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https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#1
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334071/on-the-design-and-prospects-of-direct-rna-sequencing
#2
Georgi K Marinov
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets...
February 17, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28328962/the-blood-dna-virome-in-8-000-humans
#3
Ahmed Moustafa, Chao Xie, Ewen Kirkness, William Biggs, Emily Wong, Yaron Turpaz, Kenneth Bloom, Eric Delwart, Karen E Nelson, J Craig Venter, Amalio Telenti
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches...
March 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#4
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28303552/european-radiographers-challenges-from-mammography-education-and-clinical-practice-an-integrative-review
#5
Eija Metsälä, Nicole Richli Meystre, José Pires Jorge, Anja Henner, Tiina Kukkes, Cláudia Sá Dos Reis
OBJECTIVES: This study aims to identify European radiographers' challenges in clinical performance in mammography and the main areas of mammography that require more and better training. METHODS: An extensive search was performed to identify relevant studies focused on clinical practice, education and training in mammography published between January 2010 and December 2015 in the English language. The data were analysed by using deductive thematic analysis. RESULTS: A total of 27 full text articles were read, evaluating their quality...
March 16, 2017: Insights Into Imaging
https://www.readbyqxmd.com/read/28299895/deep-sequencing-and-variant-analysis-of-an-italian-pathogenic-field-strain-of-equine-infectious-anaemia-virus
#6
K Cappelli, R F Cook, V Stefanetti, F Passamonti, G L Autorino, M T Scicluna, M Coletti, A Verini Supplizi, S Capomaccio
Equine infectious anaemia virus (EIAV) is a lentivirus with an almost worldwide distribution that causes persistent infections in equids. Technical limitations have restricted genetic analysis of EIAV field isolates predominantly to gag sequences resulting in very little published information concerning the extent of inter-strain variation in pol, env and the three ancillary open reading frames (ORFs). Here, we describe the use of long-range PCR in conjunction with next-generation sequencing (NGS) for rapid molecular characterization of all viral ORFs and known transcription factor binding motifs within the long terminal repeat of two EIAV isolates from the 2006 Italian outbreak...
March 15, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28285169/microbial-profiling-of-cpn60-universal-target-sequences-in-artificial-mixtures-of-vaginal-bacteria-sampled-by-nylon-swabs-or-self-sampling-devices-under-different-storage-conditions
#7
John J Schellenberg, Angela Yena Oh, Janet E Hill
The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT)...
March 9, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28277235/variation-in-the-level-of-detail-in-pediatric-voiding-cystourethrogram-reports
#8
Anthony J Schaeffer, Jeanne S Chow, Anastasia Ivanova, Gang Cui, Saul P Greenfield, J Michael Zerin, Alejandro Hoberman, Ranjiv I Mathews, Tej K Mattoo, Myra A Carpenter, Marva Moxey-Mims, Russell W Chesney, Caleb P Nelson
INTRODUCTION: Voiding cystourethrogram (VCUG) provides a wealth of data on urinary tract function and anatomy, but few standards exist for reporting VCUG findings. OBJECTIVE: We aimed to assess variability in VCUG reports and to test our hypothesis that VCUG reports from pediatric facilities and pediatric radiologists are more complete than those performed at other facilities or by non-pediatric radiologists. STUDY DESIGN: We analyzed original VCUG reports from children enrolled in the Randomized Intervention for Children with Vesicoureteral Reflux (RIVUR) trial...
