bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods
Authors: Hickey John M , Gorjanc Gregor 
Published: April 2012

Abstract
An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quantitative trait loci effects, and with sequence and single nucleotide polymorphism-phased alleles and genotypes. Ten replicates of a representative scenario used to study genomic selection in livestock were generated and have been made publically available. The simulated data sets were structured to encompass a spectrum of additive quantitative trait loci effect distributions, relationship structures, and single nucleotide polymorphism chip densities.
Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis
Authors: Kurihara Yukio , Schmitz Robert J , Nery Joseph R , Schultz Matthew D , Okubo-Kurihara Emiko , Morosawa Taeko , Tanaka Maho , Toyoda Tetsuro , Seki Motoaki , Ecker Joseph R 
Published: April 2012

Abstract
Eukaryotes possess several RNA surveillance mechanisms that prevent undesirable aberrant RNAs from accumulating. Arabidopsis XRN2, XRN3, and XRN4 are three orthologs of the yeast 5′-to-3′ exoribonuclease, Rat1/Xrn2, that function in multiple RNA decay pathways. XRN activity is maintained by FIERY1 (FRY1), which converts the XRN inhibitor, adenosine 3′, 5′-bisphosphate (PAP), into 5′AMP. To identify the roles of XRNs and FRY1 in suppression of non-coding RNAs, strand-specific genome-wide tiling arrays and deep strand-specific RNA-Seq analyses were carried out in fry1 and xrn single and double mutants. In fry1-6, about 2000 new transcripts were identified that extended the 3′ end of specific mRNAs; many of these were also observed in genotypes that possess the xrn3-3 mutation, a partial loss-of-function allele. Mutations in XRN2 and XRN4 in combination with xrn3-3 revealed only a minor effect on 3′ extensions, indicating that these genes may be partially redundant with XRN3. We also observed the accumulation of 3′ remnants of many DCL1-processed microRNA (miRNA) precursors in fry1-6 and xrn3-3. These findings suggest that XRN3, in combination with FRY1, is required to prevent the accumulation of 3′ extensions that arise from thousands of mRNA and miRNA precursor transcripts.
A Common Dataset for Genomic Analysis of Livestock Populations
Authors: Cleveland Matthew A , Hickey John M , Forni Selma 
Published: April 2012

Abstract
Although common datasets are an important resource for the scientific community and can be used to address important questions, genomic datasets of a meaningful size have not generally been available in livestock species. We describe a pig dataset that PIC (a Genus company) has made available for comparing genomic prediction methods. We also describe genomic evaluation of the data using methods that PIC considers best practice for predicting and validating genomic breeding values, and we discuss the impact of data structure on accuracy. The dataset contains 3534 individuals with high-density genotypes, phenotypes, and estimated breeding values for five traits. Genomic breeding values were calculated using BayesB, with phenotypes and de-regressed breeding values, and using a single-step genomic BLUP approach that combines information from genotyped and un-genotyped animals. The genomic breeding value accuracy increased with increased trait heritability and with increased relationship between training and validation. In nearly all cases, BayesB using de-regressed breeding values outperformed the other approaches, but the single-step evaluation performed only slightly worse. This dataset was useful for comparing methods for genomic prediction using real data. Our results indicate that validation approaches accounting for relatedness between populations can correct for potential overestimation of genomic breeding value accuracies, with implications for genotyping strategies to carry out genomic selection programs.
Predicting the Fission Yeast Protein Interaction Network
Authors: Pancaldi Vera , Saraç Ömer S , Rallis Charalampos , McLean Janel R , Převorovský Martin , Gould Kathleen , Beyer Andreas , Bähler Jürg 
Published: April 2012

