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Mollinari C, Cardinale A, Lupacchini L, Martire A, Chiodi V, Martinelli A, Rinaldi AM, Fini M, Pazzaglia S, Domenici MR, Garaci E, Merlo D. The DNA repair protein DNA-PKcs modulates synaptic plasticity via PSD-95 phosphorylation and stability. EMBO Rep 2024:10.1038/s44319-024-00198-3. [PMID: 39085642 DOI: 10.1038/s44319-024-00198-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
The key DNA repair enzyme DNA-PKcs has several and important cellular functions. Loss of DNA-PKcs activity in mice has revealed essential roles in immune and nervous systems. In humans, DNA-PKcs is a critical factor for brain development and function since mutation of the prkdc gene causes severe neurological deficits such as microcephaly and seizures, predicting yet unknown roles of DNA-PKcs in neurons. Here we show that DNA-PKcs modulates synaptic plasticity. We demonstrate that DNA-PKcs localizes at synapses and phosphorylates PSD-95 at newly identified residues controlling PSD-95 protein stability. DNA-PKcs -/- mice are characterized by impaired Long-Term Potentiation (LTP), changes in neuronal morphology, and reduced levels of postsynaptic proteins. A PSD-95 mutant that is constitutively phosphorylated rescues LTP impairment when over-expressed in DNA-PKcs -/- mice. Our study identifies an emergent physiological function of DNA-PKcs in regulating neuronal plasticity, beyond genome stability.
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Affiliation(s)
- Cristiana Mollinari
- Istituto Superiore di Sanita', Department of Neuroscience, 00161, Rome, Italy
- Institute of Translational Pharmacology, National Research Council, 00133, Rome, Italy
| | | | | | - Alberto Martire
- Istituto Superiore di Sanita', National Centre for Drug Research and Evaluation, 00161, Rome, Italy
| | - Valentina Chiodi
- Istituto Superiore di Sanita', National Centre for Drug Research and Evaluation, 00161, Rome, Italy
| | - Andrea Martinelli
- Istituto Superiore di Sanita', Experimental Animal Welfare Sector, 00161, Rome, Italy
| | - Anna Maria Rinaldi
- Department of Systems Medicine, "Tor Vergata" University of Rome, 00133, Rome, Italy
| | | | - Simonetta Pazzaglia
- ENEA SSPT-TECS-TEB, Casaccia Research Center, Division of Health Protection Technology (TECS), Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123, Rome, Italy
| | - Maria Rosaria Domenici
- Istituto Superiore di Sanita', National Centre for Drug Research and Evaluation, 00161, Rome, Italy
| | - Enrico Garaci
- IRCCS San Raffaele Roma, 00163, Rome, Italy
- MEBIC Consortium, 00166, Rome, Italy
| | - Daniela Merlo
- Istituto Superiore di Sanita', Department of Neuroscience, 00161, Rome, Italy.
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2
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Deluca A, Wagner A, Heimel P, Deininger C, Wichlas F, Redl H, Rohde E, Tempfer H, Gimona M, Traweger A. Synergistic effect of umbilical cord extracellular vesicles and rhBMP-2 to enhance the regeneration of a metaphyseal femoral defect in osteoporotic rats. Stem Cell Res Ther 2024; 15:144. [PMID: 38764077 PMCID: PMC11103988 DOI: 10.1186/s13287-024-03755-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/07/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND The aim of this study was to evaluate potential synergistic effects of a single, local application of human umbilical cord MSC-derived sEVs in combination with a low dose of recombinant human rhBMP-2 to promote the regeneration of a metaphyseal femoral defect in an osteoporotic rat model. METHODS 6 weeks after induction of osteoporosis by bilateral ventral ovariectomy and administration of a special diet, a total of 64 rats underwent a distal femoral metaphyseal osteotomy using a manual Gigli wire saw. Defects were stabilized with an adapted Y-shaped mini-locking plate and were subsequently treated with alginate only, or alginate loaded with hUC-MSC-sEVs (2 × 109), rhBMP-2 (1.5 µg), or a combination of sEVs and rhBMP-2 (n = 16 for each group). 6 weeks post-surgery, femora were evaluated by µCT, descriptive histology, and biomechanical testing. RESULTS Native radiographs and µCT analysis confirmed superior bony union with callus formation after treatment with hUC-MSC-sEVs in combination with a low dose of rhBMP-2. This finding was further substantiated by histology, showing robust defect consolidation 6 weeks after treatment. Torsion testing of the explanted femora revealed increased stiffness after application of both, rhBMP-2 alone, or in combination with sEVs, whereas torque was only significantly increased after treatment with rhBMP-2 together with sEVs. CONCLUSION The present study demonstrates that the co-application of hUC-MSC-sEVs can improve the efficacy of rhBMP-2 to promote the regeneration of osteoporotic bone defects.
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Affiliation(s)
- Amelie Deluca
- Institute of Tendon and Bone Regeneration, Salzburg, 5020, Austria.
- Department of Traumatology, KABEG-Klinikum Klagenfurt am Woerthersee, Klagenfurt, 9020, Austria.
| | - Andrea Wagner
- Institute of Tendon and Bone Regeneration, Salzburg, 5020, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, 1200, Austria
| | - Patrick Heimel
- Austrian Cluster for Tissue Regeneration, Vienna, 1200, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Centre in Cooperation with AUVA, Vienna, 1200, Austria
| | - Christian Deininger
- Institute of Tendon and Bone Regeneration, Salzburg, 5020, Austria
- Department of Orthopedics and Traumatology, Salzburg University Hospital, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Florian Wichlas
- Department of Orthopedics and Traumatology, Salzburg University Hospital, Paracelsus Medical University, Salzburg, 5020, Austria
| | - Heinz Redl
- Austrian Cluster for Tissue Regeneration, Vienna, 1200, Austria
- Ludwig Boltzmann Institute for Traumatology, The Research Centre in Cooperation with AUVA, Vienna, 1200, Austria
| | - Eva Rohde
- GMP Unit, Spinal Cord Injury and Tissue Regeneration Centre Salzburg, Paracelsus Medical University, Salzburg, Austria
- Department of Transfusion Medicine, Salzburger Landeskliniken GesmbH, Paracelsus Medical University, Salzburg, Austria
| | - Herbert Tempfer
- Institute of Tendon and Bone Regeneration, Salzburg, 5020, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, 1200, Austria
| | - Mario Gimona
- GMP Unit, Spinal Cord Injury and Tissue Regeneration Centre Salzburg, Paracelsus Medical University, Salzburg, Austria
- Research Program "Nanovesicular Therapies", Paracelsus Medical University, Salzburg, Austria
| | - Andreas Traweger
- Institute of Tendon and Bone Regeneration, Salzburg, 5020, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, 1200, Austria
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3
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Imirzian N, Püffel F, Roces F, Labonte D. Large deformation diffeomorphic mapping of 3D shape variation reveals two distinct mandible and head capsule morphs in Atta vollenweideri leaf-cutter worker ants. Ecol Evol 2024; 14:e11236. [PMID: 38633523 PMCID: PMC11021802 DOI: 10.1002/ece3.11236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Ants are crucial ecosystem engineers, and their ecological success is facilitated by a division of labour among sterile "workers". In some ant lineages, workers have undergone further morphological differentiation, resulting in differences in body size, shape, or both. Distinguishing between changes in size and shape is not trivial. Traditional approaches based on allometry reduce complex 3D shapes into simple linear, areal, or volume metrics; modern approaches using geometric morphometrics typically rely on landmarks, introducing observer bias and a trade-off between effort and accuracy. Here, we use a landmark-free method based on large deformation diffeomorphic metric mapping (LDDMM) to assess the co-variation of size and 3D shape in the mandibles and head capsules of Atta vollenweideri leaf-cutter ants, a species exhibiting extreme worker size-variation. Body mass varied by more than two orders of magnitude, but a shape atlas created via LDDMM on μ-CT-derived 3D mesh files revealed only two distinct head capsule and mandibles shapes-one for the minims (body mass < 1 mg) and one for all other workers. We discuss the functional significance of the identified 3D shape variation, and its implications for the evolution of extreme polymorphism in Atta.
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Affiliation(s)
| | | | - Flavio Roces
- Department of Behavioural Physiology and SociobiologyBiocenter, University of WürzburgWürzburgGermany
| | - David Labonte
- Department of BioengineeringImperial College LondonLondonUK
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Timonidis N, Rubio-Teves M, Alonso-Martínez C, Bakker R, García-Amado M, Tiesinga P, Clascá F. Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space. Neuroinformatics 2024; 22:23-43. [PMID: 37864741 PMCID: PMC10917831 DOI: 10.1007/s12021-023-09644-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
Current mesoscale connectivity atlases provide limited information about the organization of thalamocortical projections in the mouse brain. Labeling the projections of spatially restricted neuron populations in thalamus can provide a functionally relevant level of connectomic analysis, but these need to be integrated within the same common reference space. Here, we present a pipeline for the segmentation, registration, integration and analysis of multiple tract-tracing experiments. The key difference with other workflows is that the data is transformed to fit the reference template. As a test-case, we investigated the axonal projections and intranuclear arrangement of seven neuronal populations of the ventral posteromedial nucleus of the thalamus (VPM), which we labeled with an anterograde tracer. Their soma positions corresponded, from dorsal to ventral, to cortical representations of the whiskers, nose and mouth. They strongly targeted layer 4, with the majority exclusively targeting one cortical area and the ones in ventrolateral VPM branching to multiple somatosensory areas. We found that our experiments were more topographically precise than similar experiments from the Allen Institute and projections to the primary somatosensory area were in agreement with single-neuron morphological reconstructions from publicly available databases. This pilot study sets the basis for a shared virtual connectivity atlas that could be enriched with additional data for studying the topographical organization of different thalamic nuclei. The pipeline is accessible with only minimal programming skills via a Jupyter Notebook, and offers multiple visualization tools such as cortical flatmaps, subcortical plots and 3D renderings and can be used with custom anatomical delineations.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Mario Rubio-Teves
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Carmen Alonso-Martínez
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Rembrandt Bakker
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Inst. of Neuroscience and Medicine (INM-6) and Inst. for Advanced Simulation (IAS-6) and JARA BRAIN Inst. I, Jülich Research Centre, Wilhelm-Johnen-Strasse, 52425, Jülich, Germany
| | - María García-Amado
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
| | - Paul Tiesinga
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Francisco Clascá
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, C. Arzobispo Morcillo 4, 28029, Madrid, Spain
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5
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Buehler A, Brown E, Paulus L, Eckstein M, Thoma O, Oraiopoulou M, Rother U, Hoerning A, Hartmann A, Neurath MF, Woelfle J, Friedrich O, Waldner MJ, Knieling F, Bohndiek SE, Regensburger AP. Transrectal Absorber Guide Raster-Scanning Optoacoustic Mesoscopy for Label-Free In Vivo Assessment of Colitis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300564. [PMID: 37083262 PMCID: PMC10288266 DOI: 10.1002/advs.202300564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Optoacoustic imaging (OAI) enables microscale imaging of endogenous chromophores such as hemoglobin at significantly higher penetration depths compared to other optical imaging technologies. Raster-scanning optoacoustic mesoscopy (RSOM) has recently been shown to identify superficial microvascular changes associated with human skin pathologies. In animal models, the imaging depth afforded by RSOM can enable entirely new capabilities for noninvasive imaging of vascular structures in the gastrointestinal tract, but exact localization of intra-abdominal organs is still elusive. Herein the development and application of a novel transrectal absorber guide for RSOM (TAG-RSOM) is presented to enable accurate transabdominal localization and assessment of colonic vascular networks in vivo. The potential of TAG-RSOM is demonstrated through application during mild and severe acute colitis in mice. TAG-RSOM enables visualization of transmural vascular networks, with changes in colon wall thickness, blood volume, and OAI signal intensities corresponding to colitis-associated inflammatory changes. These findings suggest TAG-RSOM can provide a novel monitoring tool in preclinical IBD models, refining animal procedures and underlines the capabilities of such technologies to address inflammatory bowel diseases in humans.
