PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “trajectory analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed2004

Analysis of longitudinal studies with death and drop-out: a case study.

The analysis of longitudinal data has recently been an active area of biostatistical research. Two main approaches to analysis have emerged, the first concentrating on modelling evolution of marginal distributions of the main response variable of interest and the other on subject-specific trajectories. In epidemiology the analysis is usually complicated by missing data and by death of study participants. Motivated by a study of cognitive decline in the elderly, this paper argues that these two types of incomplete follow-up may need to be treated differently in the analysis, and proposes an extension to the marginal modelling approach. The problem of informative drop-out is also discussed. The methods are implemented in the 'Stata' statistical package.

Age Factors↗
PubMed1998

Hydrogen bonding in helical polypeptides from molecular dynamics simulations and amide hydrogen exchange analysis: alamethicin and melittin in methanol.

Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ray crystal coordinates of alamethicin as a starting structure (1 ns). The hydrogen bond patterns and stabilities were characterized by analysis of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and stabilities previously determined from high-resolution NMR structural analysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bond pattern with a high level of 3(10) hydrogen bonding involving the amide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds stabilizing amide NH's of residues C-terminal to P2 and P14 were previously proposed to explain their high amide exchange stabilities. The absence, or low levels of 3(10) hydrogen bonds at the N-terminus or for A15 NH, respectively, in the melittin simulations, is also consistent with interpretations from amide exchange analysis. Perturbation of helical hydrogen bonding in the residues before P14 (Aib10-P14, alamethicin; T11-P14, melittin) was characterized in both peptides by variable hydrogen bond patterns that included pi and gamma hydrogen bonds. The general agreement in hydrogen bond patterns determined in the simulations and from spectroscopic analysis indicates that with suitable conditions (including solvent composition and counterions where required), local hydrogen-bonded secondary structure in helical peptides may be predicted from dynamics simulations from alpha-helical starting structures. Each peptide, particularly alamethicin, underwent some large amplitude structural fluctuations in which several hydrogen bonds were cooperatively broken. The recovery of the persistent hydrogen bonding patterns after these fluctuations demonstrates the stability of intramolecular hydrogen-bonded secondary structure in methanol (consistent with spectroscopic observations), and is promising for simulations on extended timescales to characterize the nature of the backbone fluctuations that underlie amide exchange from isolated helical polypeptides.

Alamethicin↗
PubMed2003

Effects of speaking rate on second formant trajectories of selected vocalic nuclei.

The effect of speaking rate variations on second formant (F2) trajectories was investigated for a continuum of rates. F2 trajectories for the schwa preceding a voiced bilabial stop, and one of three target vocalic nuclei following the stop, were generated for utterances of the form "Put a bV here, where V was /i/,/ae/ or /oI/. Discrete spectral measures at the vowel-consonant and consonant-vowel interfaces, as well as vowel target values, were examined as potential parameters of rate variation; several different whole-trajectory analyses were also explored. Results suggested that a discrete measure at the vowel consonant (schwa-consonant) interface, the F2off value, was in many cases a good index of rate variation, provided the rates were not unusually slow (vowel durations less than 200 ms). The relationship of the spectral measure at the consonant-vowel interface, F2 onset, as well as that of the "target" for this vowel, was less clearly related to rate variation. Whole-trajectory analyses indicated that the rate effect cannot be captured by linear compressions and expansions of some prototype trajectory. Moreover, the effect of rate manipulation on formant trajectories interacts with speaker and vocalic nucleus type, making it difficult to specify general rules for these effects. However, there is evidence that a small number of speaker strategies may emerge from a careful qualitative and quantitative analysis of whole formant trajectories. Results are discussed in terms of models of speech production and a group of speech disorders that is usually associated with anomalies of speaking rate, and hence of formant frequency trajectories.

Adult↗
PubMed1999

Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations.

A method for constructing the suitable initial configuration of the membrane-protein system for molecular dynamics (MD) simulations is presented. This method could provide some hydrated initial configurations and help us to determine the best surface area of the system by contracting the surface area and comparing the optimized lowest energy of the system by energy minimization. The gramicidin A (GA) channel in;the fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer was used as our model. Three configurations with different surface areas were selected and applied for one 400 ps and two 300 ps MD simulations at constant pressure and temperature. All simulations were fairly stable without any constraints. Through analysis of the MD trajectories we found that the system with the best surface area was more stable than the other two systems, whose sizes were changed in the simulations. Further analysis of the bilayer normal length and the order parameters of the lipid alkyl tails indicates that the system with the best surface area shows some characteristics of the L(alpha) phase, while both the smaller and the larger size systems have distinct deviations from the L(alpha) phase that we expect. This illustrates that the correct surface area and the suitable initial configuration have an important influence on the phase of the membrane in the MD simulation. In addition, by comparing the root mean square differences of GA relative to the initial structure and interaction energy between different components of the system for all three systems, we find that the state of the DMPC bilayer has exerted a significant influence on the structure of GA. All these results demonstrate the validity of our method for constructing the initial configuration of the membrane-protein system for MD simulations.

