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Florian Herry, Frédéric Hérault, David Picard Druet, Amandine Varenne, Thierry Burlot, Pascale Le Roy, Sophie Allais
BACKGROUND: The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix® Axiom® HD genotyping array) for chicken has enabled the implementation of genomic selection in layer and broiler breeding, but the genotyping costs remain high for a routine use on a large number of selection candidates. It has thus been deemed interesting to develop a low density genotyping chip that would induce lower costs...
December 4, 2018: BMC Genetics
Chen Wang, Chun Liang
Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite lengths due to deficiency in mismatch repair (MMR) system. MSI is associated with several tumor types and its status can be considered as an important indicator for patient prognosis. Conventional clinical diagnosis of MSI examines PCR products of a panel of microsatellite markers using electrophoresis (MSI-PCR), which is laborious, costly, and time consuming. We developed MSIpred, a python package for automatic MSI classification using a machine learning technology - support vector machine (SVM)...
December 3, 2018: Scientific Reports
Egil Ferkingstad, Asmundur Oddsson, Solveig Gretarsdottir, Stefania Benonisdottir, Gudmar Thorleifsson, Aimee M Deaton, Stefan Jonsson, Olafur A Stefansson, Gudmundur L Norddahl, Florian Zink, Gudny A Arnadottir, Bjarni Gunnarsson, Gisli H Halldorsson, Anna Helgadottir, Brynjar O Jensson, Ragnar P Kristjansson, Gardar Sveinbjornsson, David A Sverrisson, Gisli Masson, Isleifur Olafsson, Gudmundur I Eyjolfsson, Olof Sigurdardottir, Hilma Holm, Ingileif Jonsdottir, Sigurdur Olafsson, Thora Steingrimsdottir, Thorunn Rafnar, Einar S Bjornsson, Unnur Thorsteinsdottir, Daniel F Gudbjartsson, Patrick Sulem, Kari Stefansson
Gallstones are responsible for one of the most common diseases in the Western world and are commonly treated with cholecystectomy. We perform a meta-analysis of two genome-wide association studies of gallstone disease in Iceland and the UK, totaling 27,174 cases and 736,838 controls, uncovering 21 novel gallstone-associated variants at 20 loci. Two distinct low frequency missense variants in SLC10A2, encoding the apical sodium-dependent bile acid transporter (ASBT), associate with an increased risk of gallstone disease (Pro290Ser: OR = 1...
November 30, 2018: Nature Communications
Manman Liu, Jinfei Liu, Chao Guo, Yan Li
Metal azolate frameworks (MAFs) as a subfamily of metal-organic frameworks (MOFs) have received much attention in analyzing organic volatiles owing to their remarkable structures. In this work, the headspace solid-phase microextraction (SPME) fiber based on MAF-66 has been fabricated by a layer-by-layer deposition method. To evaluate the performance of the MAF-66-coated fibers, polycyclic aromatic hydrocarbons (PAHs) were tested as analytes with gas chromatography (GC). Relevant experimental parameters were optimized including extraction temperature, extraction time, desorption temperature, desorption time, the stirring rate and salt concentration...
November 22, 2018: Journal of Chromatography. A
Matthew Herritt, Arun Prabhu Dhanapal, Larry C Purcell, Felix B Fritschi
BACKGROUND: Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited...
November 29, 2018: BMC Plant Biology
Saad Alabdulkarim, Maury A Nussbaum
We compared different passive exoskeletal designs in terms of physical demands (maximum acceptable frequency = MAF, perceived discomfort, and muscular loading) and quality in a simulated overhead drilling task, and the moderating influence of tool mass (∼2 and ∼5 kg). Three distinct designs were used: full-body and upper-body exoskeletons with attached mechanical arms; and an upper-body exoskeleton providing primarily shoulder support. Participants (n = 16, gender-balanced) simulated drilling for 15 min to determine their MAF, then maintained this pace for three additional minutes while the remaining outcome measures were obtained...
January 2019: Applied Ergonomics
Gemma Montalban, Sandra Bonache, Alejandro Moles-Fernández, Alexandra Gisbert-Beamud, Anna Tenés, Vanessa Bach, Estela Carrasco, Adrià López-Fernández, Neda Stjepanovic, Judith Balmaña, Orland Diez, Sara Gutiérrez-Enríquez
BACKGROUND: Genetic analysis of BRCA1 and BRCA2 for the diagnosis of hereditary breast and ovarian cancer (HBOC) is commonly restricted to coding regions and exon-intron boundaries. Although germline pathogenic variants in these regions explain about ~20% of HBOC cases, there is still an important fraction that remains undiagnosed. We have screened BRCA1/2 deep intronic regions to identify potential spliceogenic variants that could explain part of the missing HBOC susceptibility. METHODS: We analysed BRCA1/2 deep intronic regions by targeted gene sequencing in 192 high-risk HBOC families testing negative for BRCA1/2 during conventional analysis...
