A modified debugging infrastructure to assist real time fault injection campaigns

Fault injection is frequently used for the verification and validation of the fault tolerant features of microprocessors. This paper proposes the modification of a common on-chip debugging (OCD) infrastructure to add fault injection capabilities and improve performance. The proposed solution imposes a very low logic overhead and provides a flexible and efficient mechanism for the execution of fault injection campaigns, being applicable to different target system architectures.

Tuberculosis in patients with chronic renal failure

Nine cases of tuberculosis (TB) were diagnosed among 800 uremic patients, followed-up during 11 years, a prevalence of 1125%, 2.5 times higher than that in the general population. Six patients (66.7%) had lymph node involvement (4 cervical and 2 mediastinal). Three patients (33.3%) had pulmonary involvement (2 pleuro-pulmonary and 1 bilateral apical pulmonary). Eight patients were undergoing dialysis and 1 was pre-dialytic. The duration of dialysis ranged from 1 to 60 months. Three patients had previously received immunosuppressive drugs for unsuccessful renal transplantation. Daily fever was present in all but one patient; he was asymptomatic and TB was suspected after routine chest radiography. Biopsy was the diagnostic procedure in 7 patients (77.8%), four by direct cervical lymph node biopsy, 2 by mediastinal, performed by mediastinoscopy and 1 by pleural biopsy. In 2 other patients TB was confirmed by the presence of tubercle bacilli; in sputum (1 patient) and in a bronchial flushing specimen (the other patient). Triple therapy was used in all patients (isoniazid and ethambutol in all), plus rifampicin in 8 and streptomycin in 1. One patient had jaundice and another had optical neuritis. Five patients were cured. The other four died during treatment of causes unrelated to TB or its treatment.

Tuberculosis in renal transplant patients

Tuberculosis (TB) was diagnosed in 25 of 466 patients who underwent renal transplant over a period of 15 years. TB developed from 1 month to 9 years post-transplant. In 56% of the cases the onset was within the first post-transplant year. TB affected several isolated or combined organs. Pulmonary involvement was present in 76% of cases, either as isolated pleuro-pulmonary (56%) or associated with other sites (20%). The non-pulmonary sites were: skin, joints, tests, urinary tract, central nervous system and lymphonodules. The diagnosis was confirmed by biopsy in 64% of the cases, by identification of tubercle bacilli in 24% and only at necropsy in 12% Biopsy specimens could be classified in three histological forms: exudative, that occurred in early onset and more severe cases granulomatous in late onset and benign cases; and mixed in intermediate cases. Azathioprine dosages were similar along post-transplant time periods in TB patients and in the control groups; and in TB patients who were cured and who died. The number of steroid treated rejection crises was greater in TB than in the control group. Prednisone doses were higher and the number of rejection crises was greater in TB patients who died than in those who were cured. Fifteen patients were cured and ten died, two of them of causes unrelated to TB. Six of the eight TB-related deaths occurred in the first 6 post-transplant months. The outcome was poor in patients in whom TB arose early in post-transplant period and where the exudative or mixed forms were present; whereas the prognosis was good in patients with late onset and granulomatous form of TB. In one patient TB was transmitted by the allograft.

Predictive value of serologic tests in the diagnosis and follow-up of patients with paracoccidioidomycosis

A serologic study was undertaken in a group of 43 patients with active paracoccidioidomycosis who were treated in the same form (ketoconazole), for identical periods of time (6 months), and folio wed-up for various periods posttherapy. The tests employed were agar gel immunodiffusion (AGID) and complement fixation (FC). Also studied were 50 sera from patients with proven histoplasmosis and pulmonary aspergilloma, 30 patients with culturaly proven tuberculosis as well as 92 specimens from healthy individuals, residents in the endemic area for paracoccidioidomycosis. A single lot of yeast filtrate antigen was used throughout the study. The value of each test was measured according to GALEN and GAMBINO6. Both tests were highly sensitive, 89 and 93% respectively. Regarding their specificity, the AGID was totally specific while the CF exhibited 96.6% and 97% specificity in front of tuberculosis patients and healthy individuals respectively and 82% in comparison with patients with other mycoses. The concept of predictive value, that is, the certainty one has in accepting a positive test as diagnostic of paracoccidioidomycosis, favored the AGID procedure (100%) over the CF test. The latter could sort out with 93% certainty a patient with paracoccidioidomycosis among a group of healthy individuals and with 97.5% in the case of TB patients; when the group in question was composed by individuals with other deep mycoses, such certainty was lower (81%). The above results indicate that both the AGID and the CF tests furnish results of high confidence; one should not relay, however, in the CF alone as a means to establish the specific diagnosis of paracoccidioidomycosis.

