ExPASy: SIB bioinformatics resource portal

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPAS

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

The majority of previously deposited X-ray structures can be improved by applying current refinement methods

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Evidence for neutral neutrino current coupling to right-handed quarks

Differential cross sections dσ/dy have been measured in semileptonic neutral- and charged-current reactions induced by neutrinos and antineutrinos. The comparison of the neutral- and the charged-current differential cross sections allows the direct determination of the chiral coupling of the neutral neutrino-antineutrino current to left- and right-handed quarks. The result, with a value of g_R^2 = 0.042±0.010, is the first direct determination, with a significance of more than four standard deviations, of a non-zero value of g_R

Experimental study of x-distributions in semileptonic neutral-current neutrino and antineutrino reactions

Using the CHARM detector 36 000 deep inelastic neutral-current reactions of neutrinos (and 2000 of antineutrinos) from the 160 GeV narrow-band beam were recorded. The differential cross section in the Bjorken scaling variable x was computed by unfolding the effects of limited acceptance and of resolution of the detector as well as the ambiguity of the energy of the incoming neutrinos (produced by π- or K-decay). Combining the results from the neutrino and antineutrino data, the structure functions F2 and xF3 and the antiquark momentum distribution measured via the NC coupling were determined. The distributions are in agreement with the corresponding CC distibutions. Comparisons with deep inelastic muon scattering confirm the universality of nuclear structure functions as probed by the weak and the electromagnetic currents

Numerous potentially functional but non-genic conserved sequences on human chromosome 21.

The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes

Experimental study of neutral-current and charged-current neutrino cross sections

Samples of 9200 muon-neutrino and 3800 muon-antineutrino interactions on nuclei were obtained with the fine-grain calorimeter of the CHARM Collaboration at the CERN 200 GeV narrow-band neutrino beam. The interactions were classified as either neutral-current or charged-current processes on an event-by-event basis. Neutral-current and charged-current cross sections in neutrino and antineutrino interactions are presented. From these results we deduce a statistically significant contribution of right-handed coupling to the neutral hadronic current, and a value of the electroweak mixing angle corresponding to sin2θ = 0.220 ± 0.014

The response and resolution of a fine-grain marble calorimeter for hadronic and electromagnetic showers

The response of the fine-grained CHARM target calorimeter built to detect ν interactions has been studied in π− and e− beams of 15–140 GeV. The development of hadronic and electromagnetic showers was studied and the precision of energy measurements determined. Methods used to measure the direction of particle showers and to distinguish electromagnetic from hadronic showers have been developed and the results are given