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NMR in Biomedicine Jan 2012Diffusion tensor imaging (DTI) was used to study traumatic brain injury. The impact-acceleration trauma model was used in rats. Here, in addition to diffusivities (mean,...
Diffusion tensor imaging (DTI) was used to study traumatic brain injury. The impact-acceleration trauma model was used in rats. Here, in addition to diffusivities (mean, axial and radial), fractional anisotropy (FA) was used, in particular, as a parameter to characterize the cerebral tissue early after trauma. DTI was implemented at 7 T using fast spiral k-space sampling and the twice-refocused spin echo radiofrequency sequence for eddy current minimization. The method was carefully validated on different phantom measurements. DTI of a trauma group (n = 5), as well as a sham group (n = 5), was performed at different time points during 6 h following traumatic brain injury. Two cerebral regions, the cortex and corpus callosum, were analyzed carefully. A significant decrease in diffusivity in the trauma group versus the sham group was observed, suggesting the predominance of cellular edema in both cerebral regions. No significant FA change was detected in the cortex. In the corpus callosum of the trauma group, the FA indices were significantly lower. A net discontinuity in fiber reconstructions in the corpus callosum was observed by fiber tracking using DTI. Histological analysis using Hoechst, myelin basic protein and Bielschowsky staining showed fiber disorganization in the corpus callosum in the brains of the trauma group. On the basis of our histology results and the characteristics of the impact-acceleration model responsible for the presence of diffuse axonal injury, the detection of low FA caused by a drastic reduction in axial diffusivity and the presence of fiber disconnections of the DTI track in the corpus callosum were considered to be related to the presence of diffuse axonal injury.
Topics: Animals; Butadienes; Calibration; Corpus Callosum; Diffuse Axonal Injury; Diffusion; Diffusion Tensor Imaging; Disease Models, Animal; Elastomers; Male; Rats; Rats, Wistar; Spin Labels
PubMed: 21618304
DOI: 10.1002/nbm.1721 -
Physical Biology Jan 2023The function of many membrane-enclosed intracellular structures relies on release of diffusing particles that exit through narrow pores or channels in the membrane. The...
The function of many membrane-enclosed intracellular structures relies on release of diffusing particles that exit through narrow pores or channels in the membrane. The rate of release varies with pore size, density, and length of the channel. We propose a simple approximate model, validated with stochastic simulations, for estimating the effective release rate from cylinders, and other simple-shaped domains, as a function of channel parameters. The results demonstrate that, for very small pores, a low density of channels scattered over the boundary is sufficient to achieve substantial rates of particle release. Furthermore, we show that increasing the length of passive channels will both reduce release rates and lead to a less steep dependence on channel density. Our results are compared to previously-measured local calcium release rates from tubules of the endoplasmic reticulum, providing an estimate of the relevant channel density responsible for the observed calcium efflux.
Topics: Calcium; Diffusion; Endoplasmic Reticulum
PubMed: 36626849
DOI: 10.1088/1478-3975/acb1ea -
Physical Review. E May 2023Linear diffusions are used to model a large number of stochastic processes in physics, including small mechanical and electrical systems perturbed by thermal noise, as...
Linear diffusions are used to model a large number of stochastic processes in physics, including small mechanical and electrical systems perturbed by thermal noise, as well as Brownian particles controlled by electrical and optical forces. Here we use techniques from large deviation theory to study the statistics of time-integrated functionals of linear diffusions, considering three classes of functionals or observables relevant for nonequilibrium systems which involve linear or quadratic integrals of the state in time. For these, we derive exact results for the scaled cumulant generating function and the rate function, characterizing the fluctuations of observables in the long-time limit, and study in an exact way the set of paths or effective process that underlies these fluctuations. The results give a complete description of how fluctuations arise in linear diffusions in terms of effective forces that remain linear in the state or, alternatively, in terms of fluctuating densities and currents that solve Riccati-type equations. We illustrate these results using two common nonequilibrium models, namely, transverse diffusions in two dimensions involving a nonconservative rotating force, and two interacting particles in contact with heat baths at different temperatures.
