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 649 records · Page 36Linked to original sources

PubMed2004

The effects of rocker sole and SACH heel on kinematics in gait.

The rocker sole and solid-ankle cushion-heel (SACH) heels are the most commonly prescribed external shoe modification. Only a limited number of scientific evidence exists to support these interventions in clinical practice. The objective of this study was to determine the effects of rocker soles and SACH heels on kinematics during gait. In this study, we investigated the gait parameters during level walking, stair climbing and stair descending in healthy volunteers and assessed the effects of the modified shoes on the motion of the forefoot and hindfoot compared with the traditional shoes. Eleven normal subjects participated in this study. A six-camera motion analysis system was used to capture motion trajectories. The three-dimensional (3D) coordinates of the markers were used to calculate the angles of flexion-extension, valgus-varus, and internal-external rotation at the hindfoot and forefoot joints in a gait cycle by the custom software for foot kinematic analysis. The results showed that the rocker soles offer several advantages from the viewpoint of gait kinematics. The forefoot joint excursion in sagittal plane while wearing rocker shoes was significantly less than that while wearing traditional shoes during level walking, stair climbing and stair descending. It means that they could mimic the action of the forefoot joint, aid in roll off, and simulate forefoot dorsiflexion. Since the bony structures mechanically link the forefoot joint and hindfoot joint to a triplanar axis of motion, they could be used whenever there is minimal or no motion at the forefoot joint or hindfoot joint, because of, for example, fusion, fracture, cast immobilization, orthosis design, pain, or arthritis.

Adult↗

PubMed2002

Assessing equilibration and convergence in biomolecular simulations.

If molecular dynamics simulations are used to characterize the folding of peptides or proteins, a wide range of conformational states needs to be sampled. This study reports an analysis of peptide simulations to identify the best methods for assessing equilibration and sampling in these systems where there is significant conformational disorder. Four trajectories of a beta peptide in methanol and four trajectories of an alpha peptide in water, each of 5 ns in length, have been studied. Comparisons have also been made with two 50-ns trajectories of the beta peptide in methanol. The convergence rates of quantities that probe both the extent of conformational sampling and the local dynamical properties have been characterized. These include the numbers of hydrogen bonds populated, clusters identified, and main chain torsion angle transitions in the trajectories. The relative equilibrium rates of different quantities are found to vary significantly between the two systems studied reflecting both the differences in peptide primary structure and the different solvents used. A cluster analysis of the simulation trajectories is identified as a very effective method for judging the convergence of the simulations. This is particularly the case if the analysis includes a comparison of multiple trajectories calculated for the same system from different starting structures.

Amino Acid Sequence↗

PubMed2004

The utilization of visual feedback from peripheral and central vision in the control of direction.

Past research has demonstrated that both peripheral and central vision play an important role in the control of movement direction. However, it has been unclear whether the benefits of these sources of information are due to adjustments in the limb trajectory during movement execution (i.e., online) or modification in motor commands prior to movement initiation (i.e., offline). In the present paper, we analyzed the variability in limb trajectories in a directional aiming task to examine the relative contributions of peripheral and central vision in both the planning and execution of movements. The point of gaze was manipulated to vary where in the limb trajectory information was gained from central and peripheral vision. Analysis of the variability in directional error at various stages of the movement revealed that participants utilized information from early in the trajectory during movement execution when it appeared in both peripheral and central visual fields. Information from late in the trajectory was used offline to improve the programming of subsequent movements regardless of where this information was available in the visual field.

Adult↗

PubMed1995

Detection of temporary lateral confinement of membrane proteins using single-particle tracking analysis.

Techniques such as single-particle tracking allow the characterization of the movements of single or very few molecules. Features of the molecular trajectories, such as confined diffusion or directed transport, can reveal interesting biological interactions, but they can also arise from simple Brownian motion. Careful analysis of the data, therefore, is necessary to identify interesting effects from pure random movements. A method was developed to detect temporary confinement in the trajectories of membrane proteins that cannot be accounted for by Brownian motion. This analysis was applied to trajectories of two lipid-linked members of the immunoglobulin superfamily, Thy-1 and a neural cell adhesion molecule (NCAM 125), and the results were compared with those for simulated random walks. Approximately 28% of the trajectories for both proteins exhibited periods of transient confinement, which were < 0.07% likely to arise from random movements. In contrast to these results, only 1.5% of the simulated trajectories showed confined periods. Transient confinement for both proteins lasted on average 8 s in regions that were approximately 280 nm in diameter.

