bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of the Oral Human Attenuated Rotavirus Vaccine: A Systematic Review and Meta-analysis—2006–2016
Authors: Willame Corinne , Vonk Noordegraaf-Schouten Marije , Gvozdenović Emilia , Kochems Katrin , Oordt-Speets Anouk , Praet Nicolas , van Hoorn Rosa , Rosillon Dominique 
Published: November 2018

Abstract

Background
Gastroenteritis caused by rotavirus accounts for considerable morbidity in young children. We aimed to assess the vaccine effectiveness (VE) of the oral rotavirus vaccine Rotarix, as measured by laboratory-confirmed rotavirus infection after referral to hospital and/or emergency departments in children aged &lt;5 years with gastroenteritis.

Methods
We performed a systematic search for peer-reviewed studies conducted in real-life settings published between 2006 and 2016 and a meta-analysis to calculate the overall Rotarix VE, which was further discriminated through stratified analyses.

Results
The overall VE estimate was 69% (95% confidence interval [CI], 62% to 75%); stratified analyses revealed a non-negligible impact of factors such as study design and socioeconomic status. Depending on the control group, VE ranged from 63% (95% CI, 52% to 72%) to 81% (95% CI, 69% to 88%) for unmatched and matched rotavirus test–negative controls. VE varied with socioeconomic status: 81% (95% CI, 74% to 86%) in high-income countries, 54% (95% CI, 39% to 65%) in upper-middle-income countries, and 63% (95% CI, 50% to 72%) in lower-middle-income countries. Age, rotavirus strain, and disease severity were also shown to impact VE, but to a lesser extent.

Conclusions
This meta-analysis of real-world studies showed that Rotarix is effective in helping to prevent hospitalizations and/or emergency department visits due to rotavirus infection.
Prediction of Severe Maternal Outcome Among Pregnant and Puerperal Women in Obstetric ICU
Authors: Oliveira-Neto Antonio Francisco , Parpinelli Mary Angela , Costa Maria Laura , Souza Renato Teixeira , Ribeiro do Valle Carolina , Sousa Maria Helena , Cecatti José Guilherme 
Published: November 2018

Objective:
World Health Organization recommends the use of maternal near miss as a tool to monitor and improve quality of obstetric care. Severe maternal outcome corresponds to the sum of maternal near miss and maternal death cases. This study was aimed at validating Acute Physiology and Chronic Health Evaluation II and IV, Simplified Acute Physiology Score III, and Sequential Organ Failure Assessment in pregnant and postpartum women in predicting severe maternal outcome.

Design:
A retrospective cohort study.

Setting:
Obstetric ICU in a tertiary care hospital in Brazil.

Patients:
Pregnant and postpartum women admitted to the obstetric ICU during a 3-year period.

Interventions:
None.

Measurements and Main Results:
A total of 279 women were admitted to ICU, an admission rate of 34.6/1,000 live births, and the mortality index to severe maternal outcome (maternal death/maternal near miss + maternal death) was 7.7%. Total Sequential Organ Failure Assessment had a better overall performance than remaining scores for total hospitalizations (area under the curve, 0.86; standardized mortality ratio, 0.96; 95% CI, 0.74–1.22), for hypertensive direct causes (area under the curve, 0.81; standardized mortality ratio, 0.73; 95% CI, 0.31–1.43), and indirect causes (area under the curve, 0.89; standardized mortality ratio, 0.85; 95% CI, 0.59–1.19). The Acute Physiology and Chronic Health Evaluation II had a better overall performance than total Sequential Organ Failure Assessment for hemorrhagic causes (area under the curve, 0.75; standardized mortality ratio, 1.0; 95% CI, 0.61–1.54).

