Article
Chemistry, Medicinal
Shide Liang, Chi Zhang, Mingfu Zhu
Summary: In protein backbone refinements, calculating residue-atom interaction energy can improve the accuracy of protein loop modeling. The developed novel method shows good performance in crystal and model environments.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Computer Science, Artificial Intelligence
Xingwang Shen, Xinyu Li, Bin Zhou, Yanan Jiang, Jinsong Bao
Summary: Compared with ordinary mass-produced apparel products, custom apparel products generate more data and have complex relationships between the data at each stage of their life cycle. However, the traditional relational data storage method has drawbacks, such as high redundancy, weak correlation, and limited storage capacity. Therefore, a knowledge graph-based dynamic knowledge modeling and fusion method is proposed for the production process of custom apparel. This method includes ontology-based knowledge modeling and a bi-directional fusion approach to construct a knowledge graph, enabling dynamic knowledge fusion of the custom apparel production process. The effectiveness of the proposed method is verified using the suit production process of a custom apparel factory.
ADVANCED ENGINEERING INFORMATICS
(2023)
Article
Mathematics, Interdisciplinary Applications
Mykola Dyvak, Andriy Melnyk, Artur Rot, Marcin Hernes, Andriy Pukas
Summary: This article proposes an ontological approach as a tool for managing the processes of constructing mathematical models based on interval data and further using these models for solving applied problems. The lack of software tools for constructing this type of mathematical models complicates the application of mathematical modeling methods. However, by creating an ontological model that operates by the categories of the subject area of mathematical modeling, regardless of the modeling object, this approach allows for the generation of tools for mathematical modeling based on interval data analysis for any software development environment. The technology of creating software based on the developed ontological superstructure for mathematical modeling using interval data for different objects, as well as various forms of user interface implementation, is presented in this article.
Article
Computer Science, Artificial Intelligence
Geng Tu, Bin Liang, Dazhi Jiang, Ruifeng Xu
Summary: This article proposes a knowledge selection framework called SKSEC that incorporates sentiment emotion and context to improve emotion recognition in conversations. By eliminating and refining external knowledge, the performance of the model can be effectively enhanced.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2023)
Article
Computer Science, Artificial Intelligence
Amulya Gupta, Zhu Zhang
Summary: The study introduces three variations of vector-quantization-based topic models and demonstrates their superior performance compared to baseline models through empirical research. Furthermore, a case study highlights the powerful capabilities of these models in downstream tasks.
ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Tareq Hameduh, Michal Mokry, Andrew. D. D. Miller, Zbynek Heger, Yazan Haddad
Summary: Side-chain rotamer prediction is a critical stage in protein 3D structure building, and advanced algorithms have been developed to optimize this process. We investigated the sources of rotamer errors and found that they are associated with solvent accessibility and the tendency of certain amino acid residues to adopt non-canonical rotamers. Understanding the impact of solvent accessibility is crucial for improving side-chain prediction accuracies.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Ikuko Miyaguchi, Miwa Sato, Akiko Kashima, Hiroyuki Nakagawa, Yuichi Kokabu, Biao Ma, Shigeyuki Matsumoto, Atsushi Tokuhisa, Masateru Ohta, Mitsunori Ikeguchi
Summary: The study presents a new method, QAEmap, for evaluating and correcting protein structures generated by low-resolution electron density maps in X-ray crystallography.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Information Systems
Alisettar Huseynli, M. Ali Akcayol
Summary: Although widely used, Knowledge Graphs (KGs) often suffer from hosting false information. Previous studies have proposed methods to correct or enrich KGs by considering the KG itself or using external resources. These studies also take into account the confidence of triples in the refinement process. This study introduces a propagation approach based on triple confidence to continuously refine KGs and achieve high accuracy and precision across different datasets.
Article
Mechanics
Raj Kiran, Nhon Nguyen-Thanh, Kun Zhou
Summary: In this paper, an adaptive phase-field model is developed to study electromechanical fracture in piezoceramics. The proposed model improves the computational efficiency in cracked piezoceramics by facilitating adaptive mesh refinement. The findings are benchmarked with experiments and other numerical studies.
ENGINEERING FRACTURE MECHANICS
(2022)
Article
Mechanics
T. Coratger, G. Farag, S. Zhao, P. Boivin, P. Sagaut
Summary: The study evaluates the HRR-P LBM method for simulating complex transonic flows, solving mass and momentum conservation equations as well as the entropy equation for stability, accuracy, and computational cost. The method efficiently handles wall and open boundaries with grid refinement and includes a Vreman subgrid turbulence model for unresolved scales. The validity of the method for transonic applications is confirmed through test cases of increasing complexity.
