bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes
Authors: Zhang Xinyan , Zhao Meixia , McCarty Donald R , Lisch Damon 
Published: April 2020

AbstractTransposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
Authors: Mungan Mehmet Direnç , Alanjary Mohammad , Blin Kai , Weber Tilmann , Medema Marnix H , Ziemert Nadine 
Published: April 2020

Abstract
Multi-drug resistant pathogens have become a major threat to human health and new antibiotics are urgently needed. Most antibiotics are derived from secondary metabolites produced by bacteria. In order to avoid suicide, these bacteria usually encode resistance genes, in some cases within the biosynthetic gene cluster (BGC) of the respective antibiotic compound. Modern genome mining tools enable researchers to computationally detect and predict BGCs that encode the biosynthesis of secondary metabolites. The major challenge now is the prioritization of the most promising BGCs encoding antibiotics with novel modes of action. A recently developed target-directed genome mining approach allows researchers to predict the mode of action of the encoded compound of an uncharacterized BGC based on the presence of resistant target genes. In 2017, we introduced the ‘Antibiotic Resistant Target Seeker’ (ARTS). ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets by rapidly linking housekeeping and known resistance genes to BGC proximity, duplication and horizontal gene transfer (HGT) events. Here, we present ARTS 2.0 available at http://arts.ziemertlab.com. ARTS 2.0 now includes options for automated target directed genome mining in all bacterial taxa as well as metagenomic data. Furthermore, it enables comparison of similar BGCs from different genomes and their putative resistance genes.
Zinc supplementation combined with antidepressant drugs for treatment of patients with depression: a systematic review and meta-analysis
Authors: da Silva Laís Eloy Machado , de Santana Mônica Leila Portela , Costa Priscila Ribas de Farias , Pereira Emile Miranda , Nepomuceno Carina Márcia Magalhães , Queiroz Valterlinda Alves de Oliveira , de Oliveira Lucivalda Pereira Magalhães , Machado Maria Ester Pereira da Conceição- , de Sena Eduardo Pondé 
Published: April 2020

Abstract

Context
Zinc is an essential trace mineral required for the function of brain and neural structures. The role of zinc supplementation in the prevention and treatment of depression has been suggested in clinical studies that reported a reduction in depressive symptoms.

Objective
The aim of this review was to determine whether zinc supplementation vs placebo can prevent or improve depressive symptoms in children, adolescents, or adults.

Data Sources
Five electronic databases were searched, and studies published until September 2019 were included without language restriction.

Study Selection
Randomized, controlled, crossover trials that evaluated the effect of zinc supplementation vs a comparator for prevention or improvement of depressive symptoms in children, adolescents, or adults were eligible for inclusion.

Data Extraction
Two authors independently performed data extraction and risk-of-bias assessment.

Results
The initial search identified 12 322 studies, 5 of which were eligible for meta-analysis. The standardized mean difference (SMD) showed an average reduction of 0.36 point (95%CI, −0.67 to −0.04) in the intervention group compared with the placebo group. Forstudies in which the mean age of participants was ≥ 40 years, the SMD was reduced by 0.61 point (95%CI, −1.12 to −0.09) in the intervention group vs the placebo group. The meta-analysis by sample size (&lt; 60 individuals and  ≥ 60 individuals) did not show an effect of zinc supplementation in reducing depressive symptoms (SMD −0.28; 95%CI, −0.67 to −0.10; and SMD −0.52; 95%CI, −1.10 to 0.06).

Conclusion
Zinc supplementation may reduce depressive symptoms in individuals treated with antidepressant drugs for clinical depression.

Systematic Review Registration
PROSPERO registration number CRD42018081691.
Analysis of Mortality in Patients With COVID-19: Clinical and Laboratory Parameters
Authors: Tian Sufang , Liu Huan , Liao Meiyan , Wu Yingjie , Yang Chunxiu , Cai Yuxiang , Peng Zhiyong , Xiao Shu-Yuan 
Published: April 2020

Abstract

Background
Several reports on epidemiological and clinical features of the 2019 coronavirus disease (COVID-19) have been published. However, mortality and morbidity analyses, important for better understanding the pathogenesis of this disease, are scarce. We examine the clinical and laboratory features of 14 patients who died of COVID-19.

