Article
Computer Science, Information Systems
Na Zhao, Qian Liu, Hao Wang, Shenglong Yang, Pingzhou Li, Jian Wang
Summary: Identifying important nodes in complex networks is a growing research area. The gravity model has been proven effective in capturing node interactions in high-dimensional network space. However, traditional algorithms overlook computational overhead and complexities within this space. To address this, we propose a novel algorithm called Network Embedding and Gravity Model (NEGM), which transforms nodes into low-dimensional vectors and utilizes a gravity model to calculate relative importance. Experimental results demonstrate NEGM's potential in mining deep-seated information in various authentic networks.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2023)
Article
Engineering, Biomedical
V. V. S. Sasank, S. Venkateswarlu
Summary: This study focuses on segmenting brain tumors from MRI using a tumor growth model, where the integration of MSFO algorithm and LBM for parameter optimization has shown outstanding performance. Further analysis demonstrates that the proposed method exhibits high accuracy and precision across various metrics.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2022)
Review
Oncology
Constantino Carlos Reyes-Aldasoro
Summary: This paper reviews the different meanings and uses of the word "model" in the context of cancer research, particularly within the microenvironment of cancer tumors. It categorizes the different definitions of model into four groups and explores their respective meanings, advantages, and disadvantages. The paper also quantitatively analyzes the frequencies of these different meanings in scientific publications, as well as the specific components of the microenvironment and organs that are modeled. The findings show that while animal models, especially xenografts and mouse models, are the most commonly used, their usage is gradually decreasing, while mathematical models and prognostic and risk models are gaining popularity.
Article
Engineering, Marine
Junfeng Zhu, Wei Liu, Yanbin Yang
Summary: Shipping networks face port emergencies, which can impact connectivity and efficiency. Evaluating port importance is crucial for improving maritime transport efficiency. This study proposes a method integrating centrality and vulnerability indices to assess port importance in shipping networks. The results rank Singapore, Colombo, and Port Klang as the top three important ports. They serve as major hub ports for Asia, Europe, and Africa, occupying crucial positions in the network. This research provides a scientific basis for ensuring the efficiency, connectivity, and stability of shipping networks.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Mathematics, Applied
Biplab Dhar, Praveen Kumar Gupta, Ahmet Yildirim
Summary: This paper presents a mathematical model considering the tumour-immune interaction with the dosage effect and efficacy of a targeted chemotherapeutic drug. The model describes the dynamics of tumour cells, CD8 T-killer cells, CD4 T-helper cells, and the amount of the drug in the bloodstream. Qualitative analysis and numerical calculations demonstrate the suitability of the model for tumour removal over time, regardless of the initial population or tumour size. The dosage of the drug and its efficacy are identified as important factors in the treatment.
INTERNATIONAL JOURNAL OF COMPUTER MATHEMATICS
(2022)
Article
Infectious Diseases
Thomas Bjarnsholt, Marvin Whiteley, Kendra P. Rumbaugh, Philip S. Stewart, Peter O. Jensen, Niels Frimodt-Moller
Summary: Standard doses of antibiotics are not effective in treating chronic soft tissue and bone infections. Taking the infectious microenvironment into account could improve the treatment as the microenvironment can cause bacteria to become resistant to antibiotics. Susceptibility testing should be conducted in conditions that resemble the actual infectious microenvironments to guide antibiotic recommendations.
LANCET INFECTIOUS DISEASES
(2022)
Article
Biochemical Research Methods
Zhen-Hao Guo, Zhu-Hong You, De-Shuang Huang, Hai-Cheng Yi, Kai Zheng, Zhan-Heng Chen, Yan-Bin Wang
Summary: This paper converts MeSH tree structure into a relationship network and applies various graph embedding algorithms to represent terms. Evaluation through node classification and relationship prediction tasks shows that graph embedding algorithms can serve as an independent carrier for representation and enhance the ability of vectors. This approach has the potential to inspire researchers to study term representation in a network perspective.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Gabriel Isheden, Keith Humphreys
Summary: The aim of this article is to propose a framework for modeling breast cancer tumor growth based on human data. The framework includes a general likelihood function, stable disease assumptions, and mathematical models.
