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https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#1
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#2
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448782/amcp-partnership-forum-driving-value-and-outcomes-in-oncology
#3
(no author information available yet)
Innovation in cancer treatment has provided a wealth of recently available therapeutic agents and a healthy drug pipeline that promises to change the way we approach this disease and the lives of those affected in the years to come. However, the majority of these new agents, many of which are targeted to specific genomic features of various tumors, may challenge the health care system's ability to afford cancer care. This innovation drives the need to focus on the value of the treatments provided to patients with cancer and on methods to optimize the efficiency of the dollars we spend, in addition to the clinical value itself...
May 2017: Journal of Managed Care & Specialty Pharmacy
https://www.readbyqxmd.com/read/28447726/a-three-caller-pipeline-for-variant-analysis-of-cancer-whole-exome-sequencing-data
#4
Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis...
March 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28447476/mtbvac-from-discovery-to-clinical-trials-in-tuberculosis-endemic-countries
#5
Dessislava Marinova, Jesus Gonzalo-Asensio, Nacho Aguilo, Carlos Martin
BCG remains the only vaccine against tuberculosis (TB) in use today and despite its impressive global coverage, the nature of BCG protection against the pulmonary forms of TB remains subject to ongoing debate. Because of the limitations of BCG, novel TB vaccine candidates have been developed and several have reached the clinical pipeline. One of these candidates is MTBVAC, the first and only TB vaccine in the clinical pipeline to date based on live-attenuated Mycobacterium tuberculosis that has successfully entered clinical evaluation, a historic milestone in human vaccinology...
April 27, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28446974/stents-for-airway-strictures-selection-and-results
#6
REVIEW
Adil Ayub, Adnan M Al-Ayoubi, Faiz Y Bhora
Airway stents can provide effective and timely relief in patients with central airway obstruction. Silicone based stents are the most commonly used airway stents worldwide with a long track record of safety. Metallic stents continue to evolve from the earliest uncovered versions to a variety of newly designed covered stents. Despite the availability of a variety of stent materials and designs, minimal advances have been made towards innovation in stent technology and an ideal stent has unfortunately not yet been developed...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446765/three-dimensional-modeling-of-single-stranded-dna-hairpins-for-aptamer-based-biosensors
#7
Iman Jeddi, Leonor Saiz
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446689/bone-clarity-clearing-imaging-and-computational-analysis-of-osteoprogenitors-within-intact-bone-marrow
#8
Alon Greenbaum, Ken Y Chan, Tatyana Dobreva, David Brown, Deepak H Balani, Rogely Boyce, Henry M Kronenberg, Helen J McBride, Viviana Gradinaru
Bone tissue harbors unique and essential physiological processes, such as hematopoiesis, bone growth, and bone remodeling. To enable visualization of these processes at the cellular level in an intact environment, we developed "Bone CLARITY," a bone tissue clearing method. We used Bone CLARITY and a custom-built light-sheet fluorescence microscope to detect the endogenous fluorescence of Sox9-tdTomato(+) osteoprogenitor cells in the tibia, femur, and vertebral column of adult transgenic mice. To obtain a complete distribution map of these osteoprogenitor cells, we developed a computational pipeline that semiautomatically detects individual Sox9-tdTomato(+) cells in their native three-dimensional environment...
April 26, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28446636/insights-into-the-evolution-of-hydroxyproline-rich-glycoproteins-from-1000-plant-transcriptomes
#9
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Gane Ka-Shu Wong, Doug Soltis, Nicholas W Miles, Michael Melkonian, Barbara Melkonian, Michael K Deyholos, James Leebens-Mack, Carl J Rothfels, Dennis W Stevenson, Sean W Graham, Xumin Wang, Shuangxiu Wu, J Chris Pires, Patrick P Edger, Eric J Carpenter, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan-proteins (AGPs), extensins (EXTs) and proline-rich proteins (PRPs)...
April 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28446635/a-motif-and-amino-acid-bias-bioinformatics-pipeline-to-identify-hydroxyproline-rich-glycoproteins
#10
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signalling and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive post-translational modifications (glycosylation) and have been implicated in many biological functions...
April 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28446139/de-novo-assembly-of-highly-polymorphic-metagenomic-data-using-in-situ-generated-reference-sequences-and-a-novel-blast-based-assembly-pipeline
#11
You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, Hurng-Yi Wang
BACKGROUND: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data...
April 26, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#12
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28445076/image-based-phenotypic-screening-with-human-primary-t-cells-using-one-dimensional-imaging-cytometry-with-self-tuning-statistical-gating-algorithms
#13
Steve S Wang, Daniel J Ehrlich
The parallel microfluidic cytometer (PMC) is an imaging flow cytometer that operates on statistical analysis of low-pixel-count, one-dimensional (1D) line scans. It is highly efficient in data collection and operates on suspension cells. In this article, we present a supervised automated pipeline for the PMC that minimizes operator intervention by incorporating multivariate logistic regression for data scoring. We test the self-tuning statistical algorithms in a human primary T-cell activation assay in flow using nuclear factor of activated T cells (NFAT) translocation as a readout and readily achieve an average Z' of 0...
