bluuebunny/crossref_metadata_2025_split huggingface dataset:
ForestPMPlot: A Flexible Tool for Visualizing Heterogeneity Between Studies in Meta-analysis
Authors: Kang Eun Yong , Park Yurang , Li Xiao , Segrè Ayellet V , Han Buhm , Eskin Eleazar 
Published: August 2016

Abstract
Meta-analysis has become a popular tool for genetic association studies to combine different genetic studies. A key challenge in meta-analysis is heterogeneity, or the differences in effect sizes between studies. Heterogeneity complicates the interpretation of meta-analyses. In this paper, we describe ForestPMPlot, a flexible visualization tool for analyzing studies included in a meta-analysis. The main feature of the tool is visualizing the differences in the effect sizes of the studies to understand why the studies exhibit heterogeneity for a particular phenotype and locus pair under different conditions. We show the application of this tool to interpret a meta-analysis of 17 mouse studies, and to interpret a multi-tissue eQTL study.
Budding YeastSLX4Contributes to the Appropriate Distribution of Crossovers and Meiotic Double-Strand Break Formation on Bivalents During Meiosis
Authors: Higashide Mika , Shinohara Miki 
Published: August 2016

AbstractThe number and distribution of meiosis crossover (CO) events on each bivalent are strictly controlled by multiple mechanisms to assure proper chromosome segregation during the first meiotic division. In Saccharomyces cerevisiae, Slx4 is a multi-functional scaffold protein for structure-selective endonucleases, such as Slx1 and Rad1 (which are involved in DNA damage repair), and is also a negative regulator of the Rad9-dependent signaling pathway with Rtt107. Slx4 has been believed to play only a minor role in meiotic recombination. Here, we report that Slx4 is involved in proper intrachromosomal distribution of meiotic CO formation, especially in regions near centromeres. We observed an increase in uncontrolled CO formation only in a region near the centromere in the slx4∆ mutant. Interestingly, this phenomenon was not observed in the slx1∆, rad1∆, or rtt107∆ mutants. In addition, we observed a reduced number of DNA double-strand breaks (DSBs) and altered meiotic DSB distribution on chromosomes in the slx4∆ mutant. This suggests that the multi-functional Slx4 is required for proper CO formation and meiotic DSB formation.
Transcriptomic Analysis Identifies Candidate Genes Related to Intramuscular Fat Deposition and Fatty Acid Composition in the Breast Muscle of Squabs (Columba)
Authors: Ye Manhong , Zhou Bin , Wei Shanshan , Ding MengMeng , Lu Xinghui , Shi Xuehao , Ding Jiatong , Yang Shengmei , Wei Wanhong 
Published: August 2016

Abstract
Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.
Fluorescent Beads Are a Versatile Tool for StagingCaenorhabditis elegansin Different Life Histories
Authors: Nika Liberta , Gibson Taylor , Konkus Rebecca , Karp Xantha 
Published: August 2016

AbstractPrecise staging of Caenorhabditis elegans is essential for developmental studies in different environmental conditions. In favorable conditions, larvae develop continuously through four larval stages separated by molting periods. Distinguishing molting from intermolt larvae has been achieved using transgenes with molting reporters, therefore requiring strain constructions, or careful observation of individuals for pharyngeal pumping or behavioral quiescence. In unfavorable conditions, larvae can enter the stress-resistant and developmentally arrested dauer larva stage. Identifying dauer larvae has been based on their ability to withstand detergent selection, precluding identification of recovering animals or of mutants with defects in dauer morphogenesis. Here, we describe a simple method to distinguish molting larvae or dauer larvae from intermolt larvae that bypasses the limitations of current methods. Fluorescent latex beads are mixed with the bacterial food source and ingested by intermolt larvae and adults. Molting and dauer larvae do not feed, and therefore lack beads in their digestive tract. The presence of beads can be determined using a dissecting microscope at magnifications as low as 100 ×, or by using a wormsorter for high-throughput experiments. We find that continuously developing bead-lacking larvae display hallmarks of molting, including expression of the mlt-10::gfp molting marker and a lack of pharyngeal pumping. Furthermore, wild-type and mutant dauer larvae produced by any of three common methods are accurately identified by a lack of beads. Importantly, this method is effective in SDS-sensitive mutant backgrounds and can identify recovering dauer larvae, a stage for which there is no other method of positive selection.
ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Authors: Castandet Benoît , Hotto Amber M , Strickler Susan R , Stern David B 
Published: August 2016

