Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Kinetic modeling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed1982

Procedure for testing kinetic models of the photocycle of bacteriorhodopsin.

Given some simple kinetic models of the photocycle of bacteriorhodopsin (bR) and data taken at many wavelengths and under conditions that avoid photoselection and steady-state cycling complications, it is shown how to extract the apparent rate constants and the spectra of the intermediates. Special consideration was given to establishing the range of error of these results. There are many criteria, which we explicitly discuss, that the spectra should satisfy in order that the kinetic model be acceptable. New data for the photocycle of purple membrane fragments in dilute buffer at pH 7.0 has been obtained at 15 measuring wavelengths and four temperatures. The procedure, which can be generalized to more complex models, has been applied to these data to test two kinds of kinetic models: the unidirectional unbranched model and the undirectional model with simple branching straight back to bR from any intermediate. In these models the spectrum of the O intermediate is highly temperature sensitive, even with branching, and/or has two broad maxima. Moreover, the spectrum of the M intermediate has a secondary maximum and two M-like states appear to be required. Thus, neither model satisfies the physical criteria.

Bacteriorhodopsins↗
PubMed1998

Effect of on-line conductivity plasma ultrafiltrate kinetic modeling on cardiovascular stability of hemodialysis patients.

The aim of this multicenter, prospective, randomized cross-over study was to clarify whether on-line conductivity ultrafiltrate kinetic modeling (treatment B), as a substitute for sodium kinetic modeling, is capable of reducing intradialytic cardiovascular instability in comparison with standard treatment (treatment A), by reducing the sodium balance variability. Both treatments were performed by means of a modified hemodiafiltration technique. Treatment A was performed using fixed dialysate conductivity; treatment B made use of the dialysate conductivity derived from a conductivity kinetic model, in order to obtain an end-dialysis ultrafiltrate conductivity at each dialysis session that was equal to the mean value determined in the same patient during the four-week run-in period. Thus, during treatment B, the expected end-dialysis ultrafiltrate conductivity value of each patient should have been constant. The study was carried out according to a multicenter cross-over design of 16 weeks with two treatments (A or B), two sequences (1 = ABB and 2 = BAA), a run-in period of four weeks (period 1, treatment A), and three consecutive experimental periods of four weeks each. Analysis of variance for a cross-over design was used for the statistical analysis. Forty-nine hemodialysis patients prone to intradialytic hypotension (> 25% of sessions) were enrolled from 16 participating centers, and randomly assigned to either sequence 1 (26 patients) or sequence 2 (23 patients). Six patients dropped out and four were protocol violators, which left 39 patients selected for statistical analysis. There was no difference in the average dialysate conductivity, predialysis and end-dialysis plasma water ultrafiltrate conductivity or body weight between treatment A and treatment B. Thus, the observed mean sodium balance was not different and, as expected, only the intra-patient variability of end-dialysis ultrafiltrate conductivity (index of sodium balance variability) was reduced (21%). During treatment A, systolic blood pressure decreased by 23 mm Hg (95% confidence intervals 21 to 24 mm Hg) at the end of dialysis with respect to the pre-dialysis values. Treatment B reduced this intradialytic decrease (P = 0.001) with a maximum effect at the third hour of dialysis (4.4 mm Hg, 95% confidence intervals 1.9 to 6.9 mm Hg, 23% less than during treatment A, P 0.0005) without any period or carry-over effect (P = 0.53 and 0.08, respectively). There was no treatment effect on intradialytic diastolic blood pressure (P = 0.291). In conclusion, intradialytic cardiovascular stability was significantly improved by matching the interdialytic sodium load with intradialytic sodium removal using on-line conductivity ultrafiltrate kinetic modeling as an alternative to sodium kinetic modeling. Although highly significant, this effect was clinically not very large. By applying this conductivity kinetic model to patients with a more variable sodium intake from one session to another, a greater benefit can be expected.

Aged↗
PubMedDate not supplied

Eskimo: an epidemiological simulation kinetic model for tuberculosis.

