Article
Biology
Qing Yan, Deqiang Xiao, Yaosong Jia, Danni Ai, Jingfan Fan, Hong Song, Cheng Xu, Yining Wang, Jian Yang
Summary: This study introduces a multi-dimensional CFD framework that improves the accuracy and efficiency of FFR prediction. The framework estimates 0D patient-specific boundary conditions and generates 3D initial conditions to enhance the prediction. The study demonstrates a strong correlation between the predicted FFR and the invasive FFR, with high accuracy and sensitivity.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Kaja Gutowska, Piotr Formanowicz
Summary: The primary aim of this research is to propose algorithms for identifying significant reactions and subprocesses within biological system models constructed using classical Petri nets. These solutions enable two analysis methods: importance analysis for identifying critical individual reactions to the model's functionality and occurrence analysis for finding essential subprocesses. The utility of these methods has been demonstrated through analyses of an example model related to the DNA damage response mechanism. It should be noted that these proposed analyses can be applied to any biological phenomenon represented using the Petri net formalism. The presented analysis methods extend classical Petri net-based analyses, enhancing our comprehension of the investigated biological phenomena and aiding in the identification of potential molecular targets for drugs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Jinlian Ma, Dexing Kong, Fa Wu, Lingyun Bao, Jing Yuan, Yusheng Liu
Summary: In this study, a new method based on MDenseNet is proposed for automatic segmentation of nodular lesions from ultrasound images. Experimental results demonstrate that the proposed method can accurately extract multiple nodules from thyroid and breast ultrasound images, with good accuracy and reproducibility, and it shows great potential in other clinical segmentation tasks.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Jiabao Sheng, SaiKit Lam, Jiang Zhang, Yuanpeng Zhang, Jing Cai
Summary: Omics fusion is an important preprocessing approach in medical image processing that assists in various studies. This study aims to develop a fusion methodology for predicting distant metastasis in nasopharyngeal carcinoma by mitigating the disparities in omics data and utilizing a label-softening technique and a multi-kernel-based neural network.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Mathematical & Computational Biology
Yuxuan Tang, Shuling Shen, Linhe Zhu
Summary: In this paper, a SI reaction-diffusion rumor propagation model with nonlinear saturation incidence is studied. The conditions for the existence and local stability of the positive equilibrium point are obtained through stability analysis. The critical value and existence theorem of Turing bifurcation are obtained by selecting suitable variable as the control parameter. Different types of Turing pattern are divided and verified through numerical simulation.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS
(2024)
Article
Mathematical & Computational Biology
M. M. Abdeslami, L. Basri, M. El Fatini, I. Sekkak, R. Taki
Summary: In this work, a stochastic epidemic model with vaccination, healing and relapse is studied. The existence and uniqueness of the positive solution are proven. Sufficient conditions for extinction and persistence in mean of the stochastic system are established. Additionally, sufficient conditions for the existence of an ergodic stationary distribution to the model are also established, indicating the persistence of the infectious disease. Graphical illustrations of the approximate solutions of the stochastic epidemic model are presented.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS
(2024)
Article
Mathematical & Computational Biology
Yajing Li, Zhihua Liu
Summary: In this paper, a size-stage-structured cooperation model is proposed, which takes into account both size structure and stage structure, as well as obligate and facultative symbiosis in a cooperation system. The model is reduced to a threshold delay equations (TDEs) model using the method of characteristic, which is further transformed into a functional differential equations (FDEs) model. The results of the qualitative analysis of solutions of the FDEs model, including global existence and uniqueness, positivity and boundedness, stability and Hopf bifurcation of positive equilibrium, are established based on the classical theory of FDEs. Numerical simulations are conducted to support the analytical results, showing the importance of size structure and stage structure in the dynamic behavior of the model.
