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PubMed1995

MR image classification algorithms for neurosurgical and stereotactic radiosurgical trajectory planning and volumetric analysis.

Neurosurgical and stereotactic radiosurgical trajectory planning involves a phase of image data acquisition followed by localization of tissues to be avoided or crossed during the procedure. Success of the procedure is often assessed during follow-up by performing volumetric analysis of tissues of interest. Both localization and volumetric analysis can be facilitated by classifying the input data into different tissue types. This study compares classification results based on four different input image data: (1) MR data obtained with one TR and TE parameter combination, (2) MR data acquired with eight combinations of TR and TE parameters, (3) input data compressed into four principal components, and (4) the input data (3) together with first- and second-order texture features. The algorithms (a) to reduce the dimensionality using principal components, (b) to generate texture features, (c) to determine feature usefulness in classification using the Wilk's lambda criterion, and (d) to classify the input set are described. Classification results are found to be poor for input data 1 and much improved (qualitatively and quantatively) for input data 2. Input data 3 produces classification results (quantitatively and qualitatively) similar to that of 2. Input data 4 is found to produce quantitative results similar to those of 2 and 3, but the qualitative results show enhanced classification of some tissues and distortion of others.

Algorithms↗
PubMed2003

Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories.

A sensitivity analysis of general stoichiometric networks is considered. The results are presented as a generalization of Metabolic Control Analysis, which has been concerned primarily with system sensitivities at steady state. An expression for time-varying sensitivity coefficients is given and the Summation and Connectivity Theorems are generalized. The results are compared to previous treatments. The analysis is accompanied by a discussion of the computation of the sensitivity coefficients and an application to a model of phototransduction.

Animals↗
PubMed2005

The triplet channel in the photodissociation of ozone in the Hartley band: classical trajectory surface hopping analysis.

The triplet channel in the photodissociation of ozone in the Hartley band, O3 + hv-->O(3P) + O2(3sigma), is investigated by means of a classical trajectory surface hopping method using ab initio diabatic potential energy surfaces for the B and the R states. Because of the strong recoil in the R state along the breaking O-O bond, O2(3sigma) is produced with a high rotational energy. The nonadiabatic transition probability depends markedly on the coordinate along the crossing seam. As a consequence a unique correlation is found between the internuclear geometry at the crossing and the final vibrational state of O2(3sigma). The calculated distribution of the translational energy is in good accord with the measured distribution.

Journal Article↗
PubMed2001

Evaluation of ionic pollutants of acid fog and rain using a factor analysis and back trajectories.

Fog and rain water samples were collected at the same time in the Akita Hachimantai mountain range in northern Japan from June to September in 1998 and 1999. The various ion concentrations in these samples were analyzed, and the fog droplet sizes were measured for each fog event. As the fog droplet size increased, the ion concentration decreased. The slope of log-log plots of the concentration versus the droplet size differed with the kind of ion. In order to characterize the air pollutant, moreover, these data were quantitatively analyzed by an oblique rotational factor analysis. We found that three factors were extracted as the air pollutant source: (NH4)2SO4, acids (HNO3 + H2SO4) and sea-salt. Combining the factor analysis with the 72 h back-trajectory at 850 hPa level, we found that the contribution of each factor varied with the transport pattern of air masses.

Acid Rain↗
PubMed1996

A new system for three-dimensional kinematic trajectory acquisition and analysis--I. The application of an ultrasonic technique to human gait analysis.

This paper discusses some techniques of kinematics analysis, and describes a new system for movement recording and analysis. The new system, which is inexpensive and easy to use, consists mainly of some ultrasonic wave transmitters, receivers, a distributive multiprocessor system and software. The system can record kinematics parameters of anatomical landmarks (e.g. space coordinates, movement trajectories and angles of hips, knees and ankles). Such a system, combined with foot pressure equipment and a force plate, forms an advanced gait analysis system.

Algorithms↗
PubMed2005

Vector analysis correlating bullet trajectory to outcome after civilian through-and-through gunshot wound to the head: using imaging cues to predict fatal outcome.

