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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Kuo, Grace Monakhova, Kristina Yanny, Kyrollos Ng, Ren Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA94720 United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley BerkeleyCA94720 United States

We propose a method based on blind deconvolution to calibrate the spatially-varying point spread functions of a coded-aperture microscope system. From easy-to-acquire measurements of unstructured fluorescent beads, we... 详细信息

ISBN: (纸本)9781557528209

关键词： Optical transfer function

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Synthetic CT Generation Using MRI with Deep Learning: How Does the Selection of Input Images Affect the Resulting Synthetic CT?

Synthetic CT Generation Using MRI with Deep Learning: How Do...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Andrew P. Leynes Peder E. Z. Larson UC Berkeley - UC San Francisco Joint Graduate Program in Bioengineering

ISBN: (纸本)9781538646595

Synthetic x-ray computed tomography (CT) images derived from magnetic resonance imaging (MRI) is a recent area of focus for medical imaging researchers for applications in attenuation correction in simultaneous PET/MRI systems and MRI-guided radiotherapy planning. Several research groups have demonstrated the potential of deep learning to generate the synthetic CT images, however, there are several major open questions that remain with this approach. We investigated how the selection of MRI inputs affect the resulting output using a fixed network. We found that Dixon MRI may be sufficient for quantitatively accurate synthetic CT images and ZTE MRI may provide additional information to capture bowel air distributions.

关键词： synthetic ct deep learning mri Dixon mri zero echo-time mri

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Compressed sensing 3D fluorescence microscopy using optimized phase mask

Compressed sensing 3D fluorescence microscopy using optimize...

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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Yanny, Kyrollos Antipa, Nick Liberti, William Dehaeck, Sam Monakhova, Kristina Liu, Fanglin Linda Shen, Konlin Ng, Ren 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 Brussels1050 Belgium

We demonstrate a single-shot miniature 3D computational microscope with an optimized phase encoder. Our method uses sparsity-based reconstruction to achieve a 2.76µm lateral and 15µm axial resolution across ... 详细信息

ISBN: (纸本)9781557528209

关键词： Fluorescence microscopy

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Microfabricated bioprocessor for nanoliter-scale Sanger DNA sequencing

Microfabricated bioprocessor for nanoliter-scale Sanger DNA ...

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10th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2006

作者： Blazej, Robert G. Kumaresan, Palani Mathies, Richard A. UCSF/UC Berkeley Joint Bioengineering Graduate Group University of California Berkeley CA 94720 United States Department of Mechanical Engineering University of California Berkeley CA 94720 United States Department of Chemistry University of California Berkeley CA 94720 United States

Utilizing hybrid glass-PDMS construction, we have developed an efficient, nanoliterscale microfabricated bioprocessor that integrates all three key Sanger sequencing steps-thermal cycling, sample purification and capillary electrophoresis (CE)-into a microdevice capable of read-lengths equivalent to those used in the sequencing of the human genome. The bioprocessor incorporates a range of advanced technologies including miniaturized temperature sensing, nanoliter-scale Sanger extension reactions, microvalves/pumps, DNA affinity-capture and high-performance capillary electrophoresis. Lab-on-a-chip level integration enables sequencing of 556 continuous bases with 99% accuracy from only 1 femtomole of DNA template in a 250-nL reactor. The performance of this miniaturized DNA sequencer provides a benchmark for evaluating the ultimate cost and efficiency limits of Sanger sequencing. © 2006 Society for Chemistry and Micro-Nano Systems.

关键词： DNA sequences

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Integrated affinity capture, purification and capillary electrophoresis microdevice for quantitative double-stranded DNA analysis 11

Integrated affinity capture, purification and capillary elec...

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11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007

作者： Toriello, Nicholas M. Liu, Chung N. Thaitrong, Numrin Mathies, Richard A. UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California BerkeleyCA94720 United States Department of Chemical Engineering University of California BerkeleyCA94720 United States Department of Chemistry University of California BerkeleyCA94720 United States

A novel injection method is developed that utilizes a thermally switchable oligonucleotide affinity capture gel to mediate the concentration, purification and injection of double-stranded DNA for quantitative microchi... 详细信息

ISBN: (纸本)9780979806407

关键词： Purification

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Multichannel reverse transcription-PCR microdevice for rapid multiplex gene expression analysis

Multichannel reverse transcription-PCR microdevice for rapid...

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10th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2006

作者： Toriello, Nicholas M. Liu, Chung N. Mathies, Richard A. UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California Berkeley CA 94720 United States Department of Chemical Engineering University of California Berkeley CA 94720 United States Department of Chemistry University of California Berkeley CA 94720 United States

A microdevice is developed for rapid RNA analysis that integrates 1-step reverse transcription and 30 cycles of PCR (RT-PCR) amplification with capillary electrophoresis (CE) separation and fluorescence detection of the amplicons. The 4- layer glass-PDMS-glass-glass hybrid microdevice integrates microvalves, on-chip heaters and temperature sensors, nanoliter reaction chambers (380 nL) and 5-cm long CE separation channels. The direct integration of these processes results in attomolar detection sensitivity (

关键词： Glass

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Glucocorticoids cause mandibular bone fragility and suppress osteocyte perilacunar-canalicular remodeling

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Bone Reports 2018年 9卷 145-153页

