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General coordination principles elucidated by forward dynamics: minimum fatique does not explain muscle excitation in dynamic tasks.

The target article presents a framework for coordination of one- and two-joint muscles in a variety of tasks. Static optimization analyses were performed that minimize muscle fatigue, and it is claimed that the predicted muscle forces account for essential features of EMG activity qualitatively well. However, static optimization analyses use the observed joint moments, which implicitly assumes that they minimize the total muscle fatigue of the task. We use a forward dynamics (i.e., relationship between muscle forces and the kinematics and kinetics of task performance) modeling approach to show that this assumption does not appear to be true in cycling (which was used as an example task in the target article). Our results challenge the hypothesized coordination framework and the underlying concept that general coordination principles for dynamic tasks can be elucidated using inverse-dynamics-based analyses.

Biomechanical Phenomena↗

Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities.

The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and the presence of the photolyzed CO in the proximity of the passage; here we show that in wild-type deoxy myoglobin, opening is almost random. In wild-type deoxy myoglobin, the passage between the distal pocket and the solvent is strictly correlated to the presence/absence of a water molecule that simultaneously interacts with the distal histidine side chain and the heme iron; conversely, in the photodissociated myoglobin, the connection with the bulk solvent is always open when CO is in the vicinity of the A pyrrole ring. In YQR deoxy myoglobin, the mutated Gln(E7)64 is stably H-bonded with the mutated Tyr(B10)29. The essential dynamics analysis unveils a different behavior for the three systems. The motion amplitude is progressively restricted in going from wild-type to YQR deoxy myoglobin and to wild-type myoglobin photoproduct. In all cases, the principal motions involve mainly the same regions, but their directions are different. Analysis of the dynamics of the preexisting cavities indicates large fluctuations and frequent connections with the solvent, in agreement with the earlier hypothesis that some of the ligand may escape from the protein through these pathways.

Animals↗

Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study.

Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates reveals that the conformational rearrangement of the peptide is rather complex and occurs on at least four timescales: 1) After photoexcitation, the azobenzene unit of the molecule undergoes nonadiabatic photoisomerization within 0.2 ps. 2) On the picosecond timescale, the cooling (13 ps) and the stretching (14 ps) of the photoexcited peptide is observed. 3) Most reaction coordinates exhibit a 50-100 ps component reflecting a fast conformational rearrangement. 4) The 500-1000 ps component observed in the simulation accounts for the slow diffusion-controlled conformational equilibration of the system. The simulation of the photoinduced molecular processes is in remarkable agreement with time-resolved optical and infrared experiments, although the calculated cooling as well as the initial conformational rearrangements of the peptide appear to be somewhat too slow. Based on an ab initio parameterized vibrational Hamiltonian, the time-dependent amide I frequency shift is calculated. Both intramolecular and solvent-induced contributions to the frequency shift were found to change by < or = 2 cm(-1), in reasonable agreement with experiment. The potential of transient infrared spectra to characterize the conformational dynamics of peptides is discussed in some detail.

Computer Simulation↗

Comparison of dynamic helical CT and dynamic MR imaging in the evaluation of pelvic lymph nodes in cervical carcinoma.

OBJECTIVE: This study compares dynamic helical CT with dynamic MR imaging in the evaluation of pelvic lymph nodes in cervical carcinoma. SUBJECTS AND METHODS: Women with biopsy-proven cervical carcinoma prospectively underwent dynamic helical CT and MR imaging before surgery. A metastatic node on CT and MR imaging was defined as a rounded soft-tissue structure greater than 10 mm in maximal axial diameter or a node with central necrosis. Imaging results were compared with pathology, and receiver operating characteristic curves for size and shape were plotted on a hemipelvis basis. Nodal density and signal intensity on CT and MR images, respectively, were reviewed for differences between benign and malignant disease. RESULTS: A total of 949 lymph nodes were found at pathology in 76 hemipelves in 43 women, of which 69 lymph nodes (7%) in 17 hemipelves (22%) were metastatic. Sensitivity, specificity, positive and negative predictive values, and accuracy of helical CT and MR imaging in the diagnosis of lymph node metastasis on a hemipelvis basis was 64.7%, 96.6%, 84.6%, 90.5%, and 89.5% and 70.6%, 89.8%, 66. 7%, 91.4%, and 85.5%, respectively. Receiver operating characteristic curves for helical CT and MR imaging gave cutoff values of 9 and 12 mm in maximal axial diameter, respectively, in the prediction of metastasis. Central necrosis had a positive predictive value of 100% in the diagnosis of metastasis. Signal intensity on MR imaging and density-enhancement pattern on CT in patients with metastatic nodes did not differ from those in patients with negative nodes. CONCLUSION: Helical CT and MR imaging show similar accuracy in the evaluation of pelvic lymph nodes in patients with cervical carcinoma. Central necrosis is useful in the diagnosis of metastasis in pelvic lymph nodes in cervical cancer.

