Robust regression in biological assay: application to the evaluation of alternative experimental techniques.

Robust Huber type regression and testing of linear hypotheses are adapted to statistical analysis of parallel line and slope ratio assays. They are applied in the evaluation of results of several experiments carried out in order to compare and validate alternatives to animal experimentation based on embryo and cell cultures. Computational procedures necessary for the application of robust methods of analysis used the conversational statistical package ROBSYS. Special commands for the analysis of parallel line and slope ratio assays have been added to ROBSYS.

Purification and biochemica characterisation of endoplasmic reticulum α 1,2-mannosidase from Sporothrix schenckiil

Alpha 1,2-mannosidases from glycosyl hydrolase family 47 participate in N-glycan biosynthesis. In filamentous fungi and mammalian cells, α1,2-mannosidases are present in the endoplasmic reticulum (ER) and Golgi complex and are required to generate complex N-glycans. However, lower eukaryotes such Saccharomyces cerevisiae contain only one α1,2-mannosidase in the lumen of the ER and synthesise high-mannose N-glycans. Little is known about the N-glycan structure and the enzyme machinery involved in the synthesis of these oligosaccharides in the dimorphic fungus Sporothrix schenckii. Here, a membrane-bound α-mannosidase from S. schenckii was solubilised using a high-temperature procedure and purified by conventional methods of protein isolation. Analytical zymograms revealed a polypeptide of 75 kDa to be responsible for enzyme activity and this purified protein was recognised by anti-α1,2-mannosidase antibodies. The enzyme hydrolysed Man9GlcNAc2 into Man8GlcNAc2 isomer B and was inhibited preferentially by 1-deoxymannojirimycin. This α1,2-mannosidase was localised in the ER, with the catalytic domain within the lumen of this compartment. These properties are consistent with an ER-localised α1,2-mannosidase of glycosyl hydrolase family 47. Our results also suggested that in contrast to other filamentous fungi, S. schenckii lacks Golgi α1,2-mannosidases and therefore, the processing of N-glycans by α1,2-mannosidases is similar to that present in lower eukaryotes.

The agreement between ipsative and normative questionnaires using compositional data analysis techniques

The main instrument used in psychological measurement is the self-report questionnaire. One of its majordrawbacks however is its susceptibility to response biases. A known strategy to control these biases hasbeen the use of so-called ipsative items. Ipsative items are items that require the respondent to makebetween-scale comparisons within each item. The selected option determines to which scale the weight ofthe answer is attributed. Consequently in questionnaires only consisting of ipsative items everyrespondent is allotted an equal amount, i.e. the total score, that each can distribute differently over thescales. Therefore this type of response format yields data that can be considered compositional from itsinception.Methodological oriented psychologists have heavily criticized this type of item format, since the resultingdata is also marked by the associated unfavourable statistical properties. Nevertheless, clinicians havekept using these questionnaires to their satisfaction. This investigation therefore aims to evaluate bothpositions and addresses the similarities and differences between the two data collection methods. Theultimate objective is to formulate a guideline when to use which type of item format.The comparison is based on data obtained with both an ipsative and normative version of threepsychological questionnaires, which were administered to 502 first-year students in psychology accordingto a balanced within-subjects design. Previous research only compared the direct ipsative scale scoreswith the derived ipsative scale scores. The use of compositional data analysis techniques also enables oneto compare derived normative score ratios with direct normative score ratios. The addition of the secondcomparison not only offers the advantage of a better-balanced research strategy. In principle it also allowsfor parametric testing in the evaluation

A review of sensor fusion techniques for underwater vehicle navigation

This work provides a general description of the multi sensor data fusion concept, along with a new classification of currently used sensor fusion techniques for unmanned underwater vehicles (UUV). Unlike previous proposals that focus the classification on the sensors involved in the fusion, we propose a synthetic approach that is focused on the techniques involved in the fusion and their applications in UUV navigation. We believe that our approach is better oriented towards the development of sensor fusion systems, since a sensor fusion architecture should be first of all focused on its goals and then on the fused sensors

