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PubMed1979

Modelling in biomechanics: an overview.

The state of the art in biomechanical modelling is reviewed with specific reference being made to physical and mathematical idealizations of the human body and its segments. Scale models and anthropomorphic dummies which fall within the physical category are discussed briefly. Mathematical models which are much more prevalent and virtually synonymous with computer simulation models are then considered in two major classifications: deformable element and rigid body representations. The former include lumped parameter, discrete parameter, finite element and continuum models and are commonly used to represent the vertebral column. Examples of rigid body models of the total body response and inertial parameter variety are outlined. Finally, topics relating directly to the construction of sport and locomotion models are discussed. These include considerations for developing a static or dynamic model, utilizing Newtonian or Lagrangian equations of motion, and dealing with indeterminate systems.

Anthropometry↗
PubMed1987

[Spatial representation of basilar membrane movement with 3D computer graphics].

A mathematical model of the cochlea was implemented on a computer. The basilar membrane motion was computed for single, two, and multi-tone stimuli as well as for musical sounds and vowels. The pattern of the travelling waves were presented in three-dimensional color computer graphics. The high performance 3D graphics system performs local hidden surface removal, 3D geometric transformations and supports local lighting models to generate truly realistic shading for complex 3D objects. An addressable 1280 by 1024 pixel matrix assures crisp, precise resolution of the finest detail in the graphic images. The spatial pattern of basilar membrane motion conveys an impression of the image of acoustic stimuli on the basilar membrane. Firstly, the motion pattern of the travelling wave to a single tone is presented. The superposition of several tones (two-tone, multi-tone) causes a superposition of the travelling waves along the basilar membrane whereby the place principle in the cochlear partition becomes more clearly recognizable. Sounds (flute and violin) and vowels (German "u" and "i") evoke a complex motion pattern on the basilar membrane. The realization of the chronological order of movements on the basilar membrane can be made by computer animation. This enables the analysis of the space-time patterns of complex acoustic stimuli.

Basilar Membrane↗
PubMed2003

Computer-aided navigation in neurosurgery.

The article comprises three main parts: a historical review on navigation, the mathematical basics for calculation and the clinical applications of navigation devices. Main historical steps are described from the first idea till the realisation of the frame-based and frameless navigation devices including robots. In particular the idea of robots can be traced back to the Iliad of Homer, the first testimony of European literature over 2500 years ago. In the second part the mathematical calculation of the mapping between the navigation and the image space is demonstrated, including different registration modalities and error estimations. The error of the navigation has to be divided into the technical error of the device calculating its own position in space, the registration error due to inaccuracies in the calculation of the transformation matrix between the navigation and the image space, and the application error caused additionally by anatomical shift of the brain structures during operation. In the third part the main clinical fields of application in modern neurosurgery are demonstrated, such as localisation of small intracranial lesions, skull-base surgery, intracerebral biopsies, intracranial endoscopy, functional neurosurgery and spinal navigation. At the end of the article some possible objections to navigation-aided surgery are discussed.

Equipment Design↗
PubMed2003

Amygdala and hippocampal volumes in adolescents and adults with bipolar disorder.

