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PubMedDate not supplied

[Electrophoretic patterns of cell wall protein as a criterion for the identification and classification of Corynebacteria].

Electrophoretic patterns of cell wall protein of three industrial strains, that were used for production of lysin, and eight collection strains from the genus Corynevacterium were studied to analyze their similarity as well as to estimate an opportunity of using this parameter as an additional criterion for identification and classification of corynebacteria. Similarity coefficient of cell wall overall and main protein electrophoretic patterns were determined by a specially created computer program. Electrophoretic analysis showed that every specie had an individual protein profile. There were determined biopolymers common for the specie, genus and individual among the overall majors and minors. The obtained results showed, that the patterns of main proteins were more conservative and informative in comparison with those ones of overall proteins. The definition of similarity coefficient by the main protein patterns has correlated with the protein profile characteristics of every analyzed strain, and it managed to distribute them into the separate groups. The similarity coefficient of preparations by the main protein patterns allows to separate one specie or a strain from another, and that gives us a chance to claim that this parameter could be used as an additional criterion for differentiation and referring the corynebacteria to a certain taxonomic group.

Bacterial Proteins↗
PubMedDate not supplied

[A new method of identifying a systems based on the minimal quadratic discrepancy criterion for biophysics problems].

A wide range of biophysical systems are described by nonlinear dynamic models mathematically presented as a set of ordinary differential equations in the Cauchy explicit form: [formula: see text] Fij(X1(t),..,XN(t),t), (i = 1,...,N, j = 1,...,M), where Fij (X1(t), ..., XN(t), t) is a set of basis functions satisfying the Lipschitz condition. We investigate the problem of evaluation of model constants aij (the system identification) using experimental data about the time dependence of the dynamic parameters of the system Xi(t). A new method of system identification for the class of similar nonlinear dynamic models is proposed. It is shown that the problem of identifying an initial nonlinear model can be reduced to the solution of a system of linear equations for the matrix of the dynamic model constants [aj]i. It is proposed to determine the set of dynamic model constants aij using the criterion of minimal quadratic discrepancy for the time dependence of the set of dynamic parameters Xi(t). An important special case of the nonlinear model, the quadratic model, is considered. Test problems of identification using this method are presented for two nonlinear systems: the Van der Pol type multiparametric nonlinear oscillator and the strange attractor of Ressler, a widely known example of dynamic systems showing the stochastic behavior.

Algorithms↗
PubMed2005

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments.

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR Pulsar quadrupole-TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

Algorithms↗
PubMed2002

[Personal emergency call system based on human vital and system technical parameters in a Smart Home environment].

Progress in microtechnology and radio transmission technology has enabled the development of highly reliable emergency-call systems. The present article describes systems that have been specially designed to improve the safety and independence of handicapped and elderly persons living at home. For such persons immediate help in an emergency situation is of crucial importance. The technical state of the art of emergency-call systems specially developed for use by the elderly, is briefly discussed, in particular the well-known radio emergency-call button, with the aid of which an alarm can be activated manually. This system, however, does not offer adequate safety in all emergency situations. Alternative or complementary systems designed to automatically trigger an alarm on the basis of the recording and evaluation of so-called vital parameters, are therefore proposed. In addition, in a smart-home environment with networked devices, further parameters--so-called environment parameters can be used. It is found that the identification of an emergency situation becomes more reliable as the number of parameters employed increases.

Aged↗
PubMed1985

Retrieval of analytical data and substance identification in systematic toxicological analysis by the mean list length approach.

Chromatographic techniques are basic tools in systematic toxicological analysis. Extensive data bases with retention parameters of known drugs to aid in the identification of substances found are available or in preparation. For a search in such a data base the computer is indispenable. The commonly used window search has some disadvantages which can be overcome by a search based on the statistical concept, the mean list length. The latter retrieval system gives for each candidate in the identification process a probability value. It is shown that these probability values are highly influenced by the reproducibility of the retention parameters of the analytical systems used. Explanations for these phenomena are given.