Overview of coded light projection techniques for automatic 3D profiling

Obtaining automatic 3D profile of objects is one of the most important issues in computer vision. With this information, a large number of applications become feasible: from visual inspection of industrial parts to 3D reconstruction of the environment for mobile robots. In order to achieve 3D data, range finders can be used. Coded structured light approach is one of the most widely used techniques to retrieve 3D information of an unknown surface. An overview of the existing techniques as well as a new classification of patterns for structured light sensors is presented. This kind of systems belong to the group of active triangulation method, which are based on projecting a light pattern and imaging the illuminated scene from one or more points of view. Since the patterns are coded, correspondences between points of the image(s) and points of the projected pattern can be easily found. Once correspondences are found, a classical triangulation strategy between camera(s) and projector device leads to the reconstruction of the surface. Advantages and constraints of the different patterns are discussed

Imaging techniques and histology in the evaluation of liver fibrosis in hepatosplenic schistosomiasis mansoni in Brazil: a comparative study

Few publications have compared ultrasound (US) to histology in diagnosing schistosomiasis-induced liver fibrosis (LF); none has used magnetic resonance (MR). The aim of this study was to evaluate schistosomal LF using these three methods. Fourteen patients with hepatosplenic schistosomiasis admitted to hospital for surgical treatment of variceal bleeding were investigated. They were submitted to upper digestive endoscopy, US, MR and wedge liver biopsy. The World Health Organization protocol for US in schistosomiasis was used. Hepatic fibrosis was classified as absent, slight, moderate or intense. Histology and MR confirmed Symmers' fibrosis in all cases. US failed to detect it in one patient. Moderate agreement was found comparing US to MR; poor agreement was found when US or MR were compared to histology. Re-classifying LF as only slight or intense created moderate agreement between imaging techniques and histology. Histomorphometry did not separate slight from intense LF. Two patients with advanced hepatosplenic schistosomiasis presented slight LF. Our data suggest that the presence of the characteristic periportal fibrosis, diagnosed by US, MR or histology, associated with a sign of portal hypertension, defines the severity of the disease. We conclude that imaging techniques are reliable to define the presence of LF but fail in grading its intensity.

An overview of the advantages and constraints of coded pattern projection techniques for autonomous navigation

The absolute necessity of obtaining 3D information of structured and unknown environments in autonomous navigation reduce considerably the set of sensors that can be used. The necessity to know, at each time, the position of the mobile robot with respect to the scene is indispensable. Furthermore, this information must be obtained in the least computing time. Stereo vision is an attractive and widely used method, but, it is rather limited to make fast 3D surface maps, due to the correspondence problem. The spatial and temporal correspondence among images can be alleviated using a method based on structured light. This relationship can be directly found codifying the projected light; then each imaged region of the projected pattern carries the needed information to solve the correspondence problem. We present the most significant techniques, used in recent years, concerning the coded structured light method

Assessment of Severe Apnoea through Voice Analysis, Automatic Speech, and Speaker Recognition Techniques

This study is part of an ongoing collaborative effort between the medical and the signal processing communities to promote research on applying standard Automatic Speech Recognition (ASR) techniques for the automatic diagnosis of patients with severe obstructive sleep apnoea (OSA). Early detection of severe apnoea cases is important so that patients can receive early treatment. Effective ASR-based detection could dramatically cut medical testing time. Working with a carefully designed speech database of healthy and apnoea subjects, we describe an acoustic search for distinctive apnoea voice characteristics. We also study abnormal nasalization in OSA patients by modelling vowels in nasal and nonnasal phonetic contexts using Gaussian Mixture Model (GMM) pattern recognition on speech spectra. Finally, we present experimental findings regarding the discriminative power of GMMs applied to severe apnoea detection. We have achieved an 81% correct classification rate, which is very promising and underpins the interest in this line of inquiry.

Use of accuracy profile for the validation of a gas chromatography-negative chemical ionization tandem mass spectrometry method: quantification of ethyl glucuronide in hair

Introduction: Ethylglucuronide (EtG) is a direct and specific metabolite of ethanol. Its determination in hair is of increasing interest for detecting and monitoring alcohol abuse. The quantification of EtG in hair requires analytical methods showing highest sensitivity and specificity. We present a fully validated method based on gas chromatography-negative chemical ionization tandem mass spectrometry (GC-NCI-MS/MS). The method was validated using French Society of Pharmaceutical Sciences and Techniques (SFSTP) guidelines which are based on the determination of the total measurement error and accuracy profiles. Methods: Washed and powdered hair is extracted in water using an ultrasonic incubation. After purification by Oasis MAX solid phase extraction, the derivatized EtG is detected and quantified by GC-NCI-MS/MS method in the selected reaction monitoring mode. The transitions m/z 347 / 163 and m/z 347 / 119 were used for the quantification and identification of EtG. Four quality controls (QC) prepared with hair samples taken post mortem from 2 subjects with a known history of alcoholism were used. A proficiency test with 7 participating laboratories was first run to validate the EtG concentration of each QC sample. Considering the results of this test, these samples were then used as internal controls for validation of the method. Results: The mean EtG concentrations measured in the 4 QC were 259.4, 130.4, 40.8, and 8.4 pg/mg hair. Method validation has shown linearity between 8.4 and 259.4 pg/mg hair (r2 > 0.999). The lower limit of quantification was set up at 8.4 pg/mg. Repeatability and intermediate precision were found less than 13.2% for all concentrations tested. Conclusion: The method proved to be suitable for routine analysis of EtG in hair. GC-NCI-MS/MS method was then successfully applied to the analysis of EtG in hair samples collected from different alcohol consumers.

