Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Native and non-native speaker processing and production of contrastive focus prosody

Several studies have found that the presence of L+H* accent on a contrastive adjective assists native-speaking listeners in narrowing the referent of the noun following the adjective (e.g., Ito & Speer 2008, Weber et al. 2006). Our study addresses two questions: whether non-native speakers use prosodic cues in processing, as previous studies have shown for native speakers, and whether there is a relationship between the use of prosodic cues in processing and in production. Twenty-one Mandarin speakers living in the US and twenty-one native English speakers participated in two tasks investigating their processing and production of prosodic cues to contrastive focus. In the processing task, participants responded to the same recorded instruction containing an accented adjective in different contexts, in which the adjective was either contrastive (and therefore appropriately accented) or was repeated and followed by a contrasting noun, making focus accent on the adjective inappropriate. In the production task, participants guided an experimenter to place colored objects on a whiteboard, with some contexts designed to elicit contrastive focus. Overall results indicate that the Mandarin speakers made use of prosodic cues in both processing and production, although their focus prosody production differed from that of native speakers in several respects. Comparison of the results in the two experiments did not find strong correlations between processing and production. These results suggest that there is considerable heterogeneity even among native speakers in the use of prosodic cues in processing and production, and even those who do not use prosodic cues in processing may use them in production

Deep background subtraction of thermal and visible imagery for redestrian detection in videos

In this paper, we introduce an efficient framework to subtract the background from both visible and thermal imagery for pedestrians’ detection in the urban scene. We use a deep neural network (DNN) to train the background subtraction model. For the training of the DNN, we first generate an initial background map and then employ randomly 5% video frames, background map, and manually segmented ground truth. Then we apply a cognition-based post-processing to further smooth the foreground detection result. We evaluate our method against our previous work and 11 recently widely cited method on three challenge video series selected from a publicly available color-thermal benchmark dataset OCTBVS. Promising results have been shown that the proposed DNN-based approach can successfully detect the pedestrians with good shape in most scenes regardless of illuminate changes and occlusion problem

Increased COUP-TFII expression in adult hearts induces mitochondrial dysfunction resulting in heart failure

Mitochondrial dysfunction and metabolic remodelling are pivotal in the development of cardiomyopathy. Here, we show that myocardial COUP-TFII overexpression causes heart failure in mice, suggesting a causal effect of elevated COUP-TFII levels on development of dilated cardiomyopathy. COUP-TFII represses genes critical for mitochondrial electron transport chain enzyme activity, oxidative stress detoxification and mitochondrial dynamics, resulting in increased levels of reactive oxygen species and lower rates of oxygen consumption in mitochondria. COUP-TFII also suppresses the metabolic regulator PGC-1 network and decreases the expression of key glucose and lipid utilization genes, leading to a reduction in both glucose and oleate oxidation in the hearts. These data suggest that COUP-TFII affects mitochondrial function, impairs metabolic remodelling and has a key role in dilated cardiomyopathy. Last, COUP-TFII haploinsufficiency attenuates the progression of cardiac dilation and improves survival in a calcineurin transgenic mouse model, indicating that COUP-TFII may serve as a therapeutic target for the treatment of dilated cardiomyopathy

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Evadarstellung im Werk Gauguins : eine Auseinandersetzung mit Sünden und Tod

Die vorgelegte Arbeit behandelt Gauguins Selbstporträts und seine Darstellungen von Frauen, seinen Evas. Gauguin war sympathisch mit den europäischen Frauen; denn in seinem Auge litten sie unter den damaligen religiös-gesellschaftlichen Normen. Sie konnten keine genuine Liebe finden, welche ihr Leben glücklich machte. Andererseits sah er an dem Schicksal der Frauen zugleich sein eigenes Geschick. Deshalb lassen sich viele seiner Frauendarstellungen als Darstellungen von seinem Selbst interpretieren. Durch Analyse seiner Selbst- und Evadarstellungen gewinnt man Einsicht in Gauguins Inner- und Kunstwelt, nämlich seine inneren Konflikte, seine Entscheidung, zugunsten der Kunst auf ein bequemes Leben und damit auf eine glückliche Familie zu verzichten, seine Suche nach wahrer Liebe, die allerdings in sexuelle Ausschweifungen umschlug, und seine Auffassung von der Aufgabe der Kunst, welche eng mit Sexualität in Verbindung steht. Nicht zuletzt wird gezeigt, wie Gauguin, der von der christlichen-katholischen Religion tief geprägt war, mit Sünde und Tod rang

Association between receipt of overlapping opioid and benzodiazepine prescriptions from multiple prescribers and overdose risk.

Question: Is overdose risk increased when overlapping opioid and benzodiazepine prescriptions are written by multiple prescribers vs 1 prescriber? Findings: In this cohort study of 529 053 patients with private insurance or Medicare Advantage, overdose risk was increased 1.8-fold when opioid-benzodiazepine overlap involved prescriptions from multiple prescribers vs 1 prescriber. This increase remained statistically significant after adjusting for prescribing patterns, demographics, and comorbidities. Meaning: This study found that observed factors did not fully account for the association between receipt of overlapping opioid and benzodiazepine prescriptions from multiple prescribers and overdose risk. This finding suggests that other factors, such as poor care coordination, may play a role