Performance of Permutation Tests Using Simulated Genetic Data

Disease statuses and biological conditions are known to be greatly impacted by differences in gene expression levels. A common challenge in RNA-seq data analysis is to identify genes whose mean expression levels change across different groups of samples, or, more generally, are associated with one or more variables of interest. Such analysis is called differential expression analysis. Many tools have been developed for analyzing differential gene expression (DGE) for RNA-seq data. RNA-seq data are represented as counts. Typically, a generalized linear model with a log link and a negative binomial response is fit to the count data for each gene, and DE genes are identified by testing, for each gene, whether a model parameter or linear combination of model parameters is zero. We conducted a simulation study to compare the performance of our proposed modified permutation test to DESeq2 edgeR, Limma, LFC and Voom when applied to RNA-seq data. We considered different combinations of sample sizes and underlying distributions. In this simulation study, we first simulated data using Monte Carlo simulation in SAS and assessed True Detection rate and False Positive rate for each model involved. We then simulated data from real RNA-seq data using SimSeq algorithm and compared the performance of our proposed model to DESeq2 edgeR, Limma, LFC and Voom. The simulation results suggest that Permutation tests are a competitive alternative to traditional parametric methods for analyzing RNA-seq data when we have sufficient sample sizes. Specifically, the results show that Permutation controlled Type I error fairly well and had a comparable Power rate. Moreover, for a sample size n?10 simulation exhibited a comparable True detection rate and consistently kept the False Positive rate very low when sampling from Poisson and Negative Binomial distributions. Likewise, the results from SimSeq confirm that Permutation tests do a better job at keeping the False Positive rate the lowest

Le génocide rwandais dans la littérature africaine francophone

International audienceEn 1994 au Rwanda, entre le 6 avril et le 4 juillet, prèsd’un million de Tutsi ont trouvé la mort. Quatre ans aprèsle génocide, en 1998, une dizaine d’écrivains sont partis aupays dans le cadre du projet « Rwanda, écrire par devoirde mémoire » pour voir de plus près les ossements desvictimes exposés dans les sites de mémoire construits à ceteffet et produire des textes de témoignage. Ainsi est née lalittérature du génocide des Tutsi. Cet ouvrage tente d’analyserles œuvres issues de ce projet. Il est surtout question desouligner les différentes techniques narratives utilisées. Aprèsavoir fait un état des lieux de la tradition du témoignage dansla littérature africaine francophone de 1920 à 2000, l’auteurmontre ainsi comment les auteurs des œuvres étudiées ontpu surmonter les difficultés liées à l’indicible du génocide, qui,par sa nature, défie la raison, pour exprimer les souffrancesendurées par les victimes

Impact Assessment of agricultural research and development to reduce virus problems in tomato production in Mali: Farmers perceptions

Pests and diseases caused by bacteria, nematodes, fungi and viruses cause significant losses to tomato in West Africa. This study, carried-out within the framework of the IPM-CRSP implemented jointly by IITA, IER and Virginia Tech. and State University, assesses farmers’ perceptions on tomato pests and analyzes factors affecting pest management decision-making. Surveys were carried out in three tomato production areas where pests and diseases are major agricultural problems encountered by farmers. Data were collected a sample of from 343 farmers through a set of questionnaires on tomato production systems. Farmer’s decision-making in pest management was modeled using an econometrics Logit probability model. Results show that the main disease reported by most farmers is tomato leaf curl viruses transmitted by whitefly (Bemissia tabaci). The spray of chemicals was not effective on whitefly-transmitted viruses, but the observance of host free period could significantly reduce the population of whiteflies. Key factors affecting farmers’ pest management decision-making are gender; share of tomato income from household income and the level of farm income. Men are more involved in tomato production due to access to pesticide and effective demand for pesticides because of incomes (purchasing power). This paper concludes that tomato production can increase significantly if improved varieties tolerant to whitefly viruses are developed and disseminated, and farmers trained on the appropriate use of chemicals using a participatory approach to raise their level of awareness and information on effective pesticide use and pest-management decision-making.Agricultural and Food Policy, Agricultural Finance, Crop Production/Industries, Demand and Price Analysis, Environmental Economics and Policy, Farm Management, Food Consumption/Nutrition/Food Safety, Food Security and Poverty, International Relations/Trade, Marketing, Productivity Analysis, Research and Development/Tech Change/Emerging Technologies,

Spatial Structure Of Agricultural Biodiversity In Southern Mali

The diversity of cropping systems and varieties plays an important role in the ability of family farms to resist socio-economic and environmental shocks. For better conservation, agricultural diversity needs to be characterized and monitored in space and time. While initially dominated by the elements on price, surfaces, and productions, agricultural monitoring systems have recently incorporated diversity issues. The objective of this work is to analyze the spatial structure of agricultural biodiversity and to explain the links between this structure and the agronomic practices and results in family farms in southern Mali. The methodology was to develop, test, and maintain a conceptual model of spatial data on a sample of three villages. The analysis of these data is based on the spatial distribution of biodiversity and its correlation with the practices and agro-ecological conditions, results, and agronomic performance. The results show a very large specific and varietal diversity. We do not observe a clear link between spatial distribution and the characteristics of the physical environment, with the exception of the improved variety of Kalafoufigue located on a particular type of slope. The same observation is made when the relationship is between the spatial distribution of the variety and the technical route. Spatial analysis has developed a map of the diversity across the country village. Thus, spatial distribution points plot a surface distribution across local villages, and these results open the way for greater contributions of geographical analysis in agriculture and for scaling territories that remain a challenge for agriculture

