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PubMed1989

Altered sensory-motor control of the head as an etiological factor in space-motion sickness.

Mechanical unloading during head movements in weightlessness may be an etiological factor in space-motion sickness. We simulated altered head loading on Earth without affecting vestibular stimulation by having subjects wear a weighted helmet. Eight subjects were exposed to constant velocity rotation about a vertical axis with direction reversals every 60 sec. for eight reversals with the head loaded and eight with the head unloaded. The severity of motion sickness elicited was significantly higher when the head was loaded. This suggests that altered sensory-motor control of the head is also an etiological factor in space-motion sickness.

Gravitation↗
PubMed2000

Resolution of the phase-ambiguity problem in the centrosymmetric P [1] space group by Monte Carlo methods.

Simulated-annealing methods have been used to resolve the phase-ambiguity problem in the centrosymmetric P¿bar¿1¿ space group. First, an energy function based on the Sayre equation is introduced and a formal comparison with classical spin systems is drawn. The energy landscape is studied in detail and the validity of several energy criteria thoroughly tested. Classical Monte Carlo methods proved to be successful using a multistart optimization of the Sayre score, along with the additional monitoring of other energetic criteria. These involved the Terwilliger map quality index in reciprocal space in the absence of envelope information, and an envelope score if the shape of the molecule is known. The inherent phase-ambiguity problem of the P¿bar¿1¿ space group was therefore technically solved by Monte Carlo methods. The method should also work to resolve phase ambiguity in the SIR method of protein crystallography.

Computer Simulation↗
PubMed2005

Minimal-memory bit-vector architecture for computational mathematical morphology using subspace projections.

Computational mathematical morphology (CMM) is a nonlinear filter representation particularly amenable to real-time image processing. A windowed, translation-invariant filter is represented by a set of less-than-or-equal decisions that are executed by a parallel arrangement of comparators. In the state-of-the-art implementation, each pixel value of a windowed observation is indexed into separate lookup tables to retrieve a set of bit vectors which are "anded" together to produce a bit vector with a unique nonzero bit. The position of that bit is used to look up a filter value in a table. The number of stored bit vectors is proportional to the number of image gray levels. An architecture for CMM is presented that uses a minimal number of bit vectors so that required memory is less sensitive to the number of gray levels. The number of pixels in the observation window is the dimension of the image space. In the proposed architecure, basis elements are projected to subspaces of the image space and only bit vectors unique to each subspace are stored. Each projection corresponds to a subspace partition. Filter memory is greatly reduced by using intermediate lookup tables to map observations to unique bit vectors. We investigate two possible projection strategies: A fixed, singleton architecture, in which each subspace is one dimension, and a minimal architecture, in which a large number of subspace projections are searched for, one with minimal memory. Insensitivity to the number of gray levels is demonstrated through simulated, random-image space tessellations. We also present memory savings in a digital photocopier application.

Algorithms↗
PubMed1990

A comprehensive model of the dynamic exchange processes during hemodialysis.

The present model for the mathematical description of exchange processes during hemodialysis includes submodels for potassium, sodium, chloride, acetate, acid-base status (with CO2, bicarbonate and H(+)-ions), water distribution, oxygen, ventilation, and the uremic catabolites urea, creatinine, and vitamin B12. For potassium, sodium and urea a 2-compartment model is used consisting of the extra- and the intracellular space. For chloride, creatinine and vitamin B12 a 3-compartment model is necessary. For the description of acetate kinetics a 1-compartment model consisting of the extracellular space is sufficient. For description of the acid-base balance the model includes three submodels for CO2, bicarbonate, and hydrogen ions. All submodels are made of eight compartments, namely the intracellular and the interstitial space as well as six spaces for the blood. The three submodels are coupled to each other by the chemical reaction of CO2 to HCO3- and a H(+)-ion. Besides this reaction the diffusive exchange between the compartments, the convective transport with the blood and the elimination through the dialyzer and the lung for the molecules and ions are considered. Because of the strong buffer capacity of plasma and intracellular proteins, the functional compartments for hydrogen ions are larger than the anatomical spaces. Also the influence of extracellular pH on the electrolyte distribution at the cell membrane has been considered. With this model, which will be adapted to the patient by more than 45 individual parameters, the mass transfer and the course of concentrations during hemodialysis therapy can be reproduced adequately. Further on the values of some unknown parameters, such as the metabolic rate for acetate in the organism, can be estimated by varying the parameters systematically for several runs of the computer simulation until the simulation results are optimally fitted to measured data.

