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Results for “trajectory analysis”

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PubMed2006

Identification of patients with coronary artery disease using magnetocardiographic signal analysis.

INTRODUCTION: Magnetocardiography (MCG), which measures the magnetic component of the heart's electrical activity, offers an alternative approach for analyzing changes induced by coronary artery disease (CAD). This study examines several parameters that quantify spatial and temporal aspects of cardiac magnetic signals in CAD. MATERIALS AND METHODS: MCGs were registered at rest in 144 subjects, aged 58.3 +/- 9.8 years: 50 healthy subjects, 43 CAD patients without myocardial infarction (MI), 36 with MI, and 15 with spontaneous episodes of ventricular tachycardia (VT). Spatial characteristics of magnetic field maps (MFM), quantified using their centers of gravity, included MFM orientation and trajectory plots. Spatio-temporal analysis was performed by determining the spatial distribution of the QT interval. RESULTS: In CAD patients, MFM orientation during the QT interval deviated from normal in 67% of patients without MI and in 85% of patients with MI. Trajectory plots deviated from those of the normal group, with deviation increasing with disease severity. Quantifying the distribution of QT interval duration using a smoothness index demonstrated a significant difference between the values for healthy subjects and non-MI patients, as well as MI patients with and without VT (p < 0.001). CONCLUSION: The results reported demonstrate that disturbances in cardiac electrogenesis resulting from CAD may be assessed using MCG signal analysis.

Algorithms↗

PubMed2006

Mapping quantitative trait loci for longitudinal traits in line crosses.

Quantitative traits whose phenotypic values change over time are called longitudinal traits. Genetic analyses of longitudinal traits can be conducted using any of the following approaches: (1) treating the phenotypic values at different time points as repeated measurements of the same trait and analyzing the trait under the repeated measurements framework, (2) treating the phenotypes measured from different time points as different traits and analyzing the traits jointly on the basis of the theory of multivariate analysis, and (3) fitting a growth curve to the phenotypic values across time points and analyzing the fitted parameters of the growth trajectory under the theory of multivariate analysis. The third approach has been used in QTL mapping for longitudinal traits by fitting the data to a logistic growth trajectory. This approach applies only to the particular S-shaped growth process. In practice, a longitudinal trait may show a trajectory of any shape. We demonstrate that one can describe a longitudinal trait with orthogonal polynomials, which are sufficiently general for fitting any shaped curve. We develop a mixed-model methodology for QTL mapping of longitudinal traits and a maximum-likelihood method for parameter estimation and statistical tests. The expectation-maximization (EM) algorithm is applied to search for the maximum-likelihood estimates of parameters. The method is verified with simulated data and demonstrated with experimental data from a pseudobackcross family of Populus (poplar) trees.

Chromosome Mapping↗

PubMed1991

ADAPTU: animated dynamics analysis program at Tübingen University.

Molecular dynamics calculations are being used more and more in computational chemistry to investigate inter- and intra-molecular properties, as well as to determine structures. Visualization of a calculated trajectory is needed to allow a detailed analysis of the huge amount of data generated by such calculations. In addition to animating trajectories, ADAPTU was written to permit diagram generation in two and three dimensions for a detailed analysis, the extraction and listing of properties of a selected conformation and the visualization of the development of constraints in a restrained dynamics. The displayed trajectory, as well as the three-dimensional (3D) diagrams can be scaled, translated and rotated, and displayed in cross stereo representation. Our graphics device is a E&S PS300 system, which is connected to a host by Ethernet or by an asynchronous line.

Anti-Bacterial Agents↗

PubMed1998

[Computer-assisted analysis of sperm motility].

The fully automatic method for reconstruction of spermatozoa trajectories was presented. The method is based on computer image analysis. It allow to process pure semen without any treatment like diluting or purifying. Since no human interacting is available, this method lead to objective results. The method was used to analyse semen taken from healthy men (WHO 92 standard). The result shows absence of different populations in single sample.

Humans↗

PubMed2005

Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin.