Adult↗

[Dynamic attractor for the Berendsen thermostat an the slow dynamics of biomacromolecules].

It was shown that the nonlinear relaxation of a model system confined to the Berendsen's thermostat is determined by an attractor regime. The latter does not correspond generally to the true thermodynamic state of the system. Therefore, the use of the Berendsen's thermostat for molecular dynamics simulations, even in the case of large protein molecules at trajectory lengths of more than 10 ns, can lead to wrong conclusions. Our results agree with the concept of slow dynamics for macroscopic systems considered within the framework of the topological approach to stochastic dynamics.

Biopolymers↗

[Dynamic observation on imbalance of dynamic and static forces and degenerated cervical intervertebral disc in rats].

OBJECTIVE: To study the relation between biomechanical imbalance and the degree and course of degeneration of cervical intervertebral disc in rats. METHODS: Sixty SD rats, 8 months old, were randomly divided into 6 groups, the control and model groups of 3, 5, 7 months, 10 in each group. The cervical disc dynamic and static forces imbalance of degeneration model was established to assess the degree of degeneration as well as the content some inflammatory mediators (prostaglandin E2, 6-keto-prostaglandin F1 alpha) and collagenase (MMP-1) activity. RESULTS: (1) In 3 months model group and 5 months control group, fibrous ring of intervertebral disc showed some fissure and slight irregular arrangement, nucleus pulposus shrunken or became smaller, mild herniation of nucleus pulposus was seen in some disc. The nucleus pulposus of intervertebral disc in 5 months model group was fibrosed completely and the disc in 7 months model group herniated or became osteophytosis. (2) Compared with the control group of same time period, MMP-1 was increased significantly in the 5 months and 7 months model groups (P < 0.05), and prostaglandin E2 and 6-keto-prostaglandin F1 alpha elevated in the model groups (P < 0.05, P < 0.01). (3) Comparison between model groups, MMP-1 activity in 5 months and 7 months groups was higher than that in the 3 months group (P < 0.05), and 6-keto-prostaglandin F1 alpha was higher in 7 months group than that in 3 months group (P < 0.05). CONCLUSION: Cervical intervertebral disc undergoes a progressive degenerating process. By breaking the dynamic-static balance of neck in rats could accelerate the progression of degeneration. The fact could be used to elucidate the theory of pathogenesis of cervical spondylopathy, dynamic force imbalance in priority and static force imbalance in predominance.

Animals↗

Cell adhesion in a dynamic flow system as compared to static system. Glycosphingolipid-glycosphingolipid interaction in the dynamic system predominates over lectin- or integrin-based mechanisms in adhesion of B16 melanoma cells to non-activated endothelial cells.

Initial adhesion of B16 melanoma variants to non-activated endothelial cells is mediated through specific interaction between GM3 (NeuAc alpha 2----3Gal beta 1----4Glc beta 1----Cer) expressed on melanoma cells and lactosylceramide (LacCer, Gal beta 1----4Glc beta 1----Cer) expressed on endothelial cells. This adhesion is predominant over integrin- or lectin-mediated adhesion in a dynamic flow experimental system employing a parallel plate laminar flow chamber (Lawrence, M. B., Smith, C. W., Eskin, S. G., and McIntire, L. V. (1990) Blood 75, 227-237). In this system, a tumor cell suspension flows over a glass plate coated with glycosphingolipid, lectin, or fibronectin, and adhesion is recorded on videotape. These conditions were designed to mimic the microvascular environment in which tumor metastatic deposition takes place. In contrast, lectin- and fibronectin-based mechanisms are predominant in previously used static adhesion systems. Under static conditions, the relative degree of adhesion of the four B16 variants to endothelial cells or to LacCer-coated plates was the same as their relative degree of GM3 expression (i.e. BL6 approximately F10 greater than F1 greater than WA4), and adhesion was inhibited in the presence of methyl-beta-lactoside, or liposomes containing LacCer or GM3. Adhesion was also inhibited by pretreatment of B16 cells with anti-GM3 antibody DH2 or sialidase and by pretreatment of endothelial cells with anti-LacCer antibody T5A7. Under dynamic flow conditions, WA4 cells did not adhere to mouse endothelial cells at high shear stress (greater than 2.5 dynes/cm2) but did adhere at lower shear stress. In contrast, BL6 and F10 cells adhered strongly at both low and high shear stress. BL6 cell adhesion to endothelial cells at both low and high shear stress was inhibited in the presence of antibody DH2, ethyl-beta-lactoside, or lactose, as well as by pretreatment of BL6 cells with sialidase. Thus, some clear differences, as well as similarities, in cell adhesion under static versus dynamic conditions are demonstrated. These findings suggest that melanoma cell adhesion to endothelial cells, based on GM3/LacCer interaction, initiates metastatic deposition, which may trigger a series of "cascade" reactions leading to activation of endothelial cells and expression of Ig family or selectin receptors, thereby promoting adhesion and migration of tumor cells.