High temperature structural and magnetic properties of cobalt nanowires

We present in this paper the structural and magnetic properties of high aspect ratio Co nanoparticles (~10) at high temperatures (up to 623 K) using in situ X ray diffraction (XRD) and SQUID characterizations. We show that the anisotropic shapes, the structural and texture properties are preserved up to 500 K. The coercivity can be modelled by u0Hc=2(Kmc+Kshape)/Ms with Kmc the magnetocrystalline anisotropy constant, Kshape the shape anisotropy constant and Ms the saturation magnetization. Hc decreases linearly when the temperature is increased due to the loss of the Co magnetocrystalline anisotropy contribution. At 500K, 50% of the room temperature coercivity is preserved corresponding to the shape anisotropy contribution only. We show that the coercivity drop is reversible in the range 300 - 500 K in good agreement with the absence of particle alteration. Above 525 K, the magnetic properties are irreversibly altered either by sintering or by oxidation.Comment: 8 pages, 7 figures, submitted to Journal of Solid State Chemistr

Magnetic nanowires as permanent magnet materials

We present the fabrication of metallic magnetic nanowires using a low temperature chemical process. We show that pressed powders and magnetically oriented samples exhibit a very high coercivity (6.5 kOe at 140 K and 4.8 kOe at 300 K). We discuss the magnetic properties of these metamaterials and show that they have the suitable properties to realize "high temperature magnets" competitive with AlNiCo or SmCo permanent magnets. They could also be used as recording media for high density magnetic recording.Comment: 5 pages, 5 figure

Introduction of digital experimentation capabilities on the ELVIS iLab platform

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.Includes bibliographical references (p. 73).iLabs are online laboratories that give students access to experimental setups enabling them to conduct real experiments remotely through the internet. This circumvents a subset of the typical problems of conventional laboratories in addition to significantly increasing equipment utilization rates. In response to the lack of financial resources at partner universities in Africa, the National Instruments Educational Laboratory Virtual Instrumentation Suite (ELVIS), a low cost all-in-one electronics workbench, has become the hardware of choice for the iLab-Africa project. In this thesis, I extended the ELVIS iLab platform to support experiments in Digital Electronics complementing its analog capabilities. The new platform now offers an even greater return on investment by providing pedagogically useful laboratory exercises covering a larger portion of Electrical Engineering curricula.by Hamidou Soumare.M.Eng

A theoretical framework for trading experiments

A general framework is suggested to describe human decision making in a certain class of experiments performed in a trading laboratory. We are in particular interested in discerning between two different moods, or states of the investors, corresponding to investors using fundamental investment strategies, technical analysis investment strategies respectively. Our framework accounts for two opposite situations already encountered in experimental setups: i) the rational expectations case, and ii) the case of pure speculation. We consider new experimental conditions which allow both elements to be present in the decision making process of the traders, thereby creating a dilemma in terms of investment strategy. Our theoretical framework allows us to predict the outcome of this type of trading experiments, depending on such variables as the number of people trading, the liquidity of the market, the amount of information used in technical analysis strategies, as well as the dividends attributed to an asset. We find that it is possible to give a qualitative prediction of trading behavior depending on a ratio that quantifies the fluctuations in the model

L'impact de la divulgation des antécédents criminels des politiciens sur les résultats électoraux : le cas de l'Inde

Ce mémoire évalue l'impact de l'information sur l'élection de politiciens malhonnêtes. À partir d'un échantillon d'observations concernant un total de \ud 2105 politiciens, nous utilisons une méthode différence-en-différence pour mesurer le changement de score entraîné par la divulgation des charges criminelles des candidats aux élections en Inde. L'analyse des conséquences électorales de la malhonnêteté des politiciens revêt un caractère essentiel si l'on considère les liens importants unissant le développement économique à la qualité des élus. Contrairement à nos attentes, les estimations révèlent que même s'ils sont informés, les électeurs ne punissent pas de façon marquée la corruption des politiciens. Tandis que la divulgation des charges d'agitation politique est associée à des améliorations de score de l'ordre de 2,4 à 2,7 points de pourcentage, l'information n'a pas d'effets significatifs sur le score des candidats accusés de corruption ou de vol. Nous pensons que si les ressources financières sont déterminantes pour gagner des élections, les fonds tirés d'activités comme la corruption ou le vol donnent un avantage supplémentaire aux candidats malhonnêtes. Dans un tel contexte, l'information n'a qu'un effet limité sur la corruption des hommes politiques. Les résultats montrent par ailleurs que les électeurs ont davantage tendance à se fier à l'information divulguée lorsqu'ils ne connaissent pas le candidat. Les candidats qui au moment des élections, n'occupaient pas le poste à pouvoir sont plus durement pénalisés par la divulgation de charges criminelles. Dans le cas des candidats cherchant une réélection, les électeurs se basent surtout sur les actions et les comportements qu'ils ont adoptés au cours de leurs mandats. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Politiciens criminels, Corruption, Asymétrie d'information, Politique de divulgation