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53rd IEEE ASEE Frontiers in Education International Conference, FIE 2023

作者： Morelock, John R. Jarvie-Eggart, Michelle Chenette, Heather Hooshangi, Sara Chestnutt, Betsy Wilson, Sarah Bolhari, Azadeh Dodson, Kirsten Pavlova, Iglika Reck, Rebecca Transformations Institute University of Georgia Engineering Education AthensGA United States Michigan Technological University Engineering Fundamentals HoughtonMI United States Rose-Hulman Institute of Technology Chemical Engineering Terre HauteIN United States Virginia Tech Computer Science - Northern Virginia Center WashingtonDC United States University of Tennessee Knoxville Engineering Fundamentals KnoxvilleTN United States University of Kentucky Chemical Engineering LexingtonKY United States University of Colorado Boulder Environmental Engineering Program BoulderCO United States Lipscomb University Mechanical Engineering NashvilleTN United States University of North Carolina Greensboro Department of Biology GreensboroNC United States University of Illinois Urbana-Champaign Bioengineering ChampaignIL United States

ISBN: (纸本)9798350336429

The purpose of this workshop-designed for instructional and disciplinary STEM faculty interested in learning about qualitative research-is to (1) introduce participants to high-quality qualitative research design and (2) practice this design process alongside disciplinary STEM faculty to expand their STEM education research abilities and network. We will do so using the ProQual approach, a methodologically unencumbered and widely accessible way of thinking about qualitative research design that was deployed and refined over the last three years as part of the NSF-funded ProQual Institute for Research Methods [1]. This workshop will be conducted by ProQual Institute alumni, who are culturally sensitive to the challenges faced by disciplinary STEM faculty. Leveraging a propagation model of effecting academic change [2], the workshop leaders will serve as a community of practice to help participants move their educational research ideas forward during and after the workshop. In doing so, we strive to further FIE's mission to create a collaborative, supportive, and inclusive community of educational researchers. © 2023 IEEE.

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Study of ASIC Readout Used for Detectors in an MR Compatible, RF-Penetrable TOF-PET Insert

Study of ASIC Readout Used for Detectors in an MR Compatible...

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： Qian Dong Salar Sajedi Ilaria Sacco Peter Fischer Craig S. Levin Departments of Electrical Engineering and Radiology Stanford University Stanford CA USA Departments of Radiology Stanford University Stanford CA USA Department of Computer Science Heidelberg University Baden-Württemberg Germany Department of Radiology Electrical Engineering Bioengineering and Physics Stanford University Molecular Imaging Program at Stanford (MIPS) Stanford CA USA

Developing positron emission tomography (PET) systems with high channel number has driven the need for application-specific integrated circuits (ASICs) owing to their compactness, multi-channel readout capability, and excellent time and energy resolution performance. They can also be quite flexible by employing field-programmable gate arrays (FPGAs) in the readout circuit. In particular, the ASIC+FPGA approach provides a high performance and compact solution for TOF-PET applications. ASICs serve functions of extracting time and energy information from analog SiPM signals, and an FPGA is employed for other application-specific requirements like on-board chip configuration, communication with data acquisition (DAQ) systems, and system monitoring. Based on this foundation, we developed TOF-capable detector modules for our second generation RF-penetrable PET insert. During our previous experiments, we found that different trigger and readout methods lead to different noise pattern and intensity in MR environment, and also have different singles count loss ratio. This paper aims to study and compare different readout configurations for our MR-compatible detectors. We studied four trigger and readout methods: hit-standard, frequent-standard, hit-bypass, and frequent-bypass, and compared their singles count loss ratios with both theoretical models and experimental results. For all four methods, the theoretical results matched the experimental results well. The two methods which used bypass mode performed better than those using the standard mode approach. With the most optimized trigger and readout method (hit-bypass), we achieved 1.2% singles count loss ratio at a 20 kcps count rate per channel.

