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Chalcones from Angelica keiskei (ashitaba) inhibit key Zika virus replication proteins

BIOORGANIC CHEMISTRY 2022年 120卷 105649-105649页

作者： Mottin, Melina Caesar, Lindsay K. Brodsky, David Mesquita, Nathalya C. M. R. de Oliveira, Ketllyn Zagato Noske, Gabriela Dias Sousa, Bruna K. P. Ramos, Paulo R. P. S. Jarmer, Hannah Loh, Bonnie Zorn, Kimberley M. Foil, Daniel H. Torres, Pedro M. Guido, Rafael V. C. Oliva, Glaucius Scholle, Frank Ekins, Sean Cech, Nadja B. Andrade, Carolina H. Laster, Scott M. Univ Fed Goias Fac Farm Lab Mol Modeling & Drug Design LabMol Goiania Go Brazil Univ Brasilia Inst Ciencias Biol Lab Interacao Patogeno Hospedeiro Brasilia DF Brazil Univ N Carolina Dept Chem & Biochem Greensboro NC USA North Carolina State Univ CAVE Program Dept Biol Sci Raleigh NC 27695 USA North Carolina State Univ CAVE Program Comparat Med Inst Raleigh NC 27695 USA Univ Sao Paulo Sao Carlos Inst Phys Sao Carlos SP Brazil Collaborat Pharmaceut Inc Raleigh NC USA Univ Fed Rio de Janeiro Inst Biofis Carlos Chagas Filho Lab Modelagem & Dinam Mol Rio De Janeiro Brazil

Zika virus (ZIKV) is a dangerous human pathogen and no antiviral drugs have been approved to date. The chalcones are a group of small molecules that are found in a number of different plants, including Angelica keiskei Koidzumi, also known as ashitaba. To examine chalcone anti-ZIKV activity, three chalcones, 4-hydroxyderricin (4HD), xanthoangelol (XA), and xanthoangelol-E (XA-E), were purified from a methanol-ethyl acetate extract from A. keiskei. Molecular and ensemble docking predicted that these chalcones would establish multiple interactions with residues in the catalytic and allosteric sites of ZIKV NS2B-NS3 protease, and in the allosteric site of the NS5 RNA-dependent RNA-polymerase (RdRp). Machine learning models also predicted 4HD, XA and XA-E as potential anti-ZIKV inhibitors. Enzymatic and kinetic assays confirmed chalcone inhibition of the ZIKV NS2BNS3 protease allosteric site with IC(50)s from 18 to 50 mu M. Activity assays also revealed that XA, but not 4HD or XA-E, inhibited the allosteric site of the RdRp, with an IC50 of 6.9 mu M. Finally, we tested these chalcones for their anti-viral activity in vitro with Vero cells. 4HD and XA-E displayed anti-ZIKV activity with EC50 values of 6.6 and 22.0 mu M, respectively, while XA displayed relatively weak anti-ZIKV activity with whole cells. With their simple structures and relative ease of modification, the chalcones represent attractive candidates for hit-to-lead optimization in the search of new anti-ZIKV therapeutics.

关键词： Angelica keiskei Ashitaba Chalcones Zika virus Polymerase Protease

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Packing ellipsoids in an optimized cylinder

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EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 2020年第2期285卷 429-443页

作者： Romanova, Tatiana Litvinchev, Igor Pankratov, Alexander Natl Acad Sci Ukraine Dept Math Modeling & Optimal Design Inst Mech Engn Problems Kharkov Ukraine Kharkiv Natl Univ Radioelect Dept Syst Engn Kharkov Ukraine Nuevo Leon State Univ UANL Fac Mech & Elect Engn Grad Program Syst Engn Monterrey Mexico

The paper studies packing ellipsoids of revolution in a cylindrical container of minimum volume. Ellipsoids can be continuously rotated and translated. Two nonlinear mathematical programming models are introduced: exact and approximated. The latter uses an optimized multi-spherical approximation of ellisoids. For both models the phi-function technique is employed to describe analytically non-overlapping and containment constraints. Two solution approaches are proposed to solve the packing problem. Computational results for up to 500 ellipsoids are provided to demonstrate efficiency of the proposed approaches. (C) 2020 Elsevier B.V. All rights reserved.