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Affiliation(s)
- Adrian Buehler
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Emma Brown
- Department of Physics and Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeCB2 0REUK
| | - Lars‐Philip Paulus
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Markus Eckstein
- Institute of PathologyFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Oana‐Maria Thoma
- Department of Medicine 1University Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91052ErlangenGermany
| | - Mariam‐Eleni Oraiopoulou
- Department of Physics and Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeCB2 0REUK
| | - Ulrich Rother
- Department of Vascular SurgeryUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - André Hoerning
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Arndt Hartmann
- Institute of PathologyFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Markus F. Neurath
- Department of Medicine 1University Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91052ErlangenGermany
| | - Joachim Woelfle
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Oliver Friedrich
- Institute of Medical BiotechnologyDepartment of Chemical and Biological EngineeringFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91052ErlangenGermany
| | - Maximilian J. Waldner
- Department of Medicine 1University Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91052ErlangenGermany
| | - Ferdinand Knieling
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
| | - Sarah E. Bohndiek
- Department of Physics and Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeCB2 0REUK
| | - Adrian P. Regensburger
- Department of Pediatrics and Adolescent MedicineUniversity Hospital ErlangenFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg91054ErlangenGermany
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6
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Goldblatt D, Huang S, Greaney MR, Hamling KR, Voleti V, Perez-Campos C, Patel KB, Li W, Hillman EMC, Bagnall MW, Schoppik D. Neuronal birthdate reveals topography in a vestibular brainstem circuit for gaze stabilization. Curr Biol 2023; 33:1265-1281.e7. [PMID: 36924768 PMCID: PMC10089979 DOI: 10.1016/j.cub.2023.02.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/03/2023] [Accepted: 02/15/2023] [Indexed: 03/17/2023]
Abstract
Across the nervous system, neurons with similar attributes are topographically organized. This topography reflects developmental pressures. Oddly, vestibular (balance) nuclei are thought to be disorganized. By measuring activity in birthdated neurons, we revealed a functional map within the central vestibular projection nucleus that stabilizes gaze in the larval zebrafish. We first discovered that both somatic position and stimulus selectivity follow projection neuron birthdate. Next, with electron microscopy and loss-of-function assays, we found that patterns of peripheral innervation to projection neurons were similarly organized by birthdate. Finally, birthdate revealed spatial patterns of axonal arborization and synapse formation to projection neuron outputs. Collectively, we find that development reveals previously hidden organization to the input, processing, and output layers of a highly conserved vertebrate sensorimotor circuit. The spatial and temporal attributes we uncover constrain the developmental mechanisms that may specify the fate, function, and organization of vestibulo-ocular reflex neurons. More broadly, our data suggest that, like invertebrates, temporal mechanisms may assemble vertebrate sensorimotor architecture.
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Affiliation(s)
- Dena Goldblatt
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10004, USA
| | - Stephanie Huang
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10004, USA
| | - Marie R Greaney
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; University of Chicago, Chicago, IL 60637, USA
| | - Kyla R Hamling
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Venkatakaushik Voleti
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Citlali Perez-Campos
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kripa B Patel
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Wenze Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Elizabeth M C Hillman
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Martha W Bagnall
- Department of Neuroscience, Washington University, St. Louis, MO 63130, USA
| | - David Schoppik
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
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7
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Sailer S, Mundszinger M, Martin J, Mancini M, Wohlfahrt-Mehrens M, Kaiser U. Quantitative FIB/SEM tomogram analysis of closed and open porosity of spheroidized graphite anode materials for LiBs applications. Micron 2023; 166:103398. [PMID: 36682294 DOI: 10.1016/j.micron.2022.103398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
The electrochemical behaviour of rounded graphite particles as anode material in a lithium-ion battery strongly depends on the particle properties. The spheroidization process directly affects these properties, including the open porosity that determines the extent of direct contact between liquid electrolyte and carbon surface. Therefore, the quantification of the proportion between open and closed pores is of great interest. Here, we quantify the open and closed porosity of spheroidized porous graphite particles from FIB-SEM tomograms. Quantification is achieved based on two developments: (1) a new sample preparation strategy and (2) a newly developed image evaluation scheme based on neural networks. The sample preparation strategy involves embedding of many graphite powder particles in indium enabling the investigation of several graphite particles in one FIB/SEM tomogram with high stability and with high contrast between the conductive embedding material and porous graphite. A quantitative evaluation of closed and open porosity is achieved by machine learning in form of convolutional neural networks. The convolutional neural network is used to detect the bulk graphite and by further morphological operations, closed and open pores are identified. An error is determined by comparing automatically created quantifications with manual reference values. Our porosity data for two differently spheroidized graphite samples agree qualitatively well with corresponding results from nitrogen physisorption measurements. This approach may allow quantitative data evaluation from porous powders and support understanding of the correlation to the electrochemical behaviour in the lithium-ion battery.
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Affiliation(s)
- Stefan Sailer
- Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany.
| | - Manuel Mundszinger
- Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany
| | - Jan Martin
- Center for Solar Energy and Hydrogen Research Baden-Württemberg (ZSW), Helmholtzstraße 8, 89081 Ulm, Germany
| | - Marilena Mancini
- Center for Solar Energy and Hydrogen Research Baden-Württemberg (ZSW), Helmholtzstraße 8, 89081 Ulm, Germany
| | - Margret Wohlfahrt-Mehrens
- Center for Solar Energy and Hydrogen Research Baden-Württemberg (ZSW), Helmholtzstraße 8, 89081 Ulm, Germany
| | - Ute Kaiser
- Central Facility for Electron Microscopy, Electron Microscopy Group of Materials Science, Albert-Einstein-Allee 11, Universität Ulm, 89081 Ulm, Germany.
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8
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Spead O, Moreland T, Weaver CJ, Costa ID, Hegarty B, Kramer KL, Poulain FE. Teneurin trans-axonal signaling prunes topographically missorted axons. Cell Rep 2023; 42:112192. [PMID: 36857189 PMCID: PMC10131173 DOI: 10.1016/j.celrep.2023.112192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 01/04/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Building precise neural circuits necessitates the elimination of axonal projections that have inaccurately formed during development. Although axonal pruning is a selective process, how it is initiated and controlled in vivo remains unclear. Here, we show that trans-axonal signaling mediated by the cell surface molecules Glypican-3, Teneurin-3, and Latrophilin-3 prunes misrouted retinal axons in the visual system. Retinotopic neuron transplantations revealed that pioneer ventral axons that elongate first along the optic tract instruct the pruning of dorsal axons that missort in that region. Glypican-3 and Teneurin-3 are both selectively expressed by ventral retinal ganglion cells and cooperate for correcting missorted dorsal axons. The adhesion G-protein-coupled receptor Latrophilin-3 signals along dorsal axons to initiate the elimination of topographic sorting errors. Altogether, our findings show an essential function for Glypican-3, Teneurin-3, and Latrophilin-3 in topographic tract organization and demonstrate that axonal pruning can be initiated by signaling among axons themselves.
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Affiliation(s)
- Olivia Spead
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Trevor Moreland
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Cory J Weaver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Irene Dalla Costa
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Brianna Hegarty
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | | | - Fabienne E Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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9
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Wang C, Gordon R. RICT: Rotating image computed tomography with a one-to-one reversible image rotation algorithm. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2023; 31:463-482. [PMID: 36776028 DOI: 10.3233/xst-221248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The Mueller, Siddon and Joseph weighting algorithms are frequently used for projection and back-projection, which are relatively complicated when they are implemented in computer code. OBJECTIVE This study aims to reduce the actual complexity of the projection and back-projection. METHODS First, we neglect the exact shape of the pixel, so that its shadow is a rectangle projecting precisely to a detector bin, which implies that all the pixel weights are exactly 1 for each ray through them, otherwise are exactly 0. Next, a one-to-one reversible image rotation algorithm (RIRA) is proposed to compute the projection and back-projection, where two one-to-one mapping lists namely, U and V, are used to store the coordinates of a rotated pixel and its corresponding new coordinates, respectively. For each 2D projection, the projection is simply the column sum in each orientation according to the lists U and V. For each 2D back-projection, it is simply to arrange the projection to the corresponding column element according to the lists U and V. Thus, there is no need for an interpolation in the projection and back-projection. Last, a rotating image computed tomography (RICT) based on RIRA is proposed to reconstruct the image. RESULTS Experiments show the RICT reconstructs a good image that is close to the result of filtered back-projection (FBP) method according to the RMSE, PSNR and MSSIM values. What's more, our weight, projection and back-projection are much easier to be implemented in computer code than the FBP method. CONCLUSION This study demonstrates that the RIRA method has potential to be used to simplify many computed tomography image reconstruction algorithms.
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Affiliation(s)
- Chengxiang Wang
- School of Mathematical Sciences, Chongqing Normal University, Chongqing, China
| | - Richard Gordon
- Gulf Specimen Marine, Laboratory & Aquarium, Panacea, FL, USA
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10
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Straube C, Meyer J, Dittler A. Investigation of the local oil distribution on oleophilic mist filters applying X-ray micro-computed tomography. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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Kater MSJ, Huffels CFM, Oshima T, Renckens NS, Middeldorp J, Boddeke EWGM, Smit AB, Eggen BJL, Hol EM, Verheijen MHG. Prevention of microgliosis halts early memory loss in a mouse model of Alzheimer's disease. Brain Behav Immun 2023; 107:225-241. [PMID: 36270437 DOI: 10.1016/j.bbi.2022.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline, the neuropathological formation of amyloid-beta (Aβ) plaques and neurofibrillary tangles. The best cellular correlates of the early cognitive deficits in AD patients are synapse loss and gliosis. In particular, it is unclear whether the activation of microglia (microgliosis) has a neuroprotective or pathological role early in AD. Here we report that microgliosis is an early mediator of synaptic dysfunction and cognitive impairment in APP/PS1 mice, a mouse model of increased amyloidosis. We found that the appearance of microgliosis, synaptic dysfunction and behavioral impairment coincided with increased soluble Aβ42 levels, and occurred well before the presence of Aβ plaques. Inhibition of microglial activity by treatment with minocycline (MC) reduced gliosis, synaptic deficits and cognitive impairments at early pathological stages and was most effective when provided preventive, i.e., before the onset of microgliosis. Interestingly, soluble Aβ levels or Aβ plaques deposition were not affected by preventive MC treatment at an early pathological stage (4 months) whereas these were reduced upon treatment at a later stage (6 months). In conclusion, this study demonstrates the importance of early-stage prevention of microgliosis on the development of cognitive impairment in APP/PS1 mice, which might be clinically relevant in preventing memory loss and delaying AD pathogenesis.
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Affiliation(s)
- Mandy S J Kater
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Christiaan F M Huffels
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Takuya Oshima
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek S Renckens
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Jinte Middeldorp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands; Department of Neurobiology & Aging, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Erik W G M Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Center for Healthy Ageing, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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12
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Clark E, Battistara M, Benton MA. A timer gene network is spatially regulated by the terminal system in the Drosophila embryo. eLife 2022; 11:e78902. [PMID: 36524728 PMCID: PMC10065802 DOI: 10.7554/elife.78902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In insect embryos, anteroposterior patterning is coordinated by the sequential expression of the 'timer' genes caudal, Dichaete, and odd-paired, whose expression dynamics correlate with the mode of segmentation. In Drosophila, the timer genes are expressed broadly across much of the blastoderm, which segments simultaneously, but their expression is delayed in a small 'tail' region, just anterior to the hindgut, which segments during germband extension. Specification of the tail and the hindgut depends on the terminal gap gene tailless, but beyond this the regulation of the timer genes is poorly understood. We used a combination of multiplexed imaging, mutant analysis, and gene network modelling to resolve the regulation of the timer genes, identifying 11 new regulatory interactions and clarifying the mechanism of posterior terminal patterning. We propose that a dynamic Tailless expression gradient modulates the intrinsic dynamics of a timer gene cross-regulatory module, delineating the tail region and delaying its developmental maturation.
