14,201 research outputs found

    Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

    Get PDF
    Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

    The Spectroscopic Age of 47 Tuc

    Get PDF
    High signal-to-noise integrated spectra of the metal-rich globular cluster 47 Tuc, spanning the H-gamma(HR) and Fe4668 line indices, have been obtained. The combination of these indices has been suggested (Jones & Worthey 1995, ApJ, 446, L31) as the best available mechanism for cleanly separating the age-metallicity degeneracy which hampers the dating of distant, unresolved, elliptical galaxies. For the first time, we apply this technique to a nearby spheroidal system, 47 Tuc, for which independent ages, based upon more established methods, exist. Such an independent test of the technique's suitability has not been attempted before, but is an essential one before its application to more distant, unresolved, stellar populations can be considered valid. Because of its weak series of Balmer lines, relative to model spectra, our results imply a spectroscopic ``age'' for 47 Tuc well in excess of 20 Gyr, at odds with the colour-magnitude diagram age of 14+/-1 Gyr. The derived metal abundance, however, is consistent with the known value. Emission ``fill-in'' of the H-gamma line as the source of the discrepancy cannot be entirely excluded by existing data, although the observational constraints are restrictive.Comment: 17 pages, 4 figures, LaTeX, accepted for publication in The Astronomical Journal, also available at http://casa.colorado.edu/~bgibson/publications.htm

    Communication, Liminality, and Hope: The September 11th Missing Person Posters

    Full text link
    Immediately following the attacks on the World Trade Center on September 11, 2001, family and friends of victims missing in the towers began placing ‘‘Missing Person Posters’’ of their loved ones around New York City. In this paper, we argue that the posters represent a powerful response to a traumatic and in some ways unprecedented situation, a response that transformed the death of loved ones from a reality or future certainty into a probability made possible by the searchers’ desire, emotions, or imagination. We demonstrate how the posters, operating in the ‘‘subjunctive’’ voice, transformed the ‘‘ liminal’’ space between life and death and ‘‘haunted’’ onlookers, so that survivors and spectators alike could ponder the possibilities of a world that would ‘‘hopefully’’ turn out for the best. We also consider the implications of the posters for those who were unable to acknowledge the loss of their loved ones

    Association between a functional interleukin 6 receptor genetic variant and risk of depression and psychosis in a population-based birth cohort

    Get PDF
    OBJECTIVE: Interleukin 6 (IL-6) levels are commonly elevated in patients with depression and psychosis and in people who are at risk of developing these disorders. A common, functional variant in the IL6R gene (IL6R Asp358Ala; rs2228145 A > C) is known to dampen down inflammation by impairing IL6R signaling. We have examined the association of Asp358Ala with diagnosis of depression and psychosis, serum IL-6, CRP levels, and a number of risk factors commonly linked with inflammation, depression or psychosis. We predicted that if IL-6 were related to depression/psychosis risk causally, rather than due to confounding, Asp358Ala would be associated with risk of these disorders, serum IL-6, CRP levels, but not with any of the confounders. METHOD: We used data from the population-based ALSPAC birth cohort. Serum IL-6 and CRP levels were measured at age 9 years. Psychotic disorder, ICD-10 diagnosis of severe depressive episode, and total depression score were assessed at age 18 years. IL6R Asp358Ala was genotyped using the Illumina HumanHap550 quad genome-wide SNP genotyping platform. Risk factors assessed include sex, body mass index, social class, ethnicity, maternal education, birth weight, gestational age, maternal post-natal depression, childhood psychological and behavioral problems, and total IQ score. RESULTS: Asp358Ala was associated with decreased risk of severe depression and/or psychosis; adjusted odds ratio for those with CC, compared with AA, genotype was 0.38 (95% CI, 0.15-0.94). The variant was associated with increased serum IL-6 levels (P = 5.5 × 10-22) but decreased serum CRP levels (P = 3.5 × 10-5), consistent with an anti-inflammatory effect downstream of IL-6. Asp358Ala was not associated with total depression score. Asp358Ala was not associated with any of the other risk factors commonly linked with inflammation, depression or psychosis (all P > 0.20). CONCLUSIONS: The findings provide further evidence that the IL-6/IL6R pathways are involved in pathogenesis of severe depression and psychosis, and may be novel therapeutic targets. Previously reported associations between IL-6, depression and psychosis are unlikely to be fully explained by confounding. Based on a small number of cases, findings from the current study need replication in other samples