Conclusions:
Total Sequential Organ Failure Assessment may be used to predict severe maternal outcome in obstetric populations admitted to ICU. The Acute Physiology and Chronic Health Evaluation II may be applied to predict severe maternal outcome in hemorrhagic complications. We do not recommend Acute Physiology and Chronic Health Evaluation IV and Simplified Acute Physiology Score III for the prediction of severe maternal outcome.
CORRELATION OF GENE EXPRESSION PROFILE STATUS AND AMERICAN JOINT COMMISSION ON CANCER STAGE IN UVEAL MELANOMA
Authors: Berry Duncan E. , Schefler Amy C. , Seider Michael I. , Materin Miguel , Stinnett Sandra , Mruthyunjaya Prithvi ,   the Ocular Oncology Study Consortium
Published: November 2018

Purpose:
To study the relationship between gene expression profile (GEP) subclass and American Joint Committee on Cancer (AJCC) stage in patients with uveal melanoma (UM).

Methods:
A retrospective, multicenter study was undertaken with patients entered from nine major ocular oncology centers from across the United States. Three hundred sixty eligible patients had UM and underwent I-125 plaque brachytherapy with concurrent tumor biopsy with GEP testing between January 1, 2010, and October 28, 2014. Patient demographics and UM features were analyzed by both GEP and AJCC status.

Results:
Gene expression profile class divided the cohort into three groups: Class 1a (n = 186), Class 1b (n = 77), and Class 2 (n = 113). When classified using AJCC staging criteria, we found the following: Stage I in 91 cases (25.3%), Stage IIA in 143 cases (39.7%), Stage IIB in 89 cases (24.7%), Stage IIIA in 36 cases (10%), and Stage IIIB in 1 case (0.3%). There were no Stage IV cases, as lymph node and metastatic data were not collected as a part of this study. Among Stage I tumors, both high tumor height and high largest basal diameter were associated with a higher frequency of Class 2 status (P < 0.05). As UMs progress to a larger AJCC tumor group (T1–T4), the odds ratio of having a worse prognosis based on GEP class was 1.75 (95% CI, 1.36–2.25; P < 0.001). Similarly, as UMs progress to a higher AJCC stage, the odds ratio of having a worse prognosis based on GEP class was 1.69 (95% CI, 1.36–2.10; P < 0.001).

Conclusion:
This report details the differences in clinical features between GEP subclasses and how they are distributed among the AJCC stages. When the tumors were grouped by AJCC staging criteria, both larger AJCC tumor (T) group and worsening AJCC stage were associated with worsening predicted prognosis, based on GEP subclass.
Preferred self-administered questionnaires to assess fear of movement, coping, self-efficacy, and catastrophizing in patients with musculoskeletal pain—A modified Delphi study
Authors: Sleijser-Koehorst Marije L.S. , Bijker Lisette , Cuijpers Pim , Scholten-Peeters Gwendolyne G.M. , Coppieters Michel W. 
Published: November 2018

Abstract
The way people with musculoskeletal disorders deal with pain influences their prognosis. Psychosocial factors that influence outcomes include fear of movement, coping, self-efficacy, and catastrophizing. A 3-round modified Delphi study was conducted with the aim to reach consensus on the most appropriate questionnaires to assess these 4 psychosocial factors in patients at risk of developing persistent musculoskeletal pain. The panel consisted of 36 experts, with track records in medicine, psychology, and allied health. To be considered an expert, a minimum number of authorships were required on research articles using self-administered questionnaires to assess these psychosocial factors in relevant patient populations. In round 1, the experts proposed 30 questionnaires to assess the 4 factors. In round 2, experts rated the questionnaires on suitability, considering clinimetric properties, content, feasibility, personal experiences, and expertise. The highest ranked questionnaires (maximally 5 per factor) were retained for round 3, in which the experts made a final assessment of the questionnaires and provided their positive and negative experiences with the questionnaires. Consensus was reached for the following questionnaires to assess (1) fear of movement: Fear Avoidance Beliefs Questionnaire and Tampa Scale (full version or 11-item version); (2) coping: Coping Strategies Questionnaire (initial or revised version) and Chronic Pain Coping Index; (3) self-efficacy: Pain Self-Efficacy Questionnaire (full version or 2-item version); and (4) catastrophizing: Pain Catastrophizing Scale and the revised version of the Coping Strategies Questionnaire. Although other questionnaires can be considered in specific circumstances, these questionnaires are recommended in people with musculoskeletal pain.
Biliary tract exploration through a common bile duct incision or left hepatic duct stump in laparoscopic left hemihepatectomy for left side hepatolithiasis: which is better?
Authors: Zeng Xintao , Yang Pei , Wang Wentao 
Published: November 2018

