Metropolis-Hastings prefetching algorithms

Prefetching is a simple and general method for single-chain parallelisation of the Metropolis-Hastings algorithm based on the idea of evaluating the posterior in parallel and ahead of time. In this paper improved Metropolis-Hastings prefetching algorithms are presented and evaluated. It is shown how to use available information to make better predictions of the future states of the chain and increase the efficiency of prefetching considerably. The optimal acceptance rate for the prefetching random walk Metropolis-Hastings algorithm is obtained for a special case and it is shown to decrease in the number of processors employed. The performance of the algorithms is illustrated using a well-known macroeconomic model. Bayesian estimation of DSGE models, linearly or nonlinearly approximated, is identified as a potential area of application for prefetching methods. The generality of the proposed method, however, suggests that it could be applied in many other contexts as well.Prefetching; Metropolis-Hastings; Parallel Computing; DSGE models; Optimal acceptance rate

UV-B exposure, ROS, and stress: inseparable companions or loosely linked associates?

Ultraviolet-B (UV-B) radiation has long been perceived as a stressor. However, a conceptual U-turn has taken place, and UV-B damage is now considered rare. We question whether UV-stress and UV-B-induced reactive oxygen species (ROS) are still relevant concepts, and if ROS-mediated signaling contributes to UV-B acclimation. Measurements of antioxidants and of antioxidant genes show that both low and high UV-B doses alter ROS metabolism. Yet, there is no evidence that ROS control gene expression under low UV-B. Instead, expression of antioxidant genes is linked to the UV RESISTANCE LOCUS 8 pathway. We hypothesize that low UVB doses cause ‘eustress’ (good stress) and that stimulispecific signaling pathways pre-dispose plants to a state of low alert that includes activation of antioxidant defenses.Funding agencies are:COST Action  FA0906UV4Growth  Faculty of Business, Science, and Technology at Örebro University  Science Foundation Ireland (SFI)  11/RFP.1/EOB/3303 Hungarian Scientific Research Fund  OTKA NN-85349 UV-B-fotobiologi: mekanismer för perception och cellulära response

Adaptive hybrid Metropolis-Hastings samplers for DSGE models

Bayesian inference for DSGE models is typically carried out by single block random walk Metropolis, involving very high computing costs. This paper combines two features, adaptive independent Metropolis-Hastings and parallelisation, to achieve large computational gains in DSGE model estimation. The history of the draws is used to continuously improve a t-copula proposal distribution, and an adaptive random walk step is inserted at predetermined intervals to escape difficult points. In linear estimation applications to a medium scale (23 parameters) and a large scale (51 parameters) DSGE model, the computing time per independent draw is reduced by 85% and 65-75% respectively. In a stylised nonlinear estimation example (13 parameters) the reduction is 80%. The sampler is also better suited to parallelisation than random walk Metropolis or blocking strategies, so that the effective computational gains, i.e. the reduction in wall-clock time per independent equivalent draw, can potentially be much larger.Markov Chain Monte Carlo (MCMC); Adaptive Metropolis-Hastings; Parallel algorithm; DSGE model; Copula

Metropolis-Hastings prefetching algorithms

Prefetching is a simple and general method for single-chain parallelisation of the Metropolis-Hastings algorithm based on the idea of evaluating the posterior in parallel and ahead of time. Improved Metropolis-Hastings prefetching algorithms are presented and evaluated. It is shown how to use available information to make better predictions of the future states of the chain and increase the efficiency of prefetching considerably. The optimal acceptance rate for the prefetching random walk Metropolis-Hastings algorithm is obtained for a special case and it is shown to decrease in the number of processors employed. The performance of the algorithms is illustrated using a well-known macroeconomic model. Bayesian estimation of DSGE models, linearly or nonlinearly approximated, is identi…ed as a potential area of application for prefetching methods. The generality of the proposed method, however, suggests that it could be applied in other contexts as well

