Graph ranking for exploratory gene data analysis

<p>Abstract</p> <p>Background</p> <p>Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of analyzing, comprehending and interpreting the resulting mass of data. Selecting a subset of important genes is inevitable to address the challenge. Gene selection has been investigated extensively over the last decade. Most selection procedures, however, are not sufficient for accurate inference of underlying biology, because biological significance does not necessarily have to be statistically significant. Additional biological knowledge needs to be integrated into the gene selection procedure.</p> <p>Results</p> <p>We propose a general framework for gene ranking. We construct a bipartite graph from the Gene Ontology (GO) and gene expression data. The graph describes the relationship between genes and their associated molecular functions. Under a species condition, edge weights of the graph are assigned to be gene expression level. Such a graph provides a mathematical means to represent both species-independent and species-dependent biological information. We also develop a new ranking algorithm to analyze the weighted graph via a kernelized spatial depth (KSD) approach. Consequently, the importance of gene and molecular function can be simultaneously ranked by a real-valued measure, KSD, which incorporates the global and local structure of the graph. Over-expressed and under-regulated genes also can be separately ranked.</p> <p>Conclusion</p> <p>The gene-function bigraph integrates molecular function annotations into gene expression data. The relevance of genes is described in the graph (through a common function). The proposed method provides an exploratory framework for gene data analysis.</p

Vocational Implications of Cult Involvement

Currently, the majority of studies published on cult membership have been quantitative and have focused primarily on theories and trends about cult membership. These studies have been insufficient in shedding light on the individual’s experience. Qualitative studies are necessary to explore the individual’s accounts of their experiences with past cult involvement and the impact these experiences have on employment. Because of the potential vocational impacts of cult involvement, it is valuable to explore the psychoSocial aspects of work. A qualitative methodology informed by phenomenology was utilized to investigate the unique experience of individuals obtaining employment after leaving a cult. Seven essential themes were found through data analysis: hiding the past, fear, application difficulties, difficulty obtaining employment, inability to maintain employment, talking it out, and symptoms of psychiatric disabilities

Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

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Regional Societies: Fostering Competitive Research Through Virtual Infrastructures

The MidSouth Computational Biology and Bioinformatics Society (MCBIOS) describes its efforts to provide local opportunities for researchers to learn and connect with colleague

Interpreting the Si II and C II line spectra from the COS Legacy Spectroscopic SurveY using a virtual galaxy from a high-resolution radiation-hydrodynamic simulation

Observations of low-ionization state (LIS) metal lines provide crucial insights into the interstellar medium of galaxies, yet, disentangling the physical processes responsible for the emerging line profiles is difficult. This work investigates how mock spectra generated using a single galaxy in a radiation-hydrodynamical simulation can help us interpret observations of a real galaxy. We create 22,500 C II and Si II spectra from the virtual galaxy at different times and through multiple lines of sight and compare them with the 45 observations of low-redshift star-forming galaxies from the COS Legacy Spectroscopic SurveY (CLASSY). We find that the mock profiles provide accurate replicates to the observations of 38 galaxies with a broad range of stellar masses ($10^6$ to $10^9$ $M_\odot$) and metallicities (0.02 to 0.55 $Z_\odot$). Additionally, we highlight that aperture losses explain the weakness of the fluorescent emission in several CLASSY spectra and must be accounted for when comparing simulations to observations. Overall, we show that the evolution of a single simulated galaxy can produce a large diversity of spectra whose properties are representative of galaxies of comparable or smaller masses. Building upon these results, we explore the origin of the continuum, residual flux, and fluorescent emission in the simulation. We find that these different spectral features all emerge from distinct regions in the galaxy's ISM, and their characteristics can vary as a function of the viewing angle. While these outcomes challenge simplified interpretations of down-the-barrel spectra, our results indicate that high-resolution simulations provide an optimal framework to interpret these observations.Comment: Accepted for publication in Ap

Ecosystem and Wildlife Implications of Brush: Management System Designed to Improve Water Runoff and Percolation

With the settlement of Texas and establishment of ranchers to produce cattle, there was an effort to maximize beef production. This caused serious overgrazing. In addition, there was a reduced incidence of fires across the landscape to clear out brush. These factors led to deterioration of the grazing lands and provided an opportunity for invasive intrusion by brush and other species onto the land and riparian zones. There has been a large-scale conversion from grasslands and savannahs to wildlands over the last 150 years (Scholes and Archer, 1997). The overall impacts are significantly impaired uplands and reduced percolation and surface flow of water from rainfall which caused changes and loss in basic aquatic and terrestrial habitat. The State of Texas adopted a program to study and implement brush management systems across the state to improve the water availability in streams, rivers, reservoirs and aquifers, as well as to improve the rangelands. The feasibility studies have shown great promise for improving ranchland and improving the water situation. However, there is less known about the aquatic and wildlife species response implications of brush management. Certainly, there are opportunities for improving the viability of an ecosystem through brush management strategies and continuing management practices. The purpose of this study was to evaluate the changes in hydrology and biological diversity associated with brush management in two watersheds where significant data was already available. This study focused on assessing the aquatic and terrestrial species implications related to specified brush management strategies over time. This involved an integrated analysis including modeling of the landscape, assessing biological diversity and developing economic implications for the two watersheds (Twin Buttes and Edwards regions). Thus, this study is comprised of three parts: modeling of brush management strategies temporally, assessing biological diversity (aquatic and terrestrial) and estimating economic implications. This represents a complex analysis involving variable units and multiple disciplines. Previous feasibility studies of brush removal have been targeted at maximizing water runoff. This analysis is an extension that is designed to examine the implications of brush management under a more restrictive set of brush removal criteria that were chosen based upon wildlife considerations. To achieve the integration of hydrologic modeling, range ecology, and economic implications, there were three team meetings bringing together all components to review status and set priorities for the remainder of the work. In addition, scientists in the three basic groups of specialization interacted daily along with representatives of the Corps of Engineers to assure that each decision was reflected in other parts of the analyses. The major addition of this analysis to brush management feasibility studies being conducted as part of the Texas brush management plan is the consideration of wildlife and aquatic biota and assessing changes in biological diversity likely to result from alternative brush management scenarios