Genus-specific kinetoplast-DNA PCR and parasite culture for the diagnosis of localised cutaneous leishmaniasis: applications for clinical trials under field conditions in Brazil

The positivities of two methods for the diagnosis of localised cutaneous leishmaniasis (CL) were estimated in 280 patients enrolled in a clinical trial. The trial was conducted in an endemic area of Leishmania (Viannia) braziliensis and trial participants were patients with skin ulcers and positive leishmanin skin tests. Patients underwent aspirative skin punctures of the ulcerated lesions and lymph nodes for in vitro cultures, which were processed under field conditions at the local health centre. Skin lesion biopsies were tested at a reference laboratory using kinetoplastid DNA (kDNA)-PCR to detect DNA. The median time required to obtain a positive culture from the skin samples was seven days and the contamination rate of the samples was 1.8%. The positivities of the cultures from skin lesions, kDNA-PCR and the combination of the two methods were 78.2% (95% CI: 73-82.6%), 89.3% (95% CI: 85.1-92.4%) and 97.1% (95% CI: 94.5-98.5%). We conclude that parasite culture is a feasible method for the detection of Leishmania in field conditions and that the combination of culture and PCR has a potential role for the diagnosis of CL in candidates for clinical trials.

Malaria diagnosis from pooled blood samples: comparative analysis of real-time PCR, nested PCR and immunoassay as a platform for the molecular and serological diagnosis of malaria on a large-scale

Malaria diagnoses has traditionally been made using thick blood smears, but more sensitive and faster techniques are required to process large numbers of samples in clinical and epidemiological studies and in blood donor screening. Here, we evaluated molecular and serological tools to build a screening platform for pooled samples aimed at reducing both the time and the cost of these diagnoses. Positive and negative samples were analysed in individual and pooled experiments using real-time polymerase chain reaction (PCR), nested PCR and an immunochromatographic test. For the individual tests, 46/49 samples were positive by real-time PCR, 46/49 were positive by nested PCR and 32/46 were positive by immunochromatographic test. For the assays performed using pooled samples, 13/15 samples were positive by real-time PCR and nested PCR and 11/15 were positive by immunochromatographic test. These molecular methods demonstrated sensitivity and specificity for both the individual and pooled samples. Due to the advantages of the real-time PCR, such as the fast processing and the closed system, this method should be indicated as the first choice for use in large-scale diagnosis and the nested PCR should be used for species differentiation. However, additional field isolates should be tested to confirm the results achieved using cultured parasites and the serological test should only be adopted as a complementary method for malaria diagnosis.

Microstructural, chemical and isotopic evidence for the origin of late neolithic leather recovered from an ice field in the Swiss Alps

Archaeological leather samples recovered from the ice field at the Schnidejoch Pass (altitude 2756 m amsl) in the western Swiss Alps were studied using optical, chemical molecular and isotopic (delta(13)C and delta(15)N of the bulk leather, and compound-specific delta(13)C analyses of the organic-solvent extracted fatty acids) methods to obtain insight into the origin of the leather and ancient tanning procedures. For comparison, leathers from modern native animals in alpine environment (red deer, goat, sheep, chamois, and calf/cow) were analyzed using the same approach. Optical and electron microscopically comparisons of Schnidejoch and modern leathers showed that the gross structure (pattern of collagen fibrils and intra-fibrils material) of archaeological leather had survived essentially intact for five millennia. The SEM studies of the hairs from the most important archaeological find, a Neolithic leather legging, show a wave structure of the hair cuticle, which is a diagnostic feature for goatskins. The variations of the bulk delta(13)C and delta(15)N values, and delta(13)C values of the main fatty acids are within the range expected for pre-industrial temperate C(3) environment. The archaeological leather samples contain a mixture of indigenous (from the animal) and exogenous plant/animal lipids. An important amount of waxy n-alkanes, n-alkan-1-ols and phytosterols (beta-sitosterol, sitostanol) in all samples, and abundant biomarker of conifers (nonacosan-10-01) in the legging leathers clearly indicate that the Neolithic people were active in a subalpine coniferous forest, and that they used an aqueous extract of diverse plant material for tanning leather. (C) 2010 Elsevier Ltd. All rights reserved.

