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cool diseases go spread like butter (like a criminal undercover) [no copyright issued]

\n
", "tags": [], "relations": {}, "dateAdded": "2023-12-18T23:42:50Z", "dateModified": "2023-12-18T23:43:50Z" } }, { "key": "Z2HP37US", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/Z2HP37US", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/Z2HP37US", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Raftery and Clark", "parsedDate": "2007", "numChildren": 0 }, "data": { "key": "Z2HP37US", "version": 667, "itemType": "journalArticle", "title": "Probabilistic projections of HIV prevalence using Bayesian melding", "creators": [ { "creatorType": "author", "firstName": "Leontine Alkema, Adrian E.", "lastName": "Raftery" }, { "creatorType": "author", "firstName": "Samuel J.", "lastName": "Clark" } ], "abstractNote": "The Joint United Nations Programme on HIV/AIDS (UNAIDS) has developed the Estimation and Projection Package (EPP) for making national estimates and short-term projections of HIV prevalence based on observed prevalence trends at antenatal clinics. Assessing the uncertainty about its estimates and projections is important for informed policy decision making, and we propose the use of Bayesian melding for this purpose. Prevalence data and other information about the EPP model’s input parameters are used to derive a probabilistic HIV prevalence projection, namely a probability distribution over a set of future prevalence trajectories. We relate antenatal clinic prevalence to population prevalence and account for variability between clinics using a random effects model. Predictive intervals for clinic prevalence are derived for checking the model. We discuss predictions given by the EPP model and the results of the Bayesian melding procedure for Uganda, where prevalence peaked at around 28% in 1990; the 95% prediction interval for 2010 ranges from 2% to 7%.", "publicationTitle": "The Annals of Applied Statistics", "publisher": "", "place": "", "date": "2007", "volume": "1", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "229-248", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1214/07-AOAS111", "citationKey": "", "url": "http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1183143737", "accessDate": "2009-09-16T15:03:32Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Project Euclid", "callNumber": "0049", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:45Z" } }, { "key": "TIWXBCDC", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/TIWXBCDC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/TIWXBCDC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "Coelho et al.", "parsedDate": "2008-04", "numChildren": 0 }, "data": { "key": "TIWXBCDC", "version": 671, "itemType": "journalArticle", "title": "Complete treatment of uncertainties in a model for dengue R0 estimation", "creators": [ { "creatorType": "author", "firstName": "Flávio Codeço", "lastName": "Coelho" }, { "creatorType": "author", "firstName": "Cláudia Torres", "lastName": "Codeço" }, { "creatorType": "author", "firstName": "Claudio José", "lastName": "Struchiner" } ], "abstractNote": "In real epidemic processes, the basic reproduction number R0 is the combined outcome of multiple probabilistic events. Nevertheless, it is frequently modeled as a deterministic function of epidemiological variables. This paper discusses the importance of adequate treatment of uncertainties in such models. This is done by comparing two methods of uncertainty analysis: Monte Carlo uncertainty analysis (MCUA) and the Bayesian melding (BM) method. These methods are applied to a model for the determination of R0 of dengue fever based on entomological parameters. The BM was shown to provide a complete treatment of the uncertainties associated with model parameters. In contrast to MCUA, the incorporation of uncertainties led to realistic posterior distributions for parameter and variables. The incorporation, by the BM, of all the available information, from observational data to expert opinions, allows for the constructive use of uncertainties generating informative posterior distributions for all of the model's components that are coherent as a set.", "publicationTitle": "Cadernos De Saúde Pública / Ministério Da Saúde, Fundação Oswaldo Cruz, Escola Nacional De Saúde Pública", "publisher": "", "place": "", "date": "Apr 2008", "volume": "24", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "853-61", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cad Saude Publica", "DOI": "S0102-311X2008000400016", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18392363", "accessDate": "2008-10-21T12:14:09Z", "PMID": "18392363", "PMCID": "", "ISSN": "0102-311X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0008", "rights": "", "extra": "", "tags": [ { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Dengue", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Models, Statistical", "type": 1 }, { "tag": "Monte Carlo Method", "type": 1 }, { "tag": "uncertainty", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:13:11Z", "dateModified": "2013-04-11T12:54:44Z" } }, { "key": "T9EJMBDS", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/T9EJMBDS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/T9EJMBDS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "O'Neill and Roberts", "parsedDate": "1999", "numChildren": 0 }, "data": { "key": "T9EJMBDS", "version": 667, "itemType": "journalArticle", "title": "Bayesian Inference for Partially Observed Stochastic Epidemics", "creators": [ { "creatorType": "author", "firstName": "Philip D.", "lastName": "O'Neill" }, { "creatorType": "author", "firstName": "Gareth O.", "lastName": "Roberts" } ], "abstractNote": "The analysis of infectious disease data is usually complicated by the fact that real life epidemics are only partially observed. In particular, data concerning the process of infection are seldom available. Consequently, standard statistical techniques can become too complicated to implement effectively. In this paper Markov chain Monte Carlo methods are used to make inferences about the missing data as well as the unknown parameters of interest in a Bayesian framework. The methods are applied to real life data from disease outbreaks.", "publicationTitle": "Journal of the Royal Statistical Society. Series A (Statistics in Society)", "publisher": "", "place": "", "date": "1999", "volume": "162", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "121-129", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.jstor.org/stable/2680471", "accessDate": "2009-09-24T12:13:16Z", "PMID": "", "PMCID": "", "ISSN": "09641998", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "0146", "rights": "", "extra": "ArticleType: primary_article / Full publication date: 1999 / Copyright © 1999 Royal Statistical Society", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:43Z" } }, { "key": "R8488E95", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/R8488E95", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/R8488E95", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Spiegelhalter et al.", "parsedDate": "2002", "numChildren": 0 }, "data": { "key": "R8488E95", "version": 667, "itemType": "journalArticle", "title": "Bayesian measures of model complexity and fit", "creators": [ { "creatorType": "author", "firstName": "D. J", "lastName": "Spiegelhalter" }, { "creatorType": "author", "firstName": "N. G", "lastName": "Best" }, { "creatorType": "author", "firstName": "B. P", "lastName": "Carlin" }, { "creatorType": "author", "firstName": "A.", "lastName": "van der Linde" } ], "abstractNote": "", "publicationTitle": "Journal of the Royal Statistical Society. Series B, Statistical Methodology", "publisher": "", "place": "", "date": "2002", "volume": "64", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "583–639", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "4153", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2010-04-08T10:58:08Z", "dateModified": "2013-04-11T12:54:42Z" } }, { "key": "QGRPP89T", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/QGRPP89T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/QGRPP89T", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "B. F. Finkenstädt and B. T. Grenfell", "parsedDate": "2000", "numChildren": 0 }, "data": { "key": "QGRPP89T", "version": 667, "itemType": "journalArticle", "title": "Time series modelling of childhood diseases: a dynamical systems approach", "creators": [ { "creatorType": "author", "firstName": "", "lastName": "B. F. Finkenstädt" }, { "creatorType": "author", "firstName": "", "lastName": "B. T. Grenfell" } ], "abstractNote": "", "publicationTitle": "Journal Of The Royal Statistical Society Series C", "publisher": "", "place": "", "date": "2000", "volume": "49", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "187-205", "series": "Journal Of The Royal Statistical Society Series C", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://ideas.repec.org/a/bla/jorssc/v49y2000i2p187-205.html", "accessDate": "2009-09-24T12:06:22Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Time series modelling of childhood diseases", "language": "", "libraryCatalog": "RePEc", "callNumber": "0167", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:41Z" } }, { "key": "PTNCTA7H", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/PTNCTA7H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/PTNCTA7H", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Chowell et al.", "parsedDate": "2007-02-22", "numChildren": 0 }, "data": { "key": "PTNCTA7H", "version": 667, "itemType": "journalArticle", "title": "Comparative estimation of the reproduction number for pandemic influenza from daily case notification data", "creators": [ { "creatorType": "author", "firstName": "Gerardo", "lastName": "Chowell" }, { "creatorType": "author", "firstName": "Hiroshi", "lastName": "Nishiura" }, { "creatorType": "author", "firstName": "Luís M.A", "lastName": "Bettencourt" } ], "abstractNote": "The reproduction number, , defined as the average number of secondary cases generated by a primary case, is a crucial quantity for identifying the intensity of interventions required to control an epidemic. Current estimates of the reproduction number for seasonal influenza show wide variation and, in particular, uncertainty