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 487 records · Page 27Linked to original sources

Kinetic modeling confirms the biosynthesis of mucin core 1 (beta-Gal(1-3) alpha-GalNAc-O-Ser/Thr) O-glycan structures are modulated by neighboring glycosylation effects.

Glycoproteins containing heavily O-glycosylated, mucin-like domains serve important biological functions in which the O-linked glycans play a major role. Although not well understood, O-glycan structures are known to vary reproducibly as a function of their position in the peptide sequence. Toward understanding such behavior, an analysis of the in vivo Core 1 (beta-Gal(1-3) alpha-GalNAc-O-Ser/Thr) site-specific glycosylation pattern of the porcine salivary gland mucin 81 residue tandem repeat has been undertaken. When a kinetic modeling approach is utilized, the in vivo Core 1 glycosylation pattern could be reproduced by incorporation of the inhibitory effects of neighboring residue glycosylation plus and minus three residues of the site of glycosylation. The obtained positional weighing parameters suggest that the porcine salivary gland Core 1 transferase (UDP-galactose:glycoprotein-alpha-GalNAc beta3-galactosyltransferase) is most sensitive to the presence of glycans C terminal to the site of glycosylation. The analysis further suggests that neighboring peptide core alpha-GalNAc residues are primarily responsible for the effect. These findings further support the notion that the formation of the Core 1 structure, an important initial step in O-glycan biosynthesis, may be regulated to a large extent by neighboring residue glycosylation. As a result, the development of approaches for predicting O-glycan core structures in a site-specific manner may now appear a distinct possibility.

Amino Acid Sequence↗

A kinetic model of inorganic phosphorus mass balance in hemodialysis therapy.

BACKGROUND: There is growing evidence that inorganic phosphorus (iP) accumulation in tissues (dTiP/dt) is a risk factor for cardiac death in hemodialysis therapy (HD). The factors controlling iP mass balance in HD are dietary intake (GiP), removal by binders (JbiP) and removal by dialysis (JdiP). If iP accumulation is to be minimized, it will be necessary to regularly monitor and optimize GiP, JbiP and JdiP in individual patients. We have developed a kinetic model (iPKM) designed to monitor these three parameters of iP mass balance in individual patients and report here preliminary evaluation of the model in 23 HD patients. METHODS: GiP was calculated from PCR measured with urea kinetics; JdiP was calculated from the product of dialyzer plasma water clearance (K(pwiP)) and time average plasma iP concentration (TACiP) and treatment time (t); a new iP concentration parameter (nTAC(iP), the TACiP normalized to predialysis CoiP) was devised and shown to be a highly predictable function of the form nTAC(iP) = 1 - alpha(1 - exp[-betaK(pwiP). t/ViP]), where the coefficients alpha and beta are calculated for each patient from 2 measure values for nTAC(iP), K(pwiP).t/ViP early and late in dialysis; we measured 8-10 serial values for nTAC(iP), K(pwiP). t/ViP over a single dialysis in 23 patients; the expression derived for iP mass balance is DeltaTiP = 12(PCR) - [K(pwiP)(t) (N/7)][CoiP(1 - alpha(1 - exp[-beta(Kt/ViP)]))] - k(b).Nb. RESULTS: Calculated nTAC(iP) = 1.01(measured nTAC(iP)), r = 0.98, n = 213; calculated JdiP = 0.66(measured total dialysate iP) + 358, n = 23, r = 0.88, p < 0.001. Evaluation of 10 daily HD patients (DD) and 13 3 times weekly patients with the model predicted the number of binders required very well and showed that the much higher binder requirement observed in these DD patients was due to much higher NPCR (1.3 vs. 0.96). CONCLUSION: These results are very encouraging that it may be possible to monitor the individual effects of diet, dialysis and binders in HD and thus optimize these parameters of iP mass balance and reduce phosphate accumulation in tissues.

Death↗

Kinetic model discrimination via step-by-step experimental and computational procedure in the enzymatic oxidation of D-glucose.

