bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational profile of rare variants in inflammasome-related genes in Behçet disease: A Next Generation Sequencing approach
Authors: Burillo-Sanz Sergio , Montes-Cano Marco-Antonio , García-Lozano José-Raúl , Ortiz-Fernández Lourdes , Ortego-Centeno Norberto , García-Hernández Francisco-José , Espinosa Gerard , Graña-Gil Genaro , Sánchez-Bursón Juan , Rosa Juliá María , Solans Roser , Blanco Ricardo , Barnosi-Marín Ana-Celia , Gómez De la Torre Ricardo , Fanlo Patricia , Rodríguez-Carballeira Mónica , Rodríguez-Rodríguez Luis , Camps Teresa , Castañeda Santos , Alegre-Sancho Juan-Jose , Martín Javier , González-Escribano María Francisca 
Published: August 2017

AbstractBehçet’s disease (BD) is an immune-mediated systemic disorder with a well-established association with HLA class I and other genes. BD has clinical overlap with many autoinflammatory diseases (AIDs). The aim of this study was to investigate the role of rare variants in seven genes involved in AIDs: CECR1, MEFV, MVK, NLRP3, NOD2, PSTPIP1 and TNFRSF1A using a next generation sequencing (NGS) approach in 355 BD patients. To check global association of each gene, 4 tests: SKAT, CollapseBt, C(α) and weighted KBAC were used. Databases: 1000 Genomes Project Phase 3, Infevers, HGMD and ClinVar and algorithms: PolyPhen2 and SIFT were consulted to collect information of the 62 variants found. All the genes resulted associated using SKAT but only 3 (MVK, NOD2 and PSTPIP1) with C(α) and weighted KBAC. When all the genes are considered, 40 variants were associated to AIDs in clinical databases and 25 were predicted as pathogenic at least by one of the algorithms. Including only MVK, NOD2 and PSTPIP1, the associated to AIDs variants found in BD were 20 and the predicted as pathogenic, 12. The maxima contribution corresponds to NOD2. This study supports influence of rare variants in genes involved in AIDs in the pathogenesis of BD.
Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins
Authors: Liu Aoxing , Wang Yachun , Sahana Goutam , Zhang Qin , Liu Lin , Lund Mogens Sandø , Su Guosheng 
Published: August 2017

AbstractReduced female fertility could cause considerable economic loss and has become a worldwide problem in the modern dairy industry. The objective of this study was to detect quantitative trait loci (QTL) for female fertility traits in Chinese and Nordic Holsteins using various strategies. First, single-trait association analyses were performed for female fertility traits in Chinese and Nordic Holsteins. Second, the SNPs with P-value < 0.005 discovered in Chinese Holsteins were validated in Nordic Holsteins. Third, the summary statistics from single-trait association analyses were combined into meta-analyses to: (1) identify common QTL for multiple fertility traits within each Holstein population; (2) detect SNPs which were associated with a female fertility trait across two Holstein populations. A large numbers of QTL were discovered or confirmed for female fertility traits. The QTL segregating at 31.4~34.1 Mb on BTA13, 48.3~51.9 Mb on BTA23 and 34.0~37.6 Mb on BTA28 shared between Chinese and Nordic Holsteins were further ascertained using a validation approach and meta-analyses. Furthermore, multiple novel variants identified in Chinese Holsteins were validated with Nordic data as well as meta-analyses. The genes IL6R, SLC39A12, CACNB2, ZEB1, ZMIZ1 and FAM213A were concluded to be strong candidate genes for female fertility in Holsteins.
Quantity Matters: Children With Dyslexia Are Impaired in a Small, but Not Large, Number of Exposures During Implicit Repeated Sequence Learning
Authors: He Xinjie , Tong Shelley Xiuli 
Published: August 2017

Purpose
The present study investigated the onset of statistical learning and examined whether the number of exposures to a repeated sequence influences the learning performance of children with dyslexia on a serial reaction time task.

Method
Three groups of children (29 with dyslexia, 29 age-matched controls, and 30 reading level–matched controls) were administered a serial reaction time task, and their statistical learning performances after a small and a large number of exposures (40 vs. 180 exposures) were recorded and compared.