bounds for for the pandemic strain from 1918 to 1919 have been obtained only in a few recent studies and are yet to be fully clarified. Here, we estimate using daily case notifications during the autumn wave of the influenza pandemic (Spanish flu) in the city of San Francisco, California, from 1918 to 1919. In order to elucidate the effects from adopting different estimation approaches, four different methods are used: estimation of using the early exponential-growth rate (Method 1), a simple susceptible–exposed–infectious–recovered (SEIR) model (Method 2), a more complex SEIR-type model that accounts for asymptomatic and hospitalized cases (Method 3), and a stochastic susceptible–infectious–removed (SIR) with Bayesian estimation (Method 4) that determines the effective reproduction number at a given time . The first three methods fit the initial exponential-growth phase of the epidemic, which was explicitly determined by the goodness-of-fit test. Moreover, Method 3 was also fitted to the whole epidemic curve. Whereas the values of obtained using the first three methods based on the initial growth phase were estimated to be 2.98 (95% confidence interval (CI): 2.73, 3.25), 2.38 (2.16, 2.60) and 2.20 (1.55, 2.84), the third method with the entire epidemic curve yielded a value of 3.53 (3.45, 3.62). This larger value could be an overestimate since the goodness-of-fit to the initial exponential phase worsened when we fitted the model to the entire epidemic curve, and because the model is established as an autonomous system without time-varying assumptions. These estimates were shown to be robust to parameter uncertainties, but the theoretical exponential-growth approximation (Method 1) shows wide uncertainty. Method 4 provided a maximum-likelihood effective reproduction number 2.10 (1.21, 2.95) using the first 17 epidemic days, which is consistent with estimates obtained from the other methods and an estimate of 2.36 (2.07, 2.65) for the entire autumn wave. We conclude that the reproduction number for pandemic influenza (Spanish flu) at the city level can be robustly assessed to lie in the range of 2.0–3.0, in broad agreement with previous estimates using distinct data.", "publicationTitle": "Journal of The Royal Society Interface", "publisher": "", "place": "", "date": "February 22, 2007", "volume": "4", "issue": "12", "section": "", "partNumber": "", "partTitle": "", "pages": "155-166", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1098/rsif.2006.0161", "citationKey": "", "url": "http://rsif.royalsocietypublishing.org/content/4/12/155.abstract", "accessDate": "2009-09-24T12:27:54Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "0143", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:40Z" } }, { "key": "ENJGM57D", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/ENJGM57D", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/ENJGM57D", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Bjørnstad et al.", "parsedDate": "2002", "numChildren": 0 }, "data": { "key": "ENJGM57D", "version": 667, "itemType": "journalArticle", "title": "DYNAMICS OF MEASLES EPIDEMICS: ESTIMATING SCALING OF TRANSMISSION RATES USING A TIME SERIES SIR MODEL", "creators": [ { "creatorType": "author", "firstName": "Ottar N.", "lastName": "Bjørnstad" }, { "creatorType": "author", "firstName": "Bärbel F.", "lastName": "Finkenstädt" }, { "creatorType": "author", "firstName": "Bryan T.", "lastName": "Grenfell" } ], "abstractNote": "", "publicationTitle": "Ecological Monographs", "publisher": "", "place": "", "date": "05/2002", "volume": "72", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "169-184", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Ecological Monographs", "DOI": "10.1890/0012-9615(2002)072[0169:DOMEES]2.0.CO;2", "citationKey": "", "url": "http://www.esajournals.org/doi/abs/10.1890/0012-9615%282002%29072%5B0169%3ADOMEES%5D2.0.CO%3B2", "accessDate": "2009-09-24T11:36:51Z", "PMID": "", "PMCID": "", "ISSN": "0012-9615", "archive": "", "archiveLocation": "", "shortTitle": "DYNAMICS OF MEASLES EPIDEMICS", "language": "", "libraryCatalog": "CrossRef", "callNumber": "0178", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:14Z", "dateModified": "2013-04-11T12:54:39Z" } }, { "key": "EJAA32N6", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/EJAA32N6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/EJAA32N6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "Cauchemez et al.", "parsedDate": "2006-01", "numChildren": 1 }, "data": { "key": "EJAA32N6", "version": 671, "itemType": "journalArticle", "title": "Real-time estimates in early detection of SARS", "creators": [ { "creatorType": "author", "firstName": "Simon", "lastName": "Cauchemez" }, { "creatorType": "author", "firstName": "Pierre-Yves", "lastName": "Boelle" }, { "creatorType": "author", "firstName": "Christi A", "lastName": "Donnelly" }, { "creatorType": "author", "firstName": "Neil M", "lastName": "Ferguson" }, { "creatorType": "author", "firstName": "Guy", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Gabriel M", "lastName": "Leung" }, { "creatorType": "author", "firstName": "Anthony J", "lastName": "Hedley" }, { "creatorType": "author", "firstName": "Roy