A simple, easy to use, kinetic model allowing the simulation of the main epidemiological parameters of tuberculosis and of the financial costs associated with the implementation of different anti-tuberculous policies, has been developed and described. The model, which has been denominated "ESKIMO" (Epidemiological Simulation Kinetic Model) can be utilized on a personal computer and requires, for its use, the knowledge of a series of easily available census data relative to a given country or geographical area, an essential epidemiological profile of the disease in the same area and data which characterize one or more antituberculous treatments in therapeutic and financial terms. The rationale of the model, which is a multicompartemental system, derive from an analysis of the relationships (transfer rates) between sub-populations of individuals in relation to tuberculosis either when the dynamic state of the system is governed by "natural forces" (no treatment) or when an external action is applied to it with an aim to alter its internal pathways in a favourable sense (vaccination, long-term hospitalization, chemotherapy). The model is based on the assumption that the main objective of any antituberculous program is the reduction in size of the subpopulation of patients who can infect other individuals and therefore perpetuate the disease. Validation and projection tests carried out through Eskimo seem to indicate that concentrating the analysis on the effect of various treatments on this group of patients simplifies the calculations while the relative precision of the estimates of other parameters is very satisfactory. The results of several simulations substantiate and quantify the opinions expressed by several experts in the past that the policy of applying cheap regimens of low efficacy to a relatively small fraction of the patients' population, as frequently done in developing countries, not only does not alter the trend of the disease but produces essentially negative results (increase in the number of new cases and in the frequency of resistant M. tuberculosis). Treatment with highly effective regimens of the same number of patients as those treated now (constant coverage) and therefore without the extra costs resulting from the improvement of the available sanitary infrastructures, produces much better results in clinical terms and overall saving of financial resources.

Computer Simulation↗
PubMedDate not supplied

[A kinetic model of the cytochrome bf complex. Evaluation of kinetic parameters].

A kinetic model of the cytochrome bf complex was developed on the assumption that the Q-cycle operates. The bf complex was considered as a membrane enzyme catalyzing the electron transfer from plastoquinol to plastocyanine, which is coupled with proton translocation from the chloroplast stroma to the thylakoid lumen. The dependence of the electron transfer rates on the value of the transmembrane electric potential was taken into account. The model was applied to describe the experimental data on the flash-induced turnover of cytochromes b, plastocyanine, and the kinetics of proton deposition in the thylakoid lumen. The estimation of model parameters was performed.

Cytochrome b6f Complex↗
PubMedDate not supplied

Evaluation of kinetic models for industrial acetic fermentation: proposal of a new model optimized by genetic algorithms.

The most important kinetic models developed for acetic fermentation were evaluated to study their ability to explain the behavior of the industrial process of acetification. Each model was introduced into a simulation environment capable of replicating the conditions of the industrial plant. In this paper, it is proven that these models are not suitable to predict the evolution of the industrial fermentation by the comparison of the simulation results with an average sequence calculated from the industrial data. Therefore, a new kinetic model for the industrial acetic fermentation was developed. The kinetic parameters of the model were optimized by a specifically designed genetic algorithm. Only the representative sequence of industrial concentrations of acetic acid was required. The main novelty of the algorithm is the four-composed desirability function that works properly as the response to maximize. The new model developed is capable of explaining the behavior of the industrial process. The predictive ability of the model has been compared with that of the other models studied.

Acetic Acid↗
PubMed2000

Relevance of the conductivity kinetic model in the control of sodium pool.

