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https://www.readbyqxmd.com/read/28434198/eukaryotic-diversity-in-late-pleistocene-marine-sediments-around-a-shallow-methane-hydrate-deposit-in-the-japan-sea
#1
M Kouduka, A S Tanabe, S Yamamoto, K Yanagawa, Y Nakamura, F Akiba, H Tomaru, H Toju, Y Suzuki
Marine sediments contain eukaryotic DNA deposited from overlying water columns. However, a large proportion of deposited eukaryotic DNA is aerobically biodegraded in shallow marine sediments. Cold seep sediments are often anaerobic near the sediment-water interface, so eukaryotic DNA in such sediments is expected to be preserved. We investigated deeply buried marine sediments in the Japan Sea, where a methane hydrate deposit is associated with cold seeps. Quantitative PCR analysis revealed the reproducible recovery of eukaryotic DNA in marine sediments at depths up to 31...
April 23, 2017: Geobiology
https://www.readbyqxmd.com/read/28434085/exploring-the-oral-microflora-of-preschool-children
#2
Wen Ren, Qun Zhang, Xuenan Liu, Shuguo Zheng, Lili Ma, Feng Chen, Tao Xu, Baohua Xu
The oral cavity is one of the most important and complicated habitats in our body and supports diverse microbial communities. In this study, we aimed to determine the bacterial diversity and composition of various oral micro-niches. Samples were collected from supragingival plaque, saliva, and tongue coating from 10 preschool children (30 samples total). 16S rRNA gene pyrosequencing dataset generated 314,639 clean reads with an average of 10,488 ± 2,787 reads per sample. The phyla Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria were predominant, accounting for more than 90% of the total sequences...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28433079/utilization-of-whole-exome-next-generation-sequencing-variant-read-frequency-for-detection-of-lesion-specific-somatic-loss-of-heterozygosity-in-a-neurofibromatosis-type-1-cohort-with-tibial-pseudarthrosis
#3
Rebecca L Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A Stevenson, Rong Mao
A subset of neurofibromatosis type 1 patients develop tibial dysplasia, which can lead to pseudarthrosis. The tissue from the tibial pseudarthrosis region commonly has a somatic second hit in NF1: single-nucleotide variants, small deletions, or loss of heterozygosity (LOH). We used exome next-generation sequencing (NGS) variant frequency data (allelic imbalance analysis) to detect somatic LOH in pseudarthrosis tissue from three individuals with clinically and diagnostically confirmed neurofibromatosis type 1, and verified the results with microarray...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28432600/potentially-inappropriate-antihypertensive-prescriptions-to-elderly-patients-results-of-a-prospective-observational-study
#4
Paola H Ponte Márquez, Olga H Torres, Anonio San-José, Xavier Vidal, Antonia Agustí, Francesc Formiga, Alfonso López-Soto, Nieves Ramírez-Duque, Antonio Fernández-Moyano, Juana Garcia-Moreno, Juan A Arroyo, Domingo Ruiz
INTRODUCTION: Previous studies of antihypertensive treatment of older patients have focused on blood pressure control, cardiovascular risk or adherence, whereas data on inappropriate antihypertensive prescriptions to older patients are scarce. OBJECTIVES: The aim of the study was to assess inappropriate antihypertensive prescriptions to older patients. METHODS: An observational, prospective multicentric study was conducted to assess potentially inappropriate prescription of antihypertensive drugs, in patients aged 75 years and older with arterial hypertension (HTN), in the month prior to hospital admission, using four instruments: Beers, Screening Tool of Older Person's Prescriptions (STOPP), Screening Tool to Alert Doctors to the Right Treatment (START) and Assessing Care of Vulnerable Elders 3 (ACOVE-3)...
