Single-tube nested PCR assay with in-house DNA extraction for Mycobacterium tuberculosis detection in blood and urine

Abstract: INTRODUCTION : Molecular analyses are auxiliary tools for detecting Koch's bacilli in clinical specimens from patients with suspected tuberculosis (TB). However, there are still no efficient diagnostic tests that combine high sensitivity and specificity and yield rapid results in the detection of TB. This study evaluated single-tube nested polymerase chain reaction (STNPCR) as a molecular diagnostic test with low risk of cross contamination for detecting Mycobacterium tuberculosis in clinical samples. METHODS: Mycobacterium tuberculosis deoxyribonucleic acid (DNA) was detected in blood and urine samples by STNPCR followed by agarose gel electrophoresis. In this system, reaction tubes were not opened between the two stages of PCR (simple and nested). RESULTS: STNPCR demonstrated good accuracy in clinical samples with no cross contamination between microtubes. Sensitivity in blood and urine, analyzed in parallel, was 35%-62% for pulmonary and 41%-72% for extrapulmonary TB. The specificity of STNPCR was 100% in most analyses, depending on the type of clinical sample (blood or urine) and clinical form of disease (pulmonary or extrapulmonary). CONCLUSIONS: STNPCR was effective in detecting TB, especially the extrapulmonary form for which sensitivity was higher, and had the advantage of less invasive sample collection from patients for whom a spontaneous sputum sample was unavailable. With low risk of cross contamination, the STNPCR can be used as an adjunct to conventional methods for diagnosing TB.

Zika virus in Brazil and the danger of infestation by Aedes (Stegomyia) mosquitoes

Abstract Zika virus, already widely distributed in Africa and Asia, was recently reported in two Northeastern Brazilian: State of Bahia and State of Rio Grande do Norte, and one Southeastern: State of São Paulo. This finding adds a potentially noxious virus to a list of several other viruses that are widely transmitted by Aedes (Stegomyia) aegypti and Aedes (Stegomyia) albopictus in Brazil. The pathology and epidemiology, including the distribution and vectors associated with Zika virus, are reviewed. This review is focused on viruses transmitted by Aedes (Stegomyia) mosquitoes, including dengue, Chikungunya, Zika, Mayaro, and yellow fever virus, to emphasize the risks of occurrence for these arboviruses in Brazil and neighboring countries. Other species of Aedes (Stegomyia) are discussed, emphasizing their involvement in arbovirus transmission and the possibility of adaptation to environments modified by human activities and introduction in Brazil.

Two decades of tuberculosis in a city in Northeastern Brazil: advances and challenges in time and space

Abstract: INTRODUCTION This study presents two decades of epidemiological data on tuberculosis (TB), in order to understanding the disease profile and its spatiotemporal dynamics. METHODS This descriptive study was performed in the City of Olinda/Pernambuco, Brazil, from 1991-2010, and it analyzed new patients with TB living in the city. We used the χ²-test with a p-value <0.05 to identify differences in trends. Incidence and cluster distribution were identified using spatial scan statistics. RESULTS In total, 6202 new cases were recorded during the two decades. The highest incidence occurred in 1995 (110 cases/100,000 inhabitants), and the lowest occurred in 2009 (65 cases/100,000 inhabitants) (β=-1.44; R²=0.43; p=0.0018). The highest mortality occurred in 1998 (16 deaths/100,000 inhabitants), and the lowest occurred in 2008 (5 deaths/100,000 inhabitants) (β=-0.19; R²=0.17; p=0.07). There was a male predominance (65%), and ages ranged from 20-49 years (65%). There was a substantial increase in the number of patients that were cured after treatment (60% to 67%; p<0.001) as well as those tested for HIV (1.9% to 58.5%; p<0.001). During the first decade, clusters with p-values <0.05 included 29% of the total notified cases, and in the second decade, that percentage was 12%. CONCLUSIONS We observed a decreasing trend in incidence, which was significant, and mortality rates, which was not significant. The increased number of laboratory tests performed reflects advances in surveillance, and a reduction in the proportion of cases in primary clusters suggests, among other things, that the disease is spreading across the region.

