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At least 235 records · Page 13Linked to original sources
PubMed1998

Characterization of flexible molecules in solution: the RGDW peptide.

Molecular dynamics simulations with adaptive umbrella sampling of the potential energy are used to study conformations of the adhesion peptide RGDW. The peptide is simulated in a box of explicit water. It results in a combination of room temperature (300 K) simulations, in which conformations dominating the average properties of the system are sampled, with high temperature ( approximately 1000 K) simulations in which free energy barriers separating different local minima are crossed efficiently. The simulations with explicit water are compared to simulations of the isolated peptide using different treatments of the electrostatics, and to published experimental data. There is good agreement for data related to the backbone conformation of the peptide. Some discrepancies are evident for data related to side-chain conformations. Together the simulations and experiments provide a description of the RGDW system that is more detailed and reliable than what can be obtained by either simulations or experiments alone.

Amides↗
PubMed1990

Absolute bioavailability of pirenzepine in intensive care patients.

The absolute bioavailability (f) of pirenzepine was determined in 27 intensive care patients receiving the drug for prophylaxis and therapy of upper gastrointestinal tract bleeding. A multiple oral and intravenous dosage regimen and the times of blood sampling were adapted to individual conditions and treatment. Mean f in the patients was 0.28, which was significantly higher than in 12 normal subjects (0.14). It showed no dependence on age (range 20-82 y), nor on the risk factors cardiac insufficiency, renal and hepatic dysfunction, gastrectomy (Billroth II) and bleeding gastrointestinal ulcers, nor on concomitant administration of metoclopramide or antacids. Due to the wide therapeutic index of pirenzepine, it is concluded that individualization of therapy is not necessary for patients in intensive care.

Administration, Oral↗
PubMed1989

Relationship between the utilisation profile of individual joints and their susceptibility to primary osteoarthritis.

Two subjects were studied for 1 to 3 weeks during the course of their normal domestic activities. Utilisation profiles were derived for ten joints, using a systematic time-series sampling technique adapted from behavioural biology. At each joint the proportion of the available range utilised was noted. The results were compared with the known regional prevalence of primary osteoarthritis. There was a correlation between the degree to which a joint was incompletely utilised, and its susceptibility to osteoarthritis. The hypothesis is advanced that primary osteoarthritis may be due to incomplete joint utilisation.

Activities of Daily Living↗
PubMed1984

Effects of a rapid change in muscle glycogen availability on metabolic and hormonal responses during exercise.

To evaluate the metabolic and hormonal adaptations following a rapid change in muscle glycogen availability, 14 subjects had their muscle glycogen content increased in one leg (IG) and decreased in the other (DG). In group A (n = 7), subjects exercised on a bicycle ergometer at 70% maximal oxygen uptake for 20 min using the DG leg. Without resting these same subjects exercised another 20 min using the IG leg. Subjects in group B (n = 7) followed the same single-leg exercise protocol but in the reverse order. In order to get some information on the time sequence of these possible adaptations, blood samples were collected at rest and at the beginning and the end of each exercise period (min 5, 20, 25, and 40). Results indicated that 5 min after the switch from the DG leg to the IG leg, transient increases in plasma free fatty acids (1.20 to 1.39 meq X 1(-1)) and serum insulin (10.1 to 12 mu X 1(-1)) concentrations occurred. Between minute 25 and 40 of exercise, the DG to IG switch was accompanied by a decrease in free fatty acids and glycerol concentrations as well as an increase in lactate levels. An opposite response was observed in the IG to DG condition during the same time span. Plasma norepinephrine, epinephrine, glucagon, and serum cortisol concentrations were not significantly affected by the leg change. These results suggest a rapid preferential use of muscle glycogen when available and a time lag in the response of the extramuscular substrate mobilization factors.

Adult↗
PubMed1992

Pharmacokinetic estimations from microdialysis data.

Microdialysis has recently been adapted for sampling the extracellular fluid of various organs in order to measure drug concentrations, and the first clinical application has been published. My aim here is to provide simple rules about how to analyse pharmacokinetic data from such studies. The plotting of data on a time scale and the estimation of C (0) and slopes is not a trivial problem when multicompartmental models are assumed or sampling intervals are unequal. I have developed formulae and algorithms to solve the problem. A simple rule of thumb is given, suggesting when these formulae need to be applied. It is shown that the calculations of half-life and slopes is similar to standard methods for equal sample intervals and that calculation of AUC and clearance may be even more accurate for microdialysis data than for ordinary blood sampling, because of the time-integral character of the dialysis method. I have dealt with both zero-order and first-order kinetics.