关键词： Packing Cylindrical container Ellipsoids Phi-function technique Nonlinear optimization

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Direct imaging of liquid domains in membranes by cryo-electron tomography

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2020年第33期117卷 19713-19719页

作者： Cornell, Caitlin E. Mileant, Alexander Thakkar, Niket Lee, Kelly K. Keller, Sarah L. Univ Washington Dept Chem Seattle WA 98195 USA Univ Washington Dept Med Chem Seattle WA 98195 USA Univ Washington Biol Phys Struct & Design Grad Program Seattle WA 98195 USA Inst Dis Modeling Seattle WA 98109 USA

Images of micrometer-scale domains in lipid bilayers have pro-vided the gold standard of model-free evidence to understand the domains' shapes, sizes, and distributions. Corresponding tech-niques to directly and quantitatively assess smaller (nanoscale and submicron) liquid domains have been limited. Researchers com-monly seek to correlate activities of membrane proteins with at-tributes of the domains in which they reside;doing so hinges on identification and characterization of membrane domains. Al-though some features of membrane domains can be probed by indirect methods, these methods are often constrained by the lim-itation that data must be analyzed in the context of models that require multiple assumptions or parameters. Here, we address this challenge by developing and testing two methods of identifying submicron domains in biomimetic membranes. Both methods le-verage cryo-electron tomograms of ternary membranes under vit-rified, hydrated conditions. The first method is optimized for probe-free applications: Domains are directly distinguished from the surrounding membrane by their thickness. This technique quantitatively and accurately measures area fractions of domains, in excellent agreement with known phase diagrams. The second method is optimized for applications in which a single label is deployed for imaging membranes by both high-resolution cryo-electron tomography and diffraction-limited optical microscopy. For this method, we test a panel of probes, find that a trimeric mCherry label performs best, and specify criteria for developing future high-performance, dual-use probes. These developments have led to direct and quantitative imaging of submicron mem-brane domains in vitrified, hydrated vesicles.

关键词： probe-free height mismatch phase separation membrane

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Capacity of Two Sierra Nevada Rivers for Reintroduction of Anadromous Salmonids: Insights from a High-Resolution View

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TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY 2022年第1期151卷 13-41页

作者： Boughton, David A. Harrison, Lee R. John, Sara N. Bond, Rosealea M. Nicol, Colin L. Legleiter, Carl J. Richardson, Ryan T. Natl Marine Fisheries Serv Southwest Fisheries Sci Ctr 110 McAllister Way Santa Cruz CA 95060 USA Univ Calif Santa Barbara Earth Res Inst Santa Barbara CA 93106 USA Univ Calif Santa Cruz Inst Marine Sci Fisheries Collaborat Program 115 McAllister Way Santa Cruz CA 95060 USA US Geol Survey Integrated Modeling & Predict Div Geomorphol & Sediment Transport Lab 4620 Technol Dr Golden CO 80403 USA River Design Grp 236 Wisconsin Ave Whitefish MT 59937 USA Ocean Associates Inc Natl Marine Fisheries Serv Northwest Fisheries Sci Ctr 2725 Montlake Blvd East Washington DC 98112 USA

