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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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2
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Sun Q, Tiziana P, Khan AUM, Heuveline V, Gretz N. A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice. Int J Exp Pathol 2021; 102:218-227. [PMID: 34613652 DOI: 10.1111/iep.12399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
Optical tissue clearing (OTC) methods render tissue transparent by matching the refractive index within a sample to enable three-dimensional (3D) imaging with advanced microscopes. The application of OTC method in mediastinal organs in mice remains poorly understand. Our aim was to establish a simple protocol pipeline for 3D imaging of the mediastinal organs in mice. Trachea, oesophagus, thymus and heart were harvested from mice after retrograde perfusion via the abdominal aorta. We combined and optimized antibody labelling of thick tissue samples, OTC with cheap and non-toxic solvent ethyl cinnamate (ECi), and light-sheet fluorescence microscopy (LSFM) or laser confocal fluorescence microscopy (LCFM) to visualize the vasculature of those tissues. A high degree of optical transparency of trachea, oesophagus, thymus and heart was achieved after ECi-based OTC. With anti-CD31 antibody immunofluorescence labelling before ECi-based OTC, the vasculature of these tissues with their natural morphology, location and organizational network was imaged using LSFM or LCFM. This simple protocol pipeline provides an easy-to-setup and comprehensive way to study the vasculature of mediastinal organs in 3D without any special equipment. We anticipate that it will facilitate diverse applications in biomedical research of thoracic diseases and even other organs.
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Affiliation(s)
- Quanchao Sun
- Department of Thoracic Surgery, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China.,Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Picascia Tiziana
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Arif Ul Maula Khan
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
| | - Vincent Heuveline
- Director of the Computing Centre, Heidelberg University, Heidelberg, Germany
| | - Norbert Gretz
- Medical Research Center, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,Institute for Medical Technology, University of Heidelberg and University of Applied Sciences, Mannheim, Germany
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Leung C, Robbins S, Moss A, Heal M, Osanlouy M, Christie R, Farahani N, Monteith C, Chen J, Hunter P, Tappan S, Vadigepalli R, Cheng Z(J, Schwaber JS. 3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system. iScience 2021; 24:102795. [PMID: 34355144 PMCID: PMC8324857 DOI: 10.1016/j.isci.2021.102795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 05/05/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
We developed and analyzed a single cell scale anatomical map of the rat intrinsic cardiac nervous system (ICNS) across four male and three female hearts. We find the ICNS has a reliable structural organizational plan across individuals that provide the foundation for further analyses of the ICNS in cardiac function and disease. The distribution of the ICNS was evaluated by 3D visualization and data-driven clustering. The pattern, distribution, and clustering of ICNS neurons across all male and female rat hearts is highly conserved, demonstrating a coherent organizational plan where distinct clusters of neurons are consistently localized. Female hearts had fewer neurons, lower packing density, and slightly reduced distribution, but with identical localization. We registered the anatomical data from each heart to a geometric scaffold, normalizing their 3D coordinates for standardization of common anatomical planes and providing a path where multiple experimental results and data types can be integrated and compared.
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Affiliation(s)
- Clara Leung
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Shaina Robbins
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alison Moss
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Mahyar Osanlouy
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Richard Christie
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | | | - Jin Chen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Peter Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | | | - Rajanikanth Vadigepalli
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zixi (Jack) Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - James S. Schwaber
- Daniel Baugh Institute of Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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Ding Y, Gudapati V, Lin R, Fei Y, Sevag Packard RR, Song S, Chang CC, Baek KI, Wang Z, Roustaei M, Kuang D, Jay Kuo CC, Hsiai TK. Saak Transform-Based Machine Learning for Light-Sheet Imaging of Cardiac Trabeculation. IEEE Trans Biomed Eng 2021; 68:225-235. [PMID: 32365015 PMCID: PMC7606319 DOI: 10.1109/tbme.2020.2991754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Recent advances in light-sheet fluorescence microscopy (LSFM) enable 3-dimensional (3-D) imaging of cardiac architecture and mechanics in toto. However, segmentation of the cardiac trabecular network to quantify cardiac injury remains a challenge. METHODS We hereby employed "subspace approximation with augmented kernels (Saak) transform" for accurate and efficient quantification of the light-sheet image stacks following chemotherapy-treatment. We established a machine learning framework with augmented kernels based on the Karhunen-Loeve Transform (KLT) to preserve linearity and reversibility of rectification. RESULTS The Saak transform-based machine learning enhances computational efficiency and obviates iterative optimization of cost function needed for neural networks, minimizing the number of training datasets for segmentation in our scenario. The integration of forward and inverse Saak transforms can also serve as a light-weight module to filter adversarial perturbations and reconstruct estimated images, salvaging robustness of existing classification methods. The accuracy and robustness of the Saak transform are evident following the tests of dice similarity coefficients and various adversary perturbation algorithms, respectively. The addition of edge detection further allows for quantifying the surface area to volume ratio (SVR) of the myocardium in response to chemotherapy-induced cardiac remodeling. CONCLUSION The combination of Saak transform, random forest, and edge detection augments segmentation efficiency by 20-fold as compared to manual processing. SIGNIFICANCE This new methodology establishes a robust framework for post light-sheet imaging processing, and creating a data-driven machine learning for automated quantification of cardiac ultra-structure.
