Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models

Motivation: Blood cell development is thought to be controlled by a circuit of transcription factors (TFs) and chromatin modifications that determine the cell fate through activating cell type-specific expression programs. To shed light on the interplay between histone marks and TFs during blood cell development, we model gene expression from regulatory signals by means of combinations of sparse linear regression models. Results: The mixture of sparse linear regression models was able to improve the gene expression prediction in relation to the use of a single linear model. Moreover, it performed an efficient selection of regulatory signals even when analyzing all TFs with known motifs (>600). The method identified interesting roles for histone modifications and a selection of TFs related to blood development and chromatin remodelling. Availability: The method and datasets are available from http://www.cin.ufpe.br/~igcf/SparseMix. Contact: [email protected] Supplementary information:Supplementary data are available at Bioinformatics online

Utilisation de matrices de dissimilarité multiples pour la classification de documents

International audienceThis paper introduces a clustering algorithm that is able to partition objects taking into account simultaneously their relational descriptions given by multiple dissimilarity matrices. These matrices could have been generated using different sets of variables and a fixed dissimilarity function, using a fixed set of variables and different dissimilarity functions or using different sets of variables and dissimilarity functions. This method, which is based on the dynamic hard clustering algorithm for relational data, is designed to provided a partition and a prototype for each cluster as well as to learn a relevance weight for each dissimilarity matrix by optimizing an adequacy criterion that measures the fit between clusters and their representatives. These relevance weights change at each algorithm iteration and are different from one cluster to another. Experiments aiming at obtaining a categorization of a document data base demonstrate the usefulness of this partitional clustering method.Cet article introduit l'algorithme de classification donné dans CarvhaloLechevallier:2007:SFC capable de partitionner des objets en prenant en compte de manière simultanée plusieurs matrices de dissimilarité qui les décrivent. Ces matrices peuvent avoir été générées en utilisant différents ensembles de variables et une fonction de dissimilarité unique, un ensemble de variables donné et différentes fonctions de dissimilarité ou bien différents ensembles de variables et de fontions de dissimilarité. Cette méthode, basée sur l'algorithme de nuées dynamiques est conçu pour fournir une partition et un prototype pour chaque classe tout en découvrant une pondération pertinante pour chaque matrice de dissimilarité en optimisant un critère d'adéquation entre les classes et leurs représentants. Ces pondérations changent à chaque itération de l'algorithme et sont différentes pour chacune des classes. Ce papier se focalise sur une expérience utilisant un ensemble de documents, dont nous connaisssons une classification donnée a priori par des experts servant de référence, et montre l'utilité de cette méthode de partitionnement

Qualidade da carne DFD em diferentes tempos de maturação.

A carne DFD (do inglês, dark, firm e dry) ocorre quando o animal é submetido a condições de stress no pré-abate

Theory of Functional Connections and Nelder-Mead optimization methods applied in satellite characterization

The growing population of man-made objects with the build up of mega-constellations not only increases the potential danger to all space vehicles and in-space infrastructures (including space observatories), but above all poses a serious threat to astronomy and dark skies. Monitoring of this population requires precise satellite characterization, which is is a challenging task that involves analyzing observational data such as position, velocity, and light curves using optimization methods. In this study, we propose and analyze the application of two optimization procedures to determine the parameters associated with the dynamics of a satellite: one based on the Theory of Functional Connections (TFC) and another one based on the Nelder-Mead heuristic optimization algorithm. The TFC performs linear functional interpolation to embed the constraints of the problem into a functional. In this paper, we propose to use this functional to analytically embed the observational data of a satellite into its equations of dynamics. After that, any solution will always satisfy the observational data. The second procedure proposed in this research takes advantage of the Nealder-Mead algorithm, that does not require the gradient of the objective function, as alternative solution. The accuracy, efficiency, and dependency on the initial guess of each method is investigated, analyzed, and compared for several dynamical models. These methods can be used to obtain the physical parameters of a satellite from available observational data and for space debris characterization contributing to follow-up monitoring activities in space and astronomical observatories.Comment: Submitted to Acta Astronautic

Produção de sementes de cebola em sistemas convencional e de transição agroecológica.

