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  • Bioeconomics  (2)
  • Computational Methods, Genomics  (2)
  • Oxford University Press  (4)
  • Springer Nature
  • 2015-2019  (4)
  • 1980-1984
  • 2017  (4)
  • 1984
Collection
Publisher
  • Oxford University Press  (4)
  • Springer Nature
Years
  • 2015-2019  (4)
  • 1980-1984
Year
  • 1
    Publication Date: 2017-01-05
    Description: Stated preference scenarios often describe outcomes to be valued in terms of intermediate biophysical processes or ecosystem services with indirect utility effects, rather than in terms of final, directly welfare-relevant consequences. This article evaluates whether valid welfare estimates can emerge from this practice. We begin with a theoretical model demonstrating conditions under which stated preference scenarios that include intermediate outcomes will elicit welfare estimates identical to those from parallel scenarios that include associated final outcomes (i.e., convergent validity will hold). The model demonstrates that a necessary condition for convergent validity is the ability of respondents to correctly predict biophysical production functions linking intermediate to final outcomes. Hypotheses from the theoretical model are then evaluated empirically using an application of choice experiments to migratory fish restoration in the U.S. state of Rhode Island. Empirical results are mixed but generally reject convergent validity; welfare estimates are not robust to the use of an intermediate outcome in lieu of a related final outcome in stated preference scenarios, as predicted by theory. Results of the analysis suggest that greater attention should be given to the reliability of welfare estimation when final outcomes cannot be quantified.
    Keywords: D61 - Allocative Efficiency ; Cost-Benefit Analysis, Q51 - Valuation of Environmental Effects, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 2
    Publication Date: 2017-01-10
    Description: Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2017-01-05
    Description: Resource managers must often make difficult choices in the face of imperfectly observed and dynamically changing systems (e.g., livestock, fisheries, water, and invasive species). A rich set of techniques exists for identifying optimal choices when that uncertainty is assumed to be understood and irreducible. Standard optimization approaches, however, cannot address situations in which reducible uncertainty applies to either system behavior or environmental states. The adaptive management literature overcomes this limitation with tools for optimal learning, but has been limited to highly simplified models with state and action spaces that are discrete and small. We overcome this problem by using a recently developed extension of the Partially Observable Markov Decision Process (POMDP) framework to allow for learning about a continuous state. We illustrate this methodology by exploring optimal control of bovine tuberculosis in New Zealand cattle. Disease testing—the control variable—serves to identify herds for treatment and provides information on prevalence, which is both imperfectly observed and subject to change due to controllable and uncontrollable factors. We find substantial efficiency losses from both ignoring learning (standard stochastic optimization) and from simplifying system dynamics (to facilitate a typical, simple learning model), though the latter effect dominates in our setting. We also find that under an adaptive management approach, simplifying dynamics can lead to a belief trap in which information gathering ceases, beliefs become increasingly inaccurate, and losses abound.
    Keywords: C61 - Optimization Techniques ; Programming Models ; Dynamic Analysis, H41 - Public Goods, Q18 - Agricultural Policy ; Food Policy, Q57 - Ecological Economics: Ecosystem Services ; Biodiversity Conservation ; Bioeconomics
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 4
    Publication Date: 2017-01-10
    Description: Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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