Asymptotic Dynamics in Quantum Field Theory

A crucial element of scattering theory and the LSZ reduction formula is the assumption that the coupling vanishes at large times. This is known not to hold for the theories of the Standard Model and in general such asymptotic dynamics is not well understood. We give a description of asymptotic dynamics in field theories which incorporates the important features of weak convergence and physical boundary conditions. Applications to theories with three and four point interactions are presented and the results are shown to be completely consistent with the results of perturbation theory.Comment: 18 pages, 3 figure

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ~1 h of hands-on time

O contributo do projecto INTERFRUTA II para o desenvolvimento da fruticultura na ilha Terceira, Açores

13º Congresso da APDR (Associação Portuguesa para o Desenvolvimento Rural). Angra do Heroísmo, Julho de 2007.O Projecto Interfruta II é um projecto apoiado pelo programa Interreg III-B, desenvolvido nas Ilhas da Madeira, Tenerife (Canárias) e Terceira (Açores) destinado a contribuir para a promoção da fruticultura e viticultura nestas três regiões insulares, procurando uma melhoria dos conhecimentos sobre os problemas fitossanitários que afectam as macieiras, bananeiras, castanheiros e a vinha, aplicando técnicas que contribuam decisivamente para o conhecimento e procura de soluções, numa vertente de prospecção das pragas-chave, fauna auxiliar, doenças e vírus que afectam essas culturas. Destaca-se o facto de inicialmente se ter procedido à realização de 160 inquéritos aos produtores e ao levantamento e identificação, através de SIG, das áreas de produção frutícola da Ilha. Para a análise dos factores climáticos ao nível da parcela, foram instaladas nas três zonas em estudo, estações meteorológicas de leitura automática.ABSTRACT: The INTERFRUTA project is financed by the European Commission Interreg III-B Programme and was developed for the islands of Madeira, Tenerife and Terceira for the improvement of fruit and vineyard production in these three Atlantic regions. The project goal is a better knowledge of the phytossanitary problems that affect apples, bananas, chestnut and vineyards, applying methods that will contribute to solutions based on the survey of key pests, diseases and beneficial organisms. All these work began with a survey to 160 producers and those data permitted, applying GIS techniques to them to identify the Terceira island fruit and vineyard production areas. To register the climate conditions in each area studied fully automatic meteorological stations were put in each of the three studied areas

Comparison of two multiple-locus variable-number tandem-repeat analysis methods for molecular strain typing of human Brucella melitensis isolates from the Middle East

Brucella species are highly monomorphic, with minimal genetic variation among species, hindering the development of reliable subtyping tools for epidemiologic and phylogenetic analyses. Our objective was to compare two distinct multiple-locus variable-number tandem-repeat analysis (MLVA) subtyping methods on a collection of 101 Brucella melitensis isolates from sporadic human cases of brucellosis in Egypt (n = 83), Qatar (n = 17), and Libya (n = 1). A gel-based MLVA technique, MLVA-15IGM, was compared to an automated capillary electrophoresis-based method, MLVA-15NAU, with each MLVA scheme examining a unique set of variable-number tandem repeats. Both the MLVAIGM and MLVANAU methods were highly discriminatory, resolving 99 and 101 distinct genotypes, respectively, and were able to largely separate genotypes from Egypt and Qatar. The MLVA-15NAU scheme presented higher strain-to-strain diversity in our test population than that observed with the MLVA-15IGM assay. Both schemes were able to genetically correlate some strains originating from the same hospital or region within a country. In addition to comparing the genotyping abilities of these two schemes, we also compared the usability, limitations, and advantages of the two MLVA systems and their applications in the epidemiological genotyping of human B. melitensis strains

Cosmology of the selfaccelerating third order Galileon

In this paper we start from the original formulation of the galileon model with the original choice for couplings to gravity. Within this framework we find that there is still a subset of possible Lagrangians that give selfaccelerating solutions with stable spherically symmetric solutions. This is a certain constrained subset of the third order galileon which has not been explored before. We develop and explore the background cosmological evolution of this model drawing intuition from other even more restricted galileon models. The numerical results confirm the presence of selfacceleration, but also reveals a possible instability with respect to galileon perturbations.Comment: 30 pages, 24 figure

