An appropriate data set size for digital soil mapping in Erechim, Rio Grande do Sul, Brazil

Digital information generates the possibility of a high degree of redundancy in the data available for fitting predictive models used for Digital Soil Mapping (DSM). Among these models, the Decision Tree (DT) technique has been increasingly applied due to its capacity of dealing with large datasets. The purpose of this study was to evaluate the impact of the data volume used to generate the DT models on the quality of soil maps. An area of 889.33 km² was chosen in the Northern region of the State of Rio Grande do Sul. The soil-landscape relationship was obtained from reambulation of the studied area and the alignment of the units in the 1:50,000 scale topographic mapping. Six predictive covariates linked to the factors soil formation, relief and organisms, together with data sets of 1, 3, 5, 10, 15, 20 and 25 % of the total data volume, were used to generate the predictive DT models in the data mining program Waikato Environment for Knowledge Analysis (WEKA). In this study, sample densities below 5 % resulted in models with lower power of capturing the complexity of the spatial distribution of the soil in the study area. The relation between the data volume to be handled and the predictive capacity of the models was best for samples between 5 and 15 %. For the models based on these sample densities, the collected field data indicated an accuracy of predictive mapping close to 70 %.

Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies

The analysis of genetic data for human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1) is essential to improve treatment and public health strategies as well as to select strains for vaccine programs. However, the analysis of large quantities of genetic data requires collaborative efforts in bioinformatics, computer biology, molecular biology, evolution, and medical science. The objective of this study was to review and improve the molecular epidemiology of HIV-1 and HTLV-1 viruses isolated in Brazil using bioinformatic tools available in the Laboratório Avançado de Sáude Pública (Lasp) bioinformatics unit. The analysis of HIV-1 isolates confirmed a heterogeneous distribution of the viral genotypes circulating in the country. The Brazilian HIV-1 epidemic is characterized by the presence of multiple subtypes (B, F1, C) and B/F1 recombinant virus while, on the other hand, most of the HTLV-1 sequences were classified as Transcontinental subgroup of the Cosmopolitan subtype. Despite the high variation among HIV-1 subtypes, protein glycosylation and phosphorylation domains were conserved in the pol, gag, and env genes of the Brazilian HIV-1 strains suggesting constraints in the HIV-1 evolution process. As expected, the functional protein sites were highly conservative in the HTLV-1 env gene sequences. Furthermore, the presence of these functional sites in HIV-1 and HTLV-1 strains could help in the development of vaccines that pre-empt the viral escape process.

Mapping the Obama administration's response to the Arab Spring

When the Arab Spring broke out, the United States was in a quandary over how to handle the crisis in its attempt to balance its moral obligations and ideals without undercutting its strategic interests and those of its close allies. Flaws in US diplomatic approach have contributed to one of the most serious foreign policy crisis for a US administration to date with consequential upheaval and erosion of the US-built balance of power. The reactions and policy responses of the Obama administration highlight the difficulties in grasping with the new reality in the Middle East and in enunciating a policy platform that could combine American interests and values.

HIV testing and clinical status upon admission to a specialized health care unit in Pará, Brazil

OBJECTIVE To analyze the clinical and laboratory characteristics of HIV-infected individuals upon admission to a reference health care center.METHODS This cross-sectional study was conducted between 1999 and 2010 on 527 individuals with confirmed serological diagnosis of HIV infection who were enrolled in an outpatient health care service in Santarém, PA, Northern Brazil. Data were collected from medical records and included the reason for HIV testing, clinical status, and count of peripheral CD4+ T lymphocytes upon enrollment. The data were divided into three groups, according to the patient’s year of admission – P1 (1999-2002), P2 (2003-2006), and P3 (2007-2010) – for comparative analysis of the variables of interest.RESULTS In the study group, 62.0% of the patients were assigned to the P3 group. The reason for undergoing HIV testing differed between genders. In the male population, most tests were conducted because of the presence of symptoms suggesting infection. Among women, tests were the result of knowledge of the partner’s seropositive status in groups P1 and P2. Higher proportion of women undergoing testing because of symptoms of HIV/AIDS infection abolished the difference between genders in the most recent period. A higher percentage of patients enrolling at a more advanced stage of the disease was observed in P3.CONCLUSIONS Despite the increased awareness of the number of HIV/AIDS cases, these patients have identified their serological status late and were admitted to health care units with active disease. The HIV/AIDS epidemic in Pará presents specificities in its progression that indicate the complex characteristics of the epidemic in the Northern region of Brazil and across the country.

