bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Is Really Behavioral in Behavioral Health Policy? And Does It Work?
Authors: Galizzi Matteo M. 
Published: January 2014

AbstractAcross health systems, there is increasing interest in applying behavioral economics insights to health policy challenges. Policy decision makers have recently discussed a range of diverse health policy interventions that are commonly brought together under a behavioral umbrella. These include randomized controlled trials, comparison portals, information labels, financial incentives, sin taxes, and nudges. A taxonomy is proposed to classify such behavioral interventions. In the context of risky health behavior, each cluster of policies is then scrutinized under two respects: (i) What are its genuinely behavioral insights? (ii) What evidence exists on its practical effectiveness? The discussion highlights the main challenges in drawing a clear mapping between how much each policy is behaviorally inspired and its effectiveness.
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data
Authors: Bao Lei , Pu Minya , Messer Karen 
Published: January 2014

Abstract
Motivation: Detection and quantification of the absolute DNA copy number alterations in tumor cells is challenging because the DNA specimen is extracted from a mixture of tumor and normal stromal cells. Estimates of tumor purity and ploidy are necessary to correctly infer copy number, and ploidy may itself be a prognostic factor in cancer progression. As deep sequencing of the exome or genome has become routine for characterization of tumor samples, in this work, we aim to develop a simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data.
Results: A simulation study shows that estimates have reasonable accuracy, and that the algorithm is robust against the presence of segmentation errors and subclonal populations. We validated our algorithm against a panel of cell lines with experimentally determined ploidy. We also compared our algorithm with the well-established single-nucleotide polymorphism array-based method called ABSOLUTE on three sets of tumors of different types. Our method had good performance on these four benchmark datasets for both purity and ploidy estimates, and may offer a simple solution to copy number alteration quantification for cancer sequencing projects.
Availability and implementation: The R package absCNseq is available from http://biostats.mcc.ucsd.edu/files/absCNseq_1.0.tar.gz.
Contact: kmesser@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimization strategies for fast detection of positive selection on phylogenetic trees
Authors: Valle Mario , Schabauer Hannes , Pacher Christoph , Stockinger Heinz , Stamatakis Alexandros , Robinson-Rechavi Marc , Salamin Nicolas 
Published: January 2014

Abstract
Motivation: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution.
Results: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).
Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/.
Contact: selectome@unil.ch or nicolas.salamin@unil.ch
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data
Authors: Guan Daogang , Shao Jiaofang , Deng Youping , Wang Panwen , Zhao Zhongying , Liang Yan , Wang Junwen , Yan Bin 
Published: January 2014

Abstract
Summary: ChIP-seq technology provides an accurate characterization of transcription or epigenetic factors binding on genomic sequences. With integration of such ChIP-based and other high-throughput information, it would be dedicated to dissecting cross-interactions among multilevel regulators, genes and biological functions. Here, we devised an integrative web server CMGRN (constructing multilevel gene regulatory networks), to unravel hierarchical interactive networks at different regulatory levels. The newly developed method used the Bayesian network modeling to infer causal interrelationships among transcription factors or epigenetic modifications by using ChIP-seq data. Moreover, it used Bayesian hierarchical model with Gibbs sampling to incorporate binding signals of these regulators and gene expression profile together for reconstructing gene regulatory networks. The example applications indicate that CMGRN provides an effective web-based framework that is able to integrate heterogeneous high-throughput data and to reveal hierarchical ‘regulome’ and the associated gene expression programs.
Availability: http://bioinfo.icts.hkbu.edu.hk/cmgrn; http://www.byanbioinfo.org/cmgrn.
Contact: yanbinai6017@gmail.com or junwen@hku.hk
Supplementary Information: Supplementary data are available at Bioinformatics online.
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
Authors: Cornuet Jean-Marie , Pudlo Pierre , Veyssier Julien , Dehne-Garcia Alexandre , Gautier Mathieu , Leblois Raphaël , Marin Jean-Michel , Estoup Arnaud 
Published: January 2014

Abstract
Motivation: DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X.
Availability: Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc
Contact: estoup@supagro.inra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
CasOT: a genome-wide Cas9/gRNA off-target searching tool
Authors: Xiao An , Cheng Zhenchao , Kong Lei , Zhu Zuoyan , Lin Shuo , Gao Ge , Zhang Bo 
Published: January 2014

Abstract
Summary: The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions.
Availability: http://eendb.zfgenetics.org/casot/
Contact: zfgenetics@gmail.com or bzhang@pku.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
Authors: Schröder Jan , Hsu Arthur , Boyle Samantha E. , Macintyre Geoff , Cmero Marek , Tothill Richard W. , Johnstone Ricky W. , Shackleton Mark , Papenfuss Anthony T. 
Published: January 2014

Abstract
Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates.
Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools.
Availability and implementation: Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates.
Contact: papenfuss@wehi.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Bias from removing read duplication in ultra-deep sequencing experiments
Authors: Zhou Wanding , Chen Tenghui , Zhao Hao , Eterovic Agda Karina , Meric-Bernstam Funda , Mills Gordon B. , Chen Ken 
Published: January 2014

