bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of hematopoietic stem and progenitor cells involves a Chd1-dependent increase in total nascent transcription
Authors: Koh Fong Ming , Lizama Carlos O. , Wong Priscilla , Hawkins John S. , Zovein Ann C. , Ramalho-Santos Miguel 
Published: March 2015

Significance
Adult hematopoietic stem and progenitor cells (HSPCs) develop from a small number of specialized endothelial cells in the embryo. Very little is known about how this process, known as the endothelial-to-hematopoietic transition, is regulated. In this paper, we used mouse genetic knockout models to establish Chd1 as the first chromatin remodeler, to our knowledge, shown to regulate this transition. Chd1 is not required in the endothelium prior to the transition, nor in the blood system after the transition. We found that the emergence of HSPCs involves an increase in total nascent transcription that is dependent on Chd1. These results reveal a new paradigm of regulation of a developmental transition by modulation of transcriptional output that may be relevant in other stem/progenitor cell contexts.
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors
Authors: Owen Jeremy G. , Charlop-Powers Zachary , Smith Alexandra G. , Ternei Melinda A. , Calle Paula Y. , Reddy Boojala Vijay B. , Montiel Daniel , Brady Sean F. 
Published: March 2015

Significance
Here we use an informatics-based approach to natural product discovery that is broadly applicable to the isolation of medicinally relevant metabolites from environmental microbiomes. Combining metagenome sequencing and bioinformatics approaches with a defined set of metagenomic tools provides a template for the targeted discovery of compounds from the global metagenome. The power of this approach is demonstrated by surveying ketosynthase domain amplicon sequencing data from 185 soil microbiomes for biosynthetic gene clusters encoding epoxyketone proteasome inhibitors, leading to the isolation and characterization of seven epoxyketone natural products, including compounds with unique warhead structures. We believe this approach is applicable to any conserved biosynthetic gene and provides a higher-throughput cost-effective alternative to whole genome sequencing discovery methods.
Development of sedentary communities in the Maya lowlands: Coexisting mobile groups and public ceremonies at Ceibal, Guatemala
Authors: Inomata Takeshi , MacLellan Jessica , Triadan Daniela , Munson Jessica , Burham Melissa , Aoyama Kazuo , Nasu Hiroo , Pinzón Flory , Yonenobu Hitoshi 
Published: March 2015

Significance
The results of our research at the lowland Maya site of Ceibal add to the growing archaeological understanding that the transition to sedentism did not necessarily occur simultaneously across different social groups within a region and that monumental constructions did not always postdate fully established sedentism. Whereas sedentary and mobile populations are, in many cases, interpreted to have maintained separate communities, our study suggests that groups with different levels of mobility gathered and collaborated for constructions and public ceremonies. These data indicate that the development of sedentism was a complex process involving interactions among diverse groups, and that collaborative construction projects and communal gatherings played a critical role in this social transformation by facilitating social integration among different groups.
Sexual selection drives evolution and rapid turnover of male gene expression
Authors: Harrison Peter W. , Wright Alison E. , Zimmer Fabian , Dean Rebecca , Montgomery Stephen H. , Pointer Marie A. , Mank Judith E. 
Published: March 2015

SignificanceGenes with different expression between males and females (sex-biased genes) show rapid rates of sequence and expression divergence in a range of taxa. These characteristics have led many to assume that sex-biased genes are the product of sexual selection and sexual conflict, but this assumption remains to be rigorously tested. Using a phylogenetically controlled analysis of birds that exhibit diverse levels of sexual selection, we show a rapid turnover in sex-biased gene expression primarily through evolution of male expression levels and that the degree of sexual selection predicts the proportion of male-biased genes but does not account for rates of coding sequence evolution. We also discuss the impact of allometry on gene expression studies, an issue rarely discussed in the literature.
Regulatory vs. inflammatory cytokine T-cell responses to mutated insulin peptides in healthy and type 1 diabetic subjects
Authors: Nakayama Maki , McDaniel Kristen , Fitzgerald-Miller Lisa , Kiekhaefer Carol , Snell-Bergeon Janet K. , Davidson Howard W. , Rewers Marian , Yu Liping , Gottlieb Peter , Kappler John W. , Michels Aaron 
Published: March 2015

