Editorial Material
Multidisciplinary Sciences
Sean J. Humphrey, Elise J. Needham
Summary: A computational resource can identify candidate protein targets for a major class of kinase enzymes in humans, which is important for understanding the role of cell signaling in health and disease.
Editorial Material
Multidisciplinary Sciences
Emiliano Donadio, Sebastian Di Martino, Sofia Heinonen
Summary: A foundation is reintroducing native species to restore ecosystems and develop ecotourism.
Article
Biotechnology & Applied Microbiology
Neha Jain, Uma Shankar, Aakriti Singh, Tarun Kumar Sharma, Amit Kumar
Summary: This study identified the significant role of G-quadruplexes (GQs) in N. gonorrhoeae, an obligate human pathogen that causes gonorrhea. Five GQ motifs in the N. gonorrhoeae genome were characterized and shown to be stabilized by the GQ-specific ligand, BRACO-19, in both in vitro and in vivo conditions. BRACO-19 exhibited potent anti-gonococcal activity and altered biofilm formation as well as the adhesion and invasion of human cervical epithelial cells by N. gonorrhoeae. This study advances the knowledge of N. gonorrhoeae biology and provides insights for developing therapeutic measures against this emerging antimicrobial resistant pathogen.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Charlie Hollanders, Mathias Elsocht, Olivier Van Der Poorten, Mouhamad Jida, Evelien Renders, Bert U. W. Maes, Steven Ballet
Summary: The study introduces the use of 3-substituted 2-isocyanopyridines as convertible isocyanides in Ugi four-component reactions, which can be cleaved by amines, alcohols, and water with Zn(OAc)(2) as a catalyst. The method's applicability was demonstrated in constrained di-/tripeptides bearing acid and base sensitive protective groups obtained via Ugi-4CR post-condensation modifications.
CHEMICAL COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Cheng-Yu Tsai, Emmanuel Oluwatobi Salawu, Hongchun Li, Guan-Yu Lin, Ting-Yu Kuo, Liyin Voon, Adarsh Sharma, Kai-Di Hu, Yi-Yun Cheng, Sobha Sahoo, Lutimba Stuart, Chih-Wei Chen, Yuan-Yu Chang, Yu-Lin Lu, Simai Ke, Christopher Llynard D. Ortiz, Bai-Shan Fang, Chen-Chi Wu, Chung-Yu Lan, Hua-Wen Fu, Lee-Wei Yang
Summary: The systematic design of functional peptides has various applications and a pattern-based search engine is needed to locate desired functional motifs in primary sequences. In this study, we extracted 1.7 million helices from the PDB and compiled them into a database called TP-DB, which facilitates the identification of sequence motifs of helical structures. We demonstrated the application of TP-DB in identifying specific antibodies, designing antimicrobial peptides, and suggesting point mutations in helical peptide blockers.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Muhammad Arif, Abhishek Basu, Kaelin M. Wolf, Joshua K. Park, Lenny Pommerolle, Madeline Behee, Bernadette R. Gochuico, Resat Cinar
Summary: This study identifies gene subnetworks associated with pulmonary fibrosis and proposes peripheral CB1R antagonism as a potential therapeutic target. The findings are based on integrated multi-omics data and validate the results in both mouse models and human patients.
Article
Biochemistry & Molecular Biology
Michela Bollati, Kaliroi Peqini, Luigi Barone, Carmina Natale, Marten Beeg, Marco Gobbi, Luisa Diomede, Michelangelo Trucchi, Matteo de Rosa, Sara Pellegrino
Summary: Gelsolin amyloidosis is a disease characterized by abnormal deposition of gelsolin protein in tissues, for which there is currently no cure. Researchers have designed and synthesized three peptidomimetics that effectively inhibit the aggregation of amyloidogenic peptides and have demonstrated their efficacy in vivo. These findings provide a new pharmacological strategy against gelsolin amyloidosis and suggest potential applications in other amyloidogenic diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Caroline Jane Ross, Igor Ulitsky
Summary: This review outlines the development and limitations of methods for discovering functional elements in long noncoding RNAs (lncRNAs), and discusses the main challenges in this field.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Biochemistry & Molecular Biology
Philip Maximilian Knaff, Patrick Mueller, Christian Kersten, Lukas Wettstein, Jan Muench, Katharina Landfester, Volker Mailaender
Summary: The study developed high-affinity tetrapeptidic inhibitors using a combinatorial methodology, which can selectively inhibit the overexpression of hepsin in tumor progression.