Abstract
Laparoscopic left hemihepatectomy (LLH) followed by biliary tract exploration is used to treat left-sided hepatolithiasis (LSH). The purpose of this study was to compare the efficacy of 2 methods of biliary tract exploration in LLH:biliary tract exploration through a common bile duct (CBD) incision (with T-tube drainage) or through the left hepatic duct (LHD) stump (without T-tube drainage).
LSH patients (113 patients) were recruited retrospectively in our hospital from December 2008 to January 2016. To compare different methods of biliary tract exploration during LLH, the patients were divided into 2 groups: 41 patients underwent biliary tract exploration through the LHD stump (LHD group), and 72 patients underwent biliary tract exploration through a CBD incision (CBD group). Baseline characteristics, surgical outcomes, surgery-related complications, postoperative hospital stay (PHS) and long-term results were compared between the 2 groups.
There was no unplanned reoperation in the 2 groups. One patient in the CBD group had a residual stone, which was removed by choledochoscopy 2 months postoperation. Two patients in the LHD group and 3 patients in the CBD group had bile leakage and were cured with abdominal drainage. There were no significant differences in the total operation time, incidence of residual stones and bile leakage between the 2 groups (P > .05). The PHS and the incidence of hypokalemia or hyponatremia in the LHD group were significantly lower than those in the CBD group (P < .05). T-tube-related complications occurred in 13.9% (10/72) of the CBD patients. The mean follow-up period was 37.2 ± 13.8 months. There were no significant differences in the incidence of recurrence stones or cholangitis (P > .05) between the 2 groups.
Exploration of the biliary tract through the LHD stump without T-tube drainage is safe with satisfactory short- and long-term results for selected LSH patients.
The International Multiple Sclerosis Visual System Consortium: Advancing Visual System Research in Multiple Sclerosis
Authors: Balcer Laura J. , Balk Lisanne J. , Brandt Alexander U. , Calabresi Peter A. , Martinez-Lapiscina Elena H. , Nolan Rachel C. , Paul Friedemann , Petzold Axel , Saidha Shiv ,   on behalf of the IMSVISUAL Consortium
Published: November 2018

Background:
The International Multiple Sclerosis Visual System Consortium (IMSVISUAL) was formed in November 2014 with the primary goal of improving research, care, and education regarding the role of the visual system in multiple sclerosis (MS) and related disorders.

Methods:
In this review, we describe the formation, goals, activities, and structure of IMSVISUAL, as well as the relationship of IMSVISUAL with the Americas Committee for Treatment and Research in MS (ACTRIMS). Finally, we provide an overview of the work IMSVISUAL has completed to date, as well as an outline of research projects ongoing under the auspices of IMSVISUAL.

Results:
IMSVISUAL has 140 members worldwide and continues to grow. Through IMSVISUAL-related research, optical coherence tomography (OCT)-derived peripapillary retinal nerve fiber layer (pRNFL) thinning has been established as a predictor of future disability in MS. IMSVISUAL has also developed guidelines for reporting OCT studies in MS. Moreover, a systematic review performed by IMSVISUAL found that not only are pRNFL and ganglion cell + inner plexiform layer (GCIPL) thicknesses reduced in patients with MS (particularly in eyes with prior optic neuritis [ON]), but that inner nuclear layer measures may be higher among MS ON eyes, relative to healthy control eyes. Currently, there are several ongoing IMSVISUAL projects that will establish a role for visual outcomes in diagnosing MS and quantifying the effects of emerging therapies in clinical trials.

