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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Lai, Andre Dong, Alan Lustig, Michael Sohn, Lydia L. UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California BerkeleyCA United States Electrical Engineering and Computer Sciences University of California BerkeleyCA United States Department of Mechanical Engineering University of California BerkeleyCA United States

ISBN: (纸本)9781733419031

Biomechanics plays an integral role in cancer development and progression. Accurately quantifying the mechanical properties of cells would enable a more comprehensive understanding of cancer, complementing conventional biochemical and genetic analyses. Here, we introduce a microfluidic platform for measuring single cell viscoelasticity at multiple frequencies in a high-throughput and label-free manner. Using the Coulter principal and a unique microfluidic channel geometry, our device records resistance pulses in order to estimate a cell's viscoelastic phenotype. We demonstrate our platform's capabilities by measuring three breast epithelial cell lines. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Biomechanics

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Multiplexed resistive-pulse sensing through coded node⇓pore channel geometry 24

Multiplexed resistive-pulse sensing through coded node⇓pore...

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24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Cotner, Kristen L. Sohn, Lydia L. UC Berkeley - UCSF Graduate Program in Bioengineering Berkeley and San Francisco United States UC Berkeley Department of Mechanical Engineering Berkeley United States

ISBN: (纸本)9781733419017

Node-pore sensing (NPS) is a versatile label-free microfluidic platform to measure a variety of cell phenotypes. Yet the single-channel nature of NPS limits throughput and precludes integration with components such as cell sorting. Here we demonstrate a novel multichannel NPS design by encoding the channels with Barker and Gold codes to modulate the current pulse. Particle events are detected through matched-filter detection and successive interference cancellation (SIC), resolving overlapping signals in the same channel and across separate channels. © 2020 CBMS-0001

关键词： Matched filters

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Physics-based learned design for Fourier DiffuserScope

Physics-based learned design for Fourier DiffuserScope

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Computational Optical Sensing and Imaging, COSI 2021 - Part of OSA Imaging and Applied Optics Congress 2021

作者： Markley, Eric Liu, Fanglin Linda Kellman, Michael Antipa, Nick Waller, Laura UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States Department of Electrical Engineering and Computer Sciences University of California Berkeley United States Department of Pharmaceutical Chemistry University of California San Francisco United States Department of Electrical and Computer Engineering University of California San Diego United States

We couple a differentiable forward model of diffuser-based single-shot 3D microscopy (Fourier DiffuserScope) with an invertible and differentiable reconstruction algorithm to jointly optimize the imaging system and th... 详细信息

ISBN: (纸本)9781557528209

关键词： Imaging systems

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Optical attenuators extend dynamic range but alter angular response of planar ultraviolet-C dosimeters

arXiv

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arXiv 2021年

作者： Su, Alison Geldert, Alisha Grist, Samantha M. Herr, Amy E. University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering BerkeleyCA94720 United States Department of Bioengineering BerkeleyCA94720 United States

A challenge for sensors used in ultraviolet-C (UV-C) decontamination protocols of N95 respirators is validation that the entire N95 surface receives the minimum acceptable dose. Photochromic indicators (PCIs) can accurately measure UV-C dose on nonplanar surfaces, but often saturate below doses required to decontaminate porous, multilayered textiles such as N95s. Here, we investigate the use of optical attenuators to extend PCI dynamic range while maintaining a near-ideal angular response - critical for accurate measurements when UV-C is uncollimated. Through an analytical model, we show that tuning attenuator refractive index, attenuation coefficient, and thickness can extend dynamic range, but compromises ideal angular response unless the attenuator is an ideal diffuser. To demonstrate this tradeoff empirically, we pair PCIs with model specular (floated borosilicate) and diffuse (polytetrafluoroethylene) attenuators, characterize the angular response, and evaluate on-N95 UV-C dose measurement accuracy of each PCI-attenuator stack in a UV-C decontamination system. While both borosilicate and polytetrafluoroethylene increase PCI dynamic range >4×, both attenuators introduce angle-dependent transmittance, which causes location-dependent underestimation of UV-C dose. The PCI-borosilicate and PCI-polytetrafluoroethylene stacks underreport true on-N95 dose by 1) 14.7% and 3.6%, respectively, on a surface near-normal to the array of source lamps, and 2) 40.8% and 19.8%, respectively, on a steeply sloped location. Overall, we demonstrate that while planar optical attenuators can increase PCI dynamic range, verification of near-ideal angular response is critical for accurate UVC dose measurement. © 2021, CC BY-NC-SA.

关键词： Refractive index

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Physics-driven Deep Learning for PET/MRI

arXiv

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arXiv 2022年

作者： Rajagopal, Abhejit Leynes, Andrew P. Dwork, Nicholas Scholey, Jessica E. Hope, Thomas A. Larson, Peder E.Z. Department of Radiology and Biomedical Imaging University of California San Francisco94158 United States Uc Berkeley-UCSF Joint Graduate Program in Bioengineering University of California San Francisco United States University of California BerkeleyCA United States Department of Radiation Oncology University of California San Francisco94158 United States Departments of Pediatrics and Radiology University of Colorado Anschutz 80045 United States

In this paper, we review physics- and data-driven reconstruction techniques for simultaneous positron emission tomography (PET) / magnetic resonance imaging (MRI) systems, which have significant advantages for clinical imaging of cancer, neurological disorders, and heart disease. These reconstruction approaches utilize priors, either structural or statistical, together with a physics-based description of the PET system response. However, due to the nested representation of the forward problem, direct PET/MRI reconstruction is a nonlinear problem. We elucidate how a multi-faceted approach accommodates hybrid data- and physics-driven machine learning for reconstruction of 3D PET/MRI, summarizing important deep learning developments made in the last 5 years to address attenuation correction, scattering, low photon counts, and data consistency. We also describe how applications of these multi-modality approaches extend beyond PET/MRI to improving accuracy in radiation therapy planning. We conclude by discussing opportunities for extending the current state-of-the-art following the latest trends in physics- and deep learning-based computational imaging and next-generation detector hardware. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in Alzheimer’s disease across two brain regions.

