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Protocol for processing multivariate time-series electronic health records of COVID-19 patients.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-03-05 DOI: 10.1016/j.xpro.2025.103669
Zixiang Wang, Yinghao Zhu, Dehao Sui, Tianlong Wang, Yuntao Zhang, Yasha Wang, Chengwei Pan, Junyi Gao, Liantao Ma, Ling Wang, Xiaoyun Zhang
{"title":"Protocol for processing multivariate time-series electronic health records of COVID-19 patients.","authors":"Zixiang Wang, Yinghao Zhu, Dehao Sui, Tianlong Wang, Yuntao Zhang, Yasha Wang, Chengwei Pan, Junyi Gao, Liantao Ma, Ling Wang, Xiaoyun Zhang","doi":"10.1016/j.xpro.2025.103669","DOIUrl":"10.1016/j.xpro.2025.103669","url":null,"abstract":"<p><p>The lack of standardized techniques for processing complex health data from COVID-19 patients hinders the development of accurate predictive models in healthcare. To address this, we present a protocol for utilizing real-world multivariate time-series electronic health records of COVID-19 patients. We describe steps for covering the necessary setup, data standardization, and formatting. We then provide detailed instructions for creating datasets and for training and evaluating AI models designed to predict two key outcomes: in-hospital mortality and length of stay. For complete details on the use and execution of this protocol, please refer to Gao et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103669"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574177","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}
引用次数: 0
Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-03-05 DOI: 10.1016/j.xpro.2025.103637
Eduard M Unterauer, Eva-Maria Schentarra, Kristina Jevdokimenko, Sayedali Shetab Boushehri, Carsten Marr, Felipe Opazo, Eugenio F Fornasiero, Ralf Jungmann
{"title":"Protocol for SUM-PAINT spatial proteomic imaging generating neuronal architecture maps in rat hippocampal neurons.","authors":"Eduard M Unterauer, Eva-Maria Schentarra, Kristina Jevdokimenko, Sayedali Shetab Boushehri, Carsten Marr, Felipe Opazo, Eugenio F Fornasiero, Ralf Jungmann","doi":"10.1016/j.xpro.2025.103637","DOIUrl":"10.1016/j.xpro.2025.103637","url":null,"abstract":"<p><p>To unravel the complexity of biological processes, it is necessary to resolve the underlying protein organization down to single proteins. Here, we present a protocol for secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a DNA-PAINT-based super-resolution microscopy technique that is capable of resolving virtually unlimited protein species with single-protein resolution. We describe the steps to prepare neuronal cultures, troubleshoot and conduct SUM-PAINT experiments, and analyze the resulting feature-rich neuronal cell atlases using unsupervised machine learning approaches. For complete details on the use and execution of this protocol, please refer to Unterauer et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103637"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574181","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}
引用次数: 0
Protocol for unlocking alternative polyadenylation insights from bulk RNA-seq data with PolyAMiner-Bulk.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-28 DOI: 10.1016/j.xpro.2025.103664
Venkata Jonnakuti, Sriya Jonnakuti, Hari Krishna Yalamanchili
{"title":"Protocol for unlocking alternative polyadenylation insights from bulk RNA-seq data with PolyAMiner-Bulk.","authors":"Venkata Jonnakuti, Sriya Jonnakuti, Hari Krishna Yalamanchili","doi":"10.1016/j.xpro.2025.103664","DOIUrl":"10.1016/j.xpro.2025.103664","url":null,"abstract":"<p><p>PolyAMiner-Bulk, a deep-learning-based algorithm to decode alternative polyadenylation (APA) dynamics from bulk RNA sequencing (RNA-seq) data, enables scientists to identify and quantify APA events from processed bulk RNA-seq data. The protocol allows researchers to explore differential APA usage between two conditions and gain a better understanding of post-transcriptional regulatory mechanisms. The major steps involve input data preparation, executing PolyAMiner-Bulk, and interpreting the results. A basic familiarity with pre-processing bulk RNA-seq data and command-line tools is suggested. For complete details on the use and execution of this protocol, please refer to Jonnakuti et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103664"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538109","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}
引用次数: 0
Protocol for efficient generation of human artery and vein endothelial cells from pluripotent stem cells. 多能干细胞高效生成人动脉和静脉内皮细胞的方法。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2024-12-19 DOI: 10.1016/j.xpro.2024.103494
Kyle M Loh, Sherry Li Zheng, Kevin J Liu, Qingqing Yin, Zhainib A Amir-Ugokwe, Sawan K Jha, Yue Qi, Vanessa K Wazny, Alana T Nguyen, Angela Chen, Faith-Masong Njunkeng, Christine Cheung, Edda Spiekerkoetter, Kristy Red-Horse, Lay Teng Ang