Quantitative analysis of collagen and elastic fibers in the transversalis fascia in direct and indirect inguinal hernia

PURPOSE: Our previous studies demonstrated structural and quantitative age-related changes of the elastic fibers in transversalis fascia, which may play a role in inguinal hernia formation. To verify whether there were differences in the extracellular matrix between direct and indirect inguinal hernia, we studied the amount of collagen and elastic fibers in the transversalis fascia of 36 male patients with indirect inguinal hernia and 21 with direct inguinal hernia. MATERIAL AND METHODS: Transversalis fascia fragments were obtained during surgical intervention and underwent histological quantitative analysis of collagen by colorimetry and analysis of elastic fibers by histomorphometry. RESULTS: We demonstrated significantly lower amounts of collagen and higher amounts of elastic fibers in transversalis fascia from patients with direct inguinal hernia compared to indirect inguinal hernia patients. The transversalis fascia from direct inguinal hernia patients showed structural changes of the mature and elaunin elastic fibers, which are responsible for elasticity, and lower density of oxytalan elastic fibers, which are responsible for resistance. These changes promoted loss of resiliency of the transversalis fascia. CONCLUSION: These results improve our understanding of the participation of the extracellular matrix in the genesis of direct inguinal hernia, suggesting a relationship with genetic defects of the elastic fiber and collagen synthesis.

Microsatellite instability in solitary and sporadic gastric cancer

Recently, the presence of microsatellite instability (MSI) has been reported in gastric cancer and associated with older age of presentation, distal tumor location, early disease staging, and better overall prognosis. Different characteristics in presentation and in tumor behavior may be explained by different genetic alterations during carcinogenesis of gastric cancer. Identification of specific genetic pathways in gastric cancer may have direct impact on prognosis and selection of treatment strategies. PATIENTS AND METHODS: All 24 patients were treated by radical surgery. Fragments of normal and tumor tissues were extracted from the specimen and stored at -80ºC before DNA purification and extraction. PCR amplification utilizing microsatellite markers was performed. Tumors presenting PCR products of abnormal sizes were considered positive for microsatellite instability (MSI+). RESULTS: Five patients (21%) had tumors that were MSI+ in at least 1 marker. In the group of patients with Lauren's intestinal-type gastric carcinoma, 3 had tumors that were MSI+ (23%), while in the group of diffuse-type gastric cancer, 2 patients had tumors that were MSI+ (19%). The mean age of presentation and the male:female ratio was similar in both groups. Tumors that were MSI+ were more frequently located in proximal portion of the stomach compared to microsatellite-stable (MSS) tumors (40% vs. 16%). Although there was a trend of patients with MSI+ tumors towards a proximal gastric tumor location, early staging, and negative lymph node metastasis, there was no statistical significance compared to those with MSS tumors (P >.1). Comparison of overall and disease-free survival between gastric tumors that were MSI+ and those that were MSS found no statistically significant differences (P >.1). CONCLUSIONS: Microsatellite instability is a frequent event in gastric carcinogenesis and shows a trend towards distinct clinical and pathological characteristics of gastric cancer.

Small mammal abundances in isolated and non-isolated primary forest reserves near Manaus, Brazil

Abundances of msmall terrestrial mammals were estimated in 10 and 100-ha, isolated and non-isolated primary forest reserves near, Manaus, Brazil between October 1983 and March 1984. The smalt mammal abundance pattern In a 10 ha reserve isolated fan appoximately three years differed significantly from that in othen reserves, primarily due to higher capture rates of Marmosa cinerea, Rhipidomys mastacalis, and Onyzomys paricola in the isolated reserve. Viet type and re-invasion potential may be important factors the small mammal communities in forest patches. Variation the small mammal community among othen reserves was pnimanlty due to variatton In the abundances of Proechimys and 0. capito. At least pant of this vantation was attributable to temporal efects, but variation due to reserve effects also was suggested. Small mammals were much more abundant in the reserves during the present study than in 1982.

