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https://www.readbyqxmd.com/read/27909578/advances-in-analyzing-rna-diversity-in-eukaryotic-transcriptomes-peering-through-the-omics-lens
#1
REVIEW
Sushant Bangru, Auinash Kalsotra
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants...
2016: F1000Research
https://www.readbyqxmd.com/read/27909577/advances-in-the-understanding-and-clinical-management-of-mastocytosis-and-clonal-mast-cell-activation-syndromes
#2
REVIEW
David González-de-Olano, Almudena Matito, Alberto Orfao, Luis Escribano
Clonal mast cell activation syndromes and indolent systemic mastocytosis without skin involvement are two emerging entities that sometimes might be clinically difficult to distinguish, and they involve a great challenge for the physician from both a diagnostic and a therapeutic point of view. Furthermore, final diagnosis of both entities requires a bone marrow study; it is recommended that this be done in reference centers. In this article, we address the current consensus and guidelines for the suspicion, diagnosis, classification, treatment, and management of these two entities...
2016: F1000Research
https://www.readbyqxmd.com/read/27909576/zika-antiviral-chemotherapy-identification-of-drugs-and-promising-starting-points-for-drug-discovery-from-an-fda-approved-library
#3
Bruno S Pascoalino, Gilles Courtemanche, Marli T Cordeiro, Laura H V G Gil, Lucio Freitas-Junior
Background The recent epidemics of Zika virus (ZIKV) implicated it as the cause of serious and potentially lethal congenital conditions such microcephaly and other central nervous system defects, as well as the development of the Guillain-Barré syndrome in otherwise healthy patients. Recent findings showed that anti-Dengue antibodies are capable of amplifying ZIKV infection by a mechanism similar to antibody-dependent enhancement, increasing the severity of the disease. This scenario becomes potentially catastrophic when the global burden of Dengue and the advent of the newly approved anti-Dengue vaccines in the near future are taken into account...
2016: F1000Research
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#4
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27909574/characterization-of-5-2-18-f-fluoroethoxy-l-tryptophan-for-pet-imaging-of-the-pancreas
#5
Ahmed Abbas, Christine Beamish, Rebecca McGirr, John Demarco, Neil Cockburn, Dawid Krokowski, Ting-Yim Lee, Michael Kovacs, Maria Hatzoglou, Savita Dhanvantari
Purpose: In diabetes, pancreatic beta cell mass declines significantly prior to onset of fasting hyperglycemia. This decline may be due to endoplasmic reticulum (ER) stress, and the system L amino acid transporter LAT1 may be a biomarker of this process. In this study, we used 5-(2- (18)F-fluoroethoxy)-L-tryptophan ( (18)F-L-FEHTP) to target LAT1 as a potential biomarker of beta cell function in diabetes. Procedures: Uptake of (18)F-L-FEHTP was determined in wild-type C57BL/6 mice by ex vivo biodistribution...
2016: F1000Research
https://www.readbyqxmd.com/read/27909573/how-to-put-plant-root-uptake-into-a-soil-water-flow-model-a-documentation-with-complete-computer-code
#6
Xuejun Dong
The need for improved crop water use efficiency calls for flexible modeling platforms to implement new ideas in plant root uptake and its regulation mechanisms. This paper documents the details of modifying a soil infiltration and redistribution model to include (a) dynamic root growth, (b) non-uniform root distribution and water uptake, (c) the effect of water stress on plant water uptake, and (d) soil evaporation. The paper also demonstrates strategies of using the modified model to simulate soil water dynamics and plant transpiration considering different sensitivity of plants to soil dryness and different mechanisms of root water uptake...
2016: F1000Research
https://www.readbyqxmd.com/read/27853529/current-concepts-and-dilemmas-in-idiopathic-interstitial-pneumonias
#7
REVIEW
Jay H Ryu, Teng Moua, Natalya Azadeh, Misbah Baqir, Eunhee S Yi
Idiopathic interstitial pneumonias comprise approximately one-third of interstitial lung diseases (also called diffuse parenchymal infiltrative lung diseases). The classification of idiopathic interstitial pneumonias has undergone several revisions since the initial description of 40 years ago, and the most recent version was published in 2013. Although some aspects have been clarified, this group of heterogeneous disorders continues to be a source of confusion and misunderstanding in clinical applications...
