Using Python to Solve the Navier-Stokes Equations - Applications in the Preconditioned Iterative Methods

This article describes a new numerical solver for the Navier-Stokes equations. The proposed solver is written in Python which is a newly developed language. The Python packages are built to solve the Navier-Stokes equations with existing libraries. We have created discretized coefficient matrices from systems of the Navier-Stokes equations by the finite difference method. In addition we focus on the preconditioned Krylov subspace iterative methods in the linearized systems. Numerical results of performances for the Preconditioned iterative methods are demonstrated. The comparison between Python and Matlab is discussed at the end of the paper

Association of the triglyceride-glucose index and vascular target organ damage in a Beijing community-based population

ObjectiveWe aimed to explore the association between the triglyceride-glucose (TyG) index, a marker of insulin resistance (IR), and vascular target organ damage (TOD) in a Beijing community-based population, China.MethodsA total of 6,015 participants from an atherosclerosis cohort survey performed in the Shijingshan District in Beijing, China were included in our analysis. Vascular TOD, such as carotid-femoral pulse wave velocity (cfPWV), brachial-ankle pulse wave velocity (baPWV), and the urine albumin-to-creatinine ratio (UACR) were all evaluated.ResultsThe overall mean age of all the participants was 62.35 years, 3,951 (65.69%) were female, and mean TyG index was 8.81. In univariable regression analyzes, an increased TyG index was associated with higher cfPWV, baPWV, lnUACR, and higher risk of cfPWV ≥ 10 m/s, baPWV ≥ 1,800 cm/s, and UACR ≥ 30 mg/g, respectively. Multivariable regression analyzes showed subjects with the TyG index in top tertile had a significant increase in cfPWV (β = 0.29 m/s; 95% confidence interval [95% CI] 0.19–0.40; pfortrend < 0.001), baPWV (β = 69.28 cm/s; 95% CI 50.97–87.59; pfortrend < 0.001), lnUACR (β = 0.23; 95% CI 0.13–0.34; pfortrend < 0.001), and had a higher risk of cfPWV ≥ 10 m/s (odds ratio [OR] = 1.47; 95% CI 1.17–1.85; pfortrend < 0.001), baPWV ≥ 1,800 cm/s (OR = 1.79; 95% CI 1.48–2.17; pfortrend < 0.001), and UACR ≥ 30 mg/g (OR = 1.71; 95% CI 1.30–2.24; pfortrend < 0.001) after fully adjusting for age, sex, body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), estimated glomerular filtration rate (eGFR), self-reported coronary heart disease (CHD) and stroke, antihypertensive drugs, hypoglycemic drugs, and lipid-lowering drugs. Consistent conclusions were obtained in the subgroups without hypoglycemic and lipid-lowering medications or aged younger than 65 years old.ConclusionsThe TyG index was positively associated with artery stiffness and nephric microvascular damage in a Beijing community-based population in China. This result provides evidence that the TyG index may serve as a simple and effective indicator to reflect vascular TOD

Complete revascularization based on angiography derived fractional flow reserve versus incomplete revascularization in patients with ST-segment elevation myocardial infarction

Background: Nearly half of ST-segment elevation myocardial infarction (STEMI) patients present with significant multivessel coronary artery disease, they are at high risk of subsequent adverse events. Whether complete revascularization guided by coronary angiography-derived fractional flow reserve (caFFR) further reduces such events risk is not fully investigated. Methods: In this study, 367 consecutive STEMI patients who underwent successful primary percutaneous coronary intervention (PCI) were enrolled. caFFR of all three coronary vessels were measured, including 367 culprit vessels and 703 non-culprit vessels. Complete revascularization was defined as post-PCI caFFR > 0.8 of all three coronary vessels. The primary endpoint was major adverse cardiovascular events (MACE, a composite of cardiovascular death, non-fatal recurrent myocardial infarction, ischemia-driven revascularization and non-fatal stroke/transient ischemic attacks) during follow-up. Results: At a median follow-up of 3.8 years, MACE had occurred in 39 patients of the 220 (17.7%) in the complete revascularization group as compared with 49 patients of the 131 (37.4%) in the incomplete revascularization group (hazard ratio [HR] 1.9; 95% confidence interval [CI] 1.2–3.0; p = 0.005). The incomplete revascularization in culprit vessels evaluated by caFFR showed the highest risk for MACE occurrence. Conclusions: In STEMI patients with multivessel coronary artery disease, incomplete revascularization based on caFFR might contribute to identifying patients at high-risk

A Novel Autosomal Dominant Inclusion Body Myopathy Linked to 7q22.1-31.1

We describe a novel autosomal dominant hereditary inclusion body myopathy (HIBM) that clinically mimics limb girdle muscular dystrophy in a Chinese family. We performed a detailed clinical assessment of 36 individuals spanning four generations. The age of onset ranged from the 30s to the 50s. Hip girdle, neck flexion and axial muscle weakness were involved at an early stage. This disease progressed slowly, and a shoulder girdle weakness appeared later in the disease course. Muscle biopsies showed necrotic, regenerating, and rimmed vacuolated fibers as well as congophilic inclusions in some of the fibers. Electron micrograph revealed cytoplasmic inclusions of 15–21 nm filaments. A genomewide scan and haplotype analyses were performed using an Illumina Linkage-12 DNA Analysis Kit (average spacing 0.58 cM), which traced the disease to a new locus on chromosome 7q22.1–31.1 with a maximum multi-point LOD score of 3.65. The critical locus for this unique disorder, which is currently referred to as hereditary inclusion body myopathy 4 (HIBM4), spans 8.78 Mb and contains 65 genes. This localization raises the possibility that one of the genes clustered within this region may be involved in this disorder

