Diffuse Functions Research Articles

SNR-enhanced diffusion MRI with structure-preserving low-rank denoising in reproducing kernel Hilbert spaces.

To introduce, develop, and evaluate a novel denoising technique for diffusion MRI that leverages nonlinear redundancy in the data to boost the SNR while preserving signal information. We exploit nonlinear redundancy of the dMRI data by means of kernel principal component analysis (KPCA), a nonlinear generalization of PCA to reproducing kernel Hilbert spaces. By mapping the signal to a high-dimensional space, a higher level of redundant information is exploited, thereby enabling better denoising than linear PCA. We implement KPCA with a Gaussian kernel, with parameters automatically selected from knowledge of the noise statistics, and validate it on realistic Monte Carlo simulations as well as with in vivo human brain submillimeter and low-resolution dMRI data. We also demonstrate KPCA denoising on multi-coil dMRI data. SNR improvements up to 2.7 were obtained in real in vivo datasets denoised with KPCA, in comparison to SNR gains of up to 1.8 using a linear PCA denoising technique called Marchenko-Pastur PCA (MPPCA). Compared to gold-standard dataset references created from averaged data, we showed that lower normalized root mean squared error was achieved with KPCA compared to MPPCA. Statistical analysis of residuals shows that anatomical information is preserved and only noise is removed. Improvements in the estimation of diffusion model parameters such as fractional anisotropy, mean diffusivity, and fiber orientation distribution functions were also demonstrated. Nonlinear redundancy of the dMRI signal can be exploited with KPCA, which allows superior noise reduction/SNR improvements than the MPPCA method, without loss of signal information.

Medición de las capacidades tecnológicas para la innovación en los sistemas de conocimiento e innovación agrícola

Las funciones de generación, difusión y uso de conocimiento y tecnología en los sistemas de innovación están asociadas a las capacidades tecnológicas para la innovación (TICs, por su sigla en inglés), las cuales juegan un papel fundamental en el desempeño innovador de los sistemas de conocimiento e innovación agrícola (AKIS, por su sigla en inglés). No obstante, las metodologías actuales no exhiben perspectivas que faciliten la comprensión dinámica y organizacional de las TICs, lo que dificulta la comprensión de dichos sistemas. Este artículo presenta una propuesta metodológica para medir el nivel de las TICs al asociarlas a un modelo de comportamiento organizacional para aplicarlo en una muestra de 256 organizaciones del AKIS del café y 74 organizaciones del AKIS del aguacate en el departamento de Antioquia (Colombia). Los resultados confirman que la medición del nivel de las TICs y de sus variaciones dinámicas en el tiempo permite mejorar la comprensión de los procesos de innovación y evaluar e identificar las brechas existentes entre las TICs y las funciones de innovación de estos sistemas.

DFT study of low-energy electron interaction with pyridine, pyrazine and their halo derivatives

In this work, the density functional theory with B3LYP hybrid functional was employed to calculate quantities useful for estimating the behavior of pyridine, pyrazine and their derivatives monosubstituted with Cl or Br atom, when exposed to low-energy electron impact. Vertical electron affinities obtained in several Pople basis sets and in aug-cc-pVTZ basis set are reported. Although some of the investigated molecules do not form stable anions, the results are in a satisfactory agreement with the available, albeit sparse experimental data, if the diffuse functions are included in calculations. It was found that the 6-31+G* basis is sufficient and its further enlargement does not significantly change the results. At this level of theory, potential energy curves, supported by enthalpies of dissociation to the neutral and anion fragment, were also determined for the description of the dissociative electron attachment. According to B3LYP, the potential energy curves of the halogen bond are almost repulsive in halopyridines, whereas halopyrazine anions require small activation energy for dissociation. Vertical electron affinities, enthalpies and equilibrium C-X distances (X=H, Cl, Br) were also calculated using Møller-Plesset second-order perturbation theory.Graphic

All-electron triple zeta basis sets for ZORA calculations: Application in studies of atoms and molecules

Segmented all-electron basis set of triple zeta valence quality plus polarization functions for the elements from H to Xe to be used together with the ZORA Hamiltonian is developed. This set was augmented with diffuse functions in order to properly describe electrons distant from the nuclei. At the ZORA-CCSD(T) level of theory, ionization energies and mean dipole polarizabilities of some atoms as well as bond lengths, dissociation energies, and harmonic vibrational frequencies of a set of molecules are calculated. Scalar relativistic effects are estimated for all properties. The performances of the ZORA and DKH2 Hamiltonians are also assessed.

