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Khodadadi M, Helluy X, Güntürkün O, Behroozi M. Segmented spin-echo echo-planar imaging improves whole-brain BOLD functional MRI in awake pigeon brains. NMR Biomed 2024; 37:e5034. [PMID: 37681398 DOI: 10.1002/nbm.5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Functional magnetic resonance imaging (fMRI) in awake small animals such as pigeons or songbirds opens a new window into the neural fundaments of cognitive behavior. However, high-field fMRI in the avian brain is challenging due to strong local magnetic field inhomogeneities caused by air cavities in the skull. A spoiled gradient-echo fMRI sequence has already been used to map the auditory network in songbirds, but due to susceptibility artifacts only 50% of the whole brain could be recorded. Since whole-brain fMRI coverage is vital to reveal whole-brain networks, an MRI sequence that is less susceptible to these artifacts was required. This was recently achieved in various bird species by using a rapid acquisition with relaxation enhancement (RARE) sequence. Weak blood oxygen level-dependent (BOLD) sensitivity, low temporal resolution, and heat caused by the long train of RF refocusing pulses are the main limits of RARE fMRI at high magnetic fields. To go beyond some of these limitations, we here describe the implementation of a two-segmented spin-echo echo-planar imaging (SE-EPI). The proposed sequence covers the whole brain of awake pigeons. The sequence was applied to investigate the auditory network in awake pigeons and assessed the relative merits of this method in comparison with the single-shot RARE sequence. At the same imaging resolution but with a volume acquisition of 3 s versus 4 s for RARE, the two-segmented SE-EPI provided twice the strength of BOLD activity compared with the single-shot RARE sequence, while the image signal-to-noise ratio (SNR) and in particular the temporal SNR were very similar for the two sequences. In addition, the activation patterns in two-segmented SE-EPI data are more symmetric and larger than single-shot RARE results. Two-segmented SE-EPI represents a valid alternative to the RARE sequence in avian fMRI research since it yields more than twice the BOLD sensitivity per unit of time with much less energy deposition and better temporal resolution, particularly for event-related experiments.
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Affiliation(s)
- Mina Khodadadi
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Department of Basic Sciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Xavier Helluy
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Department of Neurophysiology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Onur Güntürkün
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
- Research Center One Health Ruhr, Research Alliance Ruhr, Ruhr University Bochum, Bochum, Germany
| | - Mehdi Behroozi
- Department of Biopsychology, Institute of Cognitive Neuroscience, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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Dang HN, Endres J, Weinmüller S, Glang F, Loktyushin A, Scheffler K, Doerfler A, Schmidt M, Maier A, Zaiss M. MR-zero meets RARE MRI: Joint optimization of refocusing flip angles and neural networks to minimize T 2 -induced blurring in spin echo sequences. Magn Reson Med 2023. [PMID: 37357374 DOI: 10.1002/mrm.29710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/28/2023] [Accepted: 05/01/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE An end-to-end differentiable 2D Bloch simulation is used to reduce T2 induced blurring in single-shot turbo spin echo sequences, also called rapid imaging with refocused echoes (RARE) sequences, by using a joint optimization of refocusing flip angles and a convolutional neural network. METHODS Simulation and optimization were performed in the MR-zero framework. Variable flip angle train and DenseNet parameters were optimized jointly using the instantaneous transverse magnetization, available in our simulation, at a certain echo time, which serves as ideal blurring-free target. Final optimized sequences were exported for in vivo measurements at a real system (3 T Siemens, PRISMA) using the Pulseq standard. RESULTS The optimized RARE was able to successfully lower T2 -induced blurring for single-shot RARE sequences in proton density-weighted and T2 -weighted images. In addition to an increased sharpness, the neural network allowed correction of the contrast changes to match the theoretical transversal magnetization. The optimization found flip angle design strategies similar to existing literature, however, visual inspection of the images and evaluation of the respective point spread function demonstrated an improved performance. CONCLUSIONS This work demonstrates that when variable flip angles and a convolutional neural network are optimized jointly in an end-to-end approach, sequences with more efficient minimization of T2 -induced blurring can be found. This allows faster single- or multi-shot RARE MRI with longer echo trains.
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Affiliation(s)
- Hoai Nam Dang
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jonathan Endres
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Simon Weinmüller
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Felix Glang
- Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
| | - Alexander Loktyushin
- Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
| | - Klaus Scheffler
- Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Arnd Doerfler
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Manuel Schmidt
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Andreas Maier
- Department of Computer Science, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Moritz Zaiss
- Institute of Neuroradiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Magnetic Resonance Center, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
- Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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Yetisir F, Poser BA, Grant PE, Adalsteinsson E, Wald LL, Guerin B. Parallel transmission 2D RARE imaging at 7T with transmit field inhomogeneity mitigation and local SAR control. Magn Reson Imaging 2022; 93:87-96. [PMID: 35940379 PMCID: PMC9789791 DOI: 10.1016/j.mri.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/15/2022] [Accepted: 08/02/2022] [Indexed: 12/26/2022]
Abstract
PURPOSE We develop and test a parallel transmit (pTx) pulse design framework to mitigate transmit field inhomogeneity with control of local specific absorption rate (SAR) in 2D rapid acquisition with relaxation enhancement (RARE) imaging at 7T. METHODS We design large flip angle RF pulses with explicit local SAR constraints by numerical simulation of the Bloch equations. Parallel computation and analytical expressions for the Jacobian and the Hessian matrices are employed to reduce pulse design time. The refocusing-excitation "spokes" pulse pairs are designed to satisfy the Carr-Purcell-Meiboom-Gill (CPMG) condition using a combined magnitude least squares-least squares approach. RESULTS In a simulated dataset, the proposed approach reduced peak local SAR by up to 56% for the same level of refocusing uniformity error and reduced refocusing uniformity error by up to 59% (from 32% to 7%) for the same level of peak local SAR compared to the circularly polarized birdcage mode of the pTx array. Using explicit local SAR constraints also reduced peak local SAR by up to 46% compared to an RF peak power constrained design. The excitation and refocusing uniformity error were reduced from 20%-33% to 4%-6% in single slice phantom experiments. Phantom experiments demonstrated good agreement between the simulated excitation and refocusing uniformity profiles and experimental image shading. CONCLUSION PTx-designed excitation and refocusing CPMG pulse pairs can mitigate transmit field inhomogeneity in the 2D RARE sequence. Moreover, local SAR can be decreased significantly using pTx, potentially leading to better slice coverage, enabling larger flip angles or faster imaging.
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Affiliation(s)
- Filiz Yetisir
- Fetal-Neonatal Neuroimaging & Developmental Science Center, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Benedikt A Poser
- Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - P Ellen Grant
- Fetal-Neonatal Neuroimaging & Developmental Science Center, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Radiology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Elfar Adalsteinsson
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 MA Avenue, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 MA Avenue, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 MA Avenue, Cambridge, MA 02139, USA
| | - Lawrence L Wald
- Department of Radiology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 MA Avenue, Cambridge, MA 02139, USA; Athinoula A. Martinos Center for Biomedical Imaging, MA General Hospital, 149 13th Street, Charlestown, MA 02129, USA
| | - Bastien Guerin
- Department of Radiology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Athinoula A. Martinos Center for Biomedical Imaging, MA General Hospital, 149 13th Street, Charlestown, MA 02129, USA
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Liu Y, Xiao H, Wang Q, Yan F, Wang H. Comparison of R1ρ Imaging between Rapid Acquisition with Relaxation Enhancement ( RARE) and Ultrashort TE (UTE) Sequence in the Assessment of Rat Liver Iron Overload at 11.7T. Curr Med Imaging 2022; 19:749-755. [PMID: 36017836 DOI: 10.2174/1573405618666220822155132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/19/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Since the most prominent effect of iron is increasing R2* and R2 relaxation rates, the iron-overload liver shows little signal with conventional T1ρ sequences like RARE. Whereas, with UTE MR imaging sequences, the signal can be detected from short T2/T2* relaxation components in tissues. This study aims to evaluate the difference in R1ρ profiles and compare the correlations between RARE-based and UTE-based sequences with LIC in the assessment of rat liver iron overload. METHODS Iron dextran (Sigma, 100 mg Fe/ml) was injected into thirty-five rats (25-100 mg/kg body weight), while the rats in the control group were injected with saline (n=5). The liver specimen was taken after one week. A portion of the largest hepatic lobe was extracted to quantify the LIC by inductively coupled plasma, and the remaining liver tissue was stored in 4% buffered paraformaldehyde for 24 h before MRI. Spin-lock preparation with RARE readout and 2D UTE readout pulses were developed to quantify R1ρ on a Bruker 11.7T MR system. RESULTS The mean R1ρ value of the rat liver with UTE-based R1ρ sequence was significantly higher compared to RARE-based R1ρ sequence (p<0.001). Spearman's correlation analysis (two-tailed) indicated that the R1ρ values were significantly correlated with LIC for both UTE-R1ρ and RARE-R1ρ sequences (r = 0.727, P < 0.001, and r = 0.712, P < 0.001, respectively). CONCLUSION The current study adds to evidence that there is a correlation between iron concentration and R1ρ. Moreover, UTE-based R1ρ sequence is more sensitive to the liver iron than the RARE-based R1ρ sequence. R1ρ might serve as a complementary imaging biomarker for liver iron overload quantification.
