On the algorithm of extension of a coordinate neighborhood on a compact manifold

Let M n be a connected, compact, closed and smooth manifold of dimension n. It is well known that there exists a smooth triangulation of the manifold Мп

Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota)

The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12,817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT 1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi

eGIFT: Mining Gene Information from the Literature

<p>Abstract</p> <p>Background</p> <p>With the biomedical literature continually expanding, searching PubMed for information about specific genes becomes increasingly difficult. Not only can thousands of results be returned, but gene name ambiguity leads to many irrelevant hits. As a result, it is difficult for life scientists and gene curators to rapidly get an overall picture about a specific gene from documents that mention its names and synonyms.</p> <p>Results</p> <p>In this paper, we present eGIFT (<url>http://biotm.cis.udel.edu/eGIFT</url>), a web-based tool that associates informative terms, called <it>i</it>Terms, and sentences containing them, with genes. To associate <it>i</it>Terms with a gene, eGIFT ranks <it>i</it>Terms about the gene, based on a score which compares the frequency of occurrence of a term in the gene's literature to its frequency of occurrence in documents about genes in general. To retrieve a gene's documents (Medline abstracts), eGIFT considers all gene names, aliases, and synonyms. Since many of the gene names can be ambiguous, eGIFT applies a disambiguation step to remove matches that do not correspond to this gene. Another additional filtering process is applied to retain those abstracts that focus on the gene rather than mention it in passing. eGIFT's information for a gene is pre-computed and users of eGIFT can search for genes by using a name or an EntrezGene identifier. <it>i</it>Terms are grouped into different categories to facilitate a quick inspection. eGIFT also links an <it>i</it>Term to sentences mentioning the term to allow users to see the relation between the <it>i</it>Term and the gene. We evaluated the precision and recall of eGIFT's <it>i</it>Terms for 40 genes; between 88% and 94% of the <it>i</it>Terms were marked as salient by our evaluators, and 94% of the UniProtKB keywords for these genes were also identified by eGIFT as <it>i</it>Terms.</p> <p>Conclusions</p> <p>Our evaluations suggest that <it>i</it>Terms capture highly-relevant aspects of genes. Furthermore, by showing sentences containing these terms, eGIFT can provide a quick description of a specific gene. eGIFT helps not only life scientists survey results of high-throughput experiments, but also annotators to find articles describing gene aspects and functions.</p

First measurements with the CMS DAQ and timing hub prototype-1

The DAQ and Timing Hub is an ATCA hub board designed for the Phase-2 upgrade of the CMS experiment. In addition to providing high-speed Ethernet connectivity to all back-end boards, it forms the bridge between the sub-detector electronics and the central DAQ, timing, and trigger control systems. One important requirement is the distribution of several high-precision, phasestable, and LHC-synchronous clock signals for use by the timing detectors. The current paper presents first measurements performed on the initial prototype, with a focus on clock quality. It is demonstrated that the current design provides adequate clock quality to satisfy the requirements of the Phase-2 CMS timing detectors

The CMS DAQ Pinball Machine

We present an interactive game for up to seven players that demonstrates the challenges of on-line event selection at the Compact Muon Solenoid (CMS) experiment to the public. The game - in the shape of a popular classic pinball machine - was conceived and prototyped by an interdisciplinary team of graphic designers, physicists and engineers at the CMS Create hackathon in 2016. Having won the competition, the prototype was turned into a fully working machine that is now exhibited on the CMS visitors’ path. Teams of 2-7 visitors can compete with one another to collect as many interesting events as possible within a simulated LHC fill. In a fun and engaging way, the game conveys concepts such as multi-level triggering, pipelined processing, event building, the importance of purity in event selection and more subtle details such as dead time. The multi-player character of the game corresponds to the distributed nature of the actual trigger and data acquisition system of the experiment. We present the concept of the game, its design and its technical implementation centered around an Arduino micro-controller controlling 700 RGB LEDs and a sound subsystem running on a Mac mini

Evaluation of Flygt Mixers for Application in Savannah River Site Tank Summary of Test Results from Phase A, B, and C Testing

Staff from the Savannah River Site (SRS), Pacific Northwest National Laboratory (PNNL), Oak Ridge National Laboratory (ORNL), and ITT Flygt Corporation in Trumbull, Connecticut, are conducting a joint mixer testing program to evaluate the applicability of Flygt mixers to SRS Tank 19 waste retrieval and waste retrieval in other U.S. Department of Energy (DOE) tanks. This report provides the results of the Phase C Flygt mixer testing and summarizes the key findings from the Phase A and B tests. Phase C Flygt mixer testing used full-scale, Model 4680 Flygt mixers (37 kW, 51-cm propeller) installed in a fall-scale tank (25.9-m diameter) at SRS. Phase A testing used a 0.45-m tank and Flygt mixers with 7.8-cm diameter propellers. Phase B testing used Model 4640 Flygt mixers (3 kW, 37-cm propeller) installed in 1.8-m and 5.7-m tanks. Powell et al. (1999z4 1999b) provide detailed descriptions of the Phase A and B tests. In Phase C, stationary submerged jet mixers manufactured by ITT Flygt Corporation were tested in the 25.9-m diameter tank at the SRS TNX facility. The Model 4680 mixers used in Phase C have 37-kW (50-hp) electric motors that drive 51-cm (20-in.) diameter propellers at 860 rpm. Fluid velocity was measured at selected locations with as many as four Model 4680 mixers operating simultaneously in the 25.9-m tank, which was filled with water to selected levels. Phase C involved no solids suspension or sludge mobilization tests