BACKGROUND: The purported functions of medial temporal lobe structures suggest their involvement in the pathophysiology of bipolar disorder (BD). Previous reports of abnormalities in the volume of the amygdala and hippocampus in patients with BD have been inconsistent in their findings and limited to adult samples. Appreciation of whether volumetric abnormalities are early features of BD or whether the abnormalities represent neurodegenerative changes associated with illness duration is limited by the paucity of data in juvenile samples. OBJECTIVE: To investigate amygdala and hippocampal volume in adults and adolescents with BD. SETTING AND PARTICIPANTS: Subjects included 36 individuals (14 adolescents and 22 adults) in outpatient treatment for BD type I at a university hospital or Veterans Affairs medical center or in the surrounding community, and 56 healthy comparison subjects (23 adolescents and 33 adults). DESIGN AND MAIN OUTCOME MEASURES: Amygdala and hippocampal volumes were defined and measured on high-resolution anatomic magnetic resonance imaging scans. We used a mixed-model, repeated-measures statistical analysis to compare amygdala and hippocampal volumes across groups while covarying for total brain volume, age, and sex. Potential effects of illness features were explored, including rapid cycling, medication, alcohol or other substance dependence, duration, and mood state. RESULTS: For both the amygdala and hippocampal regions, we found an overall significant volume reduction in the BD compared with the control group (P<.0001). Amygdala volume reductions (15.6%) were highly significant (P<.0001). We observed a nonsignificant trend (P =.054) toward reductions in hippocampal volumes of lesser magnitude (5.3%). Effects of illness features were not detected. CONCLUSIONS: These results suggest that BD is associated with decreased volumes of medial temporal lobe structures, with greater effect sizes in the amygdala than in the hippocampus. These abnormalities are likely manifested early in the course of illness, as they affected adolescent and adult subjects similarly in this sample.

Adolescent↗
PubMed2003

Gray and white matter brain abnormalities in first-episode schizophrenia inferred from magnetization transfer imaging.

BACKGROUND: Neuroimaging studies suggest that schizophrenia is associated with gray and possibly white matter changes. It is unclear whether these changes are present at illness onset or which brain structures are selectively affected. New imaging methods such as magnetization transfer imaging may be more sensitive than conventional volumetric imaging to the subtle structural brain changes in schizophrenia. METHODS: High-resolution volumetric T1-weighted images and magnetization transfer images were acquired from 30 patients (29 with first-episode schizophrenia and 1 with schizophreniform psychoses) and 30 control subjects. Images were processed using voxel-based morphometry, which allows whole-brain analysis. RESULTS: Compared with controls, the magnetization transfer ratio (an index of signal loss derived from magnetization transfer imaging) was reduced bilaterally in the medial prefrontal cortex (right greater than left), insula (left greater than right), and white matter incorporating the fasciculus uncinatus (left greater than right) in the patient group. Analysis of the T1-weighted images did not reveal significant volumetric differences between patients and controls. CONCLUSIONS: Gray and white matter abnormalities are present in schizophrenia at illness onset. The magnetization transfer ratio is sensitive to these abnormalities, which cannot be explained by detectable atrophy in our patient group.

Adolescent↗
PubMed1996

Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation.

Monte Carlo simulations are employed to investigate the thermodynamics of the first transition in writhe of a circular model filament corresponding to a 468 base-pair DNA. Parameters employed in these simulations are the torsional rigidity, C = 2.0 x 10(-19) dyne cm2, and persistence length, P = 500 A. Intersubunit interactions are modeled by a screened Coulomb potential. For a straight line of subunits this accurately approximates the nonlinear Poisson-Boltzmann potential of a cylinder with the linear charge density of DNA. Curves of relative free energy vs writhe at fixed linking difference (delta l) exhibit two minima, one corresponding to slightly writhed circles and one to slightly underwrithed figure-8's, whenever delta l lies in the transition region. The free energies of the two minima are equal when delta lc = 1.35, which defines the midpoint of the transition. At this midpoint, the free energy barrier between the two minima is found to be delta Gbar = (0.20) kBT at 298 K. Curves of mean potential energy vs writhe at fixed linking difference similarly exhibit two minima for delta l values in the transition region, and the two minimum mean potential energies are equal when delta l = 1.50. At the midpoint writhe, delta lc = 1.35, the difference in mean potential energy between the minimum free energy figure-8 and circle states is (1.3) kBT, and the difference in their entropies is 1.3 kB. Thus, the entropy of the minimum free energy figure-8 state significantly exceeds that of the circle at the midpoint of the transition. The first transition in writhe is found to occur over a rather broad range of delta l values from 0.85 to 1.85. The twist energy parameter (ET), which governs the overall free energy of supercoiling, undergoes a sigmoidal decrease, while the translational diffusion coefficient undergoes a sigmoidal increase, over this same range. The static structure factor exhibits an increase, which reflects a decrease in radius of gyration associated with the circle to figure-8 transition.