Changes in the body sodium pool caused by dialytic treatment have very important clinical implications, mainly in terms of intradialytic cardiovascular instability and interdialytic hyperhydration and hypertension with long-term cardiac hypertrophy and dilation. A kinetic model could be helpful in order to define the dialysate sodium concentration needed to match intradialytic hydrosodium removal with interdialytic sodium and water intake, but unfortunately, none of the sodium kinetic models are suitable for routine clinical application. Two conductivity kinetic models (one for hemodialysis and one for paired filtration dialysis) have been developed on the basis of the linear relationship between the sodium content and conductivity of every saline solution and plasma water and according to basic theory for ionic dialysance determination. These models make it possible to know at the start of each session the dialysate conductivity needed to obtain the desired final plasma water conductivity or to know the latter when the former is known. Clinical evaluations showed that conductivity kinetic models are very precise and accurate and may be used instead of sodium kinetic models. Furthermore, they are suitable for routine use because they do not require blood sampling or laboratory determinations. Clinical application of the conductivity kinetic model has shown that the reduced variability of end-dialysis plasma water conductivity obtained when using the model to identify dialysate conductivity significantly reduces cardiovascular instability, even without any changes in average sodium removal. Given that ionic dialysance can be easily, inexpensively, and repeatedly measured at each dialysis session, it seems realistic to expect that conductivity kinetic modeling will soon become a part of everyday clinical practice.

Blood Pressure↗
PubMed1987

[Desensitization as a reflection of receptor-enzyme system inactivation during a reaction. Kinetic model of the process].

The kinetic regularities of the processes occurring in the system: receptor-adenylate cyclase complex under the effect of a hormone, an agonist or a neuromediator, were studied. Experiments with cell cultures revealed that the effector caused an impulse increase in cAMP and a decrease in the effector-stimulated activity of the adenylate cyclase complex. The above effects were considered within the framework of a kinetic model which takes into account the enzyme complex inactivation in the course of adenylate cyclase synthesis. The data obtained permit to explain the physiological effect of desensitization of the receptor-enzyme system with respect to the effector action as a result of inactivation of this system in the course of the reaction. Possible molecular mechanisms of inactivation are discussed.

Adenylyl Cyclases↗
PubMed2004

Sequence-dependent kinetic model for transcription elongation by RNA polymerase.

We present a kinetic model for the sequence-dependent motion of RNA polymerase (RNAP) during transcription elongation. For each NTP incorporation, RNAP has a net forward translocation of one base-pair along the DNA template. However, this process may involve the exploration of back-tracked and forward-tracked translocation modes. In our model, the kinetic rates for the reaction pathway, calculated based on the stabilities of the transcription elongation complex (TEC), necessarily lead to sequence-dependent NTP incorporation rates. Simulated RNAP elongation kinetics is in good agreement with data from transcription gels and single-molecule studies. The model provides a kinetic explanation for well-known back-tracked pauses at transcript positions with unstable TECs. It also predicts a new type of pause caused by an energetically unfavorable transition from pre to post-translocation modes.

Base Pairing↗
PubMedDate not supplied

Evolution of the single-pool urea kinetic model.

Our interest in urea kinetic modeling (UKM) was stimulated some 30 years ago at the time of the advent of hollow fiber kidneys with greatly improved urea transport. This led to examination of the interaction between time and clearance in computing the dialysis dose. In early studies a fixed-volume single-pool UKM was used but this frequently gave spurious high volumes and led to the advent of the variable-volume single-pool model. The role of volume calculation in assessment of the delivered dialysis dose and the value of normalized protein catabolic rate (nPCR) calculation are reviewed. More recently quantification of double-pool effects has become simplified and now is widely used for UKM. The National Cooperative Dialysis Study (NCDS) resulted in the concept of dose quantification by Kt/V. This is reviewed, including the controversy surrounding interpretation of the NCDS. Currently there is great interest in more frequent dialysis, 4-6 days/week. The development of a new dose parameter, the standard Kt/V (stdKt/V), to enable quantitative comparison of dose with widely varying dose schedules is discussed.

Kinetics↗
PubMed2004

Calibration-free estimates of batch process yields and detection of process upsets using in situ spectroscopic measurements and nonisothermal kinetic models: 4-(dimethylamino)pyridine- catalyzed esterification of butanol.