Hairpins containing hexaloops are well represented among the diverse conformations adopted by the RNA molecules. To investigate the intrinsic properties of a backbone submitted to a hexaloop fold, we present here a molecular dynamics study of an abasic hexaloop closed by an A-form 6 basepair stem. The analysis of the 23 ns trajectory made in explicit solvent shows that both the sugars and the torsion angles in the loop undergo numerous conformational transitions. The south sugars, although not in a majority, are the major actors of the loop stretching. The five torsion angles, epsilon, zeta, alpha, beta, and gamma, are unequally variable, and only zeta and alpha exhibit trimodal distributions. The analysis of the phosphate linkages in terms of epsilonzeta'-alpha'-beta'-gamma-combinations allows us to define five conformational families, each one composed of one major substate in equilibrium with several less populated ones. The transitions between the substates within a family follow specific pathways involving the angles epsilon, zeta, and alpha. Thus, this work reveals that the backbone conformational space is both reduced and ordered even in a hexaloop devoid of bases.

Binding Sites↗

PubMed2003

Dynamic NMR structures of [Rp]- and [Sp]-phosphorothioated DNA-RNA hybrids: is flexibility required for RNase H recognition?

Chemically modified DNA oligonucleotides have been crucial to the development of antisense therapeutics. High-resolution structural studies of pharmaceutically relevant derivatives have been limited to only a few molecules. We have used NMR to elucidate the structure in solution of two DNA-RNA hybrids with the sequence d(CCTATAATCC).r(GGAUUAUAGG). The two hybrids contain an unmodified RNA target strand, whereas the DNA strand contains one of two different stereoregular sugar-phosphate backbone linkages at each nucleotide: 1), [Rp]-phosphorothioate or 2), [Sp]-phosphorothioate. Homonuclear two-dimensional spectroscopy afforded nearly complete nonlabile proton assignments. Distance bounds, calculated from the nuclear Overhauser effect (NOE) crosspeak intensities via a complete relaxation matrix approach with the program MARDIGRAS, were used to restrain the structure of the two hybrids during simulations of molecular dynamics. Analysis of restrained molecular dynamics trajectories suggests that both hybrids are flexible, requiring the use of molecular dynamics with time-averaged restraints (MDtar) to generate ensembles of structures capable of satisfying the NMR data. In particular, the deoxyribose sugars of the DNA strand show strong evidence of repuckering. Furthermore, deoxyribose sugar repuckering is accompanied by increased flexibility of overall helical geometry. These observations, together with the analysis of the crystal structure of a hybrid duplex in complex with ribonuclease H (RNase H), suggested that this flexibility may be required for recognition by RNase H.

Base Sequence↗

PubMed1990

Accessible conformations of melanin-concentrating hormone: a molecular dynamics approach.

Molecular dynamics simulations have been used to search for the accessible conformations of the melanin-concentrating hormone (MCH). The studies have been performed on native MCH and two of its peptide fragments, a cyclic MCH(5-14) fragment and a linear MCH(5-14) fragment. An analysis of the molecular dynamics trajectories of the three peptides indicates that two regions of the peptide have characteristic conformational properties that may be important for the biological activity. One is a region around Gly8, which is conformationally mobile, and the other is around Pro13, which shows unusual rigidity. The molecular dynamics simulation results are discussed in terms of backbone structural features like beta turns, side-chain interactions, and orientations of the disulfide bridge. The results of this analysis are used to suggest new analogues that will modify the conformational features of the peptide and further define the conformational requirements for activity. Finally, the results are related to nmr studies of the peptide and reveal agreements between the experimental nuclear Overhauser effect constraints and some of the accessible conformations obtained from the simulation.

Amino Acid Sequence↗

PubMed1999

The neurodevelopmental basis of schizophrenia: clinical clues from cerebro-craniofacial dysmorphogenesis, and the roots of a lifetime trajectory of disease.

A "read-back" analysis of schizophrenia, from chronic illness, through the first psychotic episode, to psychosocial and neurointegrative abnormalities of childhood and infancy, leads to the intrauterine period as a primary focus for etiological events. Evidence for a characteristic topography of cerebro-craniofacial dysmorphology in schizophrenia is reviewed, and interpreted to estimate: (i) the timing of dysmorphic event(s); (ii) the nature of early cellular and molecular mechanisms which might determine that topography of dysmorphogenesis; and (iii) the population homogeneity of these processes. It is argued that early cerebro-craniofacial dysmorphogenesis in schizophrenia should be conceptualized as a first stage not in a static but rather in a dynamic, lifetime trajectory of disease.

