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Microsnoop: A generalist tool for microscopy image representation

The Innovation 2024年第1期5卷 109-117页

作者： Dejin Xun Rui Wang Xingcai Zhang Yi Wang Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China State Key Lab of Computer-Aided Design&Computer Graphics Zhejiang UniversityHangzhou 310058China John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University Hangzhou 310018China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314100China

Accurate profiling of microscopy images from small scale to high throughput is an essential procedure in basic and applied biological ***,we present Microsnoop,a novel deep learning–based representation tool trained on large-scale microscopy images using masked self-supervised *** can process various complex and heterogeneous images,and we classified images into three categories:single-cell,full-field,and batch-experiment *** benchmark study on 10 high-quality evaluation datasets,containing over 2,230,000 images,demonstrated Microsnoop’s robust and state-ofthe-art microscopy image representation ability,surpassing existing generalist and even several custom *** can be integrated with other pipelines to perform tasks such as superresolution histopathology image and multimodal ***,Microsnoop can be adapted to various hardware and can be easily deployed on local or cloud computing *** will regularly retrain and reevaluate the model using communitycontributed data to consistently improve Microsnoop.

关键词： hardware image representation

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Software Complex and Mathematical Models for Technological design of Ozone-safe Chladones Synthesis Processes

Software Complex and Mathematical Models for Technological D...

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International Conference on Control Systems, Mathematical Modelling, Automation and Energy Efficiency (SUMMA)

作者： Tamara Balabekovna Chistyakova Inna Vasilievna Novozhilova Dmitriy Vsevolodovich Doctorov Anastasia Valerievna Egorova Olga Evgenievna Bezdudnaya Computer-Aided Design and Control Systems Department World-class Laboratory Saint-Petersburg State Institute of Technology Saint-Petersburg Russia Russian Research Center Applied Chemistry (GIPH) JSC Design Institute Saint-Petersburg Russia World-class Laboratory Saint-Petersburg State Institute of Technology Saint-Petersburg Russia Computer-Aided Design and Control Systems Department Saint-Petersburg State Institute of Technology Saint-Petersburg Russia

ISBN: (数字)9798331532178

ISBN: (纸本)9798331532185

The functional structure of the problem-oriented software complex for solving the problem of designing a technological scheme for the multi-product processes for the synthesis of ozone-safe chladones is presented in the article. The inclusion of a customizable relational database of chladone characteristics in the software complex allows selecting equipment (working volumes of reactors) to form a production flow chart based on specified criteria (productivity, energy consumption, output concentrations of the target and by-products, etc.). The mathematical models library is the basis of the software complex. Mathematical models allow performing verification calculations of various reactors for the synthesis of a wide range of chladones in accordance with the technical specification. The advantage of the software complex is the ability to analyze the effect of contact time and process temperature on the output concentrations of by-products and target products with different compositions of the initial reaction mixture. The use of the software complex allows increasing the efficiency of designing chladones synthesis processes by reducing the time spent on selecting the hardware design of processes that ensure high conversion of raw materials and the required selectivity of processes for the target component.

关键词： Productivity Relational databases Software Mathematical models Raw materials Libraries Hardware Energy efficiency Kinetic theory Inductors

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Multi-omics Approach Reveals Influenza-A Virus Target Genes Associated Genomic,Clinical and Immunological Characteristics in Cancers

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Biomedical and Environmental Sciences 2024年第7期37卷 698-715页

作者： Jiaojiao Wang Yong Liao Pinglian Yang Weile Ye Yong Liu Chunxia Xiao Weixiong Liao Chunbo Chen Zhiping Liu Zunnan Huang Center of Scientific Research Department of CardiologyMaoming People’s HospitalMaoming 525000GuangdongChina Department of Pharmacy Maoming People’s HospitalMaoming 525000GuangdongChina State Key Laboratory of Bioactive Molecules and Druggability Assessment Jinan UniversityGuangzhou 510632GuangdongChina Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research College of PharmacyJinan UniversityGuangzhou 510632GuangdongChina Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University Key Laboratory of Computer-Aided Drug Design of Dongguan CityKey Laboratory for Research and Development of Natural Drugs of Guangdong ProvinceSchool of PharmacyGuangdong Medical UniversityDongguan 523808GuangdongChina Department of Critical Care Medicine Maoming People’s HospitalMaoming 525000GuangdongChina

