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Results for “trajectory analysis”

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At least 793 records · Page 44Linked to original sources

PubMed1997

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin.

The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.

Anticodon↗

PubMed2001

Analyzing developmental trajectories of distinct but related behaviors: a group-based method.

This article presents a group-based method to jointly estimate developmental trajectories of 2 distinct but theoretically related measurement series. The method will aid the analysis of comorbidity and heterotypic continuity. Three key outputs of the model are (a) for both measurement series, the form of the trajectory of distinctive subpopulations; (b) the probability of membership in each such trajectory group; and (c) the joint probability of membership in trajectory groups across behaviors. This final output offers 2 novel features. First, the joint probabilities can characterize the linkage in the developmental course of distinct but related behaviors. Second, the joint probabilities can measure differences within the population in the magnitude of this linkage. Two examples are presented to illustrate the application of the method.

Child↗

PubMed2000

Brain electric correlates of strong belief in paranormal phenomena: intracerebral EEG source and regional Omega complexity analyses.

The neurocognitive processes underlying the formation and maintenance of paranormal beliefs are important for understanding schizotypal ideation. Behavioral studies indicated that both schizotypal and paranormal ideation are based on an overreliance on the right hemisphere, whose coarse rather than focussed semantic processing may favor the emergence of 'loose' and 'uncommon' associations. To elucidate the electrophysiological basis of these behavioral observations, 35-channel resting EEG was recorded in pre-screened female strong believers and disbelievers during resting baseline. EEG data were subjected to FFT-Dipole-Approximation analysis, a reference-free frequency-domain dipole source modeling, and Regional (hemispheric) Omega Complexity analysis, a linear approach estimating the complexity of the trajectories of momentary EEG map series in state space. Compared to disbelievers, believers showed: more right-located sources of the beta2 band (18.5-21 Hz, excitatory activity); reduced interhemispheric differences in Omega complexity values; higher scores on the Magical Ideation scale; more general negative affect; and more hypnagogic-like reveries after a 4-min eyes-closed resting period. Thus, subjects differing in their declared paranormal belief displayed different active, cerebral neural populations during resting, task-free conditions. As hypothesized, believers showed relatively higher right hemispheric activation and reduced hemispheric asymmetry of functional complexity. These markers may constitute the neurophysiological basis for paranormal and schizotypal ideation.

Adult↗

PubMed2002

MOSBY: a molecular structure viewer program with portability and extensibility.

A molecular structure viewer program, MOSBY has been developed for studies that use atomic coordinates to understand the structures of protein molecules. The program is designed to be portable with a comprehensive user interface by our high-throughput graphics library. In addition, it cooperates with extension modules customized for individual research topics and analysis. For example, an electron density module loads and displays electron density maps derived in X-ray crystallographic analysis superimposed to an atomic model. A molecular dynamics module reads a trajectory file of the results of molecular dynamics calculations and animates the structure. These plug-in modules are devised to function without modification to the MOSBY program. For variations of analysis and calculations with atomic coordinates, the portability and extensibility illustrated by MOSBY play an important rule in scientific computational tools with active software development.

Computer Graphics↗

PubMed1997

Domain motions in dihydrofolate reductase: a molecular dynamics study.

Molecular dynamics simulations have been carried out on the enzyme dihydrofolate reductase from Lactobacillus casei complexed with methotrexate, NADPH and 264 crystallographic water molecules. Analysis of correlations in atomic fluctuations reveal the presence of highly correlated motion (correlation coefficient > 0.6) in the region between residues 30 to 35 and 85 to 90 leading to the identification of two domains, an "adenosine-binding domain" and a "large domain", which rotate by 3 to 4 degrees with respect to each other. The strongest correlation (> 0.6) within the large domain involves a coupling between the motions of the "teen-loop", and the spatially contiguous loops linking beta 6-beta 7 and beta 7-beta 8. Moreover, there is a significant correlation (approximately 0.5) between the adenosine fragment of NADPH and the pteridine and p-aminobenzoyl fragments of methotrexate, which are separated by approximately 17 A, and is lost on removal of "rigid-body" motion from the original trajectory. This provides support for the idea that the relative motion of the two domains is a means by which the occupation of the binding site for the adenosine end of the coenzyme can affect methotrexate binding and vice versa. Quasiharmonic vibrational analysis of the trajectory reveals that the overall dynamics of the system are governed by domain motions whose contributions are dominant at low frequencies. In addition, different low-frequency modes are responsible for separately coupling the adenosine-binding site and parts of methotrexate.

