Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Risk prediction for weed infestation using classification rules

This paper proposes a fuzzy classification system for the risk of infestation by weeds in agricultural zones considering the variability of weeds. The inputs of the system are features of the infestation extracted from estimated maps by kriging for the weed seed production and weed coverage, and from the competitiveness, inferred from narrow and broad-leaved weeds. Furthermore, a Bayesian network classifier is used to extract rules from data which are compared to the fuzzy rule set obtained on the base of specialist knowledge. Results for the risk inference in a maize crop field are presented and evaluated by the estimated yield loss. © 2009 IEEE.

Spatial electric load forecasting using a local movement approach

An agent based model for spatial electric load forecasting using a local movement approach for the spatiotemporal allocation of the new loads in the service zone is presented. The density of electrical load for each of the major consumer classes in each sub-zone is used as the current state of the agents. The spatial growth is simulated with a walking agent who starts his path in one of the activity centers of the city and goes to the limits of the city following a radial path depending on the different load levels. A series of update rules are established to simulate the S growth behavior and the complementarity between classes. The results are presented in future load density maps. The tests in a real system from a mid-size city show a high rate of success when compared with other techniques. The most important features of this methodology are the need for few data and the simplicity of the algorithm, allowing for future scalability. © 2009 IEEE.

Existe utilização efetiva dos recursos vegetais conhecidos em comunidades caiçaras da Ilha do Cardoso, estado de São Paulo, Brasil?

This study aims to investigate if plant resources are effective used by caiçaras' communities of the Cardoso Island. We also want to verify if the biogeografic origin of plants, their uses and socioeconomic factors influence the locals' knowledge. We carried out 51 semi-structured interviews with people who have been living there for at least 5 years, who were older than 18. We concluded that the interviewees' knowledge is still diverse and that most of the plants known are used by them (82%). Native plants are largely known, while the exotic ones are the most used (95%). Knowledge and use vary according to the use of plants, although they were very similar, considering the interviewees' age and gender. We also realized that housewives use a large quantity of medicinal plants, which are mainly the exotic ones. Fishermen know and use native plants, usually for handicraft purposes. The environmental guides and people, whose job is tourism related, have a similar knowledge, especially about medicinal plants, which are less used when compared with the other professional activities.

Ecological data on road killed Amphisbaena alba linnaeus, 1758 (Squamata, Amphisbaenidae) in southeast Brazil

Vehicles running over vertebrates has been an increasing challenge to the local conservation of some herpetofauna. The Amphisbaenidae are fossorial reptiles which are poorly known ecologically. Biological and natural history data were obtained from three specimens of Amphisbaenia alba that were found dead along 8320 km survey of highways. The rarity of road kill and the importance of the species conservation are discussed.

An Educational international partnership responding to local needs: Process evaluation of the Brazil FAIMER Regional Institute

The Brazilian public health system requires competent professionals sensitive to the needs of the population. The Foundation for Advancement of International Medical Education and Research (FAIMER) provides a two-year faculty development programme for health professions educators, aiming to build leadership in education to improve health. A partnership with governmental initiatives and FAIMER was established for meeting these needs. This paper describes the initial process evaluation results of the Brazilian FAIMER Institute Fellowship (FAIMER BR). Methods: Data were analysed for the classes 2007-2010 regarding: application processes; innovation project themes; retrospective post-pre self-ratings of knowledge acquisition; and professional development portfolios. Results: Seventeen of 26 Brazilian states were represented among 98 Fellows, predominantly from public medical schools (75.5%) and schools awarded Ministry of Health grants to align education with public health services (89.8%). One-third (n = 32) of Fellows' innovation projects were related to these grants. Significant increases occurred in all topic subscales on self-report of knowledge acquisition (eff ect sizes, 1.21-2.77). In the follow up questionnaire, 63% of Fellows reported that their projects were incorporated into the curriculum or institutional policies. The majority reported that the programme deepened their knowledge (98%), provided new ideas about medical education (90%) and provided skills for conflict management (63%). One-half of the Fellows reported sustained benefits from the programme listserv and other communications, including breadth of expertise, establishment of research collaboration and receiving emotional support. Conclusion: Contributors to initial programme success included alignment of curriculum with governmental initiatives, curriculum design merging educational technology, leadership and management skills and central role of an innovation educational project responding to local needs.

Creating capabilities in local environments and production networks

Includes bibliography

Brachyuran and anomuran crabs associated with Schizoporella unicornis (Ectoprocta, Cheilostomata) from southeastern Brazil

The main goals of this investigation were to describe the community structure of anomuran and brachyuran crabs inhabiting reefs constituted by colonies of Schizoporella unicornis, and to provide a species importance ranking for this community. Collections were carried out on S. unicornis reefs at two-month intervals from May 2003 to May 2004, in the rocky sublittoral of the southeastern Brazilian coast. Relative abundance and occurrence were used to rank these species in the hierarchy importance. A total of 2,018 individuals were obtained, in 11 families, 22 genera and 31 species. Porcellanidae and Pilumnidae were the most abundant families, comprising respectively almost 60% and 15% of individuals sampled. The species ranking indicated four main groups A, B, C and D, with group A subdivided. Subgroup A1 contained 9 species, including the species of greatest ecological importance for community regarding abundance and occurrence. The great abundance of crabs associated with S. unicornis seems to be the result of its recognized importance during the crab developmental cycle, and as shelter and food for some Decapod species. These observations reveal the importance of conserving the areas occupied by these reef colonies, which appear to be an important environment for maintaining local biodiversity.