Acid-Base Equilibrium↗
PubMed2001

Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model.

Computer simulations are performed on a system of eight model peptide chains to study how the competition between protein refolding and aggregation affects the optimal conditions for refolding of four-helix bundles. The discontinuous molecular dynamics algorithm is utilized along with an intermediate-resolution protein model that we developed for this work. Physically, the model is much more detailed than any model used to date for simulations of protein aggregation. Each model residue consists of a detailed, three-bead backbone and a simplified, single-bead side-chain. Excluded volume, hydrogen bond, and hydrophobic interactions are modeled with discontinuous (i.e. hard-sphere and square-well) potentials. Simulations efficiently sample conformational space, and complete folding trajectories from random initial configurations to two four-helix bundles are possible within two days on a single processor workstation. Folding of the bundles follows two main pathways, one through a trimeric intermediate and the other through an intermediate with two dimers. The proportion of trajectories that follow each route is significantly different for the eight-peptide system in this work than in a previously studied four-peptide system, which yields one four-helix bundle, suggesting, as our previous simulations have, that protein folding properties are strongly influenced by the presence of other proteins. Folding of the bundles is optimal within a fixed temperature range, with the high-temperature boundary a function of the complexity of the protein (or oligomer) to be folded and the low-temperature boundary a function of the complexity of the protein's environment. Above the optimal temperature range for folding, the model chains tend to unfold; below the optimal range, the model chains tend to aggregate. As has been seen previously, aggregates have substantial levels of native secondary structure, suggesting that aggregates are composed largely of partially folded intermediates, not denatured chains.

Amino Acid Sequence↗
PubMed2005

A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators.

A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

Computer Graphics↗
PubMed1987

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity of transport proteins and enzymes. Different minima correspond to changes in the relative orientation of the helices coupled with side-chain rearrangements that preserve the close packing of the protein interior. The conformational space sampled by the simulation is similar to that found in the evolutionary development of the globins. Glasslike behavior is expected at low temperatures. The minima obtained from the trajectory do not satisfy certain criteria for ultrametricity.

Models, Structural↗
PubMed2006

Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli.

MOTIVATION: Many biochemical networks involve reactions localized on the cell membrane. This can give rise to spatial gradients of the concentration of cytosolic species. Moreover, the number of membrane molecules can be small and stochastic effects can become relevant. Pathways usually consist of a complex interaction network and are characterized by a large set of parameters. The inclusion of spatial and stochastic effects is a major challenge in developing quantitative and dynamic models of pathways. RESULTS: We have developed a particle-based spatial stochastic method (GMP) to simulate biochemical networks in space, including fluctuations from the diffusion of particles and reactions. Gradients emerging from membrane reactions can be resolved. As case studies for the GMP method we used a simple gene expression system and the phosphoenolpyruvate:glucose phosphotransferase system pathway. AVAILABILITY: The source code for the GMP method is available at http://www.science.uva.nl/research/scs/CellMath/GMP.

Computer Simulation↗
PubMed1976

[Occipital tumor simulating pericranial sinus (author's transl)].

A case of occipital tumor simulating sinus pericranii was reported. The patient was a 4-year-old girl who suffered from headache and nausea following head injury on midoccipital tumor, but had no remarkable neurological deficit. Her occipital tumor was soft, compressible redish and cyst-like without bruit. Conray cystography of this tumor showed superior sagittal sinus like shadow (Fig. 4). Total removal of the tumor associated with epidural hematoma was performed. Histologically this tumor was confirmed as eosinophilic granuloma. Pathogenesis of this case is following, since patient's tumor was blowed, intratumor-bleeding occurred cosequently and the bleeding flowed into epidural space. So the tumor simulated sinus pericranii (Fig. 5.).

