Optical coherence tomography detection of shear wave propagation in inhomogeneous tissue equivalent phantoms and ex-vivo carotid artery samples

PubMed Central

Razani, Marjan; Luk, Timothy W.H.; Mariampillai, Adrian; Siegler, Peter; Kiehl, Tim-Rasmus; Kolios, Michael C.; Yang, Victor X.D.

2014-01-01

In this work, we explored the potential of measuring shear wave propagation using optical coherence elastography (OCE) in an inhomogeneous phantom and carotid artery samples based on a swept-source optical coherence tomography (OCT) system. Shear waves were generated using a piezoelectric transducer transmitting sine-wave bursts of 400 μs duration, applying acoustic radiation force (ARF) to inhomogeneous phantoms and carotid artery samples, synchronized with a swept-source OCT (SS-OCT) imaging system. The phantoms were composed of gelatin and titanium dioxide whereas the carotid artery samples were embedded in gel. Differential OCT phase maps, measured with and without the ARF, detected the microscopic displacement generated by shear wave propagation in these phantoms and samples of different stiffness. We present the technique for calculating tissue mechanical properties by propagating shear waves in inhomogeneous tissue equivalent phantoms and carotid artery samples using the ARF of an ultrasound transducer, and measuring the shear wave speed and its associated properties in the different layers with OCT phase maps. This method lays the foundation for future in-vitro and in-vivo studies of mechanical property measurements of biological tissues such as vascular tissues, where normal and pathological structures may exhibit significant contrast in the shear modulus. PMID:24688822

Processing ultrasound backscatter to monitor high-intensity focused ultrasound (HIFU) therapy

NASA Astrophysics Data System (ADS)

Kaczkowski, Peter J.; Anand, Ajay; Bailey, Michael R.

2005-09-01

The development of new noninvasive surgical methods such as HIFU for the treatment of cancer and internal bleeding requires simultaneous development of new sensing approaches to guide, monitor, and assess the therapy. Ultrasound imaging using echo amplitude has long been used to map tissue morphology for diagnostic interpretation by the clinician. New quantitative ultrasonic methods that rely on amplitude and phase processing for tissue characterization are being developed for monitoring of ablative therapy. We have been developing the use of full wave ultrasound backscattering for real-time temperature estimation, and to image changes in tissue backscatter spectrum as therapy progresses. Both approaches rely on differential processing of the backscatter signal in time, and precise measurement of phase differences. Noise and artifacts from motion and nonstationary speckle statistics are addressed by constraining inversions for tissue parameters with physical models. We present results of HIFU experiments with static point and scanned HIFU exposures in which temperature rise can be accurately mapped using a new heat transfer equation (HTE) model-constrained inverse approach. We also present results of a recently developed spectral imaging method that elucidates microbubble-mediated nonlinearity not visible as a change in backscatter amplitude. [Work supported by Army MRMC.

Theory and preliminary experimental verification of quantitative edge illumination x-ray phase contrast tomography.

PubMed

Hagen, C K; Diemoz, P C; Endrizzi, M; Rigon, L; Dreossi, D; Arfelli, F; Lopez, F C M; Longo, R; Olivo, A

2014-04-07

X-ray phase contrast imaging (XPCi) methods are sensitive to phase in addition to attenuation effects and, therefore, can achieve improved image contrast for weakly attenuating materials, such as often encountered in biomedical applications. Several XPCi methods exist, most of which have already been implemented in computed tomographic (CT) modality, thus allowing volumetric imaging. The Edge Illumination (EI) XPCi method had, until now, not been implemented as a CT modality. This article provides indications that quantitative 3D maps of an object's phase and attenuation can be reconstructed from EI XPCi measurements. Moreover, a theory for the reconstruction of combined phase and attenuation maps is presented. Both reconstruction strategies find applications in tissue characterisation and the identification of faint, weakly attenuating details. Experimental results for wires of known materials and for a biological object validate the theory and confirm the superiority of the phase over conventional, attenuation-based image contrast.

A novel algorithm for fast and efficient multifocus wavefront shaping

NASA Astrophysics Data System (ADS)

Fayyaz, Zahra; Nasiriavanaki, Mohammadreza

2018-02-01

Wavefront shaping using spatial light modulator (SLM) is a popular method for focusing light through a turbid media, such as biological tissues. Usually, in iterative optimization methods, due to the very large number of pixels in SLM, larger pixels are formed, bins, and the phase value of the bins are changed to obtain an optimum phase map, hence a focus. In this study an efficient optimization algorithm is proposed to obtain an arbitrary map of focus utilizing all the SLM pixels or small bin sizes. The application of such methodology in dermatology, hair removal in particular, is explored and discussed

Wide-field high spatial frequency domain imaging of tissue microstructure

NASA Astrophysics Data System (ADS)

Lin, Weihao; Zeng, Bixin; Cao, Zili; Zhu, Danfeng; Xu, M.

2018-02-01

Wide-field tissue imaging is usually not capable of resolving tissue microstructure. We present High Spatial Frequency Domain Imaging (HSFDI) - a noncontact imaging modality that spatially maps the tissue microscopic scattering structures over a large field of view. Based on an analytical reflectance model of sub-diffusive light from forward-peaked highly scattering media, HSFDI quantifies the spatially-resolved parameters of the light scattering phase function from the reflectance of structured light modulated at high spatial frequencies. We have demonstrated with ex vivo cancerous tissue to validate the robustness of HSFDI in significant contrast and differentiation of the microstructutral parameters between different types and disease states of tissue.

Tissue Refractive Index Fluctuations Report on Cancer Development

NASA Astrophysics Data System (ADS)

Popescu, Gabriel

2012-02-01

The gold standard in histopathology relies on manual investigation of stained tissue biopsies. A sensitive and quantitative method for in situ tissue specimen inspection is highly desirable, as it will allow early disease diagnosis and automatic screening. Here we demonstrate that quantitative phase imaging of entire unstained biopsies has the potential to fulfill this requirement. Our data indicates that the refractive index distribution of histopathology slides, which contains information about the molecular scale organization of tissue, reveals prostate tumors. These optical maps report on subtle, nanoscale morphological properties of tissues and cells that cannot be recovered by common stains, including hematoxylin and eosin (H&E). We found that cancer progression significantly alters the tissue organization, as exhibited in our refractive index maps. Furthermore, using the quantitative phase information, we obtained the spatially resolved scattering mean free path and anisotropy factor g for entire biopsies and demonstrated their direct correlation with tumor presence. We found that these scattering parameters are able to distinguish between two adjacent grades, which is a difficult task and relevant for determining patient treatment. In essence, our results show that the tissue refractive index reports on the nanoscale tissue architecture and, in principle, can be used as an intrinsic marker for cancer diagnosis. [4pt] [1] Z. Wang, K. Tangella, A. Balla and G. Popescu, Tissue refractive index as marker of disease, Journal of Biomedical Optics, in press).[0pt] [2] Z. Wang, L. J. Millet, M. Mir, H. Ding, S. Unarunotai, J. A. Rogers, M. U. Gillette and G. Popescu, Spatial light interference microscopy (SLIM), Optics Express, 19, 1016 (2011).[0pt] [3] Z. Wang, D. L. Marks, P. S. Carney, L. J. Millet, M. U. Gillette, A. Mihi, P. V. Braun, Z. Shen, S. G. Prasanth and G. Popescu, Spatial light interference tomography (SLIT), Optics Express, 19, 19907-19918 (2011).[0pt] [4] Z. Wang, H. Ding and G. Popescu, Scattering-phase theorem, Optics Letters, 36, 1215 (2011).[0pt] [5] G. Popescu Quantitative phase imaging of cells and tissues (McGraw-Hill, New York, 2011).[0pt] [6] H. F. Ding, Z. Wang, F. Nguyen, S. A. Boppart and G. Popescu, Fourier Transform Light Scattering of Inhomogeneous and Dynamic Structures, Physical Review Letters, 101, 238102 (2008).

Quantitative Susceptibility Mapping by Inversion of a Perturbation Field Model: Correlation with Brain Iron in Normal Aging

PubMed Central

Poynton, Clare; Jenkinson, Mark; Adalsteinsson, Elfar; Sullivan, Edith V.; Pfefferbaum, Adolf; Wells, William

2015-01-01

There is increasing evidence that iron deposition occurs in specific regions of the brain in normal aging and neurodegenerative disorders such as Parkinson's, Huntington's, and Alzheimer's disease. Iron deposition changes the magnetic susceptibility of tissue, which alters the MR signal phase, and allows estimation of susceptibility differences using quantitative susceptibility mapping (QSM). We present a method for quantifying susceptibility by inversion of a perturbation model, or ‘QSIP’. The perturbation model relates phase to susceptibility using a kernel calculated in the spatial domain, in contrast to previous Fourier-based techniques. A tissue/air susceptibility atlas is used to estimate B0 inhomogeneity. QSIP estimates in young and elderly subjects are compared to postmortem iron estimates, maps of the Field-Dependent Relaxation Rate Increase (FDRI), and the L1-QSM method. Results for both groups showed excellent agreement with published postmortem data and in-vivo FDRI: statistically significant Spearman correlations ranging from Rho = 0.905 to Rho = 1.00 were obtained. QSIP also showed improvement over FDRI and L1-QSM: reduced variance in susceptibility estimates and statistically significant group differences were detected in striatal and brainstem nuclei, consistent with age-dependent iron accumulation in these regions. PMID:25248179

Shear Wave Imaging of Breast Tissue by Color Doppler Shear Wave Elastography.

PubMed

Yamakoshi, Yoshiki; Nakajima, Takahito; Kasahara, Toshihiro; Yamazaki, Mayuko; Koda, Ren; Sunaguchi, Naoki

2017-02-01

Shear wave elastography is a distinctive method to access the viscoelastic characteristic of the soft tissue that is difficult to obtain by other imaging modalities. This paper proposes a novel shear wave elastography [color Doppler shear wave imaging (CD SWI)] for breast tissue. Continuous shear wave is produced by a small lightweight actuator, which is attached to the tissue surface. Shear wave wavefront that propagates in tissue is reconstructed as a binary pattern that consists of zero and the maximum flow velocities on color flow image (CFI). Neither any modifications of the ultrasound color flow imaging instrument nor a high frame rate ultrasound imaging instrument is required to obtain the shear wave wavefront map. However, two conditions of shear wave displacement amplitude and shear wave frequency are needed to obtain the map. However, these conditions are not severe restrictions in breast imaging. This is because the minimum displacement amplitude is [Formula: see text] for an ultrasonic wave frequency of 12 MHz and the shear wave frequency is available from several frequencies suited for breast imaging. Fourier analysis along time axis suppresses clutter noise in CFI. A directional filter extracts shear wave, which propagates in the forward direction. Several maps, such as shear wave phase, velocity, and propagation maps, are reconstructed by CD SWI. The accuracy of shear wave velocity measurement is evaluated for homogeneous agar gel phantom by comparing with the acoustic radiation force impulse method. The experimental results for breast tissue are shown for a shear wave frequency of 296.6 Hz.

Background field removal technique based on non-regularized variable kernels sophisticated harmonic artifact reduction for phase data for quantitative susceptibility mapping.

PubMed

Kan, Hirohito; Arai, Nobuyuki; Takizawa, Masahiro; Omori, Kazuyoshi; Kasai, Harumasa; Kunitomo, Hiroshi; Hirose, Yasujiro; Shibamoto, Yuta

2018-06-11

We developed a non-regularized, variable kernel, sophisticated harmonic artifact reduction for phase data (NR-VSHARP) method to accurately estimate local tissue fields without regularization for quantitative susceptibility mapping (QSM). We then used a digital brain phantom to evaluate the accuracy of the NR-VSHARP method, and compared it with the VSHARP and iterative spherical mean value (iSMV) methods through in vivo human brain experiments. Our proposed NR-VSHARP method, which uses variable spherical mean value (SMV) kernels, minimizes L2 norms only within the volume of interest to reduce phase errors and save cortical information without regularization. In a numerical phantom study, relative local field and susceptibility map errors were determined using NR-VSHARP, VSHARP, and iSMV. Additionally, various background field elimination methods were used to image the human brain. In a numerical phantom study, the use of NR-VSHARP considerably reduced the relative local field and susceptibility map errors throughout a digital whole brain phantom, compared with VSHARP and iSMV. In the in vivo experiment, the NR-VSHARP-estimated local field could sufficiently achieve minimal boundary losses and phase error suppression throughout the brain. Moreover, the susceptibility map generated using NR-VSHARP minimized the occurrence of streaking artifacts caused by insufficient background field removal. Our proposed NR-VSHARP method yields minimal boundary losses and highly precise phase data. Our results suggest that this technique may facilitate high-quality QSM. Copyright © 2017. Published by Elsevier Inc.

Improved measurement of vibration amplitude in dynamic optical coherence elastography

PubMed Central

Kennedy, Brendan F.; Wojtkowski, Maciej; Szkulmowski, Maciej; Kennedy, Kelsey M.; Karnowski, Karol; Sampson, David D.

2012-01-01

Abstract: Optical coherence elastography employs optical coherence tomography (OCT) to measure the displacement of tissues under load and, thus, maps the resulting strain into an image, known as an elastogram. We present a new improved method to measure vibration amplitude in dynamic optical coherence elastography. The tissue vibration amplitude caused by sinusoidal loading is measured from the spread of the Doppler spectrum, which is extracted using joint spectral and time domain signal processing. At low OCT signal-to-noise ratio (SNR), the method provides more accurate vibration amplitude measurements than the currently used phase-sensitive method. For measurements performed on a mirror at OCT SNR = 5 dB, our method introduces <3% error, compared to >20% using the phase-sensitive method. We present elastograms of a tissue-mimicking phantom and excised porcine tissue that demonstrate improvements, including a 50% increase in the depth range of reliable vibration amplitude measurement. PMID:23243565

High-speed single-shot optical focusing through dynamic scattering media with full-phase wavefront shaping.

PubMed

Hemphill, Ashton S; Shen, Yuecheng; Liu, Yan; Wang, Lihong V

2017-11-27

In biological applications, optical focusing is limited by the diffusion of light, which prevents focusing at depths greater than ∼1 mm in soft tissue. Wavefront shaping extends the depth by compensating for phase distortions induced by scattering and thus allows for focusing light through biological tissue beyond the optical diffusion limit by using constructive interference. However, due to physiological motion, light scattering in tissue is deterministic only within a brief speckle correlation time. In in vivo tissue, this speckle correlation time is on the order of milliseconds, and so the wavefront must be optimized within this brief period. The speed of digital wavefront shaping has typically been limited by the relatively long time required to measure and display the optimal phase pattern. This limitation stems from the low speeds of cameras, data transfer and processing, and spatial light modulators. While binary-phase modulation requiring only two images for the phase measurement has recently been reported, most techniques require at least three frames for the full-phase measurement. Here, we present a full-phase digital optical phase conjugation method based on off-axis holography for single-shot optical focusing through scattering media. By using off-axis holography in conjunction with graphics processing unit based processing, we take advantage of the single-shot full-phase measurement while using parallel computation to quickly reconstruct the phase map. With this system, we can focus light through scattering media with a system latency of approximately 9 ms, on the order of the in vivo speckle correlation time.

High-speed single-shot optical focusing through dynamic scattering media with full-phase wavefront shaping

NASA Astrophysics Data System (ADS)

Hemphill, Ashton S.; Shen, Yuecheng; Liu, Yan; Wang, Lihong V.

2017-11-01

In biological applications, optical focusing is limited by the diffusion of light, which prevents focusing at depths greater than ˜1 mm in soft tissue. Wavefront shaping extends the depth by compensating for phase distortions induced by scattering and thus allows for focusing light through biological tissue beyond the optical diffusion limit by using constructive interference. However, due to physiological motion, light scattering in tissue is deterministic only within a brief speckle correlation time. In in vivo tissue, this speckle correlation time is on the order of milliseconds, and so the wavefront must be optimized within this brief period. The speed of digital wavefront shaping has typically been limited by the relatively long time required to measure and display the optimal phase pattern. This limitation stems from the low speeds of cameras, data transfer and processing, and spatial light modulators. While binary-phase modulation requiring only two images for the phase measurement has recently been reported, most techniques require at least three frames for the full-phase measurement. Here, we present a full-phase digital optical phase conjugation method based on off-axis holography for single-shot optical focusing through scattering media. By using off-axis holography in conjunction with graphics processing unit based processing, we take advantage of the single-shot full-phase measurement while using parallel computation to quickly reconstruct the phase map. With this system, we can focus light through scattering media with a system latency of approximately 9 ms, on the order of the in vivo speckle correlation time.

Quantitative phase imaging of human red blood cells using phase-shifting white light interference microscopy with colour fringe analysis

NASA Astrophysics Data System (ADS)

Singh Mehta, Dalip; Srivastava, Vishal

2012-11-01

We report quantitative phase imaging of human red blood cells (RBCs) using phase-shifting interference microscopy. Five phase-shifted white light interferograms are recorded using colour charge coupled device camera. White light interferograms were decomposed into red, green, and blue colour components. The phase-shifted interferograms of each colour were then processed by phase-shifting analysis and phase maps for red, green, and blue colours were reconstructed. Wavelength dependent refractive index profiles of RBCs were computed from the single set of white light interferogram. The present technique has great potential for non-invasive determination of refractive index variation and morphological features of cells and tissues.

