bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Discharge Instructions in a Pediatric Emergency Department
Authors: Akinsola Bolanle , Cheng John , Zmitrovich April , Khan Naghma , Jain Shabnam 
Published: September 2016

Background
Effective communication between physician and patient is essential to optimize care after discharge from the emergency department (ED). Written discharge care instructions (DCI) complement verbal instructions and have been shown to improve communication and patient management. In 2012, Centers for Medicare and Medicaid Services proposed a quality measure (OP-19) that assesses compliance with key elements considered essential for high-quality written DCI.

Objective
To evaluate the impact of a QI intervention on improving quality of written DCI in a pediatric emergency department (PED).

Methods
A QI initiative was conducted at a tertiary PED with greater than 60,000 annual visits. Based on Centers for Medicare and Medicaid Services OP-19 measure and group consensus, 8 elements were defined a priori as requisites for good quality DCI. These elements are:
Providers reviewed a random sample of DCI of patients. Proportion of DCI that had each element documented was compared between preintervention phase (PRE) and postintervention phase (POST).

Results
Three hundred twenty-nine DCI (PRE) and 1434 DCI (POST) were reviewed. The POST DCI showed statistically significant improvement for each of the 8 elements. The bundle measure (proportion containing all 8 elements) increased from 23% (PRE) to 79% (POST) (P < 0.001).

Conclusions
The ED DCI improved in all 8 elements after a QI intervention. A detailed DCI at ED discharge enhances the patient's ability to comply with postdischarge treatment plan. Further studies are needed to evaluate the impact of improving DCI on ED return rates and other outcomes.
Epidemiology of Pediatric Traumatic Brain Injury in a Dense Urban Area Served by a Helicopter Trauma Service
Authors: Hill Ciaran S. , McLean Aaron L. , Wilson Mark H. 
Published: September 2016

ObjectivePediatric traumatic brain injury is the most common cause of death and a major cause of morbidity in children and young adults worldwide. Despite this, our understanding of epidemiological factors relating to this type of injury is incomplete. The objective of this study was to explore a variety of factors relating to these injuries including mechanism, timing of emergency response, prehospital management, radiological diagnosis, neurosurgical care, and final outcomes.MethodsA retrospective review of all pediatric traumas attending a single large, densely populated urban area within a 2-year period was undertaken, and all cases with significant pediatric traumatic brain injury, as defined by a computed tomography scan showing an intracranial injury, were included for further analysis. Various epidemiological and treatment factors were explored.ResultsOne hundred sixteen patients fulfilled the inclusion criteria, and their injuries and management were explored further. A variety of key trends were identified. The most common mechanism of injury was pedestrian struck by car followed by falls from height. Males were injured 5 times more frequently than girls. A helicopter emergency trauma team attended 22% of the patients and intubated 11 in total. The most common intracranial injuries were skull fractures followed by contusions. Nineteen neurosurgical interventions were undertaken. Overall mortality in all patients was 8%.ConclusionsAn improved understanding of the epidemiology of pediatric brain injury will provide baselines for future outcome measurement and comparative analysis. This may improve service organization and delivery.
A National Analysis of Pediatric Trauma Care Utilization and Outcomes in the United States
Authors: Myers Sage R. , Branas Charles C. , French Benjamin , Nance Michael L. , Carr Brendan G. 
Published: September 2016

Objectives
More childhood deaths are attributed to trauma than all other causes combined. Our objectives were to provide the first national description of the proportion of injured children treated at pediatric trauma centers (TCs), and to provide clarity to the presumed benefit of pediatric TC verification by comparing injury mortality across hospital types.

Methods
We performed a population-based cohort study using the 2006 Healthcare Cost and Utilization Project Kids Inpatient Database combined with national TC inventories. We included pediatric discharges (≤16 y) with the International Classification of Diseases, Ninth Revision code(s) for injury. Descriptive analyses were performed evaluating proportions of injured children cared for by TC level. Multivariable logistic regression models were used to estimate differences in in-hospital mortality by TC type (among level-1 TCs only). Analyses were survey-weighted using Healthcare Cost and Utilization Project sampling weights.

