DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (?, G) and population differentiation statistics (D, GST ', ? test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society.

Awareness and knowledge of autism and autism interventions: A general population survey.

Recent figures show that Autism Spectrum Disorder (ASD) affects at least 1 in 88 of the population, yet for years, international public awareness of ASD was limited. Over the past 5-10 years intense efforts have been made to raise autism awareness in the general population in countries such as UK and US. In this paper we report data from a large-scale general population survey (n=1204) in which we assessed autism awareness, knowledge about autism, and perceptions about autism interventions in Northern Ireland. We found high levels of autism awareness, in fact over 80% of the sample were aware of ASD and over 60% of these respondents knew someone with ASD in their own family, circle of friends or work colleagues. Generally, knowledge of strengths and challenges faced by individuals with ASD was relatively accurate. However, perceptions of interventions and service provider responsibilities were vague and uncertain. Results show that local and international autism awareness campaigns have largely been successful and that the focus should shift towards disseminating accurate information regarding intervention and service provider responsibilities.

Dimensions of religious and national identity among Irish adolescents growing up in two jurisdictions

This poster explores the impact of growing up in different socio-political environments in the border areas of the Republic of Ireland (RoI) and Northern Ireland (NI) on adolescents’ evaluations of their religious and national identities. The vast majority of the population of the Republic of Ireland are Catholic and Irish whereas in Northern Ireland, the majority are Protestant and British. 713 adolescents (NI= 415; RoI=298), who categorised their religious identity as Catholic and their nationality as Irish completed the Collective Self – Esteem (CSE) scale (Crocker & Luhtanen, 1990) with reference to either their religious (N=350) or national identity (n=363). The overall rating of CSE for the Irish identity was significantly higher than the rating of CSE for the Catholic Identity. This result was modified by a significant interaction - adolescents in the Republic of Ireland rated the CSE of their Irish nationality higher than those in Northern Ireland (20.99 vs. 19.95), whereas adolescents in Northern Ireland rated the CSE of their Catholic religious identity higher than their peers in the Republic of Ireland (19.97 vs 18.87). Further analysis of the CSE subscales revealed differing patterns of relationships according to the scale. The evaluation of the Public Collective Self-Esteem of national and religious identities were significantly higher in the Republic of Ireland than in Northern Ireland, however Private Collective Self-esteem did not differ according to jurisdiction. These findings are discussed in relation to the social context and current theoretical accounts of collective identification processes.

Excess mortality in Type 1 diabetes diagnosed in childhood and adolescence: a systematic review of population-based cohorts

Aims: Systematic review of mortality in childhood-/adolescent-diagnosed Type 1 diabetes and examination of factors explaining the mortality variation between studies. 
Methods: Relevant studies were identified from systematic searches of MEDLINE and EMBASE. Observed and expected numbers of deaths were extracted, and standardised mortality ratios (SMRs) and 95 % confidence intervals (CIs) were calculated. Negative binomial regression was used to investigate association between mortality and study/country characteristics.
Results: Thirteen relevant publications with mortality data were identified describing 23 independent studies. SMRs varied markedly ranging from 0 to 854 (chi-squared = 70.68,df = 21, p<0.0001). Significant associations were observed between SMR and mid-year of follow-up [incidence rate ratio (IRR) 0.95, 95 % CI 0.91–0.99 equivalent to a 5 % decrease per year], between SMR and infant mortality rate (IRR 1.07, 95 % CI 1.02–1.12, a 7 % increase for each death per 1,000 live births) and, after omitting an outlier, between SMR and health expenditure as a percentage of gross domestic product (GDP) (IRR 0.79, 95 % CI 0.68–0.93, a 21 % decrease for each one percent increase in GDP). No relationship was detected between SMR and a country’s childhood diabetes incidence rate or GDP.
Conclusions: Excess mortality in childhood-/adolescent diagnosed Type 1 diabetes is apparent across countries worldwide. Excesses were less marked in more recent studies and in countries with lower infant mortality and higher health expenditure.

