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Results for “trajectory analysis”

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At least 883 records · Page 49Linked to original sources

PubMed2003

Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore.

To examine the conformational properties in aqueous solution of a 15-residue peptide that is a potential pharmacophore for AIDS vaccine development, molecular dynamics simulations were performed in water starting from structures determined experimentally in three different organic solvents. Convergence characteristics of the simulation are examined in Cartesian and conformational spaces. In addition, novel analysis tools are employed including a multidimensional scaling method to represent the distance between trajectory frames. As these methods are based on a variety of physical parameters, they provide a useful cross-check on the structural convergence. Theoretical two-dimensional (2D) 1H-NMR spectra are also generated. These are superficially quite different in appearance, demonstrating that backbone similarities difficult to identify by visual inspection of 2D NMR data can be revealed using the methods described here.

AIDS Vaccines↗

PubMed2003

Effects of race and poverty on the process and outcome of inpatient rehabilitation services among stroke patients.

BACKGROUND AND PURPOSE: The greater mortality and residual physical impairments among black stroke patients may be attributable to differential utilization of rehabilitation services. This report examines, within an equal-access healthcare system, racial differences in time to initiation of stroke rehabilitation services and in the trajectory of physical function recovery. METHODS: This study was a secondary analysis of data from an inception cohort of 1073 stroke patients hospitalized between April 1995 and March 1997 and followed up for up to 1 year. Inpatient data came from medical record reviews; follow-up data came from telephone interviews at 1, 6, and 12 months after stroke. The study included consecutive acute ischemic or intracerebral hemorrhagic stroke patients from 9 VA medical centers. The main outcome measures were time to initiation of inpatient rehabilitation services and ability to perform activities of daily living. RESULTS: There were no racial differences in receipt of inpatient rehabilitation services (blacks, 76%; whites, 70%) or in the proportion of patients referred within 3 days of admission (blacks, 43.5%; whites, 42.0%). Among patients who experienced delay in initiation of rehabilitation, only low-income blacks experienced worse functional recovery over 12 months. CONCLUSIONS: Low-income black stroke patients who experience delay in initiation of inpatient rehabilitation have a worse trajectory of functional recovery in the first year after stroke. Poverty-associated factors in the postdischarge setting may explain this phenomenon.

Activities of Daily Living↗

PubMed2003

Improved methods for the acquisition and interpretation of NMR metabolomic data.

The high spectral congestion typically observed in one-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectra of tissue extracts and biofluids limits the metabolic information that can be extracted. This study evaluates the application of two-dimensional J-resolved (JRES) spectroscopy for metabolomics, which can provide proton-decoupled projected 1D spectra (p-JRES). This approach is illustrated by an investigation of embryogenesis in Japanese medaka (Oryzias latipes), an established fish model for developmental toxicology. When combined with optimized spectral pre-processing,(2) including a 0.005-ppm bin width for data segmentation and a logarithmic transformation, the reduced congestion in the p-JRES spectra increases the likelihood that a specific metabolite can be accurately integrated and thus increases the extractable information content of the spectra. Principal components analysis of the p-JRES spectra reveals the concept of a developmental trajectory that summarizes the changes in the NMR-visible metabolome throughout medaka embryogenesis. Advantages and potential disadvantages of the p-JRES approach are discussed.

Animals↗

PubMed2003

Effect of fatigue on performance measured by a driving simulator in automobile drivers.

OBJECTIVE: To identify risk factors of performance decrement in automobile drivers. METHODS: 114 drivers (age <30 years, n=57; age > or =30 years, n=57) who stopped at a rest stop area on a freeway were recruited for the study. They filled out a questionnaire on their journey, sleep/wake patterns and performed a 30-min test on a driving simulator. The test evaluates, by computerized analysis, the lateral deviation of a virtual car from an appropriate trajectory on a virtual road. A sex/age matched control group was recruited in the community. Control subjects were studied at the same time of day as the index case driver. Controls had normal sleep wake schedule, absence of long driving and performed the same driving test. RESULTS: Drivers performed significantly worse than controls on the driving test. Age and duration of driving were the main factors associated with decreased performance. CONCLUSION: Our driving simulator can identify fatigue generated by driving but results must be considered in relation with age of subjects.

Adolescent↗

PubMed2006

Transition state of a SH3 domain detected with principle component analysis and a charge-neutralized all-atom protein model.

