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Microscopy Histopathology and Analytics, Microscopy 2020

作者： McMahon, Nathan Solanki, Allison Jones, Jocelyn Kwon, Sunjong Chang, Young-Hwan Chin, Koei Nederlof, Michel Gray, Joe Gibbs, Summer L. Department of Biomedical Engineering Computational Biology Program Oregon Health and Science University PortlandOR97201 United States Knight Cancer Institute Computational Biology Program Oregon Health and Science University PortlandOR97201 United States Center for Spatial Systems Biomedicine Computational Biology Program Oregon Health and Science University PortlandOR97201 United States Quantitative Imaging Systems PittsburghPA15238 United States

Successful targeted cancer treatment continues to elude modern medicine and its many therapeutic strategies. Herein, we propose a fluorescent imaging technique to measure drug localization and subsequent cell signalin... 详细信息

ISBN: (纸本)9781943580743

关键词： Cell signaling

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Deep Potentials for Materials science

arXiv

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arXiv 2022年

作者： Wen, Tongqi Zhang, Linfeng Wang, Han Weinan, E. Srolovitz, David J. Department of Mechanical Engineering The University of Hong Kong Hong Kong DP Technology Beijing China AI for Science Institute Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China HEDPS CAPT College of Engineering Peking University Beijing China School of Mathematical Sciences Peking University Beijing China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton United States Shenzhen China

To fill the gap between accurate (and expensive) ab initio calculations and efficient atomistic simulations based on empirical interatomic potentials, a new class of descriptions of atomic interactions has emerged and been widely applied;i.e., machine learning potentials (MLPs). One recently developed type of MLP is the Deep Potential (DP) method. In this review, we provide an introduction to DP methods in computational materials science. The theory underlying the DP method is presented along with a step-by-step introduction to their development and use. We also review materials applications of DPs in a wide range of materials systems. The DP Library provides a platform for the development of DPs and a database of extant DPs. We discuss the accuracy and efficiency of DPs compared with ab initio methods and empirical potentials. Copyright © 2022, The Authors. All rights reserved.

关键词： Calculations

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CIWARS: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

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Journal of Molecular Biology 2025年第15期437卷

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech Blacksburg 24060 VA United States Fralin Life Science Institute Virginia Tech Blacksburg 24060 VA United States Department of Civil and Environmental Engineering Virginia Tech Blacksburg 24060 VA United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg 24060 VA United States

The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://***/. © 2025 Elsevier Ltd

关键词： anomaly detection antibiotic resistance (AR) AR indicator profiling longitudinal metagenomics wastewater-based surveillance

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QCPINN: QUANTUM-CLASSICAL PHYSICS-INFORMED NEURAL NETWORKS FOR SOLVING PDES

arXiv

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arXiv 2025年

作者： Farea, Afrah Khan, Saiful Celebi, Mustafa Serdar Computational Science and Engineering Department Informatics Institute Istanbul Technical University Istanbul34469 Turkey OX11 0QX United Kingdom

Physics-informed neural networks (PINNs) have emerged as promising methods for solving partial differential equations (PDEs) by embedding physical laws within neural architectures. However, these classical approaches often require a large number of parameters to achieve reasonable accuracy, particularly for complex PDEs. In this paper, we present a quantum-classical physics-informed neural network (QCPINN) that combines quantum and classical components, allowing us to solve PDEs with significantly fewer parameters while maintaining comparable accuracy and convergence to classical PINNs. We systematically evaluated two quantum circuit architectures across various configurations on five benchmark PDEs to identify optimal QCPINN designs. Our results demonstrate that the QCPINN achieves stable convergence and comparable accuracy, while requiring approximately 10% of the trainable parameters used in classical approaches. It also results in a 40% reduction in the relative error L2 for the convection-diffusion equation. These findings demonstrate the potential of parameter efficiency as a measurable quantum advantage in physics-informed machine learning, significantly reducing model complexity while preserving solution quality. This approach presents a promising solution to the computational challenges associated with solving PDEs. © 2025, CC BY.

