bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of the “obstetric shock index” as an adjunct in identifying significant blood loss in patients with massive postpartum hemorrhage
Authors: Le Bas Abigail , Chandraharan Edwin , Addei Anthony , Arulkumaran Sabaratnam 
Published: December 2013

AbstractObjectiveTo establish the normal range for the “obstetric shock index” (OSI) after birth and to determine its usefulness as an aid to estimate blood loss in postpartum hemorrhage (PPH).MethodsA retrospective case–control analysis was conducted involving pregnant women admitted to St Georges Hospital for delivery: 50 with no PPH (control group) and 50 with massive PPH (> 30% loss of blood volume; case group). The OSI was calculated at 10 and 30 minutes from PPH onset.ResultsMean OSI in the control group at 10 and 30 minutes was 0.74 (range, 0.4–1.1) and 0.76 (range, 0.5–1.1), respectively. In the case group, mean OSI at 10 and 30 minutes was 0.91 (range, 0.4–1.5) and 0.90 (range, 0.5–1.4), respectively, with 64% requiring blood products. In the case group, 89% of women with an OSI of 1.1 or more at 10 minutes required transfusion; 75% with an OSI of 1.1 or more at 30 minutes required transfusion.ConclusionWe recommend that the normal OSI range should be 0.7–0.9. An OSI of more than 1 seems to be a useful adjunct in estimating blood loss in cases of massive PPH and in predicting the need for blood and blood products.
Eco-evolutionary feedbacks drive species interactions
Authors: Andrade-Domínguez Andrés , Salazar Emmanuel , del Carmen Vargas-Lagunas María , Kolter Roberto , Encarnación Sergio 
Published: December 2013

Abstract
In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions.
Marine viruses, a genetic reservoir revealed by targeted viromics
Authors: Martínez Joaquín Martínez , Swan Brandon K , Wilson William H 
Published: December 2013

Abstract
Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52–163 estimated genotypes, was much lower than in previous virome reports. Fragment recruitment of metagenome reads to selected reference viral genomes yields high genome coverage, suggesting little amplification and sequencing bias against some genomic regions. These results underscore the value of our approach as an effective way to target and investigate specific virus groups. In particular, it will help reveal the diversity and abundance of giant viruses in marine ecosystems.
Design of a structure with low incident and viewing angle dependence inspired by Morpho butterflies
Authors: Wang Wanlin , Zhang Wang , Gu Jiajun , Liu Qinglei , Deng Tao , Zhang Di , Lin Hai-Qing 
Published: December 2013

AbstractMorpho butterflies are well known for their brilliant iridescent colors, which arise from periodic arrays of scales. These brilliant colors have a low angle dependence, in contrast to similar phenomena that are commonly caused by the periodic structures. We designed a structure with a low incident and viewing angle dependence inspired by Morpho butterflies. This structure was studied using the finite-difference time-domain method. The lamellae distribution of tree-like structure was found to be the determining factor for producing a low incident angle dependence. Two advanced models were designed to produce a low viewing angle dependence. Model I was constructed using two layers of scales. The particle swarm optimization algorithm was used to construct Model II. The angle dependence of Model II exhibited a large viewing angle range under various incident angles.
Broad-band efficiency calibration of ITER bolometer prototypes using Pt absorbers on SiN membranes
Authors: Meister H. , Willmeroth M. , Zhang D. , Gottwald A. , Krumrey M. , Scholze F. 
Published: December 2013