The src SH3 domain has been known to be a two-state folder near room temperature. However, in a previous study with an all-atom model simulation near room temperature, the transition state of this protein was not successfully detected on a free-energy profile using two axes: the radius of gyration (R(g)) and native contact reproduction ratio (Q value). In this study, we focused on an atom packing effect to characterize the transition state and tried another analysis to detect it. To explore the atom packing effect more efficiently, we introduced a charge-neutralized all-atom model, where all of the atoms in the protein and water molecules were treated explicitly, but their partial atomic charges were set to zero. Ten molecular dynamics simulations were performed starting from the native structure at 300 K, where the simulation length of each run was 90 ns, and the protein unfolded in all runs. The integrated trajectories (10 x 90 = 900 ns) were analyzed by a principal component analysis (PCA) and showed a clear free-energy barrier between folded- and unfolded-state conformational clusters in a conformational space generated by PCA. There were segments that largely deformed when the conformation passed through the free-energy barrier. These segments correlated well with the structural core regions characterized by large phi-values, and the atom-packing changes correlated with the conformational deformations. Interestingly, using the same simulation data, no significant barrier was found in a free-energy profile using the R(g) and Q values for the coordinate axes. These results suggest that the atom packing effect may be one of the most important determinants of the transition state.

Computer Simulation↗

PubMed2005

How does self-assessed health change with age? A study of older adults in Japan.

OBJECTIVE: This research examines how the trajectories of self-rated health evolve among elderly Japanese individuals and how socioeconomic status (SES), social relations, and baseline health differentiate these trajectories. METHODS: Data came from a five-wave panel study of a national sample of 2,200 Japanese old adults between 1987 and 1999. Hierarchical linear models and cluster analysis were employed to depict major patterns of temporal changes in self-rated health. RESULT: Overall perceived health becomes worse, but only slightly, between ages 60 and 85, whereas it appears to improve a little bit after age 85. Underlying the observed age norm are four subtrajectories including constant good health, early onset of perceived health decline, late onset of perceived health decline, and a course of recovery from poor self-assessed health. DISCUSSION: Diverse subjective health trajectories exist in old age, extending well into the 90s. Prior observations of the effects of SES, social relations, and baseline health on health states and transitions can now be extended to trajectories of subjective health. Our analysis of Japanese data provides important benchmarks for comparisons with observations made in other developed nations.

Adaptation, Psychological↗

PubMed2006

Protein folding kinetics and thermodynamics from atomistic simulations.

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.

Computer Simulation↗

PubMed2003

Marital status changes and body weight changes: a US longitudinal analysis.

The role of spouse is associated with better health. The dynamics of spousal roles can be represented by marital trajectories that may remain stable or may change by entry into marriage, dissolution of marriage, or death of a spouse. Body weight is an important health-related characteristic that has been found to have mixed relationships with marital status. This analysis examined changes in marital status and body weight in 9043 adults in the US National Health and Nutrition Epidemiological Follow-up Survey (NHEFS), a longitudinal national study that interviewed and measured adults in a baseline assessment and reassessed them again in a follow-up approximately 10 years later. Men's and women's weights were differently associated with marital changes. Women who were unmarried at baseline and married at follow-up had greater weight change than those who were married at both times. Analysis of weight loss and weight gain separately revealed that sociodemographic variables, including marital change, were more predictive of variation in weight loss than weight gain. Unmarried women who married gained more weight than women married at both times. Men who remained divorced/separated and men who became widowed lost more weight than men married at both baseline and follow-up. These findings suggest that changes in social roles, such as entering or leaving marriage, influence physical characteristics such as body weight.

Adolescent↗

PubMed1995

Fast three dimensional magnetic resonance imaging.

To reduce the scan time in three-dimensional (3D) imaging, the authors consider alternative trajectories for traversing k-space. They differ from traditional 3D trajectories, such as 3DFT, in that they employ time-varying gradients allowing longer readouts and in turn a reduced scan time. Some of these trajectories reduce by an order of magnitude the number of excitations compared with 3DFT and provide flexibility for trading off signal-to-noise ratio for scan time. Other concerns are the minimum echo time and flow/motion properties. As examples, the authors show two applications: A 3D data set of the head (field of view of 30 x 30 x 7.5 cm and resolution of 1.5 x 1.5 x 1.5 mm) acquired in 56 s using a stack of spirals in 3D k-space; and a 3D movie of the heart (20 x 20 x 20 cm field of view, 2 x 2 x 2 mm resolution, and 16 time frames per cardiac cycle) acquired in 11 min using a cones trajectory.

Fourier Analysis↗

PubMed2003

A genetic analysis of axon guidance in the C elegans pharynx.

