GRAPHICAL CONFIGURATION PROGRAMMING - THE STRUCTURAL DESCRIPTION, CONSTRUCTION AND EVOLUTION OF SOFTWARE SYSTEMS USING GRAPHICS

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Detecting the signatures of helium in type Iax supernovae

Recent studies have argued that the progenitor system of type Iax supernovae must consist of a carbon-oxygen white dwarf accreting from a helium star companion. Based on existing explosion models invoking the pure deflagration of carbon-oxygen white dwarfs, we investigate the likelihood of producing spectral features due to helium in type Iax supernovae. From this scenario, we select those explosion models producing ejecta and $^{56}$Ni masses that are broadly consistent with those estimated for type Iax supernovae (0.014 - 0.478~$M_{\odot}$ and $\sim0.003$ - 0.183~$M_{\odot}$, respectively). To this end, we present a series of models of varying luminosities ($-18.4 \lesssim M_{\rm{V}} \lesssim -14.5$~mag) with helium abundances accounting for up to $\sim$36\% of the ejecta mass, and covering a range of epochs beginning a few days before B$-$band maximum to approximately two weeks after maximum. We find that the best opportunity for detecting \ion{He}{i} features is at near-infrared wavelengths, and in the post-maximum spectra of the fainter members of this class. We show that the optical spectrum of SN~2007J is potentially consistent with a large helium content (a few 10$^{-2}~M_{\odot}$), but argue that current models of accretion and material stripping from a companion struggle to produce compatible scenarios. We also investigate the presence of helium in all objects with near-infrared spectra. We show that SNe~2005hk, 2012Z, and 2015H contain either no helium or their helium abundances are constrained to much lower values ($\lesssim$10$^{-3}~M_{\odot}$). Our results demonstrate the differences in helium content among type Iax supernovae, perhaps pointing to different progenitor channels. Either SN~2007J is an outlier in terms of its progenitor system, or it is not a true member of the type Iax supernova class.Comment: 15 pages, 12 figures, 2 tables. Accepted for publication in Astronomy and Astrophysic

Extensive lava flow fields on Venus: Preliminary investigation of source elevation and regional slope variations

Large-volume lava flow fields have been identified on Venus, the most areally extensive of which are known as fluctus and have been subdivided into six morphologic types. Sheetlike flow fields (Type 1) lack the numerous, closely spaced, discrete lava flow lobes that characterize digitate flow fields. Transitional flow fields (Type 2) are similar to sheetlike flow fields but contain one or more broad flow lobes. Digitate flow fields are divided further into divergent (Types 3-5) and subparallel (Type 6) classes on the basis of variations in the amount of downstream flow divergence. As a result of our previous analysis of the detailed morphology, stratigraphy, and tectonic associations of Mylitta Fluctus, we have formulated a number of questions to apply to all large flow fields on Venus. In particular, we would like to address the following: (1) eruption conditions and style of flow emplacement (effusion rate, eruption duration), (2) the nature of magma storage zones (presence of neutral buoyancy zones, deep or shallow crustal magma chambers), (3) the origin of melt and possible link to mantle plumes, and (4) the importance of large flow fields in plains evolution. To answer these questions we have begun to examine variations in flow field dimension and morphology; the distribution of large flow fields in terms of elevation above the mean planetary radius; links to regional tectonic or volcanic structures (e.g., associations with large shield edifices, coronae, or rift zones); statigraphic relationships between large flow fields, volcanic plains, shields, and coronae; and various models of flow emplacement in order to estimate eruption parameters. In this particular study, we have examined the proximal elevations and topographic slopes of 16 of the most distinctive flow fields that represent each of the 6 morphologic types

Comparative functional genomics and the bovine macrophage response to strains of the Mycobacterium genus

Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

Football intermediaries and self‑regulation: the need for greater transparency through disciplinary law, sanctioning and qualifying criteria

This paper was first presented at the International Sports Law Conference in The Hague in October 2018. It summarises the author’s work and wider research on the introduction of new proposals for the regulation of football intermediaries (a term which the author finds unworkable and unorthodox). The author’s research critically analyses the current regulatory framework and identifies the elements that form the basis for the inadequacy and ineffectiveness of the regulations currently in force. With the use of case studies and examples drawn from the author’s private practice, recommendations are produced for new regulations that would promote transparency, equality and consistency. The author concludes that this can only be achieved via a blending of self-regulation and external regulation at an international setting

Plant Communities of Highland Heights Community Park, Cuyahoga County, Ohio

Author Institution: Dept of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OHAuthor Institution: Dept of Biology, John Carroll University, University Heights, OHAuthor Institution: Normandeau Associates, Bedford, NHWe have described the vegetation structure with respect to various community types of Highland Heights Community Park and adjoining territory. High values of Shannon’s Diversity Indexes and Floristic Quality Assessment Indexes indicate a superior quality, species-rich habitat with several high-fidelity species. Based on our research, which reveals that the study site is worthy of conservation and preservation, we suggest recommendations to the city of Highland Heights for park management and land use planning