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Protocol to study how expectations guide predictive eye movements and information sampling in humans.
IF 1.3
STAR Protocols Pub Date : 2025-04-07 DOI: 10.1016/j.xpro.2025.103737
Annika Garlichs, Mark Lustig, Matthias Gamer, Helen Blank
{"title":"Protocol to study how expectations guide predictive eye movements and information sampling in humans.","authors":"Annika Garlichs, Mark Lustig, Matthias Gamer, Helen Blank","doi":"10.1016/j.xpro.2025.103737","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103737","url":null,"abstract":"<p><p>Investigating eye movements provides a unique tool to explore how expectations influence information sampling in the visual domain. Here, we present a protocol for measuring predictive eye movements during face anticipation as well as fixations and dwell time during face recognition in humans. We describe steps for setting up two eye-tracking experiments. We then detail procedures for the measurement and analysis of eye-tracking data. For complete details on the use and execution of this protocol, please refer to Garlichs et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103737"},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804349","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}
引用次数: 0
Protocol for microbial profiling of low-biomass upper respiratory tract samples.
IF 1.3
STAR Protocols Pub Date : 2025-04-07 DOI: 10.1016/j.xpro.2025.103740
Mari-Lee Odendaal, Mei Ling J N Chu, Kayleigh Arp, Gina J van Beveren, Giske Biesbroek, Justyna Binkowska, Thijs Bosch, James A Groot, Raiza Hasrat, Sjoerd Kuiling, Elske M van Logchem, Paula Lusarreta Parga, Wouter A A de Steenhuijsen Piters, Debby Bogaert
{"title":"Protocol for microbial profiling of low-biomass upper respiratory tract samples.","authors":"Mari-Lee Odendaal, Mei Ling J N Chu, Kayleigh Arp, Gina J van Beveren, Giske Biesbroek, Justyna Binkowska, Thijs Bosch, James A Groot, Raiza Hasrat, Sjoerd Kuiling, Elske M van Logchem, Paula Lusarreta Parga, Wouter A A de Steenhuijsen Piters, Debby Bogaert","doi":"10.1016/j.xpro.2025.103740","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103740","url":null,"abstract":"<p><p>The upper respiratory tract (URT) microbiota plays a role in both acute and chronic respiratory health outcomes and consists of multiple ecologically distinct niches, all of which have low bacterial biomass. Here, we present a protocol for microbial profiling of low-biomass URT samples. We describe steps for collecting, storing, and extracting DNA. We then detail procedures for performing 16S rRNA sequencing, using an Illumina MiSeq platform, to characterize microbial communities. For complete details on the use and execution of this protocol, please refer to Odendaal et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103740"},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804343","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}
引用次数: 0
Protocol for the functional evaluation of genetic variants using saturation genome editing.
IF 1.3
STAR Protocols Pub Date : 2025-04-07 DOI: 10.1016/j.xpro.2025.103710
Sofia Obolenski, Rebeca Olvera-León, Dijue Sun, David J Adams, Andrew J Waters
{"title":"Protocol for the functional evaluation of genetic variants using saturation genome editing.","authors":"Sofia Obolenski, Rebeca Olvera-León, Dijue Sun, David J Adams, Andrew J Waters","doi":"10.1016/j.xpro.2025.103710","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103710","url":null,"abstract":"<p><p>Saturation genome editing (SGE) employs CRISPR-Cas9 and homology-directed repair (HDR) to introduce exhaustive nucleotide modifications at specific genomic sites in multiplex, enabling the functional analysis of genetic variants while preserving their native genomic context. Here, we present a protocol for SGE-based variant evaluation in HAP1-A5 cells. We describe the steps for designing variant libraries, single-guide RNAs (sgRNAs), and oligonucleotide primers for PCR. We also detail the sample preparation before the SGE screen, the cellular screening process, and subsequent next-generation sequencing (NGS) library preparation. For complete details on the use and execution of this protocol, please refer to Radford et al.,<sup>1</sup> Waters et al.,<sup>2</sup> and Olvera-León et al.<sup>3</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103710"},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804346","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}
引用次数: 0
Protocol to analyze deep-learning-predicted functional scores for noncoding de novo variants and their correlation with complex brain traits.