April 21, 2017: Drugs & Aging
https://www.readbyqxmd.com/read/28432563/complete-sequences-of-the-rna-1-and-rna-2-segments-of-chronic-bee-paralysis-virus-strain-cbpv-bj-detected-in-china
#5
Beibei Li, Shuai Deng, Dahe Yang, Chunsheng Hou, Qingyun Diao
Chronic bee paralysis virus (CBPV) is an important viral pathogen that affects adult bees. Although several CBPV strains have been reported, little information has been obtained from China. In this study, two major segments of the CBPV Chinese isolate CBPV-BJ, RNA 1 and RNA 2, were determined to be 3657 and 2267 nucleotides (nt) in length, respectively. RNA 1 and RNA 2 contained three and four open reading frames (ORFs), respectively, which agreed with known reference strains (EU122229 and EU122230). The RNA 1 had 98% nucleotide sequence identity to a known Chinese strain (KU950353), and RNA 2 had 97% nucleotide sequence identity to another Chinese strain (KU950354)...
April 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28432541/genome-characteristics-of-the-proteorhodopsin-containing-marine-flavobacterium-polaribacter-dokdonensis-dsw-5
#6
Kiyoung Yoon, Ju Yeon Song, Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim
Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28432095/mushroom-emergence-detected-by-combining-spore-trapping-with-molecular-techniques
#7
Carles Castaño, Jonàs Oliva, Juan Martínez de Aragón, Josu G Alday, Javier Parladé, Joan Pera, José Antonio Bonet
Obtaining reliable and representative mushroom production data requires time-consuming sampling schemes. In this paper, we assessed a simple methodology to detect mushroom emergence by trapping the fungal spores of the fruiting body community in plots where mushroom production was determined weekly. We compared the performance of filter paper traps with that of funnel traps and combined these spore trapping methods with species-specific quantitative real-time PCR and Illumina MiSeq to determine the spore abundance...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431310/characterization-of-bacterial-communities-of-donkey-milk-by-high-throughput-sequencing
#8
Maria de Los Dolores Soto Del Rio, Alessandra Dalmasso, Tiziana Civera, Maria Teresa Bottero
The interest in donkey milk (DM) is growing because of its functional properties and nutritional value, especially for children with allergies and food intolerances. However, most of the available reports of DM microbiota are based on culture-dependent methods to investigate food safety issues and the presence of lactic acid bacteria (LAB). The aim of this study was to determine the composition of DM bacterial communities using a high-throughput sequencing (HTS) approach. Bulk milk samples from Italian donkey dairy farms from two consecutive years were analysed using the MiSeq Illumina platform...
March 30, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28430335/reading-ability-and-quality-of-life-in-stargardt-disease
#9
Vittoria Murro, Andrea Sodi, Giovanni Giacomelli, Dario P Mucciolo, Monica Pennino, Gianni Virgili, Stanislao Rizzo
PURPOSE: To study the reading performance of patients with Stargardt disease (STGD) and the relationship between clinical vision measurements and vision-related quality of life (VRQOL). METHODS: We studied both eyes of 16 patients with STGD. Each patient was examined for best-corrected visual acuity (Early Treatment Diabetic Retinopathy Study [ETDRS]), reading ability (MNREAD and REX charts), contrast sensitivity (Pelli-Robson charts), fixation study (MP1 microperimeter), and VRQOL (25-item National Eye Institute Visual Function Questionnaire [NEI VFQ-25])...
April 14, 2017: European Journal of Ophthalmology
https://www.readbyqxmd.com/read/28429648/-the-influence-of-scene-context-on-parafoveal-processing-of-objects
#10
Monica S Castelhano, Effie J Pereira
Many studies in reading have shown the enhancing effect of context on the processing of a word before it is directly fixated (parafoveal processing of words; Balota et al., 1985; Balota & Rayner, 1983; Ehrlich & Rayner, 1981). Here, we examined whether scene context influences the parafoveal processing of objects and enhances the extraction of object information. Using a modified boundary paradigm (Rayner, 1975), the Dot-Boundary paradigm, participants fixated on a suddenly-onsetting cue before the preview object would onset 4° away...
