The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

The Murchison Widefield Array: the Square Kilometre Array Precursor at low radio frequencies

The Murchison Widefield Array (MWA) is one of three Square Kilometre Array Precursor telescopes and is located at the Murchison Radio-astronomy Observatory in the Murchison Shire of the mid-west of Western Australia, a location chosen for its extremely low levels of radio frequency interference. The MWA operates at low radio frequencies, 80-300 MHz, with a processed bandwidth of 30.72 MHz for both linear polarisations, and consists of 128 aperture arrays (known as tiles) distributed over a ~3 km diameter area. Novel hybrid hardware/software correlation and a real-time imaging and calibration systems comprise the MWA signal processing backend. In this paper the as-built MWA is described both at a system and sub-system level, the expected performance of the array is presented, and the science goals of the instrument are summarised.Comment: Submitted to PASA. 11 figures, 2 table

The Blizzard Challenge 2009

The Blizzard Challenge 2009 was the fifth annual Blizzard Challenge. As in 2008, UK English and Mandarin Chinese were the chosen languages for the 2009 Challenge. The English corpus was the same one used in 2008. The Mandarin corpus was provided by iFLYTEK. As usual, participants with limited resources or limited experience in these languages had the option of using unaligned labels that were provided for both corpora and for the test sentences. An accent-specific pronunciation dictionary was also available for the English speaker. This year, the tasks were organised in the form of ‘hubs ’ and ‘spokes ’ where each hub task involved building a general-purpose voice and each spoke task involved building a voice for a specific application. A set of test sentences was released to participants, who were given a limited time in which to synthesise them and submit the synthetic speech. An online listening test was conducted to evaluate naturalness, intelligibility, degree of similarity to the original speaker and, for one of the spoke tasks, “appropriateness.

Evaluation of options for a UK electronic thesis service: study report

The British Library (BL), JISC, UK HE institutions and CURL have funded an 18-month project to develop a national framework for the provision, preservation and open access to electronic theses produced in UK HE institutions. The project, called EThOS (Electronic Theses Online Service) was developed in response to a competitive tender invitation released by the JISC and proposes a service set up and run by the British Library. The British Library’s current service, the British Thesis Service, offers access to around 180,000 doctoral theses, predominantly from 1970 onwards, though it is estimated that overall some half million theses dating from the 1600s are in existence in the UK. Around 80% of requests are for theses published within the last 13 years and almost all of these exist only in hardcopy. Through this service, theses are acquired ‘on demand’ and delivered on microfilm at a cost of just over £60 to the user (and at this price the service runs at a loss). Whilst this service, coupled with the Index to Theses (Expert Information), enables the location of and access to relatively recent British theses by the determined seeker, no one could argue that the process is optimised. As a result, usage of theses is much lower than it might be and much research is going unnoticed and unused as a result. Conversely, it has been shown that when theses are easy to locate and access, usage is high: at Virginia Tech, a pioneer site in the provision of a formal, systematised ETD (electronic theses and dissertations) service, downloads have been shown to increase over 30-fold when a thesis is available free online and easily located. A national service for the UK that provides discovery and access to theses in electronic form via the Web will increase the utility of doctoral scholarship. A single interface that directs users to theses wherever they are held, and which addresses the issues of intellectual property, permissions, royalties, preservation, discovery, and other matters associated with the public provision of theses in electronic form, will be of great benefit to the scholarly community in the UK and across the world. The EThOS project (Electronic Theses Online Service) was commissioned to develop a model for a workable, sustainable and acceptable national service for the provision of open access to electronic doctoral theses. The EThOS project team have completed the task and UCL Library Services in partnership with Key Perspectives Ltd have been asked to undertake a consultative study to assess the acceptability of the proposed model to the UK higher education community in the context of other potential models. This document reports the results of this consultative study, including a set of recommendations to JISC and other stakeholders for setting up a UK national e-theses service. The stakeholders other than JISC are: The British Library University administrators (registrars) Graduate students and recent PhDs Librarians Institutional repository managers Other e-theses services including: DART-Europe DiVA DissOnline Australasian Digital Theses Theses Canada Networked Digital Library for Theses and Dissertations The EThOS tea

Whom to Ask? Jury Selection for Decision Making Tasks on Micro-blog Services

It is universal to see people obtain knowledge on micro-blog services by asking others decision making questions. In this paper, we study the Jury Selection Problem(JSP) by utilizing crowdsourcing for decision making tasks on micro-blog services. Specifically, the problem is to enroll a subset of crowd under a limited budget, whose aggregated wisdom via Majority Voting scheme has the lowest probability of drawing a wrong answer(Jury Error Rate-JER). Due to various individual error-rates of the crowd, the calculation of JER is non-trivial. Firstly, we explicitly state that JER is the probability when the number of wrong jurors is larger than half of the size of a jury. To avoid the exponentially increasing calculation of JER, we propose two efficient algorithms and an effective bounding technique. Furthermore, we study the Jury Selection Problem on two crowdsourcing models, one is for altruistic users(AltrM) and the other is for incentive-requiring users(PayM) who require extra payment when enrolled into a task. For the AltrM model, we prove the monotonicity of JER on individual error rate and propose an efficient exact algorithm for JSP. For the PayM model, we prove the NP-hardness of JSP on PayM and propose an efficient greedy-based heuristic algorithm. Finally, we conduct a series of experiments to investigate the traits of JSP, and validate the efficiency and effectiveness of our proposed algorithms on both synthetic and real micro-blog data.Comment: VLDB201

Programmatic and Direct Manipulation, Together at Last

Direct manipulation interfaces and programmatic systems have distinct and complementary strengths. The former provide intuitive, immediate visual feedback and enable rapid prototyping, whereas the latter enable complex, reusable abstractions. Unfortunately, existing systems typically force users into just one of these two interaction modes. We present a system called Sketch-n-Sketch that integrates programmatic and direct manipulation for the particular domain of Scalable Vector Graphics (SVG). In Sketch-n-Sketch, the user writes a program to generate an output SVG canvas. Then the user may directly manipulate the canvas while the system immediately infers a program update in order to match the changes to the output, a workflow we call live synchronization. To achieve this, we propose (i) a technique called trace-based program synthesis that takes program execution history into account in order to constrain the search space and (ii) heuristics for dealing with ambiguities. Based on our experience with examples spanning 2,000 lines of code and from the results of a preliminary user study, we believe that Sketch-n-Sketch provides a novel workflow that can augment traditional programming systems. Our approach may serve as the basis for live synchronization in other application domains, as well as a starting point for yet more ambitious ways of combining programmatic and direct manipulation.Comment: PLDI 2016 Paper + Supplementary Appendice

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al