Multiple-model based simulation of urban atmospheric methane concentration and the attributions to its seasonal variations: A case study in Hangzhou megacity, China.

Cities are treated as global methane (CH4) emission hotspots and the monitoring of atmospheric CH4 concentration in cities is necessary to evaluate anthropogenic CH4 emissions. However, the continuous and in-situ observation sites within cities are still sparsely distributed in the largest CH4 emitter as of China, and although obvious seasonal variations of atmospheric CH4 concentrations have been observed in cities worldwide, questions regarding the drivers for their temporal variations still have not been well addressed. Therefore, to quantify the contributions to seasonal variations of atmospheric CH4 concentrations, year-round CH4 concentration observations from 1st December 2020 to 30th November 2021 were conducted in Hangzhou megacity, China, and three models were chosen to simulate urban atmospheric CH4 concentration and partition its drivers including machine learning based Random Forest (RF) model, atmospheric transport processes based numerical model (WRF-STILT), and regression analysis based Multiple Linear Regression (MLR) model. The findings are as follows: (1) the atmospheric CH4 concentration showed obvious seasonal variations and were different with previous observations in other cities, the seasonality were 5.8 ppb, 21.1 ppb, and 50.1 ppb between spring-winter, summer-winter and autumn-winter, respectively, where the CH4 background contributed by -8.1 ppb, -44.6 ppb, and -1.0 ppb, respectively, and the CH4 enhancements contributed by 13.9 ppb, 65.7 ppb, and 51.1 ppb. (2) The RF model showed the highest accuracy in simulating CH4 concentrations, followed by MLR model and WRF-STILT model. (3) We further partition contributions from different factors, results showed the largest contribution was from temperature-induced increase in microbial process based CH4 emissions including waste treatment and wetland, which ranged from 38.1 to 76.3 ppb when comparing different seasons with winter. The second largest contribution was from seasonal boundary layer height (BLH) variations, which ranged from -13.4 to -6.3 ppb. And the temperature induced seasonal CH4 emission and enhancement variations were overwhelming BLH changes and other meteorological parameters.

[Identification of cardioprotective substances in Panax ginseng/P. notoginseng based on mitochondrial morphological characteristics and UPLC-Triple-TOF-MS].

Panax ginseng is reputed to be capable of replenishing healthy Qi and bolstering physical strength, and P. notoginseng can resolve blood stasis and alleviate pain. P. ginseng and P. notoginseng are frequently employed to treat ischemic heart diseases caused by blockages in the heart vessels. Mitochondrial dysfunction often coexists with abnormal mitochondrial morphology, and mitochondrial plasticity and dynamics play key roles in cardiovascular diseases. In this study, primary neonatal rat cardiomyocytes were exposed to 4 hours of hypoxia(H) followed by 2 hours of reoxygenation(R). MitoTracker Deep Red and Hoechst 33342 were used to label mitochondria and nuclei, respectively. Fluorescence images were then acquired using ImageXpress Micro Confocal. Automated image processing and parameter extraction/calculation were carried out using ImagePro Plus. Subsequently, representative parameters were selected as indicators to assess alterations in mitochondrial morphology and function. The active compounds of P. ginseng and P. notoginseng were screened out and identified based on the UPLC-Triple-TOF-MS results and mitochondrial morphometric parameters. The findings demonstrated that RS-2, RS-4, SQ-1, and SQ-4 significantly increased the values of three key morphometric parameters, including mitochondrial length, branching, and area, which might contribute to rescuing morphological features of myocardial cells damaged by H/R injury. Among the active components of the two medicinal herbs, 20(R)-ginsenoside Rg_3, ginsenoside Re, and gypenoside ⅩⅦ exhibited the strongest protective effects on mitochondria in cardiomyocytes. Specifically, 20(R)-ginsenoside Rg_3 might upregulate expression of optic atrophy 1(OPA1) and mitofusin 2(MFN2), and ginsenoside Re and gypenoside ⅩⅦ might selectively upregulate OPA1 expression. Collectively, they promoted mitochondrial membrane fusion and mitigated mitochondrial damage, thereby exerting protective effects on cardiomyocytes. This study provides experimental support for the discovery of novel therapeutic agents for myocardial ischemia-reperfusion injury from P. ginseng and P. notoginseng and offers a novel approach for large-scale screening of bioactive compounds with cardioprotective effects from traditional Chinese medicines.

