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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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Data Format Standardization and DICOM Integration for Hyperpolarized 13C MRI

arXiv

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arXiv 2024年

作者： Diaz, Ernesto Sriram, Renuka Gordon, Jeremy W. Sinha, Avantika Liu, Xiaoxi Sahin, Sule Crane, Jason Olson, Marram P. Chen, Hsin-Yu Bernard, Jenna Vigneron, Daniel B. Wang, Zhen Jane Xu, Duan Larson, Peder E.Z. Department of Radiology and Biomedical Imaging University of California - San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley United States University of California San FranciscoCA United States

Hyperpolarized (HP) 13C MRI has shown promise as a valuable modality for in vivo measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard. This includes proposing a set of minimum set of information that is specific to HP 13C MRI studies. We then show where the majority of these can be fit into existing DICOM Attributes, primarily via the "Contrast/Bolus" module. We also demonstrate pipelines for utilizing DICOM for HP 13C MRI. DICOM is the most common standard for clinical medical image storage and provides the flexibility to accommodate the unique aspects of HP 13C MRI, including the HP agent information but also spectroscopic and metabolite dimensions. The pipelines shown include creating DICOM objects for studies on human and animal imaging systems with various pulse sequences. We also show a python-based method to efficiently modify DICOM objects to incorporate the unique HP 13C MRI information that is not captured by existing pipelines. Moreover, we propose best practices for HP 13C MRI data storage that will support future multi-site trials, research studies and technical developments of this imaging technique. © 2024, CC BY.

关键词： Magnetic resonance imaging

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Resistive-pulse sensing tumor-derived exosome detection device for resrouce-limited settings 21

Resistive-pulse sensing tumor-derived exosome detection devi...

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

作者： Carey, Thomas R. Yu, Connie W. Sohn, Lydia L. UC Berkeley-UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9780692941836

We present the theory, design, and initial characterization of a tumor-derived exosome detection platform based on resistive-pulse sensing to enable cost-effective, point-of-care cancer screening. Our platform detects exosomes displaying a specific surface antigen by electronically measuring the effective size increase that occurs when exosomes bind to colloids functionalized with a specific antibody. We have demonstrated that our device can distinguish antibody-functionalized colloids from similar colloids incubated with SKBR3-derived exosomes. © 17CBMS-0001.

关键词： Colloids

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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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Technical artifacts in droplet-microfluidics-based single-nuclei RNA-sequencing 25

Technical artifacts in droplet-microfluidics-based single-nu...

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

作者： Gupta, Anushka Streets, Aaron UC Berkeley-UC San Francisco Graduate Program in Bioengineering BerkeleyCA United States Chan Zuckerberg Biohub San FranciscoCA United States

ISBN: (纸本)9781733419031

Droplet microfluidic platforms have recently become a powerful tool for sequencing the transcriptomes of single nuclei in a ultrahigh-throughput format. However, single-nuclei RNA-sequencing (snRNA-seq) introduces severe sources of technical noise and transcript detection bias which distorts true biological heterogeneity. In this work, we performed a comparative study between droplet-based single-cell RNA-sequencing (scRNA-seq) and snRNA-seq on human preadipocytes to identify and characterize primary sources of technical artifacts associated with snRNA-seq, and propose strategies to account for these artifacts. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： RNA

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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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Three-Dimensional Free-Breathing Ultrashort Echo Time (UTE) 1H MRI Regional Ventilation: Comparison With Hyperpolarized 129Xe MRI and Pulmonary Function Testing in Healthy Volunteers and People With Cystic Fibrosis

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NMR in Biomedicine 2025年第6期38卷 e70033页

作者： Tan, Fei Eddy, Rachel L. Diamond, Vanessa M. Rayment, Jonathan H. Larson, Peder E. Z. UC Berkeley–UCSF Graduate Program in Bioengineering University of California Berkeley BerkeleyCA United States Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA United States BC Children's Hospital Research Institute Vancouver Canada Centre for Heart Lung Innovation University of British Columbia Vancouver Canada Department of Pediatrics University of British Columbia Vancouver Canada