Abstract
Although RNA-Seq has revolutionized transcript analysis, organellar transcriptomes are rarely assessed even when present in published datasets. Here, we describe the development and application of a rapid and convenient method, ChloroSeq, to delineate qualitative and quantitative features of chloroplast RNA metabolism from strand-specific RNA-Seq datasets, including processing, editing, splicing, and relative transcript abundance. The use of a single experiment to analyze systematically chloroplast transcript maturation and abundance is of particular interest due to frequent pleiotropic effects observed in mutants that affect chloroplast gene expression and/or photosynthesis. To illustrate its utility, ChloroSeq was applied to published RNA-Seq datasets derived from Arabidopsis thaliana grown under control and abiotic stress conditions, where the organellar transcriptome had not been examined. The most appreciable effects were found for heat stress, which induces a global reduction in splicing and editing efficiency, and leads to increased abundance of chloroplast transcripts, including genic, intergenic, and antisense transcripts. Moreover, by concomitantly analyzing nuclear transcripts that encode chloroplast gene expression regulators from the same libraries, we demonstrate the possibility of achieving a holistic understanding of the nucleus-organelle system. ChloroSeq thus represents a unique method for streamlining RNA-Seq data interpretation of the chloroplast transcriptome and its regulators.
Analysis of Plasminogen Genetic Variants in Multiple Sclerosis Patients
Authors: Sadovnick A Dessa , Traboulsee Anthony L , Bernales Cecily Q , Ross Jay P , Forwell Amanda L , Yee Irene M , Guillot-Noel Lena , Fontaine Bertrand , Cournu-Rebeix Isabelle , Alcina Antonio , Fedetz Maria , Izquierdo Guillermo , Matesanz Fuencisla , Hilven Kelly , Dubois Bénédicte , Goris An , Astobiza Ianire , Alloza Iraide , Antigüedad Alfredo , Vandenbroeck Koen , Akkad Denis A , Aktas Orhan , Blaschke Paul , Buttmann Mathias , Chan Andrew , Epplen Joerg T , Gerdes Lisa-Ann , Kroner Antje , Kubisch Christian , Kümpfel Tania , Lohse Peter , Rieckmann Peter , Zettl Uwe K , Zipp Frauke , Bertram Lars , Lill Christina M , Fernandez Oscar , Urbaneja Patricia , Leyva Laura , Alvarez-Cermeño Jose Carlos , Arroyo Rafael , Garagorri Aroa M , García-Martínez Angel , Villar Luisa M , Urcelay Elena , Malhotra Sunny , Montalban Xavier , Comabella Manuel , Berger Thomas , Fazekas Franz , Reindl Markus , Schmied Mascha C , Zimprich Alexander , Vilariño-Güell Carles 
Published: August 2016

Abstract
Multiple sclerosis (MS) is a prevalent neurological disease of complex etiology. Here, we describe the characterization of a multi-incident MS family that nominated a rare missense variant (p.G420D) in plasminogen (PLG) as a putative genetic risk factor for MS. Genotyping of PLG p.G420D (rs139071351) in 2160 MS patients, and 886 controls from Canada, identified 10 additional probands, two sporadic patients and one control with the variant. Segregation in families harboring the rs139071351 variant, identified p.G420D in 26 out of 30 family members diagnosed with MS, 14 unaffected parents, and 12 out of 30 family members not diagnosed with disease. Despite considerably reduced penetrance, linkage analysis supports cosegregation of PLG p.G420D and disease. Genotyping of PLG p.G420D in 14446 patients, and 8797 controls from Canada, France, Spain, Germany, Belgium, and Austria failed to identify significant association with disease (P = 0.117), despite an overall higher prevalence in patients (OR = 1.32; 95% CI = 0.93–1.87). To assess whether additional rare variants have an effect on MS risk, we sequenced PLG in 293 probands, and genotyped all rare variants in cases and controls. This analysis identified nine rare missense variants, and although three of them were exclusively observed in MS patients, segregation does not support pathogenicity. PLG is a plausible biological candidate for MS owing to its involvement in immune system response, blood-brain barrier permeability, and myelin degradation. Moreover, components of its activation cascade have been shown to present increased activity or expression in MS patients compared to controls; further studies are needed to clarify whether PLG is involved in MS susceptibility.
Php4 Is a Key Player for Iron Economy in Meiotic and Sporulating Cells
Authors: Brault Ariane , Rallis Charalampos , Normant Vincent , Garant Jean-Michel , Bähler Jürg , Labbé Simon 
Published: August 2016