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Affiliation(s)
- Ying Liu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hong Xiao
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianfeng Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Fuhua Yan
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - He Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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Delgado PR, Kuehne A, Aravina M, Millward JM, Vázquez A, Starke L, Waiczies H, Pohlmann A, Niendorf T, Waiczies S. B 1 inhomogeneity correction of RARE MRI at low SNR: Quantitative in vivo 19 F MRI of mouse neuroinflammation with a cryogenically-cooled transceive surface radiofrequency probe. Magn Reson Med 2021; 87:1952-1970. [PMID: 34812528 DOI: 10.1002/mrm.29094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022]
Abstract
PURPOSE Low SNR in fluorine-19 (19 F) MRI benefits from cryogenically-cooled transceive surface RF probes (CRPs), but strong B1 inhomogeneities hinder quantification. Rapid acquisition with refocused echoes (RARE) is an SNR-efficient method for MRI of neuroinflammation with perfluorinated compounds but lacks an analytical signal intensity equation to retrospectively correct B1 inhomogeneity. Here, a workflow was proposed and validated to correct and quantify 19 F-MR signals from the inflamed mouse brain using a 19 F-CRP. METHODS In vivo 19 F-MR images were acquired in a neuroinflammation mouse model with a quadrature 19 F-CRP using an imaging setup including 3D-printed components to acquire co-localized anatomical and 19 F images. Model-based corrections were validated on a uniform 19 F phantom and in the neuroinflammatory model. Corrected 19 F-MR images were benchmarked against reference images and overlaid on in vivo 1 H-MR images. Computed concentration uncertainty maps using Monte Carlo simulations served as a measure of performance of the B1 corrections. RESULTS Our study reports on the first quantitative in vivo 19 F-MR images of an inflamed mouse brain using a 19 F-CRP, including in vivo T1 calculations for 19 F-nanoparticles during pathology and B1 corrections for 19 F-signal quantification. Model-based corrections markedly improved 19 F-signal quantification from errors > 50% to < 10% in a uniform phantom (p < 0.001). Concentration uncertainty maps ex vivo and in vivo yielded uncertainties that were generally < 25%. Monte Carlo simulations prescribed SNR ≥ 10.1 to reduce uncertainties < 10%, and SNR ≥ 4.25 to achieve uncertainties < 25%. CONCLUSION Our model-based correction method facilitated 19 F signal quantification in the inflamed mouse brain when using the SNR-boosting 19 F-CRP technology, paving the way for future low-SNR 19 F-MRI applications in vivo.
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Affiliation(s)
- Paula Ramos Delgado
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany.,Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Mariya Aravina
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany
| | - Jason M Millward
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany
| | | | - Ludger Starke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany
| | | | - Andreas Pohlmann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany
| | - Thoralf Niendorf
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany.,Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany.,MRI.TOOLS, Berlin, Germany
| | - Sonia Waiczies
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Ultrahigh Field Facility, Berlin, Germany
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Herrmann CJJ, Els A, Boehmert L, Periquito J, Eigentler TW, Millward JM, Waiczies S, Kuchling J, Paul F, Niendorf T. Simultaneous T 2 and T 2 ∗ mapping of multiple sclerosis lesions with radial RARE-EPI. Magn Reson Med 2021; 86:1383-1402. [PMID: 33951214 DOI: 10.1002/mrm.28811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/26/2022]
Abstract
PURPOSE The characteristic MRI features of multiple sclerosis (MS) lesions make it conceptually appealing to pursue parametric mapping techniques that support simultaneous generation of quantitative maps of 2 or more MR contrast mechanisms. We present a modular rapid acquisition with relaxation enhancement (RARE)-EPI hybrid that facilitates simultaneous T2 and T 2 ∗ mapping (2in1-RARE-EPI). METHODS In 2in1-RARE-EPI the first echoes in the echo train are acquired with a RARE module, later echoes are acquired with an EPI module. To define the fraction of echoes covered by the RARE and EPI module, an error analysis of T2 and T 2 ∗ was conducted with Monte Carlo simulations. Radial k-space (under)sampling was implemented for acceleration (R = 2). The feasibility of 2in1-RARE-EPI for simultaneous T2 and T 2 ∗ mapping was examined in a phantom study mimicking T2 and T 2 ∗ relaxation times of the brain. For validation, 2in1-RARE-EPI was benchmarked versus multi spin-echo (MSE) and multi gradient-echo (MGRE) techniques. The clinical applicability of 2in1-RARE-EPI was demonstrated in healthy subjects and MS patients. RESULTS There was a good agreement between T2 / T 2 ∗ values derived from 2in1-RARE-EPI and T2 / T 2 ∗ reference values obtained from MSE and MGRE in both phantoms and healthy subjects. In patients, MS lesions in T2 and T 2 ∗ maps deduced from 2in1-RARE-EPI could be just as clearly delineated as in reference maps calculated from MSE/MGRE. CONCLUSION This work demonstrates the feasibility of radially (under)sampled 2in1-RARE-EPI for simultaneous T2 and T 2 ∗ mapping in MS patients.
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Affiliation(s)
- Carl J J Herrmann
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Antje Els
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Laura Boehmert
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Joao Periquito
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Wilhelm Eigentler
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Chair of Medical Engineering, Technical University of Berlin, Berlin, Germany
| | - Jason M Millward
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sonia Waiczies
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Joseph Kuchling
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Berlin, Germany.,Department of Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Friedemann Paul
- Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine, Berlin, Germany.,NeuroCure Clinical Research Center, Charité-Universitätsmedizin, Berlin, Germany.,Department of Neurology, Charité-Universitätsmedizin, Berlin, Germany
| | - Thoralf Niendorf
- Berlin Ultrahigh Field Facility (B.U.F.F.), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Wang X, Udayakumar D, Xi Y, Rofsky NM, Pedrosa I, Madhuranthakam AJ. Single-shot RARE with Dixon: Application to robust abdominal imaging with uniform fat and water separation at 3T. Magn Reson Med 2021; 86:1463-1471. [PMID: 33929055 DOI: 10.1002/mrm.28816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/25/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE To develop a true single shot turbo spin echo (SShTSE) acquisition with Dixon for robust T2 -weighted abdominal imaging with uniform fat and water separation at 3T. METHODS The in-phase (IP) and out-of-phase (OP) echoes for Dixon processing were acquired in the same repetition time of a SShTSE using partial echoes. A phase-preserved bi-directional homodyne reconstruction was developed to compensate the partial echo and the partial phase encoding of SShTSE. With IRB approval, the SShTSE-Dixon was compared against standard SShTSE, without and with fat suppression using spectral adiabatic inversion recovery (SPAIR) in 5 healthy volunteers and 5 patients. The SNR and contrast ratio (CR) of spleen to liver were compared among different acquisitions. RESULTS The bi-directional homodyne reconstruction successfully minimized ringing artifacts because of partial acquisitions. SShTSE-Dixon achieved uniform fat suppression compared to SShTSE-SPAIR with fat suppression failures of 1/10 versus 10/10 in the axial plane and 0/5 versus 5/5 in the coronal plane, respectively. The SNRs of the liver (12.2 ± 4.9 vs. 11.7 ± 5.2; P = .76) and spleen (25.9 ± 11.6 vs. 23.7 ± 9.7; P = .14) were equivalent between fat-suppressed images (SShTSE-Dixon water-only and SShTSE-SPAIR). The SNRs of liver (14.4 ± 5.7 vs. 13.4 ± 5.0; P = .60) and spleen (26.5 ± 10.1 vs. 25.7 ± 8.5; P = .56) were equivalent between non-fat-suppressed images (SShTSE-Dixon IP and SShTSE). The CRs of spleen to liver were also similar between fat-suppressed images (2.6 ± 0.4 vs. 2.5 ± 0.5; P =.92) and non-fat-suppressed images (2.3 ± 0.6 vs. 2.2 ± 0.4; P =.84). CONCLUSION SShTSE-Dixon generates robust abdominal T2 -weighted images at 3T with and without uniform fat suppression, along with perfectly co-registered fat-only images in a single acquisition.
