Narrowing the wingless-2 mutation to a 227 kb candidate region on chicken chromosome 12.

Wingless-2 (wg-2) is an autosomal recessive mutation in chicken that results in an embryonic lethal condition. Affected individuals exhibit a multisystem syndrome characterized by absent wings, truncated legs, and craniofacial, kidney, and feather malformations. Previously, work focused on phenotype description, establishing the autosomal recessive pattern of Mendelian inheritance and placing the mutation on an inbred genetic background to create the congenic line UCD Wingless-2.331. The research described in this paper employed the complementary tools of breeding, genetics, and genomics to map the chromosomal location of the mutation and successively narrow the size of the region for analysis of the causative element. Specifically, the wg-2 mutation was initially mapped to a 7 Mb region of chromosome 12 using an Illumina 3 K SNP array. Subsequent SNP genotyping and exon sequencing combined with analysis from improved genome assemblies narrowed the region of interest to a maximum size of 227 kb. Within this region, 3 validated and 3 predicted candidate genes are found, and these are described. The wg-2 mutation is a valuable resource to contribute to an improved understanding of the developmental pathways involved in chicken and avian limb development as well as serving as a model for human development, as the resulting syndrome shares features with human congenital disorders

Visual Search and Visual Discomfort

Certain visual stimuli evoke perceptions of discomfort in non-clinical populations. We investigated the impact of stimuli previously judged as uncomfortable by non-clinical populations on a visual search task. One stimulus that has been shown to affect discomfort judgments is noise that has been filtered to have particular statistical properties (Juricevic et al, 2010 Perception39 884–899). A second type of stimulus associated with visual discomfort is striped patterns (Wilkins et al, 1984 Brain107 989–1017). These stimuli were used as backgrounds in a visual search task, to determine their influence on search performance. Results showed that, while striped backgrounds did have an impact on visual search performance, this depended on the similarity between the target and background in orientation and spatial frequency. We found no evidence for a more generalised effect of discomfort on performance

Evidence of improving antiretroviral therapy treatment delays: an analysis of eight years of programmatic outcomes in Blantyre, Malawi

Background: Impressive achievements have been made towards achieving universal coverage of antiretroviral therapy (ART) in sub-Saharan Africa. However, the effects of rapid ART scale-up on delays between HIV diagnosis and treatment initiation have not been well described. Methods: A retrospective cohort study covering eight years of ART initiators (2004–2011) was conducted at Queen Elizabeth Central Hospital (QECH) in Blantyre, Malawi. The time between most recent positive HIV test and ART initiation was calculated and temporal trends in delay to initiation were described. Factors associated with time to initiation were investigated using multivariate regression analysis. Results: From 2004–2011, there were 15,949 ART initiations at QECH (56% female; 8% children [0–10 years] and 5%adolescents [10–20 years]). Male initiators were likely to have more advanced HIV infection at initiation than female initiators (70% vs. 64% in WHO stage 3 or 4). Over the eight years studied, there were declines in treatment delay, with 2011 having the shortest delay at 36.5 days. On multivariate analysis CD4 count <50 cells/μl (adjusted geometric mean ratio [aGMR]: aGMR: 0.53, bias-corrected accelerated [BCA] 95% CI: 0.42-0.68) was associated with shorter ART treatment delay. Women (aGMR: 1.12, BCA 95% CI: 1.03-1.22) and patients diagnosed with HIV at another facility outside QECH (aGMR: 1.61, BCA 95% CI: 1.47-1.77) had significantly longer treatment delay. Conclusions: Continued improvements in treatment delays provide evidence that universal access to ART can be achieved using the public health approach adopted by Malawi However, the longer delays for women and patients diagnosed at outlying sites emphasises the need for targeted interventions to support equitable access for these groups

A simple optical coherence tomography quantification method for choroidal neovascularization

Purpose: Therapeutic efficacy is routinely assessed by measurement of lesion size using flatmounted choroids and confocal microscopy in the laser-induced choroidal neovascularization (L-CNV) rodent model. We investigated whether optical coherence tomography (OCT) quantification, using an ellipsoid volume measurement, was comparable to standard ex vivo evaluation methods for this model and whether this approach could be used to monitor treatment-related lesion changes. Methods: Bruch's membrane was ruptured by argon laser in the dilated eyes of C57BL/6J mice, followed by intravitreal injections of anti-VEGF164 or vehicle, or no injection. In vivo OCT images were acquired using Micron III or InVivoVue systems at 7, 10, and/or 14 days post-laser and neovascular lesion volume was calculated as an ellipsoid. Subsequently, lesion volume was compared to that calculated from confocal Z-stack images of agglutinin-stained choroidal flatmounts. Results: Ellipsoid volume measurement of orthogonal 2-dimensional OCT images obtained from different imaging systems correlated with ex vivo lesion volumes for L-CNV (Spearman's ρ=0.82, 0.75, and 0.82 at days 7, 10, and 14, respectively). Ellipsoid volume calculation allowed temporal monitoring and evaluation of CNV lesions in response to antivascular endothelial growth factor treatment. Conclusions: Ellipsoid volume measurements allow rapid, quantitative use of OCT for the assessment of CNV lesions in vivo. This novel method can be used with different OCT imaging systems with sensitivity to distinguish between treatment conditions. It may serve as a useful adjunct to the standard ex vivo confocal quantification, to assess therapeutic efficacy in preclinical models of CNV, and in models of other ocular diseases

Bostonia: The Boston University Alumni Magazine. Volume 9

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report

This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

A review of the discovery reach of directional Dark Matter detection

Cosmological observations indicate that most of the matter in the Universe is Dark Matter. Dark Matter in the form of Weakly Interacting Massive Particles (WIMPs) can be detected directly, via its elastic scattering off target nuclei. Most current direct detection experiments only measure the energy of the recoiling nuclei. However, directional detection experiments are sensitive to the direction of the nuclear recoil as well. Due to the Sun’s motion with respect to the Galactic rest frame, the directional recoil rate has a dipole feature, peaking around the direction of the Solar motion. This provides a powerful tool for demonstrating the Galactic origin of nuclear recoils and hence unambiguously detecting Dark Matter. Furthermore, the directional recoil distribution depends on the WIMP mass, scattering cross section and local velocity distribution. Therefore, with a large number of recoil events it will be possible to study the physics of Dark Matter in terms of particle and astrophysical properties. We review the potential of directional detectors for detecting and characterizing WIMPs

Distributed situation awareness in dynamic systems: Theoretical development and application of an ergonomics methodology

The purpose of this paper is to propose foundations for a theory of situation awareness based on the analysis of interactions between agents (i.e., both human and non-human) in subsystems. This approach may help promote a better understanding of technology-mediated interaction in systems, as well as helping in the formulation of hypotheses and predictions concerning distributed situation awareness. It is proposed that agents within a system each hold their own situation awareness which may be very different from (although compatible with) other agents. It is argued that we should not always hope for, or indeed want, sharing of this awareness, as different system agents have different purposes. This view marks situation awareness as a 1 dynamic and collaborative process that binds agents together on tasks on a moment-by-moment basis. Implications of this viewpoint for development of a new theory of, and accompanying methodology for, distributed situation awareness are offered