Digital soil mapping: strategy for data pre-processing

The region of greatest variability on soil maps is along the edge of their polygons, causing disagreement among pedologists about the appropriate description of soil classes at these locations. The objective of this work was to propose a strategy for data pre-processing applied to digital soil mapping (DSM). Soil polygons on a training map were shrunk by 100 and 160 m. This strategy prevented the use of covariates located near the edge of the soil classes for the Decision Tree (DT) models. Three DT models derived from eight predictive covariates, related to relief and organism factors sampled on the original polygons of a soil map and on polygons shrunk by 100 and 160 m were used to predict soil classes. The DT model derived from observations 160 m away from the edge of the polygons on the original map is less complex and has a better predictive performance.

Performance of an immunochromatography test for vivax malaria in the Amazon region, Brazil

The study was carried out to evaluate the diagnostic performance of the ICT malaria Pf/PvTM test for vivax malaria diagnosis in Belém, Amazon region, Brazil. The results of blood malaria parasites examination using an immunochromatography test were compared with thick blood film (TBF) examination. It was also evaluated the performance of this test storaged at three different temperatures (25°C, 30°C, and 37°C) for 24 hours before use. Overall sensitivity of ICT Pf/PvTM was 61.8% with a specificity of 100%, positive and negative predictive value of 100% and 71.8%, respectively and accuracy of 80.6%. The test sensitivity was independent of the parasite density. This test needs to be further reviewed in order to have better performance for P. vivax malaria diagnosis.

Performance of rubella suspect case definition: implications for surveillance

OBJECTIVE: To assess the performance of the rubella suspect case definition among patients with rash diseases seen at primary care units. METHODS: From January 1994 to December 2002, patients with acute rash, with or without fever, were seen at two large primary health care units and at a public general hospital in the municipality of Niterói, metropolitan area of Rio de Janeiro, Brazil. Data from clinical and serologic assessment were used to estimate the positive predictive values of the definition of rubella suspect case from the Brazilian Ministry of Health and other combination of signs/symptoms taking serologic status as the reference. Serum samples were tested for anti-rubella virus IgM using commercially available enzyme immunoassays. Positive predictive values and respective 95% confidence intervals were calculated. RESULTS: A total of 1,186 patients with an illness characterized by variable combinations of rash with fever, arthropathy and lymphadenopathy were studied. Patients with rash, regardless of other signs and symptoms, had 8.8% likelihood of being IgM-positive for rubella. The Brazilian suspect case definition (fever and lymphadenopathy in addition to rash) had low predictive value (13.5%). This case definition would correctly identify 42.3% of the IgM-positive cases, and misclassify 26.1% of the IgM-negative cases. CONCLUSIONS: These results support the recommendation to investigate and collect clinical specimens for laboratory diagnosis of all cases of rash, for surveillance purposes. Although this strategy may increase costs, the benefits of interrupting the circulation of rubella virus and preventing the occurrence of congenital rubella syndrome should pay off.

Peroxidase antibody test for mucocutaneous leishmaniasis serology performance indexes and comparison with a fluorescent antibody test: Comparação com o desempenho da reação de imunofluorescência

Performance indexes of the peroxidase antibody test were compared to that of the fluorescent antibody test. The peroxidase antibody test had a statistically higher sensitivity and negative predictive value and a higher efficiency than the fluorescent antibody test but its specificity and positive predictive value were within the 95% confidence limits for the values found for the fluorescent antibody test. Such differences did not change when Chagas' disease and visceral leishmaniasis sera were included in index calculations. Statistical analysis showed that the two tests have a substantial degree of agreement but the immunofluorescent test had a specificity index and a positive predictive value equal to 100.0% when Chagas' disease and visceral leishmaniasis sera were not included in the calculations of the performance index; in this instance, a positive test result equals a disclosure of the disease attribute due to the inexistence of false positive results. The enzyme/ protein ratio of the peroxidase conjugate, resulting in heavy or light-labeled conjugates may pose technical problems to its use in serology tests.

Performance indexes of a dot-enzime-linked immunosorbent assay (dot-ELISA) and an ezyme-linked immunosorbent assay (IgG-ELISA) for field surveys of new world leishmaniasis

Diagnostic performance indexes of sensitivity, specificity, positive predictive value and efficiency were determined for dot-ELISA and IgG-ELISA tests in 340 leishmaniasis sera. Sensitivity of the dot-ELISA was significantly lower than IgG-ELISA's; the two tests had indexes of specificity and positive predictive value of the same magnitude. Seventy-eight sera gave a negative dot-ELISA test result and a positive IgG-ELISA test result. When sera were classified according to different criteria as how to interpret this diversity, the kappa statistic did not corroborate the classification indicating that the two tests display a substantial strength of agreement. The results presented indicate that performance indexes accrued in a survey where variables arc well known may be extrapolated to other population studies if the disease presents itself as highly prevalent (due to a selection bias or not) and may be expected to discriminate a disease status among test positives.

