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Mareš J, Karjalainen J, Håkansson P, Michaeli S, Liimatainen T. Glucose exchange parameters in a subset of physiological conditions. Phys Chem Chem Phys 2023; 25:22965-22978. [PMID: 37593950 PMCID: PMC10467565 DOI: 10.1039/d3cp01973j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023]
Abstract
The chemical exchange of labile protons of the hydroxyl groups can be exploited in a variety of magnetic resonance experiments to gain information about the groups and their physicochemical environment. The exchangeable -OH protons provide important contributions to the T2 of water signals thus contributing to the T2-weighted contrast of MRI images. This exchange can be exploited more specifically and sensitively in chemical exchange saturation transfer (CEST) or longitudinal rotating frame relaxation (T1,ρ) experiments. Since glucose is omnipresent in living organisms, it may be seen as a rather universal probe. Even though the potential was first recognized many years ago, practical use has remained scarce due to numerous challenges. The major limitation is the rather low glucose concentration in most tissues. The other obstacles are related to multiple dependencies of the exchange parameters, such as temperature, pH, and concentration of various ions that are not known in sufficient detail for glucose. Thus, we embarked on evaluating the exchange parameters of a model that included every relevant chemical site for all -OH protons in both dominant enantiomers of glucose. We have (1) obtained conventional one-dimensional proton NMR spectra of glucose solutions in suitable temperature ranges, (2) we have iterated through several exchange models with various degrees of freedom determined by the number of distinguishable -OH proton sites and compared their performance, (3) we extrapolated the parameters of the best model of physiological temperature and (4) we demonstrated the use of the parameters in virtual experiments. As the main results, (1) we have obtained the temperature dependence of exchange parameters with reliable confidence intervals in three different pH values, with two of them reaching physiological temperature, and (2) we show how the parameters can be used in virtual experiments, helping to develop new applications for glucose as an NMR/MRI probe.
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Affiliation(s)
- J Mareš
- NMR Research Unit, Faculty of Science, University of Oulu, P.O. Box 3000, FIN-90014, Finland.
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Finland
| | - J Karjalainen
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Finland
| | - P Håkansson
- NMR Research Unit, Faculty of Science, University of Oulu, P.O. Box 3000, FIN-90014, Finland.
| | - S Michaeli
- Center for MR Research, Radiology Department, University of Minnesota, Minneapolis MN55455, USA
| | - T Liimatainen
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Finland
- Department of Radiology, Oulu University Hospital, Oulu, Finland
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Nazemorroaya A, Aghaeifar A, Shiozawa T, Hirt B, Schulz H, Scheffler K, Hagberg GE. Developing formalin-based fixative agents for post mortem brain MRI at 9.4 T. Magn Reson Med 2021; 87:2481-2494. [PMID: 34931721 DOI: 10.1002/mrm.29122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/07/2022]
Abstract
PURPOSE To develop fixative agents for high-field MRI with suitable dielectric properties and measure MR properties in immersion-fixed brain tissue. METHODS Dielectric properties of formalin-based agents were assessed (100 MHz-4.5 GHz), and four candidate fixatives with/without polyvinylpyrrolidone (PVP) and different salt concentrations were formulated. B1 field and MR properties (T1 , R 2 ∗ , R2 , R 2 ' , and magnetic susceptibility [QSM]) were observed in white and gray matter of pig brain samples during 0.5-35 days of immersion fixation. The kinetics were fitted using exponential functions. The immersion time required to reach maximum R 2 ∗ values at different tissue depths was used to estimate the Medawar coefficient for fixative penetration. The effect of replacing the fixatives with Fluoroinert and phosphate-buffered saline as embedding media was also evaluated. RESULTS The dielectric properties of formalin were nonlinearly modified by increasing amounts of additives. With 5% PVP and 0.04% NaCl, the dielectric properties and B1 field reflected in vivo conditions. The highest B1 values were found in white matter with PVP and varied significantly with tissue depth and embedding media, but not with immersion time. The MR properties depended on PVP yielding lower T1 , higher R 2 ∗ , more paramagnetic QSM values, and a lower Medawar coefficient (0.9 mm / h ; without PVP: 1.5). Regardless of fixative, switching to phosphate-buffered saline as embedder caused a paramagnetic shift in QSM and decreased R 2 ∗ that progressed during 1 month of storage, whereas no differences were found with Fluorinert. CONCLUSION In vivo-like B1 fields can be achieved in formalin fixatives using PVP and a low salt concentration, yielding lower T1 , higher R 2 ∗ , and more paramagnetic QSM than without additives. The kinetics of R 2 ∗ allowed estimation of fixative tissue penetration.
