Using GIS to create synthetic disease outbreaks

BACKGROUND: The ability to detect disease outbreaks in their early stages is a key component of efficient disease control and prevention. With the increased availability of electronic health-care data and spatio-temporal analysis techniques, there is great potential to develop algorithms to enable more effective disease surveillance. However, to ensure that the algorithms are effective they need to be evaluated. The objective of this research was to develop a transparent user-friendly method to simulate spatial-temporal disease outbreak data for outbreak detection algorithm evaluation. A state-transition model which simulates disease outbreaks in daily time steps using specified disease-specific parameters was developed to model the spread of infectious diseases transmitted by person-to-person contact. The software was developed using the MapBasic programming language for the MapInfo Professional geographic information system environment. RESULTS: The simulation model developed is a generalised and flexible model which utilises the underlying distribution of the population and incorporates patterns of disease spread that can be customised to represent a range of infectious diseases and geographic locations. This model provides a means to explore the ability of outbreak detection algorithms to detect a variety of events across a large number of stochastic replications where the influence of uncertainty can be controlled. The software also allows historical data which is free from known outbreaks to be combined with simulated outbreak data to produce files for algorithm performance assessment. CONCLUSION: This simulation model provides a flexible method to generate data which may be useful for the evaluation and comparison of outbreak detection algorithm performance

The Arecibo Legacy Fast ALFA Survey: The alpha.40 HI Source Catalog, its Characteristics and their Impact on the Derivation of the HI Mass Function

We present a current catalog of 21 cm HI line sources extracted from the Arecibo Legacy Fast Arecibo L-band Feed Array (ALFALFA) survey over ~2800 square degrees of sky: the alpha.40 catalog. Covering 40% of the final survey area, the alpha.40 catalog contains 15855 sources in the regions 07h30m < R.A. < 16h30m, +04 deg < Dec. < +16 deg and +24 deg < Dec. < +28 deg and 22h < R.A. < 03h, +14 deg < Dec. < +16 deg and +24 deg < Dec. < +32 deg. Of those, 15041 are certainly extragalactic, yielding a source density of 5.3 galaxies per square degree, a factor of 29 improvement over the catalog extracted from the HI Parkes All Sky Survey. In addition to the source centroid positions, HI line flux densities, recessional velocities and line widths, the catalog includes the coordinates of the most probable optical counterpart of each HI line detection, and a separate compilation provides a crossmatch to identifications given in the photometric and spectroscopic catalogs associated with the Sloan Digital Sky Survey Data Release 7. Fewer than 2% of the extragalactic HI line sources cannot be identified with a feasible optical counterpart; some of those may be rare OH megamasers at 0.16 < z < 0.25. A detailed analysis is presented of the completeness, width dependent sensitivity function and bias inherent in the current alpha.40 catalog. The impact of survey selection, distance errors, current volume coverage and local large scale structure on the derivation of the HI mass function is assessed. While alpha.40 does not yet provide a completely representative sampling of cosmological volume, derivations of the HI mass function using future data releases from ALFALFA will further improve both statistical and systematic uncertainties.Comment: 62 pages, 28 figures. See http://egg.astro.cornell.edu/alfalfa/data for ASCII and CSV datafiles corresponding to Tables 1, 2 and 3. A higher resolution PDF version can be found at http://egg.astro.cornell.edu/alfalfa/pubs.php. To appear in Nov 2011 Astron.

Cognitive rehabilitation, self-management, psychotherapeutic and caregiver support interventions in progressive neurodegenerative conditions: a scoping review

BACKGROUND: Despite their potentially significant impact, cognitive disability may be overlooked in a number of progressive neurodegenerative conditions, as other difficulties dominate the clinical picture. OBJECTIVE: We examined the extent, nature and range of the research evidence relating to cognitive rehabilitation, self-management, psychotherapeutic and caregiver support interventions in Parkinsonian disorders, multiple sclerosis (MS), frontotemporal dementias (FTD), motor neuron disease and Huntington’s disease. METHODS: Scoping review based on searches of MEDLINE and CINAHL up to 15 March 2016. RESULTS: We included 140 eligible papers. Over half of the studies, and almost all the randomised controlled trials, related to MS, while a number of single case studies described interventions for people with FTD. CR interventions addressed functional ability, communication and interaction, behaviour or memory. The majority of psychotherapy interventions involved cognitive behavioural therapy for depression or anxiety. Self-management interventions were mainly available for people with MS. There were few reports of interventions specific to caregivers. Numerous methodological challenges were identified. CONCLUSIONS: The limited range of studies for all conditions except MS suggests a need firstly to synthesise systematically the available evidence across conditions and secondly to develop well-designed studies to provide evidence about the effectiveness of CR and other psychological interventions

