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For the detection of DEGs, numerous methods are proposed. By such conventional methods, generally, DEGs are detected from one dataset consisting of group of control and treatment. However, some DEGs are easily to be detected in any experimental condition. For the detection of much experiment condition specific DEGs, each measurement value of gene expression levels should be compared in two dimensional ways, or both with other genes and other datasets simultaneously. For this purpose, we retrieve the gene expression data from public database as possible and construct", "publicationTitle": "BMC Genomics", "publisher": "", "place": "", "date": "2013-02-15", "volume": "14", "issue": "Suppl 2", "section": "", "partNumber": "", "partTitle": "", "pages": "S9", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/1471-2164-14-S2-S9", "citationKey": "", "url": "http://www.biomedcentral.com/1471-2164/14/S2/S9/abstract", "accessDate": "2013-09-23T14:29:43Z", "PMID": "", "PMCID": "", "ISSN": "1471-2164", "archive": "", "archiveLocation": "", "shortTitle": "Two-way AIC", "language": "en", "libraryCatalog": "www.biomedcentral.com", "callNumber": "", "rights": "2013 Tsuyuzaki et al.; licensee BioMed Central Ltd.", "extra": "PMID: 23445621", "tags": [ { "tag": "Tanner Clark" } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:37:48Z", "dateModified": "2015-05-01T00:37:48Z" } }, { "key": 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"application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/KMT3KVIM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/266537/items/T2S5KJ2Z", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } } }, "data": { "key": "KMT3KVIM", "version": 6, "parentItem": "T2S5KJ2Z", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-10-14T17:36:12Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20306535", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "54MTZXKU", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/54MTZXKU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/54MTZXKU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Lyczak et al.", "parsedDate": "2002-04", "numChildren": 1 }, "data": { "key": "54MTZXKU", "version": 6, "itemType": "journalArticle", "title": "Lung Infections Associated with Cystic Fibrosis", "creators": [ { "creatorType": "author", "firstName": "Jeffrey B.", "lastName": "Lyczak" }, { "creatorType": "author", "firstName": "Carolyn L.", "lastName": "Cannon" }, { "creatorType": "author", "firstName": "Gerald B.", "lastName": "Pier" } ], "abstractNote": "While originally characterized as a collection of related syndromes, cystic fibrosis (CF) is now recognized as a single disease whose diverse symptoms stem from the wide tissue distribution of the gene product that is defective in CF, the ion channel and regulator, cystic fibrosis transmembrane conductance regulator (CFTR). Defective CFTR protein impacts the function of the pancreas and alters the consistency of mucosal secretions. The latter of these effects probably plays an important role in the defective resistance of CF patients to many pathogens. As the modalities of CF research have changed over the decades from empirical histological studies to include biophysical measurements of CFTR function, the clinical management of this disease has similarly evolved to effectively address the ever-changing spectrum of CF-related infectious diseases. These factors have led to the successful management of many CF-related infections with the notable exception of chronic lung infection with the gram-negative bacterium Pseudomonas aeruginosa. The virulence of P. aeruginosa stems from multiple bacterial attributes, including antibiotic resistance, the ability to utilize quorum-sensing signals to form biofilms, the destructive potential of a multitude of its microbial toxins, and the ability to acquire a mucoid phenotype, which renders this microbe resistant to both the innate and acquired immunologic defenses of the host.", "publicationTitle": "Clinical Microbiology Reviews", "publisher": "", "place": "", "date": "2002-4", "volume": "15", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "194-222", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Clin