Comparison of the performance of polymerase chain reaction and pp65 antigenemia for the detection of human cytomegalovirus in immunosuppressed patients

INTRODUCTION: Human cytomegalovirus (HCMV) is often reactive in latently infected immunosuppressed patients. Accordingly, HCMV remains one of the most common infections following solid organ and hemopoietic stem cell transplantations, resulting in significant morbidity, graft loss and occasional mortality. The early diagnosis of HCMV disease is important in immunosuppressed patients, since in these individuals, preemptive treatment is useful. The objective of this study was to compare the performance of the in-house qualitative polymerase chain reaction (PCR) and pp65 antigenemia to HCMV infection in immunosuppressed patients in the Hospital de Clínicas of Porto Alegre (HCPA). METHODS: A total of 216 blood samples collected between August 2006 and January 2007 were investigated. RESULTS: Among the samples analyzed, 81 (37.5%) were HCMV-positive by PCR, while 48 (22.2%) were positive for antigenemia. Considering antigenemia as the gold standard, sensitivity, specificity, positive predictive values and negative predictive values for PCR were 87.5%, 76.8%, 51.8% and 95.5% respectively. CONCLUSIONS: These results demonstrated that qualitative PCR has high sensitivity and negative predictive value (NPV). Consequently PCR is especially indicated for the initial diagnosis of HCMV infection. In the case of preemptive treatment strategy, identification of patients at high-risk for HCMV disease is fundamental and PCR can be useful tool.

The performance of four molecular methods for the laboratory diagnosis of congenital toxoplasmosis in amniotic fluid samples

Introduction Toxoplasmosis may be life-threatening in fetuses and in immune-deficient patients. Conventional laboratory diagnosis of toxoplasmosis is based on the presence of IgM and IgG anti-Toxoplasma gondii antibodies; however, molecular techniques have emerged as alternative tools due to their increased sensitivity. The aim of this study was to compare the performance of 4 PCR-based methods for the laboratory diagnosis of toxoplasmosis. One hundred pregnant women who seroconverted during pregnancy were included in the study. The definition of cases was based on a 12-month follow-up of the infants. Methods Amniotic fluid samples were submitted to DNA extraction and amplification by the following 4 Toxoplasma techniques performed with parasite B1 gene primers: conventional PCR, nested-PCR, multiplex-nested-PCR, and real-time PCR. Seven parameters were analyzed, sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), negative likelihood ratio (NLR) and efficiency (Ef). Results Fifty-nine of the 100 infants had toxoplasmosis; 42 (71.2%) had IgM antibodies at birth but were asymptomatic, and the remaining 17 cases had non-detectable IgM antibodies but high IgG antibody titers that were associated with retinochoroiditis in 8 (13.5%) cases, abnormal cranial ultrasound in 5 (8.5%) cases, and signs/symptoms suggestive of infection in 4 (6.8%) cases. The conventional PCR assay detected 50 cases (9 false-negatives), nested-PCR detected 58 cases (1 false-negative and 4 false-positives), multiplex-nested-PCR detected 57 cases (2 false-negatives), and real-time-PCR detected 58 cases (1 false-negative). Conclusions The real-time PCR assay was the best-performing technique based on the parameters of Se (98.3%), Sp (100%), PPV (100%), NPV (97.6%), PLR (∞), NLR (0.017), and Ef (99%).

