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PubMed1994

Identification of a binding site for blood coagulation factor IXa on the light chain of human factor VIII.

The interaction between human factor IXa and factor VIII or its constituent units was investigated. Equilibrium binding studies were performed employing factor VIII light chain that was immobilized on a monoclonal antibody. Factor VIII light chain was observed to bind factor IXa with high affinity (Kd = 14.8 +/- 3.2 nM) and approximately 1:1 stoichiometry. Optimal interaction required NaCl concentrations below 0.2 M and the presence of Ca2+ ions. Factor VIII light chain in solution effectively inhibited binding of factor IXa to the immobilized light chain (Ki = 10.9 +/- 1.9 nM). The isolated factor VIII light chain and the factor VIII heterodimer were equally effective in factor IXa binding, demonstrating that this interaction did not require the factor VIII heavy chain. Factor Xa and activated Protein C were found to be inefficient (Ki > or = 1.2 microM) in competing with factor IXa, indicating that the high affinity for factor VIII light chain was unique for factor IXa. The factor IXa-factor VIII light chain interaction was inhibited by von Willebrand factor, but this effect was abolished by cleavage of the factor VIII light chain by thrombin. An antibody that inhibits von Willebrand factor-factor VIII complex formation did not compete for factor IXa binding. In contrast, association of factor IXa with the factor VIII light chain was inhibited by an antibody directed against the factor VIII region Gln1778-Asp1840. We propose that this sequence provides a factor IXa binding site and that its exposure requires dissociation of the factor VIII-von Willebrand factor complex.

Antibodies, Monoclonal↗
PubMed1998

Kinetic and thermodynamic principles determining the structural design of ATP-producing systems.

It is theoretically analysed whether the structural design of ATP-producing pathways, in particular the design of glycolysis, may be explained by optimization principles. On the basis of kinetic and thermodynamic principles conclusions are derived concerning the stoichiometry of these pathways in states of high ATP production rates. One of the extensions to previous investigations is that the concentrations of the adenine nucleotides are taken into account as variable quantities. This necessitates the consideration of an interaction of the ATP-producing system I with an external ATP-consuming system II. A great variety of pathways is studied which differ in the number and location of ATP-consuming reactions, ATP-producing reactions and reactions involving inorganic phosphate. The corresponding number of possible pathways may be calculated in an explicit manner as a function of the number of those reactions which do not couple to ATP or inorganic phosphate. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations and all rate equations are expressed in terms of equilibrium constants and characteristic times. A thermo-dynamical analysis of the two coupled systems yields upper and lower limits for the concentration of ATP and an explicit expression for the maximal difference between the number of ATP-producing and ATP-consuming reactions of system I. The following results of the optimization are obtained. (i) The ATP production rate always increases if the ATP-producing reactions as well as those reactions characterized by an uptake of inorganic phosphate are shifted as far as possible towards the end of system I. (ii) Explicit conditions for the optimal location of the ATP-consuming reactions are presented. The results are discussed in the context of characteristic times as well as in terms of enzyme kinetic parameters. (iii) For two sets of characteristic times the resulting stoichiometries and their corresponding steady-state fluxes are investigated in detail. One of these stoichiometries shows a close correspondence to contemporary standard glycolysis. (iv) It is shown that most possible pathways result in a very low steady-state flux, that is, the optimal stoichiometry is characterized by a significant selective advantage. (v) The standard free energy profile of a pathway with an optimal stoichiometry is discussed. It differs significantly from the free energy profiles of nonoptimized pathways.

Adenosine Triphosphate↗
PubMed2005

Discrimination between perfect and mismatched duplexes with oligonucleotide gel microchips: role of thermodynamic and kinetic effects during hybridization.

The efficiency of discrimination between perfect and mismatched duplexes during hybridization on microchips depends on the concentrations of target DNA in solution and immobilized probes, buffer composition, and temperature of hybridization and is determined by both thermodynamic relationships and hybridization kinetics. In this work, optimal conditions of discrimination were studied using hybridization of fluorescently labeled target DNA with custom-made gel-based oligonucleotide microchips. The higher the concentration of immobilized probes and the higher the association constant, the higher the concentration of the formed duplexes and the stronger the corresponding fluorescence signal, but, simultaneously, the longer the time needed to reach equilibrium. Since mismatched duplexes hybridize faster than their perfect counterparts, perfect-to-mismatch signal ratio is lower in transient regime, and short hybridization times may hamper the detection of mutations. The saturation time can be shortened by decreasing the probe concentration or augmenting the gel porosity. This improves the detection of mutations in transient regime. It is shown that the decrease in the initial concentration of oligonucleotide probes by an order of magnitude causes only 1.5-2.5-fold decrease of fluorescence signals after hybridization of perfect duplexes for 3-12 h. At the same time, these conditions improve the discrimination between perfect and mismatched duplexes more than two-fold. A similar improvement may be obtained using an optimized dissociation procedure.

