1. PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databasesTianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa, 2022, original scientific article Abstract: PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology.
Keywords: PaintOmics 4, web tools, datasets, analysis methods, molecular biology
Published in DiRROS: 17.07.2024; Views: 11; Downloads: 7
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2. Water quality characteristics and source analysis of pollutants in the Maotiao river basin (SW China)Yinjiu Li, Qiuhua Li, Shulin Jiao, Chen Liu, Liuying Yang, Guojia Huang, Si Zhou, Mengshu Han, Anton Brancelj, 2022, original scientific article Abstract: Rivers are an important mediator between human activities and the natural environment. They provide multiple functions, including irrigation, transportation, food supply, recreation, and water supply. Therefore, evaluations of water quality and pollution sources are of great significance for ecological restoration and management of rivers. In this study, the improved “vušekriterijumska optimizacija i kompromisno rješenje” (VIKOR in Serbian; in English: Multicriteria Optimization and Compromise Solution), and a geodetector were used to analyze the water quality characteristics and pollution sources of the Maotiao River Basin (Gizhou province, SW China). The results showed that the water quality of the Maotiao River Basin deteriorated significantly during the summer drought period, as was evident in the reservoirs and lakes. It improved in the wet season (i.e., during the summer period) due to runoff dilution. Water quality decreased along the river’s course, from upstream to downstream sections. The results of the geographic detector analysis showed that agricultural areas were the primary factor affecting the spatial distribution of water quality in the river basin. In July, August, and November 2020, the influence of agricultural land was 0.72, 0.60, or 0.80, respectively, and the interactions among urban, industrial, agricultural, and forested areas explained 99.2%, 83.2%, or 99.9% of the spatial differentiation of water quality, respectively. Due to the influence of spatial scale, settlements have a small influence on the spatial distribution of water quality. Their impact factors were 0.38, −0.24, and −0.05, respectively. Notably, the negative relationship of water quality and forested areas reflects that topography, types of landscapes, and soil thickness have considerable influences on the Maotiao River Basin’s water quality. Based on the findings, we infer that good farmland water conservancy projects and comprehensive management of different types of landscapes, such as forests, agriculture, and urban area and water bodies, are of great significance for improving water quality.
Keywords: water quality, statistical data, VIKOR model, CRITIC model
Published in DiRROS: 16.07.2024; Views: 2; Downloads: 4
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3. Effects of governmental data governance on urban fire risk : a city-wide analysis in ChinaZhao-Ge Liu, Xiang-Yang Li, Grunde Jomaas, 2022, original scientific article Abstract: The effects of data governance (as a means to maximize big data value creation in fire risk management) performance on fire risk was analyzed based on multi-source statistical data of 105 cities in China from 2016 to 2018. Specifically, data governance was first quantified with ten detailed indicators, which were then selected for explaining urban fire risk through correlation analysis. Next, the sample cities were clustered in terms of major socio-economic characteristics, and then the effects of data governance were examined by constructing multivariate regression models for each city cluster with ordinary least squares (OLS). The results showed that the constructed regression models produced good interpretation of fire risk in different types of cities, with coefficient of determination (R2) in each model exceeding 0.65. Among the indicators, the development of infrastructures (e.g. data collection devices and data analysis platforms), the level of data use, and the updating of fire risk related data were proved to produce significant effects on the reduction of fire frequency and fire consequence. Moreover, the organizational maturity of data governance was proved to be helpful in reducing fire frequency. For the cities with large population, the cross-department sharing of high-value data was found to be another important determinant of urban fire frequency. In comparison with existing statistical models which interpreted fire risk with general social factors (with the highest R2 = 0.60), these new regression models presented a better statistical performance (with the average R2 = 0.72). These findings are expected to provide decision support for the local governments of China and other jurisdictions to facilitate big data projects in improving fire risk management.
Keywords: urban fire risk, fire risk management, big data technologies, data governance, socio-economic factors, city-wide analysis
Published in DiRROS: 09.01.2024; Views: 284; Downloads: 68
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4. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwideYu-Rong Liu, Marcel G. A. van der Heijden, Judith Riedo, Carlos Sanz-Lazaro, David J. Eldridge, Felipe Bastida, Eduardo Moreno-Jiménez, Xin-Quan Zhou, Hang-Wei Hu, Ji-Zheng He, Tine Grebenc, Tina Unuk Nahberger, 2023, original scientific article Abstract: Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.
Keywords: soil contamination, urban greenspaces
Published in DiRROS: 28.03.2023; Views: 745; Downloads: 344
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5. Effects of Zr doping into ceria for the dry reforming of methane over ▫$Ni/CeZrO_2$▫ catalysts ein situ studies with XRD, XAFS, and AP-XPS : in situ studies with XRD, XAFS, and AP-XPSFeng Zhang, Zenghui Liu, Xiaobo Chen, Ning Rui, Luis E. Betancourt, Lili Lin, Wenqian Xu, Cheng-jun Sun, A. M. Milinda Abeykoon, José A. Rodriguez, Janvit Teržan, Kristijan Lorber, Petar Djinović, Sanjaya D. Senanayake, 2020, original scientific article Keywords: nickel, ceria, zirconia, ▫$CeZrO_2$▫ solid solution, XRD, XAFS, AP-XPS, dry reforming of methane
Published in DiRROS: 13.03.2023; Views: 676; Downloads: 421
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7. Fo Guang Shan's Expansion in the Religious Market of Thailand : a SWOT analysisGuiyu Su, Yaoping Liu, 2022, original scientific article Abstract: As one of the prominent Mahayana Buddhist institutions from Taiwan, Fo guang Shan (FgS) entered the religious market of Thailand as early as the 1990s. Its influence has grown tremendously among the local Chinese communities and Thai society. Despite this, there is a dearth of scholarship dedicated to FgS’s mar-ket expansion in Theravada-dominated Thailand. Through a SWOT analysis, this paper explores FgS’s marketing strategy for the Thai religious market. The findings suggest that FgS bears certain strengths, such as its appealing humanistic Budd-hist doctrine, gift-giving networking skills and its strong emotional bonds with the Chinese communities in Thailand. These strengths have brought and will conti-nuously provide FgS with opportunities for further expansion. However, FgS’s weakness is always there and obvious, given its foreign and non-mainstream na-ture and questionable legitimacy of existing as a Buddhist institution (or temple) in Thailand. All this has already caused threats to FgS’s missionary clergies and sanctuaries, mainly based in the Bangkok area, not to mention the growingly fierce competition from its Thai Theravada and local-born Mahayana counterparts.
Keywords: religion, Thai religion, religious market, marketing strategy, SWOT analysis, Thailand
Published in DiRROS: 28.02.2023; Views: 487; Downloads: 309
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8. Thermal-deformation model of a SR-modified A356 aluminum alloyYongyue Liu, Xianglai Xu, Jiangxiong Cheng, Hongwei Sun, Xueping Ren, Peng Jiang, 2022, original scientific article Keywords: A356 aluminum alloy, Sr modification, microstructure, thermal-deformation model
Published in DiRROS: 22.06.2022; Views: 684; Downloads: 208
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10. Structural and elastic properties of AgNi[sub]10 alloy studied with ab-initio calculationsJide Liu, Xue Wang, Xiaoming Du, Ming Xie Xie, Jinguo Li, Shangqiang Zhao, Yizhou Zhou, Qiao Zhang, Jiheng Fang, 2022, original scientific article Keywords: AgNi[sub]10 alloy, ab initio calculations, elastic anisotropy, thermodynamic properties
Published in DiRROS: 22.06.2022; Views: 693; Downloads: 178
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