6,701 research outputs found

    Optimal treatment allocations in space and time for on-line control of an emerging infectious disease

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    A key component in controlling the spread of an epidemic is deciding where, whenand to whom to apply an intervention.We develop a framework for using data to informthese decisionsin realtime.We formalize a treatment allocation strategy as a sequence of functions, oneper treatment period, that map up-to-date information on the spread of an infectious diseaseto a subset of locations where treatment should be allocated. An optimal allocation strategyoptimizes some cumulative outcome, e.g. the number of uninfected locations, the geographicfootprint of the disease or the cost of the epidemic. Estimation of an optimal allocation strategyfor an emerging infectious disease is challenging because spatial proximity induces interferencebetween locations, the number of possible allocations is exponential in the number oflocations, and because disease dynamics and intervention effectiveness are unknown at outbreak.We derive a Bayesian on-line estimator of the optimal allocation strategy that combinessimulation–optimization with Thompson sampling.The estimator proposed performs favourablyin simulation experiments. This work is motivated by and illustrated using data on the spread ofwhite nose syndrome, which is a highly fatal infectious disease devastating bat populations inNorth America

    Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

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    The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

    The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

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    Background: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. Results: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. Conclusions: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion

    Spatial genetic structure in the saddled sea bream (Oblada melanura [Linnaeus, 1758]) suggests multi-scaled patterns of connectivity between protected and unprotected areas in the Western Mediterranean Sea

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    Marine protected areas (MPAs) and networks of MPAs are advocated worldwide for the achievement of marine conservation objectives. Although the knowledge about population connectivity is considered fundamental for the optimal design of MPAs and networks, the amount of information available for the Mediterranean Sea is currently scarce. We investigated the genetic structure of the saddled sea bream ( Oblada melanura) and the level of genetic connectivity between protected and unprotected locations, using a set of 11 microsatellite loci. Spatial patterns of population differentiation were assessed locally (50-100 km) and regionally (500-1000 km), considering three MPAs of the Western Mediterranean Sea. All values of genetic differentiation between locations (Fst and Jost's D) were non-significant after Bonferroni correction, indicating that, at a relatively small spatial scale, protected locations were in general well connected with non-protected ones. On the other hand, at the regional scale, discriminant analysis of principal components revealed the presence of a subtle pattern of genetic heterogeneity that reflects the geography and the main oceanographic features (currents and barriers) of the study area. This genetic pattern could be a consequence of different processes acting at different spatial and temporal scales among which the presence of admixed populations, large population sizes and species dispersal capacity, could play a major role. These outcomes can have important implications for the conservation biology and fishery management of the saddled sea bream and provide useful information for genetic population studies of other coastal fishes in the Western Mediterranean Sea

    Fine-scale population structure and asymmetrical dispersal in an obligate salt-marsh passerine, the Saltmarsh Sparrow (Ammodramus Caudacutus)

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    Understanding the spatial scale of gene flow can yield valuable insight into the ecology of an organism and guide conservation strategies. Fine-scale genetic structure is uncommon in migratory passerines because of their high vagility and presumed high dispersal abilities. Aspects of the behavior and ecology of some migratory species, however, may promote structure on a finer scale in comparison to their mobility. We investigated population genetic structure in the Saltmarsh Sparrow (Ammodramus caudacutus), a migratory passerine that breeds along the northeastern coast of the United States, where it is restricted exclusively to a narrow strip of patchily distributed tidal marsh habitat. Using genotyping with 10 microsatellite loci, we detected weak but significant population structure among Saltmarsh Sparrows from nine marshes on the breeding grounds between Scarborough, Maine, and Oceanside, New York. Genetic variation among marshes was largely consistent with a pattern of isolation by distance, with some exceptions. One inland marsh was genetically divergent despite its proximity to other sampled marshes, which suggests that mechanisms besides geographic distance influence population genetic structure. Bayesian clustering, multivariate analyses, and assignment tests supported a population structure consisting of five groups. Estimates of migration rates indicated variation in gene flow among marshes, which suggests asymmetrical dispersal and possible source-sink population dynamics. The genetic structure that we found in Saltmarsh Sparrows may result from natal philopatry and breeding-site fidelity, combined with restricted dispersal due to obligate dependence on a patchy habitat. Our findings suggest that fine-scale population structure may be important in some migratory passerines. Received 12 July 2011, accepted 1 February 2012

