Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-eddy simulation of free-surface decaying turbulence with dynamic subgrid-scale models

This paper describes large-eddy simulations of decaying turbulence in an open channel, using different dynamic subgrade-scale models, viz. the dynamic model of Germano et al. [Phys. Fluids A 3, 1790 (1991)] (DSM), the dynamic mixed model in Zang et al. [Phys. Fluids A 5, 3186 (1993)] (DMM), and the dynamic two-parameter model of Salvetti and Banerjee [Phys. Fluids 7, 2831 (1995)] (DTM). These models are incorporated in a finite-volume solver of the Navier–Stokes equations. A direct numerical simulation of this flow conducted by Pan and Banerjee [Phys. Fluids 7, 1649 (1995)] showed that near the free surface turbulence has a quasi-two-dimensional behavior. Moreover, the quasi-two-dimensional region increases in thickness with the decay time, although the structure remains three-dimensional in the central regions of the flow. The results of the large-eddy simulations show that both the DMM and the DTM are able to reproduce the features of the decay process observed in the direct simulation and to handle the.
The Use of Electrochemical Methods to Determine the Effect of Nitrides of Alloying Elements on the Electrochemical Properties of Titanium β-Alloys

Titanium beta alloys represent the new generation of materials for the manufacturing of joint implants. Their Young’s modulus is lower and thus closer to the bone tissue compared to commonly used alloys. The surface tribological properties of these materials should be improved by ion implantation. The influence of this surface treatment on corrosion behaviour is unknown. The surface of Ti-36Nb-6Ta, Ti-36Nb-4Zr, and Ti-39Nb titanium β-alloys was modified using nitrogen ion implantation. X-ray photoelectron spectroscopy was used for surface analysis, which showed the presence of titanium, niobium, and tantalum nitrides in the treated samples and the elimination of less stable oxides. Electrochemical methods, electrochemical impedance spectra, polarisation resistance, and Mott–Schottky plot were measured in a physiological saline solution. The results of the measurements showed that ion implantation does not have a significant negative effect on the corrosion behaviour of the material. The best results of the alloys investigated were achieved by the Ti-36Nb-6Ta alloy. The combination of niobium and tantalum nitrides had a positive effect on the corrosion resistance of this alloy. After surface treatment, the polarization resistance of this alloy increased, 2.3 × 106 Ω·cm2, demonstrating higher corrosion resistance of the alloy. These results were also supported by the results of electrochemical impedance spectroscopy.
A Novel Four Mitochondrial Respiration-Related Signature for Predicting Biochemical Recurrence of Prostate Cancer

The biochemical recurrence (BCR) of patients with prostate cancer (PCa) after radical prostatectomy is high, and mitochondrial respiration is reported to be associated with the metabolism in PCa development. This study aimed to establish a mitochondrial respiratory gene-based risk model to predict the BCR of PCa. RNA sequencing data of PCa were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and mitochondrial respiratory-related genes (MRGs) were sourced via GeneCards. The differentially expressed mitochondrial respiratory and BCR-related genes (DE-MR-BCRGs) were acquired through overlapping BCR-related differentially expressed genes (BCR-DEGs) and differentially expressed MRGs (DE-MRGs) between PCa samples and controls. Further, univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analyses were performed to construct a DE-MRGs-based risk model. Then, a nomogram was established by analyzing the independent prognostic factor of five clinical features and risk scores. Moreover, Gene Set Enrichment Analysis (GSEA), tumor microenvironment, and drug susceptibility analyses were employed between high- and low-risk groups of PCa patients with BCR. Finally, qRT-PCR was utilized to validate the expression of prognostic genes. We identified 11 DE-MR-BCRGs by overlapping 132 DE-MRGs and 13 BCR-DEGs and constructed a risk model consisting of 4 genes (APOE, DNAH8, EME2, and KIF5A). Furthermore, we established an accurate nomogram, including a risk score and a Gleason score, for the BCR prediction of PCa patients. The GSEA result suggested the risk model was related to the PPAR signaling pathway, the cholesterol catabolic process, the organic hydroxy compound biosynthetic process, the small molecule catabolic process, and the steroid catabolic process. Simultaneously, we found six immune cell types relevant to the risk model: resting memory CD4+ T cells, monocytes, resting mast cells, activated memory CD4+ T cells, regulatory T cells (Tregs), and macrophages M2. Moreover, the risk model could affect the IC50 of 12 cancer drugs, including Lapatinib, Bicalutamide, and Embelin. Finally, qRT-PCR showed that APOE, EME2, and DNAH8 were highly expressed in PCa, while KIF5A was downregulated in PCa. Collectively, a mitochondrial respiratory gene-based nomogram including four genes and one clinical feature was established for BCR prediction in patients with PCa, which could provide novel strategies for further studies.
Nebulized Menthol Impairs Mucociliary Clearance via TRPM8 and MUC5AC/MUC5B in Primary Airway Epithelial Cells

