Effect of Biodiversity Changes in Disease Risk: Exploring Disease Emergence in a Plant-Virus System

The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species

A comparison of machine learning methods for predicting recurrence and death after curative-intent radiotherapy for non-small cell lung cancer: Development and validation of multivariable clinical prediction models.

Background Surveillance is universally recommended for non-small cell lung cancer (NSCLC) patients treated with curative-intent radiotherapy. High-quality evidence to inform optimal surveillance strategies is lacking. Machine learning demonstrates promise in accurate outcome prediction for a variety of health conditions. The purpose of this study was to utilise readily available patient, tumour, and treatment data to develop, validate and externally test machine learning models for predicting recurrence, recurrence-free survival (RFS) and overall survival (OS) at 2 years from treatment. Methods A retrospective, multicentre study of patients receiving curative-intent radiotherapy for NSCLC was undertaken. A total of 657 patients from 5 hospitals were eligible for inclusion. Data pre-processing derived 34 features for predictive modelling. Combinations of 8 feature reduction methods and 10 machine learning classification algorithms were compared, producing risk-stratification models for predicting recurrence, RFS and OS. Models were compared with 10-fold cross validation and an external test set and benchmarked against TNM-stage and performance status. Youden Index was derived from validation set ROC curves to distinguish high and low risk groups and Kaplan-Meier analyses performed. Findings Median follow-up time was 852 days. Parameters were well matched across training-validation and external test sets: Mean age was 73 and 71 respectively, and recurrence, RFS and OS rates at 2 years were 43% vs 34%, 54% vs 47% and 54% vs 47% respectively. The respective validation and test set AUCs were as follows: 1) RFS: 0·682 (0·575–0·788) and 0·681 (0·597–0·766), 2) Recurrence: 0·687 (0·582–0·793) and 0·722 (0·635–0·81), and 3) OS: 0·759 (0·663–0·855) and 0·717 (0·634–0·8). Our models were superior to TNM stage and performance status in predicting recurrence and OS. Interpretation This robust and ready to use machine learning method, validated and externally tested, sets the stage for future clinical trials entailing quantitative personalised risk-stratification and surveillance following curative-intent radiotherapy for NSCLC. Funding A full list of funding bodies that contributed to this study can be found in the Acknowledgements section

A Conceptual Framework for Healthy Eating Behavior in Ecuadorian Adolescents: A Qualitative Study

Objective: The objective of this study was to identify factors influencing eating behavior of Ecuadorian adolescents - from the perspective of parents, school staff and adolescents - to develop a conceptual framework for adolescents’ eating behavior. Study design: Twenty focus groups (N = 144 participants) were conducted separately with adolescents aged 11–15 y (n (focus groups) = 12, N (participants) = 80), parents (n = 4, N = 32) and school staff (n = 4, N = 32) in rural and urban Ecuador. A semi-structured questioning route was developed based on the ‘Attitude, Social influences and Self-efficacy’ model and the socio-ecological model to assess the relevance of behavioral and environmental factors in low- and middle-income countries. Two researchers independently analyzed verbatim transcripts for emerging themes, using deductive thematic content analysis. Data were analyzed using NVivo 8. Results: All groups recognized the importance of eating healthily and key individual factors in Ecuadorian adolescents’ food choices were: financial autonomy, food safety perceptions, lack of self-control, habit strength, taste preferences and perceived peer norms. Environmental factors included the poor nutritional quality of food and its easy access at school. In their home and family environment, time and convenience completed the picture as barriers to eating healthily. Participants acknowledged the impact of the changing socio-cultural environment on adolescents’ eating patterns. Availability of healthy food at home and financial constraints differed between settings and socio-economic groups. Conclusion: Our findings endorse the importance of investigating behavioral and environmental factors that influence and mediate healthy dietary behavior prior to intervention development. Several culture-specific factors emerged that were incorporated into a conceptual framework for developing health promotion interventions in Ecuador

Influences on gum feeding in primates

This chapter reviews the factors that may affect patterns of gum feeding by primates. These are then examined for mixed-species troops of saddleback (S. fuscicollis) and mustached (S. mystax) tamarins. An important distinction is made between gums produced by tree trunks and branches as a result of damage and those produced by seed pods as part of a dispersal strategy as these may be expected to differ in their biochemistry. Feeding on fruit and Parkia seed pod exudates was more prevalent in the morning whereas other exudates were eaten in the afternoon. This itinerary may represent a deliberate strategy to retain trunk gums in the gut overnight, thus maximising the potential for microbial fermentation of their β-linked oligosaccharides. Both types of exudates were eaten more in the dry than the wet season. Consumption was linked to seasonal changes in resource availability and not the tamarins’ reproductive status pro-viding no support for the suggestion that gums are eaten as a pri-mary calcium source in the later stages of gestation and lactation. The role of availability in determining patterns of consumption is further supported by the finding that dietary overlap for the trunk gums eaten was greater between species within mixed-species troops within years than it was within species between years. These data and those for pygmy marmosets (Cebuella pygmaea) suggest that patterns of primate gummivory may reflect the interaction of prefer-ence and availability for both those able to stimulate gum production and those not

Using formative research to develop CHANGE! : a curriculum-based physical activity promoting intervention

