OsCAS: a comprehensive web-based annotation platform for rice microarray data

Qingyun Shi,Yijun Meng,Dijun Chen,Fei He,Haibin Gu,Ping Wu,Ming Chen 한국바이오칩학회 2010 BioChip Journal Vol.4 No.1

OsCAS (Oryza sativa Chip Annotation System) is a comprehensive web-based tool that analyzes the results of rice (Oryza sativa) microarray experiments and the potential relationships among genes. This platform is designed to facilitate the indepth exploration of microarray data with relatively high analysis efficiency. With a user-friendly web interface, OsCAS allows chip probe IDs as inputs to retrieve relevant information according to user’s designation. Public databases, such as GenBank, UniGene, Swiss-Prot, TIGR, KOME, KEGG, Gene Ontology, and miRBase, were integrated into our platform to cover gene information, protein features, metabolic pathways and regulatory factors in rice. Besides, OsCAS includes the reprocessed information from several analytical tools such as CSRDB and miRU to obtain deep insights into the primary annotations. OsCAS is time-cost-effective in annotating large sets of chip probe IDs, and can provide some precious hints for the biological experiment design. OsCAS runs on a Linux server and is accessible at http://bis.zju.edu.cn/oscas/.

Determinants of Green Technology Diffusion and Green Trade

Qingyun Chen,조혁수 한국무역학회 2023 Journal of Korea trade Vol.27 No.6

Purpose – This study aims to explore the factors that contribute to the international diffusion of green technology and further analyze the relationship between green technology diffusion and green trade. Previous studies and theoretical foundations suggest that economic, technological, and institutional environments are important factors influencing the diffusion of green technology among countries. For this study, trade openness, intellectual property protection, the level of development of information and communication technology (ICT), research and development (R&D) investment, environmental regulations, and environmental norms were used as the key factors in the diffusion of green technology. In addition, a comparative analysis of OECD and non-OECD countries is conducted. Design/methodology – Panel data were collected from 58 countries for the period 2007–2019. The empirical analysis consists of two parts, first exploring the drivers of green technology diffusion using the feasible generalized least squares (FGLS) method, and then analyzing the linkage between green technology diffusion and green trade using the two-stage least squares (2SLS) model. The demand for green technology is expected to vary among countries because of their different economic development levels and goals. A comparative analysis was conducted based on the classification of countries by the level of economic development. Findings – We found that the level of intellectual property protection, R&D investment and environmental norms contribute positively to the diffusion of green technology. However, there is a negative correlation between trade openness, environmental regulations and green technology diffusion. Green technology diffusion positively affects green trade. Moreover, the positive impact of green technology diffusion on green trade is more pronounced in non-OECD countries than in OECD countries. Originality/value – Previous studies have focused on technology transfer and green technology innovation at the firm level; however, research on green technology diffusion is insufficient. This study investigated the determinants of green technology diffusion at the national level. The study also explored the relationship between green technology diffusion and green trade. It helps to fill the gap in the literature on green technology diffusion and provides a reference for future studies. Additionally, our findings offer valuable guidance for government and corporate decision-makers in formulating strategies for the transfer of green technologies and sustainable development initiatives.

Influence of Real-Information to Change Tourists' Travel Route

Qingyun Chen,Ruimin Ma,Maozhu Jin,Peiyu Ren 보안공학연구지원센터 2016 International Journal of u- and e- Service, Scienc Vol.9 No.11

The tourism system as a whole is becoming less sustainable, both because of its overall rapid growth and the unwillingness to change travel behavior (tourists). In the field of the tourism, the tourists' activities have influences on the protection and development of the natural scenic. In order to understand the tourist' intention to change travel route based on real-time information, this paper adds trust to the model of theory of planned behavior (TPB). Exploratory and confirmatory factor analysis are used to identify and confirm the constructs. In addition, structural equation modeling was established to test the measure model. Results indicate that the attitude, subjective norm and perceived behavioral control have positive effect on the behavioral intention of changing travel route according to real-time information. Moreover, trust also has positive influence on behavioral intention via three antecedents of intention. The findings have implications for predicting the tourist's intention of travel route change.

