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PubMed2000

Development of computational and graphical tools for analysis of movement and flexibility in large molecules.

We developed a computer program for the calculation and display of the difference distance matrices (DDMs) of macromolecules that has the ability to compare multiple structures simultaneously. To demonstrate its use, a data set of atoms for superimposition of the HIV-1 reverse transcriptase enzyme was defined using the coordinates for the 21 available crystal structures of this enzyme and its complexes. The DDM technique for superimposition data set generation allows selection of atoms that are invariant in all structures, is free from user bias, and represents the most accurate and precise method of producing such subsets. Comparison of this technique was made against other published methods of generating superimposition data sets, and it was found that significant differences in magnitude and trends of atom movements are observed depending on which data set was used.

Computer Graphics↗
PubMed2005

Is the DeVries-Rose to Weber transition empirically possible with sine-wave gratings?

Visual functioning at various retinal illuminance levels is usually measured either by determining grating acuity as a function of light level or by determining how sensitivity to sine-wave gratings changes with retinal illuminance. The former line of research has shown that grating acuity follows a two-branch relationship with retinal illuminance, with the point of discontinuity occurring at the transition from scotopic to photopic vision. Results of the latter line of research have summarily been described as a transition from the DeVries-Rose law to Weber's law, according to which log sensitivity increases linearly with log illuminance with a slope of 0.5 over a range of low illuminances (the DeVries-Rose range) and then levels off and does not increase with further increases of illuminance (the Weber range). This paper aims at determining the compatibility of the results of these two lines of research. We consider empirical constraints from data bearing on the shape of the surface describing contrast sensitivity to sine-wave gratings as a function of spatial frequency and illuminance simultaneously, in order to determine whether they are consistent with a summary description in terms of DeVries-Rose and Weber's laws. Our analysis indicates that, with sine-wave gratings, the DeVries-Rose law can only hold empirically at low spatial frequencies.

Computer Graphics↗
PubMed2004

[Modern diagnostics of tracheal stenosis].

BACKGROUND: Numerous new modalities in computertomography (CT), in particular Multislice-Spiral-CT and Virtual Endoscopy, and novel developments in endoscopy and spirometry gave us reason to review the current state of the art in diagnostics of tracheal stenosis (TS). METHODS: This review evaluates the literature of the last decade regarding new trends and methods in diagnostics of tracheal stenosis. Pros and cons are discussed, and the future trends are highlighted. CONCLUSIONS: Spiral-CT scans at collimated slices of < or = 3 mm, PITCH < or = 1.5 and a segmentation level of - 350 HE permit a valid measurement of tracheal lumina. The flow-volume-plot is still the most important investigation to evaluate respiratory function in TS. Peak-Flow-Meters are suitable for patient self monitoring. The selective estimation of the TS related airway resistance using in situ measurements and numerical flow simulation studies are likely to reach importance in future. The ability to obtain exact measures from endoscopic recordings using EndoScan serves quality control in endoscopy. An objective comparison of different treatments becomes possible. Endosonography and methods for in-vitro tissue analysis (Optical Coherence Tomography) are more focused on the early diagnosis of malignant lesions. The Synopsis of endoscopy, CT-scan and spirometry provides the highest diagnostic accuracy today.

Bronchoscopes↗
PubMed2005

[Guided surgery in a subtemporal approach in CPA tumors?].

BACKGROUND: Computer assisted surgery (CAS) permits the visualization of hidden bony covered structures invisible for the human eye with radiological 3d data sets. The surgeon might be able to orientate anatomically during surgery without having to prepare the according landmarks. This would mean less surgical traumatization and a shorter and smaller operation corridor. METHOD: We determined the use of CAS in a quality assurance analysis with the subtemporal approach in 8 patients with supra-meatal tumors type A of the cerebellopontine angle. Various navigation systems and methods for referencing for the registration of the patients' heads were used. The question was whether it is possible intraoperatively without preparation of known anatomical landmarks to define the borders of an optimal positioned temporary bone cap and to identify the bony covered inner auditory canal and its neuronal structures without orienting neurostimulation. RESULT: It was possible with CAS to assess intraoperatively the borders of a temporary bone cap above the cranially positioned mastoid cell. However, the objective inaccuracy of 2 to 28 mm observed during surgery did not allow a secure identification of the inner auditory canal. CONCLUSIONS: CAS with the subtemporal approach cannot replace the conventional preparation of known anatomical landmarks nor neurostimulation to identify neural structures, due to the expected high inaccuracy with the non-invasive referencing systems that are available today.