Methods
The cohort consisted of 11 male and 3 female patients, with 9 patients aged 70 years or above, and nearly all had underlying diseases.

Results
Fever with bilateral pneumonia was the main manifestation. Most patients had consolidations combined with ground glass opacity (GGO) on chest computed tomography scan. Laboratory tests showed lymphocytopenia in 10 patients, high blood glucose in 11, GGT in 5 of the 14 patients, and high LDH in 5 of 6 patients tested. In addition, this cohort had high level of cytokines such as interleukin-6 in all 8 patients tested.

Conclusions
The clinical and laboratory parameters in the cohort of fatal cases may be incorporated into future clinical prognosis models and will be of help in understanding the pathogenesis of this disease.
Top of the Class: The Importance of Ordinal Rank
Authors: Murphy Richard , Weinhardt Felix 
Published: April 2020

AbstractThis article establishes a new fact about educational production: ordinal academic rank during primary school has lasting impacts on secondary school achievement that are independent of underlying ability. Using data on the universe of English school students, we exploit naturally occurring differences in achievement distributions across primary school classes to estimate the impact of class rank. We find large effects on test scores, confidence, and subject choice during secondary school, even though these students have a new set of peers and teachers who are unaware of the students’ prior ranking in primary school. The effects are especially pronounced for boys, contributing to an observed gender gap in the number of Maths courses chosen at the end of secondary school. Using a basic model of student effort allocation across subjects, we distinguish between learning and non-cognitive skills mechanisms, finding support for the latter.
EVALUATION OF RADIATION PROTECTION PRINCIPLES OBSERVANCE IN DENTAL RADIOGRAPHY CENTERS (WEST OF IRAN): CROSS-SECTIONAL STUDY
Authors: Rasoul Tohidnia Mohammad , Rasool Azmoonfar , Fatemeh Amiri , Rahimi Seyed Ali , Neda Amiri , Hosna Sharafi 
Published: April 2020

AbstractThe aim of this study is to assess the evaluation of radiation protection principles observance in dental radiography centers and hazards. This cross-sectional study was designed to assess level of radiation protection principles in dentistry centers. The present cross-sectional study was conducted by enrolling 103 dentistry centers in Kermanshah province (west of Iran). Our finding illustrates 75.7% of the centers were equipped with an intraoral radiography. Although observance principles of radiation protection for patient at dentistry center were at appropriate level (97.3%), the observance of the protective principles was not adequate for the skilled workers in any center. The most commonly used protective measure was the observance of a distance from patient (97.3%) and the minimum protective measures such as the use of high-speed film (1.4%). According to results in this study, the knowledge and practice of radiation protection are not satisfactory.
Do we understand yet the nature of a partnership interest? The High Court of Australia weighs in on the debate
Authors: Nitikman Joel 
Published: April 2020

Abstract
Since before the first Partnership Act in 1865, there has been a debate as to the nature of a partner's share in a partnership. Is it a proprietary interest in the partnership property, a chose in action representing the money to be received on a dissolution of the partnership, or both at the same time? There has also been a debate as to whether one partner holds title to partnership property in trust for the other partners and, if so, the nature of that trust. Joel Nitikman explores this topics in a comment on the decision of the High Court of Australia in Commissioner of Taxation v. Rojoda.
Electroencephalogram Burst-suppression during Cardiopulmonary Bypass in Elderly Patients Mediates Postoperative Delirium
Authors: Pedemonte Juan C. , Plummer George S. , Chamadia Shubham , Locascio Joseph J. , Hahm Eunice , Ethridge Breanna , Gitlin Jacob , Ibala Reine , Mekonnen Jennifer , Colon Katia M. , Westover M. Brandon , D’Alessandro David A. , Tolis George , Houle Timothy , Shelton Kenneth T. , Qu Jason , Akeju Oluwaseun 
Published: April 2020

Background
Intraoperative burst-suppression is associated with postoperative delirium. Whether this association is causal remains unclear. Therefore, the authors investigated whether burst-suppression during cardiopulmonary bypass (CPB) mediates the effects of known delirium risk factors on postoperative delirium.

