bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contamination of urinary cultures in initial-stream versus later-stream urine in children undergoing bladder catheterization for the diagnosis of urinary tract infection
Authors: Megged Orli , Zilberstein Liron , Ben Shalom Efrat , Erlichman Matityahu 
Published: March 2016

Background
Urine cultures obtained by bladder catheterization can be contaminated by bacteria colonizing the distal urethra. Data are inconclusive regarding the potential advantage of discarding the first few urine drops obtained by bladder catheterization and testing only the sample of late-stream urine, thus reducing the likelihood of urine culture contamination.

Aim
The aim of this study was to evaluate whether the incidence of contaminated urine cultures obtained by bladder catheterization can be reduced by splitting urine samples into ‘initial’ and ‘late’ samples and using only ‘late’ samples for culture.

Methods
Urine samples obtained by bladder catheterization from children younger than 2 years being evaluated for urinary tract infection were prospectively collected. Quantitative culture results were compared between initial-stream and late-stream urine samples.

Results
A total of 199 urine culture pairs of initial and late samples were compared. When using a cutoff value of at least 10 000 colony forming units/ml, late samples were superior to the initial ones in reducing contamination of urine cultures (P=0.029).

Conclusion
When obtaining urine cultures by bladder catheterization in children younger than 2 years, discarding the first few urine drops and using only the late stream for culture reduces false-positive culture results and improves the accuracy of urinary tract infection diagnosis.
Pediatric Emergency Department Study of Cardiac Risk in the Novel Patient (PED SCReeN)
Authors: Horeczko Timothy , Park Jeanny K. , Mann Courtney , Milazzo Angelo 
Published: March 2016

Objective
We compare pediatric cardiac risk classification and management recommendations between emergency physicians (EPs) and pediatric cardiologists (PCs) in children with a suspected new cardiac disorder.

Methods
We prospectively compared the work-up, assessment, classification, and disposition of patients aged 0 to 21 years presenting to the emergency department with a potential cardiac etiology in whom an electrocardiogram (ECG) was performed. The criterion standard was a blinded assessment by the PC-electrophysiologist after review of the history, physical examination, ancillary tests, and ECG.

Results
In 508 subjects, the median age was 15 years (interquartile range, 11–17 years), with a slight female predominance (281, 55.3%). The most common reasons for obtaining an ECG were: chest pain (158, 31.1%) and syncope, presyncope, or possible seizure (146, 28.7%). The most common auxiliary study was a chest radiograph (432, 85% of subjects). A total of 617 electrocardiographic diagnoses were made by EPs and 984 diagnoses by PCs. Sensitivities and specificities varied by discrete class, but disposition decisions were concordant (home or admission). The EPs were highly accurate for the need for emergent cardiology involvement (area under the curve, 0.89).

Conclusions
The EPs and PCs agreed on the evaluation and disposition of children at either low risk or high risk for an acute cardiac presentation in the emergency department. There was considerable variation in management recommendations in the intermediate risk children needing cardiology outpatient follow-up. We recommend the development and implementation of focused training modules on emergency pediatric cardiology and increased communication with pediatric cardiology to improve patient safety and resource utilization.
How Long Does it Take to Diagnose Appendicitis? Time Point Process Mapping in the Emergency Department
Authors: Abbas Paulette I. , Zamora Irving J. , Elder Simone C. , Brandt Mary L. , Lopez Monica E. , Orth Robert C. , Bisset George S. , Cruz Andrea T. 
Published: March 2016

Objectives
Appendicitis is the most common surgical emergency encountered in the pediatric emergency department (ED). We analyzed the time course of children evaluated for suspected appendicitis in relation to implementation of a risk-stratified ultrasound scoring system and structured reporting template (Appy-Score).

Methods
In July 2013, a 6-level ultrasound (US)-based appendicitis scoring system was developed and implemented. The records of children (age ≤18 years) who underwent limited abdominal US exams for suspected appendicitis at a large academic pediatric ED were reviewed retrospectively. Time periods evaluated were from January 1 to April 1, 2013 (before implementation of the US scoring system, “PRE”) and July 1 to October 1, 2013 (after implementation of the US scoring system, “POST”). Times are presented as medians with interquartile range.