Performance of a rapid diagnostic test for the detection of visceral leishmaniasis in a large urban setting

Introduction Rapid diagnostic tests (RDTs) may improve the early detection of visceral leishmaniasis (VL), but their real-world performance requires additional study. Therefore, we evaluated the performance of an rK39-based RDT (Kalazar Detect™) for the detection of VL in an endemic, large urban area. Methods Data were collected from a registry of rK39 RDT performed at 11 emergency care units in Belo Horizonte, Brazil, and from a national database of reportable communicable diseases of the Sistema de Informação de Agravos de Notificação (SINAN). Results The rapid rK39 test was performed in 476 patients, with 114 (23.9%) positive results. The analysis of rK39 RDT performance was based on 381 (80%) cases reported to the SINAN database, of which 145 (38.1%) were confirmed cases. Estimates for sensitivity and specificity were 72.4% (95% CI: 64.6-79%) and 99.6% (95%CI: 97.6-99.9%), respectively. Positive and negative predictive values were estimated at 99.1% (95%CI: 94.9-99.8%) and 85.5% (95%CI: 80.8-89.1%), respectively. In addition, close agreement between the rK39 RDT and indirect immunofluorescence was observed. Conclusions In summary, the rK39 RDT showed a high specificity but only moderate sensitivity. In endemic areas for VL, treatment may be considered in cases with clinical manifestations and a positive rK39 RDT, but those with a negative test should be subjected to further investigation.

Performance of indirect immunofluorescence assay, immunochromatography assay and reverse transcription-polymerase chain reaction for detecting human respiratory syncytial virus in nasopharyngeal aspirate samples

Comparison of the use of indirect immunofluorescence assay (IFA), immunochromatography assay (ICA-BD) and reverse transcription-polymerase chain reaction (RT-PCR) for detecting human respiratory syncytial virus (HRSV) in 306 nasopharyngeal aspirates samples (NPA) was performed in order to assess their analytical performance. By comparing the results obtained using ICA-BD with those using IFA, we found relative indices of 85.0% for sensitivity and 91.2% for specificity, and the positive (PPV) and negative (NPV) predictive values were 85.0% and 91.2%, respectively. The relative indices for sensitivity and specificity as well as the PPV and NPV for RT-PCR were 98.0%, 89.0%, 84.0% and 99.0%, respectively, when compared to the results of IFA. In addition, comparison of the results of ICA-BD and those of RT-PCR yielded relative indices of 79.5% for sensitivity and 95.4% for specificity, as well as PPV and NPV of 92.9% and 86.0%, respectively. Although RT-PCR has shown the best performance, the substantial agreement between the ICA-BD and IFA results suggests that ICA-BD, also in addition to being a rapid and facile assay, could be suitable as an alternative diagnostic screening for HRSV infection in children.

A simple approach improving the performance of urine reagent strips for rapid diagnosis of urinary schistosomiasis in Nigerian schoolchildren

In Nigeria, schistosomiasis, caused predominantly by the species Schistosoma haematobium, is highly endemic in resource-poor communities. We performed a school-based survey in two rural communities in Osun State (Southwestern Nigeria) and assessed macrohaematuria, microhaematuria and proteinuria as indirect indicators for the presence of disease. Urine samples were inspected macroscopically for haematuria and screened for microhaematuria and proteinuria using urine reagent strips. The microscopic examination of schistosome eggs was used as the gold standard for diagnosis. In total, 447 schoolchildren were included in this study and had a 51% prevalence of urinary schistosomiasis. The sensitivity of microhaematuria (68%) and proteinuria (53%) for infection with S. haematobium was relatively low. In patients with a heavy infection (>500 eggs/10 mL), the sensitivity of microhaematuria was high (95%). When the presence of macrohaematuria and the concomitant presence of microhaematuria and proteinuria were combined, it revealed a sensitivity of 63%, a specificity of 93% and a positive predictive value of 91%. Macrohaematuria also showed high specificity (96%) and a positive predictive value of 92%, while sensitivity was < 50%. These data show that combining urine reagent strip tests (presence of proteinuria and microhaematuria) and information on macrohaematuria increased the accuracy of the rapid diagnosis of urinary schistosomiasis in an endemic rural West African setting. This simple approach can be used to increase the quality of monitoring of schistosomiasis in schoolchildren.

Performance of diagnostic biomarkers in predicting liver fibrosis among hepatitis C virus-infected Egyptian children

The aim of the present study was to identify specific markers that mirror liver fibrosis progression as an alternative to biopsy when biopsy is contraindicated, especially in children. After liver biopsies were performed, serum samples from 30 hepatitis C virus (HCV) paediatric patients (8-14 years) were analysed and compared with samples from 30 healthy subjects. All subjects were tested for the presence of serum anti-HCV antibodies. Direct biomarkers for liver fibrosis, including transforming growth factor-β1, tissue inhibitor of matrix metalloproteinase-1 (TIMP-1), hyaluronic acid (HA), procollagen type III amino-terminal peptide (PIIINP) and osteopontin (OPN), were measured. The indirect biomarkers aspartate and alanine aminotransferases, albumin and bilirubin were also tested. The results revealed a significant increase in the serum marker levels in HCV-infected children compared with the healthy group, whereas albumin levels exhibited a significant decrease. Significantly higher levels of PIIINP, TIMP-1, OPN and HA were detected in HCV-infected children with moderate to severe fibrosis compared with children with mild fibrosis (p < 0.05). The diagnostic accuracy of these direct biomarkers, represented by sensitivity, specificity and positive predictive value, emphasises the utility of PIIINP, TIMP-1, OPN and HA as indicators of liver fibrosis among HCV-infected children.