EARTHWORM ACTIVITY IN FOREST AND SAVANNA SOILS NEAR BOA VISTA, RORAIMA, BRAZIL

From May to December, 1992 we studied the earthworm activity, as part of the ECOFIT Program at Surrão ( 30km from Boa Vista), verifying the duration of the activity and quantifying it through the casts deposited on the soil surface. Three transects were stablished: a 100m long in the savanna, a 40m in the transitional area and 100m long in the forest. Specimens were collected monthly along the transects according to the method proposed by TSBF and the casts were collected from the squares previously placed on the transects. Two earthworm species were found in the three areas: Pontoscolex roraìmensis and Pontoscolex corethrurus. The first species depositing its casts on the soil surface. Rainy season wich usually occurs from April to August, determined the duration of activity for the two species (however, 1992 was atypical in that rainy season, only started in May). P. roraìmensis produced casts in the three areas from May to August followed by aestivation. In the savanna, P. corethrurus started aestivation in the same period as P. roraìmensis but remained active until November in the two other areas. P. roraìmensiswas found up 50m from the forest border, being associated to the presence of Curatella americana and Byrsonima sp, two typical savanna bushes.

Changes in population and land use over time in the Ecuadorian Amazon

This paper draws upon a detailed longitudinal survey of households living on agricultural plots in the northern three provinces of the Ecuadorian Amazon, the principal region of colonization by migrants in Ecuador since the 1970s. Following the discovery of petroleum in 1967 near what has subsequently come to be the provincial capital and largest Amazonian city of Lago Agrio, oil companies built roads to lay pipelines to extract and pump oil across the Andes for export. As a result, for the past 30 years over half of both Ecuador's export earnings and government revenues have come from petroleum extracted from this region. But the roads also facilitated massive spontaneous in-migration of families from origin areas in the Ecuadorian Sierra, characterized by minifundia and rural poverty. This paper is about those migrants and their effects on the Amazonian landscape. We discuss the data collection methodology and summarize key results on settler characteristics and changes in population, land use, land ownership, technology, labor allocation, and living conditions, as well as the relationships between changes in population and changes in land use over time. The population in the study region has been growing rapidly due to both natural population growth (high fertility) and in-migration. This has led to a dramatic process of subdivision and fragmentation of plots in the 1990's, which contrasts with the consolidation of plots that has occurred in most of the mature frontier areas of the Brazilian Amazon. This fragmentation has led to important changes in land tenure and land use, deforestation, cattle raising, labor allocation, and settler welfare.

A structured inventory of spiders (Arachnida, Araneae) in natural and artificial forest gaps at Porto Urucu, Western Brazilian Amazonia

A preliminary survey of the spider fauna in natural and artificial forest gap formations at “Porto Urucu”, a petroleum/natural gas production facility in the Urucu river basin, Coari, Amazonas, Brazil is presented. Sampling was conducted both occasionally and using a protocol composed of a suite of techniques: beating trays (32 samples), nocturnal manual samplings (48), sweeping nets (16), Winkler extractors (24), and pitfall traps (120). A total of 4201 spiders, belonging to 43 families and 393 morphospecies, were collected during the dry season, in July, 2003. Excluding the occasional samples, the observed richness was 357 species. In a performance test of seven species richness estimators, the Incidence Based Coverage Estimator (ICE) was the best fit estimator, with 639 estimated species. To evaluate differences in species richness associated with natural and artificial gaps, samples from between the center of the gaps up to 300 meters inside the adjacent forest matrix were compared through the inspection of the confidence intervals of individual-based rarefaction curves for each treatment. The observed species richness was significantly higher in natural gaps combined with adjacent forest than in the artificial gaps combined with adjacent forest. Moreover, a community similarity analysis between the fauna collected under both treatments demonstrated that there were considerable differences in species composition. The significantly higher abundance of Lycosidae in artificial gap forest is explained by the presence of herbaceous vegetation in the gaps themselves. Ctenidae was significantly more abundant in the natural gap forest, probable due to the increase of shelter availability provided by the fallen trees in the gaps themselves. Both families are identified as potential indicators of environmental change related to the establishment or recovery of artificial gaps in the study area.

