Identification of key genes in HER2-positive breast cancer with brain metastasis via bioinformatics methods.

Background: Brain metastasis (BM) represents one of the most common advanced disease states in breast cancer (BC), especially in human epidermal growth factor receptor 2 (HER2)-positive BC, and is associated with poor survival outcomes. Methods: In this study, in-depth analysis of the microarray data from the GSE43837 dataset with 19 BM samples of HER2-positive BC patients and 19 HER2-positive nonmetastatic primary BC samples was conducted. The differentially expressed genes (DEGs) between BM and primary BC samples were identified and function enrichment analysis of the DEGs was conducted to identify potential biological functions. The hub genes were identified by constructing the protein-protein interaction (PPI) network using STRING and Cytoscape. UALCAN and Kaplan-Meier plotter online tools were used to verify the clinical roles of the hub DEGs in HER2-positive BC with BM (BCBM). Results: A total of 1,056 DEGs including 767 downregulated and 289 upregulated genes were identified by comparing the microarray data of the HER2-positive BM and primary BC samples. Functional enrichment analysis demonstrated that the DEGs were mainly enriched in pathways related to extracellular matrix (ECM) organization, cell adhesion, and collagen fibril organization. PPI network analysis identified 14 hub genes. Among these, CD44, COL1A2, MMP14, POSTN, and SOX9 were associated with the survival outcomes of HER2-positive patients. Conclusions: In summary, 5 BM-specific hub genes were identified in the study; those are potential prognostic biomarkers and therapeutic targets for HER2-positive BCBM patients. However, further investigations are necessary to unravel the mechanisms by which these 5 hub genes regulate BM in HER2-positive BC.

An Efficient Short-Term Traffic Speed Prediction Model Based on Improved TCN and GCN.

Timely and accurate traffic speed predictions are an important part of the Intelligent Transportation System (ITS), which provides data support for traffic control and guidance. The speed evolution process is closely related to the topological structure of the road networks and has complex temporal and spatial dependence, in addition to being affected by various external factors. In this study, we propose a new Speed Prediction of Traffic Model Network (SPTMN). The model is largely based on a Temporal Convolution Network (TCN) and a Graph Convolution Network (GCN). The improved TCN is used to complete the extraction of time dimension and local spatial dimension features, and the topological relationship between road nodes is extracted by GCN, to accomplish global spatial dimension feature extraction. Finally, both spatial and temporal features are combined with road parameters to achieve accurate short-term traffic speed predictions. The experimental results show that the SPTMN model obtains the best performance under various road conditions, and compared with eight baseline methods, the prediction error is reduced by at least 8%. Moreover, the SPTMN model has high effectiveness and stability.

Mining urban sustainable performance: Spatio-temporal emission potential changes of urban transit buses in post-COVID-19 future.

Emission benefits of transit buses depend on ridership. Declines in ridership caused by COVID-19 leads uncertainty about the emission reduction capacity of buses. This paper provides a method framework for analyzing spatio-temporal emission patterns of buses in combination with real-time ridership and potential emission changes in the post-COVID-19 future. Based on GPS trajectory and Smart Card data of 2056 buses from 278 routes covering 1.5 million ridership in Qingdao, China, spatio-temporal emissions characteristics of buses are studied. 7589 taxis with 0.2 million passengers' trips are used for acquiring private cars' emissions to evaluate the emissions difference between buses and cars. Empirical results show that the average difference between buses and cars with 2 persons can reach up to 117 g/km-person during 7:00-8:59 and 115 g/km-person during 17:00-18:59. However, buses have various emission benefits around the city at different periods. A double increase in emissions during non-rush hours can be observed compared with rush hours. 224 online survey data are used to study the potential ridership reduction trend in post-COVID-19. Results show that 56.3% of respondents would decrease the usage of buses in the post-COVID-19 future. Based on this figure, our analysis shows that per kilometer-person emissions of buses are higher than cars during non-rush hours, however, still lower than cars during rush hours. We conclude that when ridership reduces by more than 40%, buses cannot be "greener" travel modal than cars as before. Finally, several feasible policies are suggested for this potential challenge. Our study provides convincing evidence for understanding the emission patterns of buses, to support better buses investment decisions and promotion on eco-friendly public transport service in the post-COVID-19 future.

Precision medicine in myasthenia graves: begin from the data precision.

Myasthenia gravis (MG) is a prototypic autoimmune disease with overt clinical and immunological heterogeneity. The data of MG is far from individually precise now, partially due to the rarity and heterogeneity of this disease. In this review, we provide the basic insights of MG data precision, including onset age, presenting symptoms, generalization, thymus status, pathogenic autoantibodies, muscle involvement, severity and response to treatment based on references and our previous studies. Subgroups and quantitative traits of MG are discussed in the sense of data precision. The role of disease registries and scientific bases of precise analysis are also discussed to ensure better collection and analysis of MG data.

Complex network model of the Treatise on Cold Damage Disorders.

Investigating the underlying principles of the Treatise on Cold Damage Disorder is meaningful and interesting. In this study, we investigated the symptoms, herbal formulae, herbal drugs, and their relationships in this treatise based on a multi-subnet composited complex network model (MCCN). Syndrome subnets were constructed for the symptoms and a formula subnet for herbal drugs. By subnet compounding using MCCN, a composited network was obtained that described the treatment relationships between syndromes and formulae. The results obtained by topological analysis suggested some prescription laws that could be validated in clinics. After subnet reduction using the MCCN, six channel (Tai-yang, Yang-ming, Shao-yang, Tai-yin, Shao-yin, and Jue-yin) subnets were obtained. By analyzing the strengths of the relationships among these six channel subnets, we found that the Tai-yang channel and Yang-ming channel were related most strongly with each other, and we found symptoms that implied pathogen movements and transformations among the six channels. This study could help therapists to obtain a deeper understanding of this ancient treatise.

Network propagation with dual flow for gene prioritization.

Based on the hypothesis that the neighbors of disease genes trend to cause similar diseases, network-based methods for disease prediction have received increasing attention. Taking full advantage of network structure, the performance of global distance measurements is generally superior to local distance measurements. However, some problems exist in the global distance measurements. For example, global distance measurements may mistake non-disease hub proteins that have dense interactions with known disease proteins for potential disease proteins. To find a new method to avoid the aforementioned problem, we analyzed the differences between disease proteins and other proteins by using essential proteins (proteins encoded by essential genes) as references. We find that disease proteins are not well connected with essential proteins in the protein interaction networks. Based on this new finding, we proposed a novel strategy for gene prioritization based on protein interaction networks. We allocated positive flow to disease genes and negative flow to essential genes, and adopted network propagation for gene prioritization. Experimental results on 110 diseases verified the effectiveness and potential of the proposed method.