Objective To examine the precise function of influenza A virus target genes(IATGs)in *** Using multi-omics data from the TCGA and TCPA datasets,33 tumor types were evaluated for *** expression in cancer cells was analyzed using transcriptome *** number variation(CNV)was assessed using GISTICS ***’s analysis was used to correlate mRNA expression with methylation *** was used for the enrichment ***’s correlation analysis was used to examine the association between IATG mRNA expression and *** ImmuCellAI algorithm was used to calculate the infiltration scores of 24 immune cell *** In 13 solid tumors,IATG mRNA levels were atypically *** for UCS,UVM,KICH,PCPG,THCA,CHOL,LAMI,and MESO,most cancers contained somatic IATG *** main types of CNVs in IATGs are heterozygous amplifications and *** most tumors,IATG mRNA expression is adversely associated with ***-PCR demonstrated that EGFR,ANXA5,CACNA1C,CD209,UVRAG were upregulated and CLEC4M was downregulated in KIRC cell lines,consistent with the TCGA and GTEx *** Genomic changes and clinical characteristics of IATGs were identified,which may offer fresh perspectives linking the influenza A virus to cancer.

关键词： Genomic changes Immune microenvironment Prognosis Drug resistance Experimental validation

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In silico identification of a β₂-adrenoceptor allosteric site that selectively augments canonical β₂AR-Gs signaling and function

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Proceedings of the National Academy of Sciences of the United States of America 2022年第49期119卷 e2214024119-e2214024119页

作者： Shah, Sushrut D. Lind, Christoffer De Pascali, Francesco Penn, Raymond B. MacKerell, Alexander D. Deshpande, Deepak A. Center for Translational Medicine Jane and Leonard Korman Respiratory Institute Philadelphia 19107 PA United States Department of Pharmaceutical Sciences School of Pharmacy University of Maryland Computer-Aided Drug Design Center University of Maryland Baltimore 21201 MD United States Department of Biochemistry and Molecular Biology Thomas Jefferson University Philadelphia 19107 PA United States

Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. How... 详细信息

Activation of β₂-adrenoceptors (β₂ARs) causes airway smooth muscle (ASM) relaxation and bronchodilation, and β₂AR agonists (β-agonists) are front-line treatments for asthma and other obstructive lung diseases. However, the therapeutic efficacy of β-agonists is limited by agonist-induced β₂AR desensitization and noncanonical β₂AR signaling involving β-arrestin that is shown to promote asthma pathophysiology. Accordingly, we undertook the identification of an allosteric site on β₂AR that could modulate the activity of β-agonists to overcome these limitations. We employed the site identification by ligand competitive saturation (SILCS) computational method to comprehensively map the entire 3D structure of in silico-generated β₂AR intermediate conformations and identified a putative allosteric binding site. Subsequent database screening using SILCS identified drug-like molecules with the potential to bind to the site. Experimental assays in HEK293 cells (expressing recombinant wild-type human β₂AR) and human ASM cells (expressing endogenous β₂AR) identified positive and negative allosteric modulators (PAMs and NAMs) of β₂AR as assessed by regulation of β-agonist-stimulation of cyclic AMP generation. PAMs/NAMs had no effect on β-agonist-induced recruitment of β-arrestin to β₂AR- or β-agonist-induced loss of cell surface expression in HEK293 cells expressing β₂AR. Mutagenesis analysis of β₂AR confirmed the SILCS identified site based on mutants of amino acids R131, Y219, and F282. Finally, functional studies revealed augmentation of β-agonist-induced relaxation of contracted human ASM cells and bronchodilation of contracted airways. These findings identify a allosteric binding site on the β₂AR, whose activation selectively augments β-agonist-induced Gs signaling, and increases relaxation of ASM cells, the principal thera

关键词： adrenergic receptor allosteric modulator asthma biased signaling SILCS

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Improving the binding affinity and interaction of 5-Pentyl-2-Phenoxyphenol against Mycobacterium Enoyl ACP reductase by computational approach

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Informatics in Medicine Unlocked 2021年 23卷