Conclusions:
The development of IMSVISUAL represents a major collaborative commitment to defining the role of visual outcomes in high-quality, large-scale studies that generate definitive and instructive findings in the field of MS. As a consortium, IMSVISUAL has completed several international collaborative projects, is actively engaged in numerous ongoing research studies, and is committed to expanding the role of vision research in MS and related disorders.
Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells
Authors: Higashijima Yoshiki , Matsui Yusuke , Shimamura Teppei , Tsutsumi Shuichi , Nakaki Ryo , Abe Yohei , Link Verena M. , Osaka Mizuko , Yoshida Masayuki , Watanabe Ryo , Tanaka Toshihiro , Taguchi Akashi , Miura Mai , Inoue Tsuyoshi , Nangaku Masaomi , Kimura Hiroshi , Furukawa Tetsushi , Aburatani Hiroyuki , Wada Youichiro , Glass Christopher K. , Kanki Yasuharu 
Published: November 2018

SUMMARYLysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are generally linked to gene repression. However, the functions of repressive histone methylation dynamics during inflammatory responses remain enigmatic. We found that tumor necrosis factor (TNF)-α rapidly induces the co-occupancy of lysine demethylases 7A (KDM7A) and 6A (UTX) with nuclear factor kappa-B (NF-κB) recruited elements in human endothelial cells. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and both are required for activation of NF-κB-dependent inflammatory genes. Chromosome conformation capture-based methods demonstrated increased interactions between TNF-α-induced super enhancers at NF-κB-relevant loci, coinciding with KDM7A- and UTX-recruitment. Simultaneous inhibition of KDM7A and UTX significantly reduced leukocyte adhesion in mice, establishing the biological and potential translational relevance of this mechanism. Collectively, these findings suggest that rapid erasure of repressive histone marks by KDM7A and UTX is essential for NF-κB-dependent regulation of genes that control inflammatory responses of endothelial cells.HIGHLIGHTSKDM7A and UTX cooperatively control NF-κB-dependent transcription in vascular endothelial cells.Demethylation of repressive histone marks by KDM7A and UTX is critical for early inflammatory responses.KDM7A and UTX are associated with TNF-α-induced looping of super enhancers.Pharmacological inhibition of KDM7A and UTX reduces leukocyte adhesive interactions with endothelial cells in mice.
Determinants of QTL mapping power in the realized Collaborative Cross
Authors: Keele Gregory R. , Crouse Wesley L. , Kelada Samir N. P. , Valdar William 
Published: November 2018

ABSTRACTThe Collaborative Cross (CC) is a mouse genetic reference population whose range of applications includes quantitative trait loci (QTL) mapping. The design of a CC QTL mapping study involves multiple decisions, including which and how many strains to use, and how many replicates per strain to phenotype, all viewed within the context of hypothesized QTL architecture. Until now, these decisions have been informed largely by early power analyses that were based on simulated, hypothetical CC genomes. Now that more than 50 CC strains are available and more than 70 CC genomes have been observed, it is possible to characterize power based on realized CC genomes. We report power analyses based on extensive simulations and examine several key considerations: 1) the number of strains and biological replicates, 2) the QTL effect size, 3) the presence of population structure, and 4) the distribution of functionally distinct alleles among the founder strains at the QTL. We also provide general power estimates to aide in the design of future experiments. All analyses were conducted with our R package, SPARCC (Simulated Power Analysis in the Realized Collaborative Cross), developed for performing either large scale power analyses or those tailored to particular CC experiments.
High-resolution mapping of regulatory element interactions and genome architecture using ARC-C
Authors: Huang Ni , Seow Wei Qiang , Ahringer Julie 
Published: November 2018

AbstractInteractions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.
Rapid, seamless generation of recombinant poxviruses using host-range and visual selection
Authors: Vipat Sameera , Brennan Greg , Haller Sherry L. , Rothenburg Stefan 
Published: November 2018