Results
Of 153,380 injured children, 22.3% were admitted to pediatric TCs, 45.2% to general TCs, and 32.6% to non-TCs. Overall mortality was 0.9%. Among level-1 TCs, raw mortality was 1.0% pediatric TC, 1.4% dual TC, and 2.1% general TC. In adjusted analyses, treatment at level-1 pediatric TCs was associated with a significant mortality decrease compared to level-1 general TCs (adjusted odds ratio, 0.6; 95% confidence intervals, 0.4–0.9).

Conclusions
Our results provide the first national evidence that treatment at verified pediatric TCs may improve outcomes, supporting a survival benefit with pediatric trauma verification. Given lack of similar survival advantage found for level-1 dual TCs (both general/pediatric verified), we highlight the need for further investigation to understand factors responsible for the survival advantage at pediatric-only TCs, refine pediatric accreditation guidelines, and disseminate best practices.
Variations in Patient Safety Climate in Chinese Hospitals
Authors: Zhu Junya , Li Liping , Zhou Zehui , Lou Qingqing , Wu Albert W. 
Published: September 2016

Objectives
Patient safety climate is associated with patient outcomes in hospitals around the world. A better understanding of how safety climate varies within and across hospitals will help identify improvement opportunities. We examined variations in safety climate by work area and job category in Chinese hospitals.

Methods
We administered the Chinese Hospital Survey on Patient Safety Climate in 2011 to workers in 6 hospitals in China, with completed surveys from 1464 (86% response). We calculated the percent positive response for survey items and dimensions among hospitals and compared this across work areas and job categories using general linear models.

Results
Overall, 68% of responses suggested the presence of a positive safety climate. The percent positive responses were highest for organizational learning (86.1%) and unit management support for safety (84.5%) and lowest for staffing (30.6%) and error reporting (44.5%). Workers in surgical units, intensive care units, operating rooms, and emergency departments were slightly more negative regarding overall safety climate than those in medical and ancillary units. Physicians reported worse perceptions than nurses or other hospital workers on all dimensions except for unit management support for safety and communication and peer support.

Conclusions
The perceived problem with staffing in Chinese hospitals was consistent with other studies. The lack of positive responses for error reporting may indicate a lack of awareness of the importance of learning from and reporting minor events and near misses. Variations within and across hospitals in safety climate suggest that improvement interventions should be tailored to individual units and professional groups.
Improving Incident Reporting Among Physician Trainees
Authors: Krouss Mona , Alshaikh Jumana , Croft Lindsay , Morgan Daniel J. 
Published: September 2016

Background
Preventable medical harm is a leading cause of death in the United States. Incident reporting systems have been identified as the primary method to capture medical error and harm. Incidents are rarely reported, particularly among physician trainees.

Methods
We conducted a single-center, quasi-experimental study to examine the effect of education on the importance of and how to file an incident report for physician trainees on reporting rates. Trainees were provided laminated plastic instructions, and reporting was reinforced with weekly patient safety rounds. In addition, trainees completed anonymous surveys preintervention and postintervention to determine barriers to reporting. A χ2 test compared the number of reports preintervention and postintervention.

Results
For 6 months, 73 resident physicians participated in the study. Median incident reports entered by trainees increased from 1 report per month during the preintervention period to 10 reports per month after the intervention (P = 0.005). The most common barriers to reporting incidents before intervention were not knowing how to report (72.6%), what to report (56.2%), and lack of time (42.5%). A total of 13.7% reported fear of retaliation. Most incident reports were due to delay in patient care (40.9%) and medical errors (33.3%).