Binding Sites↗

PubMed2005

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers.

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of (2)H spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of (2)H T(1) relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4 +/ -1 x 10(-8) cm(2)s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Algorithms↗

PubMed2001

[In vivo cinematic study of the trapezometacarpal joint].

The aim of this study was to assess the trapeziometacarpal joint kinematics from in vivo measurements, both quantifying the ranges of motion and suggesting a suitable joint model. A motion analysis system has been used to collect the spatial trajectories of markers, glued respectively on the thumb and on the hand's palm. A rigorous protocol was set up to make sure of the trapezoid bone's fixity relatively to the hand, and then to be able to characterize the movement of the first metacarpus with respect to the trapezium. The ranges of motion have been measured on two distinct movements: circumduction and flexion-extension, and different types of joints: healthy, pathological and prosthetic. The joint axes of rotation (for flexion-extension and ante-retroposition movements) have been determined on healthy subjects. The computation of rotation amplitudes and positions of joint axes was based upon the finite helical axis concept, which degenerates into finite rotation axis when translations can be neglected. Both the measurement protocol and the calculation method have been validated by comparing the computed joint center with that measured on a radiography, in the case of a spherical prosthesis. The ranges of motion obtained on the healthy subject series were consistent with values published by other authors. Comparisons have been realized between these reference joints and different cases: arthrodesis, arthrosis and prosthesis. The determination of rotation axes of a normal joint has lead to a generalized cardan joint, i.e. two non perpendicular converging rotation axes.

Algorithms↗

PubMed2003

NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats.

Understanding metabolic variation in "normal" animals is critical to the evaluation of drug-induced metabolic perturbation related to toxicity or pharmacology. NMR spectroscopic-based metabonomic methods were used to evaluate the acclimatization pathways of germ-free (axenic) rats to standard laboratory conditions concomitant with the associated development of gut microfloral communities. Urine samples from male Fischer 344 germ-free rats were collected over 21 days following introduction to a standard laboratory environment and analyzed using NMR spectroscopy. NMR spectra were data-reduced and analyzed using principal component analysis to visualize the changes in the host metabolic trajectory over the course of the study. At days 2 and 6 of the acclimatization process, there were marked episodes of glycosuria. In comparison to the concentrations in the 0-6 h samples, there was a reduction in the level of the tricarboxylic acid cycle intermediates (citrate, 2-oxoglutarate, and succinate) from 6 h to day 6, after which there was a sustained increase until the end of the study. The concentrations of hippurate and trimethylamine N-oxide increased over the course of the study in comparison to the levels at 0-6 h, with the most pronounced increase in the former between days 17 and 21. Phenylacetylglycine levels increased after 6 h whereas 3-hydroxypropionic acid was observed at day 12 and increased up to day 17. By day 21, the urinary metabolic profile was within the control range when compared to historical data, implying the establishment of a stable gut microflora. Although the metabolic alterations caused by the microbial alterations were not as substantial as those from metabolic dysfunction, their presence does have an effect on the interpretation of the profiles, the state of the animal, and the mechanism for the cause of such alterations. Furthermore, the use of oral drug delivery will have an effect on the microbial state, not only as a direct influence of the drug but also from it's associated vehicle. Such effects are likely to be observed particularly in the area of preclinical investigation where the data from these studies are of particular relevance.

Acclimatization↗

PubMed1986

Three-channel Lissajous' trajectory of the human short latency visual evoked potentials.