Microbiol Rev", "DOI": "10.1128/CMR.15.2.194-222.2002", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC118069/", "accessDate": "2015-04-30T23:31:15Z", "PMID": "", "PMCID": "", "ISSN": "0893-8512", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 11932230\nPMCID: PMC118069", "tags": [], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "RNN5M45T", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/RNN5M45T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/RNN5M45T", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Blanc et al.", "parsedDate": "1998-05", "numChildren": 0 }, "data": { "key": "RNN5M45T", "version": 6, "itemType": "journalArticle", "title": "Frequency and molecular diversity of Pseudomonas aeruginosa upon admission and during hospitalization: a prospective epidemiologic study", "creators": [ { "creatorType": "author", "firstName": "Dominique S.", "lastName": "Blanc" }, { "creatorType": "author", "firstName": "Christiane", "lastName": "Petignat" }, { "creatorType": "author", "firstName": "Béatrice", "lastName": "Janin" }, { "creatorType": "author", "firstName": "Jacques", "lastName": "Bille" }, { "creatorType": "author", "firstName": "Patrick", "lastName": "Francioli" } ], "abstractNote": "Objective\nTo assess the molecular epidemiology and risk factors for Pseudomonas aeruginosa colonization and infection in hospitalized patients.\nMethods\nIn a 1000-bed university hospital, newly admitted patients were assessed prospectively for colonization and infection with P. aeruginosa. Anal swabs were obtained upon admission and at discharge. Ribotyping was used for the typing of isolates. Epidemiologic and clinical data were recorded prospectively. Independent risk factors were assessed using multivariate analysis.\nResults\nThe recovery rate of patients with P. aeruginosa from anal specimens on admission was 6.7% (42/628). Infection due to P. aeruginosa was observed in 20 of 628 (3.2%) patients, of whom 10 (1.6%) were already infected on admission. Independent risk factors for colonization/infection on admission were age, indwelling urinary catheter, the presence of wound and seropositivity for HIV. Independent risk factors for nosocomial infection were anal colonization on admission, alcoholism, indwelling urinary catheter and antibiotic treatment during hospitalization.\n\nRibotyping revealed that 27 patients were colonized or infected with a unique ribotype, whereas 24 shared one or more ribotypes with other patients. Analysis of epidemiologic and molecular typing data revealed that transmission from patients to patients or from patients to environment was documented on only three occasions.\nConclusions\nA great many P. aeruginosa strains were isolated from patients and the environment, and most environmental strains were different from those recovered in patients, suggesting a low rate of hospital acquisition of P. aeruginosa from the environment. The main risk factors for hospital-acquired infection were detectable colonization on admission, antibiotic treatment and urinary catheter.", "publicationTitle": "Clinical Microbiology and Infection", "publisher": "", "place": "", "date": "May 1998", "volume": "4", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "242-247", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Clinical Microbiology and Infection", "DOI": "10.1111/j.1469-0691.1998.tb00051.x", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1198743X14650370", "accessDate": "2015-04-30T22:02:12Z", "PMID": "", "PMCID": "", "ISSN": "1198-743X", "archive": "", "archiveLocation": "", "shortTitle": "Frequency and molecular diversity of Pseudomonas aeruginosa upon admission and during hospitalization", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Pseudomonas aeruginosa", "type": 1 }, { "tag": "molecular epidemiology", "type": 1 }, { "tag": "risk factors", "type": 1 } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "HB4TJZK9", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/HB4TJZK9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/HB4TJZK9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Folsom et al.", "parsedDate": "2010-11-17", "numChildren": 0 }, "data": { "key": "HB4TJZK9", "version": 