November 24, 2018: Journal of Medical Genetics
Kifayat Ullah, Emmanuel Zubia, Mahesh Narayan, Jing Yang, Guoqiang Xu
The ubiquitin-proteasome system is an important regulatory machinery involved in proteostasis and cellular signaling. Proteins are ubiquitinated via the concerted action of E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin ligases. Although most of the studies to date focus on the significance of E3 ubiquitin ligases in disease development and therapeutic treatment, recent discoveries suggest that E2 ubiquitin-conjugating enzymes might also be potential drug targets. The ubiquitin-conjugating enzyme E2 O (UBE2O), an E3-independent E2 (i...
November 23, 2018: FEBS Journal
Nathalie Jean-Charles, Diego F Buenaventura, Mark M Emerson
BACKGROUND: Cone and rod photoreceptors are two of the primary cell types affected in human retinal disease. Potential strategies to combat these diseases are the use of gene therapy to rescue compromised photoreceptors or to generate new functional photoreceptors to replace those lost in the diseased retina. Cis-regulatory elements specific to cones, rods, or both types of photoreceptors are critical components of successful implementation of these two strategies. The purpose of this study was to identify and characterize the cell type specificity and activity of cis-regulatory elements active in developing photoreceptors...
November 22, 2018: Neural Development
Roderick A P M van Eijl, Jessie A G L van Buggenum, Sabine E J Tanis, Joost Hendriks, Klaas W Mulder
Epidermal homeostasis requires balanced and coordinated adult stem cell renewal and differentiation. These processes are controlled by both extracellular signaling and by cell intrinsic transcription regulatory networks, yet how these control mechanisms are integrated to achieve this is unclear. Here, we developed single-cell Immuno-Detection by sequencing (scID-seq) and simultaneously measured 69 proteins (including 34 phosphorylated epitopes) at single-cell resolution to study the activation state of signaling pathways during human epidermal differentiation...
November 9, 2018: iScience
Di Wu, Mei Wang, Xingang Wang, Yong-Biao Zhang, Tao Song, Ningbei Yin, Zhenmin Zhao
Single-nucleotide polymorphisms (SNPs) in protein-coding regions of genes which were previously reported to be associated with nonsyndromic cleft lip, with or without palate involvement (NSCL/P), were investigated. Twelve candidate loci [platelet-derived growth factor C (PDGFC), platelet-derived growth factor subunit A (PDGFA), platelet-derived growth factor receptor alpha (PDGFRA), glycine receptor alpha 2 (GLRA2), glycine receptor beta (GLRB), ATP binding cassette subfamily A member 4 (ABCA4), MAF bZIP transcription factor B (MAFB), interferon regulatory factor 6 (IRF6), CCDC26 long non-coding RNA (CCDC26), paired box 7 (PAX7), ventral anterior homeobox 1 (VAX1), and netrin 1 (NTN1)] covering 1...
November 21, 2018: European Journal of Oral Sciences
Emine Demir, Nazife Nur Afacan, Metin Celiker, Fatma Beyazal Celiker, Mehmet Fatih İnecikli, Suat Terzi, Engin Dursun
Objectives: We explored whether wideband tympanometry (WBT) could be used as a screening test for superior semicircular canal dehiscence (SSCD), and obtained new WBT data (given that the test is not yet in common clinical use) on patients with SSCD. Methods: We compared the WBT data of patients clinically and radiologically diagnosed with SSCD in our hospital between 2013 and 2018 to those of healthy volunteers. We compared the resonance frequency (RF), maximum absorbance frequency (MAF), and maximum absorbance ratio (MAR)...
November 22, 2018: Clinical and Experimental Otorhinolaryngology
Elizabeth Blackman, Kimlin Ashing, Denise Gibbs, Yin-Ming Kuo, Andrew Andrews, Meganathan Ramakodi, Karthik Devarajan, Jackie Bucci, Gilda Jean-Louis, Oni Richards-Waritay, Barbara Wilson, Carlene Bowen, Eric Edi, Vera Tolbert, Raphiatou Noumbissi, Daramola N Cabral, JoAnn Oliver, Robin Roberts, Marshall Tulloch-Reid, Camille Ragin
OBJECTIVE: Cancer mortality inequity among persons of African Ancestry is remarkable. Yet, Black inclusion in cancer biology research is sorely lacking and warrants urgent attention. Epidemiologic research linking African Ancestry and the African Diaspora to disease susceptibility and outcomes is critical for understanding the significant and troubling health disparities among Blacks. Therefore, in a cohort of diverse Blacks, this study examined differences in genetic ancestry informative markers (AIMs) in the DNA repair pathway and the cancer related biomarker 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL)...
