Article
Biochemistry & Molecular Biology
Daria D. Nikolaeva, Mikhail S. Gelfand, Sofya K. Garushyants
Summary: The ribosome, responsible for protein biosynthesis, is highly conserved in structure and composition across species. However, some bacteria may lack certain ribosomal proteins, especially in organisms with significantly reduced genomes. The large subunit of the ribosome shows less conservation in protein composition compared to the small subunit.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Theory & Methods
Suha S. Al-Thanyyan, Aqil M. Azmi
Summary: Text simplification (TS) reduces text complexity to improve readability and understandability, potentially preserving original information. TS is now essential for aiding low literacy levels, non-native learners, and individuals with reading comprehension difficulties. Additionally, it enhances other NLP tasks in preprocessing stages.
ACM COMPUTING SURVEYS
(2021)
Article
Computer Science, Artificial Intelligence
Junkai Ji, Yajiao Tang, Lijia Ma, Jianqiang Li, Qiuzhen Lin, Zheng Tang, Yuki Todo
Summary: ALNM is a novel single-neuron model with plastic dendritic morphology that can generate specific dendritic structures for tasks and be substituted by LCC. The MODE algorithm can optimize both the topology and weights of ALNM to produce accurate LCCs for specific tasks. Experimental results show that MODE outperforms traditional learning methods and both ALNM and LCC achieve competitive classification performances on benchmark problems.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2021)
Article
Optics
Jie Liu, Da Song, Guohua Geng, Yu Tian, Mengna Yang, Yangyang Liu, Mingquan Zhou, Kang Li, Xin Cao
Summary: In this paper, a task-driven and learnable down-sampling method named TGPS is proposed to address the issue of excessive redundant data in the dense point clouds of Terracotta Warriors obtained by a 3D scanner. The method utilizes a point-based Transformer unit to embed features and a mapping function to extract input point features for dynamic representation of global features. The contribution of each point to the global feature is estimated using the inner product between the global feature and each point feature, and high-similarity point features are retained based on descending contribution values. A Dynamic Graph Attention Edge Convolution (DGA EConv) is proposed for local feature aggregation, combined with graph convolution operation. Networks for point cloud classification and reconstruction are presented as downstream tasks. Experimental results demonstrate that the method achieves downsampling guided by global features, with TGPS-DGA-Net achieving the best accuracy on both real-world Terracotta Warrior fragments and public datasets.
Article
Computer Science, Artificial Intelligence
Jipeng Qiang, Xindong Wu
Summary: Recent approaches in Text Simplification have focused on learning simplification rewrites from parallel corpora, but the lack of such corpora has been a challenge. This paper tackles unsupervised Text Simplification without parallel sentences, introducing a phrase-based machine translation system that outperforms some supervised baselines on benchmark datasets.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2021)
Editorial Material
Medicine, General & Internal
Bob Kocher, Anuraag Chigurupati
Summary: This Viewpoint examines the conflicting incentives that hinder the reduction of administrative spending and proposes potential changes for administrative simplification.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2021)
Article
Acoustics
Jipeng Qiang, Xinyu Lu, Yun Li, Yunhao Yuan, Xindong Wu
Summary: This study focuses on the application of lexical simplification in Chinese, manually creating the first Chinese lexical simplification benchmark dataset and proposing five different types of methods as baselines for evaluation, finally discussing the advantages and disadvantages of each method.
IEEE-ACM TRANSACTIONS ON AUDIO SPEECH AND LANGUAGE PROCESSING
(2021)
Article
Biochemical Research Methods
Sebastian Prillo, Yun Deng, Pierre Boyeau, Xingyu Li, Po-Yen Chen, Yun S. Song
Summary: Phylogenetic models are widely used in biology, but estimating model parameters is computationally expensive. To overcome this challenge, researchers have introduced CherryML, which achieves significant speedup by using cherries in trees. The speedup offered by CherryML allows for the application of more complex and biologically realistic models.
Article
Biochemistry & Molecular Biology
Jarrett Man, T. A. Harrington, Kyra Lally, Madelaine E. Bartlett
Summary: The coding sequences of developmental genes and defense genes show different characteristics in evolution. LRR-RLKs, a transmembrane receptor protein family, have faster evolution rates in the LRR domains than in the RLK domains in different subfamilies with diverse functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Long Yang, Haining Liu, Yunfei Pan, Haiqiang Li, Yanhui Lu
Summary: Plant diversity has a direct influence on the occurrence of Helicoverpa armigera on marginal host walnut trees. Diverse landscapes are associated with lower pest densities and infestation rates, while weed cover in orchards increases larval density.
Article
Multidisciplinary Sciences
Catalin M. Bunduc, Dirk Fahrenkamp, Jiri Wald, Roy Ummels, Wilbert Bitter, Edith N. G. Houben, Thomas C. Marlovits
Summary: The T7SS inner-membrane complex of Mycobacterium tuberculosis is unique in structure and essential for virulence, with the protease MycP(5) playing a crucial role in complex integrity. This study reveals a previously undescribed mechanism of protein transport and provides a potential target for drug development against this major human pathogen.
Article
Astronomy & Astrophysics
Daniel Avila, Cesar Diaz, Leonardo Patino
Summary: We use the CV prescription to study the effect of a magnetic field on the computational complexity for states in the gauge theories dual to two different gravitational models. The complexity increases with the intensity of the magnetic field in one theory, while a phenomenon called magnetic simplification is discovered in the other theory. The presence of a scalar operator with a nonvanishing vacuum expectation value in the second theory leads to the indirect lowering of complexity associated with additional degrees of freedom.
Review
Biochemistry & Molecular Biology
Andreas Hanke, Riccardo Ziraldo, Stephen D. Levene
Summary: The topological properties of DNA molecules, including supercoiling, knotting, and catenation, play key roles in biological processes such as gene expression and DNA sequence recognition. Topoisomerases are essential enzymes that manage DNA topology through strand passage, with some utilizing ATP for energy. Non-equilibrium models are used to gain insights into the behavior of topoisomerases and similar enzyme systems.
Article
Biochemistry & Molecular Biology
Valerio G. Giacobelli, Kosuke Fujishima, Martin Lepsik, Vyacheslav Tretyachenko, Tereza Kadava, Mikhail Makarov, Lucie Bednarova, Petr Novak, Klara Hlouchova
Summary: RNA-peptide/protein interactions are crucial to life and have been studied in the context of early evolution. This study focused on an RNA-binding variant of the ribosomal uL11 C-terminal domain, selected from a library of prebiotically plausible amino acid sequences. The study found that the selected variant binds RNA with a similar overall affinity, utilizing ion bridging interactions for stabilization in the absence of aromatic/basic residues. These findings provide insights into how early protein-RNA interactions may have evolved.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Mathematics
Wejdan Alkaldi, Diana Inkpen
Summary: This paper proposes a system that uses deep learning techniques to simplify texts for readers based on their skills. The system includes a reinforcement learning loop with a readability classifier to decide if further simplification is needed. The simplification models are trained on annotated data from the Newsela corpus and achieve better performance than existing techniques.
Article
Multidisciplinary Sciences
Liam M. Longo, Dusan Petrovic, Shina Caroline Lynn Kamerlin, Dan S. Tawfik
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Connie A. Tenorio, Liam M. Longo, Joseph B. Parker, Jihun Lee, Michael Blaber
Article
Multidisciplinary Sciences
Liam M. Longo, Dragana Despotovic, Orit Weil-Ktorza, Matthew J. Walker, Jagoda Jablonska, Yael Fridmann-Sirkis, Gabriele Varani, Norman Metanis, Dan S. Tawfik
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Cheolmin Kim, Dong-Kyun Ryu, Jihun Lee, Young-Il Kim, Ji-Min Seo, Yeon-Gil Kim, Jae-Hee Jeong, Minsoo Kim, Jong-In Kim, Pankyeom Kim, Jin Soo Bae, Eun Yeong Shim, Min Seob Lee, Man Su Kim, Hanmi Noh, Geun-Soo Park, Jae Sang Park, Dain Son, Yongjin An, Jeong No Lee, Ki-Sung Kwon, Joo-Yeon Lee, Hansaem Lee, Jeong-Sun Yang, Kyung-Chang Kim, Sung Soon Kim, Hye-Min Woo, Jun-Won Kim, Man-Seong Park, Kwang-Min Yu, Se-Mi Kim, Eun-Ha Kim, Su-Jin Park, Seong Tae Jeong, Chi Ho Yu, Youngjo Song, Se Hun Gu, Hanseul Oh, Bon-Sang Koo, Jung Joo Hong, Choong-Min Ryu, Wan Beom Park, Myoung-don Oh, Young Ki Choi, Soo-Young Lee
Summary: A human monoclonal antibody called CT-P59 has been shown to effectively neutralize SARS-CoV-2 and demonstrate significant therapeutic effects in animal models, making it a promising candidate for COVID-19 treatment.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Liam M. Longo, Jagoda Jablonska, Pratik Vyas, Manil Kanade, Rachel Kolodny, Nir Ben-Tal, Dan S. Tawfik
Article
Biochemistry & Molecular Biology
Michael Blaber
Summary: Symmetric protein architectures have aesthetic appeal and practical value in computational design, with the role of symmetry in hydrophobic core-packing cooperativity remaining underexplored. The threefold rotational symmetry in the beta-trefoil structure promotes cooperative core-packing interactions, ensuring stability and offering optimization solutions.
Article
Multidisciplinary Sciences
Pratik Vyas, Olena Trofimyuk, Liam M. Longo, Fanindra Kumar Deshmukh, Michal Sharon, Dan S. Tawfik
Summary: The P-loop Walker A motif is essential for enzymes binding NTPs and mediating phosphoryl transfer in DNA/RNA helicases, translocases, and recombinases. Research has shown that simple polypeptides containing P-loops can exhibit helicase-like activities, including strand separation and exchange functions. Oligomeric forms of these polypeptides mediate the activity, resembling extant P-loop recombinases like RecA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Ita Gruic-Sovulj, Liam M. Longo, Jagoda Jablonska, Dan S. Tawfik
Summary: HUP, an enzyme lineage that emerged prior to the last universal common ancestor, includes AARSs and enzymes mediating NAD, FAD, and CoA biosynthesis. It catalyzes adenylation uniquely by releasing pyrophosphate, demonstrating evolutionary plasticity and innovation.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Biographical-Item
Ecology
Liam M. Longo, Dragana Despotovic, Lianet Noda-Garcia
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Cell Biology
Jessica Weant, David D. Eveleth, Amuthakannan Subramaniam, Jennifer Jenkins-Eveleth, Michael Blaber, Ling Li, David M. Ornitz, Asaf Alimardanov, Trevor Broadt, Hui Dong, Vinay Vyas, Xiaoyi Yang, Ralph A. Bradshaw
Summary: The two human FGF1 derivatives showed promising results in stimulating rabbit corneal endothelial cell proliferation, indicating their potential for regenerating corneal endothelial deficits in humans.
Article
Biochemistry & Molecular Biology
Joseph B. Parker, Connie A. Tenorio, Michael Blaber
Summary: The beta-trefoil protein architecture exhibits rotational symmetry but asymmetric features in primary and secondary structural elements. A study found that a buried solvent, participating in bridging H-bonds between three different beta-strands, is among the most conserved symmetric structural elements in this protein family.
Article
Biochemistry & Molecular Biology
Connie A. Tenorio, Joseph B. Parker, Michael Blaber
Summary: Successful protein design requires considering folding kinetics, stability thermodynamics, and biochemical functionality. The design can be simplified by separating it into two steps: initial design of a protein scaffold and subsequent functional mutation. This approach allows for broader functional adaptation.
Article
Biochemistry & Molecular Biology
Michael Blaber
Summary: Beta-trefoil proteins exhibit approximate C-3 rotational symmetry, with conserved beta-strands and divergent turn regions. Different functional families of beta-trefoils can potentially be identified by their unique turn patterns. Such analyses provide insights into the evolution and de novo protein design of beta-trefoil proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Takeshi Hiromoto, Teikichi Ikura, Eijiro Honjo, Michael Blaber, Ryota Kuroki, Taro Tamada
Summary: In this study, protein crystals are rigidified through the introduction of disulfide cross-links, resulting in improved stability and mechanical strength. The cross-linked crystals maintain diffraction in various solutions and can withstand soaking in high concentrations of organic solvents.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Editorial Material
Biochemistry & Molecular Biology
Michael Blaber, Suman Kundu
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
