Improving Term Extraction with Terminological Resources

Studies of different term extractors on a corpus of the biomedical domain revealed decreasing performances when applied to highly technical texts. The difficulty or impossibility of customising them to new domains is an additional limitation. In this paper, we propose to use external terminologies to influence generic linguistic data in order to augment the quality of the extraction. The tool we implemented exploits testified terms at different steps of the process: chunking, parsing and extraction of term candidates. Experiments reported here show that, using this method, more term candidates can be acquired with a higher level of reliability. We further describe the extraction process involving endogenous disambiguation implemented in the term extractor YaTeA

Dr. Yang Zhong: an explorer on the road forever

On the morning of September 25th 2017, grievous news spread from the remote Ordos region of Inner Mongolia to Fudan University campus in Shanghai. Professor Yang Zhong, a famous botanist and the Dean of Fudan University’s graduate school, passed away in a tragic car accident while on a business trip

New walking and cycling infrastructure and modal shift in the UK: A quasi-experimental panel study

Heavy dependency on car use leads to traffic congestion, pollution, and physical inactivity, which impose high direct and indirect costs on society. Promoting walking and cycling has been recognised as one of the means of mitigating such negative effects. Various approaches have been taken to enhance walking and cycling levels and to reduce the use of automobiles. This paper examines the effectiveness of infrastructure interventions in promoting walking and cycling for transport. Two related sets of panel data, covering elapsed time periods of one and two years, were analysed to track changes in travel behaviour following provision of new walking and cycling infrastructure so that modal shift from private car use to walking and cycling can be investigated. Two types of exposure measures were tested: distance from the infrastructure (a measure of potential usage), and actual usage of the infrastructure. Only the latter measure was statistically significantly associated with modal shift. This in turn suggested that infrastructure provision was not a sufficient condition for modal shift, but may have been a necessary condition. Along with the use of new infrastructure, the loss of employment, higher education, being male and being part of the ethnic majority were consistently found to be significantly and positively associated with modal shift towards walking and cycling. The findings of this study support the construction of walking and cycling routes, but also suggest that such infrastructure alone may not be enough to promote active travel.This paper was written on behalf of the iConnect consortium (www.iconnect.ac.uk; Christian Brand, Fiona Bull, Ashley Cooper, Andy Day, Nanette Mutrie, David Ogilvie, Jane Powell, John Preston and Harry Rutter). The iConnect consortium was funded by the Engineering and Physical Sciences Research Council (Grant reference EP/G00059X/1) and David Ogilvie is also supported by the Medical Research Council [Unit Programme number MC_UP_12015/6] and the Centre for Diet and Activity Research (CEDAR), a UKCRC Public Health Research Centre of Excellence. We thank the survey participants for their time and the consortium manager Karen Ghali for managing data collection

Prostate cancer in Asia: a collaborative report

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The H.E.S.S. extragalactic sky

The H.E.S.S. Cherenkov telescope array, located on the southern hemisphere in Namibia, studies very high energy (VHE; E>100 GeV) gamma-ray emission from astrophysical objects. During its successful operations since 2002 more than 80 galactic and extra-galactic gamma-ray sources have been discovered. H.E.S.S. devotes over 400 hours of observation time per year to the observation of extra-galactic sources resulting in the discovery of several new sources, mostly AGNs, and in exciting physics results e.g. the discovery of very rapid variability during extreme flux outbursts of PKS 2155-304, stringent limits on the density of the extragalactic background light (EBL) in the near-infrared derived from the energy spectra of distant sources, or the discovery of short-term variability in the VHE emission from the radio galaxy M 87. With the recent launch of the Fermi satellite in 2008 new insights into the physics of AGNs at GeV energies emerged, leading to the discovery of several new extragalactic VHE sources. Multi-wavelength observations prove to be a powerful tool to investigate the production mechanism for VHE emission in AGNs. Here, new results from H.E.S.S. observations of extragalactic sources will be presented and their implications for the physics of these sources will be discussed.Comment: 8 pages, 6 figures, invited review talk, in the proceedings of the "International Workshop on Beamed and Unbeamed Gamma-Rays from Galaxies" 11-15 April 2011, Lapland Hotel Olos, Muonio, Finland, Journal of Physics: Conference Series Volume 355, 201

