Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective

Predicting molecular properties (e.g., atomization energy) is an essential issue in quantum chemistry, which could speed up much research progress, such as drug designing and substance discovery. Traditional studies based on density functional theory (DFT) in physics are proved to be time-consuming for predicting large number of molecules. Recently, the machine learning methods, which consider much rule-based information, have also shown potentials for this issue. However, the complex inherent quantum interactions of molecules are still largely underexplored by existing solutions. In this paper, we propose a generalizable and transferable Multilevel Graph Convolutional neural Network (MGCN) for molecular property prediction. Specifically, we represent each molecule as a graph to preserve its internal structure. Moreover, the well-designed hierarchical graph neural network directly extracts features from the conformation and spatial information followed by the multilevel interactions. As a consequence, the multilevel overall representations can be utilized to make the prediction. Extensive experiments on both datasets of equilibrium and off-equilibrium molecules demonstrate the effectiveness of our model. Furthermore, the detailed results also prove that MGCN is generalizable and transferable for the prediction.Comment: The 33rd AAAI Conference on Artificial Intelligence (AAAI'2019), Honolulu, USA, 201

Impact of a Detailed Urban Parameterization on Modeling the Urban Heat Island in Beijing Using TEB-RAMS

The Town Energy Budget (TEB) model coupled with the Regional Atmospheric Modeling System (RAMS) is applied to simulate the Urban Heat Island (UHI) phenomenon in the metropolitan area of Beijing. This new model with complex and detailed surface conditions, called TEB-RAMS, is from Colorado State University (CSU) and the ASTER division of Mission Research Corporation. The spatial-temporal distributions of daily mean 2 m air temperature are simulated by TEB-RAMS during the period from 0000 UTC 01 to 0000 UTC 02 July 2003 over the area of 116°E~116.8°E, 39.6°N~40.2°N in Beijing. The TEB-RAMS was run with four levels of two-way nested grids, and the finest grid is at 1 km grid increment. An Anthropogenic Heat (AH) source is introduced into TEB-RAMS. A comparison between the Land Ecosystem-Atmosphere Feedback model (LEAF) and the detailed TEB parameterization scheme is presented. The daily variations and spatial distribution of the 2 m air temperature agree well with the observations of the Beijing area. The daily mean 2 m air temperature simulated by TEB-RAMS with the AH source is 0.6 K higher than that without specifying TEB and AH over the metropolitan area of Beijing. The presence of urban underlying surfaces plays an important role in the UHI formation. The geometric morphology of an urban area characterized by road, roof, and wall also seems to have notable effects on the UHI intensity. Furthermore, the land-use dataset from USGS is replaced in the model by a new land-use map for the year 2010 which is produced by the Institute of Remote Sensing and Digital Earth (RADI), Chinese Academy of Sciences (CAS). The simulated regional mean 2 m air temperature is 0.68 K higher from 01 to 02 July 2003 with the new land cover map

Screening and Identification of Hub Genes in the Development of Early Diabetic Kidney Disease Based on Weighted Gene Co-Expression Network Analysis

ObjectiveThe study aimed to screen key genes in early diabetic kidney disease (DKD) and predict their biological functions and signaling pathways using bioinformatics analysis of gene chips interrelated to early DKD in the Gene Expression Omnibus database.MethodsGene chip data for early DKD was obtained from the Gene Expression Omnibus expression profile database. We analyzed differentially expressed genes (DEGs) between patients with early DKD and healthy controls using the R language. For the screened DEGs, we predicted the biological functions and relevant signaling pathways by enrichment analysis of Gene Ontology (GO) biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways. Using the STRING database and Cytoscape software, we constructed a protein interaction network to screen hub pathogenic genes. Finally, we performed immunohistochemistry on kidney specimens from the Beijing Hospital to verify the above findings.ResultsA total of 267 differential genes were obtained using GSE142025, namely, 176 upregulated and 91 downregulated genes. GO functional annotation enrichment analysis indicated that the DEGs were mainly involved in immune inflammatory response and cytokine effects. KEGG pathway analysis indicated that C-C receptor interactions and the IL-17 signaling pathway are essential for early DKD. We identified FOS, EGR1, ATF3, and JUN as hub sites of protein interactions using a protein–protein interaction network and module analysis. We performed immunohistochemistry (IHC) on five samples of early DKD and three normal samples from the Beijing Hospital to label the proteins. This demonstrated that FOS, EGR1, ATF3, and JUN in the early DKD group were significantly downregulated.ConclusionThe four hub genes FOS, EGR1, ATF3, and JUN were strongly associated with the infiltration of monocytes, M2 macrophages, and T regulatory cells in early DKD samples. We revealed that the expression of immune response or inflammatory genes was suppressed in early DKD. Meanwhile, the FOS group of low-expression genes showed that the activated biological functions included mRNA methylation, insulin receptor binding, and protein kinase A binding. These genes and pathways may serve as potential targets for treating early DKD

Progressive Destabilization and Triggering Mechanism Analysis Using Multiple Data for Chamoli Rockslide of 7 February 2021

A catastrophic rockslide occurred on 7 February 2021 in Chamoli area in the high Himalaya. In the absence of field data, multiple satellites data of decade span have been used to investigate and understand the progressive destabilization of rockslide body. A 3D geometric model was developed using geospatial information about geology, terrain, and ice cover to understand the triggering mechanism. Several causes are uncovered as: the pronounced long-term change of land surface temperature facilitated local permafrost degradation and led to ice cover shrinking since 2010; the occurrence of ice avalanche nearby in 2016 accompanying with sidewall-to-bedrock fracturing enhanced the ice segregation beneath the rockslide body; and the development of side cracks in early February 2021 led to dropping of side support and percolating of surface water. Heavy precipitation several days before favoured the destabilization, top-corner cracks developing and top-side bergschrund breaking abruptly two days before, and ice strength reduction owing air temperature rising few hours before the event triggered finally the rockslide. The frequent disasters such as cloudburst, extreme precipitation, landslides, and snow avalanches responding to global warming and climate change in the Himalayan region needs immediate attention to the chain-like geohazards and collaborative observation with satellites and other platforms

Prevalence And Risk Factors For Cervical Neoplasia: A Cervical Cancer Screening Program In Beijing

Cervical cancer is the second most common cancer and cause of cancer-related death for women worldwide. The aims of this study were to investigate the prevalence of cervical neoplasia and examine factors associated with high-grade cervical squamous intraepithelial lesions (HSIL) among women taking part in a cervical cancer screening program in Beijing