Article
Biochemistry & Molecular Biology
Anica Dadwal, Vishal Singh, Shilpa Sharma, Amaresh Kumar Sahoo, Tulasi Satyanarayana
Summary: This study analyzed the structure and thermostability of the cellulase CBHII from Mycoeliophthora thermophila using in-silico approaches. It found that the enzyme has a high affinity for cellotetraose and exhibits tolerance to elevated temperatures.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Computer Science, Information Systems
Yan Zhang, Haoqing Xu
Summary: The novel approach of demixed sparse principal component analysis (dSPCA) proposed in this research greatly improves the interpretability of multivariate data and addresses some issues existing in traditional SPCA. By optimizing the loss function to demix dependencies between various task parameters and feature responses, and accelerating the algorithm optimization, significant progress has been made in separating neural activity into different task parameters and visualizing the demixed components.
Article
Plant Sciences
Adrien Favier, Pierre Gans, Elisabetta Boeri Erba, Luca Signor, Soumiya Sankari Muthukumar, Thomas Pfannschmidt, Robert Blanvillain, David Cobessi
Summary: PEP is a multimeric enzyme essential for proper expression of plastid genes in angiosperms, particularly for the initiation of photosynthesis gene expression and development of the photosynthetic apparatus. PAP9, an iron superoxide dismutase, exhibits unusual localization within plastids and potential association with the PEP complex. Its structural and functional features suggest unique evolutionary adaptations for protection against oxidative environments during plant evolution.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Medicinal
Jingyu Zhang, Jinxin Che, Xiaomin Luo, Mingfei Wu, Weijuan Kan, Yuheng Jin, Hanlin Wang, Ao Pang, Cong Li, Wenhai Huang, Shenxin Zeng, Weihao Zhuang, Yizhe Wu, Yongjin Xu, Yubo Zhou, Jia Li, Xiaowu Dong
Summary: In this study, dimensionality reduction analysis and model molecule validation were used to identify key structural features for improving the oral absorption of BTK-PROTACs. The newly discovered BTK-PROTACs B1 and B2 were optimized based on the results. Compound C13 with improved oral bioavailability, high BTK degradation activity, and selectivity was discovered. It showed inhibitory effects against hematologic cancer cells and attenuated the BTK-related signaling pathway. The oral administration of C13 effectively reduced BTK protein levels and suppressed tumor growth. This study led to the discovery of a new orally bioavailable BTKPROTAC for the treatment of lymphoma.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Plant Sciences
Ravi Prakash Sanyal, Vishal Prashar, Narendra Jawali, Ramanjulu Sunkar, Hari Sharan Misra, Ajay Saini
Summary: This study investigated the characteristics of two block-duplicated rice cytosolic CuZn SODs (OsCSD1, OsCSD4) and the effects of similar events in other plants. The results showed differences in gene structure, gene expression, and amino acid composition of these two OsCSDs. They were able to form heterodimers and enhance oxidative stress tolerance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Mathematics, Interdisciplinary Applications
Damjan Stojic, Dragana Radosevic
Summary: This paper successfully analyzed the morphology of astrocytes in the human brain tissue and categorized them into protoplasmic and fibrous astrocytes. By using principal component analysis, the most informative parameters were identified to differentiate astrocyte subtypes and predict their changes during aging.
FRACTAL AND FRACTIONAL
(2023)
Article
Biochemical Research Methods
Kuangnan Fang, Rui Ren, Qingzhao Zhang, Shuangge Ma
Summary: Dimension reduction techniques like PCA, PLS, and CCA are extensively used in the analysis of high-dimensional omics data. Integrative analysis, which outperforms meta-analysis and individual-data analysis, has been developed for multiple datasets with compatible designs. We developed the R package iSFun to facilitate integrative dimension reduction analysis, offering comprehensive analysis options under different models and penalties.
