Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)

Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis

Current advances in systems and integrative biology

Systems biology has gained a tremendous amount of interest in the last few years. This is partly due to the realization that traditional approaches focusing only on a few molecules at a time cannot describe the impact of aberrant or modulated molecular environments across a whole system. Furthermore, a hypothesis-driven study aims to prove or disprove its postulations, whereas a hypothesis-free systems approach can yield an unbiased and novel testable hypothesis as an end-result. This latter approach foregoes assumptions which predict how a biological system should react to an altered microenvironment within a cellular context, across a tissue or impacting on distant organs. Additionally, re-use of existing data by systematic data mining and re-stratification, one of the cornerstones of integrative systems biology, is also gaining attention. While tremendous efforts using a systems methodology have already yielded excellent results, it is apparent that a lack of suitable analytic tools and purpose-built databases poses a major bottleneck in applying a systematic workflow. This review addresses the current approaches used in systems analysis and obstacles often encountered in large-scale data analysis and integration which tend to go unnoticed, but have a direct impact on the final outcome of a systems approach. Its wide applicability, ranging from basic research, disease descriptors, pharmacological studies, to personalized medicine, makes this emerging approach well suited to address biological and medical questions where conventional methods are not ideal

Are Price Limits on Futures Markets That Cool? Evidence from the Brazilian Mercantile and Futures Exchange

This paper investigates the impact of price limits on the Brazilian futures markets using high frequency data. The aim is to identify whether there is a cool-off or a magnet effect. For that purpose, we examine a tick-by-tick data set that includes all contracts on the S�o Paulo stock index futures traded on the Brazilian Mercantile and Futures Exchange from January 1997 to December 1999. The results indicate that the conditional mean features a floor cool-off effect, whereas the conditional variance significantly increases as the price approaches the upper limit. We then build a trading strategy that accounts for the cool-off effect in the conditional mean so as to demonstrate that the latter has not only statistical, but also economic significance. The in-sample Sharpe ratio indeed is way superior to the buy-and-hold benchmarks we consider, whereas out-of-sample results evince similar performances.Cool-off effect, Futures markets, Magnet effect, Price limits, Transactions data

Detecting portuguese and english Twitter users’ gender

Existing social networking services provide means for people to communicate and express their feelings in a easy way. Such user generated content contains clues of user’s behaviors and preferences, as well as other metadata information that is now available for scientific research. Twitter, in particular, has become a relevant source for social networking studies, mainly because: it provides a simple way for users to express their feelings, ideas, and opinions; makes the user generated content and associated metadata available to the community; and furthermore provides easy-to-use web interfaces and application programming interfaces (API) to access data. For many studies, the available information about a user is relevant. However, the gender attribute is not provided when creating a Twitter account. The main focus of this study is to infer the users’ gender from other available information. We propose a methodology for gender detection of Twitter users, using unstructured information found on Twitter profile, user generated content, and later using the user’s profile picture. In previous studies, one of the challenges presented was the labor-intensive task of manually labelling datasets. In this study, we propose a method for creating extended labelled datasets in a semi-automatic fashion. With the extended labelled datasets, we associate the users’ textual content with their gender and created gender models, based on the users’ generated content and profile information. We explore supervised and unsupervised classifiers and evaluate the results in both Portuguese and English Twitter user datasets. We obtained an accuracy of 93.2% with English users and an accuracy of 96.9% with Portuguese users. The proposed methodology of our research is language independent, but our focus was given to Portuguese and English users.Os serviços de redes sociais existentes proporcionam meios para as pessoas comunicarem e exprimirem os seus sentimentos de uma forma fácil. O conteúdo gerado por estes utilizadores contém indícios dos seus comportamentos e preferências, bem como outros metadados que estão agora disponíveis para investigação científica. O Twitter em particular, tornou-se uma fonte importante para estudos das redes socias, sobretudo porque fornece um modo simples para os utilizadores expressarem os seus sentimentos, ideias e opiniões; disponibiliza o conteúdo gerado pelos utilizadores e os metadados associados à comunidade; e fornece interfaces web e interfaces de programação de aplicações (API) para acesso aos dados de fácil utilização. Para muitos estudos, a informação disponível sobre um utilizador é relevante. No entanto, o atributo de género não é fornecido ao criar uma conta no Twitter. O foco principal deste estudo é inferir o género dos utilizadores através da informação disponível. Propomos uma metodologia para a detecção de género de utilizadores do Twitter, usando informação não estruturada encontrada no perfil do Twitter, no conteúdo gerado pelo utilizador, e mais tarde usando a imagem de perfil do utilizador. Em estudos anteriores, um dos desafios apresentados foi a tarefa de etiquetar manualmente dados, que revelou exigir bastante trabalho. Neste estudo, propomos um método para a criação de conjuntos de dados etiquetados de uma forma semi-automática, utilizando um conjunto de atributos com base na informação não estruturada de perfil. Utilizando os conjuntos de dados etiquetados, associamos conteúdo textual ao seu género e criamos modelos, com base no conteúdo gerado pelos utilizadores, e na informação de perfil. Exploramos classificadores supervisionados e não supervisionados e avaliamos os resultados em ambos os conjuntos de dados de utilizadores Portugueses e Ingleses do Twitter. Obtivemos uma precisão de 93,2% com utilizadores Ingleses e uma precisão de 96,9% com utilizadores Portugueses. A metodologia proposta é independente do idioma, mas o foco foi dado a utilizadores Portugueses e Ingleses