Evaluation of rapid techniques for the detection of mycobacteria in sputum with scanty bacilli or clinically evident, smear negative cases of pulmonary and extra-pulmonary tuberculosis

The objective of the current study was to compare two rapid methods, the BBL Mycobacteria Growth Indicator Tube (MGIT TM) and Biotec FASTPlaque TB TM (FPTB) assays, with the conventional Löwenstein-Jensen (LJ) media assay to diagnose mycobacterial infections from paucibacillary clinical specimens. For evaluation of the clinical utility of the BBL MGIT TM and FPTB assays, respiratory tract specimens (n = 208), with scanty bacilli or clinically evident, smear negative cases and non-respiratory tract specimens (n = 119) were analyzed and the performance of each assay was compared with LJ media. MGIT and FPTB demonstrated a greater sensitivity (95.92% and 87.68%), specificity (94.59% and 98.78%), positive predictive value (94.91% and 99.16%) and negative predictive value (96.56% and 90.92%), respectively, compared to LJ culture for both respiratory tract and non-respiratory tract specimens. However, the FPTB assay was unable to detect nontuberculous mycobacteria and few Mycobacterium tuberculosis complex cases from paucibacillary clinical specimens. It is likely that the analytical sensitivity of FPTB is moderately low and may not be useful for the direct detection of tuberculosis in paucibacillary specimens. The current study concluded that MGIT was a dependable, highly efficient system for recovery of M. tuberculosis complexes and nontuberculous mycobacteria from both respiratory and non-respiratory tract specimens in combination with LJ media.

Evaluation of two coproscopic techniques for the diagnosis of schistosomiasis in a low-transmission area in the state of Minas Gerais, Brazil

This population study, which evaluated two parasitological methods for the diagnosis of schistosomiasis mansoni, was performed in a low-transmission area in Pedra Preta, Montes Claros, Minas Gerais, Brazil. A total of 201 inhabitants of the rural area participated in this research. Four stool samples were obtained from all participants and analysed using the Kato-Katz method (18 slides) and a commercial test, the TF-Test®, which was performed quantitatively. The data were analysed to determine prevalence, the sensitivity of the diagnostic methods, the worm burden and the definition of the "gold standard", which was obtained by totalling the results of all samples examined using the Kato-Katz technique and the TF-Test®. The results showed that the prevalence obtained from the examination of one Kato-Katz slide (the methodology adopted by the Brazilian control programme) was 8% compared to 35.8% from the "gold standard", which was a 4.5-fold difference. This result indicates that the prevalence of schistosomiasis in so-called low-transmission areas is significantly underestimated.

Laboratory detection of respiratory viruses by automated techniques.

Advances in clinical virology for detecting respiratory viruses have been focused on nucleic acids amplification techniques, which have converted in the reference method for the diagnosis of acute respiratory infections of viral aetiology. Improvements of current commercial molecular assays to reduce hands-on-time rely on two strategies, a stepwise automation (semi-automation) and the complete automation of the whole procedure. Contributions to the former strategy have been the use of automated nucleic acids extractors, multiplex PCR, real-time PCR and/or DNA arrays for detection of amplicons. Commercial fully-automated molecular systems are now available for the detection of respiratory viruses. Some of them could convert in point-of-care methods substituting antigen tests for detection of respiratory syncytial virus and influenza A and B viruses. This article describes laboratory methods for detection of respiratory viruses. A cost-effective and rational diagnostic algorithm is proposed, considering technical aspects of the available assays, infrastructure possibilities of each laboratory and clinic-epidemiologic factors of the infection.

Application of Molecular Diagnostic Techniques for Viral Testing.

Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory.