Review
Biochemical Research Methods
Stephan Struckmann, Mathias Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Moeller
Summary: Researchers are interested in finding new applications for known compounds by analyzing transcriptomics of biological samples from disease contexts. They found that matching a drug effect to the effect of the same drug at another concentration or in another cell line is a well-defined, reproducible challenge. By combining different similarity scores and heuristics, they were able to reduce the number of genes in the model and improve prediction accuracy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dongsheng Cao, Tingjun Hou
Summary: Research has shown that machine learning-based scoring functions outperform classical scoring functions in predicting protein-ligand binding affinity. Gradient boosting decision tree and random forest achieved the best predictions in most cases. The superiority of machine learning-based scoring functions is fully guaranteed when the training set contains sufficient similar targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Public, Environmental & Occupational Health
Yu-Fei Hua, Jin Lu, Bing Bai, Han-Qing Zhao
Summary: This paper explores the impact of joining China's centralized drug procurement on the profitability of medical enterprises using the difference-in-difference model. When centralized procurement does not generate sufficient cost savings, the resulting price competition can lead to a decline in enterprise profits. In the short term, the negative impact of China's drug centralized procurement policy on enterprise net profits is not evident in the year of winning the bid. However, after the government starts officially purchasing from pharmaceutical enterprises, the negative impact gradually emerges. Therefore, generic drug manufacturers should increase R&D investment and develop their own original drug products as soon as possible to enhance core competitiveness.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Computer Science, Information Systems
Jaleal Sanjak, Jessica Binder, Arjun Singh Yadaw, Qian Zhu, Ewy A. Mathe
Summary: This study utilizes a knowledge graph and node embeddings to cluster rare diseases. The clusters reveal semantically similar diseases and associated genes, and provide connections between disease clusters and drugs for further investigation.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Immunology
Robert A. Saxton, Lukas T. Henneberg, Marco Calafiore, Leon Su, Kevin M. Jude, Alan M. Hanash, K. Christopher Garcia
Summary: This study engineered a high-affinity IL-22 superagonist to investigate the molecular mechanisms of the IL-22 signaling pathway. They found that precise control of IL-22 signaling can be achieved by modulating receptor expression levels and signaling bias, leading to tissue protection effects.
Article
Computer Science, Theory & Methods
Fethi A. Rabhi, Madhushi Bandara, Kun Lu, Saif Dewan
Summary: This paper presents the design of an innovative Information Technology (IT) platform that enables data sharing and makes analytics knowledge readily available and modifiable, supporting day-to-day decision making. Organizing analytics knowledge around the concept of a research variable, this platform is particularly suitable for developing empirical data analytics applications in any domain.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Article
Multidisciplinary Sciences
Diogo L. Pires, Mark Broom
Summary: Evolutionary game theory is a powerful tool to study the self-organization of collective behavior by considering the relationship between strategy stability and population size. This study focused on analyzing the fixation probabilities of single mutants in 2x2 games in well-mixed finite populations. The results showed that in certain game scenarios, single-mutant strategies tend to benefit from larger populations, which contradicts intuition. The study also identified conditions and ways to observe increased fixation probabilities in small populations.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2022)
Article
Chemistry, Applied
Lisha Yang, Jia Wen
Summary: This paper calculated the Hamaker constant of ZIF-8 for the first time using contact angle measurement parameters and discussed its dispersion in different solvent systems. The results showed that the energy potential barrier between ZIF-8 particles was high in the water system, but the particles were unstable in the toluene system. XDLVO theory was found to better describe the dispersion of ZIF-8 particles.
