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Fast, accurate, and versatile data analysis platform for the quantification of molecular spatiotemporal signals

Cell 2025年第10期188卷 2794-2809.e21页

作者： Mi, Xuelong Chen, Alex Bo-Yuan Duarte, Daniela Carey, Erin Taylor, Charlotte R. Braaker, Philipp N. Bright, Mark Almeida, Rafael G. Lim, Jing-Xuan Ruetten, Virginia M.S. Wang, Yizhi Wang, Mengfan Zhang, Weizhan Zheng, Wei Reitman, Michael E. Huang, Yongkang Wang, Xiaoyu Li, Lei Deng, HanFei Shi, Song-Hai Poskanzer, Kira E. Lyons, David A. Nimmerjahn, Axel Ahrens, Misha B. Yu, Guoqiang Bradley Department of Electrical and Computer Engineering Virginia Polytechnic Institute and State University Arlington 22203 VA United States Janelia Research Campus Howard Hughes Medical Institute Ashburn 20147 VA United States Department of Molecular and Cellular Biology Harvard University Cambridge 02138 MA United States Graduate Program in Neuroscience Harvard Medical School Boston 02115 MA United States Waitt Advanced Biophotonics Center The Salk Institute for Biological Studies La Jolla 92037 CA United States Department of Biochemistry & Biophysics University of California San Francisco San Francisco CA United States Neuroscience Graduate Program University of California San Francisco San Francisco CA United States Centre for Discovery Brain Sciences University of Edinburgh Edinburgh BioQuarter Edinburgh EH16 4SB United Kingdom Gatsby Computational Neuroscience Unit UCL London W1T 4JG United Kingdom Kavli Institute for Fundamental Neuroscience San Francisco CA United States Department of Automation Tsinghua University Beijing 100084 China IDG/McGovern Institute for Brain Research Tsinghua University Beijing 100084 China New Cornerstone Science Laboratory Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Beijing 100084 China State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Institutes of Brain Science Fudan University Shanghai 200032 China Beijing National Research Center for Information Science and Technology Beijing 100084 China

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce activity quantification and analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine-learning techniques. It decomposes complex live-imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, microscopy techniques, and imaging approaches. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, as well as distinct sensorimotor signal propagation patterns in the mouse spinal cord. © 2025 The Author(s)

关键词： AQuA2 astrocytes cell interaction analysis functional units glial cells image analysis machine learning molecular spatiotemporal signals neurons time-lapse imaging

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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Bridging Accuracy and Efficiency: The Role of PINNs in Immune Response Simulations

Bridging Accuracy and Efficiency: The Role of PINNs in Immun...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Fernandes, Thiago E. Dos Santos, Rodrigo W. Lobosco, Marcelo Federal University of Juiz de Fora Graduate Program on Computational Modelling Juiz de Fora Brazil Federal University of Juiz de Fora Institute of Exact Sciences Department of Computer Science Juiz de Fora Brazil

ISBN: (纸本)9798350386226

Myocarditis, characterized by inflammation of the heart muscle, has seen a notable 62.2% increase in incidence over the past three decades, leading to 324,490 deaths in 2019. Despite advancements in understanding its etiology, several critical questions remain unresolved, highlighting the need for improved patient treatment strategies. computational methods play a crucial role in unraveling the complex interactions between pathogens and the immune system. This study explores the use of Physics-Informed Neural Networks (PINNs) to accelerate a newly developed model for myocardial edema formation in acute infectious myocarditis. The model describes the concentrations of pathogens and leukocytes using a nonlinear system of ordinary differential equations (ODEs). Our findings demonstrate a mean computational speedup of 5.93, while maintaining a Root Mean Squared Error of 0.0015. These results indicate that PINNs can accurately replicate the ODE system's solutions, offering substantial computational efficiency for this application. © 2024 IEEE.

关键词： Pathogens

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Explorations on system identification via higher-level application of Adaptive-Critic Approximate Dynamic programming

Explorations on system identification via higher-level appli...

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International Joint Conference on Neural Networks (IJCNN)

作者： Joshua G. Hughes George G. Lendaris Systems Science Graduate Program Portland State University Portland OR USA NW Computational Intelligence Laboratory (NWCIL) & Systems Science Graduate Program Portland State University Portland OR USA

In previous work it was shown that Adaptive- Critic-type Approximate Dynamic programming could be applied in a “higher-level” way to create autonomous agents capable of using experience to discern context and select optimal, context-dependent control policies. Early experiments with this approach were based on full a priori knowledge of the system being monitored. The experiments reported in this paper, using small neural networks representing families of mappings, were designed to explore what happens when knowledge of the system is less precise. Results of these experiments show that agents trained with this approach perform well when subject to even large amounts of noise or when employing (slightly) imperfect models. The results also suggest that aspects of this method of context discernment are consistent with our intuition about human learning. The insights gained from these explorations can be used to guide further efforts for developing this approach into a general methodology for solving arbitrary identification and control problems.