INTERNATIONAL JOURNAL OF BIOMATHEMATICS
(2024)
Article
Biochemical Research Methods
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biology
Shaherin Basith, Balachandran Manavalan, Gwang Lee
Summary: This study combined microsecond-scale unbiased molecular dynamics simulation with network analysis to elucidate the local and global conformational changes and allosteric communications in SOD1 systems. Structural analyses revealed significant variations in catalytic sites and stability due to unmetallated SOD1 systems and cysteine mutations. Dynamic motion analysis showed balanced atomic displacement and highly correlated motions in the Holo system.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Amirreza Khalili Golmankhaneh, Suemeyye Tunc, Agnieszka Matylda Schlichtinger, Dachel Martinez Asanza, Alireza Khalili Golmankhaneh
Summary: This article introduces important concepts such as fractal calculus and fractal analysis, the calculation of squared residuals, and the determination of Aikaike's information criterion for fitting cancer-related data. The study also investigates the double-size cancer in the fractal temporal dimension with respect to various mathematical models.
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biology
Christophe Noel, Nicla Settembre
Summary: This study investigates the vascular disorders caused by sustained exposure to high-level hand-transmitted vibrations. The researchers found that the diameter of the digital arteries, wall shear stress, and wall shear stress temporal gradient were the most relevant hemodynamic descriptors. Furthermore, vibration-induced wall shear stress decreased and was proportional to the acceleration level. Vibration also caused a decrease in wall shear stress power for the frequency band associated with the sympathetic nervous system's activity.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Xiaoyu Wang, Nitin Patil, Fuyi Li, Zhikang Wang, Haolan Zhan, Daniel Schmidt, Philip Thompson, Yuming Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Jiangning Song
Summary: In this study, we developed a machine learning framework called PmxPred for predicting polymyxin analogues with high antimicrobial activity against Gram-negative bacteria. The framework achieved good performance on multiple datasets, outperforming traditional transfer learning methods.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Jorg Schilcher, Alva Nilsson, Oliver Andlid, Anders Eklund
Summary: Atypical femur fractures (AFF) are rare fractures associated with drugs used to prevent fractures in the elderly. Current radiological identification is limited, but deep learning models can improve accuracy. Data fusion using both image and tabular data can further enhance identification.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Xin Zeng, Fan-Fang Meng, Xin Li, Kai -Yang Zhong, Bei Jiang, Yi Li
Summary: Accurately pinpointing protein-protein interaction site is crucial for understanding protein function and disease mechanisms. In this study, a groundbreaking graph-based computational model called GHGPR-PPIS was proposed, which utilized graph convolutional network and generalized PageRank techniques to predict PPIS. Experimental findings demonstrated the superiority of GHGPR-PPIS compared to other models, with excellent generalization performance and practical applicability.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Qianqian Wang, Mingyu Zhang, Aohan Li, Xiaojun Yao, Yingqing Chen
Summary: The development of PARP-1 inhibitors is crucial for the treatment of various cancers. This study investigates the structural regulation of PARP-1 by different allosteric inhibitors, revealing the basis of allosteric inhibition and providing guidance for the discovery of more innovative PARP-1 inhibitors.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Ramin Ranjbarzadeh, Payam Zarbakhsh, Annalina Caputo, Erfan Babaee Tirkolaee, Malika Bendechache
Summary: This study proposes an automatic and robust brain tumor segmentation framework using four MRI sequence images. The weight and bias values of the CNN model are adjusted using an Improved Chimp Optimization Algorithm (IChOA), and the best features are selected using a Support Vector Machine (SVM) classifier. The proposed framework achieves superior performance compared to existing frameworks on the BRATS 2018 dataset.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
Article
Biology
Biao Qu, Jialue Zhang, Taishan Kang, Jianzhong Lin, Meijin Lin, Huajun She, Qingxia Wu, Meiyun Wang, Gaofeng Zheng
Summary: This study proposes a deep unrolled neural network, pFISTA-DR, for radial MRI image reconstruction, which successfully preserves image details using a preprocessing module, learnable convolution filters, and adaptive threshold.
COMPUTERS IN BIOLOGY AND MEDICINE
(2024)