Pupillary and visual thresholds in young children as an index of population vitamin A status

A prototype scotopic sensitivity machine was used to evaluate pupillary and visual thresholds for 295 Indonesian children aged 1-5 y, most of whom were initially vitamin A-deficient. Subjects were tested 6 and 9 mo after receiving a high dose of vitamin A. A group of 136 older children was tested at 6 mo after dosing; all subjects underwent testing at 9 mo. After testing at 9 mo, children randomly received either a second high dose of vitamin A or placebo and were tested a final time 2 wk later. Children with abnormal pupillary thresholds had significantly higher relative dose responses (RDRs) (P < 0.01) and significantly lower serum retinol values (P = 0.05) than did normal children. The mean pupillary threshold rose (eg, retinal sensitivity fell) as vitamin A status deteriorated between 6 and 9 mo after initial dosing, and was significantly different from a group of normal American children tested previously (P < 0.001). After placebo-controlled dosing, the decline in pupillary and visual thresholds (rise in retinal sensitivity) was significant for children receiving vitamin A but not for children receiving placebo.

Prevalence of cataract and pseudophakia/aphakia among adults in the United States.

OBJECTIVES:

To determine the prevalence of cataract and pseudophakia/aphakia in the United States and to project the expected change in these prevalence figures by 2020.

METHODS:

Summary prevalence estimates of cataract and of pseudophakia/aphakia were prepared separately for black, white, and Hispanic persons (for whom only cataract surgery data were available) in 5-year age intervals starting at 40 years for women and men. The estimates were based on a standardized definition of various types of cataract: cortical, greater than 25% of the lens involved; posterior subcapsular, present according to the grading system used in each study; and nuclear, greater than or equal to the penultimate grade in the system used. Data were collected from major population-based studies in the United States, and, where appropriate, Australia, Barbados, and Western Europe. The age-, gender-, and race/ethnicity-specific rates were applied to 2000 US Census data, and projected population figures for 2020, to obtain overall estimates.

RESULTS:

An estimated 20.5 million (17.2%) Americans older than 40 years have cataract in either eye, and 6.1 million (5.1%) have pseudophakia/aphakia. Women have a significantly (odds ratio = 1.37; 95% confidence interval, 1.26-1.50) higher age-adjusted prevalence of cataract than men in the United States. The total number of persons who have cataract is estimated to rise to 30.1 million by 2020; and for those who are expected to have pseudophakia/aphakia, to 9.5 million.

CONCLUSION:

The number of Americans affected by cataract and undergoing cataract surgery will dramatically increase over the next 20 years as the US population ages.

Population and landscape genetics of the stone marten and red fox in Portugal : implications for conservation management of common carnivores

Tese de doutoramento, Biologia (Biologia da Conservação), Universidade de Lisboa, Faculdade de Ciências, 2015

Housing and neighbourhood development plans: an initial assessment of opportunities and impact of the Localism Act 2011 in England

The Localism Act 2011 created an opportunity for local communities to form Neighbourhood Forums and to prepare their own Neighbourhood Development Plans in urban and rural areas in England. Initial reactions suggested that, rather than leading to the development of more housing, these initiatives would confirm all the stereotypes of local residents blocking unwanted development in their defined neighbourhoods. However, neighbourhood plans need to be in general conformity with the Core Strategies of higher-tier plans and have to undergo an examination by an independent person appointed by government. This paper discusses the role and purpose of neighbourhood plans and the evidence base on which they are founded. It then reviews the ways in which housing strategies and evidence of need are reflected in a sample of plans which have been adopted to date. It concludes with an assessment of the broader impact of neighbourhood plans on the planning process.

Changes of overweight and obesity in the adult Swiss population according to educational level, from 1992 to 2007.

In many high income developed countries, obesity is inversely associated with educational level. In some countries, a widening gap of obesity between educational groups has been reported. The aim of this study was to assess trends in body mass index (BMI) and in prevalence of overweight and obesity and their association with educational level in the adult Swiss population. Four cross-sectional National health interview surveys conducted in 1992/93 (n = 14,521), 1997 (n = 12,474), 2002 (n = 18,908) and 2007 (n = 17,879) using representative samples of the Swiss population (age range 18-102 years). BMI was derived from self-reported data. Overweight was defined as BMI > or = 25 and <30 kg/m(2), and obesity as BMI > or = 30 kg/m(2). Mean (+/- standard deviation) BMI increased from 24.7 +/- 3.6 in 1992/3 to 25.4 +/- 3.6 kg/m2 in 2007 in men and 22.8 +/- 3.8 to 23.7 +/- 4.3 kg/m(2) in women. Between 1992/3 and 2007, the prevalence of overweight + obesity increased from 40.4% to 49.5% in men and from 22.3% to 31.3% in women, while the prevalence of obesity increased from 6.3% to 9.4% in men and from 4.9% to 8.5% in women. The rate of increase in the prevalence of obesity was greater between 1992/3 and 2002 (men: +0.26%/year; women: +0.31%/year) than between 2002 and 2007 (men: +0.10%/year; women: +0.10%/year). A sizable fraction (approximately 25%) of the increasing mean BMI was due to increasing age of the participants over time. The increase was larger in low than high education strata of the population. BMI was strongly associated with low educational level among women and this gradient remained fairly constant over time. A weaker similar gradient by educational level was apparent in men, but it tended to increase over time. In Switzerland, overweight and obesity increased between 1992 and 2007 and was associated with low education status in both men and women. A trend towards a stabilization of mean BMI levels was noted in most age categories since 2002. The increase in the prevalence of obesity was larger in low education strata of the population. These findings suggest that obesity preventive measures should be targeted according to educational level in Switzerland.