Animals↗
PubMed1998

Preparation of hair for measurement of elements by inductively coupled plasma-mass spectrometry (ICP-MS).

The preparation of hair for the determination of elements is a critical component of the analysis procedure. Open-beaker, closed-vessel microwave, and flowthrough microwave digestion are methods that have been used for sample preparation and are discussed. A new digestion method for use with inductively coupled plasma-mass spectrometry (ICP-MS) has been developed. The method uses 0.2 g of hair and 3 mL of concentrated nitric acid in an atmospheric pressure-low-temperature microwave digestion (APLTMD) system. This preparation method is useful in handling a large numbers of samples per day and may be adapted to hair sample weights ranging from 0.08 to 0.3 g. After digestion, samples are analyzed by ICP-MS to determine the concentration of Li, Be, B, Na, Mg, Al, P, S, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ge, As, Se, Rb, Sr, Zr, Mo, Pd, Ag, Cd, Sn, Sb, I, Cs, Ba, Pt, Au, Hg, Tl, Pb, Bi, Th, and U. Benefits of the APLTMD include reduced contamination and sample handling, and increased precision, reliability, and sample throughput.

Hair↗
PubMed1985

Relative abilities of phosphagens with different thermodynamic or kinetic properties to help sustain ATP and total adenylate pools in heart during ischemia.

Hearts of chicks fed the creatine analog, 1-carboxymethyl-2-iminoimidazolidine (cyclocreatine), accumulated 15 mumol/g wet wt of the synthetic phosphagen, cyclocreatine-3-P; had total creatine levels reduced from the normal 6 mumol/g to only 1.8 mumol/g; and had their glycogen levels tripled. During total ischemia in vitro these hearts utilized the cyclocreatine-P for synthesis of ATP, had greatly prolonged glycolysis, and exhibited a two- to fivefold delay in depletion of both ATP and the total adenylate pool, relative to controls. Accumulation from the diet of comparable levels of the closely related 1-carboxyethyl-2-imino-3-phosphonoimidazolidine (homocyclocreatine-P) by heart was accompanied by only slight lowering of total creatine to 4.2 mumol/g, and a tripling of glycogen levels. During ischemia these hearts exhibited prolonged glycolysis, but they did not utilize the very stable homocyclocreatine-P (200,000-fold less reactive than creatine-P) and thus formed less Pi; most significantly, there was no delay in depletion of ATP levels relative to controls. Feeding of creatine doubled total creatine levels in heart, but had no marked effect on ATP depletion during ischemia; in all dietary groups creatine-P pools had fallen to less than or equal to 1.2 mumol/g by first tissue sampling. Although adaptive responses were also involved, maximal conservation of ATP and total adenylate pools in heart during ischemia apparently required, in addition to adequate glycogen reserves, substantial levels of a kinetically competent phosphagen that is thermodynamically poised to continue to assist glycolysis in buffering decreases and oscillations in the [ATP]/[free ADP] ratio at the lower phosphorylation potentials and more acid pH characteristic of later stages of ischemia. Decreases and oscillations in the [ATP]/[free ADP] ratio cannot be buffered effectively late in ischemia by the creatine-P system for thermodynamic reasons, or by the homocyclocreatine-P system because of kinetic limitations.

Adenine Nucleotides↗
PubMed1990

Chlorophyll a fluorescence transient as an indicator of active and inactive Photosystem II in thylakoid membranes.

Upon illumination, a dark-adapted photosynthetic sample shows time-dependent changes in chlorophyll (Chl) a fluorescence yield, known as the Kautsky phenomenon or the OIDPS transient. Based on the differential effects of electron acceptors such as 2,5-dimethyl-p-benzoquinone (DMQ) and 2,6-dichloro-p-benzoquinone (DCBQ) on Chl a fluorescence transients of spinach thylakoids, we suggest that the OID phase reflects the reduction of the electron acceptor QA to QA- in the inactive PS II (see Graan, T. and Ort, D. (1986) Diochim. Biophys. Acta 852, 320-330). In spinach thylakoids, heat-induced increase of the Chl a fluorescence yield is also differentially sensitive to the addition of DMQ and DCBQ suggesting that this increase is mainly on the 'I' level, and thus heating is suggested to convert active PS II to inactive PS II centers. The kinetics of decay of QA-, calculated from variable Chl a fluorescence, was analyzed into three exponential components (365-395 microseconds; 6-7 ms; and 1.4-1.7 s). In heated samples, the decay rate of variable Chl a fluorescence is slower than the normal back-reaction rate; there is a preponderance of the slow component that may be due, partly, to the active centers undergoing slow back reaction between QA- and the S2 state of the oxygen-evolving complex.

