Publications
See a list of publications below or visit the Photonics academic staff page and click on a particular member of staff to access their personal web page, which includes a list of their own publications.
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Journal articleHarput S, Christensen-Jeffries K, Ramalli A, et al., 2020,
3-D super-resolution ultrasound imaging with a 2-D sparse array
, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, Vol: 67, Pages: 269-277, ISSN: 0885-3010High-frame-rate 3-D ultrasound imaging technology combined with super-resolution processing method can visualize 3-D microvascular structures by overcoming the diffraction-limited resolution in every spatial direction. However, 3-D super-resolution ultrasound imaging using a full 2-D array requires a system with a large number of independent channels, the design of which might be impractical due to the high cost, complexity, and volume of data produced. In this study, a 2-D sparse array was designed and fabricated with 512 elements chosen from a density-tapered 2-D spiral layout. High-frame-rate volumetric imaging was performed using two synchronized ULA-OP 256 research scanners. Volumetric images were constructed by coherently compounding nine-angle plane waves acquired at a pulse repetition frequency of 4500 Hz. Localization-based 3-D super-resolution images of two touching subwavelength tubes were generated from 6000 volumes acquired in 12 s. Finally, this work demonstrates the feasibility of 3-D super-resolution imaging and super-resolved velocity mapping using a customized 2-D sparse array transducer.
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Journal articleKumar S, Patel AK, 2020,
Purification and Characterization of Prolyl Hydroxylase 3/Pyruvate Kinase Isoform 2 Protein Complex.
, Mol Biotechnol, Vol: 62, Pages: 111-118The prolyl hydroxylase 3 (PHD3) protein is less abundant in normal oxygen conditions (normoxia) but increases under deficient oxygen condition (hypoxia). Since cancerous cells often thrive in hypoxic conditions and predominantly express the Pyruvate kinase isoforms 2 (PKM2), the PHD3/PKM2 interaction might be particularly important in cancer development. In the present study, the PHD3/PKM2 complex was co-expressed and purified by size-exclusion chromatography. The interaction of PHD3 with PKM2 was confirmed in Native gel as well as western blot analysis. The PHD3/PKM2 complex formed discreet crystals under suitable conditions, and diffraction data revealed that crystal belonged to the P1 space group with 3.0 Å resolution. This is the first crystal report of PHD3/PKM2 complex as well as this study demonstrates a direct physical binding through protein-protein interaction. The structural analysis of complex will provide the information regarding the amino acid residues critical for the catalytic mechanism. Based on the structural information thus obtained, pharmacological interference with the PHD3/PKM2 interaction could be used as a novel strategy to reduce the cancer progression.
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Conference paperHong Y, Bottrill KRH, Taengnoi N, et al., 2020,
First investigation on double- And single-sideband formats in BDFA-enabled O-band transmission
We experimentally compare 50-Gb/s single- and double-sideband formats in an O-band BDFA-amplified transmission system over different distances. The results show that single-sideband transmission is beneficial for distances beyond ~50km at more dispersive O-band wavelengths.
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Conference paperJones DC, Alexandrov Y, Curry N, et al., 2020,
A multidimensional imaging and spectroscopic microscope
We present a multidimensional luminescence microscope for characterisation of emission from defects in diamond. We have applied the photoluminescence, hyperspectral and time-resolved luminescence imaging capabilities of this novel instrument to natural and synthetic diamonds.
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Conference paperWang S, Thipparapu NK, Wang Y, et al., 2020,
Widely-Tunable bismuth-doped fiber laser for the 1305-1375nm wavelength range
We present a tunable CW Bi-doped fiber laser from 1305-1375nm by utilizing a fiber-pigtailed tunable-filter in a ring cavity. A maximum output power of 150mW at 13305nm with a slope efficiency of 35% is demonstrated.
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Conference paperWang Y, Thipparapu NK, Richardson DJ, et al., 2020,
Broadband bismuth-doped fiber amplifier with a record 115-nm bandwidth in the O and E bands
We report a bismuth-doped fiber amplifier providing >20dB gain from 1345nm-1460nm with 31dB maximum gain and 4.8dB NF at 1420nm for a -23dBm signal. The gain coefficient and temperature-dependent-gain coefficient are 0.042dB/mW and -0.015dB/?, respectively.