2016: F1000Research
https://www.readbyqxmd.com/read/27853528/recent-advances-in-understanding-and-managing-urolithiasis
#8
REVIEW
Walter L Strohmaier
During the last few years, there has been relevant progress in both understanding and managing urolithiasis. Our knowledge of stone formation has changed; although the importance of urine biochemistry was questioned by several investigators years ago, the decisive role of cellular processes (induced by oxidative stress) and the renal papilla has only recently been generally accepted as the most important step in stone formation. For calcium oxalate urolithiasis, the formation of papillary calcifications plays a key role and is of prognostic relevance...
2016: F1000Research
https://www.readbyqxmd.com/read/27853527/science-for-the-sustainable-use-of-ecosystem-services
#9
REVIEW
Elena M Bennett, Rebecca Chaplin-Kramer
Sustainability is a key challenge for humanity in the 21st century. Ecosystem services-the benefits that people derive from nature and natural capital-is a concept often used to help explain human reliance on nature and frame the decisions we make in terms of the ongoing value of nature to human wellbeing. Yet ecosystem service science has not always lived up to the promise of its potential. Despite advances in the scientific literature, ecosystem service science has not yet answered some of the most critical questions posed by decision-makers in the realm of sustainability...
2016: F1000Research
https://www.readbyqxmd.com/read/27853526/recent-advances-in-prenatal-genetic-screening-and-testing
#10
REVIEW
Ignatia B Van den Veyver
The introduction of new technologies has dramatically changed the current practice of prenatal screening and testing for genetic abnormalities in the fetus. Expanded carrier screening panels and non-invasive cell-free fetal DNA-based screening for aneuploidy and single-gene disorders, and more recently for subchromosomal abnormalities, have been introduced into prenatal care. More recently introduced technologies such as chromosomal microarray analysis and whole-exome sequencing can diagnose more genetic conditions on samples obtained through amniocentesis or chorionic villus sampling, including many disorders that cannot be screened for non-invasively...
2016: F1000Research
https://www.readbyqxmd.com/read/27853525/bacteriocin-production-a-relatively-unharnessed-probiotic-trait
#11
REVIEW
James W Hegarty, Caitriona M Guinane, R Paul Ross, Colin Hill, Paul D Cotter
Probiotics are "live microorganisms which, when consumed in adequate amounts, confer a health benefit to the host". A number of attributes are highly sought after among these microorganisms, including immunomodulation, epithelial barrier maintenance, competitive exclusion, production of short-chain fatty acids, and bile salt metabolism. Bacteriocin production is also generally regarded as a probiotic trait, but it can be argued that, in contrast to other traits, it is often considered a feature that is desirable, rather than a key probiotic trait...
2016: F1000Research
https://www.readbyqxmd.com/read/27853524/recent-advances-on-candida-albicans-biology-and-virulence
#12
REVIEW
Adnane Sellam, Malcolm Whiteway
Candida albicans is an important human fungal pathogen, in terms of both its clinical significance and its use as an experimental model for scientific investigation. Although this opportunistic pathogen is a natural component of the human flora, it can cause life-threatening infections in immunosuppressed patients. There are currently a limited number of antifungal molecules and drug targets, and increasing resistance to the front-line therapeutics, demonstrating a clear need for new antifungal drugs. Understanding the biology of this pathogen is an important prerequisite for identifying new drug targets for antifungal therapeutics...
2016: F1000Research
https://www.readbyqxmd.com/read/27853523/recent-advances-in-understanding-provoked-vestibulodynia
#13
REVIEW
Ahinoam Lev-Sagie, Steven S Witkin
Vulvodynia refers to pain in the vulva of at least 3 months' duration in the absence of a recognized underlying cause. Provoked, localized vestibulodynia is the term used to describe superficial pain confined to the vulvar vestibule, provoked by touch. This review will focus on provoked vestibulodynia with regard to its suggested causative factors and will discuss the role of inflammation, vulvovaginal infections, mucosal nerve fiber proliferation, hormonal associations, central pain mechanisms, pelvic floor muscle dysfunction, and genetic factors...
2016: F1000Research
https://www.readbyqxmd.com/read/27853522/recent-advances-in-entamoeba-biology-rna-interference-drug-discovery-and-gut-microbiome
#14
REVIEW
Pedro Morgado, Dipak Manna, Upinder Singh
In recent years, substantial progress has been made in understanding the molecular and cell biology of the human parasite Entamoeba histolytica, an important pathogen with significant global impact. This review outlines some recent advances in the Entamoeba field in the last five years, focusing on areas that have not recently been discussed in detail: (i) molecular mechanisms regulating parasite gene expression, (ii) new efforts at drug discovery using high-throughput drug screens, and (iii) the effect of gut microbiota on amoebiasis...
2016: F1000Research
https://www.readbyqxmd.com/read/27853521/zika-mosquito-vectors-the-jury-is-still-out
#15
Walter S Leal
After a 40-year hiatus, the International Congress of Entomology (ICE 2016) convened in Orlando, Florida (September 25-30, 2016). One of the symposia at ICE 2016, the Zika Symposium, covered multiple aspects of the Zika epidemic, including epidemiology, sexual transmission, genetic tools for reducing transmission, and particularly vector competence. While there was a consensus among participants that the yellow fever mosquito, Aedes aegypti, is a vector of the Zika virus, there is growing evidence indicating that the range of mosquito vectors might be wider than anticipated...
2016: F1000Research
https://www.readbyqxmd.com/read/27853520/dot-app-a-graphviz-cytoscape-conversion-plug-in
#16
Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak
dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (*.dot, *.gv) files, also known as DOT files due to the *.dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including GraphViz, Gephi, neato, smyrna, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape...
2016: F1000Research
https://www.readbyqxmd.com/read/27853519/cell5m-a-geospatial-database-of-agricultural-indicators-for-africa-south-of-the-sahara
#17
Jawoo Koo, Cindy M Cox, Melanie Bacou, Carlo Azzarri, Zhe Guo, Ulrike Wood-Sichra, Queenie Gong, Liangzhi You
Recent progress in large-scale georeferenced data collection is widening opportunities for combining multi-disciplinary datasets from biophysical to socioeconomic domains, advancing our analytical and modeling capacity. Granular spatial datasets provide critical information necessary for decision makers to identify target areas, assess baseline conditions, prioritize investment options, set goals and targets and monitor impacts. However, key challenges in reconciling data across themes, scales and borders restrict our capacity to produce global and regional maps and time series...
2016: F1000Research
https://www.readbyqxmd.com/read/27853518/metagenomic-analysis-of-medicinal-cannabis-samples-pathogenic-bacteria-toxigenic-fungi-and-beneficial-microbes-grow-in-culture-based-yeast-and-mold-tests
#18
Kevin McKernan, Jessica Spangler, Yvonne Helbert, Ryan C Lynch, Adrian Devitt-Lee, Lei Zhang, Wendell Orphe, Jason Warner, Theodore Foss, Christopher J Hudalla, Matthew Silva, Douglas R Smith
Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA...
2016: F1000Research
https://www.readbyqxmd.com/read/27853517/maternal-complications-in-a-geographically-challenging-and-hard-to-reach-district-of-bangladesh-a-qualitative-study
#19
Animesh Biswas, Koustuv Dalal, Abu Sayeed Md Abdullah, Mervyn Gifford, M A Halim
Background: Maternal complications contribute to maternal deaths in developing countries. Bangladesh still has a high prevalence of maternal mortality, which is often preventable. There are some geographically challenging and hard to reach rural districts in Bangladesh and it is difficult to get information about maternal complications in these areas. In this study, we examined the community lay knowledge of possible pregnancy complications. We also examined the common practices associated with complications and we discuss the challenges for the community...
2016: F1000Research
https://www.readbyqxmd.com/read/27853516/pattern-of-triple-negative-epithelial-ovarian-cancer-in-indigenous-african-women
#20
Mustapha Akanji Ajani, Ayodeji Akeem Salami, Olutosin Alaba Awolude, Abideen Olayiwola Oluwasola
Background: Triple negative epithelial ovarian cancer (TNEOC)  refers to ovarian carcinomas that do not express estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor- type 2 (HER-2/neu).  The aim of this study is to determine the pattern of triple negative epithelial ovarian cancer in indigenous African women. Methods: We performed a retrospective review of ER, PR and HER-2/neu expression in 90 Nigerian patients with histologically diagnosed epithelial ovarian cancer...
2016: F1000Research
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