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Direct measure of DNA bending by quantum magnetic imaging of a nano-mechanical torque-balance

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arXiv 2024年

作者： Kazi, Zeeshawn Shelby, Isaac M. Nirodi, Ruhee Turnbull, Joseph Watanabe, Hideyuki Itoh, Kohei M. Wiggins, Paul A. Fu, Kai-Mei C. Department of Physics University of Washington SeattleWA98105 United States National Institute of Advanced Industrial Science and Technology Tsukuba Central 2 1-1-1 Umezono Tsukuba Ibaraki305-8568 Japan School of Fundamental Science and Technology Keio University 3-14-1 Hiyoshi Kohoku-ku Yokohama223-8522 Japan Department of Bioengineering University of Washington SeattleWA98105 United States Department of Electrical and Computer Engineering University of Washington SeattleWA98105 United States Physical Sciences Division Pacific Northwest National Laboratory RichlandWA99354 United States

DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is detected using a nano-mechanical torque balance formed by tethering a ferromagnetic nanoparticle probe by an individual DNA molecule to a diamond magnetic field imager. The torque exerted by the DNA in response to bending caused by an applied magnetic torque is measured using wide-field imaging of quantum defects near the surface of the diamond. Qualitative measurements of differences in DNA bio-mechanical binding configuration are demonstrated, and as a proof-of-principle, a quantitative measurement of the bend response is made for individual DNA molecules. This quantum-enabled measurement approach could be applied to characterize the bend response of biophysically relevant short DNA molecules as well as the sequence dependence of DNA bending energy. © 2024, CC BY.

关键词： DNA

Noninvasive multichannel urodynamic system: Obtaining cutaneous electrical signals from the human urinary bladder

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Lifestyle Medicine

Lifestyle Medicine 2024年第1期5卷

作者： Kurniawan, Jonas F. Lee, Sanghee Le, Hoang-Kim Nguyen, Andrew K. L. Sit, Nathan L. J. Pham, Timothy Tjhia, Boris Gottlieb, Ryan Li, Carleen Shin, Andrew J. Garcia, Hassler Bueno Wu, Vincent M. Mendoza, Tris R DiPina, Thomas Ornelas, Gladys Chiang, George Jamieson, Christina A. M. Santiago-Lastra, Yahir Coleman, Todd P. Department of Bioengineering University of California San Diego La Jolla CA United States Materials Science and Engineering Program University of California San Diego La Jolla CA United States Department of Bioengineering Stanford University Stanford CA United States Department of Urology University of California San Diego La Jolla CA United States Pediatric Urology Rady Children's Hospital San Diego San Diego CA United States Department of Urology Baylor Scott & White Temple TX United States Department of Physics University of California San Diego La Jolla CA United States Department of Electrical and Computer Engineering University of California San Diego La Jolla CA United States Department of Nanoengineering University of California San Diego La Jolla CA United States Department of Materials Science and Engineering Stanford University Stanford CA United States Division of Pediatric Urology University of California San Diego La Jolla CA United States

We developed a high-resolution and noninvasive multichannel urodynamic system combined with a novel signal-processing algorithm tailored to extract electromyographic (EMG) activity from the urinary bladder. We utilized a flexible noninvasive biopotential recording system to collect an array of EMG signals from the urinary bladder of human subjects. This study also presents the use of an existing artifact rejection methodology to autonomously extract an EMG signal from an environment prone to motion artifacts. © 2023 The Authors. Lifestyle Medicine published by John Wiley & Sons Ltd.

关键词： electrical signal from the urinary bladder flexible electronics noninvasive multichannel urodynamic study voluntary voiding

Landau Polaritons in a Full-Dielectric Three-Dimensional Photonic-Crystal Cavity

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Landau Polaritons in a Full-Dielectric Three-Dimensional Pho...

