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Characterizing cellular mechanical phenotypes with mechanonode-pore sensing

Microsystems & Nanoengineering 2018年第1期4卷 438-449页

作者： Junghyun Kim Sewoon Han Andy Lei Masaru Miyano Jessica Bloom Vasudha Srivastava Martha R.Stampfer Zev J.Gartner Mark A.LaBarge Lydia L.Sohn Department of Mechanical Engineering University of California at BerkeleyBerkeleyCA 94720-1740USA Department of Bioengineering University of California at BerkeleyBerkeleyCA 94720-1762USA Department of Population Sciences Beckman Research InstituteCity of HopeDuarteCA 91010USA Department of Pharmaceutical Chemistry University of CaliforniaSan FranciscoSan FranciscoCA 94143USA Biological Systems and Engineering Division Lawrence Berkeley National LaboratoryCA 94720USA Graduate Program in Bioengineering University of CaliforniaBerkeleyand University of CaliforniaSan FranciscoBerkeleyCA 94720USA

The mechanical properties of cells change with their differentiation,chronological age,and malignant ***,these properties may be useful label-free biomarkers of various functional or clinically relevant cell ***,we demonstrate mechano-node-pore sensing(mechano-NPS),a multi-parametric single-cell-analysis method that utilizes a four-terminal measurement of the current across a microfluidic channel to quantify simultaneously cell diameter,resistance to compressive deformation,transverse deformation under constant strain,and recovery time after *** define a new parameter,the whole-cell deformability index(wCDI),which provides a quantitative mechanical metric of the resistance to compressive deformation that can be used to discriminate among different cell *** wCDI and the transverse deformation under constant strain show malignant MCF-7 and A549 cell lines are mechanically distinct from non-malignant,MCF-10A and BEAS-2B cell lines,and distinguishes between cells treated or untreated with cytoskeleton-perturbing small *** categorize cell recovery time,ΔT_(r),as instantaneous(ΔTr~0 ms),transient(ΔT_(r)≤40 ms),or prolonged(ΔT_(r)>40 ms),and show that the composition of recovery types,which is a consequence of changes in cytoskeletal organization,correlates with cellular *** the wCDI and cell-recovery time,mechano-NPS discriminates between sub-lineages of normal primary human mammary epithelial cells with accuracy comparable to flow cytometry,but without antibody ***-NPS identifies mechanical phenotypes that distinguishes lineage,chronological age,and stage of malignant progression in human epithelial cells.

关键词： microfluidics mechanical phenotyping node-pore sensing biosensors label-free

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BPS2025 - Illuminating the dynamic kinome in living cells with KARkey

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Biophysical Journal 2025年第3期124卷 502a-502a页

作者： Anne C. Lyons Tomer M. Yaron-Barir Zhou Yuan Qian-yi Zhang Daniel Stehle Dean Boecher Jared Johnson Lewis C. Cantley Danielle Schmitt Sohum Mehta Yingxiao Wang Jin Zhang Department of Pharmacology University of California San Diego La Jolla CA USA Shu Chien-Gene Lay Department of Bioengineering University of California San Diego La Jolla CA USA Vagelos College of Physicians and Surgeons Columbia University New York NY USA Alfred E. Mann Department of Biomedical Engineering University of Southern California Los Angeles CA USA Biomedical Sciences Graduate Program University of California San Diego La Jolla CA USA Meyer Cancer Center Weill Cornell Medicine New York NY USA Department of Cell Biology Harvard Medical School Boston MA USA Department of Chemistry and Biochemistry University of California Los Angeles La Jolla CA USA Department of Chemistry and Biochemistry University of California San Diego La Jolla CA USA

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Brain tumor segmentation in magnetic resonance images using genetic algorithm clustering and adaboost classifier 5

Brain tumor segmentation in magnetic resonance images using ...

