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PubMed2002

Characterisation of lavender essential oils by using gas chromatography-mass spectrometry with correlation of linear retention indices and comparison with comprehensive two-dimensional gas chromatography.

Nine samples of lavender essential oil were analysed by GC-MS using low-polarity and polar capillary columns. Linear retention indices (LRI) were calculated for each component detected. Characterisation of the individual components making up the oils was performed with the use of an mass spectrometry (MS) library developed in-house. The MS library was designed to incorporate the chromatographic data in the form of linear retention indices. The MS search routine used linear retention indices as a post-search filter and identification of the "unknowns" was made more reliable as this approach provided two independent parameters on which the identification was based. Around 70% of the total number of components in each sample were reliably characterised. A total of 85 components were identified. Semi-quantitative analysis of the same nine samples was performed by gas chromatography (GC) with flame ionisation detection (FID). The identified components accounted for more than 95% of each oil. By comparing the GC-MS results with the results from the GCxGC-FID analysis of a lavender essential oil, many more components could be found within the two-dimensional separation space.

Chromatography, Gas↗
PubMedDate not supplied

[Use of temperature coefficients of Kovach indexes in the identification of barbiturates].

The conditions of direct gas chromatographic assessment of barbiturates in reference solutions and cadaveric material extracts were analyzed with the aim of their unification. Along with the Kovach indexes, their temperature coefficients seem promising for the identification of barbiturates. Critical parameters of the evaporator temperature regimen were established, that may be used for barbiturate identification as well. The threshold values of gas chromatographic detection of phenobarbital, barbital, etaminal, hexenal, quietal, and hexobarbital were determined.

Barbiturates↗
PubMed2003

Pretherapeutic identification of high-risk acute myeloid leukemia (AML) patients from immunophenotypic, cytogenetic, and clinical parameters.

BACKGROUND: The goal of this study concerned the pretherapeutic identification of high-risk acute myeloid leukemia (AML) patients by data pattern analysis from flow cytometric immunophenotype, cytogenetic, and clinical data. METHODS: Sixty-seven parameters of AML patients at diagnosis were classified for predictive information by algorithmic data sieving using iteratively self optimizing triple matrix data pattern analysis (http://www.biochem.mpg.de/valet/classif1.html). RESULTS: Pretherapeutic predictive values for nonsurvival within five years and two years were 100.0% and 83.2%, respectively, compared to 13.9% and 47.4% for the prediction of survival at five years and two years, respectively. At diagnosis, five-year nonsurvivors showed increased patient age and higher concentration of cells in the analyzed specimen, as well as increased levels of % CD2, CD4, CD13, CD36, and CD45 positive AML blasts. Two-year nonsurvivors were characterized by a data pattern of increased patient age and levels of % CD4, CD7, CD11b, CD24, CD45, TH126, and HLA-DR positive AML blasts and decreased levels of % CD1, CD65, CD95, and TC25 positive AML blasts. Cytogenetic abnormalities were not selected for the optimized discriminatory data patterns. CONCLUSIONS: The comparatively accurate pretherapeutic identification of high-risk AML patients may prove useful for the development of individualized therapy protocols in stratified clinical patients groups.

Acute Disease↗
PubMed1993

Time-varying mechanical behavior of multijointed arm in man.

