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https://read.qxmd.com/read/30764760/ads-hcspark-a-scalable-haplotypecaller-leveraging-adaptive-data-segmentation-to-accelerate-variant-calling-on-spark
#1
Anghong Xiao, Zongze Wu, Shoubin Dong
BACKGROUND: The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious problem of computation bottlenecks, resulting in some long tail tasks when performing on large datasets. This prevents high scalability on clusters of multi-node and multi-core, and leads to long runtime and inefficient usage of computing resources...
February 14, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30747541/effects-of-cu-ii-on-the-formation-and-orientation-of-an-arachidic-acid-langmuir-blodgett-film
#2
Briana A Capistran, Gary J Blanchard
The influence of the copper (II) ion on the formation, morphology, and organization of an arachidic acid monolayer was investigated using Langmuir-Blodgett (LB) monolayers, -A isotherms and Brewster angle microscopy (BAM). Our findings indicate that a Cu2+-complexed LB film exhibits order that depends on the subphase pH, analogous to other metal ions.1-2 The metal ion facilitates formation of solid-phase films at surface pressures as low at 5 mN/m. The films exhibit a rigid, ordered phase, evidenced by the absence of a collapse point and an increase in surface pressure rather than the typical sharp decrease in surface pressure indicative of film failure...
February 12, 2019: Langmuir: the ACS Journal of Surfaces and Colloids
https://read.qxmd.com/read/30745852/ebv-mir-bart10-3p-promotes-cell-proliferation-and-migration-by-targeting-dkk1
#3
Kyoungmi Min, Suk Kyeong Lee
In Epstein-Barr virus (EBV)-infected epithelial cancers, Bam HI A rightward transcript (BART) miRNAs are highly expressed. However, only a few target genes of BART miRNAs have been investigated. Our mRNA microarray data showed that DKK1 was markedly down-regulated in EBV-associated gastric carcinoma (EBVaGC) cells. Using luciferase reporter assay we tested whether miR-BART10-3p regulates DKK1 by directly targeting the 3'-UTR of DKK1 mRNA. We observed that miR-BART10-3p transfection decreased DKK1 expression, while an LNA inhibitor of miR-BART10-3p (LNA-miR-BART10-3p(i)) increased DKK1 expression...
2019: International Journal of Biological Sciences
https://read.qxmd.com/read/30745130/-75-se-homocholic-acid-taurine-scintigraphy-75-sehcat-%C3%A2-a-standard-benchmark-test-in-bile-acid-malabsorption
#4
A Baena García, F Partida Palma, S García Martínez, M de Bonilla Candau, M Pajares Vinardell
Chronic diarrhoea due to bile acid malabsorption (BAM) is an underdiagnosed pathology. Different diagnostic tools are available. However, there is currently no consensus on which of these would be the benchmark test or gold standard. This review evaluates the possibility of using 75 Se-taurocholic acid (75 SeHCAT® ) scintigraphy as a benchmark diagnostic test and its perspective for the future. A literature review was conducted in Pubmed and OVID obtaining a total of 57 papers, 26 of which were finally used after being selected under the concepts of gold standard, diagnostic accuracy and other biomarkers...
February 7, 2019: Revista Española de Medicina Nuclear e Imagen Molecular
https://read.qxmd.com/read/30721090/lawsonia-inermis-l-leaves-aqueous-extract-as-a-natural-antioxidant-and-antibacterial-product
#5
Amin Pasandi Pour, Hassan Farahbakhsh
This study was carried out to investigate the biomedicinal potential of aqueous extract (1.25 and 2.5%) of three henna ecotypes (Shahdad, Roodbar and Bam) against Two types of Gram positive and negative bacteria, Staphylococcus aureus (ATCC 25923), Streptococcus agalactiae (ATCC 29933), Bacillus cereus (ATCC 14579), Corynebacterium pseudotuberculosis (ATCC 19410), Klebsiella pneumonia (ATCC 700603), Escherichia coli (ATCC 25922) and Salmonella enterica serovar typhi (ATCC 19430). Henna extract prevent the growth of bacteria in a dose dependent manner...