OBJECTIVE: We identify radiographic imaging similarities found on head computed tomographic (CT) scans of patients with through-and-through gunshot wounds to the head with fatal outcomes. METHODS: A retrospective analysis was conducted over an 18-month period from June 2001 through December 2002. Two hundred seventeen gunshot wound patients were evaluated. Exclusion criteria included any patient with cardiopulmonary injury and instability, airway compromise, or extracranial injuries affecting prognosis. Thirty-seven patients with isolated gunshot wounds to the head were included, 10 of which were fatal. Vital signs, examination results, Glasgow coma scale (GCS) score, intracranial pressure monitoring, surgical data, days in the intensive care unit, and CT scan appearance were collected. A Cartesian xyz coordinate system was created centered on the dorsum sella. Bullet pathways on CT scans were plotted and graphed onto a standardized magnetic resonance imaging scan. RESULTS: Ten patients progressed to brain death. GCS score and pupil irregularity were associated with fatal outcome (P < 0.0001). CT scans showed that brain shift was more common in survivors. Seventy percent of nonsurvivors had minimal brain shift. A tram-track sign on CT scans correlated with fatal outcome (P = 0.005). Vector analysis of nonsurvivors showed an area of the brain approximately 4 cm above the dorsum sella that, when penetrated through the midline, led to brain death (P = 0.0006). This zone was coined the zona fatalis. CONCLUSION: We confirm that GCS score and diabetes insipidus correlated with fatal outcome. In the setting of low-velocity gunshot wounds, fatal outcome and low GCS score were associated with a tram-track sign on CT scans. Bullet passage through a particular supra-dorsum sellar transventricular zone was associated with fatal outcome.

Adolescent↗
PubMed1997

The analysis of ontogenetic trajectories: when a change in size or shape is not heterochrony.

Heterochrony has become a central organizing concept relating development and evolution. Unfortunately, the standard definition of heterochrony--evolutionary change in the rate or timing of developmental processes--is so broad as to apply to any case of phenotypic evolution. Conversely, the standard classes of heterochrony only accurately describe a small subset of the possible ways that ontogeny can change. I demonstrate here that the nomenclature of heterochrony is meaningful only when there is a uniform change in the rate or timing of some ontogenetic process, with no change in the internal structure of that process. Given two ontogenetic trajectories, we can test for this restricted definition of heterochrony by asking if a uniform stretching or translation of one trajectory along the time axis superimposes it on the other trajectory. If so, then the trajectories are related by a uniform change in the rate or timing of development. If not, then there has been change within the ontogenetic process under study. I apply this technique to published data on fossil Echinoids and to the comparison of human and chimpanzee growth curves. For the Echinoids, some characters do show heterochrony (hypermorphosis), while others, which had previously been seen as examples of heterochrony, fail the test--implying that their evolution involved changes in the process of development, not just the rate at which it proceeded. Analysis of human and chimpanzee growth curves indicates a combination of neoteny and sequential hypermorphosis, two processes previously seen as alternate explanations for the differences between these species.

Animals↗
PubMed2006

Analysis of transient behavior in complex trajectories: application to secretory vesicle dynamics.

Analysis of trajectories of dynamical biological objects, such as breeding ants or cell organelles, is essential to reveal the interactions they develop with their environments. Many previous works used a global characterization based on parameters calculated for entire trajectories. In cases where transient behavior was detected, this usually concerned only a particular type, such as confinement or directed motion. However, these approaches are not appropriate in situations in which the tracked objects may display many different types of transient motion. We have developed a method to exhaustively analyze different kinds of transient behavior that the tracked objects may exhibit. The method discriminates stalled periods, constrained and directed motions from random dynamics by evaluating the diffusion coefficient, the mean-square displacement curvature, and the trajectory asymmetry along individual trajectories. To detect transient motions of various durations, these parameters are calculated along trajectories using a rolling analysis window whose width is variable. The method was applied to the study of secretory vesicle dynamics in the subplasmalemmal region of human carcinoid BON cells. Analysis of transitions between transient motion periods, combined with plausible assumptions about the origin of each motion type, leads to a model of dynamical subplasmalemmal organization.