Animals↗

Conformational flexibility of beta-secretase: molecular dynamics simulation and essential dynamics analysis.

AIM: Based on the structural analysis to reveal the mechanism of ligand binding to beta-secretase and the specificity of each binding sub-site. METHODS: Molecular dynamics was used to simulate on the ligand free beta-secretase and ligand bound beta-secretase. The trajectories were analyzed using the essential dynamics, and the significant conformational change was illustrated employing the DynDom program. RESULTS: The essential dynamics and DynDom analyses clearly showed that the beta-secretase experienced a large conformational change upon the substrate or inhibitor binding. The flap structure adopted a swing motion, gradually covering the active site to facilitate the ligand binding process. Residues Ser86 and Ile87 served as the hinge point. Inhibitor-enzyme interaction analysis revealed that residues at P2, P1, and P1' positions of the inhibitor were very important for the binding, and residues at P2' and P3' positions may be modified to improve the binding specificity. S3 subsite of the enzyme still had space to modify the inhibitors in increasing the binding affinity. CONCLUSION: The information presented here is valuable and could be used to identify small molecular inhibitors of beta-secretase.

Amyloid Precursor Protein Secretases↗

[The dynamics of hormonal status of developing red beet root (Beta vulgaris L.) in correlation with the dynamics of sugar accumulation].

We studied the dynamics of phytohormone levels (indole-3-acetic acid, abscisic acid, cytokinins, and gibberellin-like substances) in red beet (Beta vulgaris L.) roots at different developmental stages in comparison with the data on the dynamics of sugar accumulation in order to test possible hormonal regulation of sugar accumulation. The obtained data suggest the involvement of cytokinins and gibberellin-like substances in the control of sugar accumulation in the roots, while indole-3-acetic acid, abscisic acid, and gibberellin-like substances can control the outflow. The data on the dynamics of phytohormone levels shed light on their specific physiological role in red beet root development.

Beta vulgaris↗

[Dynamic change in respiratory mechanic dynamics and its clinical significance during mechanical ventilation in hyaline membrane disease of children].

OBJECTIVE: To explore the characteristics of changes in respiratory mechanic dynamics and clinical significance in hyaline membrane disease (HMD) under mechanical ventilation. METHODS: One hundred and twenty-six newborns with HMD undergoing mechanical ventilation were divided into two groups: complication group with 43 cases and no-complication group with 83 cases. The blood gases and indices of respiratory mechanic dynamics were monitored 2, 24, 48 and 72 hours after the first ventilation and before the first weaning from ventilation. RESULTS: Pulmonary compliance [(0.55+/-0.10) ml.cm H(2)O(-1).kg(-1), (0.43+/-0.10) ml.cm H(2)O(-1).kg(-1)] and minute volume [MV, (0.65+/-0.10) L/min, (0.62+/-0.30) L/min] were elevated compared with that after ventilation for 2-72 hours, however the oxygenation index [OI, (10.2+/-1.9)mm Hg vs. (13.6+/-4.3) mm Hg] significantly lower. The compliance and MV in no-complication group were higher than that in complication group 24 and 48 hours after ventilation. There were no differences in the airway resistance and lung inflation index between two groups. The pulmonary compliance was negatively correlated with OI (r=-0.208, P<0.01) and corrected with MV (r=0.218, P<0.01). In no-complication group, all cases ventilation was weaned successfully at once in all the patients,and their mean compliance and MV were (0.55+/-0.10) ml.cm H(2)O(-1).kg(-1) and (0.65+/-0.20) L/min respectively. However, in complication group, weaning failed 38 patients, their mean compliance and MV were (1.03+/-0.30) ml.cm H(2)O(-1).kg(-1) and (0. 33+/-0.30) L/min respectively. CONCLUSION: Respiratory mechanic dynamics monitoring is beneficial in evaluating the severity of hyaline membrane disease and complications, guiding mechanical ventilation management and weaning.

