-
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 -
Proceedings of the National Academy of... Aug 2023Real-world networks are neither regular nor random, a fact elegantly explained by mechanisms such as the Watts-Strogatz or the Barabási-Albert models, among others....
Real-world networks are neither regular nor random, a fact elegantly explained by mechanisms such as the Watts-Strogatz or the Barabási-Albert models, among others. Both mechanisms naturally create shortcuts and hubs, which while enhancing the network's connectivity, also might yield several undesired navigational effects: They tend to be overused during geodesic navigational processes-making the networks fragile-and provide suboptimal routes for diffusive-like navigation. Why, then, networks with complex topologies are ubiquitous? Here, we unveil that these models also entropically generate network bypasses: alternative routes to shortest paths which are topologically longer but easier to navigate. We develop a mathematical theory that elucidates the emergence and consolidation of network bypasses and measure their navigability gain. We apply our theory to a wide range of real-world networks and find that they sustain complexity by different amounts of network bypasses. At the top of this complexity ranking we found the human brain, which points out the importance of these results to understand the plasticity of complex systems.
Topics: Humans; Brain; Diffusion
PubMed: 37490534
DOI: 10.1073/pnas.2305001120 -
Therapeutic Advances in Vaccines and... 2023Diffusely infiltrating gliomas - including glioblastoma (GBM), isocitrate dehydrogenase (IDH) mutant gliomas, and histone 3 (H3) altered gliomas - are primary brain... (Review)
Review
Diffusely infiltrating gliomas - including glioblastoma (GBM), isocitrate dehydrogenase (IDH) mutant gliomas, and histone 3 (H3) altered gliomas - are primary brain tumors with an invariably fatal outcome. Despite advances in the understanding of their biology, standard, targeted and immune checkpoint inhibitor immunotherapies have proven ineffective in arresting their inexorable progression and associated morbidity and mortality. Recognizing the unique aspects of the immunogenicity of cancer cells, the last decade has seen the development and evaluation of vaccine-based therapies for the treatment of solid tumors, including gliomas. Here we review the current vaccine strategies for the treatment of GBM, IDH-mutant gliomas and diffuse midline glioma H3 K27M-altered. We discuss potential benefits and challenges of vaccine therapies in these specific patient populations.
PubMed: 37886714
DOI: 10.1177/25151355231206163 -
Soft Matter Jan 2024Run-and-tumble processes successfully model several living systems. While studies have typically focused on particles with isotropic tumbles, recent examples exhibit...
Run-and-tumble processes successfully model several living systems. While studies have typically focused on particles with isotropic tumbles, recent examples exhibit "tumble-turns", in which particles undergo 90° tumbles and so possess explicitly anisotropic dynamics. We study the consequences of such tumble-turn anisotropicity at both short and long-time scales. We model run-and-tumble-turn particles as self-propelled particles subjected to an angular potential that favors directions of movement parallel to Cartesian axes. Using agent-based simulations, we study the effects of the interplay between rotational diffusion and an aligning potential on the particles' trajectories, which leads to the right-angled turns. We demonstrate that the long-time effect is to alter the tumble-turn time, which governs the long-time dynamics. In particular, when normalized by this timescale, trajectories become independent of the underlying details of the potential. As such, we develop a simplified continuum theory, which quantitatively agrees with agent-based simulations. We find that the purely diffusive hydrodynamic limit still exhibits anisotropic features at intermediate times and conclude that the transition to diffusive dynamics precedes the transition to isotropic dynamics. By considering short-range repulsive and alignment particle-particle interactions, we show how the anisotropic features of a single particle are inherited by the global order of the system. We hope this work will shed light on how active systems can extend local anisotropic properties to macroscopic scales, which might be important in biological processes occurring in anisotropic environments.
PubMed: 38226730
DOI: 10.1039/d3sm00589e -
The Journal of General Physiology Oct 2023Osmosis is an important force in all living organisms, yet the molecular basis of osmosis is widely misunderstood as arising from diffusion of water across a membrane...
