Optical network planning for static applications

Traffic demands on optical transport networks continue to grow, both in numbers and in size, at an incredible rate. Consequently, the efficient use of network resources has never been as important as today. A possible solution to this problem is to plan, develop and implement efficient algorithms for static and/or dynamic applications in order to minimize the probability of blocking and/or minimizing the number of wavelengths. Static Routing and Wavelength Assignment (RWA) algorithms use a given set of optical path requests and are intended to provide a long-term plan for future traffic. Static RWA algorithms are important for current and future WDM (Wavelength-Division Multiplexing) networks, especially when there is no wavelength conversion, the network is highly connected or the traffic load is moderate to high. In this dissertation, we propose to develop an optical network planning tool capable of choosing the best optical path and assigning as few wavelengths as possible. This tool is structured in five phases: in the first phase, the network physical topology is defined by the adjacency matrix or by the cost matrix and the logical topology is defined by the traffic matrix; in a second phase, the Dijkstra algorithm is used to find the shortest path for each connection; in the third phase, the traffic routing is accomplished considering one traffic unit between the source and destination nodes; in the fourth phase, the paths are ordered using various ordering strategies, such as Shortest Path First, Longest Path First and Random Path Order; finally, in the fifth phase, the heuristic algorithms for wavelength assignment, such as Graph Coloring, First-Fit and Most-Used are used. This tool is first tested on small networks (e.g. ring and mesh topologies), and then applied to real networks (e.g. COST 239, NSFNET and UBN topologies). We have concluded that the number of wavelengths calculated for each network is almost independent of the Wavelength Assignment (WA) heuristics, as well as the ordering strategy, when a full mesh logical topology is considered.Os pedidos de tráfego nas redes de transporte ópticas continuam a crescer, tanto em número como em tamanho, a um ritmo incrível. Consequentemente, a utilização eficiente dos recursos das redes nunca foi tão importante como hoje. Uma solução possível para este problema passa por planear, desenvolver e implementar algoritmos eficientes para aplicações estáticas e/ou dinâmicas de modo a minimizar a probabilidade de bloqueio e/ou minimizar o número de comprimentos de onda. Os algoritmos de encaminhamento e de atribuição de comprimentos de onda (RWA) estáticos utilizam um determinado conjunto de pedidos de caminhos ópticos e visam fornecer um plano de longo prazo para tráfego futuro. Os algoritmos RWA estáticos são importantes para as redes em multiplexagem por divisão de comprimento de onda (WDM) atuais e futuras, especialmente quando não há conversão de comprimento de onda, a rede é altamente ligada ou a carga de tráfego é de moderada a alta. Nesta dissertação, propomos desenvolver uma ferramenta de planeamento de redes ópticas capaz de escolher o melhor caminho óptico e atribuir o mínimo de comprimentos ondas possíveis. Esta ferramenta está estruturada em cinco fases: numa primeira fase é definida a topologia física de rede pela matriz das adjacências ou pela matriz de custo e a topologia lógica é definida pela matriz de tráfego; numa segunda fase é utilizado o algoritmo Dijkstra para encontrar o caminho mais curto para cada ligação; na terceira fase o encaminhamento de tráfego é realizado considerando uma unidade de tráfego entre os nós de origem e destino; na quarta fase os caminhos são ordenados tendo em conta as várias estratégias de ordenação, tais como Shortest Path First, Longest Path First e Random Path Order; finalmente, na quinta fase, os algoritmos heurísticos são utilizados para atribuição de comprimentos de onda, como Graph Coloring, First-Fit e Most-Used. Esta ferramenta é primeiramente testada em redes pequenas (por exemplo, topologias em anel e em malha), e depois é aplicada a redes reais (por exemplo, redes COST 239, NSFNET e UBN). Concluímos que o número de comprimentos de onda calculados para cada rede é quase independente da heurística para atribuição dos cumprimentos de onda, bem como da estratégia de ordenação dos caminhos, quando uma topologia lógica em malha completa é considerada

