bluuebunny/crossref_metadata_2025_split huggingface dataset:
ARBitrator: a software pipeline for on-demand retrieval of auto-curatednifHsequences from GenBank
Authors: Heller Philip , Tripp H. James , Turk-Kubo Kendra , Zehr Jonathan P. 
Published: July 2014

AbstractMotivation: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N 2 ) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information’s GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank’s structure and tools are not conducive to searching solely by function. For some genes, such as the nifH gene commonly used to assess community potential for N 2 fixation, manual collection and curation are becoming intractable because of the large number of sequences in GenBank and the large number of highly similar paralogues. If analysis is to keep pace with sequence discovery, an automated retrieval and curation system is necessary.Results: ARBitrator uses a two-step process composed of a broad collection of potential homologues followed by screening with a best hit strategy to conserved domains. 34 420 nifH sequences were identified in GenBank as of November 20, 2012. The false-positive rate is ∼0.033%. ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted for other genes.Availability and implementation: Java source and executable code are freely available to non-commercial users at http://pmc.ucsc.edu/∼wwwzehr/research/database/ .Contact: zehrj@ucsc.eduSupplementary information: Supplementary information is available at Bioinformatics online.
RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy
Authors: Lo Kitty K. , Boustred Christopher , Chitty Lyn S. , Plagnol Vincent 
Published: July 2014

Abstract
Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting.
Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html .
Contact: kitty.lo@ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
Authors: Patel Hitesh , Grüning Björn A. , Günther Stefan , Merfort Irmgard 
Published: July 2014

Abstract
Summary : Conserved water molecules play a crucial role in protein structure, stabilization of secondary structure, protein activity, flexibility and ligand binding. Clustering of water molecules in superimposed protein structures, obtained by X-ray crystallography at high resolution, is an established method to identify consensus water molecules in all known protein structures of the same family. PyWATER is an easy-to-use PyMOL plug-in and identifies conserved water molecules in the protein structure of interest. PyWATER can be installed via the user interface of PyMOL. No programming or command-line knowledge is required for its use.
Availability and Implementation : PyWATER and a tutorial are available at https://github.com/hiteshpatel379/PyWATER . PyMOL is available at http://www.pymol.org/ or http://sourceforge.net/projects/pymol/ .
Contact : stefan.guenther@pharmazie.uni-freiburg.de
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
Authors: Güell Marc , Yang Luhan , Church George M. 
Published: July 2014

Abstract
Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility.
We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information.
Availability and implementation: CRISPR-GA Web is available at http://crispr-ga.net . Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html
Contact: mguell@genetics.med.harvard.edu
Distribution of benthic megafauna in the Barents Sea: baseline for an ecosystem approach to management
Authors: Jørgensen Lis Lindal , Ljubin Pavel , Skjoldal Hein Rune , Ingvaldsen Randi B. , Anisimova Natalia , Manushin Igor 
Published: July 2014

AbstractBenthos plays a significant role as substrate, refuge from predation and food for a wide variety of fish and invertebrates of all life stages and should therefore be considered in the ecosystem approach (EA) to management. Epibenthos from trawl catches, used in annual assessments of commercial fish stocks, was identified and measured on-board. The 2011 dataset present the baseline mapping for monitoring and included 354 taxa (218 to species level) analysed with multivariate statistical methods. This revealed four main megafaunal regions: southwestern (SW), banks/slopes in southeast and west (SEW), northwestern (NW), and northeastern (NE) which were significantly related to depth, temperature, salinity, and number of ice-days. The SW region was dominated by filter-feeders (sponges) in the inflow area of warm Atlantic water while the deeper trenches had a detritivorous fauna (echinoderms). In the SEW region, predators (sea stars, anemones and snow crabs) prevailed together with filtrating species (sea cucumber and bivalves) within a mosaic of banks and slopes. Plankton-feeding brittlestars were common in the NW and NE region, but with increasing snow crab population in NE. Climate change, potentially expanding trawling activity, and increasing snow and king crab populations might all have impacts on the benthos. Benthos should therefore be a part of an integrated assessment of a changing sea, and national agencies might consider adding benthic taxonomic expertise on-board scientific research vessels to identify the invertebrate “by-catch” as part of routine trawl surveys.
Lyman edges in supermassive black hole binaries
Authors: Generozov Aleksey , Haiman Zoltán 
Published: July 2014

