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Results for “trajectory analysis”

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At least 253 records · Page 14Linked to original sources

PubMed2006

Design and analysis of a practical 3D cones trajectory.

The 3D Cones k-space trajectory has many desirable properties for rapid and ultra-short echo time magnetic resonance imaging. An algorithm is presented that generates the 3D Cones gradient waveforms given a desired field of view and resolution. The algorithm enables a favorable trade-off between increases in readout time and decreases in the total number of required readouts. The resulting trajectory is very signal-to-noise ratio (SNR) efficient and has excellent aliasing properties. A rapid high-resolution ultra-short echo time imaging sequence is used to compare the 3D Cones trajectory to 3D projection reconstruction (3DPR) sampling schemes. For equivalent scan times, the 3D Cones trajectory has better SNR performance and fewer aliasing artifacts as compared to the 3DPR trajectory.

Algorithms↗

PubMed2006

Automatic analysis and visualization of microelectrode recording trajectories to the subthalamic nucleus: preliminary results.

Although microelectrode recordings (MER) are commonly used to confirm stereotactic targets during surgery for movement disorders, there is no consensus on whether the additional risks and cost of MER are worth the benefits. This may be due, in part, to the inconsistency and inefficiency of subjective interpretation of MER data that is currently used in practice. We describe several fully automatic visualization methods for MER that efficiently and clearly indicate segments of the microelectrode trajectories with homogeneous neural activity that correspond to expected deep brain nuclei. Specifically we demonstrate that these visualization methods can help identify the subthalamic nucleus in Parkinson's disease patients. These methods have the potential to significantly improve patient outcome by helping neurosurgeons objectively identify target structures more quickly and accurately.

Aged↗

PubMed2006

Proteomic trajectory mapping of biological transformation: Application to developmental mouse retina.

In this report we introduce a new concept "proteomic trajectory mapping" for the investigation of a complex phenomenon underlying biological transformation and transition. We define proteomic trajectory to be the kinetic trace of protein expression and present a successful proteomic trajectory mapping of complex molecular events underlying postnatal development of mouse retina. Cluster analysis of the trajectory data using a two-state model identified four proteomic trajectory types: two distinct trajectory types accounting for the decline or the rise of protein molecules actively expressed in the juvenile stage (J-type) or in the adult stage (A-type), a class of transient trajectories that mediate the transformation from the juvenile to the adult stage (T-type), and the steady trajectories throughout the entire process of transformation (C-type). The dominance of particular protein categories expressed in each trajectory characterizes the stage of retinal development. Proteomic trajectory mapping will be a powerful tool to study the systematic changes of protein expression caused by physiological, genetic, or pathological agents and the reverse of such changes to the norm by a treatment. The proteomic trajectory mapping is applicable to any biological transformation and, therefore, will be a powerful tool in biomedical sciences.

Animals↗

PubMed2001

Characteristics of cursor trajectories controlled by the computer mouse.

An analysis of computer screen cursor trajectories can provide insights into the factors limiting efficient cursor positioning and can assist in the design of human-computer interfaces. Cursor locations as controlled by a Microsoft computer mouse with standard settings were therefore sampled at 5 ms intervals and kinematic analyses addressed the proportions of time spent in the initiation, accelerative and terminal guidance phases of cursor positioning. Twelve participants used a computer mouse to move a cursor over different distances (7.5 cm, 15 cm) from a home location in the lower centre of the screen to targets of different diameters (8 mm, 16 mm), situated to the left, middle or right of the computer screen. Cursor trajectories were irregular, and participants regularly overshot their targets, spending 70% of movement duration in terminal guidance. Participants appeared to use the initial part of their movement to establish mappings between controller and display. Interventions should seek to reduce the terminal guidance phase of cursor positioning.

Adult↗

PubMed2006

Software news and updates. Carma: a molecular dynamics analysis program.

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available.

Computer Simulation↗

PubMed2005

Measurement of masticatory movement by a new jaw tracking system using a home digital camcorder.