Article
Chemistry, Medicinal
Mercedes Alfonso-Prieto, Riccardo Capelli
Summary: In this study, a protocol for molecular dynamics simulations using de novo predicted structures and machine learning algorithms for the human OR51E2 receptor has been developed. The simulations were used to refine and validate the models, and it was found that a sodium ion is required to stabilize the inactive state of the receptor near the binding site. This requirement is likely applicable to other members of the same receptor family. The protocol is proposed as a theoretical complement to the field of ORs structure determination, considering the recent publication of a CryoEM structure for the same receptor in the active state.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Physics, Applied
Tohid Shahsavarian, Yang Cao
Summary: A multiscale-multiphysics model is developed to investigate different patterns of negative discharge and discuss the challenges in finite-element-based streamer models. The model demonstrates robustness and efficiency through three different meshing techniques and achieves outstanding spatial resolution in representing streamer propagation. The extension of the model for positive streamer representation is discussed in the second part of this series, along with a thorough comparison with prior experimental results.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2022)
Article
Mechanics
Raj Kiran, Nhon Nguyen-Thanh, Hualong Yu, Kun Zhou
Summary: This paper implements an adaptive phase-field model based on polynomial splines over hierarchical T-meshes to investigate interfacial fracture in piezoelectric composites under different electromechanical loadings. The model introduces interface and crack phase-field parameters to regularize sharp interface and crack topologies, thus capturing fracture patterns including interfacial debonding, matrix cracking and their interactions. This study demonstrates the efficacy and robustness of the proposed model using various examples, accurately capturing different fracture mechanisms in composite materials.
ENGINEERING FRACTURE MECHANICS
(2023)
Article
Chemistry, Multidisciplinary
Shannon R. Petersen, Hannah Prydderch, Joshua C. Worch, Connor J. Stubbs, Zilu Wang, Jiayi Yu, Maria C. Arno, Andrey Dobrynin, Matthew L. Becker, Andrew P. Dove
Summary: This study reports the synthesis of ultra-tough, reprocessable elastomers based on linear alternating polymers. The incorporation of a rigid isohexide adjacent to urethane moieties results in elastomers with exceptional mechanical properties and optical transparency. Isosorbide-based elastomers exhibit superior tensile strength and strain recovery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Geosciences, Multidisciplinary
Zhihao Wang, Jason Goetz, Alexander Brenning
Summary: The transferability of knowledge in landslide hazard research from well-investigated areas to new study regions is becoming increasingly important. This paper compares and combines two important transfer-learning strategies, case-based reasoning (CBR) and domain adaptation (DA), for landslide susceptibility modeling. The performance evaluation shows that CBR and CBR-DA based on the proposed similarity criterion can achieve performances comparable to benchmark models trained in the target area itself.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2022)
Article
Chemistry, Medicinal
Jonathan Fine, Janez Konc, Ram Samudrala, Gaurav Chopra
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Chemistry, Multidisciplinary
Chetan Kumar Arya, Swati Yadav, Jonathan Fine, Ana Casanal, Gaurav Chopra, Gurunath Ramanathan, Kutti R. Vinothkumar, Ramaswamy Subramanian
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Editorial Material
Pharmacology & Pharmacy
William Mangione, Zackary Falls, Thomas Melendy, Gaurav Chopra, Ram Samudrala
DRUG DISCOVERY TODAY
(2020)
Article
Chemistry, Medicinal
William Mangione, Zackary Falls, Gaurav Chopra, Ram Samudrala
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biochemical Research Methods
Joao P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, Joao M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Krupal P. Jethava, Priya Prakash, Palak Manchanda, Harshit Arora, Gaurav Chopra
Summary: Targeting live cell organelles is crucial for imaging, understanding, and controlling specific biochemical processes. In this study, a modular one-step synthetic strategy was developed to create new fluorescent probes targeting lysosomal, mitochondrial, and nucleus in live cells. The differentiation in cellular localization and pH activation abilities of the probes were achieved by specific functional group changes in the central scaffold.