Probing myocardium biomechanics using quantitative optical coherence elastography

NASA Astrophysics Data System (ADS)

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2015-03-01

We present a quantitative optical coherence elastographic method for noncontact assessment of the myocardium elasticity. The method is based on shear wave imaging optical coherence tomography (SWI-OCT), where a focused air-puff system is used to induce localized tissue deformation through a low-pressure short-duration air stream and a phase-sensitive OCT system is utilized to monitor the propagation of the induced tissue displacement with nanoscale sensitivity. The 1-D scanning of M-mode OCT imaging and the application of optical phase retrieval and mapping techniques enable the reconstruction and visualization of 2-D depth-resolved shear wave propagation in tissue with ultra-high frame rate. The feasibility of this method in quantitative elasticity measurement is demonstrated on tissue-mimicking phantoms with the estimated Young's modulus compared with uniaxial compression tests. We also performed pilot experiments on ex vivo mouse cardiac muscle tissues with normal and genetically altered cardiomyocytes. Our results indicate this noncontact quantitative optical coherence elastographic method can be a useful tool for the cardiac muscle research and studies.

SU-G-BRC-15: The Potential Clinical Significance of Dose Mapping Error for Intra- Fraction Dose Mapping for Lung Cancer Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayah, N; Weiss, E; Watkins, W

Purpose: To evaluate the dose-mapping error (DME) inherent to conventional dose-mapping algorithms as a function of dose-matrix resolution. Methods: As DME has been reported to be greatest where dose-gradients overlap tissue-density gradients, non-clinical 66 Gy IMRT plans were generated for 11 lung patients with the target edge defined as the maximum 3D density gradient on the 0% (end of inhale) breathing phase. Post-optimization, Beams were copied to 9 breathing phases. Monte Carlo dose computed (with 2*2*2 mm{sup 3} resolution) on all 10 breathing phases was deformably mapped to phase 0% using the Monte Carlo energy-transfer method with congruent mass-mapping (EMCM);more » an externally implemented tri-linear interpolation method with voxel sub-division; Pinnacle’s internal (tri-linear) method; and a post-processing energy-mass voxel-warping method (dTransform). All methods used the same base displacement-vector-field (or it’s pseudo-inverse as appropriate) for the dose mapping. Mapping was also performed at 4*4*4 mm{sup 3} by merging adjacent dose voxels. Results: Using EMCM as the reference standard, no clinically significant (>1 Gy) DMEs were found for the mean lung dose (MLD), lung V20Gy, or esophagus dose-volume indices, although MLD and V20Gy were statistically different (2*2*2 mm{sup 3}). Pinnacle-to-EMCM target D98% DMEs of 4.4 and 1.2 Gy were observed ( 2*2*2 mm{sup 3}). However dTransform, which like EMCM conserves integral dose, had DME >1 Gy for one case. The root mean square RMS of the DME for the tri-linear-to- EMCM methods was lower for the smaller voxel volume for the tumor 4D-D98%, lung V20Gy, and cord D1%. Conclusion: When tissue gradients overlap with dose gradients, organs-at-risk DME was statistically significant but not clinically significant. Target-D98%-DME was deemed clinically significant for 2/11 patients (2*2*2 mm{sup 3}). Since tri-linear RMS-DME between EMCM and tri-linear was reduced at 2*2*2 mm{sup 3}, use of this resolution is recommended for dose mapping. Interpolative dose methods are sufficiently accurate for the majority of cases. J.V. Siebers receives funding support from Varian Medical Systems.« less

Confocal acoustic radiation force optical coherence elastography using a ring ultrasonic transducer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qi, Wenjuan; Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 92697; Li, Rui

2014-03-24

We designed and developed a confocal acoustic radiation force optical coherence elastography system. A ring ultrasound transducer was used to achieve reflection mode excitation and generate an oscillating acoustic radiation force in order to generate displacements within the tissue, which were detected using the phase-resolved optical coherence elastography method. Both phantom and human tissue tests indicate that this system is able to sense the stiffness difference of samples and quantitatively map the elastic property of materials. Our confocal setup promises a great potential for point by point elastic imaging in vivo and differentiation of diseased tissues from normal tissue.

Oxygen mapping: Probing a novel seeding strategy for bone tissue engineering.

PubMed

Westphal, Ines; Jedelhauser, Claudia; Liebsch, Gregor; Wilhelmi, Arnd; Aszodi, Attila; Schieker, Matthias

2017-04-01

Bone tissue engineering (BTE) utilizing biomaterial scaffolds and human mesenchymal stem cells (hMSCs) is a promising approach for the treatment of bone defects. The quality of engineered tissue is crucially affected by numerous parameters including cell density and the oxygen supply. In this study, a novel oxygen-imaging sensor was introduced to monitor the oxygen distribution in three dimensional (3D) scaffolds in order to analyze a new cell-seeding strategy. Immortalized hMSCs, pre-cultured in a monolayer for 30-40% or 70-80% confluence, were used to seed demineralized bone matrix (DBM) scaffolds. Real-time measurements of oxygen consumption in vitro were simultaneously performed by the novel planar sensor and a conventional needle-type sensor over 24 h. Recorded oxygen maps of the novel planar sensor revealed that scaffolds, seeded with hMSCs harvested at lower densities (30-40% confluence), exhibited rapid exponential oxygen consumption profile. In contrast, harvesting cells at higher densities (70-80% confluence) resulted in a very slow, almost linear, oxygen decrease due to gradual achieving the stationary growth phase. In conclusion, it could be shown that not only the seeding density on a scaffold, but also the cell density at the time point of harvest is of major importance for BTE. The new cell seeding strategy of harvested MSCs at low density during its log phase could be a useful strategy for an early in vivo implantation of cell-seeded scaffolds after a shorter in vitro culture period. Furthermore, the novel oxygen imaging sensor enables a continuous, two-dimensional, quick and convenient to handle oxygen mapping for the development and optimization of tissue engineered scaffolds. Biotechnol. Bioeng. 2017;114: 894-902. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fast photoacoustic imaging system based on 320-element linear transducer array.

PubMed

Yin, Bangzheng; Xing, Da; Wang, Yi; Zeng, Yaguang; Tan, Yi; Chen, Qun

2004-04-07

A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis.

Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging.

PubMed

Kanick, Stephen Chad; McClatchy, David M; Krishnaswamy, Venkataramanan; Elliott, Jonathan T; Paulsen, Keith D; Pogue, Brian W

2014-10-01

This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns [Formula: see text] can be used to quantitatively map the anisotropic scattering phase function distribution [Formula: see text] in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance ([Formula: see text]) in terms of dimensionless scattering [Formula: see text] and [Formula: see text], a metric of the first two moments of the [Formula: see text] distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of [Formula: see text] spectra sampled at multiple [Formula: see text] in the frequency range [0.05-0.5] [Formula: see text] allowed accurate estimation of both [Formula: see text] in the relevant tissue range [0.4-1.8] [Formula: see text], and [Formula: see text] in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited [Formula: see text]-based contrast between scar tissue and surrounding normal skin, which was not as apparent in wide field diffuse imaging. These results represent the first wide-field maps to quantify sub-diffuse scattering parameters, which are sensitive to sub-microscopic tissue structures and composition, and therefore, offer potential for fast diagnostic imaging of ultrastructure on a size scale that is relevant to surgical applications.

Mueller-matrix mapping of optically anisotropic fluorophores of molecular biological tissues in the diagnosis of death causes

NASA Astrophysics Data System (ADS)

Ushenko, A. G.; Dubolazov, A. V.; Ushenko, V. A.; Ushenko, Yu. A.; Pidkamin, L. Y.; Soltys, I. V.; Zhytaryuk, V. G.; Pavlyukovich, N.

2016-09-01

A model of generalized optical anisotropy of polycrystalline networks of albumin and globulin of human brain liquor has been suggested. The polarization-phase method of spatial and frequency differentiation of linear and circular birefringence coordinate distributions have been analytically substantiated. A set of criteria of the dynamics of necrotic changes of polarization-phase images of liquor polycrystalline films for determination of death coming prescription has been detected and substantiated.

Exploring the origins of echo-time-dependent quantitative susceptibility mapping (QSM) measurements in healthy tissue and cerebral microbleeds.

PubMed

Cronin, Matthew J; Wang, Nian; Decker, Kyle S; Wei, Hongjiang; Zhu, Wen-Zhen; Liu, Chunlei

2017-04-01

Quantitative susceptibility mapping (QSM) is increasingly used to measure variation in tissue composition both in the brain and in other areas of the body in a range of disease pathologies. Although QSM measurements were originally believed to be independent of the echo time (TE) used in the gradient-recalled echo (GRE) acquisition from which they are derived; recent literature (Sood et al., 2016) has shown that these measurements can be highly TE-dependent in a number of brain regions. In this work we systematically investigate possible causes of this effect through analysis of apparent frequency and QSM measurements derived from data acquired at multiple TEs in vivo in healthy brain regions and in cerebral microbleeds (CMBs); QSM data acquired in a gadolinium-doped phantom; and in QSM data derived from idealized simulated phase data. Apparent frequency measurements in the optic radiations (OR) and central corpus callosum (CC) were compared to those predicted by a 3-pool white matter model, however the model failed to fully explain contrasting frequency profiles measured in the OR and CC. Our results show that TE-dependent QSM measurements can be caused by a failure of phase unwrapping algorithms in and around strong susceptibility sources such as CMBs; however, in healthy brain regions this behavior appears to result from intrinsic non-linear phase evolution in the MR signal. From these results we conclude that care must be taken when deriving frequency and QSM measurements in strong susceptibility sources due to the inherent limitations in phase unwrapping; and that while signal compartmentalization due to tissue microstructure and content is a plausible cause of TE-dependent frequency and QSM measurements in healthy brain regions, better sampling of the MR signal and more complex models of tissue are needed to fully exploit this relationship. Copyright © 2017 Elsevier Inc. All rights reserved.

Multi-parametric monitoring and assessment of high-intensity focused ultrasound (HIFU) boiling by harmonic motion imaging for focused ultrasound (HMIFU): an ex vivo feasibility study

NASA Astrophysics Data System (ADS)

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E.

2014-03-01

Harmonic motion imaging for focused ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase shift during high energy HIFU treatment with tissue boiling. Forty three (n = 43) thermal lesions were formed in ex vivo canine liver specimens (n = 28). Two-dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10 s, 20 s and 30 s HIFU durations at three different acoustic powers of 8, 10, and 11 W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and passive cavitation detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δϕ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite the expectedly chaotic changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property changes throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes.

Multi-parametric monitoring and assessment of High Intensity Focused Ultrasound (HIFU) boiling by Harmonic Motion Imaging for Focused Ultrasound (HMIFU): An ex vivo feasibility study

PubMed Central

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E.

2014-01-01

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase-shift during high energy HIFU treatment with tissue boiling. Forty three (n=43) thermal lesions were formed in ex vivo canine liver specimens (n=28). Two dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10-s, 20-s and 30-s HIFU durations at three different acoustic powers of 8, 10, and 11W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and Passive Cavitation Detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δφ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite unpredictable changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property change throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes. PMID:24556974

Multi-parametric monitoring and assessment of high-intensity focused ultrasound (HIFU) boiling by harmonic motion imaging for focused ultrasound (HMIFU): an ex vivo feasibility study.

PubMed

Hou, Gary Y; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa E

2014-03-07

Harmonic motion imaging for focused ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and change in relative phase shift during high energy HIFU treatment with tissue boiling. Forty three (n = 43) thermal lesions were formed in ex vivo canine liver specimens (n = 28). Two-dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10 s, 20 s and 30 s HIFU durations at three different acoustic powers of 8, 10, and 11 W, which were selected and verified as treatment parameters capable of inducing boiling using both thermocouple and passive cavitation detection (PCD) measurements. Although a steady decrease in the displacement, compressive strain, and relative change in the focal phase shift (Δϕ) were obtained in numerous cases, indicating an overall increase in relative stiffness, the study outcomes also showed that during boiling, a reverse lesion-to-background displacement contrast was detected, indicating potential change in tissue absorption, geometrical change and/or, mechanical gelatification or pulverization. Following treatment, corresponding 2D HMI displacement images of the thermal lesions also mapped consistent discrepancy in the lesion-to-background displacement contrast. Despite the expectedly chaotic changes in acoustic properties with boiling, the relative change in phase shift showed a consistent decrease, indicating its robustness to monitor biomechanical properties independent of the acoustic property changes throughout the HIFU treatment. In addition, the 2D HMI displacement images confirmed and indicated the increase in the thermal lesion size with treatment duration, which was validated against pathology. In conclusion, multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU boiling, some of which were independent of the acoustic parameter changes.

A single-image method for x-ray refractive index CT.

PubMed

Mittone, A; Gasilov, S; Brun, E; Bravin, A; Coan, P

2015-05-07

X-ray refraction-based computer tomography imaging is a well-established method for nondestructive investigations of various objects. In order to perform the 3D reconstruction of the index of refraction, two or more raw computed tomography phase-contrast images are usually acquired and combined to retrieve the refraction map (i.e. differential phase) signal within the sample. We suggest an approximate method to extract the refraction signal, which uses a single raw phase-contrast image. This method, here applied to analyzer-based phase-contrast imaging, is employed to retrieve the index of refraction map of a biological sample. The achieved accuracy in distinguishing the different tissues is comparable with the non-approximated approach. The suggested procedure can be used for precise refraction computer tomography with the advantage of a reduction of at least a factor of two of both the acquisition time and the dose delivered to the sample with respect to any of the other algorithms in the literature.

Attenuation of Multiple Organ Damage by Continuous Low-Dose Solvent-Free Infusions of Resveratrol after Severe Hemorrhagic Shock in Rats

PubMed Central

Kirsch, Michael; Petrat, Frank

2017-01-01

Therapeutic effects of continuous intravenous infusions of solvent-free low doses of resveratrol on organ injury and systemic consequences resulting from severe hemorrhagic shock in rats were studied. Hemorrhagic shock was induced by withdrawing arterial blood until a mean arterial blood pressure (MAP) of 25–30 mmHg was reached. Following a shock phase of 60 min, rats were resuscitated with the withdrawn blood plus lactated Ringer’s. Resveratrol (20 or 60 μg/kg × h) was continuously infused intravenously starting with the resuscitation phase (30 min) and continued until the end of the experiment (total treatment time 180 min). Animals of the shock control group received 0.9% NaCl solution. After the observation phase (150 min), rats were sacrificed. Resveratrol significantly stabilized the MAP and peripheral oxygen saturation after hemorrhagic shock, decreased the macroscopic injury of the small intestine, significantly attenuated the shock-induced increase in tissue myeloperoxidase activity in the small intestine, liver, kidney and lung, and diminished tissue hemorrhages (particularly in the small intestine and liver) as well as the rate of hemolysis. Already very low doses of resveratrol, continuously infused during resuscitation after severe hemorrhagic shock, can significantly improve impaired systemic parameters and attenuate multiple organ damage in rats. PMID:28817064

Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain

NASA Astrophysics Data System (ADS)

Fang, Jinsheng; Bao, Lijun; Li, Xu; van Zijl, Peter C. M.; Chen, Zhong

2017-08-01

Background field removal is an important MR phase preprocessing step for quantitative susceptibility mapping (QSM). It separates the local field induced by tissue magnetic susceptibility sources from the background field generated by sources outside a region of interest, e.g. brain, such as air-tissue interface. In the vicinity of air-tissue boundary, e.g. skull and paranasal sinuses, where large susceptibility variations exist, present background field removal methods are usually insufficient and these regions often need to be excluded by brain mask erosion at the expense of losing information of local field and thus susceptibility measures in these regions. In this paper, we propose an extension to the variable-kernel sophisticated harmonic artifact reduction for phase data (V-SHARP) background field removal method using a region adaptive kernel (R-SHARP), in which a scalable spherical Gaussian kernel (SGK) is employed with its kernel radius and weights adjustable according to an energy "functional" reflecting the magnitude of field variation. Such an energy functional is defined in terms of a contour and two fitting functions incorporating regularization terms, from which a curve evolution model in level set formation is derived for energy minimization. We utilize it to detect regions of with a large field gradient caused by strong susceptibility variation. In such regions, the SGK will have a small radius and high weight at the sphere center in a manner adaptive to the voxel energy of the field perturbation. Using the proposed method, the background field generated from external sources can be effectively removed to get a more accurate estimation of the local field and thus of the QSM dipole inversion to map local tissue susceptibility sources. Numerical simulation, phantom and in vivo human brain data demonstrate improved performance of R-SHARP compared to V-SHARP and RESHARP (regularization enabled SHARP) methods, even when the whole paranasal sinus regions are preserved in the brain mask. Shadow artifacts due to strong susceptibility variations in the derived QSM maps could also be largely eliminated using the R-SHARP method, leading to more accurate QSM reconstruction.

Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain.