The aim of this study was to confirm the precision of our simple and inexpensive jaw tracking system which combined the use of a digital camcorder and a motion capture software developed lately. A marker was attached to the mandibular incisors of the subject, and a mirror was assembled beside the subject's face to detect antero-posterior movement during chewing. Jaw movements, including the mirror images, were recorded by a digital camcorder. The movements were traced by a motion capture software and translated into 3D data using original handmade software. To confirm the beneficial performance of our system in measuring masticatory movement, the masticatory movements of five subjects were simultaneously recorded together with a conventional jaw tracking system. Trajectories obtained from both systems were similar, and the correlation coefficient values by simple regression analysis between both trajectories were 0.9 or higher for all subjects. It was confirmed that our system could record masticatory movement with sufficient precision equivalent to that of a conventional jaw tracking system.

Adult↗

PubMed1989

Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2.

A novel method for analysing molecular dynamics trajectories has been developed, which filters out high frequencies using digital signal processing techniques and facilitates focusing on the low-frequency collective motions of proteins. These motions involve low energy slow motions, which lead to important biological phenomena such as domain closure and allosteric effects in enzymes. The filtering method treats each of the atomic trajectories obtained from the molecular dynamics simulation as a "signal". The trajectories of each of the atoms in the system (or any subset of interest) are Fourier transformed to the frequency domain, a filtering function is applied and then an inverse transformation back to the time domain yields the filtered trajectory. The filtering method has been used to study the dynamics of the enzyme phospholipase A2. In the filtered trajectory, all the high frequency bond and valence angle vibrations were eliminated, leaving only low-frequency motion, mainly fluctuations in torsions and conformational transitions. Analysis of this trajectory revealed interesting motions of the protein, including concerted movements of helices, and changes in shape of the active site cavity. Unlike normal mode analysis, which has been used to study the motion of proteins, this method does not require converged minimizations or diagonalization of a matrix of second derivatives. In addition, anharmonicity, multiple minima and conformational transitions are treated explicitly. Thus, the filtering method avoids most of the approximations implicit in other investigations of the dynamic behaviour of large systems.

Binding Sites↗

PubMedDate not supplied

[Dynamics and variability of early morphogenesis in the loach according to observations of individual developmental trajectories].

The dynamics and variability of quantitative morphological characters (morphological variables), which undergo changes upon epiboly, were studied by means of vital observations and measurements of developing loach (Misgurnus fossilis L.) embryos within equal time intervals. None of morphological variables, which characterize the dynamics of blastoderm shape, had monotonous dependence on time. In each individual embryo, the intervals of changes in morphological variables in the "normal" direction corresponding to the change of their mean values during the normal course of epiboly alternated with arrests, as well as with the changes of morphological variables in the reverse direction. The dynamics of morphological variables in time, which reflect the sequence of morphological states of the same embryo, and those of individual variations (variations of morphological states of different embryos on the same temporal section) had identical structure. This suggests instability of individual trajectories of morphogenesis or, strictly speaking, their actual absence. It was shown for the first time on the basis of analysis of individual trajectories of morphogenesis that its dynamics corresponded to so-called "determined chaos", which was previously discussed only as a theoretical possibility. The data obtained suggest that upon approach to the equatorial area of the embryo, the blastoderm marginal zone was elongated in the longitudinal direction and contracted across the axis of its movement. As a result, a positive feedback arises between the cooperated cell movement and the change of shape of the surface, over which the cells move. This leads, due to unstable radial symmetry of this movement, to the formation of embryonic shield.

Animals↗

PubMed1995

Definition of the optimal criteria for identifying hyperactivated human spermatozoa at 25 Hz using in-vitro fertilization as a functional end-point.