Noble metal nanoparticles - Au and Ag - for biodetection

Dissertation submitted for obtainment of the Master’s Degree in Biotechnology, by the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Desenvolvimento de Ontologia para Apoio ao Diagnóstico de Distúrbios do Humor

Mestrado em Computação e Instrumentação Médica

Transcranial magnetic resonance guided focused ultrasound: neurosurgery applications

Mestrado em Radiações Aplicadas às Tecnologias da Saúde

Electrochemical immunosensor for the analysis of the breast cancer biomarker HER2 ECD

Human epidermal growth factor receptor 2 (HER2) is a breast cancer biomarker that plays a major role in promoting breast cancer cell proliferation and malignant growth. The extracellular domain (ECD) of HER2 can be shed into the blood stream and its concentration is measurable in the serum fraction of blood. In this work an electrochemical immunosensor for the analysis of HER2 ECD in human serum samples was developed. To achieve this goal a screen-printed carbon electrode, modified with gold nanoparticles, was used as transducer surface. A sandwich immunoassay, using two monoclonal antibodies, was employed and the detection of the antibody–antigen interaction was performed through the analysis of an enzymatic reaction product by linear sweep voltammetry. Using the optimized experimental conditions the calibration curve (ip vs. log[HER2 ECD]) was established between 15 and 100 ng/mL and a limit of detection (LOD) of 4.4 ng/mL was achieved. These results indicate that the developed immunosensor could be a promising tool in breast cancer diagnostics, patient follow-up and monitoring of metastatic breast cancer since it allows quantification in a useful concentration range and has an LOD below the established cut-off value (15 ng/mL).

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

Respiratory complications in Brazilian patients infected with human immunodeficiency virus

PURPOSE: To determine how often and by what means an indentifiable pulmonary pathogen can be recognized in human immunodeficiency virus (HIV) infected patients with respiratory disorders in Brazil, which are the most frequently observed microorganisms and what impact specific therapy has on these agents. PATIENTS AND METHODS: Thirty-five HIV seroposiüve subjects with respiratory complaints were studied. All patients had a complete history, physical examination and blood counts. The pulmonary assessment included chest radiograms; sputum examination for bacterial and fungal pathogens; bronchoscopy with bronchoalveolar lavage and transbronchial biopsy. Patients with treatable complications received standard antimicrobial therapy. RESULTS: One or more microorganisms were found in 24 subjects and another 3 individuals showed nonspecific interstitial pneumonitis. The sputum examination identified the pulmonary pathogens in 7 cases. The bronchoalveolar lavage and the histopathologic examination were diagnostic in 14% and 83%, respectively, of the 28 individuals that were submitted to bronchoscopy. The most frequently identified microorganism was P. carinii (55%), followed by M. tuberculosis (41%) and cytomegalovirus (8%). The clinical, laboratory and radiographic findings failed to distinguish the specific pulmonary pathogens. Twenty-three individuals with P. carinii pneumonitis and/or tuberculosis received specific therapy; among the evaluable patients the therapeutic response rates were 79% for PCP and 100% for TB. CONCLUSIONS: We have determined that tuberculosis, P. carinii and cytomegalovirus pneumonitis are the most common respiratory opportunistic diseases in Brazilian patients infected with HIV. The histologic evaluation was crucial in order to identify the pulmonary pathogens. Tuberculosis in AIDS individuals displayed clinical and radiographic findings atypical for reactivation disease. However, most of the features observed in HIV infected patients had been previously described in infection of the normal host. Furthermore, the AIDS subjects showed a good therapeutic response to anti-tuberculous drugs.

Battery management system for electric racing cars

With the introduction of the electrics cars into the market new technologies regarding the battery are being developed and new problems to be solved, one of them the battery management system because each type of cell requires a specific way of handling. This research is done using the active research method to find out the actual problem on this subject and features a BMS should have, understand how they work and how to develop them applied to the purpose on this work. Once the features the BMS should have are clarified, it’s possible to develop a BMS for an electric racing car. The decisions are made taking into consideration the nature of the vehicle being developed. After the project done it’s clear to see that what was developed was not only the BMS itself but all the other factors around it, such as CAN communication, safety control, diagnostics and so on.

A Leishmaniose visceral em Portugal Continental : 1999-2009

RESUMO - As alterações climáticas alteraram a incidência e distribuição mundial de zoonoses, ao modificarem o perfil epidemiológico dos seus vectores. A leishmaniose visceral é reemergente na bacia mediterrânica, sendo o seu impacto real subestimado. Em Portugal, é endémica em três regiões, de declaração obrigatória desde 1948 e o reservatório é o canídeo. O aumento da incidência da doença no cão e a escassez de informação epidemiológica tornou pertinente investigar a realidade nacional. A partir das bases de dados das notificações e dos grupos de diagnósticos homogéneos hospitalares, foram identificados todos os casos e, consultados todos os processos clínicos dos doentes com episódios de internamento nos hospitais do continente entre 1999-2009. Ocorreram 730 internamentos para 375 indivíduos na maioria: homens, eurocaucasianos, com em média, 27 anos e, residência em Lisboa e Vale do Tejo. A sintomatologia e comorbilidades dos doentes vão de encontro ao descrito internacionalmente. A doença foi subnotificada, com uma demora média de 19 dias. A letalidade foi de 5%. A taxa de incidência média do continente foi de 0,294/100000 habitantes, sem padrão de sazonalidade. O corredor endémico de Bortman construído apresentou picos com amplitudes de 2-3 anos. O mapeamento dos doentes evidenciou casos em regiões não endémicas acompanhando a distribuição da leishmaniose canina. Seria pertinente que futuras investigações construíssem uma modelação matemática que confirmasse a tendência do corredor endémico (pico em 2011?) para accionar um sistema de alerta nos Serviços de Saúde. Seria também útil a avaliação das condições geoclimáticas das localidades com casos para evidenciar possíveis similitudes no território. -------ABSTRACT - Climate changed the incidence and worldwide distribution of zoonosis while the epidemiological profile of their vectors was changing. Visceral leishmaniasis is reemerging in the Mediterranean basin and its real impact underestimated. In Portugal, it’s endemic in three regions; the notification occurs since 1948 and dog is the reservoir. The increased incidence of the canines’ disease and the scarcity of epidemiological information relevant investigate the national reality. From Notifications and Homogeneous’ Diagnostics Groups system databases, all cases were identified and also analyze all clinical processes of inpatients’ hospitals in 1999- 2009 in Portugal. 730 admissions occurred for 375 patients. In most they were men, Caucasians, with an average of 27 years and residency in Lisboa e Vale do Tejo. The symptoms and comorbilidades patient go against described internationally. The disease was under notified, with an average delay of 19 days. Lethality was 5%. The incidence rate was 0,294/100000 inhabitants, without seasonality. The endemic’s Bortman corridor presents peak amplitudes of 2-3 years. Mapping patient’s residency shows that cases’ distribution is similar to endemic canine leishmaniasis. It would be appropriate a research to build a mathematical modeling up to confirm the trend of corridor endemic (peak in 2011?), to trigger an alert system for health services. It would also be useful to evaluate the geo-climatics conditions of localities with cases to highlight possible similarities in the territory.

Sucesso terapêutico no controlo da tuberculose em Portugal : determinantes do resultado do tratamento e a sua capacidade preditiva

