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Robot Hand Interaction Using Plastic Deformation Control with Inner Position Loop

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IEEE/ASME (AIM) International Conference on Advanced Intelligent Mechatronics

作者： Kenichi Murakami Koki Ishimoto Taku Senoo Masatoshi Ishikawa Data Science Research Division Information Technology Center The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo Japan Department of Information Physics and Computing The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo Japan Electrical Systems and Control Engineering Program Graduate School of Advanced Science and Engineering Hiroshima University 1-4-1 Kagamiyama Higashi-Hiroshima City Hiroshima Japan

ISBN: (数字)9781728167947

ISBN: (纸本)9781728167954

In this study, the inner position loop addition for plastic deformation control of the error robustness of the model and actual parameters is proposed. The inner position loop is a type of position feedback control based on the estimation of model parameters and dynamics of robots. This position control system with proportional and derivative gains modifies the trajectory of the end effector close to the desired trajectory. The robustness of the proposed control scheme is evaluated by comparing it with plastic deformation control without an inner position loop in both simulation and actual environments. Finally, the stable reaction with the proposed control is demonstrated for the case where a human pushes the robot finger.

关键词： Strain Plastics Force Deformable models Robots Friction Trajectory

Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms

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Environmental microbiology reports 2025年第3期17卷 e70121页

作者： Saru Gurung Chang-Muk Lee Hang-Yeon Weon So-Ra Han Tae-Jin Oh Department of Life Science and Biochemical Engineering SunMoon University Asan Republic of Korea. Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program SunMoon University Asan Republic of Korea. Agricultural Microbiology Division National Institute of Agricultural Sciences Rural Development Administration Jeonju Republic of Korea. Technology Services Division National Institute of Agricultural Sciences Rural Development Administration Jeonju Republic of Korea. Genome-Based BioIT Convergence Institute Asan Republic of Korea. Department of Pharmaceutical Engineering and Biotechnology SunMoon University Asan Republic of Korea.

Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2, SSBR10-3, and SSHM10-5) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.

关键词： Halobacillus sp. algicidal activity comparative genome analysis halotolerance stress response

Metrics for benchmarking and uncertainty quantification: Quality, applicability, and a path to best practices for machine learning in chemistry

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arXiv 2020年

作者： Vishwakarma, Gaurav Sonpal, Aditya Hachmann, Johannes Department of Chemical and Biological Engineering University at Buffalo State University of New York BuffaloNY14260 United States Computational and Data-Enabled Science and Engineering Graduate Program University at Buffalo State University of New York BuffaloNY14260 United States New York State Center of Excellence in Materials Informatics BuffaloNY14203 United States

This review aims to draw attention to two issues of concern when we set out to make machine learning work in the chemical and materials domain, i.e., statistical loss function metrics for the validation and benchmarking of data-derived models, and the uncertainty quantification of predictions made by them. They are often overlooked or underappreciated topics as chemists typically only have limited training in statistics. Aside from helping to assess the quality, reliability, and applicability of a given model, these metrics are also key to comparing the performance of different models and thus for developing guidelines and best practices for the successful application of machine learning in chemistry. Copyright © 2020, The Authors. All rights reserved.

关键词： Benchmarking

Author Correction: Predicting the efficiency of prime editing guide RNAs in human cells

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Nature biotechnology 2024年第3期42卷 529页

作者： Hui Kwon Kim Goosang Yu Jinman Park Seonwoo Min Sungtae Lee Sungroh Yoon Hyongbum Henry Kim Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. Electrical and Computer Engineering Seoul National University Seoul Republic of Korea. Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea. Graduate School of Data Science Seoul National University Seoul Republic of Korea. Department of Pharmacology Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Brain Korea 21 Plus Project for Medical Sciences Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Center for Nanomedicine Institute for Basic Science (IBS) Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac. Severance Biomedical Science Institute Yonsei University College of Medicine Seoul Republic of Korea. hkim1@yuhs.ac. Graduate Program of NanoScience and Technology Yonsei University Seoul Republic of Korea. hkim1@yuhs.ac.