Brain↗

PubMed1999

Single-molecule anisotropy imaging.

A novel method, single-molecule anisotropy imaging, has been employed to simultaneously study lateral and rotational diffusion of fluorescence-labeled lipids on supported phospholipid membranes. In a fluid membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in which the rotational diffusion time is on the order of the excited-state lifetime of the fluorophore rhodamine, a rotational diffusion constant, D(rot) = 7 x 10(7) rad(2)/s, was determined. The lateral diffusion constant, measured by direct analysis of single-molecule trajectories, was D(lat) = 3.5 x 10(-8) cm(2)/s. As predicted from the free-volume model for diffusion, the results exhibit a significantly enhanced mobility on the nanosecond time scale. For membranes of DPPC lipids in the L(beta) gel phase, the slow rotational mobility permitted the direct observation of the rotation of individual molecules characterized by D(rot) = 1.2 rad(2)/s. The latter data were evaluated by a mean square angular displacement analysis. The technique developed here should prove itself profitable for imaging of conformational motions of individual proteins on the time scale of milliseconds to seconds.

Anisotropy↗

PubMed2026

Integrative analysis of single-cell sequencing identifies CD8+ TIM3+ CD101+ T cell-associated genes as prognostic biomarkers in breast cancer.

BACKGROUND: Breast cancer is a prevalent and deadly malignancy that significantly impacts women's quality of life and imposes financial burdens. Despite therapeutic advancements, tumour heterogeneity and frequent relapses remain major challenges. Accordingly, this study aimed to characterize immune features associated with CD8+ TIM3+ CD101+ T cells and develop a prognostic signature for breast cancer. METHODS: This study integrated single-cell and bulk transcriptomic datasets to characterize CD8+ TIM3+ CD101+ T cell (CCT)-related immune features and construct a prognostic signature in breast cancer. Single-cell RNA-seq data were sourced from the Gene Expression Omnibus (GEO) repository, and bulk transcriptomic data were from The Cancer Genome Atlas (TCGA) and GEO databases. Analytical methods included pseudo-time trajectory reconstruction (Monocle2), intercellular signalling analysis (CellChat), functional enrichment (ClusterProfiler), and immune profiling (ssGSEA). Prognostic modeling was conducted using least absolute shrinkage and selection operator (LASSO) Cox regression, with validation via Kaplan-Meier and time-dependent receiver operating characteristic (ROC) analyses. RESULTS: Single-cell analysis identified 17 clusters spanning seven cell types, including T cells, myeloid cells, and epithelial cells. T-cell sub-clustering revealed four subtypes. Pseudotime analysis suggested a potential state-transition relationship between CD8+ CD101- TIM3+ and CD8+ CD101+ TIM3+ T-cell states. A total of 121 differentially expressed genes were enriched in vital biological processes. An 11-gene prognostic model showed strong predictive power across cohorts. Single-cell T-cell reclustering identified a CD8+ CD101+ TIM3+ T-cell subpopulation, which was primarily characterized by the expression of markers such as CD101 and HAVCR2/TIM3. CONCLUSIONS: This study maps cellular heterogeneity and molecular networks in breast cancer, offering insights for targeted therapy and improved prognosis.

Breast invasive carcinoma↗

PubMed2002

Dynamic and structural analysis of isotropically distributed molecular ensembles.

An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between "rigid" and "mobile" parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5-ns molecular dynamics trajectory of native ubiquitin and a 40-ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10-fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules.

Computer Simulation↗

PubMed2000

Conformational analysis of the Sd(a) determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations.

The conformational behaviour of the spacer-linked synthetic Sd(a) tetrasaccharide beta-D-GalpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (1) and the two mimics beta-D-Galp-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)-bet a-D-GlcpNAc-(1-->O)(CH2)5NH2 (2) and beta-D-GlcpNAc-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp-(1-->4)- beta-D-GlcpNAc-(1-->O)(CH2)5NH2 (3) were investigated by 1H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the beta-D-Hex(NAc)-(1-->4)-[alpha-Neu5Ac-(2-->3)]-beta-D-Galp fragments. The alpha-Neu5-Ac-(2-->3)-beta-D-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

Carbohydrate Conformation↗

PubMed2006

To work or not to work? The occupational trajectories of wheelchair users.

