Developing an open data portal for the ESA climate change initiative

We introduce the rationale for, and architecture of, the European Space Agency Climate Change Initiative (CCI) Open Data Portal (http://cci.esa.int/data/). The Open Data Portal hosts a set of richly diverse datasets – 13 “Essential Climate Variables” – from the CCI programme in a consistent and harmonised form and to provides a single point of access for the (>100 TB) data for broad dissemination to an international user community. These data have been produced by a range of different institutions and vary across both scientific and spatio-temporal characteristics. This heterogeneity of the data together with the range of services to be supported presented significant technical challenges. An iterative development methodology was key to tackling these challenges: the system developed exploits a workflow which takes data that conforms to the CCI data specification, ingests it into a managed archive and uses both manual and automatically generated metadata to support data discovery, browse, and delivery services. It utilises both Earth System Grid Federation (ESGF) data nodes and the Open Geospatial Consortium Catalogue Service for the Web (OGC-CSW) interface, serving data into both the ESGF and the Global Earth Observation System of Systems (GEOSS). A key part of the system is a new vocabulary server, populated with CCI specific terms and relationships which integrates OGC-CSW and ESGF search services together, developed as part of a dialogue between domain scientists and linked data specialists. These services have enabled the development of a unified user interface for graphical search and visualisation – the CCI Open Data Portal Web Presence

Hydrodynamics of the stream-disk impact in interacting binaries

We use hydrodynamic simulations to provide quantitative estimates of the effects of the impact of the accretion stream on disks in interacting binaries. For low accretion rates, efficient radiative cooling of the hotspot region can occur, and the primary consequence of the stream impact is stream overflow toward smaller disk radii. The stream is well described by a ballistic trajectory, but larger masses of gas are swept up and overflow at smaller, but still highly supersonic, velocities. If cooling is inefficient, overflow still occurs, but there is no coherent stream inward of the disk rim. Qualitatively, the resulting structure appears as a bulge extending downstream along the disk rim. We calculate the mass fraction and velocity of the overflowing component as a function of the important system parameters, and discuss the implications of the results for X-ray observations and doppler tomography of cataclysmic variables, low-mass X-ray binaries and supersoft X-ray sources.Comment: 16 pages, including 8 figures. 1 color figure as a jpeg. ApJ, in pres

Learning Disentangled Representations with Semi-Supervised Deep Generative Models

Variational autoencoders (VAEs) learn representations of data by jointly training a probabilistic encoder and decoder network. Typically these models encode all features of the data into a single variable. Here we are interested in learning disentangled representations that encode distinct aspects of the data into separate variables. We propose to learn such representations using model architectures that generalise from standard VAEs, employing a general graphical model structure in the encoder and decoder. This allows us to train partially-specified models that make relatively strong assumptions about a subset of interpretable variables and rely on the flexibility of neural networks to learn representations for the remaining variables. We further define a general objective for semi-supervised learning in this model class, which can be approximated using an importance sampling procedure. We evaluate our framework's ability to learn disentangled representations, both by qualitative exploration of its generative capacity, and quantitative evaluation of its discriminative ability on a variety of models and datasets.Comment: Accepted for publication at NIPS 201

Cohort profile: The Scottish Research Register SHARE. A register of people interested in research participation linked to NHS datasets

SHARE is a NHS Scotland Research (NRS) infrastructure initiative and is funded by the Chief Scientists Office of the Scottish Government. Additional funding and initiation of the spare blood retention in Tayside was supported by The Wellcome Trust Biomedical Resource Award Number 099177/Z/12/Z.Purpose: Recruitment to trials is often difficult. Many trials fail to meet recruitment targets resulting in underpowered studies which waste resources and the time of those who participated. While there is evidence that many people are willing to take part in research, particularly if it involves a condition from which they suffer, researchers are unable to easily contact such people often relying on busy clinicians to identify them. Many clinicians perceive themselves as too busy to take part in research activities. The Scottish Health Research Register SHARE adopts an approach which asks the public to consent to their data held in National Health Service databases to be used to determine their suitability for research projects. Additionally, participants can consent for spare blood, left after routine venepuncture to be automatically identified in the laboratory and stored for future research studies. Participants: Anyone over the age of 16 years in Scotland can participate. Participants are approached through a range of methods including directly at outpatient clinics and general practitioners practices, leaflets with hospital letters and personal email from employers. Findings to date: SHARE has recruited around 130 000 people. SHARE has demonstrated that it can quickly and efficiently recruit to studies, over 20 until now. In addition, it can be used to administer questionnaire studies by email and recruit to patient and public involvement groups. Future plans: SHARE continues to steadily recruit with the ambition of eventually achieving 1 000 000 people in Scotland. We are steadily increasing the number of data sets we use for identifying participants. We are adding a mobile app which will facilitate dissemination about research and allow the collection of physiological and activity data if desired. We anticipate that SHARE will soon become the main source of health research recruitment in Scotland.Publisher PDFPeer reviewe

Association between circulating levels of sex steroid hormones and esophageal adenocarcinoma in the FINBAR Study

Funding: The study was supported by NIH Intramural Research Program, National Cancer Institute; Cancer Focus Northern Ireland (formerly the Ulster Cancer Foundation); the Northern Ireland R&D office; and the Health Research Board, Ireland. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Explorations, Vol. 6, No. 1

