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CURRENT PROTOCOLS 2023年第10期3卷 e883页

作者： Yen, Allen Mateusiak, Chase Sarafinovska, Simona Gachechiladze, Mariam A. Guo, Juanru Chen, Xuhua Moudgil, Arnav Cammack, Alexander J. Hoisington-Lopez, Jessica Crosby, MariaLynn Brent, Michael R. Mitra, Robi D. Dougherty, Joseph D. Department of Genetics Washington University School of Medicine Saint Louis Missouri Department of Psychiatry Washington University School of Medicine Saint Louis Missouri Contribution: Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Project administration Software Supervision Validation Visualization Writing - original draft Writing - review & editing Edison Family Center for Genome Sciences and Systems Biology Washington University School of Medicine Saint Louis Missouri Contribution: Conceptualization Data curation Formal analysis Methodology Software Visualization Writing - original draft Contribution: Formal analysis Funding acquisition Investigation Visualization Writing - original draft Writing - review & editing Contribution: Formal analysis Funding acquisition Investigation Visualization Writing - review & editing Contribution: Data curation Methodology Software Writing - review & editing Contribution: Methodology Writing - review & editing Current address: Department of Ophthalmology Stanford University School of Medicine Stanford California Contribution: Conceptualization Methodology Software Validation Department of Neurology Washington University School of Medicine Saint Louis Missouri Current address: Department of Neurodegenerative Diseases University College London London United Kingdom Contribution: Conceptualization Methodology Validation Contribution: Investigation Writing - review & editing Department of Computer Science and Engineering Washington University Saint Louis Missouri Contribution: Funding acquisition Contribution: Conceptualization Funding acquisition Project administration Resources Software Supervision Writing - review & editing Intellectual and Developmental Disabilities Research Center Washington University School of Medicine Saint Louis Missouri Contribution: Conceptualization Funding acquisition Project administration Resources Supervision Writing - origin

Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next-generation sequencing. Compared with other genomic assays, readouts of which provide a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon “Calling Cards” into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile-specific transcription factor (TF) binding with custom TF-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Cards reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high-performance computing environment and to conduct downstream analyses. © 2023 Wiley Periodicals LLC. This article was corrected on 16 October 2023. See the end of the full text for details. Basic Protocol 1 : Preparation and delivery of Calling Cards reagents Support Protocol 1 : Next-generation sequencing quantification of barcode

关键词： calling cards epigenetics enhancer usage gene regulation transcription factor binding

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ERNAS: An Evolutionary Neural Architecture Search for Magnetic Resonance Image Reconstructions

arXiv

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arXiv 2022年

作者： Eslahi, Samira Vafay Tao, Jian Ji, Jim Gordon Center for Medical Imaging Massachusetts General Hospital Harvard Medical School United States Department of Visualization Texas A&M University College StationTX United States Texas A&M Institute of Data Science Texas A&M University College StationTX United States Department of Electrical and Computer Engineering Texas A&M University College StationTX United States Department of Electrical and Computer Engineering Texas A&M University at Qatar Doha Qatar

Magnetic resonance imaging (MRI) is one of the noninvasive imaging modalities that can produce high-quality images. However, the scan procedure is relatively slow, which causes patient discomfort and motion artifacts in images. Accelerating MRI hardware is constrained by physical and physiological limitations. A popular alternative approach to accelerated MRI is to undersample the k-space data. While undersampling speeds up the scan procedure, it generates artifacts in the images, and advanced reconstruction algorithms are needed to produce artifact-free images. Recently deep learning has emerged as a promising MRI reconstruction method to address this problem. However, straightforward adoption of the existing deep learning neural network architectures in MRI reconstructions is not usually optimal in terms of efficiency and reconstruction quality. In this work, MRI reconstruction from undersampled data was carried out using an optimized neural network using a novel evolutionary neural architecture search algorithm. Brain and knee MRI datasets show that the proposed algorithm outperforms manually designed neural network-based MR reconstruction models. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Associations between the Safe Prevention of Primary Cesarean Delivery Care Consensus and Maternal/Neonatal Outcomes

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American Journal of Perinatology 2023年第S 01期41卷 e1084-e1089页

作者： Pamela Estrada Laura Tipton Rylan Chong Dena Towner Kelly Yamasato Department of Obstetrics Gynecology and Women's Health University of Hawaii John A. Burns School of Medicine Honolulu Hawaii School of Natural Sciences and Mathematics Data Science Analytics and Visualization Chaminade University of Honolulu Honolulu Hawaii

