Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.

BACKGROUND: While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS: Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS: Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.

Conversion of natural forests to managed forest plantations decreases tree resistance to prolonged droughts

© 2015 Published by Elsevier B.V.Throughout the southern US, past forest management practices have replaced large areas of native forests with loblolly pine plantations and have resulted in changes in forest response to extreme weather conditions. However, uncertainty remains about the response of planted versus natural species to drought across the geographical range of these forests. Taking advantage of a cluster of unmanaged stands (85-130year-old hardwoods) and managed plantations (17-20year-old loblolly pine) in coastal and Piedmont areas of North Carolina, tree water use, cavitation resistance, whole-tree hydraulic (Ktree) and stomatal (Gs) conductances were measured in four sites covering representative forests growing in the region. We also used a hydraulic model to predict the resilience of those sites to extreme soil drying. Our objectives were to determine: (1) if Ktree and stomatal regulation in response to atmospheric and soil droughts differ between species and sites; (2) how ecosystem type, through tree water use, resistance to cavitation and rooting profiles, affects the water uptake limit that can be reached under drought; and (3) the influence of stand species composition on critical transpiration that sets a functional water uptake limit under drought conditions. The results show that across sites, water stress affected the coordination between Ktree and Gs. As soil water content dropped below 20% relative extractable water, Ktree declined faster and thus explained the decrease in Gs and in its sensitivity to vapor pressure deficit. Compared to branches, the capability of roots to resist high xylem tension has a great impact on tree-level water use and ultimately had important implications for pine plantations resistance to future summer droughts. Model simulations revealed that the decline in Ktree due to xylem cavitation aggravated the effects of soil drying on tree transpiration. The critical transpiration rate (Ecrit), which corresponds to the maximum rate at which transpiration begins to level off to prevent irreversible hydraulic failure, was higher in managed forest plantations than in their unmanaged counterparts. However, even with this higher Ecrit, the pine plantations operated very close to their critical leaf water potentials (i.e. to their permissible water potentials without total hydraulic failure), suggesting that intensively managed plantations are more drought-sensitive and can withstand less severe drought than natural forests.

Using electronic health record data for substance use Screening, Brief Intervention, and Referral to Treatment among adults with type 2 diabetes: Design of a National Drug Abuse Treatment Clinical Trials Network study.

BACKGROUND: The Affordable Care Act encourages healthcare systems to integrate behavioral and medical healthcare, as well as to employ electronic health records (EHRs) for health information exchange and quality improvement. Pragmatic research paradigms that employ EHRs in research are needed to produce clinical evidence in real-world medical settings for informing learning healthcare systems. Adults with comorbid diabetes and substance use disorders (SUDs) tend to use costly inpatient treatments; however, there is a lack of empirical data on implementing behavioral healthcare to reduce health risk in adults with high-risk diabetes. Given the complexity of high-risk patients' medical problems and the cost of conducting randomized trials, a feasibility project is warranted to guide practical study designs. METHODS: We describe the study design, which explores the feasibility of implementing substance use Screening, Brief Intervention, and Referral to Treatment (SBIRT) among adults with high-risk type 2 diabetes mellitus (T2DM) within a home-based primary care setting. Our study includes the development of an integrated EHR datamart to identify eligible patients and collect diabetes healthcare data, and the use of a geographic health information system to understand the social context in patients' communities. Analysis will examine recruitment, proportion of patients receiving brief intervention and/or referrals, substance use, SUD treatment use, diabetes outcomes, and retention. DISCUSSION: By capitalizing on an existing T2DM project that uses home-based primary care, our study results will provide timely clinical information to inform the designs and implementation of future SBIRT studies among adults with multiple medical conditions.

SMERED: A Bayesian Approach to Graphical Record Linkage and De-duplication

We propose a novel unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation is to represent the pattern of links between records as a {\em bipartite} graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible new representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate $k$-way posterior probabilities of matches across records, and propagate the uncertainty of record linkage into later analyses. Our linkage structure lends itself to an efficient, linear-time, hybrid Markov chain Monte Carlo algorithm, which overcomes many obstacles encountered by previously proposed methods of record linkage, despite the high dimensional parameter space. We assess our results on real and simulated data.

The AASK database V4.0: aircraft accident statistics and knowledge. A database to record human experience of evacuation in aviation accidents

This paper describes the AASK database. The AASK database is unique as it is a record of human behaviour during survivable aviation accidents. The AASK database is compiled from interview data compiled by agencies such as the NTSB and the AAIB. The database can be found on the website http://fseg.gre.ac.uk

CAA paper 2006/01: a database to record human experience of evacuation in aviation accidents: the aircraft accident statistics and knowledge database (AASK)

This report concerns the development of the AASK V4.0 database (CAA Project 560/SRG/R+AD). AASK is the Aircraft Accident Statistics and Knowledge database, which is a repository of survivor accounts from aviation accidents. Its main purpose is to store observational and anecdotal data from interviews of the occupants involved in aircraft accidents. The AASK database has wide application to aviation safety analysis, being a source of factual data regarding the evacuation process. It is also key to the development of aircraft evacuation models such as airEXODUS, where insight into how people actually behave during evacuation from survivable aircraft crashes is required. With support from the UK CAA (Project 277/SRG/R&AD), AASK V3.0 was developed. This was an on-line prototype system available over the internet to selected users and included a significantly increased number of passenger accounts compared with earlier versions, the introduction of cabin crew accounts, the introduction of fatality information and improved functionality through the seat plan viewer utility. The most recently completed AASK project (Project 560/SRG/R+AD) involved four main components: a) analysis of the data collected in V3.0; b) continued collection and entry of data into AASK; c) maintenance and functional development of the AASK database; and d) user feedback survey. All four components have been pursued and completed in this two-year project. The current version developed in the last year of the project is referred to as AASK V4.0. This report provides summaries of the work done and the results obtained in relation to the project deliverables.

For the record

Discusses her film, For the Record, the making of which was funded by the Arts and Humanities Research Council. The research material used in the making of FOR THE RECORD consists of official records, private diaries, personal testimony, historical expert interviews and archive footage - all related to the Internment period 1956-1960 in Northern Ireland. Through the use of clips from the film and footage that did not make it into the final cut, this talk examines how selected material is used and to what purpose. FOR THE RECORD is a film about a daughter documenting a period in her father's life and centres on PJ McClean's prison diary, secretly written on the inside of envelopes during the first 30 days in his cell. This brings the viewer into the intimate space of personal testimony. This intimacy is also reflected in the interviews between father and daughter. Throughout the film the diaries are illustrated by experimental Super8 and 16mm footage shot by the filmmaker, over a period of 10 years, of home life. The film unravels the complex story of internment; the why, the how and the ‘for what’? Official records obtained from the Public Records Office Northern Ireland (which have been closed to the public for the past fifty years) combine with archive footage of the then Northern Irish Prime Minister, Basil Brookeborough, to give a wider political perspective to this personal testament. FOR THE RECORD deals with memory, memorabilia and the question of testimony in a complex political landscape. [From the Author]