February 5, 2019: Natural Product Research
https://read.qxmd.com/read/30720799/whole-exome-sequencing-data-of-suicide-victims-who-had-suffered-from-major-depressive-disorder
#6
Dóra Tombácz, Zoltán Maróti, Tibor Kalmár, Miklós Palkovits, Michael Snyder, Zsolt Boldogkői
Suicide is one of the leading causes of mortality worldwide; it causes the death of more than one million patients each year. Suicide is a complex, multifactorial phenotype with environmental and genetic factors contributing to the risk of the forthcoming suicide. These factors first generally lead to mental disorders, such as depression, schizophrenia and bipolar disorder, which then become the direct cause of suicide. Here we present a high quality dataset (including processed BAM and VCF files) gained from the high-throughput whole-exome Illumina sequencing of 23 suicide victims - all of whom had suffered from major depressive disorder - and 21 control patients to a depth of at least 40-fold coverage in both cohorts...
February 5, 2019: Scientific Data
https://read.qxmd.com/read/30716293/influence-of-7%C3%AE-hydroxycholesterol-on-sphingomyelin-and-sphingomyelin-phosphatidylcholine-films-the-langmuir-monolayer-study-complemented-with-theoretical-calculations
#7
Anita Wnętrzak, Anna Chachaj-Brekiesz, Maria Janikowska-Sagan, Patrycja Dynarowicz-Latka
Under pathological conditions, cholesterol oxidation products (oxysterols) appear in enhanced concentration in blood and cerebrospinal fluid, which leads to cytotoxic effect, especially in central nervous system. However, the mode of action of oxysterols on the membrane level has not been fully resolved. In this paper we have investigated the interaction between 7α- hydroxycholesterol, 7α-OH (one of the most abundant oxysterol in human body) and two major membrane lipids: sphingomyelin, SM (basic component of lipid rafts and nerve membrane) and 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine, POPC (main phospholipid of mammalian cell membranes)...
February 1, 2019: Biochimica et biophysica acta. Biomembranes
https://read.qxmd.com/read/30709010/licofelone-dppc-interactions-putting-membrane-lipids-on-the-radar-of-drug-development
#8
Catarina Pereira-Leite, Daniela Lopes-de-Campos, Philippe Fontaine, Iolanda M Cuccovia, Cláudia Nunes, Salette Reis
(1) Background : Membrane lipids have been disregarded in drug development throughout the years. Recently, they gained attention in drug design as targets, but they are still disregarded in the latter stages. Thus, this study aims to highlight the relevance of considering membrane lipids in the preclinical phase of drug development. (2) Methods : The interactions of a drug candidate for clinical use (licofelone) with a membrane model system made of 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) were evaluated by combining Langmuir isotherms, Brewster angle microscopy (BAM), polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and grazing-incidence X-ray diffraction (GIXD) measurements...
January 31, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/30700791/a-suite-of-automated-sequence-analyses-reduces-the-number-of-candidate-deleterious-variants-and-reveals-a-difference-between-probands-and-unaffected-siblings
#9
Fangning Gu, Anchi Wu, M Grace Gordon, Lukas Vlahos, Shane Macnamara, Elizabeth Burke, May C Malicdan, David R Adams, Cynthia J Tifft, Camilo Toro, William A Gahl, Thomas C Markello
PURPOSE: Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. METHODS: Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target...
January 31, 2019: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://read.qxmd.com/read/30698748/smchd1-is-involved-in-de-novo-methylation-of-the-dux4-encoding-d4z4-macrosatellite
#10
Camille Dion, Stéphane Roche, Camille Laberthonnière, Natacha Broucqsault, Virginie Mariot, Shifeng Xue, Alexandra D Gurzau, Agnieszka Nowak, Christopher T Gordon, Marie-Cécile Gaillard, Claire El-Yazidi, Morgane Thomas, Andrée Schlupp-Robaglia, Chantal Missirian, Valérie Malan, Liham Ratbi, Abdelaziz Sefiani, Bernd Wollnik, Bernard Binetruy, Emmanuelle Salort Campana, Shahram Attarian, Rafaelle Bernard, Karine Nguyen, Jeanne Amiel, Julie Dumonceaux, James M Murphy, Jérôme Déjardin, Marnie E Blewitt, Bruno Reversade, Jérôme D Robin, Frédérique Magdinier
The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS)...
