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Results for “trajectory analysis”

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PubMed1982

Visual information about rigid and nonrigid motion: a geometric analysis.

A mathematical analysis is presented that attempts to describe the available visual information about rigid and nonrigid motion and the three-dimensional structure of rigidly moving objects. Unlike other approaches, the analysis is based on the geometric relations among a set of trajectories defined over an extended region of space-time. Two experiments are reported in which observers viewed computer simulations of moving objects and were required to judge whether the observed motion appeared to be rigid or nonrigid. The results suggest that the mathematical limitations of a trajectory-based analysis of visual information are consistent with the perceptual limitations of actual human observers.

Discrimination Learning↗

PubMed1999

Analysis and evaluation of the Trajectory Theory of Chronic Illness Management.

The development and testing of theories for use in nursing research and practice is essential for advancement of the profession. The Trajectory Theory of Chronic Illness Management is a middle-range nursing theory that has been proposed by Corbin and Strauss (1991a). Analysis and evaluation of this theory was performed using Fawcett and Downs's (1992) guidelines. Theory analysis and evaluation are important first steps before using a theory for practical purposes. Theory analysis makes a theory more understandable and helps to identify the strengths and weaknesses of the theory. Evaluation extends the analysis process by making judgments about the potential contribution of the theory based on published data. Results of the theory analysis and evaluation suggest that the Trajectory Theory has theoretical and social significance but that further theoretical work is necessary to enhance the internal consistency and parsimony of the theory. Although several authors have suggested that the theory has pragmatic adequacy, evidence for empirical adequacy of the theory is needed. Before more empirical studies are conducted, further theoretical work is recommended.

Chronic Disease↗

PubMed2005

Diffusional encounter of barnase and barstar.

We present an analysis of trajectories from Brownian dynamics simulations of diffusional protein-protein encounter for the well-studied system of barnase and barstar. This analysis reveals details about the optimal association pathways, the regions of the encounter complex, possible differences of the pathways for dissociation and association, the coupling of translational and rotation motion, and the effect of mutations on the trajectories. We found that a small free-energy barrier divides the energetically most favorable region into a region of the encounter complex above the barnase binding interface and a region around a second energy minimum near the RNA binding loop. When entering the region of the encounter complex from the region near the RNA binding loop, barstar has to change its orientation to increase the electrostatic attraction between the proteins. By concentrating the analysis on the successful binding trajectories, we found that the region of the second minimum is not essential for the binding of barstar to barnase. Nevertheless, this region may be helpful to steer barstar into the region of the encounter complex. When applying the same analysis to several barnase mutants, we found that single mutations may drastically change the free-energy landscape and may significantly alter the population of the two minima. Therefore, certain protein-protein pairs may require careful adaptation of the positions of encounter and transition states when interpreting mutation effects on kinetic rates of association and/or dissociation.

Bacterial Proteins↗

PubMed1984

Geometrical analysis of human three-channel Lissajous' trajectory of auditory brain-stem evoked potentials.

Three-channel Lissajous' trajectories (3CLTs) of auditory brain-stem evoked potentials (ABEPs) were obtained for a group of 15 normal humans. 3CLTs were studied using geometric spatial descriptors of rate of bending (curvature), local planarity (torsion), as well as the parameters of best fit planes along the trajectory. Point-by-point analysis enabled objective determination of apices (curvature maxima) which divided the trajectory to curvilinear segments. Consecutive apices defined planar segments (each consisting of two curvilinear segments) along the trajectory. Of the two possibilities of arranging apices in the middle of planar segments only one yielded consistently planar segments. The alternative set of apex triads represented transitions between truly planar segments. The variability of position and orientation measures of planar segments was greater than that of apex latencies and plane limits. The significance of planes, as well as their generation, in 3CLT of ABEP, remains to be studied.

Adult↗

PubMed1990

Microcomputer analysis of three-channel Lissajous' trajectory of auditory brainstem evoked potentials.

