EPIPOX:immunoinformatic characterization of the shared T-cell epitome between variola virus and related pathogenic orthopoxviruses

Concerns that variola viruses might be used as bioweapons have renewed the interest in developing new and safer smallpox vaccines. Variola virus genomes are now widely available, allowing computational characterization of the entire T-cell epitome and the use of such information to develop safe and yet effective vaccines. To this end, we identified 124 proteins shared between various species of pathogenic orthopoxviruses including variola minor and major, monkeypox, cowpox, and vaccinia viruses, and we targeted them for T-cell epitope prediction. We recognized 8,106, and 8,483 unique class I and class II MHC-restricted T-cell epitopes that are shared by all mentioned orthopoxviruses. Subsequently, we developed an immunological resource, EPIPOX, upon the predicted T-cell epitome. EPIPOX is freely available online and it has been designed to facilitate reverse vaccinology. Thus, EPIPOX includes key epitope-focused protein annotations: time point expression, presence of leader and transmembrane signals, and known location on outer membrane structures of the infective viruses. These features can be used to select specific T-cell epitopes suitable for experimental validation restricted by single MHC alleles, as combinations thereof, or by MHC supertypes

Influence of urbanisation and garden plants on the diversity and abundance of aphids and their ladybird and hoverfly predators

Urban gardens can harbour a high diversity of insects, which are critically important components of urban ecosystems. In this work, we investigate the richness and diversity of a major taxon of economic and ecological importance, the aphids (Homoptera: Aphididae), and their main insect predators, the hoverflies (Diptera: Syrphidae) and ladybirds (Coleoptera: Coccinellidae), in urban gardens. We examined how variation in environmental factors associated with urbanisation (garden host plant abundance, garden plant richness, garden size, proportion of impervious surfaces in the surrounding area) directly and indirectly (via prey and predator abundance) influence the local diversity and abundance of aphids, ladybirds, and hoverflies. Sixty-seven domestic gardens located in southern England were surveyed during the peak period of aphid abundance, and the numbers and identity of aphids and their predators were recorded. We observed 45 aphid species (179917 individuals in total), 15 hoverfly species (494 individuals) and 8 ladybird species (173 individuals). We found that aphid species richness and abundance were positively associated with utilised host plant abundance and garden plant species richness. Hoverfly abundance was positively correlated with garden plant richness. The abundance of ladybirds was positively correlated with aphid abundance and garden plant species richness, and negatively associated to the proportion of impervious surfaces in the surrounding environment. The difference in responses between the two major taxa of aphid predators may reflect differences in their behaviour and natural history. Our results indicate that overall increases in urban land cover are not favourable for ladybirds as a group, and that fine scale habitat variables that are determined by garden owners have the potential to greatly affect the general diversity of aphids and their main predators

“Hey, look at me” An {auto}ethnographic account of experiencing ADHD symptoms within sport.

This auto-ethnography presents a reflective analysis of my experiences of Attention Deficit Hyperactivity Disorder (ADHD) in sport. To date, research into ADHD has been largely confined to clinical evaluation and subjective interpretations. This, however, fails to advance cultural understandings and maintains the status quo. Using an autoethnographic approach, we aim to address this in-balance within sport and to give a voice to the voiceless. As an individual diagnosed with ADHD in early childhood, the first author, guided by the second author, shares and explores his experiences as both an athlete and a coach. By endeavouring to reveal the thoughts and feelings attached to key episodes within his sporting experience, the study functions to provide preliminary evidence to showcase how ADHD can impact upon those who participate in sport. Furthermore, the vignettes presented act as a vehicle to signpost the reader in accessing the available academic literature. As a result, it is hoped that this manuscript will bring further meaning to this often misunderstood condition, showcase how ADHD symptoms may present themselves within a sporting environment, and enable coaches to support those who experience similar episodes

Improving comprehension in adolescents with severe receptive language impairments: a randomized control trial of intervention for coordinating conjunctions

