Article
Biochemistry & Molecular Biology
Dimitrios Tsitsipatis, Ioannis Grammatikakis, Riley K. Driscoll, Xiaoling Yang, Kotb Abdelmohsen, Sophia C. Harris, Jen-Hao Yang, Allison B. Herman, Ming-Wen Chang, Rachel Munk, Jennifer L. Martindale, Krystyna Mazan-Mamczarz, Supriyo De, Ashish Lal, Myriam Gorospe
Summary: The study revealed the interaction between AUF1 and circPCNX, which can impact the production of p21 in cells and regulate cell proliferation. Eliminating the AUF1-binding region of circPCNX can abolish the increase in p21 levels and rescue proliferation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Immunology
Jialei Gong, Peng Wang, Jin-Chuan Liu, Jianlin Li, Qun-Xiong Zeng, Chen Yang, Yanfeng Li, Di Yu, Dandan Cao, Yong-Gang Duan
Summary: This study comprehensively analyzed small RNA and mRNA profiles in human chronic epididymitis (CE), identifying differentially expressed genes and miRNAs associated with CE. Functional enrichment analysis revealed the roles of these genes and miRNAs in regulating various biological processes. Moreover, a regulatory network consisting of miRNAs and mRNAs was identified as potential candidates for CE.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sung Cheon Ko, Han Min Woo
Summary: This study reports a method for bacterial RNA repression using the CRISPR-dCas13a system. By using programmable crRNAs, trans-acting and cis-acting sRNAs can be repressed, altering the regulatory mechanisms and stress-related phenotypes in bacteria. This system can be used for discovering novel sRNAs and fine-tuning bacterial RNA repression in both scientific and industrial applications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Iria Gonzalez-Vasconcellos, Maria A. Cobos-Fernandez, Michael J. Atkinson, Jose Fernandez-Piqueras, Javier Santos
Summary: Telomeric-associated long non-coding RNAs TERRA and TERC can be quantified in culture cell lines and human PBMCs using peptide nucleic acid probes with flow cytometry (RNA-Flow). This method, called RNA-Flow, allows easy and reliable quantification of lncRNAs, with broad applications in basic research and clinical diagnostics. Additionally, the staining protocol presented in this study has been proven useful for detecting and quantifying these lncRNAs on unfixed cells using confocal microscopy.
COMMUNICATIONS BIOLOGY
(2022)
Article
Cell Biology
Manyi Wei, Jiansong Huang, Guo-Wei Li, Bowen Jiang, Hong Cheng, Xiaoyan Liu, Xingyu Jiang, Xu Zhang, Li Yang, Lan Bao, Bin Wang
Summary: The study identified an axon-enriched lincRNA, ALAE, which directly interacts with KHSRP to regulate the translation of GAP43 mRNA in the axons of DRG neurons, affecting axon elongation.
Review
Biochemistry & Molecular Biology
Laura Monaghan, Dasa Longman, Javier F. Caceres
Summary: mRNA surveillance pathways play a crucial role in maintaining accurate gene expression and translation homeostasis. Studying these pathways can help us understand how cellular mRNA levels are regulated, how defective mRNAs are eliminated, and how dysregulation can contribute to human disease.
Article
Biology
Seongjin Park, Karine Prevost, Emily M. Heideman, Marie-Claude Carrier, Muhammad S. Azam, Matthew A. Reyer, Wei Liu, Eric Masse, Jingyi Fei
Summary: RNA-binding protein Hfq plays a crucial role in post-transcriptional gene regulation in bacteria, with widespread mRNA-binding activity. Short RNAs can either form a ternary complex with mRNA on Hfq or displace mRNA from Hfq in a binding face-dependent manner. Hfq binding to certain mRNAs through its distal face can recruit RNase E to promote mRNA turnover.
