Enhancing access to the Bibliome: the TREC 2004 Genomics Track

BACKGROUND: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed. RESULTS: A total of 27 research groups submitted 47 different runs. The most effective runs, as measured by the primary evaluation measure of mean average precision (MAP), used a combination of domain-specific and general techniques. The best MAP obtained by any run was 0.4075. Techniques that expanded queries with gene name lists as well as words from related articles had the best efficacy. However, many runs performed more poorly than a simple baseline run, indicating that careful selection of system features is essential. CONCLUSION: Various approaches to ad hoc retrieval provide a diversity of efficacy. The TREC Genomics Track and its test collection resources provide tools that allow improvement in information retrieval systems

Discovery of Highly Obscured Galaxies in the Zone of Avoidance

We report the discovery of twenty-five previously unknown galaxies in the Zone of Avoidance. Our systematic search for extended extra-galactic sources in the GLIMPSE and MIPSGAL mid-infrared surveys of the Galactic plane has revealed two overdensities of these sources, located around l ~ 47 and 55 degrees and |b| less than 1 degree in the Sagitta-Aquila region. These overdensities are consistent with the local large-scale structure found at similar Galactic longitude and extending from |b| ~ 4 to 40 degrees. We show that the infrared spectral energy distribution of these sources is indeed consistent with those of normal galaxies. Photometric estimates of their redshift indicate that the majority of these galaxies are found in the redshift range z = 0.01 - 0.05, with one source located at z = 0.07. Comparison with known sources in the local Universe reveals that these galaxies are located at similar overdensities in redshift space. These new galaxies are the first evidence of a bridge linking the large-scale structure between both sides of the Galactic plane at very low Galactic latitude and clearly demonstrate the feasibility of detecting galaxies in the Zone of Avoidance using mid-to-far infrared surveys.Comment: Accepted for publication in the Astronomical Journal, 28 pages, 5 tables, 11 figure

SMA/PdBI multiple line observations of the nearby Seyfert2 galaxy NGC 1068: Shock related gas kinematics and heating in the central 100pc?

We present high angular resolution (0.5-2.0") observations of the mm continuum and the 12CO(J=3-2), 13CO(J=3-2), 13CO(J=2-1), C18O(J=2-1), HCN(J=3-2), HCO+(J=4-3) and HCO+(J=3-2) line emission in the circumnuclear disk (r=100pc) of the proto-typical Seyfert type-2 galaxy NGC1068, carried out with the Submillimeter Array. We further include in our analysis new 13CO(J=1-0) and improved 12CO(J=2-1) observations of NGC1068 at high angular resolution (1.0-2.0") and sensitivity, conducted with the IRAM Plateau de Bure Interferometer. Based on the complex dynamics of the molecular gas emission indicating non-circular motions in the central ~100pc, we propose a scenario in which part of the molecular gas in the circumnuclear disk of NGC1068 is radially blown outwards as a result of shocks. This shock scenario is further supported by quite warm (Tkin>=200K) and dense (nH2=10^4cm^-3) gas constrained from the observed molecular line ratios. The HCN abundance in the circumnuclear disk is found to be [HCN]/[12CO]=10^-3.5. This is slightly higher than the abundances derived for galactic and extragalactic starforming/starbursting regions. This results lends further support to X-ray enhanced HCN formation in the circumnuclear disk of NGC1068, as suggested by earlier studies. The HCO+ abundance ([HCO+]/[12CO]=10^-5) appears to be somewhat lower than that of galactic and extragalactic starforming/starbursting regions. When trying to fit the cm to mm continuum emission by different thermal and non-thermal processes, it appears that electron-scattered synchrotron emission yields the best results while thermal free-free emission seems to over-predict the mm continuum emission.Comment: accepted for publication by ApJ; 35pages, 22 figures and 6 tables (at the end of the file); 3 figures have been decreased in quality to match size limi

Mid-Infrared Properties of the Swift Burst Alert Telescope Active Galactic Nuclei Sample of the Local Universe. I. Emission-Line Diagnostics