PURPOSE: To throw light upon the dynamic processes which may or may not lead persons with severe motor disability to employment. METHOD: A qualitative approach to the chronology of both the professional and non-professional occupations of wheelchair users between acquisition of the disability and the interview; this approach focuses upon actions and meanings, thus allowing the authors to identify the diverse factors which help build the occupation situation at the time of the study. The narratives of 36 wheelchair users of working age were used. The objective of the analysis was to reconstitute the occupation trajectories of the participants and hence to suggest a typology. This involved pinpointing the various actors, the external and cognitive contexts of their decisions and actions, and their consequences and related feelings. RESULTS: The wide diversity found in the trajectories forced the authors to go beyond any simple notion of 'work versus non-work' and to focus on the quality of the individual's process of occupation appropriation. Indeed, it is possible to successfully appropriate both work and non-work situations, just as, inversely, it is possible for a person to fail to appropriate either type of situation. Analysis of this process allows one to pinpoint different types of trajectory. On the one hand, trajectories within which people appropriate their occupations--gradual, intermittent, through rupture and successive adjustment--and, on the other hand, unstable or endured occupation trajectories. CONCLUSIONS: The findings suggest that with regard to rehabilitation practices, we should be focussing as much on the appropriation process as on return to work.

Activities of Daily Living↗

PubMed1996

Stereological analysis of the layered collagen of human intracranial aneurysms.

Intracranial saccular aneurysms are balloon-like distensions of the arterial wall; they increase in size gradually, a few to the point of bleeding or catastrophic rupture. Collagen is the primary structural component of the aneurysmal wall, and because only a small fraction of aneurysms fail, the collagen fabric must effectively reorganize in order to maintain mechanical integrity as an aneurysm changes size. Data were obtained from four human aneurysms, fixed at 110 mmHG of distending pressure with 10% buffered formalin, and sectioned completely through at 4 microns thickness. Each set of measurements included groups of data taken layer by layer from a radial corridor across the aneurysm wall. Each three-dimensional orientation measurement, for which we used a Zeiss polarizing microscope with a universal stage attachment, is defined by an azimuth and elevation angle relative to the section plane. We compared the interdependence of these measured angles with a mathematical model based on fibres following great circle trajectories, and related the measured azimuth and elevation angles to the relative depth of the section into the aneurysm. Data were plotted on Lambert equal-area projections, along with the theoretical relation between azimuth and elevation, that included wall thickness and depth of sectioning. The graphical relationship between measured azimuth and elevation for collagen fibres across the layered fabric of the aneurysmal wall is consistent with the theoretical great circle trajectories for collagen fibre alignment. Analysis was based on statistics for spherical data to give values for the mean orientation and the circular standard deviations (CSD) about that mean. The results indicate that any given region on the aneurysm wall is made up of many, very thin sublayers, most of which have a relatively coherent organization (mean CSD 8 degrees). These measurements agree well with the mathematical model and, when considered collectively, the layers provide a balanced distribution for bearing the biaxial tensile stress of the wall.

Adult↗

PubMed1990

[Study of the trajectory of erythrocyte movement in microvessels using a method of automatic image analysis].

Many physiological and pathological processes in the circulation are related to changes of blood rheological properties. Since blood represents a specific suspension of cells in plasma the mentioned changes are to a great degree dependent on behavior and interaction of red blood cells (RBC). For investigation of blood flow structure in microvessels we developed an algorithm and worked out a program for automatic treatment of RBC movement on the basis of automatic image analysis system "Leitz-TAS" (Ernst Leitz, FRG). The program was based on computation of coordinates of blood cell centers. Further we calculated the following values: the vector of displacements (S), its projection on both axes (dx, dy), their relationship (dy/dx), the relationship of RBC radial coordinate to vessel radius (y/R), and the velocity of RBC movements (V). Proceeding from these data we obtained such parameters, as e.g., the velocity profile, the radial displacements of red cells, etc. by which we could judge on the blood flow regime, the flow structure and changes of blood rheological properties.