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Extracellular matrix dynamics in aortic valve health and disease: Insights into fibrocalcific remodeling and creation of biomimetic platforms

Journal of the Heart Valve Society

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Journal of the Heart Valve Society 2024年第1期1卷

作者： Ashley J. Scott Patterson Vaidehi A. Patil Lysmarie Figueroa-Rios Alexandra N. Borelli Kristyn S. Masters Medical Scientist Training Program University of Wisconsin-Madison Madison WI USACellular and Molecular Biology Program University of Wisconsin-Madison Madison WI USA Department of Biomedical Engineering University of Wisconsin-Madison Madison WI USA Department of Bioengineering University of Colorado Denver | Anschutz Medical Campus Aurora CO USA Department of Biomedical Engineering University of Wisconsin-Madison Madison WI USADepartment of Bioengineering University of Colorado Denver | Anschutz Medical Campus Aurora CO USA

The extracellular matrix (ECM) of the aortic valve plays a pivotal role in maintaining valve function and becomes profoundly altered during the progression of calcific stenosis of the native aortic valve (CAS). CAS involves fibrocalcific ECM remodeling characterized by increased proteoglycans and glycosaminoglycans, enhanced collagen deposition, and fragmentation of elastic fibers, all of which contribute to valve thickening, fibrosis, and calcification. In this brief review, we provide an overview of these ECM changes and discuss the relationship between aberrant ECM remodeling and other pathological features of CAS - namely, differentiation of the resident valve cell types, inflammatory activity, lipid deposition, and relative hypoxia. Sexual dimorphism in ECM dynamics and the creation of disease-inspired scaffold environments to mimic CAS fibrosis are also discussed. Overall, understanding the complex interplay between cell phenotypes and ECM remodeling is crucial for elucidating the pathophysiology of CAS and developing novel treatment strategies.

关键词： aortic valve endothelial-to-mesenchymal transition valvular interstitial cells extracellular matrix fibrosis calcification

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Randomizing the human genome by engineering recombination between repeat elements

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Science (New York, N.Y.) 2025年第6733期387卷 eado3979页

作者： Koeppel, Jonas Ferreira, Raphael Vanderstichele, Thomas Riedmayr, Lisa Maria Peets, Elin Madli Girling, Gareth Weller, Juliane Murat, Pierre Liberante, Fabio Giuseppe Ellis, Tom Church, George McDonald Parts, Leopold Hinxton United Kingdom Harvard Medical School Department of Genetics Boston MA United States Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA United States Broad Institute of Massachusetts Institute of Technology and Harvard University Cambridge MA United States Department of Bioengineering Imperial College London London United Kingdom Harvard-MIT Program in Health Sciences and Technology Cambridge MA United States Harvard Medical School Boston MA United States

We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. We tracked these rearrangements over time to measure selection pressures, finding a preference for shorter variants that avoided essential genes. We characterized 29 clones with multiple rearrangements, finding an impact of deletions on expression of genes in the variant but not on nearby genes. This genome-scrambling strategy enables large deletions, sequence relocations, and the insertion of regulatory elements to explore genome dispensability and organization.

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BPS2025 - Studying self-assembly of bacterial proteins in cell-free protein synthesis systems

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Biophysical Journal 2025年第3期124卷 55a-55a页

作者： Jacob B. Miller Nolan W. Kennedy Danielle Tullman-Ercek Carolyn E. Mills Interdisciplinary Biological Sciences Program Northwestern University Evanston IL USA Department of Chemical and Biological Engineering Northwestern University Evanston IL USA Department of Bioengineering University of California Santa Barbara Santa Barbara CA USA

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Correction: Kennedy Epitope (KE)-dependent Retrograde Transport of Efficiently Cleaved HIV-1 Envelopes (Envs) and its Effect on Env Cell Surface Expression and Viral Particle Formation

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The protein journal 2024年第2期43卷 387-392页