Cover: Panthera pardus, Chui in Kiswatuli, was photographed by Dr. Linda Karbonit ar Dr. James A. Sherburne in Serengeti National Park, Tanzania. Karbonit was accompanying Sherburne who was working on the design and development of the University of Maine, U.S. Fish and Wildlife Service, assistance program in wildlife training and conservation education to Tanzania’s National Parks. Sherburne, who has worked in Tanzania for several years, was there most recently in 1988 and 1989 working on the parks project. He serves as the Director of International Natural Resources and Agricultural Programs at the University of Maine. Articles include: Research and Economic Development: from the U.S. Senate Statement, December 22, 1989, by Sen. George J. Mitchell Politics and Research: Providing a Key for Economic Development, by Sen. William S. Cohen. Publisher’s Perspective, by Gregory N. Brown, Vice President, Research and Public Service What’s EPSCoR? Editorial Reflections, by Carole J. Bombard Past and Present: Marine Geologists Explore the Old and Teach the Young, by Daniel Belknap and Joseph Kelley High Biological Productivity: Salt Marshes, by Mark E. Wood Barrier Beaches, by William Duffy Sediment Budgets & Bluff Slump, by Rebecca Smith Coastal Environments and Change, by Andrew Walsh Mapping What You Can\u27t See, by Donald Robbins Casco Bay: Sea Level and the Shoreline, by Bradley W.B. Hay Christmas at Sea, by Molly Horvath A Short Course and the Local Economy, by Richard Hale and James Philp Dr. Bernard Lown: Alumnus Receives Golden Door Award The Sky is Falling . . . well, maybe, by Carole J. Bombard A Growing Interest in Timberland, by Robert A. Strong and Bret P. Vicar

The unexpected resurgence of Weyl geometry in late 20-th century physics

Weyl's original scale geometry of 1918 ("purely infinitesimal geometry") was withdrawn by its author from physical theorizing in the early 1920s. It had a comeback in the last third of the 20th century in different contexts: scalar tensor theories of gravity, foundations of gravity, foundations of quantum mechanics, elementary particle physics, and cosmology. It seems that Weyl geometry continues to offer an open research potential for the foundations of physics even after the turn to the new millennium.Comment: Completely rewritten conference paper 'Beyond Einstein', Mainz Sep 2008. Preprint ELHC (Epistemology of the LHC) 2017-02, 92 pages, 1 figur

Comparing mutation calls in fixed tumour samples between the Affymetrix OncoScan® Array and PCR based next-generation sequencing

Background: The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. Methods: We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples. 392 fixed, clinical samples were sequenced, encompassing 641 PCR regions, 403 putative positive calls and 1528 putative negative calls. Results: A small number of mutations could not be validated, either due to large indels or pseudogenes impairing parts of the NGS pipeline. For the remainder, if calls were filtered according to simple quality metrics, both sensitivity and specificity for the OncoScan platform were over 98%. This applied even to samples with poorer sample quality and lower variant allele frequency (5–10%) than product claims indicated. Conclusions: This benchmarking study will be useful to users and potential users of this platform, who wish to compare technologies or interpret their own results

Smc5/6 coordinates formation and resolution of joint molecules with chromosome morphology to ensure meiotic divisions

During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and the regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of a subset of joint-molecule intermediates. In this regard, Smc5/6 functions independently of the major crossover pathway defined by the MutLγ complex. Furthermore, we show that Smc5/6 is required for stable chromosomal localization of the XPF-family endonuclease, Mus81-Mms4Eme1. Our data suggest that the Smc5/6 complex is required for specific recombination and chromosomal processes throughout meiosis and that in its absence, attempts at cell division with unresolved joint molecules and residual cohesin lead to severe recombination-induced meiotic catastroph

Linkage to HIV Care and Antiretroviral Therapy in Cape Town, South Africa

BACKGROUND: Antiretroviral therapy (ART) has been scaled-up rapidly in Africa. Programme reports typically focus on loss to follow-up and mortality among patients receiving ART. However, little is known about linkage and retention in care of individuals prior to starting ART. METHODOLOGY: Data on adult residents from a periurban community in Cape Town were collected at a primary care clinic and hospital. HIV testing registers, CD4 count results provided by the National Health Laboratory System and ART registers were linked. A random sample (n = 885) was drawn from adults testing HIV positive through antenatal care, sexual transmitted disease and voluntary testing and counseling services between January 2004 and March 2009. All adults (n = 103) testing HIV positive through TB services during the same time period were also included in the study. Linkage to HIV care was defined as attending for a CD4 count measurement within 6 months of HIV diagnosis. Linkage to ART care was defined as initiating ART within 6 months of HIV diagnosis in individuals with a CD4 count ≤200 cells/µl taken within 6 months of HIV diagnosis. FINDINGS: Only 62.6% of individuals attended for a CD4 count measurement within 6 months of testing HIV positive. Individuals testing through sexually transmitted infection services had the best (84.1%) and individuals testing on their own initiative (53.5%) the worst linkage to HIV care. One third of individuals with timely CD4 counts were eligible for ART and 66.7% of those were successfully linked to ART care. Linkage to ART care was highest among antenatal care clients. Among individuals not yet eligible for ART only 46.3% had a repeat CD4 count. Linkage to HIV care improved in patients tested in more recent calendar period. CONCLUSION: Linkage to HIV and ART care was low in this poor peri-urban community despite free services available within close proximity. More efforts are needed to link VCT scale-up to subsequent care