PubMed

Fang, Jinsheng; Bao, Lijun; Li, Xu; van Zijl, Peter C M; Chen, Zhong

2017-08-01

Background field removal is an important MR phase preprocessing step for quantitative susceptibility mapping (QSM). It separates the local field induced by tissue magnetic susceptibility sources from the background field generated by sources outside a region of interest, e.g. brain, such as air-tissue interface. In the vicinity of air-tissue boundary, e.g. skull and paranasal sinuses, where large susceptibility variations exist, present background field removal methods are usually insufficient and these regions often need to be excluded by brain mask erosion at the expense of losing information of local field and thus susceptibility measures in these regions. In this paper, we propose an extension to the variable-kernel sophisticated harmonic artifact reduction for phase data (V-SHARP) background field removal method using a region adaptive kernel (R-SHARP), in which a scalable spherical Gaussian kernel (SGK) is employed with its kernel radius and weights adjustable according to an energy "functional" reflecting the magnitude of field variation. Such an energy functional is defined in terms of a contour and two fitting functions incorporating regularization terms, from which a curve evolution model in level set formation is derived for energy minimization. We utilize it to detect regions of with a large field gradient caused by strong susceptibility variation. In such regions, the SGK will have a small radius and high weight at the sphere center in a manner adaptive to the voxel energy of the field perturbation. Using the proposed method, the background field generated from external sources can be effectively removed to get a more accurate estimation of the local field and thus of the QSM dipole inversion to map local tissue susceptibility sources. Numerical simulation, phantom and in vivo human brain data demonstrate improved performance of R-SHARP compared to V-SHARP and RESHARP (regularization enabled SHARP) methods, even when the whole paranasal sinus regions are preserved in the brain mask. Shadow artifacts due to strong susceptibility variations in the derived QSM maps could also be largely eliminated using the R-SHARP method, leading to more accurate QSM reconstruction. Copyright © 2017. Published by Elsevier Inc.

Systems Biology Analysis of Gene Expression during In Vivo Mycobacterium avium paratuberculosis Enteric Colonization Reveals Role for Immune Tolerance

PubMed Central

Khare, Sangeeta; Lawhon, Sara D.; Drake, Kenneth L.; Nunes, Jairo E. S.; Figueiredo, Josely F.; Rossetti, Carlos A.; Gull, Tamara; Everts, Robin E.; Lewin, Harris A.; Galindo, Cristi L.; Garner, Harold R.; Adams, Leslie Garry

2012-01-01

Survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP) in the intestinal mucosa is associated with host immune tolerance. However, the initial events during MAP interaction with its host that lead to pathogen survival, granulomatous inflammation, and clinical disease progression are poorly defined. We hypothesize that immune tolerance is initiated upon initial contact of MAP with the intestinal Peyer's patch. To test our hypothesis, ligated ileal loops in neonatal calves were infected with MAP. Intestinal tissue RNAs were collected (0.5, 1, 2, 4, 8 and 12 hrs post-infection), processed, and hybridized to bovine gene expression microarrays. By comparing the gene transcription responses of calves infected with the MAP, informative complex patterns of expression were clearly visible. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis, and genes were grouped into the specific pathways and gene ontology categories to create a holistic model. This model revealed three different phases of responses: i) early (30 min and 1 hr post-infection), ii) intermediate (2, 4 and 8 hrs post-infection), and iii) late (12 hrs post-infection). We describe here the data that include expression profiles for perturbed pathways, as well as, mechanistic genes (genes predicted to have regulatory influence) that are associated with immune tolerance. In the Early Phase of MAP infection, multiple pathways were initiated in response to MAP invasion via receptor mediated endocytosis and changes in intestinal permeability. During the Intermediate Phase, perturbed pathways involved the inflammatory responses, cytokine-cytokine receptor interaction, and cell-cell signaling. During the Late Phase of infection, gene responses associated with immune tolerance were initiated at the level of T-cell signaling. Our study provides evidence that MAP infection resulted in differentially regulated genes, perturbed pathways and specifically modified mechanistic genes contributing to the colonization of Peyer's patch. PMID:22912686

Multiscale quantification of tissue spiculation and distortion for detection of architectural distortion and spiculated mass in mammography

NASA Astrophysics Data System (ADS)

Lao, Zhiqiang; Zheng, Xin

2011-03-01

This paper proposes a multiscale method to quantify tissue spiculation and distortion in mammography CAD systems that aims at improving the sensitivity in detecting architectural distortion and spiculated mass. This approach addresses the difficulty of predetermining the neighborhood size for feature extraction in characterizing lesions demonstrating spiculated mass/architectural distortion that may appear in different sizes. The quantification is based on the recognition of tissue spiculation and distortion pattern using multiscale first-order phase portrait model in texture orientation field generated by Gabor filter bank. A feature map is generated based on the multiscale quantification for each mammogram and two features are then extracted from the feature map. These two features will be combined with other mass features to provide enhanced discriminate ability in detecting lesions demonstrating spiculated mass and architectural distortion. The efficiency and efficacy of the proposed method are demonstrated with results obtained by applying the method to over 500 cancer cases and over 1000 normal cases.

Colorectal carcinoma: Ex vivo evaluation using 3-T high-spatial-resolution quantitative T2 mapping and its correlation with histopathologic findings.

PubMed

Yamada, Ichiro; Yoshino, Norio; Hikishima, Keigo; Miyasaka, Naoyuki; Yamauchi, Shinichi; Uetake, Hiroyuki; Yasuno, Masamichi; Saida, Yukihisa; Tateishi, Ukihide; Kobayashi, Daisuke; Eishi, Yoshinobu

2017-05-01

In this study, we aimed to evaluate the feasibility of determining the mural invasion depths of colorectal carcinomas using high-spatial-resolution (HSR) quantitative T2 mapping on a 3-T magnetic resonance (MR) scanner. Twenty colorectal specimens containing adenocarcinomas were imaged on a 3-T MR system equipped with a 4-channel phased-array surface coil. HSR quantitative T2 maps were acquired using a spin-echo sequence with a repetition time/echo time of 7650/22.6-361.6ms (16 echoes), 87×43.5-mm field of view, 2-mm section thickness, 448×224 matrix, and average of 1. HSR fast-spin-echo T2-weighted images were also acquired. Differences between the T2 values (ms) of the tumor tissue, colorectal wall layers, and fibrosis were measured, and the MR images and histopathologic findings were compared. In all specimens (20/20, 100%), the HSR quantitative T2 maps clearly depicted an 8-layer normal colorectal wall in which the T2 values of each layer differed from those of the adjacent layer(s) (P<0.001). Using this technique, fibrosis (73.6±9.4ms) and tumor tissue (104.2±6.4ms) could also be clearly differentiated (P<0.001). In 19 samples (95%), the HSR quantitative T2 maps and histopathologic data yielded the same findings regarding the tumor invasion depth. Our results indicate that 3-T HSR quantitative T2 mapping is useful for distinguishing colorectal wall layers and differentiating tumor and fibrotic tissues. Accordingly, this technique could be used to determine mural invasion by colorectal carcinomas with a high level of accuracy. Copyright © 2017 Elsevier Inc. All rights reserved.

Evaluation of osteoarthritis progression using polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Nassif, Nader A.; Pierce, Mark C.; Park, B. Hyle; Cense, Barry; de Boer, Johannes F.

2004-07-01

Osteoarthritis is a prevalent medical condition that presents a diagnostic and therapeutic challenge to physicians today because of the inability to assess the integrity of the articular cartilage early in the disease. Polarization sensitive optical coherence tomography (PS-OCT) is a high resolution, non-contact imaging modality that provides cross-sectional images with additional information regarding the integrity of the collagen matrix. Using PS-OCT to image provides information regarding thickness of the articular cartilage and gives an index of biochemical changes based on alterations in optical properties (i.e. birefringence) of the tissue. We demonstrate initial experiments performed on specimens collected following total knee replacement surgery. Articular cartilage was imaged using a 1310 nm PS-OCT system where both intensity and phase images were acquired. PS-OCT images were compared with histology, and the changes in tissue optical properties were characterized. Analysis of the intensity images demonstrates differences between healthy and diseased cartilage surface and thickness. Phase maps of the tissue demonstrated distinct differences between healthy and diseased tissue. PS-OCT was able to image a gradual loss of birefringence as the tissue became more diseased. In this way, determining the rate of change of the phase provides a quantitative measure of pathology. Thus, imaging and evaluation of osteoarthritis using PS-OCT can be a useful means of quantitative assessment of the disease.

The effect of electronically steering a phased array ultrasound transducer on near-field tissue heating.

PubMed

Payne, Allison; Vyas, Urvi; Todd, Nick; de Bever, Joshua; Christensen, Douglas A; Parker, Dennis L

2011-09-01

This study presents the results obtained from both simulation and experimental techniques that show the effect of mechanically or electronically steering a phased array transducer on proximal tissue heating. The thermal response of a nine-position raster and a 16-mm diameter circle scanning trajectory executed through both electronic and mechanical scanning was evaluated in computer simulations and experimentally in a homogeneous tissue-mimicking phantom. Simulations were performed using power deposition maps obtained from the hybrid angular spectrum (HAS) method and applying a finite-difference approximation of the Pennes' bioheat transfer equation for the experimentally used transducer and also for a fully sampled transducer to demonstrate the effect of acoustic window, ultrasound beam overlap and grating lobe clutter on near-field heating. Both simulation and experimental results show that electronically steering the ultrasound beam for the two trajectories using the 256-element phased array significantly increases the thermal dose deposited in the near-field tissues when compared with the same treatment executed through mechanical steering only. In addition, the individual contributions of both beam overlap and grating lobe clutter to the near-field thermal effects were determined through comparing the simulated ultrasound beam patterns and resulting temperature fields from mechanically and electronically steered trajectories using the 256-randomized element phased array transducer to an electronically steered trajectory using a fully sampled transducer with 40 401 phase-adjusted sample points. Three distinctly different three distinctly different transducers were simulated to analyze the tradeoffs of selected transducer design parameters on near-field heating. Careful consideration of design tradeoffs and accurate patient treatment planning combined with thorough monitoring of the near-field tissue temperature will help to ensure patient safety during an MRgHIFU treatment.

Human body epigenome maps reveal noncanonical DNA methylation variation.

PubMed

Schultz, Matthew D; He, Yupeng; Whitaker, John W; Hariharan, Manoj; Mukamel, Eran A; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R; Urich, Mark A; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J; Wang, Wei; Ecker, Joseph R

2015-07-09

Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual's cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals' phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.

Mueller-matrix mapping of biological tissues in differential diagnosis of optical anisotropy mechanisms of protein networks

NASA Astrophysics Data System (ADS)

Ushenko, V. A.; Sidor, M. I.; Marchuk, Yu F.; Pashkovskaya, N. V.; Andreichuk, D. R.

2015-03-01

We report a model of Mueller-matrix description of optical anisotropy of protein networks in biological tissues with allowance for the linear birefringence and dichroism. The model is used to construct the reconstruction algorithms of coordinate distributions of phase shifts and the linear dichroism coefficient. In the statistical analysis of such distributions, we have found the objective criteria of differentiation between benign and malignant tissues of the female reproductive system. From the standpoint of evidence-based medicine, we have determined the operating characteristics (sensitivity, specificity and accuracy) of the Mueller-matrix reconstruction method of optical anisotropy parameters and demonstrated its effectiveness in the differentiation of benign and malignant tumours.

Quantitative phase imaging of biological cells and tissues using singleshot white light interference microscopy and phase subtraction method for extended range of measurement

NASA Astrophysics Data System (ADS)

Mehta, Dalip Singh; Sharma, Anuradha; Dubey, Vishesh; Singh, Veena; Ahmad, Azeem

2016-03-01

We present a single-shot white light interference microscopy for the quantitative phase imaging (QPI) of biological cells and tissues. A common path white light interference microscope is developed and colorful white light interferogram is recorded by three-chip color CCD camera. The recorded white light interferogram is decomposed into the red, green and blue color wavelength component interferograms and processed it to find out the RI for different color wavelengths. The decomposed interferograms are analyzed using local model fitting (LMF)" algorithm developed for reconstructing the phase map from single interferogram. LMF is slightly off-axis interferometric QPI method which is a single-shot method that employs only a single image, so it is fast and accurate. The present method is very useful for dynamic process where path-length changes at millisecond level. From the single interferogram a wavelength-dependent quantitative phase imaging of human red blood cells (RBCs) are reconstructed and refractive index is determined. The LMF algorithm is simple to implement and is efficient in computation. The results are compared with the conventional phase shifting interferometry and Hilbert transform techniques.

Determination of the complex refractive index segments of turbid sample with multispectral spatially modulated structured light and models approximation

NASA Astrophysics Data System (ADS)

Meitav, Omri; Shaul, Oren; Abookasis, David

2017-09-01

Spectral data enabling the derivation of a biological tissue sample's complex refractive index (CRI) can provide a range of valuable information in the clinical and research contexts. Specifically, changes in the CRI reflect alterations in tissue morphology and chemical composition, enabling its use as an optical marker during diagnosis and treatment. In the present work, we report a method for estimating the real and imaginary parts of the CRI of a biological sample using Kramers-Kronig (KK) relations in the spatial frequency domain. In this method, phase-shifted sinusoidal patterns at single high spatial frequency are serially projected onto the sample surface at different near-infrared wavelengths while a camera mounted normal to the sample surface acquires the reflected diffuse light. In the offline analysis pipeline, recorded images at each wavelength are converted to spatial phase maps using KK analysis and are then calibrated against phase-models derived from diffusion approximation. The amplitude of the reflected light, together with phase data, is then introduced into Fresnel equations to resolve both real and imaginary segments of the CRI at each wavelength. The technique was validated in tissue-mimicking phantoms with known optical parameters and in mouse models of ischemic injury and heat stress. Experimental data obtained indicate variations in the CRI among brain tissue suffering from injury. CRI fluctuations correlated with alterations in the scattering and absorption coefficients of the injured tissue are demonstrated. This technique for deriving dynamic changes in the CRI of tissue may be further developed as a clinical diagnostic tool and for biomedical research applications. To the best of our knowledge, this is the first report of the estimation of the spectral CRI of a mouse head following injury obtained in the spatial frequency domain.

Brain Injury Lesion Imaging Using Preconditioned Quantitative Susceptibility Mapping without Skull Stripping.

PubMed

Soman, S; Liu, Z; Kim, G; Nemec, U; Holdsworth, S J; Main, K; Lee, B; Kolakowsky-Hayner, S; Selim, M; Furst, A J; Massaband, P; Yesavage, J; Adamson, M M; Spincemallie, P; Moseley, M; Wang, Y

2018-04-01

Identifying cerebral microhemorrhage burden can aid in the diagnosis and management of traumatic brain injury, stroke, hypertension, and cerebral amyloid angiopathy. MR imaging susceptibility-based methods are more sensitive than CT for detecting cerebral microhemorrhage, but methods other than quantitative susceptibility mapping provide results that vary with field strength and TE, require additional phase maps to distinguish blood from calcification, and depict cerebral microhemorrhages as bloom artifacts. Quantitative susceptibility mapping provides universal quantification of tissue magnetic property without these constraints but traditionally requires a mask generated by skull-stripping, which can pose challenges at tissue interphases. We evaluated the preconditioned quantitative susceptibility mapping MR imaging method, which does not require skull-stripping, for improved depiction of brain parenchyma and pathology. Fifty-six subjects underwent brain MR imaging with a 3D multiecho gradient recalled echo acquisition. Mask-based quantitative susceptibility mapping images were created using a commonly used mask-based quantitative susceptibility mapping method, and preconditioned quantitative susceptibility images were made using precondition-based total field inversion. All images were reviewed by a neuroradiologist and a radiology resident. Ten subjects (18%), all with traumatic brain injury, demonstrated blood products on 3D gradient recalled echo imaging. All lesions were visible on preconditioned quantitative susceptibility mapping, while 6 were not visible on mask-based quantitative susceptibility mapping. Thirty-one subjects (55%) demonstrated brain parenchyma and/or lesions that were visible on preconditioned quantitative susceptibility mapping but not on mask-based quantitative susceptibility mapping. Six subjects (11%) demonstrated pons artifacts on preconditioned quantitative susceptibility mapping and mask-based quantitative susceptibility mapping; they were worse on preconditioned quantitative susceptibility mapping. Preconditioned quantitative susceptibility mapping MR imaging can bring the benefits of quantitative susceptibility mapping imaging to clinical practice without the limitations of mask-based quantitative susceptibility mapping, especially for evaluating cerebral microhemorrhage-associated pathologies, such as traumatic brain injury. © 2018 by American Journal of Neuroradiology.

Wavelet analysis of myocardium polarization images in problems of diagnostic of necrotic changes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.

2017-08-01

The paper presents the results of polarization manifestations of small - and Large-scale phase anisotropy of dead in consequence of ischemic heart disease (IHD) and acute coronary insufficiency (ACI) people myocardial tissue structures to differentiate information, the wavelet analysis method is used. The resulting maps of the of the polarizationcorrelation parameters distributions (the phase of the two-point first and second parameters of the Stokes vector) are analyzed in the framework of statistical approach. On this basis, the criteria for differential diagnosis of IHD and ACI cases have been determined.

Diagnosis of breast cancer biopsies using quantitative phase imaging

NASA Astrophysics Data System (ADS)

Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel

2015-03-01

The standard practice in the histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope. The pathologist looks at certain morphological features, visible under the stain, to diagnose whether a tumor is benign or malignant. This determination is made based on qualitative inspection making it subject to investigator bias. Furthermore, since this method requires a microscopic examination by the pathologist it suffers from low throughput. A quantitative, label-free and high throughput method for detection of these morphological features from images of tissue biopsies is, hence, highly desirable as it would assist the pathologist in making a quicker and more accurate diagnosis of cancers. We present here preliminary results showing the potential of using quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated optical path length maps of unstained breast tissue biopsies using Spatial Light Interference Microscopy (SLIM). As a first step towards diagnosis based on quantitative phase imaging, we carried out a qualitative evaluation of the imaging resolution and contrast of our label-free phase images. These images were shown to two pathologists who marked the tumors present in tissue as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on H&E stained tissue images and the number of agreements were counted. In our experiment, the agreement between SLIM and H&E based diagnosis was measured to be 88%. Our preliminary results demonstrate the potential and promise of SLIM for a push in the future towards quantitative, label-free and high throughput diagnosis.

Haemodynamic changes in trauma.

PubMed

Kirkman, E; Watts, S

2014-08-01

Trauma is the leading cause of death during the first four decades of life in the developed countries. Its haemodynamic response underpins the patient's initial ability to survive, and the response to treatment and subsequent morbidity and resolution. Trauma causes a number of insults including haemorrhage, tissue injury (nociception) and, predominantly, in military casualties, blast from explosions. This article discusses aspects of the haemodynamic responses to these insults and subsequent treatment. 'Simple' haemorrhage (blood loss without significant volume of tissue damage) causes a biphasic response: mean arterial blood pressure (MBP) is initially maintained by the baroreflex (tachycardia and increased vascular resistance, Phase 1), followed by a sudden decrease in MAP initiated by a second reflex (decrease in vascular resistance and bradycardia, Phase 2). Phase 2 may be protective. The response to tissue injury attenuates Phase 2 and may cause a deleterious haemodynamic redistribution that compromises blood flow to some vital organs. In contrast, thoracic blast exposure augments Phase 2 of the response to haemorrhage. However, hypoxaemia from lung injury limits the effectiveness of hypotensive resuscitation by augmenting the attendant shock state. An alternative strategy ('hybrid resuscitation') whereby tissue perfusion is increased after the first hour of hypotensive resuscitation by adopting a revised normotensive target may ameliorate these problems. Finally, morphine also attenuates Phase 2 of the response to haemorrhage in some, but not all, species and this is associated with poor outcome. The impact on human patients is currently unknown and is the subject of a current physiological investigation. © Crown copyright 2014. Published with the permission of the Defence Science and Technology Laboratory on behalf of the Controller of HMSO. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Quantization of liver tissue in dual kVp computed tomography using linear discriminant analysis

NASA Astrophysics Data System (ADS)

Tkaczyk, J. Eric; Langan, David; Wu, Xiaoye; Xu, Daniel; Benson, Thomas; Pack, Jed D.; Schmitz, Andrea; Hara, Amy; Palicek, William; Licato, Paul; Leverentz, Jaynne

2009-02-01

Linear discriminate analysis (LDA) is applied to dual kVp CT and used for tissue characterization. The potential to quantitatively model both malignant and benign, hypo-intense liver lesions is evaluated by analysis of portal-phase, intravenous CT scan data obtained on human patients. Masses with an a priori classification are mapped to a distribution of points in basis material space. The degree of localization of tissue types in the material basis space is related to both quantum noise and real compositional differences. The density maps are analyzed with LDA and studied with system simulations to differentiate these factors. The discriminant analysis is formulated so as to incorporate the known statistical properties of the data. Effective kVp separation and mAs relates to precision of tissue localization. Bias in the material position is related to the degree of X-ray scatter and partial-volume effect. Experimental data and simulations demonstrate that for single energy (HU) imaging or image-based decomposition pixel values of water-like tissues depend on proximity to other iodine-filled bodies. Beam-hardening errors cause a shift in image value on the scale of that difference sought between in cancerous and cystic lessons. In contrast, projection-based decomposition or its equivalent when implemented on a carefully calibrated system can provide accurate data. On such a system, LDA may provide novel quantitative capabilities for tissue characterization in dual energy CT.

Minimally invasive ultrasound thermal therapy with MR thermal monitoring and guidance

NASA Astrophysics Data System (ADS)

Diederich, Chris J.; Stafford, R. Jason; Price, Roger E.; Nau, William H.; Tyreus, Per Daniel; Rivera, Belinda; Schomer, Donald; Olsson, Lars; Hazle, John D.

2001-06-01

In this study both transurethral and interstitial ultrasound thermal therapy were applied to thermally coagulate targeted portions of the canine prostate or brain and implanted TVT tumors while using MRI-based thermal mapping techniques to monitor the therapy. MRI was also used for target definition, positioning of the applicator, and evaluation of target viability post-therapy. The complex phase-difference mapping technique using an iGE-EPI sequence with lipid suppression was used for determining temperature elevations within the in vivo prostate or brain and surrounding structures. Calculated temperature distributions, thermal dose exposures, T2-wieghted & T1-contrast enhanced images, gross inspection, and histology of sectioned prostates and brains were in good agreement with each other in defining destroyed tissue zones. Interstitial and transurethral ultrasound applicators produce directed zones of thermal coagulation within targeted tissue and implanted tumor, which can be accurately monitored and evaluated by MRI.

Segmentation of liver region with tumorous tissues

NASA Astrophysics Data System (ADS)

Zhang, Xuejun; Lee, Gobert; Tajima, Tetsuji; Kitagawa, Teruhiko; Kanematsu, Masayuki; Zhou, Xiangrong; Hara, Takeshi; Fujita, Hiroshi; Yokoyama, Ryujiro; Kondo, Hiroshi; Hoshi, Hiroaki; Nawano, Shigeru; Shinozaki, Kenji

2007-03-01

Segmentation of an abnormal liver region based on CT or MR images is a crucial step in surgical planning. However, precisely carrying out this step remains a challenge due to either connectivities of the liver to other organs or the shape, internal texture, and homogeneity of liver that maybe extensively affected in case of liver diseases. Here, we propose a non-density based method for extracting the liver region containing tumor tissues by edge detection processing. False extracted regions are eliminated by a shape analysis method and thresholding processing. If the multi-phased images are available then the overall outcome of segmentation can be improved by subtracting two phase images, and the connectivities can be further eliminated by referring to the intensity on another phase image. Within an edge liver map, tumor candidates are identified by their different gray values relative to the liver. After elimination of the small and nonspherical over-extracted regions, the final liver region integrates the tumor region with the liver tissue. In our experiment, 40 cases of MDCT images were used and the result showed that our fully automatic method for the segmentation of liver region is effective and robust despite the presence of hepatic tumors within the liver.

Focusing light through scattering media by polarization modulation based generalized digital optical phase conjugation

NASA Astrophysics Data System (ADS)

Yang, Jiamiao; Shen, Yuecheng; Liu, Yan; Hemphill, Ashton S.; Wang, Lihong V.

2017-11-01

Optical scattering prevents light from being focused through thick biological tissue at depths greater than ˜1 mm. To break this optical diffusion limit, digital optical phase conjugation (DOPC) based wavefront shaping techniques are being actively developed. Previous DOPC systems employed spatial light modulators that modulated either the phase or the amplitude of the conjugate light field. Here, we achieve optical focusing through scattering media by using polarization modulation based generalized DOPC. First, we describe an algorithm to extract the polarization map from the measured scattered field. Then, we validate the algorithm through numerical simulations and find that the focusing contrast achieved by polarization modulation is similar to that achieved by phase modulation. Finally, we build a system using an inexpensive twisted nematic liquid crystal based spatial light modulator (SLM) and experimentally demonstrate light focusing through 3-mm thick chicken breast tissue. Since the polarization modulation based SLMs are widely used in displays and are having more and more pixel counts with the prevalence of 4 K displays, these SLMs are inexpensive and valuable devices for wavefront shaping.

OCT-based approach to local relaxations discrimination from translational relaxation motions

NASA Astrophysics Data System (ADS)

Matveev, Lev A.; Matveyev, Alexandr L.; Gubarkova, Ekaterina V.; Gelikonov, Grigory V.; Sirotkina, Marina A.; Kiseleva, Elena B.; Gelikonov, Valentin M.; Gladkova, Natalia D.; Vitkin, Alex; Zaitsev, Vladimir Y.

2016-04-01

Multimodal optical coherence tomography (OCT) is an emerging tool for tissue state characterization. Optical coherence elastography (OCE) is an approach to mapping mechanical properties of tissue based on OCT. One of challenging problems in OCE is elimination of the influence of residual local tissue relaxation that complicates obtaining information on elastic properties of the tissue. Alternatively, parameters of local relaxation itself can be used as an additional informative characteristic for distinguishing the tissue in normal and pathological states over the OCT image area. Here we briefly present an OCT-based approach to evaluation of local relaxation processes in the tissue bulk after sudden unloading of its initial pre-compression. For extracting the local relaxation rate we evaluate temporal dependence of local strains that are mapped using our recently developed hybrid phase resolved/displacement-tracking (HPRDT) approach. This approach allows one to subtract the contribution of global displacements of scatterers in OCT scans and separate the temporal evolution of local strains. Using a sample excised from of a coronary arteria, we demonstrate that the observed relaxation of local strains can be reasonably fitted by an exponential law, which opens the possibility to characterize the tissue by a single relaxation time. The estimated local relaxation times are assumed to be related to local biologically-relevant processes inside the tissue, such as diffusion, leaking/draining of the fluids, local folding/unfolding of the fibers, etc. In general, studies of evolution of such features can provide new metrics for biologically-relevant changes in tissue, e.g., in the problems of treatment monitoring.

Noncontact blood perfusion mapping in clinical applications

NASA Astrophysics Data System (ADS)

Iakovlev, Dmitry; Dwyer, Vincent; Hu, Sijung; Silberschmidt, Vadim

2016-04-01

Non-contact imaging photoplethysmography (iPPG) to detect pulsatile blood microcirculation in tissue has been selected as a successor to low spatial resolution and slow scanning blood perfusion techniques currently employed by clinicians. The proposed iPPG system employs a novel illumination source constructed of multiple high power LEDs with narrow spectral emission, which are temporally modulated and synchronised with a high performance sCMOS sensor. To ensure spectrum stability and prevent thermal wavelength drift due to junction temperature variations, each LED features a custom-designed thermal management system to effectively dissipate generated heat and auto-adjust current flow. The use of a multi-wavelength approach has resulted in simultaneous microvascular perfusion monitoring at various tissue depths, which is an added benefit for specific clinical applications. A synchronous detection algorithm to extract weak photoplethysmographic pulse-waveforms demonstrated robustness and high efficiency when applied to even small regions of 5 mm2. The experimental results showed evidences that the proposed system could achieve noticeable accuracy in blood perfusion monitoring by creating complex amplitude and phase maps for the tissue under examination.

SU-E-J-219: A Dixon Based Pseudo-CT Generation Method for MR-Only Radiotherapy Treatment Planning of the Pelvis and Head and Neck

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maspero, M.; Meijer, G.J.; Lagendijk, J.J.W.

2015-06-15

Purpose: To develop an image processing method for MRI-based generation of electron density maps, known as pseudo-CT (pCT), without usage of model- or atlas-based segmentation, and to evaluate the method in the pelvic and head-neck region against CT. Methods: CT and MRI scans were obtained from the pelvic region of four patients in supine position using a flat table top only for CT. Stratified CT maps were generated by classifying each voxel based on HU ranges into one of four classes: air, adipose tissue, soft tissue or bone.A hierarchical region-selective algorithm, based on automatic thresholding and clustering, was used tomore » classify tissues from MR Dixon reconstructed fat, In-Phase (IP) and Opposed-Phase (OP) images. First, a body mask was obtained by thresholding the IP image. Subsequently, an automatic threshold on the Dixon fat image differentiated soft and adipose tissue. K-means clustering on IP and OP images resulted in a mask that, via a connected neighborhood analysis, allowing the user to select the components corresponding to bone structures.The pCT was estimated through assignment of bulk HU to the tissue classes. Bone-only Digital Reconstructed Radiographs (DRR) were generated as well. The pCT images were rigidly registered to the stratified CT to allow a volumetric and voxelwise comparison. Moreover, pCTs were also calculated within the head-neck region in two volunteers using the same pipeline. Results: The volumetric comparison resulted in differences <1% for each tissue class. A voxelwise comparison showed a good classification, ranging from 64% to 98%. The primary misclassified classes were adipose/soft tissue and bone/soft tissue. As the patients have been imaged on different table tops, part of the misclassification error can be explained by misregistration. Conclusion: The proposed approach does not rely on an anatomy model providing the flexibility to successfully generate the pCT in two different body sites. This research is founded by ZonMw IMDI Programme, project name: “RASOR sharp: MRI based radiotherapy planning using a single MRI sequence”, project number: 10-104003010.« less

Variation in the Helical Structure of Native Collagen

DTIC Science & Technology

2014-02-24

unsampled molecular transform of the sample (non-crystalline diffraction arising from the helical symmetry), these patterns also contain Bragg peaks...tissues may be treated as analogous to that from a single macromolecular crystal. Except that it arises from many fibrils within the sample , giving rise...density maps, constructed from experimentally determined phases and observed amplitudes, showed good agreement. The observed diffraction and the simulated

Optical coherence elastography assesses tissue modifications in laser reshaping of cornea and cartilages

NASA Astrophysics Data System (ADS)

Zaitsev, V. Y.; Matveyev, A. L.; Matveev, L. A.; Gelikonov, G. V.; Omelchenko, A. I.; Shabanov, D. V.; Sovetsky, A. A.; Baum, O. I.; Vitkin, A.; Sobol, E. N.

2018-02-01

Non-surgical thermo-mechanical reshaping of avascular collagenous tissues (cartilages and cornea) using moderate heating by IR-laser irradiation is an emerging technology that can find important applications in visioncorrection problems and preparation of cartilaginous implants in otolaryngology. To estimate both transient interframe strains and cumulative resultant strains produced by the laser irradiation of the tissue we use and improved version of strain mapping developed in our previous work related to compressional phase-sensitive optical coherence tomography. To reveal microstructural changes in the tissue regions where irradiation-produced strains do not disappear after temperature equilibration, we apply compressional optical coherence elastography in order to visualize the resultant variations in the tissue stiffness. The so-found regions of the stiffness reduction are attributed to formation of microscopic pores, existence of which agree with independent data obtained using methods of high-resolution microscopy.

Applications of condensed matter understanding to medical tissues and disease progression: Elemental analysis and structural integrity of tissue scaffolds

NASA Astrophysics Data System (ADS)

Bradley, D. A.; Farquharson, M. J.; Gundogdu, O.; Al-Ebraheem, Alia; Che Ismail, Elna; Kaabar, W.; Bunk, O.; Pfeiffer, F.; Falkenberg, G.; Bailey, M.

2010-02-01

The investigations reported herein link tissue structure and elemental presence with issues of environmental health and disease, exemplified by uptake and storage of potentially toxic elements in the body, the osteoarthritic condition and malignancy in the breast and other soft tissues. Focus is placed on application of state-of-the-art ionizing radiation techniques, including, micro-synchrotron X-ray fluorescence (μ-SXRF) and particle-induced X-ray emission/Rutherford backscattering mapping (μ-PIXE/RBS), coherent small-angle X-ray scattering (cSAXS) and X-ray phase-contrast imaging, providing information on elemental make-up, the large-scale organisation of collagen and anatomical features of moderate and low atomic number media. For the particular situations under investigation, use of such facilities is allowing information to be obtained at an unprecedented level of detail, yielding new understanding of the affected tissues and the progression of disease.

Monitoring of thermal therapy based on shear modulus changes: I. shear wave thermometry.

PubMed

Arnal, Bastien; Pernot, Mathieu; Tanter, Mickael

2011-02-01

The clinical applicability of high-intensity focused ultrasound (HIFU) for noninvasive therapy is today hampered by the lack of robust and real-time monitoring of tissue damage during treatment. The goal of this study is to show that the estimation of local tissue elasticity from shear wave imaging (SWI) can lead to the 2-D mapping of temperature changes during HIFU treatments. This new concept of shear wave thermometry is experimentally implemented here using conventional ultrasonic imaging probes. HIFU treatment and monitoring were, respectively, performed using a confocal setup consisting of a 2.5-MHz single-element transducer focused at 30 mm on ex vivo samples and an 8-MHz ultrasound diagnostic probe. Thermocouple measurements and ultrasound-based thermometry were used as a gold standard technique and were combined with SWI on the same device. The SWI sequences consisted of 2 successive shear waves induced at different lateral positions. Each wave was created using 100-μs pushing beams at 3 depths. The shear wave propagation was acquired at 17,000 frames/s, from which the elasticity map was recovered. HIFU sonications were interleaved with fast imaging acquisitions, allowing a duty cycle of more than 90%. Elasticity and temperature mapping was achieved every 3 s, leading to realtime monitoring of the treatment. Tissue stiffness was found to decrease in the focal zone for temperatures up to 43°C. Ultrasound-based temperature estimation was highly correlated to stiffness variation maps (r² = 0.91 to 0.97). A reversible calibration phase of the changes of elasticity with temperature can be made locally using sighting shots. This calibration process allows for the derivation of temperature maps from shear wave imaging. Compared with conventional ultrasound-based approaches, shear wave thermometry is found to be much more robust to motion artifacts.

Automatic Gleason grading of prostate cancer using SLIM and machine learning

NASA Astrophysics Data System (ADS)

Nguyen, Tan H.; Sridharan, Shamira; Marcias, Virgilia; Balla, Andre K.; Do, Minh N.; Popescu, Gabriel

2016-03-01

In this paper, we present an updated automatic diagnostic procedure for prostate cancer using quantitative phase imaging (QPI). In a recent report [1], we demonstrated the use of Random Forest for image segmentation on prostate cores imaged using QPI. Based on these label maps, we developed an algorithm to discriminate between regions with Gleason grade 3 and 4 prostate cancer in prostatectomy tissue. The Area-Under-Curve (AUC) of 0.79 for the Receiver Operating Curve (ROC) can be obtained for Gleason grade 4 detection in a binary classification between Grade 3 and Grade 4. Our dataset includes 280 benign cases and 141 malignant cases. We show that textural features in phase maps have strong diagnostic values since they can be used in combination with the label map to detect presence or absence of basal cells, which is a strong indicator for prostate carcinoma. A support vector machine (SVM) classifier trained on this new feature vector can classify cancer/non-cancer with an error rate of 0.23 and an AUC value of 0.83.

MAP3K8 (TPL2/COT) affects obesity-induced adipose tissue inflammation without systemic effects in humans and in mice.

PubMed

Ballak, Dov B; van Essen, Peter; van Diepen, Janna A; Jansen, Henry; Hijmans, Anneke; Matsuguchi, Tetsuya; Sparrer, Helmut; Tack, Cees J; Netea, Mihai G; Joosten, Leo A B; Stienstra, Rinke

2014-01-01

Chronic low-grade inflammation in adipose tissue often accompanies obesity, leading to insulin resistance and increasing the risk for metabolic diseases. MAP3K8 (TPL2/COT) is an important signal transductor and activator of pro-inflammatory pathways that has been linked to obesity-induced adipose tissue inflammation. We used human adipose tissue biopsies to study the relationship of MAP3K8 expression with markers of obesity and expression of pro-inflammatory cytokines (IL-1β, IL-6 and IL-8). Moreover, we evaluated obesity-induced adipose tissue inflammation and insulin resistance in mice lacking MAP3K8 and WT mice on a high-fat diet (HFD) for 16 weeks. Individuals with a BMI >30 displayed a higher mRNA expression of MAP3K8 in adipose tissue compared to individuals with a normal BMI. Additionally, high mRNA expression levels of IL-1β, IL-6 and IL-8, but not TNF -α, in human adipose tissue were associated with higher expression of MAP3K8. Moreover, high plasma SAA and CRP did not associate with increased MAP3K8 expression in adipose tissue. Similarly, no association was found for MAP3K8 expression with plasma insulin or glucose levels. Mice lacking MAP3K8 had similar bodyweight gain as WT mice, yet displayed lower mRNA expression levels of IL-1β, IL-6 and CXCL1 in adipose tissue in response to the HFD as compared to WT animals. However, MAP3K8 deficient mice were not protected against HFD-induced adipose tissue macrophage infiltration or the development of insulin resistance. Together, the data in both human and mouse show that MAP3K8 is involved in local adipose tissue inflammation, specifically for IL-1β and its responsive cytokines IL-6 and IL-8, but does not seem to have systemic effects on insulin resistance.

Phase-contrast microtomography using an X-ray interferometer having a 40-μm analyzer

NASA Astrophysics Data System (ADS)

Momose, A.; Koyama, I.; Hamaishi, Y.; Yoshikawa, H.; Takeda, T.; Wu, J.; Itai, Y.; Takai, , K.; Uesugi, K.; Suzuki, Y.

2003-03-01

Phase-contrast X-ray tomographic experiment using a triple Laue-case (LLL) interferometer having a 40-μm lamella which was fabricated to improve spatial resolution, was carried out using undulator X-rays at SPring-8, Japan. Three-dimensional images mapping the refractive index were measured for various animal tissues. Comparing the images with those obtained in previous experiments using conventional LLL interferometers having a 1-mm lamella, improvement in the spatial resolution was demonstrated in that histological structures, such as hepatic lobules in liver and tubules in kidney, were revealed.

Absence of rotational activity detected using 2-dimensional phase mapping in the corresponding 3-dimensional phase maps in human persistent atrial fibrillation.

PubMed

Pathik, Bhupesh; Kalman, Jonathan M; Walters, Tomos; Kuklik, Pawel; Zhao, Jichao; Madry, Andrew; Sanders, Prashanthan; Kistler, Peter M; Lee, Geoffrey

2018-02-01

Current phase mapping systems for atrial fibrillation create 2-dimensional (2D) maps. This process may affect the accurate detection of rotors. We developed a 3-dimensional (3D) phase mapping technique that uses the 3D locations of basket electrodes to project phase onto patient-specific left atrial 3D surface anatomy. We sought to determine whether rotors detected in 2D phase maps were present at the corresponding time segments and anatomical locations in 3D phase maps. One-minute left atrial atrial fibrillation recordings were obtained in 14 patients using the basket catheter and analyzed off-line. Using the same phase values, 2D and 3D phase maps were created. Analysis involved determining the dominant propagation patterns in 2D phase maps and evaluating the presence of rotors detected in 2D phase maps in the corresponding 3D phase maps. Using 2D phase mapping, the dominant propagation pattern was single wavefront (36.6%) followed by focal activation (34.0%), disorganized activity (23.7%), rotors (3.3%), and multiple wavefronts (2.4%). Ten transient rotors were observed in 9 of 14 patients (64%). The mean rotor duration was 1.1 ± 0.7 seconds. None of the 10 rotors observed in 2D phase maps were seen at the corresponding time segments and anatomical locations in 3D phase maps; 4 of 10 corresponded with single wavefronts in 3D phase maps, 2 of 10 with 2 simultaneous wavefronts, 1 of 10 with disorganized activity, and in 3 of 10 there was no coverage by the basket catheter at the corresponding 3D anatomical location. Rotors detected in 2D phase maps were not observed in the corresponding 3D phase maps. These findings may have implications for current systems that use 2D phase mapping. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Improved cancer risk stratification and diagnosis via quantitative phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Liu, Yang; Uttam, Shikhar; Pham, Hoa V.; Hartman, Douglas J.

2017-02-01

Pathology remains the gold standard for cancer diagnosis and in some cases prognosis, in which trained pathologists examine abnormality in tissue architecture and cell morphology characteristic of cancer cells with a bright-field microscope. The limited resolution of conventional microscope can result in intra-observer variation, missed early-stage cancers, and indeterminate cases that often result in unnecessary invasive procedures in the absence of cancer. Assessment of nanoscale structural characteristics via quantitative phase represents a promising strategy for identifying pre-cancerous or cancerous cells, due to its nanoscale sensitivity to optical path length, simple sample preparation (i.e., label-free) and low cost. I will present the development of quantitative phase microscopy system in transmission and reflection configuration to detect the structural changes in nuclear architecture, not be easily identifiable by conventional pathology. Specifically, we will present the use of transmission-mode quantitative phase imaging to improve diagnostic accuracy of urine cytology and the nuclear dry mass is progressively correlate with negative, atypical, suspicious and positive cytological diagnosis. In a second application, we will present the use of reflection-mode quantitative phase microscopy for depth-resolved nanoscale nuclear architecture mapping (nanoNAM) of clinically prepared formalin-fixed, paraffin-embedded tissue sections. We demonstrated that the quantitative phase microscopy system detects a gradual increase in the density alteration of nuclear architecture during malignant transformation in animal models of colon carcinogenesis and in human patients with ulcerative colitis, even in tissue that appears histologically normal according to pathologists. We evaluated the ability of nanoNAM to predict "future" cancer progression in patients with ulcerative colitis.

Identifying mitosis deep in tissue using dynamic light scattering fluctuation spectroscopy

NASA Astrophysics Data System (ADS)

An, Ran; Jeong, Kwan; Turek, John; Nolte, David

2012-03-01

In the cell cycle, mitosis is the most dramatic phase, especially in Telophase and Cytokinesis. For single cells and cell monolayer, there are precise microscopic studies of mitosis, while for 3-D tissue such as tumor spheroids the light signal is obscured by the high background of diffusely scattered light. Therefore, the mitosis phase cannot be detected deep inside 3-D tissue using conventional microscopic techniques. In this work, we detect mitosis in living tissue using Tissue Dynamic Imaging (TDI). We trace depth-gated dynamic speckles from a tumor spheroid (up to 1mm in diameter) using coherence-gated digital holography imaging. Frequency-versus-time spectrograms depend on specific types of perturbation such as cell shape change, membrane undulation and cell organelles movements. By using these spectral responses as functional finger prints, we can identify mitosis events from different voxels at a specified depth inside tumor spheroids. By performing B-scans of the tumor spheroid, we generate 3-D mitosis maps (or movies) for the entire tumor spheroids. We show that for healthy tumor spheroids, the mitosis events only happen within the proliferating shell. We also compare results when anti-cancer drugs are applied to arrest, release and synchronize mitosis. This shows the application of TDI for drug screening. The technique can identify and monitor complex motilities inside 3-D tissue with a strong potential for drug diagnosis and developmental biology studies.

Probing the regional distribution of pulmonary gas exchange through single-breath gas- and dissolved-phase 129Xe MR imaging.

PubMed

Kaushik, S Sivaram; Freeman, Matthew S; Cleveland, Zackary I; Davies, John; Stiles, Jane; Virgincar, Rohan S; Robertson, Scott H; He, Mu; Kelly, Kevin T; Foster, W Michael; McAdams, H Page; Driehuys, Bastiaan

2013-09-01

Although some central aspects of pulmonary function (ventilation and perfusion) are known to be heterogeneous, the distribution of diffusive gas exchange remains poorly characterized. A solution is offered by hyperpolarized 129Xe magnetic resonance (MR) imaging, because this gas can be separately detected in the lung's air spaces and dissolved in its tissues. Early dissolved-phase 129Xe images exhibited intensity gradients that favored the dependent lung. To quantitatively corroborate this finding, we developed an interleaved, three-dimensional radial sequence to image the gaseous and dissolved 129Xe distributions in the same breath. These images were normalized and divided to calculate "129Xe gas-transfer" maps. We hypothesized that, for healthy volunteers, 129Xe gas-transfer maps would retain the previously observed posture-dependent gradients. This was tested in nine subjects: when the subjects were supine, 129Xe gas transfer exhibited a posterior-anterior gradient of -2.00 ± 0.74%/cm; when the subjects were prone, the gradient reversed to 1.94 ± 1.14%/cm (P < 0.001). The 129Xe gas-transfer maps also exhibited significant heterogeneity, as measured by the coefficient of variation, that correlated with subject total lung capacity (r = 0.77, P = 0.015). Gas-transfer intensity varied nonmonotonically with slice position and increased in slices proximal to the main pulmonary arteries. Despite substantial heterogeneity, the mean gas transfer for all subjects was 1.00 ± 0.01 while supine and 1.01 ± 0.01 while prone (P = 0.25), indicating good "matching" between gas- and dissolved-phase distributions. This study demonstrates that single-breath gas- and dissolved-phase 129Xe MR imaging yields 129Xe gas-transfer maps that are sensitive to altered gas exchange caused by differences in lung inflation and posture.

Harmonic motion detection in a vibrating scattering medium.

PubMed

Urban, Matthew W; Chen, Shigao; Greenleaf, James

2008-09-01

Elasticity imaging is an emerging medical imaging modality that seeks to map the spatial distribution of tissue stiffness. Ultrasound radiation force excitation and motion tracking using pulse-echo ultrasound have been used in numerous methods. Dynamic radiation force is used in vibrometry to cause an object or tissue to vibrate, and the vibration amplitude and phase can be measured with exceptional accuracy. This paper presents a model that simulates harmonic motion detection in a vibrating scattering medium incorporating 3-D beam shapes for radiation force excitation and motion tracking. A parameterized analysis using this model provides a platform to optimize motion detection for vibrometry applications in tissue. An experimental method that produces a multifrequency radiation force is also presented. Experimental harmonic motion detection of simultaneous multifrequency vibration is demonstrated using a single transducer. This method can accurately detect motion with displacement amplitude as low as 100 to 200 nm in bovine muscle. Vibration phase can be measured within 10 degrees or less. The experimental results validate the conclusions observed from the model and show multifrequency vibration induction and measurements can be performed simultaneously.

Harmonic Motion Detection in a Vibrating Scattering Medium

PubMed Central

Urban, Matthew W.; Chen, Shigao; Greenleaf, James F.

2008-01-01

Elasticity imaging is an emerging medical imaging modality that seeks to map the spatial distribution of tissue stiffness. Ultrasound radiation force excitation and motion tracking using pulse-echo ultrasound have been used in numerous methods. Dynamic radiation force is used in vibrometry to cause an object or tissue to vibrate, and the vibration amplitude and phase can be measured with exceptional accuracy. This paper presents a model that simulates harmonic motion detection in a vibrating scattering medium incorporating 3-D beam shapes for radiation force excitation and motion tracking. A parameterized analysis using this model provides a platform to optimize motion detection for vibrometry applications in tissue. An experimental method that produces a multifrequency radiation force is also presented. Experimental harmonic motion detection of simultaneous multifrequency vibration is demonstrated using a single transducer. This method can accurately detect motion with displacement amplitude as low as 100 to 200 nm in bovine muscle. Vibration phase can be measured within 10° or less. The experimental results validate the conclusions observed from the model and show multifrequency vibration induction and measurements can be performed simultaneously. PMID:18986892

A study on the measurement of the core body temperature change after radiofrequency ablation (RFA) through MR temperature mapping

NASA Astrophysics Data System (ADS)

Kim, Chang-Bok; Dong, Kyung-Rae; Yu, Young; Chung, Woon-Kwan; Cho, Jae-Hwan; Joo, Kyu-Ji

2013-09-01

This study examined the change in the heat generated during radiofrequency ablation (RFA) using a self-manufactured phantom and used magnetic resonance imaging (MRI) to analyze the change in the temperature of the core body and the tissues surrounding the phantom. In this experiment, the image and the phase image were obtained simultaneously from a gradient echo-based sequence using 1.5-Tesla MRI equipment and a 12-channel head coil. The temperature mapping technique was used to calculate the change in temperature. The regions of interest (ROIs) (ROI 1 - ROI 6) were set with a focus on the area where the RFA was performed, according to the temperature distribution, before monitoring the temperature change for one hour in time intervals of five minutes. The results showed that the temperature change in the ROI with time was largest in the ROI 1 and smallest in the ROI 5. In addition, after the RFA procedure, the temperature decreased from the initial value to 0 °C in one hour. The temperature changes in the core body and the surrounding tissues were confirmed by MRI temperature mapping, which is a noninvasive method.

Cyclic motion encoding for enhanced MR visualization of slip interfaces.

PubMed

Mariappan, Yogesh K; Glaser, Kevin J; Manduca, Armando; Ehman, Richard L

2009-10-01

To develop and test a magnetic resonance imaging-based method for assessing the mechanical shear connectivity across tissue interfaces with phantom experiments and in vivo feasibility studies. External vibrations were applied to phantoms and tissue and the differential motion on either side of interfaces within the media was mapped onto the phase of the MR images using cyclic motion encoding gradients. The phase variations within the voxels of functional slip interfaces reduced the net magnitude signal in those regions, thus enhancing their visualization. A simple two-compartment model was developed to relate this signal loss to the intravoxel phase variations. In vivo studies of the abdomen and forearm were performed to visualize slip interfaces in healthy volunteers. The phantom experiments demonstrated that the proposed technique can assess the functionality of shear slip interfaces and they provided experimental validation for the theoretical model developed. Studies of the abdomen showed that the slip interface between the small bowel and the peritoneal wall can be visualized. In the forearm, this technique was able to depict the slip interfaces between the functional compartments of the extrinsic forearm muscles. Functional shear slip interfaces can be visualized sensitively using cyclic motion encoding of externally applied tissue vibrations. (c) 2009 Wiley-Liss, Inc.

Label-free tissue scanner for colorectal cancer screening

NASA Astrophysics Data System (ADS)

Kandel, Mikhail E.; Sridharan, Shamira; Liang, Jon; Luo, Zelun; Han, Kevin; Macias, Virgilia; Shah, Anish; Patel, Roshan; Tangella, Krishnarao; Kajdacsy-Balla, Andre; Guzman, Grace; Popescu, Gabriel

2017-06-01

The current practice of surgical pathology relies on external contrast agents to reveal tissue architecture, which is then qualitatively examined by a trained pathologist. The diagnosis is based on the comparison with standardized empirical, qualitative assessments of limited objectivity. We propose an approach to pathology based on interferometric imaging of "unstained" biopsies, which provides unique capabilities for quantitative diagnosis and automation. We developed a label-free tissue scanner based on "quantitative phase imaging," which maps out optical path length at each point in the field of view and, thus, yields images that are sensitive to the "nanoscale" tissue architecture. Unlike analysis of stained tissue, which is qualitative in nature and affected by color balance, staining strength and imaging conditions, optical path length measurements are intrinsically quantitative, i.e., images can be compared across different instruments and clinical sites. These critical features allow us to automate the diagnosis process. We paired our interferometric optical system with highly parallelized, dedicated software algorithms for data acquisition, allowing us to image at a throughput comparable to that of commercial tissue scanners while maintaining the nanoscale sensitivity to morphology. Based on the measured phase information, we implemented software tools for autofocusing during imaging, as well as image archiving and data access. To illustrate the potential of our technology for large volume pathology screening, we established an "intrinsic marker" for colorectal disease that detects tissue with dysplasia or colorectal cancer and flags specific areas for further examination, potentially improving the efficiency of existing pathology workflows.