Spermatozoa from fertile donors were used to select and validate criteria for the automated classification of hyperactivated (HA) motility using a computer-aided sperm analysis (CASA) system operating at 25 Hz. In the first phase of this analysis, 710 sperm trajectories were analysed and classified as forward progressive (FP), transition phase (TP) or HA. These tracks were then subjected to a CASA analysis and the various attributes of sperm movement defined for each category of motion. From this analysis, criteria were identified and subsequently validated that permitted the automated selection of FP, TP+HA and HA cells, with > 90% accuracy. To determine which attributes of movement best predicted the fertilizing potential of human spermatozoa, a detailed analysis of sperm motion was undertaken in patients undergoing in-vitro fertilization therapy. This analysis indicated that the single most important aspect of sperm movement was the incidence of HA motility (defined as curvilinear velocity > 90 microns/s, linearity < 20%, dancemean [amplitude of lateral head displacement/linearity x 100] > 45.8 microns) after 3 h of incubation. Using the latter criterion as the first incorporated variable, multiple regression equations were created that explained up to 50% of the variance in fertilization rates. None of the other patterns of motion (FP, TP, TP+HA) was correlated with fertilization rates, and none of the other published algorithms for identifying HA cells were as efficient as those described here.

Cohort Studies↗

PubMed2023

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.

Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .

Humans↗

PubMed2005

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Algorithms↗

PubMed2006

Determinants of offline processing of visual information for the control of reaching movements.

The authors investigated the use of visual feedback as a form of knowledge of results (KR) for the control of rapid (200-250 ms) reaching movements in 40 participants. They compared endpoint accuracy and intraindividual variability of a full-vision group (FV) with those of no-vision groups provided with KR regarding (a) the endpoint in numerical form, (b) the endpoint in visual form, or (c) the endpoint and the trajectory in visual form (DEL). The FV group was more accurate and less variable than were the no-vision groups, and the analysis of limb trajectory variability indicated that their superior performance resulted primarily from better movement planning rather than from online visual processes. The FV group outperformed the DEL group even though both groups were obtaining the same amount of spatial visual information from every movement. That finding suggests that the effectiveness with which visual feedback is processed offline is not a simple function of the amount of visual information available, but depends on how that information is presented.

Adult↗

PubMed2006

Echolocating bats use a nearly time-optimal strategy to intercept prey.

Acquisition of food in many animal species depends on the pursuit and capture of moving prey. Among modern humans, the pursuit and interception of moving targets plays a central role in a variety of sports, such as tennis, football, Frisbee, and baseball. Studies of target pursuit in animals, ranging from dragonflies to fish and dogs to humans, have suggested that they all use a constant bearing (CB) strategy to pursue prey or other moving targets. CB is best known as the interception strategy employed by baseball outfielders to catch ballistic fly balls. CB is a time-optimal solution to catch targets moving along a straight line, or in a predictable fashion--such as a ballistic baseball, or a piece of food sinking in water. Many animals, however, have to capture prey that may make evasive and unpredictable maneuvers. Is CB an optimum solution to pursuing erratically moving targets? Do animals faced with such erratic prey also use CB? In this paper, we address these questions by studying prey capture in an insectivorous echolocating bat. Echolocating bats rely on sonar to pursue and capture flying insects. The bat's prey may emerge from foliage for a brief time, fly in erratic three-dimensional paths before returning to cover. Bats typically take less than one second to detect, localize and capture such insects. We used high speed stereo infra-red videography to study the three dimensional flight paths of the big brown bat, Eptesicus fuscus, as it chased erratically moving insects in a dark laboratory flight room. We quantified the bat's complex pursuit trajectories using a simple delay differential equation. Our analysis of the pursuit trajectories suggests that bats use a constant absolute target direction strategy during pursuit. We show mathematically that, unlike CB, this approach minimizes the time it takes for a pursuer to intercept an unpredictably moving target. Interestingly, the bat's behavior is similar to the interception strategy implemented in some guided missiles. We suggest that the time-optimal strategy adopted by the bat is in response to the evolutionary pressures of having to capture erratic and fast moving insects.

Animals↗

PubMed2026

Seawater immersion reshapes the temporal dynamics of traumatic brain injury and reveals mitochondrial oxidative stress as a modifiable therapeutic target.