Chromatography, Gas↗
PubMed1998

Identification of the stimulated hemiretinae using a reduced number of PVEP trials.

Left and right hemifield pattern-reversal visual evoked potentials (PVEP) at P100 latency are characterised by typical field distributions of potential and the spectral parameter instantaneous frequency (IF). Both parameters can be utilised for the correct identification of the stimulated hemiretina in healthy volunteers (Hoffmann, K. et al. Electroenceph. clin. Neurophysiol., 100, 1996: 569-578). The aim of this study was the investigation of the robustness of instantaneous frequency for reduced numbers of averages. Hemifield PVEP of 15 volunteers (20 channel records) were analysed. The number of averages was reduced step-by-step (64-32-16-8-4-1). For each average, the time of P100 latency was determined by the Global field power maximum between 90 and 125 ms. The stimulated hemifield was identified using the potential or instantaneous frequency values at the occipital electrode positions O1 and O2: by maximal potential and instantaneous frequency on the stimulus-contralateral side. In summary, by reduced numbers of averages (as well as by single trials) the stimulated hemiretina was correctly identified more frequently on the basis of instantaneous frequency than of potential distribution. A number of 8 averages seems to be sufficient for the correct identification of the stimulus condition. Consequently, for the identification of left and right hemifield stimulations the recording time could be reduced immensely. Instantaneous frequency is suggested as an additional and robust parameter for the selective averaging of artefact-free trials during the recording of hemifield PVEP.

Adult↗
PubMed1997

[Identification of major gene and polygene mixed inheritance model and estimation of genetic parameters of a quantitative trait from F2 progeny].

It has been proved by many field experiments and QTL mapping results that among genes affecting some quantitative traits there are some major genes with larger genetic effect and some polygenes with smaller genetic effect. For such traits, the distribution of segregating population demonstrates multimodality, and this is the characteristic of the mixture of more than one distributions. Mixture distribution models have been used extensively as models in a wide variety of practical situations where data can be viewed as arising from two or more populations mixed in certain proportions. Akaike's Information Criterion(AIC) has been used to identify the existence of major genes affecting quantitative traits. Under the existence of major genes, the genetic effects of these genes and their genetic variance were estimated through segregation analysis. The genotype of major gene of F2 individuals of were determined by clustering using Bayesian criterion. With P1, P2, F1 and F2 populations, the likelihood ratio test was used to test the existence of polygenes. In the end, the inheritance of soybean flowering date is analyzed. One major gene was found in F2 population derived from Guludou x Shanghaihongmangzao.

Models, Genetic↗
PubMed2003

Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates.

Ribonuclease E is required for the rapid decay and correct processing of RNA in Escherichia coli. A detailed understanding of the hydrolysis of RNA by this and related enzymes will require the integration of structural and molecular data with quantitative measurements of RNA hydrolysis. Therefore, an assay for RNaseE that can be set up to have relatively high throughput while being sensitive and quantitative will be advantageous. Here we describe such an assay, which is based on the automated high pressure liquid chromatography analysis of fluorescently labeled RNA samples. We have used this assay to optimize reaction conditions, to determine for the first time the catalytic parameters for a polypeptide of RNaseE, and to investigate the RNaseE-catalyzed reaction through the modification of functional groups within an RNA substrate. We find that catalysis is dependent on both protonated and unprotonated functional groups and that the recognition of a guanosine sequence determinant that is upstream of the scissile bond appears to consist of interactions with the exocyclic 2-amino group, the 7N of the nucleobase and the imino proton or 6-keto group. Additionally, we find that a ribose-like sugar conformation is preferred in the 5'-nucleotide of the scissile phosphodiester bond and that a 2'-hydroxyl group proton is not essential. Steric bulk at the 2' position in the 5'-nucleotide appears to be inhibitory to the reaction. Combined, these observations establish a foundation for the functional interpretation of a three-dimensional structure of the catalytic domain of RNaseE when solved.