Results
A total of 926 children were included (median age, 9.5 years [range, 0.1–18 years]; 49% female). Four hundred eighty-one patients were evaluated PRE and 445 POST. When comparing the 2 groups, there were no differences in the PRE and POST periods with regard to time from US ordered to first read (102 vs 112 minutes, P = 0.30), US ordered to disposition (215 vs 208 minutes, P = 0.40) and operating room posting (121 vs 122 minutes, P = 0.59), and overall ED stay (329 vs 333 minutes, P = 0.39).

Conclusions
The development of a radiographic appendicitis score, although allowing for a standardized reporting method, did not significantly alter the ED process flow for evaluation of appendicitis. This reflects the complexities in ED throughput and reveals the need for additional factors to change to improve patient flow.
Temporal Changes of Texture Features Extracted From Pulmonary Nodules on Dynamic Contrast-Enhanced Chest Computed Tomography
Authors: Kim Hyungjin , Park Chang Min , Park Sang Joon , Song Yong Sub , Lee Jong Hyuk , Hwang Eui Jin , Goo Jin Mo 
Published: March 2016

Objectives
The aim of this study was to describe the temporal changes of various texture features extracted from pulmonary nodules on dynamic contrast-enhanced computed tomography (DCE-CT) and to compare the feature values among multiple scanning time points. We also aimed to analyze the variability of texture features across multiple scan delay times.

Materials and Methods
This retrospective study was approved by the institutional review board of Seoul National University Hospital with waiver of patients' informed consent. Twenty patients (M:F, 6:14; mean age, 60.25 ± 11.97 years) with 20 lung nodules (mean size, 24.1 ± 12.3 mm) underwent DCE-CT with multiple scan delays (30, 60, 90, 120, 150, 180, 210, 240, 300, and 480 seconds) after precontrast scans. Lung nodule segmentation and texture feature extraction were performed at each time point using in-house software. Texture feature values were compared among the multiple time points using the Friedman test with post hoc pairwise Wilcoxon signed rank test. In addition, the dynamic range (DR) reflecting the variability between 2 time points to the interpatient range was calculated. Thereafter, we determined the stable time range that met both “DR greater than 0.90” and “no statistically significant difference” between all time point pairs for each feature. The degree of variability across all scan delay times was obtained using coefficients of variation.

Results
Standard deviation, variance, entropy, sphericity, discrete compactness, gray-level cooccurrence matrix (GLCM) inverse difference moment (IDM), GLCM contrast, and GLCM entropy did not show significant differences between scan delays of 30 and 180 seconds with DR greater than 0.90 between all time point pairs. When the range was narrowed down to 60 to 150 seconds, an additional 2 values (mean and homogeneity) showed stability. Among the 13 texture features, entropy, sphericity, discrete compactness, and GLCM entropy exhibited the lowest variability (coefficient of variation ≤5%).

Conclusions
Most texture features exhibited stability with low variation between 60 and 150 seconds on DCE-CT. Thus, texture features extracted from contrast-enhanced CT with a scan delay range of 60 to 150 seconds can be used for tumor characterization despite the heterogeneity in delay time.
The Effects of Ribosome Autocatalysis and Negative Feedback in Resource Competition
Authors: Chandra Fiona A , Del Vecchio Domitilla 
Published: March 2016

