{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T21:43:05Z","timestamp":1773783785377,"version":"3.50.1"},"reference-count":43,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T00:00:00Z","timestamp":1759363200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"National Institute of Allergy and Infectious Diseases Division of Microbiology and Infectious Diseases","doi-asserted-by":"publisher","award":["AI148802"],"award-info":[{"award-number":["AI148802"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"National Institute of Allergy and Infectious Diseases Division of Microbiology and Infectious Diseases","doi-asserted-by":"publisher","award":["AI141602"],"award-info":[{"award-number":["AI141602"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015691","name":"National Institute of Allergy and Infectious Diseases Division of Microbiology and Infectious Diseases","doi-asserted-by":"publisher","award":["5T32EB032787-04"],"award-info":[{"award-number":["5T32EB032787-04"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.xpro.2025.104160","type":"journal-article","created":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T22:29:42Z","timestamp":1761949782000},"page":"104160","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Protocol for studying dynamics of parasite-host-mediated endothelial inflammation in 3D engineered brain microvessels"],"prefix":"10.1016","volume":"6","author":[{"given":"Ruoqian","family":"Hu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu Jung","family":"Shin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fatou","family":"Joof","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlin","family":"Howard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph D.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2723-9022","authenticated-orcid":false,"given":"Ying","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2025.104160_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113253","article-title":"Probing cerebral malaria inflammation in 3D human brain microvessels","volume":"42","author":"Howard","year":"2023","journal-title":"Cell Rep."},{"key":"10.1016\/j.xpro.2025.104160_bib2","series-title":"Global Malaria Programme (GMP)","year":"2024"},{"key":"10.1016\/j.xpro.2025.104160_bib3","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1056\/NEJMoa1400116","article-title":"Brain Swelling and Death in Children with Cerebral Malaria","volume":"372","author":"Seydel","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.xpro.2025.104160_bib4","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/415673a","article-title":"The pathogenic basis of malaria","volume":"415","author":"Miller","year":"2002","journal-title":"Nature"},{"key":"10.1016\/j.xpro.2025.104160_bib5","doi-asserted-by":"crossref","first-page":"291","DOI":"10.2217\/fmb.11.155","article-title":"Cerebral malaria pathogenesis: Revisiting parasite and host contributions","volume":"7","author":"Grau","year":"2012","journal-title":"Future Microbiol."},{"key":"10.1016\/j.xpro.2025.104160_bib6","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nm986","article-title":"Differentiating the pathologies of cerebral malaria by postmortem parasite counts","volume":"10","author":"Taylor","year":"2004","journal-title":"Nat. Med."},{"key":"10.1016\/j.xpro.2025.104160_bib7","doi-asserted-by":"crossref","first-page":"2146","DOI":"10.1016\/j.ajpath.2011.01.016","article-title":"The neuropathology of fatal cerebral malaria in Malawian children","volume":"178","author":"Dorovini-Zis","year":"2011","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.xpro.2025.104160_bib8","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1016\/0140-6736(90)92827-5","article-title":"TNF concentration in fatal cerebral, non-fatal cerebral, and uncomplicated Plasmodium falciparum malaria","volume":"336","author":"Kwiatkowski","year":"1990","journal-title":"Lancet"},{"key":"10.1016\/j.xpro.2025.104160_bib9","doi-asserted-by":"crossref","first-page":"e00420-19","DOI":"10.1128\/mBio.00420-19","article-title":"Binding heterogeneity of plasmodium falciparum to engineered 3d brain microvessels is mediated by EPCR and ICAM-1","volume":"10","author":"Bernabeu","year":"2019","journal-title":"mBio"},{"key":"10.1016\/j.xpro.2025.104160_bib34","series-title":"Methods in Molecular Biology","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1007\/978-1-0716-2189-9_43","article-title":"Binding of Plasmodium falciparum-Infected Red Blood Cells to Engineered 3D Microvessels","author":"Piatti","year":"2022"},{"key":"10.1016\/j.xpro.2025.104160_bib10","doi-asserted-by":"crossref","first-page":"9342","DOI":"10.1073\/pnas.1201240109","article-title":"In vitro microvessels for the study of angiogenesis and