Constraint reasoning for differential models

The basic motivation of this work was the integration of biophysical models within the interval constraints framework for decision support. Comparing the major features of biophysical models with the expressive power of the existing interval constraints framework, it was clear that the most important inadequacy was related with the representation of differential equations. System dynamics is often modelled through differential equations but there was no way of expressing a differential equation as a constraint and integrate it within the constraints framework. Consequently, the goal of this work is focussed on the integration of ordinary differential equations within the interval constraints framework, which for this purpose is extended with the new formalism of Constraint Satisfaction Differential Problems. Such framework allows the specification of ordinary differential equations, together with related information, by means of constraints, and provides efficient propagation techniques for pruning the domains of their variables. This enabled the integration of all such information in a single constraint whose variables may subsequently be used in other constraints of the model. The specific method used for pruning its variable domains can then be combined with the pruning methods associated with the other constraints in an overall propagation algorithm for reducing the bounds of all model variables. The application of the constraint propagation algorithm for pruning the variable domains, that is, the enforcement of local-consistency, turned out to be insufficient to support decision in practical problems that include differential equations. The domain pruning achieved is not, in general, sufficient to allow safe decisions and the main reason derives from the non-linearity of the differential equations. Consequently, a complementary goal of this work proposes a new strong consistency criterion, Global Hull-consistency, particularly suited to decision support with differential models, by presenting an adequate trade-of between domain pruning and computational effort. Several alternative algorithms are proposed for enforcing Global Hull-consistency and, due to their complexity, an effort was made to provide implementations able to supply any-time pruning results. Since the consistency criterion is dependent on the existence of canonical solutions, it is proposed a local search approach that can be integrated with constraint propagation in continuous domains and, in particular, with the enforcing algorithms for anticipating the finding of canonical solutions. The last goal of this work is the validation of the approach as an important contribution for the integration of biophysical models within decision support. Consequently, a prototype application that integrated all the proposed extensions to the interval constraints framework is developed and used for solving problems in different biophysical domains

Identification of Potential Inhibitors from Pyriproxyfen with Insecticidal Activity by Virtual Screening

Aedes aegypti is the main vector of dengue fever transmission, yellow fever, Zika, and chikungunya in tropical and subtropical regions and it is considered to cause health risks to millions of people in the world. In this study, we search to obtain new molecules with insecticidal potential against Ae. aegypti via virtual screening. Pyriproxyfen was chosen as a template compound to search molecules in the database Zinc_Natural_Stock (ZNSt) with structural similarity using ROCS (rapid overlay of chemical structures) and EON (electrostatic similarity) software, and in the final search, the top 100 were selected. Subsequently, in silico pharmacokinetic and toxicological properties were determined resulting in a total of 14 molecules, and these were submitted to the PASS online server for the prediction of biological insecticide and acetylcholinesterase activities, and only two selected molecules followed for the molecular docking study to evaluate the binding free energy and interaction mode. After these procedures were performed, toxicity risk assessment such as LD50 values in mg/kg and toxicity class using the PROTOX online server, were undertaken. Molecule ZINC00001624 presented potential for inhibition for the acetylcholinesterase enzyme (insect and human) with a binding affinity value of -10.5 and -10.3 kcal/mol, respectively. The interaction with the juvenile hormone was -11.4 kcal/mol for the molecule ZINC00001021. Molecules ZINC00001021 and ZINC00001624 had excellent predictions in all the steps of the study and may be indicated as the most promising molecules resulting from the virtual screening of new insecticidal agents.Federal University of Amapá, Program in Biotechnology and Biodiversity-Network BIONORTE, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for funding in the publication of this article

An In Silico Study of the Antioxidant Ability for Two Caffeine Analogs Using Molecular Docking and Quantum Chemical Methods

The antioxidant activity of molecules constitutes an important factor for the regulation of redox homeostasis and reduction of the oxidative stress. Cells affected by oxidative stress can undergo genetic alteration, causing structural changes and promoting the onset of chronic diseases, such as cancer. We have performed an in silico study to evaluate the antioxidant potential of two molecules of the zinc database: ZINC08706191 (Z91) and ZINC08992920 (Z20). Molecular docking, quantum chemical calculations (HF/6-31G**) and Pearson’s correlation have been performed. Molecular docking results of Z91 and Z20 showed both the lower binding affinity (BA) and inhibition constant (Ki) values for the receptor-ligand interactions in the three tested enzymes (cytochrome P450—CP450, myeloperoxidase—MP and NADPH oxidase—NO) than the control molecules (5-fluorouracil—FLU, melatonin—MEL and dextromethorphan—DEX, for each receptor respectively). Molecular descriptors were correlated with Ki and strong correlations were observed for the CP450, MP and NO receptors. These and other results attest the significant antioxidant ability of Z91 and Z20, that may be indicated for further analyses in relation to the control of oxidative stress and as possible antioxidant agents to be used in the pharmaceutical industry