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Affiliation(s)
- Erik Clark
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Margherita Battistara
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Matthew A Benton
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
- Developmental Biology Unit, EMBLHeidelbergGermany
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13
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Accurate and lightweight MRI super-resolution via multi-scale bidirectional fusion attention network. PLoS One 2022; 17:e0277862. [PMID: 36520931 PMCID: PMC9754592 DOI: 10.1371/journal.pone.0277862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
High-resolution magnetic resonance (MR) imaging has attracted much attention due to its contribution to clinical diagnoses and treatment. However, because of the interference of noise and the limitation of imaging equipment, it is expensive to generate a satisfactory image. Super-resolution (SR) is a technique that enhances an imaging system's resolution, which is effective and cost-efficient for MR imaging. In recent years, deep learning-based SR methods have made remarkable progress on natural images but not on medical images. Most existing medical images SR algorithms focus on the spatial information of a single image but ignore the temporal correlation between medical images sequence. We proposed two novel architectures for single medical image and sequential medical images, respectively. The multi-scale back-projection network (MSBPN) is constructed of several different scale back-projection units which consist of iterative up- and down-sampling layers. The multi-scale machine extracts different scale spatial information and strengthens the information fusion for a single image. Based on MSBPN, we proposed an accurate and lightweight Multi-Scale Bidirectional Fusion Attention Network(MSBFAN) that combines temporal information iteratively. That supplementary temporal information is extracted from the adjacent image sequence of the target image. The MSBFAN can effectively learn both the spatio-temporal dependencies and the iterative refinement process with only a lightweight number of parameters. Experimental results demonstrate that our MSBPN and MSBFAN are outperforming current SR methods in terms of reconstruction accuracy and parameter quantity of the model.
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14
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Watson CJ, Tang WJ, Rojas MF, Fiedler IAK, Morfin Montes de Oca E, Cronrath AR, Callies LK, Swearer AA, Ahmed AR, Sethuraman V, Addish S, Farr GH, Gómez AE, Rai J, Monstad-Rios AT, Gardiner EM, Karasik D, Maves L, Busse B, Hsu YH, Kwon RY. wnt16 regulates spine and muscle morphogenesis through parallel signals from notochord and dermomyotome. PLoS Genet 2022; 18:e1010496. [PMID: 36346812 PMCID: PMC9674140 DOI: 10.1371/journal.pgen.1010496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Bone and muscle are coupled through developmental, mechanical, paracrine, and autocrine signals. Genetic variants at the CPED1-WNT16 locus are dually associated with bone- and muscle-related traits. While Wnt16 is necessary for bone mass and strength, this fails to explain pleiotropy at this locus. Here, we show wnt16 is required for spine and muscle morphogenesis in zebrafish. In embryos, wnt16 is expressed in dermomyotome and developing notochord, and contributes to larval myotome morphology and notochord elongation. Later, wnt16 is expressed at the ventral midline of the notochord sheath, and contributes to spine mineralization and osteoblast recruitment. Morphological changes in wnt16 mutant larvae are mirrored in adults, indicating that wnt16 impacts bone and muscle morphology throughout the lifespan. Finally, we show that wnt16 is a gene of major effect on lean mass at the CPED1-WNT16 locus. Our findings indicate that Wnt16 is secreted in structures adjacent to developing bone (notochord) and muscle (dermomyotome) where it affects the morphogenesis of each tissue, thereby rendering wnt16 expression into dual effects on bone and muscle morphology. This work expands our understanding of wnt16 in musculoskeletal development and supports the potential for variants to act through WNT16 to influence bone and muscle via parallel morphogenetic processes. In humans, genetic variants (DNA sequences that vary amongst individuals) have been identified that appear to influence two tissues, bone and skeletal muscle. However, how single genes and genetic variants exert dual influence on both tissues is not well understood. In this study, we found that the wnt16 gene is necessary for specifying the size and shape of both muscle and bone during development in zebrafish. We also disentangled how wnt16 affects both tissues: distinct cellular populations adjacent to muscle and bone secrete Wnt16, where it acts as a signal guiding the size and shape of each tissue. This is important because in humans, genetic variants near the WNT16 gene have effects on both bone- and muscle-related traits. This study expands our understanding of the role of WNT16 in bone and muscle development, and helps to explain how genetic variants near WNT16 affect traits for both tissues. Moreover, WNT16 is actively being explored as a target for osteoporosis therapies, thus our study could have implications with regard to the potential of targeting WNT16 to treat bone and muscle simultaneously.
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Affiliation(s)
- Claire J. Watson
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - W. Joyce Tang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Maria F. Rojas
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Imke A. K. Fiedler
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ernesto Morfin Montes de Oca
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Andrea R. Cronrath
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Lulu K. Callies
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Avery Angell Swearer
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Ali R. Ahmed
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Visali Sethuraman
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Sumaya Addish
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Gist H. Farr
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Arianna Ericka Gómez
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Jyoti Rai
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Adrian T. Monstad-Rios
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Edith M. Gardiner
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, United States of America
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, Division of Cardiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Bjorn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - Ronald Young Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
- * E-mail:
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15
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Escudero Sanchez L, Brown E, Rundo L, Ursprung S, Sala E, Bohndiek SE, Partarrieu IX. Photoacoustic imaging radiomics in patient-derived xenografts: a study on feature sensitivity and model discrimination. Sci Rep 2022; 12:15142. [PMID: 36071117 PMCID: PMC9452574 DOI: 10.1038/s41598-022-19084-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022] Open
Abstract
Photoacoustic imaging is an increasingly popular method of exploring the tumour microenvironment, which can provide insight into tumour oxygenation status and potentially treatment response assessment. Currently, the measurements most commonly performed on such images are the mean and median of the pixel values of the tumour volumes of interest. We investigated expanding the set of measurements that can be extracted from these images by adding radiomic features. In particular, we found that Skewness was sensitive to differences between basal and luminal patient derived xenograft cancer models with an [Formula: see text] of 0.86, and that it was robust to variations in confounding factors such as reconstruction type and wavelength. We also built discriminant models with radiomic features that were correlated with the underlying tumour model and were independent from each other. We then ranked features by their importance in the model. Skewness was again found to be an important feature, as were 10th Percentile, Root Mean Squared, and several other texture-based features. In summary, this paper proposes a methodology to select radiomic features extracted from photoacoustic images that are robust to changes in acquisition and reconstruction parameters, and discusses features found to have discriminating power between the underlying tumour models in a pre-clinical dataset.
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Affiliation(s)
- Lorena Escudero Sanchez
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Emma Brown
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- Washington University School of Medicine in St Louis, St. Louis, MO, 63110, USA
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
- Department of Information and Electrical Engineering and Applied Mathematics (DIEM), University of Salerno, Fisciano, SA, 84084, Italy
| | - Stephan Ursprung
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Sarah E Bohndiek
- Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
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16
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Flashner S, Swift M, Sowash A, Fahmy AN, Azizkhan-Clifford J. Transcription factor Sp1 regulates mitotic chromosome assembly and segregation. Chromosoma 2022; 131:175-191. [PMID: 35916925 PMCID: PMC9470683 DOI: 10.1007/s00412-022-00778-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/14/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Aneuploidy is a pervasive feature of cancer cells that results from chromosome missegregation. Several transcription factors have been associated with aneuploidy; however, no studies to date have demonstrated that mammalian transcription factors directly regulate chromosome segregation during mitosis. Here, we demonstrate that the ubiquitously expressed transcription factor specificity protein 1 (Sp1), which we have previously linked to aneuploidy, has a mitosis-specific role regulating chromosome segregation. We find that Sp1 localizes to mitotic centromeres and auxin-induced rapid Sp1 degradation at mitotic onset results in chromosome segregation errors and aberrant mitotic progression. Furthermore, rapid Sp1 degradation results in anomalous mitotic chromosome assembly characterized by loss of condensin complex I localization to mitotic chromosomes and chromosome condensation defects. Consistent with these defects, Sp1 degradation results in reduced chromosome passenger complex activity and histone H3 serine 10 phosphorylation during mitosis, which is essential for condensin complex I recruitment and chromosome condensation. Together, these data provide the first evidence of a mammalian transcription factor acting specifically during mitosis to regulate chromosome segregation.
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Affiliation(s)
- Samuel Flashner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Michelle Swift
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Aislinn Sowash
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Alexander N Fahmy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA
| | - Jane Azizkhan-Clifford
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, MS 497, Philadelphia, PA, 19102, USA.
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17
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Savriama Y, Tautz D. Testing the accuracy of 3D automatic landmarking via genome-wide association studies. G3 (BETHESDA, MD.) 2022; 12:jkab443. [PMID: 35100368 PMCID: PMC9210295 DOI: 10.1093/g3journal/jkab443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022]
Abstract
Various advances in 3D automatic phenotyping and landmark-based geometric morphometric methods have been made. While it is generally accepted that automatic landmarking compromises the capture of the biological variation, no studies have directly tested the actual impact of such landmarking approaches in analyses requiring a large number of specimens and for which the precision of phenotyping is crucial to extract an actual biological signal adequately. Here, we use a recently developed 3D atlas-based automatic landmarking method to test its accuracy in detecting QTLs associated with craniofacial development of the house mouse skull and lower jaws for a large number of specimens (circa 700) that were previously phenotyped via a semiautomatic landmarking method complemented with manual adjustment. We compare both landmarking methods with univariate and multivariate mapping of the skull and the lower jaws. We find that most significant SNPs and QTLs are not recovered based on the data derived from the automatic landmarking method. Our results thus confirm the notion that information is lost in the automated landmarking procedure although somewhat dependent on the analyzed structure. The automatic method seems to capture certain types of structures slightly better, such as lower jaws whose shape is almost entirely summarized by its outline and could be assimilated as a 2D flat object. By contrast, the more apparent 3D features exhibited by a structure such as the skull are not adequately captured by the automatic method. We conclude that using 3D atlas-based automatic landmarking methods requires careful consideration of the experimental question.
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Affiliation(s)
- Yoland Savriama
- Department Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Diethard Tautz
- Department Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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18
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Dense channel splitting network for MR image super-resolution. Magn Reson Imaging 2022; 88:53-61. [DOI: 10.1016/j.mri.2022.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/21/2022]
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19
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Autoencoding Low-Resolution MRI for Semantically Smooth Interpolation of Anisotropic MRI. Med Image Anal 2022; 78:102393. [DOI: 10.1016/j.media.2022.102393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/20/2022]
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20
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Spead O, Weaver CJ, Moreland T, Poulain FE. Live imaging of retinotectal mapping reveals topographic map dynamics and a previously undescribed role for Contactin 2 in map sharpening. Development 2021; 148:272618. [PMID: 34698769 DOI: 10.1242/dev.199584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/07/2021] [Indexed: 11/20/2022]
Abstract
Organization of neuronal connections into topographic maps is essential for processing information. Yet, our understanding of topographic mapping has remained limited by our inability to observe maps forming and refining directly in vivo. Here, we used Cre-mediated recombination of a new colorswitch reporter in zebrafish to generate the first transgenic model allowing the dynamic analysis of retinotectal mapping in vivo. We found that the antero-posterior retinotopic map forms early but remains dynamic, with nasal and temporal retinal axons expanding their projection domains over time. Nasal projections initially arborize in the anterior tectum but progressively refine their projection domain to the posterior tectum, leading to the sharpening of the retinotopic map along the antero-posterior axis. Finally, using a CRISPR-mediated mutagenesis approach, we demonstrate that the refinement of nasal retinal projections requires the adhesion molecule Contactin 2. Altogether, our study provides the first analysis of a topographic map maturing in real time in a live animal and opens new strategies for dissecting the molecular mechanisms underlying precise topographic mapping in vertebrates.
