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1525 Publications visible to you, out of a total of 1525
Deep Learning and Explainable Artificial Intelligence for Improving Specificity and Detecting Metabolic Patterns in Newborn Screening

Abstract

Not specified

Authors: Elaine Zaunseder, Ulrike Mütze, Sven F. Garbade, Saskia Haupt, Stefan Kölker, Vincent Heuveline

Date Published: 5th Dec 2023

Publication Type: Journal

Explainable Artificial Intelligence for Improving a Session-Based Malware Traffic Classification with Deep Learning

Abstract

Not specified

Authors: Stefan Machmeier, Maximilian Hoecker, Vincent Heuveline

Date Published: 5th Dec 2023

Publication Type: Journal

An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration

Abstract (Expand)

Abstract Mitochondrial fatty acid synthesis (mtFAS) is essential for respiratory function. MtFAS generates the octanoic acid precursor for lipoic acid synthesis, but the role of longer fatty acid …thesis, but the role of longer fatty acid products has remained unclear. The structurally well-characterized component of mtFAS, human 2E -enoyl-ACP reductase (MECR) rescues respiratory growth and lipoylation defects of a Saccharomyces cerevisiae Δ etr1 strain lacking native mtFAS enoyl reductase. To address the role of longer products of mtFAS, we employed in silico molecular simulations to design a MECR variant with a shortened substrate binding cavity. Our in vitro and in vivo analyses indicate that the MECR G165Q variant allows synthesis of octanoyl groups but not long chain fatty acids, confirming the validity of our computational approach to engineer substrate length specificity. Furthermore, our data imply that restoring lipoylation in mtFAS deficient yeast strains is not sufficient to support respiration and that long chain acyl-ACPs generated by mtFAS are required for mitochondrial function.

Authors: M. Tanvir Rahman, M. Kristian Koski, Joanna Panecka-Hofman, Werner Schmitz, Alexander J. Kastaniotis, Rebecca C. Wade, Rik K. Wierenga, J. Kalervo Hiltunen, Kaija J. Autio

Date Published: 1st Dec 2023

Publication Type: Journal

Astrophysics with the Laser Interferometer Space Antenna

Abstract

Not specified

Authors: Pau Amaro-Seoane, Jeff Andrews, Manuel Arca Sedda, Abbas Askar, Quentin Baghi, Razvan Balasov, Imre Bartos, Simone S. Bavera, Jillian Bellovary, Christopher P. L. Berry, Emanuele Berti, Stefano Bianchi, Laura Blecha, Stéphane Blondin, Tamara Bogdanović, Samuel Boissier, Matteo Bonetti, Silvia Bonoli, Elisa Bortolas, Katelyn Breivik, Pedro R. Capelo, Laurentiu Caramete, Federico Cattorini, Maria Charisi, Sylvain Chaty, Xian Chen, Martyna Chruślińska, Alvin J. K. Chua, Ross Church, Monica Colpi, Daniel D’Orazio, Camilla Danielski, Melvyn B. Davies, Pratika Dayal, Alessandra De Rosa, Andrea Derdzinski, Kyriakos Destounis, Massimo Dotti, Ioana Dutan, Irina Dvorkin, Gaia Fabj, Thierry Foglizzo, Saavik Ford, Jean-Baptiste Fouvry, Alessia Franchini, Tassos Fragos, Chris Fryer, Massimo Gaspari, Davide Gerosa, Luca Graziani, Paul Groot, Melanie Habouzit, Daryl Haggard, Zoltan Haiman, Wen-Biao Han, Alina Istrate, Peter H. Johansson, Fazeel Mahmood Khan, Tomas Kimpson, Kostas Kokkotas, Albert Kong, Valeriya Korol, Kyle Kremer, Thomas Kupfer, Astrid Lamberts, Shane Larson, Mike Lau, Dongliang Liu, Nicole Lloyd-Ronning, Giuseppe Lodato, Alessandro Lupi, Chung-Pei Ma, Tomas Maccarone, Ilya Mandel, Alberto Mangiagli, Michela Mapelli, Stéphane Mathis, Lucio Mayer, Sean McGee, Barry McKernan, M. Coleman Miller, David F. Mota, Matthew Mumpower, Syeda S. Nasim, Gijs Nelemans, Scott Noble, Fabio Pacucci, Francesca Panessa, Vasileios Paschalidis, Hugo Pfister, Delphine Porquet, John Quenby, Angelo Ricarte, Friedrich K. Röpke, John Regan, Stephan Rosswog, Ashley Ruiter, Milton Ruiz, Jessie Runnoe, Raffaella Schneider, Jeremy Schnittman, Amy Secunda, Alberto Sesana, Naoki Seto, Lijing Shao, Stuart Shapiro, Carlos Sopuerta, Nicholas C. Stone, Arthur Suvorov, Nicola Tamanini, Tomas Tamfal, Thomas Tauris, Karel Temmink, John Tomsick, Silvia Toonen, Alejandro Torres-Orjuela, Martina Toscani, Antonios Tsokaros, Caner Unal, Verónica Vázquez-Aceves, Rosa Valiante, Maurice van Putten, Jan van Roestel, Christian Vignali, Marta Volonteri, Kinwah Wu, Ziri Younsi, Shenghua Yu, Silvia Zane, Lorenz Zwick, Fabio Antonini, Vishal Baibhav, Enrico Barausse, Alexander Bonilla Rivera, Marica Branchesi, Graziella Branduardi-Raymont, Kevin Burdge, Srija Chakraborty, Jorge Cuadra, Kristen Dage, Benjamin Davis, Selma E. de Mink, Roberto Decarli, Daniela Doneva, Stephanie Escoffier, Poshak Gandhi, Francesco Haardt, Carlos O. Lousto, Samaya Nissanke, Jason Nordhaus, Richard O’Shaughnessy, Simon Portegies Zwart, Adam Pound, Fabian Schussler, Olga Sergijenko, Alessandro Spallicci, Daniele Vernieri, Alejandro Vigna-Gómez