AbstractA systems-level understanding of biological processes and information flow requires the mapping of cellular component interactions, among which protein–protein interactions are particularly important. Fission yeast (Schizosaccharomyces pombe) is a valuable model organism for which no systematic protein-interaction data are available. We exploited gene and protein properties, global genome regulation datasets, and conservation of interactions between budding and fission yeast to predict fission yeast protein interactions in silico. We have extensively tested our method in three ways: first, by predicting with 70–80% accuracy a selected high-confidence test set; second, by recapitulating interactions between members of the well-characterized SAGA co-activator complex; and third, by verifying predicted interactions of the Cbf11 transcription factor using mass spectrometry of TAP-purified protein complexes. Given the importance of the pathway in cell physiology and human disease, we explore the predicted sub-networks centered on the Tor1/2 kinases. Moreover, we predict the histidine kinases Mak1/2/3 to be vital hubs in the fission yeast stress response network, and we suggest interactors of argonaute 1, the principal component of the siRNA-mediated gene silencing pathway, lost in budding yeast but preserved in S. pombe. Of the new high-quality interactions that were discovered after we started this work, 73% were found in our predictions. Even though any predicted interactome is imperfect, the protein network presented here can provide a valuable basis to explore biological processes and to guide wet-lab experiments in fission yeast and beyond. Our predicted protein interactions are freely available through PInt, an online resource on our website (www.bahlerlab.info/PInt).
FASTER MT: Isolation of Pure Populations ofaand α Ascospores fromSaccharomycescerevisiae
Authors: Chin Brian L , Frizzell Margaret A , Timberlake William E , Fink Gerald R 
Published: April 2012

AbstractThe budding yeast Saccharomyces cerevisiae has many traits that make it useful for studies of quantitative inheritance. Genome-wide association studies and bulk segregant analyses often serve as first steps toward the identification of quantitative trait loci. These approaches benefit from having large numbers of ascospores pooled by mating type without contamination by vegetative cells. To this end, we inserted a gene encoding red fluorescent protein into the MATa locus. Red fluorescent protein expression caused MATa and a/α diploid vegetative cells and MATa ascospores to fluoresce; MATα cells without the gene did not fluoresce. Heterozygous diploids segregated fluorescent and nonfluorescent ascospores 2:2 in tetrads and bulk populations. The two populations of spores were separable by fluorescence-activated cell sorting with little cross contamination or contamination with diploid vegetative cells. This approach, which we call Fluorescent Ascospore Technique for Efficient Recovery of Mating Type (FASTER MT), should be applicable to laboratory, industrial, and undomesticated, strains.
Contrasting Mutation Rates from Specific-Locus and Long-Term Mutation-Accumulation Procedures
Authors: Drake John W 
Published: April 2012

Abstract
Until recently, the two predominant ways to estimate mutation rates were the specific-locus method and the mutation-accumulation (Bateman-Mukai) method. Both involve seeding a number of parallel lines from a small, genetically uniform population, growing as long as is feasible but not so long as to allow selection to perturb mutant frequencies, and sometimes using extreme bottlenecks to facilitate the retention of deleterious mutations. In the specific-locus method, mutations are selected according to their specific phenotypes and are confirmed by sequencing. In older versions of the mutation-accumulation method, the increase in variance of a quantitative fitness trait is measured and converted into a mutation rate. More recently, a variation on the mutation-accumulation method has become possible based on phenotype-blind genomic sequencing, which might (or might not) provide improved sampling breadth, usually at the expense of sample size. In a recent study, genomic sequencing was applied to Escherichia coli lines propagated for 40,000 generations and passaged daily via 5,000,000 cells. To mitigate the impact of selection, the only targets employed for rate calculations were putatively neutral synonymous mutations. The mutation rate estimate was about 6-fold lower than obtained previously with a robust specific-locus method. Here I argue that purifying selection acting to shape the strong codon preferences of E. coli is the probable cause of the lower estimate, rather than, for instance, a lower mutation rate in nature than in the laboratory.
A Systematic Genetic Screen to Dissect the MicroRNA Pathway inDrosophila
Authors: Pressman Sigal , Reinke Catherine A , Wang Xiaohong , Carthew Richard W 
Published: April 2012

