[ { "key": "BKHARZXU", "version": 72, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/BKHARZXU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/BKHARZXU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "lastModifiedByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Yang et al.", "parsedDate": "2014", "numChildren": 1 }, "data": { "key": "BKHARZXU", "version": 72, "itemType": "journalArticle", "title": "Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing", "creators": [ { "creatorType": "author", "firstName": "Bin", "lastName": "Yang" }, { "creatorType": "author", "firstName": "Jennifer B.", "lastName": "Treweek" }, { "creatorType": "author", "firstName": "Rajan P.", "lastName": "Kulkarni" }, { "creatorType": "author", "firstName": "Benjamin E.", "lastName": "Deverman" }, { "creatorType": "author", "firstName": "Chun-Kan", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Eric", "lastName": "Lubeck" }, { "creatorType": "author", "firstName": "Sheel", "lastName": "Shah" }, { "creatorType": "author", "firstName": "Long", "lastName": "Cai" }, { "creatorType": "author", "firstName": "Viviana", "lastName": "Gradinaru" } ], "abstractNote": "", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "2014", "volume": "158", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "945-958", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.cell.2014.07.017", "citationKey": "", "url": "http://www.cell.com/article/S0092867414009313/abstract", "accessDate": "2014-08-01T13:41:35Z", "PMID": "", "PMCID": "", "ISSN": "0092-8674", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "www.cell.com", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Ian Project" } ], "collections": [], "relations": {}, "dateAdded": "2014-09-06T20:41:19Z", "dateModified": "2014-09-18T16:27:26Z" } }, { "key": "FEQPX94A", "version": 71, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/FEQPX94A", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/FEQPX94A", "type": "text/html" } }, "meta": { "createdByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Issadore et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "FEQPX94A", "version": 71, "itemType": "journalArticle", "title": "Microwave dielectric heating of drops in microfluidic devices", "creators": [ { "creatorType": "author", "firstName": "David", "lastName": "Issadore" }, { "creatorType": "author", "firstName": "Katherine J.", "lastName": "Humphry" }, { "creatorType": "author", "firstName": "Keith A.", "lastName": "Brown" }, { "creatorType": "author", "firstName": "Lori", "lastName": "Sandberg" }, { "creatorType": "author", "firstName": "David A.", "lastName": "Weitz" }, { "creatorType": "author", "firstName": "Robert M.", "lastName": "Westervelt" } ], "abstractNote": "", "publicationTitle": "Lab on a Chip", "publisher": "", "place": "", "date": "2009", "volume": "9", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "1701", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1039/b822357b", "citationKey": "", "url": "http://xlink.rsc.org/?DOI=b822357b", "accessDate": "2014-09-18T00:35:16Z", "PMID": "", "PMCID": "", "ISSN": "1473-0197, 1473-0189", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-18T00:35:16Z", "dateModified": "2014-09-18T00:35:16Z" } }, { "key": "7FD7H43K", "version": 70, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/7FD7H43K", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/7FD7H43K", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/XH78R287", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "7FD7H43K", "version": 70, "parentItem": "XH78R287", "itemType": "attachment", "linkMode": "imported_file", "title": "nm.2309.pdf", "accessDate": "", "url": "", "note": "", "contentType": "application/pdf", "charset": "", "filename": "nm.2309.pdf", "md5": "8f0a7dde66cb97395cb316895c983dd3", "mtime": 1410896235000, "tags": [], "relations": {}, "dateAdded": "2014-09-16T19:37:15Z", "dateModified": "2014-09-16T19:37:15Z" } }, { "key": "XH78R287", "version": 70, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/XH78R287", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/XH78R287", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Zhang et al.", "parsedDate": "2011-04", "numChildren": 1 }, "data": { "key": "XH78R287", "version": 70, "itemType": "journalArticle", "title": "Combating trastuzumab resistance by targeting SRC, a common node downstream of multiple resistance pathways", "creators": [ { "creatorType": "author", "firstName": "Siyuan", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Wen-Chien", "lastName": "Huang" }, { "creatorType": "author", "firstName": "Ping", "lastName": "Li" }, { "creatorType": "author", "firstName": "Hua", "lastName": "Guo" }, { "creatorType": "author", "firstName": "Say-Bee", "lastName": "Poh" }, { "creatorType": "author", "firstName": "Samuel W", "lastName": "Brady" }, { "creatorType": "author", "firstName": "Yan", "lastName": "Xiong" }, { "creatorType": "author", "firstName": "Ling-Ming", "lastName": "Tseng" }, { "creatorType": "author", "firstName": "Shau-Hsuan", "lastName": "Li" }, { "creatorType": "author", "firstName": "Zhaoxi", "lastName": "Ding" }, { "creatorType": "author", "firstName": "Aysegul A", "lastName": "Sahin" }, { "creatorType": "author", "firstName": "Francisco J", "lastName": "Esteva" }, { "creatorType": "author", "firstName": "Gabriel