October 8, 2016: Journal of Pediatric Urology
https://www.readbyqxmd.com/read/28272506/a-murine-model-to-study-epilepsy-and-sudep-induced-by-malaria-infection
#9
Paddy Ssentongo, Anna E Robuccio, Godfrey Thuku, Derek G Sim, Ali Nabi, Fatemeh Bahari, Balaji Shanmugasundaram, Myles W Billard, Andrew Geronimo, Kurt W Short, Patrick J Drew, Jennifer Baccon, Steven L Weinstein, Frank G Gilliam, José A Stoute, Vernon M Chinchilli, Andrew F Read, Bruce J Gluckman, Steven J Schiff
One of the largest single sources of epilepsy in the world is produced as a neurological sequela in survivors of cerebral malaria. Nevertheless, the pathophysiological mechanisms of such epileptogenesis remain unknown and no adjunctive therapy during cerebral malaria has been shown to reduce the rate of subsequent epilepsy. There is no existing animal model of postmalarial epilepsy. In this technical report we demonstrate the first such animal models. These models were created from multiple mouse and parasite strain combinations, so that the epilepsy observed retained universality with respect to genetic background...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28269427/colorimetric-determinations-of-lithium-levels-in-drop-volumes-of-human-plasma-for-monitoring-patients-with-bipolar-mood-disorder
#10
M Qassem, M Hickey, P A Kyriacou
Lithium preparations are considered the most reliable form of mood stabilizing medication for patients with Bipolar disorder. Nevertheless, lithium is a toxic element and its therapeutic range is extremely narrow, with levels of 0.61.0 mEq considered normal, whereas levels above 1.5 mEq are toxic. Thus unfortunately, many patients reach toxic levels that lead to unnecessary complications. It is believed that personal monitoring of blood lithium levels would benefit patients taking lithium medication. Therefore, our aim is to develop a personal lithium blood level analyzer for patients with bipolar mood disorder, and we report here our initial results of a colorimetric-based method used to test drop-volumes of human plasma that had been spiked with lithium...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28258768/quality-assessment-of-websites-providing-educational-content-for-patients-with-rheumatoid-arthritis
#11
Harish Rajashekarappa Siddhanamatha, Eric Heung, Maria de Los Angeles Lopez-Olivo, Noha Abdel-Wahab, Ana Ojeda-Prias, Irmgard Willcockson, Amye Leong, Maria Eugenia Suarez-Almazor
OBJECTIVE: We performed an environmental scan of currently available websites providing educational information about rheumatoid arthritis (RA) and evaluated the quality of these websites. METHODS: We searched three separate search engines, Google, Bing, and Ask.com, on August 27, 2015, using two search terms, "arthritis" and "rheumatoid." Only patient education websites were included. Two independent investigators evaluated the accuracy, completeness, technical elements, design and esthetics, readability, usability, and accessibility of the websites...
January 18, 2017: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/28240196/social-support-as-a-mediator-variable-of-the-relationship-between-depression-and-life-satisfaction-in-a-sample-of-saudi-caregivers-of-patients-with-alzheimer-s-disease
#12
Shatha Jamil Khusaifan, Mogeda El Sayed El Keshky
The authors would like to apologise for an error made in the acknowledgement of the above mentioned article. In the acknowledgement section of the article, paragraph 'This project was funded by the Deanship of Scientific Research (DSR), at King Abdulaziz University, Jeddah, under grant no. (G-282/ 724246/1436). The authors, therefore, acknowledge with thanks DSR for technical and financial support'. Should read: This project was funded by the Deanship of Scientific Research (DSR), at King Abdulaziz University, Jeddah, under grant no...
February 27, 2017: International Psychogeriatrics
https://www.readbyqxmd.com/read/28237189/ct-for-acute-nontraumatic-abdominal-pain-is-oral-contrast-really-required
#13
Rivka Kessner, Sophie Barnes, Pinchas Halpern, Vadim Makrin, Arye Blachar
RATIONALE AND OBJECTIVES: This study aims to compare the diagnostic performance of abdominal computed tomography (CT) performed with and without oral contrast in patients presenting to the emergency department (ED) with acute nontraumatic abdominal pain. MATERIALS AND METHODS: Between December 2013 and December 2014, 348 adult patients presenting to the ED of a large tertiary medical center with nontraumatic abdominal pain were evaluated. Exclusion criteria for the study were history of inflammatory bowel disease, recent abdominal operation and suspected renal colic, abdominal aortic aneurysm rupture, or intestinal obstruction...
February 22, 2017: Academic Radiology
https://www.readbyqxmd.com/read/28236452/multiparametric-magnetic-resonance-imaging-and-prostate-cancer-what-s-new
#14
V Catalá, J C Vilanova, J M Gaya, F Algaba, T Martí
Prostatic multi-parametric magnetic resonance imaging (MP-MRI) has recently had a wide development becoming a key tool in the diagnostic and therapeutic decisions in prostate cancer (Pca). The fast development both in technology and in reading (PIRADS V2) requires a continuous updating of knowledge within this area. The aim of this article is to present an updated revision of technical aspects, reading patterns and prostatic MP-MRI in Pca, with a multidisciplinary approach. Currently guidelines establish the use of the MP-MRI when there is a high PSA and a negative prostatic biopsy; tumor staging; evaluation in candidates to active surveillance; focal treatments plans and tumoral recurrence evaluation...