thrombosis","volume":"109","author":"Zheng","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2025.104160_bib11","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.isci.2018.05.003","article-title":"Human Organ-Specific Endothelial Cell Heterogeneity","volume":"4","author":"Marcu","year":"2018","journal-title":"iScience"},{"key":"10.1016\/j.xpro.2025.104160_bib12","first-page":"3198","article-title":"Inhibition of \u03b2-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes","volume":"142","author":"Palpant","year":"2015","journal-title":"Development"},{"key":"10.1016\/j.xpro.2025.104160_bib13","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.pt.2020.12.008","article-title":"Bioengineered 3D Microvessels for Investigating Plasmodium falciparum Pathogenesis","volume":"37","author":"Bernabeu","year":"2021","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.xpro.2025.104160_bib14","doi-asserted-by":"crossref","first-page":"e1402","DOI":"10.1093\/infdis\/jiae315","article-title":"Plasma From Older Children in Malawi Inhibits Plasmodium falciparum Binding in 3-Dimensional Brain Microvessels","volume":"230","author":"Joof","year":"2024","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.xpro.2025.104160_bib15","doi-asserted-by":"crossref","first-page":"E1782","DOI":"10.1073\/pnas.1120534109","article-title":"A restricted subset of var genes mediates adherence of Plasmodium falciparum-infected erythrocytes to brain endothelial cells","volume":"109","author":"Avril","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2025.104160_bib16","doi-asserted-by":"crossref","first-page":"E1772","DOI":"10.1073\/pnas.1120461109","article-title":"A subset of group A-like var genes encodes the malaria parasite ligands for binding to human brain endothelial cells","volume":"109","author":"Claessens","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xpro.2025.104160_bib17","doi-asserted-by":"crossref","first-page":"4243","DOI":"10.1182\/blood-2009-06-226415","article-title":"Plasmodium falciparum-infected erythrocytes induce NF-B regulated inflammatory pathways in human cerebral endothelium","volume":"114","author":"Tripathi","year":"2009","journal-title":"Blood"},{"key":"10.1016\/j.xpro.2025.104160_bib18","doi-asserted-by":"crossref","DOI":"10.15252\/emmm.201809164","article-title":"Cerebral malaria is associated with differential cytoadherence to brain endothelial cells","volume":"11","author":"Storm","year":"2019","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.xpro.2025.104160_bib19","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.01746-22","article-title":"Plasmodium falciparum and TNF-\u03b1 Differentially Regulate Inflammatory and Barrier Integrity Pathways in Human Brain Endothelial Cells","volume":"13","author":"Zuniga","year":"2022","journal-title":"mBio"},{"key":"10.1016\/j.xpro.2025.104160_bib20","series-title":"Methods in Molecular Biology","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/978-1-0716-2189-9_5","article-title":"Establishing and Maintaining In Vitro Cultures of Asexual Blood Stages of Plasmodium falciparum","author":"Lopez-Perez","year":"2022"},{"key":"10.1016\/j.xpro.2025.104160_bib21","series-title":"Methods in Malaria Research Sixth","year":"2013"},{"key":"10.1016\/j.xpro.2025.104160_bib22","doi-asserted-by":"crossref","first-page":"1584","DOI":"10.1128\/EC.00063-07","article-title":"Serum lipoproteins promote efficient presentation of the malaria virulence protein PfEMP1 at the erythrocyte surface","volume":"6","author":"Frankland","year":"2007","journal-title":"Eukaryot. Cell"},{"key":"10.1016\/j.xpro.2025.104160_bib23","doi-asserted-by":"crossref","first-page":"1820","DOI":"10.1038\/nprot.2013.110","article-title":"Formation of microvascular networks in vitro","volume":"8","author":"Morgan","year":"2013","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib24","doi-asserted-by":"crossref","first-page":"e2100031","DOI":"10.1002\/adhm.202100031","article-title":"Multiphoton-Guided Creation of Complex Organ-Specific Microvasculature","volume":"10","author":"Rayner","year":"2021","journal-title":"Adv. Healthc. Mater."