Benzoquinones↗
PubMed1996

A discontinuous method for catalase determination at 'near physiological' concentrations of H2O2 and its application to the study of H2O2 fluxes within cells.

We describe a discontinuous method for the measurement of catalase using the Ferrous Oxidation in Xylenol orange (FOX) assay. Samples containing catalase are incubated with H2O2 for varying time intervals prior to rapid mixing of aliquots of the incubation mixtures with FOX reagent, which measures residual H2O2. Absorbance is then read at 560 nm after 30-min incubation at room temperature. Decay of H2O2 is proportional to catalase activity in the original sample. An adaptation of the method involves exposure of intact cells to H2O2-generating systems in the presence of aminotriazole. The extent of catalase inactivation allows estimates of total H2O2 accumulation within the cell.

Amitrole↗
PubMed1995

Standardisation of primers and an algorithm for HIV-1 diagnostic PCR evaluated in patients harbouring strains of diverse geographical origin. The Belgian AIDS Reference Laboratories.

Eight Belgian AIDS Reference Laboratories established a multicentre quality control to evaluate the performance of their diagnostic human immunodeficiency virus type 1 (HIV-1) DNA polymerase chain reaction (PCR). A set of Belgian and African HIV-1 seropositive and seronegative patient samples, collected in Belgium, and the British Medical Research Council (MRC) HIV-1 PCR reference reagent kit, containing plasmid HIV-1 DNA at several dilutions in human carrier DNA with appropriate negative controls, were tested by the laboratories. No false positive results were reported. All laboratories were able to detect one to two copies of HIV-1 DNA. Among the 17 Belgian and African HIV-1 seropositives, some laboratories reported up to four indeterminate results, mainly due to failure of the SK38-39, SK68-69 (Ou et al. (1988) Science 239, 295-297) and/or gag881-882 (Simmonds et al. (1990) J. Virol. 64, 864-872) primers and a poorly performing algorithm. Only the H1POL4235-4538 nested pol primer set, developed by one of the laboratories, correctly identified all the tested HIV-1 positive and negative samples. Consequently, the laboratories decided to evaluate these pol primers as a reference primer set and to standardise the testing algorithm. All laboratories achieved a sensitivity and specificity of 100% on testing 10 additional Belgian and African patient samples, when adapting a standardised algorithm based on three HIV-1 primer sets, one of which is the H1POL4235-4538 primer set.

Africa↗
PubMed2005

Heavy metal contamination from mining sites in South Morocco: 1. Use of a biotest to assess metal toxicity of tailings and soils.

Our work was conducted to investigate the heavy metal toxicity of tailings and soils collected from five metal mines located in the south of Morocco. We used the MetPAD biotest Kit which detects the toxicity specifically due to the heavy metals in environmental samples. This biotest initially developed to assess the toxicity of aquatic samples was adapted to the heterogeneous physico-chemical conditions of anthropogenic soils. Contrasted industrial soils were collected from four abandoned mines (A, B, C and E) and one mine (D) still active. The toxicity test was run concurrently with chemical analyses on the aqueous extracts of tailings materials and soils in order to assess the potential availability of heavy metals. Soil pH was variable, ranging from very acidic (pH 2.6) to alkaline values (pH 8.0-8.8). The tailings from polymetallic mines (B and D) contained very high concentrations of Zn (38,000-108,000 mg kg(-1)), Pb (20,412-30,100 mg kg(-1)), Cu (2,019-8,635 mg kg(-1)) and Cd (148-228 mg kg(-1)). Water-extractable metal concentrations (i.e., soil extracts) were much lower but were highly toxic as shown by the MetPAD test, except for soils from mines A, E and site C3 from mine C. The soil extracts from mine D were the most toxic amongst all the soils tested. On this site, the toxicity of soil water extracts was mainly due to high concentrations of Zn (785-1,753 mg l(-1)), Cu (1.8-82 mg l(-1)) and Cd (2.0-2.7 mg l(-1)). The general trend observed was an increase in metal toxicity measured by the biotest with increasing available metal contents in tailings materials and soils. Therefore, the MetPAD test can be used as a rapid and sensitive predictive tool to assess the heavy metal availability in soils highly contaminated by mining activities.