Base Sequence↗
PubMed1999

Estimating the genetic architecture of quantitative traits.

Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architecture parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance. With multiple traits and multiple environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment interactions can also be estimated. We review the method and discuss issues associated with multiple interval mapping, such as likelihood analysis, model selection, stopping rules and parameter estimation. The potential power and advantages of the method for mapping multiple QTL and estimating the genetic architecture are discussed. We also point out potential problems and difficulties in resolving the details of the genetic architecture as well as other areas that require further investigation. One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.

Algorithms↗
PubMed1976

Nomemclature of the proteins of cow's milk: fourth revision.

This report reviews the nomenclature of the milk proteins of cow's milk in light of more recent advances in our knowledge. With the establishment of the primary structures of a number of these proteins, we now have a definite identification of alphas1-, kappa-, beta-, and the gamma-caseins as well as beta-lactoglobulin and alpha-lactalbumin. On the basis of new information on their primary structures and relationship to beta-casein polymorphs, changes in nomenclature have been recommended for proteins of the gamma-casein fraction. Although the primary structure serves as the unambiguous definition of proteins for which it is known, a more practical identification is necessary. We recommend that their behavior in gel electrophoresis under suitable conditions be employed for this purpose for all of the "major" milk proteins of raw skim milk except the immunoglobulins where, because of their heterogeneity and molecular genetics, physical parameters are less useful and their identification must be based upon antigenic determinants and their homology with their human counterparts. More work is needed and, with the accumulation of more information, additional changes in nomenclature can be expected for such proteins as the minor components of alphas- and kappa-caseins, alpha-lactalbumin, and the proteose-peptone fraction as well as further confirmation of the presence of immunoglobulins IgE and additional IgG subclasses. Additional components and genetic variants also can be expected.

Animals↗
PubMed2005

Effects of envelope-vocoder processing on F0 discrimination and concurrent-vowel identification.

OBJECTIVE: The aim of this study was to examine the effects of envelope-vocoder sound processing on listeners' ability to discriminate changes in fundamental frequency (F0) in anechoic and reverberant conditions and on their ability to identify concurrent vowels based on differences in F0. DESIGN: In the first experiment, F0 difference limens (F0DLs) were measured as a function of number of envelope-vocoder frequency channels (1, 4, 8, 24, and 40 channels, and unprocessed) in four normal-hearing listeners, with degree of simulated reverberation (no, mild, and severe reverberation) as a parameter. In the second experiment, vowel identification was measured as a function of the F0 difference between two simultaneous vowels in six normal-hearing listeners, with the number of vocoder channels (8 and 24 channels, and unprocessed) as a parameter. RESULTS: Reverberation was detrimental to F0 discrimination in conditions with fewer numbers of vocoder channels. Despite the reasonable F0DLs (<1 semitone) with 24- and 8-channel vocoder processing, listeners were unable to benefit from F0 differences between the competing vowels in the concurrent-vowel paradigm. CONCLUSIONS: The overall detrimental effects of vocoder processing are probably are due to the poor spectral representation of the lower-order harmonics. The F0 information carried in the temporal envelope is weak, susceptible to reverberation, and may not suffice for source segregation. To the extent that vocoder processing simulates cochlear implant processing, users of current implant processing schemes are unlikely to benefit from F0 differences between competing talkers when listening to speech in complex environments. The results provide further incentive for finding a way to make the information from low-order, resolved harmonics available to cochlear implant users.

Acoustic Stimulation↗
PubMed2006

A closed-loop identification protocol for nonlinear dynamical systems.

