Full-genome sequences of hepatitis B virus subgenotype D3 isolates from the Brazilian Amazon Region

The Brazilian Amazon Region is a highly endemic area for hepatitis B virus (HBV). However, little is known regarding the genetic variability of the strains circulating in this geographical region. Here, we describe the first full-length genomes of HBV isolated in the Brazilian Amazon Region; these genomes are also the first complete HBV subgenotype D3 genomes reported for Brazil. The genomes of the five Brazilian isolates were all 3,182 base pairs in length and the isolates were classified as belonging to subgenotype D3, subtypes ayw2 (n = 3) and ayw3 (n = 2). Phylogenetic analysis suggested that the Brazilian sequences are not likely to be closely related to European D3 sequences. Such results will contribute to further epidemiological and evolutionary studies of HBV.

The prevalence of norovirus, astrovirus and adenovirus infections among hospitalised children with acute gastroenteritis in Porto Velho, state of Rondônia, western Brazilian Amazon

Although viruses are well-established causes of acute gastroenteritis, few data on the circulation of these pathogens in Porto Velho, state of Rondônia, Brazil, are available. Thus, faecal samples from hospitalised diarrhoeic children, under six years of age, were collected and tested for the presence of norovirus (NoV), adenovirus (AdV) and astrovirus (AstV) from February 2010-February 2012. Specimens were screened by reverse-transcription polymerase chain reaction and viruses were found in 10.7% (63/591) of the cases. NoV, AdV and AstV were detected in 7.8%, 2% and 0.8% of the samples, respectively. NoV infection was observed at all ages and was most prevalent in zero-18-month-old children (84.7%; p = 0.002). A higher incidence of NoV was detected from February-April 2010, when it was found in 52.2% of the cases. Co-infections involving these viruses, rotavirus and enteropathogenic bacteria were detected in 44.4% (28/63) of the children with viral diarrhoea. Nosocomial infections were demonstrated in 28.6% (18/63) of the cases in which viruses were detected. The present paper reports, for the first time, the circulation of NoV and AstV among the paediatric population of Porto Velho and it contributes to our understanding of the roles of these pathogens in gastrointestinal infections.

New classification of natural breeding habitats for Neotropical anophelines in the Yanomami Indian Reserve, Amazon Region, Brazil and a new larval sampling methodology

Here we present the first in a series of articles about the ecology of immature stages of anophelines in the Brazilian Yanomami area. We propose a new larval habitat classification and a new larval sampling methodology. We also report some preliminary results illustrating the applicability of the methodology based on data collected in the Brazilian Amazon rainforest in a longitudinal study of two remote Yanomami communities, Parafuri and Toototobi. In these areas, we mapped and classified 112 natural breeding habitats located in low-order river systems based on their association with river flood pulses, seasonality and exposure to sun. Our classification rendered seven types of larval habitats: lakes associated with the river, which are subdivided into oxbow lakes and nonoxbow lakes, flooded areas associated with the river, flooded areas not associated with the river, rainfall pools, small forest streams, medium forest streams and rivers. The methodology for larval sampling was based on the accurate quantification of the effective breeding area, taking into account the area of the perimeter and subtypes of microenvironments present per larval habitat type using a laser range finder and a small portable inflatable boat. The new classification and new sampling methodology proposed herein may be useful in vector control programs.

Surveillance, health promotion and control of Chagas disease in the Amazon Region - Medical attention in the Brazilian Amazon Region: a proposal

We refer to Oswaldo Cruz’s reports dating from 1913 about the necessities of a healthcare system for the Brazilian Amazon Region and about the journey of Carlos Chagas to 27 locations in this region and the measures that would need to be adopted. We discuss the risks of endemicity of Chagas disease in the Amazon Region. We recommend that epidemiological surveillance of Chagas disease in the Brazilian Amazon Region and Pan-Amazon region should be implemented through continuous monitoring of the human population that lives in the area, their housing, the environment and the presence of triatomines. The monitoring should be performed with periodic seroepidemiological surveys, semi-annual visits to homes by health agents and the training of malaria microscopists and healthcare technicians to identify Trypanosoma cruzi from patients’ samples and T. cruzi infection rates among the triatomines caught. We recommend health promotion and control of Chagas disease through public health policies, especially through sanitary education regarding the risk factors for Chagas disease. Finally, we propose a healthcare system through base hospitals, intermediate-level units in the areas of the Brazilian Amazon Region and air transportation, considering the distances to be covered for medical care.

