bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imputation-Based Genomic Coverage Assessments of Current Human Genotyping Arrays
Authors: Nelson Sarah C , Doheny Kimberly F , Pugh Elizabeth W , Romm Jane M , Ling Hua , Laurie Cecelia A , Browning Sharon R , Weir Bruce S , Laurie Cathy C 
Published: August 2013

Abstract
Microarray single-nucleotide polymorphism genotyping, combined with imputation of untyped variants, has been widely adopted as an efficient means to interrogate variation across the human genome. “Genomic coverage” is the total proportion of genomic variation captured by an array, either by direct observation or through an indirect means such as linkage disequilibrium or imputation. We have performed imputation-based genomic coverage assessments of eight current genotyping arrays that assay from ~0.3 to ~5 million variants. Coverage was determined separately in each of the four continental ancestry groups in the 1000 Genomes Project phase 1 release. We used the subset of 1000 Genomes variants present on each array to impute the remaining variants and assessed coverage based on correlation between imputed and observed allelic dosages. More than 75% of common variants (minor allele frequency &gt; 0.05) are covered by all arrays in all groups except for African ancestry, and up to ~90% in all ancestries for the highest density arrays. In contrast, less than 40% of less common variants (0.01 &lt; minor allele frequency &lt; 0.05) are covered by low density arrays in all ancestries and 50–80% in high density arrays, depending on ancestry. We also calculated genome-wide power to detect variant-trait association in a case-control design, across varying sample sizes, effect sizes, and minor allele frequency ranges, and compare these array-based power estimates with a hypothetical array that would type all variants in 1000 Genomes. These imputation-based genomic coverage and power analyses are intended as a practical guide to researchers planning genetic studies.
Global Linkage Map Connects Meiotic Centromere Function to Chromosome Size in Budding Yeast
Authors: Baryshnikova Anastasia , VanderSluis Benjamin , Costanzo Michael , Myers Chad L , Cha Rita S , Andrews Brenda , Boone Charles 
Published: August 2013

AbstractSynthetic genetic array (SGA) analysis automates yeast genetics, enabling high-throughput construction of ordered arrays of double mutants. Quantitative colony sizes derived from SGA analysis can be used to measure cellular fitness and score for genetic interactions, such as synthetic lethality. Here we show that SGA colony sizes also can be used to obtain global maps of meiotic recombination because recombination frequency affects double-mutant formation for gene pairs located on the same chromosome and therefore influences the size of the resultant double-mutant colony. We obtained quantitative colony size data for ~1.2 million double mutants located on the same chromosome and constructed a genome-scale genetic linkage map at ~5 kb resolution. We found that our linkage map is reproducible and consistent with previous global studies of meiotic recombination. In particular, we confirmed that the total number of crossovers per chromosome tends to follow a simple linear model that depends on chromosome size. In addition, we observed a previously unappreciated relationship between the size of linkage regions surrounding each centromere and chromosome size, suggesting that crossovers tend to occur farther away from the centromere on larger chromosomes. The pericentric regions of larger chromosomes also appeared to load larger clusters of meiotic cohesin Rec8, and acquire fewer Spo11-catalyzed DNA double-strand breaks. Given that crossovers too near or too far from centromeres are detrimental to homolog disjunction and increase the incidence of aneuploidy, our data suggest that chromosome size may have a direct role in regulating the fidelity of chromosome segregation during meiosis.
The DrosophilaEnhancer of splitGene Complex: Architecture and Coordinate Regulation by Notch, Cohesin, and Polycomb Group Proteins
Authors: Schaaf Cheri A , Misulovin Ziva , Gause Maria , Koenig Amanda , Dorsett Dale 
Published: August 2013

AbstractThe cohesin protein complex functionally interacts with Polycomb group (PcG) silencing proteins to control expression of several key developmental genes, such as the Drosophila Enhancer of split gene complex [E(spl)-C]. The E(spl)-C contains 12 genes that inhibit neural development. In a cell line derived from the central nervous system, cohesin and the PRC1 PcG protein complex bind and repress E (spl)-C transcription, but the repression mechanisms are unknown. The genes in the E(spl)-C are directly activated by the Notch receptor. Here we show that depletion of cohesin or PRC1 increases binding of the Notch intracellular fragment to genes in the E(spl)-C, correlating with increased transcription. The increased transcription likely reflects both direct effects of cohesin and PRC1 on RNA polymerase activity at the E(spl)-C, and increased expression of Notch ligands. By chromosome conformation capture we find that the E(spl)-C is organized into a self-interactive architectural domain that is co-extensive with the region that binds cohesin and PcG complexes. The self-interactive architecture is formed independently of cohesin or PcG proteins. We posit that the E(spl)-C architecture dictates where cohesin and PcG complexes bind and act when they are recruited by as yet unidentified factors, thereby controlling the E(spl)-C as a coordinated domain.
Efficient Single-Cell Transgene Induction in Caenorhabditis elegans Using a Pulsed Infrared Laser
Authors: Churgin Matthew A , He Liping , Murray John I , Fang-Yen Christopher 
Published: August 2013