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Affiliation(s)
- Yichen Ding
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Varun Gudapati
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Ruiyuan Lin
- Ming-Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089 USA
| | - Yanan Fei
- Ming-Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089 USA
| | - René R Sevag Packard
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Sibo Song
- Ming-Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089 USA
| | - Chih-Chiang Chang
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Kyung In Baek
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Zhaoqiang Wang
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Mehrdad Roustaei
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Dengfeng Kuang
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, and Institute of Modern Optics, Nankai University, Tianjin 300350, China
| | - C.-C. Jay Kuo
- Ming-Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089 USA
| | - Tzung K. Hsiai
- Henry Samueli School of Engineering and David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
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Dejea H, Bonnin A, Cook AC, Garcia-Canadilla P. Cardiac multi-scale investigation of the right and left ventricle ex vivo: a review. Cardiovasc Diagn Ther 2020; 10:1701-1717. [PMID: 33224784 DOI: 10.21037/cdt-20-269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The heart is a complex multi-scale system composed of components integrated at the subcellular, cellular, tissue and organ levels. The myocytes, the contractile elements of the heart, form a complex three-dimensional (3D) network which enables propagation of the electrical signal that triggers the contraction to efficiently pump blood towards the whole body. Cardiovascular diseases (CVDs), a major cause of mortality in developed countries, often lead to cardiovascular remodeling affecting cardiac structure and function at all scales, from myocytes and their surrounding collagen matrix to the 3D organization of the whole heart. As yet, there is no consensus as to how the myocytes are arranged and packed within their connective tissue matrix, nor how best to image them at multiple scales. Cardiovascular imaging is routinely used to investigate cardiac structure and function as well as for the evaluation of cardiac remodeling in CVDs. For a complete understanding of the relationship between structural remodeling and cardiac dysfunction in CVDs, multi-scale imaging approaches are necessary to achieve a detailed description of ventricular architecture along with cardiac function. In this context, ventricular architecture has been extensively studied using a wide variety of imaging techniques: ultrasound (US), optical coherence tomography (OCT), microscopy (confocal, episcopic, light sheet, polarized light), magnetic resonance imaging (MRI), micro-computed tomography (micro-CT) and, more recently, synchrotron X-ray phase contrast imaging (SR X-PCI). Each of these techniques have their own set of strengths and weaknesses, relating to sample size, preparation, resolution, 2D/3D capabilities, use of contrast agents and possibility of performing together with in vivo studies. Therefore, the combination of different imaging techniques to investigate the same sample, thus taking advantage of the strengths of each method, could help us to extract the maximum information about ventricular architecture and function. In this review, we provide an overview of available and emerging cardiovascular imaging techniques for assessing myocardial architecture ex vivo and discuss their utility in being able to quantify cardiac remodeling, in CVDs, from myocyte to whole organ.
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Affiliation(s)
- Hector Dejea
- Paul Scherrer Institut, Villigen PSI, Villigen, Switzerland.,Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Anne Bonnin
- Paul Scherrer Institut, Villigen PSI, Villigen, Switzerland
| | - Andrew C Cook
- Institute of Cardiovascular Science, University College London, London, UK
| | - Patricia Garcia-Canadilla
- Institute of Cardiovascular Science, University College London, London, UK.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
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6
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Achanta S, Gorky J, Leung C, Moss A, Robbins S, Eisenman L, Chen J, Tappan S, Heal M, Farahani N, Huffman T, England S, Cheng ZJ, Vadigepalli R, Schwaber JS. A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System. iScience 2020; 23:101140. [PMID: 32460006 PMCID: PMC7327996 DOI: 10.1016/j.isci.2020.101140] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/11/2020] [Accepted: 05/01/2020] [Indexed: 12/21/2022] Open
Abstract
We have developed and integrated several technologies including whole-organ imaging and software development to support an initial precise 3D neuroanatomical mapping and molecular phenotyping of the intracardiac nervous system (ICN). While qualitative and gross anatomical descriptions of the anatomy of the ICN have each been pursued, we here bring forth a comprehensive atlas of the entire rat ICN at single-cell resolution. Our work precisely integrates anatomical and molecular data in the 3D digitally reconstructed whole heart with resolution at the micron scale. We now display the full extent and the position of neuronal clusters on the base and posterior left atrium of the rat heart, and the distribution of molecular phenotypes that are defined along the base-to-apex axis, which had not been previously described. The development of these approaches needed for this work has produced method pipelines that provide the means for mapping other organs. Comprehensive single-neuron-scale mapping of the intrinsic cardiac nervous system Whole-organ high-throughput imaging and reconstruction at a cellular resolution 3D anatomical framework for spatially tracked single-neuron molecular phenotypes Integrated histology, neuron mapping, and molecular profiles for 3D organ reconstruction
