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Journal of Biomedical Optics Jul 2023Multi-photon fluorescence recovery after photobleaching (MPFRAP) is a nonlinear microscopy technique used to measure the diffusion coefficient of fluorescently tagged...
SIGNIFICANCE
Multi-photon fluorescence recovery after photobleaching (MPFRAP) is a nonlinear microscopy technique used to measure the diffusion coefficient of fluorescently tagged molecules in solution. Previous MPFRAP fitting models calculate the diffusion coefficient in systems with diffusion or diffusion in laminar flow.
AIM
We propose an MPFRAP fitting model that accounts for shear stress in laminar flow, making it a more applicable technique for and studies involving diffusion.
APPROACH
Fluorescence recovery curves are generated using high-throughput molecular dynamics simulations and then fit to all three models (diffusion, diffusion and flow, and diffusion and shear flow) to define the limits within which accurate diffusion coefficients are produced. Diffusion is simulated as a random walk with a variable horizontal bias to account for shear flow.
RESULTS
Contour maps of the accuracy of the fitted diffusion coefficient as a function of scaled velocity and scaled shear rate show the parameter space within which each model produces accurate diffusion coefficients; the shear-flow model covers a larger area than the previous models.
CONCLUSION
The shear-flow model allows MPFRAP to be a viable optical tool for studying more biophysical systems than previous models.
Topics: Fluorescence Recovery After Photobleaching; Diffusion; Photobleaching
PubMed: 37484975
DOI: 10.1117/1.JBO.28.7.076502 -
Japanese Journal of Radiology Dec 2023This study aimed to evaluate the relationship between sleep quality as assessed using the Pittsburgh Sleep Quality Index (PSQI) and the index of diffusivity along the...
PURPOSE
This study aimed to evaluate the relationship between sleep quality as assessed using the Pittsburgh Sleep Quality Index (PSQI) and the index of diffusivity along the perivascular space (ALPS index), a possible indirect indicator of glymphatic system activity.
MATERIALS AND METHODS
This study included the diffusion magnetic resonance imaging (MRI) data of 317 people with sleep disruption and 515 healthy controls (HCs) from the Human Connectome Project (WU-MINN HCP 1200). The ALPS index was calculated automatically based on diffusion tensor image analysis (DTI)-ALPS of diffusion MRI. The ALPS index of the sleep disruption and HC groups was compared using general linear model (GLM) analysis with covariates, such as age, sex, level of education, and intracranial volume. In addition, to confirm the relationship between sleep quality and the ALPS index in the sleep disruption group as well as evaluate the effect of each PSQI component on the ALPS index, correlation analyses between the ALPS indices and PSQI scores of all the components and between the ALPS index and each PSQI component was performed using GLM analysis with the abovementioned covariates, respectively.
RESULTS
The ALPS index was significantly lower in the sleep disruption group than in the HC group (p = 0.001). Moreover, the ALPS indices showed significant negative correlations with the PSQI scores of all the components (false discovery rate [FDR]-corrected p < 0.001). Two significant negative correlations were also found between the ALPS index and PSQI component 2 (sleep latency, FDR-corrected p < 0.001) and 6 (the use of sleep medication, FDR-corrected p < 0.001).
CONCLUSION
Our findings suggest that glymphatic system impairment contributes to sleep disruption in young adults.
Topics: Young Adult; Humans; Glymphatic System; Sleep; Diffusion; Diffusion Magnetic Resonance Imaging; Image Processing, Computer-Assisted
PubMed: 37368182
DOI: 10.1007/s11604-023-01463-6 -
Journal of Chromatography. A Aug 2023We report on a new homogenization approach to solve, with drastically improved speed and accuracy, the general advection-diffusion equation in hierarchical porous media...