The energy resolved efficiency of two bolometer detector prototypes for ITER with 4 channels each and absorber thicknesses of 4.5 μm and 12.5 μm, respectively, has been calibrated in a broad spectral range from 1.46 eV up to 25 keV. The calibration in the energy range above 3 eV was performed against previously calibrated silicon photodiodes using monochromatized synchrotron radiation provided by five different beamlines of Physikalische Technische Bundesanstalt at the electron storage rings BESSY II and Metrology Light Source in Berlin. For the measurements in the visible range, a setup was realised using monochromatized halogen lamp radiation and a calibrated laser power meter as reference. The measurements clearly demonstrate that the efficiency of the bolometer prototype detectors in the range from 50 eV up to ≈6 keV is close to unity; at a photon energy of 20 keV the bolometer with the thick absorber detects 80% of the photons, the one with the thin absorber about 50%. This indicates that the detectors will be well capable of measuring the plasma radiation expected from the standard ITER scenario. However, a minimum absorber thickness will be required for the high temperatures in the central plasma. At 11.56 keV, the sharp Pt-L3 absorption edge allowed to cross-check the absorber thickness by fitting the measured efficiency to the theoretically expected absorption of X-rays in a homogeneous Pt-layer. Furthermore, below 50 eV the efficiency first follows the losses due to reflectance expected for Pt, but below 10 eV it is reduced further by a factor of 2 for the thick absorber and a factor of 4 for the thin absorber. Most probably, the different histories in production, storage, and operation led to varying surface conditions and additional loss channels.
Avalanches mediate crystallization in a hard-sphere glass
Authors: Sanz Eduardo , Valeriani Chantal , Zaccarelli Emanuela , Poon Wilson C. K. , Cates Michael E. , Pusey Peter N. 
Published: December 2013

Significance
Glasses are formed from the supercooled liquid state when motion is arrested on the scale of the particle diameter. Such states are thermodynamically unstable: An apparently deeply arrested amorphous material can transform into a crystal (devitrification) without large-scale particle motion. The prediction and avoidance of devitrification represent major formulation issues in materials science, hence the importance of understanding its mechanism. Using molecular-dynamics simulations, we study the crystallization of the simplest glass-forming system, a hard-sphere glass. We find that crystallization is caused by a subset of particles cooperatively undergoing large rearrangements in an intermittent stochastic fashion (avalanches). Particles involved in an avalanche are not themselves crystallizing, but they induce crystallization in nearby regions that already show incipient local order.
HomSI: a homozygous stretch identifier from next-generation sequencing data
Authors: Görmez Zeliha , Bakir-Gungor Burcu , Sağıroğlu Mahmut Şamil 
Published: December 2013

Abstract
Summary: In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive diseases among the members of these families. Homozygosity mapping is based on this observation, and in consanguineous families, several recessive disease genes have been discovered with the help of this technique. The researchers typically use single nucleotide polymorphism arrays to determine the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next-generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf (variant call format) files as an input file, our program identifies the majority of homozygous regions found by microarray single nucleotide polymorphism genotype data.
Availability and implementation: HomSI software is freely available at www.igbam.bilgem.tubitak.gov.tr/softwares/HomSI, with an online manual.
Contact: bakirburcu@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors
Authors: Gao Chuan , Tignor Nicole L. , Salit Jacqueline , Strulovici-Barel Yael , Hackett Neil R. , Crystal Ronald G. , Mezey Jason G. 
Published: December 2013

Abstract
Motivation: Identification of expression Quantitative Trait Loci (eQTL), the genetic loci that contribute to heritable variation in gene expression, can be obstructed by factors that produce variation in expression profiles if these factors are unmeasured or hidden from direct analysis.
Methods: We have developed a method for Hidden Expression Factor analysis (HEFT) that identifies individual and pleiotropic effects of eQTL in the presence of hidden factors. The HEFT model is a combined multivariate regression and factor analysis, where the complete likelihood of the model is used to derive a ridge estimator for simultaneous factor learning and detection of eQTL. HEFT requires no pre-estimation of hidden factor effects; it provides P-values and is extremely fast, requiring just a few hours to complete an eQTL analysis of thousands of expression variables when analyzing hundreds of thousands of single nucleotide polymorphisms on a standard 8 core 2.6 G desktop.
Results: By analyzing simulated data, we demonstrate that HEFT can correct for an unknown number of hidden factors and significantly outperforms all related hidden factor methods for eQTL analysis when there are eQTL with univariate and multivariate (pleiotropic) effects. To demonstrate a real-world application, we applied HEFT to identify eQTL affecting gene expression in the human lung for a study that included presumptive hidden factors. HEFT identified all of the cis-eQTL found by other hidden factor methods and 91 additional cis-eQTL. HEFT also identified a number of eQTLs with direct relevance to lung disease that could not be found without a hidden factor analysis, including cis-eQTL for GTF2H1 and MTRR, genes that have been independently associated with lung cancer.
Availability: Software is available at http://mezeylab.cb.bscb.cornell.edu/Software.aspx.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: jgm45@cornell.edu
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data
Authors: Suo Chen , Calza Stefano , Salim Agus , Pawitan Yudi 
Published: December 2013

