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Journal of Mathematical Biology Feb 2024Recent empirical evidence suggests that the transmission coefficient in susceptible-exposed-infected-removed-like (SEIR-like) models evolves with time, presenting random...
Recent empirical evidence suggests that the transmission coefficient in susceptible-exposed-infected-removed-like (SEIR-like) models evolves with time, presenting random patterns, and some stylized facts, such as mean-reversion and jumps. To address such observations we propose the use of jump-diffusion stochastic processes to parameterize the transmission coefficient in an SEIR-like model that accounts for death and time-dependent parameters. We provide a detailed theoretical analysis of the proposed model proving the existence and uniqueness of solutions as well as studying its asymptotic behavior. We also compare the proposed model with some variations possibly including jumps. The forecast performance of the considered models, using reported COVID-19 infections from New York City, is then tested in different scenarios. Despite the simplicity of the epidemiological model, by considering stochastic transmission, the forecasted scenarios were fairly accurate.
Topics: Humans; Epidemiological Models; COVID-19; Diffusion
PubMed: 38319446
DOI: 10.1007/s00285-023-02042-z -
Magnetic Resonance in Medical Sciences... Apr 2024Diffusion MRI is a physical measurement method that quantitatively indicates the displacement of water molecules diffusing in voxels. However, there are insufficient...
PURPOSE
Diffusion MRI is a physical measurement method that quantitatively indicates the displacement of water molecules diffusing in voxels. However, there are insufficient data to characterize the diffusion process physically in a uniform structure such as a phantom. This study investigated the transitional relationship between structure scale, temperature, and diffusion time for simple restricted diffusion using a capillary phantom.
METHODS
We performed diffusion-weighted pulsed-gradient stimulated-echo acquisition mode (STEAM) MRI with a 9.4 Tesla MRI system (Bruker BioSpin, Ettlingen, Germany) and a quadrature coil with an inner diameter of 86 mm (Bruker BioSpin). We measured the diffusion coefficients (radial diffusivity [RD]) of capillary plates (pore sizes 6, 12, 25, 50, and 100 μm) with uniformly restricted structures at various temperatures (10ºC, 20ºC, 30ºC, and 40ºC) and multiple diffusion times (12-800 ms). We evaluated the characteristics of scale, temperature, and diffusion time for restricted diffusion.
RESULTS
The RD decayed and became constant depending on the structural scale. Diffusion coefficient fluctuations with temperature occurred mostly under conditions of a large structural scale and short diffusion time. We obtained data suggesting that temperature-dependent changes in the diffusion coefficients follow physical laws.
CONCLUSION
No water molecules were observed outside the glass tubes in the capillary plates, and the capillary plates only reflected a restricted diffusion process within the structure.We experimentally evaluated the characteristics of simple restricted diffusion to reveal the transitional relationship of the diffusion coefficient with diffusion time, structure scale, and temperature through composite measurement.
Topics: Temperature; Magnetic Resonance Imaging; Diffusion Magnetic Resonance Imaging; Diffusion; Biological Transport; Phantoms, Imaging; Water
PubMed: 36754420
DOI: 10.2463/mrms.mp.2022-0103 -
Journal of Biomedical Optics Aug 2023Based on acoustic detection of optical absorption, photoacoustic tomography (PAT) allows functional and molecular imaging beyond the optical diffusion limit with high...
SIGNIFICANCE
Based on acoustic detection of optical absorption, photoacoustic tomography (PAT) allows functional and molecular imaging beyond the optical diffusion limit with high spatial resolution. However, multispectral functional and molecular PAT is often limited by decreased spectroscopic accuracy and reduced detection sensitivity in deep tissues, mainly due to wavelength-dependent optical attenuation and inaccurate acoustic inversion.
AIM
Previous work has demonstrated that reversible color-shifting can drastically improve the detection sensitivity of PAT by suppressing nonswitching background signals. We aim to develop a new color switching-based PAT method using reversibly switchable thermochromics (ReST).
APPROACH
We developed a family of ReST with excellent water dispersion, biostability, and temperature-controlled color changes by surface modification of commercial thermochromic microcapsules with the hydrophilic polysaccharide alginate.
RESULTS
The optical absorbance of the ReST was switched on and off repeatedly by modulating the surrounding temperature, allowing differential photoacoustic detection that effectively suppressed the nonswitching background signal and substantially improved image contrast and detection sensitivity. We demonstrate reversible thermal-switching imaging of ReST and using three PAT modes at different length scales.
CONCLUSIONS
ReST-enabled PAT is a promising technology for high-sensitivity deep tissue imaging of molecular activity in temperature-related biomedical applications, such as cancer thermotherapy.