{"title":"Protocol for efficient generation of human artery and vein endothelial cells from pluripotent stem cells.","authors":"Kyle M Loh, Sherry Li Zheng, Kevin J Liu, Qingqing Yin, Zhainib A Amir-Ugokwe, Sawan K Jha, Yue Qi, Vanessa K Wazny, Alana T Nguyen, Angela Chen, Faith-Masong Njunkeng, Christine Cheung, Edda Spiekerkoetter, Kristy Red-Horse, Lay Teng Ang","doi":"10.1016/j.xpro.2024.103494","DOIUrl":"10.1016/j.xpro.2024.103494","url":null,"abstract":"<p><p>Blood vessels permeate all organs and execute myriad roles in health and disease. Here, we present a protocol to efficiently generate human artery and vein endothelial cells (ECs) from pluripotent stem cells within 3-4 days of differentiation. We delineate how to seed human pluripotent stem cells and sequentially differentiate them into primitive streak, lateral mesoderm, and either artery or vein ECs. We differentiate stem cells in defined, serum-free culture media in monolayers, without feeder cells or genetic manipulations. For complete details on the use and execution of this protocol, please refer to Ang et al. <sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103494"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869708","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}
引用次数: 0
Protocol for artificial intelligence-guided neural control using deep reinforcement learning and infrared neural stimulation. 基于深度强化学习和红外神经刺激的人工智能引导神经控制方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2024-12-19 DOI: 10.1016/j.xpro.2024.103496
Brandon S Coventry, Edward L Bartlett
{"title":"Protocol for artificial intelligence-guided neural control using deep reinforcement learning and infrared neural stimulation.","authors":"Brandon S Coventry, Edward L Bartlett","doi":"10.1016/j.xpro.2024.103496","DOIUrl":"10.1016/j.xpro.2024.103496","url":null,"abstract":"<p><p>Closed-loop neural control is a powerful tool for both the scientific exploration of neural function and for mitigating deficiencies found in open-loop deep brain stimulation (DBS). Here, we present a protocol for artificial intelligence-guided neural control in rats using deep reinforcement learning (RL) and infrared neural stimulation (INS). We describe steps for integrating RL closed-loop control into neuroscience and neuromodulation studies. We then detail procedures for using and deploying infrared INS in chronic DBS applications. For complete details on the use and execution of this protocol, please refer to Coventry et al.<sup>1</sup> and Coventry and Bartlett.<sup>2</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103496"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142869706","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}
引用次数: 0
Protocol for detecting and analyzing non-oscillatory traveling waves from high-spatiotemporal-resolution human electrophysiological recordings. 从高时空分辨率人体电生理记录中检测和分析非振荡行波的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-27 DOI: 10.1016/j.xpro.2025.103659
Veronica M Zarr, Jyun-You Liou, Edward M Merricks, Tyler S Davis, Kyle Thomson, Bradley Greger, Paul A House, Ronald G Emerson, Robert R Goodman, Guy M McKhann, Sameer A Sheth, Catherine A Schevon, John D Rolston, Elliot H Smith
{"title":"Protocol for detecting and analyzing non-oscillatory traveling waves from high-spatiotemporal-resolution human electrophysiological recordings.","authors":"Veronica M Zarr, Jyun-You Liou, Edward M Merricks, Tyler S Davis, Kyle Thomson, Bradley Greger, Paul A House, Ronald G Emerson, Robert R Goodman, Guy M McKhann, Sameer A Sheth, Catherine A Schevon, John D Rolston, Elliot H Smith","doi":"10.1016/j.xpro.2025.103659","DOIUrl":"10.1016/j.xpro.2025.103659","url":null,"abstract":"<p><p>Innovations in electrophysiological recordings and computational analytic techniques enable high-resolution analysis of neural traveling waves. Here, we present a protocol for the detection and analysis of traveling waves from multi-day microelectrode array human electrophysiological recordings through a multi-linear regression statistical approach using point estimator data. We describe steps for traveling wave detection, feature characterization, and propagation pattern analysis. This protocol may improve our understanding of the coordination of neurons during non-oscillatory neural dynamics. For complete details on the use and execution of this protocol, please refer to Smith et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103659"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538077","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}
引用次数: 0
Protocol for production of tonic CAR T cells with dasatinib. 用达沙替尼生产补强型CAR - T细胞的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2024-12-30 DOI: 10.1016/j.xpro.2024.103529
Léa Rosselle, Thibault Leray, Sandy Joaquina, Benjamin Caulier, Emmet McCormack, Pascal Gelebart, Sébastien Wälchli, Else Marit Inderberg
{"title":"Protocol for production of tonic CAR T cells with dasatinib.","authors":"Léa Rosselle, Thibault Leray, Sandy Joaquina, Benjamin Caulier, Emmet McCormack, Pascal Gelebart, Sébastien Wälchli, Else Marit Inderberg","doi":"10.1016/j.xpro.2024.103529","DOIUrl":"10.1016/j.xpro.2024.103529","url":null,"abstract":"<p><p>Chimeric antigen receptors (CARs) are synthetic molecules composed of an extracellular antigen-binding domain and an intracellular signaling domain, leading to tonic signaling and manufacturing challenges. We present a protocol for the expansion of tonic CARs by using a Food and Drug Administration (FDA)-approved kinase inhibitor, dasatinib. We report steps for T cell transduction with retrovirus, expansion and verification of CAR quality using flow cytometry, and killing assay. At only 30 nM, dasatinib improves tonic CAR T cell proliferation and quality after expansion. For complete details on the use and execution of this protocol, please refer to Caulier et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103529"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750262/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142910945","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}