Topics: Stochastic Processes; Diffusion; Time Factors
PubMed: 37328997
DOI: 10.1103/PhysRevE.107.054111 -
Frontiers in Bioscience : a Journal and... Jan 2007In mammals, the O2 transport from the inspired air to the tissues is made by convective and diffusive mechanisms. The convective mechanisms are provided by the... (Review)
Review
In mammals, the O2 transport from the inspired air to the tissues is made by convective and diffusive mechanisms. The convective mechanisms are provided by the cardio-respiratory system and comprised by the basic variables of cardiac output and blood O2 content. Microcirculation in arterioles and capillaries is adjusted to match the O2 demand of local tissues. Endothelium-generated NO diffuses to the smooth muscle of microvessels and produces vasodilation that increases circulatory time in the capillaries and allows a more effective O2 extraction in the tissues. Once within the tissue, O2 diffuses to mitochondria where it is reduced in an exergonic process coupled to ATP synthesis. Both, O2 and ATP are the two most homeostatic intracellular species. In heart and muscle, both species show unchanged levels with 25-100 times increases in work load and ATP turnover rate. The linear rates of O2 uptake shown by tissue slices and perfused organs are interpreted as a fast switching of mitochondria between metabolic state 3 (with a fast rate of O2 uptake and ATP synthesis) and state 4 (with a slow rate of O2 uptake and no ADP phosphorylation). Endogenous mitochondrial NO, produced by mtNOS, sustains the concept of a physiological functional activity of this enzyme in regulating mitochondrial and cellular O2 uptake.
Topics: Animals; Biological Transport; Cell Respiration; Convection; Diffusion; Humans; Mitochondria; Oxygen; Oxygen Consumption
PubMed: 17127356
DOI: 10.2741/2121 -
Physical Review Letters Sep 2003In this Letter we present a simple and novel theoretical approach for modeling the intensity distribution from an arbitrarily shaped turbid volume in a noncontact...
In this Letter we present a simple and novel theoretical approach for modeling the intensity distribution from an arbitrarily shaped turbid volume in a noncontact geometry by considering diffuse light propagation in free space. This theory is validated with experiments for a diffusive volume of known geometry in a noncontact situation, both with and without the presence of an embedded absorber. The implications of this new formulation in the context of optical tomography in turbid media are discussed.
Topics: Diffusion; Image Processing, Computer-Assisted; Light; Models, Theoretical; Optics and Photonics; Tomography
PubMed: 14525478
DOI: 10.1103/PhysRevLett.91.103901 -
The Journal of Physical Chemistry. B Apr 2016It has been found in many experiments that the mean square displacement of a Brownian particle x(T) diffusing in a rearranging environment is strictly Fickian, obeying...
It has been found in many experiments that the mean square displacement of a Brownian particle x(T) diffusing in a rearranging environment is strictly Fickian, obeying ⟨(x(T))(2)⟩ ∝ T, but the probability distribution function for the displacement is not Gaussian. An explanation of this is that the diffusivity of the particle itself is changing as a function of time. Models for this diffusing diffusivity have been solved analytically in the limit of small time, but simulations were necessary for intermediate and large times. We show that one of the diffusing diffusivity models is equivalent to Brownian motion in the presence of a sink and introduce a class of models for which it is possible to find analytical solutions. Our solution gives ⟨(x(T))(2)⟩ ∝ T for all times and at short times the probability distribution function of the displacement is exponential which crosses over to a Gaussian in the limit of long times and large displacements.
Topics: Diffusion; Models, Theoretical; Normal Distribution
PubMed: 27029607
DOI: 10.1021/acs.jpcb.6b01527 -
Biophysical Journal Nov 2014Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We...