Abstract
Motivation: Identifying subclonal mutations and their implications requires accurate estimation of mutant allele fractions from possibly duplicated sequencing reads. Removing duplicate reads assumes that polymerase chain reaction amplification from library constructions is the primary source. The alternative—sampling coincidence from DNA fragmentation—has not been systematically investigated.
Results: With sufficiently high-sequencing depth, sampling-induced read duplication is non-negligible, and removing duplicate reads can overcorrect read counts, causing systemic biases in variant allele fraction and copy number variation estimations. Minimal overcorrection occurs when duplicate reads are identified accounting for their mate reads, inserts are of a variety of lengths and samples are sequenced in separate batches. We investigate sampling-induced read duplication in deep sequencing data with 500× to 2000× duplicates-removed sequence coverage. We provide a quantitative solution to overcorrection and guidance for effective designs of deep sequencing platforms that facilitate accurate estimation of variant allele fraction and copy number variation.
Availability and implementation: A Python implementation is freely available at https://bitbucket.org/wanding/duprecover/overview.
Contact: wzhou1@mdanderson.org, kchen3@mdanderson.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Fine-scale gas distribution in marine sediments assessed from deep-towed seismic data
Authors: Ker S. , Le Gonidec Y. , Marsset B. , Westbrook G. K. , Gibert D. , Minshull T. A. 
Published: January 2014

Abstract
In the context of seismic imaging of gas/gas-hydrate systems, the fine-scale structure of subseabed gas-related reflections is assessed by taking advantage of the source signature of the deep-towed high-resolution SYSIF seismic device. We demonstrate the value of an original wavelet-based method and associated multiscale seismic attributes, applied to seismic data recently acquired on the western margin of the Arctic archipelago of Svalbard. From analysis in the wavelet domain, we recognize two types of gas-related reflections associated with submetre-scale distribution of gas. We identify a thin gas-charged layer associated with an apparent normal polarity reflection, and we detect gas patches associated with a reverse-polarity bright spot with frequency-dependent elastic properties at small seismic wavelengths. The results provide valuable information on the scale of features through which gas migrates and resolve ambiguities in the interpretation of the seismic data.
Impact of scallop dredging on benthic epifauna in a mixed-substrate habitat
Authors: Boulcott Philip , Millar Colin P. , Fryer Rob J. 
Published: January 2014

AbstractExperimental scallop dredging was conducted to assess the vulnerability of emergent epifauna on hard substrates. Three sites were sampled before and after dredging to examine changes in the coverage of faunal turf (hydroid and bryozoan) assemblages and the composition of the wider epifaunal community. Each site had an “impact” box that was dredged, a control box that was in an area that was still open to fishing, and a control box in a special area of conservation (SAC) that had not been fished for two years. Community composition differed significantly after dredging in two of the three sites, with dredged communities becoming less similar to those in the SAC. There was no clear evidence that dredging in the impact boxes reduced the coverage of faunal turfs on hard substrates. However, the coverage of faunal turfs on hard substrates in the SAC was typically greater than in areas that were still being fished commercially, consistent with a dredging effect. The results highlight the role that substrate morphology might play in modifying the severity of dredging effects. This has relevance to marine spatial management, as it suggests that emergent epifauna living on hard substrates that are morphologically suited to dredging, such as pebble and cobble substrates, could be particularly vulnerable to dredging.
Density-dependence can be revealed by modelling the variance in the stock–recruitment process: an application to flatfish
Authors: Archambault B. , Le Pape O. , Bousquet N. , Rivot E. 
Published: January 2014

AbstractRecruitment success in marine species is mostly driven by the high and variable mortality of first life stages, and the relationships between stock and recruitment are then largely dominated by residual variability. We show that analysing the residual variability may provide insights on the density-dependence process occurring during the recruitment. Following the seminal formulation of Minto et al. (Survival variability and population density in fish populations. Nature, 2008), we show that when recruitment is considered as a sequence of a pelagic stage with stochastic density-independent mortality followed by a second stage with stochastic density-dependent mortality, then the variability of the recruitment rate per spawning biomass (RPSB) should be a decreasing function of the spawning biomass. Using stock–recruit data of 148 stocks from the RAM legacy database, we provide a test of this hypothesis by showing that the variability of RPSB is lower for fish species with the higher concentration during juvenile stages. Second, a hierarchical Bayesian model (HBM) is built to derive a meta-analysis of stock–recruit data for 39 flatfish stocks, characterized by a high concentration of juveniles in coastal nursery habitats. Results of the HBM show that the variance of the RPSB decreases with the spawning biomass for almost all stocks, thus providing strong evidence of density-dependence during the recruitment process. Finally, we attempt to relate patterns in recruitment variance to relevant life-history traits of flatfish species.
The orientation and migratory dynamics of the western rock lobster, Panulirus cygnus, in Western Australia
Authors: de Lestang Simon 
Published: January 2014