Algorithms↗

PubMed2004

Goal-directed upper limb movements by children with and without DCD: a window into perceptuo-motor dysfunction?

BACKGROUND AND PURPOSE: Developmental co-ordination disorder (DCD) occurs in at least 6% of school-aged children. Researchers agree that motor co-ordination problems evident in DCD are, in part, the result of perceptual and cognitive processes, but the limited research available remains inconclusive. The present study investigated perceptual-motor abilities, with regard to vision, kinaesthesia and cross-modal judgement, in children with and without DCD. METHOD: A cross-sectional study design was used. Nine children, aged six years (+/- six months) with DCD, and nine children without DCD, matched for age and gender, participated in the study. The children were required to point with the preferred hand to a target in three different positions under four sensory conditions, either with or without vision. Three-dimensional motion analysis was used to investigate trajectory lengths, endpoint error and movement time. The results were analysed using a generalized linear mixed model to examine the systematic effects of group, target position and task. RESULTS: Compared with children without DCD, the children with DCD produced larger endpoint errors, greater movement times and longer trajectories. Children in both groups produced larger endpoint errors, greater movement times and longer trajectories in non-visually guided aiming versus visually guided aiming tasks. CONCLUSIONS: Children with DCD moved more slowly, with longer movement trajectories and were less accurate than children without DCD when aiming to all target positions under all sensory conditions. The greatest error and trajectory length occurred for both groups when aiming movements were performed in the absence of vision. As children in the DCD group had difficulties with movement executed under kinaesthetic or visual control, the results indicate that the normal advantage of vision displayed by children without DCD is not apparent, and visual and kinaesthetic problems may be present in children with DCD.

Arm↗

PubMed1997

Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors.

Molecular models of the trans-membrane domains of delta, kappa and mu opioid receptors, members of the G-protein coupled receptor (GPCR) superfamily, were developed using techniques of homology modeling and molecular dynamics simulations. Structural elements were predicted from sequence alignments of opioid and related receptors based on (i) the consensus, periodicities and biophysical interpretations of alignment-derived properties, and (ii) tertiary structure homology to rhodopsin. Initial model structures of the three receptors were refined computationally with energy minimization and the result of the first 210 ps of a 2 ns molecular dynamics trajectory at 300K. Average structures from the trajectory obtained for each receptor subtype after release of the initial backbone constraints show small backbone deviations, indicating stability. During the molecular dynamics phase, subtype-differentiated residues of the receptors developed divergent structures within the models, including changes in regions common to the three subtypes and presumed to belong to ligand binding regions. The divergent features developed by the model structures appear to be consistent with the observed ligand binding selectivities of the opioid receptors. The results thus implicate identifiable receptor microenvironments as primary determinants of some of the observed subtype specificities in opiate ligand binding and in functional effects of mutagenesis. Networks of interacting residues observed in the models are common to the opiate receptors and other GPCRs, indicating core interfaces that are potentially responsible for structural integrity and signal transduction. Analysis of extended molecular dynamics trajectories reveals concerted motions of distant parts of ligand-binding regions, suggesting motion-sensitive components of ligand binding. The comparative modeling results from this study help clarify experimental observations of subtype differences and suggest both structural and dynamic rationales for differences in receptor properties.

Amino Acid Sequence↗

PubMed1994

Single-particle tracking: models of directed transport.

Single-particle tracking techniques make it possible to measure motion of individual particles on the cell surface. In these experiments, individual trajectories are observed, so the data analysis must take into account the randomness of individual random walks. Methods of data analysis are discussed for models combining diffusion and directed motion. In the uniform flow model, a tracer simultaneously diffuses and undergoes directed motion. In the conveyor belt model, a tracer binds and unbinds to a uniform conveyor belt moving with constant velocity. If a tracer is bound, it moves at the velocity of the conveyor belt; if it is unbound, it diffuses freely. Trajectories are analyzed using parameters that measure the extent and asymmetry of the trajectory. A method of assessing the usefulness of such parameters is presented, and pitfalls in data analysis are discussed. Joint probability distributions of pairs of extent and asymmetry parameters are obtained for a pure random walk. These distributions can be used to show that a trajectory is not likely to have resulted from a pure random walk.

Biological Transport, Active↗