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Affiliation(s)
- Xinzeng Wang
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Global MR Application and Workflow, GE Healthcare, Houston, Texas, USA
| | - Durga Udayakumar
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Yin Xi
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Population and Data Sciences, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Neil M Rofsky
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ivan Pedrosa
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ananth J Madhuranthakam
- Department of Radiology, UT Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas, USA
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Feng CW, Burnet G, Spiller CM, Cheung FKM, Chawengsaksophak K, Koopman P, Bowles J. Identification of regulatory elements required for Stra8 expression in fetal ovarian germ cells of the mouse. Development 2021; 148:dev.194977. [PMID: 33574039 DOI: 10.1242/dev.194977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/04/2021] [Indexed: 12/14/2022]
Abstract
In mice, the entry of germ cells into meiosis crucially depends on the expression of stimulated by retinoic acid gene 8 (Stra8). Stra8 is expressed specifically in pre-meiotic germ cells of females and males, at fetal and postnatal stages, respectively, but the mechanistic details of its spatiotemporal regulation are yet to be defined. In particular, there has been considerable debate regarding whether retinoic acid is required, in vivo, to initiate Stra8 expression in the mouse fetal ovary. We show that the distinctive anterior-to-posterior pattern of Stra8 initiation, characteristic of germ cells in the fetal ovary, is faithfully recapitulated when 2.9 kb of the Stra8 promoter is used to drive eGFP expression. Using in vitro transfection assays of cutdown and mutant constructs, we identified two functional retinoic acid responsive elements (RAREs) within this 2.9 kb regulatory element. We also show that the transcription factor DMRT1 enhances Stra8 expression, but only in the presence of RA and the most proximal RARE. Finally, we used CRISPR/Cas9-mediated targeted mutation studies to demonstrate that both RAREs are required for optimal Stra8 expression levels in vivo.
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Affiliation(s)
- Chun-Wei Feng
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Guillaume Burnet
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cassy M Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fiona Ka Man Cheung
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kallayanee Chawengsaksophak
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i. Vídenská 1083, 4 14220 Prague, Czech Republic
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia .,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Villano D, Romdhane F, Irrera P, Consolino L, Anemone A, Zaiss M, Dastrù W, Longo DL. A fast multislice sequence for 3D MRI-CEST pH imaging. Magn Reson Med 2020; 85:1335-1349. [PMID: 33031591 PMCID: PMC7756816 DOI: 10.1002/mrm.28516] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/30/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Purpose Chemical exchange saturation transfer MRI can provide accurate pH images, but the slow scan time (due to long saturation periods and multiple offsets sampling) reduce both the volume coverage and spatial resolution capability, hence the possibility to interrogate the heterogeneity in tumors and organs. To overcome these limitations, we propose a fast multislice CEST‐MRI sequence with high pH accuracy and spatial resolution. Methods The sequence first uses a long saturation pulse to induce the steady‐state CEST contrast and a second short saturation pulse repeated after each image acquisition to compensate for signal losses based on an uneven irradiation scheme combined with a single‐shot rapid acquisition with refocusing echoes readout. Sequence sensitivity and accuracy in measuring pH was optimized by simulation and assessed by in vitro studies in pH‐varying phantoms. In vivo validation was performed in two applications by acquiring multislice pH images covering the whole tumors and kidneys after iopamidol injection. Results Simulated and in vivo data showed comparable contrast efficiency and pH responsiveness by reducing saturation time. The experimental data from a homogeneous, pH‐varying, iopamidol‐containing phantom show that the sequence produced a uniform CEST contrast across slices and accurate values across slices in less than 10 minutes. In vivo measurements allowed us to quantify the 3D pH gradients of tumors and kidneys, with pH ranges comparable with the literature. Conclusion The proposed fast multislice CEST‐MRI sequence allows volumetric acquisitions with good pH sensitivity, accuracy, and spatial resolution for several in vivo pH imaging applications.
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Affiliation(s)
- Daisy Villano
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Feriel Romdhane
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,National Engineering School of Tunis (ENIT), University al Manar, Tunis, Tunisia
| | - Pietro Irrera
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.,Institute of Biostructures and Bioimaging, University of Campania "Luigi Vanvitelli," Italian National Research Council, Napoli, Italy
| | - Lorena Consolino
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Annasofia Anemone
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Moritz Zaiss
- Department of Neuroradiology, Friedrich-Alexander Universität Erlangen-Nürnberg, University Hospital Erlangen, Erlangen, Germany
| | - Walter Dastrù
- Molecular Imaging Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Dario Livio Longo
- Institute of Biostructures and Bioimaging, Italian National Research Council, Torino, Italy
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10
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Kuang M, Wang L, Wang Y, Xie J. An Efficient Near-Field Localization Method of Coherently Distributed Strictly Non-circular Signals. Sensors (Basel) 2020; 20:E5176. [PMID: 32927901 DOI: 10.3390/s20185176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 11/22/2022]
Abstract
For the near-field localization of non-circular distributed signals with spacial probability density functions (PDF), a novel algorithm is proposed in this paper. The traditional algorithms dealing with the distributed source are only for the far-field sources, and they need two-dimensional (2D) search or omit the angular spread parameter. As a result, these algorithms are no longer inapplicable for near-filed localization. Hence the near-filed sources that obey a classical probability distribution are studied and the corresponding specific expressions are given, providing merits for the near-field signal localization. Additionally, non-circularity of the incident signal is taken into account in order to improve the estimation accuracy. For the steering vector of spatially distributed signals, we first give an approximate expression in a non-integral form, and it provides the possibility of separating the parameters to be estimated from the spatially discrete parameters of the signal. Next, based on the rank-reduced (RARE) algorithm, direction of arrival (DOA) and range can be obtained through two one-dimensional (1-D) searches separately, and thus the computational complexity of the proposed algorithm is reduced significantly, and improvements to estimation accuracy and identifiability are achieved, compared with other existing algorithms. Finally, the effectiveness of the algorithm is verified by simulation.
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11
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Delgado PR, Kuehne A, Periquito JS, Millward JM, Pohlmann A, Waiczies S, Niendorf T. B 1 inhomogeneity correction of RARE MRI with transceive surface radiofrequency probes. Magn Reson Med 2020; 84:2684-2701. [PMID: 32447779 DOI: 10.1002/mrm.28307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/27/2020] [Accepted: 04/13/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE The use of surface radiofrequency (RF) coils is common practice to boost sensitivity in (pre)clinical MRI. The number of transceive surface RF coils is rapidly growing due to the surge in cryogenically cooled RF technology and ultrahigh-field MRI. Consequently, there is an increasing need for effective correction of the excitation field ( B 1 + ) inhomogeneity inherent in these coils. Retrospective B1 correction permits quantitative MRI, but this usually requires a pulse sequence-specific analytical signal intensity (SI) equation. Such an equation is not available for fast spin-echo (Rapid Acquisition with Relaxation Enhancement, RARE) MRI. Here we present, test, and validate retrospective B1 correction methods for RARE. METHODS We implemented the commonly used sensitivity correction and developed an empirical model-based method and a hybrid combination of both. Tests and validations were performed with a cryogenically cooled RF probe and a single-loop RF coil. Accuracy of SI quantification and T1 contrast were evaluated after correction. RESULTS The three described correction methods achieved dramatic improvements in B1 homogeneity and significantly improved SI quantification and T1 contrast, with mean SI errors reduced from >40% to >10% following correction in all cases. Upon correction, images of phantoms and mouse heads demonstrated homogeneity comparable to that of images acquired with a volume resonator. This was quantified by SI profile, SI ratio (error < 10%), and percentage of integral uniformity (PIU > 80% in vivo and ex vivo compared to PIU > 87% with the reference RF coil). CONCLUSION This work demonstrates the efficacy of three B1 correction methods tailored for transceive surface RF probes and RARE MRI. The corrected images are suitable for quantification and show comparable results between the three methods, opening the way for T1 measurements and X-nuclei quantification using surface transceiver RF coils. This approach is applicable to other MR techniques for which no analytical SI exists.