作者： Shawon, Jakaria Khan, Akib Mahmud Shahriar, Imrul Halim, Mohammad A. Division of Computer-aided Drug Design The Red-Green Research Center BICCB Dhaka Bangladesh

Tuberculosis (TB) is one of the leading causes of death worldwide. The development of new anti-tubercular drugs is required as resistant strains of M. tuberculosis to various first-line drugs are currently available. In this study, different fragments and functional groups were used to modify 5-Pentyl-2-phenoxyphenol (5PP) drug. Density functional theory was utilized for the geometric optimization of the modified drug structures. Flexible docking of the parent and all modified drugs was performed against Mycobacterium Enoyl ACP Reductase (2B36) to calculate and compare their binding affinities and non-covalent interactions. Increased non-bonded interactions along with improved binding energy are visualized for the modified drugs (J1, J2, and J3) compared to those for the parent drug J. All the modified drugs remain stably bound to the binding pocket of InhA after 100ns MD simulation. Binding free energy calculation from MD simulation also shows stable binding of the drugs with the target protein. Ensemble-based molecular docking was further performed to account for the receptor dynamics and flexibility. Variation in binding energy for a drug-protein complex is observed when protein flexibility is taken into consideration. Moreover, we found that residues Ala157, Tyr158, Ala198, Met199, and Ile215 of protein InhA are important for drug-protein interaction. Improved pharmacokinetic properties are also observed for the modified drugs compared to those for 5PP. © 2021 The Author(s)

关键词： Drug design Enoyl-acyl ACP reductase (InhA) Ensemble-based docking Molecular docking Molecular dynamics simulation Quantum mechanical calculation Tuberculosis (TB)

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Current strategies to address data scarcity in artificial intelligence-based drug discovery: A comprehensive review

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computers in Biology and Medicine 2024年 179卷 108734-108734页

作者： Gangwal, Amit Ansari, Azim Ahmad, Iqrar Azad, Abul Kalam Wan Sulaiman, Wan Mohd Azizi Department of Natural Product Chemistry Shri Vile Parle Kelavani Mandal's Institute of Pharmacy Maharashtra Dhule424001 India Computer Aided Drug Design Center Shri Vile Parle Kelavani Mandal's Institute of Pharmacy Maharashtra Dhule424001 India Department of Pharmaceutical Chemistry Prof. Ravindra Nikam College of Pharmacy Gondur Maharashtra Dhule424002 India Faculty of Pharmacy University College of MAIWP International Batu Caves Kuala Lumpur68100 Malaysia

Artificial intelligence (AI) has played a vital role in computer-aided drug design (CADD). This development has been further accelerated with the increasing use of machine learning (ML), mainly deep learning (DL), and computing hardware and software advancements. As a result, initial doubts about the application of AI in drug discovery have been dispelled, leading to significant benefits in medicinal chemistry. At the same time, it is crucial to recognize that AI is still in its infancy and faces a few limitations that need to be addressed to harness its full potential in drug discovery. Some notable limitations are insufficient, unlabeled, and non-uniform data, the resemblance of some AI-generated molecules with existing molecules, unavailability of inadequate benchmarks, intellectual property rights (IPRs) related hurdles in data sharing, poor understanding of biology, focus on proxy data and ligands, lack of holistic methods to represent input (molecular structures) to prevent pre-processing of input molecules (feature engineering), etc. The major component in AI infrastructure is input data, as most of the successes of AI-driven efforts to improve drug discovery depend on the quality and quantity of data, used to train and test AI algorithms, besides a few other factors. Additionally, data-gulping DL approaches, without sufficient data, may collapse to live up to their promise. Current literature suggests a few methods, to certain extent, effectively handle low data for better output from the AI models in the context of drug discovery. These are transferring learning (TL), active learning (AL), single or one-shot learning (OSL), multi-task learning (MTL), data augmentation (DA), data synthesis (DS), etc. One different method, which enables sharing of proprietary data on a common platform (without compromising data privacy) to train ML model, is federated learning (FL). In this review, we compare and discuss these methods, their recent applications, and limitatio

关键词： Molecules

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Immiscible-interface assisted direct metal drawing 29

Immiscible-interface assisted direct metal drawing

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29th Annual International Solid Freeform Fabrication Symposium - An Additive Manufacturing Conference, SFF 2018