AbstractBackgroundResource competition, and primarily competition for ribosomes, can lead to unexpected behavior of genetic circuits and has recently gained renewed attention with both experimental and theoretical studies. Current models studying the effects of resource competition assume a constant production of ribosomes and these models describe the experimental results well. However, ribosomes are also autocatalytic since they are partially made of protein and autocatalysis has been shown to have detrimental effects on a system’s stability and robustness. Additionally, there are known feedback regulations on ribosome synthesis such as inhibition of rRNA synthesis via ppGpp.ResultsHere, we develop two-state models of ribosome and protein synthesis incorporating autocatalysis and feedback to investigate conditions under which these regulatory actions have a significant effect in situations of increased ribosome demand. Our modeling results indicate that for sufficiently low demand, defined by the mRNA level of synthetic genes, autocatalysis has little or no effect. However, beyond a certain demand level, the system goes through a transcritical bifurcation at which the only non-negative steady state is at zero ribosome concentration. The presence of negative feedback, in turn, can shift this point to higher demand values, thus restoring the qualitative behavior observed in a model with a constant ribosome production at low demand. However, autocatalysis affects the dynamics of the system and can lead to an overshoot in the temporal response of the synthetic genes to changes in induction level.ConclusionOur results show that ribosome autocatalysis has a significant effect on the system robustness to increases in ribosome demand, however the existing negative feedback on ribosome production compensates for the effects of the necessary autocatalytic loop and restores the behavior seen in the system with constant ribosome production. These findings explain why previous models with constant ribosome production reproduce the steady state behavior well, however incorporating autocatalysis and feedback is needed to capture the transient behavior.
The Ensembl Variant Effect Predictor
Authors: McLaren William , Gil Laurent , Hunt Sarah E , Riat Harpreet Singh , Ritchie Graham R. S. , Thormann Anja , Flicek Paul , Cunningham Fiona 
Published: March 2016

ABSTRACTThe Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation and prioritization of genomic variants, including in non-coding regions.The VEP accurately predicts the effects of sequence variants on transcripts, protein products, regulatory regions and binding motifs by leveraging the high quality, broad scope, and integrated nature of the Ensembl databases. In addition, it enables comparison with a large collection of existing publicly available variation data within Ensembl to provide insights into population and ancestral genetics, phenotypes and disease.The VEP is open source and free to use. It is available via a simple web interface (http://www.ensembl.org/vep), a powerful downloadable package, and both Ensembl’s Perl and REST application program interface (API) services.
Preprint: A robust peptidomics mass spectrometry platform for measuring oxytocin in plasma and serum
Authors: Brandtzaeg Ole Kristian , Johnsen Elin , Roberg-Larsen Hanne , Seip Knut Fredrik , Leknes Siri , Lundanes Elsa , Wilson Steven Ray 
Published: March 2016

AbstractCurrent approaches to measuring the cyclic peptide oxytocin in plasma/serum are associated with poor selectivity and/or inadequate sensitivity. We here describe a high performance nano liquid chromatography-mass spectrometry platform for measuring OT in human plasma/serum. The platform is extremely robust, allowing laborious sample clean-up steps to be omitted. OT binds strongly to plasma proteins, but a reduction/alkylation procedure breaks this bond, allowing ample detection of total OT. The method showed excellent quantitation properties, and was used to determine total OT levels to 0.5-1.2 ng/mL (evaluated with human plasma and cord serum). The method is compatible with accessible mass spectrometry instrumentation, finally allowing selective and easily comparable oxytocin measurements.
A Novel Initiation Pathway inEscherichia ColiTranscription
Authors: Lerner Eitan , Chung SangYoon , Allen Benjamin L. , Wang Shuang , Lee Jookyung J. , Lu Winson S. , Grimaud Wilson L. , Ingargiola Antonino , Michalet Xavier , Alhadid Yazan , Borukhov Sergei , Strick Terence , Taatjes Dylan J. , Weiss Shimon 
Published: March 2016