We wish to understand how the trajectories of the twenty pharyngeal neurons of C. elegans are established. In this study we focused on the two bilateral M2 pharyngeal motorneurons, which each have their cell body located in the posterior bulb and send one axon through the isthmus and into the metacorpus. We used a GFP reporter to visualize these neurons in cell-autonomous and cell-non-autonomous axon guidance mutant backgrounds, as well as other mutant classes. Our main findings are: 1). Mutants with impaired growth cone functions, such as unc-6, unc-51, unc-73 and sax-3, often exhibit abnormal terminations and inappropriate trajectories at the distal ends of the M2 axons, i.e. within the metacorpus; and 2). Growth cone function mutants never exhibit abnormalities in the proximal part of the M2 neuron trajectories, i.e. between the cell body and the metacorpus. Our results suggest that the proximal and distal trajectories are established using distinct mechanisms, including a growth cone-independent process to establish the proximal trajectory. We isolated five novel mutants in a screen for worms exhibiting abnormal morphology of the M2 neurons. These mutants define a new gene class designated mnm (M neuron morphology abnormal).

Animals↗

PubMed1990

Reliability of trajectory identification for cosmic heavy ions and cytogenetic effects of their passage through plant seeds.

The potentially specific importance of the study of heavy ions from galactic cosmic rays for the understanding of radiation protection in manned spaceflight continues to stimulate spaceflight experiments in order to investigate the radiobiological properties of these ions. Chromosome aberrations as an expression of a direct assault on the genome are of particular interest in view of carcinogenesis as the primary radiation risk for man in space. An essential technical ingredient of such spaceflight experiments is the visual nuclear track detector which permits identification of those biological test organisms which have been affected by cosmic heavy ions. We describe such a technique and report on an analysis of the qualitative and quantitative reliability of this identification of particle trajectories in layers of biological test organisms. The incidence of chromosome aberrations in cells of lettuce seeds, Lactuca sativa, exposed during the Kosmos 1887 mission, was determined for seeds hit by cosmic heavy ions. In those seeds the incidence of both single and multiple chromosome aberrations was enhanced.

Chromosome Aberrations↗

PubMed2000

Consequences of scattering for spectral imaging of turbid biologic tissue.

Spectral imaging permits two-dimensional mapping of the backscattering properties of biological systems. Such mapping requires broadband illumination of the entire area of interest. However, imaging of turbid biological media under these conditions often involves mean photon path lengths that exceed the pixel size. Using a numerical Monte Carlo model, we have studied the effects of photon scattering in a hemoglobin-bearing model system. We find that photon migration and the resulting wavelength-dependent optical coupling between pixels can complicate the analysis of imaging spectroscopy data. In fact, the wavelength dependence of photon trajectories also alters the distribution of photon exit angles at the tissue surface. We therefore find that the finite optical field of view of an imaging spectrometer can affect the measured spectra in the absence of chromatic aberrations.

Hemoglobins↗

PubMed1996

Differential influence of the visual framework on end point accuracy and trajectory specification of arm movements.

In this study the influence of visual scene on both arm end point accuracy and spatial path kinematics was evaluated. Eight subjects, immersed in a virtual environment, were required to point to one of ten targets located at two distances and in five directions. Targets were presented in frameworks of different complexity. The simplest framework was constituted by a uniform background, the most complex framework was constituted by a perspective-arranged grid. In the other two conditions it consisted of lines having a direction parallel to either the subject's sagittal or frontal body axis. Movements were executed without vision of both target and framework. The results showed that pointing movements were hypometric in all conditions. No difference in end point localization was observed between movements executed after presentation of the simplest and the most complex scenes. However, hypometria significantly increased when the scene was formed by lines parallel to the subject's sagittal axis. Visual information on the scene was also used to specify hand path parameters. Trajectory curvature increased with decreasing complexity of the framework. Correspondingly, the pointing kinematics varied. Taken together, these results suggest that visual analysis of cues surrounding the target can influence both target localisation and hand path planning. However, scene complexity is directly related only to determining trajectory curvature. We conclude that planning an arm movement consists of at least two processes: target localisation and hand path specification. Environmental visual cues forming the scene are taken into account differently during the two processes.

Adult↗

PubMed1981

New methods for analysis of vision in the gerbil.

The visual behavior of gerbils has been studied by adapting natural behaviors such as food pursuit, aperture detection, barrier negotiation and ladder climbing. Methods are described for measuring detection and discrimination thresholds using visual orienting tasks. Furthermore, studies of size-distance constancy, anticipation of a moving target's trajectory, and optimal planning of barrier detours show the usefulness of film records for quantitative analysis of complex perceptual abilities. Finally, preliminary studies of gerbils following ablation of primary visual cortex indicate that some visuomotor abilities are cortically dependent.

Animals↗

PubMed2004

Model driven quantification of individual and collective cell migration.

