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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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Appendicular DXA BMC and Lean Mass Strongly Associated to Hip Fracture Risk

Appendicular DXA BMC and Lean Mass Strongly Associated to Hi...

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第六届国际骨质疏松及骨矿盐疾病学术会议

作者： John A Shepherd Serghei Malkov Kathleen Peters Jane Cauley Steve Cummings Tamara Harris Rachel Murphy Suzanne Satterfield Marjolien Visser Joseph Wilson Joseph Zmuda Peggy Cawthon Department of Radiology & Biomedical Imaging University of California San FranciscoUSA UC Berkeley-UCSF Graduate Program in Bioengineering California Pacific Medical Center Department of Epidemiology Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvaniaUSA UC Berkeley-UCSF Graduate Program in Bioengineering San FranciscoCA USA

Objective We aimto determine the utility of quantifying DXA-derived surrogates of CT measures including thigh cross-sectional muscle area(CSA) and muscle attenuation. Methods We used a retrospective case-cohort study design using data from the HealthAging and Body Composition(HealthABC) *** were 111 participants that had a hip fracture during the 8.7-year study period.A cohortof 212 non-fracture participants wasrandomly selected

关键词： DXA Appendicular DXA BMC and Lean Mass Strongly Associated to Hip Fracture Risk BMC

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Absence seizure susceptibility correlates with pre-ictal β oscillations

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Journal of Physiology Paris 2016年第4期110卷 372-381页

作者： Sorokin, Jordan M. Paz, Jeanne T. Huguenard, John R. Stanford Neurosciences Graduate Training Program United States Department of Neurology and Neurological Sciences Stanford University School of Medicine Stanford 94305 CA United States Department of Bioengineering Stanford University School of Medicine Stanford 94305 CA United States Gladstone Institutes San Francisco 94158 CA United States

Absence seizures are generalized, cortico-thalamo-cortical (CTC) high power electroencephalographic (EEG) or electrocorticographic (ECoG) events that initiate and terminate suddenly. ECoG recordings of absence seizures in animal models of genetic absence epilepsy show a sudden spike-wave-discharge (SWD) onset that rapidly emerges from normal ECoG activity. However, given that absence seizures occur most often during periods of drowsiness or quiet wakefulness, we wondered whether SWD onset correlates with pre-ictal changes in network activity. To address this, we analyzed ECoG recordings of both spontaneous and induced SWDs in rats with genetic absence epilepsy. We discovered that the duration and intensity of spontaneous SWDs positively correlate with pre-ictal 20–40 Hz (β) spectral power and negatively correlate with 4–7 Hz (Ø) power. In addition, the output of thalamocortical neurons decreases within the same pre-ictal window of time. In separate experiments we found that the propensity for SWD induction was correlated with pre-ictal β power. These results argue that CTC networks undergo a pre-seizure state transition, possibly due to a functional reorganization of cortical microcircuits, which leads to the generation of absence seizures. © 2017 Elsevier Ltd

关键词： Brain-state Epilepsy Networks Oscillations Thalamocortical

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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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Simulation of depth of interaction effects for pinhole SPECT

Simulation of depth of interaction effects for pinhole SPECT

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： A.B. Hwang K. Iwata B.H. Hasegawa Bioengineering Graduate Program University of California Berkeley and San Francisco USA Department of Radiology University of California San Francisco San Francisco CA USA Department of Nuclear Engineering University of California Berkeley Berkeley CA USA

Pinhole imaging is receiving attention as a method to enable SPECT of small animals. However, gamma rays passing through the pinhole aperture and entering the detector at an oblique angle can cause parallax errors due to the depth of interaction (DOI) of the incident gamma ray in the absorber layer of the detector. This can cause a displacement and blurring of the position coordinates recorded by the detector, resulting in an error known as the "DOI effect". The DOI effect for projection data can be analytically calculated, but the error due to the DOI effect in reconstructed SPECT images is difficult to predict analytically due to the complexity of reconstruction algorithms. Therefore, we used an analytic model of the DOI effect in the projection data to numerically simulate the acquisition of point sources to determine the point spread function at different points in the object. The resulting projection data were reconstructed using a Feldkamp algorithm, from which point spread functions were extracted to quantify loss in spatial resolution due to the DOI effect. The simulations were performed for 140-keV gamma rays and a 6 mm thick CsI scintillator with a reconstruction volume of (40 mm)/sup 3/. The simulation was repeated with a 10 mm thick high purity germanium (HPGe) detector. These detectors and parameters are representative of a system that can be used for small animal imaging. From these calculations, we estimate tomographic reconstruction contributes a resolution loss of 0.32-0.63 mm FWHM in plane and 0.21-0.42 mm FWHM out of plane of the detector. For the CsI scintillator, the DOI effect contributes a maximum resolution loss of 0.5 mm FWHM in plane and 0.3 mm FWHM out of plane. With the HPGe detector, the DOI effect contributes a spatial resolution loss of 0.6 mm FWHM in plane and 0.5 mm out of plane.