In this paper, we report the use of an NIR fiber-optic spectrometer with a high-speed diode array for calibration-free monitoring and modeling of the reaction of acetic anhydride with butanol using the catalyst 4-(dimethylamino)pyridine in a microscale batch reactor. Acquisition of spectra at 5 ms/scan gave information relevant for modeling these fast batch processes with a single multibatch kinetic model. Nonlinear fitting of a first-principles model directly to the reaction spectra gave calibration-free estimates of time-dependent concentration profiles and pure component spectra. The amount of catalyst was varied between different batches to permit accurate estimation of its effect in the multiway model. A wide range of different models with increasing complexity could be fit to each batch individually with low residuals and apparent low lack of fit. However, only one model properly estimated the concentration profiles when all five batches were fitted simultaneously in a multiway kinetic model. Inclusion of on-line temperature measurements and use of an Arrhenius model for the estimated rate constant gave significantly improved model fits compared to an isothermal kinetic model. Augmentation of prerun batches with data from an additional batch permitted model-based forecasts of reaction trajectories, reaction yield, reaction end points, and process upsets. One batch with added water to simulate a process upset was easily detected by the calibration free process model.

1-Butanol↗
PubMed1999

Uncertainty in biomonitoring and kinetic modeling.

Uncertainty in exposure assessment and uncertainty in kinetic models of early effects after exposure to a toxin are addressed in this paper. Sources of uncertainty in the determination of exposure of workers in chemical industry exposed to dioxins are exhibited and a simple kinetic model for biomonitor measurements of the concentrations from occupational exposure is derived. Model uncertainty, and uncertainty in the model parameters of physiologically-based pharmacokinetic models (PBPK models) are addressed when these models are used to estimate the effective dose in risk assessment. Uncertainty in the model parameters originating from the use of different statistical analysis methods is exhibited for Hill type nonlinear kinetics of enzyme induction mediated by a toxin.

Environmental Exposure↗
PubMed1987

The effect of urea kinetic modeling on the nutrition management of hemodialysis patients.

Urea kinetic modeling is a hemodialysis prescription technique that includes calculation of patients' protein catabolic rate (grams per kilogram body weight per day). This study compared the use of current guidelines alone with the integration of the urea kinetic modeling-derived protein catabolic rate and current guidelines for the nutrition assessment and management of 27 chronic renal failure patients on hemodialysis. In phase 1, subjects were counseled according to current renal nutrition guidelines. In phase 2, subjects were kinetically modeled and counseled with incorporation of the urea kinetic modeling-derived protein catabolic rate value. Thirteen subjects received a 1-month follow-up. Food records and time length of counseling sessions were recorded in phases 1 and 2. Significant changes seen in the mean blood urea nitrogen value during phase 2 (no. = 22, p less than or equal to .05) and follow-up phase (no. = 13, p less than or equal to 0.05) reflected an improved protein intake from phase 1 for the majority of subjects. Dietary intake and time length of counseling sessions in both phases were not significantly different. The following correlations were noted: reported protein intake and protein catabolic rate: r = .685, p less than or equal to .001; protein catabolic rate and blood urea nitrogen: r = .799, p less than or equal to .001; blood urea nitrogen and serum albumin: r = .485, p less than or equal to .05. Results suggest that the urea kinetic modeling-derived protein catabolic rate value positively affects patient adherence to diet recommendations.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1989

A kinetic model of superoxide production from single pulmonary alveolar macrophages.