Comparative Research on the Production Effects of SFS and FCH

Yuan Chen,Qingyun Chen,Lihong Gao 한국원예학회 2006 한국원예학회 기타간행물 Vol.- No.-

Providing survivability for virtual networks against substrate network failure

( Ying Wang ),( Qingyun Chen ),( Wenjing Li ),( Xuesong Qiu ) 한국인터넷정보학회 2016 KSII Transactions on Internet and Information Syst Vol.10 No.9

Network virtualization has been regarded as a core attribute of the Future Internet. In a network virtualization environment (NVE), multiple heterogeneous virtual networks can coexist on a shared substrate network. Thus, a substrate network failure may affect multiple virtual networks. In this case, it is increasingly critical to provide survivability for the virtual networks against the substrate network failures. Previous research focused on mechanisms that ensure the resilience of the virtual network. However, the resource efficiency is still important to make the mapping scheme practical. In this paper, we study the survivable virtual network embedding mechanisms against substrate link and node failure from the perspective of improving the resource efficiency. For substrate link survivability, we propose a load-balancing and re-configuration strategy to improve the acceptance ratio and bandwidth utilization ratio. For substrate node survivability, we develop a minimum cost heuristic based on a divided network model and a backup resource cost model, which can both satisfy the location constraints of virtual node and increase the sharing degree of the backup resources. Simulations are conducted to evaluate the performance of the solutions. The proposed load balancing and re-configuration strategy for substrate link survivability outperforms other approaches in terms of acceptance ratio and bandwidth utilization ratio. And the proposed minimum cost heuristic for substrate node survivability gets a good performance in term of acceptance ratio.

Spectral Clustering with Sparse Graph Construction Based on Markov Random Walk

( Jiangzhong Cao ),( Pei Chen ),( Bingo Wing-kuen Ling ),( Zhijing Yang ),( Qingyun Dai ) 한국인터넷정보학회 2015 KSII Transactions on Internet and Information Syst Vol.9 No.7

Spectral clustering has become one of the most popular clustering approaches in recent years. Similarity graph constructed on the data is one of the key factors that influence the performance of spectral clustering. However, the similarity graphs constructed by existing methods usually contain some unreliable edges. To construct reliable similarity graph for spectral clustering, an efficient method based on Markov random walk (MRW) is proposed in this paper. In the proposed method, theMRW model is defined on the raw k-NN graph and the neighbors of each sample are determined by the probability of the MRW. Since the high order transition probabilities carry complex relationships among data, the neighbors in the graph determined by our proposed method are more reliable than those of the existing methods. Experiments are performed on the synthetic and real-world datasets for performance evaluation and comparison. The results show that the graph obtained by our proposed method reflects the structure of the data better than those of the state-of-the-art methods and can effectively improve the performance of spectral clustering.

Impact of the geometric properties of intracranial vascular bifurcation and the mechanism of aneurysm occurrence and rupture

Liu, Jun,Zhang, Qingyun,Chen, Hua Techno-Press 2022 Advances in nano research Vol.13 No.4

One factor that can heighten the risk of the rapture intracranial aneurysm (IA) is bifurcations, which can cause the IA to evaluate. This study presents the effect of geometric of intracranial vascular on the bifurcation analysis of the aneurysm occurrence. The aneurysm mechanism is mathematically modeled based on the nano pipe structures under the thermal stresses, and the impact of the aneurysm geometric on the stability and bifurcation points is analyzed. Because of the dimension of these structures, the classical theories could not predict their behavior perfectly, so the nonclassical and nonlocal theories are required for the mechanical modeling of the aneurysm. The presented results show that the bifurcation point of the aneurysm mechanism is dependent on the environment temperature, and the temperature change plays an essential role in the stability of these structures.

A Max-Flow-Based Similarity Measure for Spectral Clustering

Jiangzhong Cao,Pei Chen,Yun Zheng,Qingyun Dai 한국전자통신연구원 2013 ETRI Journal Vol.35 No.2

In most spectral clustering approaches, the Gaussian kernel-based similarity measure is used to construct the affinity matrix. However, such a similarity measure does not work well on a dataset with a nonlinear and elongated structure. In this paper, we present a new similarity measure to deal with the nonlinearity issue. The maximum flow between data points is computed as the new similarity, which can satisfy the requirement for similarity in the clustering method. Additionally, the new similarity carries the global and local relations between data. We apply it to spectral clustering and compare the proposed similarity measure with other state-of-the-art methods on both synthetic and real-world data. The experiment results show the superiority of the new similarity: 1) The max-flow-based similarity measure can significantly improve the performance of spectral clustering; 2) It is robust and not sensitive to the parameters.