Genetic polymorphisms in the glutamate-rich protein of Plasmodium falciparum field isolates from a malaria-endemic area of Brazil

The genetic diversity displayed by Plasmodium falciparum, the most deadly Plasmodium species, is a significant obstacle for effective malaria vaccine development. In this study, we identified genetic polymorphisms in P. falciparum glutamate-rich protein (GLURP), which is currently being tested in clinical trials as a malaria vaccine candidate, from isolates found circulating in the Brazilian Amazon at variable transmission levels. The study was performed using samples collected in 1993 and 2008 from rural villages situated near Porto Velho, in the state of Rondônia. DNA was extracted from 126 P. falciparum-positive thick blood smears using the phenol-chloroform method and subjected to a nested polymerase chain reaction protocol with specific primers against two immunodominant regions of GLURP, R0 and R2. Only one R0 fragment and four variants of the R2 fragment were detected. No differences were observed between the two time points with regard to the frequencies of the fragment variants. Mixed infections were uncommon. Our results demonstrate conservation of GLURP-R0 and limited polymorphic variation of GLURP-R2 in P. falciparum isolates from individuals living in Porto Velho. This is an important finding, as genetic polymorphisms in B and T-cell epitopes could have implications for the immunological properties of the antigen.

Variation in haematological parameters in children less than five years of age with asymptomatic Plasmodium infection: implication for malaria field studies

During the season of high malaria transmission, most children are infected by Plasmodium, which targets red blood cells (RBCs), affecting haematological parameters. To describe these variations, we examined the haematological profiles of two groups of children living in a malaria-endemic area. A cross-sectional survey was conducted at the peak of the malaria transmission season in a rural area of Burkina Faso. After informed consent and clinical examination, blood samples were obtained from the participants for malaria diagnosis and a full blood count. Of the 414 children included in the analysis, 192 were not infected with Plasmodium, whereas 222 were asymptomatic carriers of Plasmodium infection. The mean age of the infected children was 41.8 months (range of 26.4-57.2) compared to 38.8 months (range of 22.4-55.2) for the control group (p = 0.06). The asymptomatic infected children tended to have a significantly lower mean haemoglobin level (10.8 g/dL vs. 10.4 g/dL; p < 0.001), mean lymphocyte count (4592/µL vs. 5141/µL; p = 0.004), mean platelet count (266 x 103/µL vs. 385 x 103/µL; p < 0.001) and mean RBC count (4.388 x 106/µL vs. 4.158 x 106/µL; p < 0.001) and a higher mean monocyte count (1403/µL vs. 1192/µL; p < 0.001) compared to the control group. Special attention should be applied when interpreting haematological parameters and evaluating immune responses in asymptomatic infected children living in malaria-endemic areas and enrolled in vaccine trials.

Discrepancies between Aedes aegypti identification in the field and in the laboratory after collection with a sticky trap

Currently, sticky traps are regularly employed to assist in the surveillance of Aedes aegypti infestation. We tested two alternative procedures for specimen identification performed by local health agents: directly in the field, as recommended by certain manufacturers, or after transportation to the laboratory. A total of 384 sticky traps (MosquiTRAP) were monitored monthly during one year in four geographically representative Brazilian municipalities. When the same samples were inspected in the field and in the laboratory, large differences were noted in the total number of mosquitoes recorded and in the number of specimens identified as Ae. aegypti by both procedures. Although field identification has the potential to speed vector surveillance, these results point to uncertainties in the evaluated protocol.

A sensitive, specific and reproducible real-time polymerase chain reaction method for detection of Plasmodium vivaxandPlasmodium falciparum infection in field-collected anophelines

We describe a simple method for detection of Plasmodium vivaxand Plasmodium falciparum infection in anophelines using a triplex TaqMan real-time polymerase chain reaction (PCR) assay (18S rRNA). We tested the assay on Anopheles darlingi and Anopheles stephensi colony mosquitoes fed withPlasmodium-infected blood meals and in duplicate on field collected An. darlingi. We compared the real-time PCR results of colony-infected and field collected An. darlingi, separately, to a conventional PCR method. We determined that a cytochromeb-PCR method was only 3.33% as sensitive and 93.38% as specific as our real-time PCR assay with field-collected samples. We demonstrate that this assay is sensitive, specific and reproducible.