Building predictive models of soil particle-size distribution

Is it possible to build predictive models (PMs) of soil particle-size distribution (psd) in a region with complex geology and a young and unstable land-surface? The main objective of this study was to answer this question. A set of 339 soil samples from a small slope catchment in Southern Brazil was used to build PMs of psd in the surface soil layer. Multiple linear regression models were constructed using terrain attributes (elevation, slope, catchment area, convergence index, and topographic wetness index). The PMs explained more than half of the data variance. This performance is similar to (or even better than) that of the conventional soil mapping approach. For some size fractions, the PM performance can reach 70 %. Largest uncertainties were observed in geologically more complex areas. Therefore, significant improvements in the predictions can only be achieved if accurate geological data is made available. Meanwhile, PMs built on terrain attributes are efficient in predicting the particle-size distribution (psd) of soils in regions of complex geology.

Performance de cultivares de mandioca e incidência de mosca branca no Vale do Ivinhema, Mato Grosso do Sul

O Vale do Ivinhema é a principal região produtora de mandioca de Mato Grosso do Sul. Todavia, o pequeno número de cultivares disponíveis nessa região vem contribuindo para baixas produtividades e crescente ocorrência de doen­ças e pragas. Com o objetivo de avaliar o comportamento de cultivares de mandioca nessa região, foram conduzidos, de julho/2005 a setembro/2006, experimentos em Nova Andradina, Ivinhema e Deodápolis, em delineamento em blocos casualizados, com quatro repetições. Foram avaliados 11 cultivares de mandioca quanto à produtividade e à incidência de fumagina causada pela mosca-branca (Bemisia sp.). Os cultivares IAC 12 e Fécula Branca apresentaram menor incidência de fumagina, enquanto o Cascuda destacou-se entre os de maior produção de raízes tuberosas e de massa seca em todos os ambientes.

Initial performance of pineapple and utilization of rock phosphate applied in combination with organic compounds to leaf axils

Rock phosphates have low solubility in water, but good solubility in acid. The use of organic compounds together with these phosphorus sources applied to the basal leaf axils of pineapple can increase the solubility of this phosfate source and increase the P availability to the crop. A greenhouse experiment was conducted using Araxá rock phosphate (10 g) in combination or not with solutions containing increasing concentrations of humic acids (0 to 40 mmol L-1 of carbon), with or without citric acid (0.005 mmol L-1), applied to basal leaf axils of pineapple cv. Pérola. Growth and nutritional characteristics of aerial plant parts were assessed. Growth rates of aerial parts and N, P, K, Ca and Mg contents increased curvilinearly with increasing concentration of carbon in the form of humic acids. Maximum values were found for the concentration of 9.3 mmol L-1 of carbon combined with 0.005 mmol L-1 of citric acid and natural phosphate.

Initial performance of maize in response to NPK fertilization combined with Herbaspirillum seropedicae

The inoculation with plant growth-promoting bacteria can be a technological approach useful for increasing the production of maize. The objective of this study was to evaluate the initial performance of maize in response to application of doses of NPK combined with the inoculation of the diazotrophic bacteria Herbaspirillum seropedicae in an greenhouse experiment. The experiment consisted of six fertilizer levels: 0, 25, 50, 75, 100 and 200% of the recommended dose of NPK applied to maize inoculated and non-inoculated with H. seropedicae. At 30 days after the treatment application, the growth characteristics and nutritional status of the plants were evaluated. Plant development was influenced by fertilization, but it was enhanced by combination with the bacteria, which resulted in significant increases in the dry mass of shoots (7%) and leaf area (9%) when compared with non-inoculated plants. The results showed increases in the concentration of N (11%), P (30%) and K (17%) of maize plants in response to bacterial inoculation together with NPK compared with plants that were applied fertilize only. The greater consistency and stability response of the host plant to bacterization in the presence of chemical fertilizer indicate a promissory biotechnological approach for improving the initial growth and adaptation of maize to the cultivation environment.