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Computational Optical Sensing and Imaging, COSI 2024 - Part of Optica Imaging Congress

作者： Markley, Eric Kabuli, Leyla Chien, Tiffany Pinkard, Henry 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

We present a technique for information-theoretic optimization of computational imaging systems demonstrated in snapshot 3D microscopy. By directly evaluating measurement quality and decoupling optimization from downst... 详细信息

关键词： Decoding

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Aging impairs the osteocytic regulation of collagen integrity and bone quality

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Bone Research 2024年第1期12卷 78-94页

作者： Charles A.Schurman Serra Kaya Neha Dole Nadja M.Maldonado Luna Natalia Castillo Ryan Potter Jacob P.Rose Joanna Bons Christina D.King Jordan B.Burton Birgit Schilling Simon Melov Simon Tang Eric Schaible Tamara Alliston Department of Orthopaedic Surgery University of CaliforniaSan FranciscoCA 94143USA UC Berkeley/UCSF Graduate Program in Bioengineering San FranciscoCA 94143USA Buck Institute for Research on Aging NovatoCA 94945USA Washington University in St Louis Department of OrthopedicsSt.LouisMO 63130USA Advanced Light Source Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA

Poor bone quality is a major factor in skeletal fragility in elderly *** molecular mechanisms that establish and maintain bone quality,independent of bone mass,are unknown but are thought to be primarily determined by *** hypothesize that the age-related decline in bone quality results from the suppression of osteocyte perilacunar/canalicular remodeling(PLR),which maintains bone material *** examined bones from young and aged mice with osteocyte-intrinsic repression of TGFβsignaling(TβRII^(ocy−/−))that suppresses *** control aged bone displayed decreased TGFβsignaling and PLR,but aging did not worsen the existing PLR suppression in male TβRII^(ocy−/−)*** relationship impacted the behavior of collagen material at the nanoscale and tissue scale in macromechanical *** effects of age on bone mass,density,and mineral material behavior were independent of osteocytic TGFβ.We determined that the decline in bone quality with age arises from the loss of osteocyte function and the loss of TGFβ-dependent maintenance of collagen integrity.

关键词： maintain primarily integrity

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Layered Diffusion Model for One-Shot High Resolution Text-to-Image Synthesis

arXiv

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arXiv 2024年

作者： Khwaja, Emaad Rashwan, Abdullah Chen, Ting Wang, Oliver Kothawade, Suraj Li, Yeqing UC Berkeley UCSF Joint Bioengineering Graduate Program United States Computer Science Division UC Berkeley United States Google United States Google Deepmind United Kingdom

We present a one-shot text-to-image diffusion model that can generate high-resolution images from natural language descriptions. Our model employs a layered U-Net architecture that simultaneously synthesizes images at multiple resolution scales. We show that this method outperforms the baseline of synthesizing images only at the target resolution, while reducing the computational cost per step. We demonstrate that higher resolution synthesis can be achieved by layering convolutions at additional resolution scales, in contrast to other methods which require additional models for super-resolution synthesis. © 2024, CC BY.

关键词： Diffusion

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TOWARDS SINGLE-CELL PROTEOFORM PROFILING: ON-CHIP ISOELECTRIC FOCUSING IN IMMOBILIZED PH GRADIENT GELS

TOWARDS SINGLE-CELL PROTEOFORM PROFILING: ON-CHIP ISOELECTRI...

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2022 Solid-State Sensors, Actuators and Microsystems Workshop, Hilton Head 2022

作者： Lomeli, Gabriela Herr, Amy E. UC Berkeley-UCSF Graduate Program in Bioengineering CA United States Department of Bioengineering University of California BerkeleyCA United States Chan Zuckerberg Biohub San FranciscoCA United States

ISBN: (纸本)9781940470047

Microfluidic tools are an essential capability in understanding cell-to-cell heterogeneity. Similarly, precision microanalytical tools can play an outsize role in measuring molecule-to-molecule heterogeneity, especially as protein post-translational modifications create proteoforms that execute regular and aberrant cellular functions. Although highly related, slight variations in protein charge contribute to proteoform heterogeneity. Electrophoretic methods, including immobilized pH gradient isoelectric focusing (IPG-IEF), provide the resolution to measure subtle protein-to-protein differences. However, conventional IPG-IEF can be low-throughput and requires large starting sample amounts, precluding single-cell analysis. Here, we present the first polydimethylsiloxane (PDMS)-based, immunoprobed, microfluidic IPG-IEF device to our knowledge. We demonstrate separation performance on par with our single-cell IEF device, including resolving analytes differing by only 0.1 pH. © 2022 TRF.

关键词： Electrophoresis

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Spectral DefocusCam: hyperspectral imaging using defocus and a spectral filter array

Spectral DefocusCam: hyperspectral imaging using defocus and...

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Computational Optical Sensing and Imaging, COSI 2022

作者： Foley, Christian Monakhova, Kristina Yanny, Kyrollos Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We propose a compact hyperspectral camera based on a focus-tunable lens and spectral filter array. The camera captures then fuses multiple defocused measurements to obtain a high-resolution hyperspectral volume. ©... 详细信息

ISBN: (纸本)9781557528209

关键词： Hyperspectral imaging

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OLIGONucLEOTIDE FUNCTIONALIZED POLYACRYLAMIDE BEADS FOR AMPLIFICATION BASED BIOMARKER DETECTION 25

OLIGONUCLEOTIDE FUNCTIONALIZED POLYACRYLAMIDE BEADS FOR AMPL...

