Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
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Stardust: Accessible and Transparent GPU Support for Information Visualization Rendering
Eurographics Conference on Visualization (EuroVis) 2017 Volume 36 (2017), Number 3 J. Heer, T. Ropinski and J. van Wijk (Guest Editors) Stardust: Accessible and Transparent GPU Support for Information Visualization Rendering Donghao Ren1, Bongshin Lee2, and Tobias Höllerer1 1University of California, Santa Barbara, United States 2Microsoft Research, Redmond, United States Abstract Web-based visualization libraries are in wide use, but performance bottlenecks occur when rendering, and especially animating, a large number of graphical marks. While GPU-based rendering can drastically improve performance, that paradigm has a steep learning curve, usually requiring expertise in the computer graphics pipeline and shader programming. In addition, the recent growth of virtual and augmented reality poses a challenge for supporting multiple display environments beyond regular canvases, such as a Head Mounted Display (HMD) and Cave Automatic Virtual Environment (CAVE). In this paper, we introduce a new web-based visualization library called Stardust, which provides a familiar API while leveraging GPU’s processing power. Stardust also enables developers to create both 2D and 3D visualizations for diverse display environments using a uniform API. To demonstrate Stardust’s expressiveness and portability, we present five example visualizations and a coding playground for four display environments. We also evaluate its performance by comparing it against the standard HTML5 Canvas, D3, and Vega. Categories and Subject Descriptors (according to ACM CCS): -
Civic Participation and Empowerment Through Visualization
SIGRAD 2015 L. Kjelldahl and C. Peters (Editors) Civic Participation and Empowerment through Visualization Samuel Bohmany Department of Computer and Systems Sciences, Stockholm University, Sweden Abstract This article elaborates on the use of data visualization to promote civic participation and democratic engage- ment. The power and potential of data visualization is examined through a brief historical overview and four interconnected themes that provide new opportunities for electronic participation research: data storytelling, in- fographics, data physicalization, and quantified self. The goal is to call attention to this space and encourage a larger community of researchers to explore the possibilities that data visualization can bring. Categories and Subject Descriptors (according to ACM CCS): H.5.2 [Information Interfaces and Presentation]: Screen design—User-centered design 1. Introduction The authors acknowledge that the deliberative approach to civic dialogue is “unduly restrictive, discounting other im- Since the advent of the web in the early 1990s, prospects portant ways of making, receiving, and contesting public of electronic democracy have been viewed as heralding in claims”. They therefore encourage researchers in the field to a new era of political participation and civic engagement. be more open to a wider range of practices and technologies However, empirical studies suggest most initiatives to date and suggest some of the most innovative research is being have failed to live up to expectations despite large invest- done in the area of computer-supported argument mapping ments in research. For instance, Chadwick [Cha08] states and visualization. However, the visualization research they that “the reality of online deliberation, whether judged in are referring to have primarily focused on facilitating large- terms of quantity, its quality, or its impact on political be- scale online deliberation within a conventional rationalistic haviour and policy outcomes, is far removed from the ide- framework. -
Evaluation of the Natural Prevalence of Vibrio Spp. in Uruguayan Mussels