Historically, anadromous steelhead Oncorhynchus mykiss and spring-run Chinook Salmon O. tshawytscha used high-elevation rivers in the Sierra Nevada of California but were extirpated in the 20th century by construction of impassable dams. Plans to reintroduce the fish by opening migratory passage across the dams and reservoirs can only succeed if upstream habitats have the capacity to support viable populations of each species. To estimate capacity in the Tuolumne and Merced rivers of the central Sierra Nevada, we used a high-resolution approach based on remote sensing and dynamic habitat modeling. Our results suggested that for both species in both systems, sediment grain sizes would support widespread spawning and the water temperatures, depths, and velocities would generate ample capacity for fry and juveniles. However, the unregulated Merced River was consistently too warm for adult Chinook Salmon to hold in the dry season prior to spawning, while the regulated Tuolumne River maintained a cooler, more stable thermal regime with a capacity for thousands of holding adults. In our high-resolution approach, we also discovered several specific physical controls on life history expression, including thermal constraints on the timing of spawning, hydraulic prompts for downstream migration of fry, divergence of the hydraulic niches of steelhead and Chinook Salmon, and a key but uncertain role for thermal tolerance in adult Chinook Salmon. Our results suggested that steelhead reintroduction could succeed in either system and Chinook Salmon could succeed in the Tuolumne River if passage strategies account for large numbers of migrant fry and juveniles driven downstream by winter storms and snowmelt. The Merced River appeared too warm for adult Chinook Salmon, which raises questions about the current limited understanding of thermal tolerance in holding adults. Our study shows how a high-resolution approach can provide valuable insights on specific limiting factors that mus

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Experimental study and theoretical statistical modeling of acid blue 25 remediation using activated carbon from Citrus sinensis leaf

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FLUID PHASE EQUILIBRIA 2022年第0期563卷

作者： El Messaoudi, Noureddine El Mouden, Abdelaziz El Khomri, Mohammed Bouich, Amal Fernine, Yasmine Cigeroglu, Zeynep Americo-Pinheiro, Juliana Heloisa Pine Labjar, Najoua Jada, Amane Sillanpaa, Mika Lacherai, Abdellah Ibn Zohr Univ Fac Sci Lab Appl Chem & Environm Agadir 80000 Morocco Univ Politecn Valencia Inst Design & Mfg IDF Dept Appl Phys Valencia 46000 Spain Sidi Mohamed Ben Abdellah Univ Engn Lab Organometall Mol Mat & Environm Fes 30000 Morocco Usak Univ Fac Engn Dept Chem Engn TR-64300 Usak Turkey Brazil Univ Postgrad Program Environm Sci St Carolina Fonseca 584 BR-08230030 Sao Paulo SP Brazil Mohammed V Lab Spect Mol Modeling Mat Nanomat Water & Enviro Rabat 10000 Morocco High Alsace Univ Inst Mat Sci Mulhouse IS2M F-68100 Mulhouse France Univ Johannesburg Dept Chem Engn Sch Min Met & Chem Engn ZA-2028 Doornfontein South Africa

In this study, Citrus Sinensis Leaf Activated Carbon (CSLAC), as adsorbent for acid blue 25 (AB25) dye removal from water, was synthesized from Citrus Sinensis Leaf (CSL) by using sulfuric acid (H2SO4) activation procedure. The obtained adsorbent was thereafter characterized by various methods such as FTIR, BET-BJH, and SEM-EDX. Further, the adsorption of AB25 on CSLAC was performed under different operating conditions. High CSLAC surface area of 485.16 m(2) g(-1) was obtained, affirming that the prepared adsorbent is permeable, which is an advantage for the efficient removal of contaminants. Moreover, optimal conditions for the batch removal process of the dye from water were investigated. It was found that for 100 mg L-1 AB25 dye initial concentration, the CSLAC achieved almost complete removal of 98.64% within 60 min at a temperature of 25 degrees C, by using only 0.4 g L-1 of the adsorbent dose. In addition, the Langmuir theoretical model efficiently agreed with the experimental data, and it has led to a maximum equilibrium adsorption capacity of 543.47 mg g(-1)at 25 degrees C. Kinetic studies, on the other hand, were in favor of pseudo-second-order (PSO) model to describe the dye removal from water. Others features of the CSLAC adsorbent resulted in its good regeneration and reusability. The results of theo-retical statistical modeling at temperatures varied from 25 to 40 degrees C showed a monolayer adsorption of AB25 with two energy sites of CSLAC. Various characterization methods show that the mechanism of adsorption for CSLAC towards AB25 including electrostatic attraction, hydrogen bond, and pi-pi interactions. Finally, the AB25 adsorption appeared to be an endothermic spontaneous process as evidenced by the determined thermodynamic parameters. The obtained overall data suggest that the CSLAC is an inexpensive adsorbent which has promising potential for dye removal from wastewater.

