The efficiency of concentration methods used to detect enteric viruses in anaerobically digested sludge

The presence of enteric viruses in biosolids can be underestimated due to the inefficient methods (mainly molecular methods) used to recover the viruses from these matrices. Therefore, the goal of this study was to evaluate the different methods used to recover adenoviruses (AdV), rotavirus species A (RVA), norovirus genogroup II (NoV GII) and the hepatitis A virus (HAV) from biosolid samples at a large urban wastewater treatment plant in Brazil after they had been treated by mesophilic anaerobic digestion. Quantitative polymerase chain reaction (PCR) was used for spiking experiments to compare the detection limits of feasible methods, such as beef extract elution and ultracentrifugation. Tests were performed to detect the inhibition levels and the bacteriophage PP7 was used as an internal control. The results showed that the inhibitors affected the efficiency of the PCR reaction and that beef extract elution is a suitable method for detecting enteric viruses, mainly AdV from biosolid samples. All of the viral groups were detected in the biosolid samples: AdV (90%), RVA, NoV GII (45%) and HAV (18%), indicating the viruses' resistance to the anaerobic treatment process. This is the first study in Brazil to detect the presence of RVA, AdV, NoV GII and HAV in anaerobically digested sludge, highlighting the importance of adequate waste management.

Immunologic evaluation and validation of methods using synthetic peptides derived from Mycobacterium tuberculosis for the diagnosis of tuberculosis infection

The goal of this study was to demonstrate the usefulness of an enzyme-linked immunosorbent assay (ELISA) for the serodiagnosis of pulmonary tuberculosis (PTB) and extrapulmonary TB (EPTB). This assay used 20 amino acid-long, non-overlapped synthetic peptides that spanned the complete Mycobacterium tuberculosis ESAT-6 and Ag85A sequences. The validation cohort consisted of 1,102 individuals who were grouped into the following five diagnostic groups: 455 patients with PTB, 60 patients with EPTB, 40 individuals with non-EPTB, 33 individuals with leprosy and 514 healthy controls. For the PTB group, two ESAT-6 peptides (12033 and 12034) had the highest sensitivity levels of 96.9% and 96.2%, respectively, and an Ag85A-peptide (29878) was the most specific (97.4%) in the PTB groups. For the EPTB group, two Ag85A peptides (11005 and 11006) were observed to have a sensitivity of 98.3% and an Ag85A-peptide (29878) was also the most specific (96.4%). When combinations of peptides were used, such as 12033 and 12034 or 11005 and 11006, 99.5% and 100% sensitivities in the PTB and EPTB groups were observed, respectively. In conclusion, for a cohort that consists entirely of individuals from Venezuela, a multi-antigen immunoassay using highly sensitive ESAT-6 and Ag85A peptides alone and in combination could be used to more rapidly diagnose PTB and EPTB infection.

Schistosoma mansoni in a low-prevalence area in Brazil: the importance of additional methods for the diagnosis of hard-to-detect individual carriers by low-cost immunological assays

Schistosomiasis diagnosis is based on the detection of eggs in the faeces, which is laborious and lacks sensitivity, especially for patients with a low parasite burden. Immunological assays for specific antibody detection are available, but they usually demonstrate low sensitivity and/or specificity. In this study, two simple immunological assays were evaluated for the detection of soluble Schistosoma mansoni adult worm preparation (SWAP) and egg-specific IgGs. These studies have not yet been evaluated for patients with low parasite burdens. Residents of an endemic area in Brazil donated sera and faecal samples for our study. The patients were initially diagnosed by a rigorous Kato-Katz analysis of 18 thick smears from four different stool samples. The ELISA-SWAP was successful for human diagnosis with 90% sensitivity and specificity, confirming the Kato-Katz diagnosis with nearly perfect agreement, as seen by the Kappa index (0.85). Although the ELISA-soluble S. mansoni egg antigen was 85% sensitive, it exhibited low specificity (80%; Kappa index: 0.75) and was more susceptible to cross-reactivity. We believe that immunological assays should be used in conjunction with Kato-Katz analysis as a supplementary tool for the diagnosis of schistosomiasis for patients with low infection burdens, which are usually hard to detect.

Submicroscopic malaria parasite carriage: how reproducible are polymerase chain reaction-based methods?

