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PubMed1999

Time and qualitative research.

Qualitative researchers may bear a special obligation in relation to time, as the context they hope to preserve for the phenomena they study is, in large part, temporal. Temporal concerns are integral to qualitative research, whether the focus is on disciplines in which largely qualitative methods are used, paradigms of inquiry that are primarily associated with qualitative methods, or on qualitative methods themselves. Temporal factors play a critical role in purposive sampling, the content and structure of data collection and analysis techniques, and in the re-presentation of data in the qualitative research report. Qualitative research designs may be oriented to synchronic and/or diachronic analyses. The Trajectory Model is a useful framework for sampling, data collection, and analysis. The Storyline Graph is a tool especially useful in narrative research.

Data Collection↗

PubMed2003

[Software for MR image reconstruction from data acquired on an irregular k-space trajectory].

A PC-based software was developed and programmed with VC++6 for reconstructing MR images from the data acquired on an irregular k-space trajectory. It can read clinical MRI raw data and image data, create numerical phantoms, design k-space trajectories, generate k-space data from numerical phantom, calculate weighting functions, reconstruct images, and carry out error analysis for the reconstructed images. It is helpful to the investigations of new k-space trajectories and new reconstruction algorithms.

Algorithms↗

PubMed1989

The evolution of growth trajectories and other complex quantitative characters.

Growth trajectories differ from many other quantitative characters in that they are characterized by a continuous function rather than by a finite number of discrete measurements. We review here recently developed methods for predicting the evolution of growth trajectories under the influence of natural or artificial selection. Using our method, analysis of genetic data from mice shows that the patterns of genetic variation arising from developmental processes impose constraints on evolution of growth trajectories. These constraints can be quantified to reveal the families of growth trajectories that can be produced by selection and those families that cannot. The data suggest there may be relatively few evolutionary degrees of freedom for growth trajectories despite the presence of abundant additive genetic variation to alter size and (or) growth rate at every age. The description of these constraints may be useful to both biologists who would like to determine the evolutionary options available to natural populations and to breeders who would like to alter growth trajectories to economically improve domesticated species. Our methods and conclusions can be generalized to other kinds of "infinite-dimensional" or complex characters, including morphological shapes and norms of reaction.

Age Factors↗

PubMed2003

Coordinated turn-and-reach movements. II. Planning in an external frame of reference.

The preceding study demonstrated that normal subjects compensate for the additional interaction torques generated when a reaching movement is made during voluntary trunk rotation. The present paper assesses the influence of trunk rotation on finger trajectories and on interjoint coordination and determines whether simultaneous turn-and-reach movements are most simply described relative to a trunk-based or an external reference frame. Subjects reached to targets requiring different extents of arm joint and trunk rotation at a natural pace and quickly in normal lighting and in total darkness. We first examined whether the larger interaction torques generated during rapid turn-and-reach movements perturb finger trajectories and interjoint coordination and whether visual feedback plays a role in compensating for these torques. These issues were addressed using generalized Procrustes analysis (GPA), which attempts to overlap a group of configurations (e.g., joint trajectories) through translations and rotations in multi-dimensional space. We first used GPA to identify the mean intrinsic patterns of finger and joint trajectories (i.e., their average shape irrespective of location and orientation variability in the external and joint workspaces) from turn-and-reach movements performed in each experimental condition and then calculated their curvatures. We then quantified the discrepancy between each finger or joint trajectory and the intrinsic pattern both after GPA was applied individually to trajectories from a pair of experimental conditions and after GPA was applied to the same trajectories pooled together. For several subjects, joint trajectories but not finger trajectories were more curved in fast than slow movements. The curvature of both joint and finger trajectories of turn-and-reach movements was relatively unaffected by the vision conditions. Pooling across speed conditions significantly increased the discrepancy between joint but not finger trajectories for most subjects, indicating that subjects used different patterns of interjoint coordination in slow and fast movements while nevertheless preserving the shape of their finger trajectory. Higher movement speeds did not disrupt the arm joint rotations despite the larger interaction torques generated. Rather, subjects used the redundant degrees of freedom of the arm/trunk system to achieve similar finger trajectories with differing joint configurations. We examined finger movement patterns and velocity profiles to determine the frame of reference in which turn-and-reach movements could be most simply described. Finger trajectories of turn-and-reach movements had much larger curvatures and their velocity profiles were less smooth and less bell-like in trunk-based coordinates than in external coordinates. Taken together, these results support the conclusion that turn-and-reach movements are controlled in an external frame of reference.