Three orthogonally derived voltage-time records, when plotted simultaneously on three-dimensional voltage-voltage-voltage coordinates, produce a 3-Channel Lissajous' Trajectory (3CLT). 3CLTs of short latency visual evoked potentials (SVEP) were obtained for 8 adult humans (16 eyes) in response to monocular flash stimulation. Intersubject variability of 3CLT of SVEP was small enough to enable identification along the trajectory of comparable planar-segments of approx. 3-5 ms duration across subjects. In each planar-segment, the point at which the trajectory exhibited marked bending was noted. These points were called apices and they corresponded to maxima in the trajectory's distance from the origin (Trajectory Amplitude). Intersubject variability in apex latencies was comparable to, or smaller than, peak latency variability of single-channel records. 3CLT of SVEP consisted of 8 planar-segments in each of the latency ranges of 0-40, 40-70 and 70-100 ms. Analysis of 3CLT, combining the criteria of segment planarity, apices and trajectory amplitude peaks, enabled differentiation between components that had been considered the same in surface distribution studies. 3CLT of SVEP seemed to be influenced by the direction of propagation along the visual pathway.

Adult↗

PubMed2006

Refinement trajectory and determination of eigenstates by a wavelet based adaptive method.

The detail structure of the wave function is analyzed at various refinement levels using the methods of wavelet analysis. The eigenvalue problem of a model system is solved in granular Hilbert spaces, and the trajectory of the eigenstates is traced in terms of the resolution. An adaptive method is developed for identifying the fine structure localization regions, where further refinement of the wave function is necessary.

Journal Article↗

PubMedDate not supplied

[Methods for analyzing brain evoked potentials clinically and in psychophysiology].

In the article one can find compare classification of excited brain potential analysis methods using for tasks of neurophysiology of man. Importance of visual data analysis, methods of multimeasure statistics and correlation analysis are discussed. Methods of dipoles localization and three-channel "lissa-djouson" trajectory are analysed from the position, that head is volume conductor. The last part of the article is devoted to importance of space methods of analysis of excited potentials, mainly for mapping of bio-electrical and magnetic exited potentials.

Brain Mapping↗

PubMed1999

Reliability of foot trajectory measures within and between testing sessions.

BACKGROUND: Impaired control of foot trajectory during the swing phase of gait is hypothesized to increase the risk of slipping or tripping. Before assessing the predictive validity of foot trajectory measures with respect to incidence of falls, it is necessary to establish their reliability. The purpose of this study is to assess within- and between-session reliability of foot trajectory measures and traditional temporal-distance measures in healthy elderly women during gait. METHODS: Sixteen healthy, elderly women (ages 65-79 years) completed six sets of five trials each of natural and fast cadence gait during a 3.5-hour period on each of 4 days. An optoelectric motion analysis system and heel switches were used to obtain both foot trajectory (minimum toe clearance during swing, vertical, and horizontal heel contact velocities) and temporal-distance measures (step width, cadence, velocity, stride length, and time). RESULTS: Within-session test-retest reliability of all variables at natural and fast speeds was good to excellent, with intraclass correlation coefficients (ICCs) of greater than 0.9 for all but one measure (fast cadence stride time). ICCs for between-session test-retest reliability were slightly lower, but still greater than 0.9 for all but two measures (fast cadence stride time and natural cadence vertical heel contact velocity). Heel contact velocities quantified at the instant of heel contact correlated strongly with values obtained by averaging over the last 2% of the gait cycle. DISCUSSION: The good to excellent within- and between-session reliability of these foot trajectory measures supports their use as a possible means of assessing subtle changes in gait motor control. Confirmation of an association between alterations in foot trajectory measures and incidence of falls awaits further study.

Aged↗

PubMed1997

Mesodermal guidance of pioneer axon growth.

