To be or not to be a pseudogene: a molecular epidemiological approach to the mclx genes and its impact in tuberculosis

Tuberculosis presents a myriad of symptoms, progression routes and propagation patterns not yet fully understood. Whereas for a long time research has focused solely on the patient immunity and overall susceptibility, it is nowadays widely accepted that the genetic diversity of its causative agent, Mycobacterium tuberculosis, plays a key role in this dynamic. This study focuses on a particular family of genes, the mclxs (Mycobacterium cyclase/LuxR-like genes), which codify for a particular and nearly mycobacterial-exclusive combination of protein domains. mclxs genes were found to be pseudogenized by frameshift-causing insertion(s)/deletion(s) in a considerable number of M. tuberculosis complex strains and clinical isolates. To discern the functional implications of the pseudogenization, we have analysed the pattern of frameshift-causing mutations in a group of M. tuberculosis isolates while taking into account their microbial-, patient- and disease-related traits. Our logistic regression-based analyses have revealed disparate effects associated with the transcriptional inactivation of two mclx genes. In fact, mclx2 (Rv1358) pseudogenization appears to be primarily driven by the microbial phylogenetic background, being mainly related to the Euro-American (EAm) lineage; on the other hand, mclx3 (Rv2488c) presents a higher tendency for pseudogenization among isolates from patients born on the Western Pacific area, and from isolates causing extra-pulmonary infections. These results contribute to the overall knowledge on the biology of M. tuberculosis infection, whereas at the same time launch the necessary basis for the functional assessment of these so far overlooked genes.

Photosynthetic parameters and growth in seedlings of Bertholletia excelsa and Carapa guianensis in response to pre-acclimation to full sunlight and mild water stress

Light and water are important factors that may limit the growth and development of higher plants. The aim of this study was to evaluate photosynthetic parameters and growth in seedlings of Bertholletia excelsa and Carapa guianensis in response to pre-acclimation to full sunlight and mild water stress. I used six independent pre-acclimation treatments (0, 90 (11h15-12h45), 180 (10h30-13h30), 360 (09h00-15h00), 540 (07h30-16h30) and 720 min (06h00-18h00)) varying the time of exposure to full sunlight (PFS) during 30 days, followed by whole-day outdoor exposure for 120 days. Before PFS, the plants were kept in a greenhouse at low light levels (0.8 mol m-2 day-1). The PFS of 0 min corresponded to plants constantly kept under greenhouse conditions. From the beginning to the end of the experiment, each PFS treatment was submitted to two water regimes: moderate water stress (MWS, pre-dawn leaf water potential (ΨL) of -500 to -700 kPa) and without water stress (WWS, ΨL of -300 kPa, soil kept at field capacity). Plants under MWS received only a fraction of the amount of water applied to the well-watered ones. At the end of the 120-day-period under outdoor conditions, I evaluated light saturated photosynthesis (Amax), stomatal conductance (g s), transpiration (E) and plant growth. Both Amax and g s were higher for all plants under the PFS treatment. Stem diameter growth rate and Amax were higher for C. guianensis subjected to MWS than in well-watered plants. The contrary was true for B. excelsa. The growth of seedlings was enhanced by exposure to full sunlight for 180 minutes in both species. However, plants of B. excelsa were sensitive to moderate water stress. The higher photosynthetic rates and faster growth of C. guianensis under full sun and moderate water stress make this species a promissory candidate to be tested in reforestation programs.

Influence of river ecological condition on changes in physico-chemical water parameters along rivers

Dissertação de mestrado em Ecology

Composition and structure variation for magnetron sputtered tantalum oxynitride thin films, as function of deposition parameters

Tantalum oxynitride thin films were produced by magnetron sputtering. The films were deposited usinga pure Ta target and a working atmosphere with a constant N2/O2ratio. The choice of this constant ratiolimits the study concerning the influence of each reactive gas, but allows a deeper understanding of theaspects related to the affinity of Ta to the non-metallic elements and it is economically advantageous.This work begins by analysing the data obtained directly from the film deposition stage, followed bythe analysis of the morphology, composition and structure. For a better understanding regarding theinfluence of the deposition parameters, the analyses are presented by using the following criterion: thefilms were divided into two sets, one of them produced with grounded substrate holder and the otherwith a polarization of −50 V. Each one of these sets was produced with different partial pressure of thereactive gases P(N2+ O2). All the films exhibited a O/N ratio higher than the N/O ratio in the depositionchamber atmosphere. In the case of the films produced with grounded substrate holder, a strong increaseof the O content is observed, associated to the strong decrease of the N content, when P(N2+ O2) is higherthan 0.13 Pa. The higher Ta affinity for O strongly influences the structural evolution of the films. Grazingincidence X-ray diffraction showed that the lower partial pressure films were crystalline, while X-rayreflectivity studies found out that the density of the films depended on the deposition conditions: thehigher the gas pressure, the lower the density. Firstly, a dominant -Ta structure is observed, for lowP(N2+ O2); secondly a fcc-Ta(N,O) structure, for intermediate P(N2+ O2); thirdly, the films are amorphousfor the highest partial pressures. The comparison of the characteristics of both sets of produced TaNxOyfilms are explained, with detail, in the text.

