Automatically linking MEDLINE abstracts to the Gene Ontology

Much has been written recently about the need for effective tools and methods for mining the wealth of information present in biomedical literature (Mack and Hehenberger, 2002; Blagosklonny and Pardee, 2001; Rindflesch et al., 2002)—the activity of conceptual biology. Keyword search engines operating over large electronic document stores (such as PubMed and the PNAS) offer some help, but there are fundamental obstacles that limit their effectiveness. In the first instance, there is no general consensus among scientists about the vernacular to be used when describing research about genes, proteins, drugs, diseases, tissues and therapies, making it very difficult to formulate a search query that retrieves the right documents. Secondly, finding relevant articles is just one aspect of the investigative process. A more fundamental goal is to establish links and relationships between facts existing in published literature in order to “validate current hypotheses or to generate new ones” (Barnes and Robertson, 2002)—something keyword search engines do little to support

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

Seasonal variation of the three-dimensional mean circulation over the Scotian Shelf

The seasonal-mean circulation over the Scotian Shelf is studied numerically by computing mean and tidal current fields for winter, spring, and summer using a three-dimensional nonlinear diagnostic model. The mean current fields are forced by seasonal-mean baroclinic pressure gradients, tidal rectification, uniform wind stresses, and associated barotropic pressure gradients. A historical hydrographic database is used to determine the climatological mean baroclinic forcing. Upstream open boundary conditions are estimated from the density fields to give no normal geostrophic bottom flow and are specified as either along-boundary elevation gradients or depth-integrated normal velocities. The numerical solutions for nominal bimonthly periods (January–February, April–May, and July–August) reveal the dominant southwestward nearshore and shelf-break flows of relatively cool and fresh shelf water from the Gulf of St. Lawrence and Newfoundland Shelf, with speeds up to about 20 cm/s. The seasonal intensification of the southwestward flows is reproduced by the model, with the transport increasing from 0.3 Sv in summer to 0.9 Sv in winter on the inner Halifax section. There are also pronounced topographic-scale influences of submarine banks, basins, and cross-shelf channels on the circulation, such as anticyclonic gyres over banks and cyclonic gyres over basins. Baroclinicity is the dominant forcing throughout the domain, but tidal rectification is comparable on the southwestern Scotian Shelf (e.g., about 0.2 Sv recirculating transport around Browns Bank for all the periods). The mean wind stress generates offshore surface drift in winter. The solutions are in approximate agreement with observed currents and transports over the Scotian Shelf, although there are local discrepancies

Comparison of sulfuric and oxalic acid anodizing for preparation of thermal control coatings for spacecraft

The development of thermal control surfaces, which maintain stable solar absorptivity and infrared emissivity over long periods, is challenging due to severe conditions in low-Earth orbit (LEO). Some candidate coatings are second-surface silver-coated Teflon; second-surface, silvered optical solar reflectors made of glass or quartz; and anodized aluminum. Sulfuric acid anodized and oxalic acid anodized aluminum was evaluated under simulated LEO conditions. Oxalic acid anodizing shows promise of greater stability in LEO over long missions, such as the 30 years planned for the Space Station. However, sulfuric acid anodizing shows lower solar absorptivity

Remote sensing program activity report

Major accomplishments in an effort to encourage investigation and technology transfer for practical applications of remote sensing to solve Earth resources problems in Vermont include: (1) acquisition, installation, and operation of the ORSER digital processing system on the University's IBM 3031 computer; (2) acquisition and operation of printing and CRT computer terminals for remote access to computer facilities for analysis of remotely sensed digital tape; (3) acquisition and operation of optical interpretation and image transfer devices for use with all types of aerial photography; (4) development of audio visual and other training materials for use in presentations, workshops, and short courses to enhance technology transfer; and (5) cooperation government agencies in demonstration projects to show the feasibility of using remote sensing technology

Limb-darkening functions as derived from along-track operation of the ERBE scanning radiometer for January 1985

During January 1985, the scanning radiometer aboard the Earth Radiation Budget Satellite was operated to scan along-track. These data have been analyzed to produce limb-darkening functions for Earth emitted radiation, which relate the radiance in any given direction to the radiant exitance. Limb-darkening functions are presented in tabular form and shown as figures for 10 day cases and 12 night cases, corresponding to various scene types and latitude zones. The scene types were computed using measurements within 10 deg of zenith. The limb-darkening functions have values of 1.03 to 1.09 at zenith, with 1.06 being typical. It is found that latitude causes a variation on the order of 1 percent, except for zenith angles greater than 70 deg. These limb-darkening models are about 2 percent higher at zenith than the models derived from Nimbus 7 data

Light Dark Matter Detection Prospects at Neutrino Experiments

We consider the prospects for the detection of relatively light dark matter through direct annihilation to neutrinos. We specifically focus on the detection possibilities of water Cherenkov and liquid scintillator neutrino detection devices. We find in particular that liquid scintillator detectors may potentially provide excellent detection prospects for dark matter in the 4-10 GeV mass range. These experiments can provide excellent corroborative checks of the DAMA/LIBRA annual modulation signal, but may yield results for low mass dark matter in any case. We identify important tests of the ratio of electron to muon neutrino events (and neutrino versus anti-neutrino events), which discriminate against background atmospheric neutrinos. In addition, the fraction of events which arise from muon neutrinos or anti-neutrinos ($R_{\mu}$ and $R_{\bar \mu}$) can potentially yield information about the branching fractions of hypothetical dark matter annihilations into different neutrino flavors. These results apply to neutrinos from secondary and tertiary decays as well, but will suffer from decreased detectability.Comment: 13 pages, 2 figures, pdflatex, references, one figure and comments on electron neutrino bounds and on spin-dependent scattering limits added. Figures updated

Forest Residues As An Alternate Energy Source

Forest residues, in combination with more intensified timber production systems have potential as a substantial source of fuel wood. The extent and availability of this resource is discussed, with particular reference to the energetics and economics of existing and proposed harvesting systems. Utilization of residue wood fuels is considered and recent developments in small scale automatic wood chip burning heating systems for residential and commercial use are described