Legionnaires' disease in the renal transplant unit of "Hospital das Clinicas, FMUSP": during a five year period (1988-1993)

Several reports have related Legionella pneumophila with pneumonia in renal transplant patients, however this association has not been systematically documented in Brazil. Therefore this paper reports the incidence, by serologycal assays, of Legionella pneumophila serogroup 1 in these patients during a five year period. For this purpose sera from blood samples of 70 hospitalized patients with pneumonia from the Renal Transplant Unit of Hospital das Clinicas, FMUSP collected at the acute and convalescent phase of infection were submitted to indirect immunofluorescence assay (IFA) to demonstrate anti-Legionella pneumophila serogroup 1 antibodies. Of these 70 patients studied during the period of 1988 to 1993,18 (25.71 %) had significant rises in specific antibody titers for Legionella pneumophila serogroup 1. Incidence was interrupted following Hospital water decontamination procedures, with recurrence of infections after treatment interruption. In this study, the high susceptibility (25.71%) of immunodepressed renal transplant patients to Legionella pneumophila serogroup 1 nosocomial infections is documented. The importance of the implementation and maintenance of water decontamination measures for prophylaxis of the infection is also clearly evident.

Congenital cytomegalovirus infection in a neonatal intensive care unit in Brazil evaluated by PCR and association with perinatal aspects

Cytomegalovirus (CMV) infection is the most common congenital infection, affecting 0.4% to 2.3% newborns. Most of them are asymptomatic at birth, but later 10% develop handicaps, mainly neurological disturbances. Our aim was to determine the prevalence of CMV shed in urine of newborns from a neonatal intensive care unit using the polymerase chain reaction (PCR) and correlate positive cases to some perinatal aspects. Urine samples obtained at first week of life were processed according to a PCR protocol. Perinatal data were collected retrospectively from medical records. Twenty of the 292 cases (6.8%) were CMV-DNA positive. There was no statistical difference between newborns with and without CMV congenital infection concerning birth weight (p=0.11), gestational age (p=0.11), Apgar scores in the first and fifth minutes of life (p=0.99 and 0.16), mother's age (p=0.67) and gestational history. Moreover, CMV congenital infection was neither related to gender (p=0.55) nor to low weight (<2,500g) at birth (p=0.13). This high prevalence of CMV congenital infection (6.8%) could be due to the high sensitivity of PCR technique, the low socioeconomic level of studied population or the severe clinical status of these newborns.

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

Pentamidine (PEN) is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK) into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

Lack of methicillin-resistant Staphylococcus aureus nasal carriage among patients at a primary-healthcare unit in Porto Alegre, Brazil

INTRODUCTION: Community-associated methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a pathogen in individuals without traditional risk factors. MATERIAL AND METHODS: MRSA nasal carriage was assessed in individuals consulting at a Primary Health Unit in Brazil. RESULTS: A total of 336 individuals were included: 136 were tested only for MRSA and 200 for any S. aureus. No MRSA was found among the 336 individuals and 23 (11.5%) of 200 were colonized by S. aureus. DISCUSSION: Low prevalence rates have been found in non-hospitalized individuals, but MRSA surveillance should be encouraged to monitor clinical and molecular epidemiology of CA- MRSA.

HIV-1-mother-to-child transmission and associated characteristics in a public maternity unit in Presidente Prudente, Brazil

In children, vertical transmission is the main form of HIV infection. Our aim was to determine the prevalence of HIV-1 vertical transmission in mother-infant pairs in a public maternity ward in Presidente Prudente, SP. Additionally; we sought to identify characteristics associated with this form of transmission. The files of 86 HIV-1-infected mothers and their newborns referred to a Public Hospital from March 2002 to March 2007 were analyzed. The HIV-1-RNA viral load of the newborns was determined by bDNA. The HIV-1 vertical-transmission rate was 4.6%. Children that were born in the pre-term period and breastfed were at a higher risk of HIV-1 infection (p = 0.005 and p = 0.017 respectively) than children born at term and not breastfed. Prophylactic therapy with zidovudine after birth for newborns was associated with a lower risk of infection (p = 0.003). The number of newborns weighing < 2,500 g was significantly higher for infected children (p = 0.008) than for non-infected newborns. About 22.9% of mothers did not know the HIV-1 status of their newborns eight months after delivery. The study suggests that it is necessary to increase the identification of HIV-1 infection in pregnant women and their newborns as well as to offer and explain the benefits of ARV prophylaxis.

