Article
Medicine, Research & Experimental
Jingshan Liang, Changtao Liu, Dezhi Xu, Kang Xie, Aimin Li
Summary: This study found that the long noncoding RNA NEAT1 promotes glioma progression by stabilizing PGK1. Overexpression of NEAT1 is associated with poor overall survival in GBM patients, indicating that the NEAT1/PGK1 axis may be a candidate therapeutic target for glioma treatment.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Cell Biology
Xiangying Luo, Jianwei Ge, Tao Chen, Jinfang Liu, Ziyuan Liu, Changlong Bi, Song Lan
Summary: The study observed decreased LHX9 expression in glioma tissues, with upregulation inhibiting cell growth and interacting with p53. Downregulation of LHX9 promoted PGK1 expression, accelerating glioma development.
Article
Medicine, Research & Experimental
Longzhou Zhang, Zengjin Liu, Yang Dong, Lingchang Kong
Summary: The study elucidated that E2F2 plays a crucial role in glioma malignancy progression by transcriptionally enhancing PFKFB4 expression and activating the PI3K/AKT pathway. Inhibition of E2F2 suppressed glioma growth and metastasis, indicating its potential as a therapeutic target.
Review
Biochemistry & Molecular Biology
Monika Sakowicz-Burkiewicz, Tadeusz Pawelczyk, Marlena Zysk
Summary: Neuroblastoma is a common childhood cancer with a significant risk of death. Recent studies have shown that extracellular vesicles play a crucial role in promoting tumorigenesis by carrying metabolic enzymes that influence energy metabolism. Glycolysis has been identified as playing a primary role in energy metabolism in neuroblastoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Computer Science, Artificial Intelligence
Hamidreza Mahini, Hamidreza Navidi, Fatemeh Babaei, Seyyedeh Mobarakeh Mousavirad
Summary: This paper introduces a novel inventory sharing algorithm based on population game and evolutionary dynamics, and confirms its effectiveness through theoretical derivation and implementation in MATLAB.
SWARM AND EVOLUTIONARY COMPUTATION
(2021)
Article
Cell Biology
Chenlong Li, Yan Liu, Zhonghua Lv, Hongshan Zheng, Zhenzhe Li, Jixing Zhang, Hongbo Bao, Sibin Zhang, Jinsheng Xiong, Hua Jin, Lei Yu, Siqi Ai, Yingjie Wang, Xu Xiao, Tianqi Su, Peng Liang
Summary: This study identified the novel biomarker panel consisting of the circHECTD1/miR-296-3p/SLC10A7 axis, which is critical for glioma tumorigenesis and invasiveness, representing a potential therapeutic target for intervening in glioma progression.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Cell Biology
Zhihuang Zhao, Gang Li, Yonggang Han, Yabin Li, Zhisheng Ji, Rui Guo, Xiaohong Yu
Summary: The circular RNA ZNF609 plays a critical role in regulating glioma by affecting cell growth, invasion, apoptosis, and glycolysis. ZNF609 modulates cell survival and glycolysis by targeting the miR-378b/SLC2A1 axis in glioma cells. ZNF609 and miR-378b may serve as potential therapeutic targets in treating glioma.
Article
Multidisciplinary Sciences
Alex McAvoy, John Wakeley
Summary: This study presents a method for studying evolutionary dynamics in populations with complex and heterogeneous structures. By using easily interpretable demographic measures, the long-term outcomes of evolution can be analyzed. The method can be applied to various evolutionary update mechanisms and extends the structure-coefficient theorem to better understand the mutation-selection balance under different conditions. The study applies this method to examine the production and distribution of social goods in spatially heterogeneous populations, revealing that the outcome of selection depends on the nature of the social good, spatial topology, and mutation frequency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Elizabeth A. Tripp, Feng Fu, Scott D. Pauls
Summary: Biological systems have various time-keeping mechanisms, and understanding the evolutionary development of these mechanisms is crucial. This study introduces a new evolutionary game theoretic framework to model the behavior and evolution of systems of coupled oscillators, shedding light on the relationship between synchronization and connectivity.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Cell Biology
Xiaomin Cai, Wenjin Qiu, Mengshu Qian, Shuang Feng, Chenghao Peng, Jiale Zhang, Yi Wang, Yuhai Wang
Summary: CFI is overexpressed in glioma and is associated with poor outcomes, serving as a potential prognostic biomarker and driving malignant progression in glioma.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Chuntao Li, Bo Chen, Junxia Zhang, Jingxuan Yang, Muzi Guo, Yu Ren, Zhijun Zhou, Kar-Ming Fung, Min Li, Liyang Zhang, Zhixiong Liu
Summary: SEM1 is highly expressed in gliomas and correlated with malignant features and poor prognosis. SEM1 plays a critical role in the proliferation, apoptosis, invasion, and migration of glioma cells through regulating the PI3K-Akt pathway. The SEM1 malignant regulatory network shows significant importance for the prognosis and treatment of gliomas.
