Article
Agriculture, Multidisciplinary
Ping Liao, Yanni Sun, Xiangcheng Zhu, Haiyuan Wang, Yong Wang, Jin Chen, Jun Zhang, Yanhua Zeng, Yongjun Zeng, Shan Huang
Summary: The study shows that the application of nitrification inhibitors and biochar in rice paddies can significantly increase yield and reduce global warming potential. Controlled-release nitrogen fertilisers have no effect on global warming potential, but can increase rice yield. No-tillage and non-continuous flooding can reduce global warming potential, but have different impacts on rice yield.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Environmental Sciences
Lijin Guo, Wei Lin, Cougui Cao, Chengfang Li
Summary: Integrated rice-crayfish farming system (RCS) is popular in China, but the impact of trench on greenhouse gas (GHG) emissions has been ignored. This study compared GHG emissions between rice monoculture (RM) and RCS, finding that RCS had lower CH4 emissions due to lower mcrA abundance and higher pmoA abundance. However, the trench resulted in higher CH4 emissions and lower N2O emissions compared to the RCS field. Overall, RCS does not mitigate global warming potential (GWP) compared to RM, unless the area ratio of the trench to the system is controlled below 13.9%.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Haihe Gao, Qin Liu, Changrong Yan, Qiu Wu, Daozhi Gong, Wenqing He, Hongjin Liu, Jinling Wang, Xurong Mei
Summary: Soil mulching technologies are effective in reducing non-point source pollution and carbon emissions, while ensuring grain production security and increasing water productivity. This study conducted a meta-analysis to evaluate the effects of mulching methods on rice production, greenhouse gas emissions, and water use efficiency. The results show that different mulching methods have different impacts on these indicators.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Zhaohai Bai, Xiaofei Wu, Luis Lassaletta, Alexander Haverkamp, Wei Li, Zengwei Yuan, Eduardo Aguilera, Aimable Uwizeye, Alberto Sanz-Cobena, Nannan Zhang, Xiangwen Fan, Feng Zhu, Marcel Dicke, Xuan Wang, Lin Ma
Summary: Boosting the production of insects and earthworms based on food waste and livestock manure can contribute to China's food security and carbon neutrality goals, reducing greenhouse gas emissions and dependence on feed protein imports.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Environmental Sciences
Dan Wang, Youjia Liang, Lijun Liu, Jiejun Huang, Zhangcai Yin
Summary: Global warming has a significant impact on crop production in ecologically vulnerable areas. A study in China examined the potential changes in yield and yield gaps for winter wheat and maize under different climate scenarios. The results showed that maize was more adapted to climate warming than winter wheat, and future climate change could cause fluctuations in crop yields.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Ronley C. Canatoy, Song Rae Cho, Yong Sik Ok, Seung Tak Jeong, Pil Joo Kim
Summary: Compost utilization can decrease greenhouse gas emissions within the rice cropping boundary, but increase the net global warming potential within the whole system boundary. Biochar utilization can transform paddy soil into a greenhouse gas sink and significantly reduce greenhouse gas emissions within the whole system boundary.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Fisheries
Halley E. S. Froehlich, J. Zachary Koehn, Kristin K. Holsman, Benjamin S. Halpern
Summary: Food production is a major contributor to climate change, and aquaculture is now facing increasing vulnerability to a changing climate. However, research and public awareness on the implications of climate change for aquaculture are still comparatively limited. The focus has mainly been on temperature, sea level rise, and ocean acidification, with coverage concentrated in Asia, Europe, and North/Central America.
Review
Green & Sustainable Science & Technology
Rose Tirtalistyani, Murtiningrum Murtiningrum, Rameshwar S. Kanwar
Summary: Indonesia is facing a water crisis due to mismanagement of water resources, inefficient water systems, and weak institutions and regulatory organizations. Irrigation plays a crucial role in the welfare of the Indonesian population, but the infrastructure is significantly damaged. The irrigation systems in Indonesia have existed for thousands of years and have a close relationship with the socio-cultural life of the Indonesian population.