The enzymatic oxidation of D-glucose to 2-keto-D-glucose (D-arabino-hexos-2-ulose, D-glucosone) is of prospective industrial interest. Pyranose oxidase (POx) from Peniphora gigantea is deactivated during the reaction. To develop a kinetic model including the main reaction and the enzyme inactivation, possible side-reactions of the non-stabilised enzyme with D-glucosone, hydrogen peroxide, and peroxide radicals were considered. A developed step-by-step combined experimental and computational procedure allowed to discriminate among alternative inactivation mechanisms and provides an increased model reliability. The most probable scheme is the enzyme inactivation by hydroxyl radicals formed from produced H2O2 in the presence of Fe2+ ions. This .OH reaction is supported by matrix assisted laser desorption ionisation-mass spectrometry (MALDI-MS) measurement. The estimated kinetic parameter values for the main reaction are of the same order of magnitude as those reported in the literature. The identified model allows a satisfactory process simulation and highlights measures to prevent the enzyme activity loss.

Bioreactors↗

Assessment of myocardial perfusion by dynamic N-13 ammonia PET imaging: comparison of 2 tracer kinetic models.

BACKGROUND: Measurement of myocardial blood flow (MBF) by dynamic nitrogen 13 ammonia (NH(3)) positron emission tomography (PET) uses tracer kinetic modeling to analyze time-activity curves. We compared 2 commonly used models with 2 compartments (2C) and 3 compartments (3C) for quantification of MBF and coronary flow reserve (CFR). METHODS AND RESULTS: Seventy-seven patients underwent NH(3) PET at rest and during hyperemia. Time-activity curves for blood pool and myocardial segments were obtained from short-axis images of dynamic sequences. Model fitting of the 2C and 3C models was performed to estimate regional MBF. MBF values calculated by 2C and 3C models were 0.98 +/- 0.31 mL.min(-1).g(-1) and 1.11 +/- 0.37 mL.min(-1).g(-1), respectively, at rest (P < .0001) and 2.79 +/- 1.18 mL.min(-1).g(-1) and 2.46 +/- 1.02 mL.min(-1).g(-1), respectively, during hyperemia (P < .01), resulting in a CFR of 3.02 +/- 1.31 and 2.39 +/- 1.15 (P < .0001), respectively. Significant correlation was observed between the 2 models for calculation of resting MBF (r = 0.78), hyperemic MBF (r = 0.68), and CFR (r = 0.68). CONCLUSION: Measurements of MBF and CFR by 2C and 3C models are significantly related. However, quantification of MBF and CFR significantly differs between the methods. This difference needs to be considered when normal values are established or when measurements obtained with different methods need to be compared.

Adolescent↗

Determination of flow and rate constants in a kinetic model of [99mTc]-hexamethyl-propylene amine oxime in the human brain.

The values for flow and rate constants for a kinetic model of [99mTc]-hexamethylpropyleneamine oxime (HM-PAO) distribution in the human brain were determined. The single-pass extraction ratio of HM-PAO was also determined in the rat brain by the indicator diffusion method; a value of 0.90 +/- 0.02 (mean +/- SEM, n = 5) was obtained. Time course data of brain activity and arterial blood activity of the tracer were fitted to a four compartment model: Values of blood flow and the first-order rate constants for backdiffusion of the diffusible tracer from brain to blood (k2), conversion of the lipophilic tracer to the hydrophilic one in brain (k3), and conversion of the diffusible tracer to the nondiffusible one in blood (k5) were determined. Conversion of hydrophilic tracer back to a lipophilic form in both blood and brain was assumed to be negligible during the course of the experiment. The values obtained for blood flow, k2, and k3 were, respectively, 0.40 +/- 0.03 ml/g/min, 0.38 +/- 0.04 min-1, and 0.92 +/- 0.05 min-1 in the gray matter (n = 4), and 0.23 +/- 0.01 ml/g/min, 0.17 +/- 0.01 min-1, and 1.01 +/- 0.05 min-1 in the white matter (n = 2) in patients with cerebrovascular disorder. The k5 value was 1.14 +/- 0.06 min-1 (n = 4). These experimentally determined values agree well with the theoretical ones previously reported by Lassen et al. The results suggest the relative constancy of the k3 and k5 values and the more prominent initial backdiffusion of the lipophilic HM-PAO from brain to blood in high flow regions compared to low flow regions.