Pioneer axons in insect legs are experimentally accessible model systems for the molecular identification and cellular localization of guidance cues regulating the path of axon growth. A detailed study of the Fe2 pioneer axons in the legs of the cockroach was performed to examine the diversity of guidance mechanisms. A detailed microscopic analysis of the axons at various points in their trajectory indicates that the Fe2 axons grow on a mesodermal substratum which contains the cues guiding their growth along a stereotyped path. An identified pair of muscle pioneer cells (MPC) are likely to play an important role in enabling the Fe2 growth cones to respond to mesodermal guidance cues. The addition of heparan sulfate, heparitinase, and phosphatidylinositol-specific phospholipase C to the medium perturbs the in situ path of growth of the Fe2 axons and the location of the MPC in cultured embryos. This indicates a role for heparan sulfate proteoglycans and glycosylphosphatidylinositol-anchored proteins in axon guidance. When these results are compared to those of similar experiments performed on the well-characterized Ti1 axons, they indicate significant differences in the mechanisms that are used for axon guidance. The Fe2 neurons are a good model for elucidating the mechanisms used to guide axon growth on nonmuscle mesodermal substrates often encountered in the periphery of vertebrate embryos.

Animals↗

PubMed2001

Dictyostelium cells' cytoplasm as an active viscoplastic body.

We applied a recently developed microrheology technique based on colloidal magnetic tweezers to measure local viscoelastic moduli and active forces in cells of Dictyostelium discoideum. The active transport of nonmagnetic beads taken up by phagocytosis was analyzed by single particle tracking, which allowed us to measure the length of straight steps and the corresponding velocities of the movements. The motion consists of a superposition of nearly straight long-range steps (step length in the micrometer range) and local random walks (step widths about 0.1 microm). The velocities for the former type of motion range from 1 to 3 microm/s. They decrease with increasing bead size and are attributed to rapid active transport along microtubuli. The short-range local motions exhibit velocities of less than 0.5 microm/s and reflect the internal dynamics of the cytoplasm. Viscoelastic response curves were measured by application of force pulses with amplitudes varying between 50 pN and 400 pN. Analysis of the response curves in terms of mechanical equivalent circuits yielded cytoplasmic viscosities varying between 10 and 350 Pa s. Simultaneous analysis of the response curves and of the bead trajectories showed that the motion of the beads is determined by the local yield stress within the cytoplasmic scaffold and cisternae, which varies between sigma = 30 Pa and 250 Pa. The motion of intracellular particles is interpreted in terms of viscoplastic behavior and the apparent viscosity is a measure of the reciprocal rate of bond breakage within the cytoplasmatic network. The viscoelastic moduli are interpreted as dynamic quantities which depend sensitively on the amplitude of the forces, and the rate of bond breakage is determined by the Arrhenius-Kramers law with the activation energy being reduced by the work performed by the applied force. In agreement with previous work, we provide evidence that the myosin II-deficient cells exhibit higher yield stresses, suggesting that the function of myosin II as a cross-linker is taken over by the other (non-active) cross-linkers.

Animals↗

PubMed2005

Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics.

The first example of the application of reorientational eigenmode dynamics (RED) to RNA is shown here for the small and floppy Iron Responsive Element (IRE) RNA hairpin. Order parameters calculated for bases and riboses from a 12 ns molecular dynamics trajectory are compared to experimentally determined order parameters from 13C-1H NMR relaxation experiments, and shown to be in qualitative agreement. Given the small size of the IRE hairpin and its very flexible loop, isotropic RED (iRED) was also used to analyze the trajectory in order to describe its dynamic motions. iRED analysis shows that the global and internal dynamics of the IRE are not rigorously separable, which will result in inaccurate experimental order parameters. In addition, the iRED analysis described the many correlated motions that comprise the dynamics of the IRE RNA. The combined use of NMR relaxation, RED, and iRED provide a uniquely detailed description of IRE RNA dynamics.

Magnetic Resonance Spectroscopy↗

PubMed1990

The long range transport of ozone within Europe and its control.

