Research Blogging: Indexing and Registering the Change in Science 2.0

Increasing public interest in science information in a digital and 2.0 science era promotes a dramatically, rapid and deep change in science itself. The emergence and expansion of new technologies and internet-based tools is leading to new means to improve scientific methodology and communication, assessment, promotion and certification. It allows methods of acquisition, manipulation and storage, generating vast quantities of data that can further facilitate the research process. It also improves access to scientific results through information sharing and discussion. Content previously restricted only to specialists is now available to a wider audience. This context requires new management systems to make scientific knowledge more accessible and useable, including new measures to evaluate the reach of scientific information. The new science and research quality measures are strongly related to the new online technologies and services based in social media. Tools such as blogs, social bookmarks and online reference managers, Twitter and others offer alternative, transparent and more comprehensive information about the active interest, usage and reach of scientific publications. Another of these new filters is the Research Blogging platform, which was created in 2007 and now has over 1,230 active blogs, with over 26,960 entries posted about peer-reviewed research on subjects ranging from Anthropology to Zoology. This study takes a closer look at RB, in order to get insights into its contribution to the rapidly changing landscape of scientific communication.

The SB-index and the HSB-index: efficient indices for spatial data warehouses

Spatial data warehouses (SDWs) allow for spatial analysis together with analytical multidimensional queries over huge volumes of data. The challenge is to retrieve data related to ad hoc spatial query windows according to spatial predicates, avoiding the high cost of joining large tables. Therefore, mechanisms to provide efficient query processing over SDWs are essential. In this paper, we propose two efficient indices for SDW: the SB-index and the HSB-index. The proposed indices share the following characteristics. They enable multidimensional queries with spatial predicate for SDW and also support predefined spatial hierarchies. Furthermore, they compute the spatial predicate and transform it into a conventional one, which can be evaluated together with other conventional predicates by accessing a star-join Bitmap index. While the SB-index has a sequential data structure, the HSB-index uses a hierarchical data structure to enable spatial objects clustering and a specialized buffer-pool to decrease the number of disk accesses. The advantages of the SB-index and the HSB-index over the DBMS resources for SDW indexing (i.e. star-join computation and materialized views) were investigated through performance tests, which issued roll-up operations extended with containment and intersection range queries. The performance results showed that improvements ranged from 68% up to 99% over both the star-join computation and the materialized view. Furthermore, the proposed indices proved to be very compact, adding only less than 1% to the storage requirements. Therefore, both the SB-index and the HSB-index are excellent choices for SDW indexing. Choosing between the SB-index and the HSB-index mainly depends on the query selectivity of spatial predicates. While low query selectivity benefits the HSB-index, the SB-index provides better performance for higher query selectivity.

On Equilibrium Distribution of a Reversible Growth Model

We study a probabilistic model of interacting spins indexed by elements of a finite subset of the d-dimensional integer lattice, da parts per thousand yen1. Conditions of time reversibility are examined. It is shown that the model equilibrium distribution converges to a limit distribution as the indexing set expands to the whole lattice. The occupied site percolation problem is solved for the limit distribution. Two models with similar dynamics are also discussed.

Effects of EDTA and Sodium Citrate on hormone measurements by fluorometric (FIA) and immunofluorometric (IFMA) methods

Abstract Background Measurements of hormonal concentrations by immunoassays using fluorescent tracer substance (Eu3+) are susceptible to the action of chemical agents that may cause alterations in its original structure. Our goal was to verify the effect of two types of anticoagulants in the hormone assays performed by fluorometric (FIA) or immunofluorometric (IFMA) methods. Methods Blood samples were obtained from 30 outpatients and were drawn in EDTA, sodium citrate, and serum separation Vacutainer®Blood Collection Tubes. Samples were analyzed in automatized equipment AutoDelfia™ (Perkin Elmer Brazil, Wallac, Finland) for the following hormones: Luteinizing hormone (LH), Follicle stimulating homone (FSH), prolactin (PRL), growth hormone (GH), Sex hormone binding globulin (SHBG), thyroid stimulating hormone (TSH), insulin, C peptide, total T3, total T4, free T4, estradiol, progesterone, testosterone, and cortisol. Statistical analysis was carried out by Kruskal-Wallis method and Dunn's test. Results No significant differences were seen between samples for LH, FSH, PRL and free T4. Results from GH, TSH, insulin, C peptide, SHBG, total T3, total T4, estradiol, testosterone, cortisol, and progesterone were significant different between serum and EDTA-treated samples groups. Differences were also identified between serum and sodium citrate-treated samples in the analysis for TSH, insulin, total T3, estradiol, testosterone and progesterone. Conclusions We conclude that the hormonal analysis carried through by FIA or IFMA are susceptible to the effects of anticoagulants in the biological material collected that vary depending on the type of assay.

Immunohistochemical evidence for myofibroblastlike cells associated with liver injury induced by Aflatoxin B1 in rainbow trout (Oncorhynchus mykiss)

In mammalian species, profibrogenic cells are activated to become myofibroblasts in response to liver damage. Few studies have examined hepatic myofibroblasts and their role in liver damage in teleosts. The aim of the present study was to investigate the involvement of myofibroblast-like cells in rainbow trout (Oncorhynchus mykiss) with hepatic damage induced by aflatoxin B1 (AFB1). Histopathological and immunohistochemical analyses characterized alterations in the liver stroma during the carcinogenic process. Anti-human a-smoothmuscle actin (SMA) and anti-human desmin primary antibodies were used in immunohistochemistry. Only the anti-SMA reagent labelled cells in trout liver. In the livers of control fish, only smooth muscle in blood vessels and around bile ducts was labelled. In the livers from AFB1-treated fish, SMA-positive cells were present in the stroma surrounding neoplastic lesions and in areas of desmoplastic reaction. These observations indicate that in teleosts, as in mammals, the myofibroblast-like cell is involved in fibrosis associated with liver injury. Chronic liver injury induced in trout by aflatoxin may provide a useful model system for study of the evolution of such mechanisms.

Sistema de gestão para linguagem documentária metadados e rede colaborativa no vocabulário controlado do SIBI/USP

Sistemas de gestão desenvolvidos para a web, a partir de metadados, permitem manutenção eficiente de grandes quantidades de informação. Um vocabulário controlado como o utilizado pelo Sistema Integrado de Bibliotecas da USP (SIBi/USP) necessita de atualização contínua realizada através de uma rede colaborativa com a participação de bibliotecários indexadores de todas as áreas do conhecimento. Este trabalho apresenta os resultados obtidos com o sistema de gestão desenvolvido pelo Grupo de Gerenciamento para a manutenção do Vocabulário Controlado do SIBi/USP. O fluxo deste sistema consiste em filtros de validação realizados pelos componentes do Grupo de Gerenciamento do Vocabulário. A metodologia de gestão do Vocabulário possui além deste sistema, uma política de governança. Os resultados obtidos nos seis anos desde a ativação do sistema de gestão pela Base de Sugestões consistiram em: 1192 inclusões de descritores, 240 alterações, 61 exclusões, totalizando 1493 operações. A gestão e o controle de qualidade do Vocabulário permitiram o aprimoramento do tratamento e da recuperação da informação no Banco de Dados Bibliográficos da USP – DEDALUS.

FOLKSONOMIA: UMA ANÁLISE DE SUA OPERACIONALIDADE E SUA POSSÍVEL APLICABILIDADE NA CIÊNCIA DA INFORMAÇÃO

O artigo apresenta uma análise da operacionalidade das Folksonomias e a possibilidade de aplicação dessa ferramenta nos sistemas de organização da informação da área de Ciência da Informação. Para tanto foi realizada uma análise de coerência de tags e dos recursos disponíveis para etiquetagem em dois websites, a Last.fm e o CiteULike. Por meio dessa análise constatou-se que em ambos os websites ocorreram incoerências e discrepâncias nas tags utilizadas. Todavia, o sistema da Last.fm demonstrou-se mais funcional que o do CiteULike obtendo um desempenho melhor. Por fim, sugere-se a junção das Folksonomias às Ontologias, que permitiriam a criação de sistemas automatizados de organização de conteúdos informacionais alimentados pelos próprios usuários

CID: an efficient complexity-invariant distance for time series

The ubiquity of time series data across almost all human endeavors has produced a great interest in time series data mining in the last decade. While dozens of classification algorithms have been applied to time series, recent empirical evidence strongly suggests that simple nearest neighbor classification is exceptionally difficult to beat. The choice of distance measure used by the nearest neighbor algorithm is important, and depends on the invariances required by the domain. For example, motion capture data typically requires invariance to warping, and cardiology data requires invariance to the baseline (the mean value). Similarly, recent work suggests that for time series clustering, the choice of clustering algorithm is much less important than the choice of distance measure used.In this work we make a somewhat surprising claim. There is an invariance that the community seems to have missed, complexity invariance. Intuitively, the problem is that in many domains the different classes may have different complexities, and pairs of complex objects, even those which subjectively may seem very similar to the human eye, tend to be further apart under current distance measures than pairs of simple objects. This fact introduces errors in nearest neighbor classification, where some complex objects may be incorrectly assigned to a simpler class. Similarly, for clustering this effect can introduce errors by “suggesting” to the clustering algorithm that subjectively similar, but complex objects belong in a sparser and larger diameter cluster than is truly warranted.We introduce the first complexity-invariant distance measure for time series, and show that it generally produces significant improvements in classification and clustering accuracy. We further show that this improvement does not compromise efficiency, since we can lower bound the measure and use a modification of triangular inequality, thus making use of most existing indexing and data mining algorithms. We evaluate our ideas with the largest and most comprehensive set of time series mining experiments ever attempted in a single work, and show that complexity-invariant distance measures can produce improvements in classification and clustering in the vast majority of cases.