POSTNATAL BRAIN DYSMORPHOLOGY INDUCED BY PRENATAL ALCOHOL EXPOSURE: A PRECLINICAL MRI STUDY

poster abstractBrain dysmorphology is one of the most critical features of Fetal Alcohol Spectrum Disorders (FASD). This study was designed to use high resolution preclinical MRI system to compare the brain structures between alcohol exposed C57BL/6 mice with control. The objective is to examine how alcohol affects a dose- and timing-dependent brain dysmorphology during development comparable to that of human FASD. Three treated groups, ALC (pre- and pregnancy alcohol with 4.2 % (v/v) alcohol liquid), PF (pre alcohol and a calorically matched liquid pregnancy diet), and CHOW (ad lib chow/water), were examined. Mouse heads were imaged using 9.4T preclinical MRI system with 3D gradient echo (GRE) sequence to acquire volumetric images with voxel size as low as 40 microns. Whole brain, olfactory bulbs, cortex, hypothalamus, and cerebellum were segmented and the volumes were calculated. Data was examined by ANOVA followed with paired comparison between treatment groups to test the effect of prenatal alcohol exposure. ALC group had shown consistently smaller mean volumes of difference brain regions than the other two groups. Volume of total brain, olfactory bulbs and cerebellum were observed to be significantly different for ALC compared to PF pups. This indicated that prenatal alcohol exposure caused retarded fetal brain development. Comparing PF with CHOW pups, only cerebellum volume was observed to be significantly different. For cortex volume, no significant difference was shown for any pairwise comparison. These results suggest that alcohol effect contribute to brain dysmorphology, and match with our previous craniofacial dysmorphology study. This could be important to assist in the understanding of clinical variants of human FASD patients in brain dysmorphology

Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study

BACKGROUND: C-reactive protein (CRP) is associated with immune, cardiometabolic, and psychiatric traits and diseases. Yet it is inconclusive whether these associations are causal. METHODS AND FINDINGS: We performed Mendelian randomization (MR) analyses using two genetic risk scores (GRSs) as instrumental variables (IVs). The first GRS consisted of four single nucleotide polymorphisms (SNPs) in the CRP gene (GRSCRP), and the second consisted of 18 SNPs that were significantly associated with CRP levels in the largest genome-wide association study (GWAS) to date (GRSGWAS). To optimize power, we used summary statistics from GWAS consortia and tested the association of these two GRSs with 32 complex somatic and psychiatric outcomes, with up to 123,865 participants per outcome from populations of European ancestry. We performed heterogeneity tests to disentangle the pleiotropic effect of IVs. A Bonferroni-corrected significance level of less than 0.0016 was considered statistically significant. An observed p-value equal to or less than 0.05 was considered nominally significant evidence for a potential causal association, yet to be confirmed. The strengths (F-statistics) of the IVs were 31.92-3,761.29 and 82.32-9,403.21 for GRSCRP and GRSGWAS, respectively. CRP GRSGWAS showed a statistically significant protective relationship of a 10% genetically elevated CRP level with the risk of schizophrenia (odds ratio [OR] 0.86 [95% CI 0.79-0.94]; p < 0.001). We validated this finding with individual-level genotype data from the schizophrenia GWAS (OR 0.96 [95% CI 0.94-0.98]; p < 1.72 × 10-6). Further, we found that a standardized CRP polygenic risk score (CRPPRS) at p-value thresholds of 1 × 10-4, 0.001, 0.01, 0.05, and 0.1 using individual-level data also showed a protective effect (OR < 1.00) against schizophrenia; the first CRPPRS (built of SNPs with p < 1 × 10-4) showed a statistically significant (p < 2.45 × 10-4) protective effect with an OR of 0.97 (95% CI 0.95-0.99). The CRP GRSGWAS showed that a 10% increase in genetically determined CRP level was significantly associated with coronary artery disease (OR 0.88 [95% CI 0.84-0.94]; p < 2.4 × 10-5) and was nominally associated with the risk of inflammatory bowel disease (OR 0.85 [95% CI 0.74-0.98]; p < 0.03), Crohn disease (OR 0.81 [95% CI 0.70-0.94]; p < 0.005), psoriatic arthritis (OR 1.36 [95% CI 1.00-1.84]; p < 0.049), knee osteoarthritis (OR 1.17 [95% CI 1.01-1.36]; p < 0.04), and bipolar disorder (OR 1.21 [95% CI 1.05-1.40]; p < 0.007) and with an increase of 0.72 (95% CI 0.11-1.34; p < 0.02) mm Hg in systolic blood pressure, 0.45 (95% CI 0.06-0.84; p < 0.02) mm Hg in diastolic blood pressure, 0.01 ml/min/1.73 m2 (95% CI 0.003-0.02; p < 0.005) in estimated glomerular filtration rate from serum creatinine, 0.01 g/dl (95% CI 0.0004-0.02; p < 0.04) in serum albumin level, and 0.03 g/dl (95% CI 0.008-0.05; p < 0.009) in serum protein level. However, after adjustment for heterogeneity, neither GRS showed a significant effect of CRP level (at p < 0.0016) on any of these outcomes, including coronary artery disease, nor on the other 20 complex outcomes studied. Our study has two potential limitations: the limited variance explained by our genetic instruments modeling CRP levels in blood and the unobserved bias introduced by the use of summary statistics in our MR analyses. CONCLUSIONS: Genetically elevated CRP levels showed a significant potentially protective causal relationship with risk of schizophrenia. We observed nominal evidence at an observed p < 0.05 using either GRSCRP or GRSGWAS-with persistence after correction for heterogeneity-for a causal relationship of elevated CRP levels with psoriatic osteoarthritis, rheumatoid arthritis, knee osteoarthritis, systolic blood pressure, diastolic blood pressure, serum albumin, and bipolar disorder. These associations remain yet to be confirmed. We cannot verify any causal effect of CRP level on any of the other common somatic and neuropsychiatric outcomes investigated in the present study. This implies that interventions that lower CRP level are unlikely to result in decreased risk for the majority of common complex outcomes