Diversity of sand flies in domiciliary environment of Santarém, state of Pará, Brazil: species composition and abundance patterns in rural and urban areas

This paper aimed to evaluate the richness, abundance and frequency of sand fly occurrence in rural and urban areas American visceral Leishmaniasis -AVL is endemic in the study area of Santarém municipality, Pará state. Sand flies were collected during 1995-2000, using CDC light traps placed in neighborhoods and rural areas of the municipality. A total of 53.454 individuals and 26 species of sand flies were collected. The most abundant species in both urban and rural environments was Lutzomyia longipalpis, vector of AVL in the area. The highest species richness by capture was in rural area. In all years sampled, the largest number of species of sand fly collected was always in rural areas. The species of sand flies in urban and rural area were similar in 11 species. In the rural area other 11 species were found, a total of 22 species. Shannon-Wiener index ranged from 0.12 to 0.84 at rural areas and 0.08 to 0.34 at urban ones. In general, rural localities showed higher diversity (H') of phlebotomines than urban ones. Individual-based rarefaction curves for each area demonstrated that urban localities had the lowest expected number of phlebotomine species and the richest rural ones reach higher expected values with lower amount of individuals than urban sites. The most frequent species were Lutzomyia longipalpis, Evandromyia carmelinoi and Bichromomyia flaviscutellata.

Litterfall production in intact and selectively logged forests in southern of Amazonia as a function of basal area of vegetation and plant density

Nutrient recycling in the forest is linked to the production and decomposition of litter, which are essential processes for forest maintenance, especially in regions of nutritionally poor soils. Human interventions in forest such as selecttive logging may have strong impacts on these processes. The objectives of this study were to estimate litterfall production and evaluate the influence of environmental factors (basal area of vegetation, plant density, canopy cover, and soil physicochemical properties) and anthropogenic factors (post-management age and exploited basal area) on this production, in areas of intact and exploited forest in southern Amazonia, located in the northern parts of Mato Grosso state. This study was conducted at five locations and the average annual production of litterfall was 10.6 Mg ha-1 year-1, higher than the values for the Amazon rainforest. There were differences in litterfall productions between study locations. Effects of historical logging intensity on litterfall production were not significant. Effects of basal area of vegetation and tree density on litterfall production were observed, highlighting the importance of local vegetation characteristics in litterfall production. This study demonstrated areas of transition between the Amazonia-Cerrado tend to have a higher litterfall production than Cerrado and Amazonia regions, and this information is important for a better understanding of the dynamics of nutrient and carbon cycling in these transition regions.

Migration and mental health: Japanese Brazilians in Japan and in Brazil

OBJECTIVE: Brazil is the country with the largest community of Japanese descendants in the world, from a migration movement that started in 1908. However, more recently (1988), a movement in the opposite direction began. Many of these descendants went to Japan for work purposes and suffered mental distress. Some of them sought treatment in Japan, while others returned to Brazil to seek treatment. The aim of the present study was to compare the sociodemographic profile and diagnoses of Japanese Brazilian psychiatric outpatients in Japan (remaining group) and in Brazil (returning group). METHOD: All consecutive Japanese Brazilian outpatients who received care from the psychiatric units in Japan and Brazil from April 1997 to April 2000 were compared. The diagnoses were based on ICD-10 and were made by psychiatrists. Sociodemographic data and diagnoses in Brazil and Japan were compared by means of the Chi-Squared Test. RESULTS: The individuals who returned to Brazil were mostly male and unmarried, had lived alone in Japan, had stayed there for short periods and were classified in the schizophrenia group. The individuals who remained in Japan were mostly female and married, were living with family or friends, had stayed there for long periods and were classified in the anxiety group. Logistic regression showed that the most significant factors associated with the returning group were that they had lived alone and stayed for short periods (OR = 0.93 and 40.21, respectively). CONCLUSION: We conclude that living with a family and having a network of friends is very important for mental health in the context evaluated.