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C-Net: A reliable convolutional neural network for biomedical image classification

arXiv

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arXiv 2020年

作者： Barzekar, Hosein Yu, Zeyun Big Data Analytics and Visualization Laboratory Department of Computer Science University of Wisconsin-Milwaukee MilwaukeeWI53211 United States Department of Biomedical Engineering University of Wisconsin-Milwaukee MilwaukeeWI53211 United States

Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since pathologists must examine a huge number of histopathological images to detect infinitesimal abnormalities. In this study, we propose a novel convolutional neural network (CNN) architecture composed of a Concatenation of multiple Networks, called C-Net, to classify biomedical images. The model incorporates multiple CNNs including Outer, Middle, and Inner. The first two parts of the architecture contain six networks that serve as feature extractors to feed into the Inner network to classify the images in terms of malignancy and benignancy. The C-Net is applied for histopathological image classification on two public datasets, including BreakHis and Osteosarcoma. To evaluate the performance, the model is tested using several evaluation metrics for its reliability. The C-Net model outperforms all other models on the individual metrics for both datasets and achieves zero misclassification. This approach has the potential to be extended to additional classification tasks, as experimental results demonstrate utilizing extensive evaluation metrics. Copyright © 2020, The Authors. All rights reserved.

关键词： Computer aided diagnosis

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Spin-Phonon Interactions Induced Anomalous Thermal Conductivity in Nickel (Ii) Oxide

SSRN

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SSRN 2023年

作者： Sun, Qiyang Hou, Songrui Wei, Bin Su, Yaokun Ortiz, Victor Sun, Bo Lin, Jiao Y.Y. Smith, Hillary Danilkin, Sergey Abernathy, Douglas L. Wilson, Richard Li, Chen Mechanical Engineering University of California Riverside RiversideCA92521 United States Materials Science and Engineering University of California Riverside RiversideCA92521 United States Henan Key Laboratory of Materials on Deep-Earth Engineering School of Materials Science and Engineering Henan Polytechnic University Jiaozuo454000 China Tsinghua-Berkeley Shenzhen Institute Guangdong Provincial Key Laboratory of Thermal Management Engineering and Materials TSIGS Tsinghua University Shenzhen518055 China Neutron Data Analysis and Visualization Division Oak Ridge National Laboratory Oak RidgeTN37830 United States Department of Physics and Astronomy Swarthmore College SwarthmorePA19081 United States Australian Centre for Neutron Scattering Australian Nuclear Science and Technology Organization Lucas HeightsNSW2234 Australia Neutron Scattering Division Oak Ridge National Laboratory Oak RidgeTN37830 United States

Nickel (II) oxide is a prominent candidate for spintronic and spin-caloritronic applications operating at room temperature. Although there are extensive studies on nickel oxide, the roles of magnon- and spin-phonon interactions on thermal transport are not well understood. In the present work, the relationship between spin-phonon interactions and thermal transport is investigated by performing inelastic neutron scattering, time-domain thermoreflectance thermal conductivity measurements, and atomistic thermal transport calculations. Inelastic neutron scattering measurements of the magnon lifetime imply that magnon thermal conductivity is trivial, and so heat is conducted only by phonons. Time-domain thermoreflectance measurements of the thermal conductivity vs. temperature follow T-1.47 in the antiferromagnetic phase. This temperature dependence cannot be explained by phonon-isotope and phonon-defect scattering or phonon softening. Instead, we attribute this to magnon-phonon scattering and spin-induced dynamic symmetry breaking. The spin-phonon interactions are saturated in the paramagnetic phase and lead to a weaker temperature dependence of T-1.00 at 550-700 K. These results reveal the importance of spin-phonon interactions on lattice thermal transport, shedding light on the engineering of functional antiferromagnetic spintronic and spin-caloritronic materials through these interactions. © 2023, The Authors. All rights reserved.