Abstract
We propose a new spectral signature for supermassive black hole binaries (SMBHBs) with circumbinary gas discs: a sharp drop in flux bluewards of the Lyman limit. A prominent edge is produced if the gas dominating the emission in the Lyman continuum region of the spectrum is sufficiently cold (T ≲ 20 000 K) to contain significant neutral hydrogen. Circumbinary discs may be in this regime if the binary torques open a central cavity in the disc and clear most of the hot gas from the inner region, and if any residual UV emission from the individual BHs is either dim or intermittent. We model the vertical structure and spectra of circumbinary discs using the radiative transfer code tlusty, and identify the range of BH masses and binary separations producing a Lyman edge. We find that compact supermassive (M ≳ 108 M⊙) binaries with orbital periods of ∼0.1–10 yr, whose gravitational waves are expected to be detectable by pulsar timing arrays, could have prominent Lyman edges. Such strong spectral edge features are not typically present in AGN spectra and could serve as corroborating evidence for the presence of an SMBHB.
Variations in the initial mass function in early-type galaxies: a critical comparison between dynamical and spectroscopic results
Authors: Smith Russell J. 
Published: July 2014

Abstract
I present a comparison between published dynamical (ATLAS3D) and spectroscopic (Conroy & van Dokkum) constraints on the stellar initial mass function (IMF) in early-type galaxies, using the 34 galaxies in common between the two works. Both studies infer an average IMF mass factor α (the stellar mass relative to a Kroupa-IMF population of similar age and metallicity) greater than unity, i.e. both methods favour an IMF which is heavier than that of the Milky Way, on average over the sample. However, on a galaxy-by-galaxy basis, there is no correlation between α inferred from the two approaches. I investigate how the two estimates of α are correlated systematically with the galaxy velocity dispersion, σ, and with the Mg/Fe abundance ratio. The spectroscopic method, based on the strengths of metal absorption lines, yields a correlation only with metal abundance ratios: at fixed Mg/Fe, there is no residual correlation with σ. The dynamical method, applied to exactly the same galaxy sample, yields the opposite result: the IMF variation correlates only with dynamics, with no residual correlation with Mg/Fe after controlling for σ. Hence, although both methods indicate a heavy IMF on average in ellipticals, they lead to incompatible results for the systematic trends, when applied to the same set of galaxies. The sense of the disagreement could suggest that one (or both) of the methods has not accounted fully for the main confounding factors, i.e. element abundance ratios or dark matter contributions. Alternatively, the poor agreement might indicate additional variation in the detailed shape of the IMF, beyond what can currently be inferred from the spectroscopic features.
Robustness of H0 determination at intermediate redshifts
Authors: Holanda R. F. L. , Busti V. C. , Pordeus da Silva G. 
Published: July 2014

Abstract
The most recent Hubble constant (H0) estimates from local methods (z ≪ 1), H0 = 73.8 ± 2.4 km s−1 Mpc−1, and the one from high redshifts, H0 = 67.3 ± 1.2 km s−1 Mpc−1, are discrepant at 2.4σ confidence level. Within this context, Lima & Cunha (LC) derived a new determination of H0 using four cosmic probes at intermediate redshifts (0.1 &lt; z &lt; 1.8) based on the so-called flat ΛCDM model. They obtained H0 = 74.1 ± 2.2 km s−1 Mpc−1, in full agreement with local measurements. In this Letter, we explore the robustness of the LC result searching for systematic errors and its dependence from the cosmological model used. We find that the H0 value from this joint analysis is very weakly dependent on the underlying cosmological model, but the morphology adopted to infer the distance to galaxy clusters changes the result sizeably, being the main source of systematic errors. Therefore, a better understanding of the cluster morphology is paramount to transform this method into a powerful cross-check for H0.
Kinematical fingerprints of star cluster early dynamical evolution
Authors: Vesperini Enrico , Varri Anna Lisa , McMillan Stephen L. W. , Zepf Stephen E. 
Published: July 2014

Abstract
We study the effects of the external tidal field on the violent relaxation phase of star clusters dynamical evolution, with particular attention to the kinematical properties of the equilibrium configurations emerging at the end of this phase. We show that star clusters undergoing the process of violent relaxation in the tidal field of their host galaxy can acquire significant internal differential rotation and are characterized by a distinctive radial variation of the velocity anisotropy. These kinematical properties are the result of the symmetry breaking introduced by the external tidal field in the collapse phase and of the action of the Coriolis force on the orbit of the stars. The resulting equilibrium configurations are characterized by differential rotation, with a peak located between one and two half-mass radii. As for the anisotropy, similar to clusters evolving in isolation, the systems explored in this Letter are characterized by an inner isotropic core, followed by a region of increasing radial anisotropy. However, for systems evolving in an external tidal field, the degree of radial anisotropy reaches a maximum in the cluster intermediate regions and then progressively decreases, with the cluster outermost regions being characterized by isotropy or a mild tangential anisotropy. Young or old but less-relaxed dynamically young star clusters may keep memory of these kinematical fingerprints of their early dynamical evolution.
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm
Authors: Lomsadze Alexandre , Burns Paul D. , Borodovsky Mark 
Published: July 2014

