Development of a Loop-Mediated Isothermal Amplification Method for Detection of Histoplasma capsulatum DNA in Clinical Samples

Improved methods for the detection of Histoplasma capsulatum are needed in regions with limited resources in which the organism is endemic, where delayed diagnosis of progressive disseminated histoplasmosis (PDH) results in high mortality rates. We have investigated the use of a loop-mediated isothermal amplification (LAMP) assay to facilitate rapid inexpensive molecular diagnosis of this disease. Primers for LAMP were designed to amplify the Hcp100 locus of H. capsulatum. The sensitivity and limit of detection were evaluated using DNA extracted from 91 clinical isolates of known geographic subspecies, while the assay specificity was determined using DNA extracted from 50 other fungi and Mycobacterium tuberculosis. Urine specimens (n = 6) collected from HIV-positive individuals with culture- and antigen-proven histoplasmosis were evaluated using the LAMP assay. Specimens from healthy persons (n = 10) without evidence of histoplasmosis were used as assay controls. The Hcp100 LAMP assay was 100% sensitive and specific when tested with DNA extracted from culture isolates. The median limit of detection was <= 6 genomes (range, 1 to 300 genomes) for all except one geographic subspecies. The LAMP assay detected Hcp100 in 67% of antigen-positive urine specimens (4/6 specimens), and results were negative for Hcp100 in all healthy control urine specimens. We have shown that the Hcp100 LAMP assay is a rapid affordable assay that can be used to expedite culture confirmation of H. capsulatum in regions in which PDH is endemic. Further, our results indicate proof of the concept that the assay can be used to detect Histoplasma DNA in urine. Further evaluation of this assay using body fluid samples from a larger patient population is warranted.

A fast and highly sensitive method for the detection of canine distemper virus by the naked eye

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Fast detection of the magnetic easy axis on steel sheet using the continuous rotational Barkhausen method

The magnetic behaviour of most commercial ferromagnetic steels is usually anisotropic presenting a magnetic easy axis. Changes in the direction of this axis can be related to mechanical changes and anomalies that occur in the fabrication process. The present work describes a method that uses a device with permanent magnets to create a precise rotational magnetic field. The device measures continuous Magnetic Barkhausen Noise signals related to the angle of magnetization, in order to determine the direction of the macroscopic magnetic easy axis. It also offers the possibility of obtaining real time parameters that quantify the magnetic anisotropy of the sample. (C) 2011 Elsevier Ltd. All rights reserved.

Development of an enzymeless electroanalytical method for the indirect detection of creatinine in urine samples

The aim of this study is to develop a new enzymeless electroanalytical method for the indirect quantification of creatinine from urine sample. This method is based on the electrochemical monitoring of picrate anion reduction at a glassy carbon electrode in an alkaline medium before and after it has reacted with creatinine (Jaffe's reaction). By using the differential pulse voltammetry technique under the optimum experimental conditions (step potential, amplitude potential, reaction time, and temperature), a linear analytical curve was obtained for concentrations of creatinine ranging from 1 to 80 mu mol L-1, with a detection limit of 380 nmol L-1. This proposed method was used to measure creatinine in human urine without the interference of most common organic species normally present in biological fluids (e.g., uric acid, ascorbic acid, glucose, and phosphocreatinine). The results obtained using urine samples were highly similar to the results obtained using the reference spectrophotometric method (at a 95% confidence level). (C) 2012 Elsevier B.V. All rights reserved.

