A stitch in time: The importance of water and sanitation services (WSS) infrastructure maintenance for cholera risk. A geospatial analysis in Harare, Zimbabwe.

Understanding the factors associated with cholera outbreaks is an integral part of designing better approaches to mitigate their impact. Using a rich set of georeferenced case data from the cholera epidemic that occurred in Harare from September 2018 to January 2019, we apply spatio-temporal modelling to better understand how the outbreak unfolded and the factors associated with higher risk of being a reported case. Using Call Detail Records (CDR) to estimate weekly population movement of the community throughout the city, results suggest that broader human movement (not limited to infected agents) helps to explain some of the spatio-temporal patterns of cases observed.

Appyters: Turning Jupyter Notebooks into data-driven web apps.

Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations. Here, we extended Jupyter Notebooks to broaden their accessibility with Appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications.

Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm.

Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable.

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv.

A chromosome conformation capture ordered sequence of the barley genome.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.

Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.

Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three and two with potential blast resistance. A total of 688.

transPLANT Resources for Triticeae Genomic Data.

The genome sequences of many important Triticeae species, including bread wheat ( L.) and barley ( L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy.

The Ensembl gene annotation system.

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models.

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen.

Innate Immune Response of the Pig Laryngeal Mucosa to Endotracheal Intubation.

Objective: The aim of this study was to measure the effects of endotracheal intubation on innate immune response within the pig laryngeal mucosa.

Study Design: Prospective controlled basic science study.

Setting: The animal experiments and analyses were conducted at the University of Bristol.

Identification of Cassava MicroRNAs under Abiotic Stress.

The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculenta Crantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions.

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond.

Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome.

Separating homeologs by phasing in the tetraploid wheat transcriptome.

Background: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs.

Laryngeal transplantation in minipigs: early immunological outcomes.

Despite recent tissue-engineering advances, there is no effective way of replacing all the functions of the larynx in those requiring laryngectomy. A recent clinical transplant was a success. Using quantitative immunofluorescence targeted at immunologically relevant molecules, we have studied the early (48 h and 1 week) immunological responses within larynxes transplantated between seven pairs of National Institutes of Health (NIH) minipigs fully homozygous at the major histocompatibility complex (MHC) locus.

Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.).

Background: Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity.

Laryngeal transplantation in minipigs: vascular, myologic and functional outcomes.

There is no effective way of replacing all the functions of the larynx in those requiring laryngectomy. Regenerative medicine offers promise, but cannot presently deliver implants with functioning neuromuscular units. A single well-documented laryngeal transplant in man was a qualified success, but more information is required before clinical trials may be proposed.

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers.

Ensembl 2009.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes.

Cultural competence in action for CAMHS: development of a cultural competence assessment tool and training programme.

This article details the development of a tool to measure the cultural competence of individuals working within the Children and Adolescent Mental Health Services (CAMHS). The CAMHS Cultural Competence in Action Tool - known as the CAMHS 'CCATool' - was one of the components of a national project which aimed at promoting cultural competence within CAMHS. The other component was a two day training programme.

Surface-grating distributed bragg reflector quantum-well lasers fabricated in AlGaAs-GaAs asymmetric epitaxial waveguides.

Ridge waveguide lasers, integrated with single deep-surface distributed Bragg reflectors (DBR's) in the passive section, were fabricated with a GaAs-AlGaAs double-quantum-well structure in an asymmetric waveguide. Third-order gratings, with a period of 389 nm and defined by holographic lithography, were formed by low-damage reactive ion etching processes. The grating losses and optical coupling coefficients were estimated, in particular, by use of the relationship between the real and the effective grating lengths that were computed and reexamined by measurements of grating periodicity and mode spacing.

Novel methodology for construction and pruning of quasi-median networks.

Background: Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees.