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Water Research Aug 2022Contaminants stored in the low permeability sediments will continue to threaten the adjacent shallow groundwater system after the aquifer is remediated. Understanding...
Contaminants stored in the low permeability sediments will continue to threaten the adjacent shallow groundwater system after the aquifer is remediated. Understanding the storage and discharge behavior of contaminants in the aquitards is essential for the efficient remediation of contaminated sites, but most of the previous analytical studies focused on nonreactive solutes in a single homogenous aquitard. This study presents novel analytical solutions for the forward and back diffusion of contaminants through multi-layer low permeability sediments considering abiotic and biotic environmental degradation. Three representative source depletion patterns (i.e., instantaneous, linear, and exponential patterns) were selected to describe the dissolution of dense non-aqueous phase liquids (DNAPL) in the aquifer more realistically. At the forward diffusion stage, the mass storage of contaminants in the aquitards with the instantaneous pattern is the largest, nearly twice that with the exponential pattern. A simple equivalent homogeneous model is generally adopted in the risk assessment. However, relative to the proposed multi-layer model, it will significantly underestimate the onset of the back-diffusion of heterogeneous aquitards and overestimate the persistence of aquifer plumes. The previously-reported semi-infinite boundary assumption is also not applicable, with a maximum error of over 200% in the long-term prediction of back diffusion behavior of a thin aquitard. Moreover, when the degradation half-life is less than 16 years, less than 10% of the contaminants stored in the aquitards will diffuse into the overlying aquifer, suggesting that biostimulation or bioaugmentation can effectively mitigate back-diffusion risk. Overall, the proposed diffusion-reaction coupled model with multi-layer media is of great value and high demand in predicting the back-diffusion behavior of heterogeneous aquitards and guiding the soil bioremediation.
Topics: Diffusion; Groundwater; Permeability; Solutions; Water Pollutants, Chemical
PubMed: 35932709
DOI: 10.1016/j.watres.2022.118925 -
Journal of Controlled Release :... Feb 2024Drug delivery systems which rely on diffusion for mass transport, such as hydrogels and nanoparticles, have enhanced drug targeting and extended delivery profiles to... (Review)
Review
Drug delivery systems which rely on diffusion for mass transport, such as hydrogels and nanoparticles, have enhanced drug targeting and extended delivery profiles to improve health outcomes for patients suffering from diseases including cancer and diabetes. However, diffusion-dependent systems often fail to provide >0.01-1% drug bioavailability when transporting macromolecules across poorly permeable physiological tissues such as the skin, solid tumors, the blood-brain barrier, and the gastrointestinal walls. Convection-enabling robotic ingestibles, wearables, and implantables physically interact with tissue walls to improve bioavailability in these settings by multiple orders of magnitude through convective mass transfer, the process of moving drug molecules via bulk fluid flow. In this Review, we compare diffusive and convective drug delivery systems, highlight engineering techniques that enhance the efficacy of convective devices, and provide examples of synergies between the two methods of drug transport.
Topics: Humans; Diffusion; Biological Transport; Drug Delivery Systems; Blood-Brain Barrier; Neoplasms
PubMed: 38190971
DOI: 10.1016/j.jconrel.2024.01.008 -
Magnetic Resonance in Medicine May 2020Diffusion times longer than 50 ms are typically probed with stimulated-echo sequences. Varying the diffusion time in stimulated-echo sequences affects the T weighting of...
PURPOSE
Diffusion times longer than 50 ms are typically probed with stimulated-echo sequences. Varying the diffusion time in stimulated-echo sequences affects the T weighting of subcompartments, complicating the analysis of diffusion time dependence. Although inversion recovery preparation could be used to change the T weighting, it cannot ensure equal T weighting at arbitrary mixing times. In this article, a sequence that ensures constant T weighting over a wide range of diffusion times is presented.
METHODS
The proposed sequence features 2 independent longitudinal storage periods: TM and TM . Diffusion encoding is performed during TM , effectively coupling the diffusion time and TM . Equal T weighting at arbitrary diffusion times is realized by keeping the total mixing time TM + TM constant. The sequence was compared with conventional stimulated-echo measurements of diffusion in a 2-compartment phantom consisting of distilled water and paraffinum perliquidum. Additionally, in vivo DTI of the brain was carried out for 8 healthy volunteers with diffusion times ranging from 50 to 500 ms.
RESULTS
Diffusion time dependence of the axial and radial diffusivity was detected in the brain. Both sequences resulted in almost identical diffusivities in white matter. In regions containing partial volumes of gray and white matter, a dependency on T weighting was observed.
CONCLUSION
In accordance with previous studies, little variance of T values appeared to be present in healthy white matter. However, this is likely different in diseased tissue. Here, the proposed sequence can be effective in differentiating between diffusion time dependence and T weighting effects.
Topics: Brain; Diffusion; Diffusion Magnetic Resonance Imaging; Humans; Theophylline; White Matter
PubMed: 31657868
DOI: 10.1002/mrm.28046 -
ACS Macro Letters Feb 2022The laser light scattering experiments were performed to explore the role of dextran (size (): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps;...