Background : Low childhood physical activity levels are currently one of the most pressing public health concerns. Numerous school-based physical activity interventions have been conducted with varied success. Identifying effective child-based physical activity interventions are warranted. The purpose of this formative study was to elicit subjective views of children, their parents, and teachers about physical activity to inform the design of the CHANGE! (Children\u27s Health, Activity, and Nutrition: Get Educated!) intervention programme. Methods : Semi-structured mixed-gender interviews (group and individual) were conducted in 11 primary schools, stratified by socioeconomic status, with 60 children aged 9-10 years (24 boys, 36 girls), 33 parents (4 male, 29 female) and 10 teachers (4 male, 6 female). Questions for interviews were structured around the PRECEDE stage of the PRECEDE-PROCEDE model and addressed knowledge, attitudes and beliefs towards physical activity, as well as views on barriers to participation. All data were transcribed verbatim. Pen profiles were constructed from the transcripts in a deductive manner using the Youth Physical Activity Promotion Model framework. The profiles represented analysis outcomes via a diagram of key emergent themes. Results : Analyses revealed an understanding of the relationship between physical activity and health, although some children had limited understanding of what constitutes physical activity. Views elicited by children and parents were generally consistent. Fun, enjoyment and social support were important predictors of physical activity participation, though several barriers such as lack of parental support were identified across all group interviews. The perception of family invested time was positively linked to physical activity engagement. Conclusions : Families have a powerful and important role in promoting health-enhancing behaviours. Involvement of parents and the whole family is a strategy that could be significant to increase children\u27s physical activity levels. Addressing various perceived barriers to such behaviours therefore, remains imperative. <br /

Word add-in for ontology recognition: semantic enrichment of scientific literature

<p>Abstract</p> <p>Background</p> <p>In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles.</p> <p>Results</p> <p>The Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at <url>http://www.codeplex.com/UCSDBioLit</url>.</p> <p>Conclusions</p> <p>The Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata.</p

Seasonal Movement and Distribution of Fluvial Adult Bull Trout in Selected Watersheds in the Mid-Columbia River and Snake River Basins

From 1997 to 2004, we used radio telemetry to investigate movement and distribution patterns of 206 adult fluvial bull trout (mean, 449 mm FL) from watersheds representing a wide range of habitat conditions in northeastern Oregon and southwestern Washington, a region for which there was little previous information about this species. Migrations between spawning and wintering locations were longest for fish from the Imnaha River (median, 89 km) and three Grande Ronde River tributaries, the Wenaha (56 km) and Lostine (41 km) rivers and Lookingglass Creek (47 km). Shorter migrations were observed in the John Day (8 km), Walla Walla (20 km) and Umatilla river (22 km) systems, where relatively extensive human alterations of the riverscape have been reported. From November through May, fish displayed station-keeping behavior within a narrow range (basin medians, 0.5–6.2 km). Prespawning migrations began after snowmelt-driven peak discharge and coincided with declining flows. Most postspawning migrations began by late September. Migration rates of individuals ranged from 0.1 to 10.7 km/day. Adults migrated to spawning grounds in consecutive years and displayed strong fidelity to previous spawning areas and winter locations. In the Grande Ronde River basin, most fish displayed an unusual fluvial pattern: After exiting the spawning tributary and entering a main stem river, individuals moved upstream to wintering habitat, often a substantial distance (maximum, 49 km). Our work provides additional evidence of a strong migratory capacity in fluvial bull trout, but the short migrations we observed suggest adult fluvial migration may be restricted in basins with substantial anthropogenic habitat alteration. More research into bull trout ecology in large river habitats is needed to improve our understanding of how adults establish migration patterns, what factors influence adult spatial distribution in winter, and how managers can protect and enhance fluvial populations

Fine-Scale Variation in Vector Host Use and Force of Infection Drive Localized Patterns of West Nile Virus Transmission

The influence of host diversity on multi-host pathogen transmission and persistence can be confounded by the large number of species and biological interactions that can characterize many transmission systems. For vector-borne pathogens, the composition of host communities has been hypothesized to affect transmission; however, the specific characteristics of host communities that affect transmission remain largely unknown. We tested the hypothesis that vector host use and force of infection (i.e., the summed number of infectious mosquitoes resulting from feeding upon each vertebrate host within a community of hosts), and not simply host diversity or richness, determine local infection rates of West Nile virus (WNV) in mosquito vectors. In suburban Chicago, Illinois, USA, we estimated community force of infection for West Nile virus using data on Culex pipiens mosquito host selection and WNV vertebrate reservoir competence for each host species in multiple residential and semi-natural study sites. We found host community force of infection interacted with avian diversity to influence WNV infection in Culex mosquitoes across the study area. Two avian species, the American robin (Turdus migratorius) and the house sparrow (Passer domesticus), produced 95.8% of the infectious Cx. pipiens mosquitoes and showed a significant positive association with WNV infection in Culex spp. mosquitoes. Therefore, indices of community structure, such as species diversity or richness, may not be reliable indicators of transmission risk at fine spatial scales in vector-borne disease systems. Rather, robust assessment of local transmission risk should incorporate heterogeneity in vector host feeding and variation in vertebrate reservoir competence at the spatial scale of vector-host interaction

Detection and attribution of human influence on regional precipitation

Understanding how human influence on climate is affecting precipitation around the world is immensely important for defining mitigation policies, and for adaptation planning. Yet despite increasing evidence for the influence of climate change on global patterns of precipitation, and expectations that significant changes in regional precipitation should have already occurred as a result of human influence on climate, compelling evidence of anthropogenic fingerprints on regional precipitation is obscured by observational and modelling uncertainties and is likely to remain so using current methods for years to come. This is in spite of substantial ongoing improvements in models, new reanalyses and a satellite record that spans over thirty years. If we are to quantify how human-induced climate change is affecting the regional water cycle, we need to consider novel ways of identifying the effects of natural and anthropogenic influences on precipitation that take full advantage of our physical expectations