IF 1.3
STAR Protocols Pub Date : 2025-04-07 DOI: 10.1016/j.xpro.2025.103738
Enrique Mondragon-Estrada, Sarah U Morton
{"title":"Protocol to analyze deep-learning-predicted functional scores for noncoding de novo variants and their correlation with complex brain traits.","authors":"Enrique Mondragon-Estrada, Sarah U Morton","doi":"10.1016/j.xpro.2025.103738","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103738","url":null,"abstract":"<p><p>Functional impact of noncoding variants can be predicted using computational approaches. Although predictive scores can be insightful, implementing the scores for a custom variant set and associating scores with complex traits require multiple phases of analysis. Here, we present a protocol for prioritizing variants by generating deep-learning-predicted functional scores and relating them with brain traits. We describe steps for score prediction, statistical comparison, phenotype correlation, and functional enrichment analysis. This protocol can be generalized to different models and phenotypes. For complete details on the use and execution of this protocol, please refer to Mondragon-Estrada et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103738"},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804347","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}
引用次数: 0
Protocol for affinity enrichment of polyclonal autoantibodies from human plasma.
IF 1.3
STAR Protocols Pub Date : 2025-04-07 DOI: 10.1016/j.xpro.2025.103730
Aws Aljnabi, Kelly A Hagadorn, Louisa E Neumann, Mary E Peterson, Bethany Scott, Kazutoyo Miura, Aissata Ongoiba, Safiatou Doumbo, Didier Doumtabe, Shanping Li, Kassoum Kayentao, Boubacar Traore, Silvia Bolland, Peter D Crompton, Christine S Hopp
{"title":"Protocol for affinity enrichment of polyclonal autoantibodies from human plasma.","authors":"Aws Aljnabi, Kelly A Hagadorn, Louisa E Neumann, Mary E Peterson, Bethany Scott, Kazutoyo Miura, Aissata Ongoiba, Safiatou Doumbo, Didier Doumtabe, Shanping Li, Kassoum Kayentao, Boubacar Traore, Silvia Bolland, Peter D Crompton, Christine S Hopp","doi":"10.1016/j.xpro.2025.103730","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103730","url":null,"abstract":"<p><p>Autoantibodies (AAbs) contribute to various immune-mediated diseases and are valuable biomarkers for diagnosis, classification, and disease activity. Here, we present a protocol for the affinity enrichment of AAbs from human plasma samples. We describe steps to generate a human cell line lysate, which is immobilized on Sepharose beads for affinity enrichment of AAbs. We then detail the quality-control procedure of verifying autoreactivity of AAb fractions. This protocol has potential application in functional and proteomic analyses of AAbs. For complete details on the use and execution of this protocol, please refer to Hagadorn et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103730"},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804387","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}
引用次数: 0
Protocol for high-resolution optical mapping of ex vivo rat heart for electrophysiological studies. 用于电生理学研究的体外大鼠心脏高分辨率光学制图规程。
IF 1.3
STAR Protocols Pub Date : 2025-04-05 DOI: 10.1016/j.xpro.2025.103734
Yen Ling Sung, Yuan Si Tsai, Chu Ling Chang, Yu Feng Hu
{"title":"Protocol for high-resolution optical mapping of ex vivo rat heart for electrophysiological studies.","authors":"Yen Ling Sung, Yuan Si Tsai, Chu Ling Chang, Yu Feng Hu","doi":"10.1016/j.xpro.2025.103734","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103734","url":null,"abstract":"<p><p>Cardiac optical mapping provides high-resolution spatiotemporal insights into cardiac electrophysiology. Here, we present a protocol for capturing electrical signals in rats using voltage-sensitive dyes and blebbistatin to inhibit muscle contractions. We describe steps for aortic cannulation, heart isolation, optical mapping, and detailed signal analysis. This staining strategy utilized in this protocol allows for precise signal recording while minimizing motion artifacts, thereby enhancing image quality on the cardiac surface. For complete details on the use and execution of this protocol, please refer to Hu et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103734"},"PeriodicalIF":1.3,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796650","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}
引用次数: 0
AMRLearn: Protocol for a machine learning pipeline for characterization of antimicrobial resistance determinants in microbial genomic data.
IF 1.3
STAR Protocols Pub Date : 2025-04-05 DOI: 10.1016/j.xpro.2025.103733
Xi Zhang, Yining Hu, Zhenyu Cheng, John M Archibald
{"title":"AMRLearn: Protocol for a machine learning pipeline for characterization of antimicrobial resistance determinants in microbial genomic data.","authors":"Xi Zhang, Yining Hu, Zhenyu Cheng, John M Archibald","doi":"10.1016/j.xpro.2025.103733","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103733","url":null,"abstract":"<p><p>Single-nucleotide polymorphisms (SNPs) are useful biomarkers for linking genotype to phenotype. Machine learning is powerful for predicting antimicrobial resistance (AMR) from bacterial genome sequence data. Here, we present AMRLearn, a machine learning pipeline to assist users in the prediction and visualization of AMR phenotypes associated with SNP genotypes. We describe the steps needed for input data preparation, prediction model selection, and result visualization. AMRLearn is useful for researchers wanting to extract information relevant to AMR from whole-genome sequence data.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103733"},"PeriodicalIF":1.3,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804382","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}
引用次数: 0
Protocol for dual metabolomics and proteomics using nanoflow liquid chromatography-tandem mass spectrometry.
