A statistical framework for testing functional categories in microarray data

Ready access to emerging databases of gene annotation and functional pathways has shifted assessments of differential expression in DNA microarray studies from single genes to groups of genes with shared biological function. This paper takes a critical look at existing methods for assessing the differential expression of a group of genes (functional category), and provides some suggestions for improved performance. We begin by presenting a general framework, in which the set of genes in a functional category is compared to the complementary set of genes on the array. The framework includes tests for overrepresentation of a category within a list of significant genes, and methods that consider continuous measures of differential expression. Existing tests are divided into two classes. Class 1 tests assume gene-specific measures of differential expression are independent, despite overwhelming evidence of positive correlation. Analytic and simulated results are presented that demonstrate Class 1 tests are strongly anti-conservative in practice. Class 2 tests account for gene correlation, typically through array permutation that by construction has proper Type I error control for the induced null. However, both Class 1 and Class 2 tests use a null hypothesis that all genes have the same degree of differential expression. We introduce a more sensible and general (Class 3) null under which the profile of differential expression is the same within the category and complement. Under this broader null, Class 2 tests are shown to be conservative. We propose standard bootstrap methods for testing against the Class 3 null and demonstrate they provide valid Type I error control and more power than array permutation in simulated datasets and real microarray experiments.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS146 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The 1999 Heineman Prize Address- Integrable models in statistical mechanics: The hidden field with unsolved problems

In the past 30 years there have been extensive discoveries in the theory of integrable statistical mechanical models including the discovery of non-linear differential equations for Ising model correlation functions, the theory of random impurities, level crossing transitions in the chiral Potts model and the use of Rogers-Ramanujan identities to generalize our concepts of Bose/Fermi statistics. Each of these advances has led to the further discovery of major unsolved problems of great mathematical and physical interest. I will here discuss the mathematical advances, the physical insights and extraordinary lack of visibility of this field of physics.Comment: Text of the 1999 Heineman Prize address given March 24 at the Centenial Meeting of the American Physical Society in Atlanta 20 pages in latex, references added and typos correcte

Application of lightning data to satellite-based rainfall estimation

Information on lightning may improve rain estimates made from infrared images of a geostationary satellite. We address this proposition through a case from the Cooperative Huntsville Meteorological Experiment (COHMEX). During the afternoon and evening of 13 July 1986 waves of showers and thunderstorms developed over and near the lower Tennessee River Valley. For the shower and thunderstorm region within 200 km of the National Weather Service radar at Nashville, Tennessee, we measure cold-cloud area in a sequence of GOES infrared images covering all but the end of the shower and thunderstorm period. From observations of the NASA/Marshall direction-finding network in this small domain, we also count cloud-to-ground lightning flashes and, from scans of the Nashville radar, we calculate volume rain flux. Using a modified version of the Williams and Houze scheme, over an area within roughly 240 km of the radar (the large domain), we identify and track cold cloud systems. For these systems, over the large domain, we measure area and count flashes; over the small domain, we calculate volume rain flux. For a temperature threshold of 235K, peak cloud area over the small domain lags both peak rain flux and peak flash count by about four hours. At a threshold of 226K, the lag is about two hours. Flashes and flux are matched in phase. Over the large domain, nine storm systems occur. These range in size from 300 to 60,000 km(exp 2); in lifetime, from about 2 1/2 h to 6 h or more. Storm system area lags volume rain flux and flash count; nevertheless, it is linked with these variables. In essential respects the associations were the same when clouds were defined by a threshold of 226K. Tentatively, we conclude that flash counts complement infrared images in providing significant additional information on rain flux

Screening of Irish Fruit and Vegetable Germplasm for Novel Anti-tumour and Pesticidal Compounds

Conference paperPhytochemicals are a rich source of novel therapeutic and insecticidal agents (McLaughlin and Chang, 1999). Considerable research effort has been directed at screening exotic and medicinal plants in the search for novel products. However, plants which have traditional food uses have been little explored. In addition the range, type and level of individual bioactive compounds can vary significantly between different species, different cultivars of the same species and different tissue types of the plant (Reilly, in press) Therefore, the objective of this study was to screen a range of fruits and vegetables which can be grown in Ireland for novel bioactive compounds for use in food production and as bio-pesticides.The author wishes to acknowledge the financial support from the Dublin Institute of Technology through an ABBEST fellowshi

Sum Rules for Magnetic Moments and Polarizabilities in QED and Chiral Effective-Field Theory