Automatically estimating iSAX parameters

The Symbolic Aggregate Approximation (iSAX) is widely used in time series data mining. Its popularity arises from the fact that it largely reduces time series size, it is symbolic, allows lower bounding and is space efficient. However, it requires setting two parameters: the symbolic length and alphabet size, which limits the applicability of the technique. The optimal parameter values are highly application dependent. Typically, they are either set to a fixed value or experimentally probed for the best configuration. In this work we propose an approach to automatically estimate iSAX’s parameters. The approach – AutoiSAX – not only discovers the best parameter setting for each time series in the database, but also finds the alphabet size for each iSAX symbol within the same word. It is based on simple and intuitive ideas from time series complexity and statistics. The technique can be smoothly embedded in existing data mining tasks as an efficient sub-routine. We analyze its impact in visualization interpretability, classification accuracy and motif mining. Our contribution aims to make iSAX a more general approach as it evolves towards a parameter-free method.

An epidemiological study determining blood pressure in a Portuguese cohort: the Guimaraes/Vizela study

Surveying the evolution of blood pressure (BP) levels and hypertension (HTN) prevalence is important. A stringent strategy was utilized in a population cohort study. The BP was measured at two visits at least 3 months apart, and the results were analyzed using the following two methods: the Surveillance method (three BP measurements were performed in one visit, and the results were compared with those published previously for the identical method) and the Clinical method (three measurements per visit for two visits, and the concordant results in both visits were used to determine the BP classification). A total of 2542 subjects completed the evaluation. Using the Clinical method, an average systolic/diastolic BP value of 129.8/76.8?mm?Hg was obtained, and the prevalence of HTN was 31.6%. Of the hypertensive patients, 74.3% were aware of his/her condition; 69.1% were treated and 40.8% of those treated had adequate BP control. A total of 24.7% of subjects changed his/her BP classification between visits, and 13.7% misreported HTN. Using the Surveillance method, we determined that the average global SBP has been maintained, with HTN prevalence increasing in this region, drifting from reported trends nationally and worldwide. There has been improvement in the proportion of treated and controlled subjects; however, the Surveillance method overestimated the HTN prevalence and underestimated the proportion of treated and controlled subjects. The BP levels were higher than observed worldwide in high-cardiovascular (CV) risk countries as well as higher than the minimum risk exposure level for developing CV disease.

Influence of emphysema distribution on pulmonary function parameters in COPD patients

Objective: To evaluate the impact that the distribution of emphysema has on clinical and functional severity in patients with COPD. Methods: The distribution of the emphysema was analyzed in COPD patients, who were classified according to a 5-point visual classification system of lung CT findings. We assessed the influence of emphysema distribution type on the clinical and functional presentation of COPD. We also evaluated hypoxemia after the six-minute walk test (6MWT) and determined the six-minute walk distance (6MWD). Results: Eighty-six patients were included. The mean age was 65.2 ± 12.2 years, 91.9% were male, and all but one were smokers (mean smoking history, 62.7 ± 38.4 pack-years). The emphysema distribution was categorized as obviously upper lung-predominant (type 1), in 36.0% of the patients; slightly upper lung-predominant (type 2), in 25.6%; homogeneous between the upper and lower lung (type 3), in 16.3%; and slightly lower lung-predominant (type 4), in 22.1%. Type 2 emphysema distribution was associated with lower FEV1 , FVC, FEV1 /FVC ratio, and DLCO. In comparison with the type 1 patients, the type 4 patients were more likely to have an FEV1 < 65% of the predicted value (OR = 6.91, 95% CI: 1.43-33.45; p = 0.016), a 6MWD < 350 m (OR = 6.36, 95% CI: 1.26-32.18; p = 0.025), and post-6MWT hypoxemia (OR = 32.66, 95% CI: 3.26-326.84; p = 0.003). The type 3 patients had a higher RV/TLC ratio, although the difference was not significant. Conclusions: The severity of COPD appears to be greater in type 4 patients, and type 3 patients tend to have greater hyperinflation. The distribution of emphysema could have a major impact on functional parameters and should be considered in the evaluation of COPD patients.