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Conference paperCodescu M-A, Kornilov O, Nibbering ETJ, 2020,
Switching Between Ultrafast Proton Vacancy and Excess Proton Transfer along a Methanol Solvent Bridge
, International Conference on Ultrafast Phenomena, Publisher: Optica Publishing Group<jats:p>We show how ultrafast acid-base proton transfer neutralization reactions along methanol solvent bridges can be steered from a sequential methoxide to a sequential excess proton transport pathway.</jats:p>
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Conference paperWang S, Wang Y, Thipparapu NK, et al., 2020,
All-fiber wavelength-tunable Bi-doped laser employing a fiber Bragg grating operating in the 1300nm band
, Conference on Lasers and Electro-Optics (CLEO), Publisher: IEEE, ISSN: 2160-9020 -
Conference paperGorlitz F, Wysoczanski R, Kumar S, et al., 2020,
Towards easier, faster super-resolved microscopy
, Conference on Single Molecule Spectroscopy and Superresolution Imaging XIII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Conference paperGarcia E, Guo W, Kumar S, et al., 2020,
FLIM, FRET and high content analysis
, Symposium on Multiphoton Microscopy in the Biomedical Sciences XX held at SPIE BiOS Conference, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Conference paperTawy G, Wang J, Damzen MJ, 2020,
Thermal and population induced lensing in Alexandrite lasers
, Conference on Laser Resonators, Microresonators, and Beam Control XXII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X- Author Web Link
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- Citations: 1
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Conference paperTawy G, Damzen MJ, 2020,
Narrow linewidth tunable and dual wavelength compact Alexandrite laser
, Conference on Solid State Lasers XXIX - Technology and Devices, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Conference paperTawy G, Damzen MJ, 2020,
Ultra-compact >100kHz Q-switched Alexandrite lasers
, Conference on Solid State Lasers XXIX - Technology and Devices, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X -
Conference paperZhang G, Toulemonde M, Riemer K, et al., 2020,
Effects of Mechanical Index on Repeated Sparse Activation of Nanodroplets In Vivo
, IEEE International Ultrasonics Symposium (IEEE IUS), Publisher: IEEE, ISSN: 1948-5719 -
Conference paperHarput S, Toulemonde M, Ramalli A, et al., 2020,
Quantitative Microvessel Analysis with 3-D Super-Resolution Ultrasound and Velocity Mapping
, IEEE International Ultrasonics Symposium (IEEE IUS), Publisher: IEEE, ISSN: 1948-5719- Author Web Link
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- Citations: 5
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Journal articleChandran A, Runcorn T, Murray R, et al., 2019,
Nanosecond pulsed 620 nm source by frequency-doubling a phosphosilicate Raman fiber amplifier
, Optics Letters, Vol: 44, Pages: 6025-6028, ISSN: 0146-9592We demonstrate a nanosecond pulsed source at 620 nm with watt-level average power by frequency-doubling a 1240 nm phosphosilicate Raman fiber amplifier. A gain-switched laser diode operating at 1064 nm is amplified in an ytterbium fiber master oscillator power amplifier system and then converted to 1240 nm using a phosphosilicate Raman fiber amplifier with a conversion efficiency of up to 66%. The Raman fiber amplifier is seeded with a continuous-wave 1240 nm laser diode to obtain narrow-linewidth radiation, which is subsequently frequency-doubled in a periodically poled lithium tantalate crystal. A maximum average power of 1.5 W is generated at 620 nm, corresponding to a pulse energy of 300 nJ at a repetition rate of 5 MHz. The source has excellent beam quality (M2≤1.16) and an optical efficiency (1064 nm to 620 nm) of 20%, demonstrating an effective architecture for generating red pulsed light for biomedical imaging applications.
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Conference paperZhang G, Harput S, Toulemonde M, et al., 2019,
Acoustic wave sparsely-activated localization microscopy (AWSALM): in vivo fast ultrasound super-resolution imaging using nanodroplets
, IEEE International Ultrasonics Symposium (IUS), Publisher: IEEE, Pages: 1930-1933, ISSN: 1948-5719Current localization-based super-resolution ultrasound imaging requires a low concentration of flowing microbubbles to visualize microvasculature beyond the diffraction limit and acquisition is slow. Nanodroplets offer a promising solution as they can be sparsely activated and deactivated on-demand. In this study, acoustic wave sparsely-activated localization microscopy (AWSALM) using activation and deactivation of nanodroplets, an acoustic counterpart of photo-activated localization microscopy (PALM) which is less dependent on agent concentration and the presence of flow, is demonstrated for super-resolution imaging in deep tissues in vivo. An in vivo super-resolution image of a rabbit kidney is obtained in 1.1 seconds using AWSALM, where micro-vessels with apparent sizes far below the half-wavelength of 220 μm were visualized. This preliminary result demonstrates the feasibility of applying AWSALM for in vivo super-resolution imaging.