Article
Biochemistry & Molecular Biology
Anne Grethe Hamre, Rim Al-Sadawi, Kirsti Merete Johannesen, Bastien Bisarro, Asmund Rohr Kjendseth, Hanna-Kirsti S. Leiros, Morten Sorlie
Summary: Superoxide dismutases (SODs) are enzymes that catalyze the conversion of superoxide into oxygen and hydrogen peroxide. In this study, a SOD from the thermophilic bacteria Thermobifida fusca was cloned and characterized, showing high activity and thermostability.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Anne Grethe Hamre, Rim Al-Sadawi, Kirsti Merete Johannesen, Bastien Bisarro, Asmund Rohr Kjendseth, Hanna-Kirsti S. Leiros, Morten Sorlie
Summary: In this study, a thermophilic bacteria-derived superoxide dismutase (TfSOD) was cloned and characterized. TfSOD exhibited activity towards superoxide radicals and showed thermal stability. The crystal structure and metal cofactor of TfSOD were determined.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Munishikha Kalia, Mattia Miotto, Deborah Ness, Sarah Opie-Martin, Thomas P. Spargo, Lorenzo Di Rienzo, Tommaso Biagini, Francesco Petrizzelli, Ahmad Al Khleifat, Renata Kabiljo, Tommaso Mazza, Giancarlo Ruocco, Edoardo Milanetti, Richard J. B. Dobson, Ammar Al-Chalabi, Alfredo Iacoangeli
Summary: This study investigates the influence of SOD1 gene mutations on the clinical phenotype of ALS. By analyzing structural and dynamic differences as well as clinical data, it was found that patients carrying MBR variants generally have a longer survival time compared to those with WTL variants. The results support the hypothesis of a decoupling between mechanisms of onset and progression of SOD1 ALS.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Engineering, Environmental
Selami Demir, Elif Burcu Atci
Summary: This study used activated sludge model no. 3 (ASM3) with biological phosphorus removal processes for simulation work and performed sensitivity analysis on 44 kinetic parameters, identifying 10 parameters suitable for calibration. Results showed negligible effects of the remaining parameters.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Microbiology
Xueqian Dong, Wei Wang, Shannan Li, Hongyu Han, Peiwen Lv, Chunyu Yang
Summary: A putative gene encoding superoxide dismutase (AaSOD) was identified in a thermoacidophilic Alicyclobacillus strain, with significantly higher activity observed in a medium of manganese enrichment. The optimal temperature for AaSOD reaction was found to be 35 degrees C, and it exhibited high stability across a wide pH range from 2.0 to 10.0.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Pei Li, Wenlin Zhang, Chengjun Lu, Rui Zhang, Xuelong Li
Summary: A novel robust kernel principal component analysis method with optimal mean (RKPCA-OM) is proposed to enhance the robustness of KPCA by automatically eliminating the optimal mean. The theoretical proof guarantees the convergence of the algorithm and the obtained optimal subspaces and means. Exhaustive experimental results validate the superiority of the proposed method.
Article
Energy & Fuels
S. Platikanov, R. Tauler, J. L. Cortina, C. Valderrama
Summary: The stability of an industrial Salinity Gradient Solar Pond (SGSP) was studied using Principal Component Analysis (PCA) on three datasets, revealing three main factors influencing the stability gradient. Temperature variations, solar irradiance, and wind variables were found to impact the temperature and salinity gradients significantly. This study highlights the importance of PCA in monitoring and controlling the operation process of solar ponds.
Article
Engineering, Multidisciplinary
Ana Fernandez-Navamuel, Filipe Magalhaes, Diego Zamora-Sanchez, Angel J. Omella, David Garcia-Sanchez, David Pardo
Summary: This paper proposes a Deep Learning Enhanced Principal Component Analysis (PCA) approach for outlier detection to assess the structural condition of bridges. By adding residual connections, the outlier detection ability of the network is enhanced, allowing for the detection of lighter damages.
STRUCTURAL HEALTH MONITORING-AN INTERNATIONAL JOURNAL
(2022)