1. The aim of this study was to describe the time-varying changes in the mechanical parameters of a multijointed limb. The parameters we considered are the coefficients of stiffness, viscosity, and inertia. Continuous pseudorandom perturbations were applied at the elbow joint during a catching task. A modified version of an ensemble technique was used for the identification of time-varying parameters. Torques at the elbow and wrist joints were then modeled with a linear combination of the changes in angular position and velocity weighted by the matrix of angular stiffness and the matrix of angular viscosity, respectively. Control experiments were also performed that involved the stationary maintenance of a given limb posture by resisting actively the applied perturbations. Different limb postures were examined in each such experiment to investigate the dependence of the mechanical parameters on limb geometry. 2. The technique for the identification of limb mechanical parameters proved adequate. The input perturbations applied at the elbow joint elicited angular oscillations at the wrist essentially uncorrelated with those produced at the elbow. The frequency of oscillation is much higher at the wrist than at the elbow, mainly because of the smaller inertia. The variance accounted for by the model was approximately 80% under both stationary and time-varying conditions; in the latter case the value did not vary significantly throughout the task. In addition, the model predicted values of the inertial parameters that were close to the anthropometric measures, and it reproduced the stepwise increase in limb inertia that occurs at the time the ball is held in the hand. 3. The values of angular stiffness and viscosity estimated under stationary conditions did not vary significantly with joint angle, in agreement with previous results obtained under quasi-static postural conditions. The matrix of the coefficients of angular stiffness was not symmetrical, indicating a prominent role for nonautogenic reflex feedbacks with unequal gains for elbow and wrist muscles. 4. A complex temporal modulation of angular stiffness and viscosity was observed during the catching task. The changes in the direct coefficients of angular stiffness tended to covary with those in the coupling coefficients from trial start up to approximately 30 ms before impact time. Around impact time, however, there was a complete dissociation: the direct terms peaked, whereas the coupling terms dropped. The direct terms of angular viscosity also increased before impact, whereas the viscosity coupling terms remained close to zero throughout.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗
PubMed2004

Comparison of laser-induced dissociation and high-energy collision-induced dissociation using matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) for peptide and protein identification.

The fragmentation of peptides under laser-induced dissociation (LID) as well as high-energy collision-induced dissociation (CID) conditions has been investigated. The effect of the different fragmentation mechanisms on the formation of specific fragment ion types and the usability of the resulting spectra, e.g. for high-throughput protein identification, has been evaluated. Also, basic investigations on the influence of the matrix, as well as laser fluence, on the fragment ion formation and the consequences in the spectral appearance are discussed. The preconditions for obtaining 'pure' CID spectra on matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF/TOF) instruments are evaluated and discussed as well as the differences between LID and CID in the resulting fragment ion types. While containing a wealth of information due to additional fragment ions in comparison with LID, CID spectra are significantly more complex than LID spectra and, due to different fragmentation patterns, the CID spectra are of limited use for protein identification, even under optimized parameter settings, due to significantly lower scores for the individual spectra. Conditions for optimal results regarding protein identification using MALDI-TOF/TOF instruments have been evaluated. For database searches using tandem mass spectrometric data, the use of LID as fragmentation technique in combination with parameter settings supporting the use of internal fragment ions turned out to yield the optimal results.

Amino Acid Sequence↗
PubMed2004

Depth of proteome issues: a yeast isotope-coded affinity tag reagent study.

As a test case for optimizing how to perform proteomics experiments, we chose a yeast model system in which the UPF1 gene, a protein involved in nonsense-mediated mRNA decay, was knocked out by homologous recombination. The results from five complete isotope-coded affinity tag (ICAT) experiments were combined, two using matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) and three using electrospray MS/MS. We sought to assess the reproducibility of peptide identification and to develop an informatics structure that characterizes the identification process as well as possible, especially with regard to tenuous identifications. The cleavable form of the ICAT reagent system was used for quantification. Most proteins did not change significantly in expression as a consequence of the upf1 knockout. As expected, the Upf1 protein itself was down-regulated, and there were reproducible increases in expression of proteins involved in arginine biosynthesis. Initially, it seemed that about 10% of the proteins had changed in expression level, but after more thorough examination of the data it turned out that most of these apparent changes could be explained by artifacts of quantification caused by overlapping heavy/light pairs. About 700 proteins altogether were identified with high confidence and quantified. Many peptides with chemical modifications were identified, as well as peptides with noncanonical tryptic termini. Nearly all of these modified peptides corresponded to the most abundant yeast proteins, and some would otherwise have been attributed to "single hit" proteins at low confidence. To improve our confidence in the identifications, in MALDI experiments, the parent masses for the peptides were calibrated against nearby components. In addition, five novel parameters reflecting different aspects of identification were collected for each spectrum in addition to the Mascot score that was originally used. The interrelationship between these scoring parameters and confidence in protein identification is discussed.

