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cytoNet: Spatiotemporal network analysis of cell communities (vol 18, e1009846, 2022)

PLOS COMPUTATIONAL BIOLOGY 2022年第11期18卷 e1009846页

作者： Mahadevan, A. S. Long, B. L. Hu, C. W. Ryan, D. T. Grandel, N. E. Department of Bioengineering University of Pennsylvania Philadelphia Pennsylvania United States of America. Department of Bioengineering Rice University Houston Texas United States of America. Systems Synthetic and Physical Biology Program Rice University Houston Texas United States of America. Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America. Biophysics Graduate Program University of California Berkeley California United States of America. Department of Oral & Maxillofacial Surgery University of Texas Health Science Center at San Antonio San Antonio Texas United States of America. Department of Electrical and Computer Engineering Rice University Houston Texas United States of America.

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet's capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin α4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.

关键词： Calcium imaging Fluorescence imaging Growth factors Centrality Cell cycle and cell division Endothelial cells Network analysis Stem cells

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Lightweight equivariant model for efficient machine learning interatomic potentials

arXiv

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arXiv 2023年

作者： Yang, Ziduo Wang, Xian Li, Yifan Lv, Qiujie Chen, Calvin Yu-Chian Shen, Lei Department of Mechanical Engineering National University of Singapore Singapore117575 Singapore Artificial Intelligence Medical Research Center School of Intelligent Systems Engineering Shenzhen Campus of Sun Yat-sen University Shenzhen518107 China Department of Physics National University of Singapore Singapore117551 Singapore -Preferred Program School of Electronic and Computer Engineering Peking University Shenzhen Graduate School Shenzhen518055 China State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen518055 China Guangdong L-Med Biotechnology Co. Ltd Guangdong Meizhou514699 China Research Institute Chongqing401123 China

In modern computational materials science, deep learning has shown the capability to predict interatomic potentials, thereby supporting and accelerating conventional simulations. However, existing models typically sacrifice either accuracy or efficiency. Moreover, lightweight models are highly demanded for offering simulating systems on a considerably larger scale at reduced computational costs. Here, we introduce a lightweight equivariant interaction graph neural network (LEIGNN) that can enable accurate and efficient interatomic potential and force predictions for molecules and crystals. Rather than relying on higher-order representations, LEIGNN employs a scalar-vector dual representation to encode equivariant features. By learning geometric symmetry information, our model remains lightweight while ensuring prediction accuracy and robustness through the equivariance. Our results show that LEIGNN consistently outperforms the prediction performance of the representative baselines and achieves significant efficiency across diverse datasets, which include catalysts, molecules, and organic isomers. Furthermore, we conduct molecular dynamics (MD) simulations using the LEIGNN force field across solid, liquid, and gas systems. It is found that LEIGNN can achieve the accuracy of ab initio MD across all examined systems. Copyright © 2023, The Authors. All rights reserved.

关键词： Prediction models

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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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ARCSnake: Reconfigurable snake-like robot with Archimedean screw propulsion for multi-domain mobility

arXiv

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arXiv 2021年

作者： Richter, Florian Gavrilov, Peter V. Lam, Hoi Man Degani, Amir Yip, Michael C. The Department of Electrical and Computer Engineering University of California San Diego San DiegoCA92093 United States The Department of Mechanical and Aerospace Engineering University of California San Diego San DiegoCA92093 United States The Faculty of Civil and Environmental Engineering The Technion Autonomous Systems Program Technion - Israel Institute of Technology Haifa3200003 Israel

Exploring and navigating in extreme environments, such as caves, oceans, and planetary bodies, are often too hazardous for humans, and as such, robots are possible surrogates. These robots are met with significant locomotion challenges that require traversing a wide range of surface roughnesses and topologies. Previous locomotion strategies, involving wheels or ambulatory motion, such as snake platforms, have success on specific surfaces but fail in others which could be detrimental in exploration and navigation missions. In this paper, we present a novel approach that combines snake-like robots with an Archimedean screw locomotion mechanism to provide multiple, effective mobility strategies in a large range of environments, including those that are difficult to traverse for wheeled and ambulatory robots. This work develops a robotic system called ARCSnake to demonstrate this locomotion principle and tested it in a variety of different terrains and environments in order to prove its controllable, multi-domain, navigation capabilities. These tests show a wide breadth of scenarios that ARCSnake can handle, hence demonstrating its ability to traverse through extreme terrains. Copyright © 2021, The Authors. All rights reserved.

