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Multiple roles of p53 in cancer development: Regulation of tumor microenvironment, m⁶A modification and diverse cell death mechanisms

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Journal of Advanced Research 2024年

作者： Wang, Xiangyu Yang, Jianhua Yang, Wanting Sheng, Haiyang Jia, Buyun Cheng, Peng Xu, Shanshan Hong, Xinhui Jiang, Chuanwei Yang, Yinfeng Wu, Ziyin Wang, Jinghui School of Integrated Chinese and Western Medicine Anhui University of Chinese Medicine Anhui Hefei China School of Medical Informatics Engineering Anhui University of Chinese Medicine Anhui Hefei China Global Biometrics and Data Sciences Bristol Myers Squibb New York City United States The First Affiliated Hospital Anhui University of Traditional Chinese Medicine Anhui Hefei China State Key Laboratory on Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture Jiangsu Kanion Pharmaceutical Co. Ltd Jiangsu Lianyungang China

Background: The protein p53, encoded by the most frequently mutated gene TP53 in human cancers, has diverse functions in tumor suppression. As a best known transcription factor, p53 can regulate various fundamental cellular responses, ranging from the cell-cycle arrest, DNA repair, senescence to the programmed cell death (PCD), which includes autophagy, apoptosis, ferroptosis, cuproptosis, pyroptosis and disulfidoptosis. Accumulating evidence has indicated that the tumor microenvironment (TME), N⁶-methyladenosine (m⁶A) modification and diverse PCD are important for the progression, proliferation and metastases of cancers. Aim of review: This paper aims to systematically and comprehensively summarize the multiple roles of p53 in the development of cancers from the regulation of TME, m⁶A Modification and diverse PCD. Key scientific concepts of review: TME, a crucial local homeostasis environment, influences every step of tumorigenesis and metastasis. m⁶A, the most prevalent and abundant endogenous modification in eukaryotic RNAs, plays an essential role in various biological processes, containing the progression of cancers. Additionally, PCD is an evolutionarily conserved mechanism of cell suicide and a common process in living organisms. Some forms of PCD contribute to the occurrence and development of cancer. However, the complex roles of p53 within the TME, m⁶A modification and diverse PCD mechanisms are still not completely understood. Presently, the function roles of p53 including the wild-type and mutant p53 in different context are summarized. Additionally, the interaction between the cancer immunity, cancer cell death and RNA m⁶A methylation and the p53 regulation during the development and progress of cancers were discussed. Moreover, the key molecular mechanisms by which p53 participates in the regulation of TME, m⁶A and diverse PCD are also explored. All the findings will facilitat

关键词： M6A p53 Programmed cell death Tumor microenvironment Tumor suppression

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Robust nonlinear extended prediction self-adaptive control (NEPSAC) of continuous bioreactors

Robust nonlinear extended prediction self-adaptive control (...

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2012 20th Mediterranean Conference on control and Automation, MED 2012

作者： Dutta, Abhishek De Keyser, Robain Nopens, Ingmar Department of Electrical Energy Systems and Automation Ghent University 9000 Gent Belgium Department of Applied Mathematics Biometrics and Process Control Ghent University 9000 Gent Belgium

ISBN: (纸本)9781467325318

A nonlinear predictive control strategy (NEPSAC) is formulated for a continuous bioreactor characterized by severe non-linearity and parameter time-variance, with the control objective being to regulate the fermenter operation near the optimum productivity. Robustness towards the unpredictable time-variance, which comes from cell-mass growth, is guaranteed by disturbance filter design. The dilution rate and feed substrate concentration are considered as manipulated inputs, while the state variables are the biomass, substrate and product concentrations. Results obtained with robust NEPSAC are presented and compared with those obtained with other model predictive control and various linearization based strategies. © 2012 IEEE.

关键词： Model predictive control

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Some comments to the fuzzy version of the Arrow-Sen theorem

Some comments to the fuzzy version of the Arrow-Sen theorem

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14th International Conference on Information processing and Management of Uncertainty in Knowledge-Based Systems, IPMU 2012

作者： Martinetti, Davide Montes, Susana Díaz, Susana De Baets, Bernard Dept. Statistics and O.R. University of Oviedo Oviedo Spain Dept. Appl. Math. Biometrics and Process Control University of Ghent Ghent Belgium

ISBN: (纸本)9783642317231

The Arrow-Sen Theorem is one of the most important results concerning rationality of choice functions. It states that under suitable hypothesis, several definitions of rationality given by different authors can be considered equivalent. Following the same spirit, other authors have proved that further definitions can also be considered equivalent to rationality. In this work we consider the fuzzy version of this problem, using the most general definition of fuzzy choice function possible. Older results are recalled and in many cases improved and also new theorems are proposed. © 2012 Springer-Verlag.