Methods
This was a retrospective cohort observational substudy of the Minimizing ICU [intensive care unit] Neurological Dysfunction with Dexmedetomidine-induced Sleep (MINDDS) trial. The authors analyzed data from patients more than 60 yr old undergoing cardiac surgery (n = 159). Univariate and multivariable regression analyses were performed to assess for associations and enable causal inference. Delirium risk factors were evaluated using the abbreviated Montreal Cognitive Assessment and Patient-Reported Outcomes Measurement Information System questionnaires for applied cognition, physical function, global health, sleep, and pain. The authors also analyzed electroencephalogram data (n = 141).

Results
The incidence of delirium in patients with CPB burst-suppression was 25% (15 of 60) compared with 6% (5 of 81) in patients without CPB burst-suppression. In univariate analyses, age (odds ratio, 1.08 [95% CI, 1.03 to 1.14]; P = 0.002), lowest CPB temperature (odds ratio, 0.79 [0.66 to 0.94]; P = 0.010), alpha power (odds ratio, 0.65 [0.54 to 0.80]; P < 0.001), and physical function (odds ratio, 0.95 [0.91 to 0.98]; P = 0.007) were associated with CPB burst-suppression. In separate univariate analyses, age (odds ratio, 1.09 [1.02 to 1.16]; P = 0.009), abbreviated Montreal Cognitive Assessment (odds ratio, 0.80 [0.66 to 0.97]; P = 0.024), alpha power (odds ratio, 0.75 [0.59 to 0.96]; P = 0.025), and CPB burst-suppression (odds ratio, 3.79 [1.5 to 9.6]; P = 0.005) were associated with delirium. However, only physical function (odds ratio, 0.96 [0.91 to 0.99]; P = 0.044), lowest CPB temperature (odds ratio, 0.73 [0.58 to 0.88]; P = 0.003), and electroencephalogram alpha power (odds ratio, 0.61 [0.47 to 0.76]; P < 0.001) were retained as predictors in the burst-suppression multivariable model. Burst-suppression (odds ratio, 4.1 [1.5 to 13.7]; P = 0.012) and age (odds ratio, 1.07 [0.99 to 1.15]; P = 0.090) were retained as predictors in the delirium multivariable model. Delirium was associated with decreased electroencephalogram power from 6.8 to 24.4 Hertz.

Conclusions
The inference from the present study is that CPB burst-suppression mediates the effects of physical function, lowest CPB temperature, and electroencephalogram alpha power on delirium.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
The Population-based Impact of Adjuvant Chemotherapy on Outcomes in T2N0M0 Non–Small Cell Lung Cancer
Authors: Arora Rahul K. , Gibson Amanda W. , Bebb D. Gwyn , Cheung Winson Y. 
Published: April 2020

Objectives:
The value of adjuvant chemotherapy in T2N0M0 non–small-cell lung cancer (NSCLC) is unclear. Some current guidelines suggest adjuvant chemotherapy be considered for patients with tumors ≥4 cm. Prior population-based evaluations lacked lung cancer-specific survival (LCSS) and health insurance status. The authors aimed to identify predictors of adjuvant chemotherapy use and assess its real-world benefit in T2N0M0 NSCLC.

Materials and Methods:
The authors included patients who underwent surgery for T2N0M0 NSCLC in a large Canadian province with universal health care between 2004 and 2015, grouping cases by adjuvant chemotherapy receipt. They identified predictors of chemotherapy use with logistic regression and correlates of overall survival (OS) and LCSS using Cox regression.

