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  • Open Access

    ARTICLE

    Extensive prediction of drug response in mutation-subtype-specific LUAD with machine learning approach

    KEGANG JIA1,#, YAWEI WANG2,#, QI CAO3,*, YOUYU WANG1,*

    Oncology Research, Vol.32, No.2, pp. 409-419, 2024, DOI:10.32604/or.2023.042863

    Abstract Background: Lung cancer is the most prevalent cancer diagnosis and the leading cause of cancer death worldwide. Therapeutic failure in lung cancer (LUAD) is heavily influenced by drug resistance. This challenge stems from the diverse cell populations within the tumor, each having unique genetic, epigenetic, and phenotypic profiles. Such variations lead to varied therapeutic responses, thereby contributing to tumor relapse and disease progression. Methods: The Genomics of Drug Sensitivity in Cancer (GDSC) database was used in this investigation to obtain the mRNA expression dataset, genomic mutation profile, and drug sensitivity information of NSCLS. Machine Learning (ML) methods, including Random Forest… More >

  • Open Access

    ARTICLE

    An Enhanced Equilibrium Optimizer for Solving Optimization Tasks

    Yuting Liu1, Hongwei Ding1,*, Zongshan Wang1,*, Gaurav Dhiman2,3,4, Zhijun Yang1, Peng Hu5

    CMC-Computers, Materials & Continua, Vol.77, No.2, pp. 2385-2406, 2023, DOI:10.32604/cmc.2023.039883

    Abstract The equilibrium optimizer (EO) represents a new, physics-inspired metaheuristic optimization approach that draws inspiration from the principles governing the control of volume-based mixing to achieve dynamic mass equilibrium. Despite its innovative foundation, the EO exhibits certain limitations, including imbalances between exploration and exploitation, the tendency to local optima, and the susceptibility to loss of population diversity. To alleviate these drawbacks, this paper introduces an improved EO that adopts three strategies: adaptive inertia weight, Cauchy mutation, and adaptive sine cosine mechanism, called SCEO. Firstly, a new update formula is conceived by incorporating an adaptive inertia weight to reach an appropriate balance… More >

  • Open Access

    ARTICLE

    A PSO Improved with Imbalanced Mutation and Task Rescheduling for Task Offloading in End-Edge-Cloud Computing

    Kaili Shao1, Hui Fu1, Ying Song2, Bo Wang3,*

    Computer Systems Science and Engineering, Vol.47, No.2, pp. 2259-2274, 2023, DOI:10.32604/csse.2023.041454

    Abstract To serve various tasks requested by various end devices with different requirements, end-edge-cloud (E2C) has attracted more and more attention from specialists in both academia and industry, by combining both benefits of edge and cloud computing. But nowadays, E2C still suffers from low service quality and resource efficiency, due to the geographical distribution of edge resources and the high dynamic of network topology and user mobility. To address these issues, this paper focuses on task offloading, which makes decisions that which resources are allocated to tasks for their processing. This paper first formulates the problem into binary non-linear programming and… More >

  • Open Access

    ARTICLE

    Enhanced Multi-Objective Grey Wolf Optimizer with Lévy Flight and Mutation Operators for Feature Selection

    Qasem Al-Tashi1,*, Tareq M Shami2, Said Jadid Abdulkadir3, Emelia Akashah Patah Akhir3, Ayed Alwadain4, Hitham Alhussain3, Alawi Alqushaibi3, Helmi MD Rais3, Amgad Muneer1, Maliazurina B. Saad1, Jia Wu1, Seyedali Mirjalili5,6,7,*

    Computer Systems Science and Engineering, Vol.47, No.2, pp. 1937-1966, 2023, DOI:10.32604/csse.2023.039788

    Abstract The process of selecting features or reducing dimensionality can be viewed as a multi-objective minimization problem in which both the number of features and error rate must be minimized. While it is a multi-objective problem, current methods tend to treat feature selection as a single-objective optimization task. This paper presents enhanced multi-objective grey wolf optimizer with Lévy flight and mutation phase (LMuMOGWO) for tackling feature selection problems. The proposed approach integrates two effective operators into the existing Multi-objective Grey Wolf optimizer (MOGWO): a Lévy flight and a mutation operator. The Lévy flight, a type of random walk with jump size… More >

  • Open Access

    ARTICLE

    Cloud Resource Integrated Prediction Model Based on Variational Modal Decomposition-Permutation Entropy and LSTM

    Xinfei Li2, Xiaolan Xie1,2,*, Yigang Tang2, Qiang Guo1,2

    Computer Systems Science and Engineering, Vol.47, No.2, pp. 2707-2724, 2023, DOI:10.32604/csse.2023.037351

    Abstract Predicting the usage of container cloud resources has always been an important and challenging problem in improving the performance of cloud resource clusters. We proposed an integrated prediction method of stacking container cloud resources based on variational modal decomposition (VMD)-Permutation entropy (PE) and long short-term memory (LSTM) neural network to solve the prediction difficulties caused by the non-stationarity and volatility of resource data. The variational modal decomposition algorithm decomposes the time series data of cloud resources to obtain intrinsic mode function and residual components, which solves the signal decomposition algorithm’s end-effect and modal confusion problems. The permutation entropy is used… More >

  • Open Access

    ARTICLE

    Enhanced Harris Hawks Optimization Integrated with Coot Bird Optimization for Solving Continuous Numerical Optimization Problems

