Correlation Functionals Research Articles

Upregulation of α-ENaC induces pancreatic β-cell dysfunction, ER stress, and SIRT2 degradation.

Islet beta cells (β-cells) produce insulin in response to high blood glucose levels, which is essential for preserving glucose homeostasis. Voltage-gated ion channels in β-cells, including Na +, K +, and Ca 2+ channels, aid in the release of insulin. The epithelial sodium channel alpha subunit (α-ENaC), a voltage-independent sodium ion channel, is also expressed in human pancreatic endocrine cells. However, there is no reported study on the function of ENaC in the β-cells. In the current study, we found that α-ENaC was expressed in human pancreatic glandule and pancreatic islet β-cells. In the pancreas of db/db mice and high-fat diet-induced mice, and in mouse islet β-cells (MIN6 cells) treated with palmitate, α-ENaC expression was increased. When α-ENaC was overexpressed in MIN6 cells, insulin content and glucose-induced insulin secretion were significantly reduced. On the other hand, palmitate injured islet β-cells and suppressed insulin synthesis and secretion, but increased α-ENaC expression in MIN6 cells. However, α-ENaC knockout ( Scnn1a -/-) in MIN6 cells attenuated β-cell disorder induced by palmitate. Furthermore, α-ENaC regulated the ubiquitylation and degradation of sirtuin 2 in β-cells. α-ENaC also modulated β-cell function in correlation with the inositol-requiring enzyme 1 alpha/X-box binding protein 1 (IRE1α/XBP1) and protein kinase RNA-like endoplasmic reticulum kinase/C/EBP homologous protein (PERK/CHOP) endoplasmic reticulum stress pathways. These results suggest that α-ENaC may play a novel role in insulin synthesis and secretion in the β-cells, and the upregulation of α-ENaC promotes islet β-cell dysfunction. In conclusion, α-ENaC may be a key regulator involved in islet β-cell damage and a potential therapeutic target for type 2 diabetes mellitus.

Density functional theory study of bulk properties of transition metal nitrides.

Density functional theory (DFT) calculations are performed to compute the lattice constants, formation energies and vacancy formation energies of transition metal nitrides (TMNs) for transition metals (TM) ranging from 3d-5d series. The results obtained using six different DFT exchange and correlation potentials (LDA, AM05, BLYP, PBE, rPBE, and PBEsol) show that the experimental lattice constants are best predicted by rPBE, while the values obtained using AM05, PBE, rPBE and PBEsol lie between the LDA and BLYP calculated values. A linear relationship is observed between the lattice constants and formation energies with the mean radii of TM and the difference in the electronegativity of TM and N in TMNs, respectively. Our calculated vacancy formation energies, in general, show that N-vacancies are more favorable than TM-vacancies in most TMNs. We observe that N-vacancy formation energies are linearly correlated with the calculated bulk formation energies indicating that TMNs with large negative formation energies are less susceptible to the formation of N-vacancies. Thus, our results from this extensive DFT study not only provide a systematic comparison of various DFT functionals in calculating the properties of TMNs but also serve as reference data for the computation-driven experimental design of materials.

Antenna Array Diversity Evaluation Under Multipath Environments With Digital Beamforming

This work proposes a methodology for evaluating the antenna array diversity and resultant radiation pattern from digitally-processed-based beamforming systems. Our approach enables to interpret the advanced antenna systems (AAS) coverage and massive multiple-input multiple output (mMIMO) spatial resolution, by the inspection of the array resultant multiple beams. Particularly, the impact on the mMIMO spatial resolution is conducted as a function of the channel correlation, by means of an exclusively radiofrequency (RF) approach, with the advantage of not considering the system-level features, and using a new figure of merit (factor). The new figure of merit enables to evaluate the antenna array diversity from two-and three-dimensional (2D and 3D) beamforming, by computing the number of lobes with gain higher than a unique element. In the 3D case, the figure of merit is based on a differential calculation, which enables performing an infinitesimal counting of lobes per antenna element beamwidth. Such parameter is initially applied to a theoretical dipole-based array, with the purpose of quantifying the created multiple beams by the overlapped radiation patterns from mMIMO systems. Furthermore, the factor is exploited for analyzing the performance of a 64-element and dual-polarized SICL-based slot antenna array and a 64-element dipole-based antenna prototypes, both previously developed by our research group. Finally, it is demonstrated that the factor increases as diversity increases and dipole-based antenna array could be used as an upper limit, attaining 11.46 lobes/rad.