A software package for the IBM PC computer is presented to facilitate the analysis of three-channel Lissajous' trajectories (3CLT) of auditory brainstem potentials. The program deals with 4-channel numeric or ASCII files, including three orthogonal X, Y, Z channels and standard vertex-mastoid on the stimulated side. The 3CLT analysis program implements standard measurements of peak latencies, voltage amplitude and curvature plots computed from the three orthogonal channels, interactive three-dimensional rotations of the trajectory and planar segment analysis. Parameter estimates of the best-fit plane are computed for any part of the trajectory limited by two latency cursors. Results are displayed and stored in a table including segment bounds and duration, sight vector orientation, plane equation parameters and adjustment criteria.

Evoked Potentials, Auditory↗

PubMed2026

Identification of Drug-resistant Cell Subpopulations in Colorectal Cancer Through Single-cell Analysis and Exploration of Potential Therapeutic Strategies.

INTRODUCTION: The therapeutic efficacy of Colorectal Cancer (CRC) is often compromised by resistance to the standard chemotherapy agent oxaliplatin. METHODS: This study obtained single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database. Differentially Expressed Genes (DEGs) between resistant and sensitive epithelial subpopulations were identified, followed by enrichment analysis. Pseudotemporal trajectory and cell-cell communication were analyzed using Monocle2 and CellChat, respectively. The candidate drug was predicted by Connectivity Map (cMAP) analysis. External validation included assessment of the EpC2 signature in an oxaliplatin-resistant cell line dataset (GSE76092), survival analysis using The Cancer Genome Atlas (TCGA) cohorts, and re-analysis of the GSE179784 dataset to assess the reproducibility of EpC2-like subpopulations and their DNA Damage Repair (DDR) scores. RESULTS: Cell subpopulations were divided into 10 clusters. Among them, epithelial cells comprised 5 subpopulations, with EPC2 identified as a potential oxaliplatin-resistant subset. DEGs were enriched in the TNF and IL-17 pathways. External validation confirmed the enrichment of EpC2 in resistant cell lines and its association with poor survival. Pseudotemporal trajectory revealed that epithelial cells underwent state transitions, forming two distinct branches. The resistant group exhibited enrichment in RNA splicing and NF-κB pathways. Cell-cell communication analysis revealed interactions involving MDK- NCL and PPIA-BSG. Dasatinib was predicted as a candidate drug. DISCUSSION: We identified an oxaliplatin-resistant subpopulation of Epithelial Cells (EpC2) in CRC, elucidated its multi-layered resistance mechanisms, and integrated multi- omics and cMAP database analyses to predict a potential intervention drug. CONCLUSION: This study provided potential therapeutic possibilities for oxaliplatin resistance, contributing to CRC treatment.

Humans↗

PubMed2005

Synchronized video and motion analysis for the assessment of procedures in the operating theater.

HYPOTHESIS: Objective assessment of surgical skill has recently been shown to be possible through the use of dexterity-based and video analysis systems. The aim of this study was to synchronize these 2 modalities to produce a comprehensive surgical assessment tool. DESIGN: The Imperial College Surgical Assessment Device is a dexterity-based motion analysis device that has been developed in the Department of Surgical Oncology and Technology by the Surgical Computing and Imaging Research Group. Further advances to this system have been made to enable synchronized acquisition of hand kinematics and video from real procedures, and their concurrent analysis. To test the feasibility of the system, 10 laparoscopic cholecystectomies performed by 5 different surgeons on consenting patients were recorded. Analysis focused on the entire procedure and also on specific parts of the operation such as the clipping and cutting of the cystic duct and artery. RESULTS: Dexterity analysis was performed using the objective measures of time, path length, number of movements, velocities, and trajectories. Comparative analysis of a surgeon's dexterity was carried out on the whole procedure and by using the synchronized zoom facility in the software. Kinematic signals revealed rapid changes in velocity caused by alternating between different instruments or occurring after complications such as bleeding. CONCLUSION: This new motion analysis system has been shown to be an effective tool for the comprehensive assessment of operative procedures.

Cholecystectomy, Laparoscopic↗

PubMed1995

Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories.

