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Miniscope3D:optimized single-shot miniature 3D fluorescence microscopy

Light(Science & Applications) 2020年第1期9卷 367-379页

作者： Kyrollos Yanny Nick Antipa William Liberti Sam Dehaeck Kristina Monakhova Fanglin Linda Liu Konlin Shen Ren Ng Laura Waller UCB/UCSF Joint Graduate Program in Bioengineering University of CaliforniaBerkeleyCA 94720USA Department of Electrical Engineering&Computer Sciences University of CaliforniaBerkeleyCA 94720USA TIPs Department Universite libre de Bruxelles(ULB)1050 BrusselsBelgium

Miniature fluorescence microscopes are a standard tool in systems ***,widefield miniature microscopes capture only 2D information,and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth ***,we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective’s aperture *** the phase mask at the aperture stop significantly reduces the size of the device,and varying the focal lengths enables a uniform resolution across a wide depth *** phase mask encodes the 3D fluorescence intensity into a single 2D measurement,and the 3D volume is recovered by solving a sparsity-constrained inverse *** provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the fieldvarying aberrations in miniature *** demonstrate a prototype that is 17mm tall and weighs 2.5 grams,achieving 2.76μm lateral,and 15μm axial resolution across most of the 900×700×390μm^(3) volume at 40 volumes per *** performance is validated experimentally on resolution targets,dynamic biological samples,and mouse brain *** with existing miniature single-shot volume-capture implementations,our system is smaller and lighter and achieves a more than 2×better lateral and axial resolution throughout a 10×larger usable depth *** microscope design provides single-shot 3D imaging for applications where a compact platform matters,such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

关键词： enable resolution narrow

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Segmented readout for Cherenkov time-of-flight positron emission tomography detectors based on bismuth germanate

arXiv

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arXiv 2024年

作者： Yi, Minseok Lee, Daehee Gola, Alberto Merzi, Stefano Penna, Michele Lee, Jae Sung Cherry, Simon R. Kwon, Sun Il Department of Biomedical Engineering University of California Davis United States Interdisciplinary Program in Bioengineering College of Engineering Seoul National Graduate School Korea Republic of Integrated Major in Innovative Medical Science Seoul National Graduate School Korea Republic of Fondazione Bruno Kessler Italy Brightonix Imaging Inc. Korea Republic of

Positron emission tomography (PET) is the most sensitive biomedical imaging modality for noninvasively detecting and visualizing positron-emitting radiopharmaceuticals within a subject. In PET, measuring the time-of-flight (TOF) information for each pair of 511-keV annihilation photons improves effective sensitivity but requires high timing resolution. Hybrid materials that emit both scintillation and Cherenkov photons, such as bismuth germanate (BGO), recently offer the potential for more precise timing information from Cherenkov photons while maintaining adequate energy resolution from scintillation photons. However, a significant challenge in using such hybrid materials for TOF PET applications lies in the event-dependent timing spread caused by the mixed detection of Cherenkov and scintillation photons due to relatively lower production of Cherenkov photons. This study introduces an innovative approach by segmenting silicon photomultiplier (SiPM) pixels coupled to a single crystal, rather than using traditional SiPMs that are as large as or larger than the crystals they read. We demonstrated that multiple time stamps and photon counts obtained from the segmented SiPM can classify events by providing temporal photon density, effectively addressing this challenge. The approach and findings would lead to new opportunities in applications that require precise timing and photon counting, spanning the fields of medical imaging, high-energy physics, and optical physics. © 2024, CC BY.

关键词： Photons

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Human Not in the Loop: Objective Sample Difficulty Measures for Curriculum Learning

Human Not in the Loop: Objective Sample Difficulty Measures ...

