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https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#1
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28430877/the-accessible-chromatin-landscape-during-conversion-of-human-embryonic-stem-cells-to-trophoblast-by-bmp4
#2
Yajun Liu, Dewu Ding, Hongde Liu, Xiao Sun
Human embryonic stem cells (hESC) exposed to the growth factor bone morphogenic protein 4 (BMP4) in the absence of FGF2 have been used as a model to study the development of placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. In this study, we used the public available chromatin accessibility data of hESC H1 cells and BMP4-induced trophoblast (TB)cell lines to identify DNase I hypersensitive sites (DHSs) in the two cell lines, as well as the transcription factor binding sites within the DHSs...
April 18, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28430780/the-importance-of-standardization-for-biodiversity-comparisons-a-case-study-using-autonomous-reef-monitoring-structures-arms-and-metabarcoding-to-measure-cryptic-diversity-on-mo-orea-coral-reefs-french-polynesia
#3
Emma Ransome, Jonathan B Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G Collins, Christopher P Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data...
2017: PloS One
https://www.readbyqxmd.com/read/28430181/supervised-learning-and-dimension-reduction-techniques-for-quantification-of-retinal-fluid-in-optical-coherence-tomography-images
#4
A Breger, M Ehler, H Bogunovic, S M Waldstein, A-M Philip, U Schmidt-Erfurth, B S Gerendas
PurposeThe purpose of the present study is to develop fast automated quantification of retinal fluid in optical coherence tomography (OCT) image sets.MethodsWe developed an image analysis pipeline tailored towards OCT images that consists of five steps for binary retinal fluid segmentation. The method is based on feature extraction, pre-segmention, dimension reduction procedures, and supervised learning tools.ResultsFluid identification using our pipeline was tested on two separate patient groups: one associated to neovascular age-related macular degeneration, the other showing diabetic macular edema...
April 21, 2017: Eye
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#5
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
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
#6
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/28426300/overview-of-asian-american-data-collection-release-and-analysis-national-health-and-nutrition-examination-survey-2011-2018
#7
Ryne Paulose-Ram, Vicki Burt, Lisa Broitman, Namanjeet Ahluwalia
Data System. The National Health and Nutrition Examination Survey (NHANES), conducted by the National Center for Health Statistics, is a cross-sectional survey on the health and nutritional status of US adults and children. Data Collection/Processing. A complex, multistage probability design is used to select a sample representative of the US civilian, noninstitutionalized population. NHANES includes in-home interviews, physical examinations, and biospecimen collection. About 5000 persons are examined annually...
April 20, 2017: American Journal of Public Health
https://www.readbyqxmd.com/read/28425740/-healthier-than-thou-practicing-what-you-preach-backfires-by-increasing-anticipated-devaluation-correction-to-howe-and-monin-2017
#8
(no author information available yet)
Reports an error in "Healthier Than Thou? "Practicing What You Preach" Backfires by Increasing Anticipated Devaluation" by Lauren C. Howe and Benoît Monin (Journal of Personality and Social Psychology, Advanced Online Publication, Feb 27, 2017, np). In the article, the beginning phrase of the second paragraph of the Internal Meta-Analysis of Studies 3 Through 5 section is incorrect. It should instead begin as follows: Across the three studies. The Monin et al. (2014) reference in both the References list and in text is included in error...
May 2017: Journal of Personality and Social Psychology
https://www.readbyqxmd.com/read/28424385/-korbinian-brodmann-s-scientific-profile-and-academic-works
#9
Mitsuru Kawamura
Brodmann's map is one of the best known maps of the human cerebral cortex. However, Korbinian Brodmann's 1909 monograph, containing the first map, has not been widely read by neurologists. Following the publication of the first map, Brodmann reproduced the map in 1910, and again in 1914, with several important differences. The latter map is also characterized by the exclusion of Brodmann area numbers, "12-16, and 48-51;" contrastingry numbers "1-52" have been described in the animal brain. Here, we provide a detailed explanation of the versions of Brodmann's maps, and review his academic profile and works...