Abstract
The coupling of transgenes to heat shock promoters is a widely applied method for regulating gene expression. In C. elegans, gene induction can be controlled temporally through timing of heat shock and spatially via targeted rescue in heat shock mutants. Here, we present a method for evoking gene expression in arbitrary cells, with single-cell resolution. We use a focused pulsed infrared laser to locally induce a heat shock response in specific cells. Our method builds on and extends a previously reported method using a continuous-wave laser. In our technique, the pulsed laser illumination enables a much higher degree of spatial selectivity because of diffusion of heat between pulses. We apply our method to induce transient and long-term transgene expression in embryonic, larval, and adult cells. Our method allows highly selective spatiotemporal control of transgene expression and is a powerful tool for model organism biology.
Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences BetweenArabidopsis lyrataPopulations
Authors: Remington David L , Leinonen Päivi H , Leppälä Johanna , Savolainen Outi 
Published: August 2013

AbstractCosts of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs.
High-Throughput Computer Vision Introduces the Time Axis to a Quantitative Trait Map of a Plant Growth Response
Authors: Moore Candace R , Johnson Logan S , Kwak Il-Youp , Livny Miron , Broman Karl W , Spalding Edgar P 
Published: August 2013

Abstract
Automated image acquisition, a custom analysis algorithm, and a distributed computing resource were used to add time as a third dimension to a quantitative trait locus (QTL) map for plant root gravitropism, a model growth response to an environmental cue. Digital images of Arabidopsis thaliana seedling roots from two independently reared sets of 162 recombinant inbred lines (RILs) and one set of 92 near isogenic lines (NILs) derived from a Cape Verde Islands (Cvi) × Landsberg erecta (Ler) cross were collected automatically every 2 min for 8 hr following induction of gravitropism by 90° reorientation of the sample. High-throughput computing (HTC) was used to measure root tip angle in each of the 1.1 million images acquired and perform statistical regression of tip angle against the genotype at each of the 234 RIL or 102 NIL DNA markers independently at each time point using a standard stepwise procedure. Time-dependent QTL were detected on chromosomes 1, 3, and 4 by this mapping method and by an approach developed to treat the phenotype time course as a function-valued trait. The QTL on chromosome 4 was earliest, appearing at 0.5 hr and remaining significant for 5 hr, while the QTL on chromosome 1 appeared at 3 hr and thereafter remained significant. The Cvi allele generally had a negative effect of 2.6–4.0%. Heritability due to the QTL approached 25%. This study shows how computer vision and statistical genetic analysis by HTC can characterize the developmental timing of genetic architectures.
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
Authors: Fumagalli Matteo , Vieira Filipe G , Korneliussen Thorfinn Sand , Linderoth Tyler , Huerta-Sánchez Emilia , Albrechtsen Anders , Nielsen Rasmus 
Published: August 2013

AbstractOver the past few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data. In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy for investigating population structure via principal components analysis. Through extensive simulations, we compare the new method herein proposed to approaches based on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage.
Natural History of Stuttering to 4 Years of Age: A Prospective Community-Based Study
Authors: Reilly Sheena , Onslow Mark , Packman Ann , Cini Eileen , Conway Laura , Ukoumunne Obioha C. , Bavin Edith L. , Prior Margot , Eadie Patricia , Block Susan , Wake Melissa 
Published: August 2013

OBJECTIVES:
To document the natural history of stuttering by age 4 years, including (1) cumulative incidence of onset, (2) 12-month recovery status, (3) predictors of stuttering onset and recovery, and (4) potential comorbidities. The study cohort was a prospective community-ascertained cohort (the Early Language in Victoria Study) from Melbourne, Australia, of 4-year-old children (n = 1619; recruited at age 8 months) and their mothers.

METHODS:
Outcome was stuttering onset by age 4 years and recovery within 12 months of onset, defined using concurrent monthly parent and speech pathologist ratings. Potential predictors: child gender, birth weight, birth order, prematurity, and twinning; maternal mental health and education; socioeconomic status; and family history of stuttering. Potential comorbidities: preonset and concurrent temperament, language, nonverbal cognition, and health-related quality of life.

