Protein interactions in human genetic diseases

A method is presented to identify residues that form part of an interaction interface, leading to the prediction that 1,428 OMIM mutations are related to an interaction defect

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

Dosage sensitivity is an important evolutionary force which impacts on gene dispensability and duplicability. The newly available data on human copy-number variation (CNV) allow an analysis of the most recent and ongoing evolution. Provided that heterozygous gene deletions and duplications actually change gene dosage, we expect to observe negative selection against CNVs encompassing dosage sensitive genes. In this study, we make use of several sources of population genetic data to identify selection on structural variations of dosage sensitive genes. We show that CNVs can directly affect expression levels of contained genes. We find that genes encoding members of protein complexes exhibit limited expression variation and overlap significantly with a manually derived set of dosage sensitive genes. We show that complexes and other dosage sensitive genes are underrepresented in CNV regions, with a particular bias against frequent variations and duplications. These results suggest that dosage sensitivity is a significant force of negative selection on regions of copy-number variation

Stretching Sentence-pair NLI Models to Reason over Long Documents and Clusters

Natural Language Inference (NLI) has been extensively studied by the NLP community as a framework for estimating the semantic relation between sentence pairs. While early work identified certain biases in NLI models, recent advancements in modeling and datasets demonstrated promising performance. In this work, we further explore the direct zero-shot applicability of NLI models to real applications, beyond the sentence-pair setting they were trained on. First, we analyze the robustness of these models to longer and out-of-domain inputs. Then, we develop new aggregation methods to allow operating over full documents, reaching state-of-the-art performance on the ContractNLI dataset. Interestingly, we find NLI scores to provide strong retrieval signals, leading to more relevant evidence extractions compared to common similarity-based methods. Finally, we go further and investigate whole document clusters to identify both discrepancies and consensus among sources. In a test case, we find real inconsistencies between Wikipedia pages in different languages about the same topic.Comment: Findings of EMNLP 202

Keep Your eye On The Girlie You Love / music by Ira Schuster; words by Howard Johnson, Alex Gerber, and .

Cover: a couple taking a stroll, while walking a pair of dogs; photo inset of Sophie Tucker; Publisher: Leo Feist Inc. (New York)https://egrove.olemiss.edu/sharris_c/1111/thumbnail.jp

The Anabolic Androgenic Steroid Fluoxymesterone Inhibits 11β-Hydroxysteroid Dehydrogenase 2-Dependent Glucocorticoid Inactivation

Anabolic androgenic steroids (AAS) are testosterone derivatives used either clinically, in elite sports, or for body shaping with the goal to increase muscle size and strength. Clinically developed compounds and nonclinically tested designer steroids often marketed as food supplements are widely used. Despite the considerable evidence for various adverse effects of AAS use, the underlying molecular mechanisms are insufficiently understood. Here, we investigated whether some AAS, as a result of a lack of target selectivity, might inhibit 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2)-dependent inactivation of glucocorticoids. Using recombinant human 11β-HSD2, we observed inhibitory effects for several AAS. Whereas oxymetholone, oxymesterone, danazol, and testosterone showed medium inhibitory potential, fluoxymesterone was a potent inhibitor of human 11β-HSD2 (half-maximal inhibitory concentration [IC50] of 60-100nM in cell lysates; IC50 of 160nM in intact SW-620, and 530nM in MCF-7 cells). Measurements with rat kidney microsomes and lysates of cells expressing recombinant mouse 11β-HSD2 revealed much weaker inhibition by the AAS tested, indicating that the adverse effects of AAS-dependent 11β-HSD2 inhibition cannot be investigated in rats and mice. Furthermore, we provide evidence that fluoxymesterone is metabolized to 11-oxofluoxymesterone by human 11β-HSD2. Structural modeling revealed similar binding modes for fluoxymesterone and cortisol, supporting a competitive mode of inhibition of 11β-HSD2-dependent cortisol oxidation by this AAS. No direct modulation of mineralocorticoid receptor (MR) function was observed. Thus, 11β-HSD2 inhibition by fluoxymesterone may cause cortisol-induced MR activation, thereby leading to electrolyte disturbances and contributing to the development of hypertension and cardiovascular diseas

Physical-preparation recommendations for elite rugby sevens performance

Rugby sevens, a sport new to the Olympics, features high-intensity intermittent running and contact efforts more than short match durations, normally 6 times across 2 to 3 d in a tournament format. Elite rugby sevens seasons often include over a dozen competitive tournaments over less than 9 months, demanding deliberate and careful training-stress balance and workload management alongside development of the necessary physical qualities required for competition. Focus on running and repeated power skills, strength, and match-specific conditioning capacities is advised. Partial taper approaches in combination with high-speed running (>5 m/s from GPS measures) before and between tournaments in succession may reduce injury rates and enhance performance. In a sport with substantial long-haul intercontinental travel and repetitive chronic load demands, management of logistics including nutrition and recovery is inclusive of the formula for success in the physical preparation of elite rugby sevens athletes

Deep Markov Random Field for Image Modeling

Markov Random Fields (MRFs), a formulation widely used in generative image modeling, have long been plagued by the lack of expressive power. This issue is primarily due to the fact that conventional MRFs formulations tend to use simplistic factors to capture local patterns. In this paper, we move beyond such limitations, and propose a novel MRF model that uses fully-connected neurons to express the complex interactions among pixels. Through theoretical analysis, we reveal an inherent connection between this model and recurrent neural networks, and thereon derive an approximated feed-forward network that couples multiple RNNs along opposite directions. This formulation combines the expressive power of deep neural networks and the cyclic dependency structure of MRF in a unified model, bringing the modeling capability to a new level. The feed-forward approximation also allows it to be efficiently learned from data. Experimental results on a variety of low-level vision tasks show notable improvement over state-of-the-arts.Comment: Accepted at ECCV 201

Prognostic Value of Different CMR-Based Techniques to Assess Left Ventricular Myocardial Strain in Takotsubo Syndrome

Cardiac magnetic resonance (CMR)-derived left ventricular (LV) global longitudinal strain (GLS) provides incremental prognostic information on various cardiovascular diseases but has not yet been investigated comprehensively in patients with Takotsubo syndrome (TS). This study evaluated the prognostic value of feature tracking (FT) GLS, tissue tracking (TT) GLS, and fast manual long axis strain (LAS) in 147 patients with TS, who underwent CMR at a median of 2 days after admission. Long-term mortality was assessed 3 years after the acute event. In contrast to LV ejection fraction and tissue characteristics, impaired FT-GLS, TT-GLS and fast manual LAS were associated with adverse outcome. The best cutoff points for the prediction of long-term mortality were similar with all three approaches: FT-GLS −11.28%, TT-GLS −11.45%, and fast manual LAS −10.86%. Long-term mortality rates were significantly higher in patients with FT-GLS > −11.28% (25.0% versus 9.8%; p = 0.029), TT-GLS > −11.45% (20.0% versus 5.4%; p = 0.016), and LAS > −10.86% (23.3% versus 6.6%; p = 0.014). However, in multivariable analysis, diabetes mellitus (p = 0.001), atrial fibrillation (p = 0.001), malignancy (p = 0.006), and physical triggers (p = 0.006) outperformed measures of myocardial strain and emerged as the strongest, independent predictors of long-term mortality in TS. In conclusion, CMR-based longitudinal strain provides valuable prognostic information in patients with TS, regardless of the utilized technique of assessment. Long-term mortality, however, is mainly determined by comorbidities

Pfam: clans, web tools and services

Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://pfam.cgb.ki.se/)