January 30, 2019: Nucleic Acids Research
https://read.qxmd.com/read/30691546/application-of-an-environmental-phage-based-assay-sample6-detect-ht-l-for-the-detection-of-listeria-spp-in-ice-cream
#11
Elba Veronica Arias-Rios, Kristina Tenney, Tam Mai, Sam Anderson, Ruth Marie Cantera, Jasmine M Pando, Brandon Selover, Lourdes M Nadala, Seana K Davidson, Mansour Samadpour
Background: Dairy products are common sources of Listeria outbreaks, and early detection of the pathogen is critical to prevent outbreaks of illnesses and financial losses for dairy producers. Objective: This study aimed to evaluate Sample6 Detect HT/L for effective detection of Listeria monocytogenes and L. innocua in ice cream. Methods: Performance of the Sample6 DETECT HT/L was compared with U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) Chapter 10 method for detection of Listeria spp...
January 28, 2019: Journal of AOAC International
https://read.qxmd.com/read/30674680/one-megadalton-metalloenzyme-complex-in-geobacter-metallireducens-involved-in-benzene-ring-reduction-beyond-the-biological-redox-window
#12
Simona G Huwiler, Claudia Löffler, Sebastian E L Anselmann, Hans-Joachim Stärk, Martin von Bergen, Jennifer Flechsler, Reinhard Rachel, Matthias Boll
Reversible biological electron transfer usually occurs between redox couples at standard redox potentials ranging from +0.8 to -0.5 V. Dearomatizing benzoyl-CoA reductases (BCRs), key enzymes of the globally relevant microbial degradation of aromatic compounds at anoxic sites, catalyze a biological Birch reduction beyond the negative limit of this redox window. The structurally characterized BamBC subunits of class II BCRs accomplish benzene ring reduction at an active-site tungsten cofactor; however, the mechanism and components involved in the energetic coupling of endergonic benzene ring reduction have remained hypothetical...
January 23, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30657682/application-of-trichoderma-strains-and-metabolites-enhances-soybean-productivity-and-nutrient-content
#13
Roberta Marra, Nadia Lombardi, Giada d'Errico, Jacopo Troisi, Giovanni Scala, Francesco Vinale, Sheridan Lois Woo, Giuliano Bonanomi, Matteo Lorito
Trichoderma fungi are effectively marketed worldwide as biocontrol agents and plant biostimulants on numerous crops due to their demonstrated effects in direct antagonism against fungal pathogens and plant growth promotion. Here we examined the effects of single and combined applications of Trichoderma strains and their bioactive metabolites (BAMs) harzianic acid (HA), 6-pentyl-α-pyrone (6PP) and hydrophobin1 (HYTLO1) on the growth, yield and nutrient uptake of soybean plants. Significant promotion of plant growth (up to 39%), as well as an increase in mineral content, was achieved with BAMs, used alone or combined with T...
January 18, 2019: Journal of Agricultural and Food Chemistry
https://read.qxmd.com/read/30651961/what-is-the-cost-of-delayed-diagnosis-of-bile-acid-malabsorption-and-bile-acid-diarrhoea
#14
Darren C R Fernandes, Dennis Poon, Laura L White, H Jervoise N Andreyev
Introduction: 75 Selenium taurocholic acid (SeHCAT) scanning diagnoses bile acid malabsorption/bile acid diarrhoea (BAM/BAD) and defines optimal treatment. Approximately 2% of the population have BAM/BAD. Aim: To evaluate the cost of delayed diagnosis of BAM/BAD. Methods: Patients' notes who underwent SeHCAT scanning in three hospitals over a 1-year period were reviewed retrospectively. Scan results and treatment response were recorded. Package-of-care costs were calculated using costing tools from the National Institute for Health and Care Excellence and from United Lincolnshire Hospitals Trust business unit...
January 2019: Frontline Gastroenterology
https://read.qxmd.com/read/30651164/evaluation-of-the-mc-media-pad%C3%A2-yeast-and-mold-device-for-the-enumeration-of-yeast-and-mold-collaborative-study-first-action-2018-02
#15
Patrick Bird, Benjamin Bastin, Dane Brooks, Erin Crowley, James Agin, David Goins, Charlotte Lindhardt, Renaud Chollet
Background: The MC-Media Pad™ Yeast and Mold (YM) is a ready-to use culture device that combines a test pad coated with medium and water-absorption polymers that is designed for the rapid quantification of yeast and mold in food products. Objective: The MC-Media Pad YM was compared with the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) for the enumeration of yeast and mold in frozen orange juice concentrate. Methods: The candidate method was evaluated using a paired study design in a multilaboratory collaborative study following the current AOAC Validation Guidelines...