Development of a fluorescent method for the detection in marine organisms of the respiratory electron transport system

Trabajo realizado por: Maldonado, F.; Packard, T.; Gómez, M.; Santana Rodríguez, J. J

Detection and Modeling of Boundary Layer Height

This thesis tackles the problem of the automated detection of the atmospheric boundary layer (BL) height, h, from aerosol lidar/ceilometer observations. A new method, the Bayesian Selective Method (BSM), is presented. It implements a Bayesian statistical inference procedure which combines in an statistically optimal way different sources of information. Firstly atmospheric stratification boundaries are located from discontinuities in the ceilometer back-scattered signal. The BSM then identifies the discontinuity edge that has the highest probability to effectively mark the BL height. Information from the contemporaneus physical boundary layer model simulations and a climatological dataset of BL height evolution are combined in the assimilation framework to assist this choice. The BSM algorithm has been tested for four months of continuous ceilometer measurements collected during the BASE:ALFA project and is shown to realistically diagnose the BL depth evolution in many different weather conditions. Then the BASE:ALFA dataset is used to investigate the boundary layer structure in stable conditions. Functions from the Obukhov similarity theory are used as regression curves to fit observed velocity and temperature profiles in the lower half of the stable boundary layer. Surface fluxes of heat and momentum are best-fitting parameters in this exercise and are compared with what measured by a sonic anemometer. The comparison shows remarkable discrepancies, more evident in cases for which the bulk Richardson number turns out to be quite large. This analysis supports earlier results, that surface turbulent fluxes are not the appropriate scaling parameters for profiles of mean quantities in very stable conditions. One of the practical consequences is that boundary layer height diagnostic formulations which mainly rely on surface fluxes are in disagreement to what obtained by inspecting co-located radiosounding profiles.

The Equidistant Method - a novel hip joint simulation algorithm for detection of femoroacetabular impingement

A novel computerized algorithm for hip joint motion simulation and collision detection, called the Equidistant Method, has been developed. This was compared to three pre-existing methods having different properties regarding definition of the hip joint center and behavior after collision detection. It was proposed that the Equidistant Method would be most accurate in detecting the location and extent of femoroacetabular impingement.

Simple and objective method for routine detection of the macular pigment xanthophyll

A new simple method for two-dimensional determination of optical density of macular pigment xanthophyll (ODx) in clinical routine is based on a single blue-reflection fundus image. Individual different vignetting is corrected by a shading function. For its construction, nodes are automatically found in structureless image regions. The influence of stray light in elderly crystalline lenses is compensated by a correction function that depends on age. The reproducibility of parameters in a one-wavelength reflection method determined for three subjects (47, 61, and 78 years old) was: maxODx = 6.3%, meanODx = 4.6%, volume = 6%, and area = 6% already before stray-light correction. ODx was comparable in pseudophakic and in an eye with a crystalline lens of the same 11 subjects after stray-light correction. Significant correlation in ODx was found between the one-wavelength reflection method and the two-wavelength autofluorescence method for pseudophakic and cataract eyes of 19 patients suffering from dry age-related macular degeneration (AMD) (R(2) = 0.855). In pseudophakic eyes, maxODx was significantly lower for dry AMD (n = 45) (ODx = 0.491±0.102 ODU) than in eyes with healthy fundus (n = 22) (ODx = 0.615±0.103 ODU) (p = 0.000033). Also in eyes with crystalline lens, maxODx was lower in AMD (n = 125) (ODx = 0.610±0.093 ODU) than in healthy subjects (n = 45) (ODx = 0.674±0.098 ODU) (p = 0.00019). No dependence on age was found in the pseudophakic eyes both of healthy subjects and AMD patients.

Postmortem ventilation: A new method for improved detection of pulmonary pathologies in forensic imaging

Postmortem imaging has gained prominence in the field of forensic pathology. Even with experience in this procedure, difficulties arise in evaluating pathologies of the postmortem lung. The effect of postmortem ventilation with applied pressures of 10, 20, 30 and 40mbar was evaluated in 10 corpses using simultaneous postmortem computed tomography (pmCT) scans. Ventilation was performed via a continuous positive airway pressure mask (n=5), an endotracheal tube (n=4) and a laryngeal mask (n=1) using a portable home care ventilator. The lung volumes were measured and evaluated by a segmentation technique based on reconstructed CT data. The resulting changes to the lungs were analyzed. Postmortem ventilation at 40mbar induced a significant (p<0.05) unfolding of the lungs, with a mean volume increase of 1.32l. Small pathologies of the lung such as scarring and pulmonary nodules as well as emphysema were revealed, while inner livores were reduced. Even though lower ventilation pressures resulted in a significant (p<0.05) volume increase, pathologies were best evaluated when a pressure of 40mbar was applied, due to the greater reduction of the inner livores. With the ventilation-induced expansion of the lungs, a decrease in the heart diameter and gaseous distension of the stomach was recognized. In conclusion, postmortem ventilation is a feasible method for improving evaluation of the lungs and detection of small lung pathologies. This is because of the volume increase in the air-filled portions of the lung and reduced appearance of inner livores.