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Affiliation(s)
- Azadeh Nazemorroaya
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Ali Aghaeifar
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Thomas Shiozawa
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Bernhard Hirt
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Hildegard Schulz
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Klaus Scheffler
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Institute of Biomedical Magnetic Resonance, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Gisela E Hagberg
- High-Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.,Institute of Biomedical Magnetic Resonance, Eberhard Karl's University of Tübingen, Tübingen, Germany
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van Schadewijk R, Krug JR, Shen D, Sankar Gupta KBS, Vergeldt FJ, Bisseling T, Webb AG, Van As H, Velders AH, de Groot HJM, Alia A. Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla. Sci Rep 2020; 10:971. [PMID: 31969628 PMCID: PMC6976659 DOI: 10.1038/s41598-020-57861-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Interactions between plants and the soil’s microbial & fungal flora are crucial for the health of soil ecosystems and food production. Microbe-plant interactions are difficult to investigate in situ due to their intertwined relationship involving morphology and metabolism. Here, we describe an approach to overcome this challenge by elucidating morphology and the metabolic profile of Medicago truncatula root nodules using Magnetic Resonance (MR) Microscopy, at the highest magnetic field strength (22.3 T) currently available for imaging. A home-built solenoid RF coil with an inner diameter of 1.5 mm was used to study individual root nodules. A 3D imaging sequence with an isotropic resolution of (7 μm)3 was able to resolve individual cells, and distinguish between cells infected with rhizobia and uninfected cells. Furthermore, we studied the metabolic profile of cells in different sections of the root nodule using localised MR spectroscopy and showed that several metabolites, including betaine, asparagine/aspartate and choline, have different concentrations across nodule zones. The metabolite spatial distribution was visualised using chemical shift imaging. Finally, we describe the technical challenges and outlook towards future in vivo MR microscopy of nodules and the plant root system.
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Affiliation(s)
- Remco van Schadewijk
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Julia R Krug
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Defeng Shen
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Karthick B S Sankar Gupta
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Frank J Vergeldt
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Andrew G Webb
- C.J. Gorter Center for High Field MRI, Radiology department, Leiden University Medical Centre, Leiden University, Leiden, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Henk Van As
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Aldrik H Velders
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Huub J M de Groot
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - A Alia
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands. .,Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16/18, Leipzig, 04107, Germany.
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Vučković I, Nayfeh T, Mishra PK, Periyanan S, Sussman CR, Kline TL, Macura S. Influence of water based embedding media composition on the relaxation properties of fixed tissue. Magn Reson Imaging 2019; 67:7-17. [PMID: 31821849 DOI: 10.1016/j.mri.2019.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/30/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND In MRI of formalin-fixed tissue one of the problems is the dependence of tissue relaxation properties on formalin composition and composition of embedding medium (EM) used for scanning. In this study, we investigated molecular mechanisms by which the EM composition affects T2 relaxation directly and T1 relaxation indirectly. OBJECTIVE To identify principal components of formaldehyde based EM and the mechanism by which they affect relaxation properties of fixed tissue. METHODS We recorded high resolution 1H NMR spectra of common formalin fixatives at temperatures in the range of 5 °C to 45 °C. We also measured T1 and T2 relaxation times of various organs of formalin fixed (FF) zebrafish at 7 T at 21 °C and 31 °C in several EM with and without fixative or gadolinium contrast agents. RESULTS We showed that the major source of T2 variability is chemical exchange between protons from EM hydroxyls and water, mediated by the presence of phosphate ions. The exchange rate increases with temperature, formaldehyde concentration in EM and phosphate concentration in EM. Depending on which side of the coalescence the system resides, the temperature increase can lead to either shortening or prolongation of T2, or to no noticeable change at all when very close to the coalescence. Chemical exchange can be minimized by washing out from EM the fixative, the phosphate or both. CONCLUSION The dependence of T2 in fixed tissue on the fixative origin and composition described in prior literature could be attributed to the phosphate buffer accelerated chemical exchange among the fixative hydroxyls and the tissue water. More consistent results in the relaxation measurements could be obtained by stricter control of the fixative composition or by scanning fixed tissue in PBS without fixative.
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Affiliation(s)
- Ivan Vučković
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tarek Nayfeh
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Prasanna K Mishra
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Caroline R Sussman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Timothy L Kline
- Department of Radiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Slobodan Macura
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
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Kline TL, Sussman CR, Irazabal MV, Mishra PK, Pearson EA, Torres VE, Macura SI. Three-dimensional NMR microscopy of zebrafish specimens. NMR IN BIOMEDICINE 2019; 32:e4031. [PMID: 30431194 PMCID: PMC6537090 DOI: 10.1002/nbm.4031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
While zebrafish embryos in the first five days after fertilization are clear and amenable to optical analysis, older juveniles and adults are not, due to pigmentation development and tissue growth. Thus other imaging methods are needed to image adult specimens. NMR is a versatile tool for studies of biological systems and has been successfully used for in vivo zebrafish microscopy. In this work we use NMR microscopy (MRM) for assessment of zebrafish specimens, which includes imaging of formalin fixed (FF), formalin fixed and paraffin embedded (FFPE), fresh (unfixed), and FF gadolinium doped specimens. To delineate the size and shape of various organs we concentrated on 3D MRM. We have shown that at 7 T a 3D NMR image can be obtained with isotropic resolution of 50 μm/pxl within 10 min and 25 μm/pxl within 4 h. Also, we have analyzed sources of contrast and have found that in FF specimens the best contrast is obtained by T1 weighting (3D FLASH, 3D FISP), whereas in FFPE specimens T2 weighting (3D RARE) is the best. We highlight an approach to perform segmentation of the organs in order to study morphological changes associated with mutations. The broader implication of this work is development of NMR methodology for high contrast and high resolution serial imaging and automated analysis of morphology of various zebrafish mutants.
