Perturbation measurements in highly irregular voice signals: Performances/validity of analysis software tools

In this paper we present results concerning validity of jitter measurement in strongly irregular voice signals (sustained vowels) moderately corrupted by noise. The performance of four tools for voice analysis is compared on synthetic signals as far as fundamental period and jitter estimation are concerned. Synthesised vowels offer the advantage of a perfect control of the amount of jitter put in.Though implementing the same formula for jitter estimation, the results obtained with these approaches become quite different for increasing jitter. The reason could be searched in the different methods used for the separation of voiced and unvoiced frames as well as for fundamental period estimation.Results show that all the tools give reliable results up to a jitter level J = 15%, that encompasses the maximum value J = 12% as obtained by expert raters by visual inspection. Hence, up to this limit, the tools presented here for jitter estimation can give a valid support to clinicians also in term of reproducibility of results and time saving.For jitter values larger than 15% all programs tend to underestimate the true jitter value, but with large differences among them. Just two methods succeed in estimating jitter values up to and larger than 20% and could thus be better suited for perturbation measure in strongly irregular voice signals.     

Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods

The genomic DNA-DNA hybridization (DDH) method has been widely used as a practical method for the determination of phylogenetic relationships between closely related biological strains. Traditional DDH methods have serious limitations including low reproducibility, a high background and a time-consuming procedure. The DDH method using a genome-probing microarray (GPM) has been recently developed to complement conventional methods and could be used to overcome the limitations that are typically encountered. It is necessary to compare the GPM-based DDH method to the conventional methods before using the GPM for the estimation of genomic similarities since all of the previous scientific data have been entirely dependent on conventional DDH methods. In order to address this issue we compared the DDH values obtained using the GPM, microplate and nylon membrane methods to multi-locus sequence typing (MLST) data for 9 Salmonella genomes and an Escherichia coli type strain. The results showed that the genome similarity values and the degrees of standard deviation obtained using the GPM method were lower than those obtained with the microplate and nylon membrane methods. The dendrogram from the cluster analysis of GPM DDH values was consistent with the phylogenetic tree obtained from the multi-locus sequence typing (MLST) data but was not similar to those obtained using the microplate and nylon membrane methods. Although the signal intensity had to be maximal when the targets were hybridized to their own probe, the methods using membranes and microplates frequently produced higher signals in the heterologous hybridizations than those obtained in the homologous hybridizations. Only the GPM method produced the highest signal intensity in homologous hybridizations. These results show that the GPM method can be used to obtain results that are more accurate than those generated by the other methods tested.     

Photometric determination of the DNA distribution in the 24 human chromosomes

From five normal individuals the DNA content and the DNA arm ratios of the 24 metaphase chromosomes were determined by means of scanning densitometry of photographic negatives of Feulgen-stained metaphase preparations. The results showed high reproducibility of the measuring procedure. The obtained DNA values for the 24 chromosomes showed general correspondence between the individuals. No differences between males and females were found. The DNA arm ratios showed somewhat higher inter-individual variability, especially for the acrocentric chromosomes. Our data are in agreement with other data published so far, which were obtained with somewhat different techniques, indicating that the DNA content of the individual human chromosomes in general is highly constant. Attempts were made to distinguish chromosomes by their DNA content and DNA ratio. It appears that classification of chromosomes using these parameters cannot compete with classification according to the banding patterns. Determination of the total DNA content and DNA distribution along the metaphase chromosomes may, however, provide a frame of reference for cytochemical methods directed towards the localization and quantification of molecular properties of the chromosome.     

Statistical superiority of genome-probing microarrays as genomic DNA–DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods

The genomic DNA–DNA hybridization (DDH) method has been widely used as a practical method for the determination of phylogenetic relationships between closely related biological strains. Traditional DDH methods have serious limitations including low reproducibility, a high background and a time-consuming procedure. The DDH method using a genome-probing microarray (GPM) has been recently developed to complement conventional methods and could be used to overcome the limitations that are typically encountered. It is necessary to compare the GPM-based DDH method to the conventional methods before using the GPM for the estimation of genomic similarities since all of the previous scientific data have been entirely dependent on conventional DDH methods. In order to address this issue we compared the DDH values obtained using the GPM, microplate and nylon membrane methods to multi-locus sequence typing (MLST) data for 9 Salmonella genomes and an Escherichia coli type strain. The results showed that the genome similarity values and the degrees of standard deviation obtained using the GPM method were lower than those obtained with the microplate and nylon membrane methods. The dendrogram from the cluster analysis of GPM DDH values was consistent with the phylogenetic tree obtained from the multi-locus sequence typing (MLST) data but was not similar to those obtained using the microplate and nylon membrane methods. Although the signal intensity had to be maximal when the targets were hybridized to their own probe, the methods using membranes and microplates frequently produced higher signals in the heterologous hybridizations than those obtained in the homologous hybridizations. Only the GPM method produced the highest signal intensity in homologous hybridizations. These results show that the GPM method can be used to obtain results that are more accurate than those generated by the other methods tested.     