关键词： Context Training Context modeling System identification Artificial neural networks Noise Process control

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Dynamical model of birdsong maintenance and control

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Physical Review E 2004年第5期70卷 051911-051911页

作者： Henry D. I. Abarbanel Sachin S. Talathi Gabriel Mindlin Misha Rabinovich Leif Gibb Graduate Program in Computational Neurobiology and Institute for Nonlinear Science Division of Biological Sciences University of California–San Diego La Jolla California 92093-0402 USA

The neuroethology of song learning, production, and maintenance in songbirds presents interesting similarities to human speech. We have developed a biophysical model of the manner in which song could be maintained in adult songbirds. This model may inform us about the human counterpart to these processes. In songbirds, signals generated in nucleus High Vocal center (HVc) follow a direct route along a premotor pathway to the robust nucleus of the archistriatum (RA) as well as an indirect route to RA through the anterior forebrain pathway (AFP): the neurons of RA are innervated from both sources. HVc expresses very sparse bursts of spikes having interspike intervals of about 2ms. The expressions of these bursts arrive at the RA with a time difference ΔT≈50±10ms between the two pathways. The observed combination of AMPA and NMDA receptors at RA projection neurons suggests that long-term potentiation and long-term depression can both be induced by spike timing plasticity through the pairing of the HVc and AFP signals. We present a dynamical model that stabilizes this synaptic plasticity through a feedback from the RA to the AFP using known connections. The stabilization occurs dynamically and is absent when the RA→AFP connection is removed. This requires a dynamical selection of ΔT. The model does this, and ΔT lies within the observed range. Our model represents an illustration of a functional consequence of activity-dependent plasticity directly connected with neuroethological observations. Within the model the parameters of the AFP, and thus the magnitude of ΔT, can also be tuned to an unstable regime. This means that destabilization might be induced by neuromodulation of the AFP.

关键词： Neurophysiology

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Diversity and Evolution of RNA Recognition Motifs: A Case Study on the Utility of RdRp in the phylum Duplornaviricota

Diversity and Evolution of RNA Recognition Motifs: A Case St...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Je, Mikyung Cho, Myeongji Son, Hyeon S. Seoul National University Interdisciplinary Graduate Program in Bioinformatics College of Natural Science Seoul Korea Republic of Seoul National University Lab. of Computational Biology & Bioinformatics Graduate School of Public Health Seoul Korea Republic of Seoul National University Institute of Health and Environment Seoul Korea Republic of

ISBN: (纸本)9798350337488

Viruses possess specific conserved regions known as RNA recognition motifs, which are shared within taxonomic groups. Applying these to the Baltimore virus classification system, there are genes/proteins that serve as biomarkers for each of the seven groups. Mutations in conserved sequence regions can have a significant impact on the function of a virus, especially if these conserved regions are part of a major protein. In this study, we analyzed the RdRp gene, known to be a representative RRM of RNA viruses, from viruses of five families (Alternaviridae, Chrysoviridae, Totiviridae, Sedoreoviridae, and Spinareoviridae) within the phylum Duplornaviricota. Data were retrieved from the NCBI non-redundant (nr) database (https://***/protein) applying a cut-off of 300 amino acids in length. RdRp protein sequences were aligned using PROMALS3D, and PhyML (v3.0) was used for phylogenetic analysis. In the next step, we utilized the officially provided ICTV taxonomy and bioinformatics tools to assign the phylogenetic position of RdRp. Although this analysis focused solely on RdRp, it can be concluded that using this gene as a marker may be sufficient for taxonomic assignment. Subsequent analyses will target DNA viruses and RT viruses to perform a more comprehensive assessment. This extensive analysis aims to validate the usefulness of marker genes in the overall viral taxonomy. © 2023 IEEE.

关键词： classification marker gene RdRp RNA recognition motif taxonomy virus

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An Hydro-Mechanical Model of Edema Formation Applied to Bacterial Myocarditis

An Hydro-Mechanical Model of Edema Formation Applied to Bact...

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2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

作者： Reis, R.F. Rocha, B.M. Santos, R. W. Dos Lobosco, M. Computer Science Department Federal University of Juiz de Fora Juiz de Fora MG36036-900 Brazil Graduate Program in Computational Modelling Federal University of Juiz de Fora Juiz de Fora MG36036-900 Brazil

ISBN: (纸本)9781538654880

In young adults, up to 20% of all cases of sudden death are due to myocarditis, a heart disease caused by inflammation in the myocardium. There are several reasons that lead to myocarditis, including infections caused by a virus, bacteria, protozoa, fungus, and others. Additionally, this inflammatory response is one of the consequences of an infection triggered by an immunological reaction, which causes an edema in the heart. One of the techniques used to visualize myocardial edema is the cardiovascular magnetic resonance of myocardial tissue. Using this imaging exam it is possible to visualize hyperintense signal in the edematous zone. This paper aims to model and simulate the mechanical deformation due to a bacterial infection in a two-dimensional domain that represents a short axis slice of the heart and compares qualitatively the results with data found from literature. This mathematical model consists of partial differential equations (PDEs) that use the Biot theory of poroelasticity applied to living tissue and coupled with an immune system dynamics to model the edema formation. Thus, the mathematical model used in this study is basically divided into two parts: one modelling the immune system response due to a bacterial infection, represented by neutrophils;and another representing the hydro-mechanical problem. The preliminary results show that our model is able to reproduce some key aspects related to an initial myocarditis. © 2018 IEEE.