Results:
The authors analyzed 967 patients. The median age was 68 years (interquartile range, 61 to 74), 455 (47%) were men, and 164 (17%) received adjuvant chemotherapy. Sex, tumor location, and laterality were similar between groups. Younger age, lower Charlson comorbidity score, large cell histology, and tumor size ≥4 cm were associated with a higher likelihood of chemotherapy receipt (all P<0.05). In the entire cohort and in the ≥4 and ≥5 cm subgroups, chemotherapy improved OS but not LCSS on univariate analysis. Chemotherapy was not associated with OS or LCSS in multivariate analysis (OS hazard ratio [HR], 0.925; 95% confidence interval [0.693-1.236], P=0.598, 0.725 [0.454-1.157], P=0.177 in the ≥4 cm group; LCSS HR, 1.196 [0.843-1.695], P=0.316, 0.917 [0.533-1.577], P=0.754 in the ≥4 cm group).

Conclusion:
Adjuvant chemotherapy was not associated with improved survival in this population-based T2N0M0 NSCLC cohort, even for ≥4 or ≥5 cm tumors, suggesting that it has a limited role in real-world practice.
Three-dimensional Coordinate System for Hemifacial Microsomia
Authors: Ariizumi Dai , Sakamoto Teruo , Ishii Takenobu , Sueishi Kenji , Nishii Yasushi , Sakamoto Yoshiaki , Ogata Hisao 
Published: April 2020

Background:
Hemifacial microsomia (HFM) is a congenital disorder characterized by facial asymmetry, but no midline reference has been established for evaluating facial morphology in patients with HFM. The purpose of this study was to develop a 3-dimensional coordinate system unaffected by the deformity of the external acoustic aperture or orbital circumference and to quantitatively evaluate craniofacial morphology in such patients.

Methods:
We quantitatively evaluated craniofacial morphology using 3-dimensional measurements with the skull base as a reference. Using computed tomography data from 15 patients with HFM and 15 controls, a coordinate system was created for each patient, and left–right differences between measurement points were compared.

Results:
When mandibular deformity was severe, the deformity of the posterior part of the palatine bone and lateral part of the orbit increased, but this trend was not evident for other measurement points. Thus, craniofacial deformity in HFM was not always related to mandibular deformity. Moreover, no difference was evident in the position of the hypoglossal canal between controls and patients with HFM.

Conclusions:
Quantitative assessments are possible using the coordinate system devised in this study, irrespective of the severity of HFM. The degree of mandibular deformity detailed in the Pruzansky classification was associated with the superoinferior deformity of the posterior part of the palatine bone and anteroposterior deformity of the lateral part of the orbit.
Use of Probiotics for the Management of Acute Gastroenteritis in Children
Authors: Szajewska Hania , Guarino Alfredo , Hojsak Iva , Indrio Flavia , Kolacek Sanja , Orel Rok , Salvatore Silvia , Shamir Raanan , van Goudoever Johannes B. , Vandenplas Yvan , Weizman Zvi , Zalewski Bartłomiej M. ,   Working Group on Probiotics and Prebiotics of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition
Published: April 2020

ABSTRACTSince the publication of the 2014 European Society for Paediatric Gastroenterology, Hepatology, and Nutrition Working Group (WG) on Probiotics and Prebiotics guidelines for the management of acute gastroenteritis (AGE), new evidence concerning the efficacy of probiotics has become available. This document provides updated recommendations on the use of probiotics for the treatment of AGE in previously presumed healthy infants and children. A systematic literature search was performed. All pooled analyses were explicitly performed for the current report. The WG graded the recommendations and assessed the certainty of the supporting evidence using the Grading of Recommendations, Assessment Development, and Evaluations tool. The recommendations were formulated if at least 2 randomized controlled trials that used a given probiotic were available. Despite the large number of identified trials, the WG could not identify 2 randomized controlled trial of high quality for any strain that provided benefit when used for treating AGE. The WG made weak recommendations for (in descending order in terms of the number of trials evaluating any given strain): Saccharomyces boulardii (low to very low certainty of evidence); Lactobacillus rhamnosus GG (very low certainty of evidence); L reuteri DSM 17938 (low to very low certainty of evidence); and L rhamnosus 19070‐2 and L reuteri DSM 12246 (very low certainty of evidence). The WG made a strong recommendation against L helveticus R0052 and L rhamnosus R0011 (moderate certainty of evidence) and a weak recommendation against Bacillus clausii strains O/C, SIN, N/R, and T (very low certainty of evidence).
Fully Automated Segmentation and Shape Analysis of the Thoracic Aorta in Non–contrast-enhanced Magnetic Resonance Images of the German National Cohort Study
Authors: Hepp Tobias , Fischer Marc , Winkelmann Moritz T. , Baldenhofer Sonja , Kuestner Thomas , Nikolaou Konstantin , Yang Bin , Gatidis Sergios 
Published: April 2020

