Background: The construct of physical literacy is gaining traction internationally and yet measurement of physical literacy is in its infancy. This paper describes the development of a pictorial ...child report scale of perceived physical literacy based on the comprehensive Australian Physical Literacy Framework, which includes 30 elements within four domains (physical, psychological, cognitive and social).
Methods: An expert reference committee with academic and industry representatives from physical education, sport and education was formed to provide input to each stage of the process. Qualitative research methods were used to (a) determine a character that was gender neutral, not representative of a particular race or ethnicity and appealing to children, and (b) the content (i.e. relationship between item images, wording and format with the intended construct) and response processes (i.e. interpretation of items) of the Physical Literacy in Children Questionnaire (PL-C Quest). A total of 17 children aged 4-12 years were interviewed as part of the study.
Results: A 'bunny' character was preferred by children. Overall, children interpreted most images as intended by the researchers, and, in many cases, without having to hear the words that went with the images. Some of the image scenarios were amended and redrawn according to the suggestions received from children and the expert reference group.
Discussion: This study has provided qualitative evidence based on the content of the PL-C Quest elements and domains, on the ways respondents understand, and interpret the items. This is the first step towards the development and testing of a pictorial instrument to comprehensively measure children's self-perceived physical literacy.
To assess gamma-aminobutyric acid (GABA) plus homocarnosine (GABA+) and glutamate plus glutamine (GLX) concentrations in the frontal lobes of patients with idiopathic generalized epilepsy (IGE).
...Twenty-one patients and 17 healthy volunteers were studied. A single voxel was prescribed in each frontal lobe for each subject. Point-resolved spectroscopy (PRESS)-localized short echo time MR spectroscopy (MRS) was performed to measure GLX and the metabolites N-acetylaspartate plus N-acetylaspartylglutamate (NAAt), creatine and phosphocreatine (Cr), choline-containing compounds (Cho), and myo-inositol (Ins). A double quantum GABA filter was used to measure GABA+. Segmented T1-weighted images gave the tissue composition of the prescribed voxel.
Group comparisons showed elevation of GLX and reduction of NAAt in the patient group (p < 0.05). The metabolite ratios GLX/NAAt and GLX/Ins also showed elevation in IGE (p = 0.01). No group effect was observed for GABA+, Cr, or Cho. Ins concentrations were not significantly reduced in the patient group but were less in the subgroup of patients who were taking sodium valproate.
IGE was associated with bilateral frontal lobe metabolite changes. Elevation in GLX was observed, which may imply increased neuronal excitability, whereas reduction in NAAt suggests reduced overall neuronal numbers or neuronal dysfunction.
Within many research areas, such as transcriptomics, the millions of short DNA fragments (reads) produced by current sequencing platforms need to be assembled into transcript sequences before they ...can be utilized. Despite recent advances in assembly software, creating such transcripts from read data harboring isoform variation remains challenging. This is because current approaches fail to identify all variants present or they create chimeric transcripts within which relationships between co-evolving sites and other evolutionary factors are disrupted. We present VTBuilder, a tool for constructing non-chimeric transcripts from read data that has been sequenced from sources containing isoform complexity.
We validated VTBuilder using reads simulated from 54 Sanger sequenced transcripts (SSTs) expressed in the venom gland of the saw scaled viper, Echis ocellatus. The SSTs were selected to represent genes from major co-expressed toxin groups known to harbor isoform variants. From the simulated reads, VTBuilder constructed 55 transcripts, 50 of which had a greater than 99% sequence similarity to 48 of the SSTs. In contrast, using the popular assembler tool Trinity (r2013-02-25), only 14 transcripts were constructed with a similar level of sequence identity to just 11 SSTs. Furthermore VTBuilder produced transcripts with a similar length distribution to the SSTs while those produced by Trinity were considerably shorter. To demonstrate that our approach can be scaled to real world data we assembled the venom gland transcriptome of the African puff adder Bitis arietans using paired-end reads sequenced on Illumina's MiSeq platform. VTBuilder constructed 1481 transcripts from 5 million reads and, following annotation, all major toxin genes were recovered demonstrating reconstruction of complex underlying sequence and isoform diversity.