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5th International Conference on Bioimaging, BIOIMAGING 2018 - Part of 11th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2018

作者： Oliveira, Gustavo C. Varoto, Renato Cliquet, Alberto University of São Paulo Interunits Graduate Program in Bioengineering University of São Paulo São Carlos - SP Brazil Campinas - SP Brazil Department of Electrical and Computer Engineering University of São Paulo São Carlos - SP Brazil

ISBN: (纸本)9789897582783

We present a technique for automatic brain tumor segmentation in magnetic resonance images, combining a modified version of a Genetic Algorithm Clustering method with an AdaBoost Classifier. In a group of 42 FLAIR images, segmentations produced by the algorithm were compared to the ground truth information produced by radiologists. The mean Dice similarity coefficient reached by the algorithm was 70.3%. In most cases, the AdaBoost classifier increased the quality of the segmentation, improving, on average, the DSC in about 10%. Our implementation of the Genetic Algorithm Clustering method presents improvements compared to the original method. The use of a fixed, small number of groups and smaller population allowed for less computational effort. In addition, adaptive restriction in the initial segmentation was achieved by using the information of the groups with highest and 2nd-highest mean intensities. By exploring intensity and spatial information of the pixels, the AdaBoost classifier improved segmentation results. Copyright © 2018 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved.

关键词： Image segmentation

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A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors (vol 31, e3929, 2018)

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NMR IN BIOMEDICINE 2018年第12期31卷 e3929-e3929页

作者： Vareth, M. Lupo, J. M. Larson, P. E. Z. Nelson, S. J. UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA

The goal of this study was to find the most robust algorithm for a phase‐sensitive coil combination of 3D single‐cycle and lactate‐edited, multi‐channel H‐1 point‐resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8‐ or 32‐channel array coils. Peak referencing with residual water and N‐acetyl‐aspartate, first‐point phasing, generalized least squared (GLS) and whitened singular‐value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal‐to‐noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm³) and for the 32‐channel array (25%) compared with the 8‐channel array (19%). Applying voxel‐by‐voxel phase corrections produced a larger increase in performance for the 32‐ versus 8‐channel coil. We conclude that, for clinically relevant 3D H‐1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.

关键词： coil combination techniques first‐point phasing GLS lactate editing multichannel EPSI peak referencing PRESS localization WSVD

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Lysosomal targeting of liposomes with acidic pH and Cathepsin B induces protein aggregate clearance

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Cell communication and signaling : CCS 2025年第1期23卷 296页

作者： Minsol Jeon Da-Eun Kim So Young Choi Seoyoung Kim Seongchan Kim Hyojin Lee Hyunkyung Kim Department of Biochemistry and Molecular Biology Korea University College of Medicine Seoul 02841 Republic of Korea. BK21 Graduate Program Department of Biomedical Sciences Korea University College of Medicine Seoul 02841 Republic of Korea. Biomaterials Research Center Biomedical Research Division Korea Institute of Science and Technology (KIST) Seoul 02792 Republic of Korea. School of Biomedical Engineering College of Health Science Korea University Seoul 02841 Republic of Korea. College of Pharmacy and Research Institute of Pharmaceutical Sciences Gyeongsang National University Jinju 52828 Gyeongsangnam-do Republic of Korea. Biomaterials Research Center Biomedical Research Division Korea Institute of Science and Technology (KIST) Seoul 02792 Republic of Korea. hyojinlee@kist.re.kr. Division of Bio-Medical Science & Technology KIST School Korea University of Science and Technology (UST) Seoul 02792 Republic of Korea. hyojinlee@kist.re.kr. Department of Integrative Biotechnology College of Biotechnology and Bioengineering SKKU-KIST Sungkyunkwan University Suwon 16419 Gyenggi Republic of Korea. hyojinlee@kist.re.kr. Department of Biochemistry and Molecular Biology Korea University College of Medicine Seoul 02841 Republic of Korea. hyunkkim@korea.ac.kr. BK21 Graduate Program Department of Biomedical Sciences Korea University College of Medicine Seoul 02841 Republic of Korea. hyunkkim@korea.ac.kr.

