Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work

Molecular tools to dissect the role of Dmrt2a and Dmrt2b in the left-right axis formation in zebrafish

Dissertação para obtenção do Grau de Mestre em Genética Molecular e BiomedicinaWe tend to view the vertebrate body as bilaterally symmetric, but in fact, this only happens from the outside. Internally, most of the organs from heart to liver are asymmetrically positioned. Skeleton and its associated muscles, symmetric structures of the vertebrate body, have its origins in the transient symmetric blocks of mesoderm called somites whereas the asymmetric morphogenesis of the internal organs is due to asymmetric gene expression in the lateral plate mesoderm (LPM). Previous studies using Morpholino (MO) technology have shown that dmrt2a is involved in these two processes in zebrafish. When Dmrt2a levels are reduced, asymmetric gene expression in the LPM becomes randomized and symmetric gene expression in the presomitic mesoderm (PSM) is disrupted. The paralogous of dmrt2a, the fish specific dmrt2b has been shown to be involved in regulating asymmetric gene expression in the LPM as well. Here we used the recent Transcription activator-like effector nucleases (TALENs) technology to generate dmrt2a and dmrt2b mutant alleles that will allow us in the future to uncover the downstream effectors of these transcription factors using high-throughput experiments. In addition, we overexpressed dmrt2a at the one-cell stage to characterize asymmetry versus symmetry phenotypes. The results show clearly the ability of TALEN technology to generate mutant alleles in zebrafish. Nevertheless, dmrt2a and dmrt2b homozygous mutants developed so far fail to recapitulate their previously described MO phenotypes which raise the question on what molecular mechanism(s) allow(s) zebrafish to cope with frameshift mutations. The overexpression of dmrt2a shows that a time window of opportunity during which symmetric embryonic territories are able to respond to asymmetric signals does exist during embryonic development

A stochastic modelling of the dynamical behaviour of highway bridge decks under traffic loads

In this paper an analysis methodology is developed to evaluate the dynamic response on highway bridge decks due to vehicles crossing on the rough pavement surfaces. The analysis methodology follows a statistical model running in the time domain. The mathematical model simulates the bridge structure and the vehicle series as a system, the vehicle-bridge system. The bridge deck follows a straight beam model made discrete by finite elements and nodal concentrated masses, with vertical translations and in-plane rotations as degrees of freedom. The vehicle simulation uses concentrated parameters of mass, stiffness and damping. Four different types of vehicles are modelled as rigid masses connected by springs and dampers with one, two, four or five degrees of freedom. According to each vehicle model, translational and rotational displacements are considered. The deck surface roughness is defined by a weakly stationary, second order and ergodic random process based on a well-known power spectrum density of road pavement profiles. The moving load is modelled by an infinite series of equal vehicles, regularly spaced, and running at constant velocity. Only steady-state response is considered. Response data are produced on reinforced concrete highway bridge decks made of a straight box girder cross section based on several spans and support arrangements. Conclusions are concerned with the fitness of the developed analysis methodology and the mathematical model adequacy. The influence of the vehicle type on the highway bridge decks dynamic behaviour was observed. The magnitude of the effects due to the interaction of the vehicles with an irregular pavement surface and their consequences about design and maintenance are investigated.Peer Reviewe

A universidade popular das mães de maio: saber/conhecimento do sul para o sul

1º Congresso Internacional Epistemologias do Sul: perspectivas críticas - 7 a 9 de novembro de 2016, realizada pela Universidade Federal da Integração Latino-Americana (UNILA).A Universidade, no século XXI, ainda, reforça/traz o ranço, de produções de conhecimentos altos, de produções culturais universais e conhecimentos instrumentais a mão de obra qualificada por meio do tripé: Ensino, Pesquisa e Extensão. Contudo, as demandas sociais, em suas diversidades e interculturalidades, desmitificaram a Colonialidade do Saber de reprodução de padrões de produção de conhecimentos e significações das Culturas Europeias e Norte Americana como uma sedução de acesso ao poder – Conhecimento Regulação (QUIJANO, 1992; SANTOS, 2004)

The Portuguese experience with bee pathology laboratories for the diagnosis of bee diseases

In Portugal there are two referenced laboratories responsible for the diagnosis of bee diseases, namely the National Laboratory of Veterinary Investigation (LNIV) which is the National Reference Laboratory and the Bee Pathology Laboratory which belongs to the Agrarian Superior School of Bragança (ESAB). This laboratory was created in collaboration with the Apicultural Association of Montesinho Natural Park (AAPNM) and was certified by the Veterinary Authority in 2006. The Bee Pathology Laboratory is located in the city of Bragança, integrated in the Trás – Os – Montes e Alto Douro region. Is a research and also laboratory that provides a service to individual beekeepers when requested either directly from the laboratory or through the Apicultural Association including those of Controlled Zones. These Zones are defined as areas within the national territory where the systematic control of the bee diseases is undertaken. They are regulated at the national level by the Decree – Law nº 203 of November 25th -2005, which also established which diseases are considered to be of mandatory notification in our country. The diseases referred in this regulation are: American Foulbrood (AFB), European Foulbrood (EFB), Acarapidosis, Varroosis, Small Hive Beetles (SHB) infestation, Tropilaelaps infestation, Chalkbrood (only in Controlled Zones) and Nosemosis (only in Controlled Zones)

Diagnosis of nosemosis in a Portuguese reference bee pathology laboratory

ln recent times, nosemosis was thought to be caused by the specific protozoan Nosema apis, a spore forming parasite that invades the intestinal tract of adult bees and is widespread in Europeans countries including Portugal. Ever since, in most of cases, there are no clear symptoms, the diagnosis of this disease only can be confirmed in laboratory. The Bee Pathology Laboratory from the Agrarian Superior School of Bragança (ESAB), is located in Trás-os-Montes e Alto Douro province, formed in collaboration with the Apicultural Association of Montesinho Natural Park (AAPNM). It has certification by Portuguese Veterinary Authority in the 2006

Paradigm: a bibliometric analysis of papers presented at the conferences of the POMS from 2000 to 2010

This study presents bibliometrics on Paradigm in papers presented at the Production and Operation Management Society (POMS) from 2000 to 2010, and establishes the profile of the authors and the theoretical relationships present in those papers’ content. The portal of the Production and Operation Management Society and the abstracts contained in each of the events of the period were used, seeking to highlight the concept of Paradigm and its approaches. As a result, the articles presented at the POMS from 2000 to 2010, at least three out of the four hundred papers had the concept in its title or abstract, besides being within the central arguments of these same items analyzed by this study