Acceleration↗

PubMed1996

Rational choice of molecular dynamics simulation parameters through the use of the three-dimensional autocorrelation method: application to calmodulin flexibility study.

We examined the effects of several adjustable parameters for use in molecular dynamics simulations of proteins using both standard criteria (radius of gyration, root mean square deviation from starting coordinates, molecular mechanics energy) and a new description of protein conformations by 3-D autocorrelation vectors (3-D ACV). We chose calmodulin (CaM) as a protein model and analysed 23 simulations using different combinations of the four molecular dynamics parameters studied, such as the dielectric constant (epsilon), the heating phase time (H), the thermal bath coupling time (zeta T) and the time step size (delta t). The correctness of the various trajectories generated with different parameter sets was evaluated through geometric analysis and use of a knowledge-based profile method. It is shown that 3-D ACV combined with multivariate statistical analysis provides a convenient way to describe and compare molecular dynamics simulations and constitutes a valuable complementary tool to standard methods. Using these methods, comparison of the various simulations performed on CaM indicated that the best in vacuo parameter set was epsilon = 1 x r, H = 15 ps, zeta T = 0.1 ps and delta t = 1 fs in fairly good agreement with previous less extensive comparisons of molecular dynamics trajectories.

Binding Sites↗

PubMed2004

Degradation of postural control system as a consequence of Parkinson's disease and ageing.

In this study we have shown how Parkinson's disease and ageing affect the postural control system. Our investigation of that system has involved analysis of quiet-standing center of pressure (COP) trajectories. Using the method derived from Langevin equation, we have found disease-specific and age-specific changes in the dynamics of the COP. These findings were obtained from a comparison of the diffusion matrix, the friction coefficient and the matrix of the fluctuation strength for healthy young, healthy elderly and parkinsonian (elderly) subjects under eyes-open and eyes-closed conditions. Especially the analysis of the friction coefficient and the matrix of the fluctuation strength have allowed the more detailed study of the postural control system of the parkinsonian and elderly subjects. We have found that the healthy elderly as well as parkinsonian subjects exhibit larger level of the muscular stochastic activity, compared to the young subjects. Furthermore, closure their eyes causes further increment of that activity. We have also shown that for the healthy elderly subjects a compensating mechanism, which can be described by the friction coefficient, acts under eyes-closed conditions, whereas for parkinsonian subjects this mechanism was not observed. Thus, the increase of the muscular activity is an age-specific indicator, whereas the absence of the compensation of that increase is a disease-specific indicator.

Adaptation, Physiological↗

PubMed1989

Prehension in the pigeon. II. Kinematic analysis.

During eating, the pigeon's jaw functions as a prehensile organ, i.e., as an effector organ involved in the grasping and manipulation of objects. The preceding paper provided a descriptive account of the jaw opening movements associated with each phase of the eating behavior sequence. For two of these movements, Grasping and Mandibulation, the amplitude of jaw opening is adjusted to pellet size. In the present study a kinematic analysis of these movements was carried out to clarify the motor control mechanisms mediating these adjustments. The analysis was carried out within the conceptual framework provided by a "pulse-control" model of targeted movement. For each of the movements the extent to which opening amplitude, its first and second derivatives and its rise time are scaled to pellet size was determined. Relationships among these kinematic variables were then examined in order to distinguish between "pulse-height" and "pulse-width" strategies. In addition, the possibility that "corrective adjustments" to the trajectory are made during its execution was also explored using a multiple regression analysis developed by Gordon and Ghez (1987a, b). For both movements, peak opening amplitude, acceleration and velocity are scaled to pellet size and these variables account for most of the variance in opening amplitude. The kinematic analysis suggests that critical parameters of the trajectory are determined ("programmed") prior to its initiation. Moreover, pigeons, like cats and humans, appear to utilize a "pulse-height" strategy for the control of amplitude scaling during targeted movements.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins.

We study the dependence of folding time, nucleation site, and stability of a model beta-hairpin on the location of a cross-strand hydrophobic pair, using a coarse-grained off-lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping-out, middle-out, zipping-in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the beta-turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the beta-turn encourages stability of the entire chain.

Computer Simulation↗

PubMed2001

Random Trajectory Modeling of Limited-Volume Percolation in a Microporous Structure.

The limited-volume analytical method for the evaluation of the probability of percolation (random trajectory approach) is developed. The model uses probabilistic analysis of possible percolation ways. The main equation for the probability of percolation contains parameters related to the conditions of formation of the microporous medium. Results of some computer estimations of the influence of various formation-related parameters (porosity, surface tension, coordination number, etc.) are presented. Copyright 2001 Academic Press.