Purpose:The purpose of this study was to develop and validate a deep learning-based framework for automated segmentation and vessel shape analysis on non–contrast-enhanced magnetic resonance (MR) data of the thoracic aorta within the German National Cohort (GNC) MR study.Materials and Methods:One hundred data sets acquired in the GNC MR study were included (56 men, average age 53 y [22 to 72 y]). All participants had undergone non–contrast-enhanced MR imaging of the thoracic vessels. Automated vessel segmentation of the thoracic aorta was performed using a Convolutional Neural Network in a supervised setting with manually annotated data sets as the ground truth. Seventy data sets were used for training; 30 data sets were used for quantitative and qualitative evaluation. Automated shape analysis based on centerline extraction from segmentation masks was performed to derive a diameter profile of the vessel. For comparison, 2 radiologists measured vessel diameters manually.Results:Overall, automated aortic segmentation was successful, providing good qualitative analyses with only minor irregularities in 29 of 30 data sets. One data set with severe MR artifacts led to inadequate automated segmentation results. The mean Dice score of automated vessel segmentation was 0.85. Automated aortic diameter measurements were similar to manual measurements (average difference −0.9 mm, limits of agreement: −5.4 to 3.9 mm), with minor deviations in the order of the interreader agreement between the 2 radiologists (average difference −0.5 mm, limits of agreement: −5.8 to 4.8 mm).Conclusion:Automated segmentation and shape analysis of the thoracic aorta is feasible with high accuracy on non–contrast-enhanced MR imaging using the proposed deep learning approach.
Advanced neuroimaging in neuropsychiatric systemic lupus erythematosus
Authors: Mackay Meggan , Tang Chris C. , Vo An 
Published: April 2020

Purpose of review
Neuropsychiatric lupus (NPSLE) comprises a disparate collection of syndromes affecting the central and peripheral nervous systems. Progress in the attribution of neuropsychiatric syndromes to SLE-related mechanisms and development of targeted treatment strategies has been impeded by a lack of objective imaging biomarkers that reflect specific neuropsychiatric syndromes and/or pathologic mechanisms. The present review addresses recent publications of neuroimaging techniques in NPSLE.

Recent findings
Imaging studies grouping all NPSLE syndromes together are unable to differentiate between NPSLE and non-NPSLE. In contrast, diffusion tensor imaging, FDG-PET, resting, and functional MRI techniques in patients with stable non-NPSLE demonstrate abnormal network structural and functional connectivity and regional brain activity in multiple cortical areas involving the limbic system, hippocampus, frontal, parietal, and temporal lobes. Some of these changes associate with impaired cognitive performance or mood disturbance, autoantibodies or inflammatory proteins. Longitudinal data suggest progression over time. DCE-MRI demonstrates increased Blood–brain barrier permeability.

Summary
Study design issues related to patient selection (non-NPSLE vs. NPSLE syndromes, SLE disease activity, medications) are critical for biomarker development. Regional and network structural and functional changes identified with advanced brain imaging techniques in patients with non-NPSLE may be further developed as biomarkers for cognitive and mood disorders attributable to SLE-related mechanisms.