Research Square

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Research Square 2021年

作者： Belonwu, Stella A. Li, Yaqiao Bunis, Daniel Rao, Arjun Arkal Solsberg, Caroline Warly Tang, Alice Fragiadakis, Gabriela K. Dubal, Dena B. Oskotsky, Tomiko Sirota, Marina Bakar Computational Health Sciences Institute University of California San Francisco San FranciscoCA United States Pharmaceutical Sciences and Pharmacogenomics Graduate Program University of California San Francisco San FranciscoCA United States CoLabs University of California San Francisco San FranciscoCA United States Bakar ImmunoX Initiative University of California San Francisco San FranciscoCA United States Department of Pathology University of California San Francisco San FranciscoCA United States Bioengineering Graduate Program University of California San Francisco San FranciscoCA United States Department of Medicine Division of Rheumatology University of California San Francisco San FranciscoCA United States Biomedical Sciences Graduate Program University of California San Francisco San FranciscoCA United States Neurosciences Graduate Program University of California San Francisco San FranciscoCA United States Department of Neurology Weill Institute for Neurosciences University of California San Francisco San FranciscoCA94158 United States Department of Pediatrics University of California San Francisco San FranciscoCA United States

Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can inform new therapeutic approaches for both sexes. Here, we utilized nearly 74,000 cells from human prefrontal and entorhinal cortex samples from the first two publicly available single-cell RNA sequencing AD datasets to study cell type-specific sex-stratified transcriptomic perturbations in AD. Our examination at the single-cell level revealed that sex-specific gene and pathway differences in AD were most prominently observed in glial cells of the prefrontal cortex. In the entorhinal cortex, we observed the same genes and pathways to be perturbed in opposing directions between sexes in AD relative to healthy state. Our findings contribute to growing evidence of sex differences in AD-related transcriptomic changes, which can fuel the development of therapies that may prove more effective at reversing AD pathophysiology. © 2021, CC BY.

关键词： Genes

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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

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Deep learning-guided design of dynamic proteins

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Science (New York, N.Y.) 2025年第6749期388卷 eadr7094页

作者： Amy B Guo Deniz Akpinaroglu Christina A Stephens Michael Grabe Colin A Smith Mark J S Kelly Tanja Kortemme The UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco San Francisco CA USA. Department of Bioengineering and Therapeutic Sciences University of California San Francisco San Francisco CA USA. Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA USA. Cardiovascular Research Institute University of California San Francisco San Francisco CA USA. Department of Chemistry Wesleyan University Middletown CT USA. Quantitative Biosciences Institute University of California San Francisco San Francisco CA USA. Chan Zuckerberg Biohub San Francisco CA USA.

Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-guided approach for de novo design of dynamic changes between intradomain geometries of proteins, similar to switch mechanisms prevalent in nature, with atomic-level precision. We solve four structures that validate the designed conformations, demonstrate modulation of the conformational landscape by orthosteric ligands and allosteric mutations, and show that physics-based simulations are in agreement with deep-learning predictions and experimental data. Our approach demonstrates that new modes of motion can now be realized through de novo design and provides a framework for constructing biology-inspired, tunable, and controllable protein signaling behavior de novo.

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Interoceptive modulation of emotions

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Current Opinion in Neurobiology 2025年 92卷 103049-103049页

作者： Zsembik, Leo Oldroyd, Poppy Chen, Ritchie Department of Neurological Surgery University of California San Francisco United States Weill Institute for Neurosciences University of California San Francisco United States Neuroscience Graduate Program University of California San Francisco United States Department of Psychiatry and Behavioral Sciences University of California San Francisco United States Department of Bioengineering and Therapeutic Sciences University of California San Francisco United States

The metaphorical use of the heart to represent emotions has been documented since our earliest known writings, which reflects a historical recognition of the deep connection between bodily sensations and emotions. However, it remains an active topic of investigation to determine the degree to which bodily physiology modulates emotion states. Recent advances in the neuroscience of interoception—the process by which we sense, interpret, and integrate internal bodily signals and physiology—are uncovering neurobiological mechanisms by which visceral signals can influence emotions. Here we review interoceptive pathways that relay visceral signals to the brain and discuss how these signals influence emotion states as well as challenges and opportunities to better understand interoceptive modulation of emotions. © 2025 Elsevier Ltd

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Microfluidic rheology to characterize viscoelastic properties of malignant and non-malignant epithelial cells 21

Microfluidic rheology to characterize viscoelastic propertie...

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21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017

作者： Kim, Junghyun Sohn, Lydia L. Department of Mechanical Engineering University of California at Berkeley BerkeleyCA United States Graduate Program in Bioengineering University of California Berkeley University of California San Francisco BerkeleyCA United States

ISBN: (纸本)9780692941836

This study introduces a novel microfluidic rheology platform to quantify the viscoelastic properties of cells at the single-cell level. We measured both the storage (G') and loss (G") moduli of malignant and non-malignant epithelial cells, and simultaneously evaluate the frequency dependence of the moduli through a power-law structure damping model. With our unique platform's ability to screen large cellular populations, we have established a clear difference between the viscoelastic response of malignant and non-malignant cells. © 17CBMS-0001.

关键词： Cytology

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