关键词： Qubits

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computational prediction and validation of specific EmbR binding site on PknH

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Synthetic and Systems Biotechnology 2021年第4期6卷 429-436页

作者： Insung Na Huanqin Dai Hantian Li Anvita Gupta David Kreda Powell Zhang Xiangyin Chen Lixin Zhang Gil Alterovitz Computational Health Informatics Program Boston Children’s Hospital/Harvard Medical SchoolBostonMA 02115USA Department of Medicine Brigham and Women’s Hospital/Harvard Medical SchoolBostonMA 02115USA State Key Laboratory of Mycology Institute of MicrobiologyBeijing100101 China Department of Computer Sciences Stanford UniversityStanford CA 94305USA Center for Biomedical Informatics Harvard Medical SchoolBostonMA 02115USA State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghaiChina Department of Biology The Johns Hopkins UniversityBaltimoreMD 21218USA Lexington High School BostonMA 02115USA

Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not ***(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance *** studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB ***-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B ***,the EmbR binding site on PknH was *** conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding *** bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA ***,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation *** discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding *** approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.

关键词： Disorder-to-order transition Protein intrinsic disorder Binding site prediction Drug resistance Molecular simulation

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Layer-dependent optically induced spin polarization in InSe

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Physical Review B 2023年第11期107卷 115304-115304页

作者： Jovan Nelson Teodor K. Stanev Dmitry Lebedev Trevor LaMountain J. Tyler Gish Hongfei Zeng Hyeondeok Shin Olle Heinonen Kenji Watanabe Takashi Taniguchi Mark C. Hersam Nathaniel P. Stern Applied Physics Program Northwestern University Evanston Illinois 60208 USA Department of Physics and Astronomy Northwestern University Evanston Illinois 60208 USA Department of Material Science and Engineering Northwestern University Evanston Illinois 60208 USA Computational Science Division Argonne National Laboratory Lemont Illinois 60439 USA Material Science Division Argonne National Laboratory Lemont Illinois 60439 USA Research Center for Functional Materials National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan International Center for Materials Nanoarchitectonics National Institute for Materials Science 1-1 Namiki Tsukuba 305-0044 Japan Department of Chemistry Northwestern University Evanston Illinois 60208 USA Department of Electrical Engineering and Computer Science Northwestern University Evanston Illinois 60208 USA

Optical control of spin in semiconductors has been pioneered using nanostructures of III-V and II-VI semiconductors, but the emergence of two-dimensional van der Waals materials offers an alternative low-dimensional platform for spintronic phenomena. Indium selenide (InSe), a group-III monochalcogenide van der Waals material, has shown promise for optoelectronics due to its high electron mobility, tunable direct band gap, and quantum transport. In addition to these confirmed properties, there are predictions of spin-dependent optical selection rules, suggesting the potential for all-optical excitation and control of spin in a two-dimensional layered material. Despite these predictions, layer-dependent optical spin phenomena in InSe have yet to be explored. Here, we present measurements of layer-dependent optical spin dynamics in few-layer and bulk InSe. Polarized photoluminescence reveals layer-dependent optical orientation of spin, thereby demonstrating the optical selection rules in few-layer InSe. Spin dynamics are also studied in many-layer InSe using time-resolved Kerr rotation spectroscopy. By applying out-of-plane and in-plane static magnetic fields for polarized emission measurements and Kerr measurements, respectively, the g factor for InSe was extracted. Further investigations are done by calculating precession values using a k·p model, which is supported by ab initio density functional theory. Comparison of predicted precession rates with experimental measurements highlights the importance of excitonic effects in InSe for understanding spin dynamics. Optical orientation of spin is an important prerequisite for optospintronic phenomena and devices, and these first demonstrations of layer-dependent optical excitation of spins in InSe lay the foundation for combining layer-dependent spin properties with advantageous electronic properties found in this material.