Abstract
We present a new approach to automatic training of a eukaryotic ab initio gene finding algorithm. With the advent of Next-Generation Sequencing, automatic training has become paramount, allowing genome annotation pipelines to keep pace with the speed of genome sequencing. Earlier we developed GeneMark-ES, currently the only gene finding algorithm for eukaryotic genomes that performs automatic training in unsupervised ab initio mode. The new algorithm, GeneMark-ET augments GeneMark-ES with a novel method that integrates RNA-Seq read alignments into the self-training procedure. Use of ‘assembled’ RNA-Seq transcripts is far from trivial; significant error rate of assembly was revealed in recent assessments. We demonstrated in computational experiments that the proposed method of incorporation of ‘unassembled’ RNA-Seq reads improves the accuracy of gene prediction; particularly, for the 1.3 GB genome of Aedes aegypti the mean value of prediction Sensitivity and Specificity at the gene level increased over GeneMark-ES by 24.5%. In the current surge of genomic data when the need for accurate sequence annotation is higher than ever, GeneMark-ET will be a valuable addition to the narrow arsenal of automatic gene prediction tools.
Objective and Subjective Burden of Informal Caregivers 4 Years After a Severe Traumatic Brain Injury: Results From the PariS-TBI Study
Authors: Bayen Eléonore , Jourdan Claire , Ghout Idir , Darnoux Emmanuelle , Azerad Sylvie , Vallat-Azouvi Claire , Weiss Jean-Jacques , Aegerter Philippe , Pradat-Diehl Pascale , Joël Marie-Eve , Azouvi Philippe 
Published: July 2014

Objective:
Prospective assessment of informal caregiver (IC) burden 4 years after the traumatic brain injury of a relative.

Setting:
Longitudinal cohort study (metropolitan Paris, France).

Participants:
Home dwelling adults (N = 98) with initially severe traumatic brain injury and their primary ICs.

Main Outcome Measures:
Informal caregiver objective burden (Resource Utilization in Dementia measuring Informal Care Time [ICT]), subjective burden (Zarit Burden Inventory), monetary self-valuation of ICT (Willingness-to-pay, Willingness-to-accept).

Results:
Informal caregivers were women (81%) assisting men (80%) of mean age of 37 years. Fifty-five ICs reported no objective burden (ICT = 0) and no/low subjective burden (average Zarit Burden Inventory = 12.1). Forty-three ICs reported a major objective burden (average ICT = 5.6 h/d) and a moderate/severe subjective burden (average Zarit Burden Inventory = 30.3). In multivariate analyses, higher objective burden was associated with poorer Glasgow Outcome Scale-Extended scores, with more severe cognitive disorders (Neurobehavioral Rating Scale-revised) and with no coresidency status; higher subjective burden was associated with poorer Glasgow Outcome Scale-Extended scores, more Neurobehavioral Rating Scale-revised disorders, drug-alcohol abuse, and involvement in litigation. Economic valuation showed that on average, ICs did not value their ICT as free and preferred to pay a mean Willingness-to-pay = €17 per hour to be replaced instead of being paid for providing care themselves (Willingness-to-accept = €12).

Conclusion:
Four years after a severe traumatic brain injury, 44% of ICs experienced a heavy multidimensional burden.
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
Authors: Andersson Robin , Andersen Peter Refsing , Valen Eivind , Core Leighton J. , Bornholdt Jette , Boyd Mette , Jensen Torben Heick , Sandelin Albin 
Published: July 2014

ABSTRACTMammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. While recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.
A New LxxxA Motif in the Transmembrane Helix3 of Maize Aquaporins Belonging to the Plasma Membrane Intrinsic Protein PIP2 Group Is Required for Their Trafficking to the Plasma Membrane
Authors: Chevalier Adrien S. , Bienert Gerd Patrick , Chaumont François 
Published: July 2014