Cell Line↗
PubMed1989

Single base mismatches in DNA. Long- and short-range structure probed by analysis of axis trajectory and local chemical reactivity.

We have devised a procedure to generate any single base mismatch in a constant sequence context, and have studied these from two points of view. (1) We have examined electrophoretic mobility of 458 base-pair fragments containing approximately centrally located single mismatches, in polyacrylamide gels, compared to fully matched DNA fragments. We found that no single mismatch caused a significant perturbation of gel mobility, and we conclude that all the mismatches may be accommodated within a helical geometry such that there is no alteration of the path of the helix axis in a straight DNA molecule. (2) We have studied all the single mismatches with respect to reactivity to a number of chemical probes. We found that: (a) No mispaired adenine bases are reactive to diethyl pyrocarbonate and are therefore not simply unpaired such that N-7 is exposed. (b) A number of mispaired thymine bases are reactive to osmium tetroxide, and cytosine bases to hydroxylamine. (c) Where crystal or nuclear magnetic resonance structures are available, the reactivity correlates with exposure of the pyrimidine 5,6 double bonds to attack in the major groove as a result of wobble base-pair formation. This is particularly clear for G.T and I.T base-pairs. (d) Reactivity of bases in mismatched pairs can be dependent on sequence context. (e) Reactivity of the C.C mismatch to hydroxylamine is suppressed at low pH, suggesting that a rearrangement of base-pairing occurs on protonation. The results overall are consistent with the formation of stacked intrahelical base-pairs wherever possible, resulting in no global distortion of the DNA structure, but specific enhancement of chemical reactivity in some cases.

Base Composition↗
PubMed2006

Mathematical analysis of trabecular 'trajectories' in apparent trajectorial structures: the unfortunate historical emphasis on the human proximal femur.

Wolff's "law" of the functional adaptation of bone is rooted in the trajectory hypothesis of cancellous bone architecture. Wolff often used the human proximal femur as an example of a trajectorial structure (i.e. arched trabecular patterns appear to be aligned along tension/compression stress trajectories). We examined two tenets of the trajectory hypothesis; namely, that the trabecular tracts from the tension- and compression-loaded sides of a bending environment will: (1) follow 'lines' (trajectories) of tension/compression stress that resemble an arch with its apex on a neutral axis, and (2) form orthogonal (90 degrees ) intersections. These predictions were analysed in proximal femora of chimpanzees and modern humans, and in calcanei of sheep and deer. Compared to complex loading of the human femoral neck, the chimpanzee femoral neck reputedly receives relatively simpler loading (i.e. temporally/spatially more consistent bending), and the artiodactyl calcaneus is even more simply loaded in bending. In order to directly consider Wolff's observations, measurements were also made on two-dimensional, cantilevered beams and curved beams, each with intersecting compression/tension stress trajectories. Results in the calcanei showed: (1) the same nonlinear equation best described the dorsal ("compression") and plantar ("tension") trabecular tracts, (2) these tracts could be exactly superimposed on the corresponding compression/tension stress trajectories of the cantilevered beams, and (3) trabecular tracts typically formed orthogonal intersections. In contrast, trabecular tracts in human and chimpanzee femoral necks were non-orthogonal (mean approximately 70 degrees ), with shapes differing from trabecular tracts in calcanei and stress trajectories in the beams. Although often being described by the same equations, the trajectories in the curved beams had lower r(2) values than calcaneal tracts. These results suggest that the trabecular patterns in the calcanei and stress trajectories in short beams are consistent with basic tenets of the trajectory hypothesis while those in human and chimpanzee femoral necks are not. Compared to calcanei, the more complexly loaded human and chimpanzee femoral necks probably receive more prevalent/predominant shear, which is best accommodated by non-orthogonal, asymmetric trabecular tracts. The asymmetrical trabecular patterns in the proximal femora may also reflect the different developmental 'fields' (trochanteric vs. neck/head) that formed these regions, of which there is no parallel in the calcanei.

