3,679 Works

Supplementary File 1. Candidates in the pipeline for neglected diseases, as of August 31, 2017

Ruth Young, Tewodros Bekele, Alexander Gunn, Nick Chapman, Vipul Chowdhary, Kelsey Corrigan, Lindsay Dahora, Sebastián Martinez, Sallie Permar, Johan Persson, Bill Rodriguez, Marco Schäferhoff, Kevin Schulman, Tulika Singh, Robert F Terry & Gavin Yamey

Assumptions & analysis of barriers to contracted-out Health Facilities in Sindh, Pakistan

Khurram Ansar & Million Abraha
The current issues regarding Contact-out health facilities in Sindh, Pakistan

Candidate gene methylation quantification (CandiMeth) within the Galaxy Bioinformatics Interface

Sara-Jayne Thursby, Sarah-Jayne Mackin, Rachelle Irwin & Colum Walsh
Introduction:
R packages like minfi and RnBeads allow efficient processing and high-level statistics of human DNA methylation arrays, wet-lab scientists who wish to verify methylation differences at particular loci or specific gene sets are typically uncomfortable with the command-line. They nevertheless need to visualise, compare and quantify methylation changes against identified genomic features. Therefore, we wished to develop a tool for simple intuitive mapping of methylation differences to UCSC genome browser which allows methylation differences to...

An open source machine learning tool for identifying biomarkers in next generation sequencing

Haris Ahmad, Abed Alkhateeb, Osama Hamzeh & Luis Rueda
A tool that integrates next-generation sequencing data pre-processing with machine learning techniques to extract meaningful biomarkers from next-generation sequencing data.

Manufacture of immunoglobulin therapies – relationship to thrombogenicity

Albert Farrugia
Presented to the Workshop on
Risk Mitigation Strategies to Address Procoagulant Activity in Immune Globulin Products
Universities at Shady Grove Conference Center
Rockville, Maryland
May 17-18, 2011

Solitary Median Maxillary Central Incisor (SMMCI) syndrome: an uncommon diagnosis

Manisha Joshi, Anuradha Sural, Elisheba Patras & Nittin Parkhe
Objectives of Study:
To study role of MDCT in diagnosis of Solitary Median Maxillary Central Incisor (SMMCI) Syndrome.

Material & Methods:
16 slice MDCT scanner was used to scan a new born baby with suspected choanal atresia and images were studied with Multi Planner Reformatting (MPR), Volume Rendering (VR) technique & surface Shaded Display (SSD).

Results:
MDCT images with various reformatting well demonstrated solitary central maxillary mega incisor, bilateral choanal atresia, pyriform aperture stenosis and nasolacrimal duct cysts...

Fish annotation in Ensembl

Leanne Haggerty, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Osagie Izuogu, Denye Ogeh, Fergal J. Martin & Paul Flicek
The actinopterygians, or ray-finned fish, account for nearly half of all extant vertebrates and exhibit a high level of phenotypic diversity. Previous and continuing studies have revealed divergent features of actinopterygian genomes. Specific phenotypes represented in such a diverse group can aid in extricating the set of common genes from those genes that evolved in specific lineages in response to environmental pressures.

In order to fuel research into both the evolution of fish and their...

1st INCF Workshop on Validation of Analysis Methods

The INCF Secretariat, Michael Denker, Gaute Einevoll, Felix Franke, Sonja Grün, Espen Hagen, Jason Kerr, Martin Nawrot, Torbjorn Ness, Raphael Ritz, Leslie Smith, Thomas Wachtler & Daniel Wojcik
This workshop was organized by INCF in Stockholm, Sweden, 18 - 19 June 2012.

To ensure that research results can be trusted, it is essential to use methods that are validated. This holds both for analysis and sharing of data, and has become particularly pertinent in the context of the large-scale concerted brain projects that are presently emerging both in Europe and in the US. This workshop brought together scientists concerned with the validation of methods...