Abstract
Meiosis is essential for sexually reproducing organisms, including the fission yeast Schizosaccharomyces pombe. In meiosis, chromosomes replicate once in a diploid precursor cell (zygote), and then segregate twice to generate four haploid meiotic products, named spores in yeast. In S. pombe, Php4 is responsible for the transcriptional repression capability of the heteromeric CCAAT-binding factor to negatively regulate genes encoding iron-using proteins under low-iron conditions. Here, we show that the CCAAT-regulatory subunit Php4 is required for normal progression of meiosis under iron-limiting conditions. Cells lacking Php4 exhibit a meiotic arrest at metaphase I. Microscopic analyses of cells expressing functional GFP-Php4 show that it colocalizes with chromosomal material at every stage of meiosis under low concentrations of iron. In contrast, GFP-Php4 fluorescence signal is lost when cells undergo meiosis under iron-replete conditions. Global gene expression analysis of meiotic cells using DNA microarrays identified 137 genes that are regulated in an iron- and Php4-dependent manner. Among them, 18 genes are expressed exclusively during meiosis and constitute new putative Php4 target genes, which include hry1+ and mug14+. Further analysis validates that Php4 is required for maximal and timely repression of hry1+ and mug14+ genes. Using a chromatin immunoprecipitation approach, we show that Php4 specifically associates with hry1+ and mug14+ promoters in vivo. Taken together, the results reveal that in iron-starved meiotic cells, Php4 is essential for completion of the meiotic program since it participates in global gene expression reprogramming to optimize the use of limited available iron.
Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat
Authors: Rutkoski Jessica , Poland Jesse , Mondal Suchismita , Autrique Enrique , Pérez Lorena González , Crossa José , Reynolds Matthew , Singh Ravi 
Published: August 2016

Abstract
Genomic selection can be applied prior to phenotyping, enabling shorter breeding cycles and greater rates of genetic gain relative to phenotypic selection. Traits measured using high-throughput phenotyping based on proximal or remote sensing could be useful for improving pedigree and genomic prediction model accuracies for traits not yet possible to phenotype directly. We tested if using aerial measurements of canopy temperature, and green and red normalized difference vegetation index as secondary traits in pedigree and genomic best linear unbiased prediction models could increase accuracy for grain yield in wheat, Triticum aestivum L., using 557 lines in five environments. Secondary traits on training and test sets, and grain yield on the training set were modeled as multivariate, and compared to univariate models with grain yield on the training set only. Cross validation accuracies were estimated within and across-environment, with and without replication, and with and without correcting for days to heading. We observed that, within environment, with unreplicated secondary trait data, and without correcting for days to heading, secondary traits increased accuracies for grain yield by 56% in pedigree, and 70% in genomic prediction models, on average. Secondary traits increased accuracy slightly more when replicated, and considerably less when models corrected for days to heading. In across-environment prediction, trends were similar but less consistent. These results show that secondary traits measured in high-throughput could be used in pedigree and genomic prediction to improve accuracy. This approach could improve selection in wheat during early stages if validated in early-generation breeding plots.
Parental Understanding of Hospital Course and Discharge Plan
Authors: Bhansali Priti , Washofsky Anne , Romrell Evan , Birch Sarah , Winer Jeffrey C. , Hoffner Wendy 
Published: August 2016

OBJECTIVES:
Hospital discharge marks an important transition in care from the inpatient team to the family and primary care provider. Parents must know the hospital course and discharge plan to care for their child at home and provide background for future providers. Our study aimed to determine parental knowledge of key aspects of their child’s hospital course and discharge plan and to identify markers of increased risk for incomplete or incorrect knowledge among participants.

METHODS:
We conducted a descriptive prospective cohort study of parents within 24 hours of hospital discharge. The primary outcome was concordance of parent responses to verbal interview questions about their child’s hospital treatment, laboratory testing, imaging, procedures and discharge plan with the medical record.

RESULTS:
Of 174 participants, 15% felt less than “completely prepared” to explain the hospital course to their primary care provider or to provide care after discharge. There was &gt;83% overall concordance with interview responses and the medical record, with concordance higher for hospital course events than discharge plan. There were few significant differences in understanding between trainee-based teams and the attending physician–run unit. No patient or family characteristics were consistently associated with poor understanding of hospital course or discharge plan.

CONCLUSIONS:
Although parents were generally knowledgeable about hospital course and discharge plan, areas for improved communication were identified. Individualized counseling about hospital course and discharge plan should be initiated for all parents early during hospitalization. Methods that assess and bolster caregiver comprehension and minimize dependence on written instructions may help with transition to outpatient care.
Diffuse Alveolar Hemorrhage as a Manifestation of Childhood-Onset Systemic Lupus Erythematosus
Authors: Singla Saimun , Canter Debra L. , Vece Timothy J. , Muscal Eyal , DeGuzman Marietta 
Published: August 2016