April 2017: Brain and Nerve, Shinkei Kenkyū No Shinpo
https://www.readbyqxmd.com/read/28423514/mitotic-read-out-genes-confer-poor-outcome-in-luminal-a-breast-cancer-tumors
#10
Javier Pérez-Peña, Ana Alcaraz-Sanabria, Cristina Nieto-Jiménez, Raquel Páez, Verónica Corrales-Sánchez, Leticia Serrano-Oviedo, Vikram B Wali, Gauri A Patwardhan, Eitan Amir, Balázs Győrffy, Atanasio Pandiella, Alberto Ocaña
Luminal breast tumors have been classified into A and B subgroups, with the luminal A being associated with a more favorable clinical outcome. Unfortunately, luminal A tumors do not have a universally good prognosis. We used transcriptomic analyses using public datasets to evaluate the differential expression between normal breast tissue and breast cancer, focusing on upregulated genes included in cell cycle function. Association of selected genes with relapse free survival (RFS) and overall survival (OS) was performed using the KM Plotter Online Tool (http://www...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421378/transcriptome-based-identification-of-the-desiccation-response-genes-in-marine-red-algae-pyropia-tenera-rhodophyta-and-enhancement-of-abiotic-stress-tolerance-by-ptdrg2-in-chlamydomonas
#11
Sungoh Im, Ha-Nul Lee, Hyun Shin Jung, Sunghwan Yang, Eun-Jeong Park, Mi Sook Hwang, Won-Joong Jeong, Dong-Woog Choi
Pyropia tenera (Kjellman) are marine red algae that grow in the intertidal zone and lose more than 90% of water during hibernal low tides every day. In order to identify the desiccation response gene (DRG) in P. tenera, we generated 1,444,210 transcriptome sequences using the 454-FLX platform from the gametophyte under control and desiccation conditions. De novo assembly of the transcriptome reads generated 13,170 contigs, covering about 12 Mbp. We selected 1160 differentially expressed genes (DEGs) in response to desiccation stress based on reads per kilobase per million reads (RPKM) expression values...
April 18, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28419659/making-visible-the-politics-and-ethics-of-alcohol-policy-research
#12
David Moore
Although research on alcohol policy has produced a huge international literature, alcohol research and policy itself-its cultural assumptions, methods, politics and ethics-has rarely been subject to critical analysis. In this article, I provide an appreciative review of an exception to this trend: Joseph Gusfield's 1981 classic, The Culture of Public Problems: Drinking-Driving and the Symbolic Order. I first outline Gusfield's argument that the 'problem of drinking-driving' is constructed as a 'drama of individualism' centring on the 'killer drunk'...
April 16, 2017: Addiction
https://www.readbyqxmd.com/read/28419381/enhancing-faba-bean-vicia-faba-l-genome-resources
#13
James W Cooper, Michael H Wilson, Martijn F L Derks, Sandra Smit, Karl J Kunert, Christopher Cullis, Christine H Foyer
Grain legume improvement is currently impeded by a lack of genomic resources. The paucity of genome information for faba bean can be attributed to the intrinsic difficulties of assembling/annotating its giant (~13 Gb) genome. In order to address this challenge, RNA-sequencing analysis was performed on faba bean (cv. Wizard) leaves. Read alignment to the faba bean reference transcriptome identified 16 300 high quality unigenes. In addition, Illumina paired-end sequencing was used to establish a baseline for genomic information assembly...
April 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28416714/jinglebells-a-repository-of-immune-related-single-cell-rna-sequencing-datasets
#14
Hadas Ner-Gaon, Ariel Melchior, Nili Golan, Yael Ben-Haim, Tal Shay
Recent advances in single-cell RNA-sequencing (scRNA-seq) technology increase the understanding of immune differentiation and activation processes, as well as the heterogeneity of immune cell types. Although the number of available immune-related scRNA-seq datasets increases rapidly, their large size and various formats render them hard for the wider immunology community to use, and read-level data are practically inaccessible to the non-computational immunologist. To facilitate datasets reuse, we created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level (http://jinglebells...
