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PubMed2004

Trajectories of dynamic predictors of disorder: their meanings and implications.

Developmental psychopathologists are increasingly focused on characterizing heterogeneity of trajectories of psychological disorders across the life course (e.g., developmentally limited vs. chronic forms of disorder). Although the developmental significance of trajectories has been highlighted, there has been little attention to relations between trajectories and their etiologically and clinically relevant time-varying covariates (dynamic predictors). Depending upon the functional relation between a disorder and a dynamic predictor, we expect to see different trajectories of dynamic predictors. Thus, we propose a taxonomy of trajectories of dynamic predictors of course of disorder and provide an initial investigation into its validity. Using a mixed-gender, high-risk sample of young adults followed over 7 years, we identified dynamic predictors that covary with the course of alcohol use disorder (AUD). Based on a logically derived classification to facilitate interpretation of findings, three comparison groups were examined: persons whose AUD "remitted" (n = 33), those with a chronic AUD (n = 29), and nondiagnosers (n = 274). We hypothesized seven patterns of dynamic prediction (stable vulnerability indicators, course trackers, deterioration markers, developmentally specific variables, developmental lag markers, course-referenced variables, and recovery behaviors) and found evidence for five of them. The interpretation of markers of risk for development and course of AUDs and their implications for prevention, early intervention and formal/self-change treatments are discussed.

Adult↗

PubMed2004

Taking hold of some kind of life: how developmental tasks relate to trajectories of well-being during the transition to adulthood.

The purpose of this study was to examine how successes and difficulties with various developmental tasks of early adulthood relate to the course of well-being. Three waves of national panel data spanning ages 18-26 were drawn from the Monitoring the Future study (N = 3518). Based on self-reports, respondents were assigned scores (succeeding, maintaining, or stalling) to reflect progress in seven domains of developmental tasks: education, work, financial autonomy, romantic involvement, peer involvement, substance abuse avoidance, and citizenship. We identified trajectory groups of well-being (based on self-esteem, self-efficacy, and social support) that reflect diverging trajectories during the transition: steady-high versus high-decreasing, and low-increasing versus steady-low. Logistic regression analyses were conducted to predict membership in the diverging well-being trajectory groups as a function of developmental task domain scores. Maintaining or gaining a salutary trajectory of well-being across the transition was found to be a function of more success and less stalling across the developmental tasks, specifically in the work, romantic involvement, and citizenship domains. Compensatory effects (e.g., succeeding in education compensated for not succeeding in work) and threshold effects (e.g., succeeding in both achievement and affiliation domains was necessary for a salutary trajectory) were also found.

Adolescent↗

PubMed2004

Geometric trajectory analysis of metabolic responses to toxicity can define treatment specific profiles.

Metabonomics can be viewed as the process of defining multivariate metabolic trajectories that describe the systemic response of organisms to physiological perturbations through time. We have explored the hypothesis that the homothetic geometry of a metabolic trajectory, i.e., the metabolic response irrespective of baseline values and overall magnitude, defines the mode of response of the organism to treatment and is hence the key property when considering the similarity between two sets of measurements. A modeling strategy to test for homothetic geometry, called scaled-to-maximum, aligned, and reduced trajectories (SMART) analysis, is presented that together with principal components analysis (PCA) facilitates the visualization of multivariate response similarity and hence the interpretation of metabonomic data. Several examples of the utility of this approach from toxicological studies are presented as follows: interlaboratory variation in hydrazine response, CCl(4) dose-response relationships, and interspecies comparison of bromobenzene toxicity. In each case, the homothetic trajectories hypothesis is shown to be an important concept for the successful multivariate modeling and interpretation of systemic metabolic change. Overall, geometric trajectory analysis based on a homothetic modeling strategy like SMART facilitates the amalgamation and comparison of metabonomic data sets and can improve the accuracy and precision of classification models based on metabolic profile data. Because interlaboratory variation, normal physiological variation, dose-response relationships, and interspecies differences are also key areas of concern in genomic and proteomic as well as metabonomic studies, the methods presented here may also have an impact on many other multilaboratory efforts to produce screenable "-omics" databases useful for gauging toxicity in safety assessment and drug discovery.

