The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven’t been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics

Reclaiming Indiana: The Politics of Crisis Amid the Failures of Liberal Capitalist Modernity

This ethnography examines grassroots political responses to the economic crisis that began in 2008, foremost in the US Midwest, which arguably laid the groundwork both for the election of President Donald Trump and presidential candidacy of Senator Bernie Sanders. President Obama launched his $787 billion stimulus plan in Elkhart, Indiana, in early 2009. At the height of the crisis, unemployment skyrocketed from four to 20 percent in Elkhart, and it became central to struggles over the political direction of the US. With few safety nets, Elkhart residents struggled to meet their basic needs, creating conditions for political organizing on both the Left and Right. A growing set of Left-oriented groups initially advanced cooperative experiments and alternative community projects, often with strong commitments to solidarity, building connections across historically divided groups and confronting oppression and inequality. Over time, some of these groups developed a clearer anti-capitalist critique and engaged in national-level organizing efforts (including manifestations of Occupy Wall Street and the new Poor People’s Campaign), tapping into an older generation of Left organizers, uncovering local histories of social struggle and connecting with grassroots leaders across the country. Contrary to many national pundits, this research also revealed substantial grassroots mobilization driving the Tea Party or at least chapters across northern Indiana, composed disproportionately of older adults with greater financial resources and time. Several leaders had been involved in earlier Christian Right political action. Many found their own social position precarious and the future more so for their children, and they did not see their interests represented by either political party. Especially in Indiana, the Tea Party had substantial impacts, including the election of candidates like Governor Mike Pence. Historically, Indiana was home to a series communal and cooperative experiments, giving birth to Eugene Debs and the Socialist Party of America, with the Elkhart Local securing 22.5 percent of the popular vote and winning two Elkhart City Council seats in 1917. However, following brutal repression during WWI, Indiana also became home to the American Legion, revival of the Ku Klux Klan and John Birch Society. By 1925, 26 percent of native-born white male Elkhart residents were KKK members. While emerging groups on the Right and Left diverged in substantial ways, there were points of convergence that reveal key aspects of the US political landscape. First, the self-definition of most emerging leaders across the political spectrum began with their religious and/or moral commitments, which drove and justified their political engagements and shaped their analysis. Second, in response to economic conditions, these movements asserted self-reliance within defined communities. There was a related skepticism of or active resistance to centralized government authority, intensified by decades of neoliberal rhetoric and often validated by elite capture of government policymaking. This manifest in efforts to return democracy to the local level, whether via horizontal participatory processes central to communal living experiments and organizing on the Left or by reasserting states’ rights and local government on the Right

Diagonalizing matrices over AW*-algebras

Every commuting set of normal matrices with entries in an AW*-algebra can be simultaneously diagonalized. To establish this, a dimension theory for properly infinite projections in AW*-algebras is developed. As a consequence, passing to matrix rings is a functor on the category of AW*-algebras.Comment: 24 pages. Comments very welcome

The extent of crime and anti-social behaviour facing designated heritage assets

Heritage crime has been defined as any offence which harms the value of England’s heritage assets and their settings to this and future generations. There has been growing concern at the risks of crime and anti-social behaviour faced by designated heritage assets, but the true extent of heritage crime had remained difficult to measure. This study, commissioned by English Heritage, collated and analysed data on damage from criminal behaviour to heritage assets in England. The report provides a review of the data collection procedures undertaken by the study to identify those that are most effective in building understanding of the scale and nature of heritage crime. The report then tries to answer a series of key questions about heritage crime. Finally there are some conclusions and selective recommendations aimed at improving future understanding of heritage crime. Further information on English Heritage’s information and advice regarding heritage crime can be found at http://www.english-heritage.org.uk/professional/advice/advice-by-topic/heritage-crime/

Modeling petroleum expulsion in sedimentary basins : The importance of igneous intrusion timing and basement composition

We thank Siccar Point Energy Ltd. for permission to publish this study. Thanks also to Robert Holdsworth, Simon Holford and Christian Huag Eide for their insightful feedback which has greatly improved the manuscript. 1GSA Data Repository item 2019328, supplementary data (geochemical summary, rationale and data tables), is available online at http://www.geosociety.org/datarepository/2019/, or on request from [email protected] reviewedPublisher PD

Sulfur isotopes in otoliths allow discrimination of anadromous and non-anadromous ecotypes of sockeye salmon (Oncorhynchus nerka)

