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https://www.readbyqxmd.com/read/28330322/de-novo-transcriptome-sequencing-in-monsonia-burkeana-revealed-putative-genes-for-key-metabolic-pathways-involved-in-tea-quality-and-medicinal-value
#1
Adugna A Woldesemayat, Khayalethu Ntushelo, David M Modise
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#2
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328990/gut-microbiome-analysis-of-type-2-diabetic-patients-from-the-chinese-minority-ethnic-groups-the-uygurs-and-kazaks
#3
Ye Wang, Xin Luo, Xinmin Mao, Yicun Tao, Xinjian Ran, Haixia Zhao, Jianhui Xiong, Linlin Li
The gut microbiome may have an important influence on the development of diabetes mellitus type 2 (DM2). To better understand the DM2 pandemic in ethnic minority groups in China, we investigated and compared the composition and richness of the gut microbiota of healthy, normal glucose tolerant (NGT) individuals and DM2 patients from two ethnic minority groups in Xinjiang, northwest China, the Uygurs and Kazaks. The conserved V6 region of the 16S rRNA gene was amplified by PCR from the isolated DNA. The amplified DNA was sequenced and analyzed...
2017: PloS One
https://www.readbyqxmd.com/read/28328962/the-blood-dna-virome-in-8-000-humans
#4
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/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#5
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28328396/improved-medication-adherence-and-frequency-of-blood-glucose-self-testing-using-an-m-health-platform-versus-usual-care-in-a-multisite-randomized-clinical-trial-among-people-with-type-2-diabetes-in-india
#6
Nora J Kleinman, Avani Shah, Sanjiv Shah, Sanjeev Phatak, Vijay Viswanathan
BACKGROUND: In 2015, India had an estimated 69.2 million people with diabetes and a national prevalence of 8.7%. Evidence is mounting for the benefits of telemedicine in diabetes care, but remains limited on mobile-health (m-Health) interventions. INTRODUCTION: This study assessed the impact of an m-Health diabetes platform on clinical outcomes, patient-reported outcomes, patient and provider satisfaction, and app usage. MATERIALS AND METHODS: This open-label, two-arm parallel study enrolled 91 people at 3 sites in India, aged 18-65, with type 2 diabetes, and an A1c between 7...
March 6, 2017: Telemedicine Journal and E-health: the Official Journal of the American Telemedicine Association
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#7
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/28327193/longitudinal-evaluation-of-aortic-hemodynamics-in-marfan-syndrome-new-insights-from-a-4d-flow-cardiovascular-magnetic-resonance-multi-year-follow-up-study
#8
Julia Geiger, Daniel Hirtler, Kristina Gottfried, Ozair Rahman, Emilie Bollache, Alex J Barker, Michael Markl, Brigitte Stiller
BACKGROUND: The aim of this 4D flow cardiovascular magnetic resonance (CMR) follow-up study was to investigate longitudinal changes in aortic hemodynamics in adolescent patients with Marfan syndrome (MFS). METHODS: 4D flow CMR for the assessment of in-vivo 3D blood flow with full coverage of the thoracic aorta was performed twice (baseline scan t1/follow-up scan t2) in 19 adolescent MFS patients (age at t1: 12.7 ± 3.6 years, t2: 16.2 ± 4.3 years) with a mean follow-up duration of 3...
March 22, 2017: Journal of Cardiovascular Magnetic Resonance
https://www.readbyqxmd.com/read/28326543/animal-models-for-studying-motor-axon-terminal-paralysis-and-recovery
#9
REVIEW
Michela Rigoni, Cesare Montecucco
An extraordinary property of the peripheral nervous system is that nerve terminals can regenerate after damage caused by different physical, chemical, or biological pathogens. Regeneration is the result of a complex and ill-known interplay among the nerve, the glia, the muscle, the basal lamina and, in some cases, the immune system. This phenomenon has been studied using different injury models mainly in rodents, particularly in mice, where a lesion can be produced in a chosen anatomical area. These approaches differ significantly among them for the nature of the lesion and the final outcomes...
