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https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#1
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28534779/fpga-implementation-of-the-coupled-filtering-method-and-the-affine-warping-method
#2
Chen Zhang, Tianzhu Liang, Philip Mok, Weichuan Yu
In ultrasound image analysis, speckle tracking methods are widely applied to study the elasticity of body tissue. However, "feature-motion decorrelation" still remains as a challenge for speckle tracking methods. Recently, a coupled filtering method and an affine warping method were proposed to accurately estimate strain values when the tissue deformation is large. The major drawback of these methods is the high computational complexity. Even the GPU-based program requires a long time to finish the analysis...
May 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28534166/in-silico-identification-and-validation-of-potential-micrornas-in-kinnow-mandarin-citrus-reticulata-blanco
#3
Prashant Mohanpuria, Naveen Duhan, Navraj Kaur Sarao, Manvir Kaur, Mandip Kaur
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop...
May 22, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28533770/from-vineyard-soil-to-wine-fermentation-microbiome-approximations-to-explain-the-terroir-concept
#4
REVIEW
Ignacio Belda, Iratxe Zarraonaindia, Matthew Perisin, Antonio Palacios, Alberto Acedo
Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533227/detecting-the-presence-and-progression-of-premalignant-lung-lesions-via-airway-gene-expression
#5
Jennifer Beane, Sarah A Mazzilli, Anna M Tassinari, Gang Liu, Xiaohui Zhang, Hanqiao Liu, Anne Dy Buncio, Samjot S Dhillon, Suso J Platero, Marc E Lenburg, Mary E Reid, Stephen Lam, Avrum E Spira
  Lung cancer (LC) is the leading cause of cancer death in the US. The molecular events preceding the onset of disease are poorly understood and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with LC.  Here we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in LC chemoprevention...
May 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28532469/a-pipeline-combining-multiple-strategies-for-prioritizing-heterozygous-variants-for-the-identification-of-candidate-genes-in-exome-datasets
#6
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
BACKGROUND: The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets...
May 22, 2017: Human Genomics
https://www.readbyqxmd.com/read/28532386/extremely-low-coverage-whole-genome-sequencing-in-south-asians-captures-population-genomics-information
#7
Navin Rustagi, Anbo Zhou, W Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A Gibbs, Lynn B Jorde, Fuli Yu, Jinchuan Xing
BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28532263/establishment-and-assessment-of-a-novel-in-vitro-bio-pk-pd-system-in-predicting-the-in-vivo-pharmacokinetics-and-pharmacodynamics-of-cyclophosphamide
#8
Shanshan Tong, Hong Sun, Caifu Xue, Hanmei Chen, Jing Liu, Huiying Yang, Ning Zhou, Xiaoqiang Xiang, Weimin Cai
1. A novel bio-pharmacokinetic/pharmacodynamic (PK/PD) system was established and assessed in predicting the PK parameters and PD effects of the model drug cyclophosphamide (CP) considering the interrelationships between drug metabolism, pharmacological effects and dynamic blood circulation processes in vitro. 2. The system contains a peristaltic pump, a reaction chamber with rat liver microsomes (RLMs) encapsulated in pluronic F127-acrylamide-bisacrylamide (FAB) hydrogels, an effector cell chamber and a recirculating pipeline...
May 23, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/28531174/genome-partitioner-a-web-tool-for-multi-level-partitioning-of-large-scale-dna-constructs-for-synthetic-biology-applications
#9
Matthias Christen, Luca Del Medico, Heinz Christen, Beat Christen
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs...
2017: PloS One
https://www.readbyqxmd.com/read/28530898/chronic-constipation-update-on-management
#10
REVIEW
Umar Hayat, Mohannad Dugum, Samita Garg
Managing chronic constipation involves identifying and treating secondary causes, instituting lifestyle changes, prescribing pharmacologic and nonpharmacologic therapies, and, occasionally, referring for surgery. Several new drugs have been approved, and others are in the pipeline.
May 2017: Cleveland Clinic Journal of Medicine
https://www.readbyqxmd.com/read/28529698/seven-perspectives-on-gpcr-h-d-exchange-proteomics-methods
#11
Xi Zhang
Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor...