    Accuracy of methods for detecting an irregular pulse and suspected atrial fibrillation: a systematic review and meta-analysis

    Get PDF
    Background: Pulse palpation has been recommended as the first step of screening to detect atrial fibrillation. We aimed to determine and compare the accuracy of different methods for detecting pulse irregularities caused by atrial fibrillation. Methods: We systematically searched MEDLINE, EMBASE, CINAHL and LILACS until 16 March 2015. Two reviewers identified eligible studies, extracted data and appraised quality using the QUADAS-2 instrument. Meta-analysis, using the bivariate hierarchical random effects method, determined average operating points for sensitivities, specificities, positive and negative likelihood ratios (PLR, NLR); we constructed summary receiver operating characteristic plots. Results: Twenty-one studies investigated 39 interventions (n = 15,129 pulse assessments) for detecting atrial fibrillation. Compared to 12-lead electrocardiography (ECG) diagnosed atrial fibrillation, blood pressure monitors (BPMs; seven interventions) and non-12-lead ECGs (20 interventions) had the greatest accuracy for detecting pulse irregularities attributable to atrial fibrillation (BPM: sensitivity 0.98 (95% confidence interval (CI) 0.92–1.00), specificity 0.92 (95% CI 0.88–0.95), PLR 12.1 (95% CI 8.2–17.8) and NLR 0.02 (95% CI 0.00–0.09); non-12-lead ECG: sensitivity 0.91 (95% CI 0.86–0.94), specificity 0.95 (95% CI 0.92–0.97), PLR 20.1 (95% CI 12–33.7), NLR 0.09 (95% CI 0.06–0.14)). There were similar findings for smartphone applications (six interventions) although these studies were small in size. The sensitivity and specificity of pulse palpation (six interventions) were 0.92 (95% CI 0.85–0.96) and 0.82 (95% CI 0.76–0.88), respectively (PLR 5.2 (95% CI 3.8–7.2), NLR 0.1 (95% CI 0.05–0.18)). Conclusions: BPMs and non-12-lead ECG were most accurate for detecting pulse irregularities caused by atrial fibrillation; other technologies may therefore be pragmatic alternatives to pulse palpation for the first step of atrial fibrillation screening

    T2{}^2K2{}^2: The Twitter Top-K Keywords Benchmark

    Full text link
    Information retrieval from textual data focuses on the construction of vocabularies that contain weighted term tuples. Such vocabularies can then be exploited by various text analysis algorithms to extract new knowledge, e.g., top-k keywords, top-k documents, etc. Top-k keywords are casually used for various purposes, are often computed on-the-fly, and thus must be efficiently computed. To compare competing weighting schemes and database implementations, benchmarking is customary. To the best of our knowledge, no benchmark currently addresses these problems. Hence, in this paper, we present a top-k keywords benchmark, T2{}^2K2{}^2, which features a real tweet dataset and queries with various complexities and selectivities. T2{}^2K2{}^2 helps evaluate weighting schemes and database implementations in terms of computing performance. To illustrate T2{}^2K2{}^2's relevance and genericity, we successfully performed tests on the TF-IDF and Okapi BM25 weighting schemes, on one hand, and on different relational (Oracle, PostgreSQL) and document-oriented (MongoDB) database implementations, on the other hand

    Neisseria meningitidis serogroup C sepsis and septic arthritis in an HIV-positive man

    Get PDF
    A patient with well-controlled HIV-1 infection presented with fever and rigors, a widespread maculopapular rash, and severe generalised arthralgia. Sepsis of unknown aetiology was diagnosed, and treatment with broad-spectrum antimicrobials commenced. Following initial clinical improvement, a right knee septic arthritis developed. Microscopy and culture of the joint aspirate were negative for organisms but 16S rDNA PCR identified Neisseria meningitidis DNA, subsequently verified as capsular genogroup C, thus confirming a diagnosis of disseminated meningococcal sepsis with secondary septic arthritis
    corecore