Article
Biochemistry & Molecular Biology
Reinhard Schweitzer-Stenner, Bridget Milorey, Harald Schwalbe
Summary: Flory's random coil model assumes that conformational fluctuations of amino acid residues in unfolded peptides and proteins are uncorrelated. However, recent studies have shown that the conformational propensities of amino acids depend on their nearest neighbors. Through quantitative analysis of Ramachandran plots, it was found that interactions between different pairs of amino acid residues can either stabilize or destabilize specific conformations.
Review
Biochemistry & Molecular Biology
Reinhard Schweitzer-Stenner
Summary: The Flory isolated pair hypothesis is a key concept in the random coil model, used to describe the conformational dynamics of unfolded and intrinsically disordered proteins. However, evidence suggests that nearest neighbors play a significant role in the conformational sampling of amino acid residues, leading to a lower conformational entropy than expected.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Automation & Control Systems
Hongjiao Guan, Long Zhao, Xiangjun Dong, Chuan Chen
Summary: Imbalanced data classification is a challenging problem in many applications. We propose an extended natural neighbor (ENaN) concept without parameter k to improve the quality of generated examples by accurately reflecting the local distribution. ENaN-based SMOTE (ENaNSMOTE) can improve the sample distribution obtained by SMOTE and NaNSMOTE.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Computer Science, Hardware & Architecture
Martin Aumueller, Sariel Har-Peled, Sepideh Mahabadi, Rasmus Pagh, Francesco Silvestri
Summary: This paper studies the r-NN problem in similarity search in the context of individual fairness and equal opportunities. The authors propose efficient data structures for the fair NN problem and highlight the inherent unfairness of existing NN data structures through experimental evaluation.
COMMUNICATIONS OF THE ACM
(2022)
Article
Physics, Fluids & Plasmas
Sheng Yang, Jing-Bo Xu
Summary: The study investigates ground-state quantum entanglement in a one-dimensional deconfined quantum critical point using finite-size density matrix renormalization group method. It observes two distinct behaviors of two-site entanglement and extracts accurate deconfined critical point and critical exponents. Additionally, there is a suggestion that the deconfined critical point possesses rich quantum entanglement beyond two-site entanglement from the residual entanglement perspective.
Review
Biochemistry & Molecular Biology
Veymar G. Tacias-Pascacio, Daniel Castaneda-Valbuena, Roberto Morellon-Sterling, Olga Tavano, Angel Berenguer-Murcia, Gilber Vela-Gutierrez, Irfan A. Rather, Roberto Fernandez-Lafuente
Summary: The article focuses on the application of papain in the hydrolysis of proteins from fish residues, converting the residual material into interesting products with antioxidant, nutritional, and functional activities.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Multidisciplinary
Chi-Hua Lee, Yuan-Chao Lou, Andrew H-J Wang
Summary: The formation of succinimide in proteins can alter the structure and function of peptides, leading to changes in antimicrobial activity, helicity, and serum stability.
Article
Computer Science, Artificial Intelligence
Jianhua Xia, Jinbing Zhang, Yang Wang, Lixin Han, Hong Yan
Summary: Watershed clustering is a clustering method based on watershed algorithm that can automatically determine the number of clusters in a dataset. In order to handle datasets with multiple dimensions and nonlinear structures, enhancements like KNNG, shared nearest neighbor method, and Pauta Criterion have been introduced. This approach, WC-KNNG-PC, has shown successful performance in clustering various dimensional and complex datasets with heterogeneous density and diverse shapes.
PATTERN RECOGNITION
(2022)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Forestry
James A. Westfall, Barry T. Wilson
Summary: Nonresponse in national forest inventories can lead to empirical bias in sample-based estimates, especially when estimating change over time. This study found that systematic differences in nonresponse probabilities due to ownership and forest/nonforest status result in overall change estimates that are too small. Underestimation of change hinders detection of significant shifts in forest attributes and limits effective management and policy responses. Further research is needed to address this issue, including improved strategies for defining populations and alternative estimation methods that account for differential nonresponse probabilities.
Article
Chemistry, Physical
Bridget Milorey, Harald Schwalbe, Nichole O'Neill, Reinhard Schweitzer-Stenner
Summary: Protein folding is a process where the polypeptide chain moves in a potential energy funnel, with local conformations driving the folding process and aspartic acid residues exhibiting a preference for turn-forming conformations. Nearest neighbor interactions between aspartic acid residues stabilize local turn-forming structures, while interactions with phenylalanine can decrease turn-forming propensities and increase sampling of polyproline II conformations. This suggests that the structural role of aspartic residues in intrinsically disordered proteins is determined by their neighboring residues.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Computer Science, Artificial Intelligence
Chunrong Wu, Qinglan Peng, Jia Lee, Kenji Leibnitz, Yunni Xia
Summary: Hierarchical clustering method HCNN effectively groups similar data by utilizing structural similarities in the nearest neighbor graph, identifying clusters and outliers while reducing the influence of obscure boundaries. The method merges clusters more efficiently by considering equivalence relations based on maximum similarity, leading to improved clustering efficiency and accuracy.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Materials Science, Multidisciplinary
Adam Berlie, Ian Terry
Summary: The Majumder-Ghosh point is a special point in the parameter space of a one-dimensional frustrated system, where the ground state is a superposition of singlet states without magnetic order. Szenicsite, a natural mineral with isolated one-dimensional Cu2+ chains, is predicted to be close to or on the Majumder-Ghosh point. Muon spin spectroscopy experiments show that szenicsite does not exhibit magnetic order down to 100 mK and is dominated by one-dimensional magnetic excitations.
Article
Computer Science, Information Systems
Martin Aumuller, Matteo Ceccarello
Summary: This paper revisits common benchmarking approaches to nearest neighbor search and introduces the concepts of local intrinsic dimensionality, local relative contrast, and query expansion. It is found that the distribution of these dimensionality measures affects the running time performance of implementations, and different visualization concepts are introduced to provide a more detailed understanding of the inner workings of nearest neighbor search principles.
INFORMATION SYSTEMS
(2021)
Article
Chemistry, Analytical
Tieyi Lu, Li Fu, Yu Qiu, Jifeng Zhang, Zhan Chen
Summary: The interaction between antibodies and silicone oil was studied, and it was found that surfactant can reduce the adsorption of antibodies on silicone oil but may not completely prevent it. Different antibodies require different concentrations of surfactant to prevent adsorption.
ANALYTICAL CHEMISTRY
(2022)