CLEO: science and Innovations, S and I 2022

作者： Tay, Fuyang Mojibpour, Ali Liang, Shuang Baydin, Andrey Ahmadivand, Arash Peraca, Nicolas Marquez Xu, Hongjing Gardner, Geoff C. Manfra, Michael J. Hagenmüller, David Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics and Astronomy Purdue University West LafayetteIN47907 United States Birck Nanotechnology Center Purdue University West LafayetteIN47907 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Microsoft Quantum Purdue Purdue University West LafayetteIN47907 United States School of Electrical and Computer Engineering Purdue University West LafayetteIN47907 United States School of Materials Engineering Purdue University West LafayetteIN47907 United States Université de Strasbourg CNRS Strasbourg67000 France Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

ISBN: (纸本)9781557528209

We fabricated a full-dielectric three-dimensional photonic-crystal cavity containing an ultrahigh-mobility two-dimensional electron gas. By applying a strong perpendicular magnetic field, we created Landau polaritons originating from the ultrastrong coupling of electrons with cavity modes. © Optica Publishing Group 2022, © 2022 The Author(s)

关键词： Polariton

Electrocatalytic on-site oxygenation for transplanted cell-based-therapies

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Nature Communications 2023年第1期14卷 1-11页

作者： Lee, Inkyu Surendran, Abhijith Fleury, Samantha Gimino, Ian Curtiss, Alexander Fell, Cody Shiwarski, Daniel J. Refy, Omar Rothrock, Blaine Jo, Seonghan Schwartzkopff, Tim Mehta, Abijeet Singh Wang, Yingqiao Sipe, Adam John, Sharon Ji, Xudong Nikiforidis, Georgios Feinberg, Adam W. Hester, Josiah Weber, Douglas J. Veiseh, Omid Rivnay, Jonathan Cohen-Karni, Tzahi Department of Materials Science and Engineering Carnegie Mellon University Pittsburgh PA United States Department of Biomedical Engineering Northwestern University Evanston IL United States Department of Bioengineering Rice University Houston TX United States Department of Chemical Engineering Carnegie Mellon University Pittsburgh PA United States Department of Electrical and Computer Engineering Northwestern University Evanston IL United States Department of Biomedical Engineering Carnegie Mellon University Pittsburgh PA United States Department of Physics Carnegie Mellon University Pittsburgh PA United States Department of Computer Science Northwestern University Evanston IL United States Department of Material Science and Engineering The Pennsylvania State University State College PA United States Neuroscience Institute Carnegie Mellon University Pittsburgh PA United States Simpson Querrey Institute Northwestern University Chicago IL United States Interactive Computing and Computer Science Georgia Institute of Technology Atlanta GA United States Department of Mechanical Engineering Carnegie Mellon University Pittsburgh PA United States Department of Materials Science and Engineering Northwestern University Evanston 60208 IL United States

Implantable cell therapies and tissue transplants require sufficient oxygen supply to function and are limited by a delay or lack of vascularization from the transplant host. Previous exogenous oxygenation strategies have been bulky and had limited oxygen production or regulation. Here, we show an electrocatalytic approach that enables bioelectronic control of oxygen generation in complex cellular environments to sustain engineered cell viability and therapy under hypoxic stress and at high cell densities. We find that nanostructured sputtered iridium oxide serves as an ideal catalyst for oxygen evolution reaction at neutral pH. We demonstrate that this approach exhibits a lower oxygenation onset and selective oxygen production without evolution of toxic byproducts. We show that this electrocatalytic on site oxygenator can sustain high cell loadings (>60k cells/mm³) in hypoxic conditions in vitro and in vivo. Our results showcase that exogenous oxygen production devices can be readily integrated into bioelectronic platforms, enabling high cell loadings in smaller devices with broad applicability. © 2023, The Author(s).

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CONVERGENCE SPEED AND APPROXIMATION ACCURACY OF NUMERICAL MCMC

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arXiv 2022年

作者： Cui, Tiangang Dong, Jing Jasra, Ajay Tong, Xin T. School of Mathematics Monash University Australia Graduate School of Business Columbia University United States Applied Mathematics and Computational Science Program Computer Electrical Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Saudi Arabia Department of Mathematics National University of Singapore Singapore

When implementing Markov Chain Monte Carlo (MCMC) algorithms, perturbation caused by numerical errors is sometimes inevitable. This paper studies how perturbation of MCMC affects the convergence speed and Monte Carlo estimation accuracy. Our results show that when the original Markov chain converges to stationarity fast enough and the perturbed transition kernel is a good approximation to the original transition kernel, the corresponding perturbed sampler has similar convergence speed and high approximation accuracy as well. We discuss two different analysis frameworks: ergodicity and spectral gap, both are widely used in the literature. Our results can be easily extended to obtain non-asymptotic error bounds for MCMC estimators. We also demonstrate how to apply our convergence and approximation results to the analysis of specific sampling algorithms, including Random walk Metropolis and Metropolis adjusted Langevin algorithm with perturbed target densities, and parallel tempering Monte Carlo with perturbed densities. Finally we present some simple numerical examples to verify our theoretical claims. Copyright © 2022, The Authors. All rights reserved.

