A nanopore-based stochastic detection method: Single molecule characterisation of nanoparticles using ()- hemolysin

Dissertation presented to obtain the Ph.D degree in Chemistry.

Earth-based mortars for masonry plastering

9th International Masonry Conference 2014, 7-9 July, Universidade do Minho, Guimarães

Risk factors for Leishmania chagasi infection in an urban area of Minas Gerais State

In order to understand the determinants of human infection by Leishmania chagasi in an urban area, a cross-sectional population based study was conducted using molecular and serologic methods to identify infection. Participants were interviewed using a pre-coded questionnaire. Two criteria were tested to identify risk factors: Model 1- including all participants positive in hybridization by Leishmania donovani complex probe; Model 2- including all participants positive for hybridization and at least one serologic test. In Model 1, the variables associated with infection were: ownership of birds, time spent outside house between 6:00-10:00 PM and garbage not collected. In Model 2, the variables associated with infection were: family with knowledge of the vector, garbage not collected, garbage not removed or buried, ownership of birds and eroded areas in the neighborhood. The risk factors identified were associated with household conditions, presence of animals and the likelihood of contact with phlebotomine sandflies.

Diagnosing human asymptomatic visceral leishmaniasis in an urban area of the State of Minas Gerais, using serological and molecular biology techniques

A population-based cross-sectional study was set up in Sabará country, Southeastern Brazil, to identify asymptomatic human visceral leishmaniasis in an urban area of low disease prevalence. Blood was collected on filter paper (n=1,604 inhabitants) and examined by indirect immunofluorescent test, enzyme-linked immunosorbent assay and immunochromatographic strip test. The prevalence rates of infection ranged from 2.4 to 5.6% depending on the test used. One year later, venous blood was collected in a subset of 226 participants (102 seropositive and 124 seronegative). The tests performed were IFAT, ELISA, rk39-ELISA, polymerase chain reaction and hybridization with Leishmania donovani complex probe. No clinical signs or symptoms of leishmaniasis were observed. Using hybridization as a reference test, the sensitivity and specificity of serology were respectively: 24.8 and 71% (ELISA); 26.3 and 76.3% (rk-39); 30.1 and 63.4% (IFAT). Due to disagreements, different criteria were tested to define the infection and hybridization should be considered in epidemiological studies.

Domiciliation of Triatoma pseudomaculata (Corrêa e Espínola 1964) in the Jequitinhonha Valley, State of Minas Gerais

Impact of the vector control program was evaluated eight years after implantation of epidemiological surveillance for Chagas’ disease in Berilo, a municipality in the Jequitinhonha Valley of the Brazilian State of Minas Gerais. In all 5,242 domiciliary units (96% of the total) were inspected and 10 found to be infested by the triatomine bug Triatoma pseudomaculata. Triatomines were found associated with bats inside one house and in the peridomiciles of the other nine. None of the 111 Triatoma pseudomaculata captured was infected with Trypanosoma cruzi. Noireau et al16 traps were installed in (n=8) and around (n=100) the infested house but no Trypanpsoma cruzi-infected triatomines were found. None bat, opossums (Didelphis albiventris) and rat captured in the peridomicile were infected with Trypanosoma cruzi although 24% of the inhabitants of the house infested by Triatoma pseudomaculata were seropositive for the parasite, based on ELISA, IHA and IIF.

Clinical, epidemiological and laboratory aspects of patients with American cutaneous leishmaniasis in the State of Pernambuco

The diagnosis for American cutaneous leishmaniasis is based on an association of clinical, epidemiological and laboratory characteristics. The present study identified the circulating species of Leishmania in the State of Pernambuco, described its clinical-epidemiological characteristics and diagnosed the disease. Nineteen patients presenting active lesions who had been diagnosed through clinical evaluation and laboratory tests were selected. The tests included direct investigation, in vitro culturing, Montenegro skin test, indirect immunofluorescence and polymerase chain reaction. The Montenegro Skin Test showed positive results in 89% of the patients; indirect immunofluorescence, in 79%; direct investigation, in 58%; and polymerase chain reaction in 75%. Seven Leishmania (Viannia) braziliensis samples were isolated from these patients and were characterized by means of specific monoclonal antibodies. These data confirm that a combination of different diagnosis techniques is needed in order to obtain efficient results and that, so far, Leishmania (Viannia) braziliensis is the only species responsible for American cutaneous leishmaniasis infection in Pernambuco. Thus, it is essential to identify the parasite species involved in cases of human disease in an endemic area in order to determine the clinical and epidemiological characteristics, especially with regard to diagnosis, therapy development and disease prognosis.

