Diffusion Models

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation...

This meta-analysis evaluates the efficacy and safety of chimeric antigen receptor (CAR) T-cell therapy and bispecific antibodies for relapsed/refractory diffuse large B-cell lymphoma (R/R DLBCL). We searched MEDLINE, Embase, and Cochrane databases until July 2023 for trials assessing CAR T-cell therapies and CD20×CD3 bispecific antibodies as third- or subsequent-line in R/R DLBCL. Random effects models estimated the complete response (CR) rate and secondary outcomes, with meta-regressions adjusting for relevant covariates...

Respiratory viral infections remain a leading cause of morbidity and mortality. Using a murine model of human metapneumovirus (HMPV), we identified recruitment of a C1q-expressing inflammatory monocyte population concomitant with viral clearance by adaptive immune cells. Genetic ablation of C1q led to reduced CD8+ T cell function. Production of C1q by a myeloid lineage was necessary to enhance CD8+ T cell function. Activated and dividing CD8+ T cells expressed a C1q receptor, gC1qR. Perturbation of gC1qR signaling led to altered CD8+ T cell IFN-γ production, metabolic capacity, and cell proliferation...

PURPOSE: This study is to investigate the diagnostic value of 68 Ga-PSMA-11 in improving the concordance between mpMRI-TB and combined biopsy (CB) in detecting PCa. METHODS: 115 consecutive men with 68 Ga-PSMA-11 PET/CT prior to prostate biopsy were included for analysis. PSMA intensity, quantified as maximum standard uptake value (SUVmax), minimum apparent diffusion coefficient (ADCmin) and other clinical characteristics were evaluated relative to biopsy concordance using univariate and multivariate logistic regression analyses...

A dynamic reaction-diffusion model of four variables is proposed to describe the spread of lytic viruses among phytoplankton in a poorly mixed aquatic environment. The basic ecological reproductive index for phytoplankton invasion and the basic reproduction number for virus transmission are derived to characterize the phytoplankton growth and virus transmission dynamics. The theoretical and numerical results from the model show that the spread of lytic viruses effectively controls phytoplankton blooms. This validates the observations and experimental results of Emiliana huxleyi-lytic virus interactions...

P2-type Na2/3 Ni1/3 Mn2/3 O2 (PNNMO) has been extensively studied because of its desirable electrochemical properties as a positive electrode for sodium-ion batteries. PNNMO exhibits intralayer transition-metal ordering of Ni and Mn and intralayer Na+ /vacancy ordering. The Na+ /vacancy ordering is often considered a major impediment to fast Na+ transport and can be affected by transition-metal ordering. We show by neutron/X-ray diffraction and density functional theory (DFT) calculations that Li doping (Na2/3 Li0...

The structure of solvated Li+ has a significant influence on the electrolyte/electrode interphase (EEI) components and desolvation energy barrier, which are two key factors in determining the Li+ diffusion kinetics in lithium metal batteries. Herein, the "solvent activity" concept is proposed to quantitatively describe the correlation between the electrolyte elements and the structure of solvated Li+ . Through fitting the correlation of the electrode potential and solvent concentration, we suggest a "low-activity-solvent" electrolyte (LASE) system for deriving a stable inorganic-rich EEI...

Demyelination is typically followed by a remyelination process through mature oligodendrocytes (OLs) differentiated from precursor cells (OPCs) recruited into the lesioned areas, however, this event usually results in uncompleted myelination. Potentiation of the remyelination process is an important target for designing effective therapeutic strategies against white matter loss. Here, it was evaluated the remyelinating effect of different β-carbolines that present differential allosteric modulation on the GABAA receptor expressed in OLs...

Neuronal loss in Alzheimer's disease has been reported to display features of apoptosis, pyroptosis (programmed necrosis), or necroptosis. This study thoroughly examines the production and characterization of MCM-41 based berberine (BBR)-loaded porous silica nanoparticles (MSNs) by a modified Stöber method, focusing on their possible role in inhibiting the apoptotic process. Particle size, polydispersity index, morphology, drug loading, zeta potential, entrapment efficiency, and drug release were examined...

Ischemic stroke segmentation at an acute stage is vital in assessing the severity of patients' impairment and guiding therapeutic decision-making for reperfusion. Although many deep learning studies have shown attractive performance in medical segmentation, it is difficult to use these models trained on public data with private hospitals' datasets. Here, we demonstrate an ensemble model that employs two different multimodal approaches for generalization, a more effective way to perform on external datasets...

Transdermal drug delivery is a formulation in which the drug is absorbed through the skin for systemic action. Its advantages include avoidance of first-pass effects, sustained drug supply, and ease of administration and discontinuation. Drugs administered transdermally transfer into the blood circulation through the stratum corneum, epidermis, and dermis. The stratum corneum on the skin surface plays a barrier function in skin absorption. Therefore, developing of transdermal drug delivery systems requires innovations that overcome the barrier function of the stratum corneum and improve skin permeation...

