bluuebunny/crossref_metadata_2025_split huggingface dataset:
Substantial Shifts in Ranking of California Hospitals by Hospital-Associated Methicillin-ResistantStaphylococcus aureusInfection Following Adjustment for Hospital Characteristics and Case Mix
Authors: Tehrani David M. , Phelan Michael J. , Cao Chenghua , Billimek John , Datta Rupak , Nguyen Hoanglong , Kwark Homin , Huang Susan S. 
Published: September 2014

Background.States have established public reporting of hospital-associated (HA) infections—including those of methicillin-resistantStaphylococcus aureus(MRSA)—but do not account for hospital case mix or postdischarge eventsObjective.Identify facility-level characteristics associated with HA-MRSA infection admissions and create adjusted hospital rankings.Methods.A retrospective cohort study of 2009–2010 California acute care hospitals. We defined HA-MRSA admissions as involving MRSA pneumonia or septicemia events arising during hospitalization or within 30 days after discharge. We used mandatory hospitalization and US Census data sets to generate hospital population characteristics by summarizing across admissions. Facility-level factors associated with hospitals’ proportions of HA-MRSA infection admissions were identified using generalized linear models. Using state methodology, hospitals were categorized into 3 tiers of HA-MRSA infection prevention performance, using raw and adjusted values.Results.Among 323 hospitals, a median of 16 HA-MRSA infections (range, 0–102) per 10,000 admissions was found. Hospitals serving a greater proportion of patients who had serious comorbidities, were from low-education zip codes, and were discharged to locations other than home were associated with higher HA-MRSA infection risk. Total concordance between all raw and adjusted hospital rankings was 0.45 (95% confidence interval, 0.40–0.51). Among 53 community hospitals in the poor-performance category, more than 20% moved into the average-performance category after adjustment. Similarly, among 71 hospitals in the superior-performance category, half moved into the average-performance category after adjustment.Conclusions.When adjusting for nonmodifiable facility characteristics and case mix, hospital rankings based on HA-MRSA infections substantially changed. Quality indicators for hospitals require adequate adjustment for patient population characteristics for valid interhospital performance comparisons.Infect Control Hosp Epidemiol2014;35(10):1263–1270
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface
Authors: Lajugie Julien , Fourel Nicolas , Bouhassira Eric E. 
Published: September 2014

Abstract
Summary: Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38.
Availability and implementation: GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu . The source code is available at https://github.com/JulienLajugie/GenPlay
Contact: eric.bouhassira@einstein.yu.edu or julien.lajugie@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Conditional U1 Gene Silencing inToxoplasma gondii
Authors: Pieperhoff Manuela S. , Pall Gurman S. , Jiménez-Ruiz Elena , Das Sujaan , Wong Eleanor H , Heng Joanne , Müller Sylke , Blackman Michael J , Meissner Markus 
Published: September 2014

AbstractIn absence of powerful siRNA approaches, the functional characterisation of essential genes in apicomplexan parasites, such asToxoplasma gondiiorPlasmodium falciparum,relies on conditional mutagenesis systems. Here we present a novel strategy based on U1 snRNP-mediated gene silencing. U1 snRNP is critical in pre-mRNA splicing by defining the exonintron boundaries. When a U1 recognition site is placed into the 3’-terminal exon or adjacent to the termination codon, pre-mRNA is cleaved at the 3’-end and degraded, leading to an efficient knockdown of the gene of interest (GOI). Here we describe a simple one-step approach that combines endogenous tagging with DiCre-mediated positioning of U1 recognition sites adjacent to the termination codon of the GOI which leads to a conditional knockdown of the GOI inKu80knockout and RHT. gondiitachyzoites. Specific knockdown mutants of the reporter gene GFP and several endogenous genes ofT. gondiiincluding the clathrin heavy chain gene 1(chc1), the vacuolar protein sorting gene 26 (vps26), and the dynamin-related protein C gene (drpC)were silenced using this new approach. This new gene silencing tool kit allows protein tracking and functional studies simultaneously.
Thinking aloud: effects on text comprehension by children with specific language impairment and their peers
Authors: McClintock Brenna , Pesco Diane , Martin‐Chang Sandra 
Published: September 2014