Investigation of Harmful Substances to Health Using Electronic Nose and Weight Elimination Algorithm With Correlative Gaussian Function

Investigation of Harmful Substances to Health Using Electronic Nose and Weight Elimination Algorithm With Correlative Gaussian Function

Electronic and structural properties of mixed-cation hybrid perovskites studied using an efficient spin-orbit included DFT-1/2 approach.

Fundamental understanding and optimization of the emerging mixed organic-inorganic hybrid perovskites for solar cells require multiscale modeling starting from ab initio quantum mechanics methods. Particularly, it is important to correctly predict the structural and electronic properties such as phase stability, lattice parameters, band gaps, and band structures. Although density functional theory is the method of choice to address these properties and generate the input for subsequent multiscale, high-throughput, and data-driven approaches, standard exchange correlation functionals fail to reproduce the bandgap, particularly if spin-orbit coupling (SOC) is correctly taken into account. While many SOC-included hybrid functionals suffer from low transferability between different molecular ions and are computationally costly, we propose an efficient multistep simulation protocol based on the DFT-1/2 method. We apply this approach to APbI3 with A: FA, MA, Cs, and systems with mixed cations and show how the choice of the A-cation modifies the Pb-I scaffold and the hydrogen bonding and discuss their interplay with structural stability. Furthermore, band gaps, band structures, Rashba band splitting, Born effective charges as well as partial density of states (PDOS) are compared for different cases w/wo the SOC effect and the DFT-1/2 approach.

DFT Study of Hexagonal Boron Nitride Electronic Properties Using Different Types of Exchange Correlation Functionals

DFT Study of Hexagonal Boron Nitride Electronic Properties Using Different Types of Exchange Correlation Functionals

Development of methods and means of livestock control in cattle breeding to manage the physiological state of the herd

Monitoring the temperature and pH of the contents of the rumen can be useful for assessing the health status and detecting physiological heat in cows. The purpose of the research was to develop methods and means of livestock control in cattle breeding to manage the physiological state of the herd based on mathematical models for detecting the heat, upcoming calving, initial signs of diseases, monitoring the level of feeding and water intake. The work was carried out under the production conditions of farms using existing hardware and software. The measurements were carried out using a non-invasive control method using special sensors-boluses designed to monitor the health of cows. Boluses were placed orally in the rumen of the cows under research. As a result of the research, algorithms and mathematical models were compiled to identify the heat, upcoming calving, diseases, as well as monitoring the level of feeding and water intake. The source data was imported from a standard file format compatible with other applications (csv table). Correlations between the temperature and pH of the rumen, as well as the motor activity of cows were also analyzed. As illustrations, graphs of the main indicators of vital activity, as well as graphs of mutually correlative functions and an illustration of the working console of the program have been given. Table of the results of the program for each cow, average values and standard deviation have been given. A mathematical model is a set of algorithms and calculation results. In order to implement it, a program code was created in the Matlab R2019b software package. This mathematical model can be used to process and interpret data placed in the animal’s rumen of measuring elements (boluses).