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Affiliation(s)
- Paula Ramos Delgado
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - João S Periquito
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jason M Millward
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Andreas Pohlmann
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sonia Waiczies
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thoralf Niendorf
- Berlin Ultrahigh Field Facility (B.U.F.F), Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation between the Charité Medical Faculty and the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,MRI.TOOLS GmbH, Berlin, Germany
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12
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Spencer Noakes TL, Henkelman RM, Nieman BJ. Partitioning k-space for cylindrical three-dimensional rapid acquisition with relaxation enhancement imaging in the mouse brain. NMR Biomed 2017; 30:e3802. [PMID: 28902423 DOI: 10.1002/nbm.3802] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/04/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
Three-dimensional rapid acquisition with relaxation enhancement (RARE) scans require the assignment of each phase encode step in two dimensions to an echo in the echo train. Although this assignment is frequently made across the entire Cartesian grid, collection of only the central cylinder of k-space by eliminating the corners in each phase encode dimension reduces the scan time by ~22% with negligible impact on image quality. The recipe for the assignment of echoes to grid points for such an acquisition is less straightforward than for the simple full Cartesian acquisition case, and has important implications for image quality. We explored several methods of partitioning k-space-exploiting angular symmetry in one extreme or emulating a cropped Cartesian acquisition in the other-and acquired three-dimensional RARE magnetic resonance imaging (MRI) scans of the ex vivo mouse brain. We evaluated each partitioning method for sensitivity to artifacts and then further considered strategies to minimize these through averaging or interleaving of echoes and by empirical phase correction. All scans were collected 16 at a time with multiple-mouse MRI. Although all schemes considered could be used to generate images, the results indicate that the emulation of a standard Cartesian echo assignment, by partitioning preferentially along one dimension within the cylinder, is more robust to artifacts. Samples at the periphery of the bore showed larger phase deviations and higher sensitivity to artifacts, but images of good quality could still be obtained with an optimized acquisition protocol. A protocol for high-resolution (40 μm) ex vivo images using this approach is presented, and has been used routinely with a success rate of 99% in over 1000 images.
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Affiliation(s)
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Brian J Nieman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada
- Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
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13
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Hoinkiss DC, Porter DA. Prospective motion correction in 2D multishot MRI using EPI navigators and multislice-to-volume image registration. Magn Reson Med 2017; 78:2127-2135. [PMID: 28983957 DOI: 10.1002/mrm.26951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/06/2017] [Accepted: 09/09/2017] [Indexed: 11/05/2022]
Abstract
PURPOSE Prospective motion correction reduces artifacts in MRI by correcting for subject motion in real time, but techniques are limited for multishot 2-dimensional (2D) sequences. This study addresses this limitation by using 2D echo-planar imaging (EPI) slice navigator acquisitions together with a multislice-to-volume image registration. METHODS The 2D-EPI navigators were integrated into 2D imaging sequences to allow a rapid, real-time motion correction based on the registration of three navigator slices to a reference volume. A dedicated slice-iteration scheme was used to limit mutual spin-saturation effects between navigator and image data. The method was evaluated using T2 -weighted spin echo and multishot rapid acquisition with relaxation enhancement (RARE) sequences, and its motion-correction capabilities were compared with those of periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER). Validation was performed in vivo using a well-defined motion protocol. RESULTS Data acquired during subject motion showed residual motion parameters within ±0.5 mm and ±0.5°, and demonstrated a substantial improvement in image quality compared with uncorrected scans. In a comparison to PROPELLER, the proposed technique preserved a higher level of anatomical detail in the presence of subject motion. CONCLUSIONS EPI-navigator-based prospective motion correction using multislice-to-volume image registration can substantially reduce image artifacts, while minimizing spin-saturation effects. The method can be adapted for use in other 2D MRI sequences and promises to improve image quality in routine clinical examinations. Magn Reson Med 78:2127-2135, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
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14
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Huang L, Mikolajczyk G, Küstermann E, Wilhelm M, Odenbach S, Dreher W. Adapted MR velocimetry of slow liquid flow in porous media. J Magn Reson 2017; 276:103-112. [PMID: 28167399 DOI: 10.1016/j.jmr.2017.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
MR velocimetry of liquid flow in opaque porous filters may play an important role in better understanding the mechanisms of deep bed filtration. With this knowledge, the efficiency of separating the suspended solid particles from the vertically flowing liquid can be improved, and thus a wide range of industrial applications such as wastewater treatment and desalination can be optimized. However, MR velocimetry is challenging for such studies due to the low velocities, the severe B0 inhomogeneity in porous structures, and the demand for high spatial resolution and an appropriate total measurement time during which the particle deposition will change velocities only marginally. In this work, a modified RARE-based MR velocimetry method is proposed to address these issues for velocity mapping on a deep bed filtration cell. A dedicated RF coil with a high filling factor is constructed considering the limited space available for the vertical cell in a horizontal MR magnet. Several means are applied to optimize the phase contrast RARE MRI pulse sequence for accurately measuring the phase contrast in a long echo train, even in the case of a low B1 homogeneity. Two means are of particular importance. One uses data acquired with zero flow to correct the phase contrast offsets from gradient imperfections, and the other combines the phase contrast from signals of both odd and even echoes. Results obtained on a 7T preclinical MR scanner indicate that the low velocities in the heterogeneous system can be correctly quantified with high spatial resolution and an adequate total measurement time, enabling future studies on flow during the filtration process.
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Affiliation(s)
- Li Huang
- In-vivo-MR Group, Faculty 02 (Biology/ Chemistry), University of Bremen, 28359 Bremen, Germany.
| | - Gerd Mikolajczyk
- Chair of Magnetofluiddynamics, Measuring and Automation Technology, Institute of Fluid Mechanics, Technical University of Dresden, 01062 Dresden, Germany
| | - Ekkehard Küstermann
- In-vivo-MR Group, Faculty 02 (Biology/ Chemistry), University of Bremen, 28359 Bremen, Germany
| | - Michaela Wilhelm
- Advanced Ceramics Group, Faculty 04 (Production Engineering - Mechanical Engineering and Process Engineering), University of Bremen, 28359 Bremen, Germany
| | - Stefan Odenbach
- Chair of Magnetofluiddynamics, Measuring and Automation Technology, Institute of Fluid Mechanics, Technical University of Dresden, 01062 Dresden, Germany
| | - Wolfgang Dreher
- In-vivo-MR Group, Faculty 02 (Biology/ Chemistry), University of Bremen, 28359 Bremen, Germany
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15
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Lee D, Han S, Cho H. Optimization of sparse phase encodings for variable repetition-delay turbo-spin echo (TSE) T 1 measurements for preclinical applications. J Magn Reson 2017; 274:57-64. [PMID: 27886558 DOI: 10.1016/j.jmr.2016.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 06/06/2023]
Abstract
A variable repetition-delay (TR) spin echo sequence with repeated refocusing pulses, i.e., a variable TR turbo-spin echo (TSE), provides an attractive means of acquiring an accurate T1 map information that is free from gradient echo based artifacts such as magnetic field inhomogeneities particularly for ultra-high field (at 7T and above) preclinical applications. However, the applicability of multi-slice TSE sequences is often limited by signal distortion from T2 relaxation due to echo-train acquisitions for short T2 tissues, inter-slice cross talks and magnetization transfer (MT) from repetitive slice-selective 180° pulse, and extended scan times with multiple TR excitations. These TSE shortcomings are difficult to remedy for preclinical applications, where small sizes of target organs usually limit the slice-gap control with restricted parallel imaging capabilities. In this study, compressed-sensing-assisted turbo-spin echo (CS-TSE) acquisitions for variable TR T1 measurements at 7T preclinical scanner were implemented to reduce the echo-trains by sparse phase encodings. Following the sparse signal simulation and sampling scheme optimization, the measured T1 values from CS-TSE and TSE were compared for phantoms, ex vivo, and in vivo subjects. The phantom T1 values from CS-TSE and TSE were identical to those from the inversion recovery spin echo. For both ex vivo and in vivo multi-slice T1 mapping, the shortened echo-trains of CS-TSE relieved the T2 relaxation, reduced the inter-slice interferences of multi-slice acquisition, and made room for additional slice encodings while maintaining a shorter scan time than the conventional TSE at the expense of local image smoothness from CS regularizations.