M", "lastName": "Anderson" }, { "creatorType": "author", "firstName": "Alain-Jacques", "lastName": "Valleron" } ], "abstractNote": "We propose a Bayesian statistical framework for estimating the reproduction number R early in an epidemic. This method allows for the yet-unrecorded secondary cases if the estimate is obtained before the epidemic has ended. We applied our approach to the severe acute respiratory syndrome (SARS) epidemic that started in February 2003 in Hong Kong. Temporal patterns of R estimated after 5, 10, and 20 days were similar. Ninety-five percent credible intervals narrowed when more data were available but stabilized after 10 days. Using simulation studies of SARS-like outbreaks, we have shown that the method may be used for early monitoring of the effect of control measures.", "publicationTitle": "Emerging Infectious Diseases", "publisher": "", "place": "", "date": "Jan 2006", "volume": "12", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "110-113", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Emerging Infect. Dis", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/16494726", "accessDate": "2009-09-24T15:31:10Z", "PMID": "16494726", "PMCID": "", "ISSN": "1080-6040", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0064", "rights": "", "extra": "", "tags": [ { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Computer Simulation", "type": 1 }, { "tag": "Disease Outbreaks", "type": 1 }, { "tag": "Hong Kong", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Severe Acute Respiratory Syndrome", "type": 1 }, { "tag": "Time Factors", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:38Z" } }, { "key": "ECR8CVB6", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/ECR8CVB6", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/ECR8CVB6", "type": "text/html" } }, "meta": { "createdByUser": { "id": 186478, "username": "u.alberton", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/u.alberton", "type": "text/html" } } }, "lastModifiedByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Broder et al.", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "ECR8CVB6", "version": 667, "itemType": "journalArticle", "title": "Diffractive Micro Bar Codes for Encoding of Biomolecules in Multiplexed Assays", "creators": [ { "creatorType": "author", "firstName": "Graham R.", "lastName": "Broder" }, { "creatorType": "author", "firstName": "Rohan T.", "lastName": "Ranasinghe" }, { "creatorType": "author", "firstName": "Joseph K.", "lastName": "She" }, { "creatorType": "author", "firstName": "Shahanara", "lastName": "Banu" }, { "creatorType": "author", "firstName": "Sam W.", "lastName": "Birtwell" }, { "creatorType": "author", "firstName": "Gabriel", "lastName": "Cavalli" }, { "creatorType": "author", "firstName": "Gerasim S.", "lastName": "Galitonov" }, { "creatorType": "author", "firstName": "David", "lastName": "Holmes" }, { "creatorType": "author", "firstName": "Hugo F. P.", "lastName": "Martins" }, { "creatorType": "author", "firstName": "Kevin F.", "lastName": "MacDonald" }, { "creatorType": "author", "firstName": "Cameron", "lastName": "Neylon" }, { "creatorType": "author", "firstName": "Nikolay", "lastName": "Zheludev" }, { "creatorType": "author", "firstName": "Peter L.", "lastName": "Roach" }, { "creatorType": "author", "firstName": "Hywel", "lastName": "Morgan" } ], "abstractNote": "", "publicationTitle": "Analytical Chemistry", "publisher": "", "place": "", "date": "03/2008", "volume": "80", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1902-1909", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Anal. Chem.", "DOI": "10.1021/ac7018574", "citationKey": "", "url": "http://blog.openwetware.org/community/2009/07/25/referencing-a-doi-within-openwetware/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+Openwetware+%28OpenWetWare%29", "accessDate": "2010-03-20T19:51:34Z", "PMID": "", "PMCID": "", "ISSN": "0003-2700", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "0025", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2010-03-20T19:51:34Z", "dateModified": "2013-04-11T12:54:37Z" } }, { "key": "B4F6KE2A", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/B4F6KE2A", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/B4F6KE2A", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Bettencourt and Ribeiro", "parsedDate": "2008-05-14", "numChildren": 0 }, "data": { "key": "B4F6KE2A", "version": 667, "itemType": "journalArticle", "title": "Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases", "creators": [ { "creatorType": "author", "firstName": "Luís M. A.", "lastName": "Bettencourt" }, { "creatorType": "author", "firstName": "Ruy M.", "lastName": "Ribeiro" } ], "abstractNote": "Fast changes in human demographics worldwide, coupled with increased mobility, and modified land uses make the threat of emerging infectious diseases increasingly important. Currently there is worldwide alert for H5N1 avian influenza becoming as transmissible in humans as seasonal influenza, and potentially causing a pandemic of unprecedented proportions. Here we show how epidemiological surveillance data for emerging infectious diseases can be interpreted in real time to assess changes in transmissibility with quantified uncertainty, and to perform running time predictions of new cases and guide logistics allocations.