bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fat-soluble Vitamin Deficiencies and Inflammatory Bowel Disease
Authors: Fabisiak Natalia , Fabisiak Adam , Watala Cezary , Fichna Jakub 
Published: August 2017

Background:
Vitamin deficiency is frequently associated with inflammatory bowel disease (IBD). Supplementation of vitamins could thus serve as an adjunctive therapy. The present meta-analysis reviews the deficiencies and alterations in serum fat-soluble vitamins (A, D, E, and K) reported in IBD patients.

Materials and Methods:
PubMed database search was performed to identify all primary studies up to January 2015 that evaluated the serum concentrations of fat-soluble vitamin levels in IBD patients compared with healthy individuals. We estimated pooled mean differences between groups and estimated their relations with some compounding variables (age, disease duration, C-reactive protein, albumin), using a meta-regression analysis.

Results:
Nineteen case-control studies met selection criteria. In patients with Crohn’s disease (CD), vitamin A, D, E, K status was lower than in controls [D=212 μg/L.92; 95% confidence interval (CI), 95.36-330.48 μg/L, P=0.0002; D=6.97 nmol/L, 95% CI, 1.61-12.32 nmol/L, P=0.01; D=4.72 μmol/L, 95% CI, 1.60-7.84 μmol/L, P=0.003; D=1.46 ng/mL, 95% CI, 0.48-2.43 ng/mL, P=0.003, respectively]. Patients with ulcerative colitis had lower levels of vitamin A than controls (D=223.22 μg/L, 95% CI, 44.32-402.12 μg/L, P=0.01). Patients suffering from CD for a longer time had lower levels of vitamins A (95% CI=7.1-67.58 y, P=0.02) and K (95% CI, 0.09-0.71 y, P=0.02). Meta-regression analysis demonstrated statistically significant associations between the levels of inflammatory biomarkers: C-reactive protein (P=0.03, 95% CI, −9.74 to −0.6 mgl/L) and albumin (P=0.0003, 95% CI, 402.76-1361.98 g/dL), and vitamin A status in CD patients.

Conclusion:
Our meta-analysis shows that the levels of fat-soluble vitamins are generally lower in patients with inflammatory bowel diseases and their supplementation is undoubtedly indicated.
Etiologies and Impact of Readmission Rates in the First 180 Days After Hematopoietic Stem Cell Transplantation in Children, Adolescents, and Young Adults
Authors: Maher Ossama M. , Silva Jorge G. , Huh Winston W. , Cuglievan Branko , DePombo April , Kebriaei Partow , Park Minjeong , Liu Diane , Tillman Chloe , Tarek Nidale , Cooper Laurence J.N. , Tewari Priti 
Published: August 2017

Introduction:
High rates of patients require readmission to the hospital within 6 months of hematopoietic stem cell transplantation (HSCT). We investigated the relationship between readmission rates and outcomes after HSCT in children, adolescents, and young adults (CAYA).

Materials and Methods:
A retrospective analysis of patients (26 years or younger) treated with HSCT was conducted.

Results:
A chart review of 435 CAYA who underwent HSCT from 2008 to 2015 revealed that 171 patients (39%) had at least 1 hospital readmission within 180 days of transplant; 87% received allogeneic and 13% received autologous HSCT. A total of 312 readmission events were reported. The median follow-up time was 31 months. Documented infection (n=99) and graft-versus-host disease complications (n=60) were the most common causes. Higher than 2 readmission rates were associated with lower overall survival (OS) (P=0.001) and disease-free survival (P<0.001) in patients who received allogeneic HSCT. These findings were not found in the autologous HSCT. In a multivariate analysis of those who received allogeneic HSCT, prior treatment with ≥2 chemotherapy regimens (P=0.03) was independent predictor of lower OS. There were also trends noted toward lower OS for patients with documented infections at index admission or subsequent readmissions (P=0.09).