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Affiliation(s)
- DongKyu Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Sohyun Han
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - HyungJoon Cho
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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16
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Kuczera S, Galvosas P. Advances and artefact suppression in RARE-velocimetry for flow with curved streamlines. J Magn Reson 2015; 259:135-145. [PMID: 26340434 DOI: 10.1016/j.jmr.2015.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/13/2015] [Accepted: 07/17/2015] [Indexed: 06/05/2023]
Abstract
Method and considerations are presented that allow for an improved quantitative velocity measurement of complex fluids under shear using a fast 2D PGSE-RARE technique. While this contribution is relevant for shear geometries with rotational symmetry in general, the focus here is set on cylindrical Couette cells, a device most commonly used for rheological NMR investigations. The curved nature of the flow within the shearing geometry creates challenges in accurately determining the flow profile, as conventional imaging gradients naturally operate on a Cartesian grid. In particular the appropriate slice thickness in the flow direction and the applied k-space trajectory are discussed. For the latter an MRI simulation program has been written that numerically solves the Bloch equations and allows for the investigation of out-of-pixel flow. Furthermore, we present ways of increasing the spatial resolution across the gap of cylindrical Couette cells while still providing 2D imaging capabilities under certain conditions, thus allowing for a more detailed quantification of flow profiles as necessary for the analysis of complex fluid flow.
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Affiliation(s)
- Stefan Kuczera
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Petrik Galvosas
- MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.
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17
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Walton JH, Ng KF, Anderson SE, Rutledge JC. MRI measurement of blood-brain barrier transport with a rapid acquisition refocused echo ( RARE) method. Biochem Biophys Res Commun 2015; 463:479-82. [PMID: 25998382 DOI: 10.1016/j.bbrc.2015.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/10/2015] [Indexed: 10/23/2022]
Abstract
Dynamic Contrast Enhanced (DCE) MRI is increasingly being used to assess changes in capillary permeability. Most quantitative techniques used to measure capillary permeability are based on the Fick equation that requires measurement of signal reflecting both plasma and tissue concentrations of the solute being tested. To date, most Magnetic Resonance Imaging (MRI) methods for acquiring appropriate data quickly rely on gradient recalled echo (GRE) type acquisitions, which work well in clinical low field settings. However, acquiring this type of data on high field small animal preclinical MRIs is problematic due to geometrical distortions from susceptibility mismatch. This problem can be exacerbated when using small animal models to measure blood brain barrier (BBB) permeability, where precise sampling from the superior sagittal sinus (SSS) is commonly used to determine the plasma concentration of the contrast agent. Here we present results demonstrating that a standard saturation recovery rapid acquisition refocused echo (RARE) method is capable of acquiring T1 maps with good spatial and temporal resolution for Patlak analysis (Patlak, 1983) to assess changes in BBB Gd-DTPA permeability following middle cerebral artery occlusion with reperfusion in the rat. This method limits known problems with magnetic susceptibility mismatch and may thus allow greater accuracy in BBB permeability measurement in small animals.
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Affiliation(s)
- Jeffrey H Walton
- NMR Facility and Biomedical Engineering Graduate Group, University of California, Davis, USA.
| | - Kit Fai Ng
- Division of Cardiovascular Medicine, University of California, Davis, USA
| | - Steven E Anderson
- Department of Physiology and Membrane Biology, University of California, Davis, USA
| | - John C Rutledge
- Division of Cardiovascular Medicine, University of California, Davis, USA
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18
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Neumann D, Breuer FA, Völker M, Brandt T, Griswold MA, Jakob PM, Blaimer M. Reducing contrast contamination in radial turbo-spin-echo acquisitions by combining a narrow-band KWIC filter with parallel imaging. Magn Reson Med 2014; 72:1680-6. [PMID: 24436227 PMCID: PMC4101079 DOI: 10.1002/mrm.25081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 11/08/2013] [Accepted: 11/24/2013] [Indexed: 11/06/2022]
Abstract
PURPOSE Cartesian turbo spin-echo (TSE) and radial TSE images are usually reconstructed by assembling data containing different contrast information into a single k-space. This approach results in mixed contrast contributions in the images, which may reduce their diagnostic value. The goal of this work is to improve the image contrast from radial TSE acquisitions by reducing the contribution of signals with undesired contrast information. METHODS Radial TSE acquisitions allow the reconstruction of multiple images with different T2 contrasts using the k-space weighted image contrast (KWIC) filter. In this work, the image contrast is improved by reducing the band-width of the KWIC filter. Data for the reconstruction of a single image are selected from within a small temporal range around the desired echo time. The resulting dataset is undersampled and, therefore, an iterative parallel imaging algorithm is applied to remove aliasing artifacts. RESULTS Radial TSE images of the human brain reconstructed with the proposed method show an improved contrast when compared with Cartesian TSE images or radial TSE images with conventional KWIC reconstructions. CONCLUSION The proposed method provides multi-contrast images from radial TSE data with contrasts similar to multi spin-echo images. Contaminations from unwanted contrast weightings are strongly reduced.
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Affiliation(s)
- Daniel Neumann
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
| | - Felix A. Breuer
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
| | - Michael Völker
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
| | - Tobias Brandt
- Department of Radiation Oncology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Mark A. Griswold
- Department of Radiology, University Hospitals of Cleveland and Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Peter M. Jakob
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
- Department of Experimental Physics 5, University of Würzburg, Würzburg, Germany
| | - Martin Blaimer
- Research Center Magnetic Resonance Bavaria (MRB), Würzburg, Germany
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19
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Galiana G, Peters D, Tam L, Constable RT. Multiecho acquisition of O-space data. Magn Reson Med 2014; 72:1648-57. [PMID: 24459076 PMCID: PMC4108571 DOI: 10.1002/mrm.25085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 11/08/2022]
Abstract
PURPOSE Nonlinear gradient encoding methods, such as O-Space imaging, have been shown to provide good images from very few echoes. Acquiring data in a train of spin or gradient echoes is a very flexible way to further speed acquisition time. However, combining these strategies presents significant challenges, both in terms of the contrast and artifacts. We present strategies in both pulse sequence design and image processing to mitigate these effects. THEORY AND METHODS The three strategies include a new echo ordering that takes into account the unique way that O-Space samples the k-space of the image; a new postprocessing filter that allows tuning of T2-weighting by emphasizing the contribution of low frequency spatial information at selectable points in space and time; and an offset between linear and nonlinear gradients that makes the central point of each echo unique. RESULTS Simulations indicate that these strategies mitigate artifacts introduced by T2 (or T2*) decay and produce contrast that reflects relaxation at a given echo time. CONCLUSION Turbo spin echo O-Space is theoretically feasible, and the greater undersampling should make it possible to use shorter echo trains for a given scan time.
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Affiliation(s)
- Gigi Galiana
- Yale University, Department of Diagnostic Radiology, Biomedical Engineering, Neurosurgery, New Haven, Connecticut, USA
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20
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Abstract
Germ cells are unique in undergoing meiosis to generate oocytes and sperm. In mammals, meiosis onset is before birth in females, or at puberty in males, and recent studies have uncovered several regulatory steps involved in initiating meiosis in each sex. Evidence suggests that retinoic acid (RA) induces expression of the critical pre-meiosis gene Stra8 in germ cells of the fetal ovary, pubertal testis and adult testis. In the fetal testis, CYP26B1 degrades RA, while FGF9 further antagonises RA signalling to suppress meiosis. Failsafe mechanisms involving Nanos2 may further suppress meiosis in the fetal testis. Here, we draw together the growing knowledge relating to these meiotic control mechanisms, and present evidence that they are co-ordinately regulated and that additional factors remain to be identified. Understanding this regulatory network will illuminate not only how the foundations of mammalian reproduction are laid, but also how mis-regulation of these steps can result in infertility or germline tumours.