Relation Between Growth and Developmental Status of Children in Kebon Pala, Jakarta

Background: Child development usually mentioned as related with child’s growth. Assuming that delayed growth will affect children development, but in fact, no report about this relation in national research. This study conducted to find relation between children growth and their development. Methods: this study is relational quantitative research that used a quantitative approach to measure children body height, body weight, and their developmental status. Study limited in Kebon Pala, Jakarta. Measurement were held by local administrator of Kebon Pala. Body height and weight compared with WHO growth standard, whereas developmental status measured with Developmental Screening Questioner (Kuisioner Pra Skrining Perkembangan, KPSP). Relation between body weight, body height and developmental status assessed with correlational function of Microsoft Excel. Results: there are 12.24% underweight children, 8.16% overweight children, 16.33% short children, 4.08% tall children, 4.08% delayed development children, and 20.41% children with suspicious state of development. Relation between weight and development were -0.17 and between height and development were -0.12. Conclusion: Prevalence of short children were lower than Indonesian report, and 25% children need attention to may catch their development. No relation between nutritional status and developmental status. Nutrition and development approach should be treated together.

Yukawa-Friedel-tail pair potentials for warm dense matter applications.

Accurate equationsof state (EOS) and plasma transport properties are essential for numerical simulations of warm dense matter encountered in many high-energy-density situations. Molecular dynamics (MD) is a simulation method that generates EOS and transport data using an externally provided potential to dynamically evolve the particles without further reference to the electrons. To minimize computational cost, pair potentials needed in MD may be obtained from the neutral-pseudoatom (NPA) approach, a form of single-ion density functional theory (DFT), where many-ion effects are included via ion-ion correlation functionals. Standard N-ion DFT-MD provides pair potentials via the force matching technique but at much greater computational cost. Here we propose a simple analytic model for pair potentials with physically meaningful parameters based on a Yukawa form with a thermally damped Friedel tail (YFT) applicable to systems containing free electrons. The YFT model accurately fits NPA pair potentials or the nonparametric force-matched potentials from N-ion DFT-MD, showing excellent agreement for a wide range of conditions. The YFT form provides accurate extrapolations of the NPA or force-matched potentials for small and large particle separations within a physical model. Our method can be adopted to treat plasma mixtures, allowing for large-scale simulations of multispecies warm dense matter.

Effects of rearing system and antibiotic treatment on immune function, gut microbiota and metabolites of broiler chickens

BackgroundIn China, cage systems with a high space utilization have gradually replaced ground litter systems, but the disease incidence of chickens in cages is higher. Broilers in the ground litter pens may be stimulated by more environmental microbes during the growth process and show strong immune function and status, but knowledge of which microbes and their metabolites play an immunomodulatory role is still limited. This study aimed to explore the differences and correlations in the immune function, gut microbiota and metabolites and the importance of gut microbiota of broilers raised in cages and ground litter pens.MethodsThe experiment involved a 2 × 2 factorial arrangement, with rearing systems (cages or ground litter pens) and antibiotic treatment (with or without broad-spectrum antibiotics in drinking water) as factors.ResultsThe results showed that, compared with the cage group, the ground litter broilers had stronger nonspecific immune function (Macrophages% and NO in blood), humoral immune function (IgG in blood, LPS stimulation index in ileum) and cellular immune function (T%, Tc%, ConA stimulation index and cytokines in blood). Antibiotic (ABX) treatment significantly reduced nonspecific immune function (Macrophages% and NO in blood, iNOS and Mucin2 mRNA expression in ileum), humoral immune function (IgG in blood and sIgA in ileum) and cellular immune function (T% and cytokines in blood, Th and Tc ratio, TLRs and cytokines mRNA expression in ileum). Furthermore, the ground litter broilers had higher α diversity of microbiota in ileum. The relative abundance of Staphylococcus, Jeotgalicoccus, Jeotgalibaca and Pediococcus in the ileum of ground litter broilers were higher. ABX treatment significantly reduced the α diversity of ileal microbiota, with less Chloroplast and Mitochondria. In addition, the levels of acetic acid, isobutyric acid, kynurenic acid and allolithocholic acid in the ileum of ground litter broilers were higher. Spearman correlation analysis showed that Jeotgalibaca, Pediococcus, acetic acid, kynurenic acid and allolithocholic acid were related to the immune function.ConclusionsThere were more potential pathogens, litter breeding bacteria, short-chain fatty acids, kynurenine, allolithocholic acid and tryptophan metabolites in the ileum of broilers in ground litter pens, which may be the reason for its stronger immune function and status.