Models of biological diffusion-reaction systems require accurate classification of the underlying diffusive dynamics (e.g., Fickian, subdiffusive, or superdiffusive). We use a renormalization group operator to identify the anomalous (non-Fickian) diffusion behavior from a short trajectory of a single molecule. The method provides quantitative information about the underlying stochastic process, including its anomalous scaling exponent. The classification algorithm is first validated on simulated trajectories of known scaling. Then it is applied to experimental trajectories of microspheres diffusing in cytoplasm, revealing heterogeneous diffusive dynamics. The simplicity and robustness of this classification algorithm makes it an effective tool for analysis of rare stochastic events that occur in complex biological systems.
Topics: Algorithms; Animals; Biological Transport; Diffusion; Models, Biological; Oocytes; Stochastic Processes; Xenopus
PubMed: 25418303
DOI: 10.1016/j.bpj.2014.10.005 -
Journal of the Royal Society, Interface Mar 2021Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion...
Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion of chemotactic factors. Despite the critical role of chemotactic swarming, few methods to robustly identify and quantify this phenomenon exist. Here, we present a novel method for the analysis of time series of positional data generated from realizations of agent-based processes. We convert the positional data for each individual time point to a function measuring agent aggregation around a given area of interest, hence generating a functional time series. The functional time series, and a more easily visualized of agent aggregation derived from these functions, provide useful information regarding the evolution of the underlying process over time. We extend our method to build upon the modelling of collective motility using drift-diffusion partial differential equations (PDEs). Using a functional linear model, we are able to use the functional time series to estimate the drift and diffusivity terms associated with the underlying PDE. By producing an accurate estimate for the drift coefficient, we can infer the strength and range of attraction or repulsion exerted on agents, as in chemotaxis. Our approach relies solely on using agent positional data. The spatial distribution of diffusing chemokines is not required, nor do individual agents need to be tracked over time. We demonstrate our approach using random walk simulations of chemotaxis and experiments investigating cytotoxic T cells interacting with tumouroids.
Topics: Animals; Cell Tracking; Chemotactic Factors; Chemotaxis; Diffusion; Models, Biological; Movement
PubMed: 33715400
DOI: 10.1098/rsif.2020.0879 -
The Journal of Cell Biology May 2023Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis...
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
Topics: Bacterial Proteins; Diffusion; Kinetics; Microscopy
PubMed: 36880553
DOI: 10.1083/jcb.202208059 -
Journal of Biomechanical Engineering Nov 2022Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to...
Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to resident cells. Under normal physiological conditions, the meniscus undergoes up to 20% compressive strains. While previous studies characterized solute diffusivity in the uncompressed meniscus, to date, little is known about the diffusive transport under physiological strain levels. This information is crucial to fully understand the pathophysiology of the meniscus. The objective of this study was to investigate strain-dependent diffusive properties of the meniscus fibrocartilage. Tissue samples were harvested from the central portion of porcine medial menisci and tested via fluorescence recovery after photobleaching to measure diffusivity of fluorescein (332 Da) and 40 K Da dextran (D40K) under 0%, 10%, and 20% compressive strain. Specifically, average diffusion coefficient and anisotropic ratio, defined as the ratio of the diffusion coefficient in the direction of the tissue collagen fibers to that orthogonal, were determined. For all the experimental conditions investigated, fluorescein diffusivity was statistically faster than that of D40K. Also, for both molecules, diffusion coefficients significantly decreased, up to ∼45%, as the strain increased. In contrast, the anisotropic ratios of both molecules were similar and not affected by the strain applied to the tissue. This suggests that compressive strains used in this study did not alter the diffusive pathways in the meniscus. Our findings provide new knowledge on the transport properties of the meniscus fibrocartilage that can be leveraged to further understand tissue pathophysiology and approaches to tissue restoration.
Topics: Animals; Anisotropy; Diffusion; Fibrocartilage; Fluoresceins; Meniscus; Swine
PubMed: 35789377
DOI: 10.1115/1.4054931