AbstractInitiation is a highly regulated, rate-limiting step in transcription. We employed a series of approaches to examine the kinetics of RNA polymerase (RNAP) transcription initiation in greater detail. Quenched kinetics assays, in combination with magnetic tweezer experiments and other methods, showed that, contrary to expectations, RNAP exit kinetics from later stages of initiation (e.g. from a 7-base transcript) was markedly slower than from earlier stages. Further examination implicated a previously unidentified intermediate in which RNAP adopted a long-lived backtracked state during initiation. In agreement, the RNAP-GreA endonuclease accelerated transcription kinetics from otherwise delayed initiation states and prevented RNAP backtracking. Our results indicate a previously uncharacterized RNAP initiation state that could be exploited for therapeutic purposes and may reflect a conserved intermediate among paused, initiating eukaryotic enzymes.Significance:Transcription initiation by RNAP is rate limiting owing to many factors, including a newly discovered slow initiation pathway characterized by RNA backtracking and pausing. This backtracked and paused state occurs when all NTPs are present in equal amounts, but becomes more prevalent with NTP shortage, which mimics cellular stress conditions. Pausing and backtracking in initiation may play an important role in transcriptional regulation, and similar backtracked states may contribute to pausing among eukaryotic RNA polymerase II enzymes.
Global transcriptional response of Dickeya dadantii to environmental stimuli relevant to the plant infection
Authors: Jiang Xuejiao , Zghidi‐Abouzid Ouafa , Oger‐Desfeux Christine , Hommais Florence , Greliche Nicolas , Muskhelishvili Georgi , Nasser William , Reverchon Sylvie 
Published: March 2016

SummaryDickeya species are soft rot disease‐causing bacterial plant pathogens and an emerging agricultural threat in Europe. Environmental modulation of gene expression is critical for Dickeya dadantii pathogenesis. While the bacterium uses various environmental cues to distinguish between its habitats, an intricate transcriptional control system coordinating the expression of virulence genes ensures efficient infection. Understanding of this behaviour requires a detailed knowledge of expression patterns under a wide range of environmental conditions, which is currently lacking. To obtain a comprehensive picture of this adaptive response, we devised a strategy to examine the D. dadantii transcriptome in a series of 32 infection‐relevant conditions encountered in the hosts. We propose a temporal map of the bacterial response to various stress conditions and show that D. dadantii elicits complex genetic behaviour combining common stress‐response genes with distinct sets of genes specifically induced under each particular stress. Comparison of our dataset with an in planta expression profile reveals the combined impact of stress factors and enables us to predict the major stress confronting D. dadantii at a particular stage of infection. We provide a comprehensive catalog of D. dadantii genomic responses to environmentally relevant stimuli, thus facilitating future studies of this important plant pathogen.
Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross‐fostering model
Authors: Bian Gaorui , Ma Shouqing , Zhu Zhigang , Su Yong , Zoetendal Erwin G. , Mackie Roderick , Liu Junhua , Mu Chunlong , Huang Ruihua , Smidt Hauke , Zhu Weiyun 
Published: March 2016

SummaryA reciprocal cross‐fostering model with an obese typical Chinese piglet breed and a lean Western breed was used to identify genetic and maternal effects on the acquisition and development gut bacteria from birth until after weaning. Pyrosequencing of 16S rRNA genes results revealed an age‐ and diet‐dependent bacterial succession process in piglets. During the first 3 days after birth, the bacterial community was relatively simple and dominated by Firmicutes with 79% and 65% relative abundance for Meishan and Yorkshire piglets, respectively. During the suckling period until day 14, the piglet breed and the nursing mother lead to increasing differentiation of the fecal bacterial community, with specific bacteria taxa associated with breed, and others with the nursing sow most likely due to its milk composition. Although the effect of nursing mother and the breed were evident through the suckling period, the introduction of solid feed and subsequent weaning were the major events occurring that dominated succession of the gut microbiota in the early life of piglets. This piglet cross‐fostering model is a useful tool for studying the effects of diet, host genetics and the environment on the development and acquisition of the gut microbiota and over longer studies the subsequent impact on growth, health and performance of pigs.
TRI6 and TRI10 play different roles in the regulation of deoxynivalenol (DON) production by cAMP signalling in Fusarium graminearum
Authors: Jiang Cong , Zhang Chengkang , Wu Chunlan , Sun Panpan , Hou Rui , Liu Huiquan , Wang Chenfang , Xu Jin‐Rong 
Published: March 2016