关键词： Magneto-optics Spin dynamics Chalcogenides Layered semiconductors Van der Waals systems Density functional theory Kerr effect Photoluminescence k dot p method

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Cyclic ferroelectric switching and quantized charge transport in CuInP2S6

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Physical Review B 2023年第18期108卷 L180101-L180101页

作者： Daniel Seleznev Sobhit Singh John Bonini Karin M. Rabe David Vanderbilt Department of Physics and Astronomy Center for Materials Theory Rutgers University Piscataway New Jersey 08854 USA Department of Mechanical Engineering University of Rochester Rochester New York 14627 USA Materials Science Program University of Rochester Rochester New York 14627 USA Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New York New York 10010 USA

The van der Waals layered ferroelectric CuInP2S6 has been found to exhibit a variety of intriguing properties arising from the fact that the Cu ions are unusually mobile in this system. While the polarization switching mechanism is usually understood to arise from Cu ion motion within the monolayers, a second switching path involving Cu motion across the van der Waals gaps has been suggested. In this work, we perform zero-temperature first-principles calculations on such switching paths, focusing on two types that preserve the periodicity of the primitive unit cell: “cooperative” paths preserving the system's glide mirror symmetry, and “sequential” paths in which the two Cu ions in the unit cell move independently of each other. We find that CuInP2S6 features a rich and varied energy landscape, and that sequential paths are clearly favored energetically both for cross-gap and through-layer paths. Importantly, these segments can be assembled to comprise a globally insulating cycle with the out-of-plane polarization evolving by a quantum as the Cu ions shift to neighboring layers. In this sense, we argue that CuInP2S6 embodies the physics of a quantized adiabatic charge pump.

关键词： Electric polarization Electronic structure Ferroelectricity Phonons Structural phase transition

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An In-Depth Evaluation of Federated Learning on Biomedical Natural Language Processing

arXiv

引用

arXiv 2023年

作者： Peng, Le Luo, Gaoxiang Zhou, Sicheng Chen, Jiandong Xu, Ziyue Zhang, Rui Sun, Ju Department of Computer Science and Engineering University of Minnesota MinneapolisMN United States Department of Computer and Information Science University of Pennsylvania PhiladelphiaPA United States Institute for Health Informatics University of Minnesota MinneapolisMN United States Nvidia Corporation Santa ClaraCA United States Division of Computational Health Sciences Department of Surgery University of Minnesota MinneapolisMN United States

Language models (LMs) such as BERT and GPT have revolutionized natural language processing (NLP). However, the medical field faces challenges in training LMs due to limited data access and privacy constraints imposed by regulations like the Health Insurance Portability and Accountability Act (HIPPA) and the General Data Protection Regulation (GDPR). Federated learning (FL) offers a decentralized solution that enables collaborative learning while ensuring data privacy. In this study, we evaluated FL on 2 biomedical NLP tasks encompassing 8 corpora using 6 LMs. Our results show that: 1) FL models consistently outperformed models trained on individual clients' data and sometimes performed comparably with models trained with polled data;2) with the fixed number of total data, FL models training with more clients produced inferior performance but pre-trained transformer-based models exhibited great resilience. 3) FL models significantly outperformed large language models using zero-/one-shot learning and offered lightning inference speed. © 2023, CC BY.

关键词： Data privacy

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Strategic Planning and Knowledge Management Approaches as input to remote area strategic plans: A Case study in Aru Islands Regency Maluku Province 8

Strategic Planning and Knowledge Management Approaches as in...

引用

8th International Conference on ICT for Smart Society, ICISS 2021

作者： Irena Gutandjala, Ilona Harso Supangkat, Suhono Lumban Gaol, Ford Rianti, Benny Bina Nusantara University BINUS Graduate Program-Computer Science Computer Science Department Jakarta11480 Indonesia Bandung Institute of Technology Smart City and Community Innovation Center School of Electrical and Informatics Engineering Bandung Indonesia Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781665416979

Knowledge is an important asset in an organization. Aru Islands District is one of the districts in Maluku Province. The Government of Aru Islands District Maluku has a vision and mission as outlined in the Regional Strategic Plan or commonly referred to as RENSTRA. This vision and mission are an activity that requires a policy direction that is planned and integrated with the strategic environment of all related aspects. The strategic plan is then realized with the implementation of the government with regional autonomy which is the modern governance in realizing quality public services, fast, easy, fair and unlimited for the welfare and progress of the region. In this research will be used a strategic approach as input from the analysis with knowledge management and assessment of the condition of Aru district. © 2021 IEEE.