Chemical Phenomena↗
PubMed1995

On the measurements of electrophoretic mobilities by means of capillary isotachophoresis at a constant voltage.

A method for measuring electrophoretic mobilities by means of isotachophoresis (ITP) at a constant voltage as described by H. Carchon and E. Eggermont (Electrophoresis, 1982, 3, 263-274) is analyzed. An error made in this work, disregarding the pH shift arising at the initial discontinuity on the leader-terminator boundary, has been corrected. This method has been carefully studied and generalized for the presence of constant electroosmotic flow in a capillary. The limits of its applicability and the diffusionless ITP theory in general are discussed. A detailed study of the evolution of initial discontinuity (stationary boundary) showed some anomalies not reported previously, particularly non-monotonic concentration profiles in the vicinity of stationary boundaries. Moreover, in some cases, diffusion effects and the contribution of H+ ions can also strongly influence the behavior of moving boundaries. Computer modelling (confirmed by experimental data) showed that these effects could lead to the decay of the ITP train, despite the fact that the steady state diffusionless ITP theory predicts its stability.

Computer Simulation↗
PubMed2003

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level.

Algorithms↗
PubMed2001

Determination of arterial input function using fuzzy clustering for quantification of cerebral blood flow with dynamic susceptibility contrast-enhanced MR imaging.

An accurate determination of the arterial input function (AIF) is necessary for quantification of cerebral blood flow (CBF) using dynamic susceptibility contrast-enhanced magnetic resonance imaging. In this study, we developed a method for obtaining the AIF automatically using fuzzy c-means (FCM) clustering. The validity of this approach was investigated with computer simulations. We found that this method can automatically extract the AIF, even under very noisy conditions, e.g., when the signal-to-noise ratio is 2. The simulation results also indicated that when using a manual drawing of a region of interest (ROI) (manual ROI method), the contamination of surrounding pixels (background) into ROI caused considerable overestimation of CBF. We applied this method to six subjects and compared it with the manual ROI method. The CBF values, calculated using the AIF obtained using the manual ROI method [CBF(manual)], were significantly higher than those obtained with FCM clustering [CBF(fuzzy)]. This may have been due to the contamination of non-arterial pixels into the manually drawn ROI, as suggested by simulation results. The ratio of CBF(manual) to CBF(fuzzy) ranged from 0.99-1.83 [1.31 +/- 0.26 (mean +/- SD)]. In conclusion, our FCM clustering method appears promising for determination of AIF because it allows automatic, rapid and accurate extraction of arterial pixels. J. Magn. Reson. Imaging 2001;13:797-806.

Adult↗
PubMed2006

Novel diffusion anisotropy indices: an evaluation.

PURPOSE: To systematically evaluate diffusion anisotropy (DA) using newly defined indices based on the diffusion deviation and mean diffusivity approach. MATERIALS AND METHODS: Measures of amplitude, area, and volume of the DA index (DAI) were measured and compared with regard to their sensitivity to changes in DA, susceptibility to noise in the original diffusion-weighted (DW) images, and contrast-to-noise ratio (CNR) in homogenous regions. Simulations were performed under different levels of noise and DA. Human DTI data were acquired from eight normal volunteers. RESULTS: Indices of area and volume measures provided improved resolution for characterizing the DA compared to the eigenvalue ratio. The amplitude measure showed consistent performances with good CNR and less susceptibility to noise in the original data. CONCLUSION: These indices are rotationally invariant without the requirement of eigenvalue sorting. At low anisotropy, all indices have a similar CNR. For larger DA, the first index (the deviation tensor divided by the DT) shows improved sensitivity, contrast-to-noise ratio (CNR), and noise immunity compared to the other indices.