In situ Interweaved Binder Framework Mitigating the Structural and Interphasial Degradations of High-nickel Cathodes in Lithium-ion Batteries

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Angewandte Chemie 2023年第15期135卷

作者： Dr. Biyu Jin Zehao Cui Prof. Arumugam Manthiram Materials Science and Engineering Program and Texas Materials Institute The University of Texas at Austin Austin TX 78712 USA Contribution: Conceptualization (lead) Data curation (lead) Formal analysis (lead) Investigation (lead) Methodology (equal) Writing - original draft (lead) Contribution: Conceptualization (supporting) Data curation (equal) Formal analysis (supporting) Investigation (supporting) Methodology (equal) Writing - review & editing (equal) Contribution: Conceptualization (equal) Funding acquisition (lead) Investigation (supporting) Project administration (lead) Resources (lead) Supervision (lead) Validation (equal) Writing - review & editing (equal)

The practical viability of high-nickel layered oxide cathodes is compromised by the interphasial and structural degradations. Herein, we demonstrate that by applying an in situ interweaved binder, the cycling stability of high-nickel cathodes can be significantly improved. Specifically, the results show that the resilient binder network immobilizes the transition-metal ions, suppresses electrolyte oxidative decomposition, and mitigates cathode particles pulverization, thus resulting in suppressed cathode-to-anode chemical crossover and ameliorated chemistry and architecture of electrode-electrolyte interphases. Pouch full cells with high-mass-loading LiNi 0.8 Mn 0.1 Co 0.1 O 2 cathodes achieve 0.02 % capacity decay per cycle at 1 C rate over 1 000 deep cycles at 4.4 V (vs. graphite). This work demonstrates a rational structural and compositional design strategy of polymer binders to mitigate the structural and interphasial degradations of high-Ni cathodes in lithium-ion batteries.

关键词： Cathode-to-Anode Crossover Electrode-Electrolyte Interphase High-Nickel Cathode In Situ Interweaved Binder Particles Pulverization

Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

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arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. MacDermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, David L. Chodera, John D. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

Deep learning-based frozen section to FFPE translation

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arXiv 2021年

作者： Ozyoruk, Kutsev Bengisu Can, Sermet Gokceler, Guliz Irem Başak, Kayhan Demir, Derya Serin, Gurdeniz Hacisalihoglu, Uguray Payam Kurtuluş, Emirhan Darbaz, Berkan Lu, Ming Y. Chen, Tiffany Y. Williamson, Drew F.K. Yilmaz, Funda Mahmood, Faisal Turan, Mehmet Institute of Biomedical Engineering Bogazici University Istanbul Turkey Uk Biocentre Tilbrook United Kingdom Department of Pathology Brigham and Women's Hospital Harvard Medical School BostonMA United States Cancer Data Science Program Dana-Farber Cancer Institute BostonMA United States Cancer Program Broad Institute of Harvard and Mit CambradgeMA United States Saǧlik Bilimleri University Kartal Dr.Lütfi Kirdar City Hospital Department of Pathology Istanbul Turkey Faculty of Medicine Department of Pathology Ege University Izmir Turkey Istanbul Yeni Yuzyil University Medical Faculty Gaziosmanpasa Hospital Pathology Department Turkey

