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arXiv 2020年

作者： Yeshasvi Tirupachuri, Venkata Sai University of Genova PhD Program in Bioengineering and Robotics

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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences

Dish-Trend: Intervention Modeling Simulator That Accounts fo...

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2021 Winter Simulation Conference, WSC 2021

作者： Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh PittsburghPA15213 United States

ISBN: (纸本)9781665433112

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend-and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies. © 2021 IEEE.

关键词： Directed graphs

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Advances in liposomal nanotechnology: from concept to clinics

RSC Pharmaceutics

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RSC Pharmaceutics 2024年第5期1卷 928-948页

作者： Reem M. Senjab Nour AlSawaftah Waad H. Abuwatfa Ghaleb A. Husseini Biomedical Engineering Program College of Engineering American University of Sharjah Sharjah P.O. Box 26666 United Arab Emirates ghusseini@aus.edu Materials Science and Engineering Ph.D. Program College of Arts and Sciences American University of Sharjah Sharjah P.O. Box 26666 United Arab Emirates Department of Chemical and Biological Engineering College of Engineering American University of Sharjah Sharjah P.O. Box 26666 United Arab Emirates Biosciences and Bioengineering PhD Program College of Engineering American University of Sharjah Sharjah P.O. Box 26666 United Arab Emirates

Liposomes, spherical phospholipid vesicles with a unique morphology mimicking that of body cells, have emerged as versatile nanoparticles for drug delivery. Their biocompatibility, low cytotoxicity, targeted delivery, and hydrophobic and hydrophilic characteristics make them stand out over traditional drug delivery systems. Liposomes can be tailored in size, composition, lamellarity, and surface charge, offering a unique level of customization for various applications. Extensive research in liposome technology has led to the development of a wide range of liposomal formulations with enhanced functionalities, such as PEGylated liposomes, ligand-targeted liposomes, and stimuli-responsive liposomes. Beyond their crucial role in cancer treatment, liposomes play a significant role in influenza, COVID-19, cancer, and hepatitis A vaccines. They are also utilized in pain management, fungal treatment, brain targeting, and topical and ocular drug delivery. This review offers insight into the types of liposomes, their composition, preparation methods, characterization methods, and clinical applications. Additionally, it discusses challenges and highlights potential future directions in liposome-based drug delivery.

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Extracellular respiration is a latent energy metabolism in Escherichia coli

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Cell 2025年第11期188卷 2907-2924.e23页

作者： Kundu, Biki Bapi Krishnan, Jayanth Szubin, Richard Patel, Arjun Palsson, Bernhard O. Zielinski, Daniel C. Ajo-Franklin, Caroline M. PhD Program in Systems Synthetic and Physical Biology Rice University Houston 77005 TX United States Department of Bioengineering University of California San Diego La Jolla 92093 CA United States Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Kemitorvet Building 220 Kgs. Lyngby 2800 Denmark Departments of Biosciences Bioengineering Chemical and Biomolecular Engineering and The Rice Synthetic Biology Institute Rice University Houston 77005 TX United States

Diverse microbes utilize redox shuttles to exchange electrons with their environment through mediated extracellular electron transfer (EET), supporting anaerobic survival. Although mediated EET has been leveraged for bioelectrocatalysis for decades, fundamental questions remain about how these redox shuttles are reduced within cells and their role in cellular bioenergetics. Here, we integrate genome editing, electrochemistry, and systems biology to investigate the mechanism and bioenergetics of mediated EET in Escherichia coli, elusive for over two decades. In the absence of alternative electron sinks, the redox cycling of 2-hydroxy-1,4-naphthoquinone (HNQ) via the cytoplasmic nitroreductases NfsB and NfsA enables E. coli respiration on an extracellular electrode. E. coli also exhibits rapid genetic adaptation in the outer membrane porin OmpC, enhancing HNQ-mediated EET levels coupled to growth. This work demonstrates that E. coli can grow independently of classic electron transport chains and fermentation, unveiling a potentially widespread new type of anaerobic energy metabolism. © 2025 Elsevier Inc.

关键词： adaptive laboratory evolution anaerobic metabolism electron shuttles extracellular electron transfer flux balance analysis iModulon analysis nitroreductases redox homeostasis

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Multivariate Developmental Pattern of Cortical Thickness, Brain Functional Connectivity and Behaviour: A Multi-Block Partial Least Square Discriminant Analysis 3

Multivariate Developmental Pattern of Cortical Thickness, Br...