제도환경과 조직문화가 중국 수출기업의 친환경 GVC 참여에 미치는 영향에 관한 연구

( Shi Qianyun ),조혁수 ( Cho Hyuksoo ),문희철 ( Moon Heecheol ),( Chen Qingyun ) 한국해운물류학회 2023 해운물류연구 Vol.39 No.1

글로벌 가치사슬의 확대로 인해 많은 생산시설이 개발도상국으로 이전되었다. 그 결과 해당 국가에서 환경문제가 심화하였다. 하지만 개별국가의 환경 규제가 강화되면서 GVC에서도 친환경이 강조되고 있다. 본 연구는 중국 중소수출기업 대상 친환경 GVC 참여 요인과 지속가능성에 대한 영향력을 분석하였다. 또한, GVC 전방 참여의 조절 효과도 실증적으로 확인하였다. 친환경 GVC 참여는 환경 규제와 환경 규범에 영향을 받으며, 이 중 환경 규범이 상대적으로 더 중요한 역할을 한다는 사실을 확인하였다. 이와 함께 기업 내 혁신적, 협력적 문화는 해당 기업의 친환경 GVC 활동에 긍정적인 영향을 미치며, 친환경 GVC 활동은 지속가능성으로 이어진다는 결과도 도출하였다. 마지막으로 GVC 전방 참여의 긍정적인 조절 효과도 확인하였다. With the expansion of Global Value Chain(GVC), many production facilities have been moved to developing countries. As a result, environmental problems in the countries have become increasingly serious. Eco-friendly activities are being emphasized in many areas. GVC is not an exception. This study is designed to analyze determinants and effects of eco-friendly GVC participation in terms of Chinese exporters. In addition, moderating role of forward GVC regarding the effects is investigated. According to empirical findings, environmental regulations and norms have positive impacts on eco-friendly GVC participation. In particular, environmental norm rather than regulation can be much important. A positive impact of eco-friendly GVC participation on sustainability is empirically supported. Last, forward GVC can play an important role to make the relationship between the participation and sustainability stronger.

RNA sequencing reveals lncRNA-mediated non-mendelian inheritance of feather growth change in chickens

Qiu Mohan,Yu Chunlin,Zhu Shiliang,Liu Siyang,Peng Han,Xiong Xia,Chen Jialei,Jiang Xiaosong,Du Huarui,Li Qingyun,Zhang Zengrong,Yang Chaowu 한국유전학회 2022 Genes & Genomics Vol.44 No.11

Background: Long non-coding RNAs (lncRNAs) play an essential role in biological processes. However, the expression patterns of lncRNAs that regulate the non-Mendelian inheritance feather phenotypes remain unknown. Objective: This study aimed to compare the expression profiles of lncRNAs in the follicles of the late-feathering cocks (LC) and late-feathering hens (LH) that followed genetic rules and the early-feathering hen (EH) and early-feathering cock (EC) that did not conform to the genetic laws. Methods: We performed RNA sequencing and investigated the differentially expressed lncRNAs (DElncRNAs) between the early- and late-feathering chickens, which function by cis-acting or participate in the competing endogenous RNA (ceRNA) network. Results: A total of 53 upregulated and 43 downregulated lncRNAs were identified in EC vs. LC, and 58 upregulated and 109 downregulated lncRNAs were identified in EH vs. LH. The target mRNAs regulated by lncRNAs in cis were enriched in the pentose phosphate pathway, TGF-β signaling pathway and Jak-STAT signaling pathway in EC vs. LC and were associated with the TGF-β signaling pathway, Wnt signaling pathway, p53 signaling pathway and Jak-STAT signaling pathway in EH vs. LH. In addition, the lncRNA-mediated ceRNA regulatory pathways of hair follicle formation were mainly enriched in the TGF-β signaling pathway, Wnt signaling pathway, melanogenesis, and calcium signaling pathways. The levels of ENSGALG00000047626 were significantly higher in the late-feathering chickens than in the early-feathering chickens, which regulated the expression of SSTR2 by gga-miR-1649-5p. Conclusion: This study provides a novel molecular mechanism of lncRNA's response to the feather rate that does not conform to the genetic laws in chickens.