Female↗

Quantification of myocardial blood flow using dynamic nitrogen-13-ammonia PET studies and factor analysis of dynamic structures.

UNLABELLED: In this study, factor analysis of dynamic structures (FADS) was used to extract the "pure" blood-pool time-activity curves (TACs) and to generate parametric myocardial blood flow (MBF) images (pixel unit: ml/min/g). METHODS: Ten dynamic 13N-ammonia dog PET studies (three baseline, five hyperemia and two occlusion) were included. Three factors (TACs) and their corresponding factor images (the right ventricular and left ventricular blood pools and myocardial activities) were extracted from each study. The left ventricular factors matched well with the plasma TACs. The factor images of myocardium were then converted to a parametric images of MBF using a relationship derived from a two-compartment model. RESULTS: MBF estimates obtained from FADS correlated well with MBF estimates obtained with the two-compartment model (r = 0.98, slope = 0.84) and microsphere techniques (r = 0.96, slope = 0.94). FADS-generated MBF parametric images have better image quality and lower noise levels compared to those generated with Patlak graphical analysis. CONCLUSION: Regional MBF can be measured accurately and noninvasively with 13N-ammonia dynamic PET imaging and FADS. The method is simple, accurate and produces parametric images of MBF without requiring blood sampling and spillover correction.

Ammonia↗

[201T1C1 accumulation dynamics in glioma with different grades of malignancy: an investigation using dynamic SPECT].

Dynamic SPECT was performed using 201TICI in a total of 21 gliomas, 14 cases of glioblastoma multiforme (GM) and 7 cases of anaplastic astrocytoma (AA), to investigate the relationship between test results and malignancy. The accumulation of isotope (counts/pixel) in the tumor was measured every 3 minutes with dynamic SPECT. The initial 3-minute value was reduced from subsequent accumulations (counts/minute) to obtain the time-activity curve (TAC). Thallium index (TL index), the ratio of 15-minute accumulation in the tumor to that in the same region of the contralateral normal brain, was also calculated. TL index was significantly higher (p < 0.05, Mann-Whitney test) in GM (6.25 +/- 1.97) than in AA (4.10 +/- 1.66), although no clear differential value could be determined between the two. TAC in the GM group showed that compared with the initial 3-minute value, accumulation increased significantly (p < 0.05) at every measurement point after isotope injection: 6 minutes, 0.660 +/- 0.671; 9 minutes, 1.322 +/- 1.319; 12 minutes, 1.315 +/- 1.632 and 15 minutes, 1.234 +/- 1.552. The increase in isotope accumulation in the tumor after 6 minutes or later was noted in 11 of the 14 cases in the GM group. In the AA group, however, there were no significant differences between the initial 3-minute value and value after 6 minutes (-0.283 +/- 0.462), 9 minutes (-0.574 +/- 0.681), 12 minutes (-0.690 +/- 0.611) and 15 minutes (-0.707 +/- 0.636) after isotope injection. A decrease in isotope accumulation in the tumor after 6 minutes or later was noted in 6 of the 7 cases in the AA group. Compared with static SPECT, dynamic SPECT, which can be performed easily and quickly, is more useful in clinical settings because of its high ability to differentiate the grade of malignancy of gliomas.

Adult↗

Investigation of brain dynamics in Parkinson's disease by methods derived from nonlinear dynamics.

EEGs were recorded from patients in early stages of Parkinson's disease (17 patients, 9 females) and healthy controls (12 subjects, 8 females) during rest and during execution/imagining of a complex motor task. The prediction that Parkinson's disease patients compared to controls would show more complex brain dynamics during performance of a complex motor task and imagination of the movements was confirmed by methods derived from nonlinear dynamics. In the resting state, analysis of correlation dimension of EEG time series revealed only slight topographical differences between the groups. During performance of a complex motor task, however, data from Parkinson's disease patients showed higher dimensionality than data from controls, indicating more complex EEG time series. The same difference was found when subjects did not perform any motor movements but imagined the complex movements they had just performed. The data are consistent with the hypothesis that the disturbances in Parkinson's disease result in the recruitment of superfluous cortical networks due to failed inhibition of alternative motor programs in the striatum and thus increase the complexity of cortical representation in motor conditions.

