , Md.Shamim Anower , Takenao Sugi","doi":"10.1016/j.ymeth.2025.07.009","DOIUrl":"10.1016/j.ymeth.2025.07.009","url":null,"abstract":"<div><div>Mental acuity detection is crucial for identifying cognitive impairments linked to body composition imbalances and ensuring overall mental and physical fitness. This study introduces a deep-learning neural network (NN) model with MobileNetV2 deep learning architecture to classify mental acuity levels of university students—excellent, good, and average—using bioelectrical impedance spectroscopy (BIS)-based body composition and bio-impedance measurements. Body composition and bio-impedance features such as basal metabolic rate (BMR), body cell mass (BCM), total body water (TBW), bioelectrical impedance (BI), and phase angle (PA) were utilized as inputs for a feature-based random forest (RF) machine-learning model, achieving an accuracy of 88.26% and an F1-score of 84.89%. However, an image-based NN model with MobileNetV2 deep learning architecture, leveraging 2D impedance spectrum images, outperformed RF model, achieving exceptional accuracy of 98.39% and an F1-score of 97.83%. Additionally, the Nyquist diagram showed that excellent mental acuity had the smallest semicircle, average mental acuity had the largest, and good mental acuity level was intermediate. Similarly, feature analysis revealed that excellent mental acuity level corresponded to high BMR, BCM, TBW, and PA with low BI, while average mental acuity level had the opposite trend, while good mental acuity levels fell in between. The reliability and performance of the NN model in detecting mental acuity using 2D impedance spectrum analysis highlights its potential for this task. These results emphasize the value of deep-learning approaches in integrating BIS data for accurate mental acuity assessment and their broader implications for monitoring cognitive health.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 89-96"},"PeriodicalIF":4.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144711965","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

A simple, accurate method for the measurement of lysosomal activity. 测定溶酶体活性的一种简单、准确的方法。

IF 4.2 3区生物学

Methods Pub Date : 2025-07-24 DOI: 10.1016/j.ymeth.2025.07.008

Yoshito Iwai, Yuriko Furuya, Yuji Oguro, Keiji Yamamoto

{"title":"A simple, accurate method for the measurement of lysosomal activity.","authors":"Yoshito Iwai, Yuriko Furuya, Yuji Oguro, Keiji Yamamoto","doi":"10.1016/j.ymeth.2025.07.008","DOIUrl":"https://doi.org/10.1016/j.ymeth.2025.07.008","url":null,"abstract":"<p><p>Lysosomes are responsible for the degradation of intra- and extracellular components and are thus essential for the quality control of proteins and organelles. Lysosomal dysfunction leads to lysosomal storage diseases, and it is therefore important to identify which types of stress cause functional abnormalities. Lysosomal function is generally evaluated by measuring the enzyme activity of lysosomes with fluorescent dyes. However, fluorescence microscopy can lead to different outcomes due to variations in the field of view, the analysis software used, and the parameter settings. We therefore developed a method that uses only a microplate reader and DQ Green BSA, a dye that emits fluorescence upon lysosomal degradation, to ascertain lysosomal activity. HEK293 cells were treated with DQ Green BSA with or without bafilomycin A1 and lysates extracted using radioimmunoprecipitation buffer. Fluorescence intensities and protein concentrations in the cell lysates were then measured using a microplate reader and the bicinchoninic acid method, respectively, and the fluorescence intensity divided by the protein concentration. Results indicated a significant lysosome inhibitor-induced dose-dependent decrease in the lysosomal activity. The Z'-factor of 0.77 obtained using the proposed method is a significant improvement over the - 0.06 obtained using the conventional method. The versatility of the method was evaluated with different cell types, cell lysis buffers, inhibitors, and protease substrates, with results suggesting that the method works regardless of the cells or reagents used, indicating the relative simplicity and accuracy of the proposed method as compared to the currently utilized method.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717210","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

Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives. 肿瘤蛋白-金属结合的可解释多模式学习：进展、挑战和前景。

IF 4.2 3区生物学

Methods Pub Date : 2025-07-21 DOI: 10.1016/j.ymeth.2025.07.004

Xiaokun Liu, Sayedmohammadreza Rastegari, Yijun Huang, Sxe Chang Cheong, Weikang Liu, Wenjie Zhao, Qihao Tian, Hongming Wang, Yingjie Guo, Shuo Zhou, Sina Tabakhi, Xianyuan Liu, Zheqing Zhu, Wei Sang, Haiping Lu