BACKGROUND: Little evidence exists for the effectiveness of therapy for children with receptive language difficulties, particularly those whose difficulties are severe and persistent. AIMS: To establish the effectiveness of explicit speech and language therapy with visual support for secondary school-aged children with language impairments focusing on comprehension of coordinating conjunctions in a randomized control trial with an assessor blind to group status. METHODS & PROCEDURES Fourteen participants (aged 11;3–16;1) with severe RELI (mean standard scores: CELF4 ELS = 48, CELF4 RLS = 53 and TROG-2 = 57), but higher non-verbal (Matrices = 83) and visual perceptual skills (Test of Visual Perceptual Skills (TVPS) = 86) were randomly assigned to two groups: therapy versus waiting controls. In Phase 1, the therapy group received eight 30-min individual sessions of explicit teaching with visual support (Shape Coding) with their usual SLT. In Phase 2, the waiting controls received the same therapy. The participants’ comprehension was tested pre-, post-Phase 1 and post-Phase 2 therapy on (1) a specific test of the targeted conjunctions, (2) the TROG-2 and (3) a test of passives. OUTCOMES & RESULTS: After Phase 1, the therapy group showed significantly more progress than the waiting controls on the targeted conjunctions (d = 1.6) and overall TROG-2 standard score (d = 1.4). The two groups did not differ on the passives test. After Phase 2, the waiting controls made similar progress to those in the original therapy group, who maintained their previous progress. Neither group showed progress on passives. When the two groups were combined, significant progress was found on the specific conjunctions (d = 1.3) and TROG-2 raw (d = 1.1) and standard scores (d = 0.9). Correlations showed no measures taken (including Matrices and TVPS) correlated significantly with progress on the targeted conjunctions or the TROG-2. CONCLUSIONS & IMPLICATIONS: Four hours of Shape Coding therapy led to significant gains on comprehension of coordinating conjunctions which were maintained after 4 months. Given the significant progress at a group level and the lack of reliable predictors of progress, this approach could be offered to other children with similar difficulties to the participants. However, the intervention was delivered one-to-one by speech and language therapists, thus the effectiveness of this therapy method with other methods of delivery remains to be evaluated

Cluster Analysis of Symptoms Among Patients with Upper Extremity Musculoskeletal Disorders

Introduction Some musculoskeletal disorders of the upper extremity are not readily classified. The study objective was to determine if there were symptom patterns in self-identified repetitive strain injury (RSI) patients. Methods Members (n = 700) of the Dutch RSI Patients Association filled out a detailed symptom questionnaire. Factor analysis followed by cluster analysis grouped correlated symptoms. Results Eight clusters, based largely on symptom severity and quality were formulated. All but one cluster showed diffuse symptoms; the exception was characterized by bilateral symptoms of stiffness and aching pain in the shoulder/neck. Conclusions Case definitions which localize upper extremity musculoskeletal disorders to a specific anatomical area may be incomplete. Future clustering studies should rely on both signs and symptoms. Data could be collected from health care providers prospectively to determine the possible prognostic value of the identified clusters with respect to natural history, chronicity, and return to work

Advancing the Selection of Neurodevelopmental Measures in Epidemiological Studies of Environmental Chemical Exposure and Health Effects

With research suggesting increasing incidence of pediatric neurodevelopmental disorders, questions regarding etiology continue to be raised. Neurodevelopmental function tests have been used in epidemiology studies to evaluate relationships between environmental chemical exposures and neurodevelopmental deficits. Limitations of currently used tests and difficulties with their interpretation have been described, but a comprehensive critical examination of tests commonly used in studies of environmental chemicals and pediatric neurodevelopmental disorders has not been conducted. We provide here a listing and critical evaluation of commonly used neurodevelopmental tests in studies exploring effects from chemical exposures and recommend measures that are not often used, but should be considered. We also discuss important considerations in selecting appropriate tests and provide a case study by reviewing the literature on polychlorinated biphenyls

Evaluation of the Bangor Dyslexia Test (BDT) for use with Adults

The Bangor Dyslexia Test (BDT) is a short, easy-to-administer screener for use with a broad age range, which has been in use in the UK for over three decades. A distinctive feature of the battery is its focus on skills requiring aspects of verbal and phonological processing without, however, measuring literacy skills per se. Despite its longstanding existence and usage, there has been no evaluation of the psychometric properties of the battery as an adult dyslexia screener. We examined the psychometric properties of the BDT and evaluated its capacity to discriminate between adults with and without dyslexia. A large archival sample of university students with dyslexia (n�=�193) and students with no reported literacy difficulties (n�=�40) were compared on the BDT as well as on literacy and cognitive measures. Statistical analyses revealed the BDT to be a reliable (α�=�.72) and valid dyslexia screening tool with the capacity to effectively identify adults at risk of the disorder with an overall classification rate of 94% (sensitivity 96.4% and specificity 82.5%). In addition, higher indices of dyslexia risk on the BDT were associated with lower scores on standardized measures of literac

Non-invasive beam profile monitor for medical accelerators

A beam profile monitor based on a supersonic gas-curtain is currently under development for transverse profile diagnostics of electron and proton beams in the High Luminosity LHC. This monitor uses a thin supersonic gas curtain that crosses the primary beam to be characterized under an angle of 45 degrees. The fluorescence caused by the interaction between the beam and gas-curtain is detected using a specially designed imaging system to determine the 2D transverse profile of the primary beam. Another prototype monitor based on beam induced ionization is installed at The Cockcroft Institute. This paper presents the design features of both the monitors, the gas-jet curtain formation and various experimental tests, including profile measurements of an electron beam, using helium, nitrogen and neon as gases. Such a non-invasive online beam profile monitor would be highly desirable also for medical LINAC’s and storage rings as it can characterize the beam without stopping machine operation. The paper discusses opportunities for simplifying the monitor design for integration into a medical accelerator and expected monitor performance