Identification of a glycolysis-related miRNA Signature for Predicting Breast cancer Survival.

Breast cancer (BC) is a common type of cancer and has a poor prognosis. In this study, we collected the mRNA and miRNA expression profiles of BC patients were obtained from The Cancer Genome Atlas (TCGA) to explore a novel prognostic strategy for BC patients using bioinformatics tools. We found that six glycolysis-related miRNAs (GRmiRs, including hsa-mir-1247, hsa-mir148b, hsa-mir-133a-2, has-mir-1307, hsa-mir-195 and hsa-mir-1258) were correlated with prognosis of BC samples. The risk score model was established based on 6 prognosis-associated GRmiRs. The outcome of high risk group was significantly poorer. Cox regression analysis showed that risk score was an independent prognostic factor. Differentially expressed genes identified between high and low risk groups were mainly enriched in inflammation and immune-related signaling pathways. The proportion of infiltration of 12 kinds of immune cells in high and low risk groups were significantly different. Risk score was closely associated with many immune indexes. Multiple DEGRGs and miRNAs were associated with drugs. In conclusion, glycolysis-related miRNA signature effectively predicts BC prognosis.

Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks.

MOTIVATION: Recent advances in spatially resolved transcriptomics (ST) technologies enable the measurement of gene expression profiles while preserving cellular spatial context. Linking gene expression of cells with their spatial distribution is essential for better understanding of tissue microenvironment and biological progress. However, effectively combining gene expression data with spatial information to identify spatial domains remains challenging. RESULTS: To deal with the above issue, in this paper, we propose a novel unsupervised learning framework named STMGCN for identifying spatial domains using multi-view graph convolution networks (MGCNs). Specifically, to fully exploit spatial information, we first construct multiple neighbor graphs (views) with different similarity measures based on the spatial coordinates. Then, STMGCN learns multiple view-specific embeddings by combining gene expressions with each neighbor graph through graph convolution networks. Finally, to capture the importance of different graphs, we further introduce an attention mechanism to adaptively fuse view-specific embeddings and thus derive the final spot embedding. STMGCN allows for the effective utilization of spatial context to enhance the expressive power of the latent embeddings with multiple graph convolutions. We apply STMGCN on two simulation datasets and five real spatial transcriptomics datasets with different resolutions across distinct platforms. The experimental results demonstrate that STMGCN obtains competitive results in spatial domain identification compared with five state-of-the-art methods, including spatial and non-spatial alternatives. Besides, STMGCN can detect spatially variable genes with enriched expression patterns in the identified domains. Overall, STMGCN is a powerful and efficient computational framework for identifying spatial domains in spatial transcriptomics data.

[Effects of Angong Niuhuang Pills against heart failure based on cross-scale polypharmacological study].

Angong Niuhuang Pills(AGNHP) are effective in clearing heat, removing the toxin, and eliminating phlegm for resuscitation. Clinically, it is widely used to treat various diseases such as febrile convulsion due to heat attacking pericardium, but its therapeutic effects on heart failure(HF) have not been well recognized. In this study, the profiles of differential metabolites regulated by AGNHP were identified by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry(UPLC-Q-TOF-MS). The underlying mechanism of AGNHP against HF was illustrated based on the integrated analysis of pharmacological data and metabolic molecular network. The HF model was induced by isoproterenol in mice. After oral administration of AGNHP for one week, cardiac functions in HF mice were evaluated by echocardiography, and serum samples of mice were collected for metabolomics analysis. Eight differential metabolites of AGNHP against HF were screened out through partial least square discriminant analysis(PLS-DA) and input into MetaboAnalyst for the analysis of metabolic pathways. Moreover, the critical metabolic pathways regulated by AGNHP were enriched according to the potential targets of major compounds in AGNHP. After AGNHP treatment, the recovered index of relative content of some metabolites underwent cross-scale fusion analysis with therapeutic efficacy data, followed by "compound-reaction-enzyme-gene" network analysis. It is inferred that the anti-HF effects of AGNHP may be attributed to the metabolism of arachidonic acid, amino acid, glycerophospholipid, and linoleic acid. The cross-scale polypharmacological analysis method developed in this study provides a new method to interpret scientific principles of AGNHP against HF with modern technologies.

