1,140 research outputs found

    GBA server: EST-based digital gene expression profiling

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    Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have developed a web server that implements the GBA (Guilt-by-Association) co-expression algorithm, which has been successfully used in finding disease-related genes. We have also annotated UniGene clusters with links to several important databases such as GO, KEGG, OMIM, Gene, IPI and HomoloGene. The GBA server can be accessed and downloaded at

    TGGLinesPlus: A robust topological graph-guided computer vision algorithm for line detection from images

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    Line detection is a classic and essential problem in image processing, computer vision and machine intelligence. Line detection has many important applications, including image vectorization (e.g., document recognition and art design), indoor mapping, and important societal challenges (e.g., sea ice fracture line extraction from satellite imagery). Many line detection algorithms and methods have been developed, but robust and intuitive methods are still lacking. In this paper, we proposed and implemented a topological graph-guided algorithm, named TGGLinesPlus, for line detection. Our experiments on images from a wide range of domains have demonstrated the flexibility of our TGGLinesPlus algorithm. We also benchmarked our algorithm with five classic and state-of-the-art line detection methods and the results demonstrate the robustness of TGGLinesPlus. We hope our open-source implementation of TGGLinesPlus will inspire and pave the way for many applications where spatial science matters.Comment: Our TGGLinesPlus Python implementation is open source. 27 pages, 8 figures and 4 table

    Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales

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    © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 11 (2017): 186–200, doi:10.1038/ismej.2016.95.Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.This research was supported by a KAUST-WHOI Post-doctoral Partnership Award to MN and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to CRV and AA. Research in this study was further supported by baseline research funds to CRV by KAUST and NSF award OCE-1233612 to AA. RR was supported by the ct-PIRE Project, Robert Lemelson Fellowship, Graduate Research Award (UCLA), Women Divers Hall of Fame—Sister Fund Conservation Award and a Betty and E. P. Franklin Grant in Tropical Biology and Conservation

    Giant Enhancement of Magnetostrictive Response in Directionally-Solidified Fe83Ga17Erx Compounds

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    We report, for the first time, correlations between crystal structure, microstructure and magnetofunctional response in directionally solidified [110]-textured Fe83Ga17Erx (0 < x < 1.2) alloys. The morphology of the doped samples consists of columnar grains, mainly composed of a matrix phase and precipitates of a secondary phase deposited along the grain boundary region. An enhancement of more than ~275% from ~45 to 170 ppm is observed in the saturation magnetostriction value (λs) of Fe83Ga17Erx alloys with the introduction of small amounts of Er. Moreover, it was noted that the low field derivative of magnetostriction with respect to an applied magnetic field (i.e., dλs/dHapp for Happ up to 1000 Oe) increases by ~230% with Er doping (dλs/dHapp,FeGa= 0.045 ppm/Oe; dλs/dHapp,FeGaEr= 0.15 ppm/Oe). The enhanced magnetostrictive response of the Fe83Ga17Erx alloys is ascribed to an amalgamation of microstructural and electronic factors, namely: (i) improved grain orientation and local strain effects due to deposition of Er in the intergranular region; and (ii) strong local magnetocrystalline anisotropy, due to the highly anisotropic localized nature of the 4f electronic charge distribution of the Er atom. Overall, this work provides guidelines for further improving galfenol-based materials systems for diverse applications in the power and energy sector
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