Adult↗
PubMed2003

Parkinson's disease is associated with hippocampal atrophy.

Patients with Parkinson's disease (PD) may have hippocampal atrophy compared with controls. We compared hippocampal, and extra-hippocampal volumes between PD, PDD (patients with PD who have mild cognitive impairment or dementia), Alzheimer's disease (AD) and controls using volumetric magnetic resonance imaging (MRI). Participants (10 patients with PD, 10 with PDD, 11 with AD, and 12 control subjects) had an informant interview, neurological examination, and psychometric testing. Established, reliable methods were used to measure the hippocampus, parahippocampal gyrus, temporal, frontal, and parieto-occipital lobes. Correction for intracranial volume was carried out before comparison. There was no age difference between groups (mean age, 74 years). On the Clinical Dementia Rating scale (CDR) cognitive impairment was mild (CDR = 0.5) in the majority of PDD and AD patients. Hippocampal (P < 0.0004) volumes were smaller in the patient groups. Effect sizes compared with the control group were: PD, 0.66; PDD, 1.22; and AD, 1.81. The other volumes did not differ significantly. Among PD and PDD patients, recognition memory (r = 0.54, P = 0.015) and Mini-Mental State Examination scores (r = 0.56, P = 0.01) correlated with left, but not right hippocampal volume. In conclusion, hippocampal volume showed a pattern (Control > PD > PDD > AD) suggesting progressive hippocampal volume loss in PD. Volumetric MRI imaging might provide an early marker for dementia in PD.

Aged↗
PubMed2006

Visualization and quantification of disease progression in multiple system atrophy.

To visualize and quantify disease progression in multiple system atrophy (MSA) from cerebellar type (MSA-C), we combined two magnetic resonance imaging (MRI) techniques, voxel-based morphometry (VBM) and 3D-based volumetry. Patients suffering from MSA-C (n = 14) were imaged twice with an interval of 2.0 +/- 0.2 years. We first applied VBM to map brain morphology changes between MSA patients and controls and to identify brain areas that showed a significant amount of atrophy. Using 3D-based volumetry, we confirmed that in MSA-C patients, the brainstem including medulla and pons, vermis and cerebellar hemispheres, caudate nucleus and putamen showed significant atrophy compared with controls. Next, we used 3D-based volumetry to analyze the atrophy rates. Atrophy rates in patients with MSA were significantly different from controls for putamen (-11.4% +/- 2.6%/year), vermis (-12.3% +/- 2.9%/year), and cerebellar hemispheres (-6.6% +/- 1.1%/year). The results show that 3D-based MRI volumetry is a tool that allows the disease progression of MSA to be followed over a time period of 2 years and suggest that it may serve as a surrogate marker in clinical trials to measure disease progression.

Aged↗
PubMed2006

Head of the caudate nucleus is most vulnerable in chorea-acanthocytosis: a voxel-based morphometry study.

Chorea-acanthocytosis (ChAc; OMIM 200150) is a rare autosomal recessive disease with dysfunction of the erythrocyte membrane, presenting with acanthocytes and neurological manifestations characterized by progressive hyperkinesias (chorea, dystonia) and neuropsychological impairment. Damage to the basal ganglia was described previously in neuropathological and neuroimaging investigations. We analyzed high-resolution MRI of six ChAc patients with mutations in the VPS13A gene (median age, 37 years; mean time since clinical onset, 13 years) with respect to regional atrophy by use of the observer-independent technique of voxel-based morphometry in comparison to 15 age-matched healthy controls. Additionally, global brain atrophy was determined using the standardized brain parenchymal fraction (BPF) method. A robust regional reduction of gray matter density was observed in the head of the caudate nucleus bilaterally and was nearly symmetrical (P < 0.001, corrected for small volumes). No additional gray matter changes were found. In the BPF analysis, there was no significant global brain atrophy. The predilection of atrophy in the head of the caudate nucleus, as suggested by our results, argues for a particular vulnerability of this part of the striatum in ChAc and is in agreement with pronounced neuropsychological disturbances that are thought to rely on these regions.