Article
Plant Sciences
Debarati Basu, Paul F. South
Summary: Quantitative traits are often controlled by multiple genes, requiring multi-gene transformation in synthetic biology. However, the lack of unique gene regulatory elements for simultaneous expression of nuclear transgenes in plants poses a major challenge. This study compared the transcriptional efficiencies of various promoter and UTR sequences and created new GREs with higher transcriptional efficacies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Pharmacology & Pharmacy
Liyuan Li, Xiaoying Wang, Xiao Guo, Yikun Li, Qiuhang Song, Aiying Li
Summary: LHQW and QFPD are effective traditional Chinese medicine prescriptions for treating COVID-19, relieving symptoms and preventing disease progression through different mechanisms.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Mengmeng Zheng, Chunpu Li, Mi Zhou, Ru Jia, Fengyu She, Lulu Wei, Feng Cheng, Qi Li, Jianfeng Cai, Yan Wang
Summary: The study developed an artificial antibody based on gamma-AApeptides, with small molecular weight, antibody-like properties, strong resistance to proteolysis, excellent binding affinity to HER2, effective inhibition of cell proliferation in vitro, suppression of tumor growth in vivo, and potential therapeutic applications for treating cancers.
ACTA PHARMACEUTICA SINICA B
(2021)
Article
Engineering, Multidisciplinary
Xiaoling Wang, Zhen Fan, Lin Wang, Housheng Su, James Lam
Summary: In this paper, a sensor network is utilized to tackle the distributed observer design problem for a linear time-invariant mobile target system with constant or time-varying velocity. Each sensor only has access to a partial portion of the target's output information. The sensors are equipped with consensus-based algorithms for state estimation using local measurements and leader-following flocking-like algorithms for collision avoidance, communication maintenance, and target tracking. The proposed adaptive coupling gains enable the construction of a fully distributed observer that is independent of the communication topology associated with the sensor network. Numerical simulations demonstrate the effectiveness of the proposed theoretical results.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Meimei Zhao, Lu Yao, Xiaowen Zhang, Lichao Wang, Pengfei Tu, Kewu Zeng
Summary: This study introduced a cellular target identification technology for multi-molecule systems using DHBP-bound Fe3O4 nanoparticles with photochemically induced crosslinking capacity. The technology, named the Zhao-Yao (ZY) strategy, has the potential to comprehensively interpret the pharmacological mechanism of multi-molecule systems by globally identifying cellular targets.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tomasz Wozniak, Weronika Sura, Marta Kazimierska, Marta Elzbieta Kasprzyk, Marta Podralska, Agnieszka Dzikiewicz-Krawczyk
Summary: In this study, we developed an online tool called transCRISPR for searching sequence motifs and designing sgRNAs in user-provided genomic regions. The tool provides user-friendly tables and visualizations summarizing the features of identified motifs and designed sgRNAs. Experimental validation showed that sgRNAs designed by transCRISPR efficiently disrupted MYC binding sites and affected the expression of MYC-regulated genes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Jeaphianne van Rijn, Antreas Afantitis, Mustafa Culha, Maria Dusinska, Thomas E. Exner, Nina Jeliazkova, Eleonora Marta Longhin, Iseult Lynch, Georgia Melagraki, Penny Nymark, Anastasios G. Papadiamantis, David A. Winkler, Hulya Yilmaz, Egon Willighagen
Summary: Management of nanomaterials and nanosafety data requires a unique identifier for each nanomaterial, which is provided by the European Registry of Materials Identifier. This identifier ensures the linking of internal project documentation with publicly released data and knowledge for specific nanomaterials, and has been applied in H2020-funded nanosafety projects.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Wil Gardner, David A. Winkler, Ruqaya Maliki, Suzanne M. Cutts, Sarah Ellis, Robin L. Anderson, Benjamin W. Muir, Paul J. Pigram
Summary: This study applies a convolutional neural network (CNN) fusion method to fuse ToF-SIMS hyperspectral data sets, achieving resolution-enhanced data with high spatial and mass resolution. The method is applied to ToF-SIMS images of a gold mesh sample and a tumor tissue section, and the improvement is compared to another linear fusion method used in the broader MSI community.