Article
Immunology
Min Chao, Nan Liu, Zhichuan Sun, Yongli Jiang, Tongtong Jiang, Meng Xv, Lintao Jia, Yanyang Tu, Liang Wang
Summary: Sox9, an upregulated transcription factor in clinical gliomas associated with poor prognosis, promotes migration and invasion of glioma cells and in vivo tumor development. It functions downstream of the TGF-beta pathway, where TGF-beta signaling prevents proteasomal degradation of Sox9 protein in glioma cells. These findings provide new insights into the interaction between TGF-beta signaling and oncogenic transcription factors, with implications for targeted therapy and prognostic assessment of gliomas.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
M. Taite, F. A. Fernandez-Alvarez, H. E. Braid, S. L. Bush, K. Bolstad, J. Drewery, S. Mills, J. M. Strugnell, M. Vecchione, R. Villanueva, J. R. Voight, A. L. Allcock
Summary: This study provides the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, and builds phylogenetic trees based on the collected data. The results suggest that some existing classifications may be consistent with the true evolutionary history of the suborder.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biology
Arne Traulsen, Nikoleta E. Glynatsi
Summary: Evolutionary game theory is an interdisciplinary subject that extends beyond biology, attracting mathematicians, social scientists, and computer scientists. The field has the potential for convergence or continued cross-fertilization between different disciplines, as insights are discovered and applied in various fields. The popularity of evolutionary game theory lies in its explanatory power and intuitive models.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Medicine, Research & Experimental
Wulong Liang, Jia Fang, Shaolong Zhou, Weihua Hu, Zhuo Yang, Zian Li, Lirui Dai, Yiran Tao, Xudong Fu, Xinjun Wang
Summary: Ubiquitin-specific peptidases (USPs) play a crucial role in glioma progression and have the potential to be therapeutic targets.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Review
Biology
Josue Manik Nava-Sedeno, Anja Voss-Boehme, Haralampos Hatzikirou, Andreas Deutsch, Fernando Peruani
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Physics, Multidisciplinary
Arnab Barua, Alireza Beygi, Haralampos Hatzikirou
Summary: The research investigates how cells regulate their sensing intensity and radius to ensure the required thermodynamic robustness of differentiated tissues, focusing on conditions where dedifferentiation at a cell level is possible while maintaining the spatial order and differentiation integrity of the tissue. By using stochastic thermodynamics formalism, it is found that the thermodynamic robustness of differentiated tissues depends on cell metabolism and sensing properties, with limits on the cell sensing radius to ensure the spatial order of differentiated tissues.
Article
Biochemical Research Methods
Andreas Deutsch, Josue Manik Nava-Sedeno, Simon Syga, Haralampos Hatzikirou
Summary: The model for studying collective tissue dynamics is called biological lattice-gas cellular automaton (BIO-LGCA), which can better simulate the characteristics of collective cell migration compared to classical cellular automata. This model allows for rules derivation from mathematical analysis and experimental data, enabling the study of collective cell behavior.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jasmine Foo, David Basanta, Russell C. Rockne, Carly Strelez, Curran Shah, Kimya Ghaffarian, Shannon M. Mumenthaler, Kelly Mitchell, Justin D. Lathia, David Frankhouser, Sergio Branciamore, Ya-Huei Kuo, Guido Marcucci, Robert Vander Velde, Andriy Marusyk, Sui Huang, Kishore Hari, Mohit Kumar Jolly, Haralampos Hatzikirou, Kamrine E. Poels, Mary E. Spilker, Blerta Shtylla, Mark Robertson-Tessi, Alexander R. A. Anderson
Summary: This article focuses on the role of plasticity and epigenetics in cancer, and discusses state-of-the-art mathematical and experimental approaches to study these aspects. It addresses important questions about the integration of non-genetic plasticity and mutation-driven somatic evolution, the measurement and modeling of the microenvironment's role, experimental study of non-genetic plasticity, suitable mathematical techniques, as well as the clinical and practical applications and implications.