Article
Multidisciplinary Sciences
Kevin A. Guttenplan, Maya K. Weigel, Priya Prakash, Prageeth R. Wijewardhane, Philip Hasel, Uriel Rufen-Blanchette, Alexandra E. Munch, Jacob A. Blum, Jonathan Fine, Mikaela C. Neal, Kimberley D. Bruce, Aaron D. Gitler, Gaurav Chopra, Shane A. Liddelow, Ben A. Barres
Summary: Astrocytes respond to diseases and injuries in the central nervous system by releasing long-chain saturated fatty acids contained in lipoparticles, leading to the death of neurons and mature oligodendrocytes. The elimination of saturated lipids produced by astrocytes can mitigate astrocyte-induced toxicity, suggesting a mechanism by which astrocytes kill cells in the central nervous system.
Article
Biochemistry & Molecular Biology
Shulamit Fluss Ben-Uliel, Faten Habrat Zoabi, Moriya Slavin, Hadas Sibony-Benyamini, Nir Kalisman, Nir Qvit
Summary: Mitochondria are crucial for maintaining cellular energy metabolism and function, while Pink1 is a kinase that regulates mitochondrial function. In this study, a peptide targeting Pink1 was rationally designed and molecular probes with drug-like properties were developed to investigate Pink1's structure and function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Michael Levitt, Francesco Zonta, John P. A. Ioannidis
Summary: Different modeling approaches were used to calculate excess deaths during the COVID-19 pandemic, and large variations in the number of excess deaths were found across countries. After adjusting for age, it was found that 8 out of 33 high-income countries had no overall excess deaths, there was a deficit in child deaths, and 29.7% of the excess deaths occurred in individuals under 65 years old. Additionally, there were significant differences in excess death estimates between countries like France, Germany, Italy, and Spain.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemical Research Methods
Caitlin E. Randolph, Connor H. Beveridge, Sanjay Iyer, Stephen J. Blanksby, Scott A. McLuckey, Gaurav Chopra
Summary: Despite the challenges in analyzing the extensive structural diversity of lipids, a new charge-switching mass spectrometric approach combined with liquid chromatography has been developed to differentiate isomeric lipids. This technique successfully identifies the position of anteiso-methyl branch points in fatty acids, without the need for reference standards. This method holds promise for the structural identification of branched-chain fatty acids.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Multidisciplinary
Jonathan Fine, Prageeth R. Wijewardhane, Sheik Dawood Beer Mohideen, Katelyn Smith, Jameson R. Bothe, Yogita Krishnamachari, Alexandra Andrews, Yong Liu, Gaurav Chopra
Summary: This study introduces a machine learning-based model for predicting the chemical stability of drug products using formulation conditions and aggregation curves. The results demonstrate that the machine learning models can accurately predict degradation and potency of drug products. Additionally, there is a relationship between physical stability and chemical stability.
PHARMACEUTICAL RESEARCH
(2023)
Review
Chemistry, Analytical
Caitlin E. Randolph, Palak Manchanda, Harshit Arora, Sanjay Iyer, Pooja Saklani, Connor Beveridge, Gaurav Chopra
Summary: Lipidomics, as a standalone subdiscipline of metabolomics, has received considerable attention in the past decade. Mass spectrometry has emerged as the preferred tool for lipid identification and detection due to its sensitivity and versatility. However, traditional lipidomics methods based on bulk cell samples do not capture the cellular heterogeneity present in seemingly homogeneous cell populations. This review focuses on recent advances in mass spectrometry-based single cell lipidomics and explores the reasons behind the slow development of single-cell lipidomics techniques.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Priya Prakash, Krupal P. Jethava, Nils Korte, Pablo Izquierdo, Emilia Favuzzi, Indigo V. L. Rose, Kevin A. Guttenplan, Palak Manchanda, Sayan Dutta, Jean-Christophe Rochet, Gord Fishell, Shane A. Liddelow, David Attwell, Gaurav Chopra
Summary: Phagocytosis by glial cells plays a crucial role in regulating brain function, especially in the pathogenesis and progression of Alzheimer's disease. The newly developed Aβ(pH) analogue provides a tool to study the mechanisms of glial cell clearance of Aβ, offering potential insights into Aβ clearance at different stages of AD.
Article
Chemistry, Multidisciplinary
Jonathan Fine, Judy Kuan-Yu Liu, Armen Beck, Kawthar Z. Alzarieni, Xin Ma, Victoria M. Boulos, Hilkka Kenttamaa, Gaurav Chopra
Article
Chemistry, Multidisciplinary
Jonathan A. Fine, Anand A. Rajasekar, Krupal P. Jethava, Gaurav Chopra