Results
Children with dyslexia showed impaired statistical learning after a small number of exposures to a sequence, but intact statistical learning after a large number of exposures. In contrast, the age-matched and reading level–matched control groups showed intact statistical learning after both small and large numbers of exposures. Children with dyslexia also exhibited a slower learning rate than either control group.

Conclusion
These results suggest that the amount of exposure to statistical patterns influences statistical learning performance in children with dyslexia.
CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline
Authors: Wang Xuning , Tilford Charles , Neuhaus Isaac , Mintier Gabe , Guo Qi , Feder John N , Kirov Stefan 
Published: August 2017

Abstract

Summary
The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view.

Availability and implementation
CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/.
Diverging effects of enalapril or eplerenone in primary prevention against doxorubicin-induced cardiotoxicity
Authors: Hullin Roger , Métrich Mélanie , Sarre Alexandre , Basquin Denis , Maillard Marc , Regamey Julien , Martin David 
Published: August 2017

Abstract

Aims
Clinical studies suggest beneficial effects of renin–angiotensin system blockade for prevention of left ventricular (LV) dysfunction after chemotherapy. However, the efficacy of this strategy as primary prevention has been poorly studied. This study aimed at identifying the pathophysiological mechanisms by which mineralocorticoid receptor antagonism (MRA) or angiotensin converting enzyme inhibition (ACEi) provide protection against doxorubicin-induced cardiotoxicity (DIC) in mouse models of acute and chronic toxicity.

Methods and results
Acute DIC was induced by a single injection of Dox at 15 mg/kg and chronic DIC applied 5 injections of Dox at 4 mg/kg/week. MRA was achieved using eplerenone or cardiomyocyte-specific ablation of the MR gene in transgenic mice and ACEi using enalapril. Drugs were provided with the first dose of Dox and applied until the end of the study. In both model of DIC, Dox induced cardiac atrophy with decreased LV volume, reduced cardiomyocyte cell size, and cardiac dysfunction. In the acute model, neither MRA nor ACEi protected against these manifestations of DIC. In the chronic model, concomitant treatment with eplerenone did not protect against DIC and drastically increased plasma aldosterone levels and cardiac levels of angiotensin II type 1 receptor and of connective tissue growth factor (CTGF), as observed in acute DIC. Enalapril treatment in the chronic model, however, protected against cardiac dysfunction and cardiomyocyte atrophy and was associated with increased activation of the PI3K/AKT/mTOR pathway along with normal levels of CTGF.

Conclusion
Enalapril and eplerenone disparately impact on cellular signalling in DIC. Eplerenone, on top of Dox treatment was not protective and associated with increased levels of plasma aldosterone and of cardiac CTGF. In contrast, we show that primary prevention with enalapril preserves LV morphology and function in a clinically relevant model of chronic DIC, with increased stimulation of the PI3K/AKT/mTOR axis and normal CTGF levels suggesting potential therapeutic implications.
Peripheral Blunt Dissection: Using a Microhoe-Facilitated Method for Descemet Membrane Endothelial Keratoplasty Donor Tissue Preparation
Authors: Borovik Armand M. , Perez Mauricio , Lifshitz Tova , Einan-Lifshitz Adi , Sorkin Nir , Boutin Tanguy , Showail Mahmood , Rosenblatt Amir , Rootman David S. 
Published: August 2017

Purpose:
To describe a modified technique for Descemet membrane donor tissue preparation that facilitates the original Melles stripping technique.

Methods:
Descemet membrane is prepared using a Rootman/Goldich modified Sloane microhoe, using a blunt instrument as opposed to a sharp blade or needle and begins dissection within the trabecular meshwork. The trabecular tissue is dissected for 360 degrees, and then Descemet membrane is stripped to approximately 50%. A skin biopsy punch is then used to create fenestration in the cornea, which is used to mark an “F.” on the stromal side of Descemet membrane to aid in orientation of the graft. Trephination of the membrane is then performed and stripping is completed. The tissue is stained with 0.06% trypan blue and aspirated into an injector for insertion into the anterior chamber.

Results:
Before converting to the technique described, 5 of 75 (6.7%) tissues were wasted and 7 of 75 (9.3%) tissues with radial tears were salvaged for use. Since converting to the new technique, only 1 of 171 (0.6%) (P = 0.01) tissues was wasted and 7 of 171 (4.1%) (P = 0.2) tissues with radial tears were salvaged.

