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At least 1,279 records · Page 71Linked to original sources
PubMed1994

Computer modelling of kappa carrageenan-mannan interactions.

Molecular modelling has been used as a theoretical approach to investigate the kappa carrageenan structure and its interactions with mannan chains. Calculations revealed the existence of six minima for the kappa carrageenan structure in solution. Two of them were very close to the structure found in the solid state. The methodology allowed the calculation of a theoretical counterpart of the structures based on x-ray fibre diffraction studies. In the second step of this study, we have shown that there is the possibility of interactions between kappa carrageenan double helices and mannan chains. This interacting process is allowed by the flexibility of the mannan chains and structural changes of the kappa carrageenan double helices. The calculations suggest that a disaccharide mannan fragment might be required for recognition. The results of our investigation are in good agreement with a model of gel structure based on experimental data. This approach could be applied to simulate and predict other associations in molecular assemblies.

Carbohydrate Conformation↗
PubMed1992

Computational model of the on-alpha ganglion cell receptive field based on bipolar cell circuitry.

The on-alpha ganglion cell in the area centralis of the cat retina receives approximately 450 synapses from type b1 cone bipolar cells. This bipolar type forms a closely spaced array (9 microns), which contributes from 1 to 7 synapses per b1 cell throughout the on-alpha dendritic field. Here we use a compartmental model of an on-alpha cell, based on a reconstruction from electron micrographs of serial sections, to compute the contribution of the b1 array to the on-alpha receptive field. The computation shows that, for a physiologic range of specific membrane resistance (9500-68,000 omega.cm2) and a linear synapse, inputs are equally effective at all points on the on-alpha dendritic tree. This implies that the electrotonic properties of the dendritic tree contribute very little to the domed shapes of the receptive field center and surround. Rather, these shapes arise from the domed distribution of synapses across the on-alpha dendritic field. Various sources of "jitter" in the anatomical circuit, such as variation in bipolar cell spacing and fluctuations in the number of synapses per bipolar cell, are smoothed by the overall circuit design. However, the computed center retains some minor asymmetries and lumps, due to anatomical jitter, as found in actual alpha-cell receptive fields.

Animals↗
PubMed1993

3D-structures of the lipase from Rhizomucor miehei at different temperatures and computer modelling of a complex of the lipase with trilaurylglycerol.

The lipase of Rhizomucor miehei was measured at two different wavelengths (synchroton lambda = 1.06 A and at a rotating anode lambda = 1.542 A) and two temperatures (293 and 110 K). The structure could be solved using the C alpha-coordinates from the Brookhaven data base (code name 1TGL). Both structures were refined to R-values of 18.7% (synchrotron 293 K) and 20.0% (rotating anode 110 K) at a resolution of 8-2.3 and 8-2.5 A, respectively. Both structures are almost identical to the original 1TGL data set. The side chain positions of both crystal structures differ mainly in the parts of the molecule with relatively high temperature factors in the crystallographic refinement. The low-temperature structure forms more hydrogen bridges than the room temperature structure. From the results of Brzozowski et al. (1991), a preliminary model of the active RML was constructed. A docking of trilaurylglycerol led to a first model of the complex of RML/substrate.

Amino Acid Sequence↗
PubMed1992

Estimation of survival probability in cirrhotics. Evaluation of a computer model applicable for decision-making.

In 25 randomly selected, non-alcohol-induced cirrhotics, a simple mathematical model originally designed as the "Mayo-model" for the prediction of prognosis and survival in patients with primary biliary cirrhosis, was applied using a newly developed computer program. The calculated risk scores were 4.91 for surviving patients compared to 7.65 for those who died (P less than 0.001). The survival probability at the end of the follow-up period was 88% vs 47% (P less than 0.001) for these two groups. In 12 patients of the total of 25, multiple values were calculated at yearly intervals. Usually these R values increased except in one patient with chronic active hepatitis treated effectively with corticosteroids, and for 2 others during the correction of vitamin K deficiency. Our data suggest that this model, originally designed for and validated in patients with primary biliary cirrhosis, may also be applied to predict survival in other non-alcohol-induced cirrhotics and therefore may be applicable in prospective controlled trials in cirrhotics or in evaluating the need for and the timing of liver transplantation in the (near) future in these patients.