Topics: Tomography, X-Ray Computed; Photoacoustic Techniques; Acoustics; Temperature; Diffusion; Tomography
PubMed: 36817549
DOI: 10.1117/1.JBO.28.8.082804 -
NeuroImage Oct 2023Spatial attention is often described as a mental spotlight that enhances information processing at the attended location. Using fMRI, we investigated background...
Spatial attention is often described as a mental spotlight that enhances information processing at the attended location. Using fMRI, we investigated background connectivity between the pulvinar and V1 in relation to focused versus diffused attention allocation, in weak and strong crowding contexts. Our findings revealed that focused attention led to enhanced correlations between the pulvinar and V1. Notably, this modulation was initiated by the pulvinar, and the strength of the modulation was dependent on the saliency of the target. These findings suggest that the pulvinar initiates information reweighting to V1, which underlies attentional selection in cluttered scenes.
Topics: Humans; Pulvinar; Cognition; Diffusion
PubMed: 37619793
DOI: 10.1016/j.neuroimage.2023.120341 -
Biomaterials Oct 2023Flourished in the past two decades, fluorescent probe technology provides researchers with accurate and efficient tools for in situ imaging of biomarkers in living cells... (Review)
Review
Flourished in the past two decades, fluorescent probe technology provides researchers with accurate and efficient tools for in situ imaging of biomarkers in living cells and tissues and may play a significant role in clinical diagnosis and treatment such as biomarker detection, fluorescence imaging-guided surgery, and photothermal/photodynamic therapy. In situ imaging of biomarkers depends on the spatial resolution of molecular probes. Nevertheless, the majority of currently available molecular fluorescent probes suffer from the drawback of diffusing from the target region. This leads to a rapid attenuation of the fluorescent signal over time and a reduction in spatial resolution. Consequently, the diffused fluorescent signal cannot accurately reflect the in situ information of the target. Self-immobilizing and self-precipitating molecular fluorescent probes can be used to overcome this problem. These probes ensure that the fluorescent signal remains at the location where the signal is generated for a long time. In this review, we introduce the development history of the two types of probes and classify them in detail according to different design strategies. In addition, we compare their advantages and disadvantages, summarize some representative studies conducted in recent years, and propose prospects for this field.
Topics: Fluorescent Dyes; Molecular Probes; Diagnostic Imaging; Diffusion; Photothermal Therapy
PubMed: 37643487
DOI: 10.1016/j.biomaterials.2023.122281 -
Communications Biology May 2024Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting...
Vesicles carry out many essential functions within cells through the processes of endocytosis, exocytosis, and passive and active transport. This includes transporting and delivering molecules between different parts of the cell, and storing and releasing neurotransmitters in neurons. To date, computational simulation of these key biological players has been rather limited and has not advanced at the same pace as other aspects of cell modeling, restricting the realism of computational models. We describe a general vesicle modeling tool that has been designed for wide application to a variety of cell models, implemented within our software STochastic Engine for Pathway Simulation (STEPS), a stochastic reaction-diffusion simulator that supports realistic reconstructions of cell tissue in tetrahedral meshes. The implementation is validated in an extensive test suite, parallel performance is demonstrated in a realistic synaptic bouton model, and example models are visualized in a Blender extension module.
Topics: Computer Simulation; Diffusion; Models, Biological; Software; Synaptic Vesicles; Exocytosis; Animals; Humans; Endocytosis; Neurons; Stochastic Processes
PubMed: 38750123
DOI: 10.1038/s42003-024-06276-5 -
Journal of Mathematical Biology Nov 2023Autoimmune diseases, such as Multiple Sclerosis, are often modelled through the dynamics of T-cell interactions. However, the spatial aspect of such diseases, and how...
Autoimmune diseases, such as Multiple Sclerosis, are often modelled through the dynamics of T-cell interactions. However, the spatial aspect of such diseases, and how dynamics may result in spatially heterogeneous outcomes, is often overlooked. We consider the effects of diffusion and chemotaxis on T-cell regulatory dynamics using a three-species model of effector and regulator T-cell populations, along with a chemical signalling agent. While diffusion alone cannot lead to instability and spatial patterning, the inclusion of chemotaxis can result in multiple forms of instability that produce highly complicated spatiotemporal behaviour. The parameter regimes in which different instabilities occur are determined through linear stability analysis and the full dynamics is explored through numerical simulation.
Topics: Chemotaxis; Models, Biological; T-Lymphocytes; Signal Transduction; Cell Communication; Computer Simulation; Diffusion
PubMed: 37947884
DOI: 10.1007/s00285-023-02017-0 -
Journal of Biological Physics Sep 2023We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the...