MATHEMATICAL BIOSCIENCES
(2022)
Article
Computer Science, Information Systems
Krzysztof Fiok, Waldemar Karwowski, Edgar Gutierrez-Franco, Mohammad Reza Davahli, Maciej Wilamowski, Tareq Ahram, Awad Al-Juaid, Jozef Zurada
Summary: Text classification methods have significantly improved in the last decade for text instances with less than 512 tokens, but handling longer texts comes with a high computational cost. Optimizing the attention mechanism can enhance classification performance for longer texts, while the "Text Guide" method improves performance by truncating the text.
Review
Cell Biology
Lucy M. Wang, Ellen Kuhl
Summary: Normal axon development relies on mechanical forces, but excessive forces can cause damage. Computational models assist in studying the role of mechanical forces in axon growth and damage. They evaluate interactions between different force sources within the cytoskeleton and optimize externally applied tension. They also investigate how forces distribute among axon components and how the tissue surrounding an axon affects its susceptibility to injury.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Mathematical & Computational Biology
Rui Zhen Tan
Summary: Adaptive therapy shows promise in delaying cancer recurrence by regulating the competition between drug-sensitive and drug-resistant cells. This study focuses on glandular tumors and reveals that invasive growth benefits more from adaptive therapy than glandular fission due to the migration of daughter cells into neighboring glands, which leads to enhanced competition.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2023)
Article
Mathematics, Interdisciplinary Applications
Eiko Fried, Claudia D. van Borkulo, Sacha Epskamp
Summary: In their recent paper, Forbes et al. evaluate the replicability of network models in two studies, identifying issues and criticizing current methods. They emphasize the importance of statistical tests, point out misinterpretations of tests by the authors, and highlight the failure to follow established recommendations in network estimation.
MULTIVARIATE BEHAVIORAL RESEARCH
(2021)
Article
Computer Science, Software Engineering
Gopi Krishnan Rajbahadur, Shaowei Wang, Gustavo A. Oliva, Yasutaka Kamei, Ahmed E. Hassan
Summary: The study found that the feature importance ranks computed by classifier specific and classifier agnostic methods are not always consistent for the same dataset and classifier. While classifier agnostic methods show strong agreement for specific data sets and classifiers, commonly used classifier specific methods yield vastly different results.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Julia Grajek, Jakob Nikolas Kather, Jan Poleszczuk
Summary: Immune checkpoint inhibitors (ICIs) are a revolutionary cancer treatment with mechanisms not fully understood. This study investigates the role of the enzyme carbonic anhydrase IX (CAIX) in ICI success using an in silico model of the tumor microenvironment. The model shows that CAIX-expressing tumors acidify their environment, reducing immune infiltration and increasing tumor burden. Additionally, suppressing CAIX improves the response to anti-PD-1 treatment, independent of PD-L1 expression.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Cell Biology
Aman Ullah, Minh Tuan Hoang-Trong, William Jonathan Lederer, Raimond L. Winslow, Mohsin Saleet Jafri
Summary: Calcium dynamics play a crucial role in arrhythmogenesis, and the study found that only a small number of ventricular myocytes need to be activated to trigger propagating action potentials associated with arrhythmias, with this number further decreasing under disease conditions.