Analyzing the similarity of samples and genes by MG-PCC algorithm, t-SNE-SS and t-SNE-SG maps

Abstract Background For analyzing these gene expression data sets under different samples, clustering and visualizing samples and genes are important methods. However, it is difficult to integrate clustering and visualizing techniques when the similarities of samples and genes are defined by PCC(Person correlation coefficient) measure. Results Here, for rare samples of gene expression data sets, we use MG-PCC (mini-groups that are defined by PCC) algorithm to divide them into mini-groups, and use t-SNE-SSP maps to display these mini-groups, where the idea of MG-PCC algorithm is that the nearest neighbors should be in the same mini-groups, t-SNE-SSP map is selected from a series of t-SNE(t-statistic Stochastic Neighbor Embedding) maps of standardized samples, and these t-SNE maps have different perplexity parameter. Moreover, for PCC clusters of mass genes, they are displayed by t-SNE-SGI map, where t-SNE-SGI map is selected from a series of t-SNE maps of standardized genes, and these t-SNE maps have different initialization dimensions. Here, t-SNE-SSP and t-SNE-SGI maps are selected by A-value, where A-value is modeled from areas of clustering projections, and t-SNE-SSP and t-SNE-SGI maps are such t-SNE map that has the smallest A-value. Conclusions From the analysis of cancer gene expression data sets, we demonstrate that MG-PCC algorithm is able to put tumor and normal samples into their respective mini-groups, and t-SNE-SSP(or t-SNE-SGI) maps are able to display the relationships between mini-groups(or PCC clusters) clearly. Furthermore, t-SNE-SS(m)(or t-SNE-SG(n)) maps are able to construct independent tree diagrams of the nearest sample(or gene) neighbors, where each tree diagram is corresponding to a mini-group of samples(or genes)

Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances

Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA, nirS, and nirK genes. Results showed that 1–2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity (P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile (P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria, Planctomycetes, and Cyanobacteria, the first cropping of JA with Actinobacteria, the second cropping of JA with Acidobacteria, Armatimonadetes, Gemmatimonadetes, and Proteobacteria. At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms nitrate reductase and nitrite reductase. The abundances of amoA genes decreased while nirK increased in the third cropping of JA, nirS continuously increased in the second and third cropping of JA (P < 0.05). Redundancy analysis and Mantel test found that soil organic carbon and Olsen phosphorus contents played important roles in shaping soil bacterial communities. Overall, our results revealed that continuous monocropping of JA changed soil bacterial community composition and its functional potentials

Study of quantitative structure-property relationship for density of ionic liquids based on Monte Carlo optimization

Ionic liquids (ILs) have attracted increasing interests and applications due to its unique physiochemical properties. Density is a vital physical property of ILs. In this work, a comprehensive collection of density data is conducted on 184 variable ILs. The study of quantitative structure-property relationship (QSPR) is carried out for the selected density data of ILs using simplified molecular input line entry specification (SMILES) as the representation of the molecular structure of ILs by means of CORAL software. QSPR relationships were constructed with the balance of correlations (BC) and the classic scheme. Results from three random splits displayed desirable models for predicting the external test set with the correlation coefficient (R2) and cross validated correlation coefficient (Q2) in ranges of 0.8234–0.9770 and 0.7599–0.9745, respectively. The best predictions obtained by the balance of correlations along with the global SMILES descriptors are included in the modeling process. The average statistical characteristics of the external test set are the following: n =36, R2 =0.9770, Q2= 0.9745, standard error of estimation (s)=0.023, mean absolute error (MAE) =0.018 and Fischer F-ratio (F)=144

Preparation and hydrothermal corrosion behavior of Cf/SiCN and Cf/SiHfBCN ceramic matrix composites

Cf/SiCN and Cf/SiHfBCN-based ceramic matrix composites (CMC) were fabricated using the precursor infiltration and pyrolysis technique (PIP). Their behavior in subcritical hydrothermal conditions was investigated at 150–250 °C using exposition times of 48, 96 and 240 h and shown to rely on active corrosion. The data of the mass loss as a function of the corrosion time and temperature at S/V of 0.075 were used to rationalize the corrosion kinetics of the CMCs. Both materials have been shown to exhibit excellent stability in subcritical hydrothermal conditions. The corrosion rates of Cf/SiHfBCN were lower than those determined for Cf/SiCN; furthermore, SEM investigation indicates that spallation occurred in the Cf/SiCN samples; whereas the ceramic matrix was still attached on the individual carbon fibers in Cf/SiHfBCN. The results indicate that the incorporation of Hf and B into SiCN matrix leads to a significant improvement of its hydrothermal corrosion performance