Adaptation, Physiological↗
PubMed1994

Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes.

The dynamics and stability of four DNA duplexes are studied by means of molecular dynamics simulations. The four molecules studied are combinations of 4, 15 bases long, single-stranded oligomers, F1, F2, F3, and F4. The sequence of these single strand oligomers are chosen such that F1-F2 and F3-F4 form parallel (ps) DNA double helices, whereas F1-F4 and F2-F3 form antiparallel-stranded (aps) DNA double helices. Simulations were done at low (100 K) and room (300 K) temperatures. At low temperatures the dynamics are quasi-harmonic and the analysis of the trajectories gives good estimates of the low frequency vibrational modes and density of states. These are used to estimate the linear (harmonic) contribution of local fluctuations to the configurational entropy of the systems. Estimates of the differences in enthalpy between ps and aps duplexes show that aps double helices are more stable than the corresponding ps duplexes, in agreement with experiments. At higher temperatures, the distribution of the fluctuations around the average structures are multimodal and estimates of the configurational entropy cannot be obtained. The multi-basin, nonlinear character of the dynamics at 300 K is established using a novel method which extracts large amplitude nonlinear motions from the molecular dynamics trajectories. Our analysis shows that both ps DNA exhibit much larger fluctuations than the two aps DNA. The large fluctuations of ps DNA are explained in terms of correlated transitions in the beta, epsilon, and zeta backbone dihedral angles.

Base Sequence↗
PubMed2000

Analysis of arm trajectories of everyday tasks for the development of an upper-limb orthosis.

Spatiotemporal arm and body movements of able-bodied subjects performing nine everyday tasks were recorded for the purpose of guiding the development of an upper-limb orthosis. To provide a user the opportunity to carry out these tasks with natural movements, the orthosis should allow replication of the measured trajectories. We outline the orthosis architecture, which supports the user's upper arm and forearm, and analyze the movement data to obtain orthosis design specifications. Trajectories were obtained using six-degree-of-freedom magnetic position sensors affixed to the wrist, elbow, shoulder, trunk and head. Elbow trajectory data were decomposed into ranges along the principle Cartesian axes to provide a generally useful envelope measure. The smallest Cartesian parallel-piped that contained the elbow trajectories for most tasks was approximately 30 cm front/back, 15 cm side/side, and 17 cm up/down. A rough lower bound estimate obtained by asking subjects to repeat the tasks while minimizing elbow movement substantially reduced movement in the up/down and side/side dimensions. Elbow angles were generally in the range 50 degrees-150 degrees, and the angle of the forearm with respect to vertical was 10 degrees-110 degrees. Raw trajectory data may be downloaded from www://asel.udel.edu/robotics/orthosis/range.h tml.

Activities of Daily Living↗
PubMed1989

Analysis of particle trajectories in aortic artery bifurcations with stenosis.

The fluid-particle dynamics in a two-dimensonal symmetric branching channel with local occlusions representing a diseased segment of an aortic artery bifurcation has been analyzed. The validated finite element model simulates the trajectories and landing or impact sites of spherical particles for laminar flow in bifurcation channels with generalized wall conditions. Two hypotheses relating critical wall shear stress levels and plaque formation, previously postulated by Kleinstreuer et al. (1988) and Nazemi et al. (1989), have been confirmed. Low shear stress may contribute to the onset of atherosclerotic lesions and areas of critically low and higher shear stresses are susceptible to accelerated growth of plaque.

Aorta, Abdominal↗
PubMed2006

Ensemble-based convergence analysis of biomolecular trajectories.

Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive method to self-consistently assess the convergence of trajectories generated by molecular dynamics and related methods. Our approach reports directly and systematically on the structural diversity of a simulation trajectory. Straightforward clustering and classification steps are the key ingredients, allowing the approach to be trivially applied to systems of any size. Our initial study on met-enkephalin strongly suggests that even fairly long trajectories (approximately 50 ns) may not be converged for this small--but highly flexible--system.