Adult↗
PubMed1993

Orientational sampling and rigid-body minimization in molecular docking.

The biological activities of proteins depend on specific molecular recognition and binding. Computational methods for predicting binding modes can facilitate the discovery and design of ligands and yield information on the factors governing complementarity. The DOCK suite of programs has been applied to several systems; here, the degree of orientational sampling required to reproduce and identify known binding modes, with and without rigid-body energy minimization, is investigated for four complexes. There is a tradeoff between sampling and minimization. The known binding modes can be identified with intensive sampling alone (10,000 to 20,000 orientations generated per system) or with moderate sampling combined with minimization. Optimization improves energies significantly, particularly when steric clashes are present, and brings many orientations closer to the experimentally observed position. Whether or not minimization is performed, however, sampling must be sufficient to find at least one structure in the vicinity of the presumed true binding mode. Hybrid approaches combining docking and minimization are promising and will become more viable with the use of faster algorithms and the judicious selection of fewer orientations for minimization.

Carboxypeptidases↗
PubMed1994

Parser for protein folding units.

General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering.

Actins↗
PubMed1994

Sample size determination for an exponential survival model with an unrestricted covariate.

We derive formulae for estimating sample size and power for detecting the effect of an unrestricted covariate on survival time. These are useful in designing survival studies with different patterns of recruitment and follow-up when survival time is exponentially distributed. We use the asymptotic covariance matrix, conditional expectation and Taylor's expansion techniques to develop these formulae. Computer simulations indicate that the asymptotic approximations used in developing the formulae are good over a range of parameter values and different patterns of recruitment and follow-up that are relevant to survival studies.

Computer Simulation↗
PubMed1995

Estimation of a common odds ratio under binary cluster sampling.

We present results from a simulation study for the estimation of a common odds ratio in multiple 2 x 2 tables when the data are correlated within clusters. We model the correlation of the data by the beta-binomial distribution. Through a simulation study, we compare the Mantel-Haenszel estimator with Rao and Scott's estimator in terms of their biases, observed variances, relative efficiencies of their variances and 95 per cent coverage proportions. We limit the simulation study to the case where there are the same number of subjects in each cluster and the same number of observations in each row of each stratum. When rho = 0, we recommend use of the Mantel-Haenszel estimator gamma MH with an unadjusted variance and Rao and Scott's estimator gamma RSP with a pooled design effect. In general, when rho > 0, we recommend the Mantel-Haenszel estimator gamma MH with an adjusted variance and Rao and Scott's estimator gamma RSP with a pooled design effect.

Bias↗
PubMed1993

Simultaneous measurement of two cations with the fluorescent dye indo-1.

The fluorescent chelator Indo-1 can simultaneously provide information about two ions, such as Ca2+ and Ba2+, if spectra after binding can be distinguished from each other and from the ion-free dye. In the case of extracellular Ca2+ and Ba2+, the three spectra were found to be unique and independent, in the sense that no one of them could be approximated by any combination of the other two. Upon binding Ba2+, Indo-1 experienced a peak shift from 470 to 455 nm, whereas the peak for Ca(2+)-bound Indo-1 occurred at 405 nm. The computer could distinguish a contribution from Ba2-bound Indo-1 just as well when it was in a mixture containing contributions from free dye and Ca(2+)-bound Indo-1. The program used all the spectral data in a rapid noniterative calculation. It found the unique combination of Ca(2+)-bound, Ba(2+)-bound, and metal-free Indo-1 spectra which best matched the data. The spectral weighting factors which formed the best combination spectrum then corresponded to the relative concentrations of the dye in the three states. From these and the dissociation constants for Ca2+ and Ba2+, it was possible to calculate both [Ca2+] and [Ba2+] from a single data spectrum. The method was also applied to Mn2+, a metal which does not generate a unique spectrum, but which quenches Indo-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Barium↗