A previous work introduced an optimal identification (OI) technique for reliably extracting model parameters of biochemical reaction systems from tailored laboratory experiments. The notion of optimality enters through seeking an external control in the laboratory producing data that leads to minimum uncertainties in the identified parameter distributions. A number of algorithmic and operational improvements are introduced in this paper to OI, aiming to build a more practical and efficient closed-loop identification protocol/procedure (CLIP) for nonlinear dynamical systems. The improvements in CLIP include (a) inversion cost function modification to preferably search for the upper and lower boundaries of the parameter distributions consistent with the observed data, (b) dynamic search range updating of the unknown parameters to better exploit the information from the prior iterative experiments, (c) replacing the control genetic algorithm by the simplex method to enable better balance between operational cost and inversion quality, and (d) utilizing virtual sensitivity optimization techniques to further reduce the laboratory costs. The workings of CLIP utilizing these new algorithms are illustrated in indentifying a simulated tRNA proofreading model, and the results demonstrate enhanced performance of CLIP in terms of algorithmic reliability and efficiency.

Journal Article↗
PubMed1989

Cytophotometry.

Basic differences and similarities of flow and static cytophotometric instruments are viewed with regard to technical peculiarities and applicability in the fields of biology and tumor pathology. In flow systems, precision of the information concerning quantities of constituents is high, whereas precision of information concerning morphologic parameters is low. In static systems, morphologic identification by a trained operator can be used advantageously to classify any given cell interactively, thus replacing a large number of flow parameters. This is why the vast majority of automated static machines used in pathology are still more or less semiautomatic or interactive. Carefully performed specimen-adapted cell preparation procedures in which each step is strictly supervised, highly standardized staining methods, and internal controls are prerequisites in order to obtain reliable cytochemical results. In a number of human tumors with well-controlled cytopathologic and/or histopathologic and clinical data, quantitative cytochemical analysis has been demonstrated to provide diagnostic and prognostic information complementary to that obtained by conventional clinical and morphologic methods.

Animals↗
PubMed2001

[New markers for the risk of sudden death: analysis of ventricular repolarization].

The identification of patients at high risk of sudden cardiac death is one of the greatest challenges for cardiologists. Non-invasive methods have, characteristically, low predictive sensitivities and specificities. The role of abnormalities of ventricular repolarisation (QT interval) in the genesis of ventricular arrhythmias has been well established by experimental data. For this reason, parameters of ventricular repolarisation on the surface electrocardiogram have been proposed. However, taken in isolation, these markers are limited in terms of arrhythmic risk stratification. This report analyses the value of the different parameters of ventricular repolarisation in the identification of high risk: QT dispersion, QT dynamics and T wave alternans. The dispersion of the QT interval is a marker of unhomogenous ventricular depolarisation. This concept must be applied differently in such pathologically dissimilar diseases such as myocardial infarction, cardiomyopathy or the long QT syndrome. Moreover, methodological problems make the interpretation of many experimental studies very delicate. Frequency dependence of the QT helps select high risk patients after myocardial infarction or with dilated cardiomyopathy. A common feature of pathological ventricular myocardium is the more pronounced frequency-dependency of the QT interval. The predictive value of this new index should be evaluated and compared with other non-invasive risk factors in prospective trials. Studies of T wave alternans in selected high risk populations, essentially patients with coronary artery disease and dilated cardiomyopathy, have shown this parameter to be predictive of arrhythmia. The predictive value requires confirmation in much larger populations at lower levels of risk of arrhythmia and sudden death in prospective trials. A new field of research has opened up in the study of ventricular repolarisation. Many studies have been undertaken on the duration of the QT interval, the morphology of the QT (including T wave alternans and post-pause changes) and, finally, the dynamics of the QT interval. By regrouping, analysing and using these data correctly, we should be able to identify new markers of high arrhythmic risk.

Death, Sudden, Cardiac↗
PubMed1991

Adaptive control is enhanced by background estimation.