Animals↗

Nonmonotonic temperature dependence of heat capacity through the glass transition within a kinetic model.

The heat capacity of a supercooled liquid subjected to a temperature cycle through its glass transition is studied within a kinetic model. In this model, the beta process is assumed to be thermally activated and described by a two-level system. The alpha process is described as a beta relaxation mediated cooperative transition in a double well. The overshoot of the heat capacity during the heating scan is well reproduced and is shown to be directly related to delayed energy relaxation in the double well. In addition, the calculated scan rate dependencies of the glass transition temperature T(g) and the limiting fictive temperature T(f) (L) show qualitative agreement with the known results. Heterogeneity is found to significantly reduce the overshoot of heat capacity. Furthermore, the frequency dependent heat capacity has been calculated within the present framework and found to be rather similar to the experimentally observed behavior of supercooled liquids.

Journal Article↗

A four-state kinetic model of the temporary threshold shift after loud sound based on inactivation of hair cell transduction channels.

A model of the temporary threshold shift (TTS) following loud sound is presented based on inactivation of the mechano-electrical transduction (MET) channels at the apex of the outer hair cells (OHCs). This inactivation is assumed to reduce temporarily the OHC receptor current with a consequent drop in the mechanical sensitivity of the organ of Corti. With acoustic over-stimulation some of the hair cells' MET channels are assumed to adopt one of three closed and non-transducing conformations or 'TTS states'. The sound-induced inactivation is assumed to occur because the sound makes the TTS states more energetically favourable when compared with the transducing states, and the distribution between these states is assumed to depend on the relative energies of the states and the time allowed for migration between them. By lumping the fast transducing states (one open and two closed) into a single transducing 'pseudo-state', the kinetics of the inactivation and re-activation processes (corresponding to the onset and recovery of TTS) can be described by a four-state kinetic model. The model allows an elegant description of the onset and recovery of TTS time-course in a human subject under a variety of continuous exposure conditions, and some features of intermittent exposure as well. The model also suggests that recovery of TTS may be accelerated by an intermittent tone during the recovery period which may explain some variability TTS in the literature. Other implications of the model are also discussed.

Acoustic Stimulation↗

Simple kinetic model for the study of lactate metabolic adaptation to exercise in sportsmen routine evaluation.

The interindividual specific lactate metabolic adaptation to exercise has been studied. A simple kinetic model was used which did not require labelled molecules. An one open compartment model with a first-order release rate constant described the release of lactate from the muscle. Six volunteers performed five times the same session: pedaling as long as possible at 400 W and 110 rpm. The lactate concentration was measured along the 60 min of recovery. The theoretical curve corresponding to the model was fitted to the experimental data using a non-linear regression method. The values of the following kinetic parameters were obtained: elimination rate constant (ke), release rate constant (ka), apparent amount released into the compartment divided by the volume of distribution (FQo/Vd) and area under the lactate concentration-time curve (AUC). Two way-ANOVA, Scheffé test and discriminant analysis were used to test the statistical significance of these parameters. No significant intra-individual variations were shown. Significant differences were observed between subjects (ke: P = 0.0020; ka: P less than 0.0001; FQo/Vd: P = 0.0002; AUC: P = 0.0395). A correlation was also found between FQo/Vd and ke (r = 0.72; P less than 0.001). In conclusion, the computed parameters provided by the model are sufficient to discriminate and characterize the metabolic response of each subject after short and intensive exercises.

Adaptation, Physiological↗

A simple kinetic model of PCDD/F formation by de novo synthesis.