We report on a new homogenization approach to solve, with drastically improved speed and accuracy, the general advection-diffusion equation in hierarchical porous media with localized diffusion and adsorption/desorption processes, thus opening the way to a much deeper understanding of the band broadening process in chromatographic systems. The proposed robust and efficient moment-based approach allows us to compute the exact local and integral concentration moments and hence provides exact solutions for the effective velocity and dispersion coefficients of migrating solute particles. Innovative to the proposed method is also that it not only produces the exact effective transport parameters of the long-time asymptotic solution, but also their entire transient. The analysis of the transient behaviour can be used, for example, to properly identify the time and length scales needed to achieve the macro-transport conditions. If the hierarchical porous media can be represented as the periodic repetition of a unit lattice cell, the method only requires the solution of the time-dependent advection-diffusion equations for the zeroth order and first-order exact local moments, exclusively on the unit cell. This implies an enormous reduction of the computational efforts and a significant improvement of the accuracy of the results when compared to the direct numerical simulation (DNS) approaches which require flow domains that are long enough to achieve steady-state conditions, and hence often cover tens to hundreds of unit cells. The reliability of the proposed method is verified by comparing its predictions with DNS results, in one, two and three dimensions, in both transient and asymptotic conditions. The influence of top and bottom no-slip walls on the separation performance of chromatographic columns with micromachined porous and nonporous pillars is discussed in detail.
Topics: Porosity; Reproducibility of Results; Diffusion; Computer Simulation; Adsorption
PubMed: 37271084
DOI: 10.1016/j.chroma.2023.464099 -
Environmental Science & Technology Nov 2023The development of energy-efficient and environmentally friendly lithium extraction techniques is essential to meet the growing global demand for lithium-ion batteries....
The development of energy-efficient and environmentally friendly lithium extraction techniques is essential to meet the growing global demand for lithium-ion batteries. In this work, a dual-channel ion conductor membrane was designed for a concentration-driven lithium-selective ion diffusion process. The membrane was based on a porous lithium-ion conductor, and its pores were modified with an anion-exchange polymer. Thus, the sintered lithium-ion conductors provided highly selective cation transport channels, and the functionalized nanopores with positive charges enabled the complementary permeation of anions to balance the transmembrane charges. As a result, the dual-channel membrane realized an ultrahigh Li/Na selectivity of ∼1389 with a competitive Li flux of 21.6 mmol·m·h in a diffusion process of the LiCl/NaCl binary solution, which was capable of further maintaining the high selectivity over 7 days of testing. Therefore, this work demonstrates the great potential of the dual-channel membrane design for high-performing lithium extraction from aqueous resources with low energy consumption and minimal environmental impact.
Topics: Lithium; Sodium; Diffusion
PubMed: 37918342
DOI: 10.1021/acs.est.3c05935 -
Water Research Jun 2023Low-permeability aquitards may serve as secondary sources of slow-releasing contaminants into the adjacent aquifer system, creating considerable obstacles to groundwater...
Low-permeability aquitards may serve as secondary sources of slow-releasing contaminants into the adjacent aquifer system, creating considerable obstacles to groundwater cleanup. Accurately capturing the exchange of contaminant mass between aquitards and aquifers can facilitate site management and remediation. Previous simulation studies were mainly limited to one-dimensional (1D) back diffusion from aquitards during the remediation of the source zone. In this study, a novel two-dimensional (2D) back-diffusion model is developed to investigate the storage and release of contaminants in aquitards after source isolation. This model coupled the dynamical decay of isolated sources and the diffusion-sorption process of contaminants in the layered aquitards. Exact analytical solutions for the present 2D multilayer model were derived using the finite cosine transform, Duhamel Theorem, separation of variables, and transfer matrix method. Results indicated that the previous 1D model would overestimate the contaminant concentration in the aquitard and the back-diffusion risk when the source zone was isolated. The proposed 2D back-diffusion model enables quantitative prediction of how source zone width, source concentration, and aquitard heterogeneity impact plume trailing time, thus aiding in understanding the mechanisms of aquifer contamination beyond barrier-controlled source zones.
Topics: Water Pollutants, Chemical; Computer Simulation; Diffusion; Groundwater; Permeability
PubMed: 37146396
DOI: 10.1016/j.watres.2023.120021 -
Longitudinal diffusion barriers imposed by myofilaments and mitochondria in murine cardiac myocytes.The Journal of General Physiology Oct 2023Using optical and electrical methods, we document that diffusion in the cytoplasm of BL6 murine cardiomyocytes becomes restricted >20-fold as molecular weight increases...