N", "lastName": "Hortobagyi" }, { "creatorType": "author", "firstName": "Dihua", "lastName": "Yu" } ], "abstractNote": "Trastuzumab is a successful rationally designed ERBB2-targeted therapy. However, about half of individuals with ERBB2-overexpressing breast cancer do not respond to trastuzumab-based therapies, owing to various resistance mechanisms. Clinically applicable regimens for overcoming trastuzumab resistance of different mechanisms are not yet available. We show that the nonreceptor tyrosine kinase c-SRC (SRC) is a key modulator of trastuzumab response and a common node downstream of multiple trastuzumab resistance pathways. We find that SRC is activated in both acquired and de novo trastuzumab-resistant cells and uncover a novel mechanism of SRC regulation involving dephosphorylation by PTEN. Increased SRC activation conferred considerable trastuzumab resistance in breast cancer cells and correlated with trastuzumab resistance in patients. Targeting SRC in combination with trastuzumab sensitized multiple lines of trastuzumab-resistant cells to trastuzumab and eliminated trastuzumab-resistant tumors in vivo, suggesting the potential clinical application of this strategy to overcome trastuzumab resistance.", "publicationTitle": "Nature Medicine", "publisher": "", "place": "", "date": "Apr 2011", "volume": "17", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "461-469", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Med.", "DOI": "10.1038/nm.2309", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21399647", "accessDate": "2012-04-16T03:49:09Z", "PMID": "", "PMCID": "", "ISSN": "1546-170X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 21399647", "tags": [ { "tag": "Antibodies, Monoclonal", "type": 1 }, { "tag": "Antibodies, Monoclonal, Humanized", "type": 1 }, { "tag": "Antineoplastic Agents", "type": 1 }, { "tag": "Breast Neoplasms", "type": 1 }, { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "Drug Resistance, Neoplasm", "type": 1 }, { "tag": "Enzyme Activation", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "My papers" }, { "tag": "Receptor, erbB-2", "type": 1 }, { "tag": "myself" }, { "tag": "src-Family Kinases", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-09-16T19:37:15Z", "dateModified": "2014-09-16T19:37:15Z" } }, { "key": "6XBV3CDE", "version": 69, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/6XBV3CDE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/6XBV3CDE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Kim and Paik", "parsedDate": "2010-06", "numChildren": 1 }, "data": { "key": "6XBV3CDE", "version": 69, "itemType": "journalArticle", "title": "Gene-expression-based prognostic assays for breast cancer", "creators": [ { "creatorType": "author", "firstName": "Chungyeul", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Soonmyung", "lastName": "Paik" } ], "abstractNote": "Several gene-expression-based reference laboratory tests are now available for prognostication of patients diagnosed with breast cancer. For clinical oncologists, it is important to understand the clinical contexts for which these assays were developed in order to use them properly. This Review is aimed at providing a conceptual and technical overview of the steps involved in the development of gene-expression profiling-based prognostic assays. MammaPrint and Oncotype DX, two widely utilized assays, are compared with respect to differences in the clinical contexts for their development, technologies used, and clinical utilities with the aim of providing a guide to clinical oncologists for utilization of these assays.", "publicationTitle": "Nature Reviews. Clinical Oncology", "publisher": "", "place": "", "date": "Jun 2010", "volume": "7", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "340-347", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Rev Clin Oncol", "DOI": "10.1038/nrclinonc.2010.61", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1759-4782", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20440284", "tags": [ { "tag": "Biological Assay", "type": 1 }, { "tag": "Breast Neoplasms", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Gene Expression", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Microarray Analysis", "type": 1 }, { "tag": "Prognosis", "type": 1 }, { "tag": "gene expression profiling", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-09-16T15:37:22Z", "dateModified": "2014-09-16T15:37:22Z" } }, { "key": "PZMPSXS9", "version": 69, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/PZMPSXS9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/PZMPSXS9", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/6XBV3CDE", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "PZMPSXS9", "version": 69, "parentItem": "6XBV3CDE", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-09-16T15:37:22Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20440284", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-09-16T15:37:22Z", "dateModified": "2014-09-16T15:37:22Z" } }, { "key": "FJDJ7NAD", "version": 68, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/FJDJ7NAD", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/FJDJ7NAD", "type": "text/html" } }, "meta": { "createdByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Das et al.", "parsedDate": "2014-02-26", "numChildren": 0 }, "data": { "key": "FJDJ7NAD", "version": 