MRI can provide localized assessment of lung function for monitoring people with lung disease. Hyperpolarized 129Xe MRI directly images pulmonary gas distribution but requires specialized hardware. Conventional 1H MRI acquisitions can also provide functional maps using free-breathing approaches. The purpose of this study is to evaluate regional ventilation derived from 3D ultrashort echo-time (UTE) 1H MRI using Motion-Compensated Low-Rank constrained reconstruction (MoCoLoR), by comparing against 129Xe MRI and pulmonary function testing as reference-standard. The study is retrospective in design. The study included 57 participants (25.4 ± 15.8 years, 35 males and 22 females): 12 healthy volunteers, 20 pediatric, and 25 adult people with cystic fibrosis (CF) scanned between January 2022 and February 2023. Field strength/sequence: 3T;129Xe: 2D multislice spoiled gradient-recalled sequence;UTE 1H: variable-density 3D radial sequence. K-means-based 129Xe ventilation defect percent (VDP), forced expiratory volume in 1 s (FEV1), and lung clearance index (LCI) were evaluated against UTE 1H VDP from a modified k-means method. The correspondence of ventilation defect maps from 129Xe and UTE 1H was also evaluated. Statistical tests included the Pearson correlation coefficient (r) and t tests, with p 129Xe and UTE 1H VDP were significantly correlated (r = 0.64, p = (Formula presented.)). Bland–Altman analysis showed a bias of −0.05 (p = (Formula presented.)) and limits of agreement of (0.07, −0.17). The Dice spatial accuracy of the UTE-based ventilation defect regions using 129Xe as reference was 0.64 ± 0.05. UTE 1H VDP was significantly correlated with FEV1 (r = −0.54, p = (Formula presented.)) and LCI (r = 0.48, p = (Formula presented.)) and was significantly different between healthy and CF participants (p = 0.017), although the correlations and differences were stronger for 129Xe VDP. UTE 1H VDP correlated with 129Xe VDP, FEV1, and LCI, and demonstrated high, consistent Di

关键词： Magnetic resonance imaging

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MultiWienerNet: Deep learning for fast shift-varying deconvolution

MultiWienerNet: Deep learning for fast shift-varying deconvo...

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

作者： Shuai, Richard W. Yanny, Kyrollos Monakhova, Kristina 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 present a deep-learning method based on Wiener filters and U-Nets that performs image reconstruction in systems with spatially-varying aberrations. We train on simulated microscopy measurements and test on experime... 详细信息

ISBN: (纸本)9781557528209

关键词： Image reconstruction

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MICROFLUIDIC PLATFORM FOR MULTI-FREQUENCY VISCOELASTIC PHENOTYPING OF SINGLE CELLS 25

MICROFLUIDIC PLATFORM FOR MULTI-FREQUENCY VISCOELASTIC PHENO...

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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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Creating an in vitro lung microenvironment via DNA-directed patterning to investigate the role of extracellular vesicles in metastasis 24

Creating an in vitro lung microenvironment via DNA-directed ...

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

作者： Kitayama, Sean E. Sohn, Lydia L. UC Berkeley UCSF Graduate Program in Bioengineering BerkeleyCA United States Department of Mechanical Engineering University of California Berkeley BerkeleyCA United States

ISBN: (纸本)9781733419017

We present a novel in vitro heterogenous lung microenvironment fabricated using DNA-directed patterning, a lithographic method capable of controlled spatial and temporal presentation of cells and ligands with micron-scale precision. Designed using patient histology images, this alveolar microenvironment contains five cell types in an optimized co-culture system that has a number of advantages over existing in vivo models. Our optimized platform has the ability to answer questions about breast cancer metastasis, particularly about the role of extracellular vesicles in preparing the pre-metastatic niche in the secondary lung microenvironment. © 2020 CBMS-0001

关键词： Diseases

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