It is widely accepted that the ozone concentrations experienced during photochemical episodes over large areas of Europe may exceed levels at which adverse environmental effects could be expected. These peak ozone concentrations can be reduced by controlling atmospheric emissions of the hydrocarbon and nitrogen oxide precursors. For ozone control to be successful over the spatial scale of Europe, long term international cooperation is required in the formulation of emission abatement strategies. A significant barrier to rapid progress has been the complexity of the processes that describe ozone formation. Highly sophisticated computer models of chemistry and transport have, up to now, been the only means to study the impact of abatement strategies. An alternative approach has been adopted here involving the development of a simplified long range transport model for ozone based on the analysis of over 60 experimental runs of a photochemical trajectory model applied to a wide range of hydrocarbon-nitrogen oxide emission combinations. Using the ozone-precursor relationship obtained, it has been possible to examine various policy options in the European context. Although taken together, three illustrative emission control scenarios reduce NO(x) and hydrocarbon emissions substantially through controls on motor vehicle exhaust, large combustion plant and solvent usage, a significant potential for photochemical ozone formation and long range transport may still remain after their implementation. The extents of precursor emission abatement that will be required, if the potential for ozone formation is to be reduced below published air quality criteria guidelines or critical levels, have been determined for each European country. The implied reductions in NO(x) and hydrocarbons relative to current levels amount to between 50 and 90%.

Journal Article↗

PubMed2005

Coordination of bowing and fingering in violin playing.

Playing string instruments implies motor skills including asymmetrical interlimb coordination. How special is musical skill as compared to other bimanually coordinated, non-musical skillful performances? We succeeded for the first time to measure quantitatively bimanual coordination in violinists playing repeatedly a simple tone sequence. A motion analysis system was used to record finger and bow trajectories for assessing the temporal structure of finger-press, finger-lift (left hand), and bow stroke reversals (right arm). The main results were: (1) fingering consisted of serial and parallel (anticipatory) mechanisms; (2) synchronization between finger and bow actions varied from -12 ms to 60 ms, but these 'errors' were not perceived. The results suggest that (1) bow-finger synchronization varied by about 50 ms from perfect simultaneity, but without impairing auditory perception; (2) the temporal structure depends on a number of combinatorial mechanisms of bowing and fingering. These basic mechanisms were observed in all players, including all amateurs. The successful biomechanical measures of fingering and bowing open a vast practical field of assessing motor skills. Thus, objective assessment of larger groups of string players with varying musical proficiency, or of professional string players developing movement disorders, may be helpful in music education.

Adult↗

PubMed2005

Neurocognitive impairment across the lifespan in schizophrenia: an update.

A literature review and power analysis of longitudinal studies published since 1997 investigating the trajectory of neurocognitive deficits across time in patients with schizophrenia was conducted. Ten studies were identified, evaluating a total of 834 patients with mean ages of 24.0-77.8 years at study entry. Power estimates for the 10 studies ranged widely from 0.26 to 0.99 for a medium effect size of 0.4. Despite wide inter-study differences in cognitive measures selected, sample size and phase of illness studied, several consistent themes emerged. Studies of primarily community-dwelling outpatients with schizophrenia revealed that overall measures of IQ and gross cognitive status do not show deterioration greater than that associated with benign aging. Furthermore, performance on specific measures of neurocognition was remarkably consistent across ages studied. Indeed, there is some evidence that IQ, as well as other neurocognitive measures, may show improvement over a 5-year test-retest interval. Findings were consistent whether patients were in their first episode of illness or chronic. These results support a static "encephalopathy" model of cognitive deficits in schizophrenia. In contrast, studies of middle-aged and elderly institutionalized patients with schizophrenia have revealed markedly different findings. There is evidence in this population of a decline in gross measures of cognitive status even over a brief 2.5-year test-retest interval in patients 65 or older that may, in some cases, be linked to the emergence of orofacial dyskinesia. Taken together, these studies suggest two distinct neurocognitive trajectories during the lifespan in patients with schizophrenia that may represent manifestations of distinct pathophysiological mechanisms of the illness during different phases of the disease.

Adult↗