作者： Supratik Das Hilal Ahmad Parray Adarsh Kumar Chiranjivi Prince Kumar Abhishek Goswami Manish Bansal Deepak Kumar Rathore Rajesh Kumar Sweety Samal Infection and Immunology Translational Research Program 3Rd Milestone Faridabad-Gurgaon Expressway PO box #04 Faridabad 121001 Haryana India. supratik@thsti.res.in. Translational Health Science and Technology Institute NCR Biotech Science Cluster 3Rd Milestone Faridabad-Gurgaon Expressway PO box #04 Faridabad 121001 Haryana India. supratik@thsti.res.in. Infection and Immunology Translational Research Program 3Rd Milestone Faridabad-Gurgaon Expressway PO box #04 Faridabad 121001 Haryana India. Translational Health Science and Technology Institute NCR Biotech Science Cluster 3Rd Milestone Faridabad-Gurgaon Expressway PO box #04 Faridabad 121001 Haryana India. Department of Biosciences and Bioengineering Indian Institute of Technology - Roorkee Roorkee Uttarakhand 247667 India.

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An exact mathematical description of computation with transient spatiotemporal dynamics in a complex-valued neural network

arXiv

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arXiv 2023年

作者： Budzinski, Roberto C. Busch, Alexandra N. Mestern, Samuel Martin, Erwan Liboni, Luisa H.B. Pasini, Federico W. Mináč, Ján Coleman, Todd Inoue, Wataru Muller, Lyle E. Department of Mathematics Western University LondonON Canada Western Institute for Neuroscience Western University LondonON Canada Western Academy for Advanced Research Western University LondonON Canada Graduate Program in Neuroscience Western University London Canada Huron University College LondonON Canada Department of Bioengineering Stanford University StanfordCA United States Robarts Research Institute Western University London Canada Department of Physiology and Pharmacology Western University London Canada

We study a complex-valued neural network (cv-NN) with linear, time-delayed interactions. We report the cv-NN displays sophisticated spatiotemporal dynamics, including partially synchronized "chimera" states. We then use these spatiotemporal dynamics, in combination with a nonlinear readout, for computation. The cv-NN can instantiate dynamics-based logic gates, encode shortterm memories, and mediate secure message passing through a combination of interactions and time delays. The computations in this system can be fully described in an exact, closed-form mathematical expression. Finally, using direct intracellular recordings of neurons in slices from neocortex, we demonstrate that computations in the cv-NN are decodable by living biological neurons. These results demonstrate that complex-valued linear systems can perform sophisticated computations, while also being exactly solvable. Taken together, these results open future avenues for design of highly adaptable, bio-hybrid computing systems that can interface seamlessly with other neural networks. © 2023, CC BY.

关键词： Linear systems

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Building One-Dimensional Van Der Waals Heterostructures on Atomically Precise Single-Walled Carbon Nanotubes

SSRN

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SSRN 2022年

作者： Zhang, Ruixi Feng, Ya Li, Henan Kumamoto, Akihito Wang, Shuhui Zheng, Yongjia Dai, Wanyu Liu, Ming Tanaka, Takeshi Kataura, Hiromichi Ikuhara, Yuichi Maruyama, Shigeo Xiang, Rong Department of Mechanical Engineering The University of Tokyo Tokyo113-8656 Japan Department of Bioengineering The University of Tokyo Tokyo113-8656 Japan Next Generation Electron Microscopy Social Cooperation Program The University of Tokyo Tokyo113-8656 Japan Tsukuba305-8565 Japan Institute of Engineering Innovation The University of Tokyo Tokyo113-8656 Japan