    Predicting water quality and ecological responses

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    Abstract Changes to climate are predicted to have effects on freshwater streams. Stream flows are likely to change, with implications for freshwater ecosystems and water quality. Other stressors such as population growth, community preferences and management policies can be expected to interact in various ways with climate change and stream flows, and outcomes for freshwater ecosystems and water quality are uncertain. Managers of freshwater ecosystems and water supplies could benefit from being able to predict the scales of likely changes. This project has developed and applied a linked modelling framework to assess climate change impacts on water quality regimes and ecological responses. The framework is designed to inform water planning and climate adaptation activities. It integrates quantitative tools, and predicts relationships between future climate, human activities, water quality and ecology, thereby filling a gap left by the considerable research effort so far invested in predicting stream flows. The modelling framework allows managers to explore potential changes in the water quality and ecology of freshwater systems in response to plausible scenarios for climate change and management adaptations. Although set up for the Upper Murrumbidgee River catchment in southern NSW and ACT, the framework was planned to be transferable to other regions where suitable data are available. The approach and learning from the project appear to have the potential to be broadly applicable. We selected six climate scenarios representing minor, moderate and major changes in flow characteristics for 1oC and 2oC temperature increases. These were combined with four plausible alternative management adaptations that might be used to modify water supply, urban water demand and stream flow regimes in the Upper Murrumbidgee catchment. The Bayesian Network (BN) model structure we used was developed using both a ‘top down’ and ‘bottom up’ approach. From analyses combined with expert advice, we identified the causal structure linking climate variables to stream flow, water quality attributes, land management and ecological responses (top down). The ‘bottom up’ approach focused on key ecological outcomes and key drivers, and helped produce efficient models. The result was six models for macroinvertebrates, and one for fish. In the macroinvertebrate BN models, nodes were discretised using statistical/empirical derived thresholds using new techniques. The framework made it possible to explore how ecological communities respond to changes in climate and management activities. Particularly, we focused on the effects of water quality and quantity on ecological responses. The models showed a strong regional response reflecting differences across 18 regions in the catchment. In two regions the management alternatives were predicted to have stronger effects than climate change. In three other regions the predicted response to climate change was stronger. Analyses of water quality suggested minor changes in the probability of water quality exceeding thresholds designed to protect aquatic ecosystems. The ‘bottom up’ approach limited the framework’s transferability by being specific to the Upper Murrumbidgee catchment data. Indeed, to meet stakeholder questions models need to be specifically tailored. Therefore the report proposes a general model-building framework for transferring the approach, rather than the models, to other regions.  Please cite this report as: Dyer, F, El Sawah, S, Lucena-Moya, P, Harrison, E, Croke, B, Tschierschke, A, Griffiths, R, Brawata, R, Kath, J, Reynoldson, T, Jakeman, T 2013 Predicting water quality and ecological responses, National Climate Change Adaptation Research Facility, Gold Coast, pp. 110 Changes to climate are predicted to have effects on freshwater streams. Stream flows are likely to change, with implications for freshwater ecosystems and water quality. Other stressors such as population growth, community preferences and management policies can be expected to interact in various ways with climate change and stream flows, and outcomes for freshwater ecosystems and water quality are uncertain. Managers of freshwater ecosystems and water supplies could benefit from being able to predict the scales of likely changes. This project has developed and applied a linked modelling framework to assess climate change impacts on water quality regimes and ecological responses. The framework is designed to inform water planning and climate adaptation activities. It integrates quantitative tools, and predicts relationships between future climate, human activities, water quality and ecology, thereby filling a gap left by the considerable research effort so far invested in predicting stream flows. The modelling framework allows managers to explore potential changes in the water quality and ecology of freshwater systems in response to plausible scenarios for climate change and management adaptations. Although set up for the Upper Murrumbidgee River catchment in southern NSW and ACT, the framework was planned to be transferable to other regions where suitable data are available. The approach and learning from the project appear to have the potential to be broadly applicable. We selected six climate scenarios representing minor, moderate and major changes in flow characteristics for 1oC and 2oC temperature increases. These were combined with four plausible alternative management adaptations that might be used to modify water supply, urban water demand and stream flow regimes in the Upper Murrumbidgee catchment. The Bayesian Network (BN) model structure we used was developed using both a ‘top down’ and ‘bottom up’ approach. From analyses combined with expert advice, we identified the causal structure linking climate variables to stream flow, water quality attributes, land management and ecological responses (top down). The ‘bottom up’ approach focused on key ecological outcomes and key drivers, and helped produce efficient models. The result was six models for macroinvertebrates, and one for fish. In the macroinvertebrate BN models, nodes were discretised using statistical/empirical derived thresholds using new techniques. The framework made it possible to explore how ecological communities respond to changes in climate and management activities. Particularly, we focused on the effects of water quality and quantity on ecological responses. The models showed a strong regional response reflecting differences across 18 regions in the catchment. In two regions the management alternatives were predicted to have stronger effects than climate change. In three other regions the predicted response to climate change was stronger. Analyses of water quality suggested minor changes in the probability of water quality exceeding thresholds designed to protect aquatic ecosystems. The ‘bottom up’ approach limited the framework’s transferability by being specific to the Upper Murrumbidgee catchment data. Indeed, to meet stakeholder questions models need to be specifically tailored. Therefore the report proposes a general model-building framework for transferring the approach, rather than the models, to other regions.&nbsp

    The Overlooked Potential of Generalized Linear Models in Astronomy - I: Binomial Regression

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    Revealing hidden patterns in astronomical data is often the path to fundamental scientific breakthroughs; meanwhile the complexity of scientific inquiry increases as more subtle relationships are sought. Contemporary data analysis problems often elude the capabilities of classical statistical techniques, suggesting the use of cutting edge statistical methods. In this light, astronomers have overlooked a whole family of statistical techniques for exploratory data analysis and robust regression, the so-called Generalized Linear Models (GLMs). In this paper -- the first in a series aimed at illustrating the power of these methods in astronomical applications -- we elucidate the potential of a particular class of GLMs for handling binary/binomial data, the so-called logit and probit regression techniques, from both a maximum likelihood and a Bayesian perspective. As a case in point, we present the use of these GLMs to explore the conditions of star formation activity and metal enrichment in primordial minihaloes from cosmological hydro-simulations including detailed chemistry, gas physics, and stellar feedback. We predict that for a dark mini-halo with metallicity ≈1.3×10−4Z⹀\approx 1.3 \times 10^{-4} Z_{\bigodot}, an increase of 1.2×10−21.2 \times 10^{-2} in the gas molecular fraction, increases the probability of star formation occurrence by a factor of 75%. Finally, we highlight the use of receiver operating characteristic curves as a diagnostic for binary classifiers, and ultimately we use these to demonstrate the competitive predictive performance of GLMs against the popular technique of artificial neural networks.Comment: 20 pages, 10 figures, 3 tables, accepted for publication in Astronomy and Computin

    Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

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    The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The ÎČ-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the ÎČ-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants
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