关键词： Image reconstruction Spatial resolution Animals Gamma rays Gamma ray detection Gamma ray detectors Image analysis Algorithm design and analysis Optical imaging Apertures

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QSMGAN: Improved quantitative susceptibility mapping using 3d generative adversarial networks with increased receptive field

arXiv

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arXiv 2019年

作者： Chen, Yicheng Jakary, Angela Hess, Christopher P. Lupo, Janine UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley University of California San Francisco California San FranciscoCA94158 Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States

Quantitative susceptibility mapping (QSM) is a powerful MRI technique that has shown great potential in quantifying tissue susceptibility in numerous neurological disorders. However, the intrinsic ill-posed dipole inversion problem greatly affects the accuracy of the susceptibility map. We proposed QSMGAN: A 3D deep convolutional neural network approach based on improved U-Net with increased phase receptive field and further refined the network using the WGAN-GP training strategy. Our method could generate accurate and realistic QSM from single orientation phase maps efficiently and performed significantly better than traditional non-learning-based dipole inversion algorithms. Copyright © 2019, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Association of body shape and fracture risk

Association of body shape and fracture risk

引用

第六届国际骨质疏松及骨矿盐疾病学术会议

作者： Bo Fan Joseph P Wilson John A Shepherd Department of Radiology & Biomedical Imaging University of California San FranciscoUSA Department of Radiology & Biomedical Imaging University of California San FranciscoUSA UC Berkeley-UCSF Graduate Program in BioengineeringSan FranciscoCA US

＜正＞Objective:To examine theindependent association ofbody shape（total volume,trunk volume,and trunk to leg volume ratio）tofracture risk. Methods:We performed a cross-sectional study of the NHANES 1999-2004 survey data downloaded from the study *** individualshad both a valid dual-energy Xray absorptiometry（DXA） scan and known fracture status. The body shape measureswere derived using DXA whole

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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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Design and utility of a small animal CT/SPECT system

Design and utility of a small animal CT/SPECT system

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： K. Iwata A.B. Hwang M.C. Wu H.R. Tang A.J. Da Silva K.H. Wong M.W. Dae B.H. Hasegawa Department of Radiology University of California San Francisco San Francisco CA USA Bioengineering Graduate Program University of California Berkeley and San Francisco USA Department of Radiology University of California San Francisco San Francisco USA Department of Nuclear Engineering University of California Berkeley Berkeley CA USA

Recent developments in the genetic engineering of small animals have motivated us to design an in vivo dual-modality CT/SPECT system that can be used to localize and quantify uptake of single-photon radiotracers in mice. The CT system includes a 75-W x-ray tube and a CCD camera, while the radionuclide imager incorporates a CsI(TI) scintillator coupled to a Si photodiode array with interchangeable pinhole collimators. These devices are mounted on a slip-ring gantry to image a 40-mm diameter cylindrical volume, where both modalities share a common field of view without moving the table on which the animal lies horizontally. The calculated modulation transfer function of the radionuclide system exceeds 10% at 1.01p/mm. The spatial resolution of the CT system is 0.1 mm with at scan time of 15 min and a contrast resolution of 1% for soft tissue. The high-resolution CT image can be used to provide a priori information to correct both the visual quality and the quantitative accuracy of the SPECT image. This imaging system and technique is designed for in vivo functional assessments of cancer and cardiovascular disease in small animals.

关键词： Animals Computed tomography In vivo Spatial resolution Genetic engineering Mice X-ray imaging Charge coupled devices Charge-coupled image sensors Photodiodes

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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

引用

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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