MICROPOROUS AND MESOPOROUS MATERIALS
(2022)
Article
Chemistry, Medicinal
Shu-Sen Chen, Zack Meyer, Brendan Jensen, Alex Kraus, Allison Lambert, Daniel H. Ess
Summary: Computational catalyst design requires identifying a suitable metal and ligand for desired reaction reactivity and/or selectivity. However, evaluating ligands that can be synthesized is a challenge. This study presents the ReaLigands library, which contains over 30,000 ligands obtained from dismantling experimentally reported crystal structures. Ligands were identified using a modified depth-first search algorithm and assigned charge using a machine learning model. The library enables ligands to be sorted based on ligand-to-metal atomic connections and denticity. Analysis of tridentate ligand categories revealed the diversity of ligands and their connections. The utility of the library was demonstrated in generating barriers for Rh-hydride ethylene migratory insertion with rapid speed.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Computer Science, Information Systems
Mehrdad Karajizadeh, Farid Zand, Afsaneh Vazin, Hamid Reza Saeidnia, Brady D. Lund, Sai Priya Tummuru, Roxana Sharifian
Summary: This study aimed to reduce the override rate of Drug-Drug Interaction Alerts (DDIA) in Intensive Care Units (ICUs) by designing, developing, implementing, and evaluating a severe Drug-Drug Alert System (DDIAS). The results showed that DDIAS had a good usability and a low override rate.
INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
(2023)
Article
Astronomy & Astrophysics
David Robinson, Camille Avestruz, Nickolay Y. Gnedin
Summary: This paper explores the cooling and heating functions in simulated galaxies and compares different approaches. The study finds that the actual rates of cooling and heating experienced by the gas do not correspond to the summarized functions, showing that the thermodynamics of the gas cannot be described by a single set of functions.
ASTROPHYSICAL JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Kazuhiro J. Fujimoto, Shota Minami, Takeshi Yanai
Summary: We propose a novel machine-learning-based scoring function that incorporates ligand and protein structural information into drug discovery. It accurately predicts binding affinity, surpassing conventional scoring functions. The findings provide chemical insights and are useful for rational drug discovery.
Article
Mathematics
Szilard Svitek, Norbert Annus, Ferdinand Filip
Summary: Number theory is an important area of study for mathematics education students, and visualization software can help them understand mathematical concepts and relationships.
Review
Green & Sustainable Science & Technology
Seung Yeoun Choi, Sean Hay Kim
Summary: New functions and requirements of high performance building (HPB) and reinforced regulations make it difficult for designers to decide designs alone. Not all projects can afford HPB consultants, so computer aids like design expert systems may be able to help in the near future. The effectiveness of the solution offered by the expert system relies on the quality and systemic structure of expert knowledge.
Article
Psychology, Applied
Haewon Yoon, Irene Scopelliti, Carey K. Morewedge
Summary: Observational learning can improve accuracy in judgment and decision-making, as well as increase the likelihood of taking advice. Observational learning is more effective in reducing cognitive biases and teaching decision rules compared to practice, and is equally effective as information-based interventions. Additionally, the effects of observational learning are additive for advice taking and accuracy when advice is algorithmically optimized.
ORGANIZATIONAL BEHAVIOR AND HUMAN DECISION PROCESSES
(2021)
Article
Cell Biology
Yi Zang, Mingbo Su, Qingxing Wang, Xi Cheng, Wenru Zhang, Yao Zhao, Tong Chen, Yingyan Jiang, Qiang Shen, Juan Du, Qiuxiang Tan, Peipei Wang, Lixin Gao, Zhenming Jin, Mengmeng Zhang, Cong Li, Ya Zhu, Bo Feng, Bixi Tang, Han Xie, Ming-Wei Wang, Mingyue Zheng, Xiaoyan Pan, Haitao Yang, Yechun Xu, Beili Wu, Leike Zhang, Zihe Rao, Xiuna Yang, Hualiang Jiang, Gengfu Xiao, Qiang Zhao, Jia Li
Summary: Through screening 1.8 million small molecules, we identified 1851 M(pro) inhibitors and 205 PLpro inhibitors, with 8 small molecules showing dual inhibition effects on both M(pro) and PLpro, potentially serving as better candidates for COVID-19 treatment.
Letter
Biology
Xinyuan Lin, Chi Xu, Zhaoping Xiong, Xinfeng Zhang, Ningxi Ni, Bolin Ni, Jianlong Chang, Ruiqing Pan, Zidong Wang, Fan Yu, Qi Tian, Hualiang Jiang, Mingyue Zheng, Nan Qiao
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yanqiong Liu, Zunyun Fu, Haihong Dong, Jingxuan Zhang, Yingle Mao, Mingyue Zheng, Cangsong Liao
Summary: The development of mild, efficient, and enantioselective methods for preparing chiral building blocks from simple, renewable carbon units has been a long-term goal of the sustainable chemical industry. In this study, a biocatalytic cascade using (S)-4-hydroxymandelate synthase (HmaS) as the key enzyme is reported for the synthesis of mandelate derivatives from benzaldehydes and glycine. This methodology offers a cyanide-free technology for greener and sustainable production of mandelate derivatives with high atom economy and excellent yields and enantiomeric excess values.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Shumeng Hao, Sulin Zhang, Jialin Ye, Lifan Chen, Yan Wang, Siyu Pei, Qingchen Zhu, Jing Xu, Yongzhen Tao, Neng Zhou, Huiyong Yin, Cai-Wen Duan, Chaoming Mao, Mingyue Zheng, Yichuan Xiao
Summary: Obesity is associated with elevated fatty acid beta-oxidation (FAO) and CD4(+) T cell hyperactivation, leading to enhanced induction of inflammation. The FAO rate-limiting enzyme Cpt1a stabilizes mitochondrial E3 ubiquitin ligase Goliath, promoting glycolysis and hyperactivation of CD4(+) T cells in obesity. Inhibiting the FAO-glycolysis metabolic axis with the Goliath inhibitor DC-Gonib32 reduces inflammation in obese mice.
Article
Chemistry, Medicinal
Bin Shan, Hui Hou, Keke Zhang, Rui Li, Chang Shen, Zhengyang Chen, Peijia Xu, Rongrong Cui, Zhaoming Su, Changfa Zhang, Ruirui Yang, Guizhen Zhou, Yadan Liu, Hao Guo, Kaixian Chen, Wei Fu, Hualiang Jiang, Sulin Zhang, Mingyue Zheng
Summary: Scientists have designed and synthesized a series of bipyridazine derivatives as highly potent STING agonists. Compound 12L showed significant activity in various assays and exhibited favorable pharmacokinetic properties and antitumor efficacy, suggesting its potential as an antitumor agent.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Zehui Zhou, Guizhen Zhou, Chuan Zhou, Zisheng Fan, Rongrong Cui, Yupeng Li, Rui Li, Yuejiao Gu, Huajie Li, Zhiming Ge, Xiaojia Cai, Bing Jiang, Dan Wang, Mingyue Zheng, Tianfeng Xu, Sulin Zhang
Summary: The linker moiety of a PROTAC molecule is crucial for its degradation activity, target selectivity, and physico-chemical properties. Understanding the underlying mechanisms of linker modification is important for enhancing PROTAC degradation and developing novel chemotherapies.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Plant Sciences
Haimei Li, Xu Zhu, Weihan Kong, Mingyue Zheng, Xiao Guo, Tong Wang
Summary: Urban greening plants provide the important ecosystem service of mitigating air pollution by intercepting atmospheric particulate matter. However, this study found that the dust retained by the plants can cause environmental stress to their photosynthesis and overall function. Evergreen shrub species generally performed better than deciduous shrub species in retaining dust and may be preferred for urban greening if air purification is the central goal.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Computer Science, Information Systems
Haichao Sun, Guoyin Wang, Qun Liu, Jie Yang, Mingyue Zheng
Summary: This paper proposes an explainable framework for molecular property prediction using multi-granularity representation to characterize the contribution of substructures to prediction. Several experiments are conducted to analyze the effectiveness of this framework on molecular property.
INFORMATION SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hui Zhen, Mujie Huang, Mingyue Zheng, Lili Gao, Zepeng Guo, Qiuxiang Pang, Guoxiang Jin, Zhongjun Zhou
Summary: In this study, we investigated the expression pattern and functions of the conserved WTAP gene in planarians. Knocking down WTAP resulted in severe morphological defects and lethality within 20 days. Silencing WTAP promoted the proliferation of PiwiA+ cells but impaired the differentiation of various cell types. RNA-seq analysis revealed upregulation of H4, Histone-lysine N-methyltransferase-SETMAR like, and TNF receptor-associated factor 6 (TRAF6) upon WTAP knockdown. Knocking down TRAF6 partially rescued the tissue homeostasis and regeneration defects, suggesting that WTAP maintains planarian regeneration and homeostasis via TRAF6.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Medicinal
Chang Shen, Peijia Xu, Changfa Zhang, Zhaoming Su, Bin Shan, Rui Li, Qibang Sui, Keke Zhang, Zhengyang Chen, Jingyi Zhou, Xiaojie Lu, Kaixian Chen, Mingyue Zheng, Sulin Zhang, Hui Hou
Summary: A series of 1H-pyrrole-3-carbonitrile derivatives were discovered as potential STING agonists by introducing various substituents on the aniline ring system. These compounds showed comparable activities to the reported STING agonist SR-717 in binding various hSTING alleles and inducing reporter signal in human THP1 cell lines.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Multidisciplinary Sciences
Lifan Chen, Zisheng Fan, Jie Chang, Ruirui Yang, Hui Hou, Hao Guo, Yinghui Zhang, Tianbiao Yang, Chenmao Zhou, Qibang Sui, Zhengyang Chen, Chen Zheng, Xinyue Hao, Keke Zhang, Rongrong Cui, Zehong Zhang, Hudson Ma, Yiluan Ding, Naixia Zhang, Xiaojie Lu, Xiaomin Luo, Hualiang Jiang, Sulin Zhang, Mingyue Zheng
Summary: Drug development based on target proteins has been successful. Researchers propose a sequence-to-drug concept for computational drug design based on protein sequence information and validate it through differentiable learning, demonstrating its importance in drug design.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yitian Wang, Jiacheng Xiong, Fu Xiao, Wei Zhang, Kaiyang Cheng, Jingxin Rao, Buying Niu, Xiaochu Tong, Ning Qu, Runze Zhang, Dingyan Wang, Kaixian Chen, Xutong Li, Mingyue Zheng
Summary: Lipophilicity is an important factor in drug behavior, and accurate prediction of lipophilicity is essential for successful drug discovery and design. To address the challenge of limited data availability, we developed a prediction model called RTlogD, which incorporates knowledge from multiple sources including chromatographic retention time (RT), microscopic pKa values, and logP. The RTlogD model demonstrated superior performance compared to commonly used algorithms and has the potential to improve logD prediction in drug discovery and design.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Lei Zhou, Wenzhe Yi, Zehong Zhang, Xiaoting Shan, Zitong Zhao, Xiangshi Sun, Jue Wang, Hao Wang, Hualiang Jiang, Mingyue Zheng, Dangge Wang, Yaping Li
Summary: This study designs an mRNA nanovaccine based on intelligent design, which uses machine learning techniques to ensure efficient delivery of mRNA antigen and cGAMP to targets. It activates STING, promotes mRNA-encoded antigen presentation, and enhances antitumor immunity, inhibiting tumor growth and ensuring long-term survival in tumor-bearing mice. This research provides a feasible and safe strategy for STING agonist-synergized mRNA immunization, with great potential for cancer immunotherapy enhancement.
NATIONAL SCIENCE REVIEW
(2023)
Article
Biochemistry & Molecular Biology
Lin Chen, Zehong Zhang, Zhenghao Li, Rui Li, Ruifeng Huo, Lifan Chen, Dingyan Wang, Xiaomin Luo, Kaixian Chen, Cangsong Liao, Mingyue Zheng
Summary: One key aspect of machine learning-assisted directed evolution (MLDE) is accurately understanding the fitness landscape, which maps sequence variants to desired functions. This paper describes a multi-protein training scheme that uses existing deep mutational scanning data from diverse proteins to aid in understanding the fitness landscape of a new protein. Proof-of-concept trials are conducted to validate this training scheme in multiple aspects, including extrapolating effects of single variants, predicting fitness for new proteins, and extrapolating higher-order variant effects. Results also highlight the pitfalls of MLDE and suggest improvements for developing better machine learning-assisted approaches to protein evolution. The paper includes a transparent peer review process record in the supplemental information.
Article
Chemistry, Multidisciplinary
Haiwei Shen, Bo Yang, Jiusheng Lin, Mingyue Zheng, Hualiang Jiang
Summary: A site-selective electrochemical benzylic C(sp(3))-H oxidation reaction was developed for the synthesis of desired products. This method significantly expands the scope and enhances the selectivity of aryl aldehydes and fluorinated ethers. Electricity is used as a sustainable oxidant, promoting H-2 evolution. The protocol is eco-friendly, easy to handle, and does not require any catalyst or oxidant.