Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brad

Genetic parameters for animal mortality in pasture-based, seasonal-calving dairy and beef herds

peer-reviewedIn the absence of informative health and welfare phenotypes, breeding for reduced animal mortality could improve overall health and welfare, provided genetic variability in animal mortality exists. The objective of the present study was to estimate genetic (and other) variance components for animal mortality in pasture-based, seasonal-calving dairy and beef herds across multiple life stages as well as to quantify the genetic relationship in mortality among life stages. National mortality records were available for all cattle born in the Republic of Ireland. Cattle were grouped into three life stages based on age (0 to 30 days, 31 to 365 days, 366 to 1095 days) whereas females with ≥1 calving event were also grouped into five life stages, based on parity number (1, 2, 3, 4, and 5), considering both the initial 60 days of lactation and a cow's entire lactation period, separately. The mean mortality prevalence ranged from 0.70 to 5.79% in young animals and from 0.53 to 3.86% in cows. Variance components and genetic correlations were estimated using linear mixed models using 21,637 to 100,993 records. Where heritability estimates were different from zero, direct heritability estimates for mortality in young animals (≤1095 days) ranged from 0.006 to 0.040, whereas the genetic standard deviation ranged from 0.015 to 0.034. The contribution of a maternal genetic effect to mortality in young animals was evident up to 30 days of age in dairy herds, but this was only the case in preliminary analysis of stillbirths in beef herds. Based on the estimated genetic standard deviation in the present study, the incidence of mortality in young animals could be reduced through breeding by up to 3.4 percentage units per generation. For cows, direct heritability estimates for mortality, where different from zero, ranged from 0.003 to 0.049. The genetic standard deviation for mortality in cows ranged from 0.005 to 0.016 during the initial 60 days of lactation and ranged from 0.011 to 0.032 during the cow's entire lactation. Genetic correlations among the age groups as well as between the age groups and cow parities had high standard errors. Genetic correlations among the cow parities were moderate to strongly positive (ranging from 0.66 to 0.99) and mostly different from zero. Results from the present study can be used to inform genetic evaluations for mortality in young animals and in cows as well as the potential genetic gain achievable

CREATE Project Report: Policy Assessment and Mapping of Policy Tools

The overall objective of the CREATE (Competitive Regions Employability of Adults through Education) Erasmus+ project is to enhance the performance and efficiency of Adult Education (AE) by identifying and disseminating the tools that exploit good practice in adult education policy making, implementation, and effectiveness. The EU recognises the need to act at local level to enhance coordination and planning of adult education policy, practice and funding (CEC 2012a) to achieve higher participation. Better coordination and planning will counter a mismatch between policy and reality at local level (CEC 2011). The outcome of the CREATE project will be an open accessible CREATE project virtual toolbox containing tools to enhance adult education policy making, implementation and evaluation. The development of this toolbox is one step to empower regional and local authorities with policy instruments to better shape policies and programmes for adult education, thereby better tackling the challenges of EU society and economy. This report profiles the tools, networks and platforms proposed by policy makers adn practioners in 29 local and regional authorities in 9 countries (P5 Adriatic Ionian Euroregion represents 26 regional/local authorities from 6 countries) that asssit them in adult education policy making and implementation. This Policy Assessment and Mapping of Policy Toolswas produced as part of an two year ERASMUS Project (www.projectcreate.eu)

Is birthweight associated with total and aggressive/lethal prostate cancer risks? A systematic review and meta-analysis

BACKGROUND: It has been hypothesised that intrauterine exposures are important for subsequent prostate cancer risk. Prior epidemiological studies have used birthweight as a proxy of cumulative intrauterine exposures to test this hypothesis, but results have been inconsistent partly because of limited statistical power. METHODS: We investigated birthweight in relation to prostate cancer in the Medical Research Council (MRC) National Survey of Health and Development (NSHD) using Cox proportional hazards models. We then conducted a meta-analysis of birthweight in relation to total and aggressive/lethal prostate cancer risks, combining results from the NSHD analysis with 13 additional studies on this relationship identified from a systematic search in four major scientific literature databases through January 2015. RESULTS: Random-effects models found that per kg increase in birthweight was positively associated with total (OR=1.02, 95% confidence interval (95% CI)=1.00, 1.05; I(2)=13%) and aggressive/lethal prostate cancer (OR=1.08, 95% CI=0.99, 1.19; I(2)=40%). Sensitivity analyses restricted to studies with birthweight extracted from medical records demonstrated stronger positive associations with total (OR=1.11, 95% CI=1.03, 1.19; I(2)=0%) and aggressive/lethal (OR=1.37, 95% CI=1.09, 1.74; I(2)=0%) prostate cancer. These studies heavily overlapped with those based in Nordic countries. CONCLUSIONS: This study provides evidence that heavier birthweight may be associated with modest increased risks of total and aggressive/lethal prostate cancer, which supports the hypothesis that intrauterine exposures may be related to subsequent prostate cancer risks

The Effects of Low and High Gravity on Neurospora Crassa

We studied the effects of different gravity levels on Neurospora crassa and its morphology. This research was conducted by simulating low and high gravity effects in different operating procedures. For the low gravity simulation, the experiment was conducted by using a clinostat to constantly disorient the samples at a very slow rate. For the high gravity simulation, N. crassa was subjected to different amounts of g forces by placing the samples in a centrifuge and subjected the samples to increasing amounts of revolutions per minute. The results of these experiments conclude that in low-gravity situations, the N. crassa showed sparse growth and some cytoplasmic failure. In the high gravity situations, the samples showed that at around 1,000 to 2,000 RPMs, there were no changes in the morphology, but at higher RPMs like 3,000 or 4,000, there were some signs of cytoplasmic failure but no noticeable changes to morphology

Concomitant orbital and intracranial abscess: A rare complication of sinusitis

Background:  Intracranial and orbital abscesses in combination together are rare complications of sinusitis. They can be life-threatening and can result in multiple sequelae. Case presentation: A 9-year-old female presented with left periorbital swelling, gaze restriction and headache. Following scans, she underwent emergency endoscopic sinus surgery, evacuation of the intraorbital empyema and stereotactic mini-craniectomy with the evacuation of the extradural empyema as a joint case. The patient recovered well and was discharged to complete intravenous antibiotics for 6 weeks. Conclusion: In the pediatric population intracranial complications of acute sinusitis can have more devastating consequences. Therefore prompt recognition and management are essential within a multidisciplinary team setting. We also highlight the rarity of concomitant multi-site abscess formation and the need to be vigilant for same

Development Education in Ireland. Challenges and Opportunities for the Future.

The greatest difficulty we have in describing Development Education in Ireland in the present day is that the picture is so mixed. Measured in terms of activity there is a broad and significant network of groups active in promoting development education in both the formal and non-formal sectors, yet many of these groups are not confident of their impact, their sustainability or their place in the 'bigger' development education picture