Amino Acid Sequence↗
PubMed1995

Rheumatoid factor avidity in patients with rheumatoid arthritis: identification of pathogenic RFs which correlate with disease parameters and with the gal(0) glycoform of IgG.

The standard ELISA for measuring rheumatoid factor (RF) binding was modified by treatment after the RF-Fc interaction with 2 M guanidine, which allowed a measurement of the avidity of the interaction. Incubation with 4 M guanidine eliminated RF binding. There was a direct correlation (r = 0.99) between the avidity as measured by the modified guanidine ELISA, and the dissociation constant for monoclonal RFs, as measured by competitive ELISA. Of the seropositive rheumatoid arthritis (RA) patients tested, 47% had high-avidity RFs (> or = 8% RF binding remaining after guanidine treatment). Tender joint count scores were significantly higher in the high avidity group (p = 0.05), whereas there was no significant difference in the ages, disease duration, sedimentation rate, RF titer or serum Ig levels compared to those with low-avidity RFs. Additionally 58% of those with high-avidity RFs had subcutaneous nodules, compared to 40% of the low-avidity group. A significantly higher number of nodules was present in the high-avidity RF group compared to those with low-avidity RFs (p = 0.03). Interestingly, the RF avidity was significantly higher in isolated immune complexes (IC), compared to that in circulating IgM RFs (p = 0.01). The RF avidity correlated with the presence of the glycoform of IgG lacking galactose in both circulating and IC-derived IgG (p = 0.003 and 0.009 respectively). Information about the strength of binding to Fc identifies a subgroup of IgM RFs that are likely pathological in patients with RA, as well as a specific glycoform of the target antigen.

Antibodies↗
PubMed1994

Identification of insignificant prostate cancers: analysis of preoperative parameters.

OBJECTIVES: Analyzing preoperative parameters to help determine the risk of a random or systematic prostate needle biopsy specimen detecting an incidental microscopic prostate cancer. METHODS: We reviewed the charts of 28 patients who had < or = 3 mm of Gleason grade (Glgr) < or = 2 (score < or = 4) prostate cancer in their prostate biopsy specimen and subsequently underwent a radical retropubic prostatectomy (RRP). Histopathologic review of the RRP specimen was carefully performed to determine the respective tumor volume, number of tumor foci, pathologic stage, Glgr, and score. Prostate-specific antigen (PSA) levels and the calculated PSA density (PSAD) were recorded for each case. RESULTS: Sixteen of the 28 (57%) RRP specimens contained a very small well-differentiated tumor (< or = 0.2 cc); 7 (25%) tumors were minimally larger (0.2 to 0.5 cc); and 2 specimens (7%) contained a large tumor (4 and 6 cc) only sampled by the biopsy specimen. Mean PSA levels and PSAD values both significantly differentiated tumors < or = 0.5 cc from those > 0.5 cc (p < 0.005). PSA < or = 4 vs PSAD < or = 0.1 correctly identified 12 of 23 (52%) vs 22 of 23 (96%) tumors < or = 0.5 cc, and 10 of 16 (63%) vs 15 of 16 (94%) tumors < or = 0.2 cc, respectively; both parameters excluded 4 of 5 (80%) tumors > 0.5 cc. PSA < or = 4 vs PSAD < or = 0.1 identified 13 of 25 (52%) vs 24 of 25 (96%) organ-confined tumors, respectively, and both parameters excluded the 2 specimen-confined and 1 margin-positive tumors. Thus, PSAD had an excellent ability to differentiate the tumors based on their volumes. All tumors < or = 0.5 cc in the RRP specimen were organ-confined and postoperative serial PSA levels remained < 0.4 in these patients at a mean follow-up of 24 months. CONCLUSIONS: Our data indicate that a patient who has a random or systematic prostate biopsy specimen that contains < or = 3 mm of Glgr < or = 2 prostate cancer and a PSAD < or = 0.1 is at a substantial risk (82%) of being diagnosed with an incidental, organ-confined, and probably insignificant, microscopic prostate cancer.