Methods and means of 3D diffuse Mueller-matrix tomography of depolarizing optically anisotropic biological layers

NASA Astrophysics Data System (ADS)

Dubolazov, O. V.; Ushenko, V. O.; Trifoniuk, L.; Ushenko, Yu. O.; Zhytaryuk, V. G.; Prydiy, O. G.; Grytsyuk, M.; Kushnerik, L.; Meglinskiy, I.

2017-09-01

A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular birefringence of prostate histological sections are found. The interconnections between such distributions and parameters of linear and circular birefringence of prostate tissue histological sections are defined. The comparative investigations of coordinate distributions of phase anisotropy parameters formed by fibrillar networks of prostate tissues of different pathological states (adenoma and carcinoma) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular birefringence are defined. The objective criteria of cause of Benign and malignant conditions differentiation are determined.

A super-resolution ultrasound method for brain vascular mapping

PubMed Central

O'Reilly, Meaghan A.; Hynynen, Kullervo

2013-01-01

Purpose: High-resolution vascular imaging has not been achieved in the brain due to limitations of current clinical imaging modalities. The authors present a method for transcranial ultrasound imaging of single micrometer-size bubbles within a tube phantom. Methods: Emissions from single bubbles within a tube phantom were mapped through an ex vivo human skull using a sparse hemispherical receiver array and a passive beamforming algorithm. Noninvasive phase and amplitude correction techniques were applied to compensate for the aberrating effects of the skull bone. The positions of the individual bubbles were estimated beyond the diffraction limit of ultrasound to produce a super-resolution image of the tube phantom, which was compared with microcomputed tomography (micro-CT). Results: The resulting super-resolution ultrasound image is comparable to results obtained via the micro-CT for small tissue specimen imaging. Conclusions: This method provides superior resolution to deep-tissue contrast ultrasound and has the potential to be extended to provide complete vascular network imaging in the brain. PMID:24320408

A constraint optimization based virtual network mapping method

NASA Astrophysics Data System (ADS)

Li, Xiaoling; Guo, Changguo; Wang, Huaimin; Li, Zhendong; Yang, Zhiwen

2013-03-01

Virtual network mapping problem, maps different virtual networks onto the substrate network is an extremely challenging work. This paper proposes a constraint optimization based mapping method for solving virtual network mapping problem. This method divides the problem into two phases, node mapping phase and link mapping phase, which are all NP-hard problems. Node mapping algorithm and link mapping algorithm are proposed for solving node mapping phase and link mapping phase, respectively. Node mapping algorithm adopts the thinking of greedy algorithm, mainly considers two factors, available resources which are supplied by the nodes and distance between the nodes. Link mapping algorithm is based on the result of node mapping phase, adopts the thinking of distributed constraint optimization method, which can guarantee to obtain the optimal mapping with the minimum network cost. Finally, simulation experiments are used to validate the method, and results show that the method performs very well.

Computational cell quantification in the human brain tissues based on hard x-ray phase-contrast tomograms

NASA Astrophysics Data System (ADS)

Hieber, Simone E.; Bikis, Christos; Khimchenko, Anna; Schulz, Georg; Deyhle, Hans; Thalmann, Peter; Chicherova, Natalia; Rack, Alexander; Zdora, Marie-Christine; Zanette, Irene; Schweighauser, Gabriel; Hench, Jürgen; Müller, Bert

2016-10-01

Cell visualization and counting plays a crucial role in biological and medical research including the study of neurodegenerative diseases. The neuronal cell loss is typically determined to measure the extent of the disease. Its characterization is challenging because the cell density and size already differs by more than three orders of magnitude in a healthy cerebellum. Cell visualization is commonly performed by histology and fluorescence microscopy. These techniques are limited to resolve complex microstructures in the third dimension. Phase- contrast tomography has been proven to provide sufficient contrast in the three-dimensional imaging of soft tissue down to the cell level and, therefore, offers the basis for the three-dimensional segmentation. Within this context, a human cerebellum sample was embedded in paraffin and measured in local phase-contrast mode at the beamline ID19 (ESRF, Grenoble, France) and the Diamond Manchester Imaging Branchline I13-2 (Diamond Light Source, Didcot, UK). After the application of Frangi-based filtering the data showed sufficient contrast to automatically identify the Purkinje cells and to quantify their density to 177 cells per mm3 within the volume of interest. Moreover, brain layers were segmented in a region of interest based on edge detection. Subsequently performed histological analysis validated the presence of the cells, which required a mapping from the two- dimensional histological slices to the three-dimensional tomogram. The methodology can also be applied to further tissue types and shows potential for the computational tissue analysis in health and disease.

Single shot white light interference microscopy with colour fringe analysis for quantitative phase imaging of biological cells

NASA Astrophysics Data System (ADS)

Srivastava, Vishal; Mehta, D. S.

2013-02-01

To quantitatively obtain the phase map of Onion and human red blood cell (RBC) from white light interferogram we used Hilbert transform color fringe analysis technique. The three Red, Blue and Green color components are decomposed from single white light interferogram and Refractive index profile for Red, Blue and Green colour were computed in a completely non-invasive manner for Onion and human RBC. The present technique might be useful for non-invasive determination of the refractive index variation within cells and tissues and morphological features of sample with ease of operation and low cost.

Myocardial effective transverse relaxation time T2* Correlates with left ventricular wall thickness: A 7.0 T MRI study.

PubMed

Huelnhagen, Till; Hezel, Fabian; Serradas Duarte, Teresa; Pohlmann, Andreas; Oezerdem, Celal; Flemming, Bert; Seeliger, Erdmann; Prothmann, Marcel; Schulz-Menger, Jeanette; Niendorf, Thoralf

2017-06-01

Myocardial effective relaxation time T2* is commonly regarded as a surrogate for myocardial tissue oxygenation. However, it is legitimate to assume that there are multiple factors that influence T2*. To this end, this study investigates the relationship between T2* and cardiac macromorphology given by left ventricular (LV) wall thickness and left ventricular radius, and provides interpretation of the results in the physiological context. High spatio-temporally resolved myocardial CINE T2* mapping was performed in 10 healthy volunteers using a 7.0 Tesla (T) full-body MRI system. Ventricular septal wall thickness, left ventricular inner radius, and T2* were analyzed. Macroscopic magnetic field changes were elucidated using cardiac phase-resolved magnetic field maps. Ventricular septal T2* changes periodically over the cardiac cycle, increasing in systole and decreasing in diastole. Ventricular septal wall thickness and T2* showed a significant positive correlation, whereas the inner LV radius and T2* were negatively correlated. The effect of macroscopic magnetic field gradients on T2* can be considered minor in the ventricular septum. Our findings suggest that myocardial T2* is related to tissue blood volume fraction. Temporally resolved T2* mapping could be beneficial for myocardial tissue characterization and for understanding cardiac (patho)physiology in vivo. Magn Reson Med 77:2381-2389, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Retinal nerve fiber layer thickness map and blood flow pulsation measured with SDOCT

NASA Astrophysics Data System (ADS)

Mujat, Mircea; Chan, Raymond C.; Cense, Barry; Pierce, Mark; Park, Hyle; Joo, Chulmin; Chen, Teresa C.; de Boer, Johannes F.

2006-02-01

Spectral-Domain Optical Coherence Tomography (SDOCT) allows for in-vivo video-rate investigation of biomedical tissue depth structure intended for non-invasive optical diagnostics. It has been suggested that OCT can be used for di-agnosis of glaucoma by measuring the thickness of the Retinal Nerve Fiber Layer (RNLF). We present an automated method for determining the RNFL thickness from a 3-D dataset based on edge detection using a deformable spline algo-rithm. The RNFL thickness map is combined with an integrated reflectance map and retinal cross-sectional images to provide the ophthalmologist with a familiar image for interpreting the OCT data. The video-rate capabilities of our SDOCT system allow for mapping the true retinal topography since motion artifacts are significantly reduced as com-pared to slower time-domain systems. Combined with Doppler Velocimetry, SDOCT also provides information on retinal blood flow dynamics. We analyzed the pulsatile nature of the bidirectional flow dynamics in an artery-vein pair for a healthy volunteer at different locations and for different blood vessel diameters. The Doppler phase shift is determined as the phase difference at the same point of adjacent depth profiles, and is integrated over the area delimited by two circles corresponding to the blood vessels location. Its temporal evolution clearly shows the blood flow pulsatile nature, the cardiac cycle, in both artery and vein. The artery is identified as having a stronger variation of the integrated phase shift. We observe that artery pulsation is always easily detectable, while vein pulsation seems to depend on the veins diameter.

Quantitative shear wave optical coherence elastography (SW-OCE) with acoustic radiation force impulses (ARFI) induced by phase array transducer

NASA Astrophysics Data System (ADS)

Song, Shaozhen; Le, Nhan Minh; Wang, Ruikang K.; Huang, Zhihong

2015-03-01

Shear Wave Optical Coherence Elastography (SW-OCE) uses the speed of propagating shear waves to provide a quantitative measurement of localized shear modulus, making it a valuable technique for the elasticity characterization of tissues such as skin and ocular tissue. One of the main challenges in shear wave elastography is to induce a reliable source of shear wave; most of nowadays techniques use external vibrators which have several drawbacks such as limited wave propagation range and/or difficulties in non-invasive scans requiring precisions, accuracy. Thus, we propose linear phase array ultrasound transducer as a remote wave source, combined with the high-speed, 47,000-frame-per-second Shear-wave visualization provided by phase-sensitive OCT. In this study, we observed for the first time shear waves induced by a 128 element linear array ultrasound imaging transducer, while the ultrasound and OCT images (within the OCE detection range) were triggered simultaneously. Acoustic radiation force impulses are induced by emitting 10 MHz tone-bursts of sub-millisecond durations (between 50 μm - 100 μm). Ultrasound beam steering is achieved by programming appropriate phase delay, covering a lateral range of 10 mm and full OCT axial (depth) range in the imaging sample. Tissue-mimicking phantoms with agarose concentration of 0.5% and 1% was used in the SW-OCE measurements as the only imaging samples. The results show extensive improvements over the range of SW-OCE elasticity map; such improvements can also be seen over shear wave velocities in softer and stiffer phantoms, as well as determining the boundary of multiple inclusions with different stiffness. This approach opens up the feasibility to combine medical ultrasound imaging and SW-OCE for high-resolution localized quantitative measurement of tissue biomechanical property.

Bias atlases for segmentation-based PET attenuation correction using PET-CT and MR.

PubMed

Ouyang, Jinsong; Chun, Se Young; Petibon, Yoann; Bonab, Ali A; Alpert, Nathaniel; Fakhri, Georges El

2013-10-01

This study was to obtain voxel-wise PET accuracy and precision using tissue-segmentation for attenuation correction. We applied multiple thresholds to the CTs of 23 patients to classify tissues. For six of the 23 patients, MR images were also acquired. The MR fat/in-phase ratio images were used for fat segmentation. Segmented tissue classes were used to create attenuation maps, which were used for attenuation correction in PET reconstruction. PET bias images were then computed using the PET reconstructed with the original CT as the reference. We registered the CTs for all the patients and transformed the corresponding bias images accordingly. We then obtained the mean and standard deviation bias atlas using all the registered bias images. Our CT-based study shows that four-class segmentation (air, lungs, fat, other tissues), which is available on most PET-MR scanners, yields 15.1%, 4.1%, 6.6%, and 12.9% RMSE bias in lungs, fat, non-fat soft-tissues, and bones, respectively. An accurate fat identification is achievable using fat/in-phase MR images. Furthermore, we have found that three-class segmentation (air, lungs, other tissues) yields less than 5% standard deviation of bias within the heart, liver, and kidneys. This implies that three-class segmentation can be sufficient to achieve small variation of bias for imaging these three organs. Finally, we have found that inter- and intra-patient lung density variations contribute almost equally to the overall standard deviation of bias within the lungs.

Multi-parametric monitoring of high intensity focused ultrasound (HIFU) treatment using harmonic motion imaging for focused ultrasound (HMIFU)

NASA Astrophysics Data System (ADS)

Hou, Gary Y.; Marquet, Fabrice; Wang, Shutao; Konofagou, Elisa

2012-11-01

Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a recently developed high-intensity focused ultrasound (HIFU) treatment monitoring method with feasibilities demonstrated in vitro and in vivo. Here, a multi-parametric study is performed to investigate both elastic and acoustics-independent viscoelastic tissue changes using the Harmonic Motion Imaging (HMI) displacement, axial compressive strain and relative phase-shift during high energy HIFU where tissue boiling occurs. Forty three (n=18) thermal lesions were formed in ex vivo canine liver specimens. Two dimensional (2D) transverse HMI displacement maps were also obtained before and after lesion formation. The same method was repeated in 10-, 20-and 30-s HIFU durations at three different acoustic powers of 8, 10, and 11W. For the 10-, 20-, and 30-s treatment cases, a steady decrease in the displacement (-8.67±4.80, -14.44±7.77, 24.03±12.11μm), compressive strain -0.16±0.06, -0.71±0.30, -0.68±0.36 %, and phase shift +1.80±6.80, -15.80±9.44, -18.62±13.14 ° were obtained, respectively, indicating overall increase of relative stiffness and decrease of the viscosity-to-stiffness ratio during heating. After treatment, 2D HMI displacement images of the thermal lesions showed an increased lesion-to-background contrast of 1.34±0.19, 1.98±0.30, 2.26±0.80 and lesion size of 40.95±8.06, 47.6±4.87, and 52.23±2.19 mm2, respectively, which was validated again with pathology 25.17±6.99, 42.17±1.77, 47.17±3.10 mm2. Additionally, studies also investigated the performance of mutli-parametric monitoring under the influence of boiling and attenuation change due to tissue boiling, where discrepancies were found such as deteriorated displacement SNR and reversed lesion-to-background displacement contrast with indication on possible increase in attenuation and tissue gelatification or pulverization. Despite the challenge of the boiling mechanism, the relative phase shift served as consist biomechanical tissue response independent of changes in acoustic properties throughout the HIFU treatment. In addition, the 2D HMI displacement images were able to confirm and quantify the change in dimensions of the thermal lesion site. Therefore, the multi-parametric HMIFU was shown capable of monitoring and mapping tissue viscoelastic response changes during and after HIFU treatment.

Accuracy of magnetic resonance based susceptibility measurements

NASA Astrophysics Data System (ADS)

Erdevig, Hannah E.; Russek, Stephen E.; Carnicka, Slavka; Stupic, Karl F.; Keenan, Kathryn E.

2017-05-01

Magnetic Resonance Imaging (MRI) is increasingly used to map the magnetic susceptibility of tissue to identify cerebral microbleeds associated with traumatic brain injury and pathological iron deposits associated with neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Accurate measurements of susceptibility are important for determining oxygen and iron content in blood vessels and brain tissue for use in noninvasive clinical diagnosis and treatment assessments. Induced magnetic fields with amplitude on the order of 100 nT, can be detected using MRI phase images. The induced field distributions can then be inverted to obtain quantitative susceptibility maps. The focus of this research was to determine the accuracy of MRI-based susceptibility measurements using simple phantom geometries and to compare the susceptibility measurements with magnetometry measurements where SI-traceable standards are available. The susceptibilities of paramagnetic salt solutions in cylindrical containers were measured as a function of orientation relative to the static MRI field. The observed induced fields as a function of orientation of the cylinder were in good agreement with simple models. The MRI susceptibility measurements were compared with SQUID magnetometry using NIST-traceable standards. MRI can accurately measure relative magnetic susceptibilities while SQUID magnetometry measures absolute magnetic susceptibility. Given the accuracy of moment measurements of tissue mimicking samples, and the need to look at small differences in tissue properties, the use of existing NIST standard reference materials to calibrate MRI reference structures is problematic and better reference materials are required.

Joint eigenvector estimation from mutually anisotropic tensors improves susceptibility tensor imaging of the brain, kidney, and heart.