Using optical and electrical methods, we document that diffusion in the cytoplasm of BL6 murine cardiomyocytes becomes restricted >20-fold as molecular weight increases from 30 to 2,000, roughly as expected for pores with porin channel dimensions. Bodipy-FL ATP diffuses >40-fold slower than in free water at 25°C. From several fluorophores analyzed, bound fluorophore fractions range from 0.1 for a 2 kD FITC-labeled polyethylene glycol to 0.93 for sulforhodamine. Unbound fluorophores diffuse at 0.5-8 × 10-7 cm2/s (5-80 μm2/s). Analysis of Na/K pump and veratridine-modified Na channel currents suggests that Na diffusion is nearly unrestricted at 35°C (time constant for equilibration with the pipette tip, ∼20 s). Using multiple strategies, we estimate that at 35°C, ATP diffuses four to eight times slower than in free water. To address whether restrictions are caused more by protein or membrane networks, we verified first that a protein gel, 10 g% gelatin, restricts diffusion with strong dependence on molecular weight. Solute diffusion in membrane-extracted cardiac myofilaments, confined laterally by suction into large-diameter pipette tips, is less restricted than in intact myocytes. Notably, myofilaments extracted similarly from skeletal (diaphragm) myocytes are less restrictive. Solute diffusion in myocytes with sarcolemma permeabilized by β-escin (80 µM) is similar to diffusion in intact myocytes. Restrictions are strain-dependent, being twofold greater in BL6 myocytes than in CD1/J6/129svJ myocytes. Furthermore, longitudinal diffusion is 2.5-fold more restricted in CD1/J6/129svJ myocytes lacking the mitochondrial porin, VDAC1, than in WT CD1/J6/129svJ myocytes. Thus, mitochondria networks restrict long-range diffusion while presumably optimizing nucleotide transfer between myofilaments and mitochondria. We project that diffusion restrictions imposed by both myofilaments and the outer mitochondrial membrane are important determinants of total free cytoplasmic AMP and ADP (∼10 μM). However, the capacity of diffusion to deliver ATP to myofilaments remains ∼100-fold greater than ATP consumption.
Topics: Mice; Animals; Myocytes, Cardiac; Myofibrils; Mitochondria; Diffusion; Voltage-Dependent Anion Channels; Adenosine Triphosphate; Water
PubMed: 37555782
DOI: 10.1085/jgp.202213329 -
Japanese Journal of Radiology Nov 2023This study aimed to evaluate the along the perivascular space (ALPS) index based on the diffusion tensor image ALPS (DTI-ALPS) in corticobasal degeneration with...
PURPOSE
This study aimed to evaluate the along the perivascular space (ALPS) index based on the diffusion tensor image ALPS (DTI-ALPS) in corticobasal degeneration with corticobasal syndrome (CBD-CBS) and investigate its correlation with motor and cognitive functions.
MATERIALS AND METHODS
The data of 21 patients with CBD-CBS and 17 healthy controls (HCs) were obtained from the 4-Repeat Tauopathy Neuroimaging Initiative and the Frontotemporal Lobar Degeneration Neuroimaging Initiative databases. Diffusion magnetic resonance imaging was performed using a 3-Tesla MRI scanner. The ALPS index based on DTI-ALPS was automatically calculated after preprocessing. The ALPS index was compared between the CBD-CBS and HC groups via a general linear model analysis, with covariates such as age, sex, years of education, and intracranial volume (ICV). Furthermore, to confirm the relation between the ALPS index and the motor and cognitive score in CBD-CBS, the partial Spearman's rank correlation coefficient was calculated with covariates such as age, sex, years of education, and ICV. A p value of < 0.05 was considered as statistically significant in all statistical analyses.
RESULTS
The ALPS index of CBD-CBS was significantly lower than that of HC (Cohen's d = - 1.53, p < 0.005). Moreover, the ALPS index had a significant positive correlation with the mini mental state evaluation score (r = 0.65, p < 0.005) and a significant negative correlation with the unified Parkinson's Disease Rating Scale III score (r = - 0.75, p < 0.001).
CONCLUSION
The ALPS index of patients with CBD-CBS, which is significantly lower than that of HCs, is significantly associated with motor and cognitive functions.
Topics: Humans; Corticobasal Degeneration; Glymphatic System; Databases, Factual; Diffusion; Diffusion Magnetic Resonance Imaging
PubMed: 37273112
DOI: 10.1007/s11604-023-01454-7 -
Journal of the Royal Society, Interface Feb 2024We link continuum models of reaction-diffusion systems that exhibit diffusion-driven instability to constraints on the particle-scale interactions underpinning this...