关键词： Screws

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Applying mobility business intelligence concept in analyzing oil palm plantation productivity

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AIP Conference Proceedings 2024年第1期3026卷

作者： Andreas Wahyu Krisdiarto Irya Wisnubhadra Anzaludin Samsinga Perbangsa Teddy Suparyanto Bens Pardamean Faculty of Agricultural Technology STIPER Institute of Agriculture Yogyakarta Indonesia Informatics Engineering Department Atma Jaya Yogyakarta University Yogyakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia BDSRC Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia

The palm oil business employs almost 20 million people, generates USD 21 billion in revenue, and plays a vital role in Indonesia’s social economy. The Fresh Fruit Bunches (FFB) to Palm Oil Mills (POM) distribution system is one important aspect of fruit quality. Three steps are involved in getting Oil Palm FFB from the plantation to the POM. The first part of the procedure involves cutting FFB from the tree, the second stage involves gathering the fruit at a fruit collection point (FCP), and the third stage involves transporting the fruit to the palm oil mill (POM). As of now, the cost of the FFB transportation is still considerable, accounting for roughly 15% to 20% of the FFB pricing. The use of the Business Intelligence (BI) idea in the oil palm harvesting system is presented in this study as a foundation for creating web-based applications.

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Versatile Test Reactor Open Digital engineering Ecosystem

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Insight 2022年第1期25卷 56-60页

作者： Ritter, Christopher Browning, Jeren Suyderhoud, Peter Hays, Ross Marshall, AnnMarie Han, Kevin Ashbocker, Taylor Darrington, John Nelson, Lee Idaho National Laboratory Department of Digital Systems & Engineering Versatile Test Reactor Program Idaho FallsID83401 United States Pivotal Solutions 3 Grace Avenue Suite 162 Great NeckNY11021 United States North Carolina State University Department of Civil and Environmental Engineering and Department of Computer Science University of Illinois at Urbana-Champaign 205 N. Mathews Ave. UrbanaIL61801 United States

Modern design of nuclear facilities represents unique challenges: enabling the design of complex advanced concepts, supporting geographically dispersed teams, and supporting first-of-a-kind system development. Errors made early in design can introduce silent errors. These errors can cascade causing unknown risk of complex engineering programs. The Versatile Test Reactor (VTR) program uses digital-engineering principles for design, procurement, construction, and operation to reduce risk and improve efficiencies. Digital engineering is an integrated, model-based approach which connects proven digital tools such as building information management (BIM), project controls, and systems-engineering software tools into a cohesive environment. The VTR team hypothesizes using these principals can lead to similar risk and cost reductions and schedule efficiencies observed in other engineering industries. This research investigates the use of a digital engineering ecosystem in the design of a 300-MWt sodium-cooled fast reactor. This ecosystem was deployed to over 200 engineers and used to deliver the conceptual design of the VTR. We conclude that initial results show significant reductions in user latency (1000x at peak use), the possibility of direct finite-element-analysis (FEA) integrations to computer-aided design (CAD) tools, and nuclear reactor system design descriptions (SDDs) that we can fully link throughout design in data-driven requirements-management software. These early results led to the VTR maintaining milestone performance during the COVID-19 pandemic. © 2022 by Idaho National Laboratory. Published by INCOSE with permission.

关键词： Software testing

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Spatial atlas of the mouse central nervous system at molecular resolution (vol 622, pg 552, 2023)

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NATURE 2024年第7993期625卷 E6-E6页

作者： Shi, Hailing He, Yichun Zhou, Yiming Huang, Jiahao Maher, Kamal Wang, Brandon Tang, Zefang Luo, Shuchen Tan, Peng Wu, Morgan Lin, Zuwan Ren, Jingyi Thapa, Yaman Tang, Xin Chan, Ken Y. Deverman, Benjamin E. Shen, Hao Liu, Albert Liu, Jia Wang, Xiao Broad Institute of MIT and Harvard Cambridge MA USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA USA John A. Paulson School of Engineering and Applied Sciences Harvard University Boston MA USA Computational and Systems Biology PhD Program Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge MA USA Department of Chemistry and Chemical Biology Harvard University Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA

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Utilization of response surface methodology in optimization of de-oiled olive pomace activated biochar production 6

Utilization of response surface methodology in optimization ...

引用

6th Environmental Technology and Management Conference, ETMC 2019

作者： Abarca, Ralf Ruffel De Luna, Mark Daniel Chakraborty, Sudip Curcio, Stefano Candamano, Sebastiano Department of Chemical Engineering and Technology Mindanao State University Iligan Institute of Technology Iligan City9200 Philippines Environmental Engineering Program University of the Philippines-Diliman Quezon City1101 Philippines Department of Chemical Engineering University of the Philippines-Diliman Quezon City1101 Philippines Laboratory of Transport Phenomena and Biotechnology Department of Computer Engineering Modeling Electronics and Systems University of Calabria Rende87036 Italy Department of Environmental and Chemical Engineering University of Calabria Rende87036 Italy