Correlation between TH1 response standard cytokines as biomarkers in patients with the delta virus in the western Brazilian Amazon

Hepatitis D virus (HDV) is endemic in the Amazon Region and its pathophysiology is the most severe among viral hepatitis. Treatment is performed with pegylated interferon and the immune response appears to be important for infection control. HDV patients were studied: untreated and polymerase chain reaction (PCR) positive (n = 9), anti-HDV positive and PCR negative (n = 8), and responders to treatment (n = 12). The cytokines, interleukin (IL)-2 (p = 0.0008) and IL-12 (p = 0.02) were differentially expressed among the groups and were also correlated (p = 0.0143). Future studies will be conducted with patients at different stages of treatment, associating the viral load with serum cytokines produced, thereby attempting to establish a prognostic indicator of the infection.

Complete genome sequence of Deltapapillomavirus 4 (bovine papillomavirus 2) from a bovine papillomavirus lesion in Amazon Region, Brazil

The complete genome sequence of bovine papillomavirus 2 (BPV2) from Brazilian Amazon Region was determined using multiple-primed rolling circle amplification followed by Illumina sequencing. The genome is 7,947 bp long, with 45.9% GC content. It encodes seven early (E1, E2,E4, E5, E6,E7, and E8) and two late (L1 and L2) genes. The complete genome of a BPV2 can help in future studies since this BPV type is highly reported worldwide although the lack of complete genome sequences available.

Amazon Fund: financing deforestation avoidance

The Amazon Fund, created in 2008 by the Brazilian Federal Government, is managed by Banco Nacional de Desenvolvimento Econômico e Social (BNDES). It is a pioneering initiative to fundraise and manage financial resources to cut back deforestation and support sustainable development for 30 million inhabitants in the Amazon Biome. The Amazon Fund has already received more than R$ 1.7 billion in grants (about USD 787 million). This essay analyzes the Amazon Fund's governance and management with focus on its operation and from its stakeholders' perspectives. A combination of research methods includes: documental research, in-depth interviews, and speech analysis. The study offers a comparative analysis of strengths and weaknesses related to its governance. Furthermore, it proposes ways to improve its management towards greater effectiveness. The essay also includes an assessment of the government of Norway, a major donor to the fund. The governments of Norway and Germany, in partnership with Brazil, reveal how important it is to experiment with new means of international cooperation to successfully reduce greenhouse gas emissions through rainforest preservation.

Cas d'ús HTCondor & Amazon EC2

En aquest Treball Final de Grau s'ha implementat un clúster d'alta eficiència (HTC) amb nodes físics d'una aula d'informàtica i nodes virtuals a partir d'instàncies d'Amazon EC2 (Elastic Compute Cloud). Mitjançant la creació de dos bash scripts es gestionarà la posada en marxa dels nodes del clúster, tant físics com virtuals, per tal d'optimitzar l'ús dels recursos físics, reduir el cost energètic i disposar de la flexibilitat que ofereix el sistema de màquines virtuals d'Amazon EC2.

Improving the organisation and commercialisation of small coffee and cocoa producers in the Northern Amazon Region of Ecuador

Coffee and cocoa represent the main sources of income for small farmers in the Northern Amazon Region of Ecuador. The provinces of Orellana and Sucumbios, as border areas, have benefited from investments made by many public and private institutions. Many of the projects carried out in the area have been aimed at energising the production of coffee and cocoa, strengthening the producers’ associations and providing commercialisation infrastructure. Improving the quality of life of this population threatened by poverty and high migration flows mainly from Colombia is a significant challenge. This paper presents research highlighting the importance of associative commercialisation to raising income from coffee and cocoa. The research draws on primary information obtained during field work, and from official information from the Ministry of Agriculture. The study presents an overview of current organisational structures, initiatives of associative commercialisation, stockpiling of infrastructure and ownership regimes, as well as estimates for both ‘robusta’ coffee and national cocoa production and income. The analysis of the main constraints presents different alternatives for the implementation of public land policies. These policies are aimed at mitigating the problems associated with the organisational structure of the producers, with processes of commercialisation and with environmental aspects, among others.

