7,806 research outputs found
SEMgraph: an R package for causal network inference of high-throughput data with structural equation models
No full textMotivation: With the advent of high-throughput sequencing in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms and possible experimental scenarios raised the problem of integrating large amounts of new heterogeneous data and current knowledge, to test novel hypotheses and improve our comprehension of physiological processes and diseases.Results: Combining network analysis and causal inference within the framework of structural equation modeling (SEM), we developed the R package SEMgraph. It provides a fully automated toolkit, managing complex biological systems as multivariate networks, ensuring robustness and reproducibility through data-driven evaluation of model architecture and perturbation, which is readily interpretable in terms of causal effects among system components
Novelty indicator for enhanced prioritization of predicted gene ontology annotations
No full textBiomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and might contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new annotations are both effective and efficient, especially if compared with time-consuming trials of biological validation. To limit the possibility that these techniques predict obvious and trivial high-level features, and to help prioritize their results, we introduce a new element that can improve accuracy and relevance of the results of an annotation prediction and prioritization pipeline. We propose a novelty indicator able to state the level of “originality” of the annotations predicted for a specific gene to Gene Ontology (GO) terms. This indicator, joint with our previously introduced prediction steps, helps by prioritizing the most novel interesting annotations predicted. We performed an accurate biological functional analysis of the prioritized annotations predicted with high accuracy by our indicator and previously proposed methods. The relevance of our biological findings proves effectiveness and trustworthiness of our indicator and of its prioritization of predicted annotations
Sem best shortest paths for the characterization of differentially expressed genes
No full textIn the last years, systems and computational biology focused their efforts in uncovering the causal relationships among the observable perturbations of gene regulatory networks and human diseases. This problem becomes even more challenging when network models and algorithms have to take into account slightly significant effects, caused by often peripheral or unknown genes that cooperatively cause the observed diseased phenotype. Many solutions, from community and pathway analysis to information flow simulation, have been proposed, with the aim of reproducing biological regulatory networks and cascades, directly from empirical data as gene expression microarray data. In this contribute, we propose a methodology to evaluate the most important shortest paths between differentially expressed genes in biological interaction networks, with absolutely no need of user-defined parameters or heuristic rules, enabling a free-of-bias discovery and overcoming common issues affecting the most recent network-based algorithms
Sobre as práticas e reflexões publicitárias de Fernando Pessoa
No full textNeste texto, a autora analisa alguns trabalhos publicitários de Fernando Pessoa, bem
como algumas das suas reflexões sobre esta actividade. É dada especial atenção ao slogan
“Primeiro estranha-se. Depois entranha-se”, analisado sobre a perspectiva das funções
e propriedades deste constituinte da mensagem publicitária. Por fim, recorda-se
um recente slogan que recupera o clássico de Fernando Pessoa.
On this article, the author analyses some advertising texts created by Fernando Pessoa and
some of his thoughts about this activity. The main attention goes to the famous slogan “Primeiro
estranha-se. Depois entranha-se”, analysed through the principles of the functions
and proprieties of this element of advertisements. Finally, the author presents a recent slogan, constructed through the slogan of the Portuguese writer
GenoMetric Query Language: A novel approach to large-scale genomic data management
No full textMotivation: Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art ‘big data’ computing strategies, with
abstraction levels beyond available tool capabilities.
Results: We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic ‘big data’ analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets.
Availability and implementation: The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/.
