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Fast non-iterative algorithm for 3D point-cloud holography

Optics Express 2023年第22期31卷 36468-36485页

作者： Ersaro, Nathan Tessema Yalcin, Cem Murray, Liz Kabuli, Leyla Waller, Laura Muller, Rikky Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco BerkeleyCA94720 United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA94720 United States

Recently developed iterative and deep learning-based approaches to computer-generated holography (CGH) have been shown to achieve high-quality photorealistic 3D images with spatial light modulators. However, such approaches remain overly cumbersome for patterning sparse collections of target points across a photoresponsive volume in applications including biological microscopy and material processing. Specifically, in addition to requiring heavy computation that cannot accommodate real-time operation in mobile or hardware-light settings, existing sampling-dependent 3D CGH methods preclude the ability to place target points with arbitrary precision, limiting accessible depths to a handful of planes. Accordingly, we present a non-iterative point cloud holography algorithm that employs fast deterministic calculations in order to efficiently allocate patches of SLM pixels to different target points in the 3D volume and spread the patterning of all points across multiple time frames. Compared to a matched-performance implementation of the iterative Gerchberg-Saxton algorithm, our algorithm’s relative computation speed advantage was found to increase with SLM pixel count, reaching >100,000x at 512 × 512 array format. © 2023 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement.

关键词： Iterative methods

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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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Translational Bioinformatics to Enable Precision Medicine for All: Elevating Equity across Molecular, Clinical, and Digital Realms

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Yearbook of Medical Informatics 2022年第1期31卷 106-115页

作者： Tang, Alice Woldemariam, Sarah Roger, Jacquelyn Sirota, Marina Bakar Computational Health Sciences Institute UCSF San Francisco CA United States Graduate Program in Bioengineering UCSF San Francisco CA United States School of Medicine UCSF San Francisco CA United States Graduate Program in Biological and Medical Informatics UCSF San Francisco CA United States Department of Pediatrics UCSF San Francisco CA United States

Objectives: Over the past few years, challenges from the pandemic have led to an explosion of data sharing and algorithmic development efforts in the areas of molecular measurements, clinical data, and digital health. We aim to characterize and describe recent advanced computational approaches in translational bioinformatics across these domains in the context of issues or progress related to equity and inclusion. Methods: We conducted a literature assessment of the trends and approaches in translational bioinformatics in the past few years. Results: We present a review of recent computational approaches across molecular, clinical, and digital realms. We discuss applications of phenotyping, disease subtype characterization, predictive modeling, biomarker discovery, and treatment selection. We consider these methods and applications through the lens of equity and inclusion in biomedicine. Conclusion: Equity and inclusion should be incorporated at every step of translational bioinformatics projects, including project design, data collection, model creation, and clinical implementation. These considerations, coupled with the exciting breakthroughs in big data and machine learning, are pivotal to reach the goals of precision medicine for all. © 2022 IMIA and Georg Thieme Verlag KG.

关键词： Bioinformatics genomics health equity precision medicine

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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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Advances in AAV capsid engineering: Integrating rational design, directed evolution and machine learning

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Molecular Therapy 2025年第5期33卷 1937-1945页

作者： Nisanov, Alan M. Rivera de Jesús, Julio A. Schaffer, David V. Department of Chemistry University of California Berkeley Berkeley 94720 CA United States Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley 94720 CA United States Department of Bioengineering University of California Berkeley Berkeley 94720 CA United States Graduate Program in Bioengineering University of California Berkeley San Francisco and University of California Berkeley 94720 CA United States Department of Neurological Surgery University of California San Francisco 94143 CA United States Department of Molecular and Cell Biology University of California Berkeley Berkeley 94720 CA United States

Adeno-associated virus (AAV) has emerged as a highly promising vector for human gene therapy due to its favorable safety profile, versatility, and ability to transduce a wide range of tissues. However, natural AAV serotypes have shortcomings, including suboptimal transduction efficiency, pre-existing immunity, and a lack of tissue specificity, that hinder their therapeutic potential. To address these challenges, significant efforts are being applied to engineer novel AAV capsids. Rational design leverages structural insights to enhance capsid properties, directed evolution enables unbiased selection of superior variants, and machine learning accelerates discovery by computational analysis of high-throughput screening results to enable predictive algorithms. These strategies have yielded novel capsids with improved transduction efficiency, reduced immunogenicity, and enhanced tissue targeting. Future advances that continue to integrate such multi-disciplinary approaches will further drive the clinical translation of AAV-based therapies. © 2025 The Authors

关键词： AAV directed evolution gene therapy high-throughput screening machine learning next generation sequencing NGS rational design

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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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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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DEVELOPING A DIGITAL TWIN FOR SINGLE-CELL MECHANICAL PHENOTYPING MICROFLUIDIC DEVICES 26

DEVELOPING A DIGITAL TWIN FOR SINGLE-CELL MECHANICAL PHENOTY...

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26th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2022

作者： Roychowdhury, Sayan Mahmud, Samreen T. Puleri, Daniel F. Lai, Andre Rex, Rachel Li, Brian Sohn, Lydia L. Randles, Amanda Department of Biomedical Engineering Duke University United States UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California Berkeley United States Department of Mechanical Engineering University of California Berkeley United States

ISBN: (纸本)9781733419048

Microfluidics can be used to characterize individual cells in a population based on their mechanical traits. In this work, we digitally replicate the microfluidic device developed by Li et al. [1] and perform simulations of a representative AP-1060 cell. We show that the numerical model is able to recover whole-cell deformability index, a metric used to quantify the resistance of cells to compressive deformation, within 3% of the experimental average. These results pave the way for future studies which utilize experimental and computational approaches to optimize geometric design parameters, complement signal analysis, and enhance the acquisition of mechanical information. © 2022 MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Fluid structure interaction

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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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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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