We compare mid-infrared emission-line properties, from high-resolution Spitzer spectra of a hard X-ray (14 -- 195 keV) selected sample of nearby (z < 0.05) AGN detected by the Burst Alert Telescope (BAT) aboard Swift. The luminosity distribution for the mid-infrared emission-lines, [O IV] 25.89 micron, [Ne II] 12.81 micron, [Ne III] 15.56 micron and [Ne V] 14.32/24.32 micron, and hard X-ray continuum show no differences between Seyfert 1 and Seyfert 2 populations, however six newly discovered BAT AGNs are under-luminous in [O IV], most likely the result of dust extinction in the host galaxy. The overall tightness of the mid-infrared correlations and BAT fluxes and luminosities suggests that the emission lines primarily arise in gas ionized by the AGN. We also compare the mid-infrared emission-lines in the BAT AGNs with those from published studies of ULIRGs, PG QSOs, star-forming galaxies and LINERs. We find that the BAT AGN sample fall into a distinctive region when comparing the [Ne III]/[Ne II] and the [O IV]/[Ne III] ratios. These line ratios are lower in sources that have been previously classified in the mid-infrared/optical as AGN than those found for the BAT AGN, suggesting that, in our X-ray selected sample, the AGN represents the main contribution to the observed line emission. These ratios represent a new emission line diagnostic for distinguishing between AGN and star forming galaxies.Comment: 54 pages, 9 Figures. Accepted for publication in The Astrophysical Journal

Clinical outcomes resulting from telemedicine interventions: a systematic review

BACKGROUND: The use of telemedicine is growing, but its efficacy for achieving comparable or improved clinical outcomes has not been established in many medical specialties. The objective of this systematic review was to evaluate the efficacy of telemedicine interventions for health outcomes in two classes of application: home-based and office/hospital-based. METHODS: Data sources for the study included deports of studies from the MEDLINE, EMBASE, CINAHL, and HealthSTAR databases; searching of bibliographies of review and other articles; and consultation of printed resources as well as investigators in the field. We included studies that were relevant to at least one of the two classes of telemedicine and addressed the assessment of efficacy for clinical outcomes with data of reported results. We excluded studies where the service did not historically require face-to-face encounters (e.g., radiology or pathology diagnosis). All included articles were abstracted and graded for quality and direction of the evidence. RESULTS: A total of 25 articles met inclusion criteria and were assessed. The strongest evidence for the efficacy of telemedicine in clinical outcomes comes from home-based telemedicine in the areas of chronic disease management, hypertension, and AIDS. The value of home glucose monitoring in diabetes mellitus is conflicting. There is also reasonable evidence that telemedicine is comparable to face-to-face care in emergency medicine and is beneficial in surgical and neonatal intensive care units as well as patient transfer in neurosurgery. CONCLUSIONS: Despite the widespread use of telemedicine in virtually all major areas of health care, evidence concerning the benefits of its use exists in only a small number of them. Further randomized controlled trials must be done to determine where its use is most effective

Cause of Death and Predictors of All-Cause Mortality in Anticoagulated Patients With Nonvalvular Atrial Fibrillation : Data From ROCKET AF

M. Kaste on työryhmän ROCKET AF Steering Comm jäsen.Background-Atrial fibrillation is associated with higher mortality. Identification of causes of death and contemporary risk factors for all-cause mortality may guide interventions. Methods and Results-In the Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF) study, patients with nonvalvular atrial fibrillation were randomized to rivaroxaban or dose-adjusted warfarin. Cox proportional hazards regression with backward elimination identified factors at randomization that were independently associated with all-cause mortality in the 14 171 participants in the intention-to-treat population. The median age was 73 years, and the mean CHADS(2) score was 3.5. Over 1.9 years of median follow-up, 1214 (8.6%) patients died. Kaplan-Meier mortality rates were 4.2% at 1 year and 8.9% at 2 years. The majority of classified deaths (1081) were cardiovascular (72%), whereas only 6% were nonhemorrhagic stroke or systemic embolism. No significant difference in all-cause mortality was observed between the rivaroxaban and warfarin arms (P=0.15). Heart failure (hazard ratio 1.51, 95% CI 1.33-1.70, P= 75 years (hazard ratio 1.69, 95% CI 1.51-1.90, P Conclusions-In a large population of patients anticoagulated for nonvalvular atrial fibrillation, approximate to 7 in 10 deaths were cardiovascular, whereasPeer reviewe