AbstractBackgroundMany lines of evidence now suggest that inferencing plays a substantial role in text comprehension. However, inferencing appears to be difficult for children with language impairments, many of whom are also struggling readers.AimsTo assess the effects of a ‘think‐aloud’ procedure on inference generation and narrative text comprehension by children with expressive–receptive specific language impairment (SLI) and age‐matched peers with typical language development (TLD).Methods & ProceduresAn SLI group (n = 12; mean age = 10;5) and an age‐matched TLD group (n = 12) participated in the study. Narrative passages were read silently by participants and simultaneously read aloud by the examiner in two conditions: (1) uninterrupted reading and (2) a think‐aloud, in which children verbalized their understanding as the text was read. Following the passages in both conditions, children responded to comprehension questions requiring either literal or inferential information (specifically, ‘informational’ and ‘causal’ inferences). The children's comprehension scores were analysed by group, condition and question type. The statements children generated during the think‐aloud were also compared by group and examined in relation to children's comprehension scores.Outcomes & ResultsThe SLI group scored lower than the TLD group on all questions (literal, informational and causal), in both conditions. For both groups, however, comprehension scores on all three types of questions increased when the think‐aloud procedure was implemented. During the think‐aloud, the SLI group generated a comparable number of literal statements compared with the TLD group, but fewer informational and causal statements. The number of causal statements children made correlated with their scores on the inferential comprehension questions.Conclusions & ImplicationsChildren with expressive–receptive SLI showed poorer comprehension of narrative texts than children with TLD, as expected. However, both groups’ comprehension improved when participating in the think‐aloud condition. While further investigation is warranted, the think‐aloud procedure shows promise as a strategy to enhance narrative text comprehension in school‐age children with, and without, language impairments.
Transmasculine people's vocal situations: a critical review of gender‐related discourses and empirical data
Authors: Azul David 
Published: September 2014

AbstractBackgroundTransmasculine people assigned female sex at birth but who do not identify with this classification have traditionally received little consideration in the voice literature. Some voice researchers and clinicians suggest that transmasculine people do not need attention because testosterone treatment leads to a satisfactory masculinization of their voice organs and voices. Others, however, argue that transmasculine people are a heterogeneous group whose members might not share the same body type, gender identity or desire for medical approaches to gender transitioning. Therefore, testosterone‐induced voice changes may not necessarily meet the needs and expectations of all transmasculine people.AimsTo evaluate the gender‐related discursive and empirical data about transmasculine people's vocal situations to identify gaps in the current state of knowledge and to make suggestions for future voice research and clinical practice.Methods & ProceduresA comprehensive review of peer‐reviewed academic and clinical literature was conducted. Publications were identified by searching seven electronic databases and bibliographies of relevant articles. Thirty‐one publications met inclusion criteria. Discourses and empirical data were analysed thematically. Potential problem areas that transmasculine people may experience were identified and the quality of evidence appraised.Main ContributionThe extent and quality of voice research conducted with transmasculine people so far was found to be limited. There was mixed evidence to suggest that transmasculine people's vocal situations could be regarded as problematic. The diversity that characterizes the transmasculine population received little attention and the complexity of the factors that contribute to a successful or unsuccessful vocal communication of gender in this group appeared to be under‐researched. While most transmasculine people treated with testosterone can expect a lowering of their pitch, it remains unclear whether the extent of the pitch change is enough to result in a voice that is recognized by others as male.Conclusions & ImplicationsMore research into the different factors affecting transmasculine people's vocal situations that takes account of the diversity within the population is needed.
Developing a universal reading comprehension intervention for mainstream primary schools within areas of social deprivation for children with and without language‐learning impairment: a feasibility study
Authors: McCartney Elspeth , Boyle James , Ellis Sue 
Published: September 2014

AbstractBackgroundSome children in areas of social deprivation in Scotland have lower reading attainment than neighbouring children in less deprived areas, and some of these also have lower spoken language comprehension skills than expected by assessment norms. There is a need to develop effective reading comprehension interventions that fit easily into the school curriculum and can benefit all pupils. A feasibility study of reading comprehension strategies with existing evidence of efficacy was undertaken in three mainstream primary schools within an area of social deprivation in west central Scotland, to decide whether further investigation of this intervention was warranted.AimsAims were to measure comprehension of spoken language and reading via standardised assessments towards the beginning of the school year (T1) in mainstream primary school classrooms within an area of social deprivation; to have teachers introduce previously‐validated text comprehension strategies, and to measure change in reading comprehension outcome measures towards the end of the year (T2).Methods & ProceduresA pre‐ and post‐intervention cohort design was used. Reading comprehension strategies were introduced to staff in participating schools and used throughout the school year as part of on‐going reading instruction. Spoken language comprehension was measured by TROG‐2 at T1, and reading progress by score changes from T1 to T2 on the WIAT‐IIUK‐T reading comprehension scale.Outcomes & ResultsForty‐seven pupils in five classes in three primary schools took part: 38% had TROG‐2 scores below the 10th centile. As a group, children made good reading comprehension progress, with a medium effect size of 0.46. Children with TROG‐2 scores below the 10th centile had lower mean reading scores than others at T1 and T2, although with considerable overlap. However, TROG‐2 did not make a unique contribution to reading progress: children below the 10th centile made as much progress as other children. The intervention was welcomed by schools, and the measure of reading comprehension proved responsive to change.ConclusionsThe outcomes suggest the reading intervention may be effective for children with and without spoken language comprehension difficulties, and warrants further investigation in larger, controlled, studies.
Comparing lignocellulose physiochemistry after decomposition by brown rot fungi with distinct evolutionary origins
Authors: Kaffenberger Justin T. , Schilling Jonathan S. 
Published: September 2014