Aged↗
PubMed1986

Identification of alcohol abuse and alcoholism with biological parameters.

The prevalence and incidence of heavy alcohol consumption are major problems which have been increasing in many countries in recent years. It is crucial for physicians to consistently identify early drinking problems as well as the various end disease states in order to minimize suffering and maximize recovery. This paper reviews the evolutionary development of clinical tools for detection of alcohol abuse. The focus is primarily on clinical/biochemical indicators of alcohol abuse, emphasizing but not limited to changes in hematological characteristics, liver enzyme activity, lipids, immune function factors, hormones, neurological factors, and some physically based tests. Use of test combinations and sophisticated statistical analysis of pattern changes in test batteries evidence increased diagnostic efficiency.

Alcoholism↗
PubMed2006

Identification of biomolecule mass transport and binding rate parameters in living cells by inverse modeling.

BACKGROUND: Quantification of in-vivo biomolecule mass transport and reaction rate parameters from experimental data obtained by Fluorescence Recovery after Photobleaching (FRAP) is becoming more important. METHODS AND RESULTS: The Osborne-Moré extended version of the Levenberg-Marquardt optimization algorithm was coupled with the experimental data obtained by the Fluorescence Recovery after Photobleaching (FRAP) protocol, and the numerical solution of a set of two partial differential equations governing macromolecule mass transport and reaction in living cells, to inversely estimate optimized values of the molecular diffusion coefficient and binding rate parameters of GFP-tagged glucocorticoid receptor. The results indicate that the FRAP protocol provides enough information to estimate one parameter uniquely using a nonlinear optimization technique. Coupling FRAP experimental data with the inverse modeling strategy, one can also uniquely estimate the individual values of the binding rate coefficients if the molecular diffusion coefficient is known. One can also simultaneously estimate the dissociation rate parameter and molecular diffusion coefficient given the pseudo-association rate parameter is known. However, the protocol provides insufficient information for unique simultaneous estimation of three parameters (diffusion coefficient and binding rate parameters) owing to the high intercorrelation between the molecular diffusion coefficient and pseudo-association rate parameter. Attempts to estimate macromolecule mass transport and binding rate parameters simultaneously from FRAP data result in misleading conclusions regarding concentrations of free macromolecule and bound complex inside the cell, average binding time per vacant site, average time for diffusion of macromolecules from one site to the next, and slow or rapid mobility of biomolecules in cells. CONCLUSION: To obtain unique values for molecular diffusion coefficient and binding rate parameters from FRAP data, we propose conducting two FRAP experiments on the same class of macromolecule and cell. One experiment should be used to measure the molecular diffusion coefficient independently of binding in an effective diffusion regime and the other should be conducted in a reaction dominant or reaction-diffusion regime to quantify binding rate parameters. The method described in this paper is likely to be widely used to estimate in-vivo biomolecule mass transport and binding rate parameters.

Algorithms↗
PubMed2001

Uncertainties of Monod kinetic parameters nonlinearly estimated from batch experiments.

Monod kinetic parameters (Ks, micromax, and Y) that are estimated from batch experimental data can have large uncertainties due to linear correlations between them. The degree of correlation and the resulting uncertainties of the Monod parameters are functions of the initial experimental conditions, the values of the parameters, the type and magnitude of measurement errors, and the sampling number. Careful manipulation of experimental conditions can reduce the correlations between Monod parameters allowing for the estimation of Monod kinetic parameters with the lowest degree of uncertainty. By dimensionless analysis, the correlation and relative standard deviations of Monod parameters were found to be functions of a few dimensionless variables involving the initial substrate (S0) and cell (X0) concentrations. Quantitative relationships were analyzed between the dimensionless variables and the correlation and the uncertainties of the Monod parameters. This analysis allowed for identification of the optimal experimental conditions for estimating Monod parameters under both no growth and growth conditions coupled with two kinds of measurement errors: those with constant absolute standard deviation and those with constant relative standard deviation. Examples involving the microbial reduction of iron(III) as an electron acceptor are used to illustrate the application of the developed technique.