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IEEE International Symposium on Biomedical Imaging

作者： Zhengbo Zhou Jun Luo Dooman Arefan Gene Kitamura Shandong Wu Intelligent Systems Program University of Pittsburgh Pittsburgh PA USA Department of Radiology University of Pittsburgh Pittsburgh PA USA Department of Radiology Loma Linda University Loma Linda CA USA Department of Biomedical Informatics and Department of Bioengineering University of Pittsburgh Pittsburgh PA USA

Curriculum learning is a learning method that trains models in a meaningful order from easier to harder samples. A key here is to devise automatic and objective difficulty measures of samples. In the medical domain, previous work applied domain knowledge from human experts to qualitatively assess classification difficulty of medical images to guide curriculum learning, which requires extra annotation efforts, relies on subjective human experience, and may introduce bias. In this work, we propose a new automated curriculum learning technique using the variance of gradients (VoG) to compute an objective difficulty measure of samples and evaluated its effects on elbow fracture classification from X-ray images. Specifically, we used VoG as a metric to rank each sample in terms of the classification difficulty, where high VoG scores indicate more difficult cases for classification, to guide the curriculum training process We compared the proposed technique to a baseline (without curriculum learning), a previous method that used human annotations on classification difficulty, and anti-curriculum learning. Our experiment results showed comparable and higher performance for the binary and multi-class bone fracture classification tasks.

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Drying properties of Sentang (Azadirachta excelsa) dried under different temperatures

Drying properties of Sentang (Azadirachta excelsa) dried und...

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International Conference on Science and Technology 2020, ICoST 2020

作者： Mohamad Ruddin, Noor Zulai'ha Rasid, Shaharlina Hermawan, Andi Forest Resource Technology Program Bachelor of Applied Science Faculty of Bioengineering and Technology Universiti Malaysia Kelantan Kelantan Malaysia Forest Resource Technology Centre for Post Graduate Studies Universiti Malaysia Kelantan Pangkalan Chepa Malaysia Forest Resource Technology Program Faculty of Bioengineering and Technology Universiti Malaysia Kelantan Kelantan Malaysia

In this study, we investigated the drying properties of Sentang (Azadirachta excelsa) dried at different temperatures. Sentang tree planted in Kelantan, Malaysia, was used in this study. Drying specimens with dimensions of 30 ×150 × 500 mm were dried under air-drying conditions, a constant temperature of 60, 80, 100, and 120 °C until the moisture content (MC) of the specimens reaches an equilibrium moisture content (EMC) at each drying condition. The drying properties of the specimens were then examined. The results confirmed that drying temperature had a significant effect on drying time. As expected, drying Sentang under air-drying conditions demanding considerable time than the other drying conditions. © Published under licence by IOP Publishing Ltd.

关键词： Drying

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BPS2025 - Characterization of intrinsically disordered protein-polymer interactions with fluorescence polarization

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Biophysical Journal 2025年第3期124卷 164a-164a页

作者： Wesley W. Leung Wenchang Zhou Julea Vlassakis Applied Physics Graduate Program Rice University Houston TX USA Department of Bioengineering Rice University Houston TX USA

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Development of 3D-printing composite inks based on photoreactive cartilage extracellular matrix and gelatin nanoparticles

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Bioprinting 2023年 36卷

作者： Hogan, Katie J. Perez, Marissa R. Öztatlı, Hayriye Si, Sophia Wang, Ziwen Jiang, Emily Y. Diba, Mani Garipcan, Bora Mikos, Antonios G. Department of Bioengineering Rice University Houston 77030 TX United States Baylor College of Medicine Medical Scientist Training Program Houston 77030 TX United States Institute of Biomedical Engineering Boğaziçi University İstanbul Turkey