April 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28445069/targeted-dereplication-of-microbial-natural-products-by-high-resolution-ms-and-predicted-lc-retention-time
#14
Justine Chervin, Marc Stierhof, Ming Him Tong, Doe Peace, Kine Østnes Hansen, Dagmar Solveig Urgast, Jeanette Hammer Andersen, Yi Yu, Rainer Ebel, Kwaku Kyeremeh, Veronica Paget, Gabriela Cimpan, Albert Van Wyk, Hai Deng, Marcel Jaspars, Jioji N Tabudravu
A new strategy for the identification of known compounds in Streptomyces extracts that can be applied in the discovery of natural products is presented. The strategy incorporates screening a database of 5555 natural products including 5098 structures from Streptomyces sp., using a high-throughput LCMS data processing algorithm that utilizes HRMS data and predicted LC retention times (tR) as filters for rapid identification of known compounds in the natural product extract. The database, named StrepDB, contains for each compound the structure, molecular formula, molecular mass, and predicted LC retention time...
April 26, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28444973/in-depth-comparative-phenotyping-of-blood-innate-myeloid-leukocytes-from-healthy-humans-and-macaques-using-mass-cytometry
#15
Jamila Elhmouzi-Younes, Jean-Louis Palgen, Nicolas Tchitchek, Simon Delandre, Inana Namet, Caroline L Bodinham, Kathleen Pizzoferro, David J M Lewis, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon
Comparative immune-profiling of innate responses in humans and non-human primates is important to understand the pathogenesis of infectious and chronic inflammatory diseases as well as for the preclinical development of vaccines and immune therapies. However, direct comparisons of the two species are rare and were never performed using mass cytometry. Here, whole-blood-derived leukocytes from healthy humans and cynomolgus macaques were analyzed with mass cytometry. Two similar panels of around 30 monoclonal antibodies targeting human markers associated with innate myeloid cells to stain fixed human and macaque leukocytes were constructed...
April 26, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28444330/progress-and-challenges-of-engineering-a-biophysical-carbon-dioxide-concentrating-mechanism-into-higher-plants
#16
Benjamin D Rae, Benedict M Long, Britta Förster, Nghiem D Nguyen, Christos N Velanis, Nicky Atkinson, Wei Yih Hee, Bratati Mukherjee, G Dean Price, Alistair J McCormick
Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities...
April 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28443485/letter-regarding-article-quantitative-assessment-of-parent-vessel-and-distal-intracranial-hemodynamics-following-pipeline-flow-diversion
#17
Wenqiang Li
No abstract text is available yet for this article.
January 1, 2017: Interventional Neuroradiology
https://www.readbyqxmd.com/read/28442740/deciphering-the-mode-of-action-of-cell-wall-inhibiting-antibiotics-using-metabolic-labeling-of-growing-peptidoglycan-in-streptococcus-pyogenes
#18
Atsushi Sugimoto, Asuka Maeda, Kaori Itto, Hirokazu Arimoto
Because of the scanty pipeline of antibiotics newly obtained from nature, chemical modification of established drugs is one of the major streams of current antibacterial research. Intuitive and easy-to-use assays are critical for identifying drug candidates with novel modes of action. In this study, we demonstrated that metabolic fluorescent staining of growing cell walls is a powerful tool for mode-of-action analyses of antibiotics using Streptococcus pyogenes. A set of major cell-wall-inhibiting antibiotics (bacitracin, D-cycloserine, flavomycin, oxacillin, ramoplanin, and vancomycin) was employed to validate the potential of the assay...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442722/mutational-screening-of-slc39a5-leprel1-and-lrpap1-in-a-cohort-of-187-high-myopia-patients
#19
Chun-Yun Feng, Xiao-Qiong Huang, Xue-Wen Cheng, Rong-Han Wu, Fan Lu, Zi-Bing Jin
High myopia (HM) is a leading cause of mid-way blindness with a high heritability in East Asia. Although only a few disease genes have been reported, a small proportion of patients could be identified with genetic predispositions. In order to expand the mutation spectrum of the causative genes in Chinese adult population, we investigated three genes, SLC39A5, LEPREL1 and LRPAP1, in a cohort of 187 independent Chinese patients with high myopia. Sanger sequencing was used to find possible pathogenic mutations, which were further screened in normal controls...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28441673/gateways-to-the-laboratory-how-an-md-phd-program-increased-the-number-of-minority-physician-scientists
#20
Ruth Gotian, Jemella C Raymore, Shauna-Kay Rhooms, Laura Liberman, Olaf S Andersen
Traditional underrepresented minority (URM) groups (African Americans, Hispanic Americans, Native Americans) remain underrepresented among physician-scientists. To address the dearth of URM physician-scientists, in 1993 the Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program developed a pipeline program, Gateways to the Laboratory (Gateways), which focuses on increasing the breadth and depth of the URM physician-scientist pipeline by offering an all-encompassing summer research training program which mirrors the life of a physician-scientist...
May 2017: Academic Medicine: Journal of the Association of American Medical Colleges
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