Biopolymers↗
PubMed2003

Genetic analysis of longitudinal trajectory of clinical mastitis in first-lactation Norwegian cattle.

Clinical mastitis records for 36,178 first-lactation daughters of 245 Norwegian Cattle (NRF) sires were analyzed with a Bayesian longitudinal threshold model. For each cow, the period going from 30 d before calving to 300 d after calving was divided into 11 intervals of 30 d length each. Absence or presence of clinical mastitis within each interval was scored as "0" or "1", respectively. A Bayesian threshold model consisting of a set of explanatory variables plus Legendre polynomials on time of order four was used to describe the trajectory of liability to clinical mastitis. Heritability ranged between 0.07 and 0.13 before calving, from 0.04 to 0.15 during the first 270 d after calving, and increased sharply thereafter, as a consequence of the form of the polynomial. Genetic correlations between adjacent days were close to 1, and decreased when days were further apart. Most genetic correlations were moderate to high. A measure of probability of future daughters contracting clinical mastitis during lactation was computed for each sire. A typical curve had a peak near calving followed by a decrease thereafter. The best sires had a low peak around calving and a low expected probability of mastitis among daughters throughout lactation. Expected fraction of days without mastitis was derived from the probability curves and used for ranking of sires. Rank correlations with genetic evaluations of sires obtained from cross-sectional models were high. However, sire selection was affected markedly, especially at high selection intensity. An advantage of the longitudinal model for clinical mastitis is its ability to take multiple treatments and time aspects into account.

Animals↗
PubMed2004

Folding dynamics of proteins from denatured to native state: principal component analysis.

Several trajectories starting from random configurations and ending in the native state for chymotrypsin inhibitor 2, CI2, are generated using a Go-type model where the backbone torsional angles execute random jumps on which a drift towards their native values is superposed. Bond lengths and bond angles are kept fixed, and the size of the backbone atoms and side groups are recognized. The large datasets obtained are analyzed using a particular type of principal component analysis known as Karhunen-Loeve expansion (KLE). Trajectories are decomposed separately into modes in residue space and time space. General features of different folding trajectories are compared in the modal space and relationships between the structure of CI2 and its folding dynamics are obtained. Dynamic scaling and order reduction of the folding trajectories are discussed. A continuous wavelet transform is used to decompose the nonstationary folding trajectories into windows exhibiting different features of folding dynamics. Analysis of correlations confirms the known two-state nature of folding of CI2. All of the conserved residues of the protein are shown to be stationary in the small modes of the residue space. The sequential nature of folding is shown by examining the slow modes of the trajectories. The present model of protein folding dynamics is compared with the simple Rouse model of polymer dynamics. Principal component analysis is shown to be a very effective tool for the characterization of the general folding features of proteins.

Computational Biology↗
PubMed1992

Fuzzy cluster analysis of molecular dynamics trajectories.

We propose fuzzy clustering as a method to analyze molecular dynamics (MD) trajectories, especially of proteins and polypeptides. A fuzzy cluster analysis locates classes of similar three-dimensional conformations explored during a molecular dynamics simulation. The method can be readily applied to results from both equilibrium and nonequilibrium simulations, with clustering on either global or local structural parameters. The potential of this technique is illustrated by results from fuzzy cluster analyses of trajectories from MD simulations of various fragments of human parathyroid hormone (PTH). For large molecules, it is more efficient to analyze the clustering of root-mean-square distances between conformations comprising the trajectory. We found that the results of the clustering analysis were unambiguous, in terms of the optimal number of clusters of conformations, for the majority of the trajectories examined. The conformation closest to the cluster center can be chosen as being representative of the class of structures making up the cluster, and can be further analyzed, for example, in terms of its secondary structure. The CPU time used by the cluster analysis was negligible compared to the MD simulation time.

Amino Acid Sequence↗