ADVANCED MATERIALS INTERFACES
(2022)
Review
Chemistry, Multidisciplinary
Haoxin Mai, Tu C. Le, Dehong Chen, David A. Winkler, Rachel A. Caruso
Summary: This article reviews the role of machine learning methods in clean energy applications, specifically in the design, discovery, and synthesis optimization of adsorbent materials. Through case studies, it demonstrates the importance of these methods in accelerating the development of high-performance adsorbent materials.
Article
Chemistry, Multidisciplinary
Suiying Ye, Nastaran Meftahi, Igor Lyskov, Tian Tian, Richard Whitfield, Sudhir Kumar, Andrew J. Christofferson, David A. Winkler, Chih-Jen Shih, Salvy Russo, Jean-Christophe Leroux, Yinyin Bao
Summary: In this study, a versatile and simple platform based on through-space charge transfer (TSCT) polymers was developed, which exhibited full-color-tunable emission and was aided by predictive machine learning models. By introducing electron donor groups containing simple polycyclic aromatic moieties (e.g., pyrene) through one-step copolymerization or end-group functionalization, continuous blue-to-red emission color tuning was easily achieved in solid polymers. Theoretical investigations confirmed the structurally dependent TSCT-induced emission redshifts. Additionally, the TSCT polymers were demonstrated to be a general design platform for solid-state stimuli-responsive materials, exemplified by their application in information encryption with high-contrast photochromic emission.
Article
Medicine, Research & Experimental
David Winkler, Ira Katz, Andrew Warden, Aaron Thornton, Geraldine Farjot
Summary: This study analyzed the dataset of protein-gas interactions, focusing on the potential clinical applications of xenon-protein interactions. A rational scoring method was used to generate a partial prioritized list of xenon protein targets. The study provides a preliminary analysis method for this massive dataset and emphasizes the importance of this dataset to the scientific community.
MEDICAL GAS RESEARCH
(2023)
Article
Nanoscience & Nanotechnology
Leonardo Contreas, Andrew L. Hook, David A. Winkler, Grazziela Figueredo, Paul Williams, Charles A. Laughton, Morgan R. Alexander, Philip M. Williams
Summary: Bacterial infections are becoming a greater concern due to antimicrobial resistance. The rational design of materials resistant to biofilm formation is a crucial strategy to prevent infections related to medical devices. Machine learning has been used to identify strong associations between bacterial adhesion and the physicochemical properties of polyacrylate libraries. However, the interpretability of nonlinear models is limited, making it challenging to understand the molecular interactions between materials and bacteria.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Analytical
Sarah E. Bamford, Dilek Yalcin, Wil Gardner, David A. Winkler, Thomas M. Kohl, Benjamin W. Muir, Shaun Howard, Eric A. Bruton, Paul J. Pigram
Summary: The self-organizing map with relational perspective mapping (SOM-RPM) is an unsupervised machine learning method used for visualizing and interpreting high-dimensional hyperspectral data. In this study, SOM-RPM was applied to stitched ToF-SIMS datasets to provide a direct comparison in both 2D and 3D. The quantitative assessment of annealing-induced chemical breakdown trends was conducted on spin-coated polyaniline (PANI) films, revealing differences in peak intensity ratios.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Xiliang Yan, Tongtao Yue, David A. A. Winkler, Yongguang Yin, Hao Zhu, Guibin Jiang, Bing Yan
Summary: Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. This review discusses the role of artificial intelligence (AI) and molecular simulation in transforming nanotoxicity data into critical information, by constructing quantitative nanostructure-toxicity relationships and elucidating toxicity-related molecular mechanisms. Several obstacles must be overcome for AI and molecular simulation to have their full impact, including the lack of high-quality nanomaterials, standardized nanotoxicity data, model-friendly databases, specific and universal nanodescriptors, and realistic simulation of nanomaterials. The review also provides a comprehensive summary of current capability gaps and tools required to fill these gaps, as well as a perspective on future trends and challenges.