Article
Agriculture, Multidisciplinary
Tao Wang, Hong Chen, Wei Zhou, Yong Chen, Yong Fu, Zhiping Yang, Qi Liu, Xueping Yue, Fei Deng, Malik Nkrumah, Youfeng Tao, Wanjun Ren
Summary: This study analyzed the greenhouse gas emissions, crop yield, net economic benefits, and other factors of the garlic-rice system in China, finding that it can generate high net economic benefits with low greenhouse gas emission intensity.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2022)
Article
Agriculture, Multidisciplinary
Qiang Xu, Linxiu Dai, Ziyin Shang, Ying Zhou, Jingyong Li, Zhi Dou, Xiaochun Yuan, Hui Gao
Summary: Rice-crayfish co-culturing is an important agricultural mode in China with environmental and economic advantages. This study investigated the effects of optimizing nitrogen fertilizer practices on grain yield and greenhouse gas emissions in rice-crayfish co-culture systems. The results showed that the combined application of normal and controlled-release urea improved rice yield and reduced methane and nitrous oxide emissions, making it the optimal fertilization strategy.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Environmental Sciences
Chan Guo, Xufei Liu, Xuefei He
Summary: The study collected 174 studies from 16 countries to determine appropriate nitrogen fertilization rates for enhancing crop yield while reducing greenhouse gas emissions. Results showed positive effects on crop yield and negative effects on greenhouse gas intensity, with recommendations for specific application strategies in different regions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Engineering, Environmental
Srijana Rai, Danny Hage, James Littlefield, Gabrielle Yanai, Timothy J. Skone
Summary: This study compares the life cycle global warming potential (GWP) of three major RNG pathways (anaerobic digestion, thermal gasification, and power-to-gas) with fossil natural gas (FNG) pathway. The results show that RNG production is not always carbon neutral or negative.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Adam C. Castonguay, Stephen Polasky, Matthew H. Holden, Mario Herrero, Daniel Mason-D'Croz, Cecile Godde, Jinfeng Chang, James Gerber, G. Bradd Witt, Edward T. Game, Brett A. Bryan, Brendan Wintle, Katie Lee, Payal Bal, Eve McDonald-Madden
Summary: Beef production is a complex global sustainability challenge that involves reducing poverty and hunger, as well as addressing climate change issues. Understanding the trade-offs between these goals on a global scale and at fine spatial resolution is crucial in achieving a globally sustainable beef industry.
NATURE SUSTAINABILITY
(2023)
Article
Multidisciplinary Sciences
Kuo Li, Jie Pan, Wei Xiong, Wei Xie, Tariq Ali
Summary: Climate change has a significant impact on crop yields, particularly on maize. Simulated data shows that increases in global temperatures by 1.5 degrees C and 2 degrees C result in changes in maize yields and market prices. Under the 2 degrees C scenario, the risk of reduced maize yields is more severe, leading to a noticeable decline in total maize production in major producing regions worldwide.
SCIENTIFIC REPORTS
(2022)
Article
Environmental Sciences
Jesse F. Abrams, Chris Huntingford, Mark S. Williamson, David I. Armstrong McKay, Chris A. Boulton, Joshua E. Buxton, Boris Sakschewski, Sina Loriani, Caroline Zimm, Ricarda Winkelmann, Timothy M. Lenton
Summary: This study investigates the response of the planet under fixed concentration commitments, with a focus on assessing the likelihood of exceeding temperature thresholds that trigger climate tipping points. The research finds that if today's radiative forcing is maintained until achieving equilibrium global warming, the likelihood of crossing the 1.5 degrees Celsius and 2.0 degrees Celsius thresholds is 83% and 55% respectively.
Article
Environmental Sciences
Yong Wang, Yanni Sun, Le Chen, Hua Shao, Yanhua Zeng, Yongjun Zeng, Feiyu Tang, Junhuo Cai, Shan Huang
Summary: Rice agriculture is a significant source of methane emissions and cadmium accumulation. The study investigated the combined effects of water management and lime application on CH4 emissions and rice Cd uptake. Results showed that flooding following midseason drainage effectively reduced CH4 emissions, while lime application reduced both CH4 emissions and rice Cd uptake. The recommended approach to mitigate CH4 emissions without increasing Cd uptake is continuous flooding with midseason drainage combined with lime application.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemical Research Methods
Jing-Zhe Jiang, Wen-Guang Yuan, Jiayu Shang, Ying-Hui Shi, Li-Ling Yang, Min Liu, Peng Zhu, Tao Jin, Yanni Sun, Li-Hong Yuan
Summary: The paper presents PhaGCN2, a tool that rapidly classifies viral sequences at the family level and improves the precision and recall of virus classification. It allows for high-throughput processing of viral sequences and supports visualization.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Agronomy
Ping Liao, Stephen M. Bell, Le Chen, Shan Huang, Haiyuan Wang, Jiahui Miao, Yiming Qi, Yanni Sun, Bin Liao, Yongjun Zeng, Haiyan Wei, Hui Gao, Qigen Dai, Hongcheng Zhang
Summary: Smart agronomic management practices can reduce lodging risk in rice paddies. This includes employing lodging-resistant cultivars, appropriate fertilization, and applying plant growth regulators (PGRs). Additionally, the application of silicon, potassium, prohexadione calcium, and uniconazole can improve rice yield and reduce lodging risk.
EUROPEAN JOURNAL OF AGRONOMY
(2023)
Article
Multidisciplinary Sciences
Zhixin Ma, Yifeng Liu, Lin Chai, Guochen Jin, Yanni Sun, Shaomin Zhou, Peiyuan Yin, Siwen Wang, Yuning Zhu, Dan Zhang, Shiming Lu, Bo Zhu
Summary: Intrahepatic cholestasis of pregnancy (ICP) is a rare liver disease characterized by disordered bile acid metabolism during pregnancy. Different types of ICP show distinct bile acid metabolism profiles. Elevated levels of total bile acids and glycocholic acid are associated with preterm birth in early-onset ICP (EICP), while increased levels of total bile acids and taurocholic acid are predictive of preterm birth in late-onset ICP (LICP). This study highlights the importance of assessing bile acid metabolism in ICP patients to predict perinatal complications.