AbstractA central goal of microRNA biology is to elucidate the genetic program of miRNA function and regulation. However, relatively few of the effectors that execute miRNA repression have been identified. Because such genes may function in many developmental processes, mutations in them are expected to be pleiotropic and thus are discarded in most standard genetic screens. Here, we describe a systematic screen designed to identify all Drosophila genes in ∼40% of the genome that function in the miRNA pathway. To identify potentially pleiotropic genes, the screen analyzed clones of homozygous mutant cells in heterozygous animals. We identified 45 mutations representing 24 genes, and we molecularly characterized 9 genes. These include 4 previously known genes that encode core components of the miRNA pathway, including Drosha, Pasha, Dicer-1, and Ago1. The rest are new genes that function through chromatin remodeling, signaling, and mRNA decapping. The results suggest genetic screens that use clonal analysis can elucidate the miRNA program and that ∼100 genes are required to execute the miRNA program.
Hypopigmentation and Maternal-Zygotic Embryonic Lethality Caused by a Hypomorphic Mbtps1 Mutation in Mice
Authors: Rutschmann Sophie , Crozat Karine , Li Xiaohong , Du Xin , Hanselman Jeffrey C , Shigeoka Alana A , Brandl Katharina , Popkin Daniel L , McKay Dianne B , Xia Yu , Moresco Eva Marie Y , Beutler Bruce 
Published: April 2012

Abstract
The site 1 protease, encoded by Mbtps1, mediates the initial cleavage of site 2 protease substrates, including sterol regulatory element binding proteins and CREB/ATF transcription factors. We demonstrate that a hypomorphic mutation of Mbtps1 called woodrat (wrt) caused hypocholesterolemia, as well as progressive hypopigmentation of the coat, that appears to be mechanistically unrelated. Hypopigmentation was rescued by transgenic expression of wild-type Mbtps1, and reciprocal grafting studies showed that normal pigmentation depended upon both cell-intrinsic or paracrine factors, as well as factors that act systemically, both of which are lacking in wrt homozygotes. Mbtps1 exhibited a maternal-zygotic effect characterized by fully penetrant embryonic lethality of maternal-zygotic wrt mutant offspring and partial embryonic lethality (~40%) of zygotic wrt mutant offspring. Mbtps1 is one of two maternal-zygotic effect genes identified in mammals to date. It functions nonredundantly in pigmentation and embryogenesis.
Effects of Description of Options on Parental Perinatal Decision-Making
Authors: Haward Marlyse F. , John Leslie K. , Lorenz John M. , Fischhoff Baruch 
Published: April 2012

OBJECTIVE:
To examine whether parents’ delivery room management decisions for extremely preterm infants are influenced by (1) the degree of detail with which options (comfort care [CC] or intensive care [IC]) are presented or (2) their order of presentation.

METHODS:
A total of 309 volunteers, 18 to 55 years old, were each randomized to 1 of 4 groups: (1) detailed descriptions, CC presented first; (2) detailed descriptions, IC presented first; (3) brief descriptions, CC presented first; or (4) brief descriptions, IC presented first. Each received the description of a hypothetical delivery of a 23-week gestation infant and chose either IC or CC. Open-ended and structured questions elicited reasoning. Data were analyzed by χ2 and logistic regression analysis.

RESULTS:
Neither degree of detail, comparing groups 1+2 with 3+4 (37% vs 41%, odds ratio = 0.85, 95% confidence interval = 0.54–1.34, P = .48), nor order, comparing groups 1+3 with 2+4 (40% vs 37%, odds ratio = 0.88, 95% confidence interval = 0.56–1.39; P = .59), influenced the likelihood of choosing IC. Participants choosing IC were more likely to invoke sanctity of life and religiosity as personal values. Additional reasons for choosing IC were experiences with infants born at later gestational ages, giving the infant a chance, not watching their infant die, and equating CC with euthanasia. Some choosing CC wanted to avoid infant suffering.

CONCLUSIONS:
The degree of detail and order of presentation had no effect on treatment decisions, suggesting that individuals bring well-articulated preexisting preferences to such decisions. Understanding beliefs and attitudes motivating these preferences can assist physicians in helping parents make informed decisions consistent with their values.
Complementary and Alternative Medicine Use and Adherence With Pediatric Asthma Treatment
Authors: Philp Julie C. , Maselli Judy , Pachter Lee M. , Cabana Michael D. 
Published: April 2012

BACKGROUND AND OBJECTIVE:
Complementary and alternative medicine (CAM) use for pediatric asthma is increasing. The authors of previous studies linked CAM use with decreased adherence to conventional asthma medicines; however, these studies were limited by cross-sectional design. Our objective was to assess the effect of starting CAM on pediatric adherence with daily asthma medications.

