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https://www.readbyqxmd.com/read/28645111/intersecting-transcriptomic-profiling-technologies-and-long-non-coding-rna-function-in-lung-adenocarcinoma-discovery-mechanisms-and-therapeutic-applications
#1
REVIEW
Jonathan Castillo, Theresa R Stueve, Crystal N Marconett
Previously thought of as junk transcripts and pseudogene remnants, long non-coding RNAs (lncRNAs) have come into their own over the last decade as an essential component of cellular activity, regulating a plethora of functions within multicellular organisms. lncRNAs are now known to participate in development, cellular homeostasis, immunological processes, and the development of disease. With the advent of next generation sequencing technology, hundreds of thousands of lncRNAs have been identified. However, movement beyond mere discovery to the understanding of molecular processes has been stymied by the complicated genomic structure, tissue-restricted expression, and diverse regulatory roles lncRNAs play...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644843/a-high-density-genetic-map-and-qtl-analysis-of-agronomic-traits-in-foxtail-millet-setaria-italica-l-p-beauv-using-rad-seq
#2
Jun Wang, Zhilan Wang, Xiaofen Du, Huiqing Yang, Fang Han, Yuanhuai Han, Feng Yuan, Linyi Zhang, Shuzhong Peng, Erhu Guo
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits...
2017: PloS One
https://www.readbyqxmd.com/read/28644797/spatiotemporal-gmm-for-background-subtraction-with-superpixel-hierarchy
#3
Mingliang Chen, Xing Wei, Qingxiong Yang, Qing Li, Gang Wang, Ming-Hsuan Yang
We propose a background subtraction algorithm using hierarchical superpixel segmentation, spanning trees and optical flow. First, we generate superpixel segmentation trees using a number of Gaussian Mixture Models (GMMs) by treating each GMM as one vertex to construct spanning trees. Next, we use the M-smoother to enhance the spatial consistency on the spanning trees and estimate optical flow to extend the M-smoother to the temporal domain. Experimental results on synthetic and real-world benchmark datasets show that the proposed algorithm performs favorably for background subtraction in videos against the state-of-the-art methods in spite of frequent and sudden changes of pixel values...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28644742/new-legal-requirements-for-submission-of-product-information-to-poisons-centres-in-eu-member-states
#4
Ronald de Groot, Pieter Brekelmans, Herbert Desel, Irma de Vries
In the past eight years, the European Association of Poisons Centres and Clinical Toxicologists (EAPCCT) has been intensively involved in a European Commission led process to develop EU legislation on the information of hazardous products that companies have to notify to EU Poisons Centres (or equivalent "appointed bodies"). As a result of this process, the Commission adopted Regulation (EU) No 2017/542, amending the CLP Regulation by adding an Annex on harmonised product submission requirements. Harmonised mixture information requirements: Detailed and consistent information on the composition of the hazardous product will become available to EU Poisons Centres (PC)...
June 23, 2017: Clinical Toxicology
https://www.readbyqxmd.com/read/28644739/treatment-of-hepatitis-c-with-new-fixed-dose-combinations
#5
Vicente Soriano
The advent of oral direct-acting antivirals (DAA) has revolutionized the hepatitis C virus (HCV) therapeutic landscape providing cure rates over 90%. However, a subset of patients remains at higher risk for treatment failure, including those infected with: i) genotype 3 and cirrhosis; ii) resistance-associated substitutions (RAS) occurring either as natural polymorphisms or selected after prior DAA failure; and iii) poor drug adherence associated with social disabilities (homeless, psychiatric illnesses, injection drug use, alcoholism, etc...
June 23, 2017: Expert Opinion on Pharmacotherapy
https://www.readbyqxmd.com/read/28644546/-18-f-fluoromisonidazole-uptake-in-advanced-stage-non-small-cell-lung-cancer-a-voxel-by-voxel-pet-kinetics-study
#6
Daniel R McGowan, Ruth E Macpherson, Sara L Hackett, Dan Liu, Fergus V Gleeson, W Gillies McKenna, Geoff S Higgins, John D Fenwick
PURPOSE: To determine the relative abilities of compartment models to describe time-courses of 18F-fluoromisonidazole (FMISO) uptake in tumor voxels of patients with non-small cell lung cancer (NSCLC) imaged using dynamic positron emission tomography. Also to use fits of the best-performing model to investigate changes in fitted rate-constants with distance from the tumor edge. METHODS: Reversible and irreversible two- and three-tissue compartment models were fitted to 24,662 individual voxel time activity curves (TACs) obtained from tumors in 9 patients, each imaged twice...