Animals↗

PubMedDate not supplied

Use of the wound healing trajectory as an outcome determinant for acute wound healing.

Accurate and clinically practical methods for measuring the progress of acute wound healing is necessary before interventions designed to optimize and even accelerate acute wound healing can be applied. Complete wound closure rates and operative wound closure severity are irrelevant to most acute wounds since most are closed at the time of primary tissue repair and remain closed throughout healing. Analogous to chronic wound closure, the rate of increase of incision tensile strength progressively decreases as time passes and 100% unwounded tissue strength is never achieved making the endpoint definition of "healed" vague. Conceptualizing acute wound healing in terms of its design elements with reintegration into a final outcome lends itself to the description of acute wound healing as a mathematical trajectory. Frequently such an equation is a rate expressing the change in an acute healing parameter, most often tensile strength, over time. Such an approach also normalizes misinterpretations in analysis or errors in theory developed by measuring healing parameters at fixed points in time. Distributions of fractional strength gain times (e.g., 85% normal strength) can be determined using statistical methodology similar that used for failure time of survival analysis. Preclinical studies show that acute wound healing trajectories can be shifted to the left from a "normal" or "impaired" curve to an accelerated or more "ideal" curve. A useful method for measuring acute wound healing outcomes is therefore required before the basic science of acute wound healing is inevitably applied to the problem of acute surgical wounds.

Acute Disease↗

PubMed2006

Rapid growth among term children whose birth weight was appropriate for gestational age has a longer lasting effect on body fat percentage than on body mass index.

BACKGROUND: It is not clear whether and how rapid growth in infancy, a risk factor for later obesity, differentially affects growth and body-composition development throughout childhood in term children with an appropriate-for-gestational age (AGA) birth weight. OBJECTIVE: The aim was to examine the effect of rapid growth in infancy on body mass index SD score (BMI SDS) and body fat percentage (%BF) trajectories until age 7 y. DESIGN: This analysis included 206 (50.5% female) AGA term participants of the Dortmund Nutritional and Anthropometric Longitudinally Designed Study. Repeated anthropometric measurements were obtained between 0.5 and 7 y of age. RESULTS: Fifty-nine of the 206 children (28.6%) displayed rapid growth (an increase in SDS for weight of >0.67 between birth and age 2 y). From 6 mo of age, their growth trajectories diverged from normal growers, and by age 7 y they had a higher BMI, more fat mass, and a higher risk of overweight (odds ratio: 6.2; 95% CI: 2.4, 16.5; P = 0.0002). Multilevel model analyses showed that the differences in BMI were achieved within the first 2 y of life [beta (+/-SE) SDS: 1.22 +/- 0.13], after which they persisted at this level until the age of 7 y, whereas differences in %BF, which were also already discernible by age 2 y (1.52 +/- 0.34%), became progressively larger over the next 5 y (adjusted difference: 0.23 +/- 0.11%/y; P = 0.03). CONCLUSIONS: Rapid growth in infancy and early childhood results in an increased BMI and %BF throughout childhood and an increased risk of overweight at age 7 y among AGA children. Rapid growth in AGA children has a more pronounced effect on %BF than on BMI.

Adipose Tissue↗

PubMed1986

Step-tracking movements of the wrist in humans. I. Kinematic analysis.

We have examined the kinematics of the initial trajectory of step-tracking movements performed by human subjects. Each subject tracked a target that required 5-30 degrees of radial or ulnar deviation of the wrist. All movements were to be performed as accurately as possible. Speed instructions were given before each trial. When subjects performed different amplitude movements following the same speed instruction, the peaks of velocity, acceleration, and jerk were linearly related to peak displacement. The peaks of velocity, acceleration, and jerk also changed when the speed instruction was altered. Thus, for any given movement, the peak values of the derivatives of displacement were dependent on both movement amplitude and intended speed. As a result, the peak values of the derivatives cannot be used by themselves to control or monitor peak displacement. When subjects performed different amplitude movements following the same speed instruction, movement duration tended to remain constant. In contrast, movement duration changed when the speed instruction was altered. Movements performed when subjects intended to move slowly had longer durations than when subjects intended to move quickly. These results suggest that subjects volitionally alter intended speed by selecting different movement durations. When both movement amplitude and intended speed were varied, the peak displacement of a step-tracking movement was linearly related to the product of 2 kinematic variables: the initial peak of a derivative of displacement (either velocity, acceleration, or jerk) and movement duration. On the basis of our observations, we propose that central commands generate step-tracking movements of different amplitudes and intended speeds by adjusting both the magnitude and duration of a derivative of displacement.