{"title":"Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives.","authors":"Xiaokun Liu, Sayedmohammadreza Rastegari, Yijun Huang, Sxe Chang Cheong, Weikang Liu, Wenjie Zhao, Qihao Tian, Hongming Wang, Yingjie Guo, Shuo Zhou, Sina Tabakhi, Xianyuan Liu, Zheqing Zhu, Wei Sang, Haiping Lu","doi":"10.1016/j.ymeth.2025.07.004","DOIUrl":"https://doi.org/10.1016/j.ymeth.2025.07.004","url":null,"abstract":"<p><p>In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory methods used to study such mechanisms are often costly, low throughput, and limited in capturing dynamic biological processes, machine learning (ML) has emerged as a promising alternative. Despite increasing efforts to develop protein-metal binding datasets and ML algorithms, the application of ML in tumor protein-metal binding remains limited. Key challenges include a shortage of high-quality, tumor-specific datasets, insufficient consideration of multiple data modalities, and the complexity of interpreting results due to the \"black box\" nature of complex ML models. This paper summarizes recent progress and ongoing challenges in using ML to predict tumor protein-metal binding, focusing on data, modeling, and interpretability. We present multimodal protein-metal binding datasets and outline strategies for acquiring, curating, and preprocessing them for training ML models. Moreover, we explore the complementary value provided by different data modalities and examine methods for their integration. We also review approaches for improving model interpretability to support more trustworthy decisions in cancer research. Finally, we offer our perspective on research opportunities and propose strategies to address the scarcity of tumor protein data and the limited number of predictive models for tumor protein-metal binding. We also highlight two promising directions for effective metal-based drug design: integrating protein-protein interaction data to provide structural insights into metal-binding events and predicting structural changes in tumor proteins after metal binding.</p>","PeriodicalId":390,"journal":{"name":"Methods","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697285","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

Circularization enhances RNA aptamer binding and Stability: Evidence from in-cell NMR 环状化增强RNA适体结合和稳定性：来自细胞内核磁共振的证据

IF 4.2 3区生物学

Methods Pub Date : 2025-07-16 DOI: 10.1016/j.ymeth.2025.07.006

Omar Eladl

{"title":"Circularization enhances RNA aptamer binding and Stability: Evidence from in-cell NMR","authors":"Omar Eladl","doi":"10.1016/j.ymeth.2025.07.006","DOIUrl":"10.1016/j.ymeth.2025.07.006","url":null,"abstract":"<div><div>RNA aptamers are emerging as promising molecular probes due to their high specificity and low immunogenicity. However, their clinical potential is often limited by instability under physiological conditions, primarily due to exonucleolytic degradation and structural flexibility. To address these challenges in a model system, we designed a circular RNA aptamer targeting the HIV-1 Tat protein.</div><div>Enzymatic circularization of the aptamer was performed using T4 RNA ligase, and circularization was confirmed by mobility shift assays and RNase R digestion. Binding affinity was assessed via filter dot blot assay, while structural stability was evaluated using 1D imino proton NMR and CLEANEX-PM experiments. Intracellular stability was monitored using in-cell NMR following transfection into HeLa cells.</div><div>In our study, the circular aptamer showed approximately tenfold higher binding affinity compared to its linear counterpart, as determined by filter binding assay. NMR analysis indicated improved structural rigidity, preservation of native base pairing, and reduced solvent exchange. Notably, in-cell NMR revealed that the circular aptamer remained detectable up to 18 h post-transfection, whereas the linear aptamer degraded within a few hours.</div><div>In this system, circularization substantially improved the binding performance and intracellular persistence of the RNA aptamer. These findings demonstrate the feasibility of applying RNA circularization to enhance aptamer functionality in living cells and lay the groundwork for future therapeutic exploration.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 72-79"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144655189","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

Ultrasensitive detection of MMP-2 via T7 RNA polymerase and CRISPR/Cas13a-Enhanced electrochemiluminescence biosensor for COPD diagnosis 通过T7 RNA聚合酶和CRISPR/ cas13a增强的电化学发光生物传感器超灵敏检测MMP-2在COPD诊断中的应用

IF 4.2 3区生物学

Methods Pub Date : 2025-07-15 DOI: 10.1016/j.ymeth.2025.07.005

Wensi Li , Zhichao Tang , Xiang Zhu , Beijuan Wang , Xiuqin Zhang , Ze Ji , Suhang Cheng