Safety and occlusion rates of surgical treatment of unruptured intracranial aneurysms: a systematic review and meta-analysis of the literature from 1990 to 2011.

BACKGROUND AND PURPOSE: Surgical clipping of unruptured intracranial aneurysms (UIAs) has recently been challenged by the emergence of endovascular treatment. We performed an updated systematic review and meta-analysis on the surgical treatment of UIAs, in an attempt to determine the aneurysm occlusion rates and safety of surgery in the modern era. METHODS: A detailed protocol was developed prior to conducting the review according to the Cochrane Collaboration guidelines. Electronic databases spanning January 1990-April 2011 were searched, complemented by hand searching. Heterogeneity was assessed using I(2), and publication bias with funnel plots. Surgical mortality and morbidity were analysed with weighted random effect models. RESULTS: 60 studies with 9845 patients harbouring 10 845 aneurysms were included. Mortality occurred in 157 patients (1.7%; 99% CI 0.9% to 3.0%; I(2)=82%). Unfavourable outcomes, including death, occurred in 692 patients (6.7%; 99% CI 4.9% to 9.0%; I(2)=85%). Morbidity rates were significantly greater in higher quality studies, and with large or posterior circulation aneurysms. Reported morbidity rates decreased over time. Studies were generally of poor quality; funnel plots showed heterogeneous results and publication bias, and data on aneurysm occlusion rates were scant. CONCLUSIONS: In studies published between 1990 and 2011, clipping of UIAs was associated with 1.7% mortality and 6.7% overall morbidity. The reputed durability of clipping has not been rigorously documented. Due to the quality of the included studies, the available literature cannot properly guide clinical decisions.

Demographic and genetic attributes of dispersing and resident individuals of an enclosed Microtus pennsylvanicus population

A dispersal polymorphism may exist in emigrants from cyclic populations of Microtus '~nnsylvanicus biasing trap-revealed movements of unenclosed animals in favour of sedentary or colonizing individuals. The dispersal tendency of emigrants from an enclosed population was investigated by releasing animals via tubes into one of two adjacent enclosures, one vacant and one inhabited. Individuals from the enclosed population were monitored for age, sex, weight and electrophoretically detectable serum transferrin genotype in an intensive live-trapping program. In 1973 the minimum number alive in the introduced enclosed study population reached approximately l67/ha when breeding stopped in October. In 1974 intensive breeding increased the population density to 333/ha by mid-July when a long decline in numbers and breeding intensity began without an intervening plateau. An adjacent unenclosed area had a much lower density and longer breeding season in 1974. The growth rate of young males in the enclosed population tended to be lowest during the decline period in 1974. Survival of the enclosed population was high throughout but was lowest during the decline phase in both sexes, especially males. Low transferrin heterozygote survival during the decline coincided with a significant heterozygote deficiency in females whereas in males genotype frequencies did not depart from Hardy-Weinberg equilibrium values throughout th.e study. Twenty-nine suitable ani.mals were released during the decline in five periods from July to November 1974. The proportions of males and transferrin heterozygotes in the released graun were generally greater than in the source population~ In the test enclosures 21% of the released animals continued their movement through the vacant area while 41% (no significant difference) moved through the inhabited enclosure. In the vacant test area, females had a greater tendency than males to continue dispersal whereas no difference was noted in the inhabited area. Low frequency of captures in the tubes, predator disturbances and cold weather forced the termination of the study. The role of dispersal as a population regulating mechanism was further substantiated. The genetic differences between emigrant and resident animals lend support to Howard's hypothesis that a genetic polymorphism influences the tendency to disperse. Support is also given to Myers' and Krebs' contention that among dispersers an additional density dependent polymorphism influences the distance dispersed.