Animals↗

PubMed1999

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories.

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.

Amino Acid Sequence↗

PubMed1998

Trajectories of adaptation in pediatric chronic illness: the importance of the individual.

This study used individual growth modeling to examine individual difference and group difference models of adaptation. The adaptation of 27 children with juvenile rheumatoid arthritis (JRA) and 40 children with insulin-dependent diabetes mellitus (IDDM) was tracked for 18 months from diagnosis. A control group of 62 healthy children was followed over the same time period. Clustering procedures indicated that child and family adaptation could be described by a number of distinct adaptation trajectories, independent of diagnostic group membership. In contrast, parental adaptation trajectory was associated with diagnostic group membership and control over disease activity for the JRA group and with diagnostic group membership for healthy controls. The observation of common patterns across trajectory sets, as well as the finding that trajectories were differentially related to a number of variables of interest, support the use of trajectories to represent adaptation to chronic disease.

Adaptation, Psychological↗

PubMed2006

A comparison of girls' and boys' aggressive-disruptive behavior trajectories across elementary school: prediction to young adult antisocial outcomes.

Multiple group analysis and general growth mixture modeling was used to determine whether aggressive- disruptive behavior trajectories during elementary school, and their association with young adulthood antisocial outcomes, vary by gender. Participants were assessed longitudinally beginning at age 6 as part of an evaluation of 2 school-based preventive programs. Two analogous trajectories were found for girls and boys: chronic high aggression- disruption (CHAD) and stable low aggression- disruption (LAD). A 3rd class of low moderate aggression- disruption (LMAD) for girls and increasing aggression- disruption (IAD) for boys also was found. Girls and boys in analogous CHAD classes did not differ in trajectory level and course, but girls in the CHAD and LAD classes had lower rates of antisocial outcomes than boys. Girls with the LMAD trajectory differed from boys with the IAD trajectory.

Achievement↗

PubMed2004

On-the-fly ab initio trajectory calculations of the dynamics of Cl atom reactions with methane, ethane and methanol.

The dynamics of Cl atom reactions with methane, ethane, and methanol have been studied by calculation of quasi-classical trajectories, with computation of potential energies and gradients only at the geometries through which the trajectories pass. Trajectories were started from the transition state, with 2 kcal mol(-1) of energy given to the mode with an imaginary frequency (representing the reaction coordinate at the transition state) and inclusion of zero-point energy in some or all of the remaining vibrational modes. The trajectories were propagated as far as separated products, with the majority of potential energy calculations performed at the HF/6-31G level of theory. The rotational quantum state population distributions of the HCl products from the reactions of Cl atoms with methane, ethane and methanol peaked at J'=1, 2, and 6, respectively. The calculations thereby exhibit somewhat greater rotational excitation than is found experimentally, but correctly describe the trend of increasing HCl product rotation for the three respective reactions. In agreement with previous observations, only 4% of the energy available to the products of the reaction of Cl atoms with methane was channeled into CH3 radical internal energy, and 1% into HCl rotation, with 92% ending up as translational energy. For the reaction of Cl atoms with ethane and with methanol, the corresponding values for radical internal energy, HCl rotation and product translation are 21, 3, and 78%, and 46, 13, and 42%, respectively. For the latter two reactions, the radical internal energy is mostly accounted for by rotational motion. The clear increase in rotational excitation of the HCl products from the Cl atom reaction with methanol is explained in terms of a dipole-dipole interaction between the departing polar fragments. A smaller set of more computationally expensive trajectory calculations using potentials and gradients from the MP2/6-311G(d,p) level of theory were performed for reactions of Cl atoms with methanol, and give results in better agreement with experimentally measured HCl rotational excitation, consistent with the model of dipole-induced product rotation because the MP2/6-311G(d,p) calculations give smaller dipole moments for both products than the HF/6-31G calculations. The calculated angles between the rotational angular momentum vectors and recoil velocities of the radical peak sharply at 90 degrees for the reactions of Cl atoms with ethane and methanol, but exhibit a much broader distribution for reaction with methane.