Article
Nanoscience & Nanotechnology
Xibo Yan, Maxime Remond, Zheng Zheng, Elsa Hoibian, Christophe Soulage, Stephane Chambert, Chantal Andraud, Boudewijn Van der Sanden, Francois Ganachaud, Yann Bretonniere, Julien Bernard
ACS APPLIED MATERIALS & INTERFACES
(2018)
Article
Mathematical & Computational Biology
Angelique Stephanou, Eric Fanchon, Pasquale F. Innominato, Annabelle Ballesta
ACTA BIOTHEORETICA
(2018)
Article
Biochemical Research Methods
Olivier Hugon, Boudewijn van der Sanden, Mehdi Inglebert, Olivier Jacquin, Chaouqi Misbah, Eric Lacot
BIOMEDICAL OPTICS EXPRESS
(2019)
Article
Optics
Vadim Girardeau, Olivier Jacquin, Olivier Hugon, Bathilde Riviere, Boudewijn van der Sanden, Eric Lacot
Article
Biochemical Research Methods
Boudewijn van der Sanden, Olivier Hugon, Mehdi Inglebert, Olivier Jacquin, Eric Lacot
BIOMEDICAL OPTICS EXPRESS
(2020)
Article
Biology
Pierre Jacquet, Angelique Stephanou
Summary: Using the right terminology is crucial in accurately describing biological phenomena, as inappropriate use may lead to biases in understanding, which can have negative consequences. This article focuses on the term "reprogramming" associated with cancer cell metabolism, highlighting inconsistencies in its usage and criticizing the overemphasis on the role of mutations in metabolic adaptation. With the growing interest in metabolism and the Warburg effect in cancer research, it is important to discuss these terms and concepts in detail.
Article
Engineering, Biomedical
Boudewijn van der Sanden, Laetitia Gredy, Didier Wion, Olivier Stephan
Summary: The study used two-photon polymerization to create GelMA-collagen matrixes for monitoring pO(2matrix) in 3D cell cultures. The fluorescence intensity of ruthenium complexes showed a direct and inverse relationship with local pO(2matrix), with a significant increase observed during cancer cell activities. This approach has the potential for studying cancer cell metabolic adaptations and developing new therapeutic opportunities.
ACTA BIOMATERIALIA
(2021)
Editorial Material
Biology
A. Stephanou
PHYSICS OF LIFE REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Pierre Jacquet, Angelique Stephanou
Summary: This review explores the evolving understanding of tumor cell metabolism, particularly glycolytic and oxidative metabolism, tracing its evolution from the pioneering work of Otto Warburg. Misinterpretations of Warburg's work have hindered the understanding of tumor cell metabolism, leading to new concepts like metabolic switch and metabolic reprogramming. The metabolic signature of cancer is complex and cannot be simplified to a single factor, but is expressed at the tissue level through cells' ability to dynamically explore a vast metabolic landscape in heterogeneous environments.
Article
Biology
Pierre Jacquet, Angelique Stephanou
Summary: Cancer cells' metabolism is of great interest in cancer research. However, there are few theoretical models addressing this issue due to the complexity of the metabolism. This study proposes a simplified model focusing on the interrelation of three main energy metabolites to better understand the dynamics of the core metabolic system. The model highlights the main rules allowing cells to adapt their metabolism to changing environments and suggests that metabolic features attributed to cancer cells may be due to the deregulated over-acidic environment rather than an intrinsic abnormality of the cells.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alaa Tafech, Celine Beaujean, Yves Usson, Angelique Stephanou
Summary: There are two groups of fluorescent probes for pH measurements in biological systems. The first group exhibits a single fluorescence emission peak, while the second group exhibits a dual fluorescence emission peak. This study presents a methodology using multiple wavelengths excitation to evaluate the precision of ratiometric measurements for pH determination in biological samples.
Article
Biology
Alaa Tafech, Pierre Jacquet, Celine Beaujean, Arnold Fertin, Yves Usson, Angelique Stephanou
Summary: Tumor cells have high metabolic activity, leading to increased acidity in the surrounding environment. This acidic environment promotes tumor aggressiveness and invasiveness, which are associated with a worse prognosis. This study found that different types of brain tumor cells handle acidity differently. The ability to regulate acidity appears to depend on the specific cell type and involves various mechanisms. These findings could impact treatment, as some drugs work better in certain pH environments. Adjusting the extracellular pH may improve drug effectiveness.