Abstract
Aquaporins play important roles in maintaining plant water status under challenging environments. The regulation of aquaporin density in cell membranes is essential to control transcellular water flows. This work focuses on the maize (Zea mays) plasma membrane intrinsic protein (ZmPIP) aquaporin subfamily, which is divided into two sequence-related groups (ZmPIP1s and ZmPIP2s). When expressed alone in mesophyll protoplasts, ZmPIP2s are efficiently targeted to the plasma membrane, whereas ZmPIP1s are retained in the endoplasmic reticulum (ER). A protein domain-swapping approach was utilized to demonstrate that the transmembrane domain3 (TM3), together with the previously identified N-terminal ER export diacidic motif, account for the differential localization of these proteins. In addition to protoplasts, leaf epidermal cells transiently transformed by biolistic particle delivery were used to confirm and refine these results. By generating artificial proteins consisting of a single transmembrane domain, we demonstrated that the TM3 of ZmPIP1;2 or ZmPIP2;5 discriminates between ER and plasma membrane localization, respectively. More specifically, a new LxxxA motif in the TM3 of ZmPIP2;5, which is highly conserved in plant PIP2s, was shown to regulate its anterograde routing along the secretory pathway, particularly its export from the ER.
Water Balance, Hormone Homeostasis, and Sugar Signaling Are All Involved in Tomato Resistance toTomato Yellow Leaf Curl Virus
Authors: Sade Dagan , Sade Nir , Shriki Oz , Lerner Stephen , Gebremedhin Alem , Karavani Asaf , Brotman Yariv , Osorio Sonia , Fernie Alisdair R. , Willmitzer Lothar , Czosnek Henryk , Moshelion Menachem 
Published: July 2014

AbstractVacuolar water movement is largely controlled by membrane channels called tonoplast-intrinsic aquaporins (TIP-AQPs). Some TIP-AQP genes, such as TIP2;2 and TIP1;1, are up-regulated upon exposure to biotic stress. Moreover, TIP1;1 transcript levels are higher in leaves of a tomato (Solanum lycopersicum) line resistant to Tomato yellow leaf curl virus (TYLCV) than in those of a susceptible line with a similar genetic background. Virus-induced silencing of TIP1;1 in the tomato resistant line and the use of an Arabidopsis (Arabidopsis thaliana) tip1;1 null mutant showed that resistance to TYLCV is severely compromised in the absence of TIP1:1. Constitutive expression of tomato TIP2;2 in transgenic TYLCV-susceptible tomato and Arabidopsis plants was correlated with increased TYLCV resistance, increased transpiration, decreased abscisic acid levels, and increased salicylic acid levels at the early stages of infection. We propose that TIP-AQPs affect the induction of leaf abscisic acid, which leads to increased levels of transpiration and gas exchange, as well as better salicylic acid signaling.
Inferring model‐based probability of occurrence from preferentially sampled data with uncertain absences using expert knowledge
Authors: Manceur Ameur M. , Kühn Ingolf 
Published: July 2014

Summary

For several data bases in species distribution modelling (SDM), presences are known but absences are uncertain and can be non‐detections. The environment influences both the non‐detections and the species occurrences (preferential sampling), affecting model predictions.

The objective is to estimate model‐based probability of occurrence when absences are uncertain and sampling is preferential. Our Bayesian image restoration (BIR) model has an environmental, spatial and non‐detection component. The latter is based on the number of ‘control species’ (selected by expert knowledge to have wide geographic range and occupy several habitats) observed. Control species are assumed present in all grid cells so an observed absence of the control species is a non‐detection.

The observed absence of a focal species is likely a non‐detection when the environment is conducive, the focal species was observed in the neighbourhood, and the number of control species is small.

Simulating an artificial species (true prevalence 0·31) and preferential sampling (observed prevalence 0·18), the BIR modelled prevalence was 0·32 (0·30–0·34). The estimation was robust to failure of assumptions with a mis‐specified environmental model. The restored map was close to the true map, and the true realized niche of the species was inferred (with uncertainty). The link between the non‐detection and control species is crucial, and a sensitivity analysis is recommended.

BIR restored the simulated atlas map more accurately than a covariate adjustment method. When applied to the vascular plant Asarum europaeum L., BIR changed the interpretation. The uncertainty maps assisted decision‐making. A BIR implementation new to the SDM field is presented.

BIR using control species is most fruitfully applied at coarse scale and intermediate extent, with limited environmental extremes and sufficient expert knowledge (e.g. many Central European countries).

BIR is a framework, and we studied one implementation. Any proxy (road density, distance to city, direct expert knowledge, detectability traits, etc.) associated with non‐detection can be used so BIR can be applied in diverse settings. Including non‐detections reduces model indeterminacy but often requires expert knowledge. However, the benefits of using a priori knowledge and Bayesian estimation are expected to outweigh the risks of model‐based inference.