Reliability and convergent validity of the Childhood Anxiety Sensitivity Index in children and adolescents

OBJECTIVE: The purpose of this study was to examine the reliability and the convergent validity of the Children Anxiety Sensitivity Index (CASI) with DSM-IV anxiety disorder symptoms, by comparison with the Screen for Child Anxiety Related Emotional Disorders (SCARED), in a community sample of Brazilian children and adolescents. METHODS: Children and adolescents from five schools were selected from a larger study that aimed to assess different aspects of childhood anxiety disorders. All participants completed the CASI and the SCARED. RESULTS: This study supported the reliability of the CASI total score. Girls reported higher total anxiety sensitivity scores than boys and there were no differences in total anxiety sensitivity scores between children and adolescents. This study showed moderate to high correlations between the CASI scores with SCARED scores, all correlations coefficients being positive and significant. CONCLUSIONS: Our findings demonstrate an appropriate reliability and evidence of convergent validity in the CASI in a sample of Brazilian children and adolescents.

Cognitive-behavioral therapy for anxiety disorders in children and adolescents: a systematic review of follow-up studies

Objective To conduct a systematic review about the long-term response to cognitive-behavioral therapy (CBT) for anxiety disorders (ADs) in children and adolescents. Methods The PubMed and ISI Web of Science databases were consulted. Search in the databases was performed in November 2012 and included cohort studies after CBT for ADs in children and adolescents with a follow-up period over 12 months. Results A total of 10 papers met the inclusion criteria. The follow-up period ranged from 12 months to 13 years and the results generally showed maintenance of the short-term benefits with CBT. However, the studies presented limitations, especially regarding methods, such as lack of a control group and losses to follow-up. Conclusion The long-term benefits of CBT were identified, however it would be interesting to conduct other studies with more frequent assessment periods, in order to minimize losses to follow-up, in addition to evaluating children and adolescents in the various stages of their development.

Virtual reality in assessment and treatment of schizophrenia: a systematic review

Objective To conduct a systematic review about the use of virtual reality (VR) for evaluation, treatment and/or rehabilitation of patients with schizophrenia, focused on: areas, fields and objectives; methodological issues; features of the VR used; viability and efficiency of this resource. Methods Searches were performed about schizophrenia and virtual reality in PsycINFO, Academic Search Complete, MEDLINE Complete, CINAHL with Full Text, Web of Science and Business Source Premier databases, using the following keywords: [“schizophrenia”] AND [“virtual reality” OR “serious game”] AND [“treatment” OR “therapy” OR “rehabilitation”]. The search was carried out between November 2013 and June 2014 without using any search limiters. Results A total of 101 papers were identified, and after the application of exclusion criteria, 33 papers remained. The studies analysed focused on the use of VR for the evaluation of cognitive, social, perceptual and sensory skills, and the vast majority were experimental studies, with virtual reality specifically created for them. All the reviewed papers point towards a reliable and safe use of VR for evaluating and treating cognitive and social deficits in patients with schizophrenia, with different results in terms of generalisation, motivation, assertiveness and task participation rate. Some problems were highlighted, such as its high cost and a constant need for software maintenance. Conclusion The studies show that using the virtual reality may streamline traditional evaluation/rehabilitation programmes, allowing to enhance the results achieved, both in the cognitive and in the social field, helping for the legitimisation of this population’s psycho-social inclusion.