关键词： Adsorption Acid blue 25 Citrus sinensis leaf Activated carbon Theoretical statistical modeling

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Optimized Filling of a Given Cuboid with Spherical Powders for Additive Manufacturing

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Journal of the Operations Research Society of China 2021年第4期9卷 853-868页

作者： Zoya Duriagina Igor Lemishka Igor Litvinchev Jose Antonio Marmolejo Alexander Pankratov Tatiana Romanova Georgy Yaskov Lviv Polytechnic National University Lviv 79013Ukraine Katolicki Uniwersytet Lubelski Jana Pawła II Al.Racławickie 1420950 LublinPoland Graduate Program in Systems Engineering Nuevo Leon State University(UANL)MonterreyCP 66455 San Nicolas de los GarzaNuevo LeonMexico Engineering Department Panamerican UniversityCP 03920 Mexico CityMexico Department of Mathematical Modeling and Optimal Design Institute for Mechanical Engineering Problemsthe National Academy of Sciences of UkraineKharkiv 61046Ukraine Department of Systems Engineering of Kharkiv National University of Radio Electronics Kharkiv 61166Ukraine

In additive manufacturing(also known as 3D printing),a layer-by-layer buildup process is used for manufacturing *** laser 3D printers can work with various materials including metal *** particular,mixing various-sized spherical powders of titanium alloys is considered most promising for the aerospace *** achieve desired mechanical properties of the final product,it is necessary to maintain a certain proportional ratio between different powder *** this paper,a modeling approach for filling up a rectangular 3D volume by unequal spheres in a layer-by-layer manner is proposed.A relative number of spheres of a given radius(relative frequency)are known and have to be fulfilled in the final packing.A fast heuristic has been developed to solve this special packing *** results are compared with experimental findings for titanium alloy spherical *** relative frequencies obtained by using the imposed algorithm are very close to those obtained by the *** provides an opportunity for using a cheap numerical modeling instead of expensive experimental study.

关键词： Sphere packing Heuristic algorithm Titanium alloy spherical powders 3D printing

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Localized Flexoelectric Effect Around Ba(CuNb) Nano-Clusters in Epitaxial BiFeO3 Films for Enhancement of Electric and Multiferroic Properties

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ADVANCED FUNCTIONAL MATERIALS 2025年第9期35卷

作者： Song, Hyunseok Hwang, Soo-Yoon Sung, Kil-Dong Cheng, Xiaoxing Jung, Jong Hoon Park, Jung-Min Kumar, Ashok Kim, Kee Hoon Chung, Sung-Yoon Kim, Seung-Wook Chen, Long-Qing Eom, Chang-Beom Jeong, Dae-Yong Choi, Si-Young Ryu, Jungho Yeungnam Univ Sch Mat Sci & Engn Gyongsan 38541 South Korea Pohang Univ Sci & Technol Dept Mat Sci & Engn Pohang 37673 South Korea Korea Inst Mat Sci Mat Modeling & Characterizat Dept Chang Won 51508 South Korea Penn State Univ Dept Mat Sci & Engn University Pk PA 16802 USA Inha Univ Dept Phys Incheon 22212 South Korea Inha Univ Program Semicond Convergence Incheon 22212 South Korea Osaka Univ Inst Nanosci Design Grad Sch Engn Sci Toyonaka Osaka 5608531 Japan CSIR Natl Phys Lab Dr K S Krishnan Marg New Delhi 110012 India Seoul Natl Univ Dept Phys & Astron CeNSCMR Seoul 08826 South Korea Korea Adv Inst Sci & Technol Dept Mat Sci amd Engn Daejeon 34141 South Korea Inha Univ Dept Mat Sci & Engn Incheon 22212 South Korea Univ Wisconsin Madison Dept Mat Sci & Engn Madison WI 53706 USA Ctr Van der Waals Quantum Solids Inst Basic Sci Pohang 37673 South Korea Pohang Univ Sci & Technol Dept Semicond Engn Pohang 37673 South Korea Yeungnam Univ Inst Mat Technol Gyongsan 38541 South Korea