作者： He, Li Fei, Fan Wang, Wenbo Song, Xuan Department of Industrial and Systems Engineering University of Iowa Iowa CityIA52242 United States Center for Computer Aided Design University of Iowa Iowa CityIA52242 United States

State-of-the-art metal additive manufacturing (AM) techniques construct a three-dimensional (3D) structure through sintering or melting dry metal powders in a layer-by-layer fashion, which consequently results in some typical manufacturing defects in the final structure, such as residual stress and highly-orientated microstructures. To overcome these defects, we present a new low-cost metal AM process, named Immiscible-interface assisted Direct Metal Drawing (II-DMD), which fabricates self-supported and isotropic 3D metal structures by continuously extruding a metal colloidal suspension within a second immiscible matrix colloidal suspension. The shape of the metal colloidal suspension is stabilized due to the presence of an immiscible interface between the two colloidal suspension systems. Dense metal structures can be achieved via post-consolidation of the self-stabilized metal-matrix systems, including liquid-phase drying and metal-phase sintering. In this article, the immiscible-interface-assisted self-stabilization mechanism is studied. The post-consolidation processes are discussed. Several test cases were fabricated and characterized. © Solid Freeform Fabrication 2018: Proceedings of the 29th Annual International Solid Freeform Fabrication Symposium - An Additive Manufacturing Conference, SFF 2018. All Rights Reserved.

关键词： Additives

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Cosmic voids and the kinetic analysis IV. Hubble tension and the cosmological constant

arXiv

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arXiv 2025年

作者： Gurzadyan, V.G. Fimin, N.N. Chechetkin, V.M. Center for Cosmology and Astrophysics Alikhanian National Laboratory Alikhanian Brothers str.2 0036 Armenia Yerevan State University Manukian str.1 Yerevan0025 Armenia SIA Sapienza Universita di Roma Via Salaria 851/881 Rome00191 Italy Keldysh Institute of Applied Mathematics of RAS Miusskaya Sq. 4 Moscow125047 Russia Institute of Computer Aided Design of RAS 2nd Brestskaya st. Moscow123056 Russia

The formation of cosmic structures in the late Universe was considered using the Vlasov kinetic approach. The crucial point is the use of the gravitational potential with repulsive term of the cosmological constant, which provides a solution to the Hubble tension, that is, the Hubble parameter for the late Universe has to differ from its global cosmological value. This also provides a mechanism of formation of stationary semi-periodic gravitating structures of voids and walls, so that the cosmological constant has the role of the scaling. It can therefore be compared with the observational data for given regions. The considered mechanism of the structure formation in the late cosmological epoch then succeeds the epoch described by the evolution of primordial density fluctuations. Copyright © 2025, The Authors. All rights reserved.

关键词： Cosmology

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Cosmic voids and the kinetic analysis: III. Hubble tension and structure formation in the late Universe

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Astronomy and Astrophysics 2023年 677卷

作者： Gurzadyan, V.G. Fimin, N.N. Chechetkin, V.M. Center for Cosmology and Astrophysics Alikhanian National Laboratory Yerevan State University Alikhanian Brothers str. 2 0036 Manukian str.1 Yerevan0025 Armenia SIA Sapienza Universita di Roma Via Salaria 851/881 Rome Italy Keldysh Institute of Applied Mathematics of RAS Miusskaya Sq. 4 Moscow125047 Russia Institute of Computer Aided Design of RAS 2nd Brestskaya st. Moscow123056 Russia

We study structure formation in the late Universe within the Vlasov kinetic self-consistent field approach. Our work is principally focused on the use of the modified gravitational potential with a repulsive term of the cosmological constant, which is directly linked to observations that enable characterizations of the Hubble tension as the result of local and global flows. We formulate the criteria for the formation of the semi-periodic gravitating structures, along with the predictions of their quantitative scales associated with observable parameters. Our principal conclusion is that filament formation in the Local (late) Universe can proceed as a deterministic process that is distinct from the structures at larger scales that result from the essentially stochastic dynamics of density perturbations. © The Authors 2023.

关键词： Stochastic systems

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Cosmic voids and the kinetic analysis. III. Hubble tension and structure formation in the late Universe

arXiv

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arXiv 2023年

关键词： Stochastic systems

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