Toxocariasis in children attending a Public Health Service Pneumology Unit in Paraná State, Brazil

The enzyme-linked immunosorbent assay (ELISA) is the most widely used tool to detect anti-Toxocara IgG antibodies for both serodiagnostic and seroepidemiological surveys on human toxocariasis. In the last eight years a high prevalence of toxocariasis (32.2-56.0%) has been reported in children attending public health units from municipalities in the state of Paraná, Brazil. Therefore, the aim of this work was to compare the frequency found among the general child population with that of children attending a public pneumology service in Maringá, Paraná, Brazil and describe the laboratorial, clinical and epidemiological findings. The research was conducted at the Consórcio Público Intermunicipal de Saúde do Setentrião Paranaense (CISAMUSEP) from July 2009 to July 2010 among children aged between one and 15 years. From a total of 167 children studied, only 4.2% (7/167) tested positive for anti-Toxocara spp. IgG antibodies and presented mild eosinophilia (2/7), increased serum IgE levels (6/7) and a positive allergy test for mites (5/7). The presence of pets (dogs or cats) at home did not correlate with the seroprevalence. In conclusion, cases of toxocariasis involving the respiratory tract are rare in children attending a public health pneumology unit in the northwestern region of Paraná State, despite the high prevalence of this type of toxocariasis among the infantile population attending Basic Health Units in the same geographical area.

Nosocomial infections in a Brazilian neonatal intensive care unit: a 4-year surveillance study

INTRODUCTION: Report the incidence of nosocomial infections, causative microorganisms, risk factors associated with and antimicrobial susceptibility pattern in the NICU of the Uberlândia University Hospital. METHODS: Data were collected through the National Healthcare Safety Network surveillance from January 2006 to December 2009. The patients were followed five times/week from their birth to their discharge or death. RESULTS: The study included 1,443 patients, 209 of these developed NIs, totaling 293 NI episodes, principally bloodstream infections (203; 69.3%) and conjunctivitis (52; 17.7%). Device-associated infection rates were as follows: 17.3 primary bloodstream infections per 1,000 central line-days and 3.2 pneumonias per 1000 ventilator-days. The mortality rate in neonates with NI was 11.9%. Mechanical ventilation, total parenteral nutrition, orogastric tube, previous antibiotic therapy, use of CVC and birth weight of 751-1,000g appeared to be associated with a significantly higher risk of NI (p < 0.05). In multiple logistic regression analysis for NI, mechanical ventilation and the use of CVC were independent risk factors (p < 0.05). Coagulase- negative Staphylococcus (CoNS) (36.5%) and Staphylococcus aureus (23.6%) were the most common etiologic agents isolated from cultures. The incidences of oxacillin-resistant CoNS and S. aureus were 81.8% and 25.3%, respectively. CONCLUSIONS: Frequent surveillance was very important to evaluate the association of these well-known risk factors with NIs and causative organisms, assisting in drawing the attention of health care professionals to this potent cause of morbidity.

Enteric parasites in HIV-1/AIDS-infected patients from a Northwestern São Paulo reference unit in the highly active antiretroviral therapy era

INTRODUCTION: We describe the epidemiology of intestinal parasites in patients from an AIDS reference service in Northeastern São Paulo, Brazil. METHODS: Retrospective evaluation was done for all HIV-1/AIDS-positive patients whose Hospital de Base/São José do Rio Preto laboratorial analysis was positive for enteroparasites after diagnosis of HIV-1 infection, from January 1998 to December 2008. Statistical analysis was performed using the R statistical software version 2.4.1. The level of significance adopted was 5%. RESULTS: The most frequent protozoan was Isospora belli (4.2%), followed by Giardia lamblia (3.5%), Entamoeba coli (2.8%), and Cryptosporidium parvum (0.3%). Ancylostoma duodenale (1.4%) was the most frequently detected helminth, while Taenia saginata and Strongiloides stercoralis were found in 0.7% of the samples. The results showed that diarrhea was significantly associated with giardiasis and isosporiasis. However, no association was observed between CD4+ cell counts, viral load, and the characteristics of any particular parasite. CONCLUSIONS: Our data may be useful for further comparisons with other Brazilian regions and other developing countries. The data may also provide important clues toward improving the understanding, prevention, and control of enteric parasites around the world.

