Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping.

Hispanic populations are a valuable resource that can and should facilitate the identification of complex trait genes by means of admixture mapping (AM). In this paper we focus on a particular Hispanic population living in the San Luis Valley (SLV) in Southern Colorado. We used a set of 22 Ancestry Informative Markers (AIMs) to describe the admixture process and dynamics in this population. AIMs are defined as genetic markers that exhibit allele frequency differences between parental populations >or=30%, and are more informative for studying admixed populations than random markers. The ancestral proportions of the SLV Hispanic population are estimated as 62.7 +/- 2.1% European, 34.1 +/- 1.9% Native American and 3.2 +/- 1.5% West African. We also estimated the ancestral proportions of individuals using these AIMs. Population structure was demonstrated by the excess association of unlinked markers, the correlation between estimates of admixture based on unlinked marker sets, and by a highly significant correlation between individual Native American ancestry and skin pigmentation (R2= 0.082, p < 0.001). We discuss the implications of these findings in disease gene mapping efforts

Predicting metapopulation responses to conservation in human-dominated landscapes

Loss of habitat to urbanization is a primary cause of population declines as human-dominated landscapes expand at increasing rates. Understanding how the relative effects of different conservation strategies is important to slow population declines for species in urban landscapes. We studied the wood thrush Hylocichla mustelina, a declining forest-breeding Neotropical migratory species, and umbrella species for forest-breeding songbirds, within the urbanized mid-Atlantic United States. We integrated 40 years of demographic data with contemporary metapopulation model simulations of breeding wood thrushes to predict population responses to differing conservation scenarios. We compared four conservation scenarios over a 30-year time period (2014-2044) representing (A) current observed state (Null), (B) replacing impervious surface with forest (Reforest), (C) reducing brown-headed cowbird Molothrus ater parasitism pressure (Cowbird removal), and (D) simultaneous reforesting and cowbird removal. Compared to the Null scenario, the Reforest scenario increased mean annual population trends by 54%, the Remove cowbirds scenario increased mean annual population trends by 38%, and the scenario combining reforestation and cowbird removal increased mean annual population trends by 98%. Mean annual growth rates (lambda) per site were greater in the Reforest (lambda = 0.94) and Remove cowbirds (lambda = 0.92) compared to the Null (lambda = 0.88) model scenarios. However, only by combining the positive effects of reforestation and cowbird removal did wood thrush populations stop declining (lambda = 1.00). Our results suggest that independently replacing impervious surface with forest habitat around forest patches and removing cowbirds may slow current negative population trends. Furthermore, conservation efforts that combine reforestation and cowbird removal may potentially benefit populations of wood thrushes and other similarly forest-breeding songbird species within urbanized fragmented landscapes that typify the mid-Atlantic United States

Social Ties and User Generated Content: Evidence from an Online Social Network

We use variation in wind speeds at surfing locations in Switzerland as exogenous shifters of users' propensity to post content about their surfing activity onto an online social network. We exploit this variation to test whether users' social ties on the network have a causal effect on their content generation, and whether conent generation in turn has a similar causal effect on the users' abilty to form social ties. Economically significant causal effects of this kind can produce positive feedback that generate multiplier e&curren;ects to interventions that subsidize tie formation. We argue these interventions can therefore be the basis of a strategy by the rm to indirectly faciliate content generation on the site. The exogenous variation provided by wind speeds enable us to measure this feedback empirically and to assess the return on investment from such policies. We use a detailed dataset from an online social network that comprises the complete details of social tie formation and content generation on the site. The richness of he data enable us to control for several spurious confounds that have typically plagued empirical analysis of social interactions. Our results show evidence for significant positive feedback in user generated content. We discuss the implications of the estimates for the management of the content and the growth of the network

Support for Pets Searching for Their Forever Home

For my capstone, I chose to align with the Idaho Humane Society. I wanted to select a community service project so that years from now, I could look back on this capstone and be proud of the difference I could make. The goal was to bring awareness to our communities’ needs for pets that are still looking for a forever home and assist with some of their immediate needs such as food, toys, and blankets. I networked in my personal, professional, and social groups to collect donations in the form of cash, pet food, pet treats, pet toys, blankets, and towels. I was able to organize in the community to be collected and make a final donation directly to Idaho Humane Society

USP compendial methods for analysis of heparin: chromatographic determination of molecular weight distributions for heparin sodium

Heparin is a polysaccharide product isolated from glycosaminoglycans of porcine mucosa (or occasionally other tissues and species). It is a linear non-uniform polymer consisting of alternating glucosamine and uronic acid monosaccharide residues and is highly sulfated. Heparin sodium drug product (HP) used in medicine consists of chains with molecular weight (MW) ranging from under 5,000 to over 50,000. Although HP has been used as an injectable antithrombotic medicine for more than 70 years, many aspects of its structure and purity, including its MW, have not been specified by public standards until recent years. In 2008, a number of HP lots associated with severe adverse effects, including fatalities, were found to have been contaminated with oversulfated chondroitin sulfate. This incident led to thorough revision of compendial standards worldwide. In the USA, the Food and Drug Administration (FDA) encouraged the inclusion of enhanced standards for purity and identity in the relevant monographs of the United States Pharmacopeia (USP) including acceptance criteria for MW distribution

Non-linear regression models for Approximate Bayesian Computation

Approximate Bayesian inference on the basis of summary statistics is well-suited to complex problems for which the likelihood is either mathematically or computationally intractable. However the methods that use rejection suffer from the curse of dimensionality when the number of summary statistics is increased. Here we propose a machine-learning approach to the estimation of the posterior density by introducing two innovations. The new method fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling. The new algorithm is compared to the state-of-the-art approximate Bayesian methods, and achieves considerable reduction of the computational burden in two examples of inference in statistical genetics and in a queueing model.Comment: 4 figures; version 3 minor changes; to appear in Statistics and Computin

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Biology and Management of Soybean Charcoal Rot

In the 2003 growing season, charcoal rot, a disease new to Iowa producers, was prevalent in the soybean fields of Iowa. This was the first ever statewide occurrence in Iowa with severe damage to many soybean fields. In the south, this disease has been a yield robber and has drastically reduced the yield potential by as mush as the sudden death syndrome. This article will discuss the following aspects of this disease: l) the distribution and economic importance of the pathogen; 2) identification of the disease; 3) the disease cycle and epidemiology; 4) yield loss assessment and 5) management strategies