Maximum likelihood map making with the Laser Interferometer Space Antenna

International audienceGiven the recent advances in gravitational-wave detection technologies, the detection and characterization of gravitational-wave backgrounds (GWBs) with the Laser Interferometer Space Antenna (LISA) is a real possibility. To assess the abilities of the LISA satellite network to reconstruct anisotropies of different angular scales and in different directions on the sky, we develop a map-maker based on an optimal quadratic estimator. The resulting maps are maximum likelihood representations of the GWB intensity on the sky integrated over a broad range of frequencies. We test the algorithm by reconstructing known input maps with different input distributions and over different frequency ranges. We find that, in an optimal scenario of well understood noise and high frequency, high SNR signals, the maximum scales LISA may probe are ℓmax≲15. The map-maker also allows to test the directional dependence of LISA noise, providing insight on the directional sky sensitivity we may expect

neXtProt: a knowledge platform for human proteins

neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

Carrier Screening for Spinal Muscular Atrophy (SMA) in 107,611 Pregnant Women during the Period 2005–2009: A Prospective Population-Based Cohort Study

BACKGROUND: Spinal muscular atrophy (SMA) is the most common neuromuscular autosomal recessive disorder. The American College of Medical Genetics has recently recommended routine carrier screening for SMA because of the high carrier frequency (1 in 25-50) as well as the severity of that genetic disease. Large studies are needed to determine the feasibility, benefits, and costs of such a program. METHODS AND FINDINGS: This is a prospective population-based cohort study of 107,611 pregnant women from 25 counties in Taiwan conducted during the period January 2005 to June 2009. A three-stage screening program was used: (1) pregnant women were tested for SMA heterozygosity; (2) if the mother was determined to be heterozygous for SMA (carrier status), the paternal partner was then tested; (3) if both partners were SMA carriers, prenatal diagnostic testing was performed. During the study period, a total of 2,262 SMA carriers with one copy of the SMN1 gene were identified among the 107,611 pregnant women that were screened. The carrier rate was approximately 1 in 48 (2.10%). The negative predictive value of DHPLC coupled with MLPA was 99.87%. The combined method could detect approximately 94% of carriers because most of the cases resulted from a common single deletion event. In addition, 2,038 spouses were determined to be SMA carriers. Among those individuals, 47 couples were determined to be at high risk for having offspring with SMA. Prenatal diagnostic testing was performed in 43 pregnant women (91.49%) and SMA was diagnosed in 12 (27.91%) fetuses. The prevalence of SMA in our population was 1 in 8,968. CONCLUSION: The main benefit of SMA carrier screening is to reduce the burden associated with giving birth to an affected child. In this study, we determined the carrier frequency and genetic risk and provided carrier couples with genetic services, knowledge, and genetic counseling

The Next Generation Global Gravitational Wave Observatory: The Science Book

The next generation of ground-based gravitational-wave detectors will observe coalescences of black holes and neutron stars throughout the cosmos, thousands of them with exceptional fidelity. The Science Book is the result of a 3-year effort to study the science capabilities of networks of next generation detectors. Such networks would make it possible to address unsolved problems in numerous areas of physics and astronomy, from Cosmology to Beyond the Standard Model of particle physics, and how they could provide insights into workings of strongly gravitating systems, astrophysics of compact objects and the nature of dense matter. It is inevitable that observatories of such depth and finesse will make new discoveries inaccessible to other windows of observation. In addition to laying out the rich science potential of the next generation of detectors, this report provides specific science targets in five different areas in physics and astronomy and the sensitivity requirements to accomplish those science goals. This report is the second in a six part series of reports by the GWIC 3G Subcommittee: i) Expanding the Reach of Gravitational Wave Observatories to the Edge of the Universe, ii) The Next Generation Global Gravitational Wave Observatory: The Science Book (this report), iii) 3G R&D: R&D for the Next Generation of Ground-based Gravitational Wave Detectors, iv) Gravitational Wave Data Analysis: Computing Challenges in the 3G Era, v) Future Ground-based Gravitational-wave Observatories: Synergies with Other Scientific Communities, and vi) An Exploration of Possible Governance Models for the Future Global Gravitational-Wave Observatory Network

Conserved Genes Act as Modifiers of Invertebrate SMN Loss of Function Defects

Spinal Muscular Atrophy (SMA) is caused by diminished function of the Survival of Motor Neuron (SMN) protein, but the molecular pathways critical for SMA pathology remain elusive. We have used genetic approaches in invertebrate models to identify conserved SMN loss of function modifier genes. Drosophila melanogaster and Caenorhabditis elegans each have a single gene encoding a protein orthologous to human SMN; diminished function of these invertebrate genes causes lethality and neuromuscular defects. To find genes that modulate SMN function defects across species, two approaches were used. First, a genome-wide RNAi screen for C. elegans SMN modifier genes was undertaken, yielding four genes. Second, we tested the conservation of modifier gene function across species; genes identified in one invertebrate model were tested for function in the other invertebrate model. Drosophila orthologs of two genes, which were identified originally in C. elegans, modified Drosophila SMN loss of function defects. C. elegans orthologs of twelve genes, which were originally identified in a previous Drosophila screen, modified C. elegans SMN loss of function defects. Bioinformatic analysis of the conserved, cross-species, modifier genes suggests that conserved cellular pathways, specifically endocytosis and mRNA regulation, act as critical genetic modifiers of SMN loss of function defects across species

Planck 2015 results. XIV. Dark energy and modified gravity

We study the implications of Planck data for models of dark energy (DE) and modified gravity (MG), beyond the cosmological constant scenario. We start with cases where the DE only directly affects the background evolution, considering Taylor expansions of the equation of state, principal component analysis and parameterizations related to the potential of a minimally coupled DE scalar field. When estimating the density of DE at early times, we significantly improve present constraints. We then move to general parameterizations of the DE or MG perturbations that encompass both effective field theories and the phenomenology of gravitational potentials in MG models. Lastly, we test a range of specific models, such as k-essence, f(R) theories and coupled DE. In addition to the latest Planck data, for our main analyses we use baryonic acoustic oscillations, type-Ia supernovae and local measurements of the Hubble constant. We further show the impact of measurements of the cosmological perturbations, such as redshift-space distortions and weak gravitational lensing. These additional probes are important tools for testing MG models and for breaking degeneracies that are still present in the combination of Planck and background data sets. All results that include only background parameterizations are in agreement with LCDM. When testing models that also change perturbations (even when the background is fixed to LCDM), some tensions appear in a few scenarios: the maximum one found is \sim 2 sigma for Planck TT+lowP when parameterizing observables related to the gravitational potentials with a chosen time dependence; the tension increases to at most 3 sigma when external data sets are included. It however disappears when including CMB lensing