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Predicting transcriptional changes induced by molecules with MiTCP.
Brief Bioinform
November 2024
Department of Automation, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.
View Article and Find Full Text PDFThianthrenium-Enabled Chromium-Catalyzed Deuterated Alkyl Addition to Aldehydes via a Photoactive Electron Donor-Acceptor Complex.
Org Lett
January 2025
Department of Chemistry and Materials Science, College of Science, Nanjing Forestry University, Nanjing 210037, China.
The Nozaki-Hiyama-Kishi reaction offers effective and reliable strategies for the preparation of alcohols via carbon-carbon bond formation. Typical methods usually require stoichiometric amounts of chromium salts, co-transition metals, and auxiliary reagents, which limits their practical application in industrial chemistry. To mitigate these limitations, substantial efforts have been made to develop chromium-catalytic approaches.
View Article and Find Full Text PDFFully Atomistic Molecular Dynamics Simulation of Ice Nucleation Near an Antifreeze Protein.
J Am Chem Soc
January 2025
Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, Kowloon 999077, China.
Heterogeneous ice nucleation is a widespread phenomenon in nature. Despite extensive research on ice nucleation near biological antifreeze proteins, a probe for ice nucleation and growth processes at the atomic level is still lacking. Herein, we present simulation evidence of the heterogeneous ice nucleation process on the ice-binding surface (IBS) of the antifreeze protein (TmAFP).
View Article and Find Full Text PDFExposure to Secondhand Cannabis Smoke Among Children.
JAMA Netw Open
January 2025
Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego.
Importance: The degree that in-home cannabis smoking can be detected in the urine of resident children is unclear.
Objective: Test association of in-home cannabis smoking with urinary cannabinoids in children living at home.
Design, Setting, And Participants: This cross-sectional study used baseline data from Project Fresh Air, a 2012-2016 randomized clinical trial to reduce fine particulate matter levels.
Making Mo(0) a Competitive Alternative to Ir(III) in Phosphors and Photocatalysts.
J Am Chem Soc
January 2025
Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
Iridium is used in commercial light-emitting devices and in photocatalysis but is among the rarest stable chemical elements. Therefore, replacing iridium(III) in photoactive molecular complexes with abundant metals is of great interest. First-row transition metals generally tend to yield poorer luminescence behavior, and it remains difficult to obtain excited states with redox properties that exceed those of noble-metal-based photocatalysts.
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