Adult↗
PubMed2001

Aligning gene expression time series with time warping algorithms.

UNLABELLED: motivation: Increasingly, biological processes are being studied through time series of RNA expression data collected for large numbers of genes. Because common processes may unfold at varying rates in different experiments or individuals, methods are needed that will allow corresponding expression states in different time series to be mapped to one another. RESULTS: We present implementations of time warping algorithms applicable to RNA and protein expression data and demonstrate their application to published yeast RNA expression time series. Programs executing two warping algorithms are described, a simple warping algorithm and an interpolative algorithm, along with programs that generate graphics that visually present alignment information. We show time warping to be superior to simple clustering at mapping corresponding time states. We document the impact of statistical measurement noise and sample size on the quality of time alignments, and present issues related to statistical assessment of alignment quality through alignment scores. We also discuss directions for algorithm improvement including development of multiple time series alignments and possible applications to causality searches and non-temporal processes ('concentration warping').

Algorithms↗
PubMed2002

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

Algorithms↗
PubMed1997

A population genetics model of marker-assisted selection.

A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.

Computer Simulation↗
PubMed2005

Model-based detection of partially obstructed endotracheal tube.

OBJECTIVES: A five-element lumped pulmonary model was developed to estimate respiratory mechanics automatically and noninvasively. The model was applied to diagnose obstructed endotracheal tube. Events like bronchospasm and stiff chest wall were also tested to determine the specificity of the diagnosis. Cases with positive end-expiratory pressure were also included in the analysis to see the effects of positive end-expiratory pressure on the model. DESIGN: Randomized controlled animal study. SETTING: University department of anesthesiology. SUBJECTS: Ten anesthetized, paralyzed, and mechanically ventilated mongrel dogs (19-45 kg) of either gender. INTERVENTIONS: Two levels of upper airway obstruction were induced in ten dogs by partially constricting the endotracheal tube. Acute bronchial constriction was produced in five dogs by injecting methacholine through a central venous catheter. In the same five dogs, the chest wall was stiffened by wrapping a pressure cuff around the chest. Positive end-expiratory pressure was also applied as a separate event in these five animals. MEASUREMENTS AND MAIN RESULTS: Airway pressure and flow were continuously recorded at the mouth. Model parameters were iteratively identified until the root mean square error between respiratory impedance (obtained from airway pressure and flow) and model-predicted impedance (calculated using Ohm's law) was minimum. The peak inspiratory pressure increased and the peak expiratory flow rate decreased with increasing levels of partial obstruction. The value of the model parameters R(1) and C(2) increased and C(1) decreased with partial obstructed endotracheal tube, whereas R(1) increased and L and C(2) decreased with bronchospasm. With stiff chest wall, R(2) increased and C(2) decreased. With positive end-expiratory pressure, the L parameter decreased and no significant change in other model parameters was observed. Obstructed endotracheal tube is indicated if R(1) increased > or =30%, C(1) decreased > or =10%, and C(2) increased > or =10% from baseline. The test results using 45 events, including control, three complications, and positive end-expiratory pressure, show that when the model is used to diagnose obstructed endotracheal tube, the method has a sensitivity of 90% and specificity of 97%. CONCLUSIONS: During an obstructed endotracheal tube, model parameters change such that the event can be diagnosed noninvasively, automatically, and accurately. The model differentiates between upper airway obstruction and complications like bronchospasm and stiff chest wall.

Airway Resistance↗
PubMed2005

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations.

The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson-Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines.

Animals↗
PubMed1990

Use of the impedance method to calculate 3-D power deposition patterns for hyperthermia with capacitive plate electrodes.

We have used the three-dimensional impedance method to calculate the power deposition in the human pelvic region due to a radio frequency current at 13.56 MHz applied through round or oval capacitive-plate applicators. We compare the energy deposited in several tumor sites when energy is applied using a variety of applicator sizes, locations, and boluses of various conductivities. We show detailed maps of the power deposition in these cases for selected regions of the body and suggest useful configurations of applicators for heating tumors in several locations in the body.

Computer Simulation↗
PubMed2006

In vivo profiling of focal cortical dysplasia on high-resolution MRI with computational models.