March 21, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28326156/porphyromonas-gingivalis-is-the-most-abundant-species-detected-in-coronary-and-femoral-arteries
#10
J-L C Mougeot, C B Stevens, B J Paster, M T Brennan, P B Lockhart, F K B Mougeot
An association between oral bacteria and atherosclerosis has been postulated. A limited number of studies have used 16S RNA gene sequencing-based metagenomics approaches to identify bacteria at the species level from atherosclerotic plaques in arterial walls. The objective of this study was to establish detailed oral microbiome profiles, at both genus and species level, of clinically healthy coronary and femoral artery tissues from patients with atherosclerosis. Tissue specimens were taken from clinically non-atherosclerotic areas of coronary or femoral arteries used for attachment of bypass grafts in 42 patients with atherosclerotic cardiovascular disease...
2017: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/28325132/physical-symptoms-and-working-performance-in-female-breast-cancer-survivors-a-systematic-review
#11
Kamilla Zomkowski, Bruna Cruz de Souza, Fabiana Pinheiro da Silva, Géssica Maria Moreira, Natália de Souza Cunha, Fabiana Flores Sperandio
PURPOSE: The aim of this systematic review was to summarize and systematize the information about physical symptoms and its relation with work activity on female Breast Cancer Survivors (BCS). METHODS: A systematic search was performed on the databases MEDLINE/PubMed (via National Library of Medicine), SCOPUS (Elsevier), Web of Science (Thomson Reuters Scientific) and CINAHL with full text (EBSCO), including papers about physical impairments experienced by female workers who have had breast cancer...
March 21, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28324191/planarian-homolog-of-puromycin-sensitive-aminopeptidase-djpsa-is-required-for-brain-regeneration
#12
Suge Wu, Bin Liu, Zuoqing Yuan, Xiufang Zhang, Hong Liu, Qiuxiang Pang, Bosheng Zhao
Puromycin-sensitive aminopeptidase (PSA) belongs to the M1 zinc metallopeptidase family. PSA is the most abundant aminopeptidase in the brain and plays a role in the metabolism of neuropeptides including those involved in neurodegeneration. A cDNA DjPsa was identified from the planarian Dugesia japonica cDNA library. It contains a 639-bp open reading frame corresponding to a deduced protein of 212 amino acids. Whole mount in situ hybridization revealed that DjPsa is expressed in the brain and ventral nerve cords of intact and regenerating animals and demonstrates a tissue and stage-specific expression pattern of DjPsa in developing embryos and larvae...
June 2017: Invertebrate Neuroscience: IN
https://www.readbyqxmd.com/read/28322766/characterization-of-a-molt-related-myostatin-gene-fmmstn-from-the-banana-shrimp-fenneropenaeus-merguiensis
#13
Rui Qun Zhuo, Ting Ting Zhou, Shi Ping Yang, Siuming Francis Chan
Myostatin is an important member of the Transforming Growth Factor (TGF) family that functions to regulate muscle growth in animals. In this study, the myostatin gene (FmMstn) and two slightly different (short and long forms) cDNAs of the banana shrimp Fenneropenaeus merguiensis were cloned and characterized. Similar to Mstn gene of the scallop, fish and mammal, FmMstn gene consists of 3 exons and 2 introns. The 2 kb upstream promoter region of the FmMstn gene consists of putative response elements for myocyte enhancing factor (MEF2) and E-box factors...
March 17, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28322732/glaucoma-patient-reported-concerns-and-associated-factors
#14
Rachel S Mogil, Andrew Tirsi, Jung Min Lee, Celso Tello, Sung Chul Park
PURPOSE: To assess the character and degree of concerns of glaucoma patients and identify demographic/clinical factors affecting the concerns. DESIGN: Prospective cross-sectional study. METHODS: A questionnaire that addressed patients' concerns was administered to consecutive glaucoma patients. Severity of concern was scored with a scale of 0 to 5 in order of increasing severity. Age, gender, intraocular pressure, visual field (VF) mean deviation (MD), number of anti-glaucoma medications, history of glaucoma surgery, and employment status were recorded...