The laser light scattering experiments were performed to explore the role of dextran (size (): 2.6, 6.9, and 17.0 nm) in compacting the plasmids (pBS: 2.9 kbps; pCMV-Tag2B: 4.3 kbps; and pET28a: 5.3 kbps) in vitro in the volume fraction (ϕ) range 0.01 to 0.15 of the macromolecular crowder. Two compaction regimes were observed in terms of the radius of gyration () for plasmid-dextran combinations, wherein the plasmid diffusivity is governed by normal diffusion and subdiffusion, respectively. Generalized scaling, ∼ ϕ, where represents the conformational geometry of plasmids, is reported. The plasmid conformation depends on the crowder's size, with larger conformational changes observed in the presence of smaller crowders. The second virial coefficient () and translational diffusion coefficient () indicate that entropically driven depletion of crowders, excluded volume, and interplasmid repulsive interactions govern plasmids' conformational changes, validated herein from the scaling of with molecular weight.
Topics: DNA; Dextrans; Diffusion; Molecular Conformation; Plasmids
PubMed: 35574767
DOI: 10.1021/acsmacrolett.1c00593 -
European Radiology Mar 2024Whether the alternation of the glymphatic system exists in neurodevelopmental disease still remains unclear. In this study, we investigated structural and functional...
OBJECTIVES
Whether the alternation of the glymphatic system exists in neurodevelopmental disease still remains unclear. In this study, we investigated structural and functional changes in the glymphatic system in the treatment-naïve attention-deficit/hyperactivity disorder (ADHD) children by quantitatively measuring the Virchow-Robin spaces (VRS) volume and diffusion tensor image-analysis along the perivascular space (DTI-ALPS).
METHODS
Forty-seven pediatric ADHD patients and 52 age- and gender-matched typically developing (TD) children were recruited in this prospective study. The VRS volume was calculated using a semi-automated approach in axial T2-weighted images. Diffusivities along the x-, y-, and z-axes in the projection, association, and subcortical neural fiber areas were measured. The ALPS index, a ratio that accentuated water diffusion along the perivascular space, was calculated. The Mann-Whitney U test was used to compare the quantitative parameters; Pearson's correlation was used to analyze the correlation with clinical symptoms.
RESULTS
The cerebral VRS volume (mean, 15.514 mL vs. 11.702 mL) and the VRS volume ratio in the ADHD group were larger than those in the TD group (all p < 0.001). The diffusivity along the x-axis in association fiber area and ALPS index were significantly smaller in the ADHD group vs. TD group (mean, 1.40 vs.1.59, p < 0.05 after false discovery rate adjustment). Besides, the ALPS index was related to inattention symptoms of ADHD (r = - 0.323, p < 0.05).
CONCLUSIONS
Our study suggests that the glymphatic system alternation may participate in the pathogenesis of ADHD, which may be a new research direction for exploring the mechanisms of psycho-behavioral developmental disorders. Moreover, the VRS volume and ALPS index could be used as the metrics for diagnosing ADHD.
CLINICAL RELEVANCE STATEMENT
Considering the potential relevance of the glymphatic system for exploring the mechanisms of attention deficit/hyperactivity, the Virchow-Robin spaces volume and the analysis along the perivascular space index could be used as additional metrics for diagnosing the disorder.
KEY POINTS
• Increased Virchow-Robin space volume and decreased analysis along the perivascular space index were found in the treatment-naïve attention-deficit/hyperactivity disorder children. • The results of this study indicate that the glymphatic system alternation may have a valuable role in the pathogenesis of attention-deficit/hyperactivity disorder. • The analysis along the perivascular space index is correlated with inattention symptoms of attention-deficit/hyperactivity disorder children.
Topics: Humans; Child; Attention Deficit Disorder with Hyperactivity; Prospective Studies; Benchmarking; Diffusion; Image Processing, Computer-Assisted
PubMed: 37673963
DOI: 10.1007/s00330-023-10220-2 -
Magnetic Resonance in Medicine Jun 2022To address the long echo times and relatively weak diffusion sensitization that typically limit oscillating gradient spin-echo (OGSE) experiments, an OGSE implementation...
PURPOSE
To address the long echo times and relatively weak diffusion sensitization that typically limit oscillating gradient spin-echo (OGSE) experiments, an OGSE implementation combining spiral readouts, gap-filled oscillating gradient shapes providing stronger diffusion encoding, and a high-performance gradient system is developed here and utilized to investigate the tradeoff between b-value and maximum OGSE frequency in measurements of diffusion dispersion (i.e., the frequency dependence of diffusivity) in the in vivo human brain. In addition, to assess the effects of the marginal flow sensitivity introduced by these OGSE waveforms, flow-compensated variants are devised for experimental comparison.