XA0100969 EVALUATION OF THE NATURAL PREVALENCE OF VIBRIO SPR IN URUGUAYAN MUSSELS (MYTILUS SP.) AND THEIR CONTROL USING IRRADIATION C. LOPEZ Laboratorio de Tecnicas Nucleares, Facultad de Veterinaria, Universidad de la Republica, Uruguay Abstract The presence of potentially pathogenic bacteria belonging to the Vibrionacea, especially Vibrio cholerae, and of Salmonella spp., was examined in fresh Uruguayan mussels (Mytilus sp.) during two annual seasons. The radiation decimal reduction dose (Dio) of various toxigenic strains of Vibrio cholerae was determined to vary in vitro between 0.11 and 0.19 kGy. These results and those from the examination of natural Vibrio spp. contamination in mussles were used to conclude that 1.0 kGy would be enough to render Uruguayan mussels Vibrio-safe. Mussels irradiated in the shell at the optimal dose survived long enough to allow the eventual introduction of irradiation as an effective intervention measure without affecting local marketing practices, and making it possible to market the fresh mussels live, as required by Uruguayan legislation. INTRODUCTION The Vibrionaceae are a family of facultatively anaerobic, halophilic, Gram-negative rods, polarly flagellated, motile bacteria that comprises 28 species, of which 11 are potential human pathogens (De Paola, 1981). Most of the Vibrio spp. are marine microorganisms, hence their natural occurrence in many raw seafood. Among the most prevalent species of Vibrio is V. parahaemolyticus, a fast growing bacterium that resists high salt concentrations (Battisti, R. and Moretto, E., 1994). It is reported to be the main cause of gastroenteritis in Japan, where there is a large consumption of raw fish. Vibrio vulnificus, another pathogenic species of the Vibrionaceae, is a pleomorphic, short rod that requires high salt concentrations for growth. -
Daftar Program Untuk Komputer Grafik Dan Pengolahan Citra
Daftar program untuk Komputer Grafik dan Pengolahan Citra I Made Wiryana 1 Nopember 2012 Daftar Isi 1 OpenCV 1 2 Scilab Image Processing Toolbox 2 3 VIPS 2 4 ImageJ 2 5 Marvin 2 6 MeVisLab 3 7 MVTH 3 8 Gephex 3 9 Fiji 3 10 MathMap 4 11 VTK 4 12 Tulip 4 13 PreFuse 4 1 OpenCV OpenCV - Open Source Computer Vision Library [http://www.opencv.org] is an open-source BSD- licensed library that includes several hundreds of computer vision algorithms. The document de- scribes the so-called OpenCV 2.x API, which is essentially a C++ API, as opposite to the C-based OpenCV 1.x API. The latter is described in opencv1x.pdf. OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Being a BSD-licensed product, OpenCV makes it easy for businesses to utilize and modify the code. The library has more than 2500 optimized algorithms, which includes a comprehensive set of both classic and state-of-the-art computer vision and machine learning algorithms. These algori- thms can be used to detect and recognize faces, identify objects, classify human actions in videos, track camera movements, track moving objects, extract 3D models of objects, produce 3D point clouds from stereo cameras, stitch images together to produce a high resolution image of an entire 1 scene, find similar images from an image database, remove red eyes from images taken using flash, follow eye movements, recognize scenery and establish markers to overlay it with augmented reali- ty, etc. -
The Polyomavirus Major Capsid Protein VP1 Interacts with the Nuclear Matrix Regulatory Protein
FEBS 23316 FEBS Letters 467 (2000) 359^364 View metadata, citation and similar papers at core.ac.uk brought to you by CORE The polyomavirus major capsid protein VP1 interacts with theprovided nuclearby Elsevier - Publisher Connector matrix regulatory protein YY1 Zdena Palkova¨a;b, Hana Sípanielova¨b, Vanesa Gottifredia;1, Dana Hollanderova¨b, Jitka Forstova¨b, Paolo Amatia;* aInstituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Universita© di Roma La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy bDepartment of Genetics and Microbiology, Faculty of Natural Sciences, Charles University, Vinie©na¨ 5, 12844 Prague 2, Czech Republic Received 17 December 1999 Edited by Hans-Dieter Klenk The external loops are likely to be the structures involved in Abstract Polyomavirus reaches the nucleus in a still encapsi- dated form, and the viral genome is readily found in association cell receptor recognition by virions [4] and, therefore, to be with the nuclear matrix. This association is thought to be the main antigenic determinants. The £exible C-terminal arms essential for viral replication. In order to identify the protein(s) form interpentameric contacts and the basic amino acids of involved in the virus-nuclear matrix interaction, we focused on the N terminal arm are responsible for the non-speci¢c DNA- the possible roles exerted by the multifunctional cellular nuclear binding activity of VP1 [6,7]. matrix protein Yin Yang 1 (YY1) and by the viral major capsid The necessity for viral genomes to associate to the nuclear protein VP1. In the present work we report on the in vivo matrix (NM) in order to be expressed, has been demonstrated association between YY1 and VP1. -
Learning Protein Constitutive Motifs from Sequence Data Je´ Roˆ Me Tubiana, Simona Cocco, Re´ Mi Monasson*
TOOLS AND RESOURCES Learning protein constitutive motifs from sequence data Je´ roˆ me Tubiana, Simona Cocco, Re´ mi Monasson* Laboratory of Physics of the Ecole Normale Supe´rieure, CNRS UMR 8023 & PSL Research, Paris, France Abstract Statistical analysis of evolutionary-related protein sequences provides information about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their statistical features, can efficiently model protein families from sequence information. We here apply RBM to 20 protein families, and present detailed results for two short protein domains (Kunitz and WW), one long chaperone protein (Hsp70), and synthetic lattice proteins for benchmarking. The features inferred by the RBM are biologically interpretable: they are related to structure (residue-residue tertiary contacts, extended secondary motifs (a-helixes and b-sheets) and intrinsically disordered regions), to function (activity and ligand specificity), or to phylogenetic identity. In addition, we use RBM to design new protein sequences with putative properties by composing and ’turning up’ or ’turning down’ the different modes at will. Our work therefore shows that RBM are versatile and practical tools that can be used to unveil and exploit the genotype–phenotype relationship for protein families. DOI: https://doi.org/10.7554/eLife.39397.001 Introduction In recent years, the sequencing of many organisms’ genomes has led to the collection of a huge number of protein sequences, which are catalogued in databases such as UniProt or PFAM Finn et al., 2014). Sequences that share a common ancestral origin, defining a family (Figure 1A), *For correspondence: are likely to code for proteins with similar functions and structures, providing a unique window into [email protected] the relationship between genotype (sequence content) and phenotype (biological features). -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
DECIPHER: Harnessing Local Sequence Context to Improve Protein Multiple Sequence Alignment Erik S
Wright BMC Bioinformatics (2015) 16:322 DOI 10.1186/s12859-015-0749-z RESEARCH ARTICLE Open Access DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment Erik S. Wright1,2 Abstract Background: Alignment of large and diverse sequence sets is a common task in biological investigations, yet there remains considerable room for improvement in alignment quality. Multiple sequence alignment programs tend to reach maximal accuracy when aligning only a few sequences, and then diminish steadily as more sequences are added. This drop in accuracy can be partly attributed to a build-up of error and ambiguity as more sequences are aligned. Most high-throughput sequence alignment algorithms do not use contextual information under the assumption that sites are independent. This study examines the extent to which local sequence context can be exploited to improve the quality of large multiple sequence alignments. Results: Two predictors based on local sequence context were assessed: (i) single sequence secondary structure predictions, and (ii) modulation of gap costs according to the surrounding residues. The results indicate that context-based predictors have appreciable information content that can be utilized to create more accurate alignments. Furthermore, local context becomes more informative as the number of sequences increases, enabling more accurate protein alignments of large empirical benchmarks. These discoveries became the basis for DECIPHER, a new context-aware program for sequence alignment, which outperformed other programs on largesequencesets. Conclusions: Predicting secondary structure based on local sequence context is an efficient means of breaking the independence assumption in alignment. Since secondary structure is more conserved than primary sequence, it can be leveraged to improve the alignment of distantly related proteins. -
Acholeplasma Florum, a New Species Isolated from Plants? R
