A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.

Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a 'supergene' on the sex chromosome. Here, we phenotype and genotype four guppy 'Iso-Y lines', where colour was inherited along the patriline for 40 generations.

On the genetic architecture of rapidly adapting and convergent life history traits in guppies.

The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture.

Experimental demonstration and optimization of X-ray StaticCodeCT.

As the use of X-ray computed tomography (CT) grows in medical diagnosis, so does the concern for the harm a radiation dose can cause and the biological risks it represents. StaticCodeCT is a new low-dose imaging architecture that uses a single-static coded aperture (CA) in a CT gantry. It exploits the highly correlated data in the projection domain to estimate the unobserved measurements on the detector.

Using existing knowledge for the risk evaluation of crop protection products in order to guide exposure driven data generation strategies and minimise unnecessary animal testing.

Traditionally, human health risk assessment focuses on defining the hazard through mammalian toxicity studies followed by exposure estimation. We have explored ways of predicting exposure based primarily on the use scenario and comparing the exposure to reference dose values derived by various regulatory agencies (US EPA, JMPR, and EU Commission) in order to identify mammalian toxicity studies that are relevant to human health risk assessment. Human dietary exposure was based on existing residue data for substances with comparable use on the same or similar crops.

Understanding Data Visualization Design Practice.

Professional roles for data visualization designers are growing in popularity, and interest in relationships between the academic research and professional practice communities is gaining traction. However, despite the potential for knowledge sharing between these communities, we have little understanding of the ways in which practitioners design in real-world, professional settings. Inquiry in numerous design disciplines indicates that practitioners approach complex situations in ways that are fundamentally different from those of researchers.

An evaluation of carcinogenicity predictors from short-term and sub chronic repeat-dose studies of agrochemicals in rats: Opportunities to refine and reduce animal use.

The aim of this study was to examine whether short term, repeat dose, rat studies provide sufficient information about potential carcinogenicity to enable predictions about the carcinogenic potential of agrochemicals to be made earlier in compound development. This study aimed to identify any correlations between toxicity findings obtained for short term rat studies (28 day and 90 day) and neoplastic findings obtained from 24 month rat carcinogenicity studies for agrochemical compounds (18 compounds) tested in Han Wistar and Sprague Dawley rats. The macroscopic pathology, microscopic pathology, hematology, biochemistry, organ weights, estrogen receptor activation and genotoxicity results were examined.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies.

Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata.

Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR.

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).

Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict.

Partner choice correlates with fine scale kin structuring in the paper wasp Polistes dominula.

Cooperation among kin is common in animal societies. Kin groups may form by individuals directly discriminating relatives based on kin recognition cues, or form passively through natal philopatry and limited dispersal. We describe the genetic landscape for a primitively eusocial wasp, Polistes dominula, and ask whether individuals choose cooperative partners that are nearby and/or that are genetic relatives.

Identification of 24 new microsatellite loci in the sweat bee Lasioglossum malachurum (Hymenoptera: Halictidae).

Objective: The objective here is to identify highly polymorphic microsatellite loci for the Palaearctic sweat bee Lasioglossum malachurum. Sweat bees (Hymenoptera: Halictidae) are widespread pollinators that exhibit an unusually large range of social behaviours from non-social, where each female nests alone, to eusocial, where a single queen reproduces while the other members of the colony help to rear her offspring. They thus represent excellent models for understanding social evolution.

Evolutionary divergence in life history traits among populations of the Lake Malawi cichlid fish .

During the early stages of adaptive radiation, populations diverge in life history traits such as egg size and growth rates, in addition to eco-morphological and behavioral characteristics. However, there are few studies of life history divergence within ongoing adaptive radiations. Here, we studied , a maternal mouthbrooding cichlid fish within the Lake Malawi haplochromine radiation.

Ontology-Driven Search and Triage: Design of a Web-Based Visual Interface for MEDLINE.

Background: Diverse users need to search health and medical literature to satisfy open-ended goals such as making evidence-based decisions and updating their knowledge. However, doing so is challenging due to at least two major difficulties: (1) articulating information needs using accurate vocabulary and (2) dealing with large document sets returned from searches. Common search interfaces such as PubMed do not provide adequate support for exploratory search tasks.

Reconsidering healthcare evidence as dynamic and distributed: the role of information and cognition.

Aim: The basic thrust of evidence-based healthcare is that current best evidence should be used explicitly and judiciously for diagnosis, management, and other activities in healthcare settings. For this to be possible, researchers, practitioners, and other stakeholders must have a clear and accurate conceptualization of what constitutes 'evidence' in healthcare environments, and the manner in which it is used in decision-making and other activities. Currently, the dominant conceptualization of evidence is that of a body of information that can be retrieved by stakeholders for use in healthcare practice.

Secondary contact seeds phenotypic novelty in cichlid fishes.

Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species to overcome environmental challenges and adapt to novel environments, including during adaptive radiation. To date, this has largely been considered from the perspective of interspecific hybridization at contact zones.

Guidance on classification for reproductive toxicity under the globally harmonized system of classification and labelling of chemicals (GHS).

The Globally Harmonised System of Classification (GHS) is a framework within which the intrinsic hazards of substances may be determined and communicated. It is not a legislative instrument per se, but is enacted into national legislation with the appropriate legislative instruments. GHS covers many aspects of effects upon health and the environment, including adverse effects upon sexual function and fertility or on development.

Beyond information access: Support for complex cognitive activities in public health informatics tools.

Public health professionals work with a variety of information sources to carry out their everyday activities. In recent years, interactive computational tools have become deeply embedded in such activities. Unlike the early days of computational tool use, the potential of tools nowadays is not limited to simply providing access to information; rather, they can act as powerful mediators of human-information discourse, enabling rich interaction with public health information.