ECG arrhythmia classification based on optimum-path forest

An important tool for the heart disease diagnosis is the analysis of electrocardiogram (ECG) signals, since the non-invasive nature and simplicity of the ECG exam. According to the application, ECG data analysis consists of steps such as preprocessing, segmentation, feature extraction and classification aiming to detect cardiac arrhythmias (i.e.; cardiac rhythm abnormalities). Aiming to made a fast and accurate cardiac arrhythmia signal classification process, we apply and analyze a recent and robust supervised graph-based pattern recognition technique, the optimum-path forest (OPF) classifier. To the best of our knowledge, it is the first time that OPF classifier is used to the ECG heartbeat signal classification task. We then compare the performance (in terms of training and testing time, accuracy, specificity, and sensitivity) of the OPF classifier to the ones of other three well-known expert system classifiers, i.e.; support vector machine (SVM), Bayesian and multilayer artificial neural network (MLP), using features extracted from six main approaches considered in literature for ECG arrhythmia analysis. In our experiments, we use the MIT-BIH Arrhythmia Database and the evaluation protocol recommended by The Association for the Advancement of Medical Instrumentation. A discussion on the obtained results shows that OPF classifier presents a robust performance, i.e.; there is no need for parameter setup, as well as a high accuracy at an extremely low computational cost. Moreover, in average, the OPF classifier yielded greater performance than the MLP and SVM classifiers in terms of classification time and accuracy, and to produce quite similar performance to the Bayesian classifier, showing to be a promising technique for ECG signal analysis. © 2012 Elsevier Ltd. All rights reserved.

A critical analysis of the ubiquity of linear local-regional richness relationships

Synthesis Despite theoretical criticisms, the ubiquity of linear relationships between local and regional species richness has long been used to justify it as a valid framework to conclude that local communities are not saturated with species. However, we reanalyzed published studies with a new unbiased method and found no prevalence of linear relationships and more than 40% of misclassifications, including textbook examples. We thus conclude that the prevailing argument in favor of associating a valid ecological interpretation to local-regional species richness plots, its ubiquity, is not sustained, and that ecologists could use for instance metacommunity theory to make inference on the strength of local and regional processes. Identifying the relative importance of regional and local processes to local species diversity is a central issue to many questions in basic and applied ecology. One widely-used method is to plot local species richness against its regional richness to infer whether regional or local processes determine local diversity. However, this method increases the tendency to find regional prevalence as suggested by a recent simulation. We reanalyzed studies in the literature with an unbiased method and found no prevalence of either regional or local processes. In addition, almost 40% of the studies and 50% of the ecology textbook examples using the traditional method were misclassified. Our findings reinforce the need of alternative, novel tools identified by for instance metacommunity theory to go beyond the studies of local-regional relationships in the ecological literature that focus on the interdependence of regional and local processes.© 2013 The Authors. Oikos © 2013 Nordic Society Oikos.

Ki-67 and CD100 immunohistochemical expression is associated with local recurrence and poor prognosis in soft tissue sarcomas, respectively

Soft tissue sarcomas (STSs) are a heterogeneous group of mesenchymal tumors of >50 subtypes. However, STSs represent <1% of types of cancer. Despite this low frequency, the disease is aggressive and treatment, when possible, is based on traditional chemotherapies. A number of cases of resistance to adjuvant therapies have been reported. Metastases are commonly identified in STS patients during diagnosis and the development of effective clinical parameters is crucial for correct management of the disease. The use of biological markers in cancer is a useful tool to determine patient prognosis. Ki--67 is a protein marker for proliferation of somatic cells and is widely used in prognostic studies of various types of tumor, including STSs. Cluster of differentiation 100 (CD100) is a member of the semaphorin family. The family was initially described as axon guidance molecules important for angiogenesis, organogenesis, apoptosis and neoplasia. CD100 was previously utilized as a prognostic factor in tumors and also in STSs. In the present study, protein expression of Ki--67 and CD100 was analyzed by immunohistochemistry in samples of STS patients of the Barretos Cancer Hospital (Barretos, Brazil) to establish prognostic criteria of the disease. Results demonstrate a correlation between CD100 expression and poor prognosis, consistent with a previous study. Moreover, the expression of Ki-67 was identified to correlate with presence of local or locoregional recurrence. To the best of our knowledge, no large casuistic study has revealed this correlation between Ki--67 and local recurrence in STSs. The use of Ki--67 and CD100 as markers in clinical pathological analysis may be suitable as a prognostic criterion in disease progression.

A família Pinnulariaceae (Bacillariophyceae) no estado de São Paulo: levantamento florístico

Pós-graduação em Ciências Biológicas (Biologia Vegetal) - IBRC

Leguminosas arbustivas e arbóreas de fragmentos florestais remanescentes no noroeste paulista, Brasil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Telejornalismo móvel local: novas possibilidades da televisão digital

Pós-graduação em Televisão Digital: Informação e Conhecimento - FAAC

Estudo da competitividade em empresas industriais: o caso do arranjo produtivo local (APL) de Votuporanga

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)