Oridonin inhibits tumor angiogenesis and induces vessel normalization in experimental colon cancer.

Purpose: Tumor blood vessels exhibit morphological and functional aberrancies. Its maturity and functionality are closely associated with colon cancer progression and therapeutic efficacy. The direct evidence proving whether oridonin (ORI) has vascular normalization promoting effect from which combination therapies will benefit is still lacking. Methods: We established a subcutaneous xenograft model of human colon cancer. The animals were divided into the Control and ORI-treated groups. Immunohistochemical analysis and TUNEL staining was applied to evaluate the proliferation, apoptosis and angiogenesis. Western blot analysis was employed to characterize the angiogenesis-related factors and JAK2/STAT3 signaling. Then, vascular normalization and macrophage reprogramming were assessed by immunofluorescence analysis. Results: The results showed that ORI obviously reduced tumor growth, diminished the numbers of Ki67+ cells and CD31+ microvessel density, while increased the numbers of TUNEL+ cells. The expression levels of VEGF and bFGF proteins were dramatically down-regulated while the angiostatin and endostatin levels were increased in the ORI-treated group. Moreover, ORI therapy remarkably promoted the pericyte coverage of tumor vessels from days 5 to 10, with the highest pericyte coverage rate occurred at day 7. In the time window of vascular normalization, hypoxia of the tumor microenvironment was improved by ORI, the expression of HIF-1a was downregulated. Moreover, CD206+ macrophage cells were diminished in the ORI-treated group. These anticancer effects of ORI maybe partly mediated by suppressing JAK2/STAT3 signaling pathway. Conclusions: These results highlight the potential effect of ORI on anti-angiogenesis and inducing vessel normalization roles of ORI, and probably provide optimum time point for the ORI therapy in conjunction with the chemoradiotherapy or immunotherapy.

Case report of pulmonary metastasis in a male Wistar rat glioblastoma model.

Glioblastoma (GBM) is a highly aggressive central nervous system cancer. Its extracranial metastases have rarely been reported in the past few decades. Moreover, the pathogenesis of extracranial GBM metastases remains unclear. Here, we report a case of pulmonary metastasis in a male Wistar rat of C6 GBM model. This reported Wistar male rat was one of the experimental control group without any other intervention except for C6 GBM cells orthotopic implantation. On postoperative day 15, the animal which was reported in this study showed highly cellular, pleomorphic, tumor with nuclear atypia in the brain (Ki67, approximately 65.7%) and lungs (Ki67, 49.5%). Tumor cells in the lung showed immunoreactivity for glial fibrillary acidic protein. Inflammatory CD68+ cell infiltration, weakly positive E-cadherin, and strongly positive staining for vimentin were observed both in tumors in the brain and lungs. Based on further morphological analysis, we speculate that the potential metastatic route into the lung might be hematogenous metastasis.

miR-30a regulates the proliferation and invasion of breast cancer cells by targeting Snail.

The present study aims to investigate the effect of miR-30a on the proliferative and invasive abilities of breast cancer cells, and to observe the role of miR-30a in the pathogenesis of breast cancer. With the increase of pathological grade and malignant degree of breast cancer cells, the miR-30a expression level gradually decreased (P<0.01). Transfection with miR-30a mimic significantly inhibited the proliferative and invasive ability of SK-BR-3 cells (P<0.01), while transfection with anti-miR-30a significantly improved the proliferative and invasive ability of these cells (P<0.01). It was revealed using bioinformatic methods that Snail was the functional target gene of miR-30a, and this was verified by the results of a luciferase reporter gene assay. The results of analysis of Snail expression in breast cancer tissues and breast cancer cells revealed that with the increase in pathological grade and malignant degree of breast cancer cells, Snail expression levels gradually increased (P<0.01). Western blotting revealed that miR-30a significantly inhibited Snail expression in SK-BR-3 cells, upregulated the expression of EMT-associated E-cadherin, and downregulated the expression of EMT-associated N-cadherin and Vimentin. MiR-30a was able to affect the proliferation and invasion of breast cancer cells by regulating Snail expression, and therefore has a regulatory effect on the occurrence and development of breast cancer.