http://hdl.handle.net/1957/29656 Wed, 19 Jun 2013 03:36:01 GMT 2013-06-19T03:36:01Z http://hdl.handle.net/1957/39014 Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data Di, Yanming; Emerson, Sarah C.; Schafer, Daniel W.; Kimbrel, Jeffrey A.; Chang, Jeff H. RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and consequently provides a basis for statistical analysis of gene expression. Negative binomial exact tests are available for two-group comparisons but do not extend to negative binomial regression analysis, which is important for examining gene expression as a function of explanatory variables and for adjusted group comparisons accounting for other factors. We address the adequacy of available large-sample tests for the small sample sizes typically available from RNA-Seq studies and consider a higher-order asymptotic (HOA) adjustment to likelihood ratio tests. We demonstrate that 1) the HOA-adjusted likelihood ratio test is practically indistinguishable from the exact test in situations where the exact test is available, 2) the type I error of the HOA test matches the nominal specification in regression settings we examined via simulation, and 3) the power of the likelihood ratio test does not appear to be affected by the HOA adjustment. This work helps clarify the accuracy of the unadjusted likelihood ratio test and the degree of improvement available with the HOA adjustment. Furthermore, the HOA test may be preferable even when the exact test is available because it does not require ad hoc library size adjustments. This is the publisher’s final pdf. The published article is copyrighted by De Gruyter and can be found at: http://www.degruyter.com/. Fri, 01 Mar 2013 00:00:00 GMT http://hdl.handle.net/1957/39014 2013-03-01T00:00:00Z http://hdl.handle.net/1957/38259 Estimating agreement coefficients from sample survey data Lin, Hung-Mo; Kim, Hae-Young; Williamson, John M.; Lesser, Virginia M. We present a generalized estimating equations approach for estimating the concordance correlation coefficient and the kappa coefficient from sample survey data. The estimates and their accompanying standard error need to correctly account for the sampling design. Weighted measures of the concordance correlation coefficient and the kappa coefficient, along with the variance of these measures accounting for the sampling design, are presented. We use the Taylor series linearization method and the jackknife procedure for estimating the standard errors of the resulting parameter estimates. Body measurement and oral health data from the Third National Health and Nutrition Examination Survey are used to illustrate this methodology. This is the publisher’s final pdf. The published article is copyrighted by Statistics Canada and can be found at: http://www.statcan.gc.ca/ads-annonces/12-001-x/. Fri, 01 Jun 2012 00:00:00 GMT http://hdl.handle.net/1957/38259 2012-06-01T00:00:00Z http://hdl.handle.net/1957/38032 Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus Olson, Deanna H.; Aanensen, David M.; Ronnenberg, Kathryn L.; Powell, Christopher I.; Walker, Susan F.; Bielby, Jon; Garner, Trenton W. J.; Weaver, George; The Bd Mapping Group; Fisher, Matthew C. The rapid worldwide emergence of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) is having a profound negative impact on biodiversity. However, global research efforts are fragmented and an overarching synthesis of global infection data is lacking. Here, we provide results from a community tool for the compilation of worldwide Bd presence and report on the analyses of data collated over a four-year period. Using this online database, we analysed: 1) spatial and taxonomic patterns of infection, including amphibian families that appear over-and under-infected; 2) relationships between Bd occurrence and declining amphibian species, including associations among Bd occurrence, species richness, and enigmatic population declines; and 3) patterns of environmental correlates with Bd, including climate metrics for all species combined and three families (Hylidae, Bufonidae, Ranidae) separately, at both a global scale and regional (U. S. A.) scale. These associations provide new insights for downscaled hypothesis testing. The pathogen has been detected in 52 of 82 countries in which sampling was reported, and it has been detected in 516 of 1240 (42%) amphibian species. We show that detected Bd infections are related to amphibian biodiversity and locations experiencing rapid enigmatic declines, supporting the hypothesis that greater complexity of amphibian communities increases the likelihood of emergence of infection and transmission of Bd. Using a global model including all sampled species, the odds of Bd detection decreased with increasing temperature range at a site. Further consideration of temperature range, rather than maximum or minimum temperatures, may provide new insights into Bd-host ecology. Whereas caution is necessary when interpreting such a broad global dataset, the use of our pathogen database is helping to inform studies of the epidemiology of Bd, as well as enabling regional, national, and international prioritization of conservation efforts. We provide recommendations for adaptive management to enhance the database utility and relevance. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Public Library of Science and can be found at: http://www.plos.org/. Wed, 27 Feb 2013 00:00:00 GMT http://hdl.handle.net/1957/38032 2013-02-27T00:00:00Z http://hdl.handle.net/1957/37885 Differential investment in twin offspring by female pronghorns (Antilocapra americana) Van Vuren, Dirk H.; Bray, Martin P.; Heltzel, Jeannie M. Differential investment in offspring has been reported for many mammals, often in the context of the Trivers– Willard model of male-biased investment, but evidence of differential investment in pronghorns (Antilocapra americana) is largely lacking. We assessed the causes and consequences of different birth masses of littermate fawns in a pronghorn population in Oregon. The mass differential for co-twins ranged from 0% to 89% (median ¼8.35%). Male-biased investment explained the mass differential in opposite-sex litters but not same-sex litters. The mass differential did not result from mothers producing 1 normal-size fawn and 1 runt fawn, and the smaller fawn was not deficient in physiological condition. Only 29% of fawns survived to 8 weeks and both fawns died in 56% of litters, but co-twin mortalities were largely separate events. Mass did not confer a survival advantage when considering all fawns through age 8 weeks, but there was evidence of such an advantage when comparing fawns within litters before age 18 days. Differential investment in fawns might be a bet-hedging strategy in which the mother accepts a lower expected reproductive success in exchange for a lower variance, but neither the mean nor the variance differed between mothers of different-size (.8.35% mass differential) and similar-size (,8.35%) litters. In fact, there was evidence of increased reproductive success for mothers of different-size litters, much of which stemmed from higher survival 4–6 days after birth. Having different-size fawns reduced the chances of sequential mortality, in which a predator killed one fawn then returned to kill the other. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by American Society of Mammalogists and can be found at: http://www.mammalsociety.org/. Fri, 01 Feb 2013 00:00:00 GMT http://hdl.handle.net/1957/37885 2013-02-01T00:00:00Z