The automated control of physiological variables must often contend with an unknown and time-varying background (i.e., the output level corresponding to no input). To allow for simultaneous real-time identification of background as well as the parameters of an autoregressive moving average model with exogenous inputs (ARMAX model) during adaptive control, a "floating identifier" (FI) approach was developed which may be used with most recursive identification algorithms. This method separates input and output data into low- and high-frequency components. The high-frequency components are used to identify the ARMAX model parameters and the low-frequency components to identify background. This approach was evaluated in computer simulations and animal experiments comparing an adaptive controller coupled to the FI with the same controller coupled to two other standard least squares identifiers. In the animal experiments, sodium nitroprusside was used to control mean arterial pressure of anesthetized dogs in the presence of background changes. Results showed that with the FI, the controller performed satisfactorily, while with the other identifiers, it sometimes failed. It is concluded that the FI approach is useful when applying ARMAX-based adaptive controllers to systems in which a change in background is likely.

Animals↗
PubMed1998

Endometrial carcinoma: immunohistochemically detected proliferation index is a prognosticator of long-term outcome.

AIM: To test which immunohistochemically detected tumour parameters are predictive of outcome in endometrial carcinoma. METHODS: A retrospective study of 300 patients diagnosed with endometrial carcinoma between 1980 and 1985, ensuring a follow up of at least 10 years. Paraffin wax embedded tissues from 236 patients with endometrial carcinoma were evaluated in terms of histological tumour type and grade, stage of disease, and certain immunohistochemical biological parameters. These parameters included the expression of oestrogen and progesterone receptors, the expression of p53 protein, the expression of the c-erbB-2 oncoprotein, and the expression of protease cathepsin D, together with the rate of cell proliferation. RESULTS: Using univariate analysis, the following parameters correlated significantly with adjusted survival: histological type (p = 0.025), grade (p = 0.00003), FIGO stage (p < 0.00001), proliferation rate (p = 0.00002), oestrogen receptor expression (p = 0.007), progesterone receptor expression (p = 0.0092), and p53 expression (p = 0.00028). These parameters also correlated significantly with both disease free and overall survival. There was a weak correlation of cathepsin D expression with survival, but no correlation of c-erb B-2 expression with survival. Using multivariate analysis, only FIGO stage (p = 0.0021), histological grade (p = 0.005), and proliferation rate (p = 0.0007) remained statistically significant prognosticators of adjusted survival as well as of disease free and overall survival. CONCLUSIONS: In addition to conventional histological parameters, the immunohistochemical determination of proliferative activity could contribute to the identification of a high risk subgroup of endometrial carcinomas. The other parameters tested were not of significant additional predictive value.

Adult↗
PubMed1971

Auditory evoked potentials during speech perception.

Neural responses evoked by the same binaural speech signal were recorded from ten right-handed subjects during two auditory identification tasks. One task required analysis of acoustic parameters important for making a linguistic distinction, while the other task required analysis of an acoustic parameter which provides no linguistic information at the phoneme level. In the time interval between stimulus onset and the subjects' identification responses, evoked potentials from the two tasks were significantly different over the left hemisphere but identical over the right hemisphere. These results indicate that different neural events occur in the left hemisphere during analysis of linguistic versus nonlinguistic parameters of the same acoustic signal.

Adolescent↗
PubMed2004

Splice site identification by idlBNs.

MOTIVATION: Computational identification of functional sites in nucleotide sequences is at the core of many algorithms for the analysis of genomic data. This identification is based on the statistical parameters estimated from a training set. Often, because of the huge number of parameters, it is difficult to obtain consistent estimators. To simplify the estimation problem, one imposes independent assumptions between the nucleotides along the site. However, this can potentially limit the minimum value of the estimation error. RESULTS: In this paper, we introduce a novel method in the context of identifying functional sites, that finds a reasonable set of independence assumptions supported by the data, among the nucleotides, and uses it to perform the identification of the sites by their likelihood ratio. More importantly, in many practical situations it is capable of improving its performance as the training sample size increases. We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction.

Algorithms↗