AbstractVaccinia virus (VACV) was instrumental in eradicating variola virus (VARV), the causative agent of smallpox, from nature. Since this first use as a vaccine, VACV has been developed as a vector for therapeutic vaccines and as an oncolytic virus. These applications take advantage of VACV’s easily manipulated genetics and broad host range as an outstanding platform to generate recombinant therapeutics. Several methods have been developed to generate recombinant VACV, including marker selection methods and transient dominant selection. Here, we present a refinement of a host-range selection method coupled with visual identification. Our method takes advantage of selective pressure generated by the host antiviral protein kinase R (PKR) coupled with a fluorescent fusion gene expressing mCherry-tagged E3L, one of two VACV PKR antagonists. This method permits rapid, seamless generation of rVACV in a variety of cell types.
Potassium channel regulators are differentially expressed in hippocampi of Ts65Dn and Tc1 Down syndrome mouse models
Authors: Stern Shani , Keren Rinat , Kim Yongsung , Moses Elisha 
Published: November 2018

AbstractBackground:Down syndrome remains the main genetic cause of intellectual disability, with an incidence rate of about 1 in 700 live births. The Ts65Dn mouse strain, with an extra murine chromosome that includes genes from chromosomes 10, 16 and 17 of the mouse and the Tc1 strain with an extra human chromosome 21, are currently accepted as informative and well-studied models for Down Syndrome. Using whole cell patch clamp we recently showed changes in several types of transmembrane currents in hippocampal neuronal cultures of Ts65Dn and Tc1 embryos. The associated genetic changes responsible for these changes in physiology were yet to be studied.Methods:We used qPCR to measure RNA expression level of a few of the channel genes that we suspect are implicated in the previously reported changes of measured currents, and performed statistical analysis using Matlab procedures for the standard t-test and ANOVA and for calculating correlations between the RNA expression levels of several channel genes.Results:We present differential gene expression levels measured using qPCR of the potassium channel regulators KCNE1 and KCNE2 in both Ts65Dn and Tc1 embryos and pups compared to controls. In Tc1, the human genes KCNJ6 and KCNJ15 are expressed in addition to a statistically insignificant increase of expression in the mouse genes KCNJ6 and KCNJ15. All channel genes that we have measured with large replication, have the same up-regulation or down-regulation in both mouse models, indicating that the transcription mechanism acts similarly in these two mouse models. The large dataset furthermore allows us to observe correlations between different channel genes. We find that, despite the significant changes in expression levels, channels that are known to interact have a high and significant correlation in expression both in controls and in the Down syndrome mouse model.Conclusions:We suggest the differential expression of KCNE1 and KCNE2 as a possible cause for our previously reported changes in potassium currents. We report a KCNJ6 and KCNJ15 overexpression, which plays a role in the increased input conductance and the reduced cell excitability that we previously reported in the Tc1 mouse model. The large and significant positive (KCNQ2-KCNQ3, KCNE1-KCNE2, KCNQ3-KCNE1, KCNQ2-KCNE1, KCNQ2-KCNE2, KCNQ3-KCNE2) and negative correlations (KCNE1-KCNJ15, KCNE2-KCNJ15) that we find between channel genes indicate that these genes probably work in a cooperative or in a mutually exclusive manner.
Spatiotemporal expression of FRIGIDA modulate flowering time in Arabidopsis thaliana
Authors: Kong Xiangxiang , Zhao Jinjie , Luo Landi , Chen Qian , Chang Guanxiao , Huang Jinling , Yang Yongping , Hu Xiangyang 
Published: November 2018

AbstractFRIGIDA (FRI) as the major regulator of flowering time in Arabidopsis accessions can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. Besides FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatiotemporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets MADS AFFECTING FLOWERING4 (MAF4) and MAF5 in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as pro-embryo stage is enough to upregulate FLC expression to delay flowering. Together, our findings confirm the spatiotemporal effect of FRI on delaying flowering, and propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI.HighlightRoot FRIDIGA activated the novel targets MAF4/5 to delay flowering; Temporal expressing FRIGIDA at as early as pro-embryo stage is efficient to delay flowering.