Journal Article↗

PubMed2004

Coherent switching with decay of mixing: an improved treatment of electronic coherence for non-Born-Oppenheimer trajectories.

The self-consistent decay-of-mixing (SCDM) semiclassical trajectory method for electronically nonadiabatic dynamics is improved by modifying the switching probability that determines the instantaneous electronic state toward which the system decoheres. This method is called coherent switching with decay of mixing (CSDM), and it differs from the previously presented SCDM method in that the electronic amplitudes controlling the switching of the decoherent state are treated fully coherently in the electronic equations of motion for each complete passage through a strong interaction region. It is tested against accurate quantum mechanical calculations for 12 atom-diatom scattering test cases. Also tested are the SCDM method and the trajectory surface hopping method of Parlant and Gislason that requires coherent passages through each strong interaction region, and which we call the "exact complete passage" trajectory surface hopping (ECP-TSH) method. The results are compared with previously presented results for the fewest switches with time uncertainty and Tully's fewest switches (TFS) surface hopping methods and the semiclassical Ehrenfest method. We find that the CSDM method is the most accurate of the semiclassical trajectory methods tested. Including coherent passages improves the accuracy of the SCDM method (i.e., the CSDM method is more accurate than the SCDM method) but not of the trajectory surface hopping method (i.e., the ECP-TSH method is not more accurate on average than the TFS method).

Journal Article↗

PubMed2005

Quasiclassical trajectory calculations to evaluate a kinematic constraint on internal energy in suprathreshold collision energy abstraction reactions.

Experimentally observed product quantum state distributions across a wide range of abstraction reactions at suprathreshold collision energies have shown a strong bias against product internal energy. Only a fraction, sometimes quite a small fraction, of the energetically accessible product quantum states are populated. Picconatto et al. [J. Chem. Phys. 114, 1663 (2001)] noted a simple mathematical relationship between the highest-energy rovibrational states observed and the kinematics of the reaction system. They proposed a reaction model based on reaction kinematics that quantitatively explains this behavior. The model is in excellent agreement with measured quantum state distributions. The assumptions of the model invoke detailed characteristics of reactive trajectories at suprathreshold collision energies. Here we test those assumptions using quasiclassical trajectory calculations for the abstraction reactions H+HCl-->H2+Cl, D+HCl-->HD+Cl, and H+DCl-->HD+Cl. Trajectories were run on a potential-energy surface calculated with a London-Eyring-Polyani-Sato function with a localized 3-center term (LEPS-3C) previously shown to accurately reproduce experimentally observed product state distributions for the H+HCl abstraction reaction. The trajectories sample collision energies near threshold and also substantially above it. Although the trajectories demonstrate some aspects of the model, they show that it is not valid. However, the inadequacy of the proposed model does not invalidate the apparent kinematic basis of the observed energy constraint. The present results show that there must be some other molecular behavior rooted in the reaction kinematics that is the explanation and the source of the constraint.

Journal Article↗

PubMed2006

Effect of finite trajectory length on the correlation function analysis of single molecule data.

The effect of finite trajectory length on single molecule rotational correlation functions has been studied by utilizing time series analysis and numerical simulations. Correlation functions obtained from the trajectories of length less than 100 times the correlation time constant (tau([script-l])) exhibit significant deviations from the true correlation function. The distributions of sample time constants (tau(F)) and stretching exponents (Beta(F)) are mapped by fitting a large number of rotational trajectories to stretched exponentials. As the trajectory length gets smaller, the distributions become broader and asymmetric and their mean values deviate from the true value predicted by pure rotational diffusion. Analysis based on higher order spherical harmonics is suggested as a method for minimizing the effect of the trajectory length. The distributions of time constants for different higher order spherical harmonics are also compared. While the focus of the paper is on rotational correlation functions, the general conclusions apply to any dynamical process that yields an exponentially decaying correlation function.