Article
Computer Science, Interdisciplinary Applications
I. Manifacier, A. Chauviere, C. Verdier, G. Chagnon, I. Cheddadi, N. Glade, A. Stephanou
COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING
(2020)
Article
Mathematical & Computational Biology
Angelique Stephanou, Pascal Ballet, Gibin Powathil
MATHEMATICAL MODELLING OF NATURAL PHENOMENA
(2020)
Article
Pharmacology & Pharmacy
Angelique Stephanou, Annabelle Ballesta
PHARMACOLOGY RESEARCH & PERSPECTIVES
(2019)
Article
Peripheral Vascular Disease
Jingting Yao, Justin D. Sprick, Jinhee Jeong, Jeanie Park, David A. Reiter
Summary: This study used time-frequency spectral analysis of resting near-infrared spectroscopy (NIRS) signals to evaluate the regulation of peripheral microvascular perfusion in CKD patients. The findings suggest that CKD patients have impaired neurogenic and endothelial functions, which may be associated with increased sympathetic activity and reduced endothelial function in CKD.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Yoh Sugawara, Yusuke Mizuno, Shinya Oku, Yuri Sawada, Takahisa Goto
Summary: This study investigated the role of Protein kinase D (PKD) in aortic contraction and hemodynamics, finding that PKD1 plays a crucial role in these processes through phosphorylation of MYPT1 and actin polymerization in a calcium-independent manner.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Xuenan Zhuang, Guiqin He, Yunkao Zeng, Miaoling Li, Yongyue Su, Xuelin Chen, Yining Zhang, Yuhong Gan, Feng Wen, Xiongze Zhang
Summary: This study assessed the impact of acute, heavy alcohol consumption on the ocular microvasculature. The findings suggest that excessive alcohol consumption leads to vasoconstriction in ocular arterioles and vasodilation in capillaries, particularly evident 1-hour post-consumption.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Ayuki Nakano, Akane Morita, Shiho Arima, Tohru Nagamitsu, Tsutomu Nakahara
Summary: This study examines the preventative and therapeutic effects of inhibiting mammalian target of rapamycin complex 1 (mTORC1) on abnormal retinal blood vessels in a rat model of retinopathy of prematurity (ROP). The results suggest that mTORC1 activation in proliferating endothelial cells contributes to the appearance and progression of ROP-like retinal blood vessels. Inhibition of mTORC1 may be a promising approach for selectively targeting abnormal retinal blood vessels in ROP.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Bing Wang, Xiaohong Song, Xu Zhang, Yuan Li, Mengting Xu, Xueting Liu, Bingwei Li, Sunjing Fu, Hao Ling, Yingyu Wang, Xiaoyan Zhang, Ailing Li, Mingming Liu
Summary: This study found that glycine supplementation can improve pancreatic microcirculation in T1DM mice and reverse the production of inflammatory cytokines. Furthermore, glycine supplementation also alleviates damage to pancreatic islet and vascular tissues, suggesting a potential therapeutic effect for T1DM.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Merve Erkisa Genel, Kaan Adacan, Selin Selvi, Deniz Erol Kutucu, Ayca Uvez, Elif Ilkay Armutak, Abdurrahman Sengul, Engin Ulukaya, Ebru Gurel Gurevin
Summary: This study investigated the anti-growth/cytotoxic effect of a dinuclear Pd(II) complex on breast cancer cell lines and confirmed its anti-migration and antiangiogenic properties. The results suggest the potential of this complex in the treatment of breast cancer.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Cedric Mueller, Christoph Hauser, Justin Carrard, Konstantin Gugleta, Timo Hinrichs, Arno Schmidt-Trucksass, Henner Hanssen, Lukas Streese
Summary: This study aimed to evaluate the differences in microvascular health between normotensive individuals and patients with arterial hypertension and to assess the effects of short-term high-intensity interval training (HIIT) on microvascular health in patients with arterial hypertension. The study found that short-term HIIT can ameliorate hypertension-induced retinal microvascular abnormalities in patients with arterial hypertension.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Yuyang Hou, Wenjing Du, Qiong Wu, Xinyu Chai, Yinan Wang, Yingqian Mi, Yuan Tian, Mengyan Tang, Jun Li, Dongmei Yan