March 16, 2017: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/28321845/hidradenitis-suppurativa-gains-increasing-interest-on-world-wide-web-a-source-for-patient-information
#15
Schapoor Hessam, Johannes Salem, Falk G Bechara, Axel Haferkamp, Axel Heidenreich, Pia Paffenholz, Michael Sand, Igor Tsaur, Hendrik Borgmann
BACKGROUND: Gathering health information from Internet websites is increasingly utilized by patients. No data exist about hidradenitis suppurativa (HS)-related online health information. Thus, we aimed to study the quality, popularity, readability, and timeliness of the most frequented websites on HS. METHODS: Google Trends was used to evaluate the public interest in HS. An Internet search on Google was performed for the terms "hidradenitis suppurativa," "acne inversa," and "Verneuil's disease...
March 21, 2017: International Journal of Dermatology
https://www.readbyqxmd.com/read/28321364/effect-of-method-of-deduplication-on-estimation-of-differential-gene-expression-using-rna-seq
#16
Anna V Klepikova, Artem S Kasianov, Mikhail S Chesnokov, Natalia L Lazarevich, Aleksey A Penin, Maria Logacheva
BACKGROUND: RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. RESULTS: To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI)...
2017: PeerJ
https://www.readbyqxmd.com/read/28319201/recommendations-for-patient-engagement-in-guideline-development-panels-a-qualitative-focus-group-study-of-guideline-na%C3%A3-ve-patients
#17
Melissa J Armstrong, C Daniel Mullins, Gary S Gronseth, Anna R Gagliardi
BACKGROUND: Patient and consumer engagement in clinical practice guideline development is internationally advocated, but limited research explores mechanisms for successful engagement. OBJECTIVE: To investigate the perspectives of potential patient/consumer guideline representatives on topics pertaining to engagement including guideline development group composition and barriers to and facilitators of engagement. SETTING AND PARTICIPANTS: Participants were guideline-naïve volunteers for programs designed to link community members to academic research with diverse ages, gender, race, and degrees of experience interacting with health care professionals...
2017: PloS One
https://www.readbyqxmd.com/read/28318817/clinical-and-mutational-characteristics-of-duchenne-muscular-dystrophy-patients-based-on-a-comprehensive-database-in-south-china
#18
Dan-Ni Wang, Zhi-Qiang Wang, Lei Yan, Jin He, Min-Ting Lin, Wan-Jin Chen, Ning Wang
The development of clinical trials for Duchenne muscular dystrophy (DMD) in China faces many challenges due to limited information about epidemiological data, natural history and clinical management. To provide these detailed data, we developed a comprehensive database based on registered DMD patients from South China and analysed their clinical and mutational characteristics. The database included DMD registrants confirmed by clinical presentation, family history, genetic detection, prognostic outcome, and/or muscle biopsy...
February 21, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28318503/sociotechnical-systems-as-a-framework-for-regulatory-system-design-and-evaluation-using-work-domain-analysis-to-examine-a-new-regulatory-system
#19
Tony Carden, Natassia Goode, Gemma J M Read, Paul M Salmon
Like most work systems, the domain of adventure activities has seen a series of serious incidents and subsequent calls to improve regulation. Safety regulation systems aim to promote safety and reduce accidents. However, there is scant evidence they have led to improved safety outcomes. In fact there is some evidence that the poor integration of regulatory system components has led to adverse safety outcomes in some contexts. Despite this, there is an absence of methods for evaluating regulatory and compliance systems...
March 15, 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28317510/predictors-and-outcomes-of-twelve-step-sponsorship-of-stimulant-users-secondary-analyses-of-a-multisite-randomized-clinical-trial
#20
Dennis C Wendt, Kevin A Hallgren, Dennis C Daley, Dennis M Donovan
OBJECTIVE: This secondary data analysis explored predictors and outcomes of having a 12-step sponsor among individuals receiving treatment for stimulant use disorders, inclusive of four types of 12-step groups (Narcotics Anonymous, Alcoholics Anonymous, Cocaine Anonymous, and Crystal Meth Anonymous). METHOD: For a multisite randomized clinical trial, participants (N = 471; 59% women) were recruited among adult patients in 10 U.S. community treatment programs. Participants were randomized into treatment as usual (TAU) or a 12-step facilitation (TSF) intervention: Stimulant Abuser Groups to Engage in 12-Step (STAGE-12)...
March 2017: Journal of Studies on Alcohol and Drugs
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