Flavorings enhance the palatability of e-cigarettes (e-cigs), with menthol remaining a popular choice among e-cig users. Menthol flavor remains one of the only flavors approved by the United States FDA for use in commercially available, pod-based e-cigs. However, the safety of inhaled menthol at the high concentrations used in e-cigs remains unclear. Here, we tested the effects of menthol on parameters of mucociliary clearance (MCC) in air–liquid interface (ALI) cultures of primary airway epithelial cells. ALI cultures treated with basolateral menthol (1 mM) showed a significant decrease in ciliary beat frequency (CBF) and airway surface liquid (ASL) volumes after 24 h. Menthol nebulized onto the surface of ALI cultures similarly reduced CBF and increased mucus concentrations, resulting in decreased rates of mucociliary transport. Nebulized menthol further increased the expression of mucin 5AC (MUC5AC) and mRNA expression of the inflammatory cytokines IL1B and TNFA. Menthol activated TRPM8, and the effects of menthol on MCC and inflammation could be blocked by a specific TRPM8 antagonist. These data provide further evidence that menthol at the concentrations used in e-cigs could cause harm to the airways.
Molecular Mechanisms in Genetic Aortopathy–Signaling Pathways and Potential Interventions

Thoracic aortic disease affects people of all ages and the majority of those aged <60 years have an underlying genetic cause. There is presently no effective medical therapy for thoracic aneurysm and surgery remains the principal intervention. Unlike abdominal aortic aneurysm, for which the inflammatory/atherosclerotic pathogenesis is well established, the mechanism of thoracic aneurysm is less understood. This paper examines the key cell signaling systems responsible for the growth and development of the aorta, homeostasis of endothelial and vascular smooth muscle cells and interactions between pathways. The evidence supporting a role for individual signaling pathways in pathogenesis of thoracic aortic aneurysm is examined and potential novel therapeutic approaches are reviewed. Several key signaling pathways, notably TGF-β, WNT, NOTCH, PI3K/AKT and ANGII contribute to growth, proliferation, cell phenotype and survival for both vascular smooth muscle and endothelial cells. There is crosstalk between pathways, and between vascular smooth muscle and endothelial cells, with both synergistic and antagonistic interactions. A common feature of the activation of each is response to injury or abnormal cell stress. Considerable experimental evidence supports a contribution of each of these pathways to aneurysm formation. Although human information is less, there is sufficient data to implicate each pathway in the pathogenesis of human thoracic aneurysm. As some pathways i.e., WNT and NOTCH, play key roles in tissue growth and organogenesis in early life, it is possible that dysregulation of these pathways results in an abnormal aortic architecture even in infancy, thereby setting the stage for aneurysm development in later life. Given the fine tuning of these signaling systems, functional polymorphisms in key signaling elements may set up a future risk of thoracic aneurysm. Multiple novel therapeutic agents have been developed, targeting cell signaling pathways, predominantly in cancer medicine. Future investigations addressing cell specific targeting, reduced toxicity and also less intense treatment effects may hold promise for effective new medical treatments of thoracic aortic aneurysm.
A multipurpose fiber-fed VPHG spectrograph for LAMOST