PURPOSE: On MRI, focal cortical dysplasia (FCD) is characterized by a combination of increased cortical thickness, hyperintense signal within the dysplastic lesion, and blurred transition between gray and white matter (GM-WM). The visual identification of these abnormal characteristics may be difficult, and it is unclear to what degree these features occur among different FCD lesions. Our purpose was to investigate the pattern of occurrence of abnormal MRI characteristics in FCD by using a set of computational models and to generate quantitative lesion profiling. METHODS: A set of voxel-wise operators was applied to high-resolution 3D T1-weighted MRI in 23 patients with histologically proven FCD and 39 healthy controls, creating maps of GM thickness, maps of relative intensity highlighting areas with hyperintense signal, and maps of gradient magnitude modeling the GM-WM transition. All FCD lesions were segmented manually on the T1-weighted MRI. RESULTS: FCD volumes ranged from 734 mm3 to 80,726 mm3 (mean, 8,629 mm3 +/- 16,238). The manually segmented FCD lesions were used to estimate features in the lesional area and to determine possible local variations of each feature by means of a histogram. In 78% of the patients, FCD lesions were characterized by simultaneous GM thickening, hyperintense signal, and blurring of the GM-WM transition. Moreover, in all patients, the FCD lesion had at least two of these three characteristics. CONCLUSIONS: The three features occurred regardless of the lesion volume, and they characterized not only large FCD lesions, but also subtle ones that had been overlooked by conventional radiologic inspection before surgery.

Adult↗
PubMed2004

Differences between study-specific and subject-specific heart rate corrections of the QT interval in investigations of drug induced QTc prolongation.

A computational study was designed to investigate the differences between the so-called study-specific and subject-specific heart rate corrections of QT interval. In 53 healthy subjects (25 women, mean age 26.7 +/- 8.7 years), serial 10-second electrocardiograms (ECG) were obtained during daytime hours. In each subject, 200 ECGs were selected representative of the individual QT/RR relationship. Of the population of 53 subjects, 30,000 different subgroups of 16 subjects were considered and their data used to model drug induced QT interval prolongation by 0, 5, 10, and 20 ms combined with drug induced heart rate acceleration and deceleration. In each modeled study, QTc changes were assessed by: (1) Six study-specific heart rate corrections designed by regression modeling of the baseline QT/RR data pooled from all subjects; (2) Six subject-specific heart rate corrections designed by the same regression modeling of the baseline QT/RR data in each subject separately; (3) subject optimized correction that selected the best fitting regression model for each individual; and (4) by Bazett and Fridericia corrections. In each modeled study, the errors of the correction approaches were estimated and statistically summarized over all modeled studies. The subject-specific corrections led to maximum errors in single milliseconds (error range of 2.4, 5.7, and 2.6 ms with linear, log/log linear, and exponential models, respectively) while the study-specific corrections led to substantially greater errors (error range of 17.8, 19.4, and 16.9 ms with linear, log/log linear, and exponential models, respectively). Both Bazett and Fridericia corrections led not only to substantial errors (error range of 28.3 and 16.9 ms) but also to regular bias with systematically false negative and false positive conclusions dependent on modeled heart rate acceleration and deceleration. Thus, subjects-specific corrections should be used in the intensive and definite studies aimed at providing the final answer on the ability of a drug to prolong the QT interval.

Adolescent↗
PubMed1999

Differential attenuation method for simultaneous estimation of activity and attenuation in multiemission single photon emission computed tomography.

A penalized weighted least squares reconstruction algorithm is described that simultaneously estimates activity and attenuation distributions from emission sinogram data alone. This estimation technique is based on differential attenuation information and is applicable to any single photon emission computed tomography imaging isotope with emissions at two or more distinct energies, after accurate compensation for Compton scatter. A rotation-based forward projector is used to efficiently model photon attenuation at multiple emission energies, as well as distance-dependent spatial resolution. The algorithm was tested using simulated scatter-free 201T1 projection data from a single-slice numerical cardiac phantom with and without cold myocardial defects. Poisson noise was added to the projection data to mimic clinically realistic count densities. The activity estimates resulting from the proposed method had fewer artifacts and were substantially more accurate than images reconstructed with filtered backprojection without compensation for attenuation. Several techniques were employed to reduce the time required for the iterative routine to converge and to reduce the sensitivity of the solution to noise in the projection data. These included: (1) a preconditioning image variable transformation; (2) a coarse-to-fine grid initialization schedule; and (3) a convex hull image mask determined directly from the data. The combined effect of these techniques substantially reduced the compute time required for the reconstruction.

Algorithms↗
PubMed2004

Cerebral atrophy in myotonic dystrophy: a voxel based morphometric study.