Article
Genetics & Heredity
Wenxiu Zhao, Xiangxu Meng, Jiahong Xu, Zijia Liu, Yangyang Hu, Bingyu Li, Jinhui Chen, Bing Cao
Summary: This study identified differentially expressed genes and microRNAs associated with xylem development in Dalbergia odorifera using RNA sequencing and small RNA sequencing. Further analysis revealed that these genes and miRNAs may play a role in the formation and development of xylem in D. odorifera.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Zarmik Moqtaderi, Joseph V. Geisberg, Kevin Struhl
Summary: There is a compensatory link between cleavage/polyadenylation in the nucleus and mRNA turnover in the cytoplasm. Same-gene 30 mRNA isoforms with different half-lives have similar steady-state mRNA levels, indicating an inverse relationship between cleavage/polyadenylation and mRNA isoform stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Sebastian Seibold, Jorg Mueller, Sebastian Allner, Marian Willner, Petr Baldrian, Michael D. Ulyshen, Roland Brandl, Claus Baessler, Jonas Hagge, Oliver Mitesser
Summary: Wood decomposition plays a crucial role in global carbon and nutrient cycling. Researchers have developed a new method using computed tomography (CT) scanning and image analysis to quantify wood decomposition. This non-destructive approach provides spatially explicit information and opens up new research possibilities.
SCIENTIFIC REPORTS
(2022)
Article
Geosciences, Multidisciplinary
Diandian Peng, Lijun Liu
Summary: Recent tomotectonic reconstructions provide new insights on past subduction processes, but some models violate key geological observations. This study investigates the 4D evolution of subducted slabs and finds that their sinking rate and lateral migration are influenced by various factors, cautioning the inference of past tectonic events based on seismic tomography.
EARTH-SCIENCE REVIEWS
(2022)
Review
Microbiology
Brice Felden, Yoann Augagneur
Summary: Bacterial gene expression is controlled by a complex system of molecules, with small regulatory RNAs (sRNAs) emerging as key players alongside transcription factors. sRNAs influence various biological processes and can act intracellularly or even in extracellular vesicles, impacting host cell interactions. Studies suggest that sRNA-mediated mechanisms are more diverse than previously thought, beyond traditional classifications.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marcelina Bednarczyk, Jessica K. Peters, Renata Kasprzyk, Jagoda Starek, Marcin Warminski, Tomasz Spiewla, Jeffrey S. Mugridge, John D. Gross, Jacek Jemielity, Joanna Kowalska
Summary: Several compounds were identified as inhibitors of VACV D9 decapping enzyme, with m(7)GpppCH(2)p as the most potent nucleotide inhibitor and selicidib and CP-100356 as the most potent drug-like compounds. The identified compounds efficiently inhibited D9 catalyzed decapping of 26 nt RNA substrates but showed no activity towards VACV D10 or human decapping enzyme, Dcp1/2.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lisa Kruckemeier, Zhifa Liu, Thomas Kirchartz, Uwe Rau
Summary: The extraction of photogenerated charge carriers and the generation of a photovoltage are crucial in solar cells. In this study, a new method was developed to analyze transient photovoltage measurements by comparing rise and decay times of photovoltage. Through this analysis, the rates of carrier recombination and extraction as a function of bias voltage were determined, providing insights into efficiency losses in perovskite solar cells.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Jia-Xin Chen, Shu He, Yan-Jun Wang, Xiong-Kang Gan, Ya-Qing Zhou, Lei Hua, Can Hou, Sheng Zhang, Han-Xiao Zhou, En-Zhi Jia
Summary: This study aimed to investigate mRNA expression profiling in CAD patients and identified BTRC and UBE2D2 genes as potential diagnostic biomarkers with significant diagnostic values. The study highlights the potential of these genes as novel diagnostic biomarkers and therapeutic targets for CAD.
Article
Mathematics, Applied
Xiaomeng Wang, Yijun Ran, Tao Jia
Article
Mathematics, Applied
Yijun Ran, Xiaomin Deng, Xiaomeng Wang, Tao Jia
Article
Mathematics, Interdisciplinary Applications
Lan Hou, Tao Jia, Xiangbing Wang, Tongkui Yu
Article
Physics, Multidisciplinary
Ling Zhan, Tao Jia
Summary: This article highlights the importance of Heterogeneous Information Network (HIN) embedding and proposes a new embedding method called CoarSAS2hvec. The method incorporates self-avoiding short sequence sampling and an optimized loss function to improve the performance of HIN structure embedding. CoarSAS2hvec outperforms other methods in node classification and community detection tasks, and effectively captures richer information compared to existing methods.
Article
Mathematics, Applied
Radoslaw Michalski, Damian Serwata, Mateusz Nurek, Boleslaw K. Szymanski, Przemyslaw Kazienko, Tao Jia
Summary: This research develops a temporal network epistemology model to simulate the learning process in dynamic networks. The results demonstrate that the temporal dynamics of the network significantly influence the outcome and flow of the learning process, leading to different consensus dynamics and previously unobserved phenomena. The approach and experimental results provide insights into how human communities collectively solve complex problems and spread beliefs across societies.