Crossing boundaries: Flux of aquatic winged insects toward agricultural land

Julien Raitif
Linkage between aquatic and terrestrial habitats aroused scientific interest on ecological subsidies, i.e. how the transfer of matter and energy between adjacent ecosystems can modify their own functioning. Recent attention was paid to subsidies associated with aquatic insects emerging from streams and rivers in pristine areas as they are deeply involved in adjacent terrestrial food webs. Freshwater ecosystems are widespread in agricultural landscapes, however the possible implication of aquatic subsidies is rarely considered. Substantial evidences...

List of beetles Passalidae (Coleoptera: Scarabaeoidea) from Peru

Abdhiel A. Bustamante-Navarrete, A.J. Oroz-Ramos & E. Yabar-Landa
Based on secondary information, 57 species are recorded, distributed in 6 genera, including the Passalini tribes (40 species) and Proculini (17 species), both in Passalinae. The most abundant genus is Passalus with 30 species distributed in its 3 subgenera: Passalus (Mitrorhinus) (3 species), Passalus (Passalus) (20 species) and Passalus (Pertinax) (7 species). The second most abundant genus is Veturius with 14 species also divided into 3 subgenera: Veturius (Veturius) (10 species), Veturius (Ouyana) (3 species)...

ELIXIR: 4OSS lesson development, an ELIXIR and the carpentries collaboration

Mateusz Kuzak, Jen Harrow, Rafael Jimenez, Paula Martinez, Fotis Psomopoulos, Radka Svobodová Vařeková & Allegra Via
The ELIXIR Training Platform is partnering with the Software and Data Carpentry Foundations
(The Carpentries) to train researchers to improve their computing and data management skills. Both The Carpentries and ELIXIR are interested in supporting researchers and developers to develop better software. Hence, the “ELIXIR Software development best practices” group, which is part of the ELIXIR Tools Platform, has proposed the “Four simple recommendations to encourage best practices in research software” [1] (in short “4OSS”). These...

Standardized and reproducible analysis enables identification of novel primary graft dysfunction biomarkers using exosome proteomics

Nicholas Giangreco, Guillaume Lebreton, Susan Restaino, Maryjane Farr, Paolo Colombo, Emmanuel Zorn, Pascal LePrince, Jon Kobashigawa, Nicholas Tatonetti & Barry Fine
Primary graft dysfunction (PGD) is defined as severe ventricular dysfunction within 24 hours of heart transplant and is the leading cause of mortality within the first 30 days of transplant. The etiology of primary graft dysfunction (PGD) remains unclear and prediction of PGD remains an area of active research1. Exosomes are secreted microvesicles found in numerous bodily fluids and have protein and RNA content with biomarker potential2. Here we investigate pre-transplant serum exosomes using proteomics...

Considérations clés: le contexte de la province de l’Équateur, RDC

Lys Alcayna-Stevens, Juliet Bedford & Social Science In Humanitarian Action Platform
Cette note stratégique résume les considérations clés inhérentes au contexte de la province de l’Équateur vis-à-vis de la flambée épidémique d’Ébola en RDC.

Noise masking and crowding reveal two very different kinds of spatial integration

Hörmet Yiltiz, Denis G. Pelli & 17th Vision Sciences Society Annual Meeting 2017
Yiltiz, H., & Pelli, D. G. (2017) Noise masking and crowding reveal two very different kinds of spatial integration. Journal of Vision, 17(10):802.

Recognition of a simple target, e.g. a letter, can be prevented by adding visual noise or nearby clutter. Both effects involve integration of visual information over space. The literature says that crowding integrates “features,” and noise-masking integrates contrast energy. Here we compare the spatial extent of the two kinds of integration. For...

A Microbial metabolism resource for Systems Biology: Shared semantic standards for reference data types (ELIXIR Implementation Study Deliverable Report)

Jerven Bolleman, Thierry Lombardot, Nicole Redaschi, Marco Pagni & Alan Bridge
The ELIXIR Implementation Study A microbial metabolism resource for systems biology aims to provide a practical demonstration of how existing funded resources from ELIXIR partner Nodes could be integrated into a coherent computational framework that supports studies of metabolic systems, including the creation and analysis of genome scale metabolic models.

This report presents the shared semantic standards that will be used for the representation of those reference data types that are shared between the project...

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