68, "itemType": "conferencePaper", "title": "Optically clearing tissue as an initial step for 3D imaging of core biopsies to diagnose pancreatic cancer", "creators": [ { "creatorType": "editor", "firstName": "E. Duco", "lastName": "Jansen" }, { "creatorType": "editor", "firstName": "Robert J.", "lastName": "Thomas" }, { "creatorType": "editor", "firstName": "Gerald J.", "lastName": "Wilmink" }, { "creatorType": "editor", "firstName": "Bennett L.", "lastName": "Ibey" }, { "creatorType": "author", "firstName": "Ronnie", "lastName": "Das" }, { "creatorType": "author", "firstName": "Aishwarya", "lastName": "Agrawal" }, { "creatorType": "author", "firstName": "Melissa P.", "lastName": "Upton" }, { "creatorType": "author", "firstName": "Eric J.", "lastName": "Seibel" } ], "abstractNote": "", "proceedingsTitle": "", "conferenceName": "", "publisher": "", "place": "", "date": "2014-2-26", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "89410N", "series": "", "seriesNumber": "", "DOI": "10.1117/12.2041114", "ISBN": "", "citationKey": "", "url": "http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2041114", "accessDate": "2014-09-16T04:05:13Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-16T04:05:13Z", "dateModified": "2014-09-16T04:05:13Z" } }, { "key": "477MHIB2", "version": 67, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/477MHIB2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/477MHIB2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Das et al.", "parsedDate": "2014-03-06", "numChildren": 0 }, "data": { "key": "477MHIB2", "version": 67, "itemType": "conferencePaper", "title": "Pathology in a tube: Step 1. Fixing, staining, and transporting pancreatic core biopsies in a microfluidic device for 3D imaging", "creators": [ { "creatorType": "editor", "firstName": "Bonnie L.", "lastName": "Gray" }, { "creatorType": "editor", "firstName": "Holger", "lastName": "Becker" }, { "creatorType": "author", "firstName": "Ronnie", "lastName": "Das" }, { "creatorType": "author", "firstName": "Chris W.", "lastName": "Burfeind" }, { "creatorType": "author", "firstName": "Greg M.", "lastName": "Kramer" }, { "creatorType": "author", "firstName": "Eric J.", "lastName": "Seibel" } ], "abstractNote": "", "proceedingsTitle": "", "conferenceName": "", "publisher": "", "place": "", "date": "2014-3-6", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "89760R", "series": "", "seriesNumber": "", "DOI": "10.1117/12.2041106", "ISBN": "", "citationKey": "", "url": "http://proceedings.spiedigitallibrary.org/proceeding.aspx?doi=10.1117/12.2041106", "accessDate": "2014-09-16T04:04:43Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Pathology in a tube", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-16T04:04:43Z", "dateModified": "2014-09-16T04:04:43Z" } }, { "key": "MCT8ZXPH", "version": 66, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/MCT8ZXPH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/MCT8ZXPH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Yazdi and Ardekani", "parsedDate": "2012", "numChildren": 0 }, "data": { "key": "MCT8ZXPH", "version": 66, "itemType": "journalArticle", "title": "Bacterial aggregation and biofilm formation in a vortical flow", "creators": [ { "creatorType": "author", "firstName": "Shahrzad", "lastName": "Yazdi" }, { "creatorType": "author", "firstName": "Arezoo M.", "lastName": "Ardekani" } ], "abstractNote": "", "publicationTitle": "Biomicrofluidics", "publisher": "", "place": "", "date": "12/2012", "volume": "6", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "044114", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1063/1.4771407", "citationKey": "", "url": "http://scitation.aip.org/content/aip/journal/bmf/6/4/10.1063/1.4771407", "accessDate": "2014-09-13T22:28:44Z", "PMID": "", "PMCID": "", "ISSN": "1932-1058", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-13T22:28:54Z", "dateModified": "2014-09-13T22:28:54Z" } }, { "key": "6BRFWEJ3", "version": 65, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/6BRFWEJ3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/6BRFWEJ3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 693260, "username": "hoelzle2", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/hoelzle2", "type": "text/html" } } }, "creatorSummary": "Stott et al.", "parsedDate": "2010-10-26", "numChildren": 0 }, "data": { "key": "6BRFWEJ3", "version": 65, "itemType": "journalArticle", "title": "Isolation of circulating tumor cells using a microvortex-generating herringbone-chip", "creators": [ { "creatorType": "author", "firstName": "S. L.", "lastName": "Stott" }, { "creatorType": "author", "firstName": "C.