\n\nWe develop an extension of standard epidemiological models, appropriate for emerging infectious diseases, that describes the probabilistic progression of case numbers due to the concurrent effects of (incipient) human transmission and multiple introductions from a reservoir. The model is cast in terms of surveillance observables and immediately suggests a simple graphical estimation procedure for the effective reproductive number R (mean number of cases generated by an infectious individual) of standard epidemics. For emerging infectious diseases, which typically show large relative case number fluctuations over time, we develop a Bayesian scheme for real time estimation of the probability distribution of the effective reproduction number and show how to use such inferences to formulate significance tests on future epidemiological observations.\n\nViolations of these significance tests define statistical anomalies that may signal changes in the epidemiology of emerging diseases and should trigger further field investigation. We apply the methodology to case data from World Health Organization reports to place bounds on the current transmissibility of H5N1 influenza in humans and establish a statistical basis for monitoring its evolution in real time.", "publicationTitle": "PLoS ONE", "publisher": "", "place": "", "date": "May 14, 2008", "volume": "3", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "e2185", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS ONE", "DOI": "10.1371/journal.pone.0002185", "citationKey": "", "url": "http://dx.plos.org/10.1371/journal.pone.0002185", "accessDate": "2009-09-24T11:19:47Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PLoS ONE", "callNumber": "0039", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:36Z" } }, { "key": "AH3TS8JZ", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/AH3TS8JZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/AH3TS8JZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "Cauchemez and Ferguson", "parsedDate": "2008-08-06", "numChildren": 0 }, "data": { "key": "AH3TS8JZ", "version": 671, "itemType": "journalArticle", "title": "Likelihood-based estimation of continuous-time epidemic models from time-series data: application to measles transmission in London", "creators": [ { "creatorType": "author", "firstName": "Simon", "lastName": "Cauchemez" }, { "creatorType": "author", "firstName": "Neil M", "lastName": "Ferguson" } ], "abstractNote": "We present a new statistical approach to analyse epidemic time-series data. A major difficulty for inference is that (i) the latent transmission process is partially observed and (ii) observed quantities are further aggregated temporally. We develop a data augmentation strategy to tackle these problems and introduce a diffusion process that mimics the susceptible-infectious-removed (SIR) epidemic process, but that is more tractable analytically. While methods based on discrete-time models require epidemic and data collection processes to have similar time scales, our approach, based on a continuous-time model, is free of such constraint. Using simulated data, we found that all parameters of the SIR model, including the generation time, were estimated accurately if the observation interval was less than 2.5 times the generation time of the disease. Previous discrete-time TSIR models have been unable to estimate generation times, given that they assume the generation time is equal to the observation interval. However, we were unable to estimate the generation time of measles accurately from historical data. This indicates that simple models assuming homogenous mixing (even with age structure) of the type which are standard in mathematical epidemiology miss key features of epidemics in large populations.", "publicationTitle": "Journal of the Royal Society, Interface / the Royal Society", "publisher": "", "place": "", "date": "Aug 6, 2008", "volume": "5", "issue": "25", "section": "", "partNumber": "", "partTitle": "", "pages": "885-897", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J R Soc Interface", "DOI": "10.1098/rsif.2007.1292", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18174112", "accessDate": "2009-09-24T12:21:51Z", "PMID": "18174112", "PMCID": "", "ISSN": "1742-5689", "archive": "", "archiveLocation": "", "shortTitle": "Likelihood-based estimation of continuous-time epidemic models from time-series data", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0053", "rights": "", "extra": "", "tags": [ { "tag": "Bayes Theorem", "type": 1 }, { "tag": "Computer Simulation", "type": 1 }, { "tag": "Data Interpretation, Statistical", "type": 1 }, { "tag": "Disease Outbreaks", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Likelihood Functions", "type": 1 }, { "tag": "London", "type": 1 }, { "tag": "Measles", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Time