An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients...

Deep eutectic solvents (DESs) composed of choline chloride (ChCl) and ascorbic acid (AA) were investigated using the molecular dynamics (MD) simulations. The analyses of the configuration, radial distribution function (RDFs), coordination number, spatial distribution function (SDFs), interaction energies, hydrogen bond number, and self-diffusion coefficient of the ChCl/AA binary systems of different concentrations showed that the stability of the hydrogen bond network and the mutual attraction between systems were the strongest at the experimental eutectic concentration (molar ratio of 2:1)...

Collective cell dynamics is essential for tissue morphogenesis and various biological functions. However, it remains incompletely understood how mechanical forces and chemical signaling are integrated to direct collective cell behaviors underlying tissue morphogenesis. Here, we propose a three-dimensional (3D) mechanochemical theory accounting for biochemical reaction-diffusion and cellular mechanotransduction to investigate the dynamics of multicellular lumens. We show that the interplay between biochemical signaling and mechanics can trigger either pitchfork or Hopf bifurcation to induce diverse static mechanochemical patterns or generate oscillations with multiple modes both involving marked mechanical deformations in lumens...

Deep-sea mining inevitably produces plumes, which will pose a serious threat to the marine environment with the continuous movement and diffusion of plumes along with ocean currents. The terminal settling velocity (wt ) of irregular particles is one of the crucial factors for determining the plumes' diffusion range. It is generally calculated by drag coefficient (CD ), while most existing CD models only consider single shape characteristic parameter or have a smaller range of Reynolds number (Re). In this study, a new shape factor (γ) of irregular particles is proposed by considering the thickness (one-dimension), the projected area (two-dimension), and the surface area (three-dimension) of irregular particles as well as their coupling effect to establish a modified CD model for calculating the wt ...

Most water-borne disease models ignore the advection of water flows in order to simplify the mathematical analysis and numerical computation. However, advection can play an important role in determining the disease transmission dynamics. In this paper, we investigate the long-term dynamics of a periodic reaction-advection-diffusion schistosomiasis model and explore the joint impact of advection, seasonality and spatial heterogeneity on the transmission of the disease. We derive the basic reproduction number <mml:math xmlns:mml="https://www...

Two-pore physiologically based pharmacokinetic (PBPK) modeling has demonstrated its potential in describing the pharmacokinetics (PK) of different-size proteins. However, all existing two-pore models lack either diverse proteins for validation or interspecies extrapolation. To fill the gap, here we have developed and optimized a translational two-pore PBPK model that can characterize plasma and tissue disposition of different-size proteins in mice, rats, monkeys, and humans. Datasets used for model development include more than 15 types of proteins: IgG (150 kDa), F(ab)2 (100 kDa), minibody (80 kDa), Fc-containing proteins (205, 200, 110, 105, 92, 84, 81, 65, or 60 kDa), albumin conjugate (85...

The human rotator cuff consists of four muscles, each with a complex, multipennate architecture. Despite the functional and clinical importance, the architecture of the human rotator cuff has yet to be clearly described in humans in vivo. The purpose of this study was to investigate the intramuscular, intermuscular, and interindividual variations in architecture and moment arms of the human rotator cuff. Muscle volumes, fascicle lengths, physiological cross-sectional areas (PCSAs), pennation angles, and moment arms of all four rotator cuff muscles were measured from mDixon and diffusion tensor imaging (DTI) scans of the right shoulders of 20 young adults...

When placed in an ionic surfactant gradient, charged colloids will undergo diffusiophoresis at a velocity, u DP = M DP ∇ ln  S , where M DP is the diffusiophoretic mobility and S is the surfactant concentration. The diffusiophoretic mobility depends in part on the charges and diffusivities of the surfactants and their counterions. Since micellization decreases surfactant diffusivity and alters charge distributions in a surfactant solution, M DP of charged colloids in ionic surfactant gradients may differ significantly when surfactant concentrations are above or below the critical micelle concentration (CMC)...

Rotational diffusion studies of two solutes 7-(dimethylamino)-4-methoxy-1-methyl-1,8-naphthyridin-2(1H)-one (7DM4M1M1,8, N-2(1H)-one) and 7-amino-4-(trifluoromethyl)-2H-1-benzopyran-2-one (7A4T2H1B-2-one) having equal volumes but different chemical natures are studied in series of alcohol solvents at 303 K using steady-state methods. HOMO-LUMO, Electron density, Molecular electrostatic potential (MEP), etc., are obtained from computational calculations using Gaussian 09 software. Rotational reorientation times of 7DM4M1M1,8, N-2(1H)-one solute molecule is found to be less than 7A4T2H1B-2-one solute molecule indicates it rotates slowly in chosen solvents...