The autophagy-lysosomal pathway is a cellular degradation mechanism that regulates protein quality by eliminating aggregates and maintaining normal protein function. It has been reported that aging itself reduces lysosomal proteolytic activity in age-related neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Reduction in lysosomal function may underlie the accumulation of protein aggregates such as amyloid beta (Aβ), tau, and α-synuclein. Some of these protein aggregates may cause additional lysosomal dysfunction and create a vicious cycle leading to a gradual increase in protein aggregation. In this study, liposome-based lysosomal pH-modulating particles (LPPs), containing a liquid solution to adjust lysosomal pH, have been developed to restore lysosomal function. The results demonstrate that acidic LPPs effectively restore lysosomal function by recovering lysosomal pH and facilitating the removal of protein aggregates. These findings demonstrated that acidic LPPs could effectively recover the abnormal lysosomal function via restoration of lysosomal pH and enhance the clearance of protein aggregates. Furthermore, the simultaneous introduction of Cathepsin B (CTSB) proteins and acidic LPP revealed a synergistic effect, promoting lysosomal pH recovery and enhancing aggregates removal. These findings suggest a novel strategy for improving lysosomal clearance activity in proteinopathies.

关键词： Aggregate clearance Autophagy Cathepsin Lysosome Proteinopathy

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A flexible liposomal polymer complex as a platform of specific and regulable immune regulation for individual cancer immunotherapy

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Journal of Experimental and Clinical Cancer Research 2023年第1期42卷 29-29页

作者： Chen, Chia-Hung Weng, Tzu-Han Huang, Hsiao-Hsuan Huang, Ling-Ya Huang, Kai-Yao Chen, Pin-Rong Yeh, Kuang-Yu Huang, Chi-Ting Chien, Yu-Tzu Chuang, Po-Ya Lin, Yu-Ling Tsai, Nu-Man Liu, Shih-Jen Su, Yu-Cheng Weng, Shun-Long Liao, Kuang-Wen Department of Medical Research Hsinchu MacKay Memorial Hospital Hsinchu City 30071 Taiwan Department of Dermatology MacKay Memorial Hospital Taipei City 10449 Taiwan Industrial Development Graduate Program of College of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Department of Medicine MacKay Medical College New Taipei City 25245 Taiwan Institute of Molecular Medicine and Bioengineering National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan Agricultural Biotechnology Research Center Academia Sinica Taipei 11529 Taiwan Department of Medical Laboratory and Biotechnology Chung Shan Medical University Taichung City 40201 Taiwan Department of Pathology and Clinical Laboratory Chung Shan Medical University Hospital Taichung City 40201 Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Miaoli 350401 Taiwan Department of Obstetrics and Gynecology Hsinchu MacKay Memorial Hospital Hsinchu City 30071 Taiwan MacKay Junior College of Medicine Nursing and Management Taipei City 11260 Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung City 80708 Taiwan College of Dental Medicine Kaohsiung Medical University School of Dentistry Kaohsiung City 80708 Taiwan Department of Biotechnology and Bioindustry Sciences National Cheng Kung University Tainan City 70101 Taiwan Center for Intelligent Drug Systems and Smart Bio-Devices National Yang Ming Chiao Tung University Hsinchu City 30068 Taiwan

Background: The applicability and therapeutic efficacy of specific personalized immunotherapy for cancer patients is limited by the genetic diversity of the host or the tumor. Side-effects such as immune-related adverse events (IRAEs) derived from the administration of immunotherapy have also been observed. Therefore, regulatory immunotherapy is required for cancer patients and should be developed. Methods: The cationic lipo-PEG-PEI complex (LPPC) can stably and irreplaceably adsorb various proteins on its surface without covalent linkage, and the bound proteins maintain their original functions. In this study, LPPC was developed as an immunoregulatory platform for personalized immunotherapy for tumors to address the barriers related to the heterogenetic characteristics of MHC molecules or tumor associated antigens (TAAs) in the patient population. Here, the immune-suppressive and highly metastatic melanoma, B16F10 cells were used to examine the effects of this platform. Adsorption of anti-CD3 antibodies, HLA-A2/peptide, or dendritic cells’ membrane proteins (MP) could flexibly provide pan-T-cell responses, specific Th1 responses, or specific Th1 and Th2 responses, depending on the host needs. Furthermore, with regulatory antibodies, the immuno-LPPC complex properly mediated immune responses by adsorbing positive or negative antibodies, such as anti-CD28 or anti-CTLA4 antibodies. Results: The results clearly showed that treatment with LPPC/MP/CD28 complexes activated specific Th1 and Th2 responses, including cytokine release, CTL and prevented T-cell apoptosis. Moreover, LPPC/MP/CD28 complexes could eliminate metastatic B16F10 melanoma cells in the lung more efficiently than LPPC/MP. Interestingly, the melanoma resistance of mice treated with LPPC/MP/CD28 complexes would be reversed to susceptible after administration with LPPC/MP/CTLA4 complexes. NGS data revealed that LPPC/MP/CD28 complexes could enhance the gene expression of cytokine and chemokine pathways to st