Probabilistic constraint reasoning with Monte Carlo integration to robot localization

This work studies the combination of safe and probabilistic reasoning through the hybridization of Monte Carlo integration techniques with continuous constraint programming. In continuous constraint programming there are variables ranging over continuous domains (represented as intervals) together with constraints over them (relations between variables) and the goal is to find values for those variables that satisfy all the constraints (consistent scenarios). Constraint programming “branch-and-prune” algorithms produce safe enclosures of all consistent scenarios. Special proposed algorithms for probabilistic constraint reasoning compute the probability of sets of consistent scenarios which imply the calculation of an integral over these sets (quadrature). In this work we propose to extend the “branch-and-prune” algorithms with Monte Carlo integration techniques to compute such probabilities. This approach can be useful in robotics for localization problems. Traditional approaches are based on probabilistic techniques that search the most likely scenario, which may not satisfy the model constraints. We show how to apply our approach in order to cope with this problem and provide functionality in real time.

State detection in a financial portfolio: a self-organizing maps approach for financial time series

This study analyses financial data using the result characterization of a self-organized neural network model. The goal was prototyping a tool that may help an economist or a market analyst to analyse stock market series. To reach this goal, the tool shows economic dependencies and statistics measures over stock market series. The neural network SOM (self-organizing maps) model was used to ex-tract behavioural patterns of the data analysed. Based on this model, it was de-veloped an application to analyse financial data. This application uses a portfo-lio of correlated markets or inverse-correlated markets as input. After the anal-ysis with SOM, the result is represented by micro clusters that are organized by its behaviour tendency. During the study appeared the need of a better analysis for SOM algo-rithm results. This problem was solved with a cluster solution technique, which groups the micro clusters from SOM U-Matrix analyses. The study showed that the correlation and inverse-correlation markets projects multiple clusters of data. These clusters represent multiple trend states that may be useful for technical professionals.

Entomological surveillance of Chagas disease in Berilo municipality, Jequitinhonha Valley, State of Minas Gerais, Brazil

This study aimed to evaluate the Chagas Disease Control Program which has operated since 1982 in the municipality of Berilo in the Jequitinhonha Valley, Minas Gerais, Brazil, based on evaluation of 5,242 domiciliary units (DUs) and 7,807 outbuildings over an eight-year period of epidemiological surveillance implanted in 1997. A total of 391 triatomines (280 Panstrongylus megistus and 111 Triatoma pseudomaculata) were captured, indicating the continued predominance of the former species. However, Triatoma pseudomaculata is clearly becoming more important in this region, with intradomiciliary colonies being detected in recent years. Entomological parameters, such as dispersion (17%) and intradomiciliary infestation (0.15%) indices, are compatible with the results of the epidemiological surveillance. The majority of DUs were of construction type A (plaster over bricks) or C (plaster over adobe). Twenty-five percent of the inhabitants of the DUs infested by triatomines were reactive in ELISA, IHA and IIF tests for Trypanosoma cruzi antigens.

Efficient paraconsistent reasoning with rules and ontologies for the semantic web

Ontologies formalized by means of Description Logics (DLs) and rules in the form of Logic Programs (LPs) are two prominent formalisms in the field of Knowledge Representation and Reasoning. While DLs adhere to the OpenWorld Assumption and are suited for taxonomic reasoning, LPs implement reasoning under the Closed World Assumption, so that default knowledge can be expressed. However, for many applications it is useful to have a means that allows reasoning over an open domain and expressing rules with exceptions at the same time. Hybrid MKNF knowledge bases make such a means available by formalizing DLs and LPs in a common logic, the Logic of Minimal Knowledge and Negation as Failure (MKNF). Since rules and ontologies are used in open environments such as the Semantic Web, inconsistencies cannot always be avoided. This poses a problem due to the Principle of Explosion, which holds in classical logics. Paraconsistent Logics offer a solution to this issue by assigning meaningful models even to contradictory sets of formulas. Consequently, paraconsistent semantics for DLs and LPs have been investigated intensively. Our goal is to apply the paraconsistent approach to the combination of DLs and LPs in hybrid MKNF knowledge bases. In this thesis, a new six-valued semantics for hybrid MKNF knowledge bases is introduced, extending the three-valued approach by Knorr et al., which is based on the wellfounded semantics for logic programs. Additionally, a procedural way of computing paraconsistent well-founded models for hybrid MKNF knowledge bases by means of an alternating fixpoint construction is presented and it is proven that the algorithm is sound and complete w.r.t. the model-theoretic characterization of the semantics. Moreover, it is shown that the new semantics is faithful w.r.t. well-studied paraconsistent semantics for DLs and LPs, respectively, and maintains the efficiency of the approach it extends.