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Affiliation(s)
- Chun-Wei Feng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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21
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Li Y, Cheng CN, Verdun VA, Wingert RA. Zebrafish nephrogenesis is regulated by interactions between retinoic acid, mecom, and Notch signaling. Dev Biol 2013; 386:111-22. [PMID: 24309209 DOI: 10.1016/j.ydbio.2013.11.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 01/09/2023]
Abstract
The zebrafish pronephros provides a conserved model to study kidney development, in particular to delineate the poorly understood processes of how nephron segment pattern and cell type choice are established. Zebrafish nephrons are divided into distinct epithelial regions that include a series of proximal and distal tubule segments, which are comprised of intercalated transporting epithelial cells and multiciliated cells (MCC). Previous studies have shown that retinoic acid (RA) regionalizes the renal progenitor field into proximal and distal domains and that Notch signaling later represses MCC differentiation, but further understanding of these pathways has remained unknown. The transcription factor mecom (mds1/evi1 complex) is broadly expressed in renal progenitors, and then subsequently marks the distal tubule. Here, we show that mecom is necessary to form the distal tubule and to restrict both proximal tubule formation and MCC fate choice. We found that mecom and RA have opposing roles in patterning discrete proximal and distal segments. Further, we discovered that RA is required for MCC formation, and that one mechanism by which RA promotes MCC fate choice is to inhibit mecom. Next, we determined the epistatic relationship between mecom and Notch signaling, which limits MCC fate choice by lateral inhibition. Abrogation of Notch signaling with the γ-secretase inhibitor DAPT revealed that Notch and mecom did not have additive effects in blocking MCC formation, suggesting that they function in the same pathway. Ectopic expression of the Notch signaling effector, Notch intracellular domain (NICD), rescued the expansion of MCCs in mecom morphants, indicating that mecom acts upstream to induce Notch signaling. These findings suggest a model in which mecom and RA arbitrate proximodistal segment domains, while MCC fate is modulated by a complex interplay in which RA inhibition of mecom, and mecom promotion of Notch, titrates MCC number. Taken together, our studies have revealed several essential and novel mechanisms that control pronephros development in the zebrafish.
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Affiliation(s)
- Yue Li
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
| | - Christina N Cheng
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
| | - Valerie A Verdun
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
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Kanki K, Akechi Y, Ueda C, Tsuchiya H, Shimizu H, Ishijima N, Toriguchi K, Hatano E, Endo K, Hirooka Y, Shiota G. Biological and clinical implications of retinoic acid-responsive genes in human hepatocellular carcinoma cells. J Hepatol 2013; 59:1037-44. [PMID: 23831118 DOI: 10.1016/j.jhep.2013.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Accumulating data from epidemiological and experimental studies have suggested that retinoids, which are vitamin A derivatives, exert antitumor activity in various organs. We performed a gene screening based on in silico analysis of retinoic acid response elements (RAREs) to identify the genes facilitating the antitumor activity of retinoic acid (RA) and investigated their clinical significance in hepatocellular carcinoma (HCC). METHODS In silico analysis of RAREs was performed in the 5-kb upstream region of EST clusters. Chromatin immunoprecipitation analysis of the retinoic acid receptors and gene expression analysis were performed in HuH7, HepG2, and MCF7 cells treated with all-trans RA (ATRA). mRNA expression of RA-responsive genes was investigated using tumor and non-tumor tissues of clinical HCC samples from 171 patients. The association between gene expression and survival of patients was examined by Cox regression analysis. RESULTS We identified 201 candidate genes with promoter regions containing consensus RARE and finally selected 26 RA-responsive genes. Of these, downregulation of OTU domain-containing 7B (OTUD7B) gene, which was upregulated by ATRA, in tumor tissue was associated with a low cancer-specific survival of HCC patients. Functional analyses revealed that OTUD7B negatively regulates nuclear factor κB (NF-κB) signaling and decreases the survival of HCC cells. CONCLUSIONS We identified RA-responsive genes which are regulated by retinoid signal and found that low-OTUD7B mRNA expression is associated with a poor prognosis for HCC patients. OTUD7B-mediated inhibition of NF-κB signaling may be an effective target for antitumor therapy for HCC.
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Affiliation(s)
- Keita Kanki
- Division of Molecular and Genetic Medicine, Department of Genetic Medicine and Regenerative Therapeutics, Graduate School of Medicine, Tottori University, Yonago, Japan
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23
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Daviaud N, Garbayo E, Lautram N, Franconi F, Lemaire L, Perez-Pinzon M, Montero-Menei CN. Modeling nigrostriatal degeneration in organotypic cultures, a new ex vivo model of Parkinson's disease. Neuroscience 2013; 256:10-22. [PMID: 24161279 DOI: 10.1016/j.neuroscience.2013.10.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/30/2013] [Accepted: 10/10/2013] [Indexed: 12/24/2022]
Abstract
Parkinson's disease (PD) is the second most frequent neurodegenerative disorder afflicting 2% of the population older than 65 years worldwide. Recently, brain organotypic slices have been used to model neurodegenerative disorders, including PD. They conserve brain three-dimensional architecture, synaptic connectivity and its microenvironment. This model has allowed researchers a simple and rapid method to observe cellular interactions and mechanisms. In the present study, we developed an organotypic PD model from rat brains that includes all the areas involved in the nigrostriatal pathway in a single slice preparation, without using neurotoxins to induce the dopaminergic lesion. The mechanical transection of the nigrostriatal pathway obtained during slice preparation induced PD-like histopathology. Progressive nigrostriatal degeneration was monitored combining innovative approaches, such as diffusion tensor magnetic resonance imaging (DT-RMI) to follow fiber degeneration and mass spectrometry to quantify striatal dopamine content, together with bright-field and fluorescence microscopy imaging. A substantia nigra dopaminergic cell number decrease was observed by immunohistochemistry against rat tyrosine hydroxylase (TH) reaching 80% after 2 days in culture associated with a 30% decrease of striatal TH-positive fiber density, a 15% loss of striatal dopamine content quantified by mass spectrometry and a 70% reduction of nigrostriatal fiber fractional anisotropy quantified by DT-RMI. In addition, a significant decline of medium spiny neuron density was observed from days 7 to 16. These sagittal organotypic slices could be used to study the early stage of PD, namely dopaminergic degeneration, and the late stage of the pathology with dopaminergic and GABAergic neuron loss. This novel model might improve the understanding of PD and may represent a promising tool to refine the evaluation of new therapeutic approaches.
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Affiliation(s)
- N Daviaud
- LUNAM University, Angers University, France; INSERM UMR S_1066, Angers University, France
| | - E Garbayo
- LUNAM University, Angers University, France; INSERM UMR S_1066, Angers University, France; Pharmacy and Pharmaceutical Technology Department, University of Navarra, Pamplona, Spain
| | - N Lautram
- LUNAM University, Angers University, France; INSERM UMR S_1066, Angers University, France
| | - F Franconi
- CIFAB-PRIMEX, LUNAM University, Angers University, France
| | - L Lemaire
- LUNAM University, Angers University, France; INSERM UMR S_1066, Angers University, France
| | - M Perez-Pinzon
- University of Miami, Miller School of Medicine, Miami, FL, USA
| | - C N Montero-Menei
- LUNAM University, Angers University, France; INSERM UMR S_1066, Angers University, France.
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24
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Yasmeen R, Meyers JM, Alvarez CE, Thomas JL, Bonnegarde-Bernard A, Alder H, Papenfuss TL, Benson DM, Boyaka PN, Ziouzenkova O. Aldehyde dehydrogenase-1a1 induces oncogene suppressor genes in B cell populations. Biochim Biophys Acta 2013; 1833:3218-3227. [PMID: 24080087 DOI: 10.1016/j.bbamcr.2013.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 12/11/2022]
Abstract
The deregulation of B cell differentiation has been shown to contribute to autoimmune disorders, hematological cancers, and aging. We provide evidence that the retinoic acid-producing enzyme aldehyde dehydrogenase 1a1 (Aldh1a1) is an oncogene suppressor in specific splenic IgG1(+)/CD19(-) and IgG1(+)/CD19(+) B cell populations. Aldh1a1 regulated transcription factors during B cell differentiation in a sequential manner: 1) retinoic acid receptor alpha (Rara) in IgG1(+)/CD19(-) and 2) zinc finger protein Zfp423 and peroxisome proliferator-activated receptor gamma (Pparg) in IgG1(+)/CD19(+) splenocytes. In Aldh1a1(-/-) mice, splenic IgG1(+)/CD19(-) and IgG1(+)/CD19(+) B cells acquired expression of proto-oncogenic genes c-Fos, c-Jun, and Hoxa10 that resulted in splenomegaly. Human multiple myeloma B cell lines also lack Aldh1a1 expression; however, ectopic Aldh1a1 expression rescued Rara and Znf423 expressions in these cells. Our data highlight a mechanism by which an enzyme involved in vitamin A metabolism can improve B cell resistance to oncogenesis.