O presente trabalho teve como objetivo fazer um estudo nos sistemas de produção de semente de cebola convencional e agroecológico. Foram acompanhadas três propriedades nos municípios de Candiota e Hulha Negra,RS, de produção agroecológicas e duas convencionais, sendo marcadas aleatoriamente seis unidades de amostragem,cada uma delas com dois metros sobre a linha de produção, em cada uma das propriedades. As variáveis estudadas foram peso de bulbo, diâmetro bulbo quantidade de bulbos por área, quantidade de hastes por bulbo, quantidade de flores por umbela, quantidade de sementes por flor, teor de água da semente, rendimento de sementes, germinação,primeira contagem, peso de 1000 sementes, envelhecimento acelerado, índice e velocidade de germinação e sanidade de sementes, bem como o levantamento dos custos de produção. A produção de semente de cebola através do sistema de produção agroecológico é economicamente viável e ecologicamente sustentável. A produção de semente de cebola em sistema convencional situa-se em média de 30% do seu potencial. O potencial de produção e qualidade fisiológica da semente de cebola agroecológica e convencional são similares. A variável número de flores por umbela pode ser considerada o componente principal da produção de semente de cebola

Os museus históricos e pedagógicos do estado de São Paulo

This paper analyzes the creation of the Historical and Pedagogical Museums network in the State of São Paulo between 1956 and 1973, mainly taking into consideration the concept for creation, the program, and the role of the museum in society. This work covers a period until the end of the 1990's, when the curators of the museums, which belonged to the State until that time, was transferred to the municipalities by means of a "municipalization" process coordinated by the Department of Museums and Archives of the State Department of Cultural Affairs (DEMA-SEC). It also shows that the implementation of this museums network - among other initiatives in the fields of education and of culture - addressed earlier needs of asserting an identity, emphasizing through projects of this type the hegemonic character of the State. This allowed to align the initiative of creating the museums with others actions carried out by the State before, and also enabled that this topic was take out from its long isolation from the study of State history. It also considers the web of relationships existing among the various sectors with which museums were connected, such as education, culture, and the São Paulo Historical and Geographical Institute, the Government, and Society. The implementation of Historical and Pedagogical Museums by means of State action, through its Departments of Education (from 1956 to 1968) and Cultural Affairs (from 1968 to 1998) was one of the ways through which the Government orientated its activities during those years in the fields of history, education and culture. The central thesis is that the implementation of these museums has fully addressed the aspirations of society at the time, while, at the same time, underscoring the logic behind the ideation that has oriented the characteristic mode of operation of museums during the years in which their curatorship was exercised by the Government, and proposes to consider them as a paradigm for "historical museums of the State of São Paulo".Este estudo analisa a criação da rede de museus históricos e pedagógicos do estado de São Paulo entre os anos de 1956 e 1973, sobretudo quanto ao conceito de criação, de programa e de função de museu na sociedade. Tal análise estende-se ao final da década de 1990, quando a tutela dos museus, até então estadual, é transferida às cidades por meio do processo de municipalização, coordenado pelo Departamento de Museus e Arquivos, da Secretaria de Estado da Cultura (Dema-SEC). Em meio a outras iniciativas nos campos da educação e da cultura, aborda a correspondência existente entre a implantação da rede desses museus e antigas necessidades de afirmação identitária, ao evidenciar, por meio de projetos desta natureza, o caráter hegemônico do Estado e sua atuação em campos como o da história, o da educação e o da cultura. Isso permitiu alinhar a iniciativa de criação dos museus a outras anteriormente promovidas pelo estado de São Paulo e possibilitar que o tema escapasse de um prolongado isolamento no estudo da história paulista. Trata, também, da trama de relações existentes entre diversos setores ligados aos museus - educação, cultura, Instituto Histórico e Geográfico de São Paulo (IHGSP), poder público e sociedade. A hipótese central é de que a implantação desses museus correspondeu plenamente às aspirações da sociedade de uma época, ao mesmo tempo em que evidencia a lógica da ideação que determinou o modo característico de atuação dos museus nos anos em que estiveram sob a tutela do governo estadual, propondo, assim, entendê-los como paradigma de "museu histórico do estado de São Paulo"

Measurement of the Bs0→J/ψKS0B_s^0\to J/\psi K_S^0 branching fraction

The $B_s^0\to J/\psi K_S^0$ branching fraction is measured in a data sample corresponding to 0.41$fb^{-1}$ of integrated luminosity collected with the LHCb detector at the LHC. This channel is sensitive to the penguin contributions affecting the sin2$\beta$ measurement from $B^0\to J/\psi K_S^0$ The time-integrated branching fraction is measured to be $BF(B_s^0\to J/\psi K_S^0)=(1.83\pm0.28)\times10^{-5}$. This is the most precise measurement to date