Inference of regulatory networks through temporally sparse data.

A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses, including diagnosis or prognosis of diseases and finding effective treatments for chronic diseases such as cancer. Boolean networks have emerged as a successful class of models for capturing the behavior of GRNs. In most practical settings, inference of GRNs should be achieved through limited and temporally sparse genomics data. A large number of genes in GRNs leads to a large possible topology candidate space, which often cannot be exhaustively searched due to the limitation in computational resources. This paper develops a scalable and efficient topology inference for GRNs using Bayesian optimization and kernel-based methods. Rather than an exhaustive search over possible topologies, the proposed method constructs a Gaussian Process (GP) with a topology-inspired kernel function to account for correlation in the likelihood function. Then, using the posterior distribution of the GP model, the Bayesian optimization efficiently searches for the topology with the highest likelihood value by optimally balancing between exploration and exploitation. The performance of the proposed method is demonstrated through comprehensive numerical experiments using a well-known mammalian cell-cycle network.

Effects of Selenium Doping in Zinc Telluride from First Principles

Point defects and compensation in zinc telluride have been subjects of study for several decades due to the compound’s scientific/technological applications. Despite this, there remains some disagreement in the literature as to the fine details of its defect chemistry. Recently, it has also come under renewed interest due to the emerging Cd(1–x)ZnxTe(1–y)Sey material family, used in nuclear radiation detector applications. In this article, we use state-of-the-art computational tools to re-examine the native defect chemistry of ZnTe and explore how it changes upon addition of selenium using density functional theory with screened hybrid exchange–correlation functionals, thermochemical models of the equilibration environment, and statistical mechanics models of the point defect ensemble.

Mixture Model on Development of Bivariate Product Distribution and its Properties

In the study, some bivariate distributions were developed from mixture model offspring, using the Independent (Product) distribution approach. These developments are categorized under the IID and IInD: where the Bivariate Exponential distribution, Bivariate Lindley distribution and Bivariate Juchez distribution are constructed as IIDs; and Bivariate Exponential-Lindley distribution, Bivariate Exponential-Juchez distribution and Bivariate Lindley-Juchez distribution as (IInDs). The properties of these distributions which involve: the shape of the bivariate PDFs, moments, moment generating function, mean, covariance and coefficient of correlation, maximum likelihood estimator, reliability analysis, renewal property and probability patterns; are studied across the distributions. Finally, under renewal properties, functions are derived which can model two-dimensional queuing and renewal processes, for events where the arrival and service times are dependent.

The Curious Case of the Cross-Sectional Correlation

The cross-sectional correlation is frequently used to summarize psychological data, and can be considered the basis for many statistical techniques. However, the work of Peter Molenaar on ergodicity has raised concerns about the meaning and utility of this measure, especially when the interest is in discovering general laws that apply to (all) individuals. Through using Cattell’s databox and adopting a multilevel perspective, this paper provides a closer look at the cross-sectional correlation, with the goal to better understand its meaning when ergodicity is absent. An analytical expression is presented that shows the cross-sectional correlation is a function of the between-person correlation (based on person-specific means), and the within-person correlation (based on individuals’ temporal deviations from their person-specific means). Two curiosities related to this expression of the cross-sectional correlation are elaborated on, that is: a) the difference between the within-person correlation and the (average) person-specific correlation; and b) the unexpected scenarios that can arise because the cross-sectional correlation is a weighted sum rather than a weighted average of the between-person and within-person correlations. Seven specific examples are presented to illustrate various ways in which these two curiosities may combine; R code is provided, which allows researchers to investigate additional scenarios.