We present an approach to the analysis of low-frequency (0-200 cm-1) alpha-helix vibrations in molecular dynamics simulations. The approach employs the P-Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6, pp. 46-60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repeating units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P-Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm-1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P-Curves and compared.

Algorithms↗

PubMed1991

Real-time interactive frequency filtering of molecular dynamics trajectories.

Molecular dynamics simulations of atomic motion in protein and nucleic acid molecules must be done on a femtosecond time-scale. Much of this rapid motion is unimportant for the slower changes that are most relevant to biological function (conformational changes, substrate binding, protein folding). The high-frequency motion makes simulations computationally expensive. More importantly, the high frequencies obscure visualization of the relevant dynamics processes. Sessions, Dauber-Osguthorpe and Osguthorpe presented a method for removing high-frequency motions from atomic co-ordinates of trajectories generated by simulation. While that study used fast Fourier methods and emphasized the use of filtering for analysis of trajectories, this communication describes a new method that makes it much easier to use frequency filtering in programs that display trajectories as a sequence of moving images. Tests of the method on systems extending from pure water to proteins and nucleic acid molecules in vacuo and in solution have demonstrated its general utility. Impressed with the power and simplicity of the new method, we wish to present it in sufficient detail to allow others to implement it themselves.

Fourier Analysis↗

PubMed2001

Correspondence analysis of sinogram lines. Sinogram trajectories in factor space replace raw images in the orientation of projections of macromolecular assemblies.

The lines of a large group of sinograms of projections with random orientation can be submitted to correspondence analysis. Since the number of samples per line is small, a small matrix is accumulated which is quick to orthogonalise. In the eigenvector space, the lines of a sinogram are represented by points describing a closed trajectory. Two trajectories of different sinograms intersect in the position of their common line. Determining where two trajectories cross each other is a problem of minimum chi2 distance in the space of 5-7 eigenvectors. An algorithm to determine common lines has been implemented and tested with phantom projections oriented at random, and corrupted with noise. The images were simulating a set collected with the two exposures technique, already proposed by the authors for three dimensional reconstruction from random projections. The preliminary models obtained with the new algorithm have been refined by a projection matching based on trajectories. This step requires determining which trajectory, in a set representing computed projections, matches at best with that of an experimental projection. This is a problem of minimum distance in a space with low dimensionality. The present algorithms, based on chi2 distances, run much faster than those based on correlation analysis and the quality of the reconstructed phantoms looks satisfactory.

Journal Article↗

PubMed2006

Principal component analysis of lifting waveforms.

BACKGROUND: One limiting factor in lifting research design has been the inability to effectively analyze waveform data, especially when differences in body mass, height, and load magnitude influence the derived kinetic variables. The purpose of this study was to demonstrate the sensitivity of principal component analysis to quantify clinically relevant differences in kinetic lifting waveforms over three load magnitudes and between two separate populations. METHODS: Principal component analysis was applied to five kinetic lifting waveforms. The derived principal component scores were used as the dependent measures in a two-way (clinical status x load magnitude) MANOVA. FINDINGS: Significant low back pain group differences (P<0.05) were found for three of the principal component scores on extension moment generation in the sacral and thoracic regions and for trunk compression. Significant differences were found for each variable with respect to the magnitude across the entire lift time between the three load conditions, as well as four significant differences related to inferred mechanical changes that resulted from lifting increasingly heavier loads. INTERPRETATION: Principal component analysis of kinetic lifting waveforms was shown to be insensitive to a confounding factor of different load magnitudes when attempting to identify previously determined clinically relevant differences in the waveform trajectories. The analysis was able to partition the variability attributed to the direct influence of different external load magnitudes, versus those differences in spinal loading that arose from the variations in the lifting mechanics of increasing loads. The technique could be beneficial for other kinetic analyses where confounding magnitude modifiers like body size are present.

Adult↗

PubMed1997

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.