关键词： Strategic planning

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Introducing QuantConn: Overcoming Challenging Diffusion Acquisitions with Harmonization 15th

Introducing QuantConn: Overcoming Challenging Diffusion Acqu...

引用

15th International Workshop on computational Diffusion MRI, CDMRI 2024, held in conjunction with 27th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2024

作者： Newlin, Nancy Schilling, Kurt Koudoro, Serge Chandio, Bramsh Qamar Kanakaraj, Praitayini Moyer, Daniel Kelly, Claire E. Genc, Sila Yang, Joseph Yuan-Mou Wu, Ye Adluru, Nagesh Nath, Vishwesh Pathak, Sudhir Schneider, Walter Gade, Anurag Consagra, William Rathi, Yogesh Hendriks, Tom Vilanova, Anna Chamberland, Maxime Pieciak, Tomasz Ciupek, Dominika Vega, Antonio Tristán Aja-Fernández, Santiago Malawski, Maciej Ouedraogo, Gani Machnio, Julia Thompson, Paul M. Jahanshad, Neda Garyfallidis, Eleftherios Landman, Bennett Department of Computer Science Vanderbilt University NashvilleTN United States Department of Radiology and Radiological Sciences Vanderbilt University Medical Center Nashville United States Indiana University Bloomington BloomingtonIN United States Mark and Mary Stevens Neuroimaging and Informatics Institute Keck School of Medicine of USC Los AngelesCA United States Developmental Imaging Murdoch Children’ Research Institute Melbourne Australia Murdoch Children’s Research Institute Melbourne Australia Turner Institute for Brain and Mental Health School of Psychological Sciences Monash University Melbourne Australia Department of Neurosurgery Royal Children’s Hospital Melbourne Australia Neuroscience Research Murdoch Children’s Research Institute Melbourne Australia Department of Paediatrics University of Melbourne Melbourne Australia School of Computer Science and Technology Nanjing University of Science and Technology Nanjing China Waisman Center Department of Radiology University of Wisconsin Madison United States NVIDIA Santa Clara United States Learning Research and Development Center University of Pittsburgh Pittsburgh United States Brigham and Women’s Hospital Boston United States Brigham and Women’s Hospital Harvard Medical School Boston United States Department of Computer Science and Mathmatics Eindhoven University of Technology Eindhoven Netherlands LPI ETSI Telecomunicación Universidad de Valladolid Castilla y León Spain Sano Centre for Computational Medicine Kraków30-054 Poland Aix-Marseille Université Marseille France Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States Department of Electrical and Computer Engineering Vanderbilt University NashvilleTN United States

ISBN: (纸本)9783031869198

White matter alterations are increasingly implicated in neurological diseases and their progression. Diffusion-weighted magnetic resonance imaging (DW-MRI) has been included in many international-scale studies to identify alterations in white matter microstructure and connectivity. Yet, quantitative investigation of DW-MRI data is hindered by a lack of consistency due to variations in acquisition protocols, sites, and scanners. Specifically, there is a need to harmonize the preprocessing of DW-MRI datasets to ensure that compatible and reproducible quantitative metrics are derived from each site, including (1) bundle-wise microstructure measures, (2) features of white matter fiber bundles, and (3) connectomics measures. In the MICCAI CDMRI 2023 QuantConn challenge, participants are provided raw data from the same individuals taken with two different acquisition protocols on a single 4 tesla scanner in the same scanning session and asked to preprocess the data in order to minimize acquisition differences while retaining biological variation. Here, we outline the testing framework, provide baseline pre-harmonized results, and discuss the learning implications of this challenge. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Photointerpretation

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