Base Composition↗
PubMed1996

Multiple-phase helical CT of the liver for detecting small hepatomas in patients with liver cirrhosis: contrast-injection protocol and optimal timing.

OBJECTIVE: Helical CT scanners allow multiple-phase sequential scans of the entire liver to be obtained during a single bolus injection of contrast material. The purpose of this study was to compare two injection protocols and to establish timing that would optimize detection of hepatomas less than 3 cm in diameter. SUBJECTS AND METHODS: Triple-phase helical CT of the liver was evaluated in 217 patients who had liver cirrhosis and were referred for known or suspected hepatomas. Proof of individual neoplasms was based on biopsy results, surgical findings, or findings of other imaging studies. Sixty percent nonionic contrast material, infused at 2 or 4 ml/sec, was followed by sequential arterial-phase, portal-venous phase, and equilibrium-phase helical scans of the liver. Aortic and hepatic enhancement curves were constructed by measuring CT attenuation. The CT attenuation values of individual tumor lesions were also measured. We compared the degree of enhancement of normal structures and tumors obtained with four scan protocols (injection at 2 ml/sec with a 30-sec scan delay [n = 54], injection at 2 ml/sec with a 35-sec scan delay [n = 47], injection at 4 ml/sec with a 20-sec scan delay [n = 56], and injection at 4 ml/sec with a 25-sec scan delay [n = 60] and determined the optimal injection protocol and timing for CT acquisition. RESULTS: Peak aortic and hepatic enhancement was obtained earlier with the 4-ml/sec protocol (at 24 sec and 61 sec versus 36 sec and 90 sec for the 2-ml/sec protocol). The peak attenuation value of the aorta was higher with the 4-ml/sec protocol (330 H versus 186 H for the 2-ml/sec protocol). However, peak hepatic attenuation was similar for both protocols (98 H for the 4-ml/sec protocol versus 92 H for the 2-ml/sec protocol). Liver-tumor contrast was highest in the arterial phase with both protocols. The next highest contrast was obtained during the equilibrium phase. Liver-tumor contrast in the portal-venous phase was significantly lower than that in the other two phases. Tumor enhancement was significantly higher in scans obtained using the 4-ml/sec protocol with a delay time of 25 sec than those obtained with a delay time of 20 sec. In 109 hepatomas, 35 tumors were only seen or were most conspicuous during the arterial phase, four tumors were most conspicuous during the equilibrium phase, and one tumor was most conspicuous during the portal-venous phase. CONCLUSION: Arterial-phase helical CT of the liver after 4-ml/sec injection of contrast material significantly improves detection of hepatomas less than 3 cm in diameter when performed in addition to delayed scanning. Portal-venous phase helical CT is of limited value in detecting small hepatomas.

Carcinoma, Hepatocellular↗
PubMed2003

Optical determination of anisotropic material properties of bovine articular cartilage in compression.

The precise nature of the material symmetry of articular cartilage in compression remains to be elucidated. The primary objective of this study was to determine the equilibrium compressive Young's moduli and Poisson's ratios of bovine cartilage along multiple directions (parallel and perpendicular to the split line direction, and normal to the articular surface) by loading small cubic specimens (0.9 x 0.9 x 0.8 mm, n =15) in unconfined compression, with the expectation that the material symmetry of cartilage could be determined more accurately with the help of a more complete set of material properties. The second objective was to investigate how the tension-compression nonlinearity of cartilage might alter the interpretation of material symmetry. Optimized digital image correlation was used to accurately determine the resultant strain fields within the specimens under loading. Experimental results demonstrated that neither the Young's moduli nor the Poisson's ratios exhibit the same values when measured along the three loading directions. The main findings of this study are that the framework of linear orthotropic elasticity (as well as higher symmetries of linear elasticity) is not suitable to describe the equilibrium response of articular cartilage nor characterize its material symmetry; a framework which accounts for the distinctly different responses of cartilage in tension and compression is more suitable for describing the equilibrium response of cartilage; within this framework, cartilage exhibits no lower than orthotropic symmetry.

Animals↗
PubMed1984

[Circulating immune complexes: optimization and characteristics of the C1q(I125) fixation test].