Cortical brain abnormalities in 4474 individuals with schizophrenia and 5098 control subjects via the enhancing neuro Imaging genetics through meta analysis (ENIGMA) Consortium

BACKGROUND: The profile of cortical neuroanatomical abnormalities in schizophrenia is not fully understood, despite hundreds of published structural brain imaging studies. This study presents the first meta-analysis of cortical thickness and surface area abnormalities in schizophrenia conducted by the ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis) Schizophrenia Working Group. METHODS: The study included data from 4474 individuals with schizophrenia (mean age, 32.3 years; range, 11-78 years; 66% male) and 5098 healthy volunteers (mean age, 32.8 years; range, 10-87 years; 53% male) assessed with standardized methods at 39 centers worldwide. RESULTS: Compared with healthy volunteers, individuals with schizophrenia have widespread thinner cortex (left/right hemisphere: Cohen's d = -0.530/-0.516) and smaller surface area (left/right hemisphere: Cohen's d = -0.251/-0.254), with the largest effect sizes for both in frontal and temporal lobe regions. Regional group differences in cortical thickness remained significant when statistically controlling for global cortical thickness, suggesting regional specificity. In contrast, effects for cortical surface area appear global. Case-control, negative, cortical thickness effect sizes were two to three times larger in individuals receiving antipsychotic medication relative to unmedicated individuals. Negative correlations between age and bilateral temporal pole thickness were stronger in individuals with schizophrenia than in healthy volunteers. Regional cortical thickness showed significant negative correlations with normalized medication dose, symptom severity, and duration of illness and positive correlations with age at onset. CONCLUSIONS: The findings indicate that the ENIGMA meta-analysis approach can achieve robust findings in clinical neuroscience studies; also, medication effects should be taken into account in future genetic association studies of cortical thickness in schizophrenia

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Exploration of Shared Genetic Architecture Between Subcortical Brain Volumes and Anorexia Nervosa

In MRI scans of patients with anorexia nervosa (AN), reductions in brain volume are often apparent. However, it is unknown whether such brain abnormalities are influenced by genetic determinants that partially overlap with those underlying AN. Here, we used a battery of methods (LD score regression, genetic risk scores, sign test, SNP effect concordance analysis, and Mendelian randomization) to investigate the genetic covariation between subcortical brain volumes and risk for AN based on summary measures retrieved from genome-wide association studies of regional brain volumes (ENIGMA consortium, n = 13,170) and genetic risk for AN (PGC-ED consortium, n = 14,477). Genetic correlations ranged from − 0.10 to 0.23 (all p > 0.05). There were some signs of an inverse concordance between greater thalamus volume and risk for AN (permuted p = 0.009, 95% CI: [0.005, 0.017]). A genetic variant in the vicinity of ZW10, a gene involved in cell division, and neurotransmitter and immune system relevant genes, in particular DRD2, was significantly associated with AN only after conditioning on its association with caudate volume (pFDR = 0.025). Another genetic variant linked to LRRC4C, important in axonal and synaptic development, reached significance after conditioning on hippocampal volume (pFDR = 0.021). In this comprehensive set of analyses and based on the largest available sample sizes to date, there was weak evidence for associations between risk for AN and risk for abnormal subcortical brain volumes at a global level (that is, common variant genetic architecture), but suggestive evidence for effects of single genetic markers. Highly powered multimodal brain- and disorder-related genome-wide studies are needed to further dissect the shared genetic influences on brain structure and risk for AN