We elaborate on a recently proposed extension of the Gerasimov-Drell-Hearn (GDH) sum rule which is achieved by taking derivatives with respect to the anomalous magnetic moment. The new sum rule features a {\it linear} relation between the anomalous magnetic moment and the dispersion integral over a cross-section quantity. We find some analogy of the linearized form of the GDH sum rule with the `sideways dispersion relations'. As an example, we apply the linear sum rule to reproduce the famous Schwinger's correction to the magnetic moment in QED from a tree-level cross-section calculation and outline the procedure for computing the two-loop correction from a one-loop cross-section calculation. The polarizabilities of the electron in QED are considered as well by using the other forward-Compton-scattering sum rules. We also employ the sum rules to study the magnetic moment and polarizabilities of the nucleon in a relativistic chiral EFT framework. In particular we investigate the chiral extrapolation of these quantities.Comment: 24 pages, 7 figures; several additions, published versio

Intergenerational justice of what: welfare, resources or capabilities?

An important aspect of intergenerational justice concerns the specification of a 'currency of advantage' that can be used to evaluate distributive outcomes across time. Environmental theorists have introduced several innovative currencies of justice in recent years, such as ecological space and critical natural capital. However they have often downplayed the application of established currencies (such as welfare, resources or capabilities) to issues of futurity. After exploring the merits of a number of rival currencies, it is argued that the currency of 'capabilities to function' provides a promising basis for a theory of justice that takes seriously the rights and duties of intergenerational justice

Contamination Des Laits Importes Au Mali Par La Melamine

Au Mali l’insuffisance de données scientifiques sur la contamination des aliments en général et du lait en particulier par la Mélamine a motivé la conduite de la présente étude.Dans ce travail, nous avions recherchés la Mélamine dans les laits importés au Mali.Un total de 150 échantillons de laits importés, a été récolté dans le District de Bamako.La détermination de la Mélamine a été effectuée par Immuno-affinité/Méthode ELISA. Les résultats des analyses ont montré que 38 échantillons sur les 150 de laits importés étaient contaminés par la Mélamine. Chez les importateurs, 8 échantillons sur 18 des laits importés étaient contaminés, les taux de contamination variaient de 0,03mg/kg à 0,91 mg/kg. Chez les demi-grossistes 19 échantillons sur 66 des laits importés, étaient contaminés par la Mélamine. Les taux de contamination variaient de 0,01 à 1,14mg/kg. Chez les détaillants, 11 échantillons sur 66 des laits importés étaient contaminés avec des taux de contamination qui variaient de 0,01 à 1,00mg/kg. Les taux moyens de contamination des laits pour les importateurs, les demi-grossistes et les détaillants sont respectivement de (0,20 ; 0,26 ; 0,26) mg/kg. Il est a noté que les taux obtenus sont inférieurs à la norme du Codex Alimentarius qui fixe la limite maximale pour le lait et les aliments contenant le lait à 2,5mg/kg

Ordered Measurements of Permutationally-Symmetric Qubit Strings

We show that any sequence of measurements on a permutationally-symmetric (pure or mixed) multi-qubit string leaves the unmeasured qubit substring also permutationally-symmetric. In addition, we show that the measurement probabilities for an arbitrary sequence of single-qubit measurements are independent of how many unmeasured qubits have been lost prior to the measurement. Our results are valuable for quantum information processing of indistinguishable particles by post-selection, e.g. in cases where the results of an experiment are discarded conditioned upon the occurrence of a given event such as particle loss. Furthermore, our results are important for the design of adaptive-measurement strategies, e.g. a series of measurements where for each measurement instance, the measurement basis is chosen depending on prior measurement results.Comment: 13 page

The FHD/ε\boldsymbol{\varepsilon}ppsilon Epoch of Reionization Power Spectrum Pipeline

Epoch of Reionization data analysis requires unprecedented levels of accuracy in radio interferometer pipelines. We have developed an imaging power spectrum analysis to meet these requirements and generate robust 21 cm EoR measurements. In this work, we build a signal path framework to mathematically describe each step in the analysis, from data reduction in the FHD package to power spectrum generation in the $\varepsilon$ppsilon package. In particular, we focus on the distinguishing characteristics of FHD/$\varepsilon$ppsilon: highly accurate spectral calibration, extensive data verification products, and end-to-end error propagation. We present our key data analysis products in detail to facilitate understanding of the prominent systematics in image-based power spectrum analyses. As a verification to our analysis, we also highlight a full-pipeline analysis simulation to demonstrate signal preservation and lack of signal loss. This careful treatment ensures that the FHD/$\varepsilon$ppsilon power spectrum pipeline can reduce radio interferometric data to produce credible 21 cm EoR measurements.Comment: 21 pages, 10 figures, accepted by PAS