A simple fixed-bed reactor model is used to describe experimental data about the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) from fly ash carbon. The heterogeneous oxidation of graphite-like carbon is represented by a reaction which is first order in carbon and one half order in oxygen. The same orders of reaction are assumed to be valid for PCDD/F formation, such that the oxidation of fly ash carbon would have three parallel channels leading to COx, PCDD and PCDF. In addition, PCDD/F degradation by oxygen is considered and appropriate rate constants were fitted to simulate the experimental data. The effects of water vapour and particulate copper on PCDD/F formation are included. As a result, an overall kinetic model of PCDD/F formation is obtained which describes most of the experimental data with reasonable accuracy. The main reaction channel, COx formation, needs to be understood more completely, in order to interpret PCDD/F reaction pathways better. The model can be extended to include other chlorinated aromatics and the gas/particle partitioning of the semivolatiles. It provides a basis for the qualitative and quantitative interpretation of fixed-bed and flow reactor results and it is hoped to be applicable to industrial installations like waste incinerators and metal smelters.

Benzofurans↗

Use of designed peptide linkers and recombinant hemoglobin mutants for drug delivery: in vitro release of an angiotensin II analog and kinetic modeling of delivery.

We have designed and tested specific peptide linkers for the glutathione-mediated reductive release of the angiotensin II analog N-acetyl-CGDKVYIHPF attached to recombinant human hemoglobin mutants by a disulfide bond. Inclusion of negatively charged residues decreased the rate of release by as much as 5-fold for the N-terminal linker DCD when compared to that of the control linker CG. Two different surface cysteine mutants in the second domain of the alpha,alpha-chain of recombinant human hemoglobin, D75C and K16C, were examined for their effect on the release of peptide by reduced glutathione. The reaction of the D75C-peptide conjugate with glutathione for release of the peptide is slow, with a second-order rate constant of 2.1 M-1 S-1, allowing the possibility of long term delivery. The rate of peptide release from the K16C vs the D75C mutant was decreased 15-fold. Thus, different peptide release rates can be obtained by changing both peptide linker residues and the surface location of peptide attachment. Kinetic modeling of this release using either measured or literature values for different parameters suggests boundary conditions for application to the in vivo release of peptidomimetics, small molecules, or other drugs bound to the hemoglobin surface.

Angiotensin II↗

A comprehensive kinetic model for dilute-acid hydrolysis of cellulose.

Acid-catalyzed hydrolysis is controlled not only by temperature and acid concentration but also by the physical state of the cellulose. Under low temperature and acid condition the cellulose structure stays in stable crystalline form. Therefore, the prevailing reaction mode is endwise hydrolysis. Glucose then becomes the main sugar product. However, when temperature and/or acid concentration is raised to a certain level, the cellulose structure becomes unstable by breakage of hydrogen bonding, the primary force that holds the cellulose chains. Once the crystalline structure of the cellulose is disrupted, acid molecules can penetrate into the inner layers of the cellulose chains. In support of this hypothesis, we have experimentally verified that a substantial amount of oligomers is formed as reaction intermediates under extremely low-acid and high-temperature conditions. We also found that the breakage of hydrogen bonds occurs rather abruptly in response to temperature. One such condition is 210 degrees C, 0.07% H2SO4. Glucose, once it is formed in the hydrolysate, interacts with acid-soluble lignin, forming a lignin-carbohydrate complex. This occurs concurrently with other reactions involving glucose such as decomposition and reversion. On the basis of these findings, a comprehensive kinetic model is proposed. This model is in full compliance with our recent experimental data obtained under a broad range of reaction conditions.

Animal Feed↗

Computerized urea kinetic modeling to prescribe and monitor delivered Kt/V (pKt/V, dKt/V) in peritoneal dialysis. Fresenius Randomized Dialysis Prescriptions and Clinical Outcome Study (RDP/CO).