Unlike other approaches, VTBuilder strives to maintain the relationships between co-evolving sites within the constructed transcripts, and thus increases transcript utility for a wide range of research areas ranging from transcriptomics to phylogenetics and including the monitoring of drug resistant parasite populations. Additionally, improving the quality of transcripts assembled from read data will have an impact on future studies that query these data. VTBuilder has been implemented in java and is available, under the GPL GPU V0.3 license, from http:// http://www.lstmed.ac.uk/vtbuilder .
Summary Background Observational studies report that higher intake of dietary fibre (a heterogeneous mix including non-starch polysaccharides and resistant starches) is associated with reduced risk ...of colorectal cancer, but no randomised trials with prevention of colorectal cancer as a primary endpoint have been done. We assessed the effect of resistant starch on the incidence of colorectal cancer. Methods In the CAPP2 study, individuals with Lynch syndrome were randomly assigned in a two-by-two factorial design to receive 600 mg aspirin or aspirin placebo or 30 g resistant starch or starch placebo, for up to 4 years. Randomisation was done with a block size of 16. Post-intervention, patients entered into double-blind follow-up; participants and investigators were masked to treatment allocation. The primary endpoint for this analysis was development of colorectal cancer in participants randomly assigned to resistant starch or resistant-starch placebo with both intention-to-treat and per-protocol analyses. This study is registered, ISRCTN 59521990. Findings 463 patients were randomly assigned to receive resistant starch and 455 to receive resistant-starch placebo. At a median follow-up 52·7 months (IQR 28·9–78·4), 53 participants developed 61 primary colorectal cancers (27 of 463 participants randomly assigned to resistant starch, 26 of 455 participants assigned to resistant-starch placebo). Intention-to-treat analysis of time to first colorectal cancer showed a hazard ratio (HR) of 1·40 (95% CI 0·78–2·56; p=0·26) and Poisson regression accounting for multiple primary events gave an incidence rate ratio (IRR) of 1·15 (95% CI 0·66–2·00; p=0·61). For those completing 2 years of intervention, per-protocol analysis yielded a HR of 1·09 (0·55–2·19, p=0·80) and an IRR of 0·98 (0·51–1·88, p=0·95). No information on adverse events was gathered during post-intervention follow-up. Interpretation Resistant starch had no detectable effect on cancer development in carriers of hereditary colorectal cancer. Dietary supplementation with resistant starch does not emulate the apparently protective effect of diets rich in dietary fibre against colorectal cancer. Funding European Union, Cancer Research UK, Bayer Corporation, National Starch and Chemical Co, UK Medical Research Council, Newcastle Hospitals Trustees, Cancer Council of Victoria Australia, THRIPP South Africa, The Finnish Cancer Foundation, SIAK Switzerland, and Bayer Pharma.
We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the ~160-megabase genome, ...reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
A large number of variants identified through clinical genetic testing in disease susceptibility genes are of uncertain significance (VUS). Following the recommendations of the American College of ...Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion) can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analysis of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC) and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity—findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared with classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and preformatted Excel calculators for implementation of the method for rare variants in BRCA1, BRCA2, and other high-risk genes with known penetrance.
Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is ...increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as “metrics”. As such, their one‐dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end‐user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top‐ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.
• The effects of 7 yr enhanced nitrogen (N) deposition (3.5-14 g N m-2 yr-1) in combination with phosphorus (P) additions, on growth, shoot N and P content, and root-surface phosphomonoesterase (PME) ...activities were determined along with mycorrhizal infection rates in seedlings of a sedge (Carex flacca), grass (Koeleria macrantha) and forb (Leontodon hispidus). • Seedlings were grown for 14-28 d in mesh-walled cores inserted into turfs from treated field plots enabling complete root recovery. • After 14 d, root-surface PME activity was typically more than doubled by 3.5 and 14 g N m-2 yr-1,and by 28 d the N treatments consistently gave dose-dependent effects. PME activity was reduced by P additions in the sedge and grass by 55 and 65%, respectively, and correlated with soil and shoot N and P concentrations, again most strongly in the sedge and grass. Mycorrhizal infection was least in the sedge (1%) and greater in the grass (49%) and forb (76%). • Long-term N enrichment of calcareous grassland stimulates root-surface PME in representatives of the three major higher-plant functional types. PME response to P additions was greatest in least mycorrhizal-dependant species with roots more adapted for direct P uptake.
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