PubMed

Dibb, Russell; Liu, Chunlei

2017-06-01

To develop a susceptibility-based MRI technique for probing microstructure and fiber architecture of magnetically anisotropic tissues-such as central nervous system white matter, renal tubules, and myocardial fibers-in three dimensions using susceptibility tensor imaging (STI) tools. STI can probe tissue microstructure, but is limited by reconstruction artifacts because of absent phase information outside the tissue and noise. STI accuracy may be improved by estimating a joint eigenvector from mutually anisotropic susceptibility and relaxation tensors. Gradient-recalled echo image data were simulated using a numerical phantom and acquired from the ex vivo mouse brain, kidney, and heart. Susceptibility tensor data were reconstructed using STI, regularized STI, and the proposed algorithm of mutually anisotropic and joint eigenvector STI (MAJESTI). Fiber map and tractography results from each technique were compared with diffusion tensor data. MAJESTI reduced the estimated susceptibility tensor orientation error by 30% in the phantom, 36% in brain white matter, 40% in the inner medulla of the kidney, and 45% in myocardium. This improved the continuity and consistency of susceptibility-based fiber tractography in each tissue. MAJESTI estimation of the susceptibility tensors yields lower orientation errors for susceptibility-based fiber mapping and tractography in the intact brain, kidney, and heart. Magn Reson Med 77:2331-2346, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Susceptibility Tensor Imaging (STI) of the Brain

PubMed Central

Li, Wei; Liu, Chunlei; Duong, Timothy Q.; van Zijl, Peter C.M.; Li, Xu

2016-01-01

Susceptibility tensor imaging (STI) is a recently developed MRI technique that allows quantitative determination of orientation-independent magnetic susceptibility parameters from the dependence of gradient echo signal phase on the orientation of biological tissues with respect to the main magnetic field. By modeling the magnetic susceptibility of each voxel as a symmetric rank-2 tensor, individual magnetic susceptibility tensor elements as well as the mean magnetic susceptibility (MMS) and magnetic susceptibility anisotropy (MSA) can be determined for brain tissues that would still show orientation dependence after conventional scalar-based quantitative susceptibility mapping (QSM) to remove such dependence. Similar to diffusion tensor imaging (DTI), STI allows mapping of brain white matter fiber orientations and reconstruction of 3D white matter pathways using the principal eigenvectors of the susceptibility tensor. In contrast to diffusion anisotropy, the main determinant factor of susceptibility anisotropy in brain white matter is myelin. Another unique feature of susceptibility anisotropy of white matter is its sensitivity to gadolinium-based contrast agents. Mechanistically, MRI-observed susceptibility anisotropy is mainly attributed to the highly ordered lipid molecules in myelin sheath. STI provides a consistent interpretation of the dependence of phase and susceptibility on orientation at multiple scales. This article reviews the key experimental findings and physical theories that led to the development of STI, its practical implementations, and its applications for brain research. PMID:27120169

Raman molecular imaging of brain frozen tissue sections.

PubMed

Kast, Rachel E; Auner, Gregory W; Rosenblum, Mark L; Mikkelsen, Tom; Yurgelevic, Sally M; Raghunathan, Aditya; Poisson, Laila M; Kalkanis, Steven N

2014-10-01

Raman spectroscopy provides a molecular signature of the region being studied. It is ideal for neurosurgical applications because it is non-destructive, label-free, not impacted by water concentration, and can map an entire region of tissue. The objective of this paper is to demonstrate the meaningful spatial molecular information provided by Raman spectroscopy for identification of regions of normal brain, necrosis, diffusely infiltrating glioma and solid glioblastoma (GBM). Five frozen section tissues (1 normal, 1 necrotic, 1 GBM, and 2 infiltrating glioma) were mapped in their entirety using a 300-µm-square step size. Smaller regions of interest were also mapped using a 25-µm step size. The relative concentrations of relevant biomolecules were mapped across all tissues and compared with adjacent hematoxylin and eosin-stained sections, allowing identification of normal, GBM, and necrotic regions. Raman peaks and peak ratios mapped included 1003, 1313, 1431, 1585, and 1659 cm(-1). Tissue maps identified boundaries of grey and white matter, necrosis, GBM, and infiltrating tumor. Complementary information, including relative concentration of lipids, protein, nucleic acid, and hemoglobin, was presented in a manner which can be easily adapted for in vivo tissue mapping. Raman spectroscopy can successfully provide label-free imaging of tissue characteristics with high accuracy. It can be translated to a surgical or laboratory tool for rapid, non-destructive imaging of tumor margins.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics-innervated tissues.

PubMed

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M

2016-09-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could have important impacts on fundamental scientific and clinical studies, yet realization is hampered by a lack of effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and a submillisecond temporal resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multisite stimulation and mapping to actively manipulate the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics.

Three-dimensional mapping and regulation of action potential propagation in nanoelectronics innervated tissues

PubMed Central

Dai, Xiaochuan; Zhou, Wei; Gao, Teng; Liu, Jia; Lieber, Charles M.

2016-01-01

Real-time mapping and manipulation of electrophysiology in three-dimensional (3D) tissues could impact broadly fundamental scientific and clinical studies, yet realization lacks effective methods. Here we introduce tissue-scaffold-mimicking 3D nanoelectronic arrays consisting of 64 addressable devices with subcellular dimensions and sub-millisecond time-resolution. Real-time extracellular action potential (AP) recordings reveal quantitative maps of AP propagation in 3D cardiac tissues, enable in situ tracing of the evolving topology of 3D conducting pathways in developing cardiac tissues, and probe the dynamics of AP conduction characteristics in a transient arrhythmia disease model and subsequent tissue self-adaptation. We further demonstrate simultaneous multi-site stimulation and mapping to manipulate actively the frequency and direction of AP propagation. These results establish new methodologies for 3D spatiotemporal tissue recording and control, and demonstrate the potential to impact regenerative medicine, pharmacology and electronic therapeutics. PMID:27347837

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

PubMed Central

O'Connor, Timothy R.; Bailey, Timothy L.

2014-01-01

Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088

Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

PubMed Central

Liu, Chunlei; Wei, Hongjiang; Gong, Nan-Jie; Cronin, Matthew; Dibb, Russel; Decker, Kyle

2016-01-01

Quantitative susceptibility mapping (QSM) is a recently developed MRI technique for quantifying the spatial distribution of magnetic susceptibility within biological tissues. It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue. The resulting field map is then used to determine the spatial distribution of the underlying magnetic susceptibility by solving an inverse problem. The solution is achieved by deconvolving the field map with a dipole field, under the assumption that the magnetic field is a result of the superposition of the dipole fields generated by all voxels and that each voxel has its unique magnetic susceptibility. QSM provides improved contrast to noise ratio for certain tissues and structures compared to its magnitude counterpart. More importantly, magnetic susceptibility is a direct reflection of the molecular composition and cellular architecture of the tissue. Consequently, by quantifying magnetic susceptibility, QSM is becoming a quantitative imaging approach for characterizing normal and pathological tissue properties. This article reviews the mechanism generating susceptibility contrast within tissues and some associated applications. PMID:26844301

Head-down posture in glaucoma suspects induces changes in IOP, systemic pressure and PERG that predict future loss of optic nerve tissue

PubMed Central

Porciatti, Vittorio; Feuer, William J.; Monsalve, Pedro; Triolo, Giacinto; Vazquez, Luis; McSoley, John; Ventura, Lori M.

2017-01-01

Purpose To obtain pilot data on posture-induced changes of IOP, systemic pressure and pattern electroretinogram (PERG) predictive of future optic nerve tissue loss glaucoma suspects (GS). Methods Mean peripapillary retinal fiber layer thickness (RNFLT) was measured with OCT two times/year in 28 GS aged 58 ± 8.9 years over 5.0 ± 0.73 years. All patients had a baseline PERG, IOP and brachial blood pressure measurements in the seated and – 10 degrees head-down-body-tilt position (HDT). Outcome measures were seated/HDT PERG amplitude and phase, IOP, mean arterial blood pressure (MAP), and estimated ocular perfusion pressure (OPP). An additional group of 11 similarly-aged controls (SAC) aged 56.9 ± 13 years was tested for comparison. Results While all GS had initial RNFLT in the normal range, 9/28 of them developed significant (P < 0.05) loss of mean RNFLT (thinners, T) over the follow-up period as opposed to 19/28 who did not (non-thinners, NT). Significant (P<0.05) differences between SAC, NT and T were found in PERG amplitude, PERG phase, MAP, IOP, and OPP. A nominal logistic regression using baseline PERG and hemodynamic variables was able to distinguish T from NT with an AUROC of 0.89 (SE 0.07). Conclusions Baseline PERG, IOP, and systemic blood pressure, together with their changes upon HDT, may have predictive value for future loss of optic nerve tissue in GS. This study supports the rationale for a full-scale clinical trial to identify patients at high-risk of development of glaucoma. PMID:28263259

Quantitative susceptibility mapping (QSM): Decoding MRI data for a tissue magnetic biomarker

PubMed Central

Wang, Yi; Liu, Tian

2015-01-01

In MRI, the main magnetic field polarizes the electron cloud of a molecule, generating a chemical shift for observer protons within the molecule and a magnetic susceptibility inhomogeneity field for observer protons outside the molecule. The number of water protons surrounding a molecule for detecting its magnetic susceptibility is vastly greater than the number of protons within the molecule for detecting its chemical shift. However, the study of tissue magnetic susceptibility has been hindered by poor molecular specificities of hitherto used methods based on MRI signal phase and T2* contrast, which depend convolutedly on surrounding susceptibility sources. Deconvolution of the MRI signal phase can determine tissue susceptibility but is challenged by the lack of MRI signal in the background and by the zeroes in the dipole kernel. Recently, physically meaningful regularizations, including the Bayesian approach, have been developed to enable accurate quantitative susceptibility mapping (QSM) for studying iron distribution, metabolic oxygen consumption, blood degradation, calcification, demyelination, and other pathophysiological susceptibility changes, as well as contrast agent biodistribution in MRI. This paper attempts to summarize the basic physical concepts and essential algorithmic steps in QSM, to describe clinical and technical issues under active development, and to provide references, codes, and testing data for readers interested in QSM. Magn Reson Med 73:82–101, 2015. © 2014 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited. PMID:25044035

Strategies to improve phase-stability of ultrafast swept source optical coherence tomography for single shot imaging of transient mechanical waves at 16 kHz frame rate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Shaozhen; Wei, Wei; Hsieh, Bao-Yu

We present single-shot phase-sensitive imaging of propagating mechanical waves within tissue, enabled by an ultrafast optical coherence tomography (OCT) system powered by a 1.628 MHz Fourier domain mode-locked (FDML) swept laser source. We propose a practical strategy for phase-sensitive measurement by comparing the phases between adjacent OCT B-scans, where the B-scan contains a number of A-scans equaling an integer number of FDML buffers. With this approach, we show that micro-strain fields can be mapped with ∼3.0 nm sensitivity at ∼16 000 fps. The system's capabilities are demonstrated on porcine cornea by imaging mechanical wave propagation launched by a pulsed UV laser beam, promisingmore » non-contact, real-time, and high-resolution optical coherence elastography.« less

Breast cancer diagnosis using spatial light interference microscopy

NASA Astrophysics Data System (ADS)

Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel

2015-11-01

The standard practice in histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope to diagnose whether a lesion is benign or malignant. This determination is made based on a manual, qualitative inspection, making it subject to investigator bias and resulting in low throughput. Hence, a quantitative, label-free, and high-throughput diagnosis method is highly desirable. We present here preliminary results showing the potential of quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated phase maps of unstained breast tissue biopsies using spatial light interference microscopy (SLIM). As a first step toward quantitative diagnosis based on SLIM, we carried out a qualitative evaluation of our label-free images. These images were shown to two pathologists who classified each case as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on corresponding H&E stained tissue images and the number of agreements were counted. The agreement between SLIM and H&E based diagnosis was 88% for the first pathologist and 87% for the second. Our results demonstrate the potential and promise of SLIM for quantitative, label-free, and high-throughput diagnosis.

Harmonic phases of the nanoparticle magnetization: An intrinsic temperature probe

NASA Astrophysics Data System (ADS)

Garaio, Eneko; Collantes, Juan-Mari; Garcia, Jose Angel; Plazaola, Fernando; Sandre, Olivier

2015-09-01

Magnetic fluid hyperthermia is a promising cancer therapy in which magnetic nanoparticles act as heat sources activated by an external AC magnetic field. The nanoparticles, located near or inside the tumor, absorb energy from the magnetic field and then heat up the cancerous tissues. During the hyperthermia treatment, it is crucial to control the temperature of different tissues: too high temperature can cause undesired damage in healthy tissues through an uncontrolled necrosis. However, the current thermometry in magnetic hyperthermia presents some important technical problems. The widely used optical fiber thermometers only provide the temperature in a discrete set of spatial points. Moreover, surgery is required to locate these probes in the correct place. In this scope, we propose here a method to measure the temperature of a magnetic sample. The approach relies on the intrinsic properties of the magnetic nanoparticles because it is based on monitoring the thermal dependence of the high order harmonic phases of the nanoparticle dynamic magnetization. The method is non-invasive and it does not need any additional probe or sensor attached to the magnetic nanoparticles. Moreover, this method has the potential to be used together with the magnetic particle imaging technique to map the spatial distribution of the temperature.

Estimation of elasticity map of soft biological tissue mimicking phantom using laser speckle contrast analysis

NASA Astrophysics Data System (ADS)

Suheshkumar Singh, M.; Rajan, K.; Vasu, R. M.

2011-05-01

Scattering of coherent light from scattering particles causes phase shift to the scattered light. The interference of unscattered and scattered light causes the formation of speckles. When the scattering particles, under the influence of an ultrasound (US) pressure wave, vibrate, the phase shift fluctuates, thereby causing fluctuation in speckle intensity. We use the laser speckle contrast analysis (LSCA) to reconstruct a map of the elastic property (Young's modulus) of soft tissue-mimicking phantom. The displacement of the scatters is inversely related to the Young's modulus of the medium. The elastic properties of soft biological tissues vary, many fold with malignancy. The experimental results show that laser speckle contrast (LSC) is very sensitive to the pathological changes in a soft tissue medium. The experiments are carried out on a phantom with two cylindrical inclusions of sizes 6mm in diameter, separated by 8mm between them. Three samples are made. One inclusion has Young's modulus E of 40kPa. The second inclusion has either a Young's modulus E of 20kPa, or scattering coefficient of μs'=3.00mm-1 or absorption coefficient of μa=0.03mm-1. The optical absorption (μa), reduced scattering (μs') coefficient, and the Young's modulus of the background are μa=0.01mm-1, μs'=1.00mm-1 and 12kPa, respectively. The experiments are carried out on all three phantoms. On a phantom with two inclusions of Young's modulus of 20 and 40kPa, the measured relative speckle image contrasts are 36.55% and 63.72%, respectively. Experiments are repeated on phantoms with inclusions of μa=0.03mm-1, E =40kPa and μs'=3.00mm-1. The results show that it is possible to detect inclusions with contrasts in optical absorption, optical scattering, and Young's modulus. Studies of the variation of laser speckle contrast with ultrasound driving force for various values of μa, μs', and Young's modulus of the tissue mimicking medium are also carried out.

OCT-based in vivo tissue injury mapping

NASA Astrophysics Data System (ADS)

Baran, Utku; Li, Yuandong; Wang, Ruikang K.

2016-03-01

Tissue injury mapping (TIM) is developed by using a non-invasive in vivo optical coherence tomography to generate optical attenuation coefficient and microvascular map of the injured tissue. Using TIM, the infarct region development in mouse cerebral cortex during stroke is visualized. Moreover, we demonstrate the in vivo human facial skin structure and microvasculature during an acne lesion development. The results indicate that TIM may help in the study and the treatment of various diseases by providing high resolution images of tissue structural and microvascular changes.

Detection of necrotic neural response in super-acute cerebral ischemia using activity-induced manganese-enhanced (AIM) MRI.

PubMed

Inoue, Yasuo; Aoki, Ichio; Mori, Yuki; Kawai, Yuko; Ebisu, Toshihiko; Osaka, Yasuhiko; Houri, Takashi; Mineura, Katsuyoshi; Higuchi, Toshihiro; Tanaka, Chuzo

2010-04-01

Immediate and certain determination of the treatable area is important for choosing risky treatments such as thrombolysis for brain ischemia, especially in the super-acute phase. Although it has been suggested that the mismatch between regions displaying 'large abnormal perfusion' and 'small abnormal diffusion' indicates a treatable area on an MRI, it has also been reported that the mismatch region is an imperfect approximation of the treatable region named the 'penumbra'. Manganese accumulation reflecting calcium influx into cells was reported previously in a middle cerebral artery occlusion (MCAO) model using activity-induced manganese-enhanced (AIM) MRI. However, in the super-acute phase, there have been no reports about mismatches between areas showing changes to the apparent diffusion coefficient (ADC) and regions that are enhanced in AIM MRI. It is expected that the AIM signal can be enhanced immediately after cerebral ischemia in the necrotic core region due to calcium influx. In this study, a remote embolic rat model, created using titanium-oxide macrospheres, was used to observe necrotic neural responses in the super-acute phase after ischemia. In addition, images were evaluated by comparison between ADC, AIM MRI, and histology. The signal enhancement in AIM MRI was detected at 2 min after the cerebral infarction using a remote embolic method. The enhanced area on the AIM MRI was significantly smaller than that on the ADC map. The tissue degeneration highlighted by histological analysis corresponded more closely to the enhanced area on the AIM MRI than that on the ADC map. Thus, the manganese-enhanced region in brain ischemia might indicate 'necrotic' irreversible tissue that underwent calcium influx. 2010 John Wiley & Sons, Ltd.

3D map of theranostic nanoparticles distribution in mice brain and liver by means of X-ray Phase Contrast Tomography

NASA Astrophysics Data System (ADS)

Longo, E.; Bravin, A.; Brun, F.; Bukreeva, I.; Cedola, A.; Fratini, M.; Le Guevel, X.; Massimi, L.; Sancey, L.; Tillement, O.; Zeitoun, P.; de La Rochefoucauld, O.