AbstractMotivation: RNA-sequencing technologies provide a powerful tool for expression analysis at gene and isoform level, but accurate estimation of isoform abundance is still a challenge. Standard assumption of uniform read intensity would yield biased estimates when the read intensity is in fact non-uniform. The problem is that, without strong assumptions, the read intensity pattern is not identifiable from data observed in a single sample.Results: We develop a joint statistical model that accounts for non-uniform isoform-specific read distribution and gene isoform expression estimation. The main challenge is in dealing with the large number of isoform-specific read distributions, which potentially are as many as the number of splice variants in the genome. A statistical regularization via a smoothing penalty is imposed to control the estimation. Also, for identifiability reasons, the method uses information across samples from the same region. We develop a fast and robust computational procedure based on the iterated-weighted least-squares algorithm, and apply it to simulated data and two real RNA-Seq datasets with reverse transcription–polymerase chain reaction validation. Empirical tests show that our model performs better than existing methods in terms of increasing precision in isoform-level estimation.Availability and implementation: We have implemented our method in an R package called Sequgio as a pipeline for fast processing of RNA-Seq data.Contact: yudi.pawitan@ki.seSupplementary information: Supplementary data are available at Bioinformatics online.
Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament
Authors: Fornander Louise H. , Renodon-Cornière Axelle , Kuwabara Naoyuki , Ito Kentaro , Tsutsui Yasuhiro , Shimizu Toshiyuki , Iwasaki Hiroshi , Nordén Bengt , Takahashi Masayuki 
Published: December 2013

AbstractThe Swi5-Sfr1 heterodimer protein stimulates the Rad51-promoted DNA strand exchange reaction, a crucial step in homologous recombination. To clarify how this accessory protein acts on the strand exchange reaction, we have analyzed how the structure of the primary reaction intermediate, the Rad51/single-stranded DNA (ssDNA) complex filament formed in the presence of ATP, is affected by Swi5-Sfr1. Using flow linear dichroism spectroscopy, we observe that the nucleobases of the ssDNA are more perpendicularly aligned to the filament axis in the presence of Swi5-Sfr1, whereas the bases are more randomly oriented in the absence of Swi5-Sfr1. When using a modified version of the natural protein where the N-terminal part of Sfr1 is deleted, which has no affinity for DNA but maintained ability to stimulate the strand exchange reaction, we still observe the improved perpendicular DNA base orientation. This indicates that Swi5-Sfr1 exerts its activating effect through interaction with the Rad51 filament mainly and not with the DNA. We propose that the role of a coplanar alignment of nucleobases induced by Swi5-Sfr1 in the presynaptic Rad51/ssDNA complex is to facilitate the critical matching with an invading double-stranded DNA, hence stimulating the strand exchange reaction.
DICE, an efficient system for iterative genomic editing in human pluripotent stem cells
Authors: Zhu Fangfang , Gamboa Matthew , Farruggio Alfonso P. , Hippenmeyer Simon , Tasic Bosiljka , Schüle Birgitt , Chen-Tsai Yanru , Calos Michele P. 
Published: December 2013

AbstractTo reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.
A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant Prioritization
Authors: Gagliano Sarah A. , Barnes Michael R. , Weale Michael E. , Knight Jo 
Published: December 2013