New perspectives in the use of ink evidence in forensic science: Part II. Development and testing of mathematical algorithms for the automatic comparison of ink samples analysed by HPTLC

In the first part of this research, three stages were stated for a program to increase the information extracted from ink evidence and maximise its usefulness to the criminal and civil justice system. These stages are (a) develop a standard methodology for analysing ink samples by high-performance thin layer chromatography (HPTLC) in reproducible way, when ink samples are analysed at different time, locations and by different examiners; (b) compare automatically and objectively ink samples; and (c) define and evaluate theoretical framework for the use of ink evidence in forensic context. This report focuses on the second of the three stages. Using the calibration and acquisition process described in the previous report, mathematical algorithms are proposed to automatically and objectively compare ink samples. The performances of these algorithms are systematically studied for various chemical and forensic conditions using standard performance tests commonly used in biometrics studies. The results show that different algorithms are best suited for different tasks. Finally, this report demonstrates how modern analytical and computer technology can be used in the field of ink examination and how tools developed and successfully applied in other fields of forensic science can help maximising its impact within the field of questioned documents.

Endoscopic low-coherence topography measurement for upper airways and hollow samples.

To evaluate the severity of airway pathologies, quantitative dimensioning of airways is of utmost importance. Endoscopic vision gives a projective image and thus no true scaling information can be directly deduced from it. In this article, an approach based on an interferometric setup, a low-coherence laser source and a standard rigid endoscope is presented, and applied to hollow samples measurements. More generally, the use of the low-coherence interferometric setup detailed here could be extended to any other endoscopy-related field of interest, e.g., gastroscopy, arthroscopy and other medical or industrial applications where tri-dimensional topology is required. The setup design with a multiple fibers illumination system is presented. Demonstration of the method ability to operate on biological samples is assessed through measurements on ex vivo pig bronchi.

Ant species (Hymenoptera, Formicidae) from the seasonally dry tropical forest of northeastern Brazil: a compilation from field surveys in Bahia and literature records

Ant species (Hymenoptera, Formicidae) from the seasonally dry tropical forest of northeastern Brazil: a compilation from field surveys in Bahia and literature records. The Caatingas occur predominantly in northeastern Brazil and comparatively it is the biome that received less attention than any other ecosystem in Brazil, representing the region where invertebrate groups are less known. We present here the first list of ant species of the Caatingas, compiling information from the literature, from a study of samples preserved in alcohol in the Laboratory of Entomology (Universidade Estadual de Feira de Santana), and from a field survey conducted in Milagres, Bahia, submitting standardized 1-m² samples of the leaf-litter to Winkler extractors. Summing all information, 11 subfamilies, 61 genera and 173 species (plus one subspecies) of ants are recognized in the biome. This species number does not consider morphospecies that could not be named due to the lack of reliable recent taxonomic information for some Neotropical ant genera. The list presented here for ant species of the Caatingas is therefore underestimated, but it is relevant because it allows the identification of areas to be sampled in order to improve our knowledge of the diversity of ants in this biome.

Magnetic field effect on quantum corrections to the low-temperature conductivity in mettalic perovskite oxides

The transport and magnetotransport properties of the metallic and ferromagnetic SrRuO3 (SRO) and the metallic and paramagnetic LaNiO3 (LNO) epitaxial thin films have been investigated in fields up to 55 T at temperatures down to 1.8 K . At low temperatures both samples display a well-defined resistivity minimum. We argue that this behavior is due to the increasing relevance of quantum corrections to the conductivity (QCC) as temperature is lowered; this effect being particularly relevant in these oxides due to their short mean free path. However, it is not straightforward to discriminate between contributions of weak localization and renormalization of electron-electron interactions to the QCC through temperature dependence alone. We have taken advantage of the distinct effect of a magnetic field on both mechanisms to demonstrate that in ferromagnetic SRO the weak-localization contribution is suppressed by the large internal field leaving only renormalized electron-electron interactions, whereas in the nonmagnetic LNO thin films the weak-localization term is relevant.