Aged↗

Dynamical and statistical models of vertebrate population dynamics.

Population dynamics methodology now powerfully combines discrete time models (with constant parameters, density dependence, random environment, and/or demographic stochasticity) and capture-recapture models for estimating demographic parameters. Vertebrate population dynamics has strongly benefited from this progress: survival estimates have been revised upwards, trade-offs between life history traits have been demonstrated, analyses of population viability and management are more and more realistic. Promising developments concern random effects, multistate and integrated models. Some biological questions (density dependence, links between individual and population levels, and diversification of life histories) can now be efficiently attacked.

Animals↗

Realistic population dynamics in epidemiological models: the impact of population decline on the dynamics of childhood infectious diseases. Measles in Italy as an example.

Most contributions in the field of mathematical modelling of childhood infectious diseases transmission dynamics have focused on stationary or exponentially growing populations. In this paper an epidemiological model with realistic demography is used to investigate the impact of the non-equilibrium conditions typical of the transition to sustained below replacement fertility (BRF) recently observed in a number of western countries, upon the transmission dynamics of measles. The results depend on the manner we model the relation between the (changing) age distribution of the population and contacts. Under some circumstances the transitional ageing phase typical of BRF populations might complexly interact with epidemiological variables leading to (i) a substantial reduction in the amount of vaccination effort required for eliminating the disease; (ii) a significant magnification of the perverse impact of vaccination in terms of the burden of severe age related morbidity.

Adolescent↗

Modulation of excitatory synaptic coupling facilitates synchronization and complex dynamics in a biophysical model of neuronal dynamics.

In this paper, complex dynamical synchronization in a non-linear model of a neural system is studied, and the computational significance of the behaviours is explored. The local neural dynamics is determined by voltage- and ligand-gated ion channels and feedback between densely interconnected excitatory and inhibitory neurons. A mesoscopic array of local networks is modelled by introducing coupling between the local networks via weak excitatory-to-excitatory connectivity. It is shown that with modulation of this long-range synaptic coupling, the system undergoes a transition from independent oscillations to stable chaotic synchronization. Between these states exists a 'weakly' stable state associated with complex, intermittent behaviour in the temporal domain and clusters of synchronous regions in the spatial domain. The paper concludes with a discussion of the putative relevance of such processes in the brain, including the role of neuromodulatory systems and the mechanisms underlying sensory perception, adaptation, computation and complexity.

Action Potentials↗

A dynamic life table model of Psorophora columbiae in the southern Louisiana rice agroecosystem with supporting hydrologic submodel. Part 2. Model validation and population dynamics.

In an earlier paper, the development of 2 simulation models designed to describe the interaction between key elements of the rice agroecosystem and the population dynamics of Psorophora columbiae were presented (Focks et al. 1988a). The objective of the work reported herein was to validate these models with field data. The first model (WaterMod) predicts soil hydrology conditions as a function of weather, agricultural practices, and soil characteristics for a variety of habitats found within the rice agroecosystem which are utilized by Ps. columbiae. Using a continuous series of hydrologic data collected in southwestern Louisiana during 1984 and 1985, WaterMod was demonstrated capable of adequately predicting runoff rates and the temporal timing of soil moisture and surface water. The second model (PcSim) simulates the population dynamics of Ps. columbiae based upon a host of variables including the output from WaterMod. This model was validated by comparisons made with density estimates from the literature on the temporal and spatial distribution of various life stages and by correspondence with light trap data gathered during the same time and location as the hydrologic data. PcSim was seen to respond appropriately to host animal densities and unusual meterological events occurring during 1984 and 1985 in southern Louisiana. A discussion is presented of the interaction between agricultural practices and certain key factors of the life history strategy of Ps. columbiae which permit the unusually successful exploitation of the rice agroecosystem by this species. A subsequent paper will use these models to evaluate current and proposed IPM strategies for this mosquito (Focks et al. 1988b).

Actuarial Analysis↗

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer.

The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundred systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 angstroms. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.

Biophysics↗