May 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28414882/the-effect-of-a-faith-community-nurse-network-and-public-health-collaboration-on-hypertension-prevention-and-control
#15
Jennifer Cooper, Wendy Zimmerman
BACKGROUND: As part of the Association of State and Territorial Health Official's Million Hearts State Learning Collaborative in 2014 and 2015, Washington County, Maryland formed a collaboration between the local health department, health system and faith community nurse network to address the undiagnosed and uncontrolled hypertension in the county. OBJECTIVES: Data were analyzed to determine the effect of a faith community nursing intervention of teaching blood pressure self-monitoring and coaching blood pressure and lifestyle changes in the at-risk and hypertensive population...
April 17, 2017: Public Health Nursing
https://www.readbyqxmd.com/read/28414628/fried-green-tomatoes-and-the-color-purple-a-case-study-in-lesbian-friendship-and-cultural-controversy
#16
Kristen Proehl
Published in the 1980s, Fannie Flagg's Fried Green Tomatoes at the Whistle Stop Café and Alice Walker's The Color Purple are lesbian coming-of-age narratives that share a great deal in common in terms of their thematic content, publication histories, and cultural afterlives. In both novels, female friendships are shaped by patriarchal violence and develop in the context of the rural, segregated, early twentieth-century U.S. South. But the two novels also diverge in significant ways, as differences in race, gender, class, and sexuality shape their protagonists' experiences of love and friendship...
April 17, 2017: Journal of Lesbian Studies
https://www.readbyqxmd.com/read/28413162/whole-genome-sequence-of-the-metastatic-pc3-and-lncap-human-prostate-cancer-cell-lines
#17
Inge Seim, Penny L Jeffery, Patrick B Thomas, Colleen C Nelson, Lisa K Chopin
The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ~70X coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular loss of stop codon events)...
April 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28412964/mesh-now-automatic-mesh-indexing-at-pubmed-scale-via-learning-to-rank
#18
Yuqing Mao, Zhiyong Lu
BACKGROUND: MeSH indexing is the task of assigning relevant MeSH terms based on a manual reading of scholarly publications by human indexers. The task is highly important for improving literature retrieval and many other scientific investigations in biomedical research. Unfortunately, given its manual nature, the process of MeSH indexing is both time-consuming (new articles are not immediately indexed until 2 or 3 months later) and costly (approximately ten dollars per article). In response, automatic indexing by computers has been previously proposed and attempted but remains challenging...
April 17, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28406933/transcriptomic-profiling-of-taproot-growth-and-sucrose-accumulation-in-sugar-beet-beta-vulgaris-l-at-different-developmental-stages
#19
Yong-Feng Zhang, Guo-Long Li, Xue-Feng Wang, Ya-Qing Sun, Shao-Ying Zhang
In sugar beet (Beta vulgaris L.), taproot weight and sucrose content are the important determinants of yield and quality. However, high yield and low sucrose content are two tightly bound agronomic traits. The advances in next-generation sequencing technology and the publication of sugar beet genome have provided a method for the study of molecular mechanism underlying the regulation of these two agronomic traits. In this work, we performed comparative transcriptomic analyses in the high taproot yield cultivar SD13829 and the high sucrose content cultivar BS02 at five developmental stages...
2017: PloS One
https://www.readbyqxmd.com/read/28402545/orio-online-resource-for-integrative-omics-a-web-based-platform-for-rapid-integration-of-next-generation-sequencing-data
#20
Christopher A Lavender, Andrew J Shapiro, Adam B Burkholder, Brian D Bennett, Karen Adelman, David C Fargo
Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data...
April 11, 2017: Nucleic Acids Research
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