We report the results of four new molecular dynamics (MD) simulations on the DNA duplex of sequence d(CGCGAATTCGCG)2, including explicit consideration of solvent water, and a sufficient number of Na+ counterions to provide electroneutrality to the system. Our simulations are configured particularly to characterize the latest MD models of DNA, and to provide a basis for examining the sensitivity of MD results to the treatment of boundary conditions, electrostatics, initial placement of solvent, and run lengths. The trajectories employ the AMBER 4.1 force field. The simulations use particle mesh Ewald summation for boundary conditions, and range in length from 500 ps to 5.0 ns. Analysis of the results is carried out by means of time series for conformationalm, helicoidal parameters, newly developed indices of DNA axis bending, and groove widths. The results support a dynamically stable model of B-DNA for d(CGCGAATTCGCG)2 over the entire length of the trajectory. The MD results are compared with corresponding crystallographic and NMR studies on the d(CGCGAATTCGCG)2 duplex, and placed in the context of observed behavior of B-DNA by comparisons with the complete crystallographic data base of B-form structures. The calculated distributions of mobile solvent molecules, both water and counterions, are displayed. The calculated solvent structure of the primary solvation shell is compared with the location of ordered solvent positions in the corresponding crystal structure. The results indicate that ordered solvent positions in crystals are roughly twice as structured as bulk water. Detailed analysis of the solvent dynamics reveals evidence of the incorporation of ions in the primary solvation of the minor groove B-form DNA. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces an additional source of sequence-dependent effects on local conformational, helicoidal, and morphological structure, and may have important implications for understanding the functional energetics and specificity of the interactions of DNA and RNA with regulatory proteins, pharmaceutical agents, and other ligands.

Computer Simulation↗

PubMed2005

Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes.

The lateral mobility of individual murine polyoma virus-like particles (VLPs) bound to live cells and artificial lipid bilayers was studied by single fluorescent particle tracking using total internal reflection fluorescence microscopy. The particle trajectories were analyzed in terms of diffusion rates and modes of motion as described by the moment scaling spectrum. Although VLPs bound to their ganglioside receptor in lipid bilayers exhibited only free diffusion, analysis of trajectories on live 3T6 mouse fibroblasts revealed three distinct modes of mobility: rapid random motion, confined movement in small zones (30-60 nm in diameter), and confined movement in zones with a slow drift. After binding to the cell surface, particles typically underwent free diffusion for 5-10 s, and then they were confined in an actin filament-dependent manner without involvement of clathrin-coated pits or caveolae. Depletion of cholesterol dramatically reduced mobility of VLPs independently of actin, whereas inhibition of tyrosine kinases had no effect on confinement. The results suggested that clustering of ganglioside molecules by the multivalent VLPs induced transmembrane coupling that led to confinement of the virus/receptor complex by cortical actin filaments.

Actins↗

PubMedDate not supplied

[The trajectory towards alternative medicines: an analysis of health professionals' social representations].

This article focuses on social representations of alternative medicines by a group of professors from the School of Medicine and health professionals from the public health system in the city of Campinas, São Paulo, basically physicians and nurses. The article also emphasizes personal trajectories by which these health professionals opted for a dissident theoretical and practical perspective vis-à-vis the hegemonic positivist scientific medical paradigm. The research methods were mainly ethnographic, from a phenomenological perspective. The article concludes by sustaining (in theoretical terms) the importance of these dissident perspectives for scientific development.

Adult↗

PubMed2005

Comparative metabonomics of differential hydrazine toxicity in the rat and mouse.