Room-temperature (RT) multiferroic materials have received significant research attention for various potential applications;however, their properties are not suitable for real-world implementation. In this study, a nano-scale localized flexoelectric effect is introduced to enhance the RT multiferroic performance of epitaxial bismuth iron oxide (BiFeO3;BFO) thin films by embedding 10 mol% Ba(Cu1/3Nb2/3)O-3 (BCN) nano-clusters into the host BFO film, which originally has a rhombohedral crystal structure. By utilizing nano-clustering, a large out-of-plane coherent strain is localized around the nano-clusters, resulting in a highly strained tetragonality of the BFO structure;subsequently, the films exhibit peculiar types of domains and domain walls, such as nano-scale rotational vortices and antiparallel dipole configurations. These peculiar domain structures, which originate from the localized flexoelectric effect at the nano-scale, enable excellent ferroelectric, ferromagnetic, and RT multiferroic magnetoelectric coupling. This study reveals that the local variation in the localized flexoelectric field around nano-clusters considerably impacts the formation of unusual domain-wall structures. This suggests that the controlled introduction of nano-clusters with different crystal structures is promising for achieving the desired multiferroic properties.

关键词： Ba(Cu1/3Nb2/3)O3 BiFeO3 flexoelectric magnetoelectric nano-clustering

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Energy-Efficient Hardware Implementation of Road-Lane Detection Based on Hough Transform with Parallelized Voting Procedure and Local Maximum Algorithm

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IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS 2019年第6期E102D卷 1171-1182页

作者： Guan, Jungang An, Fengwei Zhang, Xiangyu Chen, Lei Mattausch, Hans Juergen Hiroshima Univ HiSIM Res Ctr Higashihiroshima 7398527 Japan Hiroshima Univ Grad Sch Engn Higashihiroshima 7398527 Japan Hiroshima Univ TAOYAKA Program Higashihiroshima 7398527 Japan Hiroshima Univ VLSI Design Nanoelect & Compact Modeling Higashihiroshima 7398527 Japan

Efficient road-lane detection is expected to be achievable by application of the Hough transform (HT) which realizes high-accuracy straight-line extraction from images. The main challenge for HT-hardware implementation in actual applications is the trade-off optimization between accuracy maximization, power-dissipation reduction and real-time requirements. We report a HT-hardware architecture for road-lane detection with parallelized voting procedure, local maximum algorithm and FPGA-prototype implementation. Parallelization of the global design is realized on the basis of theta-value discretization in the Hough space. Four major hardware modules are developed for edge detection in the original video frames, computation of the characteristic edge-pixel values (rho,theta) in Hough-space, voting procedure for each (rho,theta) pair with parallel local-maximum-based peak voting-point extraction in Hough space to determine the detected straight lines. Implementation of a prototype system for real-time road-lane detection on a low-cost DE1 platform with a Cyclone II FPGA device was verified to be possible. An average detection speed of 135 frames/s for VGA (640x480)-frames was achieved at 50 MHz working frequency.

关键词： Hough transform paralleled voting-procedure local maximum video-based road-lane detection energy efficient

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BeeToxAI: An artificial intelligence-based web app to assess acute toxicity of chemicals to honey bees

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ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES 2021年 1卷

作者： Moreira-Filho, Jose T. Braga, Rodolpho C. Lemos, Jade Milhomem Alves, Vinicius M. Borba, Joyce V. V. B. Costa, Wesley S. Kleinstreuer, Nicole Muratov, Eugene N. Andrade, Carolina Horta Neves, Bruno J. Univ Fed Goias Fac Pharm LabMol Lab Mol Modeling & Drug Design BR-74605170 Goias GO Brazil InsilicAll Inc BR-04363090 Sao Paulo Brazil Univ N Carolina UNC Eshelman Sch Pharm Lab Mol Modeling Chapel Hill NC 27599 USA UniEVANGEL Ctr Univ Anapolis BR-75083515 Anapolis GO Brazil NIEHS Ctr Evaluat Alternat Toxicol Methods Natl Toxicol Program Interagcy Durham NC 27560 USA Univ Fed Paraiba Dept Pharmaceut Sci BR-58059900 Joao Pessoa PB Brazil