Detection of Progressive Deterioration in Early Onset Schizophrenia with a New Statistical Method

Much controversy exists over whether the course of schizophrenia, as defined by the lengths of repeated community tenures, is progressively ameliorating or deteriorating. This article employs a new statistical method proposed by Wang and Chen (2000) to analyze the Denmark registry data in Eaton, et al (1992). The new statistical method correctly handles the bias caused by induced informative censoring, which is an interaction of the heterogeneity of schizophrenia patients and long-term follow-up. The analysis shows a progressive deterioration pattern in terms of community tenures for the full registry cohort, rather than a progressive amelioration pattern as reported for a selected sub-cohort in Eaton, et al (1992). When adjusted for the long-term chronicity of calendar time, no significant progressive pattern was found for the full cohort.

OUT-OF-STEP DETECTION BASED ON ZUBOV’S APPROXIMATION BOUNDARY METHOD

Disturbances in power systems may lead to electromagnetic transient oscillations due to mismatch of mechanical input power and electrical output power. Out-of-step conditions in power system are common after the disturbances where the continuous oscillations do not damp out and the system becomes unstable. Existing out-of-step detection methods are system specific as extensive off-line studies are required for setting of relays. Most of the existing algorithms also require network reduction techniques to apply in multi-machine power systems. To overcome these issues, this research applies Phasor Measurement Unit (PMU) data and Zubov’s approximation stability boundary method, which is a modification of Lyapunov’s direct method, to develop a novel out-of-step detection algorithm. The proposed out-of-step detection algorithm is tested in a Single Machine Infinite Bus system, IEEE 3-machine 9-bus, and IEEE 10-machine 39-bus systems. Simulation results show that the proposed algorithm is capable of detecting out-of-step conditions in multi-machine power systems without using network reduction techniques and a comparative study with an existing blinder method demonstrate that the decision times are faster. The simulation case studies also demonstrate that the proposed algorithm does not depend on power system parameters, hence it avoids the need of extensive off-line system studies as needed in other algorithms.

Isotype-specific detection of ABO blood group antibodies using a novel flow cytometric method

Several methods to detect anti-A/B antibodies based on haemagglutination and haemolysis have been described. These methods measure predominantly anti-A/B immunoglobulin (Ig)M, whereas anti-A/B IgG and IgG subclasses are less well examined. We established a flow cytometry method (ABO-fluorescence-activated cell sorting; ABO-FACS) to quantify binding of anti-A/B IgM, IgG and IgG subclasses to human A or B red blood cells. Anti-A/B IgM were present in the majority of 120 blood donors, as expected from blood group typing. The sensitivity and specificity of anti-A/B IgM to predict the blood group was 93% and 96% respectively. Anti-A/B IgG was found in 34/38 blood group O samples (89%). Anti-B IgG in blood group A or anti-A IgG in blood group B was present in 4/28 (14%) and 1/28 (4%) samples, respectively, and absent in 26 AB sera. IgG2 was the predominant IgG subclass. The correlation of anti-A/B IgM and IgG in the ABO-FACS with haemagglutination titres was 0.870 and 0.783, respectively (n = 240; P < 0.001) whereas the comparison of ABO-FACS with ABO-enzyme-linked immunosorbent assay was less significant. In conclusion, ABO-FACS is a valid method to quantify anti-A/B IgM, IgG and IgG subclasses. It opens the possibility of isotype-specific monitoring of anti-A/B antibodies levels after ABO-incompatible solid organ and stem cell transplantation.