Interspecies variation between rats and mice has been studied for hydrazine toxicity using a novel metabonomics approach. Hydrazine hydrochloride was administered to male Sprague-Dawley rats (30 mg/kg, n = 10 and 90 mg/kg, n = 10) and male B6C3F mice (100 mg/kg, n = 8 and 250 mg/kg, n = 8) by oral gavage. In each species, the high dose was selected to produce the major histopathologic effect, hepatocellular lipid accumulation. Urine samples were collected at sequential time points up to 168 h post dose and analyzed by 1H NMR spectroscopy. The metabolites of hydrazine, namely diacetyl hydrazine and 1,4,5,6-tetrahydro-6-oxo-3-pyridazine carboxylic acid (THOPC), were detected in both the rat and mouse urine samples. Monoacetyl hydrazine was detected only in urine samples from the rat and its absence in the urine of the mouse was attributed to a higher activity of N-acetyl transferases in the mouse compared with the rat. Differential metabolic effects observed between the two species included elevated urinary beta-alanine, 3-D-hydroxybutyrate, citrulline, N-acetylcitrulline, and reduced trimethylamine-N-oxide excretion unique to the rat. Metabolic principal component (PC) trajectories highlighted the greater degree of toxic response in the rat. A data scaling method, scaled to maximum aligned and reduced trajectories (SMART) analysis, was used to remove the differences between the metabolic starting positions of the rat and mouse and varying magnitudes of effect, to facilitate comparison of the response geometries between the rat and mouse. Mice followed "biphasic" open PC trajectories, with incomplete recovery 7 days after dosing, whereas rats followed closed "hairpin" time profiles, indicating functional reversibility. The greater magnitude of metabolic effects observed in the rat was supported by the more pronounced effect on liver pathology in the rat when compared with the mouse.

Administration, Oral↗

PubMed2003

Ambient silver concentration anomaly in the Finnish Arctic lower atmosphere.

Mean silver concentrations in weekly particle samples collected at Kevo, northern Finland, were determined for the period of October 1964-March 1978 by neutron activation analysis. Two distinct periods were observed in the silver concentration levels over this time frame. During 1964-1970, mean weekly silver concentration levels were found in the range of 0.01-190 ng/m3 with an arithmetic mean of 2.19 ng/m3. A few very high silver concentration levels (>10 ng/m3) were observed in this period, some of which simultaneously occurred with some of the highest bromine and iodine concentration levels. During 1971-1978, silver concentration levels were in the range of 0.02-0.89 ng/m3 with a mean value of 0.09 ng/m3. The observed concentration levels in the later period matched well the data from the early 1990s reported at Sevettijärvi, northern Finland, about 60 km east of Kevo. Data analysis, historical records for this region, and residence time analysis (RTA) using wind back-trajectories show that occasional smelting of silver-rich Norilsk ores at the Nikel smelter, Kola Peninsula, was probably a significant contributor to elevated mean silver concentration levels during 1964-1970. RTA alone was not able to unambiguously identify the most probable source region for highest silver impacts at Kevo due to the weekly integrated nature of the samples collected. Critical examination of wind back-trajectories (24 per day) for specific high silver, bromine, and iodine concentration weeks was carried out to supplement the ensemble RTA analysis (2 back-trajectories per day). The supplemental back-trajectory analysis revealed that deposition of the smelter component silver as well as the sea components (bromine and iodine) could occur together at Kevo during these weekly sampling periods. The study implies that data from weekly integrated samples are insufficiently time-resolved for RTA methods alone to unambiguously resolve the sources contributing to ambient atmospheric concentrations at Kevo, Finland.

Air Pollutants↗

PubMed1998

Immigrant trajectories into homeownership: a temporal analysis of residential assimilation.

"This study explores the rate of advancement into homeownership of immigrants, relative to native borns, in Southern California, a principal region of immigrant settlement.... Recent immigrants as well as young native borns are newcomers to the housing market and have lower attainment levels than earlier arrivals or older cohorts. Cohort trajectories are tracked from 1980 to 1990, adjusting for the influence of income, education, English proficiency, and marital status. Asian immigrants achieved extraordinarily high levels of homeownership soon after arrival, whereas Hispanic immigrants demonstrated sustained advancement into homeownership from initially very low levels."

Acculturation↗

PubMed1992

A graphics program for the analysis and display of molecular dynamics trajectories.

The program SCARECROW has been developed to help the molecular modeler to analyze and display the very big and complex data files produced by molecular dynamics programs. The molecular graphics program SCARECROW is written to support the display, animation, and extensive analysis of molecular dynamics trajectories. Using the macro language it is easy to make scripts for video animation and for the automated display and analysis of time series. Extensive coloring and atom selection commands are included to help the user to focus on relevant regions of the molecule. Time series can be produced and viewed on the screen or transferred to other programs.

Chemical Phenomena↗