SummaryAmong wood‐degrading fungi, lineages holding taxa that selectively metabolize carbohydrates without significant lignin removal (brown rot) are polyphyletic, having evolved multiple times from lignin‐removing white rot fungi. Given the qualitative nature of the ‘brown rot’ classifier, we aimed to quantify and compare the temporal sequence of carbohydrate removal among brown rot clades. Lignocellulose deconstruction was compared among fungi using distinct plant substrates (angiosperm, conifer, grass). Specifically, aspen, pine and corn stalk were harvested over a 16‐week time series from microcosms containing Gloeophyllum trabeum, Fomitopsis pinicola, Ossicaulis lignatilis, Fistulina hepatica, Serpula lacrymans, Wolfiporia cocos or Dacryopinax sp. After quantifying plant mass loss, a thorough compositional analysis was complemented by a saccharification test to determine wood cell wall accessibility. Mass loss and accessibility varied depending on fungal decomposer and substrate, and trajectories of loss for hemicellulosic components and cellulose differed among plant tissue types. At any given stage of decomposition, however, lignocellulose accessibility and the fraction remaining of carbohydrates and lignin within a plant tissue type were generally the same, regardless of fungal isolate. This suggests that the sequence of plant component removal at this typical scale of characterization is shared among these brown rot lineages, despite their diverse genomes and secretomes.
Critical Urban Theory versus Critical Urban Studies: A Review Debate
Authors: Marcuse Peter , Imbroscio David , Parker Simon , Davies Jonathan S. , Magnusson Warren 
Published: September 2014

AbstractCritical urban theory and critical urban studies form the subject of two recent edited collections on approaches to the analysis and transformation of the contemporary capitalist city. In an exchange of commentaries by the respective editors and contributors, the introduction explains the genesis of each book and previews some of the key observations. Peter Marcuse then offers his assessment of Critical Urban Studies: New Directions, which is reciprocated by a commentary on Cities for People, Not for Profit: Critical Urban Theory and the Right to the City by Jonathan Davies, David Imbroscio and Warren Magnusson.
Chest wall tumors and prosthetic reconstruction: A comparative analysis on functional outcome
Authors: Leuzzi Giovanni , Nachira Dania , Cesario Alfredo , Novellis Pierluigi , Petracca Ciavarella Leonardo , Lococo Filippo , Facciolo Francesco , Granone Pierluigi , Margaritora Stefano 
Published: September 2014

AbstractBackgroundTo address the question of how much chest‐wall (CW) resections and prosthetic reconstructions influence functional outcome.MethodsWe retrospectively reviewed 175 patients who underwent surgery for CW tumors. The clinical, histological, surgical, oncological, and functional factors were analyzed.ResultsWe performed: 75 rib resections; 20 sternal resections; 15 combined resections; and 27 lung resections. In 39 cases (22.2%) CW was stabilized with non‐rigid prosthesis (Vicryl‐mesh: 8 patients; Goretex‐mesh: 31 patients). Postoperative complications occurred in 22 cases (12.6%): a correlation with lung resection was evidenced by multivariate analysis (P = 0.025). Five‐year survival for primary and secondary tumors was 50% and 36%, respectively: multivariate analysis (P = 0.048) showed a worse survival in men only. In the prosthesis subset, pulmonary function tested as percentage of forced expiratory volume in one second (%FEV1) (pre: 87.1 ± 18.9%; post: 82.3 ± 23.0%, P = ns), percentage of forced vital capacity (pre: 94.1 ± 19.3%; post: 82.0 ± 21.6%, P = ns), diffusing capacity of the lungs for carbon monoxide (pre: 15.7 ± 7.4; post: 12.1 ± 4.1, P = ns) and paO2 (pre: 82.6 ± 10.9 mmHg; post: 83.9 ± 7.3 mmHg, P = ns) was slightly modified from pre to postoperative. Interestingly, the decline of FEV1% was lower in the prosthesis‐subset (4.1 ± 15.9%) compared with the subgroup who did not undergo prosthetic stabilization (17.5 ± 16.2%), but this difference was not statistically significant (P = ns).ConclusionBecause of the low decrease of lung parameters, CW prosthetic reconstruction could be helpful for avoiding postoperative worsening of functional outcome, mostly in patients with pre‐existing pulmonary diseases.
Hypothermia after cardiac arrest does not affect serum levels of neuron‐specific enolase and protein S‐100b
Authors: PFEIFER R. , FRANZ M. , FIGULLA H. R. 
Published: September 2014

