High Heritability Is Compatible with the Broad Distribution of Set Point Viral Load in HIV Carriers.

Set point viral load in HIV patients ranges over several orders of magnitude and is a key determinant of disease progression in HIV. A number of recent studies have reported high heritability of set point viral load implying that viral genetic factors contribute substantially to the overall variation in viral load. The high heritability is surprising given the diversity of host factors associated with controlling viral infection. Here we develop an analytical model that describes the temporal changes of the distribution of set point viral load as a function of heritability. This model shows that high heritability is the most parsimonious explanation for the observed variance of set point viral load. Our results thus not only reinforce the credibility of previous estimates of heritability but also shed new light onto mechanisms of viral pathogenesis

Predictors of Employee Involvement in a Worksite Health Promotion Program

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67001/2/10.1177_109019819001700404.pd

Cancer incidence in British vegetarians

Background: Few prospective studies have examined cancer incidence among vegetarians. Methods: We studied 61 566 British men and women, comprising 32 403 meat eaters, 8562 non-meat eaters who did eat fish ('fish eaters') and 20 601 vegetarians. After an average follow-up of 12.2 years, there were 3350 incident cancers of which 2204 were among meat eaters, 317 among fish eaters and 829 among vegetarians. Relative risks (RRs) were estimated by Cox regression, stratified by sex and recruitment protocol and adjusted for age, smoking, alcohol, body mass index, physical activity level and, for women only, parity and oral contraceptive use. Results: There was significant heterogeneity in cancer risk between groups for the following four cancer sites: stomach cancer, RRs (compared with meat eaters) of 0.29 (95% CI: 0.07–1.20) in fish eaters and 0.36 (0.16–0.78) in vegetarians, P for heterogeneity=0.007; ovarian cancer, RRs of 0.37 (0.18–0.77) in fish eaters and 0.69 (0.45–1.07) in vegetarians, P for heterogeneity=0.007; bladder cancer, RRs of 0.81 (0.36–1.81) in fish eaters and 0.47 (0.25–0.89) in vegetarians, P for heterogeneity=0.05; and cancers of the lymphatic and haematopoietic tissues, RRs of 0.85 (0.56–1.29) in fish eaters and 0.55 (0.39–0.78) in vegetarians, P for heterogeneity=0.002. The RRs for all malignant neoplasms were 0.82 (0.73–0.93) in fish eaters and 0.88 (0.81–0.96) in vegetarians (P for heterogeneity=0.001). Conclusion: The incidence of some cancers may be lower in fish eaters and vegetarians than in meat eaters

An Empirical Evaluation of Evolutionary Algorithms for Unit Test Suite Generation

Context: Evolutionary algorithms have been shown to be e ective at generating unit test suites optimised for code coverage. While many speci c aspects of these algorithms have been evaluated in detail (e.g., test length and di erent kinds of techniques aimed at improving performance, like seeding), the in uence of the choice of evolutionary algorithm has to date seen less attention in the literature. Objective: Since it is theoretically impossible to design an algorithm that is the best on all possible problems, a common approach in software engineering problems is to rst try the most common algorithm, a Genetic Algorithm, and only afterwards try to re ne it or compare it with other algorithms to see if any of them is more suited for the addressed problem. The objective of this paper is to perform this analysis, in order to shed light on the in uence of the search algorithm applied for unit test generation. Method: We empirically evaluate thirteen di erent evolutionary algorithms and two random approaches on a selection of non-trivial open source classes. All algorithms are implemented in the EvoSuite test generation tool, which includes recent optimisations such as the use of an archive during the search and optimisation for multiple coverage criteria. Results: Our study shows that the use of a test archive makes evolutionary algorithms clearly better than random testing, and it con rms that the DynaMOSA many-objective search algorithm is the most e ective algorithm for unit test generation. Conclusions: Our results show that the choice of algorithm can have a substantial in uence on the performance of whole test suite optimisation. Although we can make a recommendation on which algorithm to use in practice, no algorithm is clearly superior in all cases, suggesting future work on improved search algorithms for unit test generatio

Signal Convolution Logic

We introduce a new logic called Signal Convolution Logic (SCL) that combines temporal logic with convolutional filters from digital signal processing. SCL enables to reason about the percentage of time a formula is satisfied in a bounded interval. We demonstrate that this new logic is a suitable formalism to effectively express non-functional requirements in Cyber-Physical Systems displaying noisy and irregular behaviours. We define both a qualitative and quantitative semantics for it, providing an efficient monitoring procedure. Finally, we prove SCL at work to monitor the artificial pancreas controllers that are employed to automate the delivery of insulin for patients with type-1 diabetes

Understanding Urban Demand for Wild Meat in Vietnam: Implications for Conservation Actions

Vietnam is a significant consumer of wildlife, particularly wild meat, in urban restaurant settings. To meet this demand, poaching of wildlife is widespread, threatening regional and international biodiversity. Previous interventions to tackle illegal and potentially unsustainable consumption of wild meat in Vietnam have generally focused on limiting supply. While critical, they have been impeded by a lack of resources, the presence of increasingly organised criminal networks and corruption. Attention is, therefore, turning to the consumer, but a paucity of research investigating consumer demand for wild meat will impede the creation of effective consumer-centred interventions. Here we used a mixed-methods research approach comprising a hypothetical choice modelling survey and qualitative interviews to explore the drivers of wild meat consumption and consumer preferences among residents of Ho Chi Minh City, Vietnam. Our findings indicate that demand for wild meat is heterogeneous and highly context specific. Wild-sourced, rare, and expensive wild meat-types are eaten by those situated towards the top of the societal hierarchy to convey wealth and status and are commonly consumed in lucrative business contexts. Cheaper, legal and farmed substitutes for wild-sourced meats are also consumed, but typically in more casual consumption or social drinking settings. We explore the implications of our results for current conservation interventions in Vietnam that attempt to tackle illegal and potentially unsustainable trade in and consumption of wild meat and detail how our research informs future consumer-centric conservation actions

The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities".JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131).IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributionsPeer reviewe