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Affiliation(s)
| | - Caroline R Sussman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Maria V Irazabal
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | | | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
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Kose K. Magnetic Resonance Microscopy of Chemically Fixed Human Embryos Performed in University of Tsukuba Since 1999 to 2015. Anat Rec (Hoboken) 2018; 301:987-997. [PMID: 29663733 DOI: 10.1002/ar.23787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/02/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022]
Abstract
Magnetic resonance (MR) microscopy of chemically fixed human embryos performed in University of Tsukuba since 1999 to 2015 was reviewed. More than 1,000 chemically fixed human embryos stored in the Congenital Anomaly Research Center of Kyoto University were used throughout the MR microscopy project, which was divided into three terms. In the first term (1999-2005), 3D MR images of 1,204 embryo specimens were acquired with 128 × 128 × 256 voxels by a super-parallel MR microscope using a 2.35 T horizontal-bore superconducting magnet. In the second term (2005-2006), 3D MR images of seven embryo specimens were acquired with 256 × 256 × 512 voxels by an MR microscope using a 9.4 T vertical wide-bore superconducting magnet. In the third term (2013-2015), 3D MR images of a Carnegie Stage (CS) 21 specimen were acquired with 512 × 512 × 1024 voxels by an MR microscope using a 4.7 T vertical wide-bore superconducting magnet and nuclear magnetic resonance parameters of a CS23 specimen were measured with 128 × 128 × 256-256 × 256 × 512 voxels by an MR microscope using a 9.4 T vertical narrow-bore superconducting magnet. Based on the results obtained in this project, the author has proposed the future MR microscopy project in which a number of embryo specimens will be imaged with 256 × 256 × 512-512 × 512 × 1024 voxels using a newly designed super-parallel MR microscope. Anat Rec, 301:987-997, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Katsumi Kose
- Institute of Applied Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 3058573, Japan
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Affiliation(s)
- Mari Ojakivi
- Institute of Chemistry; University of Tartu; Ravila 14a Tartu 50411 Estonia
| | - Jaanus Liigand
- Institute of Chemistry; University of Tartu; Ravila 14a Tartu 50411 Estonia
| | - Anneli Kruve
- Institute of Chemistry and Biochemistry; Free University of Berlin; Takustr. 3 14195 Berlin Germany
- Institute of Chemistry; University of Tartu; Ravila 14a Tartu 50411 Estonia
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Delcroix P, Pagliai M, Cardini G, Bégué D, Hanoune B. Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab Initio Molecular Dynamics Simulations and Quantum Chemistry Calculations. J Phys Chem A 2015; 119:9785-93. [PMID: 26352865 DOI: 10.1021/acs.jpca.5b06293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Di(oxymethylene)glycol forms in formaldehyde aqueous solutions by polymerization of methanediol. The structure and hydrogen bond interactions of di(oxymethylene)glycol with water were characterized by performing Car-Parrinello molecular dynamics simulations. The anharmonic vibrational frequencies of di(oxymethylene)glycol in solution were determined with ab initio calculations considering explicitly the hydrogen-bonded water molecules, while other interactions with solvent were described within a polarizable continuum model approach. The calculations allow for a detailed interpretation of the experimental Raman spectrum of formaldehyde aqueous solutions, leading to the assignment of the band at 920 cm(-1) to the symmetric CO stretching mode of di(oxymethylene)glycol.
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Affiliation(s)
- Pauline Delcroix
- Laboratoire de Physicochimie des Processus de Combustion et de l'Atmosphère, UMR 8522 CNRS/Université Lille 1 , F-59655 Villeneuve d'Ascq, France
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze , via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Gianni Cardini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze , via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Didier Bégué
- Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM), UMR 5254 CNRS-Equipe de Chimie Physique, Université de Pau et des Pays de l'Adour , 2 Avenue du Président Angot, 64053 Pau Cedex 9, France
| | - Benjamin Hanoune
- Laboratoire de Physicochimie des Processus de Combustion et de l'Atmosphère, UMR 8522 CNRS/Université Lille 1 , F-59655 Villeneuve d'Ascq, France
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Rivlin M, Eliav U, Navon G. NMR Studies of the Equilibria and Reaction Rates in Aqueous Solutions of Formaldehyde. J Phys Chem B 2015; 119:4479-87. [DOI: 10.1021/jp513020y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michal Rivlin
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Uzi Eliav
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Gil Navon
- School of Chemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
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Huang Y, Zhang Z, Chen H, Feng J, Cai S, Chen Z. A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples. Sci Rep 2015; 5:8390. [PMID: 25670027 PMCID: PMC4323641 DOI: 10.1038/srep08390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/19/2015] [Indexed: 01/01/2023] Open
Abstract
NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples, and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples.
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Affiliation(s)
- Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiyong Zhang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Hao Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Jianghua Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
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