{"title":"Ultrasensitive detection of MMP-2 via T7 RNA polymerase and CRISPR/Cas13a-Enhanced electrochemiluminescence biosensor for COPD diagnosis","authors":"Wensi Li , Zhichao Tang , Xiang Zhu , Beijuan Wang , Xiuqin Zhang , Ze Ji , Suhang Cheng","doi":"10.1016/j.ymeth.2025.07.005","DOIUrl":"10.1016/j.ymeth.2025.07.005","url":null,"abstract":"<div><div>In this work, an electrochemiluminescence (ECL) biosensor integrating T7 RNA polymerase amplification and CRISPR/Cas13a-mediated signal enhancement was developed for the ultrasensitive detection of matrix metalloproteinase-2 (MMP-2), a key biomarker associated with chronic inflammatory diseases such as COPD. A peptide nucleic acid (PNA) probe was designed to respond specifically to MMP-2 cleavage, enabling the release of DNA templates for subsequent T7 RNA polymerase-driven transcription amplification. The generated RNA triggers the collateral cleavage activity of CRISPR/Cas13a, resulting in a significant amplification of the ECL signal. The biosensor’s surface was constructed using a AuNPs/Ti<sub>3</sub>C<sub>2</sub>Tx/Ru(II)-PEI nanocomposite, which enhanced signal transduction and stability. Under optimized conditions, the proposed biosensor achieved a detection limit as low as 62.05 fM, demonstrating superior sensitivity compared to conventional methods, as summarized in <span><span>Table 1</span></span>. The platform also exhibited excellent specificity and anti-interference capability, ensuring reliable detection of MMP-2 in complex biological samples. This study provides a simple yet highly efficient strategy for enzymatic biomarker detection, offering great potential for clinical applications in early disease diagnosis and monitoring.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 80-88"},"PeriodicalIF":4.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658091","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

A photoactivatable chemical lipidomics approach for local sphingolipid metabolic analysis 用于局部鞘脂代谢分析的光活化化学脂组学方法

IF 4.2 3区生物学

Methods Pub Date : 2025-07-08 DOI: 10.1016/j.ymeth.2025.07.002

Xiaoxue Wang , Zhiyi Zhang , Shuwei Tian , Suihan Feng

{"title":"A photoactivatable chemical lipidomics approach for local sphingolipid metabolic analysis","authors":"Xiaoxue Wang , Zhiyi Zhang , Shuwei Tian , Suihan Feng","doi":"10.1016/j.ymeth.2025.07.002","DOIUrl":"10.1016/j.ymeth.2025.07.002","url":null,"abstract":"<div><div>In eukaryotic cells, lipid metabolism is tightly regulated depending on the subcellular localization, which is essential for maintaining lipid homeostasis. However, understanding compartmentalized lipid metabolism remains challenging due to limited availability of suitable techniques. In this study, we present a chemical lipidomics approach that combines photoactivatable probes with high resolution mass spectrometry and stable-isotope labelling to analyze lipid dynamics at subcellular resolution. We applied this method to analyze the metabolism of 1-deoxysphingolipid (DoxSL), a non-canonical lipid species linked to various metabolic diseases and neuropathy, whose metabolism remains largely unexplored. Using the photoactivatable probes, we selectively delivered 1-deoxysphinganine, a key DoxSL intermediate, to mitochondria upon photo-illumination and subsequently analyzed its local metabolic products over time. Our data show that most 1-deoxysphinganine delivered to mitochondria is rapidly converted into 1-deoxyceramides, while only a small fraction forms oxidized products. Further lipidomic analysis revealed that 1-deoxyceramides are transported to the extracellular space and that DoxSL is also present in mouse and human serum samples. In summary, we developed novel probes to track lipid dynamics with high spatiotemporal resolution in a non-invasive manner and provided new insights into sphingolipid metabolism.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 62-71"},"PeriodicalIF":4.2,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144581287","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

Fragile methods, fractured trust: rethinking scientific responsibility 脆弱的方法，破碎的信任：重新思考科学责任