Oncorhynchus nerka occur both as anadromous sockeye salmon that spend most of their life in the ocean, and as non-anadromous kokanee salmon that remain in fresh water their entire lives. We assessed whether stable isotopes of sulfur (δ34S) in otoliths could be used to distinguish sockeye salmon and kokanee ecotypes that are otherwise difficult to identify when they share a common freshwater rearing environment. We also investigated the chemical link between salmon and their diet by measuring δ34S in various fish tissues (eggs, muscle, scales) and zooplankton. δ34S (mean±SE) in sockeye salmon eggs (18.7 ± 0.4‰) and marine zooplankton (20.5 ± 0.1‰) were enriched by 10–14‰ compared with kokanee eggs and freshwater zooplankton. δ34S in the otolith cores of sockeye salmon (19.2 ± 0.7‰) and kokanee salmon (5.3 ± 1.1‰) were similar to δ34S in marine and freshwater zooplankton, respectively, indicating that the core is derived from maternal yolk tissue and reflects the maternal diet. δ34S in the freshwater growth zone of otoliths did not differ significantly between sockeye (5.9 ± 1.1‰) and kokanee salmon (4.4 ± 1.2‰), and was similar to freshwater zooplankton. The mean difference between δ34S in the otolith core and first year of growth was 13.3 ± 1.4‰ for sockeye and 0.65 ± 1.3‰ for kokanee salmon. A quadratic discriminant function developed from measurements of δ34S in otoliths of known maternal origin provided perfect classification rates in cross-validation tests. Thus, sulfur isotope ratios in otoliths are effective in discriminating between anadromous and non-anadromous ecotypes of O. nerka

Kennesaw State University Men\u27s Ensemble, Chorale, and Chamber Singers, Sacred Music of Fauré and Mozart

This KSU School of Music performance by the KSU Men\u27s Ensemble, Chorale, and Chamber Singers led by Director of Choral Activities, Dr. Leslie Blackwell, features Gabriel Fauré\u27s Requiem and Mozart\u27s Vesperae solennes de confessore (K. 339) with guest organist Brian Parks.https://digitalcommons.kennesaw.edu/musicprograms/2105/thumbnail.jp

Expression capable library for studies of Neisseria gonorrhoeae, version 1.0

Background The sexually transmitted disease, gonorrhea, is a serious health problem in developed as well as in developing countries, for which treatment continues to be a challenge. The recent completion of the genome sequence of the causative agent, Neisseria gonorrhoeae, opens up an entirely new set of approaches for studying this organism and the diseases it causes. Here, we describe the initial phases of the construction of an expression-capable clone set representing the protein-coding ORFs of the gonococcal genome using a recombination-based cloning system. Results The clone set thus far includes 1672 of the 2250 predicted ORFs of the N. gonorrhoeae genome, of which 1393 (83%) are sequence-validated. Included in this set are 48 of the 61 ORFs of the gonococcal genetic island of strain MS11, not present in the sequenced genome of strain FA1090. L-arabinose-inducible glutathione-S-transferase (GST)-fusions were constructed from random clones and each was shown to express a fusion protein of the predicted size following induction, demonstrating the use of the recombination cloning system. PCR amplicons of each ORF used in the cloning reactions were spotted onto glass slides to produce DNA microarrays representing 2035 genes of the gonococcal genome. Pilot experiments indicate that these arrays are suitable for the analysis of global gene expression in gonococci. Conclusion This archived set of Gateway® entry clones will facilitate high-throughput genomic and proteomic studies of gonococcal genes using a variety of expression and analysis systems. In addition, the DNA arrays produced will allow us to generate gene expression profiles of gonococci grown in a wide variety of conditions. Together, the resources produced in this work will facilitate experiments to dissect the molecular mechanisms of gonococcal pathogenesis on a global scale, and ultimately lead to the determination of the functions of unknown genes in the genome

The Future of Gambling Spaces: eSports and the World of Competitive Video Gaming

eSports, or competitive video gaming, are a rapidly developing segment of sport and gaming. eSports are a unique cultural and economic phenomenon, and only recently is this nascent industry garnering substantial attention from gambling operators, regulators, and researchers. In 2015, an estimated quarter of a billion dollars will be wagered on eSports, a number projected to grow to $23 billion by 2020 (Eilers Research, 2015). This panel presentation will provide a general overview of eSports, including some background on the industry, a description of the market and general business model, information about the gambling opportunities within eSports, sponsorship opportunities and conflicts, game mechanics that parallel standard sports (skill-based components) and those that incorporate chance, and opportunities for companies to integrate both responsible gaming and gambling practices. A short presentation during the panel will use Hearthstone, a popular eSport, as a case example to demonstrate some of the skill and chance components of the game. Panel participants will represent different stakeholders in eSports, including academe, media, eSports gambling operators, eSport event organizers, and participants

Where next for mathematics education in higher education? A one-day meeting in honour of Professor John Blake

On the 10 June 2016 Professor John Blake, known to many readers of MSOR Connections for his leadership of the Maths, Stats OR Network and his passionate support for mathematics education, passed away peacefully following a short illness. He was 69. In recognition of Johns work, a number of his friends and colleagues came together to organise a one-day education meeting in his honour that comprised part of a larger event celebrating his many achievements in applied mathematics. The meeting was held in July 2017 at the University of Birmingham, a place where John spent many years of his career and established a legacy for teaching and learning from which many now benefit today. John was a man for action and the purpose of this one-day meeting was to explore the current needs and priorities of the mathematical sciences community and identify mechanisms by which we can continue to work together in a changed, and changing, higher education landscape: this article comprises a record of the thoughts and ideas of those who presented in honour of Johns legacy