Activities of tabanids (Diptera, Tabanidae) attacking domestic duck-Cairina moschata (Linnaeus) (Aves, Anatidae), introduced in a forest area in the Central Amazon, Manaus, Brazil

Presented here are the feeding habits, attack behavior, daily and annual activity of adult of Phorcotabanus cinereus (Wiedeman, 1821), Chrysops laetus (Fabricius, 1805) and Phaeotabanus cajennensis (Fabricius, 1787), while biting a domestic duck, Cairina moschata (Linnaeus, 1758). The last two species were recorded for the first time attacking birds. This study comprehended monthly observations of two consecutive days from April/97 to March/98 between 5:30 a.m. and 6:30 p.m. at the Army Instructional Base ((BI-2/CIGS) near Manaus. Annual occurrence of P. cinereus was from July to September, with a daily occurrence between 9:00 a.m. and 5:00 p.m. and highest activity at 12:00 a.m. and 2:00 p.m. C. laetus ocurred from June to October; with a daily occurrence between 8:00 a.m. and 3 p.m. and highest activity at 11:00 and 12:00 a.m. Occurrence of P. cajennensis with one specimen only, was in July between 10:00 and 11:00 a.m.

A new species of the genus Pimelerodius Vanin from the Amazon Region, with notes on the geografic distribution of Pimelerodius motacilla (Boheman) (Coleoptera, Curculionidae, Otidocephalini)

Pimelerodius punctiventris sp. nov. (type locality Brazil, Amazonas, Itacoatiara) is described and illustrated. The new taxon is compared with similar species, being distinguished from the other 12 known species of the genus by the presence of punctures in ventrite I. The available published key for identification of species of Pimelerodius is adapted to include the new species. A modification of the generic description of the aedeagus of Pimelerodius is provided, a necessity due to the differences observed in the aedeagus of the new species. The occurrence of P. motacilla (Boheman, 1843) in the Amazon Region, recorded in sympatry with P. punctiventris in Itacoatiara, AM, is discussed and confirmed, based on the study of 41 available specimens.

A synopsis of the Hydrometra (Hemiptera, Heteroptera, Hydrometridae) from the Amazon River floodplain, Brazil, with redescription of Hydrometra argentina Berg

Hydrometra argentina Berg, 1879, H. caraiba Guérin-Méneville, 1857 and H. guianana Hungerford & Evans, 1934 are newly recorded in the Amazon River floodplain, Brazil. A redescription of H. argentina is also given, as the original description is incomplete. A key to the three known species occurring in this region is provided. Hydrometra argentina can be distinguished from H. caraiba and H. guianana by the body length smaller than 12.50 mm, anteoculus/postoculus ratio between 1.80 and 2.00, clypeus narrow and conical, metacetabulum with no circular pits, and projections on male abdominal sternite VI in the shape of simple spines. The other species can be distinguished mainly by the anteoculus/postoculus ratio and position of projections on male abdominal sternite VI.

Weighted metric multidimensional scaling

This paper establishes a general framework for metric scaling of any distance measure between individuals based on a rectangular individuals-by-variables data matrix. The method allows visualization of both individuals and variables as well as preserving all the good properties of principal axis methods such as principal components and correspondence analysis, based on the singular-value decomposition, including the decomposition of variance into components along principal axes which provide the numerical diagnostics known as contributions. The idea is inspired from the chi-square distance in correspondence analysis which weights each coordinate by an amount calculated from the margins of the data table. In weighted metric multidimensional scaling (WMDS) we allow these weights to be unknown parameters which are estimated from the data to maximize the fit to the original distances. Once this extra weight-estimation step is accomplished, the procedure follows the classical path in decomposing a matrix and displaying its rows and columns in biplots.

Culicidae (Diptera, Culicomorpha) from the western Brazilian Amazon: Juami-Japurá Ecological Station

With 312 trap-hours of sampling effort, 1554 specimens of Culicidae (Diptera) were collected, using CDC and Malaise traps, in nine different locations along the Juami River, within the Juami-Japurá Ecological Station, Amazonas State, Brazil. A list of mosquito species with 54 taxa is presented, which includes three new distributional records for the state of Amazonas. The species found belong to the genera Anopheles, Aedeomyia, Aedes, Psorophora, Culex, Coquillettidia, Sabethes, Wyeomyia and Uranotaenia.

Richardia Robineau-Desvoidy (Diptera, Tephritoidea, Richardiidae) from Central Amazon, Brazil

Richardia Robineau-Desvoidy (Diptera, Tephritoidea, Richardiidae) from Central Amazon, Brazil. There are 11 species of Richardia known to Brazil. Of these, only four are known to occur in the Brazilian Amazon Region, where the diversity of Richardia is underestimated. Herein we describe and illustrate Richardia intemperata sp. nov. and Richardia parispina sp. nov. from Amazonas, Brazil. An illustrated key to males from this region is also provided.