The polymerase chain reaction (PCR)-based methods for the diagnosis of malaria infection are expected to accurately identify submicroscopic parasite carriers. Although a significant number of PCR protocols have been described, few studies have addressed the performance of PCR amplification in cases of field samples with submicroscopic malaria infection. Here, the reproducibility of two well-established PCR protocols (nested-PCR and real-time PCR for the Plasmodium 18 small subunit rRNA gene) were evaluated in a panel of 34 blood field samples from individuals that are potential reservoirs of malaria infection, but were negative for malaria by optical microscopy. Regardless of the PCR protocol, a large variation between the PCR replicates was observed, leading to alternating positive and negative results in 38% (13 out of 34) of the samples. These findings were quite different from those obtained from the microscopy-positive patients or the unexposed individuals; the diagnosis of these individuals could be confirmed based on the high reproducibility and specificity of the PCR-based protocols. The limitation of PCR amplification was restricted to the field samples with very low levels of parasitaemia because titrations of the DNA templates were able to detect < 3 parasites/µL in the blood. In conclusion, conventional PCR protocols require careful interpretation in cases of submicroscopic malaria infection, as inconsistent and false-negative results can occur.

Evaluation of four molecular methods for the diagnosis of tuberculosis in pulmonary and blood samples from immunocompromised patients

The present study analysed the concordance among four different molecular diagnostic methods for tuberculosis (TB) in pulmonary and blood samples from immunocompromised patients. A total of 165 blood and 194 sputum samples were collected from 181 human immunodeficiency virus (HIV)-infected patients with upper respiratory complaints, regardless of suspicious for TB. The samples were submitted for smear microscopy, culture and molecular tests: a laboratory-developed conventional polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR) and the Gen-Probe and Detect-TB Ampligenix kits. The samples were handled blindly by all the technicians involved, from sample processing to results analysis. For sputum, the sensitivity and specificity were 100% and 96.7% for qPCR, 81.8% and 94.5% for Gen-Probe and 100% and 66.3% for Detect-TB, respectively. qPCR presented the best concordance with sputum culture [kappa (k) = 0.864)], followed by Gen-Probe (k = 0.682). For blood samples, qPCR showed 100% sensitivity and 92.3% specificity, with a substantial correlation with sputum culture (k = 0.754) and with the qPCR results obtained from sputum of the corresponding patient (k = 0.630). Conventional PCR demonstrated the worst results for sputa and blood, with a sensitivity of 100% vs. 88.9% and a specificity of 46.3% vs. 32%, respectively. Commercial or laboratory-developed molecular assays can overcome the difficulties in the diagnosis of TB in paucibacillary patients using conventional methods available in most laboratories.

Molecular diagnosis of strongyloidiasis in tropical areas: a comparison of conventional and real-time polymerase chain reaction with parasitological methods

This study aimed to evaluate the use of conventional polymerase chain reaction (cPCR) and real-time quantitative PCR (qPCR) in the diagnosis of human strongyloidiasis from stool samples in tropical areas. Stool samples were collected from individuals and were determined to be positive for Strongyloides stercoralis (group I), negative for S. stercoralis (group II) and positive for other enteroparasite species (group III). DNA specific to S. stercoralis was found in 76.7% of group I samples by cPCR and in 90% of group I samples by qPCR. The results show that molecular methods can be used as alternative tools for detecting S. stercoralis in human stool samples in tropical areas.

Integrative Review: Concepts And Methods Used In Nursing


Integrative review (IR) has an international reputation in nursing research and evidence-based practice. This IR aimed at identifying and analyzing the concepts and methods recommended to undertaking IR in nursing. Nine information resources,including electronic databases and grey literature were searched. Seventeen studies were included. The results indicate that: primary studies were mostly from USA; it is possible to have several research questions or hypotheses and include primary studies in the review from different theoretical and methodological approaches; it is a type of review that can go beyond the analysis and synthesis of findings from primary studies allowing exploiting other research dimensions, and that presents potentialities for the development of new theories and new problems for research. Conclusion: IR is understood as a very complex type of review and it is expected to be developed using standardized and systematic methods to ensure the required rigor of scientific research and therefore the legitimacy of the established evidence.