RESULTS:
By age 4 years, the cumulative incidence of stuttering onset was 11.2% (95% confidence interval [CI]: 9.7% to 12.8%). Higher maternal education (P = .004), male gender (P = .02), and twinning (P = .005) predicted stuttering onset. At outcome, stuttering children had stronger language (mean [SD]: 105.0 [13.0] vs 99.6 [14.6]; mean difference 5.5, 95% CI: 3.1 to 7.8; P &lt; .001) and nonverbal cognition (mean [SD]: 106.5 [11.4] vs 103.9 [13.7], mean difference 2.6, 95% CI: 0.4 to 4.8; P = .02) and better health-related quality of life but were otherwise similar to their nonstuttering peers. Only 9 of 142 children (6.3%; 95% CI: 2.9% to 11.7%) recovered within 12 months of onset.

CONCLUSIONS:
Although stuttering onset is common in preschoolers, adverse affects are not the norm in the first year after onset.
Measuring Hospital Quality Using Pediatric Readmission and Revisit Rates
Authors: Bardach Naomi S. , Vittinghoff Eric , Asteria-Peñaloza Renée , Edwards Jeffrey D. , Yazdany Jinoos , Lee Henry C. , Boscardin W. John , Cabana Michael D. , Dudley R. Adams 
Published: August 2013

OBJECTIVE:
To assess variation among hospitals on pediatric readmission and revisit rates and to determine the number of high- and low-performing hospitals.

METHODS:
In a retrospective analysis using the State Inpatient and Emergency Department Databases from the Healthcare Cost and Utilization Project with revisit linkages available, we identified pediatric (ages 1–20 years) visits with 1 of 7 common inpatient pediatric conditions (asthma, dehydration, pneumonia, appendicitis, skin infections, mood disorders, and epilepsy). For each condition, we calculated rates of all-cause readmissions and rates of revisits (readmission or presentation to the emergency department) within 30 and 60 days of discharge. We used mixed logistic models to estimate hospital-level risk-standardized 30-day revisit rates and to identify hospitals that had performance statistically different from the group mean.

RESULTS:
Thirty-day readmission rates were low (&lt;10.0%) for all conditions. Thirty-day rates of revisit to the inpatient or emergency department setting ranged from 6.2% (appendicitis) to 11.0% (mood disorders). Study hospitals (n = 958) had low condition-specific visit volumes (37.0%–82.8% of hospitals had &lt;25 visits). The only condition with &gt;1% of hospitals labeled as different from the mean on 30-day risk-standardized revisit rates was mood disorders (4.2% of hospitals [n = 15], range of hospital performance 6.3%–15.9%).

CONCLUSIONS:
We found that when comparing hospitals’ performances to the average, few hospitals that care for children are identified as high- or low-performers for revisits, even for common pediatric diagnoses, likely due to low hospital volumes. This limits the usefulness of condition-specific readmission or revisit measures in pediatric quality measurement.
ADHD and Learning Disabilities in Former Late Preterm Infants: A Population-Based Birth Cohort
Authors: Harris Malinda N. , Voigt Robert G. , Barbaresi William J. , Voge Gretchen A. , Killian Jill M. , Weaver Amy L. , Colby Christopher E. , Carey William A. , Katusic Slavica K. 
Published: August 2013

BACKGROUND AND OBJECTIVE:
Previous studies suggest that former late preterm infants are at increased risk for learning and behavioral problems compared with term infants. These studies have primarily used referred clinical samples of children followed only until early school age. Our objective was to determine the cumulative incidence of attention deficit/hyperactivity disorder (ADHD) and learning disabilities (LD) in former late preterm versus term infants in a population-based birth cohort.

METHODS:
Subjects included all children born 1976 to 1982 in Rochester, MN who remained in the community after 5 years. This study focused on the comparison of subjects in 2 subgroups, late preterm (34 to &lt;37 weeks) and term (37 to &lt;42 weeks). School and medical records were available to identify individuals who met research criteria for ADHD and LD in reading, written language, and math. The Kaplan-Meier method was used to estimate the cumulative incidence of each condition by 19 years of age. Cox models were fit to evaluate the association between gestational age group and condition, after adjusting for maternal education and perinatal complications.

RESULTS:
We found no statistically significant differences in the cumulative incidence of ADHD or LD between the late preterm (N = 256) versus term (N = 4419) groups: ADHD (cumulative incidence by age 19 years, 7.7% vs 7.2%; P = .84); reading LD (14.2% vs 13.1%; P = .57); written language LD (13.5% vs 15.7%; P = .36), and math LD (16.1% vs 15.5%; P = .89).