We link continuum models of reaction-diffusion systems that exhibit diffusion-driven instability to constraints on the particle-scale interactions underpinning this instability. While innumerable biological, chemical and physical patterns have been studied through the lens of Alan Turing's reaction-diffusion pattern-forming mechanism, the connections between models of pattern formation and the nature of the particle interactions generating them have been relatively understudied in comparison with the substantial efforts that have been focused on understanding proposed continuum systems. To derive the necessary reactant combinations for the most parsimonious reaction schemes, we analyse the emergent continuum models in terms of possible generating elementary reaction schemes. This analysis results in the complete list of such schemes containing the fewest reactions; these are the simplest possible hypothetical mass-action models for a pattern-forming system of two interacting species.
Topics: Models, Biological; Diffusion
PubMed: 38412962
DOI: 10.1098/rsif.2023.0490 -
Brain Communications 2023White matter is often severely affected after human ischaemic stroke. While animal studies have suggested that various factors may contribute to white matter structural...
White matter is often severely affected after human ischaemic stroke. While animal studies have suggested that various factors may contribute to white matter structural damage after ischaemic stroke, the characterization of damaging processes to the affected hemisphere after human stroke remains poorly understood. Thus, the present study aims to thoroughly describe the longitudinal pattern of evolution of diffusion magnetic resonance imaging metrics in different parts of the ipsilesional white matter after stroke. We acquired diffusion and anatomical images in 17 patients who had suffered from a single left hemisphere ischaemic stroke, at 24-72 h, 8-14 days and 6 months post-stroke. For each patient, we created three regions of interest: (i) the white matter lesion; (ii) the perilesional white matter; and (iii) the remaining white matter of the left hemisphere. We extracted diffusion metrics (fractional anisotropy, mean, axial and radial diffusivities) for each region and conducted two-way repeated measures ANOVAs with stage post-stroke (acute, subacute and chronic) × regions of interest (white matter lesion, perilesional white matter and remaining white matter). Fractional anisotropy values stayed consistent across time-points, with significantly lower values in the white matter lesion compared to the perilesional white matter and remaining white matter tissue. Fractional anisotropy values of the perilesional white matter were also significantly lower than that of the remaining white matter. Mean, axial and radial diffusivities in the white matter lesion were all decreased in the acute stage compared to perilesional white matter and remaining white matter, but significantly increased in both the subacute and chronic stages. Significant increases in mean and radial diffusivities in the perilesional white matter were seen in the later stages of stroke. Our findings suggest that various physiological processes are at play in the acute, subacute and chronic stages following ischaemic stroke, with the infarct territory and perilesional white matter affected by ischaemia at different rates and to different extents throughout the stroke recovery stages. The examination of multiple diffusivity metrics may inform us about the mechanisms occurring at different time-points, i.e. focal swelling, axonal damage or myelin loss.
PubMed: 38075947
DOI: 10.1093/braincomms/fcad313 -
Angewandte Chemie (International Ed. in... Feb 2024Electrocatalytic CO reduction has developed into a broad field, spanning fundamental studies of enzymatic 'model' catalysts to synthetic molecular catalysts and... (Review)
Review
Electrocatalytic CO reduction has developed into a broad field, spanning fundamental studies of enzymatic 'model' catalysts to synthetic molecular catalysts and heterogeneous gas diffusion electrodes producing commercially relevant quantities of product. This diversification has resulted in apparent differences and a disconnect between seemingly related approaches when using different types of catalysts. Enzymes possess discrete and well understood active sites that can perform reactions with high selectivity and activities at their thermodynamic limit. Synthetic small molecule catalysts can be designed with desired active site composition but do not yet display enzyme-like performance. These properties of the biological and small molecule catalysts contrast with heterogeneous materials, which can contain multiple, often poorly understood active sites with distinct reactivity and therefore introducing significant complexity in understanding their activities. As these systems are being better understood and the continuously improving performance of their heterogeneous active sites closes the gap with enzymatic activity, this performance difference between heterogeneous and enzymatic systems begins to close. This convergence removes the barriers between using different types of catalysts and future challenges can be addressed without multiple efforts as a unified picture for the biological-synthetic catalyst spectrum emerges.
Topics: Carbon Dioxide; Diffusion; Electrodes; Thermodynamics
PubMed: 37983571
DOI: 10.1002/anie.202310547