Insects associated with exposed decomposing bodies in the Colombian Andean Coffee Region

In Colombia, mainly classic forensic medicine methods were used to clarify crimes until 2004. However, other disciplines, including forensic entomology, started to be considered only after the New Accusatory System introduction in Bogotá and the Coffee Region in 2005. In order to provide tools for obtaining evidentiary material elements in judicial trials, it is presented here the succession of insects throughout the decomposition process of an exposed carcass of Sus scrofa Linnaeus 1758 (Suidae) and the Occurrence Matrix of colonizing species. This process was evaluated under ambient conditions in the Andean rural area of the city of Pereira, in the Mundo Nuevo district, located in a pre-montane Wet Forest area, from October to November 2006. A sampling period of 27 days and 3198 individuals were collected. We found these colonizing species in the following stages of decomposition: Lucilia eximia (Wiedemann, 1819) fresh; Hemilucilia semidiaphana (Rondani, 1850), Oxelytrum discicolle (Brullé, 1840), and Cochliomyia macellaria (Fabricius 1775) bloated; Chrysomya albiceps (Wiedemann 1819), Compsomyiops verena (Walker, 1849), Ophyra aenescens (Wiedemann, 1830) and Musca domestica Linnaeus, 1758 active; Fannia sp. advanced and Stearibia nigriceps (Meigen, 1826) remains. This study provides support tools to define the Post Mortem Interval that may be used by experts from government institutions and laboratories officially accredited.

When rare is just a matter of sampling: unexpected dominance of clubtail dragonflies (Odonata, Gomphidae) through different collecting methods at Parque Nacional da Serra do Cipó, Minas Gerais State, Brazil

When rare is just a matter of sampling: Unexpected dominance of clubtail dragonflies (Odonata, Gomphidae) through different collecting methods at Parque Nacional da Serra do Cipó, Minas Gerais State, Brazil. Capture of dragonfly adults during two short expeditions to Parque Nacional da Serra do Cipó, Minas Gerais State, using three distinct collecting methodsaerial nets, Malaise and light sheet trapsis reported. The results are outstanding due the high number of species of Gomphidae (7 out of 26 Odonata species), including a new species of Cyanogomphus Selys, 1873, obtained by two non-traditional collecting methods. Because active collecting with aerial nets is the standard approach for dragonfly inventories, we discuss some aspects of the use of traps, comparing our results with those in the literature, suggesting they should be used as complementary methods in faunistic studies. Furthermore, Zonophora campanulata annulata Belle, 1983 is recorded for the first time from Minas Gerais State and taxonomic notes about Phyllogomphoides regularis (Selys, 1873) and Progomphus complicatus Selys, 1854 are also given.

Comparative abundance and diversity of Dryininae (Hymenoptera, Dryinidae) in three savannah phytophysiognomies in southeastern Brazil, under three sampling methods

Comparative abundance and diversity of Dryininae (Hymenoptera, Dryinidae) in three savannah phytophysiognomies in southeastern Brazil, under three sampling methods. This study aimed to assess the abundance and diversity of Dryininae in riparian vegetation, Brazilian savannah, and savannah woodland vegetation at the Estação Ecológica de Jataí, in Luiz Antônio, State of São Paulo, Brazil, by using Moericke, Malaise, and light traps. The sampling was carried out from December 2006 to November 2009, and 371 specimens of Dryininae were caught, with the highest frequencies in spring and summer. Fourteen species of Dryinus Latreille, 1804 and one of Thaumatodryinus Perkins, 1905 were identified. The highest frequencies of Dryinus in the riparian vegetation differed significantly from those obtained in the Brazilian savannah and savannah woodland vegetation. In the riparian vegetation, the highest number of Dryinus was collected using light traps and the interactions between abundance and the collection method used were significant. The number of specimens of Dryinus collected in the Brazilian savannah and savannah woodland vegetation using Malaise traps did not differ significantly from those obtained using Moericke traps. Males significantly outnumbered females in the sex ratio of Dryinus. The species diversity of Dryinus based on females collected using Malaise traps was high in the Brazilian savannah. Furthermore, high species richness of female Dryinus was observed in riparian vegetation (six species) and Brazilian savannah (five). The light trap was the most successful method for sampling diversity of Dryininae.