-H.", "lastName": "Hsu" }, { "creatorType": "author", "firstName": "D. I.", "lastName": "Tsukrov" }, { "creatorType": "author", "firstName": "M.", "lastName": "Yu" }, { "creatorType": "author", "firstName": "D. T.", "lastName": "Miyamoto" }, { "creatorType": "author", "firstName": "B. A.", "lastName": "Waltman" }, { "creatorType": "author", "firstName": "S. M.", "lastName": "Rothenberg" }, { "creatorType": "author", "firstName": "A. M.", "lastName": "Shah" }, { "creatorType": "author", "firstName": "M. E.", "lastName": "Smas" }, { "creatorType": "author", "firstName": "G. K.", "lastName": "Korir" }, { "creatorType": "author", "firstName": "F. P.", "lastName": "Floyd" }, { "creatorType": "author", "firstName": "A. J.", "lastName": "Gilman" }, { "creatorType": "author", "firstName": "J. B.", "lastName": "Lord" }, { "creatorType": "author", "firstName": "D.", "lastName": "Winokur" }, { "creatorType": "author", "firstName": "S.", "lastName": "Springer" }, { "creatorType": "author", "firstName": "D.", "lastName": "Irimia" }, { "creatorType": "author", "firstName": "S.", "lastName": "Nagrath" }, { "creatorType": "author", "firstName": "L. V.", "lastName": "Sequist" }, { "creatorType": "author", "firstName": "R. J.", "lastName": "Lee" }, { "creatorType": "author", "firstName": "K. J.", "lastName": "Isselbacher" }, { "creatorType": "author", "firstName": "S.", "lastName": "Maheswaran" }, { "creatorType": "author", "firstName": "D. A.", "lastName": "Haber" }, { "creatorType": "author", "firstName": "M.", "lastName": "Toner" } ], "abstractNote": "", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "2010-10-26", "volume": "107", "issue": "43", "section": "", "partNumber": "", "partTitle": "", "pages": "18392-18397", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1073/pnas.1012539107", "citationKey": "", "url": "http://www.pnas.org/cgi/doi/10.1073/pnas.1012539107", "accessDate": "2014-09-13T22:21:57Z", "PMID": "", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-13T22:21:57Z", "dateModified": "2014-09-13T22:21:57Z" } }, { "key": "EQCMDFIA", "version": 64, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/EQCMDFIA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/EQCMDFIA", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/RZ3XUKUH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "EQCMDFIA", "version": 64, "parentItem": "RZ3XUKUH", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2014-09-12T22:20:57Z", "url": "http://www.nature.com/nm/journal/vaop/ncurrent/pdf/nm.3488.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Angelo et al. - 2014 - Multiplexed ion beam imaging of human breast tumor.pdf", "md5": "0347551f681175a5d89f2ef9684eb1c5", "mtime": 1410560461000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T22:20:57Z", "dateModified": "2014-09-12T22:21:01Z" } }, { "key": "9SGUMNHU", "version": 64, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/9SGUMNHU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/9SGUMNHU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/RZ3XUKUH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "9SGUMNHU", "version": 64, "parentItem": "RZ3XUKUH", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2014-09-12T22:20:58Z", "url": "http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3488.html", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "nm.3488.html", "md5": "83865f3b4a1145d4f0e9e102a467509a", "mtime": 1410560459000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T22:20:58Z", "dateModified": "2014-09-12T22:20:58Z" } }, { "key": "RZ3XUKUH", "version": 64, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/RZ3XUKUH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/RZ3XUKUH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Angelo et al.", "parsedDate": "2014-03-02", "numChildren": 2 }, "data": { "key": "RZ3XUKUH", "version": 64, "itemType": "journalArticle", "title": "Multiplexed ion beam imaging of human breast tumors", "creators": [ { "creatorType": "author", "firstName": "Michael", "lastName": "Angelo" }, { "creatorType": "author", "firstName": "Sean C.", "lastName": "Bendall" }, { "creatorType": "author", "firstName": "Rachel", "lastName": "Finck" }, { "creatorType": "author", "firstName": "Matthew B.", "lastName": "Hale" }, { "creatorType": "author", "firstName": "Chuck", "lastName": "Hitzman" }, { "creatorType": "author", "firstName": "Alexander D.", "lastName": "Borowsky" }, { "creatorType": "author", "firstName": "Richard M.", "lastName": "Levenson" }, { "creatorType": "author", "firstName": "John B.", "lastName": "Lowe" }, { "creatorType": "author", "firstName": "Scot D.", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Shuchun", "lastName": "Zhao" }, { "creatorType": "author", "firstName": "Yasodha", "lastName": "Natkunam" }, { "creatorType": "author", "firstName": "Garry P.", "lastName": "Nolan" } ], "abstractNote": "Immunohistochemistry (IHC) is a tool for visualizing protein expression that is employed as part of the diagnostic workup for the majority of solid tissue malignancies. Existing IHC methods use antibodies tagged with fluorophores or enzyme reporters that generate colored pigments. Because these reporters exhibit spectral and spatial overlap when used simultaneously, multiplexed IHC is not routinely used in clinical settings. We have developed a method that uses secondary ion mass spectrometry to image antibodies tagged with isotopically pure elemental metal reporters. Multiplexed ion beam imaging (MIBI) is capable of analyzing up to 100 targets simultaneously over a five-log dynamic range. Here, we used MIBI to analyze formalin-fixed, paraffin-embedded human breast tumor tissue sections stained with ten labels simultaneously. The resulting data suggest that MIBI can provide new insights into disease pathogenesis that will be valuable for basic research, drug discovery and clinical diagnostics.", "publicationTitle": "Nature Medicine", "publisher": "", "place": "", "date": "March 2, 2014", "volume": "advance online