Journal Article↗

PubMed1984

Invariants in loaded goal directed movements.

Goal directed movements, executed by means of a manipulator with various dynamics, were investigated in order to establish to what extent the loading affects the executed movement. The desired movement concept, together with a describing function model for goal directed movements, was applied to parameterize the movements. Analysis of the results showed that the position trajectories, when scaled by means of a fundamental scale property, with respect to the maximum velocity of the desired movements, were invariant under variation of the manipulator dynamics. From this invariance in the phasing of the movements, it was concluded that the subjects fully adapted to the applied loads.

Goals↗

PubMed2006

Cognitive load affects postural control in children.

Inferring relations between cognitive processes and postural control is a relatively topical challenge in developmental neurology. This study investigated the effect of a concurrent cognitive task on postural control in a sample of 50 nine-year-old children. Each subject completed two balance trials of 60 s, one with a concurrent cognitive task (cognitive load) and another with no cognitive load. The concurrent cognitive task consisted of mentally counting backwards in steps of 2. Twelve posturographic parameters (PPs) were extracted from the centre of pressure (CoP) trajectory obtained through a load cell force plate. Analysis of variance revealed significant differences in the majority of the extracted PPs. CoP was found to travel faster, farther, and with substantially different features demonstrating an overall broadening of the spectrum in the frequency domain. Nonlinear stability factors revealed significant differences when exposed to a concurrent cognitive task, showing an increase of instability in the intervention rate of the postural control system. By grouping children through selected items from Teachers Ratings and PANESS assessment, specific significant differences were also found both in time and frequency domain PPs, thus confirming the hypothesis of an interaction between cognitive processes (and their development), and postural control.

Attention↗

PubMed1994

Sensitivity functions of a human head movement model.

With time as the criterion to be optimized, the divergences from optimal head movements show systematic differences of their control signal variables with respect to single behaviours. To clarify these relationships, this study uses manipulation and mathematical analysis of the 6th order nonlinear head movement model, i.e. the threefold approach of sensitivity analysis. In addition to sensitivity coefficients, graphs and trajectories sensitivity functions have been analysed. This is the sensitivity of a nominal head movement to changes of the model parameters during the time course of the movement. This demonstrated both the specific change of the visco-inertial properties of the head movement model during the movement and also the potential pathological deficits that may occur.

Computer Simulation↗

PubMed2026

Divergent evolutionary strategies in spider venoms: A comparative proteomic profiling of four sympatric species from Yunnan.

Spider venoms comprise complex cocktails of bioactive molecules evolved for predation and defense, representing a valuable resource for biological research and pharmaceutical discovery. In this study, we performed a systematic analysis of venom gland extracts from four common spider species indigenous to Yunnan, China: Agelena limbata, Hippasa lycosina, Lycosa grahami, and Sinopoda pengi. Using an integrated transcriptomic and proteomic targeted profiling approach, we successfully annotated 141 distinct toxins. Comparative analysis revealed significant interspecific heterogeneity, suggesting distinct evolutionary trajectories and "weapon system economics." Both A. limbata and L. grahami exhibited a "peptide-dominant" profile anchored by neurotoxic peptides and isomerases, optimized for rapid chemical paralysis. In contrast, S. pengi displayed a distinct "protein-dominant" signature enriched with high-molecular-weight enzymes and CAP superfamily proteins, likely functioning to facilitate tissue degradation and toxin diffusion. Occupying an intermediate position, H. lycosina demonstrated a hybrid composition. These findings suggest that although these species share the same geographical range, their venom systems have undergone divergent evolutionary adaptations driven by specific ecological niches and hunting strategies. This study represents the first systematic proteomic characterization of these venom components, providing a valuable reservoir of molecular candidates while highlighting the bioinformatic nuances of analyzing whole-gland homogenates.

Animals↗

PubMed2005

Analysis of regional and temporal characteristics of PM10 during an Asian dust episode in Korea.

This study analyzes the regional and temporal distributions of PM10 concentrations observed in major metropolitan cities in Korea before, during and after a recent Asian dust episode in 2002. There were spatial and temporal variations in PM10 concentrations among the mid-western, the southwestern, the southeastern, and the southern parts of Korea during this Asian dust period due to the different air mass movement time and the different wind directions and speeds of prevailing winds in each city or region. The origins of the three-day Asian dust episode were identified by an analysis of two-day backward isentropic air trajectories. The different origins for each day also significantly contributed to the spatial and temporal variations in PM10 concentrations. A significant relationship was found between PM10 concentrations on the day preceding the first peak day and the first peak day of the Asian dust period but only in the mid-western areas. The concentrations of PM10 just after the Asian dust episode were much higher than those just before. There was a significant increase in a coarse fraction, having soil origins, of particles during the Asian dust episode. Concentrations of Mn, Fe, Ni and Cr extracted from the total suspended particulate (TSP) samples collected in 7 cities during the Asian dust episode were much higher when compared with other days in 2001. However, the Asian dust did not consistently increase the concentrations of lead, cadmium and copper as they are influenced by local sources such as local traffic or industrial emissions.

