Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license

Simulation of Alternative Marketing Strategies for U.S. Cotton

Three marketing strategies (selling a put option, cash sale at harvest, and cash sale in June) are simulated based on historical values and ranked based on certainty equivalents for a representative irrigated and dryland cotton farm Scenario analysis is also used to compare varying yield values.Simulation, Marketing, Cotton, Risk, Marketing, Research Methods/ Statistical Methods,

Supersolutions for a class of semilinear heat equations

A semilinear heat equation $u_{t}=\Delta u+f(u)$ with nonnegative initial data in a subset of $L^{1}(\Omega)$ is considered under the assumption that $f$ is nonnegative and nondecreasing and $\Omega\subseteq \R^{n}$. A simple technique for proving existence and regularity based on the existence of supersolutions is presented, then a method of construction of local and global supersolutions is proposed. This approach is applied to the model case $f(s)=s^{p}$, $\phi\in L^{q}(\Omega)$: new sufficient conditions for the existence of local and global classical solutions are derived in the critical and subcritical range of parameters. Some possible generalisations of the method to a broader class of equations are discussed.Comment: Expanded version of the previous submission arXiv:1111.0258v1. 14 page

NURBS modeling and structural shape optimization of cardiovascular stents

Cardiovascular stents have been used since the 1990s to treat atherosclerosis, one of leading causes of death in the western world, and structural optimization has led to significant improvements in stent performance. Much of the potential variation in stent geometry, however, has remained unconsidered. This paper presents a non-uniform rational basis spline (NURBS) parameterization of a stent, the inclusion of structural fatigue resistance as a design consideration, and the results of a design optimization based on response surface techniques. Results show the feasibility and merits of the NURBS approach, which models a much broader range of shapes than was previously possible. Multi-objective optimization produces a range of geometrically diverse Pareto-optimal designs; these can be used to develop future clinical design guides, accounting for the variation observed across patients. We conclude by motivating future work with increasingly complex physical modeling and optimization capabilities

Structure formation by cosmic strings with a cosmological constant

Final published version.Comment: 4 Page

Differing instructional needs for children of similar reading achievement grades two, four, and six

Thesis (Ed.M.)--Boston Universit

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation