Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm

We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. From the results of the multicanonical-multioverlap molecular dynamics simulation, furthermore, we obtain a new local-minimum state of the Met-enkephalin system.Comment: 15 pages, (Revtex4), 9 figure

A Technique for the Quantitative Estimation of Soil Micro-organisms

RESP-269

Les enjeux de l’équivalence écologique pour la conception et le dimensionnement de mesures compensatoires d’impacts sur la biodiversité et les milieux naturels,

L’évolution du contexte réglementaire a renforcé l’obligation de compenser " en nature " les impacts sur la biodiversité qui n’ont pas pu être évités ou réduits. Dans ce contexte, l’évaluation de l’équivalence entre les pertes causées par ces impacts et les gains de biodiversité attendus des actions de compensation suscite des questions scientifiques et techniques quant aux concepts et connaissances à mobiliser et aux méthodes d’évaluation à développer et mettre en ½uvre. On y trouve en particulier l'identification des éléments de biodiversité à considérer, le développement d’indicateurs appropriés permettant de comparer pertes et gains, la sélection d’un état de référence pour le calcul des pertes et gains, et la prise en compte des dynamiques écologiques et des incertitudes dans l’évaluation du devenir des sites de compensation. Par ces questions, l'équivalence écologique donne un cadre de raisonnement explicite à la conception et au dimensionnement de la compensation qui est appropriable par chacun des acteurs concernés. / Since 2007 France has seen a radical strengthening of its legislation concerning the mitigation of development impacts on biodiversity and ecosystems. Under pressure from the European Union and as an outcome of a national consultative process called the “Grenelle de l’Environnement”, the scope of the mitigation hierarchy of avoiding, reducing and offsetting impacts of plans, programs and projects has been expanded. It now includes stronger requirements in terms of monitoring and effective implementation. These changes – which have strong financial and legal implications for developers - have revealed the lack of technical guidelines for designing and sizing offsets. Assessing the ecological equivalence between losses caused by impacts and the gains expected from offset actions raises scientific and technical issues that remain unresolved. These include the identification of relevant components of biodiversity, the development of appropriate indicators, the identification of reference states and the incorporation of ecological dynamics and uncertainties into offset design and sizing

Scherben bringen Glück ...: Digitale Präsentation der mitteldeutschen Ostrakasammlungen im "Papyrusportal Deutschland"

Die Papyrus- und Ostrakasammlung der UB Leipzig besitzt seit Anfang des 20. Jahrhunderts ca. 1.544 aus Ägypten stammende Ostraka. Durch ein von der DFG gefördertes Projekt konnten die beschrifteten Tonscherben katalogisiert, digitalisiert und dreidimensional in der Datenbank „Papyrus- und Ostrakaprojekt Halle-Jena-Leipzig“ präsentiert werden. Diese stellt den Nutzern zwei Suchmasken zur Verfügung. In der einen können in den Schriftträgern technische Details sowie die Aufbewahrung abgefragt werden und in der anderen ist im Text u.a. der Inhalt sowie bei publizierten Stücken die Transkription und die Übersetzung suchbar

Bases génétiques et fonctionnelles de la durabilité des résistances polygéniques au virus Y de la pomme de terre (PVY) chez le piment (Capsicum annuum)

Les résistances génétiques permettent une lutte efficace contre les maladies des plantes cultivées mais sont limitées par les capacités d évolution des bioagresseurs ciblés. Chez le piment, le fonds génétique peut améliorer la durabilité de la résistance au PVY conférée par le gène majeur pvr23. L objectif de ma thèse était de caractériser les facteurs génétiques de l hôte conditionnant la durabilité du gène majeur en répondant aux questions suivantes : (i) Quels sont leurs actions sur l évolution des populations virales ? (ii) Correspondent-ils aux QTL (quantitative trait loci) de résistance partielle ? (iii) Sont-ils répandus au sein des ressources génétiques du piment ? Différentes expérimentations incluant des tests de résistances, d évolution expérimentale et de compétition entre différents variants viraux, ont montré que les facteurs du fonds génétique augmentant la durabilité de pvr23 agissaient en : (i) diminuant la concentration virale dans la plante, (ii) en réduisant les probabilités de mutations du PVY vers le contournement du gène pvr23 et (iii) en ralentissant la sélection des variants viraux contournants. La détection de QTL et la cartographie des facteurs génétiques affectant la fréquence de contournement de pvr23 (QTL de durabilité) a mis en évidence quatre régions du génome du piment qui, par des effets additifs ou épistatiques, expliquent 70% de la variabilité phénotypique observée. La cartographie comparée montre que trois des quatre QTL de durabilité co-localisent avec des QTL affectant la résistance partielle, suggérant que les QTL de résistance partielle ont un effet pléiotropique sur la durabilité d un gène majeur de résistance. L étude d une collection de 20 accessions de piment, porteuses de pvr23 ou pvr24(allèle très proche de pvr23) dans des fonds génétiques variés, a montré que les fonds génétiques favorables à la durabilité de ces allèles de résistance sont fréquents dans les ressources génétiques du piment. Ces résultats mettent en évidence que la durabilité d un gène majeur de résistance peut-être fortement augmentée lorsqu il est associé à des facteurs génétiques réduisant la multiplication du pathogène. De plus, la fréquence de contournement du gène majeur s est révélée être un caractère très héritable (h =0.87) et la détection de QTL affectant ce caractère est possible. La sélection directe pour de tels QTL est donc envisageable et ouvre de nouvelles perspectives pour préserver la durabilité des gènes majeurs de résistance utilisés en sélection variétale.Genetic resistances provide an efficient control of crop diseases but are limited by pathogen adaptation.In pepper, the durability of the pvr23 allele, conferring resistance to Potato virus Y (PVY), was demonstrated todepend on the plant genetic background. The aim of my PhD thesis was to characterize the host genetic factorsaffecting the durability of the major resistance gene pvr23 and to answer to the following question s: (i) What istheir action on the evolution of the viral population? (ii) Is there identity between the QTLs (quantitative traitloci) controlling the partial resistance and the QTLs affecting the durability of pvr23? (iii) Are these genetic factorswidespread among the genetic resources of pepper? Various experiments including resistance testing,experimental evolution and competition between various PVY variants, enabled to show that the genetic factorsaffecting the durability of pvr23 acted in: (i) decreasing the viral accumulation, (ii) decreasing the probability ofacquisition of resistance breaking (RB) mutations by PVY and (iii) slowing down the selection of RB variants. QTLdetection and mapping of genetic factors affecting the frequency of pvr23 RB showed that four loci actingadditively and in epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency.Comparative mapping between these QTLs and QTLs affecting partial resistance showed that three of the fourQTLs controlling the frequency of pvr23 RB are also involved in quantitative resistance, suggesting that QTLs forquantitative resistance have a pleiotropic effect on the durability of the major resistance gene. Analysis of acollection of 20 pepper accessions, carrying pvr23 or pvr24 (allele closely related to pvr23) in various geneticbackgrounds, showed that genetic backgrounds favorable to the durability of the pvr2-mediated resistance arewidespread in the genetic resources of pepper. These results highlight that the durability of a major resistancegene can be strongly increased when associated with genetic factors decreasing the pathogen multiplication.Moreover, the frequency of a major gene RB is a highly heritable trait and QTLs detection for this trait isachievable. The direct selection for such QTLs opens new prospects to preserve the durability of major resistancegenes used by breeders.AVIGNON-Bib. numérique (840079901) / SudocSudocFranceF

Bias in parametric estimation: reduction and useful side-effects

The bias of an estimator is defined as the difference of its expected value from the parameter to be estimated, where the expectation is with respect to the model. Loosely speaking, small bias reflects the desire that if an experiment is repeated indefinitely then the average of all the resultant estimates will be close to the parameter value that is estimated. The current paper is a review of the still-expanding repository of methods that have been developed to reduce bias in the estimation of parametric models. The review provides a unifying framework where all those methods are seen as attempts to approximate the solution of a simple estimating equation. Of particular focus is the maximum likelihood estimator, which despite being asymptotically unbiased under the usual regularity conditions, has finite-sample bias that can result in significant loss of performance of standard inferential procedures. An informal comparison of the methods is made revealing some useful practical side-effects in the estimation of popular models in practice including: i) shrinkage of the estimators in binomial and multinomial regression models that guarantees finiteness even in cases of data separation where the maximum likelihood estimator is infinite, and ii) inferential benefits for models that require the estimation of dispersion or precision parameters

Fixed Effect Estimation of Large T Panel Data Models

This article reviews recent advances in fixed effect estimation of panel data models for long panels, where the number of time periods is relatively large. We focus on semiparametric models with unobserved individual and time effects, where the distribution of the outcome variable conditional on covariates and unobserved effects is specified parametrically, while the distribution of the unobserved effects is left unrestricted. Compared to existing reviews on long panels (Arellano and Hahn 2007; a section in Arellano and Bonhomme 2011) we discuss models with both individual and time effects, split-panel Jackknife bias corrections, unbalanced panels, distribution and quantile effects, and other extensions. Understanding and correcting the incidental parameter bias caused by the estimation of many fixed effects is our main focus, and the unifying theme is that the order of this bias is given by the simple formula p/n for all models discussed, with p the number of estimated parameters and n the total sample size.Comment: 40 pages, 1 tabl

Electromagnetic vertex function of the pion at T > 0

The matrix element of the electromagnetic current between pion states is calculated in quenched lattice QCD at a temperature of $T = 0.93 T_c$. The nonperturbatively improved Sheikholeslami-Wohlert action is used together with the corresponding ${\cal O}(a)$ improved vector current. The electromagnetic vertex function is extracted for pion masses down to $360 {\rm MeV}$ and momentum transfers $Q^2 \le 2.7 {\rm GeV}^2$.Comment: 17 pages, 8 figure

Measuring Malnutrition

Summary The nutritional condition of an individual, or the extent of malnutrition in a population, can be measured either in terms of outcomes , i.e. current status, or in terms of inputs , i.e rates of consumption of nutrients and/or energy in diets. A review of the methods of measurement in common use for these two approaches, and of their technical limitations, is followed by an account of the problems of interpretation of these in the light of contemporary ideas about the causes of growth faltering in children. Also discussed is the basis for standards of normality for growth and for nutrient intake levels, and the extent to which adaptive changes in behaviour or physiology may compensate for low levels of intake. It is concluded that, provided these problems are recognised, nutritional indicators can play a useful role in assessing overall food and health situations, particularly when accompanied by other complementary measurements of the effects of the health environment of the households and their social and economic characteristics