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Affiliation(s)
- Olivia Spead
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Cory J Weaver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Trevor Moreland
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Fabienne E Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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21
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Smith B, Datta A, Lee J, Evans D, Fleiszig S. Quantification of relative neurite tortuosity using Fourier transforms. J Neurosci Methods 2021; 361:109266. [PMID: 34166700 PMCID: PMC10964090 DOI: 10.1016/j.jneumeth.2021.109266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/16/2021] [Accepted: 06/17/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The tortuosity of nerve fibers has been shown to be important for identifying and monitoring clinically relevant manifestations resulting from of a variety of ocular and systemic disease pathologies and disorders. However, quantifying tortuosity in dense neurite networks can prove challenging, as existing methods require manual scoring and/or complete segmentation of the neurite network. NEW METHOD We measured neurite tortuosity by quantifying the degree of directional coherence in the Fourier transform of segmented neurite masks. This allowed for the analysis of neurite tortuosity without requiring complete segmentation of the neurite network. We were also able to adapt this method to measure tortuosity at different length and size scales. RESULTS With this novel method, neurite tortuosity was accurately quantified in simulated data sets at multiple length scales and scale variant and scale invariant tortuosity was accurately distinguished. Use of this method on images of murine corneal neurites correctly distinguished known differences between neurite tortuosity in the peripheral and central cornea. COMPARISON WITH EXISTING METHOD(S) Other methods require complete segmentation of neurites, which can be prohibitive in dense and/or sparsely labeled neurite networks such as in the cornea. Additionally, other methods require manual curation, manual scoring, or generation of a curated training set, while our novel method directly measures tortuosity as an intrinsic property of the image. CONCLUSIONS We report the use of Fourier transforms for quantification of neurite tortuosity at multiple length scales, and with an image input that contains incompletely segmented neurites. This new method does not require manual training or curation, allowing a direct and rapid measurement of neurite tortuosity, thereby enhancing the accuracy and utility of neurite tortuosity measurements for evaluation of ocular and systemic disease pathology.
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Affiliation(s)
- Benjamin Smith
- School of Optometry, University of California, Berkeley, CA 94720, USA; Graduate Program in Vision Science, University of California, Berkeley, CA 94720, USA.
| | - Ananya Datta
- School of Optometry, University of California, Berkeley, CA 94720, USA
| | - Justin Lee
- School of Optometry, University of California, Berkeley, CA 94720, USA
| | - David Evans
- School of Optometry, University of California, Berkeley, CA 94720, USA; College of Pharmacy, Touro University California, Vallejo, CA 94592, USA
| | - Suzanne Fleiszig
- School of Optometry, University of California, Berkeley, CA 94720, USA; Graduate Program in Vision Science, University of California, Berkeley, CA 94720, USA
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22
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23
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Guillaume F, Le Cann S, Tengattini A, Törnquist E, Falentin-Daudre C, Albini Lomami H, Petit Y, Isaksson H, Haïat G. Neutron microtomography to investigate the bone-implant interface-comparison with histological analysis. Phys Med Biol 2021; 66. [PMID: 33831846 DOI: 10.1088/1361-6560/abf603] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/08/2021] [Indexed: 12/20/2022]
Abstract
Bone properties and especially its microstructure around implants are crucial to evaluate the osseointegration of prostheses in orthopaedic, maxillofacial and dental surgeries. Given the intrinsic heterogeneous nature of the bone microstructure, an ideal probing tool to understand and quantify bone formation must be spatially resolved. X-ray imaging has often been employed, but is limited in the presence of metallic implants, where severe artifacts generally arise from the high attenuation of metals to x-rays. Neutron tomography has recently been proposed as a promising technique to study bone-implant interfaces, thanks to its lower interaction with metals. The aim of this study is to assess the potential of neutron tomography for the characterisation of bone tissue in the vicinity of a metallic implant. A standardised implant with a bone chamber was implanted in rabbit bone. Four specimens were imaged with neutron tomography and subsequently compared to non-decalcified histology to stain soft and mineralised bone tissues, used here as a ground-truth reference. An intensity-based image registration procedure was performed to place the 12 histological slices within the corresponding 3D neutron volume. Significant correlations (p < 0.01) were obtained between the two modalities for the bone-implant contact (BIC) ratio (R = 0.77) and the bone content inside the chamber (R = 0.89). The results indicate that mineralised bone tissue can be reliably detected by neutron tomography. However, theBICratio and bone content were found to be overestimated with neutron imaging, which may be explained by its sensitivity to non-mineralised soft tissues, as revealed by histological staining. This study highlights the suitability of neutron tomography for the analysis of the bone-implant interface. Future work will focus on further distinguishing soft tissues from bone tissue, which could be aided by the adoption of contrast agents.
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Affiliation(s)
- Florian Guillaume
- Département de génie mécanique, École de technologie supérieure, Montréal, Canada.,MSME, CNRS UMR 8208, Univ Paris Est Creteil, Univ Gustave Eiffel, F-94010 Creteil, France
| | - Sophie Le Cann
- MSME, CNRS UMR 8208, Univ Paris Est Creteil, Univ Gustave Eiffel, F-94010 Creteil, France
| | - Alessandro Tengattini
- Institut Laue Langevin, Grenoble, France.,Laboratoire 3SR, Université Grenoble Alpes, Gières, France
| | - Elin Törnquist
- Department of Biomedical Engineering, Lund University, SE-221 00 Lund, Sweden
| | - Céline Falentin-Daudre
- LBPS/CSPBAT, UMR CNRS 7244, Institut Galilée, Université Sorbonne Paris Nord, 99 avenue JB Clément 93430- Villetaneuse, France
| | - Hugues Albini Lomami
- MSME, CNRS UMR 8208, Univ Paris Est Creteil, Univ Gustave Eiffel, F-94010 Creteil, France
| | - Yvan Petit
- Département de génie mécanique, École de technologie supérieure, Montréal, Canada
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, SE-221 00 Lund, Sweden
| | - Guillaume Haïat
- MSME, CNRS UMR 8208, Univ Paris Est Creteil, Univ Gustave Eiffel, F-94010 Creteil, France
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24
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Saha PK, Oweis RR, Zhang X, Letuchy E, Eichenberger-Gilmore JM, Burns TL, Warren JJ, Janz KF, Torner JC, Snetselaar LG, Levy SM. Effects of fluoride intake on cortical and trabecular bone microstructure at early adulthood using multi-row detector computed tomography (MDCT). Bone 2021; 146:115882. [PMID: 33578032 PMCID: PMC8009824 DOI: 10.1016/j.bone.2021.115882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/28/2021] [Accepted: 02/07/2021] [Indexed: 11/18/2022]
Abstract
PURPOSE The aim of this study was to examine the effects of period-specific and cumulative fluoride (F) intake on bone at the levels of cortical and trabecular bone microstructural outcomes at early adulthood using emerging multi-row detector computed tomography (MDCT)-based novel techniques. METHODS Ultra-high resolution MDCT distal tibia scans were collected at age 19 visits under the Iowa Bone Development Study (IBDS), and cortical and trabecular bone microstructural outcomes were computed at the distal tibia using previously validated methods. CT scans of a tissue characterization phantom were used to calibrate CT numbers (Hounsfield units) into bone mineral density (mg/cc). Period-specific and cumulative F intakes from birth up to the age of 19 years were assessed for IBDS participants through questionnaire, and their relationships with MDCT-derived bone microstructural outcomes were examined using bivariable and multivariable analyses, adjusting for height, weight, maturity offset (years since age of peak height velocity (PHV)), physical activity (questionnaire for adolescents (PAQ-A)), healthy eating index version 2010 (HEI-2010) scores, and calcium and protein intakes. RESULTS MDCT distal tibia scans were acquired for 324 participants from among the total of 329 participants at age 19 visits. No motion artifacts were observed in any MDCT scans, and all images were successfully processed to measure cortical and trabecular bone microstructural outcomes. At early adulthood, males were observed to have stronger trabecular bone microstructural features, as well as thicker cortical bone (p < 0.01), as compared to age-similar females; however, females were found to have less cortical bone porosity as compared to males. Among participants with available F intake estimates (75 to 91% of the 324 with MDCT scans, depending on the period-specific F intake measure), no statistically significant associations were detected between any period-specific or cumulative F intake and bone microstructural outcomes of the tibia at the p < 0.01 level. Only for females, statistically suggestive associations (p < 0.05) were found between recent F intake (from 14 to 19 years) and trabecular mean plate width and trabecular thickness at the tibia. Those associations became somewhat weaker, but still statistically suggestive, for trabecular thickness in fully adjusted analysis with height, weight, PHV, calcium and protein intake, and HEI-2010 and PAQ-A scores as covariates. CONCLUSION The findings show that the effects of lifelong or period-specific F intake from combined sources for adolescents typical to the United States Midwest region are not strongly associated with bone microstructural outcomes at age 19 years. These findings are generally consistent with previously reported results of IBDS analyses, which further confirms that effects of lifelong or period-specific F intake on skeletons in early adulthood are absent or weak, even at the levels of cortical and trabecular bone microstructural details.
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Affiliation(s)
- Punam K Saha
- Department of Electrical and Computer Engineering, College of Engineering, The University of Iowa, Iowa City, IA, USA; Department of Radiology, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA.
| | - Reem Reda Oweis
- Department of Preventive and Community Dentistry, College of Dentistry, Iowa City, IA, USA
| | - Xiaoliu Zhang
- Department of Electrical and Computer Engineering, College of Engineering, The University of Iowa, Iowa City, IA, USA
| | - Elena Letuchy
- Department of Epidemiology, College of Public Health, Iowa City, IA, USA
| | - Julie M Eichenberger-Gilmore
- Department of Epidemiology, College of Public Health, Iowa City, IA, USA; Formerly with Department of Preventive and Community Dentistry, College of Dentistry, Iowa City, IA, USA; Nutrition and Food Services, Iowa City VA Health Care System, Iowa City, IA, USA
| | - Trudy L Burns
- Department of Epidemiology, College of Public Health, Iowa City, IA, USA
| | - John J Warren
- Department of Preventive and Community Dentistry, College of Dentistry, Iowa City, IA, USA
| | - Kathleen F Janz
- Department of Health and Human Physiology, College of Liberal Arts and Sciences, Iowa City, IA, USA
| | - James C Torner
- Department of Epidemiology, College of Public Health, Iowa City, IA, USA
| | - Linda G Snetselaar
- Department of Epidemiology, College of Public Health, Iowa City, IA, USA
| | - Steven M Levy
- Department of Preventive and Community Dentistry, College of Dentistry, Iowa City, IA, USA; Department of Epidemiology, College of Public Health, Iowa City, IA, USA
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25
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Ibrahim A, Refaee T, Primakov S, Barufaldi B, Acciavatti RJ, Granzier RWY, Hustinx R, Mottaghy FM, Woodruff HC, Wildberger JE, Lambin P, Maidment ADA. The Effects of In-Plane Spatial Resolution on CT-Based Radiomic Features' Stability with and without ComBat Harmonization. Cancers (Basel) 2021; 13:cancers13081848. [PMID: 33924382 PMCID: PMC8103509 DOI: 10.3390/cancers13081848] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Handcrafted radiomic features (HRFs) are quantitative features extracted from medical images, and they are mined for associations with different clinical endpoints. While many studies reported on the potential of HRFs to unravel clinical endpoints, the sensitivity of HRFs to variations in scanning parameters is affecting the inclusion of radiomic signatures in clinical decision-making. In this study, we investigated the effects of variations in the in-plane resolution of scans, while all other scanning parameters were fixed. Moreover, we investigated the effects of ten different image resampling methods and ComBat harmonization on the reproducibility of HRFs. Our results show that the majority of HRFs are significantly and variably affected by the differences in in-plane resolution. The majority of image resampling methods resulted in a higher number of reproducible HRFs compared to ComBat harmonization. Our developed framework guides identifying the reproducible and harmonizable HRFs in different scenarios. Abstract While handcrafted radiomic features (HRFs) have shown promise in the field of personalized medicine, many hurdles hinder its incorporation into clinical practice, including but not limited to their sensitivity to differences in acquisition and reconstruction parameters. In this study, we evaluated the effects of differences in in-plane spatial resolution (IPR) on HRFs, using a phantom dataset (n = 14) acquired on two scanner models. Furthermore, we assessed the effects of interpolation methods (IMs), the choice of a new unified in-plane resolution (NUIR), and ComBat harmonization on the reproducibility of HRFs. The reproducibility of HRFs was significantly affected by variations in IPR, with pairwise concordant HRFs, as measured by the concordance correlation coefficient (CCC), ranging from 42% to 95%. The number of concordant HRFs (CCC > 0.9) after resampling varied depending on (i) the scanner model, (ii) the IM, and (iii) the NUIR. The number of concordant HRFs after ComBat harmonization depended on the variations between the batches harmonized. The majority of IMs resulted in a higher number of concordant HRFs compared to ComBat harmonization, and the combination of IMs and ComBat harmonization did not yield a significant benefit. Our developed framework can be used to assess the reproducibility and harmonizability of RFs.