关键词： Nickel oxide

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Deciphering boundary layer dynamics in high-Rayleigh-number convection using 3360 GPUs and a high-scaling in-situ workflow

arXiv

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arXiv 2025年

作者： Bode, Mathis Alvarez, Damian Fischer, Paul Frouzakis, Christos E. Göbbert, Jens Henrik Insley, Joseph A. Lan, Yu-Hsiang Mateevitsi, Victor A. Min, Misun Papka, Michael E. Rizzi, Silvio Samuel, Roshan J. Schumacher, Jörg Jülich Supercomputing Centre Forschungszentrum Jülich GmbH Jülich52425 Germany Siebel School of Computing and Data Science University of Illinois at Urbana-Champaign 201 N Goodwin Ave UrbanaIL61801 United States Mathematics and Computer Science Division Argonne National Laboratory 9700 S Cass Ave LemontIL60439 United States CAPS Laboratory Department of Mechanical and Process Engineering ETH Zürich Zürich8092 Switzerland Argonne Leadership Computing Facility Argonne National Laboratory 9700 S Cass Ave LemontIL60439 United States Electronic Visualization Laboratory University of Illinois Chicago 1200 W Harrison St ChicagoIL60607 United States Institute of Thermodynamics and Fluid Mechanics Technische Universität Ilmenau P.O. Box 100565 Ilmenau98684 Germany Tandon School of Engineering New York University New York CityNY11201 United States

Turbulent heat and momentum transfer processes due to thermal convection cover many scales and are of great importance for several natural and technical flows. One consequence is that a fully resolved three-dimensional analysis of these turbulent transfers at high Rayleigh numbers, which includes the boundary layers, is possible only using supercomputers. The visualization of these dynamics poses an additional hurdle since the thermal and viscous boundary layers in thermal convection fluctuate strongly. In order to track these fluctuations continuously, data must be tapped at high frequency for visualization, which is difficult to achieve using conventional methods. This paper makes two main contributions in this context. First, it discusses the simulations of turbulent Rayleigh-Bénard convection up to Rayleigh numbers of Ra = 1012 computed with NekRS on GPUs. The largest simulation was run on 840 nodes with 3360 GPU on the JUWELS Booster supercomputer. Secondly, an in-situ workflow using ASCENT is presented, which was successfully used to visualize the high-frequency turbulent fluctuations. © 2025, CC BY.

关键词： Rayleigh number

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POSTER: Will Sentiment of Forex News Effect Forecast of the RMB Exchange Rate? 16

POSTER: Will Sentiment of Forex News Effect Forecast of the ...

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16th ACM International Conference on Computing Frontiers, CF 2019

作者： Cheng, Zhou Wang, Jixiang Qi, Tianmei Zhao, Junfeng Wang, Zhihong Guo, Yi Zhou, Yu Co. Ltd Shanghai China Department of Computer Science and Engineering East China University of Science and Technology Shanghai China Business Intelligence and Visualization Research Center National Engineering Laboratory for Big Data Distribution and Exchange Technologies Shanghai China

ISBN: (纸本)9781450366854

The forecast and analysis of the trend of the RMB exchange rate have been deeply explored by many researchers in the financial field, but the combination of public opinion sentiment data and historical market data to forecast the RMB exchange rate in the short term has been studied little. With the rapid development of the Internet, the influence of public opinion sentiment on the economy and society is increasing. Online public opinion sentiment data not only have an impact on stock prices [1] and commodity prices, but also have a significant impact on foreign exchange (Forex) rates. However, the public opinion data are not applied for the RMB exchange rate forecast, because the impact of public events on the exchange rate is ignored. Besides, the lack of exact temporal sliding window of public opinion ignores its timeliness and sensibility. © 2019 Association for Computing Machinery.

关键词： Forecasting

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3-hydroxybutyrate in the brain: Biosynthesis, function, and disease therapy

Brain‐X

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Brain‐X 2023年第1期1卷

作者： Bing-Long Wang Jian-Fei Wu Da Xiao Bo Wu Dai-Xu Wei Zigong Affiliated Hospital of Southwest Medical University Zigong Psychiatric Research Center Zigong Institute of Brain Science Zigong Sichuan Province China Contribution: Conceptualization Supervision Visualization Writing - original draft Writing - review & editing Contribution: Validation Visualization Writing - original draft Writing - review & editing Department of Chemical System Engineering The University of Tokyo Tokyo Japan Contribution: Visualization Department of Biochemistry and Structural Biology University of Texas Health San Antonio San Antonio Texas USA Key Laboratory of Resource Biology and Biotechnology in Western China Department of Life Sciences and Medicine Ministry of Education School of Medicine Northwest University Xi'an Shaanxi Province China Contribution: Conceptualization Data curation Funding acquisition Investigation Methodology Project administration Resources Supervision Visualization Writing - original draft Writing - review & editing