Article
Biochemistry & Molecular Biology
Sakshi Piplani, Puneet Singh, Nikolai Petrovsky, David A. A. Winkler
Summary: Drugs targeting novel targets are necessary for treating COVID-19 patients due to the rapid mutation of SARS-CoV-2. In silico simulations can quickly identify existing drugs with known safety profiles that can be repurposed for COVID-19 treatment. This study provides new insights into the SARS-CoV-2 spike protein and its potential regulation by endogenous hormones and drugs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
See Yoong Wong, Andrew L. Hook, Wil Gardner, Chien-Yi Chang, Ying Mei, Martyn C. Davies, Paul Williams, Morgan R. Alexander, Davide Ballabio, Benjamin W. Muir, David A. Winkler, Paul J. Pigram
Summary: Biofilm formation is a major problem in hospitals, and researching biofilm-resistant materials is critical. Polymer microarrays can efficiently discover new biofilm-resistant polymers. This study investigates bacterial attachment and surface chemistry on a polymer microarray to better understand Pseudomonas aeruginosa biofilm formation. Analyzing the data using linear multivariate analysis and a nonlinear self-organizing map reveals fragment ions associated with bacterial biofilm formation. Considering these insights, a second analysis is conducted that explicitly considers interactions between key fragments. This improved model provides chemical insights for designing materials that prevent pathogen attachment.
ADVANCED MATERIALS INTERFACES
(2023)
Article
Materials Science, Coatings & Films
Wil Gardner, David A. Winkler, David L. J. Alexander, Davide Ballabio, Benjamin W. Muir, Paul J. Pigram
Summary: In this study, two different ToF-SIMS imaging datasets were used to evaluate the impact of data preprocessing methods and SOM hyperparameters on the performance of SOM. It was found that preprocessing is generally more important than hyperparameter selection, and there are complex interactions between different parameters. The results of this study are important for understanding the effects of data processing on hyperspectral imaging data.
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY A
(2023)
Article
Chemistry, Multidisciplinary
Alexander Corletto, Marco Fronzi, Alexis Krywula Joannidis, Peter C. Sherrell, Michael J. Ford, David A. Winkler, Joseph G. Shapter, James Bullock, Amanda V. Ellis
Summary: A new model is proposed to explain how the electrostatics and strain at the MoS2/metal interface influence the monolayer-selectivity of MME. The study demonstrates the significance of electrostatics in nanomaterial van der Waals interactions.
ADVANCED MATERIALS INTERFACES
(2023)
Editorial Material
Pharmacology & Pharmacy
David Alan Winkler
PHARMACEUTICAL SCIENCES
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Aayush Kumar, Jimiama M. Mase, Divish Rengasamy, Benjamin Rothwell, Mercedes Torres Torres, David A. Winkler, Grazziela P. Figueredo
Summary: This paper presents an open-source Python toolbox called Ensemble Feature Importance (EFI) which provides robust and accurate feature importance quantification and reliable interpretation for prediction problems using fuzzy sets. EFI addresses uncertainties in feature importance quantification due to diverse machine learning algorithms and calculation methods, and it merges results from multiple models using decision fusion techniques.
MACHINE LEARNING, OPTIMIZATION, AND DATA SCIENCE, LOD 2022, PT II
(2023)
Article
Chemistry, Multidisciplinary
Xuying Li, Haoxin Mai, Junlin Lu, Xiaoming Wen, Tu C. Le, Salvy P. Russo, David A. Winkler, Dehong Chen, Rachel A. Caruso
Summary: This study used a combination of machine learning models and theoretical calculations to efficiently screen substitution elements that enhanced the photoactivity of Cs2AgBiBr6 perovskites. The results showed that d10-configured Zn2+ significantly boosted the photocatalytic activity. Experimental verification confirmed a 13-fold increase in toluene conversion compared to the unsubstituted counterpart. This research exemplifies the application of computational modeling in photocatalyst design and elucidating structure-property relationships.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