The present paper describes the optimisation of a liquid phase [125I] C1q binding assay for the detection of circulating immune complexes. Blood must be collected without any anticoagulant. The serum can be stored or transported as usual without damage. A 90 min incubation is needed to reach the equilibrium of the reaction; polyethylene glycol (2,5% final concentration) is added to precipitate the [125I] C1q-CIC complex. By its simplicity and reproducibility, this test can be currently employed, especially in the case of treatment by plasmapheresis.

Antigen-Antibody Complex↗
PubMed1996

Reproductive bionomics of the soft tick, Ornithodoros turicata (Acari: Argasidae).

The effects of different temperatures and relative humidities (RHs) were tested on various reproductive parameters of Ornithodoros turicata, an argasid tick that inhabits gopher tortoise burrows in Florida, USA. The pre-oviposition, oviposition and incubation periods of the ticks decreased as temperature increased. These periods were also affected by the RH. The number of eggs oviposited was affected significantly by the combined effect of temperature and RH. Fewer eggs were laid by ticks in the 24 degrees C regimes and the 27 degrees C/95% RH regime compared to those in the other temperature/RH groups. There was an inverse relationship between the number of eggs oviposited and the percentage of hatched larvae that was correlated with the temperature and RH. Ticks reared at 27 degrees C/90% RH and 30 degrees C/90% RH laid more eggs than those reared in the other combinations of temperature and humidity but fewer larvae hatched from these eggs. The reproductive fitness index (RFI) values were highest in females held in the 24 degrees C groups and the 30 degrees C/95% RH group, although significantly more larvae hatched at the lower temperatures. The optimum reproductive conditions for O. turicata under laboratory conditions appear to be 24 degrees C and 90-95% RH. While mating occurred at all temperatures, none of the females laid eggs at 22 degrees C. The ticks may move preferentially to low temperatures when not feeding to remain above the critical equilibrium humidity and/or below the critical metabolic level necessary for prolonged survival. However, most female ticks oviposited after 45 days when moved to 27 degrees C/95% RH. Ornithodoros turicata females may have a limited capability to delay oviposition until an optimal microenvironment for egg deposition can be located in the burrow.

Animals↗
PubMed1979

RIA system programming by means of kinetic parameters.

Insulin-125I antibody reaction was optimized by physical-chemical parameters. After the activation energies Ea and Ed for association and dissociation, respectively were calculated from the experimental data, the theoretical values of the reaction rate constants ka and kd were determined as well as equilibrium constants K. By means of the empirical formulae, the approximate incubation time for the RIA kit and maximal percent of insulin-125I binding to antibody (%B) in relation to temperature were computed. The proposed method may be applied to the new antigen-binder systems preparation (new antibodies, shortening of the incubation time, temperature changes, influence of different ions and kind of buffer).

Animals↗
PubMed2005

Extended flip-back schemes for sensitivity enhancement in multidimensional HSQC-type out-and-back experiments.

In many NMR experiments, only polarisation of a limited sub-set of all protons is converted into observable coherence. As recently shown by the "longitudinal" TROSY implementation (Pervushin et al. (2002) J. Am. Chem. Soc., 124, 12898-12902) and SOFAST-HMQC (Schanda and Brutscher (2005) J. Am. Chem. Soc., 127, 8014-8015), recovery of unused polarisation can be used indirectly and unspecifically to cool the proton lattice and, thus, accelerate re-equilibration for the selected proton subset. Here we illustrate transfer of this principle to HSQC-based multi-dimensional out-and-back experiments that exploit only polarisation of 15N-bound protons. The presented modifications to the pulse sequences can be implemented broadly and easily, extending standard flip-back of water polarisation to a much larger pool of protons that may comprise all non-15N-bound protons. The underlying orthogonal separation of H(N) polarisation (selected by the main transfer path) from unused H(u) polarisation (flipped-back on the recovery path) is thereby achieved through positive or negative selection by J-coupling, or using band-selective pulses. In practice, H(u) polarisation recovery degrades mostly through cumulative pulse imperfections and transverse relaxation; we present, however, strategies to substantially minimise such losses particularly during interim proton decoupling. Depending on the protein's relaxation properties and the extended flip-back scheme employed, we recovered up to 60% H(u) equilibrium polarisation. The concomitant cooling of the proton lattice afforded substantial gains of more than 40%, relative to the water-only flip-back version, in the fast pulsing regime with re-equilibration delays tau much shorter than optimal (tau(opt) = 1.25 x T1(H(N))). These would be typically employed if resolution requirements dominate the total measurement time. Contrarily, if sensitivity is limiting and optimal interscan delays tau(opt) can be set (optimal pulsing regime), the best of the presented flip-back schemes may still afford up to ca. 10% absolute sensitivity enhancement.