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

作者： Chaves, Rodrigo Cotrim Streets, Aaron University of California BerkeleyCA United States UC Berkeley UCSF Graduate Program in Bioengineering CA United States

ISBN: (纸本)9781733419031

Single-cell quantitative biomarker analysis is a powerful technique for studying tissue heterogeneity, but commonly used staining techniques cannot detect markers with lower than 100 target molecules per cell [1]. Here we report a droplet microfluidic platform for encapsulation of samples in Polyacrylamide (PA) hydrogel beads, and staining for fluorescence analysis. This is achieved by functionalizing the PA with oligonucleotides designed to capture biomarkers of interest, and amplifying targets through PCR, enabling sensitive detection of DNA, RNA or protein molecules with low copy number for quantification of cellular populations with traditional flow cytometry. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Oligonucleotides

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Spectral DiffuserScope - Computational Snapshot Hyperspectral Imager for Microscopy

Spectral DiffuserScope - Computational Snapshot Hyperspectra...

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2023 Computational Optical Sensing and Imaging, COSI 2023 in Optica Imaging Congress - Part of Imaging and Applied Optics Congress 2023

作者： Aggarwal, Neerja Markley, Eric Raniwala, Yashovardhan Houck, William D. Lee, Kyung Chul Bae, Junghyun Baek, Nakkyu Park, Wook Lee, Seung Ah Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States VIAVI Solutions Inc Santa Rosa United States School of Electrical and Electronic Engineering Yonsei University Seoul Korea Republic of

We introduce a computational snapshot hyperspectral imager for benchtop microscopy. The compact device uses a diffuser and spectral filter array to multiplex spatio-spectral information into a 2D measurement, then rec... 详细信息

ISBN: (纸本)9781957171289

关键词： Blue light emitting diodes Diffusers Fluorescence microscopy Image sensors Spatial resolution Ultraviolet light emitting diodes

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MULTIPLEXED DNA-DIRECTED PATTERNING OF ANTIBODIES FOR SINGLE-CELL SURFACE MARKER ANALYSIS 25

MULTIPLEXED DNA-DIRECTED PATTERNING OF ANTIBODIES FOR SINGLE...

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

作者： Kozminsky, Molly Scheideler, Olivia J. Li, Brian Liu, Nathaniel K. Sohn, Lydia L. California Institute of Quantitative Biosciences Berkeley United States 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)9781733419031

Cell surface marker expression is a ubiquitously measured property of single-cell phenotypes. However, measuring several markers with exogenous labels can be costly and complex. We applied a novel bioconjugation chemistry known as DNA-directed patterning to functionalize glass substrates with great specificity and flexibility. Combined with a newly-designed node-pore sensing device, we have developed a flexible and label-free platform for multiplexed surface-marker screening of single cells. In this work, we present our design and demonstrate our platform's capability to screen two example cell types for surface-marker expression. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： DNA

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CELL-E 2: translating proteins to pictures and back with a bidirectional text-to-image transformer 23

CELL-E 2: translating proteins to pictures and back with a b...

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Proceedings of the 37th International Conference on Neural Information Processing Systems

作者： Emaad Khwaja Yun S. Songt Aaron Agarunov Bo Huang UC Berkeley - UCSF Joint Bioengineering Graduate Program and Computer Science Division UC Berkeley CA Department of Statistics UC Berkeley CA and Computer Science Division UC Berkeley CA Department of Pathology Memorial Sloan Kettering Cancer Center Department of Pharmaceutical Chemistry UCSF San Francisco CA and Department of Biochemistry and Biophysics UCSF San Francisco CA and Chan Zuckerberg Biohub - San Francisco San Francisco CA

We present CELL-E 2, a novel bidirectional transformer that can generate images depicting protein subcellular localization from the amino acid sequences (and vice versa). Protein localization is a challenging problem that requires integrating sequence and image information, which most existing methods ignore. CELL-E 2 extends the work of CELL-E, not only capturing the spatial complexity of protein localization and produce probability estimates of localization atop a nucleus image, but also being able to generate sequences from images, enabling de novo protein design. We train and finetune CELL-E 2 on two large-scale datasets of human proteins. We also demonstrate how to use CELL-E 2 to create hundreds of novel nuclear localization signals (NLS). Results and interactive demos are featured at https://***/CELL-E_2/.

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FABRICATION OF STABLE GRADIENTS IN A HYDROGEL-FILLED MICROFLUIDIC DEVICE 25

FABRICATION OF STABLE GRADIENTS IN A HYDROGEL-FILLED MICROFL...

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

ISBN: (纸本)9781733419031

Gradients play a key role in mimicking biological conditions in situ and in separating biological species for analysis. Current methods to generate microscale gradients typically require high reagent consumption and enclosed microfluidic devices. Here, we introduce a simple and controllable method to generate stable immobilized gradients in a hydrogel-filled PDMS channel using only 7 µL of reagent. The versatile fabrication technique forms gradients of compounds containing an abstractable hydrogen (C-H) bond. Moreover, the PDMS can be detached from the glass substrate for open access to the gradient gel. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Hydrogels

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