Trophic roles of scavenger beetles in relation to decomposition stages and seasons

Carcasses represent a trophic and reproductive resource or shelter for arthropods, which are a representative component of the decomposition process. Four experiments, one per season, were conducted in a semi-rural area of Bahía Blanca, Argentina, to study the trophic roles of cadaveric beetles, evaluating the abundance, composition and dominance during all decomposition stages and seasons. Species of necrophagous, necrophilous and omnivorous habits were found. Abundance, composition and dominance of beetles in relation to their trophic roles changed according to seasons and decomposition stages. Guilds and patterns of succession were established in relation to those periods. Trophic roles could be an indicator of beetle associations with decomposition stages and seasons.

Surface and subsurface decomposition of a desiccated grass pasture biomass related to erosion and its prediction with RUSLE

Erosion is deleterious because it reduces the soil's productivity capacity for growing crops and causes sedimentation and water pollution problems. Surface and buried crop residue, as well as live and dead plant roots, play an important role in erosion control. An efficient way to assess the effectiveness of such materials in erosion reduction is by means of decomposition constants as used within the Revised Universal Soil Loss Equation - RUSLE's prior-land-use subfactor - PLU. This was investigated using simulated rainfall on a 0.12 m m-1 slope, sandy loam Paleudult soil, at the Agriculture Experimental Station of the Federal University of Rio Grande do Sul, in Eldorado do Sul, State of Rio Grande do Sul, Brazil. The study area had been covered by native grass pasture for about fifteen years. By the middle of March 1996, the sod was mechanically mowed and the crop residue removed from the field. Late in April 1996, the sod was chemically desiccated with herbicide and, about one month later, the following treatments were established and evaluated for sod biomass decomposition and soil erosion, from June 1996 to May 1998, on duplicated 3.5 x 11.0 m erosion plots: (a) and (b) soil without tillage, with surface residue and dead roots; (c) soil without tillage, with dead roots only; (d) soil tilled conventionally every two-and-half months, with dead roots plus incorporated residue; and (e) soil tilled conventionally every six months, with dead roots plus incorporated residue. Simulated rainfall was applied with a rotating-boom rainfall simulator, at an intensity of 63.5 mm h-1 for 90 min, eight to nine times during the experimental period (about every two-and-half months). Surface and subsurface sod biomass amounts were measured before each rainfall test along with the erosion measurements of runoff rate, sediment concentration in runoff, soil loss rate, and total soil loss. Non-linear regression analysis was performed using an exponential and a power model. Surface sod biomass decomposition was better depicted by the exponential model, while subsurface sod biomass was by the power model. Subsurface sod biomass decomposed faster and more than surface sod biomass, with dead roots in untilled soil without residue on the surface decomposing more than dead roots in untilled soil with surface residue. Tillage type and frequency did not appreciably influence subsurface sod biomass decomposition. Soil loss rates increased greatly with both surface sod biomass decomposition and decomposition of subsurface sod biomass in the conventionally tilled soil, but they were minimally affected by subsurface sod biomass decomposition in the untilled soil. Runoff rates were little affected by the studied treatments. Dead roots plus incorporated residues were effective in reducing erosion in the conventionally tilled soil, while consolidation of the soil surface was important in no-till. The residual effect of the turned soil on erosion diminished gradually with time and ceased after two years.

Organic material decomposition and nutrient dynamics in a mulch system enriched with leguminous trees in the Amazon

The new techniques proposed for agriculture in the Amazon region include rotational fallow systems enriched with leguminous trees and the replacement of biomass burning by mulching. Decomposition and nutrient release from mulch were studied using fine-mesh litterbags with five different leguminous species and the natural fallow vegetation as control. Samples from each treatment were analyzed for total C, N, P, K, Ca, Mg, lignin, cellulose content and soluble polyphenol at different sampling times over the course of one year. The decomposition rate constant varied with species and time. Weight loss from the decomposed litter bag material after 96 days was 30.1 % for Acacia angustissima, 32.7 % for Sclerolobium paniculatum, 33.9 % for Iinga edulis and the Fallow vegetation, 45.2 % for Acacia mangium and 63.6 % for Clitoria racemosa. Immobilization of N and P was observed in all studied treatments. Nitrogen mineralization was negatively correlated with phenol, C-to-N ratio, lignin + phenol/N ratio, and phenol/phosphorus ratios and with N content in the litterbag material. After 362 days of field incubation, an average (of all treatments), 3.3 % K, 32.2 % Ca and 22.4 % Mg remained in the mulch. Results confirm that low quality and high amount of organic C as mulch application are limiting for the quantity of energy available for microorganisms and increase the nutrient immobilization for biomass decomposition, which results in competition for nutrients with the crop plants.