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Journal articleWang Y, Thipparapu NK, Wang S, et al., 2019,
Study on the temperature dependent characteristics of O-band bismuth-doped fiber amplifier
, OPTICS LETTERS, Vol: 44, Pages: 5650-5653, ISSN: 0146-9592 -
Journal articleDavis SPX, Kumar S, Alexandrov Y, et al., 2019,
Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish.
, Journal of Biophotonics, Vol: 12, ISSN: 1864-063XOptical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images. For sparse samples, this can be addressed with iterative algorithms to reconstruct 3D images from undersampled OPT data, but the data processing times present a significant challenge for studies imaging multiple animals. We show here that convolutional neural networks (CNN) can be used in place of iterative algorithms to remove artifacts - reducing processing time for an undersampled in vivo zebrafish dataset from 77 to 15 minutes. We also show that using CNN produces reconstructions of equivalent quality to CS with 40% fewer projections. We further show that diverse training data classes, for example ex vivo mouse tissue data, can be used for CNN-based reconstructions of OPT data of other species including live zebrafish.
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Journal articleRamuz M, Hasan A, Gruscheski L, et al., 2019,
A software tool for high-throughput real-time measurement of intensity-based ratio-metric FRET
, Cells, Vol: 8, ISSN: 2073-4409Förster resonance energy transfer (FRET) is increasingly used for non-invasive measurement of fluorescently tagged molecules in live cells. In this study, we have developed a freely available software tool MultiFRET, which, together with the use of a motorised microscope stage, allows multiple single cells to be studied in one experiment. MultiFRET is a Java plugin for Micro-Manager software, which provides real-time calculations of ratio-metric signals during acquisition and can simultaneously record from multiple cells in the same experiment. It can also make other custom-determined live calculations that can be easily exported to Excel at the end of the experiment. It is flexible and can work with multiple spectral acquisition channels. We validated this software by comparing the output of MultiFRET to that of a previously established and well-documented method for live ratio-metric FRET experiments and found no significant difference between the data produced with the use of the new MultiFRET and other methods. In this validation, we used several cAMP FRET sensors and cell models: i) isolated adult cardiomyocytes from transgenic mice expressing the cytosolic epac1-camps and targeted pmEpac1 and Epac1-PLN sensors, ii) isolated neonatal mouse cardiomyocytes transfected with the AKAP79-CUTie sensor, and iii) human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) transfected with the Epac-SH74 sensor. The MultiFRET plugin is an open source freely available package that can be used in a wide area of live cell imaging when live ratio-metric calculations are required.
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Journal articleDamzen M, Kerridge-Johns W, Geberbauer J, 2019,
Vortex mode transformation interferometry
, Journal of Optics, Vol: 22, Pages: 1-9, ISSN: 1464-4258Whilst many techniques exist for generation of an optical vortex, there remains a need for new devices and methods that can also provide vortex generation withhigher powers, greater flexibility of wavelength, and generation beyondthe lowest-order Laguerre-Gaussian 𝐿𝐺01modeto address a broader range of practical applications.This work revealshow an all-mirror based interferometricmode transformation system can provide these propertiesincludingrevealing, for the first time,the generation ofa much richer set of vortex mode patterns than might have been thought possible previously.Anew developed theoreticalformulation, confirmed with excellent agreement by experimental demonstrationsin an imbalanced Sagnac interferometer,showsinterferometric transformation is possible for all orders of Laguerre-Gaussian 𝐿𝐺0𝑙modes into a rich set of high quality higher-order vortex and vortex superposition. The interferometric approachis shown to be configurabletoincrease or decrease vorticity. The new mathematical formulation provides the ability to perform a fullmodal power analysis of both the mode-transformed transmitted vortex and the complementary reflected beam at the Sagnac beamsplitter port.A discussion is made on the origin of the orbital angular momentum transferred to the vortex output from the Sagnac beamsplitter.