Brain Diseases↗
PubMed2000

Simulated seizures and spreading depression in a neuron model incorporating interstitial space and ion concentrations.

Sustained inward currents in neuronal membranes underlie tonic-clonic seizure discharges and spreading depression (SD). It is not known whether these currents flow through abnormally operating physiological ion channels or through pathological pathways that are not normally present. We have now used the NEURON simulating environment of Hines, Moore, and Carnevale to model seizure discharges and SD. The geometry and electrotonic properties of the model neuron conformed to a hippocampal pyramidal cell. Voltage-controlled transient and persistent sodium currents (I(Na,T) and I(Na,P)), potassium currents (I(K,DR) and I(K,A)), and N-methyl-D-aspartate (NMDA) receptor-controlled currents (I(NMDA)), were inserted in the appropriate regions of the model cell. The neuron was surrounded by an interstitial space where extracellular potassium and sodium concentration ([K(+)](o) and [Na(+)](o)) could rise or fall. Changes in intra- and extracellular ion concentrations and the resulting shifts in the driving force for ionic currents were continuously computed based on the amount of current flowing through the membrane. A Na-K exchange pump operated to restore ion balances. In addition, extracellular potassium concentration, [K(+)](o), was also controlled by a "glial" uptake function. Parameters were chosen to resemble experimental data. As long as [K(+)](o) was kept within limits by the activity of the Na-K pump and the "glial" uptake, a depolarizing current pulse applied to the cell soma evoked repetitive firing that ceased when the stimulating current stopped. If, however, [K(+)](o) was allowed to rise, then a brief pulse provoked firing that outlasted the stimulus. At the termination of such a burst, the cell hyperpolarized and then slowly depolarized and another burst erupted without outside intervention. Such "clonic" bursting could continue indefinitely maintained by an interplay of the rise and fall of potassium and sodium concentrations with membrane currents and threshold levels. SD-like depolarization could be produced in two ways, 1) by a dendritic NMDA-controlled current. Glutamate was assumed to be released in response to rising [K(+)](o). And 2) by the persistent (i.e., slowly inactivating) Na-current, I(Na,P). When both I(NMDA) and I(Na,P) were present, the two acted synergistically. We conclude that epileptiform neuronal behavior and SD-like depolarization can be generated by the feedback of ion currents that change ion concentrations, which, in turn, influence ion currents and membrane potentials. The normal stability of brain function must depend on the efficient control of ion activities, especially that of [K(+)](o).

Action Potentials↗
PubMed2005

A model for CD2/CD58-mediated adhesion strengthening.

Stable cell adhesion is vital for structural integrity and functional efficacy. Yet how low affinity adhesion molecules such as CD2 and CD58 can produce stable cell adhesion is still not completely understood. In this paper, we present a theoretical model that simulates the accumulation of CD2 and CD58 in the contact area of a Jurkat T lymphoblast and a CD58-containing substrate. The cell is assumed to have a spherical shape initially and it is allowed to spread gradually on a circular substrate. Mobile CD2 and CD58 can diffuse freely on both the cell and substrate. Their binding in the contact area is controlled by first-order kinetics. The contact area grows linearly with the total number of CD2/CD58 bonds. Cellular deformation and cytoskeleton involvement were not considered. This time-dependent moving-boundary problem was solved with the Crank-Nicolson finite difference scheme and the variable space grid method. Our simulated results are in reasonable agreement with the experimental observations. The role of diffusion becomes more and more prominent during the contact area increase, which is not sensitive to the kinetic rate constants tested in this study. However, it is very sensitive to the dissociation equilibrium constant and the concentrations of CD2 and CD58.

Adhesiveness↗
PubMed1986

The temporal response of bone to unloading.