Date Published: 1st Dec 2023

Publication Type: Journal

Simulations of common-envelope evolution in binary stellar systems: physical models and numerical techniques

Abstract

Not specified

Authors: Friedrich K. Röpke, Orsola De Marco

Date Published: 1st Dec 2023

Publication Type: Journal

Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance

Abstract (Expand)

Abstract The propensity of poorly water-soluble drugs to aggregate at supersaturation impedes their bioavailability. Supersaturated amorphous drug-salt-polymer systems provide an emergent approach to …r systems provide an emergent approach to this problem. However, the effects of polymers on drug-drug interactions in aqueous phase are largely unexplored and it is unclear how to choose an optimal salt-polymer combination for a particular drug. Here, we describe a comparative experimental and computational characterization of amorphous solid dispersions containing the drug celecoxib, and a polymer, polyvinylpyrrolidone vinyl acetate (PVP-VA) or hydroxypropyl methylcellulose acetate succinate, with or without Na + /K + salts. Classical models for drug-polymer interactions fail to identify the best drug-salt-polymer combination. In contrast, more stable drug-polymer interaction energies computed from molecular dynamics simulations correlate with prolonged stability of supersaturated amorphous drug-salt-polymer systems, along with better dissolution and pharmacokinetic profiles. The celecoxib-salt-PVP-VA formulations exhibit excellent biopharmaceutical performance, offering the prospect of a low-dosage regimen for this widely used anti-inflammatory, thereby increasing cost-effectiveness, and reducing side-effects.

Authors: Sumit Mukesh, Goutam Mukherjee, Ridhima Singh, Nathan Steenbuck, Carolina Demidova, Prachi Joshi, Abhay T. Sangamwar, Rebecca C. Wade

Date Published: 1st Dec 2023

Publication Type: Journal

Host–guest interactions in framework materials: Insight from modeling

Abstract (Expand)

The performance of metal–organic and covalent organic framework materials in sought-after applications—capture, storage, and delivery of gases and molecules, and separation of their mixtures—heavily …xtures—heavily depends on the host–guest interactions established inside the pores of these materials. Computational modeling provides information about the structures of these host–guest complexes and the strength and nature of the interactions present at a level of detail and precision that is often unobtainable from experiment. In this Review, we summarize the key simulation techniques spanning from molecular dynamics and Monte Carlo methods to correlate ab initio approaches and energy, density, and wavefunction partitioning schemes. We provide illustrative literature examples of their uses in analyzing and designing organic framework hosts. We also describe modern approaches to the high-throughput screening of thousands of existing and hypothetical metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) and emerging machine learning techniques for predicting their properties and performances. Finally, we discuss the key methodological challenges on the path toward computation-driven design and reliable prediction of high-performing MOF and COF adsorbents and catalysts and suggest possible solutions and future directions in this exciting field of computational materials science.

Authors: Michelle Ernst, Jack D. Evans, Ganna Gryn'ova

Date Published: 1st Dec 2023

Publication Type: Journal

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