AbstractLarge-scale migrations are known to occur in numerous species, and in the case of the Western Rock Lobster, Panulirus cygnus, result in juveniles moving from nursery areas into deeper offshore breeding grounds. In 2008 the Western Rock Lobster fishery reduced harvest rates to increase legal and spawning biomass throughout the fishery, which also allowed greater numbers of lobsters to migrate. Increased lobster migration could potentially reduce biomass in some areas, thus adversely impacting commercial catch rates. Over 20 000 tag–recaptured lobsters were analysed to determine the dynamics underlying migration in this species and to assess the impact reduced harvest rates may have had on catches. This study showed that P. cygnus migration was associated with body size and water depth, and that magnetism and oceanic currents appear to be the most likely guideposts used for orientation. Size at migration varied in a constant fashion along the coast, being larger towards the southern end of the fishery and smallest at the offshore Abrolhos Islands. During the migration period, up to 50% of lobsters at their mean size of migration moved from coastal areas out towards deeper waters (>40 m), whereas <15% of those in deeper water at the same size moved significant distances northward. This behaviour appears to be contranatant, counteracting the downstream redistribution of larvae after their 9–11 month larval life. Reduced harvest rates and catches being focussed onto higher valued sedentary lobsters have allowed more lobsters to migrate. However, the numbers moving between management areas are relatively small, with the biological and economic benefits of fishing at a reduced exploitation rate outweighing losses to catches.
Weak lensing with 21 cm intensity mapping at z ∼ 2–3
Authors: Pourtsidou A. , Metcalf R. Benton 
Published: January 2014

Abstract
We study how 21 cm intensity mapping can be used to measure gravitational lensing over a wide range of redshift. This can extend weak lensing measurements to higher redshifts than are accessible with conventional galaxy surveys. We construct a convergence estimator taking into account the discreteness of galaxies and calculate the expected noise level as a function of redshift and telescope parameters. At z ∼ 2–3, we find that a telescope array with a collecting area ∼0.2 km2 spread over a region with diameter ∼2 km would be sufficient to measure the convergence power spectrum to high accuracy for multipoles between 10 and 1000. We show that these measurements can be used to constrain interacting dark energy models.
Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing
Authors: Kunde-Ramamoorthy Govindarajan , Coarfa Cristian , Laritsky Eleonora , Kessler Noah J. , Harris R. Alan , Xu Mingchu , Chen Rui , Shen Lanlan , Milosavljevic Aleksandar , Waterland Robert A. 
Published: January 2014

Abstract
Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered &gt;70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage.
Beyond species: why ecological interaction networks vary through space and time
Authors: Poisot T. , Stouffer D.B. , Gravel D. 
Published: January 2014

AbstractCommunity ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological mechanisms act locally on the existence of interspecific interactions. Here we argue that the current conceptualization of species interaction networks is ill-suited for this task. Instead, we propose that future research must start to account for the intrinsic variability of species interactions, then scale up from here onto complex networks. This can be accomplished simply by recognizing that there exists intra-specific variability, in traits or properties related to the establishment of species interactions. By shifting the scale towards population-based processes, we show that this new approach will improve our predictive ability and mechanistic understanding of how species interact over large spatial or temporal scales.
Heterologous Expression of Methylketone Synthase1 and Methylketone Synthase2 Leads to Production of Methylketones and Myristic Acid in Transgenic Plants
Authors: Yu Geng , Pichersky Eran 
Published: January 2014

AbstractSome plants produce methylketones as potent defense compounds against various insects. Wild tomato (Solanum habrochaites), a relative of the cultivated tomato (Solanum lycopersicum), synthesizes large amounts of 2-methylketones in its glandular trichomes, but cultivated tomato trichomes contain little or no methylketones. Two enzymes, Solanum habrochaites methylketone synthase1 (ShMKS1) and ShMKS2, are required to convert β-ketoacyl acyl-carrier protein intermediates of the fatty acid biosynthetic pathway to methylketones. ShMKS2 is a thioesterase that hydrolyzes β-ketoacyl acyl-carrier protein, and ShMKS1 is a decarboxylase that converts the resulting 3-ketoacids to 2-methylketones. We introduced ShMKS2 by itself or together with ShMKS1 to Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana tabacum), and cultivated tomato under the control of the 35S, Rubisco small subunit, and tomato trichome-specific promoters. Young tobacco and Arabidopsis plants expressing both genes under the control of 35S and Rubisco small subunit promoters produced methylketones in their leaves but had serious growth defects. As plants matured, they ceased to produce methylketones. Tobacco plants but not Arabidopsis or tomato plants expressing only ShMKS2 under the 35S promoter also synthesized methylketones, but at a lower rate. Transgenic cultivated tomato plants expressing ShMKS1 and ShMKS2 under trichome-specific promoters had slightly elevated levels of methylketone. Trace amounts of myristic acid were also detected in transgenic plants constitutively expressing ShMKS2 with or without ShMKS1. These results suggest that increases in methylketone production in plants will require the targeting of the pathway to self-contained structures in the plant and may also require increasing the flux of fatty acid biosynthesis.