Adult↗

PubMed2004

Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations.

Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion. The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1.

Anisotropy↗

PubMed2003

Three dimensional k-space trajectory design using genetic algorithms.

Image quality and total scan time in MRI are determined in large part by the trajectory employed to sample the Fourier space. Each trajectory has different properties like coverage of k-space, scan time, sensitivity to off-resonance conditions, etc. These properties are often contradictory, therefore a universal optimal trajectory does not exist and ultimately, it will depend on the image characteristics sought. Most trajectories used today are designed based on intuition and k-space analysis more than with optimization methods. This work presents a 3D k-space trajectory design method based on Genetic Algorithm optimization. Genetic Algorithms have been chosen because they are particularly good for searching large solution spaces. They emulate the natural evolutionary process allowing better offsprings to survive. The objective function searches the maximum of the trajectory's k-space coverage subject to hardware constraints for a fixed scanning time using the trajectory's torsion as its optimization variable. The method proved to be effective for generating k-space trajectories. They are compared with well-established trajectories. The results of simulated experiments show that they can be appropriate for image acquisition under certain special conditions, like off-resonance and undersampling. This design method can be extended to include other objective functions for different behaviors.

Algorithms↗

PubMed2003

Evaluation of trajectories and contact pressures for the straight nucleus cochlear implant electrode array - a two-dimensional application of finite element analysis.

A two-dimensional (2D) finite element analysis has been used in this study to model the insertion of the Nucleus electrode array with different stiffness properties in order to evaluate the propensity of damage by visualizing the predicted trajectories and by comparing the buckling stresses and the contact pressures at the tip (and its distribution along the length) of the electrode array. Previous temporal bone studies have shown that damage during insertion of an electrode array around the basal turn of the cochlear spiral could be related to the design and the stiffness properties of the electrode array. However, it is difficult to evaluate different designs of electrode arrays purely by experimental methods as the experimental conditions and their results are difficult to reproduce. Three electrode arrays with different mechanical properties, i.e. uniform stiffness, graded stiffness, and a soft tip have been modelled. Buckling stress and contact pressure at the tip of the electrode array were found to be highest for the arrays with uniform stiffness. The contact pressures at the tip of the electrode array appeared strongly influenced by the stiffness profile and were optimal for graded stiffness. The results indicate the importance of the electrode array design and stiffness properties in minimizing trauma. However, there are a number of limitations in the present 2D evaluation which will require further analysis using a three-dimensional model to obtain definitive results.

Cochlea↗

PubMed2004

BioSimGrid: towards a worldwide repository for biomolecular simulations.

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

Acetylcholinesterase↗

PubMed2026

Exploratory single-nucleus multiomics analysis of myeloid cell states associated with neoadjuvant chemotherapy response in pancreatic ductal adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) continues to be one of the most lethal human malignancies, with the vast majority of patients ineligible for immunotherapy. Tumour-associated macrophages (TAMs) are key regulators of the PDAC tumour microenvironment (TME), yet their transcriptional and epigenomic heterogeneity in the context of chemotherapy response is poorly understood. Therefore, we performed an exploratory single nucleus multiomics analysis of PDAC tumors stratified by histopathologic response to neoadjuvant chemotherapy. METHODS: Surgical resection specimens from PDAC patients were classified as responders or non-responders using the American College of Pathologists (CAP) histopathologic criteria. Frozen tissue underwent simultaneous snRNA-seq and snATAC-seq on the 10x Genomics Chromium Single Cell Multiome platform, followed by downstream analyses such as differential gene expression, GO and hallmark pathway enrichment, pseudotime trajectory inference and ChromVAR transcription factor motif analysis. RESULTS: Multiomics profiling of 30 840 high-quality nuclei revealed a myeloid compartment that differed in composition and transcriptional state between CAP-defined responders and non-responders in this small cohort. We observed a trend toward higher LAM-like state proportions in the responders than non-responders (38.4% vs. 26.7%), although this disparity did not achieve statistical significance. The transcriptional programs of the responder myeloid cells are associated with phagocytosis and lipid handling. Chromatin accessibility analysis further suggested candidate response-associated transcription factor motif accessibility patterns. CONCLUSIONS: Neoadjuvant-treated PDAC tumours from CAP-defined responders in this cohort myeloid landscape with apparent enrichment of LAM-like states and immune-activating transcriptional/epigenetic programs. However, these findings are preliminary and hypothesis-generating because of the small cohort size, heterogeneous treatment regimens, absence of matched pre-treatment biopsies, and lack of knockout validation. Larger treatment cohorts and functional/mechanistic studies are needed to determine whether LAM-like myeloid programs contribute to chemotherapy response or reflect a consequence of chemotherapy treatment.