publication", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Med", "DOI": "10.1038/nm.3488", "citationKey": "", "url": "http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3488.html", "accessDate": "2014-09-12T22:20:57Z", "PMID": "", "PMCID": "", "ISSN": "1078-8956", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "© 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-12T22:20:57Z", "dateModified": "2014-09-12T22:20:57Z" } }, { "key": "EDE6N2CH", "version": 64, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/EDE6N2CH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/EDE6N2CH", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/3Q9Q4EBI", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "EDE6N2CH", "version": 64, "parentItem": "3Q9Q4EBI", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2014-09-12T22:17:57Z", "url": "http://www.nature.com/nbt/journal/v24/n10/abs/nbt1250.html", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "nbt1250.html", "md5": "11e075d8261f5e5702f1d02099980311", "mtime": 1410560276000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T22:17:57Z", "dateModified": "2014-09-12T22:17:57Z" } }, { "key": "KB6Q32QE", "version": 64, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/KB6Q32QE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/KB6Q32QE", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/3Q9Q4EBI", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "KB6Q32QE", "version": 64, "parentItem": "3Q9Q4EBI", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2014-09-12T22:17:54Z", "url": "http://www.nature.com/nbt/journal/v24/n10/pdf/nbt1250.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Schubert et al. - 2006 - Analyzing proteome topology and function by automa.pdf", "md5": "f74898a1e72b18399563f5def1e866b2", "mtime": 1410560275000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T22:17:54Z", "dateModified": "2014-09-12T22:17:56Z" } }, { "key": "3Q9Q4EBI", "version": 62, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/3Q9Q4EBI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/3Q9Q4EBI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Schubert et al.", "parsedDate": "2006-10", "numChildren": 2 }, "data": { "key": "3Q9Q4EBI", "version": 62, "itemType": "journalArticle", "title": "Analyzing proteome topology and function by automated multidimensional fluorescence microscopy", "creators": [ { "creatorType": "author", "firstName": "Walter", "lastName": "Schubert" }, { "creatorType": "author", "firstName": "Bernd", "lastName": "Bonnekoh" }, { "creatorType": "author", "firstName": "Ansgar J.", "lastName": "Pommer" }, { "creatorType": "author", "firstName": "Lars", "lastName": "Philipsen" }, { "creatorType": "author", "firstName": "Raik", "lastName": "Böckelmann" }, { "creatorType": "author", "firstName": "Yanina", "lastName": "Malykh" }, { "creatorType": "author", "firstName": "Harald", "lastName": "Gollnick" }, { "creatorType": "author", "firstName": "Manuela", "lastName": "Friedenberger" }, { "creatorType": "author", "firstName": "Marcus", "lastName": "Bode" }, { "creatorType": "author", "firstName": "Andreas W. M.", "lastName": "Dress" } ], "abstractNote": "Temporal and spatial regulation of proteins contributes to function. We describe a multidimensional microscopic robot technology for high-throughput protein colocalization studies that runs cycles of fluorescence tagging, imaging and bleaching in situ. This technology combines three advances: a fluorescence technique capable of mapping hundreds of different proteins in one tissue section or cell sample; a method selecting the most prominent combinatorial molecular patterns by representing the data as binary vectors; and a system for imaging the distribution of these protein clusters in a so-called toponome map. By analyzing many cell and tissue types, we show that this approach reveals rules of hierarchical protein network organization, in which the frequency distribution of different protein clusters obeys Zipf's law, and state-specific lead proteins appear to control protein network topology and function. The technology may facilitate the development of diagnostics and targeted therapies.", "publicationTitle": "Nature Biotechnology", "publisher": "", "place": "", "date": "October 2006", "volume": "24", "issue": "10", "section": "", "partNumber": "", "partTitle": "", "pages": "1270-1278", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt1250", "citationKey": "", "url": "http://www.nature.com/nbt/journal/v24/n10/abs/nbt1250.html", "accessDate": "2014-09-12T22:17:54Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "© 2006 Nature Publishing Group", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2014-09-12T22:17:54Z", "dateModified": "2014-09-12T22:17:54Z" } }, { "key": "9RSQ7H6V", "version": 61, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/9RSQ7H6V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/9RSQ7H6V", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/V3ZBWCX7", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "9RSQ7H6V", "version": 61, "parentItem": "V3ZBWCX7", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-09-12T12:24:32Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/23473796", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-09-12T12:24:32Z", "dateModified": "2014-09-12T12:24:32Z" } }, { "key": "V3ZBWCX7", "version": 61, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/V3ZBWCX7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/V3ZBWCX7", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Bond