Improvement of conditions for boundedness in a fully parabolic chemotaxis system with nonlinear signal production

under homogeneous Neumann boundary conditions in a bounded domain Ω⊂ℝ n (n≥2). The diffusion function D(s)∈C 2 ([0,∞)) and the chemotactic sensitivity function S(s)∈C 2 ([0,∞)) are given by D(s)≥C d (1+s) -α and 0<S(s)≤C s s(1+s) β-1 for all s≥0 with C d ,C s >0 and α,β∈ℝ. The nonlinear signal secretion function g(s)∈C 1 ([0,∞)) is supposed to satisfy g(s)≤C g s γ foralls≥0 with C g ,γ>0. Global boundedness of solution is established under the specific conditions:

Efficient parallel computing on the game theory-aware robust influence maximization problem

Influence maximization (IM) is a problem of finding the most influential nodes with limited budgets under the given propagation model, which finally maximizes the spread of influence into the network. This work considers the robustness assumption in the IM problem, named the robust influence maximization (RIM) problem, which focuses on the uncertainty factors among the influence propagation models and algorithms, so as to find nodes that can achieve robust performance with different diffusion functions in networks. For modeling the uncertainty, we generate parameter space by adding noises into the independent cascade (IC) propagation model, in which each edge has an interval to deposit its all possible activation probabilities. Then, a novel robust optimal objective function is proposed for the RIM problem, which based on the calculation of the Shapley value, one classical and crucial concept in cooperative game theory. Particularly, to face the computing time explosion for traversing various uncertainty scenarios, we first give a complete parallel computing based framework to improve the proposed algorithm’s efficiency, which will definitely motivate the research that how to fully use the computing resources to speed up the RIM problem solving. Through extensive experiments with nine real-world/synthetic networks and four centrality-based IC models, we find one exciting rule that the worst case on the perturbation interval model occurs when edge probability is equal to the endpoint of the interval, and the influence spread effect is positively correlated with the difference of probabilities between two directions over an edge. The seed nodes selected by the proposed robust algorithm outperforms other state-of-the-art methods under the worst diffusion case.

Safety and efficacy of rituximab in connective tissue disease-associated interstitial lung disease: A systematic review and meta-analysis

ObjectiveRituximab (RTX) is widely used in the treatment of connective tissue disease (CTD) because it can target and eliminate pathogenic B cells. Interstitial lung disease (ILD) is one of the common complications of CTD; however, the clinical benefits of RTX in connective tissue disease-associated interstitial lung disease (CTD-ILD) are still controversial. This meta-analysis was performed to systematically evaluate the efficacy and safety of RTX in CTD-ILD patients. MethodsWe performed a systematic online query in PubMed, Cochrane, and Embase up to February 2020. Randomized controlled trials and observational studies on the use of RTX and conventional treatment in CTD-ILD patients were comprehensively reviewed and investigated. ResultsIn total, 6 studies, including 242 participants, were analysed. The pooled results showed that RTX is superior to conventional treatment methods in improving forced vital capacity and modified Rodnan skin scores (MRSS) in patients with systemic sclerosis (P＜0. 05), but there was no statistically significant difference between RTX and conventional treatment method in the improvement of lung diffusion function. The risk of adverse effects declined in the RTX therapy groups compared with the conventional therapy groups in terms of infection and the blood system. ConclusionThe pooled results of this meta-analysis indicated that RTX is well tolerated, and RTX is able to improve or stabilize pulmonary function in CTD-ILD patients.

New Cu(II), Co(II) and Ni(II) azo-Schiff base complexes: Synthesis, characterization, catalytic oxidation of alkenes and DFT study

Three new complexes with general formula of ML (M = Cu (1), Co (2), Ni (3)) containing an azo-Schiff base ligand (H2L) derived from 2,3-butanediamine and 4-(benzeneazo) salicylaldehyde were synthesized by template method. Characterization of the ligand and complexes were accomplished with FT-IR, UV–Vis, and 1H NMR. The catalytic activity of the complexes (1–3) were tested for the oxidation of various alkenes (cyclooctene, cyclohexene, styrene, α-methyl styrene, and norbornene) applying tert-butyl hydroperoxide (TBHP) as an oxidizing agent, and it was found that they were acceptable catalysts. Under the optimized reaction conditions, CuL complex displayed 94% conversion for the oxidation of cyclooctene, and CoL and NiL complexes exhibited 90 and 85% conversions for oxidizing α-methyl styrene, respectively. Based on our density functional computations, diffuse functions are compulsory in the basis set for geometry optimization of these systems. Therefore, the most stable structures and the vibrational frequencies were calculated at the M06-2X/6–311++G(d,p) level. By establishing the correlation between observed and calculated frequencies, the assignment of the vibrational modes was performed. Based on natural charge analysis (NAO), the back electron transfer from ML to the TBHP breaks the OO bond and facilitates the formation of tert-butoxyl radicals.