Article
Computer Science, Artificial Intelligence
Yansong Wang, Xiaomeng Wang, Yijun Ran, Radoslaw Michalski, Tao Jia
Summary: One important task in the study of information cascade is to predict the future recipients of a message given its past spreading trajectory. The proposed method CasSeqGCN combines the network structure and temporal feature to accurately predict the future cascade size. The experiment demonstrates that the improved prediction comes from the design of the input and the GCN layer.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Psychiatry
Yunsong Luo, Wenyu Chen, Jiang Qiu, Tao Jia
Summary: This study used a large-scale resting-state fMRI dataset from China to develop a stacking machine learning model that estimates the brain aging of MDD patients. The results showed that MDD patients have a higher brain-predicted age difference compared to healthy controls, and antidepressant users in the MDD subgroup have an even greater age difference. This study confirms the presence of accelerated brain aging in MDD patients and verifies existing findings using functional brain connectivity.
TRANSLATIONAL PSYCHIATRY
(2022)
Article
Automation & Control Systems
Tianyang Cai, Tao Jia, Sridhar Adepu, Yuqi Li, Zheng Yang
Summary: With the widespread innovation of IoT, SDN, and cloud computing, cyber-physical systems (CPSs) have been developed to facilitate daily life and economy. However, the shutdown of critical CPSs and the increasing threat of DDoS attacks pose serious consequences. This article presents an adaptive DDoS attack mitigation scheme called ADAM, which combines information entropy and unsupervised anomaly detection methods to accurately detect and mitigate DDoS attacks. Experimental results show that ADAM has a high accuracy in mitigating DDoS attacks and reduces the false-positive rate compared to similar work.
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS
(2023)
Article
Information Science & Library Science
Yang Li, Tao Jia
Summary: The purpose of this study is to propose an improved credit allocation method that enhances the distinguishability of the leading author and the robustness to malicious manipulations. By using a modified Sigmoid function and excluding the target paper in calculating co-citation contributions, the proposed method (NCCAS) is tested on Nobel Prize-winning papers and a large dataset of computer science articles. The findings indicate that NCCAS provides the most accurate prediction of Nobel laureates, ensures the distinguishability of the leading author, and exhibits robustness against malicious manipulations.
JOURNAL OF DATA AND INFORMATION SCIENCE
(2023)
Article
Mathematics, Interdisciplinary Applications
Yijun Ran, Si-Yuan Liu, Xiaoyao Yu, Ke-Ke Shang, Tao Jia
Summary: This article discusses the importance of link prediction in evolving systems and proposes a new method to address the temporal link prediction problem with new nodes.
JOURNAL OF PHYSICS-COMPLEXITY
(2022)
Article
Information Science & Library Science
Linlin Liu, Jianfei Yu, Junming Huang, Feng Xia, Tao Jia
Summary: A recent study shows that research in China is more dominated by large teams, particularly in the field of natural science. Despite the global trend of more papers being written by big teams, China has seen a significant drop in output from small teams. This imbalance highlights the need to strike a balance between small and big teams for fostering innovation and originality.
QUANTITATIVE SCIENCE STUDIES
(2021)
Article
Information Science & Library Science
Wenyu Chen, Zhangqian Zhu, Tao Jia
Summary: The study found that a university's position in different rankings is not consistent, but the relative positions for a particular set of universities are more similar. A university's best rank strongly correlates with its consensus rank, usually 38% higher on average. This means the best rank reflects the collective opinion of experts, can be trusted, but with caution.
QUANTITATIVE SCIENCE STUDIES
(2021)
Article
Physics, Fluids & Plasmas
Zhen Su, Chao Gao, Jiming Liu, Tao Jia, Zhen Wang, Juergen Kurths
Proceedings Paper
Computer Science, Artificial Intelligence
Yixin Tan, Xiaomeng Wang, Tao Jia
SEMANTIC WEB - ISWC 2020, PT I
(2020)
Article
Psychology, Biological
Tao Jia, Dashun Wang, Boleslaw K. Szymanski
NATURE HUMAN BEHAVIOUR
(2017)