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Affiliation(s)
- Abdalla Ibrahim
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6200 Maastricht, The Netherlands; (T.R.); (S.P.); (H.C.W.); (P.L.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands; (F.M.M.); (J.E.W.)
- Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, University Hospital of Liège and GIGA CRC-In Vivo Imaging, University of Liège, 4000 Liege, Belgium;
- Department of Nuclear Medicine and Comprehensive Diagnostic Center Aachen (CDCA), University Hospital RWTH Aachen University, 52074 Aachen, Germany
- Correspondence:
| | - Turkey Refaee
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6200 Maastricht, The Netherlands; (T.R.); (S.P.); (H.C.W.); (P.L.)
- Department of Diagnostic Radiology, Faculty of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Sergey Primakov
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6200 Maastricht, The Netherlands; (T.R.); (S.P.); (H.C.W.); (P.L.)
- Department of Nuclear Medicine and Comprehensive Diagnostic Center Aachen (CDCA), University Hospital RWTH Aachen University, 52074 Aachen, Germany
| | - Bruno Barufaldi
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (B.B.); (R.J.A.); (A.D.A.M.)
| | - Raymond J. Acciavatti
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (B.B.); (R.J.A.); (A.D.A.M.)
| | - Renée W. Y. Granzier
- Department of Surgery, GROW—School for Oncology, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands;
| | - Roland Hustinx
- Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, University Hospital of Liège and GIGA CRC-In Vivo Imaging, University of Liège, 4000 Liege, Belgium;
| | - Felix M. Mottaghy
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands; (F.M.M.); (J.E.W.)
- Department of Nuclear Medicine and Comprehensive Diagnostic Center Aachen (CDCA), University Hospital RWTH Aachen University, 52074 Aachen, Germany
| | - Henry C. Woodruff
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6200 Maastricht, The Netherlands; (T.R.); (S.P.); (H.C.W.); (P.L.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands; (F.M.M.); (J.E.W.)
| | - Joachim E. Wildberger
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands; (F.M.M.); (J.E.W.)
| | - Philippe Lambin
- The D-Lab, Department of Precision Medicine, GROW—School for Oncology, Maastricht University, 6200 Maastricht, The Netherlands; (T.R.); (S.P.); (H.C.W.); (P.L.)
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre+, 6200 Maastricht, The Netherlands; (F.M.M.); (J.E.W.)
| | - Andrew D. A. Maidment
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (B.B.); (R.J.A.); (A.D.A.M.)
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26
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Quantification of Tumor Vasculature by Analysis of Amount and Spatial Dispersion of Caliber-Classified Vessels. Methods Mol Biol 2021. [PMID: 32754817 DOI: 10.1007/978-1-0716-0916-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This protocol focuses on the quantitative description of the angioarchitecture of experimental tumor xenografts. This semiautomatic analysis is carried out on functional vessels and microvessels acquired by confocal imaging and processed into progressively reconstructed angioarchitectures following a caliber-classification step. The protocol can be applied also to the quantification of pathological angioarchitectures other than tumor grafts as well as to the microvasculature of physiological tissue samples.
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27
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Zhang X, Comellas AP, Regan EA, Guha I, Shibli-Rahhal A, Rubin MR, DiCamillo PA, Letuchy EM, Barr RG, Hoffman EA, Saha PK. Quantitative CT-Based Methods for Bone Microstructural Measures and Their Relationships With Vertebral Fractures in a Pilot Study on Smokers. JBMR Plus 2021; 5:e10484. [PMID: 33977202 PMCID: PMC8101620 DOI: 10.1002/jbm4.10484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 11/05/2022] Open
Abstract
Osteoporosis causes fragile bone, and bone microstructural quality is a critical determinant of bone strength and fracture risk. This study pursues technical validation of novel CT-based methods for assessment of peripheral bone microstructure together with a human pilot study examining relationships between bone microstructure and vertebral fractures in smokers. To examine the accuracy and reproducibility of the methods, repeat ultra-high-resolution (UHR) CT and micro-CT scans of cadaveric ankle specimens were acquired. Thirty smokers from the University of Iowa COPDGene cohort were recruited at their 5-year follow-up visits. Chest CT scans, collected under the parent study, were used to assess vertebral fractures. UHR CT scans of distal tibia were acquired for this pilot study to obtain peripheral cortical and trabecular bone (Cb and Tb) measures. UHR CT-derived Tb measures, including volumetric bone mineral density (BMD), network area, transverse trabecular density, and mean plate width, showed high correlation (r > 0.901) with their micro-CT-derived values over small regions of interest (ROIs). Both Cb and Tb measures showed high reproducibility-intra-class correlation (ICC) was greater than 0.99 for all Tb measures except erosion index and greater than 0.97 for all Cb measures. Female sex was associated with lower transverse Tb density (p < 0.1), higher Tb spacing (p < 0.05), and lower cortical thickness (p < 0.001). Participants with vertebral fractures had significantly degenerated values (p < 0.05) for all Tb measures except thickness. There were no statistically significant differences for Cb measures between non-fracture and fracture groups. Vertebral fracture-group differences of Tb measures remained significant after adjustment with chronic obstructive pulmonary disease (COPD) status. Although current smokers at baseline had more fractures-81.8% versus 63.2% for former smokers-the difference was not statistically significant. This pilot cross-sectional human study demonstrates CT-based peripheral bone microstructural differences among smokers with and without vertebral fractures. © 2021 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Xiaoliu Zhang
- Department of Electrical and Computer Engineering, College of Engineering University of Iowa Iowa City IA USA
| | - Alejandro P Comellas
- Department of Internal Medicine, Carver College of Medicine University of Iowa Iowa City IA USA
| | - Elizabeth A Regan
- Division of Rheumatology, Department of Medicine National Jewish Health Denver CO USA
| | - Indranil Guha
- Department of Electrical and Computer Engineering, College of Engineering University of Iowa Iowa City IA USA
| | - Amal Shibli-Rahhal
- Department of Internal Medicine, Carver College of Medicine University of Iowa Iowa City IA USA
| | - Mishaela R Rubin
- Department of Clinical Medicine Columbia University New York NY USA
| | - Paul A DiCamillo
- Department of Radiology, Carver College of Medicine University of Iowa Iowa City IA USA
| | - Elena M Letuchy
- Department of Epidemiology, College of Public Health University of Iowa Iowa City IA USA
| | - R Graham Barr
- Department of Medicine Columbia University New York NY USA
| | - Eric A Hoffman
- Department of Radiology, Carver College of Medicine University of Iowa Iowa City IA USA.,Department of Biomedical Engineering, College of Engineering University of Iowa Iowa City IA USA
| | - Punam K Saha
- Department of Electrical and Computer Engineering, College of Engineering University of Iowa Iowa City IA USA.,Department of Radiology, Carver College of Medicine University of Iowa Iowa City IA USA
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28
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Oh SY, Dieterich M, Lee BN, Boegle R, Kang JJ, Lee NR, Gerb J, Hwang SB, Kirsch V. Endolymphatic Hydrops in Patients With Vestibular Migraine and Concurrent Meniere's Disease. Front Neurol 2021; 12:594481. [PMID: 33776877 PMCID: PMC7991602 DOI: 10.3389/fneur.2021.594481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/09/2021] [Indexed: 12/17/2022] Open
Abstract
Objective: Intravenous contrast agent enhanced, high-resolution magnetic resonance imaging of the inner ear (iMRI) confirmed that patients with Menière's disease (MD) and vestibular migraine (VM) could present with endolymphatic hydrops (EH). The present study aimed to investigate EH characteristics and their interrelation to neurotologic testing in patients with VM, MD, or VM with concurrent MD (VM-MD). Methods: Sixty–two patients (45 females, aged 23–81 years) with definite or probable VM (n = 25, 19 definite), MD (n = 29, 17 definite), or showing characteristics of both diseases (n = 8) were included in this study. Diagnostic workup included neurotologic assessments including video-oculography (VOG) during caloric stimulation and head-impulse test (HIT), ocular and cervical vestibular evoked myogenic potentials (o/cVEMP), pure tone audiometry (PTA), as well as iMRI. EH's degree was assessed visually and via volumetric quantification using a probabilistic atlas-based segmentation of the bony labyrinth and volumetric local thresholding (VOLT). Results: Although a relevant number of VM patients reported varying auditory symptoms (13 of 25, 52.0%), EH in VM was only observed twice. In contrast, EH in VM-MD was prevalent (2/8, 25%) and in MD frequent [23/29, 79.3%; χ2(2) = 29.1, p < 0.001, φ = 0.7]. Location and laterality of EH and neurophysiological testing classifications were highly associated (Fisher exact test, p < 0.005). In MD, visual semi-quantitative grading and volumetric quantification correlated highly to each other (rS = 0.8, p < 0.005, two-sided) and to side differences in VOG during caloric irrigation (vestibular EH ipsilateral: rS = 0.6, p < 0.05, two-sided). In VM, correlations were less pronounced. VM-MD assumed an intermediate position between VM and MD. Conclusion: Cochlear and vestibular hydrops can occur in MD and VM patients with auditory symptoms; this suggests inner ear damage irrespective of the diagnosis of MD or VM. The EH grades often correlated with auditory symptoms such as hearing impairment and tinnitus. Further research is required to uncover whether migraine is one causative factor of EH or whether EH in VM patients with auditory symptoms suggests an additional pathology due to MD.
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Affiliation(s)
- Sun-Young Oh
- Department of Neurology, School of Medicine, Jeonbuk National University, Jeonju, South Korea.,Research Institute of Clinical Medicine, Jeonbuk National University Hospital-Biomedical Research Institute, Jeonbuk National University, Jeonju, South Korea
| | - Marianne Dieterich
- Department of Neurology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.,German Center for Vertigo and Balance Disorders-IFB, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Bit Na Lee
- Department of Neurology, School of Medicine, Jeonbuk National University, Jeonju, South Korea
| | - Rainer Boegle
- Department of Neurology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.,German Center for Vertigo and Balance Disorders-IFB, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jin-Ju Kang
- Department of Neurology, School of Medicine, Jeonbuk National University, Jeonju, South Korea
| | - Na-Ri Lee
- Research Institute of Clinical Medicine, Jeonbuk National University Hospital-Biomedical Research Institute, Jeonbuk National University, Jeonju, South Korea.,Division of Oncology and Hematology, Department of Internal Medicine, Jeonbuk National University Hospital and School of Medicine, Jeonju, South Korea
| | - Johannes Gerb
- Department of Neurology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.,German Center for Vertigo and Balance Disorders-IFB, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Seung-Bae Hwang
- Research Institute of Clinical Medicine, Jeonbuk National University Hospital-Biomedical Research Institute, Jeonbuk National University, Jeonju, South Korea.,Department of Radiology, Jeonbuk National University Hospital and School of Medicine, Jeonju, South Korea
| | - Valerie Kirsch
- Department of Neurology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.,German Center for Vertigo and Balance Disorders-IFB, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
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29
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Dalle Nogare DE, Natesh N, Vishwasrao HD, Shroff H, Chitnis AB. Zebrafish Posterior Lateral Line primordium migration requires interactions between a superficial sheath of motile cells and the skin. eLife 2020; 9:58251. [PMID: 33237853 PMCID: PMC7688310 DOI: 10.7554/elife.58251] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
The Zebrafish Posterior Lateral Line primordium migrates in a channel between the skin and somites. Its migration depends on the coordinated movement of its mesenchymal-like leading cells and trailing cells, which form epithelial rosettes, or protoneuromasts. We describe a superficial population of flat primordium cells that wrap around deeper epithelialized cells and extend polarized lamellipodia to migrate apposed to the overlying skin. Polarization of lamellipodia extended by both superficial and deeper protoneuromast-forming cells depends on Fgf signaling. Removal of the overlying skin has similar effects on superficial and deep cells: lamellipodia are lost, blebs appear instead, and collective migration fails. When skinned embryos are embedded in Matrigel, basal and superficial lamellipodia are recovered; however, only the directionality of basal protrusions is recovered, and migration is not rescued. These observations support a key role played by superficial primordium cells and the skin in directed migration of the Posterior Lateral Line primordium.