Influence of field slope and coffee plantation age on the physical properties of a red-yellow Latosol

In modern agriculture, several factors cause changes in the soil physical properties. The time of establishment of a crop (plantation age) and the slope are examples of factors that moderate the impact of mechanized operations on the soil structure. The objective of this study was to analyze the effect of machinery traffic on the physical properties of a Red-Yellow Latosol under coffee plantations with different ages (2, 7, 18, and 33 years) and slope positions (3, 9 and 15 %). Samples were collected from three positions between coffee rows (lower wheel track, inter-row and upper wheel track) and at two depths (surface layer and sub-surface). Changes in the total porosity, macroporosity, microporosity, organic matter, bulk density, and aggregate stability were investigated. Our results showed that the slope influenced the organic matter content, microporosity and aggregate stability. The soil samples under the inter-row were minimally damaged in their structure, compared to those from under the lower and upper wheel track, while the structure was better preserved under the lower than the upper track. The time since the establishment of the crop, i.e., the plantation age, was the main factor determining the extent of structural degradation in the coffee plantation.

Bacterial bioassay for rapid and accurate analysis of arsenic in highly variable groundwater samples.

In this study, we report the first ever large-scale environmental validation of a microbial reporter-based test to measure arsenic concentrations in natural water resources. A bioluminescence-producing arsenic-inducible bacterium based on Escherichia coli was used as the reporter organism. Specific protocols were developed with the goal to avoid the negative influence of iron in groundwater on arsenic availability to the bioreporter cells. A total of 194 groundwater samples were collected in the Red River and Mekong River Delta regions of Vietnam and were analyzed both by atomic absorption spectroscopy (AAS) and by the arsenic bioreporter protocol. The bacterial cells performed well at and above arsenic concentrations in groundwater of 7 microg/L, with an almost linearly proportional increase of the bioluminescence signal between 10 and 100 microg As/L (r2 = 0.997). Comparisons between AAS and arsenic bioreporter determinations gave an overall average of 8.0% false negative and 2.4% false positive identifications for the bioreporter prediction at the WHO recommended acceptable arsenic concentration of 10 microg/L, which is far betterthan the performance of chemical field test kits. Because of the ease of the measurement protocol and the low application cost, the microbiological arsenic test has a great potential in large screening campaigns in Asia and in other areas suffering from arsenic pollution in groundwater resources.

Topological magnetic irreversibility in superconducting Pb samples of various shapes

The magnetic-field dependence of the magnetization of cylinders, disks, and spheres of pure type-I superconducting lead was investigated by means of isothermal measurements of first magnetization curves and hysteresis cycles. Depending on the geometry of the sample and the direction and intensity of the applied magnetic field, the intermediate state exhibits different irreversible features that become particularly highlighted in minor hysteresis cycles. The irreversibility is noticeably observed in cylinders and disks only when the magnetic field is parallel to the axis of revolution and is very subtle in spheres. When the magnetic field decreases from the normal state, the irreversibility appears at a temperature-dependent value whose distance to the thermodynamic critical field depends on the sample geometry. The irreversible features in the disks are altered when they are submitted to an annealing process. These results agree well with very recent high-resolution magneto-optical experiments in similar materials that were interpreted in terms of transitions between different topological structures for the flux configuration in the intermediate state. A discussion of the relative role of geometrical barriers for flux entry and exit and pinning effects as responsible for the magnetic irreversibility is given.

Revisiting Field Capacity (FC): variation of definition of FC and its estimation from pedotransfer functions

Taking into account the nature of the hydrological processes involved in in situ measurement of Field Capacity (FC), this study proposes a variation of the definition of FC aiming not only at minimizing the inadequacies of its determination, but also at maintaining its original, practical meaning. Analysis of FC data for 22 Brazilian soils and additional FC data from the literature, all measured according to the proposed definition, which is based on a 48-h drainage time after infiltration by shallow ponding, indicates a weak dependency on the amount of infiltrated water, antecedent moisture level, soil morphology, and the level of the groundwater table, but a strong dependency on basic soil properties. The dependence on basic soil properties allowed determination of FC of the 22 soil profiles by pedotransfer functions (PTFs) using the input variables usually adopted in prediction of soil water retention. Among the input variables, soil moisture content θ (6 kPa) had the greatest impact. Indeed, a linear PTF based only on it resulted in an FC with a root mean squared residue less than 0.04 m³ m-3 for most soils individually. Such a PTF proved to be a better FC predictor than the traditional method of using moisture content at an arbitrary suction. Our FC data were compatible with an equivalent and broader USA database found in the literature, mainly for medium-texture soil samples. One reason for differences between FCs of the two data sets of fine-textured soils is due to their different drainage times. Thus, a standardized procedure for in situ determination of FC is recommended.