SCIENTIFIC REPORTS
(2023)
Article
Agriculture, Multidisciplinary
Ping Liao, Lei Liu, Stephen M. Bell, Jinsong Liu, Yanni Sun, Yongjun Zeng, Hongcheng Zhang, Shan Huang
Summary: Ammonia (NH3) emissions are a significant source of nitrogen (N) losses in rice paddies. Lime application and straw retention are commonly used practices to improve soil fertility in acidic soils. However, the interaction between lime and straw application on NH3 emissions from rice paddies is still unclear.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Biochemical Research Methods
Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun
Summary: Understanding the host range of plasmids is essential for studying their roles in bacterial evolution and adaptation. Existing tools for predicting plasmid hosts face challenges in sensitivity and precision. This study presents a hierarchical classification tool called HOTSPOT, which uses a state-of-the-art language model, Transformer, to accurately predict the host taxonomy of input plasmid contigs.
Article
Chemistry, Multidisciplinary
Qing Feng, Xianchao Chen, Ning Zhang, Xiaonan Li, Jingchao Zhou, Shengsheng Li, Xiaorong Zhang, Yanni Sun, Yuehui She
Summary: Bohai Oilfield has developed a bio-nano-depressurization and injection-increasing composite system solution to address the high injection pressure and insufficient injection volume in offshore oilfields. The new technology has the advantages of efficient decompression, long-term injection, and wide adaptation. However, there is a need for optimization schemes and application effect prediction methods to further promote and apply the bio-nano-composite system solution. This paper optimizes the injection volume, concentration, and speed of the bio-nano-augmentation fluid and evaluates the application effect using well testing, water absorption index, and numerical simulation methods.
Article
Biochemical Research Methods
Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun
Summary: In this study, a computational method called PhaVIP was developed for fast and accurate classification and annotation of phage virion proteins (PVPs). By encoding protein sequences into unique images and utilizing the Vision Transformer model, PhaVIP can learn both local and global features from sequence images. Experimental results demonstrated the superior performance of PhaVIP, and its output was further applied to phage taxonomy classification and phage host prediction with beneficial results.
Article
Biochemical Research Methods
Runzhou Yu, Syed Muhammad Umer Abdullah, Yanni Sun
Summary: Accessing accurate viral genomes is crucial for downstream data analysis. Although third-generation sequencing (TGS) is commonly used for virus sequencing due to its long read length, its higher per-base error rate poses a challenge. In this study, we developed HMMPolish, a novel pipeline for correcting errors in protein-coding regions of known RNA viruses. Using profile Hidden Markov Models, HMMPolish can correct errors that are ignored by other polishing tools. Extensive validation on different datasets demonstrated the superior performance of HMMPolish in error correction compared to popular polishers.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Xubo Tang, Jiayu Shang, Yongxin Ji, Yanni Sun
Summary: In this study, a plasmid detection tool called PLASMe was developed, which combines alignment and learning-based methods to effectively identify closely related and diverged plasmids. By encoding plasmid sequences as a language defined on the protein cluster-based token set, the Transformer model in PLASMe can learn the importance of proteins and their correlation. Comparative analysis showed that PLASMe achieved the highest F1-score in detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data, and exhibited more reliable performance than other tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Weidun Xie, Xingjian Chen, Zetian Zheng, Fuzhou Wang, Xiaowei Zhu, Qiuzhen Lin, Yanni Sun, Ka-Chun Wong
Summary: This study presents a method called lncRNA-Top to predict lncRNA-gene regulation relationships and constructs controlled deep-learning models. Through case studies, it is found that the predictions are accurate, and additional software is provided for target candidate annotation.
Article
Biochemical Research Methods
Jiayu Shang, Xubo Tang, Yanni Sun
Summary: Researchers have developed a tool called PhaTYP that accurately predicts the lifestyle of bacteriophages, especially for short contigs. Experimental results show that PhaTYP outperforms other existing methods and achieves more stable performance on short contigs. Additionally, the utility of PhaTYP for analyzing phage lifestyle in human neonates' gut data has been demonstrated, which helps extend our understanding of microbial communities.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Runzhou Yu, Dehan Cai, Yanni Sun
Summary: RNA viruses mutate constantly, but accurate assembly of viral genomes is crucial for studying virus evolution and understanding the relationship between genotypes and virus properties. A new tool called AccuVIR has been developed for viral genome assembly and polishing using error-prone long reads. It can distinguish sequencing errors from true variants, resulting in more accurate viral genomes compared to other tools.
Article
Biochemical Research Methods
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.
Article
Soil Science
Ping Liao, Lei Liu, Jin Chen, Yanni Sun, Shan Huang, Yongjun Zeng, Kees Jan van Groenigen
Summary: Liming materials can increase rice yield and nitrogen uptake, but decrease the efficiency of fertilizer nitrogen and promote nitrogen losses. Long-term studies on the impact of liming on nitrogen dynamics in paddy soils are necessary.
SOIL & TILLAGE RESEARCH
(2024)