Sex chromosomes and genetic association studies.

Although the literature concerning statistical testing for genotype-phenotype association in family-based and population-based studies is very extensive, until recently the sex chromosomes have received little attention. Here it is shown that the X chromosome in particular presents special problems with respect to efficient analysis of mixed-sex population studies, and as a result of X inactivation. This paper reviews recent developments in approaching these problems.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Review of best management practices for aquatic vegetation control in stormwater ponds, wetlands, and lakes

Auckland Council (AC) is responsible for the development and operation of a stormwater network across the region to avert risks to citizens and the environment. Within this stormwater network, aquatic vegetation (including plants, unicellular and filamentous algae) can have both a positive and negative role in stormwater management and water quality treatment. The situations where management is needed to control aquatic vegetation are not always clear, and an inability to identify effective, feasible and economical control options may constrain management initiatives. AC (Infrastructure and Technical Services, Stormwater) commissioned this technical report to provide information for decision- making on aquatic vegetation management with in stormwater systems that are likely to experience vegetation-related issues. Information was collated from a comprehensive literature review, augmented by knowledge held by the authors. This review identified a wide range of management practices that could be potentially employed. It also demonstrated complexities and uncertainties relating to these options that makes the identification of a best management practice difficult. Hence, the focus of this report was to enable users to screen for potential options, and use reference material provided on each option to confirm the best practice to employ for each situation. The report identifies factors to define whether there is an aquatic vegetation problem (Section 3.0), and emphasises the need for agreed management goals for control (e.g. reduction, mitigation, containment, eradication). Resources to screen which management option(s) to employ are provided (Section 4.0), relating to the target aquatic vegetation, likely applicability of options to the system being managed, indicative cost, and ease of implementation. Initial screening allows users to shortlist potential control options for further reference (Section 5.0). Thirty-five control options are described (Section 5.0) in sufficient detail to consider applicability to individual sites and species. These options are grouped under categories of biological, chemical or physical control. Biological control options involve the use of organisms to predate, infect or control vegetation growth (e.g. classical biological control) or manipulate conditions to control algal growth (e.g. pest fish removal, microbial products). Chemical control options involve the use of pesticides and chemicals (e.g. glyphosate, diquat), or the use of flocculants and nutrient inactivation products that are used to reduce nutrient loading, thereby decreasing algal growth. Physical control options involve removing vegetation or algal biomass (e.g. mechanical or manual harvesting), or setting up barriers to their growth (e.g. shading, bottom lining, sediment capping). Preventative management options are usually the most cost effective, and these are also briefly described (Section 6.0). For example, the use of hygiene or quarantine protocols can reduce weed introductions or spread. Catchment- based practices to reduce sediment and nutrient sources to stormwater are likely to assist in the avoidance of algal and possibly aquatic plant problems. Nutrient removal may be a co-benefit where harvesting of submerged weed biomass is undertaken in stormwater systems. It should also be considered that removal of substantial amounts of submerged vegetation may result in a sudden and difficult-to-reverse s witch to a turbid, phytoplankton dominated state. Another possible solution is the conversion of systems that experience aquatic vegetation issues, to systems that are less likely to experience issues. The focus of this report is on systems that receive significant stormwater inputs, i.e. constructed bodies, including ponds, amenity lakes, wetlands, and highly-modified receiving bodies. However, some information will have application to other natural water bodies

The ongoing pursuit of R Coronae Borealis stars: the ASAS-3 survey strikes again

CONTEXT: R Coronae Borealis stars( RCBs) are rare, hydrogen-deficient, carbon rich super giant variable stars that are likely the evolved merger products of pairs of CO and He white dwarfs. Only 55 RCB stars have been found in our galaxy and their distribution on the sky is weighted heavily by microlensing survey field positions. A less biased wide-area survey would enable us to test competing evolutionary scenarios, understand the population or populations that produce RCBs, and constrain their formation rate. AIMS: The ASAS-3 survey monitored the sky south of declination +28deg between 2000 and 2010 to a limiting magnitude of V = 14. We searched ASAS-3 for RCB variables using several different methods to ensure that the probability of RCB detection was as high as possible and to reduce selection biases based on luminosity, temperature, dust production activity and shell brightness. METHODS: Candidates whose light curves were visually inspected were pre-selected based on their infrared (IR) excesses due to warm dust in their circumstellar shells using the WISE and/or 2MASS catalogues. Criteria on light curve variability were also applied when necessary to minimise the number of objects. Initially, we searched for RCB stars among the ASAS-3 ACVS1.1 variable star catalogue, then among the entire ASAS-3 south source catalogue, and finally directly interrogated the light curve database for objects that were not catalogued in either of those. We then acquired spectra of 104 stars to determine their real nature using the SSO/WiFeS spectrograph. RESULTS: We report 21 newly discovered RCB stars and 2 new DY Per stars. Two previously suspected RCB candidates were also spectroscopically confirmed. Our methods allowed us to extend our detection efficiency to fainter magnitudes that would not have been easily accessible to discovery techniques based onlight curve variability. The overall detection efficiencyis about 90% for RCBs with maximum light brighter than V ∼13. CONCLUSIONS: With these new discoveries, 76 RCBs are now known in our Galaxy and 22 in the Magellanic Clouds. This growing sample is of great value to constrain the peculiar and disparate atmosphere composition of RCBs. Most importantly, we show that the spatial distribution and apparent magnitudes of Galactic RCB stars is consistent with RCBs being part of the Galactic bulge population.Department of HE and Training approved lis