Article
Multidisciplinary Sciences
Simon Syga, Diana David-Rus, Yannik Schaelte, Haralampos Hatzikirou, Andreas Deutsch
Summary: This study investigates the impact of NPIs during the first wave of COVID-19 infections in Germany by combining Bayesian parameter inference with an agent-based epidemiological model. The results show that NPIs significantly reduced random contacts in the transmission network, increased network clustering, and led to a previously unrecognized transition in the number of new cases from exponential to constant.
SCIENTIFIC REPORTS
(2021)
Article
Mathematics
Haralampos Hatzikirou, Nikos I. Kavallaris, Marta Leocata
Summary: A novel averaging method is introduced to address a specific type of random ordinary differential equations, which is then applied to evaluate intratumoral heterogeneity impact on tumor dynamics. Modeling tumors and stochastic processes, it is found that the introduction of white noise leads to monostable tumor growth, even when considering spatial cell diffusion.
Correction
Materials Science, Multidisciplinary
Haralampos Hatzikirou
JOURNAL OF THE MECHANICAL BEHAVIOR OF MATERIALS
(2022)
Editorial Material
Biology
Haralampos Hatzikirou
PHYSICS OF LIFE REVIEWS
(2022)
Article
Multidisciplinary Sciences
Konstantinos Spiliotis, Constantinos Chr Koutsoumaris, Andreas Reppas, Lito A. Papaxenopoulou, Jens Starke, Haralampos Hatzikirou
Summary: This study uses an agent-based network model to explore optimal policies against pandemics, including social distancing and vaccination strategies. The results show that prioritizing the first vaccine dose along with mild social restrictions can effectively control the pandemic.
Article
Multidisciplinary Sciences
Elisa Setten, Alessandra Castagna, Josue Manik Nava-Sedeno, Jonathan Weber, Roberta Carriero, Andreas Reppas, Valery Volk, Jessica Schmitz, Wilfried Gwinner, Haralampos Hatzikirou, Friedrich Feuerhake, Massimo Locati
Summary: This study presents a mathematical model based on an in vitro system to simulate the interaction between macrophages and fibroblasts, as well as the metabolic and immunologic signals affecting kidney fibrosis. Through transcriptome-based mathematical modeling, the study reveals the association between specific metabolic and inflammatory cues and irreversible fibrosis development. The model is validated on human transplanted kidney biopsies, demonstrating its feasibility in understanding fibrosis pathogenesis.
NATURE COMMUNICATIONS
(2022)
Review
Immunology
Pejman Shojaee, Federica Mornata, Andreas Deutsch, Massimo Locati, Haralampos Hatzikirou
Summary: This article reviews the role of mathematical modelling in elucidating the impact of tumor-associated macrophages (TAMs) in tumor progression and therapy design, aiming to identify synergies between biological and mathematical approaches to address current clinical challenges.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Lito A. Papaxenopoulou, Gang Zhao, Sahamoddin Khailaie, Konstantinos Katsoulis-Dimitriou, Ingo Schmitz, Eva Medina, Haralampos Hatzikirou, Michael Meyer-Hermann
Summary: This study developed a mathematical model to investigate chronic Staphylococcus aureus infection. The model suggested a therapeutic strategy using heat-killed S. aureus, which was tested in vivo. The results showed that the treatment protocol eliminated the infection and restored immune system function.
Article
Engineering, Chemical
Hongtao Zhang, Symeon Savvopoulos, Haralampos Hatzikirou, Isam Janajreh
Summary: Supercooling is a challenge in various fields, and the study of freezing droplets provides insights into the supercooling and crystallization processes. Experimental measurements show that the supercooling-degree increases with decreasing cooling temperature, but decreases with increasing droplet size. The addition of AgI nucleating agent significantly reduces the supercooling-degree.
Article
Physics, Multidisciplinary
Arnab Barua, Haralampos Hatzikirou
Summary: Cell decision making is the process of cells gathering information from their local microenvironment and regulating their internal states to create appropriate responses. Microenvironmental cell sensing plays a key role in this process. This article explores the implications of the Bayesian learning hypothesis for the temporal evolution of internal states and proposes a formalism to understand cell state dynamics even without exact biochemical information about cell sensing processes.
Article
Medicine, Research & Experimental
Pietro Mascheroni, Symeon Savvopoulos, Juan Carlos Lopez Alfonso, Michael Meyer-Hermann, Haralampos Hatzikirou
Summary: This study addresses the challenges in analyzing clinical data and proposes a novel method that combines Bayesian approach of mathematical modeling and machine learning to improve individualized predictions. Testing on synthetic dataset and real patient cohorts show that this method can accurately predict clinical outcomes in the context of data sparsity and limited knowledge of disease mechanisms.
COMMUNICATIONS MEDICINE
(2021)