Factors", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:10Z", "dateModified": "2013-04-11T12:54:35Z" } }, { "key": "93DBSNTB", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/93DBSNTB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/93DBSNTB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Brown et al.", "parsedDate": "2008-08-01", "numChildren": 0 }, "data": { "key": "93DBSNTB", "version": 667, "itemType": "journalArticle", "title": "Progress and challenges in modelling country-level HIV/AIDS epidemics: the UNAIDS Estimation and Projection Package 2007", "creators": [ { "creatorType": "author", "firstName": "T", "lastName": "Brown" }, { "creatorType": "author", "firstName": "J A", "lastName": "Salomon" }, { "creatorType": "author", "firstName": "L", "lastName": "Alkema" }, { "creatorType": "author", "firstName": "A E", "lastName": "Raftery" }, { "creatorType": "author", "firstName": "E", "lastName": "Gouws" } ], "abstractNote": "The UNAIDS Estimation and Projection Package (EPP) was developed to aid in country-level estimation and short-term projection of HIV/AIDS epidemics. This paper describes advances reflected in the most recent update of this tool (EPP 2007), and identifies key issues that remain to be addressed in future versions. The major change to EPP 2007 is the addition of uncertainty estimation for generalised epidemics using the technique of Bayesian melding, but many additional changes have been made to improve the user interface and efficiency of the package. This paper describes the interface for uncertainty analysis, changes to the user interface for calibration procedures and other user interface changes to improve EPP's utility in different settings. While formal uncertainty assessment remains an unresolved challenge in low-level and concentrated epidemics, the Bayesian melding approach has been applied to provide analysts in these settings with a visual depiction of the range of models that may be consistent with their data. In fitting the model to countries with longer-running epidemics in sub-Saharan Africa, a number of limitations have been identified in the current model with respect to accommodating behaviour change and accurately replicating certain observed epidemic patterns. This paper discusses these issues along with their implications for future changes to EPP and to the underlying UNAIDS Reference Group model.", "publicationTitle": "Sex Transm Infect", "publisher": "", "place": "", "date": "August 1, 2008", "volume": "84", "issue": "Suppl_1", "section": "", "partNumber": "", "partTitle": "", "pages": "i5-10", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1136/sti.2008.030437", "citationKey": "", "url": "http://sti.bmj.com/cgi/content/abstract/84/Suppl_1/i5", "accessDate": "2009-09-16T15:01:41Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Progress and challenges in modelling country-level HIV/AIDS epidemics", "language": "", "libraryCatalog": "HighWire", "callNumber": "0052", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:34Z" } }, { "key": "5IXKHCC5", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/5IXKHCC5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/5IXKHCC5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "O'Neill", "parsedDate": "2009-10", "numChildren": 0 }, "data": { "key": "5IXKHCC5", "version": 671, "itemType": "journalArticle", "title": "Bayesian inference for stochastic multitype epidemics in structured populations using sample data", "creators": [ { "creatorType": "author", "firstName": "Philip D", "lastName": "O'Neill" } ], "abstractNote": "This paper is concerned with the development of new methods for Bayesian statistical inference for structured-population stochastic epidemic models, given data in the form of a sample from a population with known structure. Specifically, the data are assumed to consist of final outcome information, so that it is known whether or not each individual in the sample ever became a clinical case during the epidemic outbreak. The objective is to make inference for the infection rate parameters in the underlying model of disease transmission. The principal challenge is that the required likelihood of the data is intractable in all but the simplest cases. Demiris and O'Neill (2005b) used data augmentation methods involving a certain random graph in a Markov chain Monte Carlo setting to address this situation in the special case where the sample is the same as the entire population. Here, we take an approach relying on broadly similar principles, but for which the implementation details are markedly different. Specifically, to cover the general case of sample data, we use an alternative data augmentation scheme and employ noncentering methods. The methods are illustrated using data from an influenza outbreak.", "publicationTitle": "Biostatistics (Oxford, England)", "publisher": "", "place": "", "date": "Oct 2009", "volume": "10", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "779-791", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Biostatistics", "DOI": "10.1093/biostatistics/kxp031", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/19648227", "accessDate": "2009-09-24T12:19:49Z", "PMID": "19648227", "PMCID": "", "ISSN": "1468-4357", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0007", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:33Z" } }, { "key": "5G8X7TWW", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/5G8X7TWW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/5G8X7TWW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Kass