Biomarker of food intake for assessing the consumption of dairy and egg products

Foods of animal origin constitute one of the predominant food groups consumed in Western diets. They play an essential role in human nutrition as they represent an excellent source of high quality proteins, vitamins, minerals and fats. Foods of animal origin are highly diverse (e.g. meat, fish, dairy products and eggs) and their associations with a range of nutritional and health outcomes are therefore heterogeneous. Such associations are also often weak or debated due to the difficulty in establishing correct assessments of dietary intake. Therefore, in order to better characterize associations between the consumption of specific foods of animal origin and health outcomes, it is important to identify reliable biomarkers of food intake (BFIs). BFIs provide a more accurate measure of intake and are independent of the memory and sincerity of the subjects as well as of their knowledge about the consumed foods. To date, only a very limited number of compounds have been proposed as biomarkers of the intake of foods of animal origin and further studies are necessary to validate them and to discover new candidate BFIs. We have, therefore, conducted a systematic search of the scientific literature to evaluate the current status of potential BFIs for each category of foods of animal origin commonly consumed in Europe. This review reports on candidate biomarkers for dairy products and eggs intake, while biomarkers for fish and meat intake will be published separately. Remarkably, validated BFIs for dairy products and eggs are not available. A series of challenges hinders their identification and validation, in particular the heterogeneous composition of each food within a product category and the lack of specificity of the markers identified so far. Untargeted metabolomic strategies may allow the identification of novel food biomarkers, that, when taken separately or in combination, could be used to assess the intake of dairy products and eggs

O projecto INTERFRUTA II e o seu papel no desenvolvimento da fruticultura na ilha Terceira

I Congresso de Fruticultura e Viticultura. Angra do Heroísmo 17-19 Abril 2008.Trabalho de investigação desenvolvido no projecto INTERFRUTA II, financiado pelo programa INTERREG III-B (05/MAC/3.1/A4).O Projecto INTERFRUTA II é um projecto desenvolvido nas Ilhas da Madeira, Tenerife (Canárias) e Terceira (Açores) destinado a contribuir para a promoção da fruticultura e viticultura nestas três regiões insulares, procurando uma melhoria dos conhecimentos sobre as culturas de macieiras, bananeiras, castanheiros e vinha. Englobando um estudo integrado que envolve a climatologia, fenologia, pedologia, problemas fitossanitários, pragas-chave e a fauna auxiliar presente nas parcelas estudadas, distribuídas pela zona Norte e Sul da Ilha, aplicando técnicas que contribuam decisivamente para o conhecimento e procura de soluções inovadoras que conduzam ao acréscimo do rendimento dos produtores e a uma menor utilização e aplicação de pesticidas. Para atingir estes objectivos numa fase inicial realizaram-se 160 inquéritos aos produtores e foi possível a identificação, através de SIG, das áreas de produção frutícola da Ilha. Para a análise dos factores climáticos ao nível da parcela, foram instaladas estações meteorológicas de leitura automática. Na parte relativa ao estudo da fenologia e produção para além da caracterização foi avaliado o impacto da polinização na taxa de vingamento dos frutos de macieira. Dentro dos problemas fitossanitários, na identificação das pragas-chave de cada cultura foi utilizada a observação visual de órgãos predefinidos e a monitorização através de armadilhas com feromona sexual e utilizadas placas cromotrópicas com cola. Nos fungos foi utilizada a observação visual e na prospecção de vírus e fitoplasmas utilizaram-se técnicas moleculares (ELISA) e PCR. Na prospecção da fauna auxiliar foi a técnica dos batimentos (ou pancadas) e a armadilha Malaise. Foi também realizado o levantamento das plantas auxiliares de produção e feita a sua identificação. Nas pragas-chave de cada uma das culturas, centrou-se a investigação sobre as mais importantes. A mosca-do-Mediterrâneo (C. capitata Wied.) foi uma delas, onde com o objectivo da sua monitorização, recorrendo aos SIG, foi montada uma rede de armadilhas em toda a ilha. Na bananeira, centrou-se todo o trabalho no gorgulho-da-bananeira (Cosmopolites sordidus Germar) e nas tripes. No castanheiro, no bichado-da-castanha (Cydia splendana Hubner) tendo sido avaliados os prejuízos que causa e conhecida a sua curva de voo através da sua monitorização usando armadilhas com feromona sexual. Na vinha, o míldio é a doença que mais contribuiu para a diminuição da produção de uva para vinho. Nas macieiras, os principais problemas decorrem da presença de aranhiço vermelho (Panonychus ulmi Koch), traça-oriental (Cydia molesta) e bichado (Cydia pomonella L.). Para a recolha e divulgação de toda a informação foi construída uma página Web do projecto, disponível na Internet (www.interfuta.angra.uac.pt) e uma base de dados fitossanitários de diagnóstico da Macaronésia (PROFITOMAC) para a identificação de todos os problemas que afectam estas culturas nos três arquipélagos em que o projecto de desenvolve. No âmbito das actividades do projecto foram ainda realizados alguns cursos de formação de curta duração para técnicos e produtores

SUPPA2:fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Supplementary methods. (PDF 315 kb

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function