AbstractThe increasing quantity and quality of functional genomic information motivate the assessment and integration of these data with association data, including data originating from genome-wide association studies (GWAS). We used previously described GWAS signals (“hits”) to train a regularized logistic model in order to predict SNP causality on the basis of a large multivariate functional dataset. We show how this model can be used to derive Bayes factors for integrating functional and association data into a combined Bayesian analysis. Functional characteristics were obtained from the Encyclopedia of DNA Elements (ENCODE), from published expression quantitative trait loci (eQTL), and from other sources of genome-wide characteristics. We trained the model using all GWAS signals combined, and also using phenotype specific signals for autoimmune, brain-related, cancer, and cardiovascular disorders. The non-phenotype specific and the autoimmune GWAS signals gave the most reliable results. We found SNPs with higher probabilities of causality from functional characteristics showed an enrichment of more significant p-values compared to all GWAS SNPs in three large GWAS studies of complex traits. We investigated the ability of our Bayesian method to improve the identification of true causal signals in a psoriasis GWAS dataset and found that combining functional data with association data improves the ability to prioritise novel hits. We used the predictions from the penalized logistic regression model to calculate Bayes factors relating to functional characteristics and supply these online alongside resources to integrate these data with association data.Author SummaryLarge-scale genetic studies have had success identifying genes that play a role in complex traits. Advanced statistical procedures suggest that there are still genetic variants to be discovered, but these variants are difficult to detect. Incorporating biological information that affect the amount of protein or other product produced can be used to prioritise the genetic variants in order to identify which are likely to be causal. The method proposed here uses such biological characteristics to predict which genetic variants are most likely to be causal for complex traits.
FROGG high‐risk prostate cancer workshop: Patterns of practice and literature review
Authors: Lehman Margot , Hayden Amy J , Martin Jarad M , Christie David , Kneebone Andrew B , Sidhom Mark , Skala Marketa , Tai Keen‐Hun 
Published: December 2013

SummaryAustralian and New Zealand radiation oncologists with an interest in uro‐oncology were invited to participate in a pattern‐of‐practice survey dealing with the management of intact high‐risk prostate cancer. Responses from 46 practitioners (representing 73% of all potential respondents) revealed that high‐dose radiation therapy is the standard of care. However, there is variability in practice with regard to the methods used to achieve dose escalation, the use of whole‐pelvic radiation therapy and the optimal duration of androgen deprivation therapy employed. A review of the literature outlining the current body of knowledge and the planned and ongoing studies in intact high‐risk prostate cancer is presented.
Deletion variant near ZNF389 is associated with control of ovine lentivirus in multiple sheep flocks
Authors: White S. N. , Mousel M. R. , Reynolds J. O. , Herrmann‐Hoesing L. M. , Knowles D. P. 
Published: December 2013

SummaryOvine lentivirus (OvLV) is a macrophage‐tropic lentivirus found in many countries that causes interstitial pneumonia, mastitis, arthritis and cachexia in sheep. There is no preventive vaccine and no cure, but breed differences suggest marker‐assisted selective breeding might improve odds of infection and control of OvLV post‐infection. Although variants in TMEM154 have consistent association with odds of infection, no variant in any gene has been associated with host control of OvLV post‐infection in multiple animal sets. Proviral concentration is a live‐animal diagnostic measure of OvLV control post‐infection related to severity of OvLV‐induced lesions. A recent genome‐wide association study identified a region including four zinc finger genes associated with proviral concentration in one Rambouillet flock. To refine this region, we tested additional variants and identified a small insertion/deletion variant near ZNF389 that showed consistent association with proviral concentration in three animal sets (P < 0.05). These animal sets contained Rambouillet, Polypay and crossbred sheep from multiple locations and management conditions. Strikingly, one flock had exceptionally high prevalence (>87%, including yearlings) and mean proviral concentration (>950 copies/μg), possibly due to needle sharing. The best estimate of proviral concentration by genotype, obtained from all 1310 OvLV‐positive animals tested, showed insertion homozygotes had less than half the proviral concentration of other genotypes (P < 0.0001). Future work will test additional breeds, management conditions and viral subtypes, and identify functional properties of the haplotype this deletion variant tracks. To our knowledge, this is the first genetic variant consistently associated with host control of OvLV post‐infection in multiple sheep flocks.