Conclusions
Real-time education and regular reinforcement increased incident reporting among resident physicians. This educational approach may increase incidence reporting in other institutions.
Using Broken Windows Theory as the Backdrop for a Proactive Approach to Threat Identification in Health Care
Authors: Boquet Albert J. , Cohen Tara N. , Cabrera Jennifer S. , Litzinger Tracy L. , Captain Kevin A. , Fabian Michael A. , Miles Steven G. , Shappell Scott A. 
Published: September 2016

Objectives
Historically, health care has relied on error management techniques to measure and reduce the occurrence of adverse events. This study proposes an alternative approach for identifying and analyzing hazardous events. Whereas previous research has concentrated on investigating individual flow disruptions, we maintain the industry should focus on threat windows, or the accumulation of these disruptions. This methodology, driven by the broken windows theory, allows us to identify process inefficiencies before they manifest and open the door for the occurrence of errors and adverse events.

Methods
Medical human factors researchers observed disruptions during 34 trauma cases at a Level II trauma center. Data were collected during resuscitation and imaging and were classified using a human factors taxonomy: Realizing Improved Patient Care Through Human-Centered Operating Room Design for Threat Window Analysis (RIPCHORD-TWA).

Results
Of the 576 total disruptions observed, communication issues were the most prevalent (28%), followed by interruptions and coordination issues (24% each). Issues related to layout (16%), usability (5%), and equipment (2%) comprised the remainder of the observations. Disruptions involving communication issues were more prevalent during resuscitation, whereas coordination problems were observed more frequently during imaging.

Conclusions
Rather than solely investigating errors and adverse events, we propose conceptualizing the accumulation of disruptions in terms of threat windows as a means to analyze potential threats to the integrity of the trauma care system. This approach allows for the improved identification of system weaknesses or threats, affording us the ability to address these inefficiencies and intervene before errors and adverse events may occur.
A framework for RNA quality correction in differential expression analysis
Authors: Jaffe Andrew E. , Tao Ran , Norris Alexis L. , Kealhofer Marc , Nellore Abhinav , Jia Yankai , Hyde Thomas M. , Kleinman Joel E. , Straub Richard E. , Leek Jeffrey T. , Weinberger Daniel R. 
Published: September 2016

AbstractRNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment employing existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from a molecular degradation experiment of human brain tissue, we introduce the quality surrogate variable (qSVA) analysis framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show this approach results in greatly improved replication rates (>3x) across two large independent postmortem human brain studies of schizophrenia. Finally, we explored public datasets to demonstrate potential RNA quality confounding when comparing expression levels of different brain regions and diagnostic groups beyond schizophrenia. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from the human brain.
MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQ
Authors: Fang Rongxin , Yu Miao , Li Guoqiang , Chee Sora , Liu Tristin , Ren Bing 
Published: September 2016

AbstractWe report a highly sensitive and cost-effective method for genome-wide identification of chromatin interactions in eukaryotic cells. Combining proximity ligation with chromatin immunoprecipitation and sequencing, the method outperforms the state of art approach in sensitivity, accuracy and ease of operation. Application of the method to mouse embryonic stem cells improves mapping of enhancer-promoter interactions.
Fitness effects of thermal stress differ between outcrossing and selfing populations inCaenorhabditis elegans
Authors: Plesnar-Bielak Agata , Labocha Marta K. , Kosztyła Paulina , Woch Katarzyna R. , Banot Woronika M. , Markot Karolina , Skarboń Magdalena , Prus Monika A. , Prokop Zofia M. 
Published: September 2016

AbstractThe maintenance of males and outcrossing is widespread, despite considerable costs of males. By enabling recombination between distinct genotypes, outcrossing may be advantageous during adaptation to a novel environments and if so, it should be selected for under environmental challenge. However, a given environmental change may influence fitness of male, female, and hermaphrodite or asexual individuals differently, and hence the relationship between reproductive system and dynamics of adaptation to novel conditions may not be driven solely by the level of outcrossing and recombination. This has important implications for studies investigating the evolution of reproductive modes in the context of environmental changes, and for the extent to which their findings can be generalized. Here, we useCaenorhabditis elegans– a free-living nematode species in which hermaphrodites (capable of selfing but not cross-fertilizing each other) coexist with males (capable of fertilizing hermaphrodites) – to investigate the response of wild type as well as obligatorily outcrossing and obligatorily selfing lines to stressfully increased ambient temperature. We found that thermal stress affects fitness of outcrossers much more drastically than that of selfers. This shows that apart from the potential for recombination, the selective pressures imposed by the same environmental change can differ between populations expressing different reproductive systems and affect their adaptive potential.
A single intracellular protein governs the critical transition from an individual to a coordinated population response during quorum sensing: Origins of primordial language
Authors: Vila-Sanjurjo Celina , Engwer Christoph , Qin Xiaofei , Hembach Lea , Verdía-Cotelo Tania , Remuñán-López Carmen , Vila-Sanjurjo Antón , Goycoolea Francisco M. 
Published: September 2016

Quorum sensing (QS) explains a type of bacterial cell-cell communication mediated by exocellular compounds that act as autoinducers (AIs). As such, QS can be considered the most primordial form of language. QS has profound implications for the control of many important traits (e.g.biofilm formation, secretion of virulence factors, etc.). Conceptually, the QS response can be split into its “listening” and “speaking” components,i.e.the power to sense AI levelsvs.the ability to synthesize and release these molecules. By explaining the cell-density dependence of QS behavior as the consequence of the system’s arrival to a threshold AI concentration, models of QS have traditionally assumed a salient role for the “QS speaking” module during bacterial cell-to-cell communication. In this paper, we have provided evidence that challenges this AI-centered view of QS and establishes LuxR-like activators at the center of QS. Our observation that highly coordinated, cell-density dependent responses can occur in the absence of AI production, implies that the ability to launch such responses is engrained within the “QS listening” module. Our data indicates that once a critical threshold of intracellular activator monomers in complex with AI is reached, a highly orchestrated QS response ensues. While displaying a clear cell-density dependence, such response does not strictly require the sensing of population levels by individual cells. We additionally show, bothin vivoandin silico, that despite their synchronous nature, QS responses do not require that all the cells in the population participate in the response. Central to our analysis was the discovery that percolation theory (PT) can be used to mathematically describe QS responses. While groundbreaking, our results are in agreement with and integrate the latest conclusions reached in the field. We explain for the first time, the cell-density-dependent synchronicity of QS responses as the function of a single protein, the LuxR-like activator, capable of coordinating the temporal response of a population of cells in the absence of cell-to-cell communication. Being QS the most primordial form of speech, our results have important implications for the evolution of language in its ancient chemical form.Abbreviations3Dthree dimensionalacwthreshold intracellular concentration of activator moleculesAHLacyl-homoserine lactoneAHLfischN-(3-oxohexanoyl)-L-homoserine lactoneAHLviolN-hexanoyl-DL-homoserine-lactoneAIautoinducera.uarbitrary unitsBMBbromophenol blueCAtrans-cinnamaldehydeFlfluorescence intensityFI/OD600density-normalized fluorescence intensityGFPgreen fluorescent proteinMwmolecular weightPTpercolation theoryQSquorum sensingtcpercolation critical timewtwild type
Stochastic dynamics of genetic broadcasting networks
Authors: Potoyan Davit A. , Wolynes Peter G. 
Published: September 2016

AbstractThe complex genetic programs of eukaryotic cells are often regulated by key transcription factors occupying or clearing out of a large number of genomic locations. Orchestrating the residence times of these factors is therefore important for the well organized functioning of a large network. The classic models of genetic switches sidestep this timing issue by assuming the binding of transcription factors to be governed entirely by thermodynamic protein-DNA affinities. Here we show that relying on passive thermodynamics and random release times can lead to a “time-scale crisis” of master genes that broadcast their signals to large number of binding sites. We demonstrate that this “time-scale crisis” can be resolved by actively regulating residence times through molecular stripping. We illustrate these ideas by studying the stochastic dynamics of the genetic network of the central eukaryotic master regulatorNFκBwhich broadcasts its signals to many downstream genes that regulate immune response, apoptosis etc.
The impact of rare variation on gene expression across tissues
Authors: Li Xin , Kim Yungil , Tsang Emily K. , Davis Joe R. , Damani Farhan N. , Chiang Colby , Zappala Zachary , Strober Benjamin J. , Scott Alexandra J. , Ganna Andrea , Merker Jason ,   GTEx Consortium, Hall Ira M. , Battle Alexis , Montgomery Stephen B. 
Published: September 2016