关键词： Costimulatory molecules Immunotherapy LPPC personalized cancer therapy Tumor heterogenicity

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Control of brain network dynamics across diverse scales of space and time

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Physical Review E 2020年第6期101卷 062301-062301页

作者： Evelyn Tang Harang Ju Graham L. Baum David R. Roalf Theodore D. Satterthwaite Fabio Pasqualetti Danielle S. Bassett Department of Bioengineering School of Engineering & Applied Science University of Pennsylvania Pennsylvania 19104 USA Max Planck Institute for Dynamics and Self-Organization Göttingen 37079 Germany Neuroscience Graduate Program Perelman School of Medicine University of Pennsylvania Pennsylvania 19104 USA Department of Psychiatry Perelman School of Medicine University of Pennsylvania Pennsylvania 19104 USA Department of Mechanical Engineering University of California Riverside Riverside California 92521 USA Department of Physics & Astronomy College of Arts & Sciences University of Pennsylvania Pennsylvania 19104 USA Department of Electrical & Systems Engineering School of Engineering & Applied Science University of Pennsylvania Pennsylvania 19104 USA Department of Neurology Perelman School of Medicine University of Pennsylvania Pennsylvania 19104 USA Santa Fe Institute Santa Fe New Mexico 87501 USA

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow timescales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast timescales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure.

关键词： Network diffusion Synchronization Brain network Magnetic resonance imaging

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Concentric Micromirror Array for High-Speed Optical Dynamic Focusing

Concentric Micromirror Array for High-Speed Optical Dynamic ...

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IEEE/LEOS International Conference on Optical MEMS

作者： Nathan Tessema Ersumo Cem Yalcin Nicolas Pégard Laura Waller Daniel Lopez Rikky Muller San Francisco Graduate Program in Bioengineering University of California Berkeley - University of California USA Departement of Electrical Engineering & Computer Sciences University of California Berkeley USA Department of Applied Physical Sciences University of North Carolina at Chapel Hill Chapel Hill USA Center for Nanoscale Materials Argonne National Laboratory Argonne USA

Optical dynamic focusing has emerged as a speed, complexity and efficiency bottleneck across various applications, which include scanning multi-photon microscopy in biology, maskless lithography and micromachining in material processing, and wavefront correction. Here, we present a 32-ring 23,852-pixel concentric micromirror array capable of performing dynamic focusing for wavelengths of up to 1040 nm with a response rate of up to 8.75 kHz, 30 V drive and a focusing full-width-half-maximum to range ratio of 4.8%.

关键词： Optimized production technology High-speed optical techniques Micromechanical devices Nanophotonics Micromirrors Focusing

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Stimuli-responsive gyroid Scaffolds: hierarchical architecture and electric stimulation promote bone regeneration

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Materials Today 2025年

作者： Rafael R.A. Silva Frederico Barbosa Guilherme Ferreira Carlos Ureña Eduardo H. Backes José M. Inácio José A. Belo Rui Igreja João C. Silva Luiz H.C. Mattoso Elvira Fortunato Henrique M.V. Almeida Rodrigo Martins Caio G. Otoni Graduate Program in Materials Science and Engineering (PPGCEM) Federal University of São Carlos (UFSCar) Rod. Washington Luís km 235 13565-905 São Carlos SP Brazil Nanotechnology National Laboratory for Agriculture (LNNA) Embrapa Instrumentation 13560-970 São Carlos SP Brazil CENIMAT/i3N Department of Materials Science NOVA School of Science and Technology NOVA University Lisbon (NOVA FCT) and CEMOP/UNINOVA Campus de Caparica 2829-516 Caparica Portugal Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisboa Portugal Associate Laboratory i4HB – Institute for Health and Bioeconomy Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisboa Portugal Stem Cells and Development Laboratory iNOVA4Health NOVA Medical School Faculdade de Ciências Médicas Universidade NOVA de Lisboa 1169-056 Lisbon Portugal Department of Mechanical and Aerospace Engineering and PolitoBIOMed Lab Politecnico di Torino Corso Duca Degli Abruzzi 24 Turin 10129 Italy Institute of Chemistry University of Campinas (UNICAMP) Campinas SP Brazil