Computer Simulation↗

PubMed2006

Quasiclassical trajectories on a finite element density functional potential energy surface: The C++H2O reaction revisited.

A new method for the representation of potential energy surfaces (PESs) based on the p version of the finite element method is presented and applied to the PES of the [COH2]+ system in order to study the C++H2O-->[COH]++H reaction through the quasiclassical trajectory method. Benchmark ab initio computations have been performed on the most relevant stationary points of the PES through a procedure that incorporates basis set extrapolations, the contribution of the core correlation energy, and scalar relativistic corrections. The electronic structure method employed to compute the many points needed to construct the PES is a hybrid density functional approach of the B3LYP type with geometry-dependent parameters, which improves dramatically the performance with respect of the B3LYP method. The trajectory computations shed light on the behavior of the COH2+ complex formed in the collision. At a fixed relative translational energy of 0.62 eV, which corresponds to the crossed beam experiments [D. M. Sonnenfroh et al., J. Chem. Phys. 83, 3985 (1985)], the complex dissociates significantly into the reactants (37%). However, the behavior for a thermal sampling at T=300 K is significantly different because only 9% of the trajectories where capture occurs lead to dissociation into the reactants. The latter kind of behavior is coherent with the view that simple ion-molecule reactions proceed quite often at the capture rate provided it is corrected by the fraction of the electronic states which, being nearly degenerate for the reactants, become attractive at short distances. For both T=300 K and crossed beam conditions, the trajectory computations indicate that COH2+ is the critical intermediate, in agreement with a recent work [Y. Ishikawa et al., Chem. Phys. Lett. 370, 490 (2003)] and in contrast with the interpretation of the crossed beam experiments. Besides, virtually all trajectories generate COH++H (>99%), but a significant proportion of the isoformyl cation is formed with enough vibrational energy as to surmount the COH+-HCO+ isomerization barrier, about 37% at T=300 K.

Journal Article↗

PubMed1998

Minimum sperm trajectory length for reliable determination of the fractal dimension.

The aim of this study was to determine the minimum track length required for the reliable calculation of the fractal dimension of trajectories of capacitating human spermatozoa. Manually reconstructed trajectories classified previously as hyperactivated or non-hyperactivated were re-analyzed. The trajectories were reconstructed at 60 Hz, and each comprised 61 points (corresponding to 1 s movement). The trajectories were 'split' to give the equivalent of 2 x 31 point, 3 x 21 point, 4 x 16 point and 6 x 11 point track segments and the fractal dimension determined for each. The fractal dimensions of each track segment within each trajectory were compared using paired t-tests. No significant difference was observed between the fractal dimensions of track segments of equal length, irrespective of the motility pattern. However, significant differences in fractal dimension values were observed when segments of different lengths were compared (P<0.01). For the non-hyperactivated tracks, the fractal dimension was consistently below the hyperactivation threshold level for only the 31 point segments. The hyperactivated tracks consistently had fractal dimension values above the threshold level when segments of 16 points or longer were analysed. Therefore, the minimum track length for the determination of reliable fractal dimension values was 31 points, corresponding to an image sampling time of 0.5 s at 60 Hz, although it could be used as a screening method for the identification of hyperactivated motility for track segments of greater than 11 points (corresponding to 0.17 s movement).

False Positive Reactions↗

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↗

PubMed2025

An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training.

MOTIVATION: Accurate prediction of protein-ligand binding (PLB) relationships plays a crucial role in drug discovery, which helps identify drugs that modulate the activity of specific targets. Traditional biological assays for measuring PLB relationships are time consuming and costly. In addition, models for predicting PLB relationships have been developed and widely used in drug discovery tasks. However, learning more accurate PLB representations is essential to meet the stringent standards required for drug discovery. RESULTS: We propose an image-based PLB representation learning framework, called ImagePLB, which equips ligand representation learner (LRL) and protein representation learner (PRL) to accept 3D multi-view ligand images and protein graphs as input, respectively, and learns rich interaction information between ligand and protein through a binding representation learner (BRL). Considering the scarcity of protein-ligand pairs, we further propose a multi-level next trajectory prediction (MLNTP) task to pre-train ImagePLB on the 4D flexible dynamics trajectory of 16 972 complexes, including ligand level, protein level, and complex level, to learn information related to trajectories. Besides, by introducing trajectory regularization (TR), we effectively alleviate the problem of high (even almost identical) feature similarity caused by adjacent trajectories. Compared with the current state-of-the-art methods, ImagePLB has achieved competitive improvements on PLB-related prediction tasks, including protein-ligand affinity and efficacy prediction tasks. This study opens the door to the image-based PLB learning paradigm. AVAILABILITY AND IMPLEMENTATION: All data and implementation details of code can be obtained from https://github.com/HongxinXiang/ImagePLB.