Analysis of flux estimates based on (13)C-labelling experiments.

Modelling of the fluxes in central metabolism can be performed by combining labelling experiments with metabolite balancing. Using this approach, multiple samples from a cultivation of Saccharomyces cerevisiae in metabolic and isotopic steady state were analysed, and the metabolic fluxes in central metabolism were estimated. In the various samples, the estimates of the central metabolic pathways, the tricarboxylic acid cycle, the oxidative pentose phosphate pathway and the anaplerotic pathway, showed an unprecedented reproducibility. The high reproducibility was obtained with fractional labellings of individual carbon atoms as the calculational base, illustrating that the more complex modelling using isotopomers is not necessarily superior with respect to reproducibility of the flux estimates. Based on these results some general difficulties in flux estimation are discussed.     

Estimation of the absolute density of adult Ixodes persulcatus ticks according to the results of collecting per flag-hour (Ixodidae)

The results of two methods of estimation of abundance of adult Ixodes persulcatus ticks, the absolute (at the sample plots) and the relative (per flag-hour) estimations, were compared. Collecting of ticks and estimation of their abundance was conducted during 9 years at the forests of the Far East and Pre-Ural region. The total of 1995 plots (100 sq. m each) were studied and 865 flag-hours were carried out. A good correlation of the data, obtained by these methods, was revealed. The average number of adult ticks, collected per flag-hour, approximately corresponds to the average number of ticks, activated during the season at 100 sq. m. The possibility of corresponding re-calculation of the results of estimation per flag-hour into the parameters of tick population density was evaluated. It was shown that such re-calculation gives good results. Their inexactitude usually doesn't exceed the statistical error of the parameters, obtained by the estimation of tick density at sample plots.     

Multivariate assessment of activated sludge stability in lab-scale experiments

In wastewater research, the transfer of activated sludge from large-scale plants to lab-scale reactors induces a transient period. It is crucial to quantitatively assess the stability of activated sludge before starting any experimental procedure. Otherwise, the transient interferes with the experimental results, jeopardizing reproducibility and accuracy. This paper presents a novel multivariate technique to assess activated sludge stability based on the combination of principal component analysis (PCA) with the squared prediction error (SPE) statistic. The proposed method allows for a more accurate estimation of activated sludge stability than existing univariate methods and also eliminates the need to establish thresholds for every single variable. The procedure is validated on experimental data obtained by Van den Broeck et al. [1].     

Comparison of two measuring methods for the evaluation of C-heterochromatin in human chromosomes

Summary In this study two different methods for evaluating the size of the C heterochromatin blocks of human chromosomes 1, 9, 16, and Y were compared. The first method measured the lengths of both the euchromatin and the C heterochromatin parts of the p and q arms of chromosomes 1, 9, 16, and Y. The second method analyzed the same chromosome segments, but by measuring the areas.In the comparison, the relative C heterochromatin value (length or surface) of each chromosome, the mean for each individual, the standard deviation, and the coefficient of variation were taken into account. It is proposed that the best estimation for the size of a C heterochromatin segment is the ratio of its length to the total length of the chromosome; accurate estimation requires at least 20 metaphases.     

Utility of the hot-wire spirometer

A comparative study has been carried out to investigate the performance of the hot-wire spirometer and the Rollingseal spirometer; the reproducibility of the data generated by an individual examiner; and the validity of data obtained by an "inexperienced examiner" using the hot-wire spirometer. The following results were obtained: 1. The experimental data given by the hot-wire spirometer were about 5-6% higher for FVC and FEV1, and about 10-12% higher for PFR, V50, and V25, respectively, when compared to the data generated by the Rollingseal spirometer. 2. The reproducibility of the data produced by the hot-wire spirometer operated by an "experienced examiner" was good, as the percent difference was about +/- 3%. 3. Reliable data were obtained with the spirometer even by an "inexperienced examiner" if he/she has gone through an on-site training concerning instrumentation and measurement methods for spirography.     