AbstractRare genetic variants are abundant in humans yet their functional effects are often unknown and challenging to predict. The Genotype-Tissue Expression (GTEx) project provides a unique opportunity to identify the functional impact of rare variants through combined analyses of whole genomes and multi-tissue RNA-sequencing data. Here, we identify gene expression outliers, or individuals with extreme expression levels, across 44 human tissues, and characterize the contribution of rare variation to these large changes in expression. We find 58% of underexpression and 28% of overexpression outliers have underlying rare variants compared with 9% of non-outliers. Large expression effects are enriched for proximal loss-of-function, splicing, and structural variants, particularly variants near the TSS and at evolutionarily conserved sites. Known disease genes have expression outliers, underscoring that rare variants can contribute to genetic disease risk. To prioritize functional rare regulatory variants, we develop RIVER, a Bayesian approach that integrates RNA and whole genome sequencing data from the same individual. RIVER predicts functional variants significantly better than models using genomic annotations alone, and is an extensible tool for personal genome interpretation. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues with potential health consequences, and provide an integrative method for interpreting rare variants in individual genomes.
Local genetic effects on gene expression across 44 human tissues
Authors: Aguet François , Brown Andrew A. , Castel Stephane E. , Davis Joe R. , Mohammadi Pejman , Segrè Ayellet V. , Zappala Zachary , Abell Nathan S. , Frésard Laure , Gamazon Eric R. , Gelfand Ellen , Gloudemans Michael J. , He Yuan , Hormozdiari Farhad , Li Xiao , Li Xin , Liu Boxiang , Garrido-Martín Diego , Ongen Halit , Palowitch John J. , Park YoSon , Peterson Christine B. , Quon Gerald , Ripke Stephan , Shabalin Andrey A. , Shimko Tyler C. , Strober Benjamin J. , Sullivan Timothy J. , Teran Nicole A. , Tsang Emily K. , Zhang Hailei , Zhou Yi-Hui , Battle Alexis , Bustamonte Carlos D. , Cox Nancy J. , Engelhardt Barbara E. , Eskin Eleazar , Getz Gad , Kellis Manolis , Li Gen , MacArthur Daniel G. , Nobel Andrew B. , Sabbati Chiara , Wen Xiaoquan , Wright Fred A. ,   GTEx Consortium, Lappalainen Tuuli , Ardlie Kristin G. , Dermitzakis Emmanouil T. , Brown Christopher D. , Montgomery Stephen B. 
Published: September 2016

AbstractExpression quantitative trait locus (eQTL) mapping provides a powerful means to identify functional variants influencing gene expression and disease pathogenesis. We report the identification of cis-eQTLs from 7,051 post-mortem samples representing 44 tissues and 449 individuals as part of the Genotype-Tissue Expression (GTEx) project. We find a cis-eQTL for 88% of all annotated protein-coding genes, with one-third having multiple independent effects. We identify numerous tissue-specific cis-eQTLs, highlighting the unique functional impact of regulatory variation in diverse tissues. By integrating large-scale functional genomics data and state-of-the-art fine-mapping algorithms, we identify multiple features predictive of tissue-specific and shared regulatory effects. We improve estimates of cis-eQTL sharing and effect sizes using allele specific expression across tissues. Finally, we demonstrate the utility of this large compendium of cis-eQTLs for understanding the tissue-specific etiology of complex traits, including coronary artery disease. The GTEx project provides an exceptional resource that has improved our understanding of gene regulation across tissues and the role of regulatory variation in human genetic diseases.