Hydrogen-Ion Concentration↗
PubMed1988

Extraction of estrogens by human perfused uterus. Effects of membrane permeability and binding by serum proteins on differential influx into endometrium and myometrium.

The present study was undertaken to examine the extractions of estradiol, estrone, and estrone sulfate from the circulation of the human perfused uterus. The differential permeability of endometrial and myometrial vascular beds to estrogens was evaluated in uteri samples obtained during the proliferative and secretive phases of the menstrual cycle. The effects of binding by human serum proteins on estrogen influx into the endometrium and myometrium were also determined by the use of double-isotope, single-injection, timed tissue sampling techniques adapted to the extracorporeal perfusion of human uterus. Tritiated test estrogen was injected into the uterine artery as a mixture with 14C-butanol, a free diffusible reference substance. The influx of 14C-dextran (a membrane-impermeable compound) was used to test the aspecific influx from vasculature to extravascular space. Results show that in the human perfused uterus: (1) membrane permeability plays different roles in estrogen influxes between the endometrium and myometrium; (2) during the proliferative and secretive phase of the menstrual cycle the uterine microvessels are differently permeable to the free plus protein-bound estrogens; and (3) plasma proteins decrease the endometrial and myometrial uptakes of estrogens.

Blood Proteins↗
PubMed2001

Effective object recognition for automated counting of colonies in Petri dishes (automated colony counting).

Determination of the number of colonies (colony forming units, CFU) is a standard method in microbiological analysis to ensure the quality of drinking water. Normally this tedious work is still performed manually. A PC-based method for the automated counting of digitized images of Petri dishes is presented. The method includes highly specific and effective object recognition algorithms that ensure very high detection accuracy. The processing sequence implies internal controls therefore enabling reliable automated evaluations of series of images. Use of the Fuzzy formalism and the high adaptivity of the algorithms lead to an extraordinary user-friendliness. For digitization different devices like flatbed scanners or CCD-cameras can be used. Due to the highly adaptive algorithms samples from the routine standard preparation process in laboratories can be evaluated. The accuracy and quality of the method aim at advancement in objectivity of colony counting and quality control and assurance. The algorithms and the evaluation of the method are presented.

Algorithms↗
PubMed1999

Deformable meshes with automated topology changes for coarse-to-fine three-dimensional surface extraction.

This work presents a generic deformable model for extracting objects from volumetric data with a coarse-to-fine approach. This model is based on a dynamic triangulated surface which alters its geometry according to internal and external constraints to perform shape recovery. A new framework for topology changes is proposed to extract complex objects: within this framework, the model dynamically adapts its topology to the geometry of its vertices according to simple distance constraints. In order to speed up the process, an algorithm of pyramid construction with any reduction factor transforms the image into a set of images with progressively higher resolutions. This organization into a hierarchy, combined with a model which can adapt its sampling to the resolution of the workspace, enables a fast estimation of the shapes included in the image. After that, the model searches for finer and finer details while relying successively on the different levels of the pyramid.

Algorithms↗
PubMed2004

Synchronized conformational fluctuations and binding site desolvation during molecular recognition.

Binding site desolvation is a poorly understood prerequisite to ligand binding. Although structural fluctuations may be expected to have an important role, little is known about which fluctuations are important or the mechanism by which they promote desolvation. This investigation examines whether and how specific structural fluctuations contribute to desolvation of the ligand binding site in glycopeptide antibiotics. Backbone peptide group rotations in vancomycin, known to occur by experimental observation, were examined in this work with a two-dimensional adaptive umbrella sampling molecular dynamics simulation technique. Results indicate that energetic barriers to rotation are relatively small for two of the peptide groups intimately involved in ligand recognition. When they occur, these rotations strip water molecules away from key hydrogen bond donors and simultaneously cause significant distortions in the macrocyclic rings of the antibiotic that force water into and out of the binding site. Both events are intricately synchronized on the molecular level and have consequences that are clearly necessary to prepare the binding site for receiving a ligand. These results suggest that previously reported observations concerning structural dynamics and binding kinetics in these compounds are mechanistically linked, and they illustrate a heretofore unrecognized degree of preorganization, complexity, and synchronization that may be involved in specific molecular recognition. They also suggest that strategies for increasing antibiotic affinity through covalent dimerization may be counterproductive.

Amides↗
PubMed2001

Effect of roasting conditions on reduction of ochratoxin a in coffee.