Carbon↗
PubMed2006

Automatic microelectrode recording analysis and visualization of the globus pallidus interna and stereotactic trajectory.

Locating deep brain neuronal structures is required to accurately place deep brain stimulation (DBS) electrodes during stereotactic surgery in patients with Parkinson's disease and other movement disorders. This study investigates the efficacy of automatic microelectrode visualization and analysis methods to help neurosurgeons locate target structures more objectively, consistently, and easily during surgery. Ten patients (4 males and 6 females) who underwent bilateral implantation of DBS electrodes in the globus pallidus interna (Gpi), from 2001 to 2003, at the Oregon Health and Science University and the Portland Veterans Administration Medical Center were included. We compared the efficacy of the microelectrode recording signal energy, power spectral density (PSD), marginal probability density (mPDF), autocorrelation function (ACF), and partial ACF. mPDF and PSD estimates most accurately indicated the borders of the GPi target structure.

Aged↗
PubMed1999

Hydration effects on the electrostatic potential around tuftsin.

The electrostatic potential and component dielectric constants from molecular dynamics (MD) trajectories of tuftsin, a tetrapeptide with the amino acid sequence Thr-Lys-Pro-Arg in water and in saline solution are presented. The results obtained from the analysis of the MD trajectories for the total electrostatic potential at points on a grid using the Ewald technique are compared with the solution to the Poisson-Boltzmann (PB) equation. The latter was solved using several sets of dielectric constant parameters. The effects of structural averaging on the PB results were also considered. Solute conformational mobility in simulations gives rise to an electrostatic potential map around the solute dominated by the solute monopole (or lowest order multipole). The detailed spatial variation of the electrostatic potential on the molecular surface brought about by the compounded effects of the distribution of water and ions close to the peptide, solvent mobility, and solute conformational mobility are not qualitatively reproducible from a reparametrization of the input solute and solvent dielectric constants to the PB equation for a single structure or for structurally averaged PB calculations. Nevertheless, by fitting the PB to the MD electrostatic potential surfaces with the dielectric constants as fitting parameters, we found that the values that give the best fit are the values calculated from the MD trajectories. Implications of using such field calculations on the design of tuftsin peptide analogues are discussed.

Computer Simulation↗
PubMed2005

Effects of polychlorinated biphenyls on the schooling behavior of Japanese medaka (Oryzias latipes).

The effects of polychlorinated biphenyls (PCBs; Kanechlor 400) on the schooling behavior of Japanese medaka (Oryzias latipes) were tested after feeding with various concentrations of PCBs (0, 1, 5, 25, and 125 microg/g). To test schooling, three PCB-exposed medaka and three untreated fish were placed in one chamber, and their swimming trajectories were recorded. Swimming velocity, turning angle, and nearest-neighbor distance (NND) were analyzed individually, and the polarization and expanse of each schooling group were analyzed. Fractal dimension analysis was performed for trajectory, swimming velocity, and turning angle. Six behaviors (school formed by six swimming medaka, school formed by six stationary medaka, school formed by three to five swimming medaka, school formed by three to five stationary medaka, swimming without schooling, and stationary without schooling) were quantified with time. Behavioral parameters were the same for PCB-exposed and unexposed medaka in the same schooling group. Swimming velocity decreased in a dose-dependent manner, and NND in the group exposed to 25 microg/g of PCBs was significantly longer (126%) than that in the controls. The fractal dimensions of trajectory and turning angle increased significantly in the highest PCB-exposure group, indicating that schools containing PCB-exposed individuals frequently changed direction. The PCBs shortened the time of school formed by six swimming fish, which was 23.7% of the control value in the group exposed to 25 microg/g of PCBs. The frequency of collisions between individuals was significantly greater in the highest-exposure group (31.3) than in the controls (13.3). Thus, PCB exposure influences the behavior of unexposed fish in the same school, consequently affecting schooling behavior.

Animals↗
PubMed1997

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme.

Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations. For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by modes of motion external to the domains. To analyze the molecular dynamics trajectory, a principal component analysis tailored specifically to analyze interdomain motions is applied. A method based on the curl of the atomic displacements is described, which yields a sharp discrimination of domains, and which defines a unique interdomain screw-axis. Hinge axes are defined and classified as twist or closure axes depending on their direction. The methods have been tested on lysozyme. A remarkable correspondence was found between the first normal mode axis and the first principal mode axis, with both axes passing within 3 A of the alpha-carbon atoms of residues 2, 39, and 56 of human lysozyme, and near the interdomain helix. The axes of the first modes are overwhelmingly closure axes. A lesser degree of correspondence is found for the second modes, but in both cases they are more twist axes than closure axes. Both analyses reveal that the interdomain connections allow only these two degrees of freedom, one more than provided by a pure mechanical hinge.