Brain involvement in myotonic dystrophy type 1 (DM1) is characterised by cortical atrophy and white matter lesions. We compared the magnetic resonance imaging derived grey matter maps of 22 DM1 patients with those of matched, healthy controls using voxel based morphometry to evaluate the extension of global and regional cortical atrophy in DM1, as well as its relationships with clinical and genetic features. Patients had significantly reduced brain tissue volumes. Grey matter volume was inversely correlated with age; this inverse correlation was significantly stronger in DM1 than in controls. Neither the clinical and genetic characteristics nor white matter lesions were correlated with cortical atrophy. Grey matter atrophy was located mainly in the bilateral frontal and parietal lobes, in the bilateral middle temporal gyrus, and in the left superior temporal and occipital gyrus.

Adult↗
PubMed2005

Traumatic brain injury and grey matter concentration: a preliminary voxel based morphometry study.

BACKGROUND: Magnetic resonance imaging (MRI) studies have shown diffuse cerebral atrophy following traumatic brain injury. In the past, quantitative volumetric analysis of these changes was carried out by manually tracing specific regions of interest. In contrast, voxel based morphometry (VBM) is a fully automated technique that allows examination of the whole brain on a voxel by voxel basis. OBJECTIVE: To use VBM to evaluate changes in grey matter concentration following traumatic brain injury. METHODS: Nine patients with a history of traumatic brain injury (ranging from mild to severe) about one year previously were compared with nine age and sex matched healthy volunteers. T1 weighted three dimensional MRI images were acquired and then analysed with statistical parametric mapping software (SPM2). The patients with traumatic brain injury also completed cognitive testing to determine whether regional grey matter concentration correlated with a measure of attention and initial injury severity. RESULTS: Compared with controls, the brain injured patients had decreased grey matter concentration in multiple brain regions including frontal and temporal cortices, cingulate gyrus, subcortical grey matter, and the cerebellum. Decreased grey matter concentration correlated with lower scores on tests of attention and lower Glasgow coma scale scores. CONCLUSIONS: Using VBM, regions of decreased grey matter concentration were observed in subjects with traumatic brain injury compared with well matched controls. In the brain injured patients, there was a relation between grey matter concentration and attentional ability.

Adult↗
PubMed2003

Linkage analysis of quantitative trait loci in the presence of heterogeneity.

Variance component modeling for linkage analysis of quantitative traits is a powerful tool for detecting and locating genes affecting a trait of interest, but the presence of genetic heterogeneity will decrease the power of a linkage study and may even give biased estimates of the location of the quantitative trait loci. Many complex diseases are believed to be influenced by multiple genes and therefore genetic heterogeneity is likely to be present for many real applications of linkage analysis. We consider a mixture of multivariate normals to model locus heterogeneity by allowing only a proportion of the sampled pedigrees to segregate trait-influencing allele(s) at a specific locus. However, for mixtures of normals the classical asymptotic distribution theory of the maximum likelihood estimates does not hold, so tests of linkage and/or heterogeneity are evaluated using resampling methods. It is shown that allowing for genetic heterogeneity leads to an increase in power to detect linkage. This increase is more prominent when the genetic effect of the locus is small or when the percentage of pedigrees not segregating trait-influencing allele(s) at the locus is high.

Chromosome Mapping↗
PubMed2003

Increases in regional subarachnoid CSF without apparent cortical gray matter deficits in schizophrenia: modulating effects of sex and age.

OBJECTIVE: The authors investigated the modulating effects of biological sex and age on regional decreases in cortical gray matter and increases in subarachnoid CSF in 25 patients with chronic schizophrenia and 28 group-matched healthy comparison subjects. METHOD: Computational cortical pattern-matching methods were employed to measure the local proportions of gray matter and subarachnoid CSF at thousands of homologous cortical surface locations in each subject using high-resolution magnetic resonance images. Principal-component analysis reduced tissue proportion values obtained at each cortical surface point into component scores for each subject. Principal-component analysis scores were used as dependent variables in statistical analyses that included diagnosis, age, and sex as predictor variables. To reveal more regional changes in tissue proportions, statistical differences in gray matter and CSF were compared at each cortical surface location and mapped in three dimensions. RESULTS: Principal-component analyses revealed main effects of diagnosis, sex, and age for the CSF increases seen in the schizophrenia patients, in male subjects, and in association with age. Significant diagnosis-by-age, diagnosis-by-sex, and diagnosis-by-sex-by-age interactions were also observed, revealing CSF increases in male patients at younger ages. Statistical maps showed regional increases in subarachnoid CSF in association with the above effects. For cortical gray matter measurements, only main effects of age were observed. CONCLUSIONS: Regionally specific increases in sulcal and subarachnoid CSF occur during adulthood and appear prematurely in male schizophrenia patients. Cortical gray matter reductions show aging effects but are below the threshold of significance in schizophrenia.

Adult↗