April 21, 2017: Quarterly Journal of Experimental Psychology: QJEP
https://www.readbyqxmd.com/read/28429584/dna-metabarcoding-of-unfractionated-water-samples-relates-phyto-zoo-and-bacterioplankton-dynamics-and-reveals-a-single-taxon-bacterial-bloom
#11
Christian Wurzbacher, Katrin Attermeyer, Marie Therese Kettner, Clara Flintrop, Norman Warthmann, Sabine Hilt, Hans-Peter Grossart, Michael T Monaghan
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring...
April 21, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28429252/analysis-of-global-gene-expression-profiles-during-the-flowering-initiation-process-of-lilium%C3%A2-%C3%A3-%C3%A2-formolongi
#12
Yu-Fan Li, Ming-Fang Zhang, Meng Zhang, Gui-Xia Jia
The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70...
April 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28429088/an-snp-panel-for-the-analysis-of-paternally-inherited-alleles-in-maternal-plasma-using-ion-torrent-pgm
#13
Donggui Yang, Hao Liang, Shaobin Lin, Qing Li, Xiaoyan Ma, Jun Gao, Hongyu Sun, Qingqing Chen, Jianzhu Wu, Xueling Ou
Researchers have sought to develop an effective protocol for paternity analysis using cell-free DNA (cfDNA) in maternal plasma. The use of massively parallel sequencing (MPS) technology for SNP testing is attractive because of its high-throughput capacity and resolution to single-base precision. In this study, we designed a customized SNP panel for cfDNA sequencing that includes 720 short amplicons (< 140 bp) targeting SNPs on the autosome and Y chromosome. The systemic performance was evaluated using the Ion Torrent PGM, indicating balanced coverage among most of the included loci, except for 78 poorly performing SNPs that were observed to have an inconsistent allele balance, lower coverage reads or high background signals...
April 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28428172/how-are-non-numerical-prognostic-statements-interpreted-and-are-they-subject-to-positive-bias
#14
Anne Moyer, Samantha Siess, Sumeet Bhinder
OBJECTIVES: Frank, clear communication with family members of terminally ill or incapacitated patients has important implications for well-being, satisfaction with care and sound decision-making. However, numerical prognostic statements, particularly more negative ones, have been found to be interpreted in a positively biased manner. Less precise non-numerical statements, preferred by physicians, and particularly statements using threatening terms (dying vs surviving) may be even more subject to such biases...
April 20, 2017: BMJ Supportive & Palliative Care
https://www.readbyqxmd.com/read/28428036/giantcell-tumor-of-tendon-sheath-open-surgery-or-arthroscopic-synovectomy-a-systematic-review-of-the-literature
#15
REVIEW
Thibaut Noailles, Kevin Brulefert, Sylvain Briand, Pierre Marie Longis, Kevin Andrieu, Antoine Chalopin, François Gouin
PURPOSE: Giantcell tumor of tendon sheath(GCTTS)formelyknowned as pigmented villonodular synovitis (PVNS) is a benign, locally aggressive, proliferative disorder of the synovium involving a joint, bursa, or tendon sheath. Treatment ofGCTTSinvolves early surgical resection to limit articular destruction and the risk of recurrence. Synovectomy remains the treatment of choice forGCTTSbut without clear consensus to make an open or arthroscopic synovectomy andno certainty on the responsibility of surgery in the evolution towards the degenerative osteoarthritis...
April 17, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28427935/the-manifolded-dynamics-of-hiv-1-transmission-in-northern-alberta-a-combined-analysis-of-virus-genetic-and-public-health-data
#16
B Vrancken, D Adachi, M Benedet, A Singh, R Read, S Shafran, G D Taylor, S Houston, K Simmonds, S Plitt, C Sikora, P Lemey, C L Charlton, J W Tang
Molecular epidemiology has become a key tool for tracking infectious disease epidemics. Here, the spread of the most prevalent HIV-1 subtypes in Northern Alberta, Canada, was characterized with a Bayesian phylogenetic approach using 1146 HIV-1 pol sequences collected between 2007 and 2013 for routine clinical management purposes. Available patient metadata were qualitatively interpreted and correlated with onwards transmission using Fisher exact tests and logistic regression. Most infections were from subtypes A (n=36), B (n=815) and C (n=211)...
April 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28427933/high-molecular-weight-genomic-dna-mini-prep-for-filamentous-fungi
#17
Mi-Kyung Lee, Hee-Soo Park, Kap-Hoon Han, Seung-Beom Hong, Jae-Hyuk Yu
Purification of high quality genomic DNA (gDNA) from filamentous fungi suitable for whole genome sequencing has previously involved many steps. Here, we report a simple and easy-to-follow mini-preparation protocol for high molecular weight (∼20 kb) gDNA from filamentous fungi including Aspergillus and Eurotium. This comprehensive protocol includes graphic step-by-step instructions for inoculation, homogenization, and purification of gDNA. The most critical step is a thorough 3 ∼ 5 min homogenization of the freeze-dried mycelium using a motorized hand-held homogenizer with a mini spatula inserted...
April 18, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28427066/intravitreal-ranibizumab-in-diabetic-macular-edema-long-term-outcomes
#18
Ilaria Zucchiatti, Francesco Bandello
Intravitreal ranibizumab (RBZ) has been shown in multiple randomized clinical trials to be a valuable treatment for diabetic macular edema (DME), promoting a significant improvement in best-corrected visual acuity (BCVA) and in anatomic outcomes. Compared to sham (RISE and RIDE studies), RBZ rapidly and sustainably improved BCVA and decreased macular edema at 2 years, reducing the risk of further vision loss, with low rates of local or systemic side effects. Compared to macular laser photocoagulation (READ-2 study), RBZ provided a greater improvement in BCVA and regression in foveal thickness, but required a higher number of injections compared to patients treated with both RBZ and laser...
2017: Developments in Ophthalmology
https://www.readbyqxmd.com/read/28426889/concurrent-and-longitudinal-predictors-of-reading-for-deaf-and-hearing-children-in-primary-school
#19
Margaret Harris, Emmanouela Terlektsi, Fiona Elizabeth Kyle
Forty-one children with severe-profound prelingual hearing loss were assessed on single word reading, reading comprehension, English vocabulary, phonological awareness and speechreading at three time points, 1 year apart (T1-T3). Their progress was compared with that of a group of hearing children of similar nonverbal IQ, initially reading at the same level. Single word reading improved at each assessment point for the deaf children but there was no growth in reading comprehension from T2 to T3. There were no differences between children with cochlear implants and those with hearing aids on either reading measure but orally educated children had higher scores than children who signed in the classroom...
April 1, 2017: Journal of Deaf Studies and Deaf Education
https://www.readbyqxmd.com/read/28426749/molecular-characterization-tissue-tropism-and-genetic-variability-of-the-novel-mupapillomavirus-type-hpv204-and-phylogenetically-related-types-hpv1-and-hpv63
#20
Anja Šterbenc, Lea Hošnjak, Diego Chouhy, Elisa M Bolatti, Anja Oštrbenk, Katja Seme, Boštjan J Kocjan, Boštjan Luzar, Adriana A Giri, Mario Poljak
HPV204 is the only newly identified Mupapillomavirus (Mu-PV) type in more than a decade. To comprehensively characterize HPV204, we performed a detailed molecular analysis of the viral genome and evaluated its clinical relevance in comparison to the other Mu-PVs, HPV1 and HPV63. The 7,227-bp long genome of HPV204 exhibits typical genomic organization of Mu-PVs with eight open reading frames (ORFs) (E6, E7, E1, E2, E8, E4, L2, and L1). We developed three type-specific quantitative real-time PCRs and used them to test a representative collection (n = 1,006) of various HPV-associated benign and malignant neoplasms, as well as samples of clinically normal cutaneous, mucosal, and mucocutaneous origins...
2017: PloS One
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