Decellularized extracellular matrix (dECM)-based materials possess innate biochemical cues to drive cell recruitment and differentiation and are of interest for cartilage tissue engineering. While 3D-printing (3DP) provides a means for achieving the precise architecture needed for cartilage tissue engineering, dECM hydrogels have proven difficult to translate to 3DP due to low viscosity and weak mechanical properties. In this study, a cartilage dECM (cdECM, 3 w/v%) was combined with varied amounts of gelatin nanoparticles (GNPs;10, 12.5, 15 w/v%) to form novel hydrogel-colloidal composite materials for 3DP. The addition of GNPs increased the viscosity and rheological properties of the cdECM hydrogel in a dose-dependent manner, directly improving the printability of cdECM 3DP inks. Additionally, functionalization of both materials yielded a UV-crosslinkable material for post-printing crosslinking, and increased GNP content increased post-UV storage moduli with 15 w/v% GNPs yielding a storage modulus 26x greater than that of cdECM alone. 3DP construct swelling and degradation were decreased as a function of increased UV-crosslinking dosage (0, 1.5, and 3 J/cm²). After 14 d of swelling in PBS, construct non-porous area was increased by ∼40 % and pore area was increased by ∼30 % for uncrosslinked (0 J/cm²) constructs versus highly crosslinked (3 J/cm²) constructs. Roughly 40 % higher mass retention was observed across GNP content groups for 3 J/cm² versus 0 J/cm² UV exposure after 14 d of enzymatic degradation, showing the potential for tuning physicochemical properties via UV exposure. Likewise, the retention of key biochemical components of cdECM over the course of degradation was evaluated. Sulfated glycosaminoglycans, a key reservoir for tissue-specific growth factors, were found to be retained within scaffolds over 14 d of degradation and to be released relative to construct degradation and UV-crosslinking. The

关键词： 3D-printing Cartilage tissue engineering Colloidal gel Decellularized extracellular matrix

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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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Brain MRI Synthesis using Enhanced Denoising Diffusion Probabilistic Models from Brain PET and CT scans

Brain MRI Synthesis using Enhanced Denoising Diffusion Proba...

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： Y.J. Seol J.S. Lee Interdisciplinary Program in Bioengineering Seoul National University Seoul Republic of Korea Integrated Major in Innovative Medical Science Seoul National University Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Seoul Republic of Korea Brightonix Imaging Inc Seoul Republic of Korea

Denoising diffusion probabilistic models (DDPM) has shown superior performance in image synthesis for various fields. In this study, we propose an enhanced DDPM framework with the joint probability for synthesizing brain MRI from brain PET/CT. Although PET/MRI scans provide high-resolution structural information for partial evaluation and image reconstruction, it is costly and time-consuming compared to PET/CT. Also, synthesizing MRI from PET/CT including anatomical details has not been extensively studied. We achieved significant performance of proposed network compared with U-Net and cGAN in various input.

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Droplet digital quantification of nucleic acids with Cas13a 25

Droplet digital quantification of nucleic acids with Cas13a

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

作者： Liu, Frank X. Cui, Johnson Q. Yao, Shuhuai Department of Mechanical and Aerospace Engineering The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong Bioengineering Graduate Program Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong

ISBN: (纸本)9781733419031

The isothermal amplification coupled with CRISPR detection has attracted tremendous interest for the sensitive, specific, and qualitative detection of nucleic acids. We report here a Microfluidics Enabled Digital Isothermal CRISPR-cas13a Assay (MEDICA) which leverages the droplet microfluidics technology to enable recombinase polymerase amplification (RPA) and Cas13a trans-cleavage reporting in individual droplet partitions for absolute quantification. The optimal one-pot MEDICA achieved single nucleic acid molecule detection within 30 min. We applied MEDICA to quantify HPV 16 and 18 viral loads in clinical samples, indicating complete accordance with quantitative polymerase chain reaction (qPCR) results. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Drops

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Integrating computational and experimental insights into osmolyte-driven activation of Geobacillus kaustophilus L-asparaginase for acrylamide mitigation

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Journal of Molecular Liquids 2025年 423卷

作者： Özdemir, F.İnci Servili, Burak Demirtaş, Özge Şükür, Gözde Tülek, Ahmet Yildirim, Deniz Gebze Technical University Department of Molecular Biology and Genetics Kocaeli Gebze41400 Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program İstanbul Fatih35430 Turkey Iğdır University Postgraduate Education Institute Department of Bioengineering and Sciences Iğdır Merkez76000 Turkey Cukurova University Faculty of Ceyhan Engineering Department of Chemical Engineering Adana Ceyhan01950 Turkey

Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.

关键词： Maltose

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