METHODS:
We used a retrospective cohort study design. Telephone surveys were administered to caregivers of patients with asthma annually from 2004 to 2007. Dependent variables were percent missed doses per week and a previously validated “Medication Adherence Scale score.” Independent variables included demographic factors, caregiver perception of asthma control, and initiation of CAM for asthma. We used multivariate linear regression to assess the relationship between medication adherence and previous initiation of CAM.

RESULTS:
From our longitudinal data set of 1322 patients, we focused on 187 children prescribed daily medications for all 3 years of our study. Patients had high rates of adherence. The mean percent missed asthma daily controller medication doses per week was 7.7% (SD = 14.2%). Medication Adherence Scale scores (range: 4–20, with lower scores reflecting higher adherence) had an overall mean of 7.5 (SD = 2.9). In multivariate analyses, controlling for demographic factors and asthma severity, initiation of CAM use was not associated with subsequent adherence (P &gt; .05).

CONCLUSIONS:
The data from this study suggest that CAM use is not necessarily “competitive” with conventional asthma therapies; families may incorporate different health belief systems simultaneously in their asthma management. As CAM use becomes more prevalent, it is important for physicians to ask about CAM use in a nonjudgmental fashion.
Parental Separation and Pediatric Cancer: A Danish Cohort Study
Authors: Grant Sally , Carlsen Kathrine , Bidstrup Pernille Envold , Bastian Gro Samsø , Lund Lasse Wegener , Dalton Susanne Oksbjerg , Johansen Christoffer 
Published: April 2012

OBJECTIVE:
The purpose of this study was to determine the risk for separation (ending cohabitation) of the parents of a child with a diagnosis of cancer.

METHODS:
In a nationwide cohort, we compared the risk for ending cohabitation of the parents of 2450 children (aged 0–20 years) given a diagnosis of cancer with the risk of parents of 44 853 randomly selected, gender- and age-matched cancer-free children. We adjusted for socioeconomic position and demographic factors. Rate ratios and 95% confidence intervals for separation were estimated in a Cox proportional hazards model.

RESULTS:
The parents of children with cancer did not have a higher risk for separation than the general population (rate ratio: 1.00 [95% confidence interval: 0.91–1.10]). Separate analyses according to type of cancer and survival of the child similarly yielded null results.

CONCLUSIONS:
Experiencing cancer in a child does not seem to be a risk factor for separation. Our study will allow clinicians to reassure parents and to support them in facing the trauma of cancer in their child.
The Dance Between Attending Physicians and Senior Residents as Teachers and Supervisors
Authors: Balmer Dorene F. , Giardino Angelo P. , Richards Boyd F. 
Published: April 2012

OBJECTIVE:
To examine how attending physicians and senior residents negotiated shared responsibilities for teaching and supervising on clinical work rounds.

METHODS:
As part of a larger ethnographic field study, we observed clinical work rounds on a General Pediatrics ward over 8 months, and interviewed 14 of 18 attending physicians and 9 of 11 senior residents whom we observed. Struck by the frequency of 2 codes in that data set (“stand back” and “step up”), we used the metaphor of a dance as an analytic strategy for understanding the dynamic relationship between attending physicians and senior residents.

RESULTS:
Like a traditional dance with a priori choreography, and consistent with the traditional premise in graduate medical education, attending physicians frequently “stood back” and senior residents, accordingly, “stepped up” and took on teaching and supervising responsibilities. Less often, both attending physicians and senior residents assumed the lead, or attending physicians stepped up rather than entrust senior residents. The complex clinical context sometimes changed the choreography. Attending physicians and senior residents understood their mutual responsibilities but were not bound by them; they improvised to maintain high-quality patient care.