Osmosis is an important force in all living organisms, yet the molecular basis of osmosis is widely misunderstood as arising from diffusion of water across a membrane separating solutions of differing osmolarities, and hence different water concentrations. In 1923, Peter Debye proposed a physical model for a semipermeable membrane emphasizing the repulsive forces between solute molecules and membrane that prevent the solute from entering the membrane. His work was hardly noticed at the time and slipped out of view. We show that Debye's analysis of van 't Hoff's law for osmotic equilibrium also provides a consistent and plausible mechanism for osmotic flow. A difference in osmolyte concentrations in solutions separated by a semipermeable membrane leads to different pressures at the two water-membrane interfaces because the total repulsive force between solute molecules and the membrane is different at the two interfaces. Water is therefore driven through the membrane for exactly the same reason that pure water flows in response to an imposed hydrostatic pressure difference. In this paper, we present the Debye model in both equilibrium and flow conditions. We point out its applicability regardless of the nature of the membrane with examples ranging from the predominantly convective flow of water through synthetic membranes and capillary walls to the purely diffusive flow of independent water molecules through a lipid bilayer and the flow of a single-file column of water molecules in narrow protein channels.
Topics: Diffusion; Lipid Bilayers; Osmosis; Pressure; Water
PubMed: 37624228
DOI: 10.1085/jgp.202313332 -
Northern Clinics of Istanbul 2023This article aimed to study two different parameters of basal cell carcinoma (BCC): First, to analyze the expression of antihuman epithelial antigen (Ber-EP4) on the...
OBJECTIVE
This article aimed to study two different parameters of basal cell carcinoma (BCC): First, to analyze the expression of antihuman epithelial antigen (Ber-EP4) on the primary and recurrent BCCs on the head, neck, and other body parts and second, to find Ber-EP4's staining pattern and staining intensities correlation between histological type, demographic data, tumor, and its prognostic parameters.
METHODS
We evaluated the Ber-EP4 staining patterns of 201 patients diagnosed with BCC. We analyzed the possible correlation between the tumor's prognostic parameters and the Ber-EP4 staining intensity and its pattern (peripheral, superficial, or diffused).
RESULTS
In 199 out of the 201 cases, staining was observed. Two cases were unstained. In 25.6% (n=51) of the cases with staining, the staining was weak, on the 25.6% (n=51), it was moderate, and on the 48.8% (n=97), it was severe. The staining pattern was 31.2% (n=62) peripheral, 4.0% (n=8) superficial, 54.7% (n=109) diffuse, and 10.1% (n=20) peripheral and superficial.
CONCLUSION
Ber-EP4 is the only antibody commonly used for BCC diagnosis; the existence of different staining intensities and patterns in BCC tumor cells in routine dermatopathology practice limit the pathologists. The studies investigating Ber-EP4 staining in BCCs were conducted with very small numbers of cases. In these studies, even the presence of staining in the focal area was considered to be a positive acceptance criterion; the staining intensity and pattern were not evaluated. Therefore, our study is the first study with a high number of cases and the first to include an evaluation of Ber-EP4 staining's intensity and localization.
PubMed: 37829747
DOI: 10.14744/nci.2022.25675 -
Frontiers in Molecular Neuroscience 2023Chronic progressive neuroinflammation is a hallmark of neurological lysosomal storage diseases, including mucopolysaccharidosis III (MPS III or Sanfilippo disease)....
INTRODUCTION
Chronic progressive neuroinflammation is a hallmark of neurological lysosomal storage diseases, including mucopolysaccharidosis III (MPS III or Sanfilippo disease). Since neuroinflammation is linked to white matter tract pathology, we analyzed axonal myelination and white matter density in the mouse model of MPS IIIC and post-mortem brain samples of MPS III patients.