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1984, p. 11-15 Vol. 34, No. 1 0020-7713/84/010011-05$02.OO/O Copyright 0 1984, International Union of Microbiological Societies Acholeplasma florum, a New Species Isolated from Plants? R. E. McCOY,l* H. G. BASHAM,' J. G. TULLY,* D. L. ROSE,2 P. CARLE,3 AND J. M. BOVE3 University of Florida Agricultural Research and Education Center, Fort Lauderdale, Florida 33314'; Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Frederick, Maryland 21 70i2;and lnstitut National de la Recherche Agronomique, Pont de la Maye 33140, France3 Three acholeplasmas isolated from floral surfaces of healthy plants in Florida were found to be similar in their biochemical and serological properties. These organisms did not require serum or cholesterol for growth, although addition of some supplementary fatty acids (as represented by Tween 80) was necessary for growth to occur in serum-free medium. The three strains possessed biochemical properties typical of the Acholeplasmataceae and were distinguished from the nine previously recognized Acholeplasma species by serological and deoxyribopucleic acid-deoxyribonucleic acid hybridization techniques. The genome molec- ular weight of the three Acholeplasma strains was lo9, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 27 to 28 mol%. On the basis of these results and other morphological, biological, and serological properties, we propose that these organisms represent a new species, Acholeplasmaflorurn. Strain L1 (= ATCC 33453) is the type strain. Plant surfaces, particularly flowers, have recently been Media and cultivation procedures. Isolates were routinely proven to be fertile sites for isolation of members of the grown in MC broth or in the serum fraction medium de- Mycoplasrnatales (5, 11-13, 26). -
Microbial Gene Identification Using Interpolated Markov Models Steven L
544–548 Nucleic Acids Research, 1998, Vol. 26, No. 2 1998 Oxford University Press Microbial gene identification using interpolated Markov models Steven L. Salzberg1,2,*, Arthur L. Delcher3, Simon Kasif4 and Owen White1 1The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, 2Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA, 3Department of Computer Science, Loyola College in Maryland, Baltimore, MD 21210, USA and 4Department of Electrical Engineering and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA Received September 10, 1997; Revised and Accepted November 11, 1997 ABSTRACT in new genomes still have no significant homology to known genes (1). For these genes, we must rely on computational methods of This paper describes a new system, GLIMMER, for scoring the coding region to identify the genes. The best-known finding genes in microbial genomes. In a series of tests program for this task is GeneMark (5), which uses a Markov chain on Haemophilus influenzae, Helicobacter pylori and model to score coding regions. GeneMark has been highly effective other complete microbial genomes, this system has and was used in the H.influenza and more recent genome projects. proven to be very accurate at locating virtually all the We have developed a new system, GLIMMER, that uses a technique genes in these sequences, outperforming previous called interpolated Markov models (IMMs) to find coding regions methods. A conservative estimate based on experiments in microbial sequences. IMMs are in principle more powerful than on H.pylori and H.influenzae is that the system finds Markov chains, and the computational experiments described below >97% of all genes. -
Opportunistic Intruders: How Viruses Orchestrate ER Functions to Infect Cells
REVIEWS Opportunistic intruders: how viruses orchestrate ER functions to infect cells Madhu Sudhan Ravindran*, Parikshit Bagchi*, Corey Nathaniel Cunningham and Billy Tsai Abstract | Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co‑opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus–ER interactions has become available, these insights may lead to the development of crucial therapeutic agents. Morphogenesis Viruses have evolved sophisticated strategies to establish The ER is a membranous system consisting of the The process by which a virus infection. Some viruses bind to cellular receptors and outer nuclear envelope that is contiguous with an intri‑ particle changes its shape and initiate entry, whereas others hijack cellular factors that cate network of tubules and sheets1, which are shaped by structure. disassemble the virus particle to facilitate entry. After resident factors in the ER2–4. The morphology of the ER SEC61 translocation delivering the viral genetic material into the host cell and is highly dynamic and experiences constant structural channel the translation of the viral genes, the resulting proteins rearrangements, enabling the ER to carry out a myriad An endoplasmic reticulum either become part of a new virus particle (or particles) of functions5. -
Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment
antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton,