Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction by Andreas Denger, Volkhard Helms

“…In this study, we leverage recent advances in deep learning, such as amino acid sequence embeddings with protein language models (pLMs), highly accurate 3D structure predictions with AlphaFold 2, and structure-encoding 3Di sequences from FoldSeek, for predicting substrates of membrane transporters. …”
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Public antibodies: convergent signatures in human humoral immunity against pathogens by Vishal N. Rao, Camila H. Coelho

“…In this Minireview, we examine and compare public antibody identification methods, including the identification criteria used based on V(D)J gene usage and similarity in the complementarity-determining region three sequences, and explore the molecular features of public antibodies elicited against common pathogens, including viruses, protozoa, and bacteria. …”
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Neutral markers reveal complex population structure across the range of a widespread songbird by Aaron Veale, Matthew W. Reudink, Theresa M. Burg

“…Abstract Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. …”
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Geological study of sediments from the Negro and Solimões rivers by Patricia Ramos Carvalho, Casimiro Munita, Emílio Soares, Ricieri Tarabossi

“…   The Amazon is the largest and most complex ecosystem on the planet, and its entire evolutionary history was influenced by the dynamics of the Amazon River System. …”
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Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery by Vaishali P. Waman, Sundeep Chaitanya Vedithi, Sherine E. Thomas, Bridget P. Bannerman, Asma Munir, Marcin J. Skwark, Sony Malhotra, Tom L. Blundell

“…We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. …”
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CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence by Zongguo Wang, Ziyi Chen, Yang Yuan, Yangang Wang

“…The software consists of three key modules, an evolutionary optimization algorithm (EOA) that searches for all possible crystal structure configurations, density functional theory (DFT) that provides the accurate energy values for these structures, and a deep neural network (DNN) that learns the relationship between crystal structures and their corresponding energies. …”
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An adaptive differential evolution algorithm based on adaptive evolution strategy and diversity enhancement by Shengke Lin, Huarong Xu

“…Second, we introduce a novel individual ranking factor that divides the generation of the scaling factor into three distinct phases, thereby optimizing balanced exploration and exploitation throughout the evolutionary process. …”
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Dimorphic Sessile Apterae of the Aphid Neothoracaphis glaucae (Hemiptera) on the Evergreen Oak Quercus glauca by Shigeyuki Aoki, Utako Kurosu, Keigo Uematsu, Takema Fukatsu, Mayako Kutsukake

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Comparative analysis of the global innovation index combining the graph visualization and topological data analysis approaches by Rolando Ismael Yépez, Maricela Fernanda Ormaza

“… This study analyzes the Global Innovation Index (GII) of the 100 most innovative countries in 2022 and 2023, applying the Fruchterman-Reingold algorithm to obtain a spatial distribution of the data and utilizing persistent homology with Vietoris-Rips complexes at three scales (ε = 0.3, 1.0, and 1.5) to form connected components or structures. …”
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Application of Hybrid MOPSO Algorithm to Optimal Reactive Power Dispatch Problem Considering Voltage Stability by Yujiao Zeng, Yanguang Sun

“…This problem is formulated as a challenging nonlinear constrained multiobjective optimization problem considering three objectives, that is, power losses minimization, voltage profile improvement, and voltage stability enhancement simultaneously. …”
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Empirical study on the evolution of telecom fraud risks driven by artificial intelligence generated content by ZHOU Shengli, XU Rui, CHEN Tinggui, WANG Shaojie, WANG Zhenbo

“…The evolution patterns of telecom fraud risks driven by AIGC were categorized into three types: the long-chain type evolution pattern systematically identifies complete risk events and their inter-event evolutionary trajectories within cases, while investigation of the star-shaped and composite type evolution patterns enable recognition of divergent risk behavioral patterns and localization of core risk event nodes across homogeneous case clusters, there by establishing a theoretical foundation for developing scientifically rational governance strategies in telecom fraud countermeasures.…”
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Divergence of the bZIP Gene Family in Strawberry, Peach, and Apple Suggests Multiple Modes of Gene Evolution after Duplication by Xiao-Long Wang, Yan Zhong, Zong-Ming Cheng, Jin-Song Xiong

“…The comparative analysis of bZIP genes in three species provides information on the evolutionary fate of bZIP genes in apple and peach after they diverged from strawberry.…”
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Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: A first report from South India. by Yamuna Devi Bakthavatchalam, Priyanka Babu, Elakkiya Munusamy, Hariharan Triplicane Dwarakanathan, Priscilla Rupali, Marcus Zervos, Peter John Victor, Balaji Veeraraghavan

“…Significant pbp2 upregulation was noted in three TR-MRSA strains, which had teicoplanin MICs of 16 or 32 μg/ml, whilst significant pbp4 downregulation was not noted in these strains. …”
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Correlation Between Individual Body Condition and Seasonal Activity in Buresch’s Crested Newt, <i>Triturus ivanbureschi</i> by Simeon Lukanov, Irena Atanasova

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Classification, Functions, Development and Outlook of Photoanode Block Layer for Dye-Sensitized Solar Cells by Youqing Wang, Wenxuan Wu, Peiling Ren

“…We categorize block layer architectures into three distinct configurations: single layer, doped layer, and multilayer structures. …”
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Global agricultural trade network characteristics and its influencing factors by Junwen Cao, Qingya Lei

“…Abstract This study investigates the evolutionary process of the global agricultural trade network and identifies key influencing factors. …”
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Chromosomal periodicity and positional networks of genes in Escherichia coli by Anthony Mathelier, Alessandra Carbone

“…This finding generates new questions on evolutionary pressures imposed on the chromosome. Our methodological approach is based on single genome analysis. …”
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Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses. by Zhonglou Sun, Tao Pan, Chaochao Hu, Lu Sun, Hengwu Ding, Hui Wang, Chenling Zhang, Hong Jin, Qing Chang, Xianzhao Kan, Baowei Zhang

“…Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. …”
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Extending Long‐Term Avian Studies Alters Temporal and Climate‐Driven Trend Conclusions by Irene Zanandrea, Juan Moreno, Alejandro Cantarero

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Using principal component analysis to identify the component affecting skull weight of Japanese Quail by israa Abd Alsada

“…The analysis extracted three principal components for both sexes, explaining 52.76% of the variance in males and 56.52% in females. …”
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