A multipurpose fiber-fed double-beam Schmidt spectrograph using VPHG (volume phase holographic gratings) is under construction for LAMOST (The Large Sky Area Multi-Object Fiber Spectroscopic Telescope). There are 16 such spectrographs (hereafter referred to as LRSs) for the project. The spectrographs are designed with wavelength coverage from 370 to 900 nm, with spectral resolutions of 1000-10000, and with multi-object capability over a 5 degrees field of view. Each spectrograph will be accommodating 250 fibers of 320 microns diameter (corresponding 3.3 arcsecs). The 200 mm diameter collimated beam is split into two separate channels. The blue channel is optimized for 370nm-590nm, and the red channel for 570nm-900nm. The LRS can work in several varied resolution modes. The optical design and performance is described. The spectrograph is of simple design with moderate image quality and good throughput. Progress on the construction of LRS is reported as well.
Fabrication of Mechanically Enhanced, Suturable, Fibrous Hydrogel Membranes

Poly(vinyl-alcohol) hydrogels have already been successfully utilised as drug carrier systems and tissue engineering scaffolds. However, lacking mechanical strength and suturability hinders any prospects for clinical and surgical applications. The objective of this work was to fabricate mechanically robust PVA membranes, which could also withstand surgical manipulation and suturing. Electrospun membranes and control hydrogels were produced with 61 kDa PVA. Using a high-speed rotating cylindrical collector, we achieved fibre alignment (fibre diameter: 300 ± 50 nm). Subsequently, we created multilayered samples with different orientations to achieve multidirectional reinforcement. Finally, utilising glutaraldehyde as a cross-linker, we created insoluble fibrous-hydrogel membranes. Mechanical studies were performed, confirming a fourfold increase in the specific loading capacities (from 0.21 to 0.84 Nm2/g) in the case of the monolayer samples. The multilayered membranes exhibited increased resistance from both horizontal and vertical directions, which varies according to the specific arrangement. Finally, the cross-linked fibrous hydrogel samples not only exhibited specific loading capacities significantly higher than their counterpart bulk hydrogels but successfully withstood suturing. Although cross-linking optimisation and animal experiments are required, these membranes have great prospects as alternatives to current surgical meshes, while the methodology could also be applied in other systems as well.
Fundamentally different representations of color and motion revealed by individual differences in perceptual scaling

Significance The visual attributes of color and motion have often been compared to identify different processing streams within the visual system. Here, we show that the judgments people make about hue and motion direction – in similar tasks – also reveal very different representational principles. Individual differences in perceived motion direction reflect the structure of visual space (e.g., varying in the relative weighting of horizontal and vertical), while variations in hue percepts do not reveal privileged chromatic axes or a global coordinate frame. This distinction may reflect fundamental differences in how information about hue and motion direction are used for vision.
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data

Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. On both a synthetic spike-in RNA sample and human RNA samples, ESPRESSO outperforms multiple contemporary tools in not only transcript isoform discovery but also transcript isoform quantification. In total, we generated and analyzed ~1.1 billion nanopore RNA-seq reads covering 30 human tissue samples and three human cell lines. ESPRESSO and its companion dataset provide a useful resource for studying the RNA repertoire of eukaryotic transcriptomes.
An Overview of Circulating Cell-Free Nucleic Acids in Diagnosis and Prognosis of Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer due to its molecular heterogeneity and poor clinical outcomes. Analysis of circulating cell-free tumor nucleic acids (ctNAs) can improve our understanding of TNBC and provide efficient and non-invasive clinical biomarkers that may be representative of tumor heterogeneity. In this review, we summarize the potential of ctNAs to aid TNBC diagnosis and prognosis. For example, tumor fraction of circulating cell-free DNA (TFx) may be useful for molecular prognosis of TNBC: high TFx levels after neoadjuvant chemotherapy have been associated with shorter progression-free survival and relapse-free survival. Mutations and copy number variations of TP53 and PIK3CA/AKT genes in plasma may be important markers of TNBC onset, progression, metastasis, and for clinical follow-up. In contrast, the expression profile of circulating cell-free tumor non-coding RNAs (ctncRNAs) can be predictive of molecular subtypes of breast cancer and thus aid in the identification of TBNC. Finally, dysregulation of some circulating cell-free tumor miRNAs (miR17, miR19a, miR19b, miR25, miR93, miR105, miR199a) may have a predictive value for chemotherapy resistance. In conclusion, a growing number of efforts are highlighting the potential of ctNAs for future clinical applications in the diagnosis, prognosis, and follow-up of TNBC.
Controlled Assembly of Fluorophores inside a Nanoliposome

Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.
A Study of the Ping An Health App Based on User Reviews with Sentiment Analysis

By mining the dimensional sentiment and dimension weight of the Ping An Health App reviews, this paper explores the changing trend of the influence of dimensions on user satisfaction and provides suggestions for the Ping An Health App operators to improve user satisfaction. Firstly, the topic model is used to identify the topic of user comments, and then the fine-grained sentiment analysis method is used to calculate the sentiment and weight of each dimension. Finally, the changing trend of the weight of each dimension and the changing trend of user satisfaction of each dimension are drawn. Based on the reviews of the Ping An Health App in the Apple App Store, users’ concerns about Ping An Health App can be summarized into seven main dimensions: Usage, Bug report, Reliability, Feature information, Services, Other apps, and User Background. The “Feature information” dimension and “Reliability” dimension have a great impact on user satisfaction with the Ping An Health App, while the “Bug report” dimension has the lowest user satisfaction.
Prevalence of Smoking Various Tobacco Types in the Kazakhstani Adult Population in 2021: A Cross-Sectional Study

Tobacco use was the second-leading risk factor for death, accounting for 15.4% of total deaths in 2019. In 2019, 20.4% (2.7 million) of the adult population in Kazakhstan, 36.5% of men, and 6.0% of women smoked tobacco. A cross-sectional study of a random sample (n = 1201) was conducted between October and December 2021 in accordance with the STEPwise approach. The tobacco-use questions were focused on current and previous smoking status, initiation and duration of smoking, amount of tobacco use, exposure to secondhand smoke, and information related to quitting smoking. From 20.8% of smokers, 93.8% of men and 80.2% of women use tobacco products daily, χ2 = 10.983, p-score < 0.001. The earliest initiation of smoking was 6 years old. The prevalence of smoking tobacco products in Kazakhstan is 20.8%, which means that every fifth adult smokes. In addition, the proportion of smokers among men was 38.5%, and among women, it was 10.1%. A total of 93.8% of men and 80.2% of women smoked daily. The role of healthcare professionals in smoking prevention is very low, and only 16.9% of respondents have been advised to quit smoking in the last 12 months. New interventions for tobacco smoking prevention are urgently needed in Kazakhstan.
Recent Pharmacological Options in Type 2 Diabetes and Synergic Mechanism in Cardiovascular Disease

Diabetes Mellitus is a multifactorial disease with a critical impact worldwide. During prediabetes, the presence of various inflammatory cytokines and oxidative stress will lead to the pathogenesis of type 2 diabetes. Furthermore, insulin resistance and chronic hyperglycemia will lead to micro- and macrovascular complications (cardiovascular disease, heart failure, hypertension, chronic kidney disease, and atherosclerosis). The development through the years of pharmacological options allowed us to reduce the persistence of chronic hyperglycemia and reduce diabetic complications. This review aims to highlight the specific mechanisms with which the new treatments for type 2 diabetes reduce oxidative stress and insulin resistance and improve cardiovascular outcomes.
Prenatal Lipopolysaccharide Exposure Alters Hepatic Drug-Metabolizing Enzyme Expression in Mouse Offspring via Histone Modifications