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3rd IEEE International Conference on Metrology for eXtended Reality, Artificial Intelligence and Neural Engineering, MetroXRAINE 2024

作者： Tassi, Emma Goffi, Federica Bonivento, Carolina Mauri, Maddalena Agarwal, Nivedita Girometti, Rossano Torrente, Yvan Bianchi, Anna Maria Nobile, Maria Maggioni, Eleonora Brambilla, Paolo Irccs Ca' Granda Ospedale Maggiore Policlinico Dept. of Neurosciences and Mental Health Milan Italy Politecnico di Milano Department of Electronics Information and Bioengineering Milan Italy Polo Fvg Scientific Institute Irccs 'Eugenio Medea' Pasian di Prato Udine Italy Child Psychopathology Unit Scientific Institute Irccs Eugenio Medea Bosisio Parini Italy School of Medicine and Surgery University of Milano-Bicocca PhD program in Neuroscience Milan Italy Scientific Institute Irccs E. Medea Neuroimaging Lab Bosisio Parini Italy Institute of Radiology University of Udine Department of Medicine Udine Italy Universita degli Studi di Milano Department of Pathophysiology and Transplantation Milan Italy

ISBN: (纸本)9798350378009

The intricate relationship between emotional and behavioral traits and brain anatomy and function during childhood and adolescence is crucial for elucidating the neurobiological basis of diverse psychopathological disorders but it still largely unknown. In this study, we aimed to quantitatively evaluate the multivariate patterns of association between brain activity, cortical brain characteristics, and core clinical and behavioral features in a sample of forty subjects with age ranging between 11-21 years who were referred for emotional-behavioral problems. By exploiting a multi-block partial least square discriminant analysis (MBPLS-DA) framework, we attempt to explain the multivariate relations among the Child Behavior Checklist (CBCL) and brain structure and function assessed via magnetic resonance imaging (MRI). Based on individual importance of each block, our findings showed a prominent contribution of regional cortical thickness data in explaining the variance of CBCL scales. By analyzing each block's loadings individually, a prominent positive association was found among regional cortical thickness in paracentral, lateral occipital cortex, precuneus and CBCL composite scores of psychotic, autism spectrum disorder risk profiles and withdrawn scale. Furthermore, the same CBCL scores were also found positively associated with functional connections involving regions of anterior and median cingulate cortex, caudate nucleus, inferior parietal lobule and angular gyrus. Our investigation suggests a key role of brain structure and function in shaping behavioral traits that might be predispose to psychopathology during childhood and adolescence. The proposed MBPLS-DA application promotes broader adoption of this technique across diverse and multimodal MRI and clinical datasets. © 2024 IEEE.

关键词： Magnetic resonance imaging

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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences

Dish-Trend: Intervention Modeling Simulator That Accounts fo...

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Simulation Winter Conference

作者： Stefan Andjelkovic Natasa Miskov-Zivanov Computational and Systems Biology Joint Carnegie Mellon University and University of Pittsburgh Computational Biology PhD Program University of Pittsburgh Pittsburgh PA USA Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh Pittsburgh PA USA

ISBN: (纸本)9781665433129

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend- and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies.

关键词： Regulators Toy manufacturing industry Stochastic processes Predictive models Market research Regulation Data models

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BPS2025 - Flexible and robust labeling and tracking of non-repetitive genomic loci

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Biophysical Journal 2025年第3期124卷 353a-353a页

作者： Alex Raterink Rajarshi P. Ghosh Quanming Shi Linfeng Yang Minh Khue Nguyen Anna-Karin Gustavsson Systems Synthetic and Physical Biology PhD Program Rice University Houston TX USA Howard Hughes Medical Institute University of California Berkeley CA USA Department of Bioengineering Stanford University Stanford CA USA Department of Chemistry Rice University Houston TX USA Department of Biosciences Rice University Houston TX USA

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Dish-trend: Intervention modeling simulator that accounts for trend influences

arXiv

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arXiv 2021年

作者： Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh 4420 Bayard St PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh 4420 Bayard St PittsburghPA15213 United States

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend- and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies. Copyright © 2021, The Authors. All rights reserved.