Traumatic brain injury (TBI) evolves through time-dependent secondary injury, but whether seawater (SW) immersion merely amplifies pathology or reshapes the temporal trajectory of post-traumatic biology remains unclear. Here, we applied time-resolved proteomics to mouse brains after controlled cortical impact (CCI) with or without artificial SW immersion at 1, 3, 7, and 28 days post-injury. Trajectory-based proteomic analysis revealed that SW immersion altered the direction, magnitude, timing, persistence, and recovery of protein responses, rather than simply intensifying TBI-induced changes. This remodeled trajectory exhibited phase-specific patterns, including SW-dominant, synergistically enhanced, and attenuated responses, highlighting mitochondrial oxidative stress, inflammatory activation, complement/coagulation disturbance, and impaired structural repair. Phenotypic validation confirmed phase-specific deficits, including acute inflammatory-redox injury, impaired neuronal survival, chronic axon-myelin disruption, and incomplete behavioral recovery. SS-31 partially mitigated selected inflammatory, redox, neuronal, and white matter abnormalities, supporting mitochondrial oxidative stress as a modifiable node rather than the sole driver of trajectory remodeling. These findings identify seawater immersion as a temporal modifier of secondary injury and emphasize that environmental trauma may require trajectory-informed, phase-specific therapeutic interventions.

Animals↗

PubMed2004

Identifying and predicting adolescent smokers' developmental trajectories.

Very few studies have defined trajectories of smoking. In the present study, we modeled growth in adolescent smoking and empirically identified prototypical trajectories. We conceptualized escalation of smoking as a growth process and modeled rates of change and heterogeneity of these patterns using latent growth mixture modeling. The analysis identified six trajectories with low ambiguity about group membership (early rapid escalators, late rapid escalators, late moderate escalators, late slow escalators-smokers, stable puffers, and late slow escalators-puffers). A trajectory of quitters was not identified. We also examined predictors of the smoking trajectories. The predictors were assessed across the adolescent years and included variables related to smoking and other substance use, as well as a range of variables related to sociodemographic factors and mental health. Observed change in the pattern of predictors across age has implications for the mechanism of effect of these variables in relation to smoking trajectories, including predictors that differentiated among daily smokers, variables that may determine the trajectory (e.g., friends smoking), and variables that may result from the trajectory (e.g., marijuana use, less attachment to friends).

Adolescent↗

PubMed2003

Trajectories of delinquent behaviour in adolescence and their covariates: relations with initial and time-averaged factors.

This longitudinal study examined individual, family, and peer covariates of distinctive trajectories of juvenile delinquency, using data from a community sample of 318 German adolescents (mean age at the first wave was 11.45 years). Latent growth mixture modelling analysis revealed four trajectory groups: high-level offenders, medium-level offenders, low-level offenders, and rare offenders. The trajectory groups were discriminated better by time-averaged covariates than by initial status covariates. High peer tolerance of deviance and low parental empathy were consistently linked to varying offending trajectories, whereas gender, low academic achievement, and low parental monitoring appeared to be trajectory-specific covariates.

Adolescent↗

PubMed2004

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1.

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 3(10)-helix/turn to alpha helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.

Biophysical Phenomena↗

PubMed1995

Structure, dynamics and energetics of initiation sites in protein folding: I. Analysis of a 1 ns molecular dynamics trajectory of an early folding unit in water: the helix I/loop I-fragment of barnase.

The dynamic and energetic behavior of an initiation site of protein folding (helix I/loop I fragment of barnase) isolated from the tertiary environment of the rest protein is investigated in a 1 ns molecular dynamics simulation. All atom representation, explicit solvent description, and periodic boundary conditions are applied. In the course of the simulation several steps of structural disintegration are observed, followed by events partially rebuilding the initial structure. The phase of disintegration results in a fragment conformation completely lacking hydrogen bonds, with one residue in the center of the helix changed from alpha to beta conformation. The transition state of helix disintegration is characterized by a complete i-->i + 4/i + 5 hydrogen bonding network which undergoes gradual hydrolysis starting at the solvent exposed flank and proceeding towards the interior of the fragment perpendicular to the axis of the helix. Energetic analysis of the helix transitions shows that the i-->i + 4/i-->i + 5 network of hydrogen bonds accommodates one helical residue in beta conformation with only slightly worse hydrogen bonding energy and Van der Waals packing compared to the regular alpha-helix. The stability of the fragment is primarily due to hydrophobic interactions of residues shown to be essential in mutagenesis experiments.

Amino Acid Sequence↗