REAPR: a universal tool for genome assembly evaluation.

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/

Meanings in motion and faces: Developmental associations between the processing of intention from geometrical animations and gaze detection accuracy

Aspects of face processing, on the one hand, and theory of mind (ToM) tasks, on the other hand, show specific impairment in autism. We aimed to discover whether a correlation between tasks tapping these abilities was evident in typically developing children at two developmental stages. One hundred fifty-four normal children (6-8 years and 16-18 years) and 13 high-IQ autistic children (11-17 years) were tested on a range of face-processing and IQ tasks, and a ToM test based oil the attribution of intentional movement to abstract shapes in a cartoon. By midchildhood, the ability accurately and spontaneously to infer the locus of attention of a face with direct or averted gaze was specifically associated with the ability to describe geometrical animations using mental state terms. Other face-processing and animation descriptions failed to show the association. Autistic adolescents were impaired at both gaze processing and ToM descriptions. using these tests. Mentalizing and gaze perception accuracy are associated in typically developing children and adolescents. The findings are congruent with the possibility that common neural Circuitry underlies, at least in part, processing implicated in these tasks. They are also congruent with the possibility that autism may lie at one end of a developmental continuum with respect to these skills, and to the factor(s) underpinning them

Confabulation in children with autism

Some children with high-functioning autistic spectrum conditions (ASC) have been noted clinically to produce accounts and responses akin to confabulations in neurological patients. Neurological confabulation is typically associated with abnormalities of the frontal lobes and related structures, and some forms have been linked to poor performance on source monitoring and executive function tasks. ASC has also been linked to atypical development of the frontal lobes, and impaired performance on source monitoring and executive tasks. But confabulation in autism has not to our knowledge previously been examined experimentally. So we investigated whether patterns of confabulation in autism might share similarities with neurologically-based confabulation. Tests of confabulation elicitation, source monitoring (reality monitoring, plus temporal and task context memory) and executive function were administered to four adolescents with ASC who had previously been noted to confabulate spontaneously in everyday life. Scores were compared to a typically developing (TD) and an ASC control group. One confabulating participant was significantly impaired at reality monitoring, and one was significantly worse at a task context test, relative to both the ASC and TD controls. Three of the confabulators showed impairment on measures of executive function (Brixton test; Cognitive Estimates test; Hayling Test B errors) relative to both control groups. Three were significantly poorer than the TD controls on two others (Hayling A and B times), but the ASC control group was also significantly slower at this test than the TD controls. Compared to TD controls, two of the four confabulating participants produced an abnormal number of confabulations during a confabulation elicitation questionnaire, where the ASC controls and TD controls did not differ from each other. These results raise the possibility that in at least some cases, confabulation in autism may be less related to social factors than it is to impaired source memory or poor executive function

Beneficial physiological effects with blackcurrant intake in endurance athletes

Blackcurrant contains anthocyanins, known to influence vasorelaxation and peripheral blood flow. We examined the effects of 7 days intake of Sujon New Zealand blackcurrant powder (6g/day) on the lactate curve, maximum oxygen uptake, and cardiovascular responses at rest and during cycling. Thirteen trained triathletes with >3 yrs experience (8 men, age: 38±8 yrs, body mass: 71±9 kg, BF%: 19±5%, mean±SD) performed two incremental cycling protocols with recording of physiological and cardiovascular responses (Portapres® Model 2). Cardiovascular function was also measured in rest. Experimental design was double-blind, placebo-controlled, randomized and cross-over (wash-out 4 wks). Data was analysed with two-tailed t-tests and 2-way ANOVA and significance accepted at p<0.05. Plasma lactate was lower at 40%, 50%, 60% and 70% of maximum power by 27%, 22%, 17% and 13%. Intensity at 4 mmol∙L-1 OBLA was 6% higher with blackcurrant without effect on heart rate and oxygen uptake. Maximum values of oxygen uptake, heart rate and power were not affected by blackcurrant, but obtained with 14% lower lactate. In rest, blackcurrant increased stroke volume and cardiac output by 25% and 26%, and decreased total peripheral resistance by 16%, with no changes in blood pressure and heart rate. Cardiovascular responses during exercise at 40%, 50%, 60%, 70% and 80% intensity were not affected. Sujon New Zealand blackcurrant powder affects lactate production and/or clearance during exercise. Sujon New Zealand blackcurrant powder affects physiological and cardiovascular responses in rest and during exercise that may have implications for exercise performance

Protocol for a systematic review of the use of narrative storytelling and visual-arts-based approaches as knowledge translation tools in healthcare

BACKGROUND: The arts are powerful, accessible forms of communication that have the potential to impart knowledge by attracting interest and developing meaningful connections. Knowledge translation aims to reduce the ‘evidence-practice’ gap by developing, implementing and evaluating strategies designed to enhance awareness and promote behavior change congruent with research evidence. Increasingly, innovative approaches such as narrative storytelling and other arts-based interventions are being investigated to bridge the growing gap between practice and research. This study is the first to systematically identify and synthesize current research on narrative storytelling and visual art to translate and disseminate health research. METHODS: A health research librarian will develop and implement search strategies designed to identify relevant evidence. Studies will be included if they are primary research employing narrative storytelling and/or visual art as a knowledge translation strategy in healthcare. Two reviewers will independently perform study selection, quality assessment, and data extraction using standard forms. Disagreements will be resolved through discussion or third party adjudication. Data will be grouped and analyzed by research design, type of knowledge translation strategy (that is, a narrative or visual-arts-based approach), and target audience. An overall synthesis across all studies will be conducted. DISCUSSION: The findings from this research project will describe the ‘state of the science’ regarding the use of narrative storytelling and visual art as knowledge translation strategies. This systematic review will provide critical information for: (1) researchers conducting knowledge translation intervention studies; (2) nursing, medicine, and allied healthcare professionals; (3) healthcare consumers, including patients and families; and (4) decision makers and knowledge users who are charged to increase use of the latest research in healthcare settings