Significance
Certain class II major histocompatibility alleles confer disease risk for type 1 diabetes (T1D). Insulin-specific and other autoantibodies often precede T1D development, but major efforts at disease prevention using insulin preparations (subcutaneous, oral, and intranasal) to induce tolerance have not been effective. Measuring insulin-specific T-cell responses from the peripheral blood has been a challenging feat but would allow for assessment of therapeutic response in these trials. In our study, we report CD4 T-cell responses to a mutated insulin B-chain peptide in new-onset and established T1D as well as control subjects dependent on HLA-DQ genotype. Our results have important implications for the application and monitoring of insulin-specific therapies to prevent diabetes onset.
Sae2 promotes DNA damage resistance by removing the Mre11–Rad50–Xrs2 complex from DNA and attenuating Rad53 signaling
Authors: Chen Huan , Donnianni Roberto A. , Handa Naofumi , Deng Sarah K. , Oh Julyun , Timashev Leonid A. , Kowalczykowski Stephen C. , Symington Lorraine S. 
Published: March 2015

Significance
Chromosomal double-strand breaks (DSBs) are cytotoxic forms of DNA damage that must be accurately repaired to maintain genome integrity. The conserved Mre11–Rad50–Xrs2/NBS1 nuclease/ATPase complex plays an important role in repair by functioning as a damage sensor and by regulation of DNA end processing to ensure repair by the most appropriate mechanism. Yeast Sae2 is known to function with Mre11 to process DNA ends, but its precise role is poorly understood. Here we show that it is the failure to remove Mre11 from DNA ends, leading to persistent DNA damage signaling and cell cycle arrest, that causes sensitivity of Sae2-deficient cells to DNA damaging agents.
A multistage mathematical approach to automated clustering of high-dimensional noisy data
Authors: Friedman Alexander , Keselman Michael D. , Gibb Leif G. , Graybiel Ann M. 
Published: March 2015

Significance
Organizing large, multidimensional datasets by subgrouping data as clusters is a major challenge in many fields, including neuroscience, in which the spike activity of large numbers of neurons is recorded simultaneously. We present a mathematical approach for clustering such multidimensional datasets in a relatively high-dimensional space using as a prototype datasets characterized by high background spike activity. Our method incorporates features allowing reliable clustering in the presence of such strong background activity and, to deal with large size of datasets, incorporates automated implementation of clustering. Our approach effectively identifies individual neurons in spike data recorded with multiple tetrodes, and opens the way to use this method in other domains in which clustering of complex datasets is needed.
Tryptophan-independent auxin biosynthesis contributes to early embryogenesis in
Arabidopsis
Authors: Wang Bing , Chu Jinfang , Yu Tianying , Xu Qian , Sun Xiaohong , Yuan Jia , Xiong Guosheng , Wang Guodong , Wang Yonghong , Li Jiayang 
Published: March 2015

Significance
The phytohormone indole-3-acetic acid (IAA) plays a vital role in plant growth and development. IAA can be synthesized through the precursor tryptophan (Trp), known as the Trp-dependent IAA biosynthetic pathway. However, IAA may also be synthesized through a proposed Trp-independent IAA biosynthetic pathway. Although the Trp-independent IAA biosynthesis was hypothesized 20 years ago, it remains a mystery. In this paper, we provide compelling evidence that the cytosol-localized indole synthase (INS) initiates the Trp-independent IAA biosynthetic pathway and that the spatial and temporal expression of INS plays an important role in the establishment of the apical–basal pattern during early embryogenesis, demonstrating that the Trp-dependent and -independent IAA biosynthetic pathways coordinately regulate embryogenesis of higher plants.
Bible
Authors: Campbell Gordon 
Published: March 2015