IF 1.3
STAR Protocols Pub Date : 2025-04-05 DOI: 10.1016/j.xpro.2025.103745
Weiwei Lin, Fatemeh Mousavi, Benjamin C Blum, Christian F Heckendorf, Matthew Lawton, Noah Lampl, Ryan Hekman, Mark McComb, Andrew Emili
{"title":"Protocol for dual metabolomics and proteomics using nanoflow liquid chromatography-tandem mass spectrometry.","authors":"Weiwei Lin, Fatemeh Mousavi, Benjamin C Blum, Christian F Heckendorf, Matthew Lawton, Noah Lampl, Ryan Hekman, Mark McComb, Andrew Emili","doi":"10.1016/j.xpro.2025.103745","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103745","url":null,"abstract":"<p><p>Nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS) benefits untargeted metabolomics by enhancing sensitivity and integrating proteomics for the same sample. Here, we present a protocol to enable nLC-MS for dual metabolomics and proteomics. We describe steps for solid-phase micro-extraction (SPME)-assisted metabolite cleaning and enrichment, which avoids capillary column blockage. We then detail nLC-MS data acquisition and analysis. This protocol has been applied in diverse specimens including biofluids, cell lines, and tissues. For complete details on the use and execution of this protocol, please refer to Lin et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103745"},"PeriodicalIF":1.3,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796642","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}
引用次数: 0
Protocol to profile tumor and microenvironment from ovarian cancer patient samples and evaluate cell-based therapy using in vitro killing assays.
IF 1.3
STAR Protocols Pub Date : 2025-04-05 DOI: 10.1016/j.xpro.2025.103742
Yan-Ruide Li, Christopher J Ochoa, Zibai Lyu, Yichen Zhu, Yuning Chen, Gabriella DiBernardo, Lauryn Ruegg, Sanaz Memarzadeh, Lili Yang
{"title":"Protocol to profile tumor and microenvironment from ovarian cancer patient samples and evaluate cell-based therapy using in vitro killing assays.","authors":"Yan-Ruide Li, Christopher J Ochoa, Zibai Lyu, Yichen Zhu, Yuning Chen, Gabriella DiBernardo, Lauryn Ruegg, Sanaz Memarzadeh, Lili Yang","doi":"10.1016/j.xpro.2025.103742","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103742","url":null,"abstract":"<p><p>Ovarian cancer (OC) presents significant challenges due to late diagnosis and high recurrence rates, necessitating a deeper understanding of the molecular and cellular characteristics of OC and the exploration of novel therapeutic approaches. Here, we provide a protocol to characterize primary OC patient samples, including the tumor and the tumor microenvironment (TME), using flow cytometry. Additionally, we detail the design and evaluation of various cell-based immunotherapies aimed at targeting primary OC tumor and the TME through in vitro killing assays. For complete details on the use and execution of this protocol, please refer to Li et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103742"},"PeriodicalIF":1.3,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796654","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}
引用次数: 0
Protocol for fabricating optically transparent, pinhole-free NiO thin film for memory devices using the spin-coating technique.
IF 1.3
STAR Protocols Pub Date : 2025-04-04 DOI: 10.1016/j.xpro.2025.103732
Adiba Adiba, Franco Mayanglambam, Tufail Ahmad
{"title":"Protocol for fabricating optically transparent, pinhole-free NiO thin film for memory devices using the spin-coating technique.","authors":"Adiba Adiba, Franco Mayanglambam, Tufail Ahmad","doi":"10.1016/j.xpro.2025.103732","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103732","url":null,"abstract":"<p><p>Fabricating visibly transparent and uniform metal oxide thin films is a significant challenge. Here, we present a protocol for the fabrication of NiO thin films. We detail the essential steps for substrate preparation. We then describe the optimized steps for spin coating, considering various parameters such as the concentration of the precursor solution, drying temperature, annealing temperature, and spin-coating speed.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103732"},"PeriodicalIF":1.3,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789191","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}
引用次数: 0
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