METHODS
Using DTI sequences, OGSE acquisitions were performed on three volunteers at b-values of 300, 500, and 1000 s/mm and frequencies up to 125, 100, and 75 Hz, respectively; scans were performed for gap-filled oscillating gradient shapes with and without flow sensitivity. Pulsed gradient spin-echo DTI acquisitions were also performed at each b-value. Upon reconstruction, mean diffusivity (MD) maps and maps of the diffusion dispersion rate were computed.
RESULTS
The power law diffusion dispersion model was found to fit best to MD measurements acquired at b = 1000 s/mm despite the associated reduction of the spectral range; this observation was consistent with Monte Carlo simulations. Furthermore, diffusion dispersion rates without flow sensitivity were slightly higher than flow-sensitive measurements.
CONCLUSION
The presented OGSE implementation provided an improved depiction of diffusion dispersion and demonstrated the advantages of measuring dispersion at higher b-values rather than higher frequencies within the regimes employed in this study.
Topics: Brain; Diffusion; Diffusion Magnetic Resonance Imaging; Humans; Monte Carlo Method
PubMed: 35049104
DOI: 10.1002/mrm.29161 -
Physical Review Letters Aug 2020Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous...
Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation, and filtration processes. Their current description via diffusion equations with mixed boundary conditions is limited to simple surface reactions with infinite or constant reactivity. In this Letter, we propose a probabilistic approach based on the concept of boundary local time to investigate the intricate dynamics of diffusing particles near a reactive surface. Reformulating surface-particle interactions in terms of stopping conditions, we obtain in a unified way major diffusion-reaction characteristics such as the propagator, the survival probability, the first-passage time distribution, and the reaction rate. This general formalism allows us to describe new surface reaction mechanisms such as for instance surface reactivity depending on the number of encounters with the diffusing particle that can model the effects of catalyst fooling or membrane degradation. The disentanglement of the geometric structure of the medium from surface reactivity opens far-reaching perspectives for modeling, optimization, and control of diffusion-mediated surface phenomena.
Topics: Cell Membrane; DNA; Diffusion; Models, Biological; Models, Chemical; Proteins; Surface Properties; Thermodynamics
PubMed: 32857533
DOI: 10.1103/PhysRevLett.125.078102 -
Bioinformatics (Oxford, England) Sep 2023As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest...
MOTIVATION
As an important player in transcriptome regulation, microRNAs may effectively diffuse somatic mutation impacts to broad cellular processes and ultimately manifest disease and dictate prognosis. Previous studies that tried to correlate mutation with gene expression dysregulation neglected to adjust for the disparate multitudes of false positives associated with unequal sample sizes and uneven class balancing scenarios.
RESULTS
To properly address this issue, we developed a statistical framework to rigorously assess the extent of mutation impact on microRNAs in relation to a permutation-based null distribution of a matching sample structure. Carrying out the framework in a pan-cancer study, we ascertained 9008 protein-coding genes with statistically significant mutation impacts on miRNAs. Of these, the collective miRNA expression for 83 genes showed significant prognostic power in nine cancer types. For example, in lower-grade glioma, 10 genes' mutations broadly impacted miRNAs, all of which showed prognostic value with the corresponding miRNA expression. Our framework was further validated with functional analysis and augmented with rich features including the ability to analyze miRNA isoforms; aggregative prognostic analysis; advanced annotations such as mutation type, regulator alteration, somatic motif, and disease association; and instructive visualization such as mutation OncoPrint, Ideogram, and interactive mRNA-miRNA network.
AVAILABILITY AND IMPLEMENTATION
The data underlying this article are available in MutMix, at http://innovebioinfo.com/Database/TmiEx/MutMix.php.
Topics: Humans; Diffusion; Glioma; MicroRNAs; Mutation; RNA, Messenger
PubMed: 37624931
DOI: 10.1093/bioinformatics/btad520 -
Journal of Mathematical Biology May 2023The effects of habitat heterogeneity on a diffusing population are investigated here. We formulate a reaction-diffusion system of partial differential equations to...
The effects of habitat heterogeneity on a diffusing population are investigated here. We formulate a reaction-diffusion system of partial differential equations to analyze the effect of resource allocation in an ecosystem with resource having its own dynamics in space and time. We show a priori estimates to prove the existence of state solutions given a control. We formulate an optimal control problem of our ecosystem model such that the abundance of a single species is maximized while minimizing the cost of inflow resource allocation. In addition, we show the existence and uniqueness of the optimal control as well as the optimal control characterization. We also establish the existence of an optimal intermediate diffusion rate. Moreover, we illustrate several numerical simulations with Dirichlet and Neumann boundary conditions with the space domain in 1D and 2D.
Topics: Ecosystem; Population Dynamics; Models, Biological; Diffusion
PubMed: 37217639
DOI: 10.1007/s00285-023-01932-6 -
The Journal of Chemical Physics Aug 2022Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in...
Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different real-time feedback-driven single-particle tracking (RT-FD-SPT) approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the knight's tour (grid scan) method, and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the knight's tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows for an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.
Topics: Diffusion; Feedback; Particle Size; Single Molecule Imaging
PubMed: 36050025
DOI: 10.1063/5.0096729