Conclusions:
More than 2 hospital readmissions within 6 months of allogeneic HSCT in CAYA, who are either heavily pretreated or had documented infections at index admission or subsequent readmissions adversely affected the outcomes.
Longitudinal Analysis of Echocardiographic Abnormalities in Children With Sickle Cell Disease
Authors: Harrington Jamie K. , Krishnan Usha , Jin Zhezhen , Mardy Christopher , Kobsa Serge , Lee Margaret T. 
Published: August 2017

Background:Cardiac abnormalities have been described in echocardiograms of children with sickle cell disease (SCD). However, longitudinal studies investigating progression of echocardiographic abnormalities across the pediatric age spectrum in SCD are lacking.Methods:A retrospective longitudinal analysis of 829 echocardiograms from pediatric patients with SCD at steady-state was performed. Left heart parameters included left ventricular end-systolic, end-diastolic diameters, fractional shortening, and mass. Right ventricular pressure was estimated by tricuspid regurgitation gradient. Tricuspid regurgitation gradient ≥25 mm Hg, az-score ≥2 for LV parameters and ≤−2 for left ventricular fractional shortening were considered abnormal.Results:Kaplan-Meier analysis revealed that echocardiographic abnormalities were detected by 5 years of age, and the cumulative incidence progressively increased throughout childhood. Age, male gender, HbSS and Sβθthalassemia genotype, white blood cell count, platelet count, total bilirubin, admissions for pain crises and acute chest syndrome were positively, whereas hemoglobin was negatively associated with cardiac abnormalities.Conclusion:Cardiac abnormalities began early in childhood and progressively increased with age. Our study highlights the high cumulative incidence of cardiac abnormalities in children with SCD, which could represent a marker of disease severity.
Subarachnoid Hemorrhage Revealing Moyamoya Syndrome in a Patient With May-Hegglin Anomaly
Authors: Béjot Yannick , Barnay José-Luis , Chavent Adrien , Daubail Benoit , Jacquin Agnès , Kazemi Apolline , Ricolfi Frédéric , Giroud Maurice 
Published: August 2017

Introduction:
Moyamoya syndrome is a rare progressive cerebrovascular occlusive disease for which several associated conditions have been described.

Case Report:
We report the case of a 76-year-old woman with a history of May-Hegglin anomaly who presented with an isolated unusual diffuse headache. Initial laboratory investigations showed only thrombocytopenia (platelet count 95000/μL). Unenhanced brain computed tomography scan revealed a small subarachnoid hemorrhage in the left frontal lobe. Computed tomography angiography showed occlusion of the terminal portion of the left internal carotid artery (ICA) and narrowing of the terminal portion of the right ICA with abnormal collateral vessels. Conventional angiography confirmed the tight stenosis of the extremity of the right ICA, and the occlusion of the left ICA, associated with an extensive collateral network consistent with moyamoya syndrome. No aneurysm was identified.

Conclusions:
The rarity of these 2 diseases makes a fortuitous association very unlikely. We thus concluded that this observation could be the first reported case of May-Hegglin anomaly as a cause of moyamoya syndrome.
In Vitro Synergy Testing of Gentamicin, an Old Drug Suggested as Future Treatment Option for Gonorrhoea, in Combination With Six Other Antimicrobials Against Multidrug-Resistant Neisseria gonorrhoeae Strains
Authors: Singh Vikram , Bala Manju , Bhargava Aradhana , Kakran Monika , Bhatnagar Ravi 
Published: August 2017

Background
Emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Neisseria gonorrhoeae is a serious concern and combination therapy has been recommended to delay the onset of treatment failures. Gentamicin, an old and inexpensive antibiotic, is recommended in combination with azithromycin for treatment failures cases with the first-line regimen as per the latest Centers for Disease Control and Prevention sexually transmitted disease treatment guidelines. However, not much literature is available on in vitro and in vivo efficacy of this combination. Therefore, this study was carried out to evaluate the in vitro synergy of gentamicin in combination with azithromycin and 5 other antimicrobials.

Methods
In vitro synergy of gentamicin in combination with cefixime, ceftriaxone, spectinomycin, azithromycin, moxifloxacin, and ertapenem was determined by Etest for 75 N. gonorrhoeae strains, of which 65 were MDR and one was XDR. Fractional inhibitory concentration index (FICI) of ≤0.5 and >4.0 denoted synergy and antagonism respectively.

Results
Maximum efficacy of gentamicin was observed in combination with ertapenem (geometric mean FICI, 0.56) followed by cefixime (FICI, 0.87). There was no antagonism for both these combinations. However, antagonism was demonstrated in 5.3%, 8%, 8%, and 10.7% strains when gentamicin was paired with spectinomycin (FICI, 1.34), ceftriaxone (FICI, 1.13), azithromycin (FICI, 1.49), and moxifloxacin (FICI, 1.30), respectively.