Aged↗
PubMed1993

Animated visualization of a high resolution color three dimensional digital computer model of the whole human head.

The interactive visualization of animated images through a computerized three dimensional (3D) full color model of an unstained cadaveric human head is presented. Serial full color images were taken of the blockface of a cryomicrotomed frozen human head every 200 microns. From this series of images a three dimensional digital model with a resultant pixel resolution of 200 microns3 was created on a UNIX workstation. Using this database, resampled images were computed along orthogonal axes and written sequentially to a write-once-read-many times (WORM) videodisc unit. Playback of this customized videodisc dataset provides animations of the digitally reconstructed slices and 3D reconstructed surface models. An interactive interface to the animated sequences is provided through a PC based tutorial package. This tutorial program is able to access videodisc frames to display animations and labeled still images in a software window to illustrate various neuroanatomic topics. The technique of animation as applied to this high resolution 3D model provides insight into complex spatial relationships and has great potential in research and as a teaching tool in the neurosciences.

Brain↗
PubMed2006

Downloadable computer models for renal replacement therapy.

Mathematical models can predict solute clearances and solute concentrations during renal replacement therapy. At present, however, most nephrologists cannot use these models because they require mathematical software. In this report, we describe models of solute transport by convection and diffusion adapted to run on the commonly available software program Excel for Macintosh computers and PCs running Windows. Two programs have been created that can be downloaded from http://www.stanford.edu/~twmeyer/ or http://dev.satellitehealth.com/research/journal.asp. The first, called 'Dr Addis Clearance Calculator', calculates clearance values from inputs including the blood flow Q(b), the hematocrit, the ultrafiltration rate Q(f), the dialysate flow rate Q(d), the reflection coefficient sigma and the mass transfer area coefficient K(o)A for the solute of interest, and the free fraction f if the solute is protein bound. Solute concentration profiles along the length of the artificial kidney are displayed graphically. The second program, called 'Dr Coplon Dialysis Simulator', calculates plasma solute concentrations from the clearance values obtained by the first program and from additional input values including the number of treatments per week, the duration of the treatments, and the solute's production rate and volumes of distribution. The program calculates the time-averaged solute concentration and provides a graphic display of the solute concentration profile through a week-long interval.

Animals↗
PubMed1987

Computer modeling and analysis of cross-sectional bone density studies with respect to age and the menopause.

Controversy exists about rates of bone mineral loss from the lumbar spine at the menopause. Cross-sectional studies of lumbar bone mineral against age have been interpreted as evidence for or against a menopause-related change in lumbar bone loss, depending on their goodness of fit to either linear or nonlinear equations. To investigate the ability of cross-sectional studies to detect accelerated lumbar bone loss at the menopause, we constructed models of different patterns of loss and evaluated the findings in cross-sectional analyses of computer-simulated populations of normal women. A sample size of greater than 300 was needed to distinguish between linear and nonlinear patterns of bone loss with a power of 90% when the data was analyzed throughout life. Examining for differences between the slopes of the regressions of pre- and postmenopausal women was more useful for detecting nonlinear bone loss under some circumstances. A difference between slopes was apparent in studies containing 100 subjects if lumbar bone density (BMD) was assumed to be unchanged prior to the menopause, but a larger study size was needed (greater than 1000) if BMD was assumed to fall before the menopause. We also measured lumbar BMD by dual photon absorptiometry in 141 normal females. When the data was analyzed against age throughout life, a nonlinear pattern of bone loss was found, and comparison of pre- and postmenopausal subjects showed a significant difference in the slopes of the linear regressions. Our patient data support the concept of a relatively stable lumbar BMD prior to the menopause with a rapid but transient decline postmenopausally.(ABSTRACT TRUNCATED AT 250 WORDS)

Aging↗
PubMed2001

Social effects in simple computer model of aging.

A simple evolutionary model for biological aging is modified such that it requires a minimum population for survival, like in human society. This social effect leads to a transition between extinction and survival of the species.

Aging↗