CONCLUSIONS:
These data from a population-based birth cohort indicate that former late preterm infants have similar rates of LD and ADHD as term infants.
The Modernization of the Energy Sector in Poland vs. Poland’s Energy Security / Modernizacja sektora energii w polsce a bezpieczeństwo energetyczne Polski
Authors: Frączek Paweł , Kaliski Maciej , Siemek Paweł 
Published: August 2013

The paper discusses the essence of Poland’s energy security, decisive factors for its attainment and the structure of primary energy sources of the country. It describes the main problem areas in functioning of the energy sector in Poland, as well as the conditions for its modernization. The issues of increasing the natural gas share in the country’s structure of primary energy sources and a construction of the first nuclear power plant in Poland have been particularly emphasised. The paper stresses that without modernizing actions it will be impossible for Poland to fulfil international obligations concerning changes in the functioning of the energy sector.
The study, analysing the conditions for increasing the role of natural gas in Poland, points at the necessity to expand the gas infrastructure, to increase a scale of gas production from domestic deposits and to complete liberalization of the energy industry. It also emphasises that a potential delay in the construction of the country’s first nuclear power plant may limit competitiveness of the economy.
Experimental and Numerical Analysis of the air Flow in T-Shape Channel Flow / Eksperymentalna i numeryczna analiza przepływu powietrza przez skrzyżowanie kanałów w kształcie litery T
Authors: Szmyd Janusz , Branny Marian , Karch Michal , Wodziak Waldemar , Jaszczur Marek , Nowak Remigiusz 
Published: August 2013

This paper presents the results of experimental and numerical investigations of air flow through the crossing of a mining longwall and ventilation gallery. The object investigated consists of airways (headings) arranged in a T-shape. Maintained for technological purposes, the cave is exposed particularly to dangerous accumulations of methane.
The laboratory model is a certain simplification of a real longwall and ventilation gallery crossing. Simplifications refer to both the object’s geometry and the air flow conditions. The aim of the research is to evaluate the accuracy with which numerical simulations model the real flow. Stereo Particle Image Velocimetry (SPIV) was used to measure all velocity vector components. Three turbulence models were tested: standard k-ε, k-ε realizable and the Reynolds Stress Model (RSM). The experimental results have been compared against the results of numerical simulations. Good agreement is achieved between all three turbulence model predictions and measurements in the inflow and outflow of the channel. Large differences between the measured and calculated velocity field occur in the cavity zone. Two models, the standard k-ε and k-ε realizable over-predict the measure value of the streamwise components of velocity. This causes the ventilation intensity to be overestimated in this domain. The RSM model underestimates the measure value of streamwise components of velocity and therefore artificially decreases the intensity of ventilation in this zone. The RSM model provides better predictions than the standard k-ε and k-ε realizable in the cavity zone.
Cuttings Transport with Foam in Highly Inclined Wells at Simulated Downhole Conditions / Transport urobku wiertniczego przy użyciu piany w silnie nachylonych otworach w symulowanych warunkach w otworze
Authors: Xu Jiafu , Ozbayoglu Evren , Miska Stefan Z. , Yu Mengjiao , Takach Nicholas 
Published: August 2013

Along with the rapidly growing demand and development activities in unconventional resources, is the growth of environmental awareness and concerns among the public. Foam, as an alternative to traditional drilling fluid, is gaining more and more momentum in the drilling industry. Drilling with foam can minimize formation damage, water usage, and drag and torque. Foam also costs less and leaves a much smaller environmental footprint than other commonly used drilling fluids, such as synthetic oil-based fluids, when developing vulnerable formations such as shale gas. As drilling in horizontal and near horizontal sections has become very common, and the need for such sections is increasing, it is very important to understand cuttings transport and hole cleaning issues when drilling with foam in such sections.
A team from University of Tulsa Drilling Research Projects (TUDRP) conducted a series of experiments focused on studying the effects of change in hole inclination angle from 90 degrees to 70 degrees on cuttings transport with foam under Elevated Pressure and Elevated Temperature (EPET) conditions. This experimental and theoretical study also includes other influential parameters such as foam quality, foam flow rate, polymer concentration and drill pipe rotary speed. We have observed that there is no significant difference in cuttings concentration and frictional pressure losses as inclination changes from 70 to 90 degrees. Also, an increase in superficial foam velocity reduces cuttings concentration within the annulus. Pipe rotation influences cuttings concentration and frictional pressure losses for low quality foams, but does not have a significant effect on high quality foams.
A correlation for the cuttings bed area and a computer simulator are developed for practical design and field applications. The predicted results are compared with experimental results from this study and previous studies. The comparison shows good agreement.
We believe that the findings of this paper will help designers with the choice of optimal drilling fluid for drilling horizontal wells in unconventional (shale) gas/oil reservoirs.