June 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28643921/whole-exome-sequencing-identified-a-variant-in-eftud2-gene-in-establishing-a-genetic-diagnosis
#7
S Rengasamy Venugopalan, E G Farrow, M Lypka
OBJECTIVES: Craniofacial anomalies are complex and have an overlapping phenotype. Mandibulofacial Dysostosis and Oculo-Auriculo-Vertebral Spectrum are conditions that share common craniofacial phenotype and present a challenge in arriving at a diagnosis. In this report, we present a case of female proband who was given a differential diagnosis of Treacher Collins syndrome or Hemifacial Microsomia without certainty. Prior genetic testing reported negative for 22q deletion and FGFR screenings...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643865/characterization-and-biological-function-of-milk-derived-mirnas
#8
Regina Golan-Gerstl, Yaffa Elbaum Shiff, Vardit Lavi-Moshayoff, Daniel Schecter Dena Leshkowitz, Shimon Reif
SCOPE: Breastfeeding is associated with reduced risk of infection, immune mediated disorders, obesity and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. METHODS AND RESULTS: This study applied Next Generation Sequencing and quantitative real time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas...
June 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28643680/-towards-precision-medicine-in-myeloma-new-evidence-and-challenges
#9
Verónica González-Calle, Rafael Fonseca
In the last few years, next-generation sequencing studies have provided insights into the mutational landscape of multiple myeloma. The identification of actionable mutations might give a precious opportunity for exploring new targeted therapies. Thus, the implementation of promising precision medicine strategies seems to be closer than ever. Throughout this review we describe the main challenges that should to be dealt with in this new era, in order to achieve the main goal of precision medicine, namely matching patients with their right drug...
2017: Medicina
https://www.readbyqxmd.com/read/28643429/advances-and-challenges-in-metal-sulfides-selenides-for-next-generation-rechargeable-sodium-ion-batteries
#10
REVIEW
Zhe Hu, Qiannan Liu, Shu-Lei Chou, Shi-Xue Dou
Rechargeable sodium-ion batteries (SIBs), as the most promising alternative to commercial lithium-ion batteries, have received tremendous attention during the last decade. Among all the anode materials for SIBs, metal sulfides/selenides (MXs) have shown inspiring results because of their versatile material species and high theoretical capacity. They suffer from large volume expansion, however, which leads to bad cycling performance. Thus, methods such as carbon modification, nanosize design, electrolyte optimization, and cut-off voltage control are used to obtain enhanced performance...
June 23, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28643380/microscopy-visualisation-confirms-multi-species-biofilms-are-ubiquitous-in-diabetic-foot-ulcers
#11
Khalid Johani, Matthew Malone, Slade Jensen, Iain Gosbell, Hugh Dickson, Honhua Hu, Karen Vickery
Increasing evidence within the literature has identified the presence of biofilms in chronic wounds and proposed that they contribute to delayed wound healing. This research aimed to investigate the presence of biofilm in diabetic foot ulcers (DFUs) using microscopy and molecular approaches and define if these are predominantly mono- or multi-species. Secondary objectives were to correlate wound observations against microscopy results in ascertaining if clinical cues are useful in detecting wound biofilm. DFU tissue specimens were obtained from 65 subjects...
June 23, 2017: International Wound Journal
https://www.readbyqxmd.com/read/28643354/diffusion-mri-microstructure-models-with-in-vivo-human-brain-connectome-data-results-from-a-multi-group-comparison
#12
Uran Ferizi, Benoit Scherrer, Torben Schneider, Mohammad Alipoor, Odin Eufracio, Rutger H J Fick, Rachid Deriche, Markus Nilsson, Ana K Loya-Olivas, Mariano Rivera, Dirk H J Poot, Alonso Ramirez-Manzanares, Jose L Marroquin, Ariel Rokem, Christian Pötter, Robert F Dougherty, Ken Sakaie, Claudia Wheeler-Kingshott, Simon K Warfield, Thomas Witzel, Lawrence L Wald, José G Raya, Daniel C Alexander
A large number of mathematical models have been proposed to describe the measured signal in diffusion-weighted (DW) magnetic resonance imaging (MRI). However, model comparison to date focuses only on specific subclasses, e.g. compartment models or signal models, and little or no information is available in the literature on how performance varies among the different types of models. To address this deficiency, we organized the 'White Matter Modeling Challenge' during the International Symposium on Biomedical Imaging (ISBI) 2015 conference...