Conclusions:
The peripheral blunt dissection technique offers an improvement over the technique originally described by Melles et al, as the incidence of tissue wastage and tears is lower, it is easy to learn, has low stress, and is reproducible. Combining this with a stromal surface letter mark ensures correct orientation of the tissue against the corneal stroma of the recipient.
Recognition and Management of Acute Dacryocystic Retention
Authors: McGrath Lindsay A. , Satchi Kahmi , McNab Alan A. 
Published: August 2017

Purpose:
Acute noninfectious dacryocystic retention is an under-recognized condition heralded by painful lacrimal sac swelling, obstruction, and epiphora. This longitudinal chart review aimed to estimate the incidence of this condition in an urban Australian population, while further defining the signs and symptoms of the disease and options for management.

Methods:
We retrospectively reviewed the charts of 1,593 consecutive patients presenting with acquired nasolacrimal duct obstruction and epiphora between 1990 and 2015. The records of patients with acute dacryocystic retention were analyzed for age, gender, clinical features, and management.

Results:
Of all patients presenting with nasolacrimal duct obstruction, 20 were found to have acute dacryocystic retention. The mean age was 42.2 ± 9.3. There was an equal distribution of laterality, and only 2 cases (10%) were bilateral. There was a statistically significant female predominance, and most patients presented reporting 2 to 3 previous episodes. At presentation, 30% of patients reported spontaneous passage of a dacryolith. Despite this, 70% of affected patients required surgical management, with a 64% incidence of stones noted at the time of dacryocystorhinostomy.

Conclusions:
Acute dacryocystic retention is an uncommon, but even less frequently identified condition, most common in middle-aged women. Improved understanding of this condition and its natural history is likely to enhance patient counseling and avoid ineffective use of antibiotics in affected patients.
FISH Analysis of TOP2A and HER-2 Aberrations in Female Breast Carcinoma on Archived Material: Egyptian NCI Experience
Authors: Badawy Omnia M. , Loay Iman 
Published: August 2017

Background:

HER-2 and TOP2A genes are considered of great importance in breast cancer. Their copy number variability has been proposed to be a marker for the degree of chromosomal instability. Owing to the close proximity of TOP2A gene to HER-2 gene chromosome 17, TOP2A status is believed to affect therapeutic plan. The percentage of TOP2A aberrations is greatly variable among different studies.

Aim of Work:
Is to investigate the relation between TOP2A and HER-2 gene amplification using fluorescence in situ hybridization technique.

Materials and Methods:
Archival blocks of 112 breast cancer Egyptian female patients were retrieved from the pathology department at NCI, Cairo University were retrieved and investigated using fluorescence in situ hybridization technique for TOP2A and HER-2 gene assessment. In addition, correlation with some clinicopathologic parameters was done.

Results:

HER-2 gene amplification was encountered in about 33% of cases. TOP2A gene amplification and deletion were detected in 23.9% and 2.8% of studied cases. Moderate agreement was obtained between results of HER-2 gene and TOP2A gene amplification.

Conclusions:

HER-2 and TOP2A genes amplification are 2 separate genetic yet closely related events in breast cancer. Polysomy of chromosome 17 is proposed to be an early event in occurrence of TOP2A gene amplification. Further studies regarding effect of TOP2A gene in response to anthracyclines in Egyptian population should be planned for to establish its role in therapeutic planning.
Basic Hemodynamic Monitoring Using Ultrasound or Electrical Cardiometry During Transportation of Neonates and Infants*
Authors: Boet Angele , Jourdain Gilles , Demontoux Serge , Hascoet Sebastien , Tissieres Pierre , Rucker-Martin Catherine , De Luca Daniele 
Published: August 2017

Objectives:
Electrical cardiometry and heart ultrasound might allow hemodynamic evaluation during transportation of critically ill patients. Our aims were 1) to test feasibility of stroke volume monitoring using electrical cardiometry or ultrasound during transportation and 2) to investigate if transportation impacts on electrical cardiometry and ultrasound reliability.

Design:
Prospective, pragmatic, feasibility cohort study.

Setting:
Mobile ICUs specialized for neonatal and pediatric transportation.

Patients:
Thirty hemodynamically stable neonates and infants.