CONCLUSIONS:
The metaphor of a dance enabled us to better understand not only how attending physicians and senior residents negotiate shared responsibilities for teaching and supervision on clinical work rounds, but also how the clinical context impacts this negotiation. A better understanding of this negotiated relationship may help to clarify assumptions and set realistic expectations for what it might take for senior residents to assume progressive responsibility for these responsibilities in today’s clinical context.
Metabolic Effects of Replacing Sucrose by Isomaltulose in Subjects With Type 2 Diabetes
Authors: Brunner Stefanie , Holub Ines , Theis Stephan , Gostner Andrea , Melcher Ralph , Wolf Petra , Amann-Gassner Ulrike , Scheppach Wolfgang , Hauner Hans 
Published: April 2012

OBJECTIVE
To test the hypothesis that replacement of sucrose with isomaltulose in sweet foods and beverages improves metabolic control in patients with type 2 diabetes.

RESEARCH DESIGN AND METHODS
One hundred ten patients with type 2 diabetes were randomized to receive sweet foods containing either 50 g/day isomaltulose or sucrose for 12 weeks as part of their habitual diet under free-living conditions. HbA1c at 12 weeks was the primary outcome parameter.

RESULTS
In the final analysis comprising 101 patients, isomaltulose did not significantly affect HbA1c at 12 weeks (sucrose: 7.39 ± 0.78%; isomaltulose: 7.24 ± 0.76%; regression coefficient [b]: 0.02 [95% CI: −0.21 to 0.25], P = 0.844). Triglycerides at 12 weeks were significantly lower in the isomaltulose versus the sucrose group (b: 34.01 [6.59–61.44], P = 0.016). Other secondary parameters did not significantly differ between groups.

CONCLUSIONS
Isomaltulose did not influence glycemic control assessed as HbA1c in type 2 diabetes under free-living conditions but was associated with lower triglyceride levels.
Spring-block approach for crack patterns in glass
Authors: Horvát Emőke-Ágnes , Járai-Szabó Ferenc , Brechet Yves , Néda Zoltán 
Published: April 2012

Abstract
Fracture patterns resulting from point-like impact acting perpendicularly on the plane of a commercial sodalime glass plate is modelled by a spring-block system. The characteristic patterns consist of crack lines that are spreading radially from the impact point and concentric arcs intersecting these radial lines. Experimental results suggest that the number of radial crack lines is scaling linearly with the energy dissipated during the crack formation process. The elaborated spring-block model reproduces with success the observed fracture patterns and scaling law.
The Carter constant for inclined orbits about a massive Kerr black hole: near-circular, near-polar orbits
Authors: Komorowski Peter , Valluri Sree , Houde Martin 
Published: April 2012

Abstract
In an extreme mass-ratio binary black hole system, a non-equatorial orbit will list (i.e. increase its angle of inclination, i) as it evolves in Kerr spacetime. The abutment, a set of evolving, near-polar, retrograde orbits, for which the instantaneous Carter constant (Q) is at its maximum value (Q
X) for given values of latus rectum (l̃) and eccentricity (e), has been introduced as a laboratory in which the consistency of dQ/dt with corresponding evolution equations for d
l̃/dt and de/dt might be tested independently of a specific radiation back-reaction model. To demonstrate the use of the abutment as such a laboratory, a derivation of dQ/dt, based only on published formulae for d
l̃/dt and de/dt, was performed for elliptical orbits on the abutment. The resulting expression for dQ/dt matched the published result to the second order in e. We believe the abutment is a potentially useful tool for improving the accuracy of evolution equations to higher orders of e and l̃−.
Measurements of heavy flavor and di-electron production at STAR
Authors: Wang Gang 
Published: April 2012

Abstract
Heavy quarks are produced early in the relativistic heavy ion collisions, and provide an excellent probe into the hot and dense nuclear matter created at RHIC. In these proceedings, we will discuss recent STAR measurements of heavy flavor production, to investigate the heavy quark interaction with the medium. Electromagnetic probes, such as electrons, provide information on the various stages of the medium evolution without modification by final stage interactions. Di-electron production measurements by STAR will also be discussed.