June 23, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28643254/gene-targeting-in-rabbits-single-step-generation-of-knock-out-rabbits-by-microinjection-of-crispr-cas9-plasmids
#13
Yoshihiro Kawano, Arata Honda
The development of genome editing technology has allowed gene disruptions to be achieved in various animal species and has been beneficial to many mammals. Gene disruption using pluripotent stem cells is difficult to achieve in rabbits, but thanks to advances in genome editing technology, a number of gene disruptions have been conducted. This paper describes a simple and easy method for carrying out gene disruptions in rabbits using CRISPR/Cas9 in which the gene to be disrupted is marked, the presence or absence of off-target candidates is checked, and a plasmid allowing simultaneous expression of Cas9 and sgRNA is constructed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643016/screening-for-lynch-syndrome-in-young-saudi-colorectal-cancer-patients-using-microsatellite-instability-testing-and-next-generation-sequencing
#14
Masood Alqahtani, Caitlin Edwards, Natasha Buzzacott, Karen Carpenter, Khalid Alsaleh, Abdulmalik Alsheikh, Waleed Abozeed, Miral Mashhour, Afnan Almousa, Yousef Housawi, Shareefa Al Hawwaj, Barry Iacopetta
Individuals with Lynch syndrome (LS) have germline variants in DNA mismatch repair (MMR) genes that confer a greatly increased risk of colorectal cancer (CRC), often at a young age. Identification of these individuals has been shown to increase their survival through improved surveillance. We previously identified 33 high risk cases for LS in the Saudi population by screening for microsatellite instability (MSI) in the tumor DNA of 284 young CRC patients. The aim of the present study was to identify MMR gene variants in this cohort of patients...
June 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28643015/the-role-of-screening-mri-in-the-era-of-next-generation-sequencing-and-moderate-risk-genetic-mutations
#15
REVIEW
Sarah Macklin, Jennifer Gass, Ghada Mitri, Paldeep S Atwal, Stephanie Hines
With the advent of next-generation sequencing, the ability to rapidly analyze numerous genes simultaneously has led to the creation of large cancer gene panels. Some of these genes, like BRCA1 and BRCA2, have been heavily researched and have well-established management guidelines. Other more newly established genes, like ATM, CHEK2, and PALB2, have previously had less robust research surrounding them which has limited the ability to create accurate risk estimates. With their inclusion on gene panels, there has been more pressure to produce management guidelines for patients discovered to carry pathogenic variants in these genes...
June 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28642701/the-market-of-biopharmaceutical-medicines-a-snapshot-of-a-diverse-industrial-landscape
#16
Evelien Moorkens, Nicolas Meuwissen, Isabelle Huys, Paul Declerck, Arnold G Vulto, Steven Simoens
Background: Biopharmaceutical medicines represent a growing share of the global pharmaceutical market, and with many of these biopharmaceutical products facing loss of exclusivity rights, also biosimilars may now enter the biopharmaceutical market. Objectives: This study aims to identify and document which investment and development strategies are adopted by industrial players in the global biopharmaceutical market. Methods: A descriptive analysis was undertaken of the investment and development strategies of the top 25 pharmaceutical companies according to 2015 worldwide prescription drug sales...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28642611/engineered-newcastle-disease-virus-expressing-the-f-and-g-proteins-of-ampv-c-confers-protection-against-challenges-in-turkeys
#17
Haixia Hu, Jason P Roth, Laszlo Zsak, Qingzhong Yu
Avian metapneumovirus (AMPV) infects the respiratory and reproductive tracts of domestic poultry, resulting in substantial economic losses for producers. Live attenuated vaccines appear to be the most effective in countries where the disease is prevalent. However, reversion to virulence has been demonstrated in several studies. Therefore, the development of a stable and safe next generation vaccine against the AMPV disease is needed. In the present study, we generated a recombinant Newcastle disease virus (NDV) vectoring the fusion (F) protein and glycoprotein (G) genes of AMPV subtype-C (AMPV-C) as a bivalent vaccine candidate using reverse genetics technology...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642609/microbial-signatures-associated-with-oropharyngeal-and-oral-squamous-cell-carcinomas
#18
Sagarika Banerjee, Tian Tian, Zhi Wei, Kristen N Peck, Natalie Shih, Ara A Chalian, Bert W O'Malley, Gregory S Weinstein, Michael D Feldman, James Alwine, Erle S Robertson
The microbiome is fundamentally one of the most unique organs in the human body. Dysbiosis can result in critical inflammatory responses and result in pathogenesis contributing to neoplastic events. We used a pan-pathogen array technology (PathoChip) coupled with next-generation sequencing to establish microbial signatures unique to human oral and oropharyngeal squamous cell carcinomas (OCSCC/OPSCC). Signatures for DNA and RNA viruses including oncogenic viruses, gram positive and negative bacteria, fungi and parasites were detected...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#19
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642364/the-accuracy-and-bias-of-single-step-genomic-prediction-for-populations-under-selection
#20
Wan-Ling Hsu, Dorian J Garrick, Rohan Luigi Fernando
In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, using the means of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is not straightforward. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean μg of unselected individuals as a fixed effect. Centering the entire matrix of observed and imputed genotypes using their sample means can be done to improve numerical properties of the analysis, in addition to fitting μg...
June 22, 2017: G3: Genes—Genomes—Genetics
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