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Affiliation(s)
- Damian E Dalle Nogare
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Naveen Natesh
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Harshad D Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, United States
| | - Hari Shroff
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, United States.,Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Ajay B Chitnis
- Section on Neural Developmental Dynamics, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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30
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Jeevakala S, Sreelakshmi C, Ram K, Rangasami R, Sivaprakasam M. Artificial intelligence in detection and segmentation of internal auditory canal and its nerves using deep learning techniques. Int J Comput Assist Radiol Surg 2020; 15:1859-1867. [PMID: 32964338 DOI: 10.1007/s11548-020-02237-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/14/2020] [Indexed: 11/29/2022]
Abstract
PURPOSE Artificial intelligence (AI) in medical imaging is a burgeoning topic that involves the interpretation of complex image structures. The recent advancements in deep learning techniques increase the computational powers to extract vital features without human intervention. The automatic detection and segmentation of subtle tissue such as the internal auditory canal (IAC) and its nerves is a challenging task, and it can be improved using deep learning techniques. METHODS The main scope of this research is to present an automatic method to detect and segment the IAC and its nerves like the facial nerve, cochlear nerve, inferior vestibular nerve, and superior vestibular nerve. To address this issue, we propose a Mask R-CNN approach driven with U-net to detect and segment the IAC and its nerves. The Mask R-CNN with its backbone network of the RESNET50 model learns a background-based localization policy to produce an actual bounding box of the IAC. Furthermore, the U-net segments the structure related information of IAC and its nerves by learning its features. RESULTS The proposed method was experimented on clinical datasets of 50 different patients including adults and children. The localization of IAC using Mask R-CNN was evaluated using Intersection of Union (IoU), and segmentation of IAC and its nerves was evaluated using Dice similarity coefficient. CONCLUSIONS The localization result shows that mean IoU of RESNET50, RESNET101 are 0.79 and 0.74, respectively. The Dice similarity coefficient of IAC and its nerves using region growing, PSO and U-net method scored 92%, 94%, and 96%, respectively. The result shows that the proposed method outperform better in localization and segmentation of IAC and its nerves. Thus, AI aids the radiologists in making the right decisions as the localization and segmentation of IAC is accurate.
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Affiliation(s)
- S Jeevakala
- Healthcare Technology Innovation Centre, Indian Institute of Technology Madras, Chennai, India.
| | - C Sreelakshmi
- Healthcare Technology Innovation Centre, Indian Institute of Technology Madras, Chennai, India
| | - Keerthi Ram
- Healthcare Technology Innovation Centre, Indian Institute of Technology Madras, Chennai, India
| | | | - Mohanasankar Sivaprakasam
- Healthcare Technology Innovation Centre, Indian Institute of Technology Madras, Chennai, India.,Indian Institute of Technology Madras, Chennai, India
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Mascheroni L, Scherer KM, Manton JD, Ward E, Dibben O, Kaminski CF. Combining sample expansion and light sheet microscopy for the volumetric imaging of virus-infected cells with super-resolution. BIOMEDICAL OPTICS EXPRESS 2020; 11:5032-5044. [PMID: 33014598 PMCID: PMC7510880 DOI: 10.1364/boe.399404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 05/25/2023]
Abstract
Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution owing to their physical magnification, which is achieved through water-absorbing polymers. The technique uses readily available chemicals and does not require sophisticated equipment, thus offering super-resolution to laboratories that are not microscopy-specialised. Here we present a protocol combining sample expansion with light sheet microscopy to generate high-contrast, high-resolution 3D reconstructions of whole virus-infected cells. The results are superior to those achievable with comparable imaging modalities and reveal details of the infection cycle that are not discernible before expansion. An image resolution of approximately 95 nm could be achieved in samples labelled in 3 colours. We resolve that the viral nucleoprotein is accumulated at the membrane of vesicular structures within the cell cytoplasm and how these vesicles are positioned relative to cellular structures. We provide detailed guidance and a video protocol for the optimal application of the method and demonstrate its potential to study virus-host cell interactions.
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Affiliation(s)
- Luca Mascheroni
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- These authors contributed equally
| | - Katharina M Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- These authors contributed equally
| | | | - Edward Ward
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Oliver Dibben
- Flu-MSAT, Biopharmaceutical Development, R&D, AstraZeneca, Liverpool, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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32
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Le Cann S, Tudisco E, Tägil M, Hall SA, Isaksson H. Bone Damage Evolution Around Integrated Metal Screws Using X-Ray Tomography - in situ Pullout and Digital Volume Correlation. Front Bioeng Biotechnol 2020; 8:934. [PMID: 32850760 PMCID: PMC7419699 DOI: 10.3389/fbioe.2020.00934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022] Open
Abstract
Better understanding of the local deformation of the bone network around metallic implants subjected to loading is of importance to assess the mechanical resistance of the bone-implant interface and limit implant failure. In this study, four titanium screws were osseointegrated into rat tibiae for 4 weeks and screw pullout was conducted in situ under x-ray microtomography, recording macroscopic mechanical behavior and full tomographies at multiple load steps before failure. Images were analyzed using Digital Volume Correlation (DVC) to access internal displacement and deformation fields during loading. A repeatable failure pattern was observed, where a ∼300–500 μm-thick envelope of bone detached from the trabecular structure. Fracture initiated close to the screw tip and propagated along the implant surface, at a distance of around 500 μm. Thus, the fracture pattern appeared to be influenced by the microstructure of the bone formed closely around the threads, which confirmed that the model is relevant for evaluating the effect of pharmacological treatments affecting local bone formation. Moreover, cracks at the tibial plateau were identified by DVC analysis of the tomographic images acquired during loading. Moderate strains were first distributed in the trabecular bone, which localized into higher strains regions with subsequent loading, revealing crack-formation not evident in the tomographic images. The in situ loading methodology followed by DVC is shown to be a powerful tool to study internal deformation and fracture behavior of the newly formed bone close to an implant when subjected to loading. A better understanding of the interface failure may help improve the outcome of surgical implants.
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Affiliation(s)
- Sophie Le Cann
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Erika Tudisco
- Division of Geotechnical Engineering, Lund University, Lund, Sweden
| | - Magnus Tägil
- Department of Orthopaedics, Clinical Sciences, Lund University, Lund, Sweden
| | - Stephen A Hall
- Division of Solid Mechanics, Lund University, Lund, Sweden.,Lund Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, Lund, Sweden.,Department of Orthopaedics, Clinical Sciences, Lund University, Lund, Sweden
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Low-Cost PVD Shadow Masks with Submillimeter Resolution from Laser-Cut Paper. MICROMACHINES 2020; 11:mi11070676. [PMID: 32664500 PMCID: PMC7407583 DOI: 10.3390/mi11070676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/29/2022]
Abstract
We characterize an affordable method of producing stencils for submillimeter physical vapor deposition (PVD) by using paper and a benchtop laser cutter. Patterning electrodes or similar features on top of organic or biological substrates is generally not possible using standard photolithography. Shadow masks, traditionally made of silicon-based membranes, circumvent the need for aggressive solvents but suffer from high costs. Here, we evaluate shadow masks fabricated by CO2 laser processing from quantitative filter papers. Such papers are stiff and dimensionally stable, resilient in handling, and cut without melting or redeposition. Using two exemplary interdigitated electrode designs, we quantify the line resolution achievable with both high-quality and standard lenses, as well as the positional accuracy across multiple length scales. Additionally, we assess the gap between such laser-cut paper masks and a substrate, and quantify feature reproduction onto polycarbonate membranes. We find that ~100 µm line widths are achievable independent of lens type and that average positional accuracy is better than ±100 µm at 4”-wafer scale. Although this falls well short of the micron-size features achievable with typical shadow masks, resolution in the tenths to tens of millimeters is entirely sufficient for applications from contact pads to electrochemical cells, allowing new functionalities on fragile materials.
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Dias A, Lozovska A, Wymeersch FJ, Nóvoa A, Binagui-Casas A, Sobral D, Martins GG, Wilson V, Mallo M. A Tgfbr1/Snai1-dependent developmental module at the core of vertebrate axial elongation. eLife 2020; 9:56615. [PMID: 32597756 PMCID: PMC7324159 DOI: 10.7554/elife.56615] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022] Open
Abstract
Formation of the vertebrate postcranial body axis follows two sequential but distinct phases. The first phase generates pre-sacral structures (the so-called primary body) through the activity of the primitive streak on axial progenitors within the epiblast. The embryo then switches to generate the secondary body (post-sacral structures), which depends on axial progenitors in the tail bud. Here we show that the mammalian tail bud is generated through an independent functional developmental module, concurrent but functionally different from that generating the primary body. This module is triggered by convergent Tgfbr1 and Snai1 activities that promote an incomplete epithelial to mesenchymal transition on a subset of epiblast axial progenitors. This EMT is functionally different from that coordinated by the primitive streak, as it does not lead to mesodermal differentiation but brings axial progenitors into a transitory state, keeping their progenitor activity to drive further axial body extension.
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Affiliation(s)
- André Dias
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Filip J Wymeersch
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Ana Nóvoa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Anahi Binagui-Casas
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Gabriel G Martins
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Valerie Wilson
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Moises Mallo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Kunz PJ, Barthel L, Meyer V, King R. Vesicle transport and growth dynamics in Aspergillus niger: Microscale modeling of secretory vesicle flow and centerline extraction from confocal fluorescent data. Biotechnol Bioeng 2020; 117:2875-2886. [PMID: 32510171 DOI: 10.1002/bit.27452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 12/15/2022]
Abstract
In this paper, we present a mathematical model to describe filamentous fungal growth based on intracellular secretory vesicles (SVs), which transport cell wall components to the hyphal tip. Vesicular transport inside elongating hyphae is modeled as an advection-diffusion-reaction equation with a moving boundary, transformed into fixed coordinates, and discretized using a high-order weighted essentially nonoscillatory discretization scheme. The model describes the production and the consumption of SVs with kinetic functions. Simulations are subsequently compared against distributions of SVs visualized by enhanced green fluorescent protein in young Aspergillus niger hyphae after germination. Intensity profile data are obtained using an algorithm scripted in ImageJ that extracts mean intensity distributions from 3D time-lapse confocal measurement data. Simulated length growth is in good agreement with the experimental data. Our simulations further show that a decrease of effective vesicle transport velocity towards the tip can explain the observed tip accumulation of SVs.
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Affiliation(s)
- Philipp J Kunz
- Chair of Measurement and Control, Technische Universität Berlin, Berlin, Germany
| | - Lars Barthel
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, Germany
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Technische Universität Berlin, Berlin, Germany
| | - Rudibert King
- Chair of Measurement and Control, Technische Universität Berlin, Berlin, Germany
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36
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Sogabe M, Ohzeki M, Fujimoto K, Sehara-Fujisawa A, Nishimura S. Restored interlaced volumetric imaging increases image quality and scanning speed during intravital imaging in living mice. JOURNAL OF BIOPHOTONICS 2020; 13:e201960204. [PMID: 32078253 DOI: 10.1002/jbio.201960204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/07/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Dynamic intravital imaging is essential for revealing ongoing biological phenomena within living organisms and is influenced primarily by several factors: motion artifacts, optical properties and spatial resolution. Conventional imaging quality within a volume, however, is degraded by involuntary movements and trades off between the imaged volume, imaging speed and quality. To balance such trade-offs incurred by two-photon excitation microscopy during intravital imaging, we developed a unique combination of interlaced scanning and a simple image restoration algorithm based on biological signal sparsity and a graph Laplacian matrix. This method increases the scanning speed by a factor of four for a field size of 212 μm × 106 μm × 130 μm, and significantly improves the quality of four-dimensional dynamic volumetric data by preventing irregular artifacts due to the movement observed with conventional methods. Our data suggest this method is robust enough to be applied to multiple types of soft tissue.