BackgroundWe investigated the brain‐derived proteins neuron‐specific enolase (NSE) and protein S‐100b (S‐100b) in survivors of cardiac arrest who had either received therapeutic hypothermia (TH) or had not.MethodsIn a retrospective cohort study, we analysed serum levels of these two proteins over 5 days in 201 adult cardiac arrest survivors admitted to our intensive care unit between 2003 and 2010. These were all survivors that remained comatose and survived at least 48 h. Of these, 140 received therapeutic hypothermia (hypothermia group). The remainder received only standard therapy without hypothermia (normothermia group).ResultsThere was no difference in survival between the hypothermia and normothermia groups. At 4 weeks after arrest, 61 (43.6%) patients of the hypothermia group and 26 (42.6%) patients of the normothermia group were still alive with favourable to moderate neurological outcome (Cerebral Performance Category Scale 1–3). We observed no change in the mean serum levels of either protein between the two groups. Within each group, we found significantly higher serum levels of NSE and S‐100b in patients with unfavourable neurological outcome (Cerebral Performance Category Scale 4 and 5) than in those with moderate to favourable outcome. Cut‐off levels 3 days after cardiac arrest predicting an unfavourable outcome were > 40 ng/ml for NSE [specificity 95.2%, Sensitivity 74.1%, areas under the curve (AUC):0.889], false positive rate 4 [confidence interval (CI): 0.0131–0.1175] and > 1.03 μg/1 for S‐100b (specificity 95.6%, Sensitivity 57.8%, AUC: 0.875) false positive rate 3 (CI: 0.0091–01218).ConclusionsAdditional application of TH was not associated with significant changes in serum levels of NSE and S‐100b in comatose survivors of cardiac arrest, compared to those treated without TH.
Identification of contemporary selection signatures using composite log likelihood and their associations with marbling score in Korean cattle
Authors: Ryu Jihye , Lee Chaeyoung 
Published: September 2014

SummaryPositive selection not only increases beneficial allele frequency but also causes augmentation of allele frequencies of sequence variants in close proximity. Signals for positive selection were detected by the statistical differences in subsequent allele frequencies. To identify selection signatures in Korean cattle, we applied a composite log‐likelihood (CLL)‐based method, which calculates a composite likelihood of the allelic frequencies observed across sliding windows of five adjacent loci and compares the value with the critical statistic estimated by 50 000 permutations. Data for a total of 11 799 nucleotide polymorphisms were used with 71 Korean cattle and 209 foreign beef cattle. As a result, 147 signals were identified for Korean cattle based on CLL estimates (P < 0.01). The signals might be candidate genetic factors for meat quality by which the Korean cattle have been selected. Further genetic association analysis with 41 intragenic variants in the selection signatures with the greatest CLL for each chromosome revealed that marbling score was associated with five variants. Intensive association studies with all the selection signatures identified in this study are required to exclude signals associated with other phenotypes or signals falsely detected and thus to identify genetic markers for meat quality.
A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations
Authors: Chan Jackie T. , Sherwin William B. , Taylor Matthew D. 
Published: September 2014

SummaryStock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive‐bred organisms into natural systems. Use of wild‐caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild‐caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment‐limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post‐larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post‐larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild‐caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre‐release hatchery stocks.
Fibrinous pericarditis and pericardial effusion in three neonatal foals
Authors: Armstrong SK , Raidal SL , Hughes KJ 
Published: September 2014

Case seriesThree foals, aged between 5 and 10 days, were presented for assessment of lethargy, abdominal pain and joint effusion. Fibrinous pericarditis and pericardial effusion (PE) were recognised in each foal and considered as sequelae to systemic inflammatory response syndrome (SIRS) and suspected or confirmed septicaemia.Clinical course and outcomeDiagnosis of pericarditis was made in two foals by echocardiographic examination and analysis of pericardial fluid, and during postmortem examination of the third foal. In both of the foals that underwent pericardiocentesis,PEwas an exudate, no bacteria were identified on cytological analysis and bacterial culture was negative. Despite apparent response to treatment, two foals died 2 and 3 weeks, respectively, after discharge from hospital. One foal was euthanased during hospitalisation.Conclusion and clinical relevanceThis report highlights the need to consider the development of pericarditis andPEin foals withSIRSand signs of cardiorespiratory dysfunction, and the requirement for protracted follow‐up to monitor for clinical resolution.