Variability of the C-segment sizes of chromosomes 1, 9, 16 and Y in the human chromosome set]

The investigation of chromosome polymorphism by quantitative methods is a rather hard task. The manual method for measuring C-segments of chromosomes 1, 9, 16 and Y in man is suggested, which is not difficult, being reasonably precise for the population research. Metaphases of the average level of chromosome condensation were taken for analysis. Only the C-segments were measured without measuring chromosomes. The negative chromosome image was 4000-fold magnified, compared to the chromosome natural size, and the boundaries of C-segments of each chromosome were five-fold dotted on a sheet of paper specially printed for this purpose. C-segments were measured by magnifying glass with 0.025 mcm scale unit. For every individuum, C-segments were measured in 5-7 cells only. The data are presented on the estimation of measurement errors and on individual (intercellular) and population (interindividual) variations of C-segments of chromosomes.     

Principles of cytogenetic examination for detecting occupational hazards

The main principles are stated of carrying out a cytogenetic examination of human populations on the basis of critical analysis of data from literature and the authors' own experience in this field. The method for estimation of sister chromatid exchanges is shown expedient to be used together with the chromosome aberration analysis in carrying out cytogenetic examinations. Statistically ascertained approaches are adduced to select the necessary amount of persons examined in groups and the number of cells for analysis when using methods for estimation of sister chromatid exchanges and chromosome aberrations.     

Preparation of samples of biological fluids for electron spin resonance (ESR) examination

The ESR (Electron Spin Resonance) Technique, is usually used in the study of Free Radicals and Metal - Proteins, in biological fluids, but the most apt method for the preparation of the sample has still to be defined. In this work the A.A. describe and analyse the negative and positive aspects of several methods. The results of the E.S.R. spectra, obtained by means of lyophilization, that is the most used method in literature, have been compared with those obtained by means of concentration of some biological fluid (serum and synovial fluid). The A.A. demonstrated that the lyophilization does not permit the reproducibility of the spectra, for different spectra are obtained from the same lyophilized serum and synovial fluid samples. A high reproducibility of the spectra is instead obtained by the concentration of the sample means of the "collodion bag" or "Aquacide" methods. The A.A. are convinced that for on exact investigation of the E.S.R. Signals, only the concentration method is useful, and not the lyophilization method as reported in literature.     

An evaluation of the analysis system of video transects used to sample subtidal epibiota

Two popular methods of benthic cover estimation (the point intercept technique with two sets of position points, and digital interactive color segmentation) were compared with an alternative method of digital cover estimation using Bezier curves as a tool for outlining the objects on an images and AutoCAD® software for the final evaluation of abundance. The comparison was done using still video images obtained from two 10-m transects on subtidal rocks off the Rimsky-Korsakov islands in the Sea of Japan (Russia). Ten rectangular sectors (1×0.4 m each) selected randomly within both video transects were analyzed. One-way ANOVA for repeated measurements was used to test the differences between methods. The point intercept technique differed significantly from both methods of digital estimation and had an essential positive bias. The Tukey multiple comparison test revealed the differences among digital estimation methods in the species, which have the complicated color with many contrast spots. The proposed approach using Bezier curves has an advantage over the interactive color segmentation if the objects under selection are lit at different levels or have a contrast coloration or are hidden by canopy organisms. Besides, estimation of cover in the field of AutoCAD® software is more precise and takes less time than that obtained using a scaled grid, available for automatically segmented species. The results showed that digital cover estimation using Bezier curves and AutoCAD® software is a convenient method for analyzing benthic samples at large spatial scales.     

Application of ethidium bromide for high-resolution banding analysis of chromosomes from human malignant cells

Ethidium bromide was added to cultured human leukemic bone marrow and solid tumor cells to evaluate its inhibitory effect on mitotic chromosome condensation and its possible application to high-resolution banding analysis. In most experiments ethidium bromide treatment resulted in a high proportion of mitotic cells having elongated chromosomes, without remarkable reduction in either the mitotic index or quality of metaphase chromosomes. Optimal effect on chromosome length was obtained by adding 10 micrograms/ml of ethidium bromide during the final 2 hr of culture. Because of the simplicity and reproducibility of the technique involved, ethidium bromide can be used routinely to extend the length of chromosomes for fine-banding analysis of malignant cells.     

A Comparison of Generalized Poisson Distribution for Modeling Chromosome Aberrations

Various models have been developed for modeling the distribution of chromosome aberrations in the literature (e. g. Consul, 1989). Generalized Poisson distribution is among the popular ones. The parameters of this distribution provide meaningful interpretation of the induction mechanism of the chromosome aberrations. In this article, we apply several estimation methods to estimate the generalized Poisson parameters for fitting the number of chromosome aberrations under different dosages of radiations. The methods compared are moment, maximum likelihood, minimum chi-square, weighted discrepancy and empirically weighted rates of change. Our study suggests that the empirically weighted rates of change method results in smallest Mean Square Error and Mean Absolute Error for most dosages of radiations. The data used for this comparison are from Janardan and Schaeffer (1977).     