Boundedness in a quasilinear two-species chemotaxis system with two chemicals in higher dimensions

In this paper, a nonlinear diffusion two-species chemotaxis model with two chemicals{ut=∇⋅(D(u)∇u)−∇⋅(u∇v),τvt=Δv−v+w,wt=∇⋅(S(w)∇w)−∇⋅(w∇z),τzt=Δz−z+u, is considered in a bounded domain x∈Ω⊂Rd(d≥2) with homogeneous Neumann boundary conditions, where t≥0, and τ=0 or τ=1. The diffusion functions (D,S)∈(C2([0,∞)))2 are assumed to take forms like D(u)=(u+1)m1−1 and S(w)=(w+1)m2−1 with some m1,m2>1, respectively. In the fully parabolic case τ=1, it is proved that global classical bounded solutions exist if m1>2−2/d and m2>2−2/d. While for the case τ=0, by the means of the Lyapunov functional, the range of m1 and m2 to ensure the global existence of solutions can be extended to m1m2+2m1/d>m1+m2 or m1m2+2m2/d>m1+m2.

Hypersensitivity pneumonia diagnosed by excisional lung biopsy: a clinicopathological features of 47 cases

Objective: To analyze the clinicopathological and immunohistochemical characteristics of the hypersensitivity pneumonia (HP) cases that were diagnosed by excisional lung biopsy, to improve the diagnosis accuracy of HP. Methods: The data of 47 HP cases diagnosed by excisional lung biopsy during the last 20 years were collected in Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, from January 2000 to June 2020. The clinicopathological features and the immunohistochemical profiles of CD3, CD4, CD8 and CD20 were analyzed using light microscopy and immunohistochemical stains. Results: The age of the patients ranged from 15 to 68 years, while the ratio of male to female was 22∶25. The main symptoms were shortness of breath and cough, and 32 cases had a history of allergen exposure. Most of the patients had restrictive impaired ventilatory function, and impaired diffusion function. The proportion of lymphocytes in bronchoalveolar lavage fluid (BALF) increased in 85.3%(29/34) of the patients, and the CD4+/CD8+ T cell ratio was not higher than 0.8 in 31.3%(10/32) of the patients. Microscopically, 59.6%(28/47) of the cases showed nonnecrotizing granuloma/giant cells in the stroma, and 40.4% (19/47) of the cases had only giant cells. Ninety-three-point six percent of the cases(44/47) had peribronchiolar metaplasia, while 70.2%(33/47) had focal cell-rich inflammation. Forty-four cases (93.6%, 44/47) had fibrosis, which was manifested as usual interstitial pneumonia-like fibrosis (47.7%, 21 cases), nonspecific interstitial pneumonia-like fibrosis (29.5%, 13 cases), purely peribronchiolar fibrosis (6.8%, 3 cases) and mixed fibrosis (15.9%, 7 cases). Immunohistochemistry showed that CD4+ T cells were fewer than CD8+ T cells in 24 cases (55.8%, 24/43) of HP. Thirty-two HP patients had follow-up data. Among them, 7 patients had improved symptoms, 12 patients were stable, and 13 patients had worsening symptoms. Conclusions: The most common type of HP diagnosed by excisional lung biopsy is chronic HP. The clinical characteristics are long course of disease, restricted ventilation disorder and impaired diffusion function with the increase of lymphocyte proportion in BALF. Nearly 1/3 of the patients have no known history of allergen contact. The degree of fibrosis in HP patients diagnosed by excisional lung biopsy is severe, and the histologic types of fibrosis varies, but the UIP-like and/or NSIP-like fibrosis is most common. The CD4+/CD8+ T cell ratio in lung tissues is less than 1 in more than half of the cases. Pulmonary fibrosis continued to increase in some of the patients with chronic HP, even after treatment.