and Kinnamon", "parsedDate": "2013-04-30", "numChildren": 1 }, "data": { "key": "V3ZBWCX7", "version": 61, "itemType": "journalArticle", "title": "Microwave processing of gustatory tissues for immunohistochemistry", "creators": [ { "creatorType": "author", "firstName": "Amanda", "lastName": "Bond" }, { "creatorType": "author", "firstName": "John C.", "lastName": "Kinnamon" } ], "abstractNote": "We use immunohistochemistry to study taste cell structure and function as a means to elucidate how taste receptor cells communicate with nerve fibers and adjacent taste cells. This conventional method, however, is time consuming. In the present study we used taste buds from rat circumvallate papillae to compare conventional immunohistochemical tissue processing with microwave processing for the colocalization of several biochemical pathway markers (PLCβ2, syntaxin-1, IP3R3, α-gustducin) and the nuclear stain, Sytox. The results of our study indicate that in microwave versus conventional immunocytochemistry: (1) fixation quality is improved; (2) the amount of time necessary for processing tissue is decreased; (3) antigen retrieval is no longer needed; (4) image quality is superior. In sum, microwave tissue processing of gustatory tissues is faster and superior to conventional immunohistochemical tissue processing for many applications.", "publicationTitle": "Journal of Neuroscience Methods", "publisher": "", "place": "", "date": "Apr 30, 2013", "volume": "215", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "132-138", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Neurosci. Methods", "DOI": "10.1016/j.jneumeth.2013.02.014", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1872-678X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 23473796 \nPMCID: PMC3782387", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Antibodies", "type": 1 }, { "tag": "Biological Markers", "type": 1 }, { "tag": "Cell Nucleus", "type": 1 }, { "tag": "Coloring Agents", "type": 1 }, { "tag": "Image Processing, Computer-Assisted", "type": 1 }, { "tag": "Immunohistochemistry", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Microscopy, Confocal", "type": 1 }, { "tag": "Microwaves", "type": 1 }, { "tag": "Organic Chemicals", "type": 1 }, { "tag": "Phospholipase C beta", "type": 1 }, { "tag": "Qa-SNARE Proteins", "type": 1 }, { "tag": "Rats", "type": 1 }, { "tag": "Rats, Sprague-Dawley", "type": 1 }, { "tag": "Taste", "type": 1 }, { "tag": "Taste Buds", "type": 1 }, { "tag": "Tissue Fixation", "type": 1 }, { "tag": "Transducin", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-09-12T12:24:32Z", "dateModified": "2014-09-12T12:24:32Z" } }, { "key": "CD732B4V", "version": 61, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/CD732B4V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/CD732B4V", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/7IGTJBRW", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "CD732B4V", "version": 61, "parentItem": "7IGTJBRW", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2014-09-12T12:21:07Z", "url": "http://link.springer.com/chapter/10.1007%2F978-3-319-10470-6_15", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "10.html", "md5": "32724c842dc3d98fb6a07134f5437e52", "mtime": 1410524467000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T12:21:07Z", "dateModified": "2014-09-12T12:21:07Z" } }, { "key": "VT5METNH", "version": 61, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/VT5METNH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/VT5METNH", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/7IGTJBRW", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "VT5METNH", "version": 61, "parentItem": "7IGTJBRW", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2014-09-12T12:21:05Z", "url": "http://link.springer.com/content/pdf/10.1007%2F978-3-319-10470-6_15.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Chen et al. - 2014 - A Matching Model Based on Earth Mover’s Distance f.pdf", "md5": "1ec2e1107bf43bb4cb115c2c10b1514b", "mtime": 1410524466000, "tags": [], "relations": {}, "dateAdded": "2014-09-12T12:21:05Z", "dateModified": "2014-09-12T12:21:06Z" } }, { "key": "7IGTJBRW", "version": 75, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/7IGTJBRW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/7IGTJBRW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "lastModifiedByUser": { "id": 445611, "username": "jzartman", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jzartman", "type": "text/html" } } }, "creatorSummary": "Chen et al.", "parsedDate": "2014-01-01", "numChildren": 2 }, "data": { "key": "7IGTJBRW", "version": 75, "itemType": "bookSection", "title": "A Matching Model Based on Earth Mover’s Distance for Tracking Myxococcus Xanthus", "creators": [ { "creatorType": "author", "firstName": "Jianxu", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Cameron W.", "lastName": "Harvey" }, { "creatorType": "author", "firstName": "Mark S.", "lastName": "Alber" }, { "creatorType": "author", "firstName": "Danny Z.", "lastName": "Chen" }, { "creatorType": "editor", "firstName": "Polina", "lastName": "Golland" }, { "creatorType": "editor", "firstName": "Nobuhiko", "lastName": "Hata" }, { "creatorType": "editor", "firstName": "Christian", "lastName": "Barillot" }, { "creatorType": "editor", "firstName": "Joachim", "lastName": "Hornegger" }, { "creatorType": "editor", "firstName": "Robert", "lastName": "Howe" } ], "abstractNote": "Tracking