Chromosome banding in sturgeons

The article reviews the present knowledge of chromosome banding in sturgeons and summarizes recent findings obtained by both classical banding techniques (C-banding, fluorescent and silver staining) and molecular methods, such as fluorescent in situ hybridization (FISH). The results are discussed in relation to karyotype organization and chromosome evolution in sturgeons.     

A Critical Review of Home Range Studies

Abstract No consensus currently exists for the methods of estimation of home range size or for reporting home-range analysis results. Studies currently employ a variety of disparate methods or provide inadequate information for reproducing their analyses. We reviewed 161 home range studies published in 2004, 2005, and 2006 to assess what methods are currently employed and how results are reported. We found that home range reporting was generally inadequate for reproducing studies; that the methods employed varied considerably; that home range estimates were often reported and analyzed using inappropriate methods; and that many comparisons were made between studies that may produce spurious results. We urge for minimum editorial standards for reporting home range studies and we urge researchers to follow a unified methodology for estimating animal home ranges. We supply recommendations for such reporting and methodology. These recommendations will increase the reproducibility of studies and allow for more robust comparisons between studies.     

PCC-FISH in skin fibroblasts for local dose assessment: biodosimetric analysis of a victim of the Georgian radiological accident

We propose a new method of biodosimetry that could be applied in cases of localized irradiation. The approach is based on excess chromosome segments determination by the PCC-FISH technique in fibroblasts isolated from skin biopsy. Typically, 0 to 10 Gy ex vivo gamma-irradiated human skin biopsies were dissociated and fibroblasts were isolated and grown for several days. Cells next underwent PCC-FISH painting of whole chromosome 4, and the number of excess chromosome segments per metaphase was determined. An ex vivo reference curve correlating the number of excess chromosome segments per metaphase to the radiation dose was established and used to assess the dose delivered to the skin of one of the victims of the radiological accident that occurred at Lia in Georgia in December 2001. Specifically, the victim suffering from moist desquamation underwent skin excision in Hospital Percy (France). Measurement of excess chromosome segments per metaphase was done in fibroblasts isolated and grown from removed wounded skin and subsequent conversion to radiation doses was performed. The radiation dose map obtained was shown to be in accordance with clinical data and physical dosimetry as well as with conventional biodosimetry. These results demonstrated that PCC-FISH painting applied to skin fibroblasts may be a suitable technique for dose estimation. To assess its worth, this approach needs to be extended to future accidents involving localized radiation exposure.     

Application of Ethidium Bromide for High-Resolution Banding Analysis of Chromosomes from Human Malignant Cells

Ethidium bromide was added to cultured human leukemic bone marrow and solid tumor cells to evaluate its inhibitory effect on mitotic chromosome condensation and its possible application to high-resolution banding analysis. In most experiments ethidium bromide treatment resulted in a high proportion of mitotic cells having elongated chromosomes, without remarkable reduction in either the mitotic index or quality of metaphase chromosomes. Optimal effect on chromosome length was obtained by adding 10 μg/ml of ethidium bromide during the final 2 hr of culture. Because of the simplicity and reproducibility of the technique involved, ethidium bromide can be used routinely to extend the length of chromosomes for fine-banding analysis of malignant cells.     

Comparison of image registration performed with MV cone beam CT and CT on rails and Syngo™ Adaptive Targeting software

BackgroundMinimization of geometric errors in treatment delivery is essential in modern conformal and intensity-modulated techniques.AimIn this paper two Siemens systems, MVision megavoltage cone beam CT, and CTVision (CT on rails), are compared.Material and MethodsThe reproducibility and uncertainty of the image registration procedure performed with Adaptive Targeting (AT) software were evaluated. Both systems were evaluated by means of simulating the clinical situation with an anthropomorphic phantom in three anatomical sites: head & neck, thorax and pelvis.ResultsThe results for two methods of image registration, manual and automatic, were evaluated separately. The manual procedure was used by two users, more and less experienced.ConclusionsThe MVision system and CTVision and the Therapist Adaptive software ensure image registration with the uncertainty of about 2.0 mm (2 standard deviations). In the case of the automatic registration method better reproducibility of image registration was obtained for MVision. For CTVision the necessity of manual identification of the machine isocentre made the registration less reproducible. In the case of MVision, the automatic method was more reproducible than the manual one (smaller dispersion of results). In the case of CTVision, similar results were obtained for both registration methods. In the case of manual registration slightly better reproducibility for CT data acquired at 2 mm slice thickness and 2 mm slice separation than for data acquired at 5 mm slice thickness and 5 mm slice separation were obtained. Similar results of manual registration performed by more and less experienced users were obtained.