Euler angles, Bryant angles and Euler parameters

This chapter deals with the different approaches for describing the rotational coordinates in spatial multibody systems. In this process, Euler angles and Bryant angles are briefly characterized. Particular emphasis is given to Euler parameters, which are utilized to describe the rotational coordinates in the present work. In addition, for all the types of coordinates considered in this chapter, a characterization of the transformation matrix is fully described.

Why do we need randomized and epidemiological studies on cardiovascular disease? Evidence-based cardiology VII

Over the last two decades the results of randomized clinical studies, which are powerful aids for correctly assessing therapeutical strategies, have consolidated cardiological practice. In addition, scientifically interesting hypotheses have been generated through the results of epidemiological studies. Properly conducted randomized studies without systematic errors and with statistical power adequate for demonstrating moderate and reasonable benefits in relevant clinical outcomes have provided reliable and strong results altering clinical practice, thus providing adequate treatment for patients with cardiovascular disease (CVD). The dissemination and use of evidence-based medicine in treating coronary artery disease (CAD), heart failure (HF), and in prevention will prevent hundreds of thousands of deaths annually in developed and developing countries. CVD is responsible for approximately 12 million deaths annually throughout the world, and approximately 60% of these deaths occur in developing countries. During recent years, an increase in mortality and morbidity rates due to CVD has occurred in developing countries. This increase is an indication that an epidemiological (demographic, economical, and health-related) transition is taking place in developing countries and this transition implies a global epidemic of CVD, which will require wide-ranging and globally effective strategies for prevention. The identification of conventional and emerging risk factors for CVD, as well as their management in high-risk individuals, has contributed to the decrease in the mortality rate due to CVD. Through a national collaboration, several multi-center and multinational randomized and epidemiological studies have been carried out throughout Brazil, thus contributing not only to a generalized scientific growth in different Brazilian hospitals but also to the consolidation of an increasingly evidence-based clinical practice.

The effect of siesta in parameters of cardiac structure and in interpretation of ambulatory arterial blood pressure monitoring

OBJECTIVE: To evaluate the influence of the siesta in ambulatory blood pressure (BP) monitoring and in cardiac structure parameters. METHODS: 1940 ambulatory arterial blood pressure monitoring tests were analyzed (Spacelabs 90207, 15/15 minutes from 7:00 to 22:00 hours and 20/20 minutes from 22:01 to 6.59hours) and 21% of the records indicated that the person had taken a siesta (263 woman, 52±14 years). The average duration of the siesta was 118±58 minutes. RESULTS: (average ± standard deviation) The average of systolic/diastolic pressures during wakefulness, including the napping period, was less than the average for the period not including the siesta (138±16/85±11 vs 139±16/86±11 mmHg, p<0.05); 2) pressure loads during wakefulness including the siesta, were less than those observed without the siesta); 3) the averages of nocturnal sleep blood pressures were similar to those of the siesta, 4) nocturnal sleep pressure drops were similar to those in the siesta including wakefulness with and without the siesta; 5) the averages of BP in men were higher (p<0.05) during wakefulness with and without the siesta, during the siesta and nocturnal sleep in relation to the average obtained in women; 6) patients with a reduction of 0- 5% during the siesta had thickening of the interventricular septum and a larger posterior wall than those with a reduction during the siesta >5%. CONCLUSION: The siesta influenced the heart structure parameters and from a statistical point of view the average of systolic and diastolic pressures and the respective pressure loads of the wakeful period.

Epidemiological characteristics of congenital heart diseases in Londrina, Paraná South Brazil

OBJECTIVE: To determine the prevalence and other epidemiological characteristics of congenital heart diseases. METHODS: A retrospective population based study of children who were born in Londrina, from January '89 to December '98 (80,262 live births). Diagnoses were confirmed through autopsy, surgery, catheterization, or echocardiography. RESULTS: A total of 441 patients was as certained what corresponds to a prevalence of 5.494:1,000 live births. Ventricular septal defect was the commonest lesion. A small number of transpositions of the great vessels and of left ventricular hypoplasia was observed. A high propation of ventricular septal defect (28.3%) and atrioventricular septal defects (8.1%) occurred. Fifty-one (11.35%) affected children had syndromic diseases and 52 (12.01%) children had nonsyndromic anomalies. CONCLUSION: The prevalence of congenital heart diseases in Londrina is in accordance with that of other regions of the globe. This prevalence also may reflect the reality in the southern region of Brazil, because population characteristics are very similar in the 3 southernmost Brazilian states.