2017: F1000Research
https://www.readbyqxmd.com/read/28529006/validation-of-a-next-generation-sequencing-pipeline-for-the-molecular-diagnosis-of-multiple-inherited-cancer-predisposing-syndromes
#12
Paula Paulo, Pedro Pinto, Ana Peixoto, Catarina Santos, Carla Pinto, Patrícia Rocha, Isabel Veiga, Gabriela Soares, Catarina Machado, Fabiana Ramos, Manuel R Teixeira
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer...
May 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28527344/harnessing-plant-metabolic-diversity
#13
REVIEW
Charlie Owen, Nicola J Patron, Ancheng Huang, Anne Osbourn
Advances in DNA sequencing and synthesis technologies in the twenty-first century are now making it possible to build large-scale pipelines for engineering plant natural product pathways into heterologous production species using synthetic biology approaches. The ability to decode the chemical potential of plants by sequencing their transcriptomes and/or genomes and to then use this information as an instruction manual to make drugs and other high-value chemicals is opening up new routes to harness the vast chemical diversity of the Plant Kingdom...
May 17, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28527154/structure-based-classification-for-bile-salt-export-pump-bsep-inhibitors-using-comparative-structural-modeling-of-human-bsep
#14
Sankalp Jain, Melanie Grandits, Lars Richter, Gerhard F Ecker
The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline...
May 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28526974/the-health-equity-scholars-program-innovation-in-the-leaky-pipeline
#15
Carole C Upshur, Diedra M Wrighting, Gonzalo Bacigalupe, Joan Becker, Laura Hayman, Barbara Lewis, Sylvia Mignon, Megan E Rokop, Elizabeth Sweet, Marie Idali Torres, Paul Watanabe, Cedric Woods
Despite attempts to increase enrollment of under-represented minorities (URMs: primarily Black/African American, Hispanic/Latino, and Native American students) in health professional programs, limited progress has been made. Compelling reasons to rectify this situation include equity for URMs, better prepared health professionals when programs are diverse, better quality and access to health care for UMR populations, and the need for diverse talent to tackle difficult questions in health science and health care delivery...
May 19, 2017: Journal of Racial and Ethnic Health Disparities
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#16
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#17
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526081/comprehensive-detection-of-germline-variants-by-msk-impact-a-clinical-diagnostic-platform-for-solid-tumor-molecular-oncology-and-concurrent-cancer-predisposition-testing
#18
Donavan T Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E Robson, Kenneth Offit, Michael F Berger, Khedoudja Nafa, Marc Ladanyi, Liying Zhang
BACKGROUND: The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families. METHODS: Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes...
May 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28525878/vaccine-development-for-respiratory-syncytial-virus
#19
REVIEW
Barney S Graham
Respiratory syncytial virus (RSV) is an important and ubiquitous respiratory pathogen for which no vaccine is available notwithstanding more than 50 years of effort. It causes the most severe disease at the extremes of age and in settings of immunodeficiency. Although RSV is susceptible to neutralizing antibody, it has evolved multiple mechanisms of immune evasion allowing it to repeatedly infect people despite relatively little genetic diversity. Recent breakthroughs in determining the structure and antigenic content of the fusion (F) glycoprotein in its metastable untriggered prefusion form (pre-F) and the stable rearranged postfusion form (post-F) have yielded vaccine strategies that can induce potent neutralizing antibody responses and effectively boost pre-existing neutralizing activity...
May 16, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28523014/harnessing-plant-biodiversity-for-the-discovery-of-novel-anticancer-drugs-targeting-microtubules
#20
REVIEW
Songbo Xie, Jun Zhou
The microtubule cytoskeleton plays a critical role in a wide range of cellular activities and has been shown to be a highly effective target for the treatment of human malignancies. Despite the recent focus on proteomics and high-throughput profiling, it is clear that analysis of plant extracts has yielded several highly efficacious microtubule-targeting agents (MTAs) currently in clinical use, as well as agents in the current pipeline with promising efficacy. To date, a large proportion of the world's plant biodiversity remains untapped by the pharmaceutical industry, presenting a major opportunity for the discovery of novel pharmacologically active lead compounds...
2017: Frontiers in Plant Science
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