    Hao Cui, Yanling Guo*, Yaning Xiao, Yangwei Wang*, Jian Li, Yapeng Zhang, Haoyu Zhang

    CMES-Computer Modeling in Engineering & Sciences, Vol.137, No.2, pp. 1635-1675, 2023, DOI:10.32604/cmes.2023.026019

    Abstract Harris Hawks Optimization (HHO) is a novel meta-heuristic algorithm that imitates the predation characteristics of Harris Hawk and combines Lévy flight to solve complex multidimensional problems. Nevertheless, the basic HHO algorithm still has certain limitations, including the tendency to fall into the local optima and poor convergence accuracy. Coot Bird Optimization (CBO) is another new swarm-based optimization algorithm. CBO originates from the regular and irregular motion of a bird called Coot on the water’s surface. Although the framework of CBO is slightly complicated, it has outstanding exploration potential and excellent capability to avoid falling into local optimal solutions. This paper… More > Graphic Abstract

    Enhanced Harris Hawks Optimization Integrated with Coot Bird Optimization for Solving Continuous Numerical Optimization Problems

  • Open Access

    ARTICLE

    In silico Prediction and Analysis of Potential Off-Targets and Off-Target Mutation Detection in StERF3-Gene Edited Potato Plants

    Hafiza Arooj Razzaq1, Siddra Ijaz1,*, Imran Ul Haq2, Faisal Saeed Awan1

    Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2451-2460, 2023, DOI:10.32604/phyton.2023.030501

    Abstract The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 approach. The 201 off-targets… More >

  • Open Access

    ARTICLE

    Mutations in epigenetic regulator KMT2C detected by liquid biopsy are associated with worse survival in prostate cancer patients

    SHA ZHU#, NANWEI XU#, JIAYU LIANG, FENGNIAN ZHAO, ZILIN WANG, YUCHAO NI, JINDONG DAI, JINGE ZHAO, XINGMING ZHANG, JUNRU CHEN, GUANGXI SUN, PENGFEI SHEN*, HAO ZENG*

    Oncology Research, Vol.31, No.4, pp. 605-614, 2023, DOI:10.32604/or.2023.028321

    Abstract Background: KMT2 (lysine methyltransferase) family enzymes are epigenetic regulators that activate gene transcription. KMT2C is mainly involved in enhancer-associated H3K4me1, and is also one of the top mutated genes in cancer (6.6% in pan-cancer). Currently, the clinical significance of KMT2C mutations in prostate cancer is understudied. Methods: We included 221 prostate cancer patients diagnosed between 2014 and 2021 in West China Hospital of Sichuan University with cell-free DNA-based liquid biopsy test results in this study. We investigated the association between KMT2C mutations, other mutations, and pathways. Furthermore, we evaluated the prognostic value of KMT2C mutations, measured by overall survival (OS)… More >

  • Open Access

    REVIEW

    Targeting DNA repair for cancer treatment: Lessons from PARP inhibitor trials

    DHANYA K. NAMBIAR1, DEEPALI MISHRA2, RANA P. SINGH2,3,*

    Oncology Research, Vol.31, No.4, pp. 405-421, 2023, DOI:10.32604/or.2023.028310

    Abstract Ionizing radiation is frequently used to treat solid tumors, as it causes DNA damage and kill cancer cells. However, damaged DNA is repaired involving poly-(ADP-ribose) polymerase-1 (PARP-1) causing resistance to radiation therapy. Thus, PARP-1 represents an important target in multiple cancer types, including prostate cancer. PARP is a nuclear enzyme essential for single-strand DNA breaks repair. Inhibiting PARP-1 is lethal in a wide range of cancer cells that lack the homologous recombination repair (HR) pathway. This article provides a concise and simplified overview of the development of PARP inhibitors in the laboratory and their clinical applications. We focused on the… More > Graphic Abstract

    Targeting DNA repair for cancer treatment: Lessons from PARP inhibitor trials

  • Open Access

    ARTICLE

    A novel mutation in ROR2 led to the loss of function of ROR2 and inhibited the osteogenic differentiation capability of bone marrow mesenchymal stem cells (BMSCs)

    WENQI CHEN1,#, XIAOYANG CHU2,#, YANG ZENG3,#, YOUSHENG YAN4, YIPENG WANG4, DONGLAN SUN1, DONGLIANG ZHANG5, JING ZHANG1,*, KAI YANG4,*

    BIOCELL, Vol.47, No.7, pp. 1561-1569, 2023, DOI:10.32604/biocell.2023.028851

    Abstract Background: Receptor tyrosine kinase-like orphan receptor 2 (ROR2) has a vital role in osteogenesis. However, the mechanism underlying the regulation of ROR2 in osteogenic differentiation is still poorly comprehended. A previous study by our research group showed that a novel compound heterozygous ROR2 variation accounted for the autosomal recessive Robinow syndrome (ARRS). This study attempted to explore the impact of the ROR2: c.904C>T variant specifically on the osteogenic differentiation of BMSCs. Methods: Coimmunoprecipitation (CoIP)-western blotting was carried out to identify the interaction between ROR2 and Wnt5a. Double-immunofluorescence staining was used for determining the expressions and co-localization of ROR2 and Wnt5a… More > Graphic Abstract

    A novel mutation in <i>ROR2</i> led to the loss of function of <i>ROR2</i> and inhibited the osteogenic differentiation capability of bone marrow mesenchymal stem cells (BMSCs)

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