A computerized urea kinetic model of peritoneal urea transport (PACK-PD) has been developed and used to calculate prescription parameters which would result in the prescribed weekly peritoneal urea clearance (pKpt/V) required to achieve levels of weekly summed renal + peritoneal urea clearance (pKprt/ V) targeted at 1.75 and 2.16. Baseline kinetic data were obtained and analyzed with PACK-PD on 88 patients, and the program then used these data to calculate the required pKpt/V and subsequently the delivered Kpt/V (dKpt/V) from the dialysate collections. A total of 108 prescriptions were written and compared to dKpt/V measured over one to 24 months in the 88 patients. Both continuous ambulatory peritoneal dialysis and automated peritoneal dialysis (APD) were studied (APD consisted of PD+ with one or two diurnal and two to four nocturnal cycler exchanges). The correlation of dKpt/V to pKpt/V showed r = 0.93 with 95% confidence limits (CL) on agreement of +/-20% over a range of pKpt/V 0.52-2.55. The 95% CL on (dKpt/V-pKpt/V) were +/-0.30. We concluded: (1) that the prescription can be modeled as reliably in peritoneal dialysis as in hemodialysis (HD) where dKt/V and pKt/V agree to +/-25%, (2) that any individual weekly dKpt/V may vary as much as 0.3-0.4 from pKpt/V, and (3) that frequent measurement of dKpt/V and adjustment of pKpt/V as needed are required (as in HD) to control mean dKpt/V to within +/-10% of mean pKpt/V.

Capillary Permeability↗

Optimal decolorization and kinetic modeling of synthetic dyes by Pseudomonas strains.

Pseudomonas spp were isolated from an anaerobic-aerobic dyeing house wastewater treatment facility as the most active azo-dye degraders. Decolorization of azo dyes and non-azo dyes including anthraquinone, metal complex and indigo was compared with individual strains and a bacterial consortium consisting of the individual strain and municipal sludge (50 50wt). The consortium showed a significant improvement on decolorization of two recalcitrant non-azo dyes, but little effect on the dyes that the individual strains could degrade to a great or moderate extent. Decolorization of Acid violet 7 (monoazo) by a Pseudomonas strain GM3 was studied in detail under various conditions. The optimum decolorization activity was observed in a narrow pH range (7-8), a narrow temperature range (35-40 degrees C), and at the presence of organic and ammonium nitrogen. Nitrate had a severe inhibitory effect on azo dye decolorization: 10 mg/L led to 50% drop in decolorization activity and 1000 mg/L to complete activity depression. A kinetic model is established giving the dependence of decolorization rate on cell mass concentration (first-order) and dye concentration (half order). The rate increased with temperature from 10 to 35 C, which can be predicted by Arrhenius equation with the activation energy of 16.87 kcal/mol and the frequency factor of 1.49 x 10(11) (mg L)1/2/g DCM min.

Coloring Agents↗

Use of urea kinetic model and haemofiltration to improve nitrogen balance in haemodialysed children.

To improve nitrogen balance and nutritional status, 10 paediatric patients (11.2 +/- 2.7 years; 28.5 +/- 5.1 kg) on regular haemodialysis (HD) for 25.3 +/- 1.2 months were treated with haemofiltration (HF) for 12.2 +/- 3.4 months. HF was prescribed using a urea kinetic model to ensure a pre-treatment blood urea nitrogen (BUN) of 130 mg/100ml. Urea generation rate (Gu) and protein catabolic rate (PCR) were computed by urea kinetics. Protein and calorie intake was assessed in the children on an unrestricted diet by analysis of 10 days' dietary records obtained every two months. During HF treatment a significant decrease of Gu and PCR was obtained and nitrogen balance increased in all the children.

Adolescent↗

[Purification of total flavones from Morus alba L.by macroporous adsorbents and kinetic model for the process].

OBJECTIVE: To establish the separation and purification technology for the total flavones from Morus alba L.(MTF), and present a kinetic model for this process. METHODS: Three types of macroporous adsorbents were tested to separate and purify MTF, and to evaluated by adsorption capacity, elution ratio and product purity. The curves of dynamic adsorption-elution process was plotted and the kinetic equations were presented. RESULT: Among three types of macroporous adsorbents, the NKA-9 type showed better property with the adsorption capacity of 43.4 mg.g(-1)and the elution ratio of 98.2%. The purity of MTF product reached to 58.2 % in the technological conditions following: extract sample concentration of 20 mg.ml(-1), 6 times washing water and elution reagent of 70% ethanol. The adsorbent could be used for 4 times repeatedly. The kinetic equation was y=u(1 - e(-kx)). CONCLUSION: The NKA-9 type of macroporous absorbent is suitable to purify the MTF.

Adsorption↗

A kinetic model of intermediate formation during assembly of cholera toxin B-subunit pentamers.