Investigation of measles IgM-seropositive cases of febrile rash illnesses in the absence of documented measles virus transmission, State of São Paulo, Brazil, 2000-2004

INTRODUCTION: To review measles IgM-positive cases of febrile rash illnesses in the State of São Paulo, Brazil, over the five-year period following interruption of measles virus transmission. METHODS: We reviewed 463 measles IgM-positive cases of febrile rash illness in the State of São Paulo, from 2000 to 2004. Individuals vaccinated against measles < 56 days prior to specimen collection were considered to be exposed to the vaccine. Serum from the acute and convalescent phases was tested for evidence of measles, rubella, parvovirus B19 and human herpes virus-6 infection. In the absence of seroconversion to measles immunoglobulin-G, measles IgM-positive cases were considered false positives in individuals with evidence of other viral infections. RESULTS: Among the 463 individuals with febrile rash illness who tested positive for measles IgM antibodies during the period, 297 (64%) were classified as exposed to the vaccine. Among the 166 cases that were not exposed to the vaccine, 109 (66%) were considered false positives based on the absence of seroconversion, among which 21 (13%) had evidence of rubella virus infection, 49 (30%) parvovirus B19 and 28 (17%) human herpes virus-6 infection. CONCLUSIONS: Following the interruption of measles virus transmission, thorough investigation of measles IgM-positive cases is required, especially among cases not exposed to the vaccine. Laboratory testing for etiologies of febrile rash illness aids interpretation of these cases.

Poisoning due to Philodryas olfersii (Lichtenstein, 1823) attended at Restauração Hospital in Recife, State of Pernambuco, Brazil: case report

Few papers have been published on snake bites caused by Philodryas olfersii. We report here the first case identified at the Centro de Assistência Toxicológica do Hospital da Restauração, Recife, State of Pernambuco. This case was described based on medical protocols, interviewing the patient and identifying the animal that caused the bite. The patient presented pain, heat, erythema, edema and ecchymosis, without other laboratory abnormalities or coagulation disorders. The treatment consisted of administration of eight ampoules of antibothropic serum, and post-administration allergenic reactions were observed. The importance of bites by opistoglyph snakes needs to be reconsidered in research and at specialized treatment centers.

A SARIMA forecasting model to predict the number of cases of dengue in Campinas, State of São Paulo, Brazil

INTRODUCTION: Forecasting dengue cases in a population by using time-series models can provide useful information that can be used to facilitate the planning of public health interventions. The objective of this article was to develop a forecasting model for dengue incidence in Campinas, southeast Brazil, considering the Box-Jenkins modeling approach. METHODS: The forecasting model for dengue incidence was performed with R software using the seasonal autoregressive integrated moving average (SARIMA) model. We fitted a model based on the reported monthly incidence of dengue from 1998 to 2008, and we validated the model using the data collected between January and December of 2009. RESULTS: SARIMA (2,1,2) (1,1,1)12 was the model with the best fit for data. This model indicated that the number of dengue cases in a given month can be estimated by the number of dengue cases occurring one, two and twelve months prior. The predicted values for 2009 are relatively close to the observed values. CONCLUSIONS: The results of this article indicate that SARIMA models are useful tools for monitoring dengue incidence. We also observe that the SARIMA model is capable of representing with relative precision the number of cases in a next year.

Notification of the first isolation of Cacipacore virus in a human in the State of Rondônia, Brazil

Flavivirus is a genus of arthropod-transmitted viruses of the family Flaviviridae, and in Brazil, up to eleven different Flavivirus have been isolated. We collected blood from farmers in the municipality of Theobroma, which is located 320km from the City of Porto Velho, the former capital of the Brazilian State of Rondônia. For viral isolation, we used newborn mouse brain, followed by RT-PCR with specific universal Flavivirus primers. We obtained fragments 958bp and 800bp in length. Based on BLAST, these sequences were 91% similar to a sequence of Cacipacore virus.

Study on Chagas disease occurrence in the municipality of Monte Negro, State of Rondônia, Brazilian Amazon

INTRODUCTION: Studies on Chagas disease deal with the perspective of its occurrence in the Amazon region, which is directly correlated to the population growth and the spread of the bug biotope. The state of Rondônia has an immense source of vectors (Triatomine) and reservoirs of Trypanosoma cruzi. Environmental changes brought forth by the deforestation in the region may cause vector behavior changes and bring these vectors to a closer contact with humans, increasing the probability of vector infection. METHODS: This study was carried out to check the occurrence of Chagas disease in the municipality of Monte Negro, Rondônia, Brazil, based on a random sampling of the farms and people wherein blood collection from the population and capturing triatomines were done. The blood samples were submitted to serologic tests to detect antibodies of the IgG class against T. cruzi. The triatomines that were collected had their digestive tract checked for the presence of trypanosomatidae with morphology resembling that of the T. cruzi. RESULTS: The population examined was mostly from other states. From the 322 bugs examined on the microscope, 50% showed parasites with morphology compatible with T. cruzi. From the serology of 344 random samples of human blood, 1.2% was found positive, 6% showed inconclusive results, and 92.8% were negative. CONCLUSIONS: Monte Negro shows low prevalence of human infection by T. cruzi and none active vector transmission; however, preventive and surveying measures, which are not performed until now, shall be taken due to the abundance of vectors infected by trypanosomatidae.