6, "itemType": "journalArticle", "title": "Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis", "creators": [ { "creatorType": "author", "firstName": "James P.", "lastName": "Folsom" }, { "creatorType": "author", "firstName": "Lee", "lastName": "Richards" }, { "creatorType": "author", "firstName": "Betsey", "lastName": "Pitts" }, { "creatorType": "author", "firstName": "Frank", "lastName": "Roe" }, { "creatorType": "author", "firstName": "Garth D.", "lastName": "Ehrlich" }, { "creatorType": "author", "firstName": "Albert", "lastName": "Parker" }, { "creatorType": "author", "firstName": "Aurélien", "lastName": "Mazurie" }, { "creatorType": "author", "firstName": "Philip S.", "lastName": "Stewart" } ], "abstractNote": "PMID: 21083928", "publicationTitle": "BMC Microbiology", "publisher": "", "place": "", "date": "2010-11-17", "volume": "10", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "294", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/1471-2180-10-294", "citationKey": "", "url": "http://www.biomedcentral.com/1471-2180/10/294/abstract", "accessDate": "2015-04-27T23:25:50Z", "PMID": "", "PMCID": "", "ISSN": "1471-2180", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.biomedcentral.com", "callNumber": "", "rights": "2010 Folsom et al; licensee BioMed Central Ltd.", "extra": "PMID: 21083928", "tags": [], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "UFBT46UZ", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/UFBT46UZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/UFBT46UZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Flemming et al.", "parsedDate": "2007-11-15", "numChildren": 1 }, "data": { "key": "UFBT46UZ", "version": 6, "itemType": "journalArticle", "title": "The EPS Matrix: The “House of Biofilm Cells”", "creators": [ { "creatorType": "author", "firstName": "Hans-Curt", "lastName": "Flemming" }, { "creatorType": "author", "firstName": "Thomas R.", "lastName": "Neu" }, { "creatorType": "author", "firstName": "Daniel J.", "lastName": "Wozniak" } ], "abstractNote": "", "publicationTitle": "Journal of Bacteriology", "publisher": "", "place": "", "date": "11/15/2007", "volume": "189", "issue": "22", "section": "", "partNumber": "", "partTitle": "", "pages": "7945-7947", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Bacteriol.", "DOI": "10.1128/JB.00858-07", "citationKey": "", "url": "http://jb.asm.org/content/189/22/7945", "accessDate": "2013-10-03T19:48:34Z", "PMID": "", "PMCID": "", "ISSN": "0021-9193, 1098-5530", "archive": "", "archiveLocation": "", "shortTitle": "The EPS Matrix", "language": "en", "libraryCatalog": "jb.asm.org", "callNumber": "", "rights": "", "extra": "PMID: 17675377", "tags": [], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "HNA29PVI", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/HNA29PVI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/HNA29PVI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Waite et al.", "parsedDate": "2005-09-15", "numChildren": 1 }, "data": { "key": "HNA29PVI", "version": 6, "itemType": "journalArticle", "title": "Transcriptome Analysis of Pseudomonas aeruginosa Growth: Comparison of Gene Expression in Planktonic Cultures and Developing and Mature Biofilms", "creators": [ { "creatorType": "author", "firstName": "Richard D.", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Anastasia", "lastName": "Papakonstantinopoulou" }, { "creatorType": "author", "firstName": "Eddie", "lastName": "Littler" }, { "creatorType": "author", "firstName": "Michael A.", "lastName": "Curtis" } ], "abstractNote": "The transcriptomes of logarithmic- and stationary-phase Pseudomonas aeruginosa planktonic cultures and static biofilms of different stages of development were compared. Developing and confluent biofilm transcriptomes were found to be related to those of logarithmic- and stationary-phase planktonic cultures, respectively. In addition, a number of novel genes were up-regulated in developing and confluent biofilms, including genes encoding putative solute transport proteins and transcriptional regulators, respectively.", "publicationTitle": "Journal of