引用次数: 0
Protocol for assessing T cell receptor-mediated human T cell cytotoxicity. 评估T细胞受体介导的人T细胞毒性的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-04 DOI: 10.1016/j.xpro.2024.103541
Kathryne E Marks, Ifeoluwakiisi Adejoorin, John Sowerby, Deepak A Rao
{"title":"Protocol for assessing T cell receptor-mediated human T cell cytotoxicity.","authors":"Kathryne E Marks, Ifeoluwakiisi Adejoorin, John Sowerby, Deepak A Rao","doi":"10.1016/j.xpro.2024.103541","DOIUrl":"10.1016/j.xpro.2024.103541","url":null,"abstract":"<p><p>Measuring the cytotoxicity of human T cells is a valuable but challenging task. We present a protocol for assessing the ability of polyclonal human T cells to kill target cells upon T cell receptor (TCR) triggering. We describe steps for preparing L and T cells for the assay and incubation of target cells with effector cells. We detail procedures for assessing cell death by flow cytometry. This protocol can be applied to small numbers of effector cells isolated from patient samples. For complete details on the use and execution of this protocol, please refer to Wang et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103541"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932886","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}
引用次数: 0
Protocol for generating a pancreatic cancer organoid associated with heterogeneous tumor microenvironment. 生成与异质肿瘤微环境相关的胰腺癌类器官的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-07 DOI: 10.1016/j.xpro.2024.103539
Kenta Takeuchi, Shunsuke Tabe, Yuya Yamamoto, Kenta Takahashi, Megumi Matsuo, Yasuharu Ueno, Masayuki Ohtsuka, Soichiro Morinaga, Yohei Miyagi, Tomoyuki Yamaguchi, Naoki Tanimizu, Hideki Taniguchi
{"title":"Protocol for generating a pancreatic cancer organoid associated with heterogeneous tumor microenvironment.","authors":"Kenta Takeuchi, Shunsuke Tabe, Yuya Yamamoto, Kenta Takahashi, Megumi Matsuo, Yasuharu Ueno, Masayuki Ohtsuka, Soichiro Morinaga, Yohei Miyagi, Tomoyuki Yamaguchi, Naoki Tanimizu, Hideki Taniguchi","doi":"10.1016/j.xpro.2024.103539","DOIUrl":"10.1016/j.xpro.2024.103539","url":null,"abstract":"<p><p>Pancreatic ductal adenocarcinoma (PDAC) organoids that simulate the tumor microenvironment (TME) are an effective tool to identify how TME affects PDAC malignancy. We present a protocol for generating a fused pancreatic cancer organoid (FPCO) that partly reproduces the TME, including heterogeneous cancer-associated fibroblasts (CAFs), using patient-derived PDAC cells and human-induced pluripotent cell-derived endothelial and mesenchymal cells. We also describe the procedure for analyzing FPCO characteristics. FPCO can provide a platform for establishing a reliable drug screening system. For complete details on the use and execution of this protocol, please refer to Takeuchi et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103539"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11760323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142956073","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}
引用次数: 0
Protocol for generating liver metastasis microtissues to decipher cellular interactions between metastatic intestinal cancer and liver tissue. 生成肝转移微组织的方案，以破译转移性肠癌和肝组织之间的细胞相互作用。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-20 DOI: 10.1016/j.xpro.2024.103575
Maria Lamprou, Ana Krotenberg Garcia, Saskia Jacoba Elisabeth Suijkerbuijk
{"title":"Protocol for generating liver metastasis microtissues to decipher cellular interactions between metastatic intestinal cancer and liver tissue.","authors":"Maria Lamprou, Ana Krotenberg Garcia, Saskia Jacoba Elisabeth Suijkerbuijk","doi":"10.1016/j.xpro.2024.103575","DOIUrl":"10.1016/j.xpro.2024.103575","url":null,"abstract":"<p><p>Cell competition is a quality control mechanism that promotes elimination of suboptimal cells relative to fitter neighbors. Cancer cells exploit these mechanisms for expansion, but the underlying molecular pathways remain elusive. Here, we present a protocol for generating matrix-free microtissues recapitulating cellular interactions between intestinal cancer and hepatocyte-like cells using microscopy or transcriptomics/proteomics. We describe steps for generating and differentiating liver progenitor organoids and microtissue formation. We then detail procedures for immunofluorescence staining, mounting microtissues, and sorting cells. For complete details on the use and execution of this protocol, please refer to Krotenberg Garcia et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103575"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11787675/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013060","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}
引用次数: 0
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