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Journal articleTawy G, Wang J, Damzen M, 2019,
Pump-induced lensing effects in diode pumped Alexandrite lasers
, Optics Express, Vol: 27, Pages: 35865-35883, ISSN: 1094-4087It is essential to understand the pump-induced lensing and aberration effects in solid-state lasers, such as Alexandrite, since these set limits on laser power scaling whilst maintaininghigh spatial TEM00beam quality. In this work, we present direct wavefront measurements ofpump-induced lensing and spherical aberration using a Shack-Hartmann wavefront sensor, for thefirst time, in a diode-pumped Alexandrite laser, and under both non-lasing and lasing conditions.The lens dioptric power is found to be weakly sub-linear with respect to the absorbed pumppower, and under lasing, the lensing power is observed to decrease to60 %of its non-lasingvalue. The results are inconsistent with a thermal lens model but a fuller theoretical formulationis made of a combined thermal and population lens model giving good quantitative agreementto the observed pump power dependence of the induced-lensing under non-lasing conditionsand the reduced lensing under lasing conditions. The deduced value for the difference inexcited to ground state polarizability is consistent with prior measurement estimates for otherchromium-doped gain media. The finding of this paper provide new insight into pump-inducedlensing in Alexandrite and also provides a basis for a fast saturable population lens mechanism toaccount for self-Q-switching observed recently in Alexandrite laser systems.
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Journal articleCorcoran D, Juskaite V, Xu Y, et al., 2019,
DDR1 autophosphorylation is a result of aggregation into dense clusters
, Scientific Reports, Vol: 9, ISSN: 2045-2322The collagen receptor DDR1 is a receptor tyrosine kinase that promotes progression ofa wide range of human disorders. Little is known about how ligand binding triggers DDR1 kinase activity. We previously reported that collagen induces DDR1 activation through lateral dimer association and phosphorylation between dimers, a process that requires specific transmembrane association. Here we demonstrate ligand-induced DDR1 clustering by widefield and super-resolution imaging and provide evidence for a mechanism whereby DDR1 kinase activity is determined by its molecular density. Ligand binding resulted in initial DDR1 reorganisation into morphologically distinct clusters with unphosphorylated DDR1. Further compaction over time led to clusters with highly aggregated and phosphorylated DDR1. Ligand-induced DDR1 clustering was abolished by transmembrane mutations but did not require kinase activity. Our results significantly advance our understanding of the molecular events underpinning ligand-induced DDR1 kinase activity and provide an explanation for the unusually slow DDR1 activation kinetics.
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Journal articleJones DC, Kumar S, Lanigan PMP, et al., 2019,
Multidimensional luminescence microscope for imaging defect colour centres in diamond
, Methods and Applications in Fluorescence, Vol: 8, ISSN: 2050-6120We report a multidimensional luminescence microscope providing hyperspectral imaging and time-resolved (luminescence lifetime) imaging for the study of luminescent diamond defects. The instrument includes crossed-polariser white light transmission microscopy to reveal any birefringence that would indicate strain in the diamond lattice. We demonstrate the application of this new instrument to defects in natural and synthetic diamonds including N3, nitrogen and silicon vacancies. Hyperspectral imaging provides contrast that is not apparent in conventional intensity images and the luminescence lifetime provides further contrast.
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Conference paperPetropoulos P, Hong Y, Bottrill K, et al., 2019,
Extending the optical bandwidth of optical communication systems
, ISSN: 2162-108XThis talk discusses the new avenues facilitated through the adoption of ultra-broadband hollow-core optical transmission fibres, paired with amplifiers covering alternative wavelength bands. Transmission experiments using these technologies over an extended optical bandwidth are presented.
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Conference paperThipparapu NK, Wang Y, Wang S, et al., 2019,
Bi-doped silica-based fiber amplifier for O-band transmission
, ISSN: 2162-108XBismuth (Bi)-doped fibers offer a great potential to develop fiber sources in the 1150-1800nm wavelength region. Here, we review our recent work on Bi-doped fiber amplifiers in the O-band covering from 1300-1360nm.
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Journal articleAndrew Y, Bähner JP, Battle R, et al., 2019,
H-Mode Power Threshold Studies on MAST †
, Plasma, Vol: 2, Pages: 328-338Analysis of the L–H and H–L transition power thresholds (Pth) and pedestal parameters are presented for the mega ampere spherical tokamak (MAST). The dependencies of Pth on the average, core plasma electron density, X-point height, and plasma current are described. Increasing X-point distance from the divertor floor over 10–12 cm is found to increase Pth by a factor of three, while X-point heights greater than this have no further influence. The X-point height dependence of Pth is also observed to be sensitive to the plasma current. An Ip decrease from 0.77 MA to 0.65 MA, is observed to lower Pth by a factor of three across the X-point height scan and increases the maximum X-point height at which Pth stops increasing by 3 cm. Finally, a comparison of the experimental results with the predictions by the finite beta drift wave model is made, which provides a reasonable condition for the transition into and out of the H-mode.
