Minimum Energy Reliable Paths Using Unreliable Wireless Links

We address the problem of energy-efcient reliable wireless communication in the presence of unreliable or lossy wireless link layers in multi-hop wireless networks. Prior work [1] has provided an optimal energy efcient solution to this problem for the case where link layers implement perfect reliability. However, a more common scenario — a link layer that is not perfectly reliable, was left as an open problem. In this paper we rst present two centralized algorithms, BAMER and GAMER, that optimally solve the minimum energy reliable communication problem in presence of unreliable links. Subsequently we present a distributed algorithm, DAMER, that approximates the performance of the centralized algorithm and leads to signicant performance improvement over existing singlepath or multi-path based techniques

RICHEST ‐ a web server for richness estimation in biological data

Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. We have developed a web server, RICHness ESTimator (RICHEST), which implements three non-parametric statistical methods for richness estimation. Its user-friendly web interface allows users to analyze and compare their data conveniently over the web

Minimum Energy Reliable Paths using Unreliable Wireless Links

We address the problem of energy-efficient reliable wireless communication in the presence of unreliable or lossy wireless link layers in multi-hop wireless networks. Prior work [1] has provided an optimal energy efficient solution to this problem for the case where link layers implement perfect reliability. However, a more common scenario — a link layer that is not perfectly reliable, was left as an open problem. In this paper we first present two centralized algorithms, BAMER and GAMER, that optimally solve the minimum energy reliable communication problem in presence of unreliable links. Subsequently we present a distributed algorithm, DAMER, that approximates the performance of the centralized algorithm and leads to significant performance improvement over existing singlepath or multi-path based techniques. Categories and Subject Descriptor

GSV: a web-based genome synteny viewer for customized data

<p>Abstract</p> <p>Background</p> <p>The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis.</p> <p>Results</p> <p>We have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation.</p> <p>Conclusions</p> <p>GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at <url>http://cas-bioinfo.cas.unt.edu/gsv</url>, and the software is also freely available for local installations.</p

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features

The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/

BOV – a web-based BLAST output visualization tool

Article discussing research on BOV, a web-based BLAST output visualization tool

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

Article discussing the draft genome sequence of the cyanide-utilizing bacterium 'Pseudomonas fluorescens' strain NCIMB 11764

Genome-wide mutagenesis of Zea mays L. using RescueMu transposons

Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants

Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women.

We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI &lt; 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value &lt; 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p &lt; 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value &lt; 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity