3,936 Works

FROGS: Find Rapidly OTU with Galaxy Solution

Frederic Escudie, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, Sarah Maman, Mahendra Mariadassou, Guillermina Hernandez-Raquet & Geraldine Pascal
High-throughput sequencing of 16S/18S/23S RNA amplicons has opened new horizons in the study of microbe communities. With the sequencing at great depth the current processing pipelines struggle to run rapidly and the most effective solutions are often designed for specialists. These tools are designed to give both the abundance table of operational taxonomic units (OTUs) and their taxonomic affiliation. In this context we developed the pipeline FROGS: « Find Rapidly OTU with Galaxy Solution »....

Auxin regulatory module evolution during C4 plant evolution

Yao-Ming Chang, Arthur Chun-Chieh Shih & Wen-Hsiung Li
Auxin, a plant phytohormone, plays an important role in vasculature development of vascular plants through the feedback regulation between auxin responsive factors (ARFs) and AUX/IAA proteins. In flowering plants, more than twenty genes in both ARF and AUX/IAA families have been identified but their regulatory relationships are still largely unknown. In this study, we analyzed three time-course transcriptome datasets from maize foliar (C4), husk (C3-like) and rice (C3) embryonic leaves and found that most ARF...

An introduction to sharing medical knowledge

Alin Teodosiu
A presentation highlighting the intrinsic importance of teaching for the medical culture as a whole while also providing useful guidelines for beginners as well as experienced teachers alike.

Estimating population density and size of a social forest-dwelling mammal using gas movement theory and spatially explicit distribution model

Maria Luisa Jorge, Joan Coker, Daniel Gorczynski & Mauro Galetti
Accurate estimates of density and population size are fundamental for appropriate monitoring of populations. Forest dwelling large mammals that live in herds are particularly difficult for estimating population density and size because of the heterogeneity of their spatial distribution at local scales and the difficulty of counting groups. Previous work has dealt with heterogeneity of spatial-temporal distribution by the independent use of gas movement theory and spatially explicit distribution models. Here we propose to combine...

Keep your eye on the prize: the relation between biased attention and reward processing among dysphoric individuals

W. Michael Vanderlind, Narun Pornpattananangkul, James Glazer, Arielle R. Baskin-Sommers, Robin Nusslock & Jutta Joormann

Touch epithelial samples

Ye Jin Kwon, Cristina E. Stanciu, M. Katherine Philpott & Christopher J. Ehrhardt
Flow cytometry source data for all samples are provided in Flow Cytometry Standard (.fcs) format files. Source data files are organized into three different repositories labeled, “HLA Hybridization”, “Cytokeratin Hybridization”, and “Autofluorescence”. Flow cytometry data collected on aged touch samples is contained within the Autofluorescence data folder. File names are labeled with the anonymized sample ID number, date of analysis, and the instrument platform used. Source data files are also labeled by the specific probe...

Scaling up access to HIV treatment: what can we learn for NCDs?

Helen Bygrave

Establishing the end-users requirements before designing a web-based learning platform to improve clinical ultrasound credentialing success within a resource limited setting

Hein Lamprecht
Using 2-step individual interviews and thematic analysis approach to establish both the trainee and trainer endusers requirements before embarking on the design of a web-based learning platform to improve doctors clinical ultrasound credentialing success within a resource limited setting

Color spectrographic respiratory monitoring from the external ear canal

Daniel John Doyle
Background & Objectives: The need for a simple and reliable means of respiratory monitoring has become stronger in recent years with the widespread use of opioids such as morphine for acute pain management. In this preliminary report we describe the use of color spectrographic analysis of breath sounds recorded from the external ear canal as a candidate technology to meet this important clinical need.

Materials & Methods: A miniature electret microphone was modified with the...

GeneSeqToFamily: the Ensembl GeneTrees pipeline as a Galaxy workflow

Anil Thanki, Nicola Soranzo & Robert Davey
GeneSeqToFamily is an open-source Galaxy workflow based on the Ensembl GeneTrees pipeline. The workflow helps users to run their analyses without using the command-line while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. It also allows users to subsequently visualise these gene families using the Aequatus.js interactive tool, which is developed as part of the Aequatus software.

Nonnegative matrix factorization clustering for time series cancer progression data

Abed Alkhateeb, Iman Rezaeian & Luis Rueda
An important aspect of studying cancer is to consider the progression of the disease in time. In this study, we focus on a prostate cancer data set that contains different samples at different progression stages. Pre-processing was done by aligning the sample's reads to the human genome, and constructing and quantifying the transcripts at each stage thereafter. This results in a matrix of vectors (V) that contains the transcript's profiles quantified as fragments per kilo...

Community-based HIV testing strategies among sex workers in the transport corridor in Mozambique

Humberto Jassitene
The MSF Corridor project aims to implement a comprehensive intervention for sex workers (SW) along the transport corridor in Mozambique and Malawi. This community-based model includes outreach services, HIV testing and counselling, condom distribution, follow-up testing for HIV negative SW and access to STI and HIV care. Humberto Jassitene from MSF Mozambique describes testing, retesting and seroconversion among SWs in Tete and Sofala and explores sex workers peer educators’ perspectives on their role.

Personalized neoantigen vaccination with synthetic long peptides

John P. Finnigan, Alex Rubinsteyn, Tavi Nathanson, Nicholas Akers, Nina Bhardwaj, Jeff Hammerbacher, Bojan Losic & Eric Schadt
Mutations in cancer may give rise to novel antigenic peptides, known as tumor neoantigens, that are promising targets for immunotherapy. However, due to the complexity and heterogeneity of most cancers, a single antigenic target is often insufficient for achieving a durable response or remission. Vaccines using single, short synthetic peptides are vulnerable to immune evasion or may even promote immune tolerance and/or anergy, leading to increased tumor growth. Cancer vaccination has moved in two promising...

Concomitant O-GlcNAcylation and phosphorylation of a plant virus capsid protein

Sandra Martínez-Turiño, Jesús Pérez, Marta Hervás, S Ciordia, R Navajas, MC Mena & Juan Antonio García Álvarez
O-linked b-D-N-acetylglucosamine modification has been shown to play a very important role in a number of pathophysiological human conditions. However, contrary to animals, this PTM has been barely studied in plants.

Plum pox virus (PPV) (genus Potyvirus) causes sharka, one of the most damaging diseases affecting stone fruit trees. PPV genome is a positive-sense single-stranded RNA encapsidated by a single type of capsid protein (CP) in flexuous rod particles. The PPV CP is the best-characterized target...

Electro-acupuncture stimulation modulates Hippocampal VEGF-C, CXCR4 and IP-10 in rats exposed to unpredictably chronic-mild stress

Huili Jiang, Tuya Bao, Danmei Zhang, Yu Wang, Xuhui Zhang, Jing Li, Xinjing Yang, Bingcong Zhao, Miao Yu & Yu Guo
Objective: Based on the differential protein expression analysis in antibody microarrays, this study was to investigate the effect of electro-acupuncture (EA) on hippocampal vascular endothelial growth factor C (VEGF-C), chemokine cys-x-cys receptor 4 (CXCR4) and interferon-inducible protein-10 (IP-10) in a rat model of depression disorder.

Conclusions: The differential protein expression analysis of hippocampal VEGF-C, CXCR4 and IP-10 in antibody microarrays might elucidate the mechanism of the antidepressive effect of EA therapy.

Dataset 3: Raw data for Figure 3, Incremental cost-effectiveness plane for once daily (QD) versus twice-daily regimen (BID).

Muinat B. Sanni-Oba, Olalekan A. Uthman & Jean B. Nachega

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