Osteoporotic fractures in older adults place a significant burden on healthcare systems due to prolonged healing times and escalating costs. Innovative approaches closely mimicking the human bone microenvironment are paramount for advancing bone tissue regeneration. This study leverages a sacrificial template methodology to develop hierarchical 3D porous gelatin-NaNbO 3 @PDMS scaffolds with gyroid structures mimicking cancellous bone architecture, tailored for enhanced stimuli-responsive biological performance. Modulating porosity levels (∼0%, 18 %, and 63 %) enables macro-to-micro pore transitions, highlighting how porosity and zero-curvature surfaces impact critical properties for bioactive scaffold applications. Under simulated physical activity pressures, lower scaffold porosity enhances structural integrity, mechanical stability, and damping capacity, driven by reduced thickness plastic deformation. Corona discharge poling generates electrically charged stimuli-responsive scaffolds, enhancing electric field intensity through charge trapping. Combined with ultrasound stimulation (50 and 250 mW·cm −2 ), it boosts metabolic activity, gene expression, and mineralization, increasing calcium deposition by up to 1200 % compared to unstimulated controls. Finite element analysis reveals that the 63 % porosity scaffolds generate a sixfold stronger electric field than its 18 % counterpart, enhancing stimuli-responsive cell alignment, with ultrasound stimulation boosting it by ∼10 %. These discoveries in zero-curvature geometries and stimuli-responsive systems redefine bone regeneration strategies by mimicking bone anisotropy through electric field stimulation, offering transformative insights for advanced biomaterials in implants and physiotherapy.

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Iterative Motion Compensation reconstruction ultra-short TE(iMoCo UTE) for high resolution free breathing pulmonary MRI

arXiv

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arXiv 2020年

作者： Zhu, Xucheng Chan, Marilynn Lustig, Michael Johnson, Kevin Larson, Peder E.Z. UCSF/UC Berkeley Graduate Program in Bioengineering University of California San Francisco San FranciscoCA United States Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA United States Department of Pediatrics Division of Pediatric Pulmonology University of California San Francisco San FranciscoCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Department of Medical Physics University of Wisconsin Madison MadisonWI United States Department of Radiology University of Wisconsin Madison MadisonWI United States

Purpose: To develop a high scanning efficiency, motion corrected imaging strategy for free-breathing pulmonary MRI by combining a motion compensation reconstruction with a UTE acquisition, called iMoCo UTE. Methods: An optimized golden angle ordering radial UTE sequence was used to continuously acquire data for 5 minutes. All readouts were grouped to different respiratory motion states based on self-navigator signals, then motion resolved data was reconstructed by XD Golden-angle RAdial Sparse Parallel reconstruction (XD-GRASP). One state from the motion resolved images was selected as a reference, and motion fields from the other states to the reference were derived via non-rigid registration. Finally, all motion resolved data and motion fields were reconstructed by using an iterative motion compensation reconstruction with a total generalized variation sparse constraint. Results: The iMoCo UTE strategy was evaluated in volunteers and non-sedated pediatric patient(4-6 y/o) studies. Images reconstructed with iMoCo UTE provided sharper anatomical lung structures, and higher apparent SNR and CNR, compared to using other motion correction strategies, such as soft-gating, motion resolved reconstruction, and non-rigid motion compensation(MoCo). iMoCo UTE also showed promising results in an infant study. Conclusions: The proposed iMoCo UTE combines self-navigation, motion modeling, and a compressed sensing reconstruction to increase scan efficiency, SNR, and reduce respiratory motion in lung MRI. This proposed strategy shows improvements in free breathing lung MRI scans, especially in very challenging application situations, such as pediatric MRI studies. Copyright © 2020, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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