A commercial lot of green coffee, naturally contaminated with ochratoxin A (OTA), was roasted under various conditions, and the effects on its final OTA content were determined. Precautions were taken in sampling the coffee to cope with OTA inhomogeneity. The roasting conditions were kept within the range of commercial practice. Roasting time was varied from 2.5 to 10 min, and the roast color varied from light medium to dark. The differences in OTA reduction between the different levels of roasting times and colors did not reach statistical significance. However, for all roasting conditions, the reduction was highly significant, 69% reduction over the combined results. In total, nine studies by various authors about OTA reduction during coffee roasting are now available. Seven out of these nine reported that the relevant range of OTA reductions was between 69 and 96%. Among these seven,are all four studies that reported using naturally contaminated beans, a sampling procedure adapted to mycotoxin inhomogeneity, and roasting conditions within the range of actual practice. Three different explanations are available for this reduction: physical removal of OTA with chaff, isomerization at the C-3 position into another diastereomer, and thermal degradation with possible involvement of moisture. All three explanations may play a partial role in the OTA reduction during coffee roasting.

Coffee↗
PubMed2005

Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models.

The method of histogram-reweighting was integrated with a recently developed approach using aggregation-volume-bias Monte Carlo and self-adaptive umbrella sampling to develop the AVUS-HR algorithm that allows for exceedingly efficient calculations of nucleation properties over a wide range of thermodynamic conditions. Simulations were carried out for water using both fixed-charge and polarizable force fields belonging to the TIP4P family (namely, TIP4P, TIP4P-FQ, TIP4P-pol2, and TIP4P-pol3) to investigate the nucleation of water over a temperature range from 200 to 300 K and the concentration of water clusters in the atmosphere at elevations up to 15 km. It was found that the nucleation free energy barriers and atmospheric concentrations are extremely sensitive to the force field, albeit all of the models investigated in this study support the following general conclusions: (i) ice nucleation is not present under the thermodynamic conditions and cluster-size range investigated here, i.e., the critical nuclei possess liquidlike structures, and (ii) the atmospheric concentrations of water clusters under homogeneous conditions are very low with the mole fraction of hexamers being about 10(-10), a number probably too low to influence the solar radiation balance. Compared to the experimental data, the TIP4P-pol3 model yields the most accurate nucleation results, consistent with its excellent performance for the second virial coefficient and the minimum cluster energies.

Journal Article↗
PubMed2006

Probing the nucleation mechanism for the binary n-nonane/1-alcohol series with atomistic simulations.

The AVUS-HR approach, which combines histogram reweighting with aggregation-volume-bias Monte Carlo nucleation simulations using self-adaptive umbrella sampling, was extended to multicomponent nucleation systems. It was applied to investigate the homogeneous vapor-liquid nucleation for the binary n-nonane/1-alcohol series, including the n-nonane/methanol, n-nonane/ethanol, n-nonane/1-propanol, n-nonane/1-butanol, n-nonane/1-hexanol, and n-nonane/1-decanol systems. The simple transferable potentials for phase equilibria-united atom force field was used in this investigation. It was found that the nucleation free energy (NFE) contour plots obtained for these binary n-nonane/1-alcohol nucleation systems exhibit rather interesting mechanistic features, some of which are distinct from other binary systems previously studied (such as water/ethanol and water/n-nonane). In addition, the NFE profiles show a subtle evolution with the increase in alcohol chain length, from a somewhat two-pathway type of shape as observed for the n-nonane/methanol system to a more normal single-pathway one for systems involving longer alcohols (1-hexanol and 1-decanol). In contrast, the NFE maps obtained for the other three binary systems involving those medium-length alcohols display the most striking feature with the saddle point stretched almost all the way from the n-nonane-enriched to the alcohol-enriched domain, implying that multiple pathways coexist on the nucleation map. These free energy profiles were shown to be consistent with the non-ideal nucleation behavior observed experimentally for this binary series, namely, a rather reluctant conucleation of the alcohols with n-nonane. In particular, this non-ideal behavior becomes more severe with a decrease in the alcohol chain length. Also, analysis of the compositions of the critical nuclei indicates a reluctant mixing behavior between these two species, i.e., depletion of the alcohol at low alcohol activity or depletion of n-nonane at low n-nonane activity, in agreement with the experimental interpretations. Furthermore, a microscopic inhomogeneity is present inside these critical nuclei, that is, alcohols aggregate via hydrogen bonds forming alcohol-enriched domains.

Alcohols↗