3-hydroxybutyrate (3HB), or BHB, is an anionic small molecule acid metabolite with a hydroxyl group. 3HB is the major ketone body that is distributed in the human brain and its primary energy source when glucose is absent. A better understanding of 3HB and how to adapt neuronal response mechanisms is expected to facilitate the development of new interventions to promote cognitive brain function and prevent neurodegenerative diseases. It provides important concepts for the clinical application of 3HB therapy. This review summarizes the distribution of 3HB in the brain, its properties, and its mechanism in brain and nerve regulation. We focus on 3HB biosynthesis in natural human cells and engineered bacteria via synthetic biology platforms and 3HB treatment in various brain and nerve diseases, including epilepsy, multiple sclerosis, stroke, Parkinson's disease, Alzheimer's disease, Huntington's disease, depressive disorder, and schizophrenia. Ultimately, this review explores the future development trend of 3HB as a potential small-molecule drug for brain and nerve diseases.

关键词： 3-hydroxybutyrate ketogenic diet ketone body polyhydroxyalkanoates synthetic biology

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The mechanism of bone healing after traumatic brain injury

Brain‐X

引用

Brain‐X 2023年第3期1卷

作者： Yuan Xiong Wenbin Zhong Bobin Mi School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore Singapore Department of Orthopedics Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei China Contribution: Data curation Resources Software Supervision Writing - original draft Contribution: Data curation Software Supervision Writing - original draft Contribution: Conceptualization Investigation Supervision Validation Visualization Writing - review & editing

A growing body of evidence suggests that patients who experience traumatic brain injuries (TBIs) exhibit significantly shorter healing periods compared to those with isolated fractures. However, the precise underlying mechanism behind this phenomenon remains unclear. Recent studies have shed light on the potential role of hormonal signals and neural circuits originating in the hypothalamus, which play vital roles in regulating the skeletal system. Despite these advances, there is a lack of comprehensive research summarizing the crucial role of bone healing in TBIs and the underlying mechanisms. This review aimed to explore the underlying mechanisms responsible for the accelerated bone healing observed in TBI patients, with a specific focus on the intricate crosstalk between TBI and bone remodeling. Additionally, we comprehensively discuss and summarize the beneficial effects of TBI on the skeletal system and examine the TBI-induced signaling pathways that result in accelerated fracture healing and bone remodeling. By dissecting these pathways, we aim to identify potential targets for intervention and bone repair promotion.

关键词： bone crosstalk mechanisms TBI

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Triptycene-Fused Sterically Shielded Multi-Resonance TADF Emitter Enables High-Efficiency Deep Blue OLEDs with Reduced Dexter Energy Transfer

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Angewandte Chemie 2023年第32期135卷

作者： Hanif Mubarok Al Amin Taehwan Lee Prof. Jaehoon Jung Prof. Jeong-Hwan Lee Prof. Min Hyung Lee Department of Chemistry University of Ulsan 44610 Ulsan Republic of Korea Contribution: Data curation (equal) Investigation (lead) Department of Materials Science and Engineering and 3D Convergence Center Inha University 22212 Incheon Republic of Korea Contribution: Data curation (equal) Investigation (equal) Contribution: Formal analysis (equal) Visualization (supporting) Contribution: Methodology (equal) Writing - original draft (equal) Contribution: Conceptualization (lead) Methodology (lead) Writing - review & editing (lead)

Designing multi-resonance (MR) emitters that can simultaneously achieve narrowband emission and suppressed intermolecular interactions is challenging for realizing high color purity and stable blue organic light-emitting diodes (OLEDs). Herein, a sterically shielded yet extremely rigid emitter based on a triptycene-fused B,N core (Tp-DABNA) is proposed to address the issue. Tp-DABNA exhibits intense deep blue emissions with a narrow full width at half maximum (FWHM) and a high horizontal transition dipole ratio, superior to the well-known bulky emitter, t -DABNA. The rigid MR skeleton of Tp-DABNA suppresses structural relaxation in the excited state, with reduced contributions from the medium- and high-frequency vibrational modes to spectral broadening. The hyperfluorescence (HF) film composed of a sensitizer and Tp-DABNA shows reduced Dexter energy transfer compared to those of t -DABNA and DABNA-1. Notably, deep blue TADF-OLEDs with the Tp-DABNA emitter display higher external quantum efficiencies (EQE max =24.8 %) and narrower FWHMs (≤26 nm) than t -DABNA-based OLEDs (EQE max =19.8 %). The HF-OLEDs based on the Tp-DABNA emitter further demonstrate improved performance with an EQE max of 28.7 % and mitigated efficiency roll-offs.

关键词： Deep Blue OLEDs Hyperfluorescence Multi-Resonance TADF Triptycene

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