5,581 Works

Togo – recent developments in agricultural research

&
Togo - recent developments in agricultural research

Malodor Detection for FSM Technologies by an Integrated Gas Sensors System

, Peter Coggan, Claire Welling, Sonia Grego & Marc Deshusses
Malodors in and around toilets, and released during fecal sludge management activities remain an important risk factor for adoption of sanitation products and technologies. Many challenges and knowledge gaps exist ranging from identifying odor release points, quantifying odor emissions, adopting designs and best practices that minimize odors, to testing for compliance. One critical need is to develop an instrument that can monitor odor, even crudely, to provide feedback in the event a significant system malfunction....

Data integration and visualization at the 4D nucleome data portal

Burak Alver, Alexander Balashov, Shannon Ehmsen, Koray Kirli, , Luisa Mercado, Sarah Reiff, Andrew Schroeder, Chad Serrant, Carl Vitzthum, Nils Gehlenborg & Peter J. Park
The 4D Nucleome Consortium aims to elucidate the nature of DNA conformation in the nucleus both spatially and temporally. The 4DN Data Portal (https://data.4dnucleome.org) was created as a community resource to collect and disseminate data generated by the Consortium with complete experimental metadata following a FAIR approach. The data portal contains many innovative experiment types that probe the 3D interactions of chromatin, including Hi-C methods, DamID-seq, Repli-seq, super-resolution microscopy, and more. In addition to making...

Characterization of the Livestock Production Systems and the Potential of Feed-based Interventions for Improving Livestock Productivity in Ol'lessos Division of Nandy County (Kenya)

Sylvia Wafula, Josephine Kirui & Ben Lukuyu
Characterization of the Livestock Production Systems and the Potential of Feed-based Interventions for Improving Livestock Productivity in Ol'lessos Division of Nandy County (Kenya)

Fast and accurate 16S microbial community analysis using Kraken 2

Jennifer Lu & Steven Salzberg
Over the last decade, QIIME “Quantitative Insights Into Microbial Ecology” arose as the most commonly cited bioinformatic tool for analyzing 16S rRNA data[1]. Last year, Almeida et. al. (2018) showed that QIIME 2 outperforms QIIME, MAPseq, and mothur in the accurate classification of bacterial genera in simulated human gut, ocean, and soil metagenomes[2]. This experiment tested each rRNA classifier against the 16S Greengenes, RDP, and SILVA databases. However, while the QIIME 2 proved to have...

Counterfeiting in African agriculture inputs--challenges & solutions: comprehensive findings

Walter De Boef, Orin Hasson, Ben Pierson, Daniel Kim, John Mennel, Carl Engle, Pradeep Prabhala, John Bryce, , Alyssa Jethani & Aliza Hoffman
Counterfeiting in African agriculture inputs--challenges & solutions: comprehensive findings

KBBQ: A reference-free method for base quality score recalibration

Adam Orr & Reed Cartwright
Next-generation DNA sequencing is commonly used to detect genetic variation in many organisms. Quality scores are associated with the sequencing data that predict the accuracy of the base call in each read and statistical models for detecting variants utilize these scores to determine which bases are reliable and which are not. Despite their importance, base quality scores are often poorly calibrated and underestimate the probability of error, causing overconfidence in the accuracy of the resulting...

Country Brief--Pakistan

Bill
Country Brief--Pakistan

NovoAlign performance optimisation

Colin Hercus &
NovoAlign is an NGS sequence alignment software for accurate mapping of short reads onto a reference genome. We have recently updated the software from the previous version (V3.09.02) to version 4 (V4) which includes runtime reduction, revision of default options for alignment scoring, removal of obsolete functions and changes in command line options. Run time reductions included new SIMD dynamic programming routines and an alignment cache function. To determine the optimum settings for gap penalties,...

Improving our knowledge of how seagrass meadows support global fisheries production using the Indo-Pacific Seagrass Network.

Lina Mtwana Nordlund, Leanne Cullen-Unsworth & Richard Unsworth

PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis

& Adrian R. Krainer
Splicing-detection tools were developed to report alternative pre-mRNA splicing (AS) changes in short-read RNA-seq data. We now developed PSISigma for both short- and long-read RNA-seq analysis. We employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins)
to benchmark its performance (i.e., precision, recall, false positive rate, and correlation) in comparison with three leading tools (rMATS, SUPPA2, and Whippet). PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and...

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