We previously demonstrated the experimental synthesis of one-dimensional van der Waals (1D vdW) heterostructures, where single-crystal boron nitride nanotubes (BNNT) and/or molybdenum disulfide nanotubes seamlessly wrap around a single-walled carbon nanotube (SWCNT) and form a coaxial hetero-nanotube with a diameter of only several nm. This opens up a plethora of function-designable 1D heterostructures but being able to accurately control the atomic structure and property of each shell is an initial and critical step . Here, we demonstrate the possibility of building 1D vdW heterostructures on atomically precise, i.e. electronic-property-specific, single-chirality SWCNTs. This is achieved by a long route of dispersing, sorting, re-depositing and cleaning SWCNTs before performing the synthesis of 1D heterostructures. We employ five different single-chirality SWCNT solutions as examples and confirm that 1D heterostructures can be fabricated on these solution-sorted SWCNT templates if the surfactant can be readily removed. Cutting-edge transmission electron microscopy unambiguously reveals the high-quality coaxial geometry as well as the crystal orientation of inner and outer nanotubes, and visualizes that all zigzag, near-armchair, and chiral BNNTs can form on (6, 5) SWCNTs. © 2022, The Authors. All rights reserved.

关键词： High resolution transmission electron microscopy

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An overview of deep learning in medical imaging

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Informatics in Medicine Unlocked 2021年 26卷

作者： Anaya-Isaza, Andrés Mera-Jiménez, Leonel Zequera-Diaz, Martha Pontificia Universidad Javeriana Bogotá 110231 Colombia Faculty of Engineering Bioengineering Program Universidad de Antioquia Medellín 050010 Colombia School of Engineering BASPI/FootLab (Bioengineering Signal Analysis And Image Processing Research Group) Pontificia Universidad Javeriana Bogotá 110231 Colombia INDIGO Research Bogotá 110221 Colombia

Deep learning (DL) is one of the branches of artificial intelligence that has seen exponential growth in recent years. The scientific community has focused its attention on DL due to its versatility, high performance, high generalization capacity, and multidisciplinary uses, among many other qualities. In addition, a large amount of medical data and the development of more powerful computers has also fostered an interest in this area. This paper presents an overview of current deep learning methods, starting from the most straightforward concept but accompanied by the mathematical models that are behind the functionality of this type of intelligence. In the first instance, the fundamental concept of artificial neural networks is introduced, progressively covering convolutional structures, recurrent networks, attention models, up to the current structure known as the Transformer. Secondly, all the basic concepts involved in training and other common elements in the design of the architectures are introduced. Thirdly, some of the key elements in modern networks for medical image classification and segmentation are shown. Subsequently, a review of some applications realized in the last years is shown, where the main features related to DL are highlighted. Finally, the perspectives and future expectations of deep learning are presented. © 2021 The Authors

关键词： Attention models Convolutional neural networks Deep learning Medical imaging Recurrent neural networks Transformers

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Alerting Network Alteration in Idiopathic Rapid Eye Movement Sleep Behavior Disorder Patients with Mild Cognitive Impairment

Alerting Network Alteration in Idiopathic Rapid Eye Movement...

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亚洲睡眠医学会2021年学术大会暨第十三届中国睡眠研究会年会

作者： Jeong,El Cha,Kwang Su Sunwoo,Jun-Sang Jung,Ki-Young El Jeong Interdisciplinary Program in Bioengineering College of EngineeringSeoul National University Department of Neurology Seoul National University HospitalNeuroscience Research InstituteSeoul National University College of Medicine Department of Neurosurgery Seoul National University Hospital

Objective: It is reported that idiopathic REM sleep behavior disorder (iRBD) is associated with alteration of attention,executive functions,and visuospatial abilities. In addition,it is known that about half of the iRBD patients have mild cognitive impairment (MCI). The aim of this study was to explore the differences between iRBD patients with MCI and ones without MCI. Methods: 14 healthy controls (HC),24 iRBD patients without MCI (iRBD-nMCI),and 24 iRBD patients with MCI (iRBD-MCI) were recruited.

关键词： Alerting Network Alteration in Idiopathic Rapid Eye Movement Sleep Behavior Disorder Patients with Mild Cognitive Impairment

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