Magnetic Resonance Spectroscopy↗
PubMed1988

Solid phase enzyme-linked competitive binding assay for riboflavin.

A new solid-phase enzyme-linked assay for riboflavin (vitamin B2) is described. The assay is based on the competition between analyte vitamin molecules and a glucose-6-phosphate dehydrogenase-3-carboxymethylriboflavin conjugate for a limited number of riboflavin-binding protein sites immobilized on Sepharose particles. Significant improvements in conjugate catalytic activity and thus detectability are achieved by optimizing the reaction conditions used to covalently link 3-carboxymethylriboflavin to the enzyme. Optimization experiments include studying the effects of reaction pH and organic solvent composition. Final assay detection limits and the sensitivity of the dose-response curves are dependent on the ratio of conjugate to binding protein sites utilized in an equilibrium assay protocol. Selectivity of the method correlates well with that predicted based on the known association constants of riboflavin-binding protein with flavin analogs. The assay is shown to offer adequate detection limits and selectivity for direct measurement of riboflavin in urine, infant formula, and vitamin capsules.

Binding Sites↗
PubMed2005

A process to prepare a synthetic filter material containing nutrients for biofiltration.

In this study, an optimal process to prepare a synthetic filter material (poly(vinyl alcohol) (PVA)/peat/KNO(3) composite bead) containing nutrients was developed for biofiltration. The optimal preparing condition was that each of the peat and PVA aqueous solutions contains 6.4 g KNO(3) and the nitrogen content in the boric and phosphate aqueous solutions must retain higher than 3.94 and 1.52 g N/l, respectively. The equilibrium amount of water-soluble nitrogen dissolved out of the prepared composite bead was between 7.95 and 8.21mg N/g dry solid. The path of water-soluble nitrogen dissolving out of the A-type bead was the water-soluble nitrogen dispersed in the peat phase initially diffused into the outer PVA phase and then it diffused out of the bead surface. And the path of water-soluble nitrogen dissolving out of the H-type bead was the water-soluble nitrogen dispersed in both the peat and PVA phases simultaneously diffused into the outer PVA phase and out of the bead surface, respectively. The microbial growth rate k(g) of the H-type composite bead was higher than that of the A-type composite bead approximately 1.09-1.58 times, and its value was between 0.100 and 0.417 day(-1) as the composite bead was immersed in 0-0.896 M KNO(3) solution. The maximum value of k(g) appeared at the composite bead immersed in 0.384 M KNO(3) solution and was higher than that of the compost by a factor approximately 1.49. The percentage of removed volatile organic compounds (VOCs) remained at more than 98% during the biofilter operating 230 days as the composite bead was immersed in KNO(3) aqueous solution before packing. This composite bed was without the further addition of nutrients during this operating period. It was proved that this composite bead was superior to the compost as a filter material.

Air Pollutants↗
PubMed2006

Interaction between anionic dyes and cationic flocculant P(AM-DMC) in synthetic solutions.

Copolymer of acrylamide and 2-[(methacryloyloxy)ethyl]trimethylammonium chloride [P(AM-DMC)] is found to be effective to combine anionic dyes with strong aqueous solubility. This work aims mainly at revealing the interaction between anionic dyes and [P(AM-DMC)] by running jar test, spectra analysis and equilibrium dialysis experiments. The results show that P(AM-DMC) effectively decolorizes the tested strong water soluble anionic dyes, such as acidic, reactive and direct dyes, from their aqueous solutions under mild acidic and neutral conditions. Higher cationicity and optimal dose of flocculant P(AM-DMC) have to be used to achieve satisfactory and effective decolorization. Comparison of IR spectra of dye, flocculant P(AM-DMC) and the floc formed indicates chemical interaction occurred between sulfonic groups of dye and quaternary ammonium of flocculant. Plots of r-logC suggest cooperative interaction exists evidently for some dyes tested. Addition of KCl or urea reduces binding extent evidently, which shows the importance of electrostatic and hydrophobic interaction. Therefore the interaction between dyes tested and P(AM-DMC) might be controlled by hydrophobic, cooperative interaction and energetic interaction which includes chemical and electrostatic interactions.

Acrylamides↗
PubMed1997

Enzyme catalyzed esterification.