Mapping of Chagas disease research: analysis of publications in the period between 1940 and 2009

INTRODUCTION: Publications are often used as a measure of success in research work. Chagas disease occurs in Central and Southern America. However, during the past years, the disease has been occurring outside Latin America due to migration from endemic zones. This article describes a bibliometric review of the literature on Chagas disease research indexed in PubMed during a 70-year period. METHODS: Medline was used via the PubMed online service of the U.S. National Library of Medicine from 1940 to 2009. The search strategy was: Chagas disease [MeSH] OR Trypanosoma cruzi [MeSH]. RESULTS: A total of 13,989 references were retrieved. The number of publications increased steadily over time from 1,361 (1940-1969) to 5,430 (2000-2009) (coefficient of determination for linear fit, R²=0.910). Eight journals contained 25% of the Chagas disease literature. Of the publications, 64.2% came from endemic countries. Brazil was the predominant country (37%), followed by the United States (17.6%) and Argentina (14%). The ranking in production changed when the number of publications was normalized by estimated cases of Chagas disease (Panama and Uruguay), population (Argentina and Uruguay), and gross domestic product (Bolivia and Brazil). CONCLUSIONS: Several Latin American countries, where the prevalence of T. cruzi infection was not very high, were the main producers of the Chagas disease literature, after adjusting for economic and population indexes. The countries with more estimated cases of Chagas disease produced less research on Chagas disease than some developed countries.

Reduction of catheter-associated bloodstream infections through procedures in newborn babies admitted in a university hospital intensive care unit in Brazil

INTRODUCTION: Catheter-associated bloodstream infection (CA-BSI) is the most common nosocomial infection in neonatal intensive care units. There is evidence that care bundles to reduce CA-BSI are effective in the adult literature. The aim of this study was to reduce CA-BSI in a Brazilian neonatal intensive care unit by means of a care bundle including few strategies or procedures of prevention and control of these infections. METHODS: An intervention designed to reduce CA-BSI with five evidence-based procedures was conducted. RESULTS: A total of sixty-seven (26.7%) CA-BSIs were observed. There were 46 (32%) episodes of culture-proven sepsis in group preintervention (24.1 per 1,000 catheter days [CVC days]). Neonates in the group after implementation of the intervention had 21 (19.6%) episodes of CA-BSI (14.9 per 1,000 CVC days). The incidence of CA-BSI decreased significantly after the intervention from the group preintervention and postintervention (32% to 19.6%, 24.1 per 1,000 CVC days to 14.9 per 1,000 CVC days, p=0.04). In the multiple logistic regression analysis, the use of more than 3 antibiotics and length of stay >8 days were independent risk factors for BSI. CONCLUSIONS: A stepwise introduction of evidence-based intervention and intensive and continuous education of all healthcare workers are effective in reducing CA-BSI.

Relationship between antibiotic consumption, oropharyngeal colonization, and ventilator-associated pneumonia by Staphylococcus aureus in an intensive care unit of a Brazilian teaching hospital

INTRODUCTION: his study evaluated the consumption of major classes of antibiotics, the colonization of the oropharynx of patients on mechanical ventilation, and the risk of ventilator-associated pneumonia (VAP) caused by Staphylococcus aureus in an intensive care unit for adults. METHODS: A case-control study was carried out using colonized patients (cases) by oxacillin-resistant S. aureus (ORSA) and (controls) oxacillin-sensitive S. aureus (OSSA) from May 2009 to August 2010. The occurrence of VAP by S. aureus was also evaluated in the same period. Antibiotic consumption was expressed as the number of defined daily doses (DDD)/1,000 patient-days for glycopeptides, carbapenems, and extended-spectrum cephalosporins. RESULTS: Three hundred forty-six (56.1%) patients underwent mechanical ventilation with a frequency of oropharyngeal colonization of 36.4%, corresponding to 63.5% for ORSA and 36.5% for OSSA. The risk of illness for this organism was significant (p<0.05), regardless of whether colonization/infection was by ORSA or OSSA. The consumption of antibiotics was high, mainly for broad-spectrum cephalosporins (551.26 DDDs/1,000 patient-days). The high density of use of glycopeptides (269.56 DDDs/1,000 patient-days) was related to colonization by ORSA (Pearson r=0.57/p=0.02). Additionally, age >60 years, previous antibiotic therapy, and previous use of carbapenems were statistically significant by multivariate analysis. CONCLUSIONS: There was a significant relationship between the colonization of the oropharyngeal mucosa and the risk of VAP by both phenotypes. The use of glycopeptides was related to colonization by ORSA.