A model of weightlessness in which the hindlimbs of rats are elevated by their tails at a 40 degrees angle to unload the hindlimbs while maintaining normal weight bearing on the forelimbs has been used to simulate certain conditions of space flight. When we used this model in growing rats, we found that growth in bone weight ceased by 1 week in the hindlimbs and lumbar vertebrae, whereas growth in bone weight in the forelimbs and cervical vertebrae remained unaffected. Within 2 weeks, however, the accretion of bone weight in the hindlimbs and lumbar vertebrae returned to normal despite continued skeletal unloading. Since bone weight in the growing rat is primarily determined by bone formation (bone resorption is modest), we investigated the effects of selective skeletal unloading on bone formation during 2 weeks of hindlimb elevation using radioisotope incorporation (with 45Ca and [3H]proline) and histomorphometry (with tetracycline labeling). The studies using radioisotope incorporation showed that bone formation was inhibited by the fifth day of skeletal unloading. By the 10th to 12th day, bone formation had returned toward normal. In comparison with cortical bone, cancellous bone (lumbar vertebrae and proximal tibiae) incorporated more 45Ca and [3H]proline (indicating greater metabolic activity) and had a greater absolute response to skeletal unloading. The results of these studies were confirmed by histomorphometric measurements of bone formation using triple tetracycline labeling. We conclude that this model of simulated weightlessness results in an initial inhibition of bone formation in the unloaded bones. This temporary cessation of bone formation is followed by a cessation in the accretion of bone weight, which then resumes at a normal rate by 14 days despite continued skeletal unloading. We believe that this cycle of inhibition and resumption of bone formation has profound implications for understanding bone dynamics during space flight, immobilization, or bed rest and offers an opportunity to study the hormonal and mechanical factors that regulate bone formation.

Animals↗
PubMed2004

A STAP algorithm approach to fMRI: a simulation study.

PURPOSE: To adapt the space-time adaptive processing (STAP) algorithm, previously developed in the field of sensor array processing and applied to radar signal processing, for use in construction of brain activation maps in functional magnetic resonance imaging (fMRI). MATERIALS AND METHODS: STAP is a two-dimensional filter in which both the spatial and temporal responses are controlled adaptively. It processes space-time data as a complete spatiotemporal set. Unlike presently used fMRI techniques, STAP locates activated regions both spatially and in frequency. RESULTS: Computer simulations incorporating actual MRI noise indicate that STAP exhibits a high degree of accuracy in detecting the small signal intensity changes inherent in fMRI. CONCLUSION: Because STAP processes space-time data as a single data matrix, it exhibits potential over currently available fMRI methods in providing a measure of the full spatiotemporal extent of a task-related activity.

Algorithms↗
PubMedDate not supplied

Space flight effects on bacterial physiology.

The study of bacterial behavior under space flight conditions is highly important for the early detection of changes in bacterial communities and bacteria with medical, environmental, or life support consequences for survival of the crew in closed space environments. Although many species of prokaryotes have been studied in ground simulation facilities or have been flown in space flights, at present only few hard research data are available to predict the effects of cosmic radiation, microgravity, vibration and hypervelocity on microbial behavior in space flight. The results that are available tend to be fragmentary and often lack a classical, controlled experimental context to interpret them. Thus, many basic questions concerning the effects of space on microbial behavior have yet to be resolved.

Bacteria↗
PubMed2002

Roles of mutation and recombination in the evolution of protein thermodynamics.

We present a comprehensive study of the evolutionary origin of the thermodynamic behavior of proteins. With the use of a simplified model, we exhaustively enumerate the space of all sequences and the space of all structures, simulate the evolutionary relationship between sequences and structures, and characterize the steady-state sequence distribution for all structures in terms of several thermodynamic variables. We assess the effects of two major forces of evolution: mutation and recombination. Three simplifications are made. First, a two-dimensional lattice model is used to represent protein sequences and structures. Second, proteins undergo neutral evolution so that the fitness landscape has a flat allowed region inside of which all sequences are equally fit. Third, we ignore otherwise important factors such as finite population size and evolutionary time. Two scenarios emerge from our study. The first occurs when evolution is dominated by mutation events. Even though the prototype sequence that is most mutationally robust is preferred by evolution, the preference is not strong enough to offset the huge size of sequence space. Most native sequences are located near the boundary of the fitness region and are marginally compatible with the native structure. The second scenario occurs when evolution is dominated by recombination events. Now evolutionary preference for prototype sequence is strong enough to overcome the size of sequence space so that most native sequences are located near the center of sequence-structure compatibility. We conclude that the relative frequency of mutation and recombination events is a major determinant of how optimal protein sequences are for their structures.