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Affiliation(s)
- Maina Sogabe
- Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masayuki Ohzeki
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Koji Fujimoto
- Graduate School of Medicine, Human Brain Research Center, Kyoto University, Kyoto, Japan
| | - Atsuko Sehara-Fujisawa
- Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Satoshi Nishimura
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
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37
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Susaki EA, Shimizu C, Kuno A, Tainaka K, Li X, Nishi K, Morishima K, Ono H, Ode KL, Saeki Y, Miyamichi K, Isa K, Yokoyama C, Kitaura H, Ikemura M, Ushiku T, Shimizu Y, Saito T, Saido TC, Fukayama M, Onoe H, Touhara K, Isa T, Kakita A, Shibayama M, Ueda HR. Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat Commun 2020; 11:1982. [PMID: 32341345 PMCID: PMC7184626 DOI: 10.1038/s41467-020-15906-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Whole-organ/body three-dimensional (3D) staining and imaging have been enduring challenges in histology. By dissecting the complex physicochemical environment of the staining system, we developed a highly optimized 3D staining imaging pipeline based on CUBIC. Based on our precise characterization of biological tissues as an electrolyte gel, we experimentally evaluated broad 3D staining conditions by using an artificial tissue-mimicking material. The combination of optimized conditions allows a bottom-up design of a superior 3D staining protocol that can uniformly label whole adult mouse brains, an adult marmoset brain hemisphere, an ~1 cm3 tissue block of a postmortem adult human cerebellum, and an entire infant marmoset body with dozens of antibodies and cell-impermeant nuclear stains. The whole-organ 3D images collected by light-sheet microscopy are used for computational analyses and whole-organ comparison analysis between species. This pipeline, named CUBIC-HistoVIsion, thus offers advanced opportunities for organ- and organism-scale histological analysis of multicellular systems.
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Affiliation(s)
- Etsuo A Susaki
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-5241, Japan.
| | - Chika Shimizu
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-5241, Japan
| | - Akihiro Kuno
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, 951-8585, Japan
| | - Xiang Li
- Neutron Science Laboratory, The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Kengo Nishi
- Neutron Science Laboratory, The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Ken Morishima
- Neutron Science Laboratory, The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Hiroaki Ono
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-5241, Japan
| | - Yuki Saeki
- Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazunari Miyamichi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- ERATO Touhara Chemosensory Signal Project, Japan Science and Technology Agency, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kaoru Isa
- Department of Neuroscience, Graduate School of Medicine and Faculty of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Chihiro Yokoyama
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hiroki Kitaura
- Department of Pathology, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, 951-8585, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8601, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hirotaka Onoe
- Human Brain Research Center, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- ERATO Touhara Chemosensory Signal Project, Japan Science and Technology Agency, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tadashi Isa
- Department of Neuroscience, Graduate School of Medicine and Faculty of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8501, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata, 951-8585, Japan
| | - Mitsuhiro Shibayama
- Neutron Science Laboratory, The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka, 565-5241, Japan.
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Mateus R, Holtzer L, Seum C, Hadjivasiliou Z, Dubois M, Jülicher F, Gonzalez-Gaitan M. BMP Signaling Gradient Scaling in the Zebrafish Pectoral Fin. Cell Rep 2020; 30:4292-4302.e7. [PMID: 32209485 PMCID: PMC7109522 DOI: 10.1016/j.celrep.2020.03.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 02/07/2020] [Accepted: 03/09/2020] [Indexed: 01/25/2023] Open
Abstract
Secreted growth factors can act as morphogens that form spatial concentration gradients in developing organs, thereby controlling growth and patterning. For some morphogens, adaptation of the gradients to tissue size allows morphological patterns to remain proportioned as the organs grow. In the zebrafish pectoral fin, we found that BMP signaling forms a two-dimensional gradient. The length of the gradient scales with tissue length and its amplitude increases with fin size according to a power-law. Gradient scaling and amplitude power-laws are signatures of growth control by time derivatives of morphogenetic signaling: cell division correlates with the fold change over time of the cellular signaling levels. We show that Smoc1 regulates BMP gradient scaling and growth in the fin. Smoc1 scales the gradient by means of a feedback loop: Smoc1 is a BMP agonist and BMP signaling represses Smoc1 expression. Our work uncovers a layer of morphogen regulation during vertebrate appendage development.
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Affiliation(s)
- Rita Mateus
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Laurent Holtzer
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Carole Seum
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Zena Hadjivasiliou
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Marine Dubois
- Department of Biochemistry, Faculty of Sciences, University of Geneva, Switzerland
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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Neumann JO, Campos B, Younes B, Jakobs M, Unterberg A, Kiening K, Hubert A. Evaluation of three automatic brain vessel segmentation methods for stereotactical trajectory planning. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019; 182:105037. [PMID: 31445207 DOI: 10.1016/j.cmpb.2019.105037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Stereotactical procedures require exact trajectory planning to avoid blood vessels in the trajectory path. Innovation in imaging and image recognition techniques have facilitated the automatic detection of blood vessels during the planning process and may improve patient safety in the future. To assess the feasibility of a vessel detection and warning system using currently available imaging and vessel segmentation techniques. METHODS Image data were acquired from post-contrast, isovolumetric T1-weighted sequences (T1CE) and time.-of-flight MR angiography at 3T or 7T from a total of nine subjects. Vessel segmentation by a combination of a vessel-enhancement filter with subsequent level-set segmentation was evaluated using three different methods (Vesselness, FastMarching and LevelSet) in 45 stereotactic trajectories. Segmentation results were compared to a gold-standard of manual segmentation performed jointly by two human experts. RESULTS The LevelSet method performed best with a mean interclass correlation coefficient (ICC) of 0.76 [0.73, 0.81] compared to the FastMarching method with ICC 0.70 [0.67, 0.73] respectively. The Vesselness algorithm achieved clearly inferior overall performance with a mean ICC of 0.56 [0.53, 0.59]. The differences in mean ICC between all segmentation methods were statistically significant (p < 0.001 with post-hoc p < 0.026). The LevelSet method performed likewise good in MPRAGE and 3T-TOF images and excellent in 7T-TOF image data. The negative predictive value (NPV) was very high (>97%) for all methods and modalities. Positive predictive values (PPV) were found in the overall range of 65-90% likewise depending on algorithm and modality. This pattern reflects the disposition of all segmentation methods - in case of misclassification - to produce preferentially false-positive than false-negative results. In a clinical setting, two to three potential collision warnings would be given per trajectory on average with a PPV of around 50%. CONCLUSIONS It is feasible to integrate a clinically meaningful vessel detection and collision warning system into stereotactical planning software. Both, T1CE and MRA sequences are suitable as image data for such an application.
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Affiliation(s)
- Jan-Oliver Neumann
- Division Stereotactical and Functional Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Germany.
| | - Benito Campos
- Department of Neurosurgery, University Hospital Heidelberg, Germany
| | - Bilal Younes
- Department of Neurosurgery, University Hospital Heidelberg, Germany
| | - Martin Jakobs
- Division Stereotactical and Functional Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Germany
| | | | - Karl Kiening
- Division Stereotactical and Functional Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Germany
| | - Alexander Hubert
- Department of Neuroradiology, University Hospital Heidelberg, Germany
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40
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Microstructure anisotropy of La0.6Sr0.4Co0.2Fe0.8O3- film on rigid Gd0.1Ce0.9O1.95 substrate during constrained sintering. Ann Ital Chir 2019. [DOI: 10.1016/j.jeurceramsoc.2019.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Moraes T, Amorim P, Da Silva JV, Pedrini H. Medical image interpolation based on 3D Lanczos filtering. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING: IMAGING & VISUALIZATION 2019. [DOI: 10.1080/21681163.2019.1683469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Thiago Moraes
- Division of 3D Technologies, Center for Information Technology Renato Archer, Campinas, Brazil
| | - Paulo Amorim
- Division of 3D Technologies, Center for Information Technology Renato Archer, Campinas, Brazil
| | - Jorge Vicente Da Silva
- Division of 3D Technologies, Center for Information Technology Renato Archer, Campinas, Brazil
| | - Helio Pedrini
- Institute of Computing, University of Campinas, Campinas, Brazil
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42
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Sotiriou V, Rolfe RA, Murphy P, Nowlan NC. Effects of Abnormal Muscle Forces on Prenatal Joint Morphogenesis in Mice. J Orthop Res 2019; 37:2287-2296. [PMID: 31297860 DOI: 10.1002/jor.24415] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/02/2019] [Indexed: 02/04/2023]
Abstract
Fetal movements are essential for normal development of the human skeleton. When fetal movements are reduced or restricted, infants are at higher risk of developmental dysplasia of the hip and arthrogryposis (multiple joint contractures). Joint shape abnormalities have been reported in mouse models with abnormal or absent musculature, but the effects on joint shape in such models have not been quantified or characterized in detail. In this study, embryonic mouse forelimbs and hindlimbs at a single developmental stage (Theiler Stage 23) with normal, reduced, or absent muscle were imaged in three-dimensions. Skeletal rudiments were virtually segmented and rigid image registration was used to reliably align rudiments with each other, enabling repeatable assessment and measurement of joint shape differences between normal, reduced-muscle and absent-muscle groups. We demonstrate qualitatively and quantitatively that joint shapes are differentially affected by a lack of, or reduction in, skeletal muscle, with the elbow joint being the most affected of the major limb joints. Surprisingly, the effects of reduced muscle were often more pronounced than those of absent skeletal muscle, indicating a complex relationship between muscle mass and joint morphogenesis. These findings have relevance for human developmental disorders of the skeleton in which abnormal fetal movements are implicated, particularly developmental dysplasia of the hip and arthrogryposis. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2287-2296, 2019.
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Affiliation(s)
- Vivien Sotiriou
- Department of Bioengineering, Imperial College London, London, SW6 7NA, UK
| | - Rebecca A Rolfe
- Department of Bioengineering, Imperial College London, London, SW6 7NA, UK.,Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Paula Murphy
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Niamh C Nowlan
- Department of Bioengineering, Imperial College London, London, SW6 7NA, UK
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Amson E, Kilbourne BM. Trabecular bone architecture in the stylopod epiphyses of mustelids (Mammalia, Carnivora). ROYAL SOCIETY OPEN SCIENCE 2019; 6:190938. [PMID: 31824706 PMCID: PMC6837213 DOI: 10.1098/rsos.190938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/20/2019] [Indexed: 05/04/2023]
Abstract
Mustelidae, a carnivoran clade that includes for instance weasels, badgers, otters and martens, has undergone several evolutionary transitions of lifestyle, resulting in specializations for fossorial, natatorial and scansorial locomotion, in addition to more generalized species. The family is therefore regarded as offering an adequate framework for morpho-functional analyses. However, the architecture of the epiphyseal trabecular bone, which is argued to be particularly responsive to the biomechanical environment, has never been studied. Here, we quantify trabecular bone parameters of the proximal and distal epiphyses of the humerus and femur in 29 species of mustelids and assess the differences of these parameters among groups defined a priori based on the aforementioned locomotor types. The parameters are assessed in a phylogenetic framework, taking into account the potential effect on an individual's body mass. The range of variation described by the acquired parameters is relatively restricted when compared to that of other clades. Generalists, however, are featuring a wider range of variation than the other types. While clear discrimination of locomotor types is difficult, some differences were highlighted by our analysis, such as a greater bone fraction associated with the natatorial taxa, which we discuss in a functional context.
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Affiliation(s)
- E. Amson
- Author for correspondence: E. Amson e-mail:
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Benton MA, Frey N, Nunes da Fonseca R, von Levetzow C, Stappert D, Hakeemi MS, Conrads KH, Pechmann M, Panfilio KA, Lynch JA, Roth S. Fog signaling has diverse roles in epithelial morphogenesis in insects. eLife 2019; 8:47346. [PMID: 31573513 PMCID: PMC6794076 DOI: 10.7554/elife.47346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The Drosophila Fog pathway represents one of the best-understood signaling cascades controlling epithelial morphogenesis. During gastrulation, Fog induces apical cell constrictions that drive the invagination of mesoderm and posterior gut primordia. The cellular mechanisms underlying primordia internalization vary greatly among insects and recent work has suggested that Fog signaling is specific to the fast mode of gastrulation found in some flies. On the contrary, here we show in the beetle Tribolium, whose development is broadly representative for insects, that Fog has multiple morphogenetic functions. It modulates mesoderm internalization and controls a massive posterior infolding involved in gut and extraembryonic development. In addition, Fog signaling affects blastoderm cellularization, primordial germ cell positioning, and cuboidal-to-squamous cell shape transitions in the extraembryonic serosa. Comparative analyses with two other distantly related insect species reveals that Fog's role during cellularization is widely conserved and therefore might represent the ancestral function of the pathway.