关键词： Knowledge based systems

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On some properties of the negative transitivity obtained from transitivity 1

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9th International Conference on Modeling Decisions for Artificial Intelligence, MDAI 2012

作者： Díaz, Susana Montes, Susana De Baets, Bernard Dept. of Statistics and O.R. University of Oviedo Calvo Sotelo s/n 33007 Oviedo Spain Dept. of Appl. Math. Biometrics and Process Control Ghent University Coupure Links 653 B-9000 Gent Belgium

ISBN: (数字)9783642346200

ISBN: (纸本)9783642346194

For crisp relations the transitivity of a relation and the negative transitivity of its dual are equivalent conditions. Particularly, a crisp complete large preference relation is transitive if and only if its associated strict preference relation is negatively transitive. In this contribution we focus on one of those implications for fuzzy relations. Recall that in the context of fuzzy relations there are multiple ways of obtaining the strict preference relation from the large preference relation, and also multiple ways for defining transitivity. We analyze the type of negative transitivity we can assure for the strict preference relation, departing from a large preference relation that satisfies almost any kind of transitivity. We recall the general expression we obtained and study some interesting properties. Finally, we pay special attention to the particular case of the minimum t-norm both in the role of generator and in the role of conjunctor defining the transitivity of the original reflexive relation. © 2012 Springer-Verlag.

关键词： Knowledge based systems

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Robust nonlinear extended prediction self-adaptive control (NEPSAC) of continuous bioreactors

Robust nonlinear extended prediction self-adaptive control (...

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Mediterranean Conference on control and Automation (MED)

作者： Abhishek Dutta Robain De Keyser Ingmar Nopens Department of Applied Mathematics Biometrics and Process Control Ghent University Gent Belgium Department of Electrical Energy Systems and Automation Ghent University Gent Belgium Universiteit Gent Gent BE

关键词： Computational modeling

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Monotonicity of fuzzy rule bases: On differences between graded and non-graded approaches

Monotonicity of fuzzy rule bases: On differences between gra...

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Joint 7th Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2011 and 17th French Days on Fuzzy Logic and Applications, LFA 2011

作者： Daňková, Martina Ŝteňpnicňka, Martin De Baets, Bernard Institute for Research and Applications of Fuzzy Modeling University of Ostrava Ostrava Czech Republic Department of Applied Mathematics Biometrics and Process Control Ghent University Gent Belgium

ISBN: (纸本)9789078677000

This contribution provides an exhaustive explanation of the graded approach to the monotonicity property (of a fuzzy relation) and its non-graded version. Our framework is algebraic. We present a wide variety of examples to support our claims relating to the well defined notion and suitability for fuzzy rule base applications and moreover, to improve the readability of the related mathematical formulae. © 2011. The authors-Published by Atlantis Press.

关键词： Fuzzy rules

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Semantic systems biology: Enabling integrative biology via semantic web technologies 11

Semantic systems biology: Enabling integrative biology via s...

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Proceedings of the International Conference on Web Intelligence, Mining and Semantics

作者： Antezana, Erick Blondé, Ward Venkatesan, Aravind De Baets, Bernard Mironov, Vladimir Kuiper, Martin Department of Biology Høgskoleringen 5 7491 Trondheim Norway Ghent University Department of Applied Mathematics Biometrics and Process Control Coupure links 653 9000 Ghent Belgium

ISBN: (纸本)9781450301480

The vast amounts of knowledge in the biomedical domain have paved the way for a new paradigm in biological research called Systems Biology, essentially an approach that relies on the integration of all available knowledge of a biological system in a single model. This approach promotes a comprehensive understanding of biological systems, driven by data integration and mathematical modelling. However, the sheer volume, variation and complexity of the current biological data pose a number of hurdles in knowledge management that need to be overcome. The Semantic Web offers various solutions to these challenges. With our initiative, named Semantic Systems Biology (SSB), we augment the systems biology approach with semantic web technologies to enable smooth data integration, rigorous knowledge representation, efficient querying, and hypothesis generation. Here we present an overview of the projects associated with the SSB initiative. Access to our resources developed within the SSB frame is provided on our website: http://***. © 2011 ACM.