Interventions:
Patients enrolled underwent paired stroke volume measurements (180 before/after and 180 during the transfer) by electrical cardiometry (SVEC) and ultrasound (SVUS).

Measurements and Main Results:
No problems or malfunctioning occurred neither with electrical cardiometry nor with ultrasound. Ultrasound lasted on average 90 (10) seconds, while 45 (15) seconds were needed to instigate electrical cardiometry monitoring. Coefficient of variation was higher for SVUS (before/after: 0.57; during: 0.66) than for SVEC (before/after: 0.38; during: 0.36). Correlations between SVEC and SVUS before/after and during the transfer were r equal to 0.57 and r equal to 0.8, respectively (p always < 0.001). Bland-Altman analysis showed that stroke volume tends to be higher if measured by electrical cardiometry. SVEC measured before (5.5 [2.4] mL), during (5.4 [2.4] mL), and after the transfer (5.4 [2.3] mL) are similar (p = 0.955); same applies for SVUS before (2.6 [1.5] mL), during (2.4 [2] mL), and after (2.9 [2] mL) the transfer (p = 0.268).

Conclusions:
Basic hemodynamic monitoring is feasible during pediatric and neonatal transportation both with electrical cardiometry and ultrasound. These two techniques show comparable reliability, although stroke volume was higher if measured by electrical cardiometry. The transportation itself does not affect the reliability of stroke volume measurements.
The Antimalarial Drug Artesunate Attenuates Cardiac Injury in A Rodent Model of Myocardial Infarction
Authors: Khan Areeg I. , Kapoor Amar , Chen Jianmin , Martin Lukas , Rogazzo Mara , Mercier Thomas , Decosterd Laurent , Collino Massimo , Thiemermann Christoph 
Published: August 2017

ABSTRACT
Ischemic heart disease remains the leading cause of morbidity and mortality in the Western world. Artesunate is the WHO-recommended drug of choice for complicated malaria (with organ failure). The administration of high doses of artesunate is safe in healthy volunteers (up to 8 mg/kg i.v.) and patients with severe malaria (2.4 mg/kg i.v.). We investigated the effects of artesunate (1 mg/kg) or its active metabolite dihydroartemisinin (DHA; 0.1 mg/kg) in a model of transient myocardial ischemia/reperfusion (I/R) and evaluated the mechanism of action of the observed cardioprotective effects of artesunate and DHA. We report here for the first time that the administration of artesunate at the onset of reperfusion attenuates the myocardial injury associated with I/R. The observed beneficial effects of artesunate are associated with activation of the PI3K/Akt/ERK 1/2 (RISK) pathway, activation of endothelial nitric oxide synthase, inhibition of glycogen synthase kinase-3β, inhibition of nuclear factor kappa B, and activation of the STAT3 (SAFE) pathway. In conclusion, as artesunate has an excellent safety profile, the above data should stimulate clinical trials in patients with acute coronary syndromes.
Science with no fiction: measuring the veracity of scientific reports by citation analysis
Authors: Grabitz Peter , Lazebnik Yuri , Nicholson Josh , Rife Sean 
Published: August 2017

AbstractThe current crisis of veracity in biomedical research is enabled by the lack of publicly accessible information on whether the reported scientific claims are valid. One approach to solve this problem is to replicate previous studies by specialized reproducibility centers. However, this approach is costly or unaffordable and raises a number of yet to be resolved concerns that question its effectiveness and validity. We propose to use an approach that yields a simple numerical measure of veracity, the R-factor, by summarizing the outcomes of already published studies that have attempted to test a claim. The R-factor of an investigator, a journal, or an institution would be the average of the R-factors of the claims they reported. We illustrate this approach using three studies recently tested by a replication initiative, compare the results, and discuss how using the R-factor can help improve the veracity of scientific research.
Tryptophan and Cysteine Oxidation Products Dominate in α‐Lactalbumin‐Derived Peptides Analyzed with LC–MSn
Authors: Koivumäki Tuuli P. , Gürbüz Göker , Heinonen I. Marina 
Published: August 2017