Small Tidal Channels Improve Foraging Opportunities for Calidris Shorebirds

Estuarine intertidal habitats are heterogeneous, therefore migratory shorebirds are expected to forage in microhabitats where they can maximize their energy intake. Identifying proximate factors that migratory shorebirds use to accept or reject a particular habitat patch will help land managers make conservation and restoration decisions that provide the greatest benefits to shorebird populations during migration, a period of intense energy usage. We examined whether small semipermanent tidal channels were preferentially used by foraging Western Sandpipers (Calidris mauri) and Dunlins (C. alpina) during a spring migratory stopover in Bandon Marsh, an Oregon, USA, estuary. Further, we tested alternative hypotheses about how channels might be beneficial to shorebirds by examining infauna abundance, composition, and depth alongside channels compared with that in open mudflats. The densities of Western Sandpipers and Dunlins were at least 4 times higher along channels than in open mudflat habitats. Infauna along channels were twice as abundant as those in the surrounding mudflats, and infauna were generally found closer to the surface. Furthermore, sediment alongside channels required less than half the force to probe, probably increasing shorebirds\u27 overall access to prey. We conclude that shorebirds selected microhabitats near channels because of the greater food abundance and availability. Additional evidence suggested that another microhabitat, patches of red algae (Gracilaria sp.), may also have conferred advantages on foraging shorebirds. Channels may be a valuable microhabitat to consider when selecting conservation areas for shorebirds, and maintaining channels (e.g., through maintaining natural hydrology and sedimentation patterns) should be considered in management practices

Clinical description of a completed outbreak of SARS in Vietnam, February-May 2003

We investigated the clinical manifestations and course of all probable severe acute respiratory syndrome (SARS) patients in the Vietnam outbreak. Probable SARS cases were defined by using the revised World Health Organization criteria. We systematically reviewed medical records and undertook descriptive statistical analyses. All 62 patients were hospitalized. On admission, the most prominent symptoms were malaise (82.3%) and fever (79.0%). Cough, chest pain, and shortness of breath were present in approximately one quarter of the patients; 79.0% had lymphopenia; 40.3% had thrombocytopenia; 19.4% had leukopenia; and 75.8% showed changes on chest radiograph. Fever developed on the first day of illness onset, and both respiratory symptoms and radiographic changes occurred on day 4. On average, maximal radiographic changes were observed on day 10, and fevers subsided by day 13. Symptoms on admission were nonspecific, although fever, malaise, and lymphopenia were common. The complications of SARS included invasive intubation and ventilation (11.3%) and death (9.7%)

Cronicidad y multimorbilidad, un análisis bajo el concepto de red global mediante análisis de redes

Objectius: Descriure i visualitzar l'estructura de les xarxes de cronicitat, malalties cròniques i multimorbilitat. Mètodes: Estudi descriptiu i observacional amb una població d'estudi de 22.406 individus entre els 18 anys i sense límit d'edat, assignats durant l'any 2013, a tres àrees bàsiques de salut urbanes de la ciutat de Barcelona. Resultats. La cronicitat, des d'un enfocament de xarxa, està altament agrupada per malalties cròniques i connectada mitjançant les persones que pateixen més d’una malaltia creant un sistema complex altament heterogeni. El mètode d'anàlisi d'associació per individus permet, en la xarxa de malalties cròniques i de multimorbilitat, visualitzar les interrelacions entre malalties, arribant a un nivell de relació i de comprensió de la multimorbilitat superior que la diada o la triada, aconseguint una visualització de la multimorbilitat d’un total de 19 grups de malalties cròniques. Addicionalment, permet visualitzar i interpretar la comorbiditat mitjançant la mida dels arcs en la xarxa.Objetivos: Describir y visualizar la estructura de las redes de cronicidad, enfermedades crónicas y multimorbilidad. Métodos: Estudio descriptivo y observacional con una población de estudio de 22.406 individuos entre a los 18 años y sin límite de edad, asignados durante el año 2013, a tres áreas básicas de salud urbanas de la ciudad de Barcelona. Resultados: La cronicidad, desde un enfoque de red, está altamente agrupada por enfermedades crónicas y conectada mediante las personas que sufren más de una enfermedad creando un sistema complejo altamente heterogéneo. El método de análisis según asociación por individuos permite, en la red de enfermedades crónicas y de multimorbilidad, visualizar las interrelaciones entre enfermedades, llegando a un nivel de relación y de comprensión de la multimorbilidad superior que la diada o triada, consiguiendo una visualización de la multimorbilidad de un total de 19 grupos de enfermedades crónicas. Adicionalmente, permite visualizar e interpretar la comorbilidad mediante la medida de los arcos en la red.Objectives. Describe and visualize the network structure of chronicity, chronic diseases, and multi-morbidity. Methods. Descriptive and observational study with a sample of 22,406 individuals of 18 years or more who belonged during 2013 to one of the three basic urban healthcare areas of Barcelona. Results. Chronicity from a network perspective is a network that his highly concentrated around chronic diseases and connected through people who have one or several diseases, thereby creating a complex and highly heterogeneous system. The method of analysis by association of individuals allows visualization of the interdependencies between diseases in networks of chronic diseases and multi-morbidity. This improves the understanding of multi-morbidity beyond that offered by dyads and triads, expanding the visualization to a total of 19 groups of chronic disease. In addition, this allows to visualize and interpret comorbidity by the size of network edges