关键词： Biological systems

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On the role of acyclicity in the study of rationality of fuzzy choice functions

On the role of acyclicity in the study of rationality of fuz...

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2011 11th International Conference on Intelligent Systems Design and Applications, ISDA'11

作者： Martinetti, Davide De Baets, Bernard Diaz, Susana Montes, Susana Dept. Statistics and O. R. University of Oviedo Oviedo Spain Dept. Appl. Math. Biometrics and Process Control University of Ghent Ghent Belgium

ISBN: (纸本)9781457716751

Fuzzy choice functions obtained from preference relations have been recently used to develop automated negotiation systems. This contribution contains a theoretical study of coherence conditions in the process of creating a fuzzy choice function from a preference relation. In particular, the role of the acyclicity property of fuzzy preference relations is studied in the framework of rationality of fuzzy choice functions. Two different definitions of fuzzy acyclicity are compared. The two classical ways of constructing a fuzzy choice function from a given fuzzy preference relation are considered and properties such as acyclicity and completeness are proved to be sufficient conditions to ensure that the constructed function is a rational choice function. Special attention has been paid to the choice of the t-norm too. The results obtained are also compared to the classical results on rationality in the theory of crisp choice functions. © 2011 IEEE.

关键词： Rational functions

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Towards the Full Lyapunov Spectrum of Elementary Cellular Automata

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AIP Conference Proceedings 2011年第1期1389卷 981-986页

作者： J. M. Baetens B. De Baets KERMIT Department of Applied Mathematics Biometrics and Process Control Ghent University Coupure links 653 Gent Belgium

Throughout the decades following the postulation of cellular automata (CA) halfway the previous century, numerous studies have been conducted to gain insight into the dynamical properties of these uttermost discrete dynamical systems. Mostly, these studies were motivated by the fact that CA turned out capable of evolving intriguing spatio‐temporal dynamics notwithstanding their intrinsically simple nature. Though many measures have been proposed for gaining insight into CA dynamics, the use of Lyapunov exponents that measure how their phase space trajectories evolve with respect to each other has proved particularly fruitful. Yet, to this day, in all studies relying on this measure the conclusions are drawn upon the so‐called maximum Lyapunov exponent (MLE), whereas the determination of the full Lyapunov spectrum has been neglected despite its demonstrated usefulness in elucidating the dynamics of continuous dynamical systems and maps. In this preliminary study, we outline how the Lyapunov spectrum of so‐called elementary CA can be obtained, we show the validity of the proposed computational methodology and, finally, we present the full spectra of some renowned elementary CA.

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The RDF foundry: Call for an initiative to build enhanced RDF resources for biological data integration 11

The RDF foundry: Call for an initiative to build enhanced RD...

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Proceedings of the International Conference on Web Intelligence, Mining and Semantics

作者： Venkatesan, Aravind Blondé, Ward Antezana, Erick Skillingstad, Mats Marshall, M. Scott De Baets, Bernard Mironov, Vladimir Kuiper, Martin Department of Biology Høgskoleringen 5 7491 Trondheim Norway Ghent University Department of Applied Mathematics Biometrics and Process Control Coupure links 653 9000 Ghent Belgium Informatics Institute University of Amsterdam Netherlands

ISBN: (纸本)9781450301480

Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concepts within the biomedical domain. The ontologies within the OBO Foundry are usually represented in the OBO ontology language. While being human-readable, this language lacks the computational rigour required for the Semantic Web (SW). Consequently, the RDF and OWL languages, both fundamental components of the SW technology stack, are being increasingly adopted by the biomedical community to exchange biological knowledge in a computer intelligible form. Some of the OBO- formatted ontologies have been made available in OWL, thus signalling a move towards the SW. OWL provides support for automated reasoning, which is its raison d'être. Unfortunately, automated reasoning on the massive volumes of data that are typical of the biomedical domain is riddled with performance limitations. Due to consistent support for the SPARQL specification in triple store implementations, as well as the ability to simulate some types of reasoning with pre-computed closures, RDF has evolved into a language of choice for knowledge exchange within the framework of the SW. Here, we discuss the need to establish a foundry charged with the task of harmonizing biomedical RDF resources, acting along the same lines as the OBO Foundry. To substantiate the need for an RDF Foundry, we provide the outcome of a small survey we have conducted to highlight the domain coverage, redundancies, and comprehensiveness of results obtained from a few representative distributed resources available today. © 2011 ACM.

关键词： Data integration

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