Mass-zero constrained dynamics for simulations based on orbital-free density functional theory.

A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case, the recently introduced Mass-Zero (MaZe) constrained dynamics. The formalism ensures that full adiabatic separation is enforced between nuclear and electronic degrees of freedom and, consequently, that the exact Born-Oppenheimer probability for the nuclei is sampled. Numerical integration of the MaZe dynamics combines standard molecular dynamics algorithms, e.g., Verlet or velocity Verlet, with the SHAKE method to impose the minimum conditions on the electronic degrees of freedom as a set of constraints. The developments presented in this work, which include a bespoke adaptation of the standard SHAKE algorithm, ensure that the quasilinear scaling of OFDFT is preserved by the new method for a broad range of kinetic and exchange-correlation functionals, including nonlocal ones. The efficiency and accuracy of the approach are demonstrated via calculations of static and dynamic properties of liquid sodium in the constant energy and constant temperature ensembles.

S61 Postoperative Ustekinumab Drug Levels and Disease Activity in Patients With Crohn’s Disease

Background: Ustekinumab is a biologic that targets and blocks the IL-12 and IL-23 receptors and effectively reduces clinical and endoscopic activity of Crohn’s Disease (CD) (1-3). Despite advances in CD treatment, including novel biologic therapies, surgical intervention is still common (4). Preventing postoperative recurrence of disease is critical to avoid subsequent procedures as these operations are expensive and invasive with risk for complications. Studies have previously evaluated for the association of postoperative drug levels, specifically of tumor necrosis factor inhibitors in relation to endoscopic disease recurrence (5-6). However, no study has been conducted to explore the association between postoperative ustekinumab levels and both endoscopic and clinical CD activity. Methods: This was a retrospective study of CD patients from a tertiary referral center that had an ustekinumab level taken postoperatively. Thirty-two total patients were identified. Ustekinumab drug levels were taken within 2 years postoperatively. Harvey-bradshaw index (HBI) was used to evaluate clinical disease activity and a combination of Rutgeerts’ and simple endoscopic score (SES) for Crohn’s Disease was used for endoscopic activity. Values for labs, clinical scores, and endoscopic scores were taken closest to surgery preoperatively with at least a one-month delay after surgery for postoperative values. Delta was the numeric difference between pre and postoperative measurements. Surgical procedures included small or large bowel resection, proctectomy, and fistulectomy. Patients were separated into groups depending on if their ustekinumab level was adequate, defined as greater than or equal to 4 μg/mL, or suboptimal, defined as below 4 μg/mL. All statistics were completed using built-in Excel functions for linear regression, linear correlation, and one-tailed t-test for unequal variance. P values of <0.05 and correlations above 0.8 were considered significant. Results: Average time drug levels taken postoperatively was 257 days. Postoperative hemoglobin levels were significantly higher in the adequate level group, 13.3 g/dL compared to 12.0 g/dL (P = 0.028). Hematocrit levels were also higher in the adequate ustekinumab level group, 40.5 versus 37.1 (P = 0.027). Clinically, patients with adequate ustekinumab levels had a greater change of their HBI score compared to preoperatively, delta HBI of -3 compared to 0.4 (P = 0.046). Only the suboptimal group showed a significant average decrease in endoscopic disease activity preoperatively to postoperatively, 85.7% to 37.5% (P = 0.029). No significant linear correlations were observed when comparing ustekinumab level to postoperative lab values, clinical scores, and endoscopic scores or their deltas. Conclusion(s): Adequate levels of ustekinumab yielded higher postoperative hemoglobin and hematocrit levels in addition to a greater reduction in HBI score. Only the suboptimal ustekinumab level group showed a significant reduction in average endoscopic disease activity compared to preoperative scores, which is consistent with findings that HBI does not necessarily correlate to endoscopic disease activity. The data suggests that adequate ustekinumab levels following CD surgery reduces the risk of anemia postoperatively and results in better clinical CD remission (HBI < 5) and response (delta HBI >=3). Future studies are needed to find the optimal ustekinumab levels both pre and postoperatively in order to maintain CD remission.

