A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

Mixtures of Common Skew-t Factor Analyzers

A mixture of common skew-t factor analyzers model is introduced for model-based clustering of high-dimensional data. By assuming common component factor loadings, this model allows clustering to be performed in the presence of a large number of mixture components or when the number of dimensions is too large to be well-modelled by the mixtures of factor analyzers model or a variant thereof. Furthermore, assuming that the component densities follow a skew-t distribution allows robust clustering of skewed data. The alternating expectation-conditional maximization algorithm is employed for parameter estimation. We demonstrate excellent clustering performance when our model is applied to real and simulated data.This paper marks the first time that skewed common factors have been used

Design of two-dimensional particle assemblies using isotropic pair interactions with an attractive well

Using ground-state and relative-entropy based inverse design strategies, isotropic interactions with an attractive well are determined to stabilize and promote as- sembly of particles into two-dimensional square, honeycomb, and kagome lattices. The design rules inferred from these results are discussed and validated in the dis- covery of interactions that favor assembly of the highly open truncated-square and truncated-hexagonal lattices.Comment: 11 pages, 5 figures and supplemental materia

Constructing a gazebo: supporting teamwork in a tightly coupled, distributed task in virtual reality

Many tasks require teamwork. Team members may work concurrently, but there must be some occasions of coming together. Collaborative virtual environments (CVEs) allow distributed teams to come together across distance to share a task. Studies of CVE systems have tended to focus on the sense of presence or copresence with other people. They have avoided studying close interaction between us-ers, such as the shared manipulation of objects, because CVEs suffer from inherent network delays and often have cumbersome user interfaces. Little is known about the ef-fectiveness of collaboration in tasks requiring various forms of object sharing and, in particular, the concurrent manipu-lation of objects. This paper investigates the effectiveness of supporting teamwork among a geographically distributed group in a task that requires the shared manipulation of objects. To complete the task, users must share objects through con-current manipulation of both the same and distinct at-tributes. The effectiveness of teamwork is measured in terms of time taken to achieve each step, as well as the impression of users. The effect of interface is examined by comparing various combinations of walk-in cubic immersive projection technology (IPT) displays and desktop devices

Development of explosive welding techniques for fabrication of regeneratively cooled thrust chambers for large rocket engine requirements Final report, 28 Jun. 1967 - 15 Sep. 1970

Explosive welding techniques in fabricating regeneratively cooled thrust chambers for large rocket engine requirements including ultrasonic inspection, metallography, and burst testin