A kinetic model was developed to describe the production of superoxide (O2-) by single pulmonary alveolar macrophages (PAM). Model predictions were compared with experimental results obtained from single rat PAM. The O2- was quantified by measuring the reduction of nitro blue tetrazolium (NBT) to a diformazan precipitate (NBTH2) from video-recorded images of individual cells. The kinetic model considered three reactions: 1) the production of extracellular O2- from the reduction of oxygen by NADPH oxidase using intracellular NADPH as the substrate, 2) the subsequent dismutation of O2- to form H2O2, and 3) the reaction of O2- and NBT to form diformazan. NBT specificity for O2- was analyzed by comparing results in the presence and absence of superoxide dismutase (SOD) that catalyzes the dismutation of O2- to H2O2. Measured PAM heterogeneity was accounted for by varying the concentration of intracellular NADPH, its rate of depletion, and the concentration of intracellular NADPH oxidase in the kinetic model. Model predictions compared favorably with experimental results except when SOD was present. This discrepancy may be due to diffusional limitations because NBT is a relatively small molecule (818 mol wt) compared with SOD (34,000 mol wt). In addition, the cell surface is both ruffled and negatively charged, which may introduce steric hindrances and/or electrostatic effects, since SOD is also negatively charged, whereas NBT is positively charged.

Animals↗
PubMed2006

Reaction mechanism and kinetic modeling of DEET degradation by flow-through anodic fenton treatment (FAFT).

The previously developed batch anodic Fenton treatment (AFT) technology has been successfully applied to degrade various pesticides in aqueous solution. The goal of this work is the development of a flow-through AFT system (FAFT) which is critical to bringing this technology into practical general use in the field. For this purpose, the degradation of DEET (N,N-diethyl-3-methylbenzamide), an insect repellent, and nine model amides was studied. Oxidation products of these compounds in FAFT were identified by GC/MS, and the results revealed that various -OH additions (most likely on the aromatic ring), quinone/keto product formation, and dimerization/bimolecular disproportionation are the major reaction pathways. This proposed overall reaction mechanism was then combined with the basic Fenton's mechanism to model the kinetics of various active species in FAFT including DEET, Fe2+, H2O2, and total iron under different reaction conditions. In addition, both initial and steady-state hydroxyl radical concentrations were measured in FAFT using benzoic acid as a chemical probe; the measured *OH concentrations were best-fitted exponentially. On the basis of the obtained [*OH] trend and the mass balance of the FAFT system, a simple FAFT model was developed to fit all of the degradation data of DEET and the model amides.

DEET↗
PubMed2002

Structure-based kinetic modeling of excited-state transfer and trapping in histidine-tagged photosystem II core complexes from synechocystis.

Chlorophyll fluorescence decay kinetics in photosynthesis are dependent on processes of excitation energy transfer, charge separation, and electron transfer in photosystem II (PSII). The interpretation of fluorescence decay kinetics and their accurate simulation by an appropriate kinetic model is highly dependent upon assumptions made concerning the homogeneity and activity of PSII preparations. While relatively simple kinetic models assuming sample heterogeneity have been used to model fluorescence decay in oxygen-evolving PSII core complexes, more complex models have been applied to the electron transport impaired but more highly purified D1-D2-cyt b(559) preparations. To gain more insight into the excited-state dynamics of PSII and to characterize the origins of multicomponent fluorescence decay, we modeled the emission kinetics of purified highly active His-tagged PSII core complexes with structure-based kinetic models. The fluorescence decay kinetics of PSII complexes contained a minimum of three exponential decay components at F(0) and four components at F(m). These kinetics were not described well with the single radical pair energy level model, and the introduction of either static disorder or a dynamic relaxation of the radical pair energy level was required to simulate the fluorescence decay adequately. An unreasonably low yield of charge stabilization and wide distribution of energy levels was required for the static disorder model, and we found the assumption of dynamic relaxation of the primary radical pair to be more suitable. Comparison modeling of the fluorescence decay kinetics from PSII core complexes and D1-D2-cyt b(559) reaction centers indicated that the rates of charge separation and relaxation of the radical pair are likely altered in isolated reaction centers.

Cyanobacteria↗
PubMed2000

A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates.