Efficient Kohn–Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions

For general exchange–correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only ∼25% (one-photon off-resonance regions) and ∼50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

Study of pressure induced physical variations in the electronic and optical properties of MgA2Te4 (A = Sc, Y)

In this work, the electrical, and optical properties are investigated for MgSc2Te4 and MgY2Te4 spinel compounds under the effect of pressure up to 15 and 30 GPa, respectively. These compounds are suitable for optoelectronics and photovoltaic applications. Trans-Blaha modified Becke Johnson (TB-mBJ) approximation exchange and correlation functionals were used to uncover electronic and optical properties. The electronic band gaps of both compounds appear to be direct despite the effect of pressure. MgSc2Te4 exhibits metallic behavior at 15 GPa, while MgY2Te4 exhibits metallic behavior at 30 GPa. Density of states spectra used to identify the atomic contribution of states by ions in the bands. Real part of the dielectric function, optical reflectivity and refractive index upshifted with the increase in energy while the imaginary parts of the dielectric function, optical conductivity and absorption coefficient red-shifted with the increase of hydrostatic pressure.

Energy Correlations of Non-Integrable Ising Models: The Scaling Limit in the Cylinder

We consider a class of non-integrable 2D Ising models whose Hamiltonian, in addition to the standard nearest neighbor couplings, includes additional weak multi-spin interactions which are even under spin flip. We study the model in cylindrical domains of arbitrary aspect ratio and compute the multipoint energy correlations at the critical temperature via a multiscale expansion, uniformly convergent in the domain size and in the lattice spacing. We prove that, in the scaling limit, the multipoint energy correlations converge to the same limiting correlations as those of the nearest neighbor Ising model in a finite cylinder with renormalized horizontal and vertical couplings, up to an overall multiplicative constant independent of the shape of the domain. The proof is based on a representation of the generating function of correlations in terms of a non-Gaussian Grassmann integral, and a constructive Renormalization Group (RG) analysis thereof. A key technical novelty compared with previous works is a systematic analysis of the effect of the boundary corrections to the RG flow, in particular a proof that the scaling dimension of boundary operators is better by one dimension than their bulk counterparts. In addition, a cancellation mechanism based on an approximate image rule for the fermionic Green’s function is of crucial importance for controlling the flow of the (superficially) marginal boundary terms under RG iterations.

Absorption Spectra of Flexible Fluorescent Probes by a Combined Computational Approach: Molecular Dynamics Simulations and Time-Dependent Density Functional Theory.

A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3H-xanthen-3-one molecule, depicted by a combined classical-quantum chemical approach. Particularly, first classical molecular dynamics (MD) has been used to explore the configurational space, and next, the absorption spectrum has been reconstructed by averaging the results of time-dependent density functional theory (TD-DFT) calculations performed on equispaced molecular conformations extracted from MD to properly sample the configurational space explored at finite temperature. To verify the effect of molecular conformation on the spectral profile, the generated electronic absorption spectra were compared with those obtained considering a single structure corresponding to the optimized one, an approach also referred to as static. This comparison allows one to highlight a sizable though small shift between the maxima of the corresponding reconstructed absorption spectra, highlighting the importance of conformational sampling in the case of this rather flexible molecule. Four different exchange and correlation functionals (PBE, BLYP, PBE0, B3LYP) were considered to compute vertical transition via TD-DFT calculations. From the results obtained in gas and in condensed, here solution, phases, it appears that the magnitude of the shift is actually more affected by the phase in which the system is found than by the functional used. This fact underlines the central importance of conformational mobility, that is flexibility, of this molecule. From a more quantitative point of view, a comparison with available experimental data shows that hybrid functionals, such as PBE0 and B3LYP, enable one to faithfully reproduce the observed absorption maxima.