Cholera toxin is the most important virulence factor produced by Vibrio cholerae. The pentameric B-subunit of the toxin can bind to GM1-ganglioside receptors, leading to toxin entry into mammalian cells. Here, the in vitro disassembly and reassembly of CtxB(5) (the B subunit pentamer of cholera toxin) is investigated. When CtxB(5) was acidified at pH 1.0 and then neutralized, the B-subunits disassembled and could no longer migrate as SDS-stable pentamers on polyacrylamide gels or be captured by GM1. However, continued incubation at neutral pH resulted in the B-subunits regaining the capacity to be detected by GM1 enzyme-linked immunosorbent assay (t(12) approximately 8 min) and to migrate as SDS-stable pentamers (t(12) approximately 15 min). Time-dependent changes in Trp fluorescence intensity during B-subunit reassembly occurred with a half-time of approximately 8 min, similar to that detected by GM1 enzyme-linked immunosorbent assay, suggesting that both methods monitor earlier events than B-pentamer formation alone. Based on the Trp fluorescence intensity measurements, a kinetic model of the pathway of CtxB(5) reassembly was generated that depended on trans to cis isomerization of Pro-93 to give an interface capable of subunit-subunit interaction. The model suggests formation of intermediates in the reaction, and these were successfully detected by glutaraldehyde cross-linking.

Cholera Toxin↗

Urea kinetic modeling with a prototype urea sensor in the spent dialysate stream.

The authors have previously demonstrated the feasibility and accuracy of urea kinetic modeling (UKM) based on monitoring urea concentration in the spent dialysate stream (SDS) throughout the hemodialysis (HD) session. They describe here a prototype urea sensor for this purpose and initial experience with HD patients. The sensor is based on ammonium ion and reference electrodes housed in a cell through which the entire SDS passes. The two electrode tips are bathed in urease solution on one side of a dialysis membrane; the SDS flows along the adjacent side. Urea diffusing across the membrane from the SDS is converted by the urease into ammonium ion, which is measured by the electrode pair. For evaluation, the prototype flowthrough urea sensor was installed in the SDS of a Cobe Centry 3 HD machine for 36 HD sessions. Independent measurement demonstrated a linear relationship between mv output of the sensor and logarithm of SDS urea concentration. The use of SDS urea concentration time profiles obtained with this sensor to obtain accurate values of patient protein catabolic rate (PCR) and KT/V is illustrated. Incorporation of urea sensors such as this prototype into HD machines, will permit complete automation of UKM in the near future.

Dialysis Solutions↗

Phospholipid binding and transfer by the nonspecific lipid-transfer protein (sterol carrier protein 2). A kinetic model.

The nonspecific lipid-transfer protein (nsL-TP) from bovine liver was studied by measuring the binding and transfer of the fluorescent phospholipid 1-palmitoyl-2-[6-(1-pyrenyl)-hexanoyl]-sn-glycero-3-phosphocholine (PamPryGroPCho). A kinetic model is presented involving three steps: (a) interaction of nsL-TP with a membrane surface; (b) equilibration of PamPyrGroPCho monomers between the membrane and nsL-TP; and (c) dissociation of the nsL-TP/PamPyrGroPCho complex from the membrane surface. Steady-state analysis of the model yielded theoretical equations describing both binding and transfer kinetics. Computer analysis, using these equations, showed good fits with the experimental results and several kinetic constants could be calculated. From these constants it was inferred that incorporation of acidic phospholipids into vesicles enhanced the interaction of nsL-TP with the membrane interface (step a), without affecting the equilibrium binding of phospholipid monomers to nsL-TP (step b). As a result, the rate of nsL-TP-mediated PamPyrGroPCho transfer from donor to acceptor vesicles was greatly affected. Under the conditions of incubation, incorporation of the acidic lipids in the donor membrane vesicles stimulated transfer, whereas incorporation of these lipids in the acceptor membranes could lead to a virtually complete inhibition of transfer. From the results it is concluded that the formation of a soluble lipid-nsL-TP complex is the key step in nsL-TP-mediated phospholipid transfer.

Animals↗