Contact: [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online
Fragments of the self: self-awareness, identity, and heteronymy in the works of Fernando Pessoa
No full textopenLa presente tesi esplora il tema dell'autocoscienza nell'opera di Fernando Pessoa, con particolare attenzione alla relazione tra identità ed eteronimia. Pessoa, attraverso la creazione dei suoi eteronimi, affronta questioni fondamentali legate alla frammentazione del sé e alla complessità dell'identità umana. L'analisi si concentra sulla natura poliedrica dell'autore, indagando come ogni eteronimo rappresenti un aspetto distinto della sua interiorità nel tentativo di comprendere e superare i limiti dell'individualità.This thesis explores the theme of self-awareness in the works of Fernando Pessoa, with a particular focus on the relashionship between identity and heteronymy. Through the creation of his heteronymys, Pessoa addresses fundamental questions related to the fragmentation of the self and the complexity of human identity. The analysis centers on the multifaceted nature of the author, investigating how each heteronym represents a distinct aspect of his inner world and an attempt to understand and transcend the limits of individuality
Recommended from our members
Fernando Moral Iglesias writes to Dr. Hector P. Garcia about Bill Neeley, author of the book "Hispanic Patriots of the Texas Revolution." (Correspondence)
No full textFernando Moral Iglesias writes to Dr. Hector P. Garcia about Bill Neeley, author of the book "Hispanic Patriots of the Texas Revolution." Two newspaper articles about Bill Neeley are included
Fernando Henrique Cardoso e o pensamento político brasileiro
No full textTese (doutorado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas, Programa de Pós-Graduação em Sociologia Política, Florianópolis, 2015.A construção do legado de Fernando Henrique Cardoso tem transcorrido a partir do signo de rupturas e dicotomias estruturantes, características que se articulam em torno da ideia da transição da atividade intelectual para a atividade política, num processo que reforça traços marcantes da imaginação política brasileira. Partindo da crítica dessa visão, este trabalho investiga o que o processo de formação do legado do autor como levado a cabo até aqui tem a dizer sobre os modos pelos quais se produz e se reinventa o ?pensamento político brasileiro?, ou, em outras palavras, o que sua trajetória intelectual individual representa em relação à trajetória coletiva de pensamento designada por esta expressão. Duas teses interpretativas principais são desenvolvidas ao longo deste trabalho: a primeira, de que o fio de continuidade e de unidade entre os diversos momentos da trajetória intelectual de Cardoso, negado pelas abordagens que até o presente vão dando conta da sistematização de seu legado, pode ser reconstruído e recuperado se a ênfase da análise recair na especificidade política de seus escritos, reconstrução e recuperação que, obviamente, não se furtam a considerar possíveis inconsistências, incoerências e mudanças nas crenças ao longo de sua trajetória; e a segunda, de que tal pensamento político, sem desconsiderar outras fontes genericamente rotuladas como ?universais?, estrutura-se a partir de um diálogo seletivo, sistemático e contínuo com algumas das principais matrizes de interpretação do político no país, diálogo este que, de um lado, torna possível evidenciar a existência de uma cosmovisão a atuar como ?fio condutor? para o conjunto de seu pensamento (conferindo a ele um sentido de coerência) e, de outro, entender o impacto ressignificador desse pensamento sobre tais matrizes. O trabalho está organizado em três partes: na primeira, produz-se uma reflexão teórico-metodológica do campo do pensamento político brasileiro; na segunda, discute-se a especificidade da reflexão política do autor a partir de dois momentos distintos (o do estabelecimento e o da consolidação das suas crenças políticas); e na terceira, num exercício de tentar aproximar as duas primeiras, discute-se a especificidade da inscrição do pensamento político do autor no campo do pensamento político brasileiro a partir de duas variáveis: as filiações e as recepções.Abstract : The construction of Fernando Henrique Cardoso?s legacy has been developed based on the mark of structuring ruptures and dichotomies, characteristics that are both articulated around the idea of the transition from the intellectual to the political activity, in a process that reinforces strong features of the Brazilian political imagination. Anchored in a criticism of this view, this study investigates what the process of formation of the author?s legacy developed until the present moment reveal about the forms through which the ?Brazilian political thought? is produced and reinvented, or, in other words, what his personal intellectual trajectory represents in relation to the collective thought trajectory designated by this expression. Two main interpretative theses are tested throughout this work: the first one is that the continuity and the unity between the several moments of Cardoso?s intellectual trajectory (denied by the approaches that, until the present moment, have been systematizing his legacy) can be reconstructed and recuperated if the emphasis of the analysis lies in the political specificity of his writings - assuming that both the reconstructing and the recuperation, obviously, do not fail to consider possible inconsistencies, incoherences and changes in the beliefs of the author throughout his trajectory; and second , that such political thought , without disregarding other sources generally labeled as ?universal? , is structured from a selective, systematic and continuous dialogue with some of the main forms of interpretation of the policy in the country, this dialogue , on the one hand , makes it possible to show the existence of a worldview to act as ?common thread? for all of his thought (giving him a sense of coherence), and on the other, to understand the impact of this ressignificador thinking about such matrices. The work is organized in three parts: in the first, the field of the Brazilian political thought is theoretical and methodologically questioned; in the second part, the specificity of the author?s political reflection is discussed based on two different moments (the establishment and the consolidation of his political beliefs); and, in the third part, in an attempt of approximating the two previous parts, the specificity of the insertion of the author?s political thought in the Brazilian political thought field is discussed, which is based on two variables: the filiations and the receptions
- …