关键词： Stochastic systems

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Multivariate Developmental Pattern of Cortical Thickness, Brain Functional Connectivity and Behaviour: a Multi-Block Partial Least Square Discriminant Analysis

Multivariate Developmental Pattern of Cortical Thickness, Br...

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Metrology for Extended Reality, Artificial Intelligence and Neural Engineering (MetroXRAINE), IEEE International Conference on

作者： Emma Tassi Federica Goffi Carolina Bonivento Maddalena Mauri Nivedita Agarwal Rossano Girometti Yvan Torrente Anna Maria Bianchi Maria Nobile Eleonora Maggioni Paolo Brambilla Dept. of Neurosciences and Mental Health IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milan Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy Polo FVG Scientific Institute IRCCS ‘Eugenio Medea’ Pasian di Prato Udine Italy Child Psychopathology Unit Scientific Institute IRCCS Eugenio Medea Bosisio Parini Italy PhD program in Neuroscience School of Medicine and Surgery University of Milano-Bicocca Milan Italy Neuroimaging Lab Scientific Institute IRCCS E. Medea Bosisio Parini Italy Department of Medicine Institute of Radiology University of Udine Udine Italy Department of Pathophysiology and Transplantation Universita degli Studi di Milano Milan Italy

ISBN: (数字)9798350378009

ISBN: (纸本)9798350378016

The intricate relationship between emotional and behavioral traits and brain anatomy and function during childhood and adolescence is crucial for elucidating the neurobiological basis of diverse psychopathological disorders but it still largely unknown. In this study, we aimed to quantitatively evaluate the multivariate patterns of association between brain activity, cortical brain characteristics, and core clinical and behavioral features in a sample of forty subjects with age ranging between 11–21 years who were referred for emotional-behavioral problems. By exploiting a multi-block partial least square discriminant analysis (MBPLS-DA) framework, we attempt to explain the multivariate relations among the Child Behavior Checklist (CBCL) and brain structure and function assessed via magnetic resonance imaging (MRI). Based on individual importance of each block, our findings showed a prominent contribution of regional cortical thickness data in explaining the variance of CBCL scales. By analyzing each block's loadings individually, a prominent positive association was found among regional cortical thickness in paracentral, lateral occipital cortex, precuneus and CBCL composite scores of psychotic, autism spectrum disorder risk profiles and withdrawn scale. Furthermore, the same CBCL scores were also found positively associated with functional connections involving regions of anterior and median cingulate cortex, caudate nucleus, inferior parietal lobule and angular gyrus. Our investigation suggests a key role of brain structure and function in shaping behavioral traits that might be predispose to psychopathology during childhood and adolescence. The proposed MBPLS-DA application promotes broader adoption of this technique across diverse and multimodal MRI and clinical datasets.

关键词： Brain Magnetic resonance imaging Computed tomography Loading Neural engineering Focusing Metrology Resonance Thickness measurement Periodic structures

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High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH

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Cell 2025年

作者： Zhu, Yanyu Balaji, Ashwin Han, Mengting Andronov, Leonid Roy, Anish R. Wei, Zheng Chen, Crystal Miles, Leanne Cai, Sa Gu, Zhengxi Tse, Ariana Yu, Betty Chentzu Uenaka, Takeshi Lin, Xueqiu Spakowitz, Andrew J. Moerner, W.E. Qi, Lei S. Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Chemistry Stanford University Stanford 94305 CA United States Biophysics PhD Program Stanford University Stanford 94305 CA United States Computational Biology Program Public Health Sciences Division and Translational Data Science IRC Fred Hutchinson Cancer Center Seattle 98109 WA United States Department of Chemical Engineering Stanford University Stanford 94305 CA United States Department of Materials Science and Engineering Stanford University Stanford 94305 CA United States Institute for Stem Cell Biology & Regenerative Medicine and Department of Pathology Stanford University School of Medicine Stanford 94305 CA United States Sarafan ChEM-H Stanford University Stanford 94305 CA United States Chan Zuckerberg Biohub San Francisco 94080 CA United States

Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease. © 2025 Elsevier Inc.

关键词： CRISPR imaging DNA communication dynamic tracking enhancer-promoter interaction high-resolution imaging live DNA imaging non-repetitive genome imaging Oligo-LiveFISH polymer modeling primary cell

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