the motion of Myxococcus xanthus is a crucial step for fundamental bacteria studies. Large number of bacterial cells involved, limited image resolution, and various cell behaviors (e.g., division) make tracking a highly challenging problem. A common strategy is to segment the cells first and associate detected cells into moving trajectories. However, known detection association algorithms that run in polynomial time are either ineffective to deal with particular cell behaviors or sensitive to segmentation errors. In this paper, we propose a polynomial time hierarchical approach for associating segmented cells, using a new Earth Mover’s Distance (EMD) based matching model. Our method is able to track cell motion when cells may divide, leave/enter the image window, and the segmentation results may incur false alarm, detection lost, and falsely merged/split detections. We demonstrate it on tracking M. xanthus. Applied to error-prone segmented cells, our algorithm exhibits higher track purity and produces more complete trajectories, comparing to several state-of-the-art detection association algorithms.", "bookTitle": "Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014", "series": "Lecture Notes in Computer Science", "seriesNumber": "8674", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2014/01/01", "publisher": "Springer International Publishing", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "113-120", "ISBN": "978-3-319-10469-0 978-3-319-10470-6", "DOI": "", "citationKey": "", "url": "http://link.springer.com/chapter/10.1007/978-3-319-10470-6_15", "accessDate": "2014-09-12T12:21:05Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "link.springer.com", "callNumber": "", "rights": "©2014 Springer International Publishing Switzerland", "extra": "", "tags": [ { "tag": "Artificial Intelligence (incl. Robotics)", "type": 1 }, { "tag": "Computer Graphics", "type": 1 }, { "tag": "Health Informatics", "type": 1 }, { "tag": "Image Processing and Computer Vision", "type": 1 }, { "tag": "Imaging / Radiology", "type": 1 }, { "tag": "Pattern Recognition", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-09-12T12:21:05Z", "dateModified": "2014-09-12T12:21:05Z" } }, { "key": "FB4CZPMI", "version": 58, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/FB4CZPMI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/FB4CZPMI", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/EHDSKA42", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "FB4CZPMI", "version": 58, "parentItem": "EHDSKA42", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2014-09-09T16:46:19Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/23818604", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2014-09-09T16:46:19Z", "dateModified": "2014-09-09T16:46:19Z" } }, { "key": "EHDSKA42", "version": 58, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/EHDSKA42", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/EHDSKA42", "type": "text/html" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "creatorSummary": "Gerdes et al.", "parsedDate": "2013-07-16", "numChildren": 1 }, "data": { "key": "EHDSKA42", "version": 58, "itemType": "journalArticle", "title": "Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue", "creators": [ { "creatorType": "author", "firstName": "Michael J.", "lastName": "Gerdes" }, { "creatorType": "author", "firstName": "Christopher J.", "lastName": "Sevinsky" }, { "creatorType": "author", "firstName": "Anup", "lastName": "Sood" }, { "creatorType": "author", "firstName": "Sudeshna", "lastName": "Adak" }, { "creatorType": "author", "firstName": "Musodiq O.", "lastName": "Bello" }, { "creatorType": "author", "firstName": "Alexander", "lastName": "Bordwell" }, { "creatorType": "author", "firstName": "Ali", "lastName": "Can" }, { "creatorType": "author", "firstName": "Alex", "lastName": "Corwin" }, { "creatorType": "author", "firstName": "Sean", "lastName": "Dinn" }, { "creatorType": "author", "firstName": "Robert J.", "lastName": "Filkins" }, { "creatorType": "author", "firstName": "Denise", "lastName": "Hollman" }, { "creatorType": "author", "firstName": "Vidya", "lastName": "Kamath" }, { "creatorType": "author", "firstName": "Sireesha", "lastName": "Kaanumalle" }, { "creatorType": "author", "firstName": "Kevin", "lastName": "Kenny" }, { "creatorType": "author", "firstName": "Melinda", "lastName": "Larsen" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Lazare" }, { "creatorType": "author", "firstName": "Qing", "lastName": "Li" }, { "creatorType": "author", "firstName": "Christina", "lastName": "Lowes" }, { "creatorType": "author", "firstName": "Colin C.", "lastName": "McCulloch" }, { "creatorType": "author", "firstName": "Elizabeth", "lastName": "McDonough" }, { "creatorType": "author", "firstName": "Michael C.", "lastName": "Montalto" }, { "creatorType": "author", "firstName": "Zhengyu", "lastName": "Pang" }, { "creatorType": "author", "firstName": "Jens", "lastName": "Rittscher" }, { "creatorType": "author", "firstName": "Alberto", "lastName": "Santamaria-Pang" }, { "creatorType": "author", "firstName": "Brion D.", "lastName": "Sarachan" }, { "creatorType": "author", "firstName": "Maximilian