SummaryThe biosynthesis of mycotoxin deoxynivalenol (DON) in Fusarium graminearum is regulated by two pathway‐specific transcription factors Tri6 and Tri10 and affected by various host and environmental factors. In this study, we showed that cyclic adenosine monophosphate (cAMP) treatment induced DON production by stimulating TRI gene expression and DON‐associated cellular differentiation in F. graminearum. Interestingly, exogenous cAMP had no effects on the tri6 mutant but partially recovered the defect of tri10 mutant in DON biosynthesis. Although the two cAMP phosphodiesterase genes PDE1 and PDE2 had overlapping functions in vegetative growth, conidiation, sexual reproduction and plant infection, deletion of PDE2 but not PDE1 activated intracellular PKA activities and increased DON production. Whereas the tri6 pde2 mutant failed to produce DON, the tri10 pde2 double mutant produced a significantly higher level of DON than the tri10 mutant. Cellular differentiation associated with DON production was stimulated by exogenous cAMP or deletion of PDE2 in both tri10 and tri6 mutants. These data indicate that TRI6 is essential for the regulation of DON biosynthesis by cAMP signalling but elevated PKA activities could partially bypass the requirement of TRI10 for TRI gene‐expression and DON production, and Pde2 is the major cAMP phosphodiesterase to negatively regulate DON biosynthesis in F. graminearum.
Exchange of core chromosomes and horizontal transfer of lineage‐specific chromosomes in Fusarium oxysporum
Authors: Vlaardingerbroek Ido , Beerens Bas , Rose Laura , Fokkens Like , Cornelissen Ben J. C. , Rep Martijn 
Published: March 2016

SummaryHorizontal transfer of supernumerary or lineage‐specific (LS) chromosomes has been described in a number of plant pathogenic filamentous fungi. So far it was not known whether transfer is restricted to chromosomes of certain size or properties, or whether ‘core’ chromosomes can also undergo horizontal transfer. We combined a directed and a non‐biased approach to determine whether such restrictions exist. Selection genes were integrated into the genome of a strain of Fusarium oxysporum pathogenic on tomato, either targeted to specific chromosomes by homologous recombination or integrated randomly into the genome. By testing these strains for transfer of the marker to another strain we could confirm transfer of a previously described mobile pathogenicity chromosome. Surprisingly, we also identified strains in which (parts of) core chromosomes were transferred. Whole genome sequencing revealed that this was accompanied by the loss of the homologous region from the recipient strain. Remarkably, transfer of the mobile pathogenicity chromosome always accompanied this exchange of core chromosomes.
The frequency of mucosal‐associated invariant T cells is selectively increased in dermatitis herpetiformis
Authors: Li Jane , Reantragoon Rangsima , Kostenko Lyudmila , Corbett Alexandra Jane , Varigos George , Carbone Francis Robert 
Published: March 2016

AbstractBackground/ObjectivesMucosal‐associated invariant T (MAIT) cells are a novel subset of innate‐like T‐cells that are enriched in mucosal tissues. Their presence in human skin has only recently been recognised. We describe the expression of skin‐tropic molecules on human skin MAIT cells at steady state and investigate their contribution to various dermatoses with known T‐cell involvement.MethodsTo examine the expression of skin‐tropic molecules by MAIT cells at steady state, we performed a flow cytometric analysis of blood and skin samples from healthy donors. To investigate any potential wider contribution of MAIT cells to skin disease, we examined psoriasis, alopecia areata and dermatitis herpetiformis biopsies using immunofluorescent staining to identify the proportion of T‐cells expressing MAIT cell surface markers.ResultsWe found that MAIT cells constituted a small population of T‐cells in normal human skin, similar to the percentage found in peripheral blood. Like other skin T‐cells, skin MAIT cells expressed high levels of the skin‐associated markers, cutaneous lymphocyte antigen and CD103. In psoriasis and alopecia areata the proportion of MAIT cells was similar to that found in normal skin, but in dermatitis herpetiformis it was significantly elevated.ConclusionsThe expression of skin‐tropic molecules by skin MAIT cells is consistent with their resident status in normal human skin. Our results suggest that MAIT cells may play a role in the pathogenesis of dermatitis herpetiformis.