Gamma-ray signatures of cosmic ray acceleration, propagation, and confinement in the era of CTA

Galactic cosmic rays are commonly believed to be accelerated at supernova remnants via diffusive shock acceleration. Despite the popularity of this idea, a conclusive proof for its validity is still missing. Gamma-ray astronomy provides us with a powerful tool to tackle this problem, because gamma rays are produced during cosmic ray interactions with the ambient gas. The detection of gamma rays from several supernova remnants is encouraging, but still does not constitute a proof of the scenario, the main problem being the difficulty in disentangling the hadronic and leptonic contributions to the emission. Once released by their sources, cosmic rays diffuse in the interstellar medium, and finally escape from the Galaxy. The diffuse gamma-ray emission from the Galactic disk, as well as the gamma-ray emission detected from a few galaxies is largely due to the interactions of cosmic rays in the interstellar medium. On much larger scales, cosmic rays are also expected to permeate the intracluster medium, since they can be confined and accumulated within clusters of galaxies for cosmological times. Thus, the detection of gamma rays from clusters of galaxies, or even upper limits on their emission, will allow us to constrain the cosmic ray output of the sources they contain, such as normal galaxies, AGNs, and cosmological shocks. In this paper, we describe the impact that the Cherenkov Telescope Array, a future ground-based facility for very-high energy gamma-ray astronomy, is expected to have in this field of research.Comment: accepted to Astroparticle Physics, special issue on Physics with the Cherenkov Telescope Arra

Repeatability of quantitative18F-FLT uptake measurements in solid tumors: an individual patient data multi-center meta-analysis

INTRODUCTION: 3'-deoxy-3'-[18F]fluorothymidine (18F-FLT) positron emission tomography (PET) provides a non-invasive method to assess cellular proliferation and response to antitumor therapy. Quantitative18F-FLT uptake metrics are being used for evaluation of proliferative response in investigational setting, however multi-center repeatability needs to be established. The aim of this study was to determine the repeatability of18F-FLT tumor uptake metrics by re-analyzing individual patient data from previously published reports using the same tumor segmentation method and repeatability metrics across cohorts. METHODS: A systematic search in PubMed, EMBASE.com and the Cochrane Library from inception-October 2016 yielded five18F-FLT repeatability cohorts in solid tumors.18F-FLT avid lesions were delineated using a 50% isocontour adapted for local background on test and retest scans. SUVmax, SUVmean, SUVpeak, proliferative volume and total lesion uptake (TLU) were calculated. Repeatability was assessed using the repeatability coefficient (RC = 1.96 × SD of test-retest differences), linear regression analysis, and the intra-class correlation coefficient (ICC). The impact of different lesion selection criteria was also evaluated. RESULTS: Images from four cohorts containing 30 patients with 52 lesions were obtained and analyzed (ten in breast cancer, nine in head and neck squamous cell carcinoma, and 33 in non-small cell lung cancer patients). A good correlation was found between test-retest data for all18F-FLT uptake metrics (R2 ≥ 0.93; ICC ≥ 0.96). Best repeatability was found for SUVpeak(RC: 23.1%), without significant differences in RC between different SUV metrics. Repeatability of proliferative volume (RC: 36.0%) and TLU (RC: 36.4%) was worse than SUV. Lesion selection methods based on SUVmax ≥ 4.0 improved the repeatability of volumetric metrics (RC: 26-28%), but did not affect the repeatability of SUV metrics. CONCLUSIONS: In multi-center studies, differences ≥ 25% in18F-FLT SUV metrics likely represent a true change in tumor uptake. Larger differences are required for FLT metrics comprising volume estimates when no lesion selection criteria are applied

Identification of a novel protein containing two C2 domains selectively expressed in the rat brain and kidney

AbstractWe have isolated and characterized a rat brain cDNA clone which encodes a new protein of 474 amino acids in length which contains two C2 domains structurally homologous to those present in synaptotagmins. The overall amino acid identity in C2 domains between this protein and the synaptotagmins is 36–44%. This protein also contains 3 putative consensus sequences for phosphorylation by cAMP-dependent protein kinase. RNA blot hybridization revealed a 3.0 kb transcript abundantly expressed only in the rat brain and the kidney. Thus, we called this brain/kidney protein (B/K). In situ hybridization and Northern blot analyses showed that the B/K transcript was found in forebrain including the olfactory bulb, cerebral cortex, hippocampus, and hypothalamus. In the kidney, high levels of B/K transcript were expressed in the papillary region of the inner medulla, the inner stripe of the outer medulla and the cortex. The selective expression in forebrain and kidney suggests that B/K may be involved in similar cAMP-dependent processes at these very different sites