Chagas' heart disease: evolutive evaluation of electrocardiographic and echocardiographic parameters in patients with the indeterminate form

OBJECTIVE: To identify and associate potential electrocardiographic and echocardiographic changes in patients with the indeterminate form of Chagas' disease during long-term follow-up. METHODS: One hundred sixty patients underwent standard electrocardiography and two-dimensional guided M-mode echocardiography for left ventricular ejection fraction determination. Patients were followed up for 98.6±30.4 months, undergoing repeat electrocardiographic studies at 6-month intervals and echocardiographic studies at 12-month intervals. RESULTS: Based on the electrocardiographic findings, the patients were divided into group I, 125 patients (78.6%) with normal electrocardiograms throughout follow-up, and group II, 34 patients (21.3%) who developed electrocardiographic changes. Group II was further divided into group IIA (9 patients, 5.6%) with permanent electrocardiographic changes, group IIB (14 patients, 8.8%) with transitory electrocardiographic changes, and group IIC (11 patients, 6.9%) with changes appearing only on the final electrocardiogram. Left ventricular ejection fractions remained normal in the entire population studied and did not differ among groups. CONCLUSION: The indeterminate form of Chagas' disease clearly represents a benign condition with a favorable long-term prognosis. Although some patients develop electrocardiographic changes, left ventricular systolic function is well preserved.

Epidemiological aspects of adherence to the treatment of hypertension

OBJECTIVE: To analyze the reasons given by patients for interrupting their pharmacological treatment of hypertension. METHODS: We carried out an observational cross-sectional study, in which a questionnaire was applied and blood pressure was measured in 401 patients in different centers of the state of Bahia. The patients selected had been diagnosed with hypertension and were not on antihypertensive treatment for at least 60 days. Clinical and epidemiological characteristics of the groups were analyzed. RESULTS: Of the 401 patients, 58.4% were females, 55.6% of whom white; 60.5% of the males were white. The major reasons alleged for not adhering to treatment were as follows (for males and females respectively): normalization of blood pressure (41.3% and 42.3%); side effects of the medications (31.7% and 24.8%); forgetting to use the medication (25.2% and 20.1%); cost of medication (21.6% and 20.1%); fear of mixing alcohol and medication (23.4% and 3.8%); ignoring the need for continuing the treatment (15% and 21.8%); use of an alternative treatment (11.4% and 17.1%); fear of intoxication (9.6% and 12.4%); fear of hypotension (9.6% and 12%); and fear of mixing the medication with other drugs (8.4% and 6.1%). CONCLUSION: Our data suggest that most factors concerning the abandonment of the treatment of hypertension are related to lack of information, and that, despite the advancement in antihypertensive drugs, side effects still account for most abandonments of treatment.

Malolactic fermentation in winemaking: evaluation of operational parameters

Dissertação de mestrado em Bioengenharia

Epidemiological study of congenital heart defects in children and adolescents: analysis of 4,538 cases

OBJECTIVE: To analyze the frequency and prevalence of congenital heart defects in a tertiary care center for children with heart diseases. METHODS: We carried out an epidemiological assessment of the first medical visit of 4,538 children in a pediatric hospital from January 1995 to December 1997. All patients with congenital heart defects had their diagnoses confirmed at least on echocardiography. The frequency and prevalence of the anomalies were computed according to the classification of sequential analysis. Age, weight, and sex were compared between the groups of healthy individuals and those with congenital heart defects after distribution according to the age group. RESULTS: Of all the children assessed, 2,017 (44.4%) were diagnosed with congenital heart disease, 201 (4.4%) with acquired heart disease, 52 (1.2%) with arrhythmias, and 2,268 (50%) were healthy children. Congenital heart diseases predominated in neonates and infants, corresponding to 71.5% of the cases. Weight and age were significantly lower in children with congenital heart defects. Ventricular septal defect was the most frequent acyanotic anomaly, and tetralogy of Fallot was the most frequent cyanotic anomaly. CONCLUSION: Children with congenital heart defects are mainly referred during the neonatal period and infancy with impairment in gaining weight. Ventricular septal defect is the most frequent heart defect.