Animals↗
PubMed2006

Imaging of dynamic secretory vesicles in living pollen tubes of Picea meyeri using evanescent wave microscopy.

Evanescent wave excitation was used to visualize individual, FM4-64-labeled secretory vesicles in an optical slice proximal to the plasma membrane of Picea meyeri pollen tubes. A standard upright microscope was modified to accommodate the optics used to direct a laser beam at a variable angle. Under evanescent wave microscopy or total internal reflection fluorescence microscopy, fluorophores localized near the surface were excited with evanescent waves, which decay exponentially with distance from the interface. Evanescent waves with penetration depths of 60 to 400 nm were generated by varying the angle of incidence of the laser beam. Kinetic analysis of vesicle trafficking was made through an approximately 300-nm optical section beneath the plasma membrane using time-lapse evanescent wave imaging of individual fluorescently labeled vesicles. Two-dimensional trajectories of individual vesicles were obtained from the resulting time-resolved image stacks and were used to characterize the vesicles in terms of their average fluorescence and mobility, expressed here as the two-dimensional diffusion coefficient D2. The velocity and direction of vesicle motions, frame-to-frame displacement, and vesicle trajectories were also calculated. Analysis of individual vesicles revealed for the first time, to our knowledge, that two types of motion are present, and that vesicles in living pollen tubes exhibit complicated behaviors and oscillations that differ from the simple Brownian motion reported in previous investigations. Furthermore, disruption of the actin cytoskeleton had a much more pronounced effect on vesicle mobility than did disruption of the microtubules, suggesting that actin cytoskeleton plays a primary role in vesicle mobility.

Actin Cytoskeleton↗
PubMed1999

Molecular dynamics study of kaliotoxin in water.

Kaliotoxin (KTX), a potassium channel blocker found in the venom of the scorpion Androctonous Mauretanicus is a 38 residue polypeptide with a well defined structure consisting of a alpha-helix and a three strand antiparallel beta-sheet interconnected by three disulfide bonds. Although the 3D structure has been determined by NMR, there is a number of features, mainly concerning the conformation and flexibility of the side chains, but also the long range order in the peptide and its fluctuations, that may have escaped the experimental study. These questions are now being addressed using molecular dynamics (MD) simulations. Accordingly, the present work reports the analysis of a 430 ps molecular dynamics trajectory of the polypeptide soaked with 4700 TIP3 water molecules inside a 56 A box. MD calculations were performed with periodic boundary conditions. Analysis of the conformational space sampled by each of the residues along the trajectory, suggests a special behavior of Pro17 and Lys19 both located on the helix. Furthermore, analysis of the relative movements of the secondary structure elements indicates that the alpha-helix and beta-sheets fluctuate in a correlated motion, preserving the tertiary structure of the polypeptide along the trajectory. Finally, analysis of the charge distribution was also examined. The direction of the dipole moment, computed from the center of masses appears to be an interesting feature of the structure probably related to the biological function of the molecule.

Computer Simulation↗
PubMed2005

Exploratory study of the electron-density relocalization process in benzene through a time-dependent topological analysis.

A time-dependent topological analysis of the electron density in benzene provides quantitative information about charge oscillation processes, and particularly about the two highest pi orbitals contributions to carbon topological basins. In this exploratory study coupling one molecular-dynamic trajectory to a topological analysis, Fourier transform of the topological time data autocorrelation functions indicates frequencies of oscillations, and shows that carbon atoms, though identical in average, would be more or less highest occupied molecular-orbital reactive with a cyclic behavior.

Journal Article↗
PubMed2004

Simulation of ultrashort electron pulse generation from optical injection into wake-field plasma waves.

A laser-plasma-based source of relativistic electrons is described in detail, and analyzed in two dimensions using theoretical and numeric techniques. Two laser beams are focused in a plasma, one exciting a wake-field electron plasma wave while another locally alters some electron trajectories in such a way that they can be trapped and accelerated by the wave. Previous analyses dealt only with one-dimensional models. In this paper two-dimensional particle-in-cell simulations and analysis of single particle trajectories show that the radial wake field plays an important role. The simulation results are interpreted to evaluate the accelerated electron beam's properties and compared with existing devices.

Journal Article↗
PubMed2006

Ischemic and nephrotoxic acute renal failure are distinguished by their broad transcriptomic responses.