November 19, 2018: Ethnicity & Health
Tatjana Škarić-Jurić, Željka Tomas, Matea Zajc Petranović, Nada Božina, Nina Smolej Narančić, Branka Janićijević, Marijana Peričić Salihović
The products of the polymorphic ADME genes are involved in Absorption, Distribution, Metabolism, and Excretion of drugs. The pharmacogenetic data have been studied extensively due to their clinical importance in the appropriate drug prescription, but such data from the isolated populations are rather scarce. We analyzed the distribution of 95 polymorphisms in 31 core ADME genes in 20 populations worldwide and in newly genotyped samples from the Roma (Gypsy) population living in Croatia. Global distribution of ADME core gene loci differentiated three major clusters; (1) African, (2) East Asian, and (3) joint European, South Asian and South American cluster...
2018: PloS One
Dominik Aschenbrenner, Mathilde Foglierini, David Jarrossay, Dan Hu, Howard L Weiner, Vijay K Kuchroo, Antonio Lanzavecchia, Samuele Notarbartolo, Federica Sallusto
In the version of this article initially published, in the legend to Fig. 1b, the description of the frequency of TH 17-IL-10+ clones was incomplete for the first group; this should read as follows: "...13 experiments with clones isolated from CCR6+ CCR4+ CXCR3- T cells...". Also, the label along the vertical axis of the bottom right plot in Figure 5b was incomplete; the correct label is 'IFN-γ+ cells (%)'. Finally, in the first sentence of the final paragraph of the final Results subsection, the description of the regions analyzed was incorrect; that sentence should begin: "DNA motif-enrichment analysis of the subset-specific H3K27ac-positive regions...
November 17, 2018: Nature Immunology
Magali Fournier, Amol Saxena, Nicola Maffulli
Hallux valgus is a common disorder characterized by a medial deviation of the 1st metatarsal, eventually leading to subluxation and pain of the 1st metatarsophalangeal joint. This can inhibit sports activity. Despite being a common forefoot pathology, debate exists regarding the appropriate surgical approach in the athletic population. Paucity in literature exists with reporting of outcomes of 1st metatarsal procedures leading to best outcomes. This review was able to identify 5 studies of surgical correction of hallux valgus in athletes published to date...
November 14, 2018: Journal of Foot and Ankle Surgery: Official Publication of the American College of Foot and Ankle Surgeons
Kang-Yi Su, Jeng-Sen Tseng, Keng-Mao Liao, Tsung-Ying Yang, Kun-Chieh Chen, Kuo-Hsuan Hsu, Pan-Chyr Yang, Sung-Liang Yu, Gee-Chen Chang
Several ultra-sensitive methods for T790M in plasma cell-free DNA (cfDNA) have been developed for lung cancer. The correlation between mutation-allele frequency (MAF) cut-off, drug responsiveness, and outcome prediction is an unmet needs and not fully addressed. An innovative combination of peptide nucleic acid (PNA) and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) was used to proof of concept for monitoring cfDNA T790M in EGFR-mutant patients. Mutant enrichment by PNA was optimized and the detection limit was evaluated through serial dilutions...
2018: PloS One
Sheikh Firdous Ahmad, Manjit Panigrahi, Supriya Chhotaray, Dhan Pal, Anuj Chauhan, Arvind Sonwane, Subhashree Parida, Bharat Bhushan, Gyanendra Kumar Gaur, Bishnu Prasad Mishra, Raj Kumar Singh
The present study was aimed to assess parameters related to genetic diversity, population structure and admixture in the Frieswal crossbred cattle of India. A total of three datasets were analyzed during this study. Dataset A (n = 80) consisted of data on two purebred populations, i.e., Shorthorn (n = 35) and Brahman (n = 25) and one crossbred strain Santa Gertrudis (n = 20). The dataset B (n = 71) consisted of data on three populations that included Holstein-Friesian (n = 30), Sahiwal (n = 27) and Frieswal (n = 14) cattle...
November 16, 2018: Animal Biotechnology
Jariya Upadia, Alicia Gomes, Peter Weiser, Maria Descartes
Multicentric carpotarsal osteolysis syndrome (MCTO) is a rare skeletal disorder caused by heterozygous mutations in the MAFB gene (v-maf musculoaponeurotic fibrosarcoma oncogene ortholog B). This is an autosomal dominant condition with a high frequency of sporadic cases. MCTO is characterized by osteolysis of the carpal, metacarpal, and tarsal bones beginning in early childhood with musculoskeletal rheumatologic symptoms such as pain and disability. Renal involvement can be seen in more than half of the patients; from ages 16 months to 42 years and manifests from proteinuria to end-stage renal failure requiring renal transplantation...
December 2018: Journal of Pediatric Genetics
Barry S Mason, Viola C Altmann, Victoria L Goosey-Tolfrey
PURPOSE: To determine the effect of trunk and arm impairment on physical and technical performance during wheelchair rugby (WR) competition. METHODS: Thirty-one highly trained WR players grouped according to their trunk (no trunk [NT]; some trunk [T] function) and arm impairment (poor [PAF]; moderate [MAF]; good [GAF] arm function) participated in 5 WR matches. Player's physical (wheelchair mobility) and technical (ball handling) activities were analysed using an indoor tracking system and video analysis respectively...
November 14, 2018: International Journal of Sports Physiology and Performance
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