Abstract
Produced during the lifetime of William Shakespeare and John Donne, the King James Version (KJV) of the Bible has long been viewed as the most elegantly written and poetic of the many English translations. Now reaching its 400th anniversary, it remains one of the most frequently used Bibles in the English-speaking world, especially in America. This book offers an authoritative history of this renowned translation, ranging from the Bible's inception to the present day. The text tells the complex story of how this translation came to be commissioned, who the translators were, and how the translation was accomplished. The book does not end with the printing of that first edition, but also traces the textual history from 1611 to the establishment of the modern text by Oxford University Press in 1769, shedding light on the subsequent generations who edited and interacted with the text and bringing to life the controversies surrounding later revisions. In addition, the book examines the reception of the KJV, showing how its popularity has shifted through time and territory, ranging from adulation to deprecation and attracting the attention of a wide variety of adherents. Since the KJV is more widely read in America today than in any other country, the book pays particular attention to the history of the KJV in the United States. Finally, the volume includes appendices that contain short biographies of the translators and a guide to the 74-page preliminaries of the 1611 edition.
Introduction
Authors: Campbell Gordon 
Published: March 2015

Abstract
This book chronicles the history of the King James Version (KJV) of the Bible from 1611 to 2011. Known in the United Kingdom as the Authorised Version, the KJV is the most celebrated book in the English-speaking world, particularly the United States. The book tells the complex story of how this translation came to be commissioned and accomplished, as well as the people behind the translation. Aside from its printing history, it traces the KJV's political, ecclesiastical, and cultural history from 1611 to Oxford University Press's publication of the modern version in 1769, along with the subsequent generations who edited and interacted with the text and the controversies surrounding later revisions. The reception of the King James Version is considered as well.
The Eighteenth Century
Authors: Campbell Gordon 
Published: March 2015

Abstract
This chapter focuses on editions of the King James Version (KJV) of the Bible that were published in the eighteenth century. It first looks at the editions published by John Baskett at Oxford University Press before turning to the editions published by John Baskerville and F. S. Parris at Cambridge University Press. It then considers Benjamin Blayney's edition and concludes by assessing the reception of the KJV in the eighteenth century.
The Revised Version
Authors: Campbell Gordon 
Published: March 2015

Abstract
This chapter focuses on the revised edition of the King James Version (KJV) of the Bible. It first considers the rationale for the revision of the KJV and the proposals for revision, along with the rules that were devised to govern the process of revision. It then assesses the reception of the Revised Version of the New Testament before turning to a discussion of the revision of the Old Testament and of the Revised Version of the KJV. Finally, it examines whether the Revised Version of the KJV can be viewed as a modernisation of the KJV or as a new version of the Bible.
Cognitive Fusion and Pain Experience in Young People
Authors: Solé Ester , Tomé-Pires Catarina , de la Vega Rocío , Racine Mélanie , Castarlenas Elena , Jensen Mark P. , Miró Jordi 
Published: March 2015

Objectives:
Acceptance and Commitment Therapy (ACT) has been shown to be an effective treatment for chronic pain in young people. Cognitive fusion is a key concept of ACT that is hypothesized to contribute to distress and suffering. In this study, we sought to: (1) test hypothesized associations between cognitive fusion and pain intensity, disability, and catastrophizing; and (2) examine the function of cognitive fusion as a possible mediator between catastrophizing and disability.

Methods:
A community sample of 281 young people (11 to 20 y) completed measures assessing cognitive fusion, pain intensity, disability, and pain catastrophizing.

Results:
Cognitive fusion was positively related to pain intensity (r=0.24, P<0.01), disability (r=0.32, P<0.001), and pain catastrophizing (r=0.47, P<0.001). Moreover, cognitive fusion was found to mediate the association between pain catastrophizing and disability (β=0.01, 95% confidence interval=0.002-0.024, 5000 bootstrap resamples).