Chapter Integrative Systems Biology Resources and Approaches in Disease Analytics

Currently, our analytical competences are struggling to keep-up the pace of in-deep analysis of all generated large-scale data resultant of high-throughput omics platforms. While, a substantial effort was spent on methods enhancement regarding technical aspects across many detection omics platforms, the development of integrative down-stream approaches is still challenging. Systems biology has an immense applicability in the biomedical and pharmacological areas since the main goal of those focuses in the translation of measured outputs into potential markers of a Human ailment and/or to provide new compound leads for drug discovery. This approach would become more straightforward and realistic to use in standard analysis workflows if the collation of all available information of every component of a biological system was ensured into a single database framework, instead of search and fetch a single component at time across a scatter of databases resources. Here, we will describe several database resources, standalone and web-based tools applied in disease analytics workflows based in data-driven integration of outputs of multi-omic detection platforms

Case study: a Jerónimo Martins snapshot

Este estudo tem como objectivo dar a conhecer o Grupo Jerónimo Martins, que é actualmente a empresa líder no sector da distribuição e cujas insígnias têm uma posição de liderança nos segmentos retalhista e grossista no mercado português, e no segmento de hard discount na Polónia, o outro país onde actualmente se encontra estabelecida a empresa. De modo a cumprir essa finalidade e de que forma ela se relaciona com a realidade presente, é realizada uma breve contextualização sobre a conjuntura económica sobre os países e sectores onde a Jerónimo Martins está inserida, passando em seguida para uma descrição sobre a empresa bem como uma análise à sua situação financeira e às suas perspectivas futuras tendo em conta o conjunto de decisões que é tomado pela sua administração com vista ao crescimento e desenvolvimento sustentáveis dos seus negócios. A conclusão do estudo centra-se exclusivamente na recomendação sobre a acção da empresa de acordo os devidos critérios de avaliação do preço-alvo da mesma, ao mesmo tempo que tal valor é confrontado com os resultados obtidos por outras entidades especializadas na avaliação de títulos financeiros de forma a conseguir apurar se a conclusão obtida está dentro de um intervalo de valores considerados verosímeis para a situação em causa e para comparar recomendações de modo a que seja possível a um investidor obter um conjunto mais alargado de recomendações que apontam para uma postura específica face à acção da Jerónimo Martins em uma determinada data.This case study has the objective to provide an insight regarding Jerónimo Martins Group, which is the leader in the distribution sector and whose banners hold the lead position in the Portuguese Retail and Wholesale market segments, as well as the hard discount one in Poland, which is the only other country where the company is established. In order to do so and to relate it toward the present, it begins with a small contextualization over the economic conjuncture concerning both countries and their respective sectors where Jerónimo Martins operates, followed by its thorough description and a detailed financial status analysis. Finally it is laid out what are the Group‟s future prospects bearing in mind the set of managerial decisions taken in order to keep the healthy business growth and development. This study concludes by issuing a recommendation over the company‟s stock price according to some suitable valuation methods and by making a comparison between the result achieved and a few other recommendations from other financial entities to see whether the recommendation made is somewhat in line with the other ones and in order for a given investor to get a larger set of opinions pointing out a certain stance regarding Jerónimo Martins stock and its price at a given date