The arecibo legacy fast ALFA survey: The ALFALFA extragalactic HI source catalog

We present the catalog of ∼31,500 extragalactic H i line sources detected by the completed Arecibo Legacy Fast ALFA (ALFALFA) survey out to z 6.5) detections and ones of lower quality that coincide in both position and recessional velocity with galaxies of known redshift. We review the observing technique, data reduction pipeline, and catalog construction process, focusing on details of particular relevance to understanding the catalog's compiled parameters. We further describe and make available the digital H i line spectra associated with the cataloged sources. In addition to the extragalactic H i line detections, we report nine confirmed OH megamasers (OHMs) and 10 OHM candidates at 0.16 < z < 0.22 whose OH line signals are redshifted into the ALFALFA frequency band. Because of complexities in data collection and processing associated with the use of a feed-horn array on a complex single-dish antenna in the terrestrial radio frequency interference environment, we also present a list of suggestions and caveats for consideration by users of the ALFALFA extragalactic catalog for future scientific investigations.© 2018. The American Astronomical Society. All rights reserved.The authors acknowledge the work of the entire ALFALFA collaboration who have contributed to the many aspects of the survey over the years. The ALFALFA team at Cornell has been supported by NSF grants AST-0607007, AST-1107390, and AST-1714828 and grants from the Brinson Foundation. Participation of the Undergraduate ALFALFA Team has been made possible by NSF grants AST-0724918, AST-0725267, AST-0725380, AST-0902211, AST-0903394, AST-1211005, AST-1637339, AST-1637271, AST-1637299, AST-1637262, and AST-1637276. EAKA is supported by the WISE research program, which is financed by the Netherlands Organisation for Scientific Research (NWO). BRK acknowledges the National Radio Astronomy Observatory (NRAO). The NRAO is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc. MGJ acknowledges support from grant AYA2015-65973-C3-1-R (MINECO/FEDER, UE). We thank Dmitry Makarov for comments and suggestions on cross-identifications. This work is based on observations made with the Arecibo Observatory. The Arecibo Observatory has been operated by SRI International under a cooperative agreement with the National Science Foundation (AST-1100968) and in alliance with Ana G. Mendez-Universidad Metropolitana and the Universities Space Research Association. We thank the staff of the Arecibo Observatory, especially Phil Perillat, Ganesh Rajagopalan, Arun Venkataraman, Hector Hernandez, and the telescope operations group for their outstanding support of the ALFALFA survey program. We acknowledge the use of NASA's SkyView facility (http://skyview.gsfc.nasa.gov), located at NASA Goddard Space Flight Center, and the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. The Digitized Sky Surveys were produced at the Space Telescope Science Institute under U.S. Government grant NAG W-2166. The images of these surveys are based on photographic data obtained using the Oschin Schmidt Telescope on Palomar Mountain and the UK Schmidt Telescope. The plates were processed into the present compressed digital form with the permission of these institutions. The Second Palomar Observatory Sky Survey (POSS-II) was made by the California Institute of Technology with funds from the National Science Foundation, the National Geographic Society, the Sloan Foundation, the Samuel Oschin Foundation, and the Eastman Kodak Corporation. This research used data from the Sloan Digital Sky Survey. Funding for the SDSS and SDSS-II has been provided by the Alfred P. Sloan Foundation, the Participating Institutions, the National Science Foundation, the U.S. Department of Energy, the National Aeronautics and Space Administration, the Japanese Monbukagakusho, the Max Planck Society, and the Higher Education Funding Council for England