Zinc-substituted desulfovibrio gigas desulforedoxins

Protein Science (2002), 11:2464–2470

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

A importância da Polícia Municipal na segurança

The challenge of this work is to assess the importance of the municipal police in improving the safety of citizens, if gauging from this reality through contributions from the Municipal Police Guimarães. The IV Constitutional Review in 1997, enabled the Portuguese municipalities creating administrative police bodies. These services, known as Municipal Police, have gradually come up in several municipalities. Currently the Municipal Police have their fundamental legal regulations of Law No. 19/2004 of 20 May, which, according to the Portuguese Constitution provides that these must be seen as municipal services, which act in a space territorially delimited, which corresponds to the municipality that each belongs. Under Article 237, paragraph 3, of the Constitution, the Municipal Police are municipal services, which shall cooperate in the maintenance of public order and protection of local communities, acting in cooperation with the security forces, public security functions. The safety concept has been taking an increasingly significant importance within the population. Is also no doubt say that, currently, insecurity affects all of society and is a major concern of law enforcement authorities. To find suitable answers we found that there are several studies on these subjects. In order to be able to make our contribution, text looks us on this subject, having had the support of the Municipal Police Guimarães, in the preparation of this work. Thus, based on a survey, they were sounded out, as privileged actors, agents of the Municipal Police Guimarães, in order to know their perceptions with regard to security issues faced in the context of security. We understand ask them to answer in particular the following questions: What are the most facilitators situations of crime? How important is the Municipal Police Guimarães in crime prevention? What are the strategies for prevention of incivilities? What other skills that can be conferred upon the Municipal Police? The results obtained allowed us to conclude that incivilities facilitate the occurrence of crimes and that the Municipal Police may have a more active role in the security of the population. If you were given other duties, in addition to that already have, the Municipal Police could reach another level of effectiveness. However we understand that any change to the tasks of this police need a serious and profound reflection, to find complementary alternatives with the security forces, which does not conflict with current assignments of any of the parties or with the interests of citizens.

O serviço fiscal aduaneiro criminal e contraordenacional da GNR

At a time of global economic instability, to which Portugal is not oblivious, and aware that the main source of Portuguese State revenue relies on the collection of tribute, the National Republican Guard holds within its mission relevant assignments to the protection of the financial interests of the country, in particular, fiscal and customs. These assignments were inherited from the century - old institution Guarda Fiscal - with evidence given in this domain, which was integrated into the National Republican Guard in 1993, to adopt, a 1St model, that held a specialized unit – Brigada Fiscal, with surveillance and patrolling missions of costa and fiscal and customs supervision, throughout the national territory and maritime zone of respect. In 2009, the result of political decisions, reorganization the State's central administration, appears de 2Nd model, because the Brigada Fiscal assignments were divided by two specialized units - UAF with investigation skills, and UCC for patrolling and surveillance of the coast. Analyzed the legal spectrum of special legislation leading the criminal and transgression sector punitive (RGIT), in essence, is in the UAF that resides the role assignments from the scope of the investigation and supervision of goods in the national territory on a par with the tax authority. Tax inspection assignments, fiscal and customs of the National Republican Guard, are unmatched in the National Tribute System, constituting itself as a potentiality of this special body, in similarity of their counterparts - Spain and Italy; however, have some constraints, that urge to clarify and repair. Foreseeing the future, face the announced news of a new restructuring, on behalf of the interests of the country, and in order to raise the quality of performance of the tax inspection, fiscal and customs, the National Republican Guard shall maintain a model based on the experience already accumulated, obviously adapted to the new demands of a changing society. Despite the current model gain in efficiency, loses in effectiveness. However, the efficiency of a model, without the necessary resources, can never bring “the letter to Garcia” against any kind of infringements, criminal or transgressions. Unless better opinion, both tax structures of the National Republican Guard are valid as an instrument for the prevention and combat of these illegal types. Because they are strategic in pursuing the public interest, given the scarce resources of the country and be the National Republican Guard, the force with the means and know-how of this nature. The political power has the final word.

The call for sailing uncharted seas: Motivations and expectations of recently graduated individuals

We explore the motivations and expectations that are impacting Portuguese recently graduated individuals in their decision of becoming international managers. Throughout a qualitative analysis over 20 interviews we construct a theoretical framework of recent graduates actual expectations and motivations regarding their international assignments. Accordingly, individuals are conducted by the desire of cultural-diversity experiences, social pressures and challenging environments. Expectations are not a result of a straightforward process; instead, they are dynamic and influenced by the challenges that international managers have to cope with during their international journey. Moreover, expectations and motivations are not mutually exclusive; they produce impact on each other, characterizing a dynamic process of international managers‟ lives.