Highlights of the Brazilian Thoracic Association guidelines for interstitial lung diseases

Interstitial lung diseases (ILDs) are heterogeneous disorders, involving a large number of conditions, the approach to which continues to pose an enormous challenge for pulmonologists. The 2012 Brazilian Thoracic Association ILD Guidelines were established in order to provide Brazilian pulmonologists with an instrument that can facilitate the management of patients with ILDs, standardizing the criteria used for the diagnosis of different conditions and offering guidance on the best treatment in various situations. The objective of this article was to briefly describe the highlights of those guidelines.As doenças pulmonares intersticiais (DPIs) são afecções heterogêneas, envolvendo um elevado número de condições, cuja abordagem ainda é um grande desafio para o pneumologista. As Diretrizes de DPIs da Sociedade Brasileira de Pneumologia e Tisiologia, publicadas em 2012, foram estabelecidas com o intuito de fornecer aos pneumologistas brasileiros um instrumento que possa facilitar a abordagem dos pacientes com DPIs, padronizando-se os critérios utilizados para a definição diagnóstica das diferentes condições, além de orientar sobre o melhor tratamento nas diferentes situações. Esse artigo teve como objetivo descrever resumidamente os principais destaques dessas diretrizes.Universidade de São Paulo Faculdade de Medicina Hospital das ClínicasUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Curso de Pós-Graduação de Doenças Pulmonares IntersticiaisUniversidade Federal de Ciências da Saúde de Porto AlegreSanta Casa de Porto Alegre Ambulatório de Doenças IntersticiaisSES Hospital Regional da Asa Norte Serviço de Doenças TorácicasFundação Jorge Duprat Figueiredo de Segurança e Medicina do Trabalho Serviço de MedicinaUniversidade Estadual de Campinas Faculdade de Ciências Médicas Departamento de Clínica MédicaUniversidade Federal do Estado do Rio de JaneiroUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Departamento de PatologiaHospital do Servidor Público Estadual de São Paulo Serviço de Anatomia PatológicaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUniversidade de São Paulo Faculdade de Medicina de Ribeirão Preto Divisão de PneumologiaUniversidade Federal de Santa Catarina Departamento de Clínica MédicaUniversidade Federal de Santa Catarina Hospital UniversitárioHospital de Messejana Ambulatório de Doenças IntersticiaisHospital do Servidor Público Estadual de São Paulo Ambulatório de Doenças IntersticiaisUniversidade de São Paulo Faculdade de Medicina Instituto do CoraçãoUniversidade Federal FluminenseUniversidade de São Paulo Faculdade de MedicinaHospital Sírio Libanês Núcleo Avançado de TóraxUniversidade Federal da BahiaHospital do Servidor Público Estadual de São PauloHospital do Câncer Antônio Cândido CamargoUNIFESP, EPM, Curso de Pós-Graduação de Doenças Pulmonares IntersticiaisUNIFESP, EPM, Depto. de PatologiaUNIFESP, EPMSciEL

Highlights of the Brazilian Thoracic Association guidelines for interstitial lung diseases

Interstitial lung diseases (ILDs) are heterogeneous disorders, involving a large number of conditions, the approach to which continues to pose an enormous challenge for pulmonologists. The 2012 Brazilian Thoracic Association ILD Guidelines were established in order to provide Brazilian pulmonologists with an instrument that can facilitate the management of patients with ILDs, standardizing the criteria used for the diagnosis of different conditions and offering guidance on the best treatment in various situations. The objective of this article was to briefly describe the highlights of those guidelines.As doenças pulmonares intersticiais (DPIs) são afecções heterogêneas, envolvendo um elevado número de condições, cuja abordagem ainda é um grande desafio para o pneumologista. As Diretrizes de DPIs da Sociedade Brasileira de Pneumologia e Tisiologia, publicadas em 2012, foram estabelecidas com o intuito de fornecer aos pneumologistas brasileiros um instrumento que possa facilitar a abordagem dos pacientes com DPIs, padronizando-se os critérios utilizados para a definição diagnóstica das diferentes condições, além de orientar sobre o melhor tratamento nas diferentes situações. Esse artigo teve como objetivo descrever resumidamente os principais destaques dessas diretrizes.28229

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km 2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km 2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co-occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data. © 2018 by the The Authors. Ecology © 2018 The Ecological Society of Americ