Ligands↗

PubMed2006

Risk and protective factors of different functional trajectories in older persons: are these the same?

We examined whether risk and protective factors of different functional trajectories were the same in 1,765 Dutch older persons. We assessed disability in 1993 and reassessed it in 2001. For 2001 as compared with 1993, we distinguished three trajectory groups: substantially poorer, somewhat poorer, and no change or better functioning. We assessed sociodemographic, health, and psychosocial potential risk or protective factors in 1993. When we analyzed them separately, risk and protective factors had similar (but mirrored) associations with functional trajectories. However, in a multivariate approach, we identified old age, depressive symptoms, and low mastery as risk factors for functional decline, whereas we identified young age, good perceived health, and self-efficacy expectancies as factors that predicted trajectories of healthy functioning. Risk and protective factors of functional trajectories in older persons are not the same.

Aged↗

PubMed1992

Left hemisphere preponderance in trajectorial learning.

The present study examines the organisational principle of a trajectorial storage mechanism for isochronically controlled overlearned movements. 48 right-handed subjects were trained on new ideograms at five different sizes. After the trajectory had been overtrained with one hand, learning transfer to the contralateral hand was analysed. Results indicate a significant transfer of trajectorial information after training with the right hand towards the left hand which points to a preponderance of the dominant left hemisphere in generalizing storage of learned trajectories to either upper extremity. The trajectorial storage system has clear geometrical restraints.

Female↗

PubMed2002

Bullet trajectory predicts the need for damage control: an artificial neural network model.

BACKGROUND: Effective use of damage control in trauma hinges on an early decision to use it. Bullet trajectory has never been studied as a marker for damage control. We hypothesize that this decision can be predicted by an artificial neural network (ANN) model based on the bullet trajectory and the patient's blood pressure. METHODS: A multilayer perceptron ANN predictive model was developed from a data set of 312 patients with single abdominal gunshot injuries. Input variables were the bullet path, trajectory patterns, and admission systolic pressure. The output variable was either a damage control laparotomy or intraoperative death. The best performing ANN was implemented on prospectively collected data from 34 patients. RESULTS: The model achieved a correct classification rate of 0.96 and area under the receiver operating characteristic curve of 0.94. External validation showed the model to have a sensitivity of 88% and specificity of 96%. Model implementation on the prospectively collected data had a correct classification rate of 0.91. Sensitivity analysis showed that systolic pressure, bullet path across the midline, and trajectory involving the right upper quadrant were the three most important input variables. CONCLUSION: Bullet trajectory is an important, hitherto unrecognized, factor that should be incorporated into the decision to use damage control.

Abdominal Injuries↗

PubMed1992

Trajectories of changing refractive status.

Refractive status can be represented as a point plotted on a three-dimensional graph. As the refractive status changes a curve is traced out on the graph. Trajectories of changing refractive status are illustrated in a number of representative ideal cases. The three-dimensional graphs are shown by means of stereo-pairs. Trajectories are constructed from clinical data and interpreted with reference to the ideal examples. They show changing refractive status with age, after cataract extraction, and after radial keratotomy. The trajectories may prove to be a useful tool for both clinician and researcher. They show overall trends and allow prediction of future changes. Certain types of trajectories could prove to be characteristic of certain conditions and thus be useful for diagnosis. Trajectories allow monitoring of change after intervention.

Adolescent↗