关键词： Inverse problems

Towards a Prosodic Model for Synthesized Speech of Mathematical Expressions in MathML 9

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Towards a Prosodic Model for Synthesized Speech of Mathemati...

9th International Conference on Software Development and Technologies for Enhancing Accessibility and Fighting Info-Exclusion, DSAI 2020

作者： Souza, Adriana Freitas, Diamantino Bahia Federal Institute of Education Science and Technology Porto Seguro Brazil Doctoral Program in Digital Media Faculty of Engineering University of Porto Porto Portugal Department of Electrical and Computer Engineering Faculty of Engineering University of PortoPorto Portugal

ISBN: (纸本)9781450389372

The use of the MathML language made possible to improve the accessibility of mathematics for blind or low-vision persons in digital media. Synthetic speech technologies have advanced significantly using MathML, however, the speech synthesizers' standard reading style is still not suitable for mathematics. Making mathematical reading of the speech synthesizers more natural and expressive is still a challenge. The creation of models to produce the appropriate prosody in the synthesized speech of math content is therefore necessary, as shown in previous research. This article presents a proposal for a model to improve prosody in the synthesized speech of mathematical expressions based on MathML. A corpus of mathematical expressions spoken by Mathematics teachers was created to support the model's development. The Fujisaki intonation model was adopted for intonation control, accent and phrase commands have been extracted from the corpus, and some adjustments have been made to manipulate prosodic parameters in the speech of mathematical expression in correlation with the MathML tree;additionally, a pattern of pauses control is being created. © 2020 ACM.

关键词： Digital storage

A micromirror array with annular partitioning for high-speed random-access axial focusing

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Light(science & Applications) 2020年第1期9卷 241-255页

作者： Nathan Tessema Ersumo Cem Yalcin Nick Antipa Nicolas Pegard Laura Waller Daniel Lopez Rikky Muller The University of California Berkeley and University of CaliforniaSan Francisco Graduate Program in BioengineeringBerkeleyCA 94720USA Department of Electrical Engineering&Computer Sciences University of CaliforniaBerkeleyCA 94720USA Department of Applied Physical Sciences University of North Carolina at Chapel HillChapel HillNC 27514USA Chan Zuckerberg Biohub San FranciscoCA 94158USA Physical Measurement Laboratory National Institute of Standards and TechnologyGaithersburgMD 20899USA

Dynamic axial focusing functionality has recently experienced widespread incorporation in microscopy,augmented/virtual reality(AR/VR),adaptive optics and material ***,the limitations of existing varifocal tools continue to beset the performance capabilities and operating overhead of the optical systems that mobilize such *** varifocal tools that are the least burdensome to operate(*** crystal,elastomeric or optofluidic lenses)suffer from low(≈100 Hz)refresh ***,the fastest devices sacrifice either critical capabilities such as their dwelling capacity(*** gradient lenses or monolithic micromechanical mirrors)or low operating overhead(*** mirrors).Here,we present a general-purpose random-access axial focusing device that bridges these previously conflicting features of high speed,dwelling capacity and lightweight drive by employing lowrigidity micromirrors that exploit the robustness of defocusing phase ***,the device consists of an 8.2mm diameter array of piston-motion and 48-μm-pitch micromirror pixels that provide 2πphase shifting for wavelengths shorter than 1100 nm with 10-90% settling in 64.8μs(i.e.,15.44 kHz refresh rate).The pixels are electrically partitioned into 32 rings for a driving scheme that enables phase-wrapped operation with circular symmetry and requires<30 V per *** experiments demonstrated the array’s wide focusing range with a measured ability to target 29 distinct resolvable depth ***,the features of the proposed array offer the potential for compact,straightforward methods of tackling bottlenecked applications,including high-throughput single-cell targeting in neurobiology and the delivery of dense 3D visual information in AR/VR.