Frozen sectioning (FS) is the preparation method of choice for microscopic evaluation of tissues during surgical operations. The high speed of procedure allows pathologists to rapidly assess the key microscopic features, such as tumor margins and malignant status to guide surgical decision-making and minimise disruptions to the course of the operation. However, FS is prone to introducing many misleading artificial structures (histological artefacts), such as nuclear ice crystals, compression, and cutting artefacts, hindering timely and accurate diagnostic judgement of the pathologist. Additional training and prolonged experience is often required to make highly effective and time critical diagnosis on frozen sections. On the other hand, the gold standard tissue preparation technique of formalin-fixation and paraffin-embedding (FFPE) provides significantly superior image quality, but is a very time-consuming process (12-48 hours), making it unsuitable for intra-operative use. In this paper, we propose an artificial intelligence (AI) method that improves FS image quality by computationally transforming frozen-sectioned whole-slide images (FS-WSIs) into whole-slide FFPE-style images in minutes. AI-FFPE rectifies FS artefacts with the guidance of an attention-mechanism that puts a particular emphasis on artefacts while utilising a self-regularization mechanism established between FS input image and synthesized FFPE-style image that preserves clinically relevant features. As a result, AI-FFPE method successfully generates FFPE-style images without significantly extending tissue processing time and consequently improves diagnostic accuracy. We demonstrate the efficacy of AI-FFPE on lung and brain frozen sections using a variety of different qualitative and quantitative metrics including visual Turing tests from 20 board certified pathologists. Additionally, we demonstrate that deep models trained on FFPE tissue can adapt to frozen sections which a much higher efficacy whe

关键词： Surgery

An overview of facial micro-expression analysis: data, methodology and challenge

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arXiv 2020年

作者： Xie, Hong-Xia Lo, Ling Shuai, Hong-Han Cheng, Wen-Huang The Institute of of Electronics National Chiao Tung Univresity Hsinchu300 Taiwan The Department of Electrical and Computer Engineering National Chiao Tung Univresity Hsinchu300 Taiwan The Institute of Electronics National Chiao Tung Univresity Hsinchu300 Taiwan The Artificial Intelligence and Data Science Program National Chung Hsing University Taichung400 Taiwan

Facial micro-expressions indicate brief and subtle facial movements that appear during emotional communication. In comparison to macro-expressions, micro-expressions are more challenging to be analyzed due to the short span of time and the fine-grained changes. In recent years, micro-expression recognition (MER) has drawn much attention because it can benefit a wide range of applications, e.g. police interrogation, clinical diagnosis, depression analysis, and business negotiation. In this survey, we offer a fresh overview to discuss new research directions and challenges these days for MER tasks. For example, we review MER approaches from three novel aspects: macro-to-micro adaptation, recognition based on key apex frames, and recognition based on facial action units. Moreover, to mitigate the problem of limited and biased ME data, synthetic data generation is surveyed for the diversity enrichment of micro-expression data. Since micro-expression spotting can boost micro-expression analysis, the state-of-the-art spotting works are also introduced in this paper. At last, we discuss the challenges in MER research and provide potential solutions as well as possible directions for further investigation. Copyright © 2020, The Authors. All rights reserved.

关键词： Surveys

Generative models of simultaneously heavy-tailed distributions of inter-event times on nodes and edges

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arXiv 2020年

作者： dos Reis, Elohim Fonseca Li, Aming Masuda, Naoki Department of Mathematics State University of New York at Buffalo BuffaloNY United States Department of Zoology University of Oxford Oxford United Kingdom Department of Biochemistry University ofOxford Oxford United Kingdom Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY United States

Intervals between discrete events representing human activities, as well as other types of events, often obey heavy-tailed distributions, and their impacts on collective dynamics on networks such as contagion processes have been intensively studied. The literature supports that such heavy-tailed distributions are present for inter-event times associated with both individual nodes and individual edges in networks. However, the simultaneous presence of heavy-tailed distributions of inter-event times for nodes and edges is a non-trivial phenomenon, and its origin has been elusive. In the present study, we propose a generative model and its variants to explain this phenomenon. We assume that each node independently transits between a high-activity and low-activity state according to a continuous-time two-state Markov process and that, for the main model, events on an edge occur at a high rate if and only if both end nodes of the edge are in the high-activity state. In other words, two nodes interact frequently only when both nodes prefer to interact with others. The model produces distributions of inter-event times for both individual nodes and edges that resemble heavy-tailed distributions across some scales. It also produces positive correlation in consecutive inter-event times, which is another stylized observation for empirical data of human activity. We expect that our modeling framework provides a useful benchmark for investigating dynamics on temporal networks driven by non-Poissonian event sequences. Copyright © 2020, The Authors. All rights reserved.

关键词： Continuous time systems