Comparison of estimation methods of soil strength in five soils

In agriculture, the soil strength is used to describe the susceptibility to deformation by pressure caused by agricultural machine. The purpose of this study was to compare different methods for estimating the inherent soil strength and to identify their suitability for the evaluation of load support capacity, compaction susceptibility and root growth. The physical, chemical, mineralogical and intrinsic strength properties of seven soil samples, collected from five sampling pits at different locations in Brazil, were measured. Four clay (CS) and three sandy clay loam (SCL) soils were used. The clay soils were collected on a farm in Santo Ângelo, RS (28 º 16 ' 16 '' S; 54 º 13 ' 11 '' W 290 m); A and B horizons at the Universidade Federal de Lavras, Lavras, MG (21 º 13 ' 47 '' S; 44 º 58 ' 6'' W; 918 m) and on the farm Sygenta, in Uberlandia, MG (18 º 58 ' 37 '' S; 48 º 12 ' 05 '' W 866 m). The sandy clay loam soils were collected in Aracruz, ES (19 º 47 ' 10 '' S; 40 º 16 ' 29 '' W 81 m), and on the farm Xavier, Lavras, MG (21 º 13 ' 24 '' S; 45 º 05 ' 00 '' W; 844 m). Soil strength was estimated based on measurements of: (a) a pneumatic consolidometer, (b) manual pocket (non-rotating) penetrometer; and (c) automatic (rotating) penetrometer. The results of soil strength properties were similar by the three methods. The soil structure had a significant influence on soil strength. Results of measurements with both the manual pocket and the electric penetrometer were similar, emphasizing the influence of soil texture. The data showed that, to enhance the reliability of predictions of preconsolidation pressure by penetrometers, it is better to separate the soils into the different classes, rather than analyze them jointly. It can be concluded that the consolidometer method, although expensive, is the best when evaluations of load support capacity and compaction susceptibility of soil samples are desired.

Root system distribution of sugar cane as related to nitrogen fertilization, evaluated by two methods: monolith and probes

Few studies on sugar cane have evaluated the root system of the crop, in spite of its importance. This is mainly due to the difficulty of evaluation and high variability of results. The objective of this study was to develop an evaluation method of the cane root system by means of probes so as to evaluate the mass, distribution and metabolically active roots related to N fertilization at planting. For this purpose, an experiment was conducted in an Arenic Kandiustults with medium texture in Jaboticabal/SP, in a randomized block design with four replications and four treatments: control (without N) and 40, 80 and 120 kg ha-1 of N applied in the form of urea in the planting furrow of the cane variety SP81 3250. One week before harvest, a urea-15N solution was applied at the cane stalk base to detect active metabolism in the root system. Trenches of 1.5 m length and 0.6 m depth were opened between two sugar cane rows for root sampling by two methods: monoliths (0.3, 0.2 and 0.15 m wide, deep and long respectively) taken from the trench wall and by probe (internal diameter 0.055 m). For each method, 15 samples per plot were collected. The roots were separated from the soil in a sieve (2 mm mesh), oven-dried (at 65 ºC) and the dry matter was measured. Root sampling by probes resulted in root mass that did not differ from the evaluation in monoliths, indicating that this evaluation method may be used for sugar cane root mass, although neither the root distribution in the soil profile nor the rhizome mass were efficiently evaluated, due to the small sample volume. Nitrogen fertilization at planting did not result in a greater root accumulation in the sugar cane plant, but caused changes in the distribution of the root system in the soil. The absence of N fertilization led to a better root distribution in the soil profile, with 50, 34 and 16 % in the 0-0.2, 0.2-0.4 and 0.4-0.6 m layers, respectively; in the fertilized treatments the roots were concentrated in the surface layer, with on average 70, 17 and 13 % for the same layers. The metabolically active roots were concentrated in the center of the cane stool, amounting to 40 % of the total root mass, regardless of N fertilization (application of 120 kg ha-1 N or without N).