Cell Division↗
PubMed2006

Universal reduced potential function for diatomic systems.

The potential energy functions of 200 diatomic systems, with dissociation energies De ranging from few eV to hundreds of mueV, are well described by a new three-parameter potential energy function. Identification of the evaluated values of a dimensionless quantity, xin=L2/Ln [Ln=(n!De/fn)1/n, a scaled length parameter, and fn, the nth force constant evaluated at the equilibrium internuclear distance Re], is proposed as a reliable criterion to search for the universal scaling features of potentials and spectroscopic constants for bound diatomic systems. Our study suggests a useful approach to predicting future molecular spectroscopic constants.

Journal Article↗
PubMed2006

Novel two-parameter flow cytometry (MIL4/SSC followed by MIL4/CT7) allows for identification of five fractions of guinea pig leukocytes in peripheral blood and lymphoid organs.

Though the guinea pig has been an extremely useful animal model for a variety of diseases, the tools necessary to undertake a full-scale immunological analysis of the guinea pig have been lacking. For instance, traditional two-parameter forward/side scatter (FSC/SSC) flow cytometry, though effective in human and other animal models, is unable to adequately identify the distinct fractions of guinea pig peripheral blood leukocytes (PBL). We introduce here a new flow cytometric technique (MIL4/SSC followed by MIL4/CT7) which redresses this lack by identifying and characterizing five distinct fractions of PBL: neutrophils, lymphocytes, monocytes, eosinophils plus basophils, and the novel MIL4(-)SSC(large)CT7(high) population. The MIL4(-)SSC(large)CT7(high) cells possess cytoplasmic inclusion bodies of variable size that were positive for periodic acid Schiff (PAS). Their cell surface stained positive for the helper/inducer lymphocyte markers, T cell markers, CD45, Thy-1, asialo GM1 and FcR, but negative for B cell markers, such as membrane-type IgM, CD8 and MHC class II. The novel flow cytometric technique also allowed us to establish that the five leukocyte fractions were found in PBL, splenocytes, thymocytes and lymph node cells. Cells which were positive for inclusion bodies comprised 16.6% of splenocytes, 9.9% of PBL and 4.3% of liver cells, but were comparatively rare in lymph node cells, thymocytes, and BM cells. The novel flow cytometric technique introduced here will allow a better understanding of the response of each type of guinea pig leukocyte and thereby shed light on the diseases with which they are associated.

Animals↗
PubMed1992

The step response of left ventricular pressure to ejection flow: a system oriented approach.

Left ventricular pressure is dependent on both ventricular volume and ventricular ejection flow. These dependencies are usually expressed by ventricular elastance, and resistance, respectively. Resistance is a one-valued effect only, when ejection flow either is constant or increases. Decreasing ejection flow elicits a third effect: a decrease of elastance. The effects of elastance, resistance and elastance depression were modeled in a three-compartment model consisting of a dead-volume compartment, an elastance compartment, and a second series-elastance compartment connected to the elastance compartment by a resistance. This model was identified with the pressure response determined experimentally by imposing pumped constant-flow ejection epochs on isolated rabbit hearts. The experimental flow epochs consisted of two phases of constant flow separated by an increasing or decreasing flow step. It was found that elastance is not changed after the flow step if this is positive or zero. Negative flow steps induced a deactivation of elastance that is linearly dependent on the difference between isovolumic pressure that would be developed at the volume existing at the time of measurement and actual pressure. The parameters found from the identification procedure are ventricular active volume, nondepressed elastance, series-elastance, resistance, and the elastance deactivation factor. The first four parameter values were found in agreement with other results reported in literature. The elastance depression factor is a new parameter that could be of physiological or clinical significance since it may be related to the inability of the force generators in the heart muscle to be restored to their full number, after being inactivated or decoupled by filament sliding associated with ejection. On the basis of the results, an alinear state-model of the ventricle, for arbitrary, including physiological flow patterns is proposed.