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Affiliation(s)
- Matthew Alan Benton
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Nadine Frey
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | | | - Cornelia von Levetzow
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Dominik Stappert
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Muhammad Salim Hakeemi
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Kai H Conrads
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Matthias Pechmann
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
| | - Kristen A Panfilio
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany.,School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois, Chicago, United States
| | - Siegfried Roth
- Institute for Zoology/Developmental Biology, Biocenter, University of Cologne, Köln, Germany
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Oravec D, Flynn MJ, Zauel R, Rao S, Yeni YN. Digital tomosynthesis based digital volume correlation: A clinically viable noninvasive method for direct measurement of intravertebral displacements using images of the human spine under physiological load. Med Phys 2019; 46:4553-4562. [PMID: 31381174 DOI: 10.1002/mp.13750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/17/2019] [Accepted: 07/26/2019] [Indexed: 01/23/2023] Open
Abstract
PURPOSE We have developed a clinically viable method for measurement of direct, patient-specific intravertebral displacements using a novel digital tomosynthesis based digital volume correlation technique. These displacements may be used to calculate vertebral stiffness under loads induced by a patient's body weight; this is particularly significant because, among biomechanical variables, stiffness is the strongest correlate of bone strength. In this proof of concept study, we assessed the feasibility of the method through a preliminary evaluation of the accuracy and precision of the method, identification of a range of physiological load levels for which displacements are measurable, assessment of the relationship of measured displacements with microcomputed tomography based standards, and demonstration of the in vivo application of the technique. METHODS Five cadaveric T11 vertebrae were allocated to three groups in order to study (a) the optimization of digital volume correlation algorithm input parameters, (b) accuracy and precision of the method and the ability to measure displacements at a range of physiological load levels, and (c) the correlation between displacements measured using tomosynthesis based digital volume correlation vs. high resolution microcomputed tomography based digital volume correlation and large scale finite element models. Tomosynthesis images of one patient (Female, 60 yr old) were used to calculate displacement maps, and in turn stiffness, using images acquired in both standing and standing-with-weight (8 kg) configurations. RESULTS We found that displacements were accurate (2.28 µm total error) and measurable at physiological load levels (above 267 N) with a linear response to applied load. Calculated stiffness among three tested vertebral bodies was within an acceptable range relative to reported values for vertebral stiffness (5651-13260 N/mm). Displacements were in good qualitative and quantitative agreement with both microcomputed tomography based finite element (r2 = 0.762, P < 0.001) and digital volume correlation (r2 = 0.799, P < 0.001) solutions. For one patient tested twice, once standing and once holding weights, results demonstrated excellent qualitative reproducibility of displacement distributions with superior endplate displacements increasing by 22% with added weight. CONCLUSIONS The results of this work collectively suggest the feasibility of the method for in vivo measurement of intravertebral displacements and stiffness in humans. These findings suggest that digital volume correlation using digital tomosynthesis imaging may be useful in understanding the mechanical response of bone to disease and may further enhance our ability to assess fracture risk and treatment efficacy for the spine.
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Affiliation(s)
- Daniel Oravec
- Bone and Joint Center, Henry Ford Hospital, Detroit, MI, USA
| | - Michael J Flynn
- Department of Radiology, Henry Ford Hospital, Detroit, MI, USA
| | - Roger Zauel
- Bone and Joint Center, Henry Ford Hospital, Detroit, MI, USA
| | - Sudhaker Rao
- Department of Endocrinology, Henry Ford Hospital, Detroit, MI, USA
| | - Yener N Yeni
- Bone and Joint Center, Henry Ford Hospital, Detroit, MI, USA
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Fertin A, Laforgue L, Duperray A, Laurent VM, Usson Y, Verdier C. Displacement fields using correlation methods as a tool to investigate cell migration in 3D collagen gels. J Microsc 2019; 275:172-182. [PMID: 31301069 DOI: 10.1111/jmi.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/11/2019] [Indexed: 01/22/2023]
Abstract
Living cells embedded in a complex extra-cellular matrix migrate in a sophisticated way thanks to adhesions to matrix fibres and contractility. It is important to know what kind of forces are exerted by the cells. Here, we use reflectance confocal microscopy to locate fibres accurately and determine displacement fields. Correlation techniques are used to this aim, coupled with proper digital image processing. Benchmark tests validate the method in the case of shear and stretching motions. Finally, the method is tested successfully for studying cancer cells migrating in collagen gels of different concentration.
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Affiliation(s)
- Arnold Fertin
- CNRS, TIMC-IMAG, University Grenoble Alpes, Grenoble, France
| | - Laure Laforgue
- Institute for Advanced Biosciences, INSERM U 1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.,CNRS, LIPhy, University Grenoble Alpes, Grenoble, France
| | - Alain Duperray
- Institute for Advanced Biosciences, INSERM U 1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | | | - Yves Usson
- CNRS, TIMC-IMAG, University Grenoble Alpes, Grenoble, France
| | - Claude Verdier
- CNRS, LIPhy, University Grenoble Alpes, Grenoble, France
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Abstract
In this paper, a set of techniques used for downsampling and upsampling of 2D images is analyzed on various image datasets. The comparison takes into account a significant number of interpolation kernels, their parameters, and their algebraical form, focusing mostly on linear interpolation methods with symmetric kernels. The most suitable metrics for measuring the performance of upsampling and downsampling filters’ combinations are presented, discussing their strengths and weaknesses. A test benchmark is proposed, and the obtained results are analyzed with respect to the presented metrics, offering explanations about specific filter behaviors in general, or just in certain circumstances. In the end, a set of filters and parameters recommendations is offered based on extensive testing on carefully selected image datasets. The entire research is based on the study of a large set of research papers and on a solid discussion of the underlying signal processing theory.
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Kumar M, Kozorovitskiy Y. Tilt-invariant scanned oblique plane illumination microscopy for large-scale volumetric imaging. OPTICS LETTERS 2019; 44:1706-1709. [PMID: 30933127 PMCID: PMC7263705 DOI: 10.1364/ol.44.001706] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This Letter presents the first demonstration of multi-tile stitching for large scale 3D imaging in single objective light-sheet microscopy. We show undistorted 3D imaging spanning complete zebrafish larvae and over 1 mm3 volumes for thick mouse brain sections. We use remote galvo scanning for light-sheet creation and develop a processing pipeline for 3D tiling across different axes. With the improved one photon (1p) tilt-invariant scanned oblique plane illumination (SOPi, /sōpī/) microscope presented here, we demonstrate cellular resolution imaging at depths exceeding 330 μm in optically scattering mouse brain samples and dendritic imaging in more superficial layers.
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NIR-Fluorescent Multidye Silica Nanoparticles with Large Stokes Shifts for Versatile Biosensing Applications. J Fluoresc 2019; 29:293-305. [PMID: 30613851 DOI: 10.1007/s10895-018-02339-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/26/2018] [Indexed: 02/07/2023]
Abstract
We have synthesized and characterized of a series of single and multidye copolymerized nanoparticles with large to very large Stokes shifts (100 to 255 nm) for versatile applications as standalone or multiplexed probes in biological matrices. Nanoparticles were prepared via the Stöber method and covalently copolymerized with various combinations of three dyes, including one novel aminocyanine dye. Covalently encapsulated dyes exhibited no significant leakage from the nanoparticle matrix after more than 200 days of storage in ethanol. Across multiple batches of nanoparticles with varying dye content, the average yields and average radii were found to be highly reproducible. Furthermore, the batch to batch variability in the relative amounts of dye incorporated was small (relative standard deviations <2.3%). Quantum yields of dye copolymerized nanoparticles were increased 50% to 1000% relative to those of their respective dye-silane conjugates, and fluorescence intensities were enhanced by approximately three orders of magnitude. Prepared nanoparticles were surface modified with polyethylene glycol and biotin and bound to streptavidin microspheres as a proof of concept. Under single wavelength excitation, microsphere-bound nanoparticles displayed readily distinguishable fluorescence signals at three different emission wavelengths, indicating their potential applications to multicolor sensing. Furthermore, nanoparticles modified with polyethylene glycol and biotin demonstrated hematoprotective qualities and reduced nonspecific binding of serum proteins, indicating their potential suitability to in vivo imaging applications.
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Koneti S, Borges J, Roiban L, Rodrigues MS, Martin N, Epicier T, Vaz F, Steyer P. Electron Tomography of Plasmonic Au Nanoparticles Dispersed in a TiO 2 Dielectric Matrix. ACS APPLIED MATERIALS & INTERFACES 2018; 10:42882-42890. [PMID: 30457319 DOI: 10.1021/acsami.8b16436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plasmonic Au nanoparticles (AuNPs) embedded into a TiO2 dielectric matrix were analyzed by combining two-dimensional and three-dimensional electron microscopy techniques. The preparation method was reactive magnetron sputtering, followed by thermal annealing treatments at 400 and 600 °C. The goal was to assess the nanostructural characteristics and correlate them with the optical properties of the AuNPs, particularly the localized surface plasmon resonance (LSPR) behavior. High-angle annular dark field-scanning transmission electron microscopy results showed the presence of small-sized AuNPs (quantum size regime) in the as-deposited Au-TiO2 film, resulting in a negligible LSPR response. The in-vacuum thermal annealing at 400 °C induced the formation of intermediate-sized nanoparticles (NPs), in the range of 10-40 nm, which led to the appearance of a well-defined LSPR band, positioned at 636 nm. Electron tomography revealed that most of the NPs are small-sized and are embedded into the TiO2 matrix, whereas the larger NPs are located at the surface. Annealing at 600 °C promotes a bimodal size distribution with intermediate-sized NPs embedded in the matrix and big-sized NPs, up to 100 nm, appearing at the surface. The latter are responsible for a broadening and a redshift, to 645 nm, in the LSPR band because of increase of scattering-to-absorption ratio. Beyond differentiating and quantifying the surface and embedded NPs, electron tomography also provided the identification of "hot-spots". The presence of NPs at the surface, individual or in dimers, permits adsorption sites for LSPR sensing and for surface-enhanced spectroscopies, such as surface-enhanced Raman scattering.
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Affiliation(s)
- Siddardha Koneti
- Université Lyon, INSA-Lyon, MATEIS UMR CNRS 5510 , 21 Avenue Jean Capelle , 69621 Villeurbanne Cedex , France
| | - Joel Borges
- Centro de Física , Universidade do Minho , Campus de Gualtar , 4710 057 Braga , Portugal
| | - Lucian Roiban
- Université Lyon, INSA-Lyon, MATEIS UMR CNRS 5510 , 21 Avenue Jean Capelle , 69621 Villeurbanne Cedex , France
| | - Marco S Rodrigues
- Centro de Física , Universidade do Minho , Campus de Gualtar , 4710 057 Braga , Portugal
| | - Nicolas Martin
- Institut FEMTO-ST, UMR 6174 CNRS, Université Bourgogne Franche-Comté , 15B, Avenue des Montboucons , 25030 Besançon Cedex , France
| | - Thierry Epicier
- Université Lyon, INSA-Lyon, MATEIS UMR CNRS 5510 , 21 Avenue Jean Capelle , 69621 Villeurbanne Cedex , France
| | - Filipe Vaz
- Centro de Física , Universidade do Minho , Campus de Gualtar , 4710 057 Braga , Portugal
| | - Philippe Steyer
- Université Lyon, INSA-Lyon, MATEIS UMR CNRS 5510 , 21 Avenue Jean Capelle , 69621 Villeurbanne Cedex , France
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