Air↗

PubMed2004

The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.

Reverse transcriptases (RTs) are multidomain enzymes of variable architecture that couple both RNA- and DNA-directed DNA polymerase activities with an RNase H activity specific for an RNA:DNA hybrid in order to replicate the single-stranded RNA genome of the retrovirus. Previous structural work has been reported for the heterodimeric HIV-1 and HIV-2 RTs. We now report the first crystal structure of the full-length Moloney murine leukemia virus (MMLV) RT at 3.0 A resolution. The structure reveals a clamp-shaped molecule resulting from the relative positions of the thumb, connection, and RNase H domains that is strikingly different from the HIV-1 RT and provides the first example of a monomeric reverse transcriptase. A comparative analysis with related DNA polymerases suggests a unique trajectory for the template-primer exiting the polymerase active site and provides insights regarding processive DNA synthesis by MMLV RT.

Amino Acid Sequence↗

PubMed2002

Synergic analysis of upper limb target-reaching movements.

The topological invariance and synergies of human movements are discussed through the analysis and comparison of upper-limb target-reaching tasks. Five subjects were asked to perform different target-reaching tasks with different indices of difficulty, and the movements were captured using a Vicon 3D motion analysis system. Topological invariance was observed in the trajectories of different task performances. After normalization, the trajectories of the arm tips had very close patterns for different target-reaching tasks. Synergy in the target-reaching movements of the upper limbs was also found among the different joint angles. The joint angles can be fitted using the same format of functions proposed in this study. The parameters in the function can be taken as a characteristic feature of target-reaching movement patterns. A target-reaching movement can be determined by these parameters and the start and end positions.

Adult↗

PubMed2006

Modeling late-life adaptation in affective well-being under a severe chronic health condition: the case of age-related macular degeneration.

Age-related macular degeneration (AMD) was used as a case model to longitudinally study adaptation in affective well-being under a prevalent chronic health condition. Measures of positive and negative affect, obtained at 5 subsequent measurement occasions with 3-month intervals in between, were analyzed in 90 older adults diagnosed with AMD. The authors proposed a pattern of adaptation that shows initial decline in affective well-being after disease outbreak, followed by a turnaround into a restorative phase of increase, implying nonlinear intraindividual trajectories, with changes substantially related to disease duration. Analysis was conducted by means of a nonlinear mixed models approach. Results confirmed the hypothesized adaptation pattern for positive affect but not for negative affect, which was found more stable across measurement occasions.

Adaptation, Psychological↗

PubMed1997

Augmented Feedback Presented in a Virtual Environment Accelerates Learning of a Difficult Motor Task.

One can use a number of techniques (e.g., from videotaping to computer enhancement of the environment) to augment the feedback that a subject usually receives during training on a motor task. Although some forms of augmented feedback have been shown to enhance performance on isolated isometric tasks during training, when the feedback has been removed subjects have sometimes not been able to perform as well in the "real-world" task as controls. Indeed, for realistic, nonisometric motor tasks, improved skill acquisition because of augmented feedback has not been demonstrated. In the present experiments, subjects (Experiment 1, N = 42; Experiment 2, N = 21) performed with a system that was designed for teaching a difficult multijoint movement in a table tennis environment. The system was a fairly realistic computer animation of the environment and included paddles for the teacher and subject, as well as a virtual ball. Each subject attempted to learn a difficult shot by matching the pattern of movements of the expert teacher. Augmented feedback focused the attention of the subject on a minimum set of movement details that were most relevant to the task; feedback was presented in a form that required the least perceptual processing. Effectiveness of training was determined by measuring their performance in the real task. Subjects who received the virtual environment training performed significantly better than subjects who received a comparable amount of real-task practice or coaching. Kinematic analysis indicated that practice with the expert's trajectory served as a basis for performance on the real-world task and that the movements executed after training were subject-specific modifications of the expert's trajectory. Practice with this trajectory alone was not sufficient for transfer to the real task, however: When a critical component of the virtual environment was removed, subjects showed no transfer to the real task.

augmented feedback↗