Image Denoising using Modified Diffusion Functions on Nonlinear Second-Order Hyperbolic Model

Partial Differential Equations have been effective in solving numerous issues in image processing and computer vision fields. Image denoising is an essential process in image processing as the existence of noise affects an image’s quality. Various nonlinear PDE-based models for removal and edge-preserving in the images have been proposed in literatures. Due to the undesirable effect problems, which are the blocky effect and the edge detectors that falsely recognize it as edges, several improved nonlinear PDE-based denoising approaches are introduced. A nonlinear second-order hyperbolic model was introduced because of the linear hyperbolic equation’s weakness that is not completely reducing the blurring effects. Besides improving image quality using the model, an appropriate diffusion function is crucial for satisfactory denoising results. This paper aims to propose a modified diffusion function to be implemented on a nonlinear second-order hyperbolic model and evaluate the model’s performance that acts as an image denoising process. A set of images with different noise levels are processed using different modified diffusion functions and implemented to preserve the image details. Then, the proposed diffusion function’s performance is evaluated using the peak signal-to-noise ratio (PSNR) and compared with the performance of existing filters that are Gaussian filter, average filter and Wiener filter. The implementation of the experiment is completed using MATLAB. As a result, the modified functions have successfully removed the different levels of noise and improve the image quality with a higher value of PSNR as compared with Gaussian filter, average filter and Wiener filter. It can be concluded that the modified diffusion function is outperforming existing filters and significantly produced a better image noise removal method with better details preservation.

Energy Partitions of Seismic Waves in Interfaces: Numerical Results

The energy propagated by a seismic event has been of great interest to the community of geophysics and seismologists. In recent times, several studies have been published with the purpose of showing the contributions of each type of seismic wave to the total energy propagated. In this context, diffuse field theory, Green functions and motion correlations have been used to determine energy contributions or partitions based on the type of propagated seismic waves or the degrees of freedom of the medium. In this work, we implement the boundary element method to derive seismic wave energy partitions in interfaces (vacuum–solid, fluid–solid and solid–solid). Theoretical results for two-dimensional infinite spaces show that for a Poisson solid, the energy partitions are 25% for P waves and 75% for SV waves; our results are coincident with such values. However, for interfaces, energy partitions are strongly dependent on the propagation velocities and Poisson's ratio of the media they join. For the case of a vacuum–solid half-space, our results are coincident with those already published and whose energy amplification reaches a value of 2.0 for a Poisson solid.

Reduced white matter microstructure in bipolar disorder with and without psychosis.

Affective and psychotic features overlap considerably in bipolar I disorder, complicating efforts to determine its etiology and develop targeted treatments. In order to clarify whether mechanisms are similar or divergent for bipolar disorder with psychosis (BDP) and bipolar disorder with no psychosis (BDNP), neurobiological profiles for both the groups must first be established. This study examines white matter structure in the BDP and BDNP groups, in an effort to identify portions of white matter that may differ between the bipolar and healthy groups or between the bipolar subgroups themselves. Diffusion-weighted imaging data were acquired from participants with BDP (n=45), BDNP (n=40), and healthy comparisons (HC) (n=66). Fractional anisotropy (FA), radial diffusivity (RD), and spin distribution function (SDF) values indexing white matter diffusivity or spin density were calculated and compared between the groups. In comparisons between both the bipolar groups and HC, FA (FDR<0.00001) and RD (FDR=0.0037) differed minimally, in localized portions of the left cingulum and corpus callosum, while reductions in SDF (FDR=0.0002) were more widespread. The bipolar subgroups did not differ from each other on FA, RD, or SDF metrics. Together, these results demonstrate a novel profile of white matter differences in bipolar disorder and suggest that this white matter pathology is associated with the affective disturbance common to those with bipolar disorder rather than the psychotic features unique to some. The white matter alterations identified in this study may provide substrates for future studies examining specific mechanisms that target affective domains of illness.

Evaluation of an analytical method for relationship between soil hydraulic diffusivity and sorptivity under zeolite application

ABSTRACT-Zeolite is used to improve the soil hydraulic properties, i.e., soil hydraulic diffusivity (D) and sorptivity (S) that should be determined. A simple method that relates S to D was evaluated by horizontal water absorption experiment in sandy loam, loam and silty clay soils and zeolite application rates of 0, 4, 8, and 12 g kg-1 soil. Results indicated that zeolite application was not effective on the a and b values of hydraulic diffusivity function (D=aEXP(bθ), θ is the soil water content, cm3 cm-3), while maximum value of a and b in sandy loam and silty clay soils, respectively occurred by zeolite application of 8 g kg -1 soil. The values of a and b for loam soil were not influenced by zeolite application rates. Sorptivity for sandy loam soil was reduced by zeolite application rate, while minimum value of S for loam and silty clay soils occurred at zeolite application rate of 8 g kg-1 soil. It is indicated that indirect determination of S for different soil textures and zeolite application rates were closely similar to the direct determination of S. Therefore, by determination of S value by simple horizontal absorption test at two different initial soil water contents or two different absorption suction heads in tension infiltrometer the values of Ds and α for hydraulic diffusivity function (D=Dsθα) can be estimated.

Time-Dependent Fractional Diffusion and Friction Functions for Anomalous Diffusion

The precise determination of diffusive properties is presented for a system described by the generalized Langevin equation. The time-dependent fractional diffusion function and the Green-Kubo relation as well as the generalized Stokes-Einstein formula, in the spirit of ensemble averages, are reconfigured. The effective friction function is introduced as a measure of the influence of frequency-dependent friction on the evolution of the system. This is applied to the generalized Debye model, from which self-oscillation emerges as indicative of ergodicity that breaks due to high finite-frequency cutoff. Moreover, several inconsistent conclusions that have appeared in the literature are revised.

Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals.

In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the 13C and 1H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For 13C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the 1H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental 13C and 1H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for 13C chemical shift calculations, but not for the 1H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the 13C and 1H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.

A review on asymptotic inference in stochastic differential equations with mixed effects

This paper is a survey of recent contributions on estimation in stochastic differential equations with mixed effects. These models involve N stochastic differential equations with common drift and diffusion functions but random parameters that allow for differences between processes. The main objective is to estimate the distribution of the random effects and possibly other fixed parameters that are common to the N processes. While many algorithms have been proposed, the theoretical aspects related to estimation have been little studied. This review article focuses only on theoretical inference for stochastic differential equations with mixed effects. It has so far only been considered in some very specific classes of mixed-effect diffusion models, observed without measurement error, where explicit estimators can be defined. Within this framework, the asymptotic properties of several estimators, either parametric or nonparametric, are discussed. Different schemes of observations are considered according to the approach, associating a large number of individuals with, in most cases, high-frequency observations of the trajectories.

The Vibronic Absorption Spectrum and Electronic States of Nile Red in Aqueous Solution

AbstractThe TD‐DFT was applied to calculate the vibronic absorption spectrum of Nile red (NR) in an aqueous solution. Various hybrid functionals have been used. The O3LYP/6‐31G(d,p) theory level gave an excellent agreement with the experimental absorption spectrum both in the position of the maximum and in the shape. Extended basis sets with diffuse functions and showed the worst results compared to the compact 6‐31G(d,p) basis. The dipole moments and atomic charges of the ground and excited states of the NR molecule have been calculated. According to our calculations, the dipole moment of a molecule increases upon photoexcitation, which is consistent with the positive solvatochromism of NR. An insignificant photoinduced electron transfer from the aminodiethyl group to the center of the chromophore and carbonyl group was found. According to our calculations, vibronic coupling plays a significant role in the absorption spectrum of the NR.

Preconditioning for symmetric positive definite systems in balanced fractional diffusion equations

In this paper, we study the finite volume discretization method for balanced fractional diffusion equations where the fractional differential operators are comprised of both Riemann-Liouville and Caputo fractional derivatives. The main advantage of this approach is that new symmetric positive definite Toeplitz-like linear systems can be constructed for solving balanced fractional diffusion equations when diffusion functions are non-constant. It is different from non-symmetric Toeplitz-like linear systems usually obtained by existing numerical methods for fractional diffusion equations. The preconditioned conjugate gradient method with circulant and banded preconditioners can be applied to solve the proposed symmetric positive definite Toeplitz-like linear systems. Numerical examples, for both of one- and two- dimensional cases, are given to demonstrate the good accuracy of the finite volume discretization method and the fast convergence of the preconditioned conjugate gradient method.

Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study.

We have performed a hierarchical ab initio benchmark and DFT performance study of D2Ch•••A− chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA‐relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all‐electron relativistically contracted variants of Karlsruhe basis sets (ZORA‐def2‐SVP, ZORA‐def2‐TZVPP, ZORA‐def2‐QZVPP) with and without diffuse functions. The highest‐level ZORA‐CCSD(T)/ma‐ZORA‐def2‐QZVPP counterpoise‐corrected complexation energies (ΔE CPC) are converged within 1.1–3.4 kcal mol−1 and 1.5–3.1 kcal mol−1 with respect to the method and basis set, respectively. Next, we used the ZORA‐CCSD(T)/ma‐ZORA‐def2‐QZVPP (ΔE CPC) as reference data for analyzing the performance of 13 different ZORA‐relativistic DFT approaches in combination with the Slater‐type QZ4P basis set. We find that the three‐best performing functionals are M06‐2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol−1, respectively. The MAE for BLYP‐D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol−1, respectively.