},{"key":"10.1016\/j.xpro.2025.104160_bib25","doi-asserted-by":"crossref","first-page":"2753","DOI":"10.1038\/nprot.2006.430","article-title":"Preparation of ready-to-use, storable and reconstituted type I collagen from rat tail tendon for tissue engineering applications","volume":"1","author":"Rajan","year":"2007","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib26","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1089\/ten.tea.2010.0724","article-title":"Decellularized porcine brain matrix for cell culture and tissue engineering scaffolds","volume":"17","author":"Dequach","year":"2011","journal-title":"Tissue Eng. Part A"},{"key":"10.1016\/j.xpro.2025.104160_bib27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0000910","article-title":"Disruption of Var2CSA gene impairs placental malaria associated adhesion phenotype","volume":"2","author":"Viebig","year":"2007","journal-title":"PLoS One"},{"key":"10.1016\/j.xpro.2025.104160_bib28","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-018-2486-6","article-title":"iDEP: An integrated web application for differential expression and pathway analysis of RNA-Seq data","volume":"19","author":"Ge","year":"2018","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.xpro.2025.104160_bib29","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.xpro.2025.104160_bib30","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: a graphical gene-set enrichment tool for animals and plants","volume":"36","author":"Ge","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xpro.2025.104160_bib31","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2025.104160_bib42","first-page":"7","article-title":"Analysis of Plasmodium falciparum-infected red blood cells","volume":"4","author":"Uhlemann","year":"2000","journal-title":"MACS & More"},{"key":"10.1016\/j.xpro.2025.104160_bib32","series-title":"Volume Flow and Wall Shear Stress Quantification in the Human Conjunctival Capillaries and Post-capillary Venules in Vivo","author":"Koutsiaris","year":"2007"},{"key":"10.1016\/j.xpro.2025.104160_bib33","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.molbiopara.2004.05.009","article-title":"Localization of organellar proteins in Plasmodium falciparum using a novel set of transfection vectors and a new immunofluorescence fixation method","volume":"137","author":"Tonkin","year":"2004","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.xpro.2025.104160_bib43","first-page":"177","article-title":"Endothelial permeability assays in vitro","author":"Adil","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.xpro.2025.104160_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2022.101204","article-title":"Isolation and freezing of human peripheral blood mononuclear cells from pregnant patients","volume":"3","author":"Efthymiou","year":"2022","journal-title":"STAR Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib37","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib35","series-title":"Methods in Molecular Biology","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/978-1-59745-551-0_17","article-title":"Methods for Forming Human Microvascular Tubes In Vitro and Measuring Their Macromolecular Permeability","author":"Price","year":"2011"},{"key":"10.1016\/j.xpro.2025.104160_bib38","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41596-021-00635-w","article-title":"Engineered human blood\u2013brain barrier microfluidic model for vascular permeability analyses","volume":"17","author":"Hajal","year":"2022","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib39","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2024.102950","article-title":"Protocol for fabricating and characterizing microvessel-on-a-chip for human umbilical vein endothelial cells","volume":"5","author":"Cacheux","year":"2024","journal-title":"STAR Protoc."},{"key":"10.1016\/j.xpro.2025.104160_bib40","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1016\/j.pt.2019.04.010","article-title":"Blood\u2013Brain Barrier in Cerebral Malaria: Pathogenesis and Therapeutic Intervention","volume":"35","author":"Nishanth","year":"2019","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.xpro.2025.104160_bib41","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-24775-5","article-title":"Microfluidic device with brain extracellular matrix promotes structural and functional maturation of human brain organoids","volume":"12","author":"Cho","year":"2021","journal-title":"Nat. Commun."}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166725005660?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166725005660?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T18:03:49Z","timestamp":1773770629000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166725005660"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":43,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["S2666166725005660"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2025.104160","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for studying dynamics of parasite-host-mediated endothelial inflammation in 3D engineered brain microvessels","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2025.104160","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2023.113253","name":"associatedlink","label":"CrossRef DOI link to the associated document"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104160"}}