IF 4.2 3区生物学

Methods Pub Date : 2025-07-07 DOI: 10.1016/j.ymeth.2025.07.003

Stephen A. Bustin , Carl T. Wittwer

{"title":"Fragile methods, fractured trust: rethinking scientific responsibility","authors":"Stephen A. Bustin , Carl T. Wittwer","doi":"10.1016/j.ymeth.2025.07.003","DOIUrl":"10.1016/j.ymeth.2025.07.003","url":null,"abstract":"<div><div>Science has a credibility problem, and it is not just the fault of politicians, journalists, or conspiracy theorists. It begins within science itself. This review examines how flawed methods and selective reporting, combined with overly polished communications that prioritise image over clarity, have normalised bad practice in molecular biology, diagnostics, and related applied sciences. The quantitative real-time polymerase chain reaction (qPCR) offers a clear example: a conceptually simple, technically mature technology that is nonetheless routinely misused, despite published standards and repeated calls for methodological rigour over the past two decades. If qPCR is so often misapplied, what does that suggest about confidence in more complex, less transparent technologies? An additional problem lies in the way scientific findings are misreported or exaggerated. Such distortions have far-reaching consequences beyond individual studies. From the MMR-autism scare to COVID-19 testing and vaccine hesitancy, they have fuelled confusion, eroded public trust, and endangered public health. Consequently, when flawed or overstated findings shape public policy or clinical decisions, the damage undermines science’s role as a reliable source of knowledge and informed choice. Credibility must rest on transparent practice, ethical responsibility, and attention to both how results are produced and how they are communicated. Until scientists recognise that communication is not value-neutral, and that our public voice carries consequences far beyond the lab, public scepticism will be justified.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 54-61"},"PeriodicalIF":4.2,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144581286","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

Immunoinformatics-based multi-epitope vaccine design using transforming growth factor beta-2 proprotein (TGFB2) for glioblastoma multiforme (GBM): GVac 基于免疫信息学的多形性胶质母细胞瘤（GBM）转化生长因子-2蛋白（TGFB2）多表位疫苗设计

IF 4.2 3区生物学

Methods Pub Date : 2025-07-06 DOI: 10.1016/j.ymeth.2025.07.001

Deniz Tülümen , Esra Aydemir , Furkan Ayaz

{"title":"Immunoinformatics-based multi-epitope vaccine design using transforming growth factor beta-2 proprotein (TGFB2) for glioblastoma multiforme (GBM): GVac","authors":"Deniz Tülümen , Esra Aydemir , Furkan Ayaz","doi":"10.1016/j.ymeth.2025.07.001","DOIUrl":"10.1016/j.ymeth.2025.07.001","url":null,"abstract":"<div><div>Glioblastoma multiforme (GBM), a malignant glioma, is a central nervous system tumor with a high mortality rate in the world. Despite its high mortality rate, there is no effective treatment yet. Classical treatment methods are usually applied to patients, but patients lose their lives in a short time. A strong vaccine or drug that will extend the life of patients has not yet emerged. In this study, various bioinformatic analyses were performed on the Transforming growth factor beta-2 proprotein (TGFB2) belonging to GBM, and a multi-epitope vaccine design was made. These analyses include allergenicity, antigenicity and toxicity tests, various epitope selections, molecular docking, molecular dynamics simulation and immune simulation analyses. As a result of all analyses, a vaccine candidate called GVac was revealed. Gvac is enhanced with an adjuvant called batroxicidin (BatxC), an antimicrobial peptide. While analyses of Gvac generally yield strong results, it offers the potential to be used in various clinical studies if carried forward. With developing technologies, it is now necessary to move away from classical treatment methods and apply to treatment methods that can provide faster and more effective results. This is also the aim of this study. Gvac may offer hope to GBM patients awaiting treatment around the world and the studies need to be carried forward.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 38-53"},"PeriodicalIF":4.2,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144569839","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

A prognostic gene signature and subtype-specific drug sensitivity in TNBC revealed by single-cell and bulk RNA sequencing: Insights into stemness and tumor heterogeneity 单细胞和大量RNA测序揭示了TNBC的预后基因特征和亚型特异性药物敏感性：对干细胞和肿瘤异质性的见解

IF 4.2 3区生物学

Methods Pub Date : 2025-06-18 DOI: 10.1016/j.ymeth.2025.06.007

Do Thi Minh Xuan , Doan Phuong Quy Nguyen , Van Thi Ngoc Tram , Hoang Dang Khoa Ta