L.", "lastName": "Seel" }, { "creatorType": "author", "firstName": "Antti", "lastName": "Seppo" }, { "creatorType": "author", "firstName": "Kashan", "lastName": "Shaikh" }, { "creatorType": "author", "firstName": "Yunxia", "lastName": "Sui" }, { "creatorType": "author", "firstName": "Jingyu", "lastName": "Zhang" }, { "creatorType": "author", "firstName": "Fiona", "lastName": "Ginty" } ], "abstractNote": "Limitations on the number of unique protein and DNA molecules that can be characterized microscopically in a single tissue specimen impede advances in understanding the biological basis of health and disease. Here we present a multiplexed fluorescence microscopy method (MxIF) for quantitative, single-cell, and subcellular characterization of multiple analytes in formalin-fixed paraffin-embedded tissue. Chemical inactivation of fluorescent dyes after each image acquisition round allows reuse of common dyes in iterative staining and imaging cycles. The mild inactivation chemistry is compatible with total and phosphoprotein detection, as well as DNA FISH. Accurate computational registration of sequential images is achieved by aligning nuclear counterstain-derived fiducial points. Individual cells, plasma membrane, cytoplasm, nucleus, tumor, and stromal regions are segmented to achieve cellular and subcellular quantification of multiplexed targets. In a comparison of pathologist scoring of diaminobenzidine staining of serial sections and automated MxIF scoring of a single section, human epidermal growth factor receptor 2, estrogen receptor, p53, and androgen receptor staining by diaminobenzidine and MxIF methods yielded similar results. Single-cell staining patterns of 61 protein antigens by MxIF in 747 colorectal cancer subjects reveals extensive tumor heterogeneity, and cluster analysis of divergent signaling through ERK1/2, S6 kinase 1, and 4E binding protein 1 provides insights into the spatial organization of mechanistic target of rapamycin and MAPK signal transduction. Our results suggest MxIF should be broadly applicable to problems in the fields of basic biological research, drug discovery and development, and clinical diagnostics.", "publicationTitle": "Proceedings of the National Academy of Sciences of the United States of America", "publisher": "", "place": "", "date": "Jul 16, 2013", "volume": "110", "issue": "29", "section": "", "partNumber": "", "partTitle": "", "pages": "11982-11987", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc. Natl. Acad. Sci. U.S.A.", "DOI": "10.1073/pnas.1300136110", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 23818604 \nPMCID: PMC3718135", "tags": [ { "tag": "3,3'-Diaminobenzidine", "type": 1 }, { "tag": "Breast Neoplasms", "type": 1 }, { "tag": "Cell Line, Tumor", "type": 1 }, { "tag": "Colonic Neoplasms", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Formaldehyde", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Image Processing, Computer-Assisted", "type": 1 }, { "tag": "Immunohistochemistry", "type": 1 }, { "tag": "In Situ Hybridization, Fluorescence", "type": 1 }, { "tag": "Microscopy, Fluorescence", "type": 1 }, { "tag": "Paraffin Embedding", "type": 1 }, { "tag": "Receptor, erbB-2", "type": 1 }, { "tag": "Receptors, Androgen", "type": 1 }, { "tag": "Receptors, Estrogen", "type": 1 }, { "tag": "Statistics, Nonparametric", "type": 1 }, { "tag": "Tumor Markers, Biological", "type": 1 }, { "tag": "Tumor Suppressor Protein p53", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2014-09-09T16:46:19Z", "dateModified": "2014-09-09T16:46:19Z" } }, { "key": "U92V9NCM", "version": 57, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/U92V9NCM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/U92V9NCM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/HH2JR52D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } } }, "data": { "key": "U92V9NCM", "version": 57, "parentItem": "HH2JR52D", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2013-03-26T12:47:29Z", "url": "http://breast-cancer-research.com/content/11/5/R66/", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "R66.html", "md5": "e4c00abe209ece76c587f73a9df70fa5", "mtime": 1410280071000, "tags": [], "relations": {}, "dateAdded": "2014-09-09T16:27:51Z", "dateModified": "2014-09-09T16:27:51Z" } }, { "key": "D3QPX7D6", "version": 57, "library": { "type": "group", "id": 279223, "name": "IMCT-R21", "links": { "alternate": { "href": "https://www.zotero.org/groups/imct-r21", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/279223/items/D3QPX7D6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/imct-r21/items/D3QPX7D6", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/279223/items/HH2JR52D", "type": "application/json" } }, "meta": { "createdByUser": { "id": 990056, "username": "syzm2000", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/syzm2000", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "D3QPX7D6", "version": 57, "parentItem": "HH2JR52D", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2013-03-26T12:47:25Z", "url": "http://breast-cancer-research.com/content/pdf/bcr2358.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Behbod et al. - 2009 - An intraductal human-in-mouse transplantation mode.pdf", "md5": "d604e966b46d6bf598cb12cb3bcbaf14", "mtime": 1410280071000, "tags": [], "relations": {}, "dateAdded": "2014-09-09T16:27:51Z", "dateModified": "2014-09-09T16:27:51Z" } } ]