Bacteriology", "publisher": "", "place": "", "date": "09/15/2005", "volume": "187", "issue": "18", "section": "", "partNumber": "", "partTitle": "", "pages": "6571-6576", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Bacteriol.", "DOI": "10.1128/JB.187.18.6571-6576.2005", "citationKey": "", "url": "http://jb.asm.org/content/187/18/6571", "accessDate": "2013-09-19T01:08:24Z", "PMID": "", "PMCID": "", "ISSN": "0021-9193, 1098-5530", "archive": "", "archiveLocation": "", "shortTitle": "Transcriptome Analysis of Pseudomonas aeruginosa Growth", "language": "en", "libraryCatalog": "jb.asm.org.prx.library.gatech.edu", "callNumber": "", "rights": "", "extra": "PMID: 16159792", "tags": [ { "tag": "Tanner Clark" } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "T2S5KJ2Z", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/T2S5KJ2Z", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/T2S5KJ2Z", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Smyth et al.", "parsedDate": "2010-04", "numChildren": 1 }, "data": { "key": "T2S5KJ2Z", "version": 6, "itemType": "journalArticle", "title": "Garlic as an inhibitor of Pseudomonas aeruginosa quorum sensing in cystic fibrosis--a pilot randomized controlled trial", "creators": [ { "creatorType": "author", "firstName": "Alan R", "lastName": "Smyth" }, { "creatorType": "author", "firstName": "Paramita M", "lastName": "Cifelli" }, { "creatorType": "author", "firstName": "Catharine A", "lastName": "Ortori" }, { "creatorType": "author", "firstName": "Karima", "lastName": "Righetti" }, { "creatorType": "author", "firstName": "Sarah", "lastName": "Lewis" }, { "creatorType": "author", "firstName": "Penny", "lastName": "Erskine" }, { "creatorType": "author", "firstName": "Elaine D", "lastName": "Holland" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Givskov" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Williams" }, { "creatorType": "author", "firstName": "Miguel", "lastName": "Cámara" }, { "creatorType": "author", "firstName": "David A", "lastName": "Barrett" }, { "creatorType": "author", "firstName": "Alan", "lastName": "Knox" } ], "abstractNote": "Pseudomonas aeruginosa forms biofilms in the cystic fibrosis lung. Quorum sensing (QS) controls biofilm maturation, immune evasion, antibiotic tolerance and virulence factor production. Garlic shows QS inhibitory activity in vitro and in animal models. We report the first clinical trial in man of a QS inhibitor.We randomized 34 patients to garlic or olive oil capsules (both 656 mg daily). Clinical outcomes and safety bloods were measured at baseline and after 8 weeks treatment. In this exploratory study, analysis was per protocol.Eight patients withdrew, leaving 26 for analysis (13 garlic). With placebo, there was a greater decline in mean (SD) percentage change from baseline FEV(1) [-3.6% (11.3)] than with garlic [-2.0% (12.3)]. This was not significant (mean difference = 1.6, 95% CI -12.7 to 15.9, P = 0.8). The mean (SD) increase in weight was greater with garlic [1.0% (2.0)] than with placebo [0.6% (2.0)]--non-significant (mean difference = 0.4%, 95% CI -1.3 to 2.0, P = 0.6). The median (range) change in clinical score with garlic was -1 (-3 to 5) and 1 (-1 to 4) with placebo (negative score means improvement). This was non-significant [median difference = -1 (-3 to 0), P = 0.16]. In the garlic group, seven patients had IV antibiotics versus five placebo. There was a highly significant correlation between plasma and sputum measurements of the QS molecule 3-oxo-C12-HSL (Pearson correlation coefficient = 0.914, P = 0.004). At the end of treatment five patients in each group had abnormal liver function or triglycerides and five garlic patients (one placebo) reported minor adverse effects.Garlic capsules were well tolerated. Although there was no significant effect of garlic compared to placebo in this pilot study, there was a suggestion of improvement with garlic which should be investigated in a larger trial.", "publicationTitle": "Pediatric pulmonology", "publisher": "", "place": "", "date": "Apr 2010", "volume": "45", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "356-362", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Pediatr. Pulmonol.", "DOI": "10.1002/ppul.21193", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1099-0496", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "PMID: 20306535", "tags": [ { "tag": "4-Butyrolactone", "type": 1 }, { "tag": "Adolescent", "type": 