Debt dynamics and monetary policy: A note

"Leaning against the wind" - a tighter monetary policy than necessary for stabilizing inflation around the inflation target and unemployment around a long-run sustainable rate - has been justified as a way of reducing household indebtedness. In a recent paper Lars Svensson claims that this policy is counterproductive, since a higher policy rate actually leads to an increase (and not a decrease) in real debt and the debt-to-GDP ratio. In this note we offer some comments and extensions to Svensson's analysis. In particular, we take Svensson's debt model to the data and show that it provides an incomplete account of short term debt dynamics. Further, the overall analysis of the effects of monetary policy on debt rests on the rather strong assumption that debt is independent of the policy rate, conditional on housing prices. The policy responses advocated by Svensson can therefore be questioned. More importantly, our exercises with a modified model of debt dynamics enables further understanding of how different assumptions affect the assessment of the effects of monetary policy on debt

Bark beetles facilitate the establishment of wood decay fungi

Forests in the northern hemisphere are largely dominated by conifers and provide a key habitat for a multitude of species. Wood decay fungi, i.e. basidiomycetes, are important for nutrient cycling. Saproxylic insects may facilitate the fungal colonization by opening up bark layer, provide a court for introduction, or they can specifically or loosely vector fungal propagules to the substrate. The aim of the thesis was to clarify the role of insects for dispersal of fungal spores and propagules to Norway spruce stem sections, determine whether mycelial establishment was aided by holes in the bark created by the bark beetle, examine the early succession of fungal diversity in dead wood, and determine whether the hibernation environments for Ips typographus have an impact on the fungal community dispersed by the bark beetle. Further analysis was conducted on wood material from high stumps and stem sections, mycelia from high stumps, and bark beetles from high stumps, stem sections, standing trees and forest litter. Pure culture isolation, T-RFLP, cloning and 454-sequencing were methods used to explain the fungal community composition. It was concluded that (i) bark beetles contribute to the establishment of wood decay fungi and act as random vectors; (ii) the fungal community vectored by the bark beetle is depending on the hibernation environment; (iii) beetle entrance and emergence holes on their own have little or no effect on the substrate availability for air-dispersed fungal species; (iv) the fungal community changes drastically in newly created dead wood and the ecological interaction between fungi and dead wood is complex; and (v) the complexity of the fungal community detected is influenced by the method used to analyze it. Overall, bark beetles have a major impact on fungal dispersal and colonization success of wood-decay fungi

Ecosystem properties and principles of living systems as foundation for sustainable agriculture – Critical reviews of environmental assessment tools, key findings and questions from a course process

With increasing demands on limited resources worldwide, there is a growing interest in sustainable patterns of utilisation and production. Ecological agriculture is a response to these concerns. To assess progress and compliance, standard and comprehensive measures of resource requirements, impacts and agro-ecological health are needed. Assessment tools should also be rapid, standardized, userfriendly, meaningful to public policy and applicable to management. Fully considering these requirements confounds the development of integrated methods. Currently, there are many methodologies for monitoring performance, each with its own foundations, assumptions, goals, and outcomes, dependent upon agency agenda or academic orientation. Clearly, a concept of sustainability must address biophysical, ecological, economic, and sociocultural foundations. Assessment indicators and criteria, however, are generally limited, lacking integration, and at times in conflict with one another. A result is that certification criteria, indicators, and assessment methods are not based on a consistent, underlying conceptual framework and often lack a management focus. Ecosystem properties and principles of living systems, including self-organisation, renewal, embeddedness, emergence and commensurate response provide foundation for sustainability assessments and may be appropriate focal points for critical thinking in an evaluation of current methods and standards. A systems framework may also help facilitate a comprehensive approach and promote a context for meaningful discourse. Without holistic accounts, sustainable progress remains an illdefined concept and an elusive goal. Our intent, in the work with this report, was to use systems ecology as a pedagogic basis for learning and discussion to: - Articulate general and common characteristics of living systems. - Identify principles, properties and patterns inherent in natural ecosystems. - Use these findings as foci in a dialogue about attributes of sustainability to: a. develop a model for communicating scientific rationale. b. critically evaluate environmental assessment tools for application in land-use. c. propose appropriate criteria for a comprehensive assessment and expanded definition of ecological land use

Recent progress in plant taxonomy and floristic studies in Greece

A survey of developments in plant taxonomy, floristics, and phytogeography in Greece during 2005 to 2016 is presented. Species diversity in different areas and on different scales is summarised in five maps. A list of new taxa described during this period is provided, together with their type citations and taxonomic comments where relevant; almost all of the taxa are based on Greek plant material