Mystical orientation and the perceiving process : a study among Anglican clergymen

This study examines the hypothesised link between mystical orientation and the perceiving process within the Jungian model of psychological type. Data were provided by 232 Anglican clergymen serving in the Church in Wales who completed both the Francis-Louden Mystical Orientation Scale and the Francis Psychological Type Scales. The data demonstrated that intuitive types recorded significantly higher scores than sensing types on the index of mystical orientation, supporting the hypothesis based on Ross' thesis

Factors affecting continuation of clean intermittent catheterisation in people with multiple sclerosis: results of the COSMOS mixed-methods study

Background:  Clean intermittent catheterisation (CIC) is often recommended for people with multiple sclerosis (MS).  Objective:  To determine the variables that affect continuation or discontinuation of the use of CIC.  Methods:  A three-part mixed-method study (prospective longitudinal cohort (n = 56), longitudinal qualitative interviews (n = 20) and retrospective survey (n = 456)) was undertaken, which identified the variables that influenced CIC continuation/discontinuation. The potential explanatory variables investigated in each study were the individual’s age, gender, social circumstances, number of urinary tract infections, bladder symptoms, presence of co-morbidity, stage of multiple sclerosis and years since diagnosis, as well as CIC teaching method and intensity.  Results:  For some people with MS the prospect of undertaking CIC is difficult and may take a period of time to accept before beginning the process of using CIC. Ongoing support from clinicians, support at home and a perceived improvement in symptoms such as nocturia were positive predictors of continuation. In many cases, the development of a urinary tract infection during the early stages of CIC use had a significant detrimental impact on continuation.  Conclusion:  Procedures for reducing the incidence of urinary tract infection during the learning period (i.e. when being taught and becoming competent) should be considered, as well as the development of a tool to aid identification of a person’s readiness to try CIC

A randomised controlled trial of PEGASUS, a psychoeducational programme for young people with high-functioning autism spectrum disorder.

Psychoeducation is an essential component of postdiagnostic care for people with ASD (autism spectrum disorder), but there is currently no evidence base for clinical practice. We designed, manualised and evaluated PEGASUS (psychoeducation group for autism spectrum understanding and support), a group psychoeducational programme aiming to enhance the self-awareness of young people with ASD by teaching them about their diagnosis

Rural Clinician Scarcity and Job Preferences of Doctors and Nurses in India: A Discrete Choice Experiment

The scarcity of rural doctors has undermined the ability of health systems in low and middle-income countries like India to provide quality services to rural populations. This study examines job preferences of doctors and nurses to inform what works in terms of rural recruitment strategies. Job acceptance of different strategies was compared to identify policy options for increasing the availability of clinical providers in rural areas. In 2010 a Discrete Choice Experiment was conducted in India. The study sample included final year medical and nursing students, and in-service doctors and nurses serving at Primary Health Centers. Eight job attributes were identified and a D-efficient fractional factorial design was used to construct pairs of job choices. Respondent acceptance of job choices was analyzed using multi-level logistic regression. Location mattered; jobs in areas offering urban amenities had a high likelihood of being accepted. Higher salary had small effect on doctor, but large effect on nurse, acceptance of rural jobs. At five times current salary levels, 13% (31%) of medical students (doctors) were willing to accept rural jobs. At half this level, 61% (52%) of nursing students (nurses) accepted a rural job. The strategy of reserving seats for specialist training in exchange for rural service had a large effect on job acceptance among doctors, nurses and nursing students. For doctors and nurses, properly staffed and equipped health facilities, and housing had small effects on job acceptance. Rural upbringing was not associated with rural job acceptance. Incentivizing doctors for rural service is expensive. A broader strategy of substantial salary increases with improved living, working environment, and education incentives is necessary. For both doctors and nurses, the usual strategies of moderate salary increases, good facility infrastructure, and housing will not be effective. Non-physician clinicians like nurse-practitioners offer an affordable alternative for delivering rural health care

Eyebrow hairs from actinic keratosis patients harbor the highest number of cutaneous human papillomaviruses

BACKGROUND: Cutaneous human papillomavirus (HPV) infections seem to be associated with the onset of actinic keratosis (AK). This study compares the presence of cutaneous HPV types in eyebrow hairs to those in tissues of normal skin and skin lesions of 75 immunocompetent AK patients. METHODS: Biopsies from AK lesions, normal skin and plucked eyebrow hairs were collected from each patient. DNA from these specimens was tested for the presence of 28 cutaneous HPV (betaPV and gammaPV) by a PCR based method. RESULTS: The highest number of HPV prevalence was detected in 84% of the eyebrow hairs (63/75, median 6 types) compared to 47% of AK lesions (35/75, median 3 types) (p< 0.001) and 37% of normal skin (28/75, median 4 types) (p< 0.001), respectively. A total of 228 HPV infections were found in eyebrow hairs compared to only 92 HPV infections in AK and 69 in normal skin. In all three specimens HPV20, HPV23 and/or HPV37 were the most prevalent types. The highest number of multiple types of HPV positive specimens was found in 76% of the eyebrow hairs compared to 60% in AK and 57% in normal skin. The concordance of at least one HPV type in virus positive specimens was 81% (three specimens) and 88-93% of all three combinations with two specimens. CONCLUSIONS: Thus, eyebrow hairs revealed the highest number of cutaneous HPV infections, are easy to collect and are an appropriate screening tool in order to identify a possible association of HPV and AK