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Affiliation(s)
- Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan Gorky
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Clara Leung
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Alison Moss
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Shaina Robbins
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leonard Eisenman
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jin Chen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | | | | | | | | | | | - Zixi Jack Cheng
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - James S Schwaber
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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7
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Becher T, Riascos-Bernal DF, Kramer DJ, Almonte VM, Chi J, Tong T, Oliveira-Paula GH, Koleilat I, Chen W, Cohen P, Sibinga NES. Three-Dimensional Imaging Provides Detailed Atherosclerotic Plaque Morphology and Reveals Angiogenesis After Carotid Artery Ligation. Circ Res 2020; 126:619-632. [PMID: 31914850 DOI: 10.1161/circresaha.119.315804] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RATIONALE Remodeling of the vessel wall and the formation of vascular networks are dynamic processes that occur during mammalian embryonic development and in adulthood. Plaque development and excessive neointima formation are hallmarks of atherosclerosis and vascular injury. As our understanding of these complex processes evolves, there is a need to develop new imaging techniques to study underlying mechanisms. OBJECTIVE We used tissue clearing and light-sheet microscopy for 3-dimensional (3D) profiling of the vascular response to carotid artery ligation and induction of atherosclerosis in mouse models. METHODS AND RESULTS Adipo-Clear and immunolabeling in combination with light-sheet microscopy were applied to image carotid arteries and brachiocephalic arteries, allowing for 3D reconstruction of vessel architecture. Entire 3D neointima formations with different geometries were observed within the carotid artery and scored by volumetric analysis. Additionally, we identified a CD31-positive adventitial plexus after ligation of the carotid artery that evolved and matured over time. We also used this method to characterize plaque extent and composition in the brachiocephalic arteries of ApoE-deficient mice on high-fat diet. The plaques exhibited inter-animal differences in terms of plaque volume, geometry, and ratio of acellular core to plaque volume. A 3D reconstruction of the endothelium overlying the plaque was also generated. CONCLUSIONS We present a novel approach to characterize vascular remodeling in adult mice using Adipo-Clear in combination with light-sheet microscopy. Our method reconstructs 3D neointima formation after arterial injury and allows for volumetric analysis of remodeling, in addition to revealing angiogenesis and maturation of a plexus surrounding the carotid artery. This method generates complete 3D reconstructions of atherosclerotic plaques and uncovers their volume, geometry, acellular component, surface, and spatial position within the brachiocephalic arteries. Our approach may be used in a number of mouse models of cardiovascular disease to assess vessel geometry and volume. Visual Overview: An online visual overview is available for this article.
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Affiliation(s)
- Tobias Becher
- From the Laboratory of Molecular Metabolism (T.B., D.J.K., J.C., P.C.), The Rockefeller University, NY.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (T.B.).,First Department of Medicine (Division of Cardiology), University Medical Center Mannheim, Germany (T.B.)
| | - Dario F Riascos-Bernal
- (Cardiology Division) Department of Medicine, Department of Developmental and Molecular Biology, Wilf Family Cardiovascular Research Institute (D.F.R.-B., V.M.A., G.H.O.-P., N.E.S.S.), Albert Einstein College of Medicine, Bronx, NY
| | - Daniel J Kramer
- From the Laboratory of Molecular Metabolism (T.B., D.J.K., J.C., P.C.), The Rockefeller University, NY
| | - Vanessa M Almonte
- (Cardiology Division) Department of Medicine, Department of Developmental and Molecular Biology, Wilf Family Cardiovascular Research Institute (D.F.R.-B., V.M.A., G.H.O.-P., N.E.S.S.), Albert Einstein College of Medicine, Bronx, NY
| | - Jingy Chi
- From the Laboratory of Molecular Metabolism (T.B., D.J.K., J.C., P.C.), The Rockefeller University, NY
| | - Tao Tong
- Bio-Imaging Resource Center (T.T.), The Rockefeller University, NY
| | - Gustavo H Oliveira-Paula
- (Cardiology Division) Department of Medicine, Department of Developmental and Molecular Biology, Wilf Family Cardiovascular Research Institute (D.F.R.-B., V.M.A., G.H.O.-P., N.E.S.S.), Albert Einstein College of Medicine, Bronx, NY
| | - Issam Koleilat
- Department of Cardiothoracic and Vascular Surgery (Division of Vascular Surgery), Montefiore Medical Center, Bronx, NY (I.K.)
| | - Wei Chen
- Department of Medicine (Nephrology Division) (W.C.), Albert Einstein College of Medicine, Bronx, NY.,Department of Medicine, University of Rochester School of Medicine and Dentistry, NY (W.C.)
| | - Paul Cohen
- From the Laboratory of Molecular Metabolism (T.B., D.J.K., J.C., P.C.), The Rockefeller University, NY
| | - Nicholas E S Sibinga
- (Cardiology Division) Department of Medicine, Department of Developmental and Molecular Biology, Wilf Family Cardiovascular Research Institute (D.F.R.-B., V.M.A., G.H.O.-P., N.E.S.S.), Albert Einstein College of Medicine, Bronx, NY
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