Enzyme catalyzed esterification reactions have found many applications, ranging from the modification of vegetable oils for human consumption to the production of optically pure chemicals. To displace the equilibrium in favor of synthesis, rather than hydrolysis, these reactions are performed in non-aqueous or microaqueous media. The influence of the amount of water, and of the nature of organic solvent, are new parameters to consider in the optimization of industrial processes. They also add a new perspective to our knowledge of the functioning of enzymes.

Journal Article↗
PubMed2000

Structure and thermodynamic properties of a binary liquid in a porous matrix: the formalism

Using the replica trick we derive a formalism to describe the structure and the thermodynamic properties of a binary liquid in equilibrium with a porous medium. We present the replica Ornstein-Zernike equations for the general case of a k-component liquid inside a porous matrix; besides the usual liquid-state closure relations, we consider in particular the optimized random phase approximation (ORPA) restricting ourselves at present to hard-core potentials exclusively. We present furthermore several thermodynamic relations: the Gibbs-Duhem equation, the compressibility, and the viral equation. Within the framework of the ORPA (mean spherical approximation), closed expressions for the perturbation contribution to the free energy and the chemical potentials can be presented. Finally, we offer suggestions for numerical implementations.

Journal Article↗
PubMed2001

Learning to coordinate in a complex and nonstationary world.

We study analytically and by computer simulations a complex system of adaptive agents with finite memory. Borrowing the framework of the minority game and using the replica formalism we show the existence of an equilibrium phase transition as a function of the ratio between the memory lambda and the learning rates Gamma of the agents. We show that, starting from a random configuration, a dynamic phase transition also exists, which prevents agents from reaching optimal coordination. Furthermore, in a nonstationary environment, we show by numerical simulations that the phase transition becomes discontinuous.

Game Theory↗
PubMed2000

On the synthesis of brain-state-in-a-box neural models with application to associative memory.

In this article we present techniques for designing associative memories to be implemented by a class of synchronous discrete-time neural networks based on a generalization of the brain-state-in-a-box neural model. First, we address the local qualitative properties and global qualitative aspects of the class of neural networks considered. Our approach to the stability analysis of the equilibrium points of the network gives insight into the extent of the domain of attraction for the patterns to be stored as asymptotically stable equilibrium points and is useful in the analysis of the retrieval performance of the network and also for design purposes. By making use of the analysis results as constraints, the design for associative memory is performed by solving a constraint optimization problem whereby each of the stored patterns is guaranteed a substantial domain of attraction. The performance of the designed network is illustrated by means of three specific examples.

Association Learning↗
PubMed1977

[An ion exchange method to determine free metal concentrations, adapted for use in biological fluids: methods and determination of (Mg2+)].

An ion exchange method for measuring concentrations of free (ionized) metal ions and its application to the determination of [Mg2+] is described. A surface sulfonated polystyrene material is used as the "twodimensional" cation exchanger. The sample-volume is 1 ml. About 50 determinations can be performed within 1 hr having a standard error of +/- (2-4)% in the optimal range of measurement. Advantages and disadvantages of the method compared with other ones are demonstrated and discussed. Free Mg2+ ion concentrations were measured in solutions containing pyrophosphate as well as haemoglobin and compared with those which were determined by equilibrium calculation or ultrafiltration.

Cation Exchange Resins↗
PubMed1983

Clinical results of long-term treatment with a low protein diet and a new amino acid preparation in patients with chronic uremia.

15 patients with severe uremia (mean serum creatinine concentration 965, range 568-1383 mumoles/l) were treated with an unselected protein restricted (16-20 g protein/day) diet and a new amino acid preparation, containing the essential amino acids in proportions which differed from those recommended by Rose for normal man and which contained in addition histidine and tyrosine, for an average period of 224 (range 33-737) days. Plasma urea concentration decreased and the uremic symptoms disappeared. Ten nitrogen balance studies were performed in 6 patients after a mean treatment time of 151 days. The mean nitrogen balance, corrected for changes in total urea pool, was + 0.4 +/- 0.22 g N/day. In 4 patients, in whom progression of the renal insufficiency was assessed by plots of the reciprocal of serum creatinine concentration versus time, retardation of progression was observed after institution of the regimen. The results show that nitrogen equilibrium can be maintained during long-term treatment with this regimen and suggest that better nitrogen utilization is achieved with the new amino acid preparation than when essential amino acids are given to uremic patients in the proportions considered optimal for normal man. It is further shown that the progression of renal insufficiency may be retarded by this regimen.

Adult↗