There is now convincing evidence that the proteasome contributes to the generation of most of the peptides presented by major histocompatibility complex class I molecules. Here we present a model-based kinetic analysis of fragment patterns generated by the 20S proteasome from 20 to 40 residues long oligomeric substrates. The model consists of ordinary first-order differential equations describing the time evolution of the average probabilities with which fragments can be generated from a given initial substrate. First-order rate laws are used to describe the cleavage of peptide bonds and the release of peptides from the interior of the proteasome to the external space. Numerical estimates for the 27 unknown model parameters are determined across a set of five different proteins with known cleavage patterns. Testing the validity of the model by a jack knife procedure, about 80% of the observed fragments can be correctly identified, whereas the abundance of false-positive classifications is below 10%. From our theoretical approach, it is inferred that double-cleavage fragments of length 7-13 are predominantly cut out in "C-N-order" in that the C-terminus is generated first. This is due to striking differences in the further processing of the two fragments generated by the first cleavage. The upstream fragment exhibits a pronounced tendency to escape from second cleavage as indicated by a large release rate and a monotone exponential decline of peptide bond accessibility with increasing distance from the first scissile bond. In contrast, the release rate of the downstream fragment is about four orders of magnitude lower and the accessibility of peptide bonds shows a sharp peak in a distance of about nine residues from the first scissile bond. This finding strongly supports the idea that generation of fragments with well-defined lengths is favored in that temporary immobilization of the downstream fragment after the first cleavage renders it susceptible for a second cleavage.

Adenosine Triphosphatases↗
PubMed2004

A novel mathematical method based on urea kinetic modeling for computing the dialysis dose.

A novel normalized single pool urea kinetic model (nspUKM) for the quantification of the urea removal, dialyzer urea clearance and urea generation rate during a dialysis session, is presented. Its major goal is the computation of an accurate estimate of the fractional dialyzer urea clearance (dKt/V), which is denoted nKt/V, in contrast to the equilibrated Kt/V (eKt/V). This work clarifies the significance of dKt/V as a complement to eKt/V in hemodialysis (HD) prescription and quantification. This new model emerges from a generalization of the standard single pool urea kinetic model (spUKM) of the US National Cooperative Dialysis Study (NCDS), identified as gspUKM. Due to their significance, the standard single pool Kt/V (spKt/V) and the eKt/V are also analyzed from gspUKM in this work, with the aim of achieving a better interpretation of the results. Indices nKt/V, eKt/V and spKt/V have been compared with the dKt/V computed from a published and validated two-pool urea kinetic model (2pUKM). We present the results obtained from a clinical study carried out on a group of 30 end stage renal disease (ESRD) patients. The limits of agreement (mean+/-2S.D. (standard deviation) of the difference) between nKt/V and 2pKt/V were -0.077+/-0.72% (percentage of the dKt/V mean), while between eKt/V and 2pKt/V were -13.75+/-17.39% and between spKt/V and 2pKt/V were -1.61+/-6.54%. These scores prove that the nspUKM model is able to provide a very accurate estimate of 2pKt/V and thus dKt/V, even with high flux (HF) HD. The presented method joins the simplicity of single-pool models to the accuracy of double-pool models, when the target is the identification of the dialyzer urea clearance, urea removal and urea generation rate, although it does not provide a good prediction of the urea dynamics. Finally, we think that our analytical and experimental findings throw light on the behavior and applicability of the different Kt/V indices analyzed.

Blood Urea Nitrogen↗
PubMed2001

Kinetic model for phenolic compound oxidation by Fenton's reagent.

A kinetic model is developed for the oxidation of phenolic compounds by Fenton's reagent. In the first stage a rigorous kinetic model is applied to calculate the different kinetic rate constants for the oxidation process of p-hydroxybenzoic acid. In a second phase a competitive method is applied to calculate these kinetic constants for another 10 phenolic compounds present in agroindustrial and pulp paper wastewaters. These 10 phenolic compounds were: beta-resorcylic acid, 3-(4-hydroxyphenyl)-propionic acid, ferulic acid, protocatechuic acid, caffeic acid, p-coumaric acid, vanillic acid, syringic acid, veratric acid and 3,4,5-trimethoxybenzoic acid.

Hydrogen Peroxide↗