February 21, 2017: Radiología
https://www.readbyqxmd.com/read/28230889/quantification-of-the-borderline-range-and-implications-for-evaluating-non-animal-testing-methods-precision
#15
Maria Leontaridou, Daniel Urbisch, Susanne N Kolle, Katharina Ott, Denis S Mulliner, Silke Gabbert, Robert Landsiedel
Testing methods to assess the skin sensitisation potential of a substance usually use threshold criteria to dichotomise continuous experimental read-outs into yes/no conclusions. The threshold criteria are prescribed in the respective OECD test guidelines and the conclusion is used for regulatory hazard assessment, i.e. classification and labelling of the substance. We can identify a borderline range (BR) around the classification threshold within which test results are non-conclusive due to a testing method's biological and technical variability...
February 23, 2017: ALTEX
https://www.readbyqxmd.com/read/28227673/colorimetric-determinations-of-lithium-levels-in-drop-volumes-of-human-plasma-for-monitoring-patients-with-bipolar-mood-disorder
#16
M Qassem, M Hickey, P A Kyriacou, M Qassem, M Hickey, P A Kyriacou, M Qassem, M Hickey, P A Kyriacou
Lithium preparations are considered the most reliable form of mood stabilizing medication for patients with Bipolar disorder. Nevertheless, lithium is a toxic element and its therapeutic range is extremely narrow, with levels of 0.61.0 mEq considered normal, whereas levels above 1.5 mEq are toxic. Thus unfortunately, many patients reach toxic levels that lead to unnecessary complications. It is believed that personal monitoring of blood lithium levels would benefit patients taking lithium medication. Therefore, our aim is to develop a personal lithium blood level analyzer for patients with bipolar mood disorder, and we report here our initial results of a colorimetric-based method used to test drop-volumes of human plasma that had been spiked with lithium...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28159771/improving-and-correcting-the-contiguity-of-long-read-genome-assemblies-of-three-plant-species-using-optical-mapping-and-chromosome-conformation-capture-data
#17
Wen-Biao Jiao, Gonzalo Garcia Accinelli, Benjamin Hartwig, Christiane Kiefer, David Baker, Edouard Severing, Eva-Maria Willing, Mathieu Piednoel, Stefan Woetzel, Eva Madrid-Herrero, Bruno Huettel, Ulrike Hümann, Richard Reinhard, Marcus A Koch, Daniel Swan, Bernardo Clavijo, George Coupland, Korbinian Schneeberger
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes, however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated PacBio long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding...
February 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28148242/exome-qtl-seq-maps-monogenic-locus-and-qtls-in-barley
#18
Hiroshi Hisano, Kazuki Sakamoto, Hiroki Takagi, Ryohei Terauchi, Kazuhiro Sato
BACKGROUND: QTL-seq, in combination with bulked segregant analysis and next-generation sequencing (NGS), is used to identify loci in small plant genomes, but is technically challenging to perform in species with large genomes, such as barley. A combination of exome sequencing and QTL-seq (exome QTL-seq) was used to map the mono-factorial Mendelian locus black lemma and pericarp (Blp) and QTLs for resistance to net blotch disease, a common disease of barley caused by the fungus Pyrenophora teres, which segregated in a population of 100 doubled haploid barley lines...
February 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28134443/challenges-and-opportunities-for-whole-genome-sequencing-based-surveillance-of-antibiotic-resistance
#19
Anita C Schürch, Willem van Schaik
Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)-based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore)...
January 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28130155/ms-read-quantitative-measurement-of-amino-acid-incorporation
#20
Kyle Mohler, Hans-Rudolph Aerni, Brandon Gassaway, Jiqiang Ling, Michael Ibba, Jesse Rinehart
Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored...
January 24, 2017: Biochimica et Biophysica Acta
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