关键词： mirror axial random

AI-driven 3D Spatial Transcriptomics

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arXiv 2025年

作者： Almagro-Pérez, Cristina Song, Andrew H. Weishaupt, Luca Kim, Ahrong Jaume, Guillaume Williamson, Drew F.K. Hemker, Konstantin Lu, Ming Y. Singh, Kritika Chen, Bowen Le, Long Phi Baras, Alexander S. Jiang, Sizun Bashashati, Ali Liu, Jonathan T.C. Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Department of Computer Science & Technology University of Cambridge Cambridge United Kingdom Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Rutgers Robert Wood Johnson Medical School New BrunswickNJ United States Department of Pathology Johns Hopkins Hospital BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins Hospital BaltimoreMD United States Broad Institute of Harvard and MIT CambridgeMA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States Department of Pathology Dana Farber Cancer Institute BostonMA United States Department of Pathology and Laboratory Medicine University of British Columbia VancouverBC Canada School of Biomedical Engineering University of British Columbia VancouverBC Canada Department of Mechanical Engineering Bioengineering Laboratory Medicine & Pathology University of Washington SeattleWA United States Harvard Data Science Initiative Harvard University CambridgeMA United States

A comprehensive three-dimensional (3D) map of tissue architecture and gene expression is crucial for illuminating the complexity and heterogeneity of tissues across diverse biomedical applications1. However, most spatial transcriptomics (ST) approaches remain limited to two-dimensional (2D) sections of tissue2–4. Although current 3D ST methods hold promise, they typically require extensive tissue sectioning, are complex, are not compatible with non-destructive 3D tissue imaging technologies, and often lack scalability5–8. Here, we present VOlumetrically Resolved Transcriptomics EXpression (VORTEX), an AI framework that leverages 3D tissue morphology and minimal 2D ST to predict volumetric 3D ST. By pretraining on diverse 3D morphology–transcriptomic pairs from heterogeneous tissue samples and then fine-tuning on minimal 2D ST data from a specific volume of interest, VORTEX learns both generic tissue-related and sample-specific morphological correlates of gene expression. This approach enables dense, high-throughput, and fast 3D ST, scaling seamlessly to large tissue volumes far beyond the reach of existing 3D ST techniques. By offering a cost-effective and minimally destructive route to obtaining volumetric molecular insights, we anticipate that VORTEX will accelerate biomarker discovery and our understanding of morphomolecular associations and cell states in complex tissues. Interactive 3D ST volumes can be viewed at https://***/. © 2025, CC BY-NC-ND.

关键词： Vortex flow

Broadband Coherent Wave Control Through Photonic Collisions at Time Interfaces

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arXiv 2022年

作者： Galiffi, Emanuele Xu, Gengyu Yin, Shixiong Moussa, Hady Ra'di, Younes Alù, Andrea Photonics Initiative Advanced Science Research Center City University of New York 85 St. Nicholas Terrace New York10031 United States Department of Electrical Engineering City College City University of New York United States Physics Program Graduate Center City University of New York United States Department of Electrical Engineering and Computer Science Syracuse University SyracuseNY13244 United States

Coherent wave control exploits the interference among multiple waves impinging on a system to suppress or enhance outgoing signals based on their relative phase and amplitude. This process inherently requires the combination of non-Hermiticity, in order to enable energy exchanges among the waves, and spatial interfaces in order to tailor their scattering. Here we explore the temporal analogue of this phenomenon, based on time-interfaces that support instantaneous non-Hermitian scattering events for photons. Based on this mechanism, we demonstrate ultra-broadband temporal coherent wave control and the photonic analogue of mechanical collisions with phase-tunable elastic features. We apply them to erase, enhance and reshape arbitrary pulses by suitably tailoring the amplitude and phase of counterpropagating signals. Our findings provide a pathway to effectively sculpt broadband light with light without requiring spatial boundaries, within an ultrafast and low-energy platform. © 2022, CC BY.

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