Inflammation is a major regulator of drug-metabolizing enzymes (DMEs), therefore contributing to the interindividual variability of drug effects. However, whether prenatal inflammation affects DMEs expression in offspring remains obscure. This study investigated the effects of prenatal lipopolysaccharide (LPS) exposure on hepatic expression of inflammatory-related genes, nuclear receptors, and DMEs in offspring mice. Prenatal LPS exposure on gestational day (GD) 10 led to higher expression of NF-κB, Pxr, and Cyp2b10, while lower expression of Car, Ahr, Cyp3a11, and Ugt1a1 in postnatal day (PD) 30 offspring. However, multiple doses of LPS exposure on GD10-14 resulted in higher levels of inflammatory-related genes, Cyp1a2, and Cyp2b10, and lower levels of Pxr and Cyp3a11 in PD30 offspring liver. For PD60 offspring, decreased hepatic expression of NF-κB and IL-6, and increased expression of Pxr and Cyp3a11 were seen in single-dose LPS groups, whereas opposite results were observed in the multiple-dose LPS groups. Notably, enhanced H3K4me3 levels in the PXR response elements of the Cyp3a11 promoter were observed in the liver of PD60 offspring mice from dams treated with multiple doses of LPS during pregnancy. Overall, this study suggests that parental LPS exposure could persistently alter the hepatic expression of DMEs, and histone modifications may contribute to the long-term effects.
Dynamic epi‐transcriptomic landscape mapping with disease progression in estrogen receptor‐positive breast cancer

Dear Editor, The molecular determinants that drive breast cancer progression tometastasis are complex and partly controlled by nucleic acid epi-modifications [1]. Although DNA-methyl modifications in breast cancer metastasis have been well described, there is limited understanding of the role of RNA methylation in advanced disease [2]. This study aimed to provide an understanding on the role of the epitranscriptome in estrogen receptor-positive (ER+) breast cancer progression to metastasis. Numerous RNA modifications have been described to date, of which N-methyladenosine (m6A) modifications are the most common [3]. Here, we mapped dynamic global m6A-specific methylated RNA immunoprecipitation sequencing (MeRIPseq), with corresponding RNA-sequencing (RNA-seq) and mass spectrometry, in cell models of disease progression to metastasis: endocrine-sensitive (MCF7/luminal A), endocrineresistant (LY2/luminal B) and endocrine-resistant brain metastatic (T347/patient-derived luminal B metastatic) (Figure 1A). The relevance of this model system was verified using comparative analysis of patient-matched brain metastatic samples [4] with RNA-seq data from our cells (LY2 vs. MCF7 and T347 vs. MCF7) [4] (Supplementary Table S1). Consistent differential gene expression in key oncogenic pathways such as Kirsten rat sarcoma virus (KRAS), nuclear factor-κB (NF-κB) and epithelial-
The Contribution of Disks and Envelopes to the Millimeter Continuum Emission from Very Young Low-Mass Stars

We investigate the question of disk formation during the protostar phase. We model the dust continuum emission from the dense cloud core using the cloud-collapse models of Terebey et al. (1984) and show that dust emission from the dense core is important when measured with large single-dish telescopes at 1.3 mm, but nearly negligible with interferometers at 2.7 mm. From published and new data, we conclude that massive disks are also seen toward a number of other sources including L1448 IRS 3, whose disk mass is estimated to be 0.5 solar mass. However, 1.3 mm data show that massive disks are relatively rare, occurring around perhaps 5 percent of young embedded stars. This implies that either massive disks occur briefly during the embedded phase or that relatively few young stars form massive disks. The median 1.3 mm flux density of IRAS-Dense cores in our sample is nearly the same as T Tauri stars in the sample of Beckwith et al. (1990). We conclude that the typical disk mass is not significantly higher during the embedded phase than during the later T Tauri phase.