While the control of cell migration by biochemical and biophysical factors is largely documented, a precise quantification of cell migration parameters in different experimental contexts is still questionable. Indeed, these phenomenological parameters can be evaluated from data obtained either at the cell population level or at the individual cell level. However, the range within which both characterizations of cell migration are equivalent remains unclear. We analyse here to which extent both sources of data could be integrated within a unified description of cell migration by considering the motility of the endothelial cell line EAhy926. Using time-lapse video-microscopy and associated analysis of digital image time series, we quantified EAhy926 random motility coefficient, migration speed and trajectory persistence time in two different migration assays: the in vitro wound healing assay, and the cell-populated agarose drop assay. In order to analyse the agreement between independent quantifications of cell motility based either on individual cell analysis or cell population dynamic analysis, a theoretical multi-agents cellular model was developed and discussed as a possible theoretical framework able to unify these multi-scale data. Model simulations especially reveal the potential bias induced by cell proliferation and cell-cell adhesion when cell migration parameters are estimated from the extensively used in vitro wound healing assay.

Cell Line↗

PubMed1997

Chemotaxis of Amoeba proteus in the developing pH gradient within a pocket-like chamber studied with the computer assisted method.

A new "U" shaped, pocket-like chamber was used to observe the chemotactic responses of individual cells. This method permits monitoring of both the development of the concentration gradient of a tested substance and cell locomotion. We investigated the chemotactic responses of Amoeba proteus and observed that the amoebae moved in positively and negatively developing [H+] gradients towards the solution of lower pH in a pH range 5.75-7.75. The chemotactic response of amoebae to [H+] gradients required the presence of extracellular calcium ions. It was blocked and random locomotion was restored by the replacement of calcium with magnesium in the cell medium. Time-lapse video recording and data processing were accomplished with computer-assisted methods. This made it possible to compare selected methods of data presentation and analysis for cells locomoting in isotropic and anisotropic conditions. The cell trajectories were determined and displayed in circular diagrams, lengths of cell tracks and final cell displacements were estimated and a few parameters characterizing cell locomotion were computed.

Amoeba↗

PubMed1999

Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.

Hyperthermophilic proteins often possess an increased number of surface salt bridges compared with their mesophilic homologues. However, salt bridges are generally thought to be of minor importance in protein stability at room temperature. In an effort to understand why this may no longer be true at elevated temperatures, we performed molecular dynamics simulations of the hyperthermophilic protein Sac7d at 300 K, 360 K, and 550 K. The three trajectories are stable on the nanosecond timescale, as evidenced by the analysis of several time-resolved properties. The simulations at 300 K and (to a lesser extent) 360 K are also compatible with nuclear Overhauser effect-derived distances. Raising the temperature from 300 K to 360 K results in a less favourable protein-solvent interaction energy, and a more favourable intraprotein interaction energy. Both effects are almost exclusively electrostatic in nature and dominated by contributions due to charged side-chains. The reduced solvation is due to a loss of spatial and orientational structure of water around charged side-chains, which is a consequence of the increased thermal motion in the solvent. The favourable change in the intraprotein Coulombic interaction energy is essentially due to the tightening of salt bridges. Assuming that charged side-chains are on average more distant from one another in the unfolded state than in the folded state, it follows that salt bridges may contribute to protein stability at elevated temperatures because (i) the solvation free energy of charged side-chains is more adversely affected in the unfolded state than in the folded state by an increase in temperature, and (ii) due to the tightening of salt bridges, unfolding implies a larger unfavourable increase in the intraprotein Coulombic energy at higher temperature. Possible causes for the unexpected stability of the protein at 550 K are also discussed.

Archaeal Proteins↗

PubMed1990

Dynamic transitions in stance support accompanying leg flexion movements in man.

The control processes underlying dynamic transitions in stance support during single leg flexion movements were investigated in human subjects as a function of the intended speed of movement, by examining the vertical and lateral horizontal components of the ground reaction forces, the frontal plane trajectory of the body center of mass (CM) recorded via motion analysis, and the electromyographic (EMG) recordings of selected lower limb muscles. For the slowest movements, the measured vertical force beneath the flexing and single stance limbs closely matched the vertical force-time history predicted by a quasi-static mechanical model, whereas, the more rapid natural and fast speeds showed progressively larger discrepancies between measured and predicted forces. The initial resultant horizontal force component was exerted in the flexing to stance limb direction but was proportionately greater (4:1) beneath the flexing versus the stance limb during fast and natural speeds, and became equivalent for slow movements. Speed related EMG differences included an early phasic recruitment of the lateral hip muscle of the flexing limb which always preceded the ground reaction force changes for fast and natural but not slow movements, and a considerably earlier onset of the stance leg knee extensor relative to the flexing limb knee flexor for slow versus fast and natural speeds. Overall, the findings suggested two different speed related strategies for linking the postural and intentional movement components, where the choice of the strategy selected appeared to reflect the mechanical requirements needed to overcome the inertial force of the body mass during transitions from bipedal to single limb stance support.

Adult↗