We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the modified diffusive epidemic process using the Monte Carlo method by computational analysis. Our model may be helpful for modeling systems closer to reality consisting of two classes of individuals: susceptible (A) and infected (B). The individuals can diffuse in a network according to constant diffusion rates [Formula: see text] and [Formula: see text], for the classes A and B, respectively, and obeying three diffusive regimes, i.e., [Formula: see text], [Formula: see text], and [Formula: see text]. Into the same site i, the reaction occurs according to the dynamical rule based on Gillespie's algorithm. Finite-size scaling analysis has shown that our model exhibits continuous phase transition to an absorbing state with a set of critical exponents given by [Formula: see text], [Formula: see text], and [Formula: see text] familiar to every investigated regime. In summary, the continuous phase transition, characterized by this set of critical exponents, does not have the same exponents of the mean-field universality class in both regular lattices and complex networks.
Topics: Humans; Computer Simulation; Algorithms; Epidemics; Models, Biological; Diffusion
PubMed: 37118345
DOI: 10.1007/s10867-023-09634-2 -
ACS Sensors Sep 2023Diffusion limitations and nonspecific surface absorption are great challenges for developing micro-/nanoscale affinity biosensors. There are very limited approaches that...
Diffusion limitations and nonspecific surface absorption are great challenges for developing micro-/nanoscale affinity biosensors. There are very limited approaches that can solve these issues at the same time. Here, an acoustic streaming approach enabled by a gigahertz (GHz) resonator is presented to promote mass transfer of analytes through the jet mode and biofouling removal through the shear mode, which can be switched by tuning the deviation angle, α, between the resonator and the sensor. Simulations show that the jet mode (α ≤ 0) drives the analytes in the fluid toward the sensing surface, overcomes the diffusion limitation, and enhances the binding; while the shear mode (0 < α < π/4) provides a scouring action to remove the biofouling from the sensor. Experimental studies were performed by integrating this GHz resonator with optoelectronic sensing systems, where a 34-fold enhancement for the initial binding rate was obtained. Featuring high efficiency, controllability, and versatility, we believe that this GHz acoustic streaming approach holds promise for many kinds of biosensing systems as well as lab-on-chip systems.
Topics: Acoustics; Biofouling; Diffusion
PubMed: 37639526
DOI: 10.1021/acssensors.3c00982 -
The Journal of Physiology Jun 2024Neurons in the central nervous system communicate with each other by activating billions of tiny synaptic boutons distributed along their fine axons. These presynaptic...
Neurons in the central nervous system communicate with each other by activating billions of tiny synaptic boutons distributed along their fine axons. These presynaptic varicosities are very crowded environments, comprising hundreds of synaptic vesicles. Only a fraction of these vesicles can be recruited in a single release episode, either spontaneous or evoked by action potentials. Since the seminal work by Fatt and Katz, spontaneous release has been modelled as a memoryless process. Nevertheless, at central synapses, experimental evidence indicates more complex features, including non-exponential distributions of release intervals and power-law behaviour in their rate. To describe these features, we developed a probabilistic model of spontaneous release based on Brownian motion of synaptic vesicles in the presynaptic environment. To account for different diffusion regimes, we based our simulations on fractional Brownian motion. We show that this model can predict both deviation from the Poisson hypothesis and power-law features in experimental quantal release series, thus suggesting that the vesicular motion by diffusion could per se explain the emergence of these properties. We demonstrate the efficacy of our modelling approach using electrophysiological recordings at single synaptic boutons and ultrastructural data. When this approach was used to simulate evoked responses, we found that the replenishment of the readily releasable pool driven by Brownian motion of vesicles can reproduce the characteristic binomial release distributions seen experimentally. We believe that our modelling approach supports the idea that vesicle diffusion and readily releasable pool dynamics are crucial factors for the physiological functioning of neuronal communication. KEY POINTS: We developed a new probabilistic model of spontaneous and evoked vesicle fusion based on simple biophysical assumptions, including the motion of vesicles before they dock to the release site. We provide closed-form equations for the interval distribution of spontaneous releases in the special case of Brownian diffusion of vesicles, showing that a power-law heavy tail is generated. Fractional Brownian motion (fBm) was exploited to simulate anomalous vesicle diffusion, including directed and non-directed motion, by varying the Hurst exponent. We show that our model predicts non-linear features observed in experimental spontaneous quantal release series as well as ultrastructural data of synaptic vesicles spatial distribution. Evoked exocytosis based on a diffusion-replenished readily releasable pool might explain the emergence of power-law behaviour in neuronal activity.
Topics: Synaptic Vesicles; Animals; Synaptic Transmission; Models, Neurological; Presynaptic Terminals; Rats; Diffusion
PubMed: 38723211
DOI: 10.1113/JP284926