January 16, 2019: Journal of AOAC International
https://read.qxmd.com/read/30644360/global-dna-methylation-remodeling-during-direct-reprogramming-of-fibroblasts-to-neurons
#16
Chongyuan Luo, Qian Yi Lee, Orly Wapinski, Rosa Castanon, Joseph R Nery, Moritz Mall, Michael S Kareta, Sean M Cullen, Margaret A Goodell, Howard Y Chang, Marius Wernig, Joseph R Ecker
Direct reprogramming of fibroblasts to neurons induces widespread cellular and transcriptional reconfiguration. Here, we characterized global epigenomic changes during the direct reprogramming of mouse fibroblasts to neurons using whole-genome base-resolution DNA methylation (mC) sequencing. We found that the pioneer transcription factor Ascl1 alone is sufficient for inducing the uniquely neuronal feature of non-CG methylation (mCH), but co-expression of Brn2 and Mytl1 was required to establish a global mCH pattern reminiscent of mature cortical neurons...
January 15, 2019: ELife
https://read.qxmd.com/read/30643419/effects-of-phenylalanine-on-the-liquid-expanded-and-liquid-condensed-states-of-phosphatidylcholine-monolayers
#17
Andrea C Cutro, E Anibal Disalvo, María A Frías
Background: Phenylalanine (Phe) is involved in physiological and pathological processes in cell membranes in which expanded and condensed states coexist. In this direction, it was reported that surface hydration is important for the binding affinity of the amino acid which significantly perturbs 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) monolayer structure and morphology. A deeper insight showed that Phe inserts in DPPC monolayer defects as a monomer at pH 5 and forms aggregates that adsorb to the membrane surface generating a reconfiguration of the lipid arrangement in areas of higher packing...
2019: Lipid Insights
https://read.qxmd.com/read/30629405/osteoinductivity-of-porous-biphasic-calcium-phosphate-ceramic-spheres-with-nanocrystalline-and-their-efficacy-in-guiding-bone-regeneration
#18
Xiangfeng Li, Tao Song, Xuening Chen, Menglu Wang, Xiao Yang, Yumei Xiao, Xingdong Zhang
Conventional biphasic calcium phosphate (BCP) bioceramics are facing many challenges to meet the demands of regenerative medicine, their biological properties are limited to a large extent due to the large grain size in comparison with nanocrystalline of natural bone mineral. Herein, this study aimed to fabricate porous BCP ceramic spheres with nanocrystalline (BCP-N) by combining alginate gelatinizing with microwave hybrid sintering methods, and investigated their in vitro and in vivo combinational osteogenesis potential...
January 10, 2019: ACS Applied Materials & Interfaces
https://read.qxmd.com/read/30597848/pre-bed-casein-protein-supplementation-does-not-enhance-acute-functional-recovery-in-physically-active-males-and-females-when-exercise-is-performed-in-the-morning
#19
Eva Apweiler, David Wallace, Sarah Stansfield, Dean M Allerton, Meghan A Brown, Emma J Stevenson, Tom Clifford
This study examined whether consuming casein protein (CP) pre-sleep could accelerate acute recovery following muscle-damaging exercise. Thirty-nine active males and females performed 100 drop jumps in the morning, consumed their habitual diet during the day, and then within 30 min pre-bed consumed either ~40 g of CP ( n = 19) or ~40 g of a carbohydrate-only control (CON) ( n = 20). Maximal isometric voluntary contractions (MIVC), countermovement jumps (CMJ), pressure-pain threshold (PPT), subjective muscle soreness and the brief assessment of mood adapted (BAM+) were measured pre, 24 and 48 h following the drop jumps...
December 28, 2018: Sports
https://read.qxmd.com/read/30584610/lack-of-association-between-epstein-barr-virus-and-mammary-tumours-in-dogs
#20
Gustavo A Roa López, Jhon Jairo Suárez, Paola Barato, Noel Verján García
Introduction: Epstein-Barr virus (EBV) is a γ-herpesvirus associated with various neoplasms in humans and is a probable aetiological agent in breast cancer; however, a causal relationship has not yet been established. Because of the epidemiological and clinicopathological similarities between breast cancer and canine mammary tumours, dogs have been proposed as a valid model for breast cancer. Material and Methods: A total of 47 canine mammary gland tumour tissues were processed by routine histopathological technique with haematoxylin-eosin staining and classified according to the type of neoplasm...
September 2018: Journal of Veterinary Research
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