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Affiliation(s)
- R Yasmeen
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - J M Meyers
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - C E Alvarez
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - J L Thomas
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - A Bonnegarde-Bernard
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - H Alder
- Nucleic Acid Shared Resource, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - T L Papenfuss
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - D M Benson
- Division of Hematology, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - P N Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - O Ziouzenkova
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA.
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25
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Marcinkiewicz KM, Gudas LJ. Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells. Exp Cell Res 2013; 320:128-43. [PMID: 24076275 DOI: 10.1016/j.yexcr.2013.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/11/2013] [Accepted: 09/17/2013] [Indexed: 12/18/2022]
Abstract
To gain insight into oral squamous cell carcinogenesis, we performed deep sequencing (RNAseq) of non-tumorigenic human OKF6-TERT1R and tumorigenic SCC-9 cells. Numerous homeobox genes are differentially expressed between OKF6-TERT1R and SCC-9 cells. Data from Oncomine, a cancer microarray database, also show that homeobox (HOX) genes are dysregulated in oral SCC patients. The activity of Polycomb repressive complexes (PRC), which causes epigenetic modifications, and retinoic acid (RA) signaling can control HOX gene transcription. HOXB7, HOXC10, HOXC13, and HOXD8 transcripts are higher in SCC-9 than in OKF6-TERT1R cells; using ChIP (chromatin immunoprecipitation) we detected PRC2 protein SUZ12 and the epigenetic H3K27me3 mark on histone H3 at these genes in OKF6-TERT1R, but not in SCC-9 cells. In contrast, IRX1, IRX4, SIX2 and TSHZ3 transcripts are lower in SCC-9 than in OKF6-TERT1R cells. We detected SUZ12 and the H3K27me3 mark at these genes in SCC-9, but not in OKF6-TERT1R cells. SUZ12 depletion increased HOXB7, HOXC10, HOXC13, and HOXD8 transcript levels and decreased the proliferation of OKF6-TERT1R cells. Transcriptional responses to RA are attenuated in SCC-9 versus OKF6-TERT1R cells. SUZ12 and H3K27me3 levels were not altered by RA at these HOX genes in SCC-9 and OKF6-TERT1R cells. We conclude that altered activity of PRC2 is associated with dysregulation of homeobox gene expression in human SCC cells, and that this dysregulation potentially plays a role in the neoplastic transformation of oral keratinocytes.
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Affiliation(s)
- Katarzyna M Marcinkiewicz
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA; Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences of Cornell University, 1300 York Avenue, New York, NY 10065, USA
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26
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Hawkes HJ, Karlenius TC, Tonissen KF. Regulation of the human thioredoxin gene promoter and its key substrates: a study of functional and putative regulatory elements. Biochim Biophys Acta Gen Subj 2014; 1840:303-14. [PMID: 24041992 DOI: 10.1016/j.bbagen.2013.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 07/26/2013] [Accepted: 09/06/2013] [Indexed: 02/08/2023]
Abstract
BACKGROUND The thioredoxin system maintains redox balance through the action of thioredoxin and thioredoxin reductase. Thioredoxin regulates the activity of various substrates, including those that function to counteract cellular oxidative stress. These include the peroxiredoxins, methionine sulfoxide reductase A and specific transcription factors. Of particular relevance is Redox Factor-1, which in turn activates other redox-regulated transcription factors. SCOPE OF REVIEW Experimentally defined transcription factor binding sites in the human thioredoxin and thioredoxin reductase gene promoters together with promoters of the major thioredoxin system substrates involved in regulating cellular redox status are discussed. An in silico approach was used to identify potential putative binding sites for these transcription factors in all of these promoters. MAJOR CONCLUSIONS Our analysis reveals that many redox gene promoters contain the same transcription factor binding sites. Several of these transcription factors are in turn redox regulated. The ARE is present in several of these promoters and is bound by Nrf2 during various oxidative stress stimuli to upregulate gene expression. Other transcription factors also bind to these promoters during the same oxidative stress stimuli, with this redundancy supporting the importance of the antioxidant response. Putative transcription factor sites were identified in silico, which in combination with specific regulatory knowledge for that gene promoter may inform future experiments. GENERAL SIGNIFICANCE Redox proteins are involved in many cellular signalling pathways and aberrant expression can lead to disease or other pathological conditions. Therefore understanding how their expression is regulated is relevant for developing therapeutic agents that target these pathways.
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27
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Nicholls PK, Harrison CA, Rainczuk KE, Wayne Vogl A, Stanton PG. Retinoic acid promotes Sertoli cell differentiation and antagonises activin-induced proliferation. Mol Cell Endocrinol 2013; 377:33-43. [PMID: 23831638 DOI: 10.1016/j.mce.2013.06.034] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/25/2013] [Accepted: 06/26/2013] [Indexed: 12/12/2022]
Abstract
From puberty and throughout adult spermatogenesis, retinoid signalling is essential for germ cell differentiation and male fertility. The initiation of spermatogonial differentiation and germ cell meiosis occurs under the direction of local retinoid signalling in the testis, and corresponds with the final phase of somatic Sertoli cell differentiation at puberty. Here, we consider the cellular and molecular basis of retinoid actions upon Sertoli cell differentiation. Primary rat Sertoli cells were isolated during the pubertal proliferative and quiescent phases at postnatal days 10- and 20- respectively, and cultured with all-trans-retinoic acid. We show that retinoid signalling can potently suppress activin-induced proliferation by antagonising G1 phase progression and entry into the cell cycle. Retinoid signalling was also found to initiate tight junction formation in primary Sertoli cells, consistent with a pro-differentiative role. This study implicates retinoid signalling in the differentiation of both somatic and germ cells in the testis at puberty.
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Affiliation(s)
- Peter K Nicholls
- Prince Henry's Institute of Medical Research, Clayton, Victoria 3168, Australia
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28
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Ahn JH, Shin JE, Chung BY, Lee HM, Kang HH, Chung JW, Pak JH. Involvement of retinoic acid-induced peroxiredoxin 6 expression in recovery of noise-induced temporary hearing threshold shifts. Environ Toxicol Pharmacol 2013; 36:463-471. [PMID: 23792233 DOI: 10.1016/j.etap.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/23/2013] [Accepted: 05/27/2013] [Indexed: 06/02/2023]
Abstract
All-trans retinoic acid (ATRA) is reported to reduce hair cell loss and hearing deterioration caused by noise-induced hearing loss (NIHL). The present study investigates the involvement of peroxiredoxin 6 (Prdx 6) in ATRA-mediated protection of temporary threshold shift of hearing. Mice fed with ATRA before or after exposure to white noise showed a faster recovery than untreated controls within 1 week, with a concomitant increase of cochlear Prdx 6 expression. Treatment of mouse auditory cells with ATRA induced Prdx 6 expression. A putative retinoic acid (RA)-response element (RARE) was identified in a murine Prdx 6 promoter region. Prdx 6 promoter activities were elevated in wild-type reporter plasmid-transfected cells, whereas no significant change in activity was in those with RARE-disrupted mutant reporter. RA receptor α (RARα) functions as a transactivator of Prdx 6 gene expression. These findings suggest that ATRA-induced Prdx 6 expression may be associated with rapid recovery from temporary NIHL.