Humans↗

PubMed2004

UCSF Chimera--a visualization system for exploratory research and analysis.

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

Amino Acid Sequence↗

PubMed2004

Does space in the jaw influence the timing of molar crown initiation? A model using baboons (Papio anubis) and great apes (Pan troglodytes, Pan paniscus).

Radiographic and histological studies of baboon (Papio hamadryas, P. anubis) and chimpanzee (Pan troglodytes) permanent tooth development have found that periods of molar crown mineralization overlap markedly in chimpanzees but are staggered in baboons. Here we test the hypothesis that these intertaxon differences in molar initiation are primarily due to the space available in the mandibles of each species for these teeth. This study includes radiographic, linear measurement, and three-dimensional (3D) coordinate landmark data taken from baboon (Papio anubis n=51) and great ape (Pan paniscus n=43, P. troglodytes n=60) mandibles and permanent molars across a broad developmental range for each taxon. Unexpectedly, 3D multivariate statistical shape analysis of the molar crypt, crown, and root data shows that all three species trajectories of molar row shape change are indistinguishable from each other. Qualitative analysis of these 3D data reveals subtle and inconclusive intergeneric differences in the space maintained between adjacent molars during growth. The space distal to each newly initiated molar is slightly greater in the baboon. Bivariate analyses comparing molar row and mandibular corpus proportions in Papio and Pan fail to show clear or consistent taxonomic differences in the ratio of space afforded developing molars in the alveolar bone. Thus, there is a poor correlation between mandibular proportion and both intermolar spacing and 3D molar development pattern. Contrary to earlier studies, these results suggest that pattern of molar crown initiation and temporal overlap of adjacent mineralizing crowns is not significantly different between Papio and Pan. This may be due in part to the inclusion here of not only 3D molar crown data but also 3D molar crypt data. This study strongly refutes the hypothesis that space available in the mandible directly underlies different times of permanent molar crown initiation between Papio and Pan.

Animals↗

PubMed1990

Temperature dependence of the structure and dynamics of myoglobin. A simulation approach.

The results of simulations of the structure and internal motions of carbonomonoxymyoglobin (MbCO) at two different temperatures (325 and 80 K) are presented and compared with experimental data. Properties calculated from the 120 ps trajectory at 325 K are used as a reference in the analysis of the motion of the protein at 80 K. Three separate 80 K molecular dynamics trajectories were calculated; they were started with different coordinate sets from the 325 K simulation and the lower temperature was achieved by scaling the velocities. The simulations yield results for the structural changes between 325 and 80 K that are in general accord with those from X-ray data. Both the experimental and calculated radii of gyration, distances from the center of mass and main-chain difference distance matrices show that there is a significant but inhomogeneous shrinkage with decreasing temperature. For the atomic fluctuations, by contrast, the calculated temperature dependence is very different from the X-ray results; i.e. the calculated root-mean-square backbone fluctuations decrease to 0.11 A at 80 K from 0.51 A at 325 K, while the fluctuations obtained from the X-ray B factors go from 0.56 A at 260 K to 0.47 A at 80 K. The smaller temperature dependence of the B factors suggests that there is significant conformational disorder in MbCO crystals at lower temperatures. This is in accord with the simulation results, which show that the protein is trapped in restricted regions of conformational space at 80 K, while at 325 K a much larger region is accessible to the protein. Analysis of the fluctuations at 325 K and 80 K shows that the room temperature flexibility of the protein is determined by the mobility of the loop regions and by side-chain torsional motions (in accord with earlier simulation results), while the low temperature fluctuations involve motion within a single well. Examination of the calculated iron atom fluctuations and comparison with Mossbauer data show good agreement. It is found that the dominant contribution to the iron motion arises from heme sliding; motion of the iron relative to the heme are much smaller.