{"title":"A prognostic gene signature and subtype-specific drug sensitivity in TNBC revealed by single-cell and bulk RNA sequencing: Insights into stemness and tumor heterogeneity","authors":"Do Thi Minh Xuan , Doan Phuong Quy Nguyen , Van Thi Ngoc Tram , Hoang Dang Khoa Ta","doi":"10.1016/j.ymeth.2025.06.007","DOIUrl":"10.1016/j.ymeth.2025.06.007","url":null,"abstract":"<div><div>Triple-negative breast cancer (TNBC) remains one of the most aggressive Triple-negative breast cancer (TNBC) remains one of the most aggressive and therapeutically challenging breast cancer subtypes, largely due to its lack of targetable receptors and its intrinsic chemoresistance. In this study, we applied an integrative multi-omics approach − combining single-cell RNA sequencing (scRNA-seq) with bulk transcriptomic, epigenomic, and mutational analyses, to investigate the cellular heterogeneity and underlying mechanisms of drug resistance in TNBC. Analysis of the scRNA-seq dataset (GSE176078) revealed a complex tumor microenvironment with a highly plastic cancer epithelial subpopulation (Cluster C4) exhibiting elevated multipotency and distinct intercellular communication patterns. Concurrently, unsupervised clustering of TCGA-BRCA data delineated three molecular subtypes (CS1, CS2, and CS3) with unique biological and metabolic profiles, where CS3 notably exhibited unique molecular features associated with chromatin remodeling and high proliferative activity, suggesting distinct therapeutic vulnerabilities. An overlap analysis between scRNA-seq and bulk RNA-seq data identified 220 common differentially expressed genes (DEGs), from which a four-gene prognostic signature (CTSF, GBP1, BCL2A1, and EMP1) was derived. This signature robustly stratified patients by overall survival across both internal and external cohorts. Overall, our findings provide critical insights into the molecular drivers of chemoresistance in TNBC and offer a foundation for personalized therapeutic strategies.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 24-37"},"PeriodicalIF":4.2,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320849","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

Multifunctional nanophotonic photoacoustic biosensors: a new era in molecular imaging–guided deep-tissue cancer monitoring 多功能纳米光子光声生物传感器：分子成像引导深部组织癌症监测的新时代。

IF 4.2 3区生物学

Methods Pub Date : 2025-06-16 DOI: 10.1016/j.ymeth.2025.06.005

Bakr Ahmed Taha , Ghassan M. Sulaiman , Ali J. Addie , Khalil A.A. Khalil , Elsadig M. Ahmed , Vishal Chaudhary , Norhana Arsad

{"title":"Multifunctional nanophotonic photoacoustic biosensors: a new era in molecular imaging–guided deep-tissue cancer monitoring","authors":"Bakr Ahmed Taha , Ghassan M. Sulaiman , Ali J. Addie , Khalil A.A. Khalil , Elsadig M. Ahmed , Vishal Chaudhary , Norhana Arsad","doi":"10.1016/j.ymeth.2025.06.005","DOIUrl":"10.1016/j.ymeth.2025.06.005","url":null,"abstract":"<div><div>Monitoring cancer therapy is difficult because of restricted imaging depth, inadequate molecular specificity, and delayed response evaluation. Moreover, conventional imaging techniques fail to provide high-resolution, real-time views of the dynamic tumor microenvironment during therapy. Among emerging technologies, nanophotonic photoacoustic biosensors have gained prominence as multifunctional platforms that enable real-time, non-invasive imaging and dynamic monitoring of cancer therapy. This review discusses advances in nanophotonic engineering, including plasmonic nanostructures, NIR-II fluorophore-integrated systems, SERS-active materials, fiber-optic probes, and hybrid nanosystems, all tailored to enhance molecular targeting and signal specificity. In addition, biomimetic and biologically inspired nanosystems with enhanced tissue penetration and reduced autofluorescence in the NIR-II spectrum can be specifically highlighted. The key aspects of clinical translation are examined including biosafety, molecular specificity, and scalability. Furthermore, further explore the convergence of these biosensors with artificial intelligence and Internet of Things (IoT) frameworks to support adaptive, patient-specific decision-making in oncology. As a result of these multifunctional systems that combine nanophotonics, machine learning, and molecular diagnostics, oncology could shift towards precision-guided treatment. Finally, it proposes strategic avenues for clinical adoption, placing PAS at the vanguard of the next generation of cancer diagnostics.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"242 ","pages":"Pages 1-23"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293159","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