作者： Alemi, A. Sean Mazur, Courtney M. Fowler, Tristan W. Woo, Jonathon J. Knott, P. Daniel Alliston, Tamara Department of Otorhinolaryngology Head and Neck Surgery University of California San Francisco United States Department of Orthopaedic Surgery University of California San Francisco United States UC Berkeley-UCSF Graduate Program in Bioengineering United States

Osteocytes support dynamic, cell-intrinsic resorption and deposition of bone matrix through a process called perilacunar/canalicular remodeling (PLR). In long bones, PLR depends on MMP13 and is tightly regulated by PTH, sclerostin, TGFβ, and glucocorticoids. However, PLR is regulated differently in the cochlea, suggesting a mechanism that is anatomically distinct. Unlike long bones, the mandible derives from neural crest and exhibits unique susceptibility to medication and radiation induced osteonecrosis. Therefore, we sought to determine if PLR in the mandible is suppressed by glucocorticoids, as it is in long bone. Hemimandibles were collected from mice subcutaneously implanted with prednisolone or vehicle containing pellets for 7, 21, or 55 days (n = 8/group) for radiographic and histological analyses. Within 21 days, micro-computed tomography revealed a glucocorticoid-dependent reduction in bone volume/total volume and trabecular thickness and a significant decrease in bone mineral density after 55 days. Within 7 days, glucocorticoids strongly and persistently repressed osteocytic expression of the key PLR enzyme MMP13 in both trabecular and cortical bone of the mandible. Cathepsin K expression was significantly reduced only after 55 days of glucocorticoid treatment, at which point histological analysis revealed a glucocorticoid-dependent reduction in the lacunocanalicular surface area. In addition to reducing bone mass and suppressing PLR, glucocorticoids also reduced the stiffness of mandibular bone in flexural tests. Thus, osteocyte PLR in the neural crest-derived mandible is susceptible to glucocorticoids, just as it is in the mesodermally-derived femur, highlighting the need to further study PLR as a target of drugs, and radiation in mandibular osteonecrosis. © 2018

关键词： Glucocorticoids Mandible Osteocyte Perilacunar/canalicular remodeling

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Motion artifacts on 240Hz OLED stereoscopic 3D displays

Motion artifacts on 240Hz OLED stereoscopic 3D displays

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2014 SID International Symposium

作者： Johnson, Paul Kim, Joohwan Hoffman, David M. Vargas, Andres Banks, Martin S. UC Berkeley - UCSF Graduate Program in Bioengineering United States University of California Berkeley Vision Science Program 360 Minor Hall Berkeley CA United States Samsung Display Americas Lab San Jose CA United States

We examined the visibility of motion artifacts-judder, motion blur, and edge banding-on a Samsung 240Hz stereoscopic 3D (S3D) OLED display. We determined the relative contributions of the frame rate of the content, update rate of the panel, duty cycle, and flash number. We compared the visibility of artifacts on the Samsung display with those on a 60Hz S3D LCD. Short duty cycles and low flash numbers reduce the visibility of motion artifacts. © 2014 SID.

关键词： Visibility

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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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Osteocyte dysfunction promotes osteoarthritis through MMP13-dependent suppression of subchondral bone homeostasis

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Bone Research 2019年第4期7卷 354-370页

作者： Courtney MMazur Jonathon JWoo Cristal SYee Aaron JFields Claire Acevedo Karsyn NBailey Serra Kaya Tristan WFowler Jeffrey CLotz Alexis Dang Alfred CKuo Thomas PVail Tamara Alliston Department of Orthopaedic Surgery University of CaliforniaSan FranciscoCA 94143USA UC Berkeley-UCSF Graduate Program in Bioengineering San FranciscoCA 94143USA Department of Mechanical Engineering University of UtahSalt Lake CityUT 84112USA San Francisco Veterans Affairs Medical Center San FranciscoCA 94121USA

Osteoarthritis(OA),long considered a primary disorder of articular cartilage,is commonly associated with subchondral bone ***,the cellular mechanisms responsible for changes to subchondral bone in OA,and the extent to which these changes are drivers of or a secondary reaction to cartilage degeneration,remain *** knee joints from human patients with end-stage OA,we found evidence of profound defects in osteocyte *** of osteocyte perilacunar/canalicular remodeling(PLR)was most severe in the medial compartment of OA subchondral bone,with lower protease expression,diminished canalicular networks,and disorganized and hypermineralized extracellular *** a step toward evaluating the causality of PLR suppression in OA,we ablated the PLR enzyme MMP13 in osteocytes while leaving chondrocytic MMP13 intact,using Cre recombinase driven by the 9.6-kb DMP1 *** only did osteocytic MMP13 deficiency suppress PLR in cortical and subchondral bone,but it also compromised *** in the absence of injury,osteocytic MMP13 deficiency was sufficient to reduce cartilage proteoglycan content,change chondrocyte production of collagen II,aggrecan,and MMP13,and increase the incidence of cartilage lesions,consistent with early ***,in humans and mice,defects in PLR coincide with cartilage ***-derived MMP13 emerges as a critical regulator of cartilage homeostasis,likely via its effects on ***,these findings implicate osteocytes in bone-cartilage crosstalk in the joint and suggest a causal role for suppressed perilacunar/canalicular remodeling in osteoarthritis.

关键词： MMP13 homeostasis likely

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