Acute renal failure (ARF) has a high morbidity and mortality. In animal ARF models, effective treatments must be administered before or shortly after the insult, limiting their clinical potential. We used microarrays to identify early biomarkers that distinguish ischemic from nephrotoxic ARF or biomarkers that detect both injury types. We compared rat kidney transcriptomes at 2 and 8 h after ischemia/reperfusion and after mercuric chloride. Quality control and statistical analyses were necessary to normalize microarrays from different lots, eliminate outliers, and exclude unaltered genes. Principal component analysis revealed distinct ischemic and nephrotoxic trajectories and clear array groupings. Therefore, we used supervised analysis, t-tests, and fold changes to compile gene lists for each group, exclusive or nonexclusive, alone or in combination. There was little network connectivity, even in the largest group. Some microarray-identified genes were validated by TaqMan assay, ruling out artifacts. Western blotting confirmed that heme oxygenase-1 (HO-1) and activating transcription factor-3 (ATF3) proteins were upregulated; however, unexpectedly, their localization changed within the kidney. HO-1 staining shifted from cortical (early) to outer stripe of the outer medulla (late), primarily in detaching cells, after mercuric chloride but not ischemia/reperfusion. ATF3 staining was similar, but with additional early transient expression in the outer stripe after ischemia/reperfusion. We conclude that microarray-identified genes must be evaluated not only for protein levels but also for anatomical distribution among different zones, nephron segments, or cell types. Although protein detection reagents are limited, microarray data lay a rich foundation to explore biomarkers, therapeutics, and the pathophysiology of ARF.

Activating Transcription Factor 3↗
PubMed2006

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation.

The structure and molecular packing density of a "mismatched" solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data on comparable systems. The local density or molecular packing in DMPC-hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested a positive volume change, DeltaV(m), of 4 cm(3) mol(-1) hexanol partitioned at 310 K in good accordance with experimental values. Analysis of the apparent volumes of each component in the pure and mixed states further showed that DeltaV(m) reflects a balance between a substantial increase in the packing density of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8) is stretched by about 4%. Concomitantly, the average lateral area per chain decreases and these two effects compensate so that the overall packing density in the outer region, where the hexanol molecules are located, remains practically constant. The core of the bilayer (C9-C13) is slightly thinned. The average lateral area per chain in this region expands, resulting in a looser packing density. The net effect in the core is a 2-3% decrease in density corresponding to a total volume increase of approximately 14 cm(3) mol(-1) hexanol partitioned.

Computer Simulation↗
PubMed2004

Trajectories of depressive symptoms among high risk African-American adolescents.

PURPOSE: To examine the trajectories of depressive symptoms among African-American youth and the psychosocial factors associated with these trajectories. METHODS: The sample included 579 African-American adolescents who were at risk of dropping out of school, interviewed annually starting from ninth grade for 4 years. The measures included depressive symptoms, anxiety symptoms, self-esteem, stress, and active coping; all self-reported. We used cluster analysis to develop longitudinal trajectories of depression in our sample. RESULTS: Four different trajectories of depressive symptoms were found that represented the changes in depressive symptoms among the participants. These trajectories are: consistently high (15.9%), consistently low (21.1%), decreasing (41.8%), and increasing (21.2%) depressive symptoms. The results from the comparisons of the trajectories indicated that adolescents who presented consistently high levels of depressive symptoms were more likely to be female, reported more anxiety symptoms, lower self-esteem, higher stress, and lower grade point average (GPA) compared with adolescent members of the other trajectories. DISCUSSION: Depressive symptoms may be manifested in different ways according to the patterns of change. Different correlates are associated with these trajectories of depressive symptoms and provide insights about the antecedents and consequences of the patterns of change in depressive symptoms.

Adaptation, Psychological↗
PubMed2005

Determination of photophysical parameters from photon arrival time trajectories in single molecule fluorescence spectroscopy.

Triplet blinking is a phenomenon observed commonly in single molecule fluorescence spectroscopy. At high to moderate excitation intensities one can distinguish bright (on) and dark (off) periods in the fluorescence intensity trajectory caused by sojourns into the nonemissive triplet state. In this work, we focus on triplet blinking of an immobilized molecule in the low excitation regime, where a threshold between on and off intensity levels cannot be set, and, therefore, a standard on/off analysis of fluorescence intensity trajectories is not possible. In the low excitation regime triplet blinking parameters can be recovered from photon arrival time trajectories, i.e., records of individual photon arrival time. We use computer-generated data to compare the recovery of the triplet blinking parameters from the intensity correlation function (ICF) and the histogram of interarrival time. We have found that the ICF offers a better statistics for the recovery of the triplet blinking parameters.

Journal Article↗