Animals↗
PubMed1996

Coupled Markov chain model: characterization of membrane channel currents with multiple conductance sublevels as partially coupled elementary pores.

A parameterized Markov chain model is developed to represent the characteristics of channel currents that either are the superposition of many single channels or show multiple conductance sublevels. The simplified model takes the form of a set of binary chains that are interdependent according to a simple lumped coupling parameter. When varied, this parameter realizes a range of behaviors from tight coupling to complete independence. Other model parameters describe the intrinsic characteristics of the binary chains. An identification procedure for the model parameters is developed based on hidden Markov modeling ideas but incorporating a novel parameter estimation. The usefulness of the model in analyzing certain types of data is demonstrated with examples of real channel currents.

Animals↗
PubMed1995

Can manometric parameters predict response to biofeedback therapy in fecal incontinence?

PURPOSE: Biofeedback therapy may improve fecal control in up to 50 percent to 92 percent of patients with fecal incontinence. Identification of favorable manometric parameters before biofeedback therapy may help in selection of patients suitable for such therapy. METHODS: Twenty-eight patients with fecal incontinence (idiopathic, 11; iatrogenic trauma, 8; obstetric trauma, 9) who underwent biofeedback therapy were studied to determine whether manometric parameters could predict the result of therapy. Biofeedback was given using a computer software program designed to strengthen the external anal sphincter with auditory and visual feedback. RESULTS: Thirteen patients (46.4 percent) achieved excellent results; eight patients (28.6 percent) had good results, but seven patients (24.5 percent) failed to improve after biofeedback therapy. Resting or squeeze anal canal pressure, pressure volume, sphincter length, sphincter fatigue rate, and cross-sectional asymmetry of the entire sphincter before biofeedback failed to reveal any statistically significant differences between responders and nonresponders. However, the cross-sectional asymmetry of the high-pressure zone within the sphincter at rest was greater in nonresponders than in responders (not improved, 25.8 percent; good result, 20.2 percent; excellent result, 15.4 percent; P < 0.07). This difference was even greater on squeeze (not improved, 21 percent; good result, 17.6 percent; excellent result, 13.2 percent; P < 0.04). The number of biofeedback sessions, response on bearing down, and quality of rectoanal excitatory reflex were not reliable indicators of outcome. No statistical difference was found in mean resting and squeeze pressures after biofeedback between responders and non-responders. CONCLUSIONS: Except for increased cross-sectional asymmetry in the high-pressure zone, which may be a forerunner of adverse outcome, manometric parameters before biofeedback do not predict response to biofeedback therapy. Improvement in continence may be independent of resting and squeeze pressures achieved after biofeedback therapy.

Adult↗
PubMed1999

Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection.

We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point and molecular weight, as well as chemical modifications or number of missed cleavages of a protein, the program performs a fully automated identification of the protein. The first step is a peak detection algorithm, which allows precise and fast determination of peptide masses, even if the peaks are of low intensity or they overlap. In the second step the masses and environmental data are used by the identification algorithm to search in protein sequence databases (SWISS-PROT and/or TrEMBL) for protein entries that match the input data. Consequently, a list of candidate proteins is selected from the database, and a score calculation provides a ranking according to the quality of the match. To define the most discriminating scoring calculation we analyzed the respective role of each parameter in two directions. The first one is based on filtering and exploratory effects, while the second direction focuses on the levels where the parameters intervene in the identification process. Thus, according to our analysis, all input parameters contribute to the score, however with different weights. Since it is difficult to estimate the weights in advance, they have been computed with a generic algorithm, using a training set of 91 protein spectra with their environmental data. We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs.

Algorithms↗