关键词： Tissue

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Using SYCLomatic to Migrate CUDA Code to oneAPI Adapting NVIDIA GPU

Using SYCLomatic to Migrate CUDA Code to oneAPI Adapting NVI...

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IEEE International Conference on Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS)

作者： Wentao Liang Norihisa Fujita Ryohei Kobayashi Taisuke Boku Master's Program in Computer Science Degree Program in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Center for Computational Sciences University of Tsukuba

ISBN: (数字)9798350383454

ISBN: (纸本)9798350383461

Nowadays, the use of accelerators in high performance computing has become more common than ever before. The most used accelerators must be the Graphics Processing Unit (GPU). It has emerged as an important component in most of the parallel computing scenarios, surpassing the capabilities of the traditional Central Processing Unit (CPU) in perspective of both performance and energy efficiency.

关键词： Codes Conferences High performance computing Graphics processing units Cluster computing Parallel processing Energy efficiency Central Processing Unit

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Development of an Application to Assess Quality of Life 27th

Development of an Application to Assess Quality of Life

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27th Brazilian Congress on Biomedical Engineering, CBEB 2020

作者： Oliveira, D.S. Santos, W.S. Ribeiro, L.M. Oliveira, G.S. Magalhães, D.S.F. Frade-Barros, A.F. Brazil University Bioengineering Department Rua A 208 Novo Jaçanã São Paulo Itabuna-Bahia Brazil Nutrition Department UniFTC Itabuna Brazil Graduate Program in Computational Modelling in Science and Technology State University of Santa Cruz Ilhéus Brazil

ISBN: (纸本)9783030706005

Quality of life (QOL) is how the individual perceives himself as having an impact on his physical-emotional integrity, functional capacity, and self-esteem. Quality of life assessment tools can be generic or specific. Generics evaluate various aspects of quality of life and health status, and can be useful for patients, regardless of disease or condition, and can also be used for healthy individuals. The Medical questionnaire Outcomes Study 36 (SF-36) is one of the main instruments used to assess the health-related quality of life. This study aimed to develop the first application software (APP) for assessing the quality of life in Portuguese. This is an experimental study, of analytical, observational, and transversal nature that seeks associations or correlations between variables of interest. The application was developed on the Unity Engine to facilitate port for Android and its graphical interface. The Sarcvida app contemplates the SF-36 questionnaire and the SARC-F+CC. The application has undergone structural and functional tests and the next step is the evaluation of the app by health professionals. Sarcvida app is composed of SF-36 QOL questionnaire, SARC-F+CC, and D-score. The application proved to be functional, corresponding to initial research expectations for the project. The app presented usability and functionality for the evaluation of QOL in the tests to which it has been submitted so far. In Brazil there are no applications composed of SF-36 QOL questionnaire, SARC-F+CC, and the D-score, therefore, this study is innovative, presenting the first Portuguese version available in the app. Besides, mobile technology developed here is a tool to help monitor patients by contributing health professionals in possible interventions for health promotion. © 2022, Springer Nature Switzerland AG.

关键词： Application programs

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Electronic properties of 3d transition metal dihalide monolayers predicted by DFT methods: Is there a pattern or are the results random?

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Journal of the Chinese Chemical Society 2023年第3期70卷 359-371页

作者： Chiu, Cheng-chau Wang, Chung-Yu Huang, Bo-Jie Kuo, Jer-Lai Department of Chemistry National Sun Yat-sen University Kaohsiung Taiwan Center for Theoretical and Computational Physics National Sun Yat-sen University Kaohsiung Taiwan Green Hydrogen Research Center National Sun Yat-sen University Kaohsiung Taiwan Institute of Atomic and Molecular Sciences Academia Sinica Taipei Taiwan Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Department of Chemistry National Tsing Hua University Hsinchu Taiwan International Graduate Program of Molecular Science and Technology (NTU-MST) National Taiwan University Taipei Taiwan

We use periodic DFT calculations at LDA and PBE level to investigate 3d transition metal dihalide (TMDH) monolayers in H- and T-phase. By analyzing the phonon dispersion, we have obtained a rough overview which combinations may form stable structures. We have focused on identifying and explaining trends in the predicted electronic properties. Although their geometric structures are simple, the associated electronic and magnetic properties are not as easy to understand. At first glance, it seems that there is no clear trend, as even isovalence-electronic TMDH monolayers formed from the same metal but different halides can feature different magnetic moments. The identification of potential trends is further complicated by the fact that for a significant number of species, LDA results and PBE results predict different ground-state electronic structures. By rigorously analyzing the potential energy surfaces associated with different magnetic moments, we could show that the apparent inconsistencies can be easily understood as a result of the differences in the relative energy between electronic states of different magnetic moments. We further show that the trends in the band gaps can be easily rationalized by an electron counting rule based on simple symmetry arguments. © 2022 Chemical Society Located in Taipei and Wiley-VCH GmbH.

关键词： 2D materials DFT electronic structure monolayer spin transition metal dihalides

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