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MESH Headings
- Animals
- Auditory Fatigue/drug effects
- Binding Sites
- Cell Line
- Cochlea/drug effects
- Cochlea/metabolism
- Cochlea/physiopathology
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Hearing/drug effects
- Hearing Loss, Noise-Induced/etiology
- Hearing Loss, Noise-Induced/metabolism
- Hearing Loss, Noise-Induced/physiopathology
- Mice
- Mice, Inbred BALB C
- Mutation
- Peroxiredoxin VI/genetics
- Peroxiredoxin VI/metabolism
- Promoter Regions, Genetic
- Receptors, Retinoic Acid/agonists
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/metabolism
- Recovery of Function
- Response Elements
- Retinoic Acid Receptor alpha
- Signal Transduction
- Time Factors
- Transcriptional Activation
- Transfection
- Tretinoin/pharmacology
- Up-Regulation
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Affiliation(s)
- Joong Ho Ahn
- Department of Otolaryngology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea
| | - Jung-Eun Shin
- Department of Otolaryngology (Head and Neck Surgery), Konkuk University Hospital, Seoul 143-729, Republic of Korea
| | - Bom Yi Chung
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea
| | - Hye Mi Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea
| | - Hun Hee Kang
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea
| | - Jong Woo Chung
- Department of Otolaryngology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea.
| | - Jhang Ho Pak
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-736, Republic of Korea.
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Gudas LJ. Retinoids induce stem cell differentiation via epigenetic changes. Semin Cell Dev Biol 2013; 24:701-5. [PMID: 23973942 DOI: 10.1016/j.semcdb.2013.08.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/24/2013] [Accepted: 08/10/2013] [Indexed: 12/20/2022]
Abstract
Vitamin A (all-trans retinol) and its active metabolites, collectively called retinoids, exert potent effects on stem cell differentiation and thus, the formation of the entire organism, in part via the modulation of the epigenome. All-trans retinoic acid (RA), through binding to the retinoic acid receptors (RARs), alters interactions of the RARs with various protein components of the transcription complex at numerous genes in stem cells, and some of these protein components of the transcription complex then either place or remove epigenetic marks on histones or on DNA, altering chromatin structure and leading to an exit from the self-renewing, pluripotent stem cell state. Different epigenetic mechanisms, i.e. first, primarily H3K27me3 marks and then DNA methylation, may be employed by embryonic stem cells and other stem cells for control of early vs. late stages of cell differentiation. Creating these stable epigenetic changes requires the actions of many molecules, including tet1, polycomb protein complexes (PRCs), miRNAs, DNA methyltransferases (DNMTs), and telomerase reverse transcriptase. A more complete understanding of retinoid-dependent stem cell differentiation should reward us with new insights into the failure to maintain a differentiated state that is an essential part of neoplastic cell transformation and cancer.
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Affiliation(s)
- Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA; Department of Medicine, Weill Medical College of Cornell University, New York, NY 10065, USA.
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30
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Sarang Z, Garabuczi É, Joós G, Kiss B, Tóth K, Rühl R, Szondy Z. Macrophages engulfing apoptotic thymocytes produce retinoids to promote selection, differentiation, removal and replacement of double positive thymocytes. Immunobiology 2013; 218:1354-60. [PMID: 23932496 DOI: 10.1016/j.imbio.2013.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/04/2013] [Accepted: 06/17/2013] [Indexed: 11/30/2022]
Abstract
The thymus provides the microenvironment in which thymocytes develop into mature T-cells, and interactions with thymic stromal cells are thought to provide the necessary signals for thymocyte maturation. Recognition of self-MHC by T-cells is a basic requirement for mature T-cell functions, and those thymocytes that do not recognize or respond too strongly to the peptide-loaded self-MHC molecules found in the thymus undergo apoptosis. As a result, 95% of the thymocytes produced will die and be subsequently cleared by macrophages. This review describes a complex crosstalk between developing thymocytes and engulfing macrophages which is mediated by retinoids produced by engulfing macrophages. The interaction results in the harmonization of the rate of cell death of dying double positive cells with their clearance and replacement, and in promotion of the differentiation of the selected cells in the thymus.
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Affiliation(s)
- Zsolt Sarang
- Section of Dental Biochemistry, Department of Biochemistry and Molecular Biology, Research Center of Molecular Medicine, University of Debrecen, Nagyerdei krt. 98, 4012 Debrecen, Hungary
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31
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Pérez RJ, Benoit YD, Gudas LJ. Deletion of retinoic acid receptor β (RARβ) impairs pancreatic endocrine differentiation. Exp Cell Res 2013; 319:2196-204. [PMID: 23756134 DOI: 10.1016/j.yexcr.2013.05.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 12/20/2022]
Abstract
All-trans retinoic acid (RA) signals via binding to retinoic acid receptors (RARs α, β, and γ). RA directly influences expression of Pdx1, a transcription factor essential for pancreatic development and beta-cell (β-cell) maturation. In this study we follow the differentiation of cultured wild-type (WT) vs. RARβ knockout (KO) embryonic stem (ES) cells into pancreatic islet cells. We found that RARβ KO ES cells show greatly reduced expression of some important endocrine markers of differentiated islet cells, such as glucagon, islet amyloid polypeptide (Iapp), and insulin 1 (Ins1) relative to WT. We conclude that RARβ activity is essential for proper differentiation of ES cells to pancreatic endocrine cells.
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Affiliation(s)
- Ronald J Pérez
- Pharmacology Department, Weill Medical College of Cornell University, New York, NY 10065, USA
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32
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Abele TA, Lee SL, Twickler DM. MR imaging quantitative analysis of fetal Chiari II malformations and associated open neural tube defects: balanced SSFP versus half-Fourier RARE and interobserver reliability. J Magn Reson Imaging 2013; 38:786-93. [PMID: 23390087 DOI: 10.1002/jmri.24032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/12/2012] [Indexed: 11/10/2022] Open
Abstract
PURPOSE To evaluate bSSFP (balanced steady state free precession) and half-Fourier RARE (rapid acceleration with relaxation enhancement) MRI sequences in their ability to demonstrate fetal anatomic landmarks, quantify the degree of cerebellar herniation in Chiari II malformations and level and length of the associated open neural tube defects, as well as evaluate interobserver reliability of these measurements. MATERIALS AND METHODS Two independent observers retrospectively reviewed MRIs of 37 fetuses with Chiari II malformations and associated open neural tube defects (mean gestational age: 27 weeks 2 days). Comparison of bSSFP and RARE included: (i) Ability to confidently identify anatomic landmarks of the posterior fossa and spine; (ii) Measurements of the foramen magnum, cerebellar tonsillar herniation length, intervertebral disc space level of tonsillar herniation, open neural tube defect length, and disc space start and end level of the open neural tube defect; (iii) Observed conspicuity of anatomic landmarks. RESULTS There was no significant difference in assessment of cerebellar tonsillar herniation or open neural tube defect level between bSSFP and RARE for either observer. Intervertebral discs were more conspicuous on bSSFP while cerebellar tonsils were more conspicuous on RARE (P < 0.05). Interobserver reliability was strong for both sequences in assessing the foramen magnum (r = 0.95, 0.94), tonsillar herniation length (r = 0.93, 0.95), and open neural tube defect length (r = 0.97, 0.96). CONCLUSION Despite improved conspicuity of the intervertebral discs with bSSFP and cerebellar tonsils with RARE, there is no significant difference in measurement of hindbrain herniation or open neural tube defect level; interobserver reliability is excellent for both sequences.
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Affiliation(s)
- Travis A Abele
- Department of Radiology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA
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Castana O, Rempelos G, Anagiotos G, Fonia E, Kiskira O. Acute acalculous cholecystitis - a rare complication of burn injury. Ann Burns Fire Disasters 2009; 22:48-50. [PMID: 21991152 PMCID: PMC3188211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Indexed: 05/31/2023]
Abstract
The aim of this study is to draw attention to acute acalculous cholecystitis, a rare complication that may occur during the post-burn period (usually within 20-30 days). A 42-yr-old male patient, the victim of 35% TBSA high-voltage electrical burns that caused the amputation of both upper extremities by day 45 post-burn, was brought to our operating theatre suffering from acute acalculous cholecystitis. Mild epigastric pain followed by reflex nausea, vomiting, and pain that shifts to the upper quadrant and considerably increases during the post-burn period should make the therapist think of acalculous cholecystitis and react immediately with an urgent operation. Diagnosis of acute acalculous cholecystitis in a burn patient depends on recognizing a combination of signs and symptoms which are often attributed to other problems. Once diagnosed, the best choice of treatment for acalculous cholecystitis is cholecystectomy in an otherwise clinically stable patient.
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Affiliation(s)
- O Castana
- Department of Plastic and Reconstructive Surgery, Evangelismos General Hospital of Athens, Greece
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