BACKGROUND:Diffuse alveolar hemorrhage (DAH) is a devastating clinical syndrome characterized by a falling hematocrit, respiratory insufficiency, and radiographic evidence of pulmonary infiltrates. Literature regarding management of DAH in childhood-onset SLE (cSLE) is limited.METHODS:We reviewed the presentation, management, and outcome of DAH in a pediatric tertiary medical center with one of the largest cSLE cohorts in North America. During a 10 year period 7 of 410 children with cSLE had DAH.RESULTS:The majority of cSLE patients with DAH were male (71%) and Hispanic (57%). The median age at the time of DAH diagnosis was 14 years (range 3 -15 years). DAH was the presenting manifestation of cSLE in 29% of children; 71% presented with DAH within 3 months of their diagnosis. All patients had cough, 86% had dyspnea, and 29% had hemoptysis. All patients had anemia and 71% had thrombocytopenia. Eighty-six percent had hematuria/proteinuria, and a positive anti-double stranded DNA antibody. Chest imaging showed diffuse ground glass opacities in all events. All patients developed respiratory insufficiency (29% supplemental oxygenation and 71% mechanical ventilation). Transfusions were required in 57% of cases. All patients received corticosteroids and additional immunomodulation to achieve disease control. Eighty-six percent of our DAH/cSLE cohort survived their initial event (median follow-up 2.5 years). No survivor required supplemental oxygen or had a DAH recurrence.CONCLUSIONS:SLE should be in the hospitalist's differential diagnosis for any child with respiratory insufficiency, cytopenias, and/or urinary abnormalities. Once cSLE is identified, initiation of aggressive immune suppression with multiple agents may enhance outcomes.
Trampoline Park and Home Trampoline Injuries
Authors: Kasmire Kathryn E. , Rogers Steven C. , Sturm Jesse J. 
Published: August 2016

BACKGROUND AND OBJECTIVE:Trampoline parks, indoor recreational facilities with wall-to-wall trampolines, are increasing in number and popularity. The objective was to identify trends in emergency department visits for trampoline park injuries (TPIs) and compare TPI characteristics with home trampoline injuries (HTIs).METHODS:Data on trampoline injuries from the National Electronic Injury Surveillance System from 2010 to 2014 were analyzed. Sample weights were applied to estimate yearly national injury trends; unweighted cases were used for comparison of injury patterns.RESULTS:Estimated US emergency department visits for TPI increased significantly, from 581 in 2010 to 6932 in 2014 (P = .045), whereas HTIs did not increase (P = .13). Patients with TPI (n = 330) were older than patients with HTI (n = 7933) (mean 13.3 vs 9.5 years, respectively, P &lt; .001) and predominantly male. Sprains and fractures were the most common injuries at trampoline parks and homes. Compared with HTIs, TPIs were less likely to involve head injury (odds ratio [OR] 0.64; 95% confidence interval [CI], 0.46–0.89), more likely to involve lower extremity injury (OR 2.39; 95% CI, 1.91–2.98), more likely to be a dislocation (OR 2.12; 95% CI, 1.10–4.09), and more likely to warrant admission (OR 1.76; 95% CI, 1.19–2.61). TPIs necessitating hospital admission included open fractures and spinal cord injuries. TPI mechanisms included falls, contact with other jumpers, and flips.CONCLUSIONS:TPI patterns differed significantly from HTIs. TPIs are an emerging concern; additional investigation and strategies are needed to prevent injury at trampoline parks.
Spring 2012
Authors: Lal Hamish 
Published: August 2016

It is an absolute pleasure to welcome readers to this issue of the ICE Construction Law Quarterly. In this issue, we look at a range of dispute avoidance/resolution procedures. Dispute Adjudication Boards are covered twice: firstly, we have an excellent article by Frederic Gillion dealing with the practical difficulties of enforcing a decision of a Dispute Adjudication Board and secondly we are delighted to publish an article from Dr Robert Gaitskell QC. Dr Gaitskell gives a view from the Board which will inform and perhaps tempt some readers to become more involved with DABs. Mediation is often viewed as an unnecessary expense (both in terms of cost and time) and we have reported on recent Court of Appeal guidance that suggests that a party needs to respond reasonably to an offer to mediate. We have also looked at more hard-edged procedures. In the context of adjudication please note that the ICE’s own adjudication procedure was examined by the Court of Appeal in Lanes Group plc v. Galliford Try Infrastructure Ltd and we report on the latest position on so-called ‘forum shopping’. We also consider whether an adjudicator still has the right to payment in circumstances where his decision is found to be non-binding. A related issue is discussed in the context of arbitration where we consider the concept of bias. Finally, as set out below we issue a ‘warning’ about the Bribery Act. This is a self-explanatory article and merits inclusion primarily because it deals with the first conviction. Feedback is very important to us and so please do email (hlal@jonesday.com) with your comments, thoughts and suggestions. This newsletter is for our readers and I strive to ensure that we make it as relevant and interesting as possible. May I please wish readers a very happy, healthy and constructive New Year.