and Raftery", "parsedDate": "1995-06", "numChildren": 0 }, "data": { "key": "5G8X7TWW", "version": 667, "itemType": "journalArticle", "title": "Bayes Factors", "creators": [ { "creatorType": "author", "firstName": "Robert E.", "lastName": "Kass" }, { "creatorType": "author", "firstName": "Adrian E.", "lastName": "Raftery" } ], "abstractNote": "", "publicationTitle": "Journal of the American Statistical Association", "publisher": "", "place": "", "date": "Jun., 1995", "volume": "90", "issue": "430", "section": "", "partNumber": "", "partTitle": "", "pages": "773-795", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.jstor.org/stable/2291091", "accessDate": "2009-09-21T12:30:56Z", "PMID": "", "PMCID": "", "ISSN": "01621459", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "5804", "rights": "", "extra": "ArticleType: primary_article / Full publication date: Jun., 1995 / Copyright © 1995 American Statistical Association", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:10:18Z", "dateModified": "2013-04-11T12:54:32Z" } }, { "key": "4BAR6VXE", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/4BAR6VXE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/4BAR6VXE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "Anderson and May", "parsedDate": "1979-08-02", "numChildren": 0 }, "data": { "key": "4BAR6VXE", "version": 671, "itemType": "journalArticle", "title": "Population biology of infectious diseases: Part I", "creators": [ { "creatorType": "author", "firstName": "R M", "lastName": "Anderson" }, { "creatorType": "author", "firstName": "R M", "lastName": "May" } ], "abstractNote": "If the host population is taken to be a dynamic variable (rather than constant, as conventionally assumed), a wider understanding of the population biology of infectious diseases emerges. In this first part of a two-part article, mathematical models are developed, shown to fit data from laboratory experiments, and used to explore the evolutionary relations among transmission parameters. In the second part of the article, to be published in next week's issue, the models are extended to include indirectly transmitted infections, and the general implications for infectious diseases are considered.", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "Aug 2, 1979", "volume": "280", "issue": "5721", "section": "", "partNumber": "", "partTitle": "", "pages": "361-367", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/460412", "accessDate": "2009-09-24T14:49:17Z", "PMID": "460412", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "Population biology of infectious diseases", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "1711", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Bacterial Infections", "type": 1 }, { "tag": "Communicable Diseases", "type": 1 }, { "tag": "Disease Outbreaks", "type": 1 }, { "tag": "Ectromelia, Infectious", "type": 1 }, { "tag": "Mice", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Pasteurella Infections", "type": 1 }, { "tag": "Population Dynamics", "type": 1 }, { "tag": "Virus Diseases", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:02Z", "dateModified": "2013-04-11T12:54:31Z" } }, { "key": "26E7XH4H", "version": 667, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/26E7XH4H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/26E7XH4H", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Mckay et al.", "parsedDate": "2000-02", "numChildren": 0 }, "data": { "key": "26E7XH4H", "version": 667, "itemType": "journalArticle", "title": "A Comparison of Three Methods for Selecting Values of Input Variables in the Analysis of Output from a Computer Code", "creators": [ { "creatorType": "author", "firstName": "M. D.", "lastName": "Mckay" }, { "creatorType": "author", "firstName": "R. J.", "lastName": "Beckman" }, { "creatorType": "author", "firstName": "W. J.", "lastName": "Conover" } ], "abstractNote": "Two types of sampling plans are examined as alternatives to simple random sampling in Monte Carlo studies. These plans are shown to be improvements over simple random sampling with respect to variance for a class of estimators which includes the sample mean and the empirical distribution function.", "publicationTitle": "Technometrics", "publisher": "", "place": "", "date": "Feb., 2000", "volume": "42", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "55-61", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.jstor.org/stable/1271432", "accessDate": "2009-09-21T10:38:03Z", "PMID": "", "PMCID": "", "ISSN": "00401706", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "JSTOR", "callNumber": "0178", "rights": "", "extra": "ArticleType: primary_article / Issue Title: Special 40th Anniversary Issue / Full publication date: Feb., 2000 / Copyright © 2000 American Statistical Association and American Society for Quality", "tags": [ { "tag": "latin-hypercube-sampling" } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:11:39Z", "dateModified": "2013-04-11T12:54:30Z" } }, { "key": "UHE7VITM", "version": 1, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/UHE7VITM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/UHE7VITM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "creatorSummary": "Coelho et al.", "parsedDate": "2008", "numChildren": 0 }, "data": { "key": "UHE7VITM", "version": 1, "itemType": "journalArticle", "title": "Epigrass: a tool to study disease spread in complex networks", "creators": [ { "creatorType": "author", "firstName": "Flavio", "lastName": "Coelho" }, { "creatorType": "author", "firstName": "Oswaldo", "lastName": "Cruz" }, { "creatorType": "author", "firstName": "Claudia", "lastName": "Codeco" } ], "abstractNote": "BACKGROUND:The construction of complex spatial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most, if not all, these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior.RESULTS:A Network epidemiological model representing the spread of a directly transmitted disease through a bus-transportation network connecting mid-size cities in Brazil. Results show that the topological context of the starting point of the epidemic is of great importance from both control and preventive perspectives.CONCLUSION:Epigrass is shown to facilitate greatly the construction, simulation and analysis of complex network models. The output of model results in standard GIS file formats facilitate the post-processing and analysis of results by means of sophisticated GIS software.", "publicationTitle": "Source Code for Biology and Medicine", "publisher": "", "place": "", "date": "2008", "volume": "3", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "3", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1186/1751-0473-3-3", "citationKey": "", "url": "http://www.scfbm.org/content/3/1/3", "accessDate": "2008-05-23T20:40:58Z", "PMID": "", "PMCID": "", "ISSN": "1751-0473", "archive": "", "archiveLocation": "", "shortTitle": "Epigrass", "language": "", "libraryCatalog": "BioMed Central and More", "callNumber": "0000", "rights": "", "extra": "", "tags": [ { "tag": "epigrass" } ], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:13:19Z", "dateModified": "2010-04-23T09:26:28Z" } }, { "key": "7BAJFD82", "version": 671, "library": { "type": "group", "id": 4426, "name": "Biomathematics", "links": { "alternate": { "href": "https://www.zotero.org/groups/biomathematics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/4426/items/7BAJFD82", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/biomathematics/items/7BAJFD82", "type": "text/html" } }, "meta": { "createdByUser": { "id": 27767, "username": "fccoelho", "name": "Flávio Codeço Coelho", "links": { "alternate": { "href": "https://www.zotero.org/fccoelho", "type": "text/html" } } }, "lastModifiedByUser": { "id": 231445, "username": "zigong", "name": "Yannick Delbecque", "links": { "alternate": { "href": "https://www.zotero.org/zigong", "type": "text/html" } } }, "creatorSummary": "Codeço and Coelho", "numChildren": 0 }, "data": { "key": "7BAJFD82", "version": 671, "itemType": "journalArticle", "title": "[Networks: epidemiology of transmissible diseases from a systemic perspective]", "creators": [ { "creatorType": "author", "firstName": "Cláudia Torres", "lastName": "Codeço" }, { "creatorType": "author", "firstName": "Flávio Codeço", "lastName": "Coelho" } ], "abstractNote": "The direct or indirect physical contact between human beings as a basic condition for the transmission of infectious diseases stimulated epidemiologists to put forth great efforts to understanding and describing the process of human contacts. It is through these contacts that disease spreads over populations and emerges, at the systemic level, in the form of epidemics. During the 20th century, many researchers dedicated themselves to revealing the population patterns that favor or not the emergence of epidemics and their temporal and spatial dynamics. The first insights came from population models adapted from the physical sciences, in which non-structured populations are considered. Later on it became clear that a more detailed description of social structures was required to correctly describe epidemic dynamics, and concepts such as social group, social network and social cohesion became important terms in the quantitative study of epidemics. The approximation between epidemiology and the social sciences turns obvious as their concepts are interacting more and more. To give a brief overview of this trajectory is the purpose of this article.", "publicationTitle": "Ciência & Saúde Coletiva", "publisher": "", "place": "", "date": "", "volume": "13", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1767-74", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cien Saude Colet", "DOI": "S1413-81232008000600011", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pubmed/18833353", "accessDate": "2008-10-21T12:13:50Z", "PMID": "18833353", "PMCID": "", "ISSN": "1678-4561", "archive": "", "archiveLocation": "", "shortTitle": "[Networks", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "0000", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-09-25T09:13:31Z", "dateModified": "2010-04-23T09:26:16Z" } } ]