Chemically induced toxicity is the leading cause of recent extinction of honey bees. In this regard, we developed an innovative artificial intelligence-based web app (BeeToxAI) for assessing the acute toxicity of chemicals Apis mellifera. . Initially, we developed and externally validated QSAR models for classification (external set racy similar to 91%) through the combination of Random Forest and molecular fingerprints to predict the potential chemicals to cause acute contact toxicity and acute oral toxicity to honey bees. Then, we developed and nally validated regression QSAR models (R-2 = 0.75) using Feedforward Neural Networks (FNNs). Afterward, best models were implemented in the publicly available BeeToxAI web app ( http://***/ ) . The outputs of BeeToxAI are: toxicity predictions with estimated confidence, applicability domain estimation, and color-coded maps of relative structure fragment contributions to toxicity. As an additional assessment BeeToxAI performance, we collected an external set of pesticides with known bee toxicity that were not included in our modeling dataset. BeeToxAI classification models were able to predict four out of five pesticides correctly. The acute contact toxicity model correctly predicted all of the eight pesticides. Here we demonstrate that ToxAI can be used as a rapid new approach methodology for predicting acute toxicity of chemicals in bees.

关键词： Apis mellifera Artificial intelligence Pollinators Ecotoxicology Machine learning Predictive modeling

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Novel computational models offer alternatives to animal testing for assessing eye irritation and corrosion potential of chemicals

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ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES 2021年 1卷 100028页

作者： Silva, Arthur C. Borba, Joyce V. V. B. Alves, Vinicius M. Hall, Steven U. S. Furnham, Nicholas Kleinstreuer, Nicole Muratov, Eugene Tropsha, Alexander Andrade, Carolina Horta Univ Fed Goias UFG Fac Farm LabMol Lab Mol Modeling & Drug Design Goiania Go Brazil Univ N Carolina UNC Eshelman Sch Pharm Lab Mol Modeling Chapel Hill NC USA London Sch Hyg & Trop Med Dept Infect Biol London WC1E 7HT England NIEHS Natl Toxicol Program Interagcy Ctr Evaluat Alternat Toxicol Methods Durham NC 27709 USA Univ Fed Paraiba Dept Pharmaceut Sci BR-58059 Joao Pessoa PB Brazil

Eye irritation and corrosion are fundamental considerations in developing chemicals to be used in or near the eye, from cleaning products to ophthalmic solutions. Unfortunately, animal testing is currently the standard method to identify compounds that cause eye irritation or corrosion. Yet, there is growing pressure on the part of regulatory agencies both in the USA and abroad to develop New Approach Methodologies (NAMs) that help reduce the need for animal testing and address unmet need to modernize safety evaluation of chemical hazards. In furthering the development and applications of computational NAMs in chemical safety assessment, in this study we have collected the largest expertly curated dataset of compounds tested for eye irritation and corrosion, and employed this data to build and validate binary and multi-classification Quantitative Structure-Activity Relationships (QSAR) models that can reliably assess eye irritation/corrosion potential of novel untested compounds. QSAR models were generated with Random Forest (RF) and Multi-Descriptor Read Across (MuDRA) machine learning (ML) methods, and validated using a 5-fold external cross-validation protocol. These models demonstrated high balanced accuracy (CCR of 0.68-0.88), sensitivity (SE of 0.61-0.84), positive predictive value (PPV of 0.65-0.90), specificity (SP of 0.56-0.91), and negative predictive value (NPV of 0.68-0.85). Overall, MuDRA models outperformed RF models and were applied to predict compounds' irritation/corrosion potential from the Inactive Ingredient Database, which contains components present in FDA-approved drug products, and from the Cosmetic Ingredient Database, the European Commission source of information on cosmetic substances. All models built and validated in this study are publicly available at the STopTox web portal ( https://***/ ). These models can be employed as reliable tools for identifying potential eye irritant/corrosive compounds.

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