A Method to Address Differential Bias in Genotyping in Large-Scale Association Studies

In a previous paper we have shown that, when DNA samples for cases and controls are prepared in different laboratories prior to high-throughput genotyping, scoring inaccuracies can lead to differential misclassification and, consequently, to increased false-positive rates. Different DNA sourcing is often unavoidable in large-scale disease association studies of multiple case and control sets. Here, we describe methodological improvements to minimise such biases. These fall into two categories: improvements to the basic clustering methods for identifying genotypes from fluorescence intensities, and use of “fuzzy” calls in association tests in order to make appropriate allowance for call uncertainty. We find that the main improvement is a modification of the calling algorithm that links the clustering of cases and controls while allowing for different DNA sourcing. We also find that, in the presence of different DNA sourcing, biases associated with missing data can increase the false-positive rate. Therefore, we propose the use of “fuzzy” calls to deal with uncertain genotypes that would otherwise be labeled as missing

Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13

Following the recent success of genome-wide association studies in uncovering disease-associated genetic variants, the next challenge is to understand how these variants affect downstream pathways. The most proximal trait to a disease-associated variant, most commonly a single nucleotide polymorphism (SNP), is differential gene expression due to the cis effect of SNP alleles on transcription, translation, and/or splicing gene expression quantitative trait loci (eQTL). Several genome-wide SNP–gene expression association studies have already provided convincing evidence of widespread association of eQTLs. As a consequence, some eQTL associations are found in the same genomic region as a disease variant, either as a coincidence or a causal relationship. Cis-regulation of RPS26 gene expression and a type 1 diabetes (T1D) susceptibility locus have been colocalized to the 12q13 genomic region. A recent study has also suggested RPS26 as the most likely susceptibility gene for T1D in this genomic region. However, it is still not clear whether this colocalization is the result of chance alone or if RPS26 expression is directly correlated with T1D susceptibility, and therefore, potentially causal. Here, we derive and apply a statistical test of this hypothesis. We conclude that RPS26 expression is unlikely to be the molecular trait responsible for T1D susceptibility at this locus, at least not in a direct, linear connection

Treating and Preventing Influenza in Aged Care Facilities: A Cluster Randomised Controlled Trial

PMCID: PMC3474842This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Interventions in measles outbreaks: the potential reduction in cases associated with school suspension and vaccination interventions

Background: Measles is resurgent in the US, with more cases in 2019 than any year since 1992. Many of the cases were concentrated in three outbreaks in New York and Washington states, where local governments enacted intervention strategies in an attempt to limit the spread of measles. Regulations differed by location, suggesting guidance on the optimal interventions may be beneficial. Methods: We simulate the daily interactions of the populations of six metropolitan areas of Texas, US, using an agent-based model. The real-life vaccination rates of each school in these metropolitan areas are applied to simulated equivalents. A single case of measles is introduced to the population and the resulting number of cases counted. A range of public health interventions, focused on suspending unvaccinated students and mandatory vaccinations, were simulated during measles outbreaks and the reduction in the number of measles cases, relative to no intervention, recorded. Interventions were simulated only in schools with measles cases and in all schools in each metropolitan area. Results: Suspending unvaccinated students from school was associated with the greatest reduction in measles cases. In a plausible worst-case outbreak scenario, the number of cases is forecast to reduce by 68-96%. Interventions targeting all schools in a metropolitan area is not found to be associated with fewer measles cases than only targeting schools with measles cases, at 2018 vaccination rates. Targeting all schools also increases the cumulative number of school days missed by suspended students by a factor of 10-100, depending on the metropolitan area, compared to targeting only schools with measles cases. If vaccination rates drop 5% in the schools which are under-vaccinated in 2018, metropolitan area-wide interventions are forecast to be associated with fewer cases than school-specific interventions. Conclusions: Interventions that are quickly implemented and widely followed may reduce the size of measles outbreaks by up 96%. If vaccination rates continue to fall in Texas, metropolitan area-wide interventions should be considered in the event of an outbreak