Chemical Phenomena↗

PubMed1999

From atomic to mesoscopic descriptions of the internal dynamics of DNA.

An analysis of four 1-ns molecular dynamics trajectories for two different 15-bp oligonucleotides is presented. Our aim is to show which groups of atoms can be treated as rigid bodies within a bead representation of DNA, independently of the base sequence and for any conformations belonging to the A/B family. Five models with moderate intragroup deformations are proposed in which the groups are formed of atoms belonging to a single nucleotide or to a complementary nucleotide pair. The influence of group deformation in two of these models is studied using canonical correlation analysis, and it is shown that the internal DNA dynamics is indeed dominated by the rigid motion of the defined atom groups. Finally, using one of the models within a bead representation of duplex DNA makes it possible to obtain stretching, torsional, and bending rigidities in reasonable agreement with experiment but points to strongly correlated stretching motions.

Base Sequence↗

PubMed1993

Operation Everest II: an indication of deterministic chaos in human heart rate variability at simulated extreme altitude.

It has been shown that fluctuation of human heartbeat intervals (heart rate variability, HRV) reflects variations in autonomic nervous system activity. We studied HRV at simulated altitudes of over 6000 m from Holter electrocardiograms recorded during the Operation Everest II study (Houston et al. 1987). Stationary, approximately 30-min segments of HRV data from six subjects at sea level and over 6000 m were supplied to (1) spectral analysis to evaluate sympathetic and parasympathetic nervous system (SNS, PNS) activity, (2) the analysis of Poincaré section of the phase space trajectory reconstructed on a delayed coordinate system to evaluate whether there was fluctuation with deterministic dynamics, (3) the estimation of the correlation dimension to evaluate a static property of putative attractors, and (4) the analysis of nonlinear predictability of HRV time series which could reflect a dynamic property of the attractor. Unlike HRV at sea level, the recordings at over 6000 m showed a strong periodicity (period of about 20 s) with small cycle-to-cycle perturbation. When this perturbation was expressed on a Poincaré section, it seemed to be likely that the perturbation itself obeyed a deterministic law. The correlation dimensions of these recordings showed low dimensional values (3.5 +/- 0.4, mean +/- SD), whereas those of the isospectral surrogates showed significantly (P < 0.05) higher values (5.3 +/- 0.5) with embedding dimensions of 5.6 +/- 0.9.(ABSTRACT TRUNCATED AT 250 WORDS)

Altitude↗

PubMed2002

The incidence and the risk of pneumothorax and chest tube placement after percutaneous CT-guided lung biopsy: the angle of the needle trajectory is a novel predictor.

STUDY OBJECTIVE: Pneumothorax remains the most common complication of percutaneous CT-guided lung biopsy, despite improved techniques. The rate of pneumothorax reported in the literature ranges from 19 to 60%. The aims of this study were to estimate the risk of pneumothorax in patients undergoing CT-guided lung biopsy, and to determine which factors affect its occurrence. DESIGN: Retrospective study. PATIENTS AND METHODS: This study involved 289 consecutive patients who underwent biopsy in our hospital under consistent methods, using only one type of needle, the 19-gauge Tokyo Medical College (TMC) Needle (Takei; Tokyo, Japan), under CT guidance. RESULT: Seventy-seven patients (26.6%) had pneumothorax after percutaneous CT-guided lung biopsy. Forty-one of the 77 patients (53.2%) who had pneumothorax (14.2% of the entire series) required placement of a chest tube. Our present study, using multivariate logistic regression analysis, confirmed that greater lesion depth, wider trajectory angle, and increasing FVC percent predicted are independent risk factors of pneumothorax, and that two former factors are independent risk factors of chest tube placement following percutaneous CT-guided lung biopsy. CONCLUSIONS: The angle of needle route is a novel predictor of this complication. Our findings suggest that low pneumothorax rates are achieved by combining several techniques to reduce the risk of pneumothorax.

Adult↗