bluuebunny/crossref_metadata_2025_split huggingface dataset:
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study inArabidopsis thaliana
Authors: Froussios Kimon , Schurch Nick J , Mackinnon Katarzyna , Gierliński Marek , Duc Céline , Simpson Gordon G , Barton Geoffrey J 
Published: February 2019

AbstractMotivationRNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, differential gene expression (DGE) tools typically assume the form of the underlying gene expression distribution. In this paper, the statistical properties of gene expression from RNA-seq are investigated in the complex eukaryote, Arabidopsis thaliana, extending and generalizing the results of previous work in the simple eukaryote Saccharomyces cerevisiae.ResultsWe show that, consistent with the results in S.cerevisiae, more gene expression measurements in A.thaliana are consistent with being drawn from an underlying negative binomial distribution than either a log-normal distribution or a normal distribution, and that the size and complexity of the A.thaliana transcriptome does not influence the false positive rate performance of nine widely used DGE tools tested here. We therefore recommend the use of DGE tools that are based on the negative binomial distribution.Availability and implementationThe raw data for the 17 WT Arabidopsis thaliana datasets is available from the European Nucleotide Archive (E-MTAB-5446). The processed and aligned data can be visualized in context using IGB (Freese et al., 2016), or downloaded directly, using our publicly available IGB quickload server at https://compbio.lifesci.dundee.ac.uk/arabidopsisQuickload/public_quickload/ under ‘RNAseq&gt;Froussios2019’. All scripts and commands are available from github at https://github.com/bartongroup/KF_arabidopsis-GRNA.Supplementary informationSupplementary data are available at Bioinformatics online.
RiboD: a comprehensive database for prokaryotic riboswitches
Authors: Mukherjee Sumit , Das Mandal Sukhen , Gupta Nikita , Drory-Retwitzer Matan , Barash Danny , Sengupta Supratim 
Published: February 2019

Abstract

Summary
Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location and gene/operon it regulates. RiboD provides a very useful resource that can be utilized for the better understanding of riboswitch-based gene regulation in bacteria and archaea.

Availability and implementation
RiboD can be freely accessed on the web at http://ribod.iiserkol.ac.in/.
Influenza Vaccine Effectiveness Against Hospitalization in Fully and Partially Vaccinated Children in Israel: 2015–2016, 2016–2017, and 2017–2018
Authors: Segaloff Hannah E , Leventer-Roberts Maya , Riesel Dan , Malosh Ryan E , Feldman Becca S , Shemer-Avni Yonat , Key Calanit , Monto Arnold S , Martin Emily T , Katz Mark A 
Published: February 2019

Abstract

Background
Influenza vaccine effectiveness (VE) varies by season, circulating influenza strain, age, and geographic location. There have been few studies of influenza VE among hospitalized children, particularly in Europe and the Middle East.

Methods
We estimated VE against influenza hospitalization among children aged 6 months to 8 years at Clalit Health Services hospitals in Israel in the 2015–2016, 2016–2017, and 2017–2018 influenza seasons, using the test-negative design. Estimates were computed for full and partial vaccination.

Results
We included 326 influenza-positive case patients and 2821 influenza-negative controls (140 case patients and 971 controls from 2015–2016, 36 case patients and 1069 controls from 2016–2017, and 150 case patients and 781 controls from 2017–2018). Over all seasons, VE was 53.9% for full vaccination (95% confidence interval [CI], 38.6%–68.3%), and 25.6% for partial vaccination (−3% to 47%). In 2015–2016, most viruses were influenza A(H1N1) and vaccine lineage–mismatched influenza B/Victoria; the VE for fully vaccinated children was statistically significant for influenza A (80.7%; 95% CI, 40.3%–96.1%) but not B (23.0%; −38.5% to 59.4%). During 2016–2017, influenza A(H3N2) predominated, and VE was (70.8%; 95% CI, 17.4%–92.4%). In 2017–2018, influenza A(H3N2), H1N1 and lineage-mismatched influenza B/Yamagata cocirculated; VE was statistically significant for influenza B (63.0%; 95% CI, 24.2%–83.7%) but not influenza A (46.3%; −7.2% to 75.3%).