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Journal articleChristensen-Jeffries K, Brown J, Harput S, et al., 2019,
Poisson statistical model of ultrasound super-resolution imaging acquisition time
, IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control, Vol: 66, Pages: 1246-1254, ISSN: 0885-3010A number of acoustic super-resolution techniques have recently been developed to visualize microvascular structure and flow beyond the diffraction limit. A crucial aspect of all ultrasound (US) super-resolution (SR) methods using single microbubble localization is time-efficient detection of individual bubble signals. Due to the need for bubbles to circulate through the vasculature during acquisition, slow flows associated with the microcirculation limit the minimum acquisition time needed to obtain adequate spatial information. Here, a model is developed to investigate the combined effects of imaging parameters, bubble signal density, and vascular flow on SR image acquisition time. We find that the estimated minimum time needed for SR increases for slower blood velocities and greater resolution improvement. To improve SR from a resolution of λ/10 to λ/20 while imaging the microvasculature structure modeled here, the estimated minimum acquisition time increases by a factor of 14. The maximum useful imaging frame rate to provide new spatial information in each image is set by the bubble velocity at low blood flows (<;150 mm/s for a depth of 5 cm) and by the acoustic wave velocity at higher bubble velocities. Furthermore, the image acquisition procedure, transmit frequency, localization precision, and desired super-resolved image contrast together determine the optimal acquisition time achievable for fixed flow velocity. Exploring the effects of both system parameters and details of the target vasculature can allow a better choice of acquisition settings and provide improved understanding of the completeness of SR information.
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Journal articleTawy G, Damzen M, 2019,
Tunable, dual wavelength and self-Q-switched Alexandrite laser using crystal birefringence control
, Optics Express, Vol: 27, Pages: 17507-17520, ISSN: 1094-4087We present a red-diode-pumped Alexandrite laser with continuous wavelength tunability, dual wavelength and self-Q-switching in an ultra-compact resonator containing only the gain medium. Wavelength tuning is obtained by varying the geometrical path length and birefringence by tilting a Brewster-cut Alexandrite crystal. Two crystals from independent suppliers are used to demonstrate and compare the performance. Wavelength tuning between 750 and 764 nm is demonstrated in the first crystal and between 747 and 768 nm in the second crystal. Stable dual wavelength operation is also obtained in both crystals with wavelength separation determined by the crystal free spectral range. Temperature tuning was also demonstrated to provide finer wavelength tuning at a rate of −0.07 nm K −1. Over a narrow tuning range, stable self-Q-switching is observed with a pulse duration of 660 ns at 135 kHz, which we believe is the highest Q-switched pulse rate in Alexandrite to date. Theoretical modelling is performed showing good agreement with the wavelength tuning and dual wavelength results.
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Journal articleLagarto J, Dyer B, Dunsby C, et al., 2019,
In vivo label-free optical monitoring of structural and metabolic remodeling of myocardium following infarction
, Biomedical Optics Express, Vol: 10, Pages: 3506-3521, ISSN: 2156-7085Cardiac remodeling following myocardial infarction (MI) involves structural and functional alterations in the infarcted and remote viable myocardium that can ultimately lead to heart failure. The underlying mechanisms are not fully understood and, following our previous study of the autofluorescence lifetime and diffuse reflectance signatures of the myocardium in vivo at 16 weeks post MI in rats [Biomed. Opt. Express 6(2), 324 (2015)], we here present data obtained at 1, 2 and 4 weeks post myocardial infarction that help follow the temporal progression of these changes. Our results demonstrate that both structural and metabolic changes in the heart can be monitored from the earliest time points following MI using label-free optical readouts, not only in the region of infarction but also in the remote non-infarcted myocardium. Changes in the autofluorescence intensity and lifetime parameters associated with collagen type I autofluorescence were indicative of progressive collagen deposition in tissue that was most pronounced at earlier time points and in the region of infarction. In addition to significant collagen deposition in infarcted and non-infarcted myocardium, we also report changes in the autofluorescence parameters associated with reduced nicotinamide adenine (phosphate) dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD), which we associate with metabolic alterations throughout the heart. Parallel measurements of the diffuse reflectance spectra indicated an increased contribution of reduced cytochrome c. Our findings suggest that combining time-resolved spectrofluorometry and diffuse reflectance spectroscopy could provide a useful means to monitor cardiac function in vivo at the time of surgery.
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