METHODS
Brain and spinal cord tissues of human MPS III patients, 6-month-old mice and age- and sex-matching wild type mice were analyzed by immunofluorescence to assess levels of myelin-associated proteins, primary and secondary storage materials, and levels of microgliosis. Corpus callosum (CC) region was studied by transmission electron microscopy to analyze axon myelination and morphology of oligodendrocytes and microglia. Mouse brains were analyzed by high-filed MRI using Diffusion Basis Spectrum Imaging in Python-Diffusion tensor imaging algorithms.
RESULTS
Analyses of CC and spinal cord tissues by immunohistochemistry revealed substantially reduced levels of myelin-associated proteins including Myelin Basic Protein, Myelin Associated Glycoprotein, and Myelin Oligodendrocyte Glycoprotein. Furthermore, ultrastructural analyses revealed disruption of myelin sheath organization and reduced myelin thickness in the brains of MPS IIIC mice and human MPS IIIC patients compared to healthy controls. Oligodendrocytes (OLs) in the CC of MPS IIIC mice were scarce, while examination of the remaining cells revealed numerous enlarged lysosomes containing heparan sulfate, GM3 ganglioside or "zebra bodies" consistent with accumulation of lipids and myelin fragments. In addition, OLs contained swollen mitochondria with largely dissolved cristae, resembling those previously identified in the dysfunctional neurons of MPS IIIC mice. Diffusion Basis Spectrum Imaging revealed compelling signs of demyelination (26% increase in radial diffusivity) and tissue loss (76% increase in hindered diffusivity) in CC of MPS IIIC mice.
DISCUSSION
Our findings demonstrate an important role for white matter injury in the pathophysiology of MPS III. This study also defines specific parameters and brain regions for MRI analysis and suggests that it may become a crucial non-invasive method to evaluate disease progression and therapeutic response.
PubMed: 38163061
DOI: 10.3389/fnmol.2023.1323449 -
Molecules (Basel, Switzerland) Nov 2023We review the milestones in the century-long development of the theory of diffusion-controlled reactions. Starting from the seminal work by von Smoluchowski, who... (Review)
Review
We review the milestones in the century-long development of the theory of diffusion-controlled reactions. Starting from the seminal work by von Smoluchowski, who recognized the importance of diffusion in chemical reactions, we discuss perfect and imperfect surface reactions, their microscopic origins, and the underlying mathematical framework. Single-molecule reaction schemes, anomalous bulk diffusions, reversible binding/unbinding kinetics, and many other extensions are presented. An alternative encounter-based approach to diffusion-controlled reactions is introduced, with emphasis on its advantages and potential applications. Some open problems and future perspectives are outlined.
PubMed: 38005291
DOI: 10.3390/molecules28227570 -
International Journal of Molecular... Nov 2023Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We... (Review)
Review
Using the framework of a continuous diffusion model based on the Smoluchowski equation, we analyze particle dynamics in the confinement of a transmembrane nanopore. We briefly review existing analytical results to highlight consequences of interactions between the channel nanopore and the translocating particles. These interactions are described within a minimalistic approach by lumping together multiple physical forces acting on the particle in the pore into a one-dimensional potential of mean force. Such radical simplification allows us to obtain transparent analytical results, often in a simple algebraic form. While most of our findings are quite intuitive, some of them may seem unexpected and even surprising at first glance. The focus is on five examples: (i) attractive interactions between the particles and the nanopore create a potential well and thus cause the particles to spend more time in the pore but, nevertheless, increase their net flux; (ii) if the potential well-describing particle-pore interaction occupies only a part of the pore length, the mean translocation time is a non-monotonic function of the well length, first increasing and then decreasing with the length; (iii) when a rectangular potential well occupies the entire nanopore, the mean particle residence time in the pore is independent of the particle diffusivity inside the pore and depends only on its diffusivity in the bulk; (iv) although in the presence of a potential bias applied to the nanopore the "downhill" particle flux is higher than the "uphill" one, the mean translocation times and their distributions are identical, i.e., independent of the translocation direction; and (v) fast spontaneous gating affects nanopore selectivity when its characteristic time is comparable to that of the particle transport through the pore.
Topics: Nanopores; Diffusion
PubMed: 37958906
DOI: 10.3390/ijms242115923