Conclusions
The findings suggest that gentamicin significantly enhances the in vitro therapeutic potency of ertapenem and cefixime which will be potentially effective to control the spread of MDR and XDR N. gonorrhoeae. The study warrants more in vitro studies and clinical trials for gentamicin + azithromycin and other 3 combinations because of considerable antagonism.
Multiple Sclerosis
Authors: Sommer Nora N. , Saam Tobias , Coppenrath Eva , Kooijman Hendrik , Kümpfel Tania , Patzig Maximilian , Beyer Sebastian E. , Sommer Wieland H. , Reiser Maximilian F. , Ertl-Wagner Birgit , Treitl Karla M. 
Published: August 2017

Objectives
The aim of this study was to assess the diagnostic accuracy of a modified high-resolution whole-brain three-dimensional T1-weighted black-blood sequence (T1-weighted modified volumetric isotropic turbo spin echo acquisition [T1-mVISTA]) in comparison to a standard three-dimensional T1-weighted magnetization-prepared rapid gradient echo (MP-RAGE) sequence for detection of contrast-enhancing cerebral lesions in patients with relapsing-remitting multiple sclerosis (MS).

Materials and Methods
After institutional review board approval and informed consent, 22 patients (8 men; aged 31.0 ± 9.2 years) with relapsing-remitting MS were included in this monocentric prospective cohort study.
Contrast-enhanced T1-mVISTA and MP-RAGE, both with 0.8 mm3 resolution, were performed in all patients. In a substudy of 12 patients, T1-mVISTA was compared with a T1-mVISTA with 1.0 mm3 resolution (T1-mVISTA_1.0). Reference lesions were defined by an experienced neuroradiologist using all available sequences and served as the criterion standard. T1-mVISTA, T1-mVISTA_1.0, and MP-RAGE sequences were read in random order 4 weeks apart. Image quality, visual contrast enhancement, contrast-to-noise-ratio (CNR), diagnostic confidence, and lesion size were assessed and compared by Wilcoxon and Mann-Whitney U tests.

Results
Eleven of 22 patients displayed contrast-enhancing lesions. Visual contrast enhancement, CNR, and diagnostic confidence of contrast-enhancing MS lesions were significantly increased in T1-mVISTA compared with MP-RAGE (P < 0.001). Significantly more contrast-enhancing lesions were detected with T1-mVISTA than with MP-RAGE (71 vs 39, respectively; P < 0.001). With MP-RAGE, 25.6% of lesions were missed in the initial reading, whereas only 4.2% of lesions were missed with T1-mVISTA. Increase of the voxel volume from 0.8 mm to 1.0 mm isotropic in T1-mVISTA_1.0 did not affect the detectability of lesions, whereas scan time was decreased from 4:43 to 1:55 minutes.

Conclusions
Three-dimensional T1-mVISTA improves the detection rates of contrast-enhancing cerebral MS lesions compared with conventional 3D MP-RAGE sequences by increasing CNR of lesions and might, therefore, be useful in patient management.
Stable, metastable and unstable cellulose solutions
Authors: Gubitosi Marta , Nosrati Pegah , Koder Hamid Mona , Kuczera Stefan , Behrens Manja A. , Johansson Eric G. , Olsson Ulf 
Published: August 2017

We have characterized the dissolution state of microcrystalline cellulose (MCC) in aqueous tetrabutylammonium hydroxide, TBAH(aq), at different concentrations of TBAH, by means of turbidity and small-angle X-ray scattering. The solubility of cellulose increases with increasing TBAH concentration, which is consistent with solubilization driven by neutralization. When comparing the two polymorphs, the solubility of cellulose I is higher than that of cellulose II. This has the consequence that the dissolution of MCC (cellulose I) may create a supersaturated solution with respect to cellulose II. As for the dissolution state of cellulose, we identify three different regimes. (i) In the stable regime, corresponding to concentrations below the solubility of cellulose II, cellulose is molecularly dissolved and the solutions are thermodynamically stable. (ii) In the metastable regime, corresponding to lower supersaturations with respect to cellulose II, a minor aggregation of cellulose occurs and the solutions are kinetically stable. (iii) In the unstable regime, corresponding to larger supersaturations, there is macroscopic precipitation of cellulose II from solution. Finally, we also discuss strong alkali solvents in general and compare TBAH(aq) with the classical NaOH(aq) solvent.
Vegetative compatibility groups explain variation in the virulence ofVerticillium dahliaeon strawberry
Authors: Fan Rong , Cockerton Helen , Armitage Andrew D. , Bates Helen , Cascant-Lopez Emma , Antanaviciute Laima , Xu Xiangming , Hu Xiaoping , Harrison Richard J. 
Published: August 2017