1 }, { "tag": "Adult", "type": 1 }, { "tag": "Child", "type": 1 }, { "tag": "Cystic Fibrosis", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Homoserine", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Male", "type": 1 }, { "tag": "Middle Aged", "type": 1 }, { "tag": "Phytotherapy", "type": 1 }, { "tag": "Pilot Projects", "type": 1 }, { "tag": "Plant Oils", "type": 1 }, { "tag": "Plasma", "type": 1 }, { "tag": "Pseudomonas Infections", "type": 1 }, { "tag": "Pseudomonas aeruginosa", "type": 1 }, { "tag": "Quorum sensing", "type": 1 }, { "tag": "Respiratory Function Tests", "type": 1 }, { "tag": "Sputum", "type": 1 }, { "tag": "Treatment Outcome", "type": 1 }, { "tag": "Young Adult", "type": 1 }, { "tag": "garlic", "type": 1 } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "83ZMS835", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/83ZMS835", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/83ZMS835", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/266537/items/9X5CWUV4", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } } 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"linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2013-09-19T01:08:24Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/16159792", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "9X5CWUV4", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/9X5CWUV4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/9X5CWUV4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Hancock", "parsedDate": "1998-08", "numChildren": 1 }, "data": { "key": "9X5CWUV4", "version": 6, "itemType": "journalArticle", "title": "Resistance mechanisms in Pseudomonas aeruginosa and other nonfermentative gram-negative bacteria", "creators": [ { "creatorType": "author", "firstName": "R. E.", "lastName": "Hancock" } ], "abstractNote": "Nonfermentative gram-negative bacilli are still a major concern in compromised individuals. By far the most important of these organisms is Pseudomonas aeruginosa, although Acinetobacter baumannii (previously Acinetobacter calcoaceticus), Stenotrophomonas maltophilia (previously Pseudomonas and Xanthomonas maltophilia), and Burkholderia cepacia (previously Pseudomonas cepacia) are also of substantative concern because of their similar high intrinsic resistances to antibiotics. The basis for the high intrinsic resistance of these organisms is the lower outer-membrane permeability of these species, coupled with secondary resistance mechanisms such as an inducible cephalosporinase or antibiotic efflux pumps, which take advantage of low outer-membrane permeability. Even a small change in antibiotic susceptibility of these organisms can result in an increase in the MIC of a drug to a level that is greater than the clinically achievable level. In this review, the major mechanisms of resistance observed in the laboratory and clinic are summarized.", "publicationTitle": "Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America", "publisher": "", "place": "", "date": "Aug 1998", "volume": "27 Suppl 1", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "S93-99", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Clin. Infect. Dis.", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1058-4838", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 9710677", "tags": [ { "tag": "Drug Resistance, Microbial", "type": 1 }, { "tag": "GRAM-negative bacteria", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Pseudomonas aeruginosa", "type": 1 } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } }, { "key": "VG4CGHZI", "version": 6, "library": { "type": "group", "id": 266537, "name": "Shared Biofilm", "links": { "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/266537/items/VG4CGHZI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shared_biofilm/items/VG4CGHZI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1559687, "username": "tanner.clark.h", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/tanner.clark.h", "type": "text/html" } } }, "creatorSummary": "Stover et al.", "parsedDate": "2000-08-31", "numChildren": 1 }, "data": { "key": "VG4CGHZI", "version": 6, "itemType": "journalArticle", "title": "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen", "creators": [ { "creatorType": "author", "firstName": "C. K.", "lastName": "Stover" }, { "creatorType": "author", "firstName": "X. Q.", "lastName": "Pham" }, { "creatorType": "author", "firstName": "A. L.", "lastName": "Erwin" }, { "creatorType": "author", "firstName": "S. D.", "lastName": "Mizoguchi" }, { "creatorType": "author", "firstName": "P.", "lastName": "Warrener" }, { "creatorType": "author", "firstName": "M. J.", "lastName": "Hickey" }, { "creatorType": "author", "firstName": "F. S.", "lastName": "Brinkman" }, { "creatorType": "author", "firstName": "W. O.", "lastName": "Hufnagle" }, { "creatorType": "author", "firstName": "D. J.", "lastName": "Kowalik" }, { "creatorType": "author", "firstName": "M.", "lastName": "Lagrou" }, { "creatorType": "author", "firstName": "R. L.", "lastName": "Garber" }, { "creatorType": "author", "firstName": "L.", "lastName": "Goltry" }, { "creatorType": "author", "firstName": "E.", "lastName": "Tolentino" }, { "creatorType": "author", "firstName": "S.", "lastName": "Westbrock-Wadman" }, { "creatorType": "author", "firstName": "Y.", "lastName": "Yuan" }, { "creatorType": "author", "firstName": "L. L.", "lastName": "Brody" }, { "creatorType": "author", "firstName": "S. N.", "lastName": "Coulter" }, { "creatorType": "author", "firstName": "K. R.", "lastName": "Folger" }, { "creatorType": "author", "firstName": "A.", "lastName": "Kas" }, { "creatorType": "author", "firstName": "K.", "lastName": "Larbig" }, { "creatorType": "author", "firstName": "R.", "lastName": "Lim" }, { "creatorType": "author", "firstName": "K.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "D.", "lastName": "Spencer" }, { "creatorType": "author", "firstName": "G. K.", "lastName": "Wong" }, { "creatorType": "author", "firstName": "Z.", "lastName": "Wu" }, { "creatorType": "author", "firstName": "I. T.", "lastName": "Paulsen" }, { "creatorType": "author", "firstName": "J.", "lastName": "Reizer" }, { "creatorType": "author", "firstName": "M. H.", "lastName": "Saier" }, { "creatorType": "author", "firstName": "R. E.", "lastName": "Hancock" }, { "creatorType": "author", "firstName": "S.", "lastName": "Lory" }, { "creatorType": "author", "firstName": "M. V.", "lastName": "Olson" } ], "abstractNote": "Pseudomonas aeruginosa is a ubiquitous environmental bacterium that is one of the top three causes of opportunistic human infections. A major factor in its prominence as a pathogen is its intrinsic resistance to antibiotics and disinfectants. Here we report the complete sequence of P. aeruginosa strain PAO1. At 6.3 million base pairs, this is the largest bacterial genome sequenced, and the sequence provides insights into the basis of the versatility and intrinsic drug resistance of P. aeruginosa. Consistent with its larger genome size and environmental adaptability, P. aeruginosa contains the highest proportion of regulatory genes observed for a bacterial genome and a large number of genes involved in the catabolism, transport and efflux of organic compounds as well as four potential chemotaxis systems. We propose that the size and complexity of the P. aeruginosa genome reflect an evolutionary adaptation permitting it to thrive in diverse environments and resist the effects of a variety of antimicrobial substances.", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "Aug 31, 2000", "volume": "406", "issue": "6799", "section": "", "partNumber": "", "partTitle": "", "pages": "959-964", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "10.1038/35023079", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "PMID: 10984043", "tags": [ { "tag": "Bacterial Proteins", "type": 1 }, { "tag": "Computational biology", "type": 1 }, { "tag": "DNA, Bacterial", "type": 1 }, { "tag": "Drug Resistance, Microbial", "type": 1 }, { "tag": "Gene Expression Regulation, Bacterial", "type": 1 }, { "tag": "Genome, Bacterial", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Molecular Sequence Data", "type": 1 }, { "tag": "Pseudomonas Infections", "type": 1 }, { "tag": "Pseudomonas aeruginosa", "type": 1 }, { "tag": "Sequence Analysis, DNA", "type": 1 }, { "tag": "Species Specificity", "type": 1 } ], "collections": [ "DB2RNWSC" ], "relations": {}, "dateAdded": "2015-05-01T00:24:35Z", "dateModified": "2015-05-01T00:24:35Z" } } ]