Olive activated biochar (OAB) was prepared from waste de-oiled olive pomace (sansa esausta, SE) through carbonization followed by combined KOH and thermal activation. The activation process was optimized using central composite design (CCD) with pyrolysis temperature, activation time and KOH to pyrolized SE mass ratio (KOH/PSE) as independent variables, and yield, methylene blue number (MBN) and iodine number (ID) as responses. Optimized OAB was subjected to fixed bed adsorption of 100 mg L-1 methylene blue dye. Numerical optimization resulted in optimum process setting of 362°C pyrolysis temperature, 61-min activation time and 0.81 KOH/PSE under which the optimized activated biochar produced 31% OAB, MBN of 679 and ID of 899. Thomas and Yoon-Nelson models best fit the fixed bed adsorption data implying that methylene blue adsorption conforms to Langmuir isotherm and obeys pseudo-second order reversible reaction kinetics with no axial dispersion. The theoretical adsorption capacity of OAB is 131 mg g-1 with theoretical time required for 50% sorbate breakthrough of 54.69 h. These results show the potential application of OAB in dye adsorption. © 2020 The Authors, published by EDP Sciences.

关键词： Carbonization

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Clarifying Assumptions about Artificial Intelligence before Revolutionising Patent Law

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GRUR International 2022年第4期71卷 295-321页

作者： Kim, Daria Alber, Maximilian Kwok, Man Wai Mitrovic, Jelena Ramirez-Atencia, Cristian Perez, Jesus Alberto Rodriguez Zille, Heiner Max Planck Institute for Innovation and Competition Munich Germany Charite Institute of Pathology Berlin Germany Chinese University of Hong Kong Department of Physics (Formerly) Hong Kong BMBF Program for Women in AI Faculty of Computer Science and Mathematics Chair of Data Science University of Passau Germany Department of Computer Systems Universidad Politecnica de Madrid Spain School of Computing Science College of Science and Engineering University of Glasgow United Kingdom Faculty of Computer Science Otto von Guericke University Magdeburg Germany

This paper examines several widespread assumptions about artificial intelligence, particularly machine learning, that are often taken as factual premises in discussions on the future of patent law in the wake of 'artificial ingenuity'. The objective is to draw a more realistic and nuanced picture of the human-computer interaction in solving technical problems than where 'intelligent' systems autonomously yield inventions. A detailed technical perspective is presented for each assumption, followed by a discussion of pertinent uncertainties for patent law. Overall, it is argued that implications of machine learning for the patent system in its core tenets appear far less revolutionary than is often posited. © 2022 Published by OUP and CH Beck on behalf of GRUR e.V.

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Accelerating Real-Time Imaging for Radiotherapy: Leveraging Multi-GPU Training with PyTorch

Accelerating Real-Time Imaging for Radiotherapy: Leveraging ...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Ruth Obe Brandt Kaufmann Kaelen Baird Sam Kadel Yasmin Soltani Mostafa Cham Matthias K. Gobbert Carlos A. Barajas Zhuoran Jiang Vijay R. Sharma Lei Ren Stephen W. Peterson Jerimy C. PoIf Dept. of Computer Science and of Software Engineering U. of Houston-Clear Lake USA Dept. of Mathematics and Statistics U. of San Francisco USA Dept. of Computer Science and of Mathematics Skidmore College USA Dept. of Computer Science and of Psychology Mount Holyoke College USA Dept. of Biomedical Engineering U. of Houston USA Dept. of Information Systems U. of Maryland Baltimore County Dept. of Mathematics and Statistics U. of Maryland Baltimore County Medical Physics Graduate Program Duke University USA Dept. of Radiation Oncology U. of Maryland School of Medicine USA Department of Radiation Oncology U. of Maryland School of Medicine USA Dept. of Physics U. of Cape Town South Africa H3D Inc. USA

Proton beam therapy is an advanced form of cancer radiotherapy that uses high-energy proton beams to deliver precise and targeted radiation to tumors. This helps to mit-igate unnecessary radiation exposure in healthy tissues. Real-time imaging of prompt gamma rays with Compton cameras has been suggested to improve therapy efficacy. However, the camera's non-zero time resolution leads to incorrect interaction classifications and noisy images that are insufficient for accurately assessing proton delivery in patients. To address the challenges posed by the Compton camera's image quality, machine learning techniques are employed to classify and refine the generated data. These machine-learning techniques include recurrent and feedforward neural networks. A PyTorch model was designed to improve the data captured by the Compton camera. This decision was driven by PyTorch's flexibility, powerful capabilities in handling sequential data, and enhanced G PU usage. This accelerates the model's computations on large-scale radiotherapy data. Through hyperparameter tuning, the validation accuracy of our PyTorch model has been improved from an initial 7 % to over 60 %. Moreover, the PyTorch Distributed Data Parallelism strategy was used to train the RNN models on multiple G PU s, which significantly reduced the training time with a minor impact on model accuracy.

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