Abstractα‐Lactalbumin (α‐La), a major milk whey protein, is comprised of several amino acids prone to metal‐catalyzed oxidation (MCO) typical in processing and during storage of foods. New tools are needed for the detection of characteristic oxidation products especially from tryptophan and cysteine that often remain unrecognized when using the traditional methods of carbonyl formation monitoring. In this study, the oxidative changes in α‐La were investigated through tryptic digestion and collection of 3 descriptive peptides fitted into a metal‐catalyzed oxidation (Fenton reaction) model. The peptide samples were oxidized at +37 °C for 14 d and explored with liquid chromatography–quadrupole ion trap‐mass spectrometer (LC–MSn). The fractionated α‐La peptides were valyl‐glycyl‐isoleucyl‐asparaginyl‐tyrosyl‐tryptophyl‐leucyl‐alanyl‐histidyl‐lysine (VGINYWLAHK), leucyl‐aspartyl‐glutaminyl‐tryptophyl‐leucyl‐cysteinyl‐glutamyl‐lysine (LDQWLCEK), and tryptophyl+16‐leucyl‐alanyl‐histidyl‐lysyl‐alanyl‐leucyl‐cysteine (W+16LAHKALC). Oxidation of several amino acids, such as cysteine, histidine, lysine, and tryptophan was observed. In the peptide LDQWLCEK, cysteine was rapidly trioxidized to sulfonic acid, followed by other amino acid side chains as secondary oxidation sites. Tryptophan oxidation was more pronounced in the peptides W+16LAHKALC and VGINYWLAHK, and also formation of the harmful N‐formylkynurenine was observed. As a conclusion, several stable and promising oxidation markers are proposed for α‐La, which could be implemented in the evaluation of quality and safety of dairy protein‐containing products.
Low‐Temperature Blanching as a Tool to Modulate the Structure of Pectin in Blueberry Purees
Authors: Chevalier Laura M. , Rioux Laurie‐Eve , Angers Paul , Turgeon Sylvie L. 
Published: August 2017

AbstractBlueberry composition was characterized for 6 cultivars. It contains a good amount of dietary fiber (10% to 20%) and pectin (4% to 7%) whose degree of methylation (DM) is sensitive to food processing. A low temperature blanching (LTB: 60 °C/1 h) was applied on blueberry purees to decrease pectin DM, in order to modulate puree properties and functionalities (that is, viscosity and stability), and to enhance pectin affinity toward other components within food matrices. Fiber content, viscosity, pectin solubility, DM, and monosaccharide composition were determined for both pasteurized, and LTB+pasteurized blueberry purees. The results showed that neither the amount of fiber, nor the viscosity were affected by LTB, indicating that this treatment did not result in any significant pectin depolymerization and degradation. LTB caused a decrease both in pectin DM from 58–67% to 45–47% and in the amount of water‐soluble pectin fraction, the latter remaining the major fraction of total pectin at 52% to 57%. A LTB is a simple and mild process to produce blueberry purees with mostly soluble and low‐methylated pectin in order to extend functionality and opportunities for interactions with other food ingredients.
Fortification of Wheat Bread with Agroindustry By‐Products: Statistical Methods for Sensory Preference Evaluation and Correlation with Color and Crumb Structure
Authors: Martins Z. E. , Pinho O. , Ferreira I.M.P.L.V.O. 
Published: August 2017

AbstractThe use of agroindustry by‐products (BP) for fortification of wheat bread can be an alternative to waste disposal because BP are appealing sources of dietary fiber. Moreover, it may also contribute to indirect income generation. In this study, sensory, color, and crumb structure properties of breads fortified with fiber rich fraction recovered from four types of agroindustry BP were tested, namely orange (OE), pomegranate (PE), elderberry (EE), and spent yeast (YE). Statistical models for sensory preference evaluation and correlation with color and crumb structure were developed. External preference mapping indicated consumer preferences and enabled selection of the concentrations of BP fibre‐rich fraction with best acceptance, namely 7.0% EE, 2.5% OE, 5.0% PE, and 2.5% YE. Data collected from image analysis complemented sensory profile information, whereas multivariate PLS regression provided information on the relationship between “crust color” and “crumb color” and instrumental data. Regression models developed for both sensory attributes presented good fitting (R2Y > 0.700) and predictive ability (Q2 > 0.500), with low RMSE. Crust and crumb a* parameters had a positive influence on “crust color” and “crumb color” models, while crust L* and b* had a negative influence.