Conclusions
Influenza vaccine was effective in preventing hospitalizations among fully vaccinated Israeli children over 3 influenza seasons, but not among partially vaccinated children. There was cross-lineage protection in a season where the vaccine contained B/Victoria and the circulating strain was B/Yamagata, but not in a season with the opposite vaccine-circulating strain distribution.
Identification of Chitinase-3-Like Protein 1 as a Novel Neutrophil Antigenic Target in Crohn’s Disease
Authors: Deutschmann Claudia , Sowa Mandy , Murugaiyan Jayaseelan , Roesler Uwe , Röber Nadja , Conrad Karsten , Laass Martin W , Bogdanos Dimitrios , Sipeki Nora , Papp Maria , Rödiger Stefan , Roggenbuck Dirk , Schierack Peter 
Published: February 2019

AbstractBackground and AimsThere is an increasing incidence of inflammatory bowel disease [IBD]. Autoimmune responses are involved in the pathophysiology of IBD, but their underlying pathways and target antigens have not yet been fully elucidated.MethodsAutoantigenic targets in IBD were identified after separation of whole cell proteins isolated from neutrophils using two-dimensional electrophoresis and matrix assisted laser desorption ionization – time of flight mass spectrometry-based protein identification of the spots that displayed Western blotting signals with anti-neutrophil cytoplasmic antibody-positive sera. The prevalence of IgG, IgA and secretory IgA [sIgA] to chitinase 3-like protein 1 [CHI3L1] was analysed by enzyme-linked immunosorbent assays using recombinant CHI3L1 in 110 patients with Crohn’s disease [CD], 95 with ulcerative colitis [UC], 126 with coeliac disease [CeD] and 86 healthy controls [HCs].ResultsThe 18-glycosylhydrolase family member CHI3L1 was identified as a neutrophil autoantigenic target. CD patients displayed significantly higher levels of IgG to CHI3L1 than patients with UC and CeD (p < 0.0001, respectively). IgA and sIgA to CHI3L1 was significantly higher in CD than in UC, CeD and HCs [p < 0.0001, respectively]. IgA and sIgA to CHI3L1 demonstrated the highest prevalence in CD [25.5%, 28/110; and 41.8%%, 46/110] compared to HCs [2.3%, 2/86; and 4.7%%, 4/86; p = 0.0015 and p < 0.0001] and are associated with a more complicated progression of CD.ConclusionCHI3L1 is a novel neutrophil autoantigenic target in CD. IgA and sIgA to CHI3L1 may serve as novel markers for CD and may facilitate the serological diagnosis of IBD.
Handmade stent graft fenestration to preserve left subclavian artery in thoracic endovascular aortic repair†
Authors: Kuo Huey-Shiuan , Huang Jih-Hsin , Chen Jer-Shen 
Published: February 2019

Abstract

OBJECTIVES
This study aimed to evaluate the efficacy and safety of a handmade fenestrated stent graft over an aortic stent graft for preserving the left subclavian artery (LSA) in thoracic endovascular aortic repair (TEVAR).

METHODS
From July 2015 to October 2018, a total of 32 consecutive patients with various thoracic aortic pathologies who underwent TEVAR in which handmade fenestration over a thoracic aortic stent graft was used for LSA were included. Outcomes including technical success, procedure-related complications, perioperative mortality and morbidity and graft patency were analysed.

RESULTS
Twenty-four patients (75.00%) presented with aortic dissection, 5 patients (15.63%) with thoracic aortic aneurysm and 2 patients (6.25%) with penetrating aortic ulcer; 1 patient (3.13%) required re-TEVAR due to endoleak and sac expansion from previous TEVAR for thoraco-abdominal aneurysm. TEVAR was performed in a zone 2 landing with single fenestration for LSA (26 patients, 81.25%), zone 1 landing with double fenestration for both LSA and left common carotid artery (5 patients, 15.63%) or zone 1 landing with single fenestration for LSA and a chimney graft for left common carotid artery (1 patient, 3.13%). The technical success rate, defined as the successful alignment of fenestration to LSA, was 93.75%. At a mean follow-up of 17.3 months, 4 cases of endoleak and 2 cases of stent graft-induced new entry were noted, 3 of which were treated endovascularly.

CONCLUSIONS
Our preliminary results demonstrate the viability of preserving LSA blood flow in TEVAR using a handmade stent graft fenestration to treat various aortic pathologies in various clinical situations and the technical feasibility and short-term results that may justify the use of this method in emergency cases.
Real-world referral pattern and outcomes of diabetic patients who undergo revascularization: data from the prospective Multi-vessel Coronary Artery Disease (MULTICAD) Israeli Registry†
Authors: Ram Eilon , Goldenberg Ilan , Sternik Leonid , Peled Yael , Segev Amit , Kogan Alexander , Vorobeichik Pechersky Dina , Shlomo Nir , Raanani Ehud 
Published: February 2019

Abstract

OBJECTIVES
Diabetes mellitus patients with multivessel coronary artery disease present with a poor prognosis. We aimed to explore real-life clinical outcomes of diabetic patients who were referred for coronary revascularization.

METHODS
We used data from the Multi-vessel Coronary Artery Disease (MULTICAD) Israeli Registry. Using descriptive statistics, Kaplan–Meier, Cox and logistic regression, we described a revascularization referral pattern, short-term outcomes and long-term survival among 475 diabetic patients with multivessel and/or left main disease, 48% of whom underwent surgical and 52% percutaneous revascularization.