AbstractVerticillium dahliaeinfection of strawberry (Fragaria × ananassa) is a major cause of disease-induced wilting in soil-grown strawberries across the world. To understand what components of the pathogen are affecting disease expression, the presence of the known effectorVdAve1was screened in a sample ofVerticillium dahliaeisolates. Isolates from strawberry were found to containVdAve1and were divided into two major clades, based upon their vegetative compatibility groups (VCG); no UK strawberry isolates containedVdAve1. VC clade was strongly related to their virulence levels.VdAve1-containing isolates pathogenic on strawberry were found in both clades, in contrast to some recently published findings.On strawberry,VdAve1-containing isolates had significantly higher virulence during early infection, which diminished in significance as the infection progressed. Transformation of a virulent non-VdAve1containing isolate, withVdAve1was found neither to increase nor decrease virulence when inoculated on a susceptible strawberry cultivar. There are therefore virulence factors that are epistatic toVdAve1and potentially multiple independent routes to high virulence on strawberry inV. dahliaelineages.Genome sequencing a subset of isolates across the two VCGs revealed that isolates were differentiated at the whole genome level and contained multiple changes in putative effector content, indicating that different clonal VCGs may have evolved different strategies for infecting strawberry, leading to different virulence levels in pathogenicity tests. It is therefore important to consider both clonal lineage and effector complement as the adaptive potential of each lineage will differ, even if they contain the same race determining effector.
A Portable Software Library that Implements the Gillespie Direct Method
Authors: Sauro Herbert M 
Published: August 2017

AbstractA common approach to simulating chemical reaction systems is to formulate the problem as a set of ordinary differential equation and solve them using standard numerical procedures. Such a formulation works well when the number of molecules involved in the simulation is large and assumes a deterministic formulation for the underling chemical kinetics. However for systems such as gene regulatory networks where the number of molecules of a specific species can be of the order of 10s of molecules, the deterministic approach fails to capture important dynamical features. At low molecular numbers stochastic events dominate the dynamics. As a result much research has been devoted to developing numerical algorithms for computing the stochastic trajectories. One of the most common approaches is based on Gillespie’s stochastic simulation algorithm, for example the direct method. Due to its simplicity the direct method has been implemented many times in software. However, unusually, there does not appear to be a C based reusable software library. This article describes the development of such a library. All source code is licensed under the liberal Apache 2.0 open source license and is available at Github:https://github.com/sys-bio/libStochastic
ACaenorhabditis elegansmodel of adenylosuccinate lyase deficiency reveals neuromuscular and reproductive phenotypes of distinct etiology
Authors: Fenton Adam R. , Janowitz Haley N. , McReynolds Melanie R. , Wang Wenqing , Hanna-Rose Wendy 
Published: August 2017

AbstractInborn errors of purine metabolism are rare syndromes with an array of complex phenotypes in humans. One such disorder, adenylosuccinate lyase deficiency (ASLD), is caused by a decrease in the activity of the bi-functional purine biosynthetic enzyme, adenylosuccinate lyase (ADSL). Mutations in human ADSL cause epilepsy, muscle ataxia, and autistic-like symptoms. Although the genetic basis of ASLD syndrome is known, the molecular mechanisms driving phenotypic outcome are not. Here, we characterize neuromuscular and reproductive phenotypes associated with a deficiency ofadsl-1inCaenorhabditis elegans.Characterization of the neuromuscular phenotype reveals a disruption of cholinergic transmission affecting muscular contraction. Using genetics, pharmacological supplementation, and metabolite measurements, we correlate phenotypes with distinct metabolic perturbations. The neuromuscular defect is associated with a toxic accumulation of a purine biosynthetic intermediate whereas the reproductive defect can be ameliorated by purine supplementation, indicating differing molecular mechanisms behind the phenotypes of ASLD. Because purine metabolism is highly conserved in metazoans, we suggest that similar separable metabolic perturbations result in the varied symptoms in the human disorder and that a dual-approach therapeutic strategy may be beneficial.
Anaerobic methanotrophic communities thrive in deep submarine permafrost
Authors: Winkel Matthias , Mitzscherling Julia , Overduin Pier P. , Horn Fabian , Winterfeld Maria , Rijkers Ruud , Grigoriev Mikhail N. , Knoblauch Christian , Mangelsdorf Kai , Wagner Dirk , Liebner Susanne 
Published: August 2017

AbstractThawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic (ANME-2a/b, ANME-2d) assemblages in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in AOM we found a large diversity of archaea mainly belonging toBathyarchaeota,Thaumarchaeota, andEuryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential anaerobic oxidation of methane (AOM) coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescencein situhybridization (FISH) corroborate AOM communities in submarine permafrost sediments potentially active at low temperatures. Extrapolating potential AOM rates, when scaled to the total area of expected submarine permafrost thaw, reveals that methane could be consumed at rates between 8 and 120 Tg C per year, which is comparable to other AOM habitats such as seeps, continental SMTZ and wetlands. We thus propose that AOM is active where submarine permafrost thaws and needs to be accounted for in global methane budgets.
A high-throughput analysis method of microdroplet PCR coupled with fluorescence spectrophotometry
Authors: Du Yanan , Zhao Xiao , Zhao Binan , Xu Yan , Shi Wei , Ren Fangfang , Wu Yangyang , Hu Ruili , Fan Xiaorui , Zhang Qi , Zhang Xiaoxia , Shi Bin , Zhao Huanzhen , Zhao Kai 
Published: August 2017

AbstractHere we report a novel microdroplet PCR method combined with fluorescence spectrophotometry (MPFS), which allows for qualitative, quantitative and high -throughput detection of multiple DNA targets. In this study, each pair of primers was labeled with a specific fluorophore. Through microdroplet PCR, a target DNA was amplified and labeled with the same fluorophore. After products purification, the DNA products tagged with different fluorophores could be analyzed qualitatively by the fluorescent intensity determination. The relative fluorensence unit was also measured to construct the standard curve and to achieve quantitative analysis. In a reaction, the co -amplified products with different fluorophores could be simultaneously analyzed to achieve high -throughput detection. We used four kinds of GM maize as a model to confirm this theory. The qualitative results revealed high specificity and sensitivity of 0.5% (w / w). The quantitative results revealed that the limit of detection was 103copies and with good repeatability. Moreover, reproducibility assay were further performed using four foodborne pathogenic bacteria. Consequently, the same qualitative, quantitative and high-throughput results were confirmed as the four GM maize.
GVC: An ultra-fast and all-round genome variant caller
Authors: Zhang Zhongbo , Yin Longhui , Hao Lingtong , Cao Lihua , Liu Changlin , Chen Mengzhu , Li Cheng , Xu Zhao , Ling Shaoping 
Published: August 2017

ABSTRACTGenome variant detection is a challenge task in cancer genome analysis. Current software for variant detection is very time-consuming and in the same time not accurate enough to satisfy the requirements of clinical applications in precision oncology. We developed an all-round ultra-fast Genomic Variant Caller (GVC), which can detect Germline and Somatic variants, including SNVs and INDELs from genome sequencing data with super high speed and accuracy. GVC achieved mean F1-measure of 99.34% and 97.92% for Germline SNVs in WGS and WES datasets, respectively. And GVC reached mean F1-measure of 97.34% and 89.03% for Germline INDELs in WGS and WES datasets, respectively. GVC achieved mean F1-measure of 90.79% and 86.3% for Somatic SNVs in WGS and WES datasets, respectively. GVC reached mean F1-measure of 76.88% and 68.36% for Somatic INDELs in WGS and WES datasets, respectively. GVC outperformed all the other widely used pipelines. GVC showed super-fast processing speed, exhibiting 128-fold and 54-fold increase in comparison to GATK in WGS and WES datasets processing, respectively. GVC webtool is available from GVC Web Toolhttps://gvc.0cancer.cn. Basing on the accurate GVC algorithm, we also released tumor mutation burden (TMB) results of TCGA datasets on GVC Web Tool.