A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

The question of “evidence” in the emergence of evidence-based or evidence-aware policies in agriculture

Evidence-based or evidence-aware policy approaches are used in many different sectors (health, education, etc.). These approaches are less common in agriculture but are gradually emerging. Analysis of debates surrounding this trend sheds light on the particular nature of the difficulties faced by public decision-makers who are willing to use available scientific knowledge. After examining certain misunderstandings which arise in the international debate over evidence-based policy approaches, this paper addresses two specific issues: (i) the problems of competing evidence for using knowledge in the design of public policies and (ii) the potential role of rationalization tools in a possible "depoliticisation" of public decision-making.knowledge, agriculture, policy, evidence, Agricultural and Food Policy, B29, D8, Q01, O3,

Incomplete Markets, Growth, and the Business Cycle

We introduce a Ramsey growth model with incomplete markets, decentralized production, and idiosyncratic technological risk. The combination of uninsurable shocks with the precautionary motive can slow down capital accumulation or give rise to persistent fluctuations even when agents are very patient and technology is strictly convex. The model generates closed-form expressions for the equilibrium dynamics under a finite or infinite horizon. Multiple steady states and poverty traps can arise from the endogeneity of the interest rate instead of the usual wealth effect. Depending on the economy's parameters, the local dynamics around a steady state are locally unique, totally unstable or locally undetermined, and the equilibrium path can be attracted to a limit cycle. In calibrated examples, financial incompleteness substantially slows down convergence to the steady state and thus increases the persistence of aggregate shocks.

Multifrequency Jump-Diffusions: An Equilibrium Approach

This paper proposes that equilibrium valuation is a powerful method to generate endogenous jumps in asset prices, which provides a structural alternative to traditional reduced-form specifications with exogenous discontinuities. We specify an economy with continuous consumption and dividend paths, in which endogenous price jumps originate from the market impact of regime-switches in the drifts and volatilities of fundamentals. We parsimoniously incorporate shocks of heterogeneous durations in consumption and dividends while keeping constant the number of parameters. Equilibrium valuation creates an endogenous relation between a shock's persistence and the magnitude of the induced price jump. As the number of frequencies driving fundamentals goes to infinity, the price process converges to a novel stochastic process, which we call a multifractal jump-diffusion.

Effect of microchannel aspect ratio on residence time distributions and the axial dispersion coefficient

The effect of microchannel aspect ratio (channel depth/channel width) on residence time distributions and the axial dispersion coefficient have been investigated for Newtonian and shear thinning non-Newtonian flow using computational fluid dynamics. The results reveal that for a fixed cross sectional area and throughput, there is a narrowing of the residence time distribution as the aspect ratio decreases. This is quantified by an axial dispersion coefficient that increases rapidly for aspect ratios less than 0.3 and then tends towards an asymptote as the aspect ratio goes to 1. The results also show that the axial dispersion coefficient is related linearly to the Reynolds number when either the aspect ratio or the mean fluid velocity is varied. However, the fluid Péclet number is a linear function of the Reynolds number only when the aspect ratio (and therefore hydraulic diameter) is varied. Globally, the results indicate that microchannels should be designed with low aspect ratios (≤ 0.3) for reduced axial dispersion

Idiosyncratic Production Risk, Growth and the Business Cycle

We introduce a neoclassical growth economy with idiosyncratic production risk and incomplete markets. The general equilibrium is characterized in closed form. Uninsurable production shocks introduce a risk premium on private equity and typically result in a lower steady-state level of capital than under complete markets. In the presence of such risks, the anticipation of low investment and high interest rates in the future discourages risk-taking and feeds back into low investment in the present. An endogenous macroeconomic complementarity thus arises, which slows down convergence and amplifies the magnitude and persistence of the business cycle. These results — contrasting sharply with those of Aiyagari (1994) and Krusell and Smith (1998) — highlight that idiosyncratic production or capital-income risk can have significant adverse effects on capital accumulation and aggregate volatility. Keywords: Capital income, Entrepreneurial risk, Fluctuations, Growth, Investment, Precautionary savings.

Diablo Canyon power plant site ecological study Quarterly Report No. 13; July 1 - September 30, 1976

Surveys of 39 random 30-m2 subtidal stations and 56 random 1/4-m2 subtidal stations in Diablo Cove and the North Control were completed. The mean density of red abalones, Haliotis rufescens, in Diablo Cove was greater this year (0.02/m2) than last year (0.005/m2). This difference probably reflects sampling variation rather than density change. A total of 29 sportfish catch-per-unit-of-effort stations was sampled in Diablo Cove and 12 in the North Control. Foam observations in Diablo Cove were continued. The cooling water pumps were not in operation. The amounts of foam appeared to be about the same during certain weather conditions as those when the pumps are in operation, although not as thick. The number of sea otters, Enhydra lutris, decreased substantially between Pt. Buchon and Pecho Rock. This was due to their annual migration (or "pulling back") into the more central parts of their range. Random surveys of the intertidal areas during the upwelling period were completed. (11pp.

Optimisation of solvent replacement procedures according to economic and environmental criteria in pharmaceutical industry

During pharmaceutical syntheses, the reaction solvent has often to be switched off from one reaction step to the following one. Because of the standard industrial practices, solvent replacement generally constitutes a slow and high solvent-consuming operation. In this paper, a specific methodology, based on a batch processes optimisation framework, is proposed for the optimisation of solvent replacement procedures. Optimisation may be performed at different levels according to economic and environmental criteria and satisfying safety and waste treatment constraints. In fact, the proposed methodology allows both to design new procedures of solvent replacement and to improve existing industrial processes. Two industrial applications are detailed to emphasize the benefits related to this methodology. In each case, the proposed methodology leads to the suitable recipe from comparison of traditional and empirical replacement procedures generally used in the pharmaceutical industry