RESUMO - Enquadramento/objectivos: Apesar do elevado nível de comprometimento em estratégias eficazes para o controlo da tuberculose, em todo o mundo, esta constitui ainda um sério problema de Saúde Pública, com uma estimativa global de 9,4milhões de casos novos em 2008 e 1,8milhões de mortes/ano. O reduzido conhecimento das barreiras e facilitadores para o sucesso terapêutico constitui um importante obstáculo na procura de soluções eficazes de melhoramento da qualidade dos programas de controlo da tuberculose. Este estudo procura contribuir para a identificação atempada de doentes com perfis preditivos de insucesso terapêutico, através da identificação inicial de potenciais determinantes do resultado, com base num modelo epidemiológico e estatístico. Métodos: Foi desenvolvido um estudo de caso-controlo para a população de casos notificados ao Programa Nacional de Controlo da Tuberculose (n=24491), entre 2000-2007. Os factores preditivos de insucesso terapêutico foram identificados na análise bivariada e multivariada, com um nível de significância de 5%; a regressão logística foi utilizada para estimar a odds ratio de insucesso terapêutico, em comparação com o sucesso terapêutico, para diversos factores identificados na literatura, e para os quais os dados se encontravam disponíveis. Resultados: A dependência alcoólica (OR=2,889), o país de origem (OR=3,910), a situação sem-abrigo (OR=3.919), a co-infecção pelo VIH (OR=5,173), a interrupção (OR=60.615) ou falha terapêutica no tratamento anterior (OR=67.345) e a duração do tratamento inferior a 165 dias (OR=1930,133) foram identificados como factores preditivos de insucesso terapêutico. A duração do tratamento inferior a 165 dias provou ser o mais importante determinante do resultado terapêutico. Conclusões: Os resultados sugerem que um doente imigrante, em situação de sem-abrigo, dependente alcoólico, com tratamentos anteriores para a tuberculose e co-infectado pelo VIH apresenta uma elevada probabilidade de insucesso terapêutico. Assim, deverão ser definidas estratégias específicas, centradas no doente por forma a impedir este resultado. A base de dados (SVIG-TB), provou ser uma ferramenta de qualidade para a investigação sobre diversos aspectos do controlo da tuberculose. ------------------------------- ABSTRACT - Background/Objective: Despite the high commitment in good strategies for tuberculosis control worldwide, this is still a serious Public Health problem, with global estimates of 9,4million new cases in 2008 and 1,8million deaths/year. The poor understanding of the barriers and facilitators to treatment success is a major obstacle to find effective solutions to improve the quality of tuberculosis programs. This study tries to contribute to the timely identification of patients with predictive profiles of unsuccessful treatment outcomes, through the initial identification of characteristics probably affecting treatment outcome, found on the basis of an epidemiological and statistical model. Methods: A case-control study was conducted for the population of cases notified to the National Program for Tuberculosis Control (n=24 491), between 2000-2007. Predictive factors for unsuccessful outcome were assessed in a bivariate and multivariate analysis, using a significance level of 5%; a logistic regression was used to estimate the odds-ratio of unsuccessful, as compared to successful outcome, for several factors identified in the literature and to which data was available. Results: Alcohol abuse (OR=2,889), patient´s foreign origin (OR=3,910), homelessness (OR=3,919), HIV co-infection (OR=5,173), interruption (OR=60,615) or unsuccessful outcome in the previous treatment (OR=67,345) and treatment duration below 165 days (OR=1930,133) were identified as predictive of unsuccessful outcomes. A low treatment duration proved to be the most powerful factor affecting treatment outcome. Conclusions: Results suggest that a foreign-born patient, alcohol abuser, who has had a previous treatment for tuberculosis and is co-infected with HIV is very likely to have an unsuccessful outcome. Therefore, specific, patient-centered strategies should be taken to prevent an unsuccessful outcome. The database (SVIG-TB), has proved to be a quality tool on research of various aspects of tuberculosis control.

Verificação interna periódica de esfigmomanómetros digitais

Os equipamentos de medição utilizados nos hospitais têm uma função muito importante na deteção e diagnóstico de doenças como é o caso da pressão arterial. Entre esses equipamentos encontram-se os esfigmomanómetros digitais portáteis que são em muitos casos os primeiros a serem utilizados e a fornecerem um primeiro diagnóstico da pressão arterial do doente como é no caso das urgências hospitalares. Para que os diagnósticos prescritos pelos profissionais de saúde - médicos e enfermeiros seja o mais correto é necessário conhecer as condições de trabalho em que se encontram os esfigmomanómetros digitais existentes nas unidades de saúde. Sendo os esfigmomanómetros digitais equipamentos com uma importância relevante na vida do ser humano, estes deveriam fazer parte da lista de equipamentos que estão englobados na metrologia legal, situação que neste momento ainda não foi concretizada e cada hospital toma a decisão espontânea se efetua a calibração ou verificação internamente dos seus esfigmomanómetros digitais. Pretende-se com este trabalho dar a conhecer o estado ao nível dos erros de alguns esfigmomanómetros digitais existentes nos hospitais envolvidos no trabalho e desenvolver um procedimento de verificação interna dos mesmos com auxílio de um manómetro analógico calibrado e um estetoscópio duplo – método de medição auscultatório - e comparar esses resultados com a utilização de um simulador – método de medição oscilométrico.

Seroprevalence of toxoplasmosis in Fortaleza, Ceará, Brazil

A serological survey of Toxoplasma gondii infection in population groups in Fortaleza, Brazil, was conducted, in order to identify seroprevalence rates according to age and risk factors associated with acquired infection. A Toxoplasma IgG-antibody enzyme immunoassay (Sanofi Pasteur Diagnostics, Marnes la Coquette, France) was employed to assess the immunity. Public day-care centers and schools were randomly selected, while three large antenatal clinics and maternity units were choosen by its importance. Population groups and results of 997 blood tests were: 227 children (mean age 3.8 years), 22.8% seropositives; 584 students (mean 11.4 years), 58.4%, and pregnant and postpartum women (mean 24 years), 71.5% seropositives (p < 0.001). Of 256 participants reporting close contact with cats, 59.8% were seropositive, in contrast with 51% seropositives without contact (relative risk 1.17; 95% confidence interval 1.04-1.33; p = 0.01). Having three or more siblings at home was related to higher seroprevalence in children and students (relative risk 1.39; 95% confidence interval 1.21-1.60; p < 0.01). In conclusion, toxoplasmosis seroprevalence showed a rapid increase during the first ten years of life, in association with close contact with cats and larger households, probably related to inappropriate hygiene and child-care practices.