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  • Biodiversity Conservation  (2)
  • Computational Methods
  • Oxford University Press  (3)
  • 2025-2025
  • 2015-2019  (3)
  • 1985-1989
  • 1980-1984
  • 2017  (3)
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  • Oxford University Press  (3)
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  • 2025-2025
  • 2015-2019  (3)
  • 1985-1989
  • 1980-1984
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  • 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: 2017-01-05
    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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  • 3
    Publication Date: 2017-01-10
    Description: RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting. In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA–protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html .
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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