Evolution, Molecular↗
PubMed1993

First web space contracture and hand function.

We studied 125 normal volunteers to determine the normal first web space angle and to evaluate the influence of thumb-index finger web space contracture on hand function. One hundred ninety-five hands were measured and found to have a mean web space angle of 100 degrees. There was no significant difference in the mean angle in relation to sex or hand dominance. The mean angle was significantly smaller for persons 50 to 79 years of age than for the two younger age groups. Twenty-five normal volunteers (50 hands) took the Jebsen-Taylor test three times: first, with no restrictions; second, with splints simulating a 60-degree web space contracture; and third, with splints simulating a 30-degree contracture. More than half of the volunteers had abnormal small-object subtests. Other abnormal subtests included card turning, feeding, and stacking checkers. Grasping large light and heavy objects was less difficult because of compensatory techniques used by the volunteers.

Adolescent↗
PubMed1995

Exobiology research on Space Station Freedom.

The Gas-Grain Simulation Facility (GGSF) is a multidisciplinary experiment laboratory being developed by NASA at Ames Research Center for delivery to Space Station Freedom in 1998. This facility will employ the low-gravity environment of the Space Station to enable aerosol experiments of much longer duration than is possible in any ground-based laboratory. Studies of fractal aggregates that are impossible to sustain on Earth will also be enabled. Three research areas within exobiology that will benefit from the GGSF are described here. An analysis of the needs of this research and of other suggested experiments has produced a list of science requirements which the facility design must accommodate. A GGSF design concept developed in the first stage of flight hardware development to meet these requirements is also described.

Cosmic Dust↗
PubMed2003

Definition of displacement probability and diffusion time in q-space magnetic resonance measurements that use finite-duration diffusion-encoding gradients.

In q-space diffusion NMR, the probability P(r,td) of a molecule having a displacement r in a diffusion time td is obtained under the assumption that the diffusion-encoding gradient g has an infinitesimal duration. However, this assumption may not always hold, particularly in human MRI where the diffusion-encoding gradient duration delta is typically of the same order of magnitude as the time offset Delta between encoding gradients. In this case, finite-delta effects complicate the interpretation of displacement probabilities measured in q-space MRI, and the form by which the signal intensity relates to them. By considering the displacement-specific dephasing, , of a set of spins accumulating a constant displacement vector r in the total time Delta+delta during which diffusion is encoded, the probability recovered by a finite-delta q-space experiment can be interpreted. It is shown theoretically that a data analysis using a modified q-space index q=gammadeltaetag, with gamma the gyromagnetic ratio and eta=square root (Delta-delta/3)/(Delta+delta), recovers the correct displacement probability distribution if diffusion is multi-Gaussian free diffusion. With this analysis, we show that the displacement distribution P(r,texp) is measured at the experimental diffusion-encoding time texp=Delta+delta, and not at the reduced diffusion time tr=Delta-delta/3 as is generally assumed in the NMR and MRI literature. It is also shown that, by defining a probability P(y,Delta) that a time t deltac then eta is not equal to square root (Delta-delta/3)/(Delta+delta) which implies that we can no longer obtain the correct displacement probability from the displacement distribution. In the case that /g/=18 mT/m and Delta-delta=5 ms, the parameter deltac in ms is given by "deltac=0.49a2+0.24" where a is the sphere's radius expressed in microm. Simulation of q-space restricted diffusion MRI experiments indicate that if eta=square root (Delta-delta/3)/(Delta+delta), the recovered displacement probability is always better than the Gaussian approximation, and the measured diffusion coefficient matches the diffusion coefficient at time texp=Delta+delta better than it matches the diffusion coefficient at time tr=Delta-delta/3. These results indicate that q-space MRI measurements of displacement probability distributions are theoretically possible in biological tissues using finite-duration diffusion-encoding gradients provided certain compartment size and diffusion encoding gradient duration constraints are met.

Journal Article↗