Summary: This study identified a prognostic signature consisting of four genes in bladder cancer patients and utilized angiogenesis-related genes and molecular subtypes to construct this signature, which could help predict survival outcomes. The study also evaluated immune cell infiltration and predicted chemotherapeutic responses, confirming the effectiveness of this prognostic signature.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Sean D. Mcgarry, Cynthia Adjekukor, Suchit Ahuja, Jasper Greysson-Wong, Idy Vien, Kristina D. Rinker, Sarah J. Childs
Summary: The article introduces a software tool called Vessel Metrics for analyzing developmental vascular microscopy images, which can expedite the analysis process and ensure consistency between research groups. The tool includes a segmentation algorithm that accurately quantifies different image types and has been validated in zebrafish and mouse models.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Y. P. Latul, C. Ince, N. E. van Trommel, A. van den Brandhof-van den Berg, J. P. W. R. Roovers, A. W. Kastelein
Summary: This study evaluated the real-time detection capability of handheld vital microscopy (HVM) for cervical intraepithelial neoplasia (CIN) and cervical cancer (CC). The results showed that HVM enables easy, real-time, and non-invasive assessment of cervical lesions through the detection of microvascular alterations. This method has the potential to be used for point-of-care screening, reducing unnecessary surgical interventions.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Zhifei Liu, Jieqiong Zhang, Xue Li, Qiumei Hu, Xi Chen, Linlin Luo, Liqianyu Ai, Jian Ye
Summary: The study revealed that astrocytic YAP can alleviate retinal pathological angiogenesis by inhibiting overactivation of astrocytes, thereby suppressing excessive VEGF-A production and neuroinflammation.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Robert G. Hahn
Summary: The fast-exchange interstitial fluid compartment is directly connected to the circulating blood, while the slow-exchange compartment is not.
MICROVASCULAR RESEARCH
(2024)
Review
Peripheral Vascular Disease
Nadia Hamjane, Mohcine Bennani Mechita, Naima Ghailani Nourouti, Amina Barakat
Summary: Gut microbiota dysbiosis plays a crucial role in the development of obesity-related metabolic abnormalities, including insulin resistance, type 2 diabetes, and cardiovascular diseases. Inflammation is a major mechanism linking gut microbiota dysbiosis to obesity-associated metabolic complications.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Guangzhen Zhou, Yan Gao, Yanbin Shi, Shengnan Qiu, Guimei Lin, Xinbing Ding, Wenguang Wang, Yihua Feng, Fei Wang, Jinwei Qiao
Summary: This study utilized an in vitro biomimetic experimental system to investigate the transvascular transport of nano-preparations, and found that the pressure gradient between vascular fluid pressure and interstitial fluid pressure determines the existence of the enhanced penetration and retention effect of nanopreparations.
MICROVASCULAR RESEARCH
(2024)
Article
Peripheral Vascular Disease
Kenji Chamoto, Barry C. Gibney, Willi L. Wagner, Maximilian Ackermann, Hassan A. Khalil, Steven J. Mentzer
Summary: In the study, the process of angiogenesis in adult regenerating tissue was investigated by grafting portions of the regenerating lung onto the chick chorioallantoic membrane. The results showed peri-graft angiogenesis, particularly in the cardiac lobe. Functional vascular connections were observed between the cardiac lobe and the chick chorioallantoic membrane vascular network. Elevated gene expression levels were found in the cardiac lobe compared to other lobes.
MICROVASCULAR RESEARCH
(2024)