An ordered subset approach to including covariates in the transmission disequilibrium test

Clinical heterogeneity of a disease may reflect an underlying genetic heterogeneity, which may hinder the detection of trait loci. Consequently, many statistical methods have been developed that allow for the detection of linkage and/or association signals in the presence of heterogeneity

Seroprevalence and risk factors for Neospora caninum in small dairy farms in central Chile

Indexación: Scopus.Objetivos. Proveer información sobre la seroprevalencia y factores de riesgo asociados a la infección por Neospora caninum en bovinos en Chile central. Materiales y métodos. La población estudiada corresponde a pequeñas lecherías que son parte de un programa gubernamental de Asistencia Técnica (SAT), en la región de O´Higgins en Chile central. Muestras de suero fueron recolectadas desde vacas en lactancia y analizadas mediante un kit comercial ELISA. Además, se aplicó un cuestionario a los dueños de los animales para la identificación de factores de riesgo a través de regresión logística. Resultados. Se identificó una prevalencia a nivel de granja del 67%, mientras que dentro de las granjas positivas, esta fue en promedio de 55%. El historial de abortos (p= 0.037, OR=5.09), la fuente de alimentación de perros (p= 0.0429, OR=6), la fuente de agua de bebida de las vacas (p=0.034, OR=4.5) y el manejo de los abortos (p=0.017, OR=7.43) fueron identificados como factores de riesgo para la infección. Conclusiones. Se observa una alta seroprevalencia de N. caninum en pequeños productores lecheros pertenecientes al SAT en Chile central. Los resultados presentados resaltan la necesidad de mejorar las acciones de vigilancia de esta enfermedad y el desarrollo de medidas preventivas para evitar las pérdidas asociadas a esta enfermedad.Objective. To provide information about seroprevalence and risk factors of Neospora caninum infection in bovines of central Chile. Material and Methods. The study population are small dairy farms that are part of a Government Technical Support Service (SAT) in the O'Higgins region in central Chile. Sera samples were collected from milking cows and analyzed by a commercial ELISA kit. Additionally, a questionnaire was applied to farmers to identify risk factors through logistic regression. Results. The farm level prevalence was found to be 67%, and within farms seroprevalence 55%. Abortion history (p= 0.037, OR=5.09), dogs feed source (p= 0.0429, OR=6), cattle drinking water source (p=0.034, OR=4.5) and abortions management (p=0.017, OR=7.43) were found as significant risk factors for infection. Conclusion. There is a high N. caninum seroprevalence in small SAT's dairy farms in O'Higgins region. These results highlight the need of improving N. caninum surveillance, and the development of preventive measures to avoid losses related with this disease.http://revistas.unicordoba.edu.co/index.php/revistamvz/article/view/92

Towards IASI-New Generation (IASI-NG): impact of improved spectral resolution and radiometric noise on the retrieval of thermodynamic, chemistry and climate variables

Besides their strong contribution to weather forecast improvement through data assimilation, thermal infrared sounders onboard polar-orbiting platforms are now playing a key role for monitoring atmospheric composition changes. The Infrared Atmospheric Sounding Interferometer (IASI) instrument developed by the French space agency (CNES) and launched by Eumetsat onboard the Metop satellite series is providing essential inputs for weather forecasting and pollution/climate monitoring owing to its smart combination of large horizontal swath, good spectral resolution and high radiometric performance. EUMETSAT is currently preparing the next polar-orbiting program (EPS-SG) with the Metop-SG satellite series that should be launched around 2020. In this framework, CNES is studying the concept of a new instrument, the IASI-New Generation (IASI-NG), characterized by an improvement of both spectral and radiometric characteristics as compared to IASI, with three objectives: (i) continuity of the IASI/Metop series; (ii) improvement of vertical resolution; (iii) improvement of the accuracy and detection threshold for atmospheric and surface components. In this paper, we show that an improvement of spectral resolution and radiometric noise fulfill these objectives by leading to (i) a better vertical coverage in the lower part of the troposphere, thanks to the increase in spectral resolution; (ii) an increase in the accuracy of the retrieval of several thermodynamic, climate and chemistry variables, thanks to the improved signal-to-noise ratio as well as less interferences between the signatures of the absorbing species in the measured radiances. The detection limit of several atmospheric species is also improved. We conclude that IASI-NG has the potential for strongly benefiting the numerical weather prediction, chemistry and climate communities now connected through the European GMES/Copernicus initiative

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.</p> <p>Results</p> <p>We have developed <it>ChIPpeakAnno </it>as a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with <it>ChIPpeakAnno </it>can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. In addition, we have implemented functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, the package includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes.</p> <p>Conclusions</p> <p><it>ChIPpeakAnno </it>enables batch annotation of the binding sites identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a large number of enriched genomic regions within the statistical programming environment R. Allowing users to pass their own annotation data such as a different Chromatin immunoprecipitation (ChIP) preparation and a dataset from literature, or existing annotation packages, such as <it>GenomicFeatures </it>and <it>BSgenom</it>e, provides flexibility. Tight integration to the <it>biomaRt </it>package enables up-to-date annotation retrieval from the BioMart database.</p

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Внедрение и принцип работы системы сейсмического мониторинга горного массива для работы в условиях ООО "Шахта "Усковская"

The status of the Silicon Microvertex Detector (SMD) and its installation into the LEP-L3 experiment are presented, highlighting novel features and sophisticated techniques. Preliminary results based on 1993 data are given and compared with Monte Carlo predictions, to understand the detector performances and its tracking capabilities

Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections

Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies

Energy Resolution Performance of the CMS Electromagnetic Calorimeter

The energy resolution performance of the CMS lead tungstate crystal electromagnetic calorimeter is presented. Measurements were made with an electron beam using a fully equipped supermodule of the calorimeter barrel. Results are given both for electrons incident on the centre of crystals and for electrons distributed uniformly over the calorimeter surface. The electron energy is reconstructed in matrices of 3 times 3 or 5 times 5 crystals centred on the crystal containing the maximum energy. Corrections for variations in the shower containment are applied in the case of uniform incidence. The resolution measured is consistent with the design goals

Prognostic impact of CEBPA mutational subgroups in adult AML

Despite recent refinements in the diagnostic and prognostic assessment of CEBPA mutations in AML, several questions remain open, i.e. implications of different types of basic region leucin zipper (bZIP) mutations, the role of co-mutations and the allelic state. Using pooled primary data analysis on 1010 CEBPA-mutant adult AML patients, a comparison was performed taking into account the type of mutation (bZIP: either typical in-frame insertion/deletion (InDel) mutations (bZIPInDel), frameshift InDel or nonsense mutations inducing translational stop (bZIPSTOP) or single base-pair missense alterations (bZIPms), and transcription activation domain (TAD) mutations) and the allelic state (single (smCEBPA) vs. double mutant (dmCEBPA)). Only bZIPInDel patients had significantly higher rates of complete remission and longer relapse free and overall survival (OS) compared with all other CEBPA-mutant subgroups. Moreover, co-mutations in bZIPInDel patients (e.g. GATA2, FLT3, WT1 as well as ELN2022 adverse risk aberrations) had no independent impact on OS, whereas in non-bZIPInDel patients, grouping according to ELN2022 recommendations added significant prognostic information. In conclusion, these results demonstrate bZIPInDel mutations to be the major independent determinant of outcome in CEBPA-mutant AML, thereby refining current classifications according to WHO (including all dmCEBPA and smCEBPA bZIP) as well as ELN2022 and ICC recommendations (including CEBPA bZIPms)