Discussion:
The findings indicate that cognitive fusion is moderately to strongly associated with pain-related outcomes, which support the need for further research to (1) better understand the relationship between cognitive fusion and adjustment to chronic pain, and (2) determine whether the benefits of treatments such as ACT are mediated, at least in part, by reductions in cognitive fusion.
Celiac Disease Alone and Associated With Type 1 Diabetes Mellitus
Authors: Tsouka Alexandra , Mahmud Farid H. , Marcon Margaret A. 
Published: March 2015

ABSTRACTObjectives:The aim of the study was to evaluate complication screening and follow‐up patterns in a population with type 1 diabetes mellitus and celiac disease (T1D/CD) in relation to a matched cohort with celiac disease (CD) alone at our center.Methods:We retrospectively reviewed the health charts of 41 children with T1D and biopsy‐proven CD and compared anthropometrics and complication of screening within 2 years from CD diagnosis. Follow‐up patterns were determined 3 years postdiagnosis. This population was then compared with a population with both symptomatic and asymptomatic CD matched for age and sex.Results:In comparison with T1D/CD, patients with CD alone had a significantly lower height, weight and body mass index (BMI z score 0.01 vs 0.81, P = 0.001) and higher rates of screening for anemia (95% vs 71%, P = 0.003) and bone health (49% vs 29%, P = 0.05). Minimal rates of laboratory abnormalities were observed in either group, irrespective of symptoms at presentation, but CD alone more often presented with anemia than T1D/CD. Repeat serology testing was significantly more frequently performed in the T1D/CD group. Follow‐up was equally variable with a median of 3 (range 0–4) visits with a gastroenterologist during the first 3 years postdiagnosis.Conclusions:These results suggest that patients with T1D/CD represent a distinct and possibly milder phenotype from CD alone. Complication screening was variable and negative for the majority of the patients. Guidelines for follow‐up may need to be tailored to specific groups to standardize evaluation and complication screening, especially with regard to bone health.
A Measure of Barriers Toward Medical Disclosure Among Health Professionals in the United Arab Emirates
Authors: Zaghloul Ashraf Ahmad , Elsergany Moetaz , Mosallam Rasha 
Published: March 2015

Background
There has been a growing awareness that patients are subject to injuries that can be prevented as a direct consequence of health care. Error disclosure is an effective technique to restore the lost trust with the health care system.

Objective
The current study aimed to develop a valid and reliable scale to determine the factors facilitating the disclosure of health professionals in health organizations.

Methods
This study had a cross-sectional design that consisted of 722 responses (response rate of 68.3%) from 1 private and 1 public hospital in Sharjah, United Arab Emirates. The data collection tool included 23 items rated on a Likert scale ranging from 5, strongly agree, to 1, strongly disagree.
The internal consistency was established through calculating the split-half reliability for part 1 (12 items), which had a Cronbach coefficient of 0.65, and part 2 (11 items), which had a Cronbach coefficient of 0.62. Scale validity was assessed with the Kaiser-Meyer-Olkin measure of sampling adequacy, which had a value of 0.62, and the Bartlett test of sphericity (approximated χ2 = 13012.2, P = 0.0001) supported the factorability of the correlation matrix. The varimax rotation revealed 5 components that explained 77.8% of the total variance.

Results
The varimax rotation revealed 21 items loaded on the following 5 factors: fear of disclosure and provider image consequences (factor 1), apology (factor 2), organizational culture toward patient safety (factor 3), professional ethics and transparency (factor 4), as well as patient and provider education (factor 5).

Conclusions
The disclosure of medical mistakes requires preliminary considerations to effectively and compassionately disclose these events to patients. The validity and reliability of the results support the use of this scale at hospitals as part of the health care providers' disclosure processes.
Impact of Inpatient Harms on Hospital Finances and Patient Clinical Outcomes
Authors: Adler Lee , Yi David , Li Michael , McBroom Barry , Hauck Loran , Sammer Christine , Jones Cason , Shaw Terry , Classen David 
Published: March 2015

Objective
The aim of this study was to determine the impact of all-cause inpatient harms on hospital finances and patient clinical outcomes.

