Crustal deformation at the Sumatran Subduction Zone revealed by coral rings

Analyses of coral rings grown in the interval 1970–1997 reveal a geographically distinct pattern of interseismic uplift off Sumatra's western coast. At distances less than 110 km from the Sumatran trench, coral reefs are submerging as fast as 5 mm/y. At 130 and 180 km distance from the trench, they are emerging at similar rates. We suggest that a locked, or partially locked patch, located above 30 km depth on the upper surface of the subducting oceanic plate, generates this pattern

Marginal likelihoods in phylogenetics: a review of methods and applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation (ABC) to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.Comment: 33 pages, 3 figure

Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending.

Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium, and Salmonella. Consumer microbial risks of surface source water quality (impacted by 0-100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0-100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10-4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10-4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR

Why HITnet kiosks didn\u27t hit the mark for sexual health education of Western Australian Aboriginal youth

Objective: To assess the use, appropriateness of, and staff feedback on specific sexual health modules, which were installed on Heuristic Interactive Technology (HITnet) kiosks at Aboriginal Community Controlled Health Services (ACCHS). The HITnet kiosks were aimed at Aboriginal youth visiting these sites. Methods: Modules on the HITnet kiosks were assessed for (1) cultural appropriateness using Yunkaporta’s Aboriginal pedagogy framework and (2) compliance with the World Health Organization’s (WHO) advice on key elements for comprehensive sexual health education for young people. Data measuring kiosk use were obtained through HITnet kiosk activity reports. An online survey of ACCHS staff was used to qualitatively assess use of, and staff perceptions of, HITnet kiosks. Results: Kiosk modules were consistent with seven of the eight elements of Yunkaporta’s framework and all of the WHO recommendations. The most popular module generated 3,066 purposeful sessions and the least popular module generated 724 purposeful sessions across nine sites in 2012. While teenagers were the most frequent of the kiosk user groups (39.5% in 2012), the majority of users (56%) were not in the target group (i.e. elders 4%, adults 25%, children 27%). Key issues reported by ACCHS staff (n=11) included: lack of clarity regarding staff responsibility for overseeing kiosk functionality; kiosks attracting “inappropriate ages”; and “lack of privacy” based on kiosk location, screen visibility, and absence of headphones preventing discreet access. Conclusions: The modules were tailored to a young Aboriginal audience through technology thought to be appealing to this group. However, barriers to use of the kiosk included kiosk design features, location, and lack of clarity around responsibility for kiosk operation. Implications: Aboriginal youth need easy access to sexual health messages in a ‘safe’, non-judgmental space. Information and communication that is accessible via personal and mobile devices may be a better vehicle than public kiosks

Timing of progression from Chlamydia trachomatis infection to pelvic inflammatory disease: a mathematical modelling study

PMCID: PMC3505463The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2334/12/187. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Characterization of serine proteinase expression in agaricus bisporus and coprinopsis cinerea by using green fluorescent protein and the A. bisporus SPR1 Promoter

The Agaricus bisporus serine proteinase 1 (SPR1) appears to be significant in both mycelial nutrition and senescence of the fruiting body. We report on the construction of an SPR promoter::green fluorescent protein (GFP) fusion cassette, pGreen_hph1_SPR_GFP, for the investigation of temporal and developmental expression of SPR1 in homobasidiomycetes and to determine how expression is linked to physiological and environmental stimuli. Monitoring of A. bisporus pGreen_hph1_SPR_GFP transformants on media rich in ammonia or containing different nitrogen sources demonstrated that SPR1 is produced in response to available nitrogen. In A. bisporus fruiting bodies, GFP activity was localized to the stipe of postharvest senescing sporophores. pGreen_hph1_SPR_GFP was also transformed into the model basidiomycete Coprinopsis cinerea. Endogenous C. cinerea proteinase activity was profiled during liquid culture and fruiting body development. Maximum activity was observed in the mature cap, while activity dropped during autolysis. Analysis of the C. cinerea genome revealed seven genes showing significant homology to the A. bisporus SPR1 and SPR2 genes. These genes contain the aspartic acid, histidine, and serine residues common to serine proteinases. Analysis of the promoter regions revealed at least one CreA and several AreA regulatory motifs in all sequences. Fruiting was induced in C. cinerea dikaryons, and fluorescence was determined in different developmental stages. GFP expression was observed throughout the life cycle, demonstrating that serine proteinase can be active in all stages of C. cinerea fruiting body development. Serine proteinase expression (GFP fluorescence) was most concentrated during development of young tissue, which may be indicative of high protein turnover during cell differentiatio

Rapid descriptive consumer analysis using simultaneous and monadic sample presentation for coffee

The objective of this study was to investigate how rapid descriptive consumer analysis using simultaneous presentation of samples compared with monadic presentation of samples, using both affective and descriptive sensory evaluation methods. Simultaneous presentation of coffee samples for sensory acceptance testing, using ranking analysis, was conducted using naïve assessors. In a separate session, assessors evaluated the same coffee samples, using monadic presentation and employing the same scales. Similarly, descriptive consumer analysis, using simultaneous and monadic sample presentation, was conducted using descriptive attributes chosen by the panel. For RDA (Ranking descriptive analysis), coffee samples were presented simultaneously (randomised) to assessors and subsequently ranked. The process was then repeated using the same assessors; however, samples were presented in monadic and randomised presentation order. Data accumulated from the study were analysed by Analysis of Variance (APLSR-ANOVA Partial Least Squares Regression). Results obtained indicate that simultaneous presentation of samples was more effective than monadic presentation, as a larger amount of attributes with significant (P < 0.05) intensity differences were observed using RDA. Thus, simultaneous presentation of samples also allows ranking in SAT evaluation and proved a useful tool in establishing the hedonic attributes of products. We propose to call this method Ranking Acceptance Analysis (RAA)

The Youth Risk Behavior Survey (YRBS): Evolution of the Survey and Development of Customized Forms

The Youth Risk Behavior Survey is an effective tool in surveillance of youth risk behaviors. Since 1991, Centers for Disease Control and Prevention have been a rich source of support for implementing the YRBS. CDC provides sample surveys, nation-wide data for comparison purposes, and many other resources designed for successful implementation of a YRBS. CDC YRBS have some limitations and implementing their versions of the surveys might be problematic for some communities so it is common to see customization of the CDC YRBS. This paper highlights a brief history of the YRBS, mobilizing the community for input into the YRBS and examples of questions for customizing YRBS