RESULTS
Factors independently associated with referral for surgery included the presence of left main stenosis [odds ratio (OR) 1.89; P = 0.030] and a higher Syntax score (OR 1.15 per point increment; P < 0.001), whereas an older age (OR 1.03 per 1-year increment in age; P = 0.019), prior percutaneous coronary intervention (OR 1.83; P = 0.009) and the presence of renal impairment (OR 2; P = 0.026) were associated with percutaneous coronary intervention referral. At 7 months of follow-up, multivariable analysis did not reveal any difference in mortality risk between the surgical and percutaneous revascularization groups [hazard ratio (HR) 1.23, 95% confidence interval (CI) 0.5–3.04; P = 0.649], whereas after 7 months, surgical revascularization was associated with a significant survival benefit (HR 2.24, 95% CI 1.03–4.87; P = 0.042).

CONCLUSIONS
Our observation suggests that in a real-world setting, only approximately one-half of diabetic patients with multivessel disease are referred to surgical revascularization despite guideline indications. Surgical compared to percutaneous revascularization in this population was associated with improved long-term survival that became evident 7 months after the revascularization procedure.
Chaotic dynamics from a pseudo-linear system
Authors: Ghane Hamed , Sterk Alef E , Waalkens Holger 
Published: February 2019

Abstract
Investigating the possibility of applying techniques from linear systems theory to the setting of non-linear systems has been the focus of many papers. The pseudo-linear (PL) form representation of non-linear dynamical systems has led to the concept of non-linear eigenvalues (NEValues) and non-linear eigenvectors (NEVectors). When the NEVectors do not depend on the state vector of the system, then the NEValues determine the global qualitative behaviour of a non-linear system throughout the state space. The aim of this paper is to use this fact to construct a non-linear dynamical system of which the trajectories of the system show continual stretching and folding. We first prove that the system is globally bounded. Next we analyse the system numerically by studying bifurcations of equilibria and periodic orbits. Chaos arises due to a period doubling cascade of periodic attractors. Chaotic attractors are presumably of Hénon-like type, which means that they are the closure of the unstable manifold of a saddle periodic orbit. We also show how PL forms can be used to control the chaotic system and to synchronize two identical chaotic systems.
A Systematic Review and Recommendation for Reporting of Surrogate Endpoint Evaluation Using Meta-analyses
Authors: Xie Wanling , Halabi Susan , Tierney Jayne F , Sydes Matthew R , Collette Laurence , Dignam James J , Buyse Marc , Sweeney Christopher J , Regan Meredith M 
Published: February 2019

AbstractBackgroundMeta-analysis of randomized controlled trials (RCTs) has been widely conducted for the evaluation of surrogate endpoints in oncology, but little attention has been given to the adequacy of reporting and interpretation. This review evaluated the reporting quality of published meta-analyses on surrogacy evaluation and developed recommendations for future reporting.MethodsWe searched PubMed through August 2017 to identify studies that evaluated surrogate endpoints using the meta-analyses of RCTs in oncology. Both individual patient data (IPD) and aggregate data (AD) meta-analyses were included for the review.ResultsEighty meta-analyses were identified: 22 used IPD and 58 used AD from multiple RCTs. We observed variability and reporting deficiencies in both IPD and AD meta-analyses, especially on reporting of trial selection, endpoint definition, study and patient characteristics for included RCTs, and important statistical methods and results. Based on these findings, we proposed a checklist and recommendations to improve completeness, consistency, and transparency of reports of meta-analytic surrogacy evaluation. We highlighted key aspects of the design and analysis of surrogate endpoints and presented explanations and rationale why these items should be clearly reported in surrogacy evaluation.ConclusionsOur reporting of surrogate endpoint evaluation using meta-analyses (ReSEEM) guidelines and recommendations will improve the quality in reporting and facilitate the interpretation and reproducibility of meta-analytic surrogacy evaluation. Also, they should help promote greater methodological consistency and could also serve as an evaluation tool in the peer review process for assessing surrogacy research.
Expression of ERG11 and efflux pump genes CDR1, CDR2 and SNQ2 in voriconazole susceptible and resistant Candida glabrata strains
Authors: Navarro-Rodríguez Patricia , Martin-Vicente Adela , López-Fernández Loida , Guarro Josep , Capilla Javier 
Published: February 2019