Research Design
A retrospective analysis of inpatient harm from 24 hospitals in a large multistate health system was conducted during 2009 to 2012 using the Institute of Healthcare Improvement Global Trigger Tool for Measuring Adverse Events. Inpatient harms were detected and categorized into harm (F–I), temporary harm (E), and no harm.

Results
Of the 21,007 inpatients in this study, 15,610 (74.3%) experienced no harm, 2818 (13.4%) experienced temporary harm, and 2579 (12.3%) experienced harm. A patient with harm was estimated to have higher total cost ($4617 [95% confidence interval (CI), $4364 to 4871]), higher variable cost ($1774 [95% CI, $1648 to $1900]), lower contribution margin (−$1112 [95% CI, −$1378 to −$847]), longer length of stay (2.6 d [95% CI, 2.5 to 2.8]), higher mortality probability (59%; odds ratio, 1.4 [95% CI, 1.0 to 2.0]), and higher 30-day readmission probability (74.4%; odds ratio, 2.9 [95% CI, 2.6 to 3.2]). A patient with temporary harm was estimated to have higher total cost ($2187 [95% CI, $2008 to $2366]), higher variable cost ($800 [95% CI, $709 to $892]), lower contribution margin (−$669 [95% CI, −$891 to −$446]), longer length of stay (1.3 d [95% CI, 1.2 to 1.4]), mortality probability not statistically different, and higher 30-day readmission probability (54.6%; odds ratio, 1.2 [95% CI, 1.1 to 1.4]). Total health system reduction of harm was associated with a decrease of $108 million in total cost, $48 million in variable cost, an increase of contribution margin by $18 million, and savings of 60,000 inpatient care days.

Conclusions
This all-cause harm safety study indicates that inpatient harm has negative financial outcomes for hospitals and negative clinical outcomes for patients.
Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression
Authors: Shen Shensi , Rodrigo Guillermo , Prakash Satya , Majer Eszter , Landrain Thomas E. , Kirov Boris , Daròs José-Antonio , Jaramillo Alfonso 
Published: March 2015

AbstractOrganisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves thede novodesign of RNA modules enabling dynamic signal processing in live cells. This requires a scalable methodology for sensing, transmission, and actuation, which could be assembled into larger signaling networks. Here, we present a biochemical strategy to design RNA-mediated signal transduction cascades able to sense small molecules and small RNAs. We design switchable functional RNA domains by using strand-displacement techniques. We experimentally characterize the molecular mechanism underlying our synthetic RNA signaling cascades, show the ability to regulate gene expression with transduced RNA signals, and describe the signal processing response of our systems to periodic forcing in single live cells. The engineered systems integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to engineer arbitrary complex gene circuits.
“Safe handover saves lives”: results from clinical audit
Authors: Advani Rajeev , Stobbs Nicola Marie , Killick Neil , Kumar B Nirmal 
Published: March 2015

Purpose
– The implementation of the European Working Time Directive and its subsequent impact on the hours worked by doctors in training has resulted in shift-working rotas being the norm and greater cross-cover between specialties. As such, the need for continuity of information and comprehensiveness of handover between shifts has become more important than ever. The purpose of this paper is to show how handover can be improved by the implementation of an electronic handover system and subsequent Quality Improvement Rapid Cycle Change Model of clinical audit.

Design/methodology/approach
– Initial data were collected using a standardised questionnaire collected prospectively from all junior doctors within the surgical division. Following the first audit cycle, changes were implemented in a Quality Improvement Rapid Cycle Change Model of clinical audit and a Surgical Division Electronic Handover Shared Drive was developed. Three further prospective cycles of clinical audit were carried out over a period of 12 months.

Findings
– The results show a more effective handover system to be in place. Effects of change measured as an 80 per cent standard was achieved in all categories and maintained throughout all cycles of re-audit.

Practical implications
– A surgical division shared electronic handover drive was developed and subsequent audits have shown improved handover practice in a foundation trust. This has positive benefits on patient safety and quality of care.

Originality/value
– This work is of interest to those looking to set up an electronic handover system and additionally to all those working in specialities where cross-cover is required.