AbstractCandida glabrata causes difficult to treat invasive candidiasis due to its antifungal resistance, mainly to azoles. The aim of the present work was to study the role of the genes ERG11, CDR1, CDR2, and SNQ2 on the resistance to voriconazole (VRC) in a set of C. glabrata strains with known in vitro and in vivo susceptibility to this drug. Eighteen clinical isolates of C. glabrata were exposed in vitro to VRC, and the expression of the cited genes was quantified by real time quantitative polymerase chain reaction (q-PCR). In addition, the ERG11 gene was amplified and sequenced to detect possible mutations. Ten synonymous mutations were found in 15 strains, two of them being reported for the first time; however, no amino acid changes were detected. ERG11 and CDR1 were the most expressed genes in all the strains tested, while the expression of CDR2 and SNQ2 was modest. Our results show that gene expression does not directly correlate with the VRC MIC. In addition, the expression profiles of ERG11 and efflux pump genes did not change consistently after exposure to VRC. Although individual analysis did not result in a clear correlation between MIC and gene expression, we did observe an increase in ERG11 and CDR1 expression in resistant strains. It is of interest that considering both in vitro and in vivo results, the slight increase in such gene expression correlates with the observed resistance to VRC.
Triggering magnetar outbursts in 3D force-free simulations
Authors: Carrasco Federico , Viganò Daniele , Palenzuela Carlos , Pons Jose A 
Published: February 2019

Abstract
In this letter, we present the first 3D force-free general relativity simulations of the magnetosphere dynamics related to the magnetar outburst/flare phenomenology. Starting from an initial dipole configuration, we adiabatically increase the helicity by twisting the footprints of a spot on the stellar surface and follow the succession of quasi-equilibrium states until a critical twist is reached. Twisting beyond that point triggers instabilities that results in the rapid expansion of magnetic field lines, followed by reconnection, as observed in previous axi-symmetric simulations. If the injection of magnetic helicity goes on, the process is recurrent, periodically releasing a similar amount of energy, of the order of a few per cent of the total magnetic energy. From our current distribution, we estimate the local temperature assuming that dissipation occurs mainly in the highly resistive outermost layer of the neutron star. We find that the temperature smoothly increases with injected twist, being larger for spots located in the tropical regions than in polar regions, and rather independent of their sizes. After the injection of helicity ceases, the magnetosphere relaxes to a new stable state, in which the persistent currents maintain the footprints area slightly hotter than before the onset of the instability.
Comparison of polarization at two lunar eclipse events
Authors: Takahashi Jun , Itoh Yoichi , Watanabe Makoto , Akitaya Hiroshi , Takaki Katsutoshi , Kawabata Koji S , Itoh Ryosuke , Oasa Yumiko 
Published: February 2019

Abstract
We present the results of imaging polarimetry of the eclipsed Moon on 2014 October 8. The observed polarization degree was less than 1% in both the V and R bands, which contrasts with the reported 2%–3% polarization during the eclipse of 2015 April 4. We examined the Earth’s atmospheric data on the two dates and found that the high (≥7 km) cloud distribution was more inhomogeneous for the 2015 eclipse than it was for the 2014 eclipse. The polarization position angle observed during the 2015 eclipse can be explained if the major polarizing source was high clouds with an intermediate horizontal optical thickness. We suggest a possible dependence of the lunar eclipse polarization on the Earth’s high cloud distribution.
Assessing Combinability of Phylogenomic Data Using Bayes Factors
Authors: Neupane Suman , Fučíková Karolina , Lewis Louise A , Kuo Lynn , Chen Ming-Hui , Lewis Paul O 
Published: February 2019

Abstract
With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence and provides a way to assess the statistical significance of D values. We use BFs to assess data combinability using an empirical data set comprising 56 plastid genes from the green algal order Volvocales. We also discuss the potential need for calibrating BFs and demonstrate that BFs used in this study are correctly calibrated.
Robust Design for Coalescent Model Inference
Authors: Parag Kris V , Pybus Oliver G 
Published: February 2019

AbstractThe coalescent process describes how changes in the size or structure of a population influence the genealogical patterns of sequences sampled from that population. The estimation of (effective) population size changes from genealogies that are reconstructed from these sampled sequences is an important problem in many biological fields. Often, population size is characterized by a piecewise-constant function, with each piece serving as a population size parameter to be estimated. Estimation quality depends on both the statistical coalescent inference method employed, and on the experimental protocol, which controls variables such as the sampling of sequences through time and space, or the transformation of model parameters. While there is an extensive literature on coalescent inference methodology, there is comparatively little work on experimental design. The research that does exist is largely simulation-based, precluding the development of provable or general design theorems. We examine three key design problems: temporal sampling of sequences under the skyline demographic coalescent model, spatio-temporal sampling under the structured coalescent model, and time discretization for sequentially Markovian coalescent models. In all cases, we prove that 1) working in the logarithm of the parameters to be inferred (e.g., population size) and 2) distributing informative coalescent events uniformly among these log-parameters, is uniquely robust. “Robust” means that the total and maximum uncertainty of our parameter estimates are minimized, and made insensitive to their unknown (true) values. This robust design theorem provides rigorous justification for several existing coalescent experimental design decisions and leads to usable guidelines for future empirical or simulation-based investigations. Given its persistence among models, this theorem may form the basis of an experimental design paradigm for coalescent inference.