2018-01-01

The word "theranostic" derives from the fusion of two terms: therapeutic and diagnostic. It is a promising research field that aims to develop innovative therapies with high target specificity by exploiting the therapeutic and diagnostic properties, in particular for metal-based nanoparticles (NPs) developed to erase cancer. In the framework of a combined research program on low dose X-ray imaging and theranostic nanoparticles (NPs), high resolution Phase-Contrast Tomography images of mice organs injected with gadolinium and gold-NPs were acquired at the European Synchrotron Radiation Facility (ESRF). Both compounds are good X-ray contrast agents due to their high attenuation coefficient with respect to biological tissues, especially immediately above K-edge energy. X-ray tomography is a powerful non-invasive technique to image the 3D vasculature network in order to detect abnormalities. Phase contrast methods provide more detailed anatomical information with higher discrimination among soft tissues. We present the images of mice liver and brain injected with gold and gadolinium NPs, respectively. We discuss different image processing methods used aiming at enhancing the accuracy on localizing nanoparticles.

Transcriptome profiling analysis of Vibrio vulnificus during human infection.

PubMed

Bisharat, Naiel; Bronstein, Michal; Korner, Mira; Schnitzer, Temima; Koton, Yael

2013-09-01

Vibrio vulnificus is a waterborne pathogen that was responsible for an outbreak of severe soft-tissue infections among fish farmers and fish consumers in Israel. Several factors have been shown to be associated with virulence. However, the transcriptome profile of the pathogen during human infection has not been determined yet. We compared the transcriptome profile, using RNA sequencing, of a human-pathogenic strain harvested directly from tissue of a patient suffering from severe soft-tissue infection with necrotizing fasciitis, with the same strain and three other environmental strains grown in vitro. The five sequenced libraries were aligned to the reference genomes of V. vulnificus strains CMCP6 and YJ016. Approximately 47.8 to 62.3 million paired-end raw reads were generated from the five runs. Nearly 84 % of the genome was covered by reads from at least one of the five runs, suggesting that nearly 16 % of the genome is not transcribed or is transcribed at low levels. We identified 123 genes that were differentially expressed during the acute phase of infection. Sixty-three genes were mapped to the large chromosome, 47 genes mapped to the small chromosome and 13 genes mapped to the YJ016 plasmid. The 123 genes fell into a variety of functional categories including transcription, signal transduction, cell motility, carbohydrate metabolism, intracellular trafficking and cell envelope biogenesis. Among the genes differentially expressed during human infection we identified genes encoding bacterial toxin (RtxA1) and genes involved in flagellar components, Flp-coding region, GGDEF family protein, iron acquisition system and sialic acid metabolism.

Ethical aspects of tissue engineering: a review.

PubMed

de Vries, Rob B M; Oerlemans, Anke; Trommelmans, Leen; Dierickx, Kris; Gordijn, Bert

2008-12-01

Tissue engineering (TE) is a promising new field of medical technology. However, like other new technologies, it is not free of ethical challenges. Identifying these ethical questions at an early stage is not only part of science's responsibility toward society, but also in the interest of the field itself. In this review, we map which ethical issues related to TE have already been documented in the scientific literature. The issues that turn out to dominate the debate are the use of human embryonic stem cells and therapeutic cloning. Nevertheless, a variety of other ethical aspects are mentioned, which relate to different phases in the development of the field. In addition, we discuss a number of ethical issues that have not yet been raised in the literature.

Motion-induced error reduction by combining Fourier transform profilometry with phase-shifting profilometry.

PubMed

Li, Beiwen; Liu, Ziping; Zhang, Song

2016-10-03

We propose a hybrid computational framework to reduce motion-induced measurement error by combining the Fourier transform profilometry (FTP) and phase-shifting profilometry (PSP). The proposed method is composed of three major steps: Step 1 is to extract continuous relative phase maps for each isolated object with single-shot FTP method and spatial phase unwrapping; Step 2 is to obtain an absolute phase map of the entire scene using PSP method, albeit motion-induced errors exist on the extracted absolute phase map; and Step 3 is to shift the continuous relative phase maps from Step 1 to generate final absolute phase maps for each isolated object by referring to the absolute phase map with error from Step 2. Experiments demonstrate the success of the proposed computational framework for measuring multiple isolated rapidly moving objects.

Amplitude-modulated ultrasound radiation force combined with phase-sensitive optical coherence tomography for shear wave elastography

NASA Astrophysics Data System (ADS)

Nguyen, Thu-Mai; Song, Shaozhen; Arnal, Bastien; Wong, Emily Y.; Shen, Tueng T.; Wang, Ruikang K.; O'Donnell, Matthew

2015-03-01

Tissue stiffness can be measured from the propagation speed of shear waves. Acoustic radiation force (ARF) can generate shear waves by focusing ultrasound in tissue for ~100 μs. Safety considerations and electronics abilities limit ultrasound pressures. We previously presented shear wave elastography combining ARF and phase-sensitive optical coherence tomography (PhS-OCT) [1]. Here, we use amplitude-modulated ARF to enhance shear wave signal-to-noise ratio (SNR) at low pressures. Experiments were performed on tissue-mimicking phantoms. ARF was applied using a single-element transducer, driven by a 7.5 MHz, 3-ms, sine wave modulated in amplitude by a linear-swept frequency (1 to 7 kHz). Pressures between 1 to 3 MPa were tested. Displacements were tracked using PhS-OCT and numerically compressed using pulse compression methods detailed in previous work [2]. SNR was compared to that of 200-μs bursts. Stiffness maps were reconstructed using time-of-flight computations. 200-μs bursts give barely detectable displacements at 1 MPa (3.7 dB SNR). Pulse compression gives 36.2 dB at 1.5 MPa. In all cases with detectable displacements, shear wave speeds were determined in 5%-gelatin and 10%-gelatin phantoms and compared to literature values. Applicability to ocular tissues (cornea, intraocular lens) is under investigation.

Combined use of X-ray fluorescence microscopy, phase contrast imaging for high resolution quantitative iron mapping in inflamed cells

NASA Astrophysics Data System (ADS)

Gramaccioni, C.; Procopio, A.; Farruggia, G.; Malucelli, E.; Iotti, S.; Notargiacomo, A.; Fratini, M.; Yang, Y.; Pacureanu, A.; Cloetens, P.; Bohic, S.; Massimi, L.; Cutone, A.; Valenti, P.; Rosa, L.; Berlutti, F.; Lagomarsino, S.

2017-06-01

X-ray fluorescence microscopy (XRFM) is a powerful technique to detect and localize elements in cells. To derive information useful for biology and medicine, it is essential not only to localize, but also to map quantitatively the element concentration. Here we applied quantitative XRFM to iron in phagocytic cells. Iron, a primary component of living cells, can become toxic when present in excess. In human fluids, free iron is maintained at 10-18 M concentration thanks to iron binding proteins as lactoferrin (Lf). The iron homeostasis, involving the physiological ratio of iron between tissues/secretions and blood, is strictly regulated by ferroportin, the sole protein able to export iron from cells to blood. Inflammatory processes induced by lipopolysaccharide (LPS) or bacterial pathoge inhibit ferroportin synthesis in epithelial and phagocytic cells thus hindering iron export, increasing intracellular iron and bacterial multiplication. In this respect, Lf is emerging as an important regulator of both iron and inflammatory homeostasis. Here we studied phagocytic cells inflamed by bacterial LPS and untreated or treated with milk derived bovine Lf. Quantitative mapping of iron concentration and mass fraction at high spatial resolution is obtained combining X-ray fluorescence microscopy, atomic force microscopy and synchrotron phase contrast imaging.

Evaluation of bioreactor-cultivated bone by magnetic resonance microscopy and FTIR microspectroscopy.

PubMed

Chesnick, Ingrid E; Avallone, Francis A; Leapman, Richard D; Landis, William J; Eidelman, Naomi; Potter, Kimberlee

2007-04-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of 9 weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 microm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro.

Evaluation of Bioreactor-Cultivated Bone by Magnetic Resonance Microscopy and FTIR Microspectroscopy

PubMed Central

Chesnick, Ingrid E.; Avallone, Frank; Leapman, Richard D.; Landis, William J.; Eidelman, Naomi; Potter, Kimberlee

2007-01-01

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of nine weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 μm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro. PMID:17174620

Quantitative susceptibility mapping (QSM) of white matter multiple sclerosis lesions: interpreting positive susceptibility and the presence of iron

PubMed Central

Wisnieff, Cynthia; Ramanan, Sriram; Olesik, John; Gauthier, Susan; Wang, Yi; Pitt, David

2014-01-01

Purpose Within multiple sclerosis (MS) lesions iron is present in chronically activated microglia. Thus, iron detection with MRI might provide a biomarker for chronic inflammation within lesions. Here, we examine contributions of iron and myelin to magnetic susceptibility of lesions on quantitative susceptibility mapping (QSM). Methods Fixed MS brain tissue was assessed with MRI including gradient echo data, which was processed to generate field (phase), R2* and QSM. Five lesions were sectioned and evaluated by immunohistochemistry for presence of myelin, iron and microglia/macrophages. Two of the lesions had an elemental analysis for iron concentration mapping, and their phospholipid content was estimated from the difference in the iron and QSM data. Results Three of the five lesions had substantial iron deposition that was associated with microglia and positive susceptibility values. For the two lesions with elemental analysis, the QSM derived phospholipid content maps were consistent with myelin labeled histology. Conclusion Positive susceptibility values with respect to water indicate the presence of iron in MS lesions, though both demyelination and iron deposition contribute to QSM. PMID:25137340

Propagation-based phase-contrast x-ray tomography of cochlea using a compact synchrotron source.

PubMed

Töpperwien, Mareike; Gradl, Regine; Keppeler, Daniel; Vassholz, Malte; Meyer, Alexander; Hessler, Roland; Achterhold, Klaus; Gleich, Bernhard; Dierolf, Martin; Pfeiffer, Franz; Moser, Tobias; Salditt, Tim

2018-03-21

We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which - due to the large performance gap with respect to conventional laboratory instruments - so far were usually limited to synchrotron sources. We demonstrate the potential by mapping the functional soft tissue within the guinea pig and marmoset cochlea, including in the latter case an electrical cochlear implant. We show how 3d microanatomical studies without dissection or microscopic imaging can enhance future research on cochlear implants.

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions

PubMed Central

Acharya, Kamal R.; Dhand, Navneet K.; Whittington, Richard J.; Plain, Karren M.

2017-01-01

Johne’s disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen’s kappa statistic) and no significant difference to the reference tests (McNemar’s Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption. PMID:29312970

Culture-Independent Identification of Mycobacterium avium Subspecies paratuberculosis in Ovine Tissues: Comparison with Bacterial Culture and Histopathological Lesions.

PubMed

Acharya, Kamal R; Dhand, Navneet K; Whittington, Richard J; Plain, Karren M

2017-01-01

Johne's disease is a chronic debilitating enteropathy of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Current abattoir surveillance programs detect disease via examination of gross lesions and confirmation by histopathological and/or tissue culture, which is time-consuming and has relatively low sensitivity. This study aimed to investigate whether a high-throughput quantitative PCR (qPCR) test is a viable alternative for tissue testing. Intestine and mesenteric lymph nodes were sourced from sheep experimentally infected with MAP and the DNA extracted using a protocol developed for tissues, comprised enzymatic digestion of the tissue homogenate, chemical and mechanical lysis, and magnetic bead-based DNA purification. The extracted DNA was tested by adapting a previously validated qPCR for fecal samples, and the results were compared with culture and histopathology results of the corresponding tissues. The MAP tissue qPCR confirmed infection in the majority of sheep with gross lesions on postmortem (37/38). Likewise, almost all tissue culture (61/64) or histopathology (52/58) positives were detected with good to moderate agreement (Cohen's kappa statistic) and no significant difference to the reference tests (McNemar's Chi-square test). Higher MAP DNA quantities corresponded to animals with more severe histopathology (odds ratio: 1.82; 95% confidence interval: 1.60, 2.07). Culture-independent strain typing on tissue DNA was successfully performed. This MAP tissue qPCR method had a sensitivity equivalent to the reference tests and is thus a viable replacement for gross- and histopathological examination of tissue samples in abattoirs. In addition, the test could be validated for testing tissue samples intended for human consumption.

Human Induced Pluripotent Stem Cell-Derived Cardiac Cell Sheets Expressing Genetically Encoded Voltage Indicator for Pharmacological and Arrhythmia Studies.

PubMed

Shaheen, Naim; Shiti, Assad; Huber, Irit; Shinnawi, Rami; Arbel, Gil; Gepstein, Amira; Setter, Noga; Goldfracht, Idit; Gruber, Amit; Chorna, Snizhanna V; Gepstein, Lior

2018-06-05

Fulfilling the potential of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes for studying conduction and arrhythmogenesis requires development of multicellular models and methods for long-term repeated tissue phenotyping. We generated confluent hiPSC-derived cardiac cell sheets (hiPSC-CCSs), expressing the genetically encoded voltage indicator ArcLight. ArcLight-based optical mapping allowed generation of activation and action-potential duration (APD) maps, which were validated by mapping the same hiPSC-CCSs with the voltage-sensitive dye, Di-4-ANBDQBS. ArcLight mapping allowed long-term assessment of electrical remodeling in the hiPSC-CCSs and evaluation of drug-induced conduction slowing (carbenoxolone, lidocaine, and quinidine) and APD prolongation (quinidine and dofetilide). The latter studies also enabled step-by-step depiction of drug-induced arrhythmogenesis ("torsades de pointes in the culture dish") and its prevention by MgSO 4 and rapid pacing. Phase-mapping analysis allowed biophysical characterization of spiral waves induced in the hiPSC-CCSs and their termination by electrical cardioversion and overdrive pacing. In conclusion, ArcLight mapping of hiPSC-CCSs provides a powerful tool for drug testing and arrhythmia investigation. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Eccentricity mapping of the human visual cortex to evaluate temporal dynamics of functional T1ρ mapping.

PubMed

Heo, Hye-Young; Wemmie, John A; Johnson, Casey P; Thedens, Daniel R; Magnotta, Vincent A

2015-07-01

Recent experiments suggest that T1 relaxation in the rotating frame (T(1ρ)) is sensitive to metabolism and can detect localized activity-dependent changes in the human visual cortex. Current functional magnetic resonance imaging (fMRI) methods have poor temporal resolution due to delays in the hemodynamic response resulting from neurovascular coupling. Because T(1ρ) is sensitive to factors that can be derived from tissue metabolism, such as pH and glucose concentration via proton exchange, we hypothesized that activity-evoked T(1ρ) changes in visual cortex may occur before the hemodynamic response measured by blood oxygenation level-dependent (BOLD) and arterial spin labeling (ASL) contrast. To test this hypothesis, functional imaging was performed using T(1ρ), BOLD, and ASL in human participants viewing an expanding ring stimulus. We calculated eccentricity phase maps across the occipital cortex for each functional signal and compared the temporal dynamics of T(1ρ) versus BOLD and ASL. The results suggest that T(1ρ) changes precede changes in the two blood flow-dependent measures. These observations indicate that T(1ρ) detects a signal distinct from traditional fMRI contrast methods. In addition, these findings support previous evidence that T(1ρ) is sensitive to factors other than blood flow, volume, or oxygenation. Furthermore, they suggest that tissue metabolism may be driving activity-evoked T(1ρ) changes.

Noninvasive OCT imaging of the retinal morphology and microvasculature based on the combination of the phase and amplitude method

NASA Astrophysics Data System (ADS)

Qin, Lin; Fan, Shanhui; Zhou, Chuanqing

2017-04-01

To implement the optical coherence tomography (OCT) angiography on the low scanning speed OCT system, we developed a joint phase and amplitude method to generate 3-D angiograms by analysing the frequency distribution of signals from non-moving and moving scatterers and separating the signals from the tissue and blood flow with high-pass filter dynamically. This approach firstly compensates the sample motion between adjacent A-lines. Then according to the corrected phase information, we used a histogram method to determine the bulk non-moving tissue phases dynamically, which is regarded as the cut-off frequency of a high-pass filter, and separated the moving and non-moving scatters using the mentioned high-pass filter. The reconstructed image can visualize the components of moving scatters flowing, and enables volumetric flow mapping combined with the corrected phase information. Furthermore, retinal and choroidal blood vessels can be simultaneously obtained by separating the B-scan into retinal part and choroidal parts using a simple segmentation algorithm along the RPE. After the compensation of axial displacements between neighbouring images, three-dimensional vasculature of ocular vessels has been visualized. Experiments were performed to demonstrate the effectiveness of the proposed method for 3-D vasculature imaging of human retina and choroid. The results revealed depth-resolved vasculatures in retina and choroid, suggesting that our approach can be used for noninvasive and three-dimensional angiography with a low-speed clinical OCT, and it has a great potential for clinic application.

Investigation of Thermal Effects of Photocoagulation on Retinal Tissue Using Fine-Motion-Sensitive Dynamic Optical Coherence Tomography.

PubMed

Kurokawa, Kazuhiro; Makita, Shuichi; Yasuno, Yoshiaki

2016-01-01

To enable an objective evaluation of photocoagulation, we characterize thermal tissue changes induced by laser irradiation with different laser parameters using optical coherence tomography (OCT). Spectral-domain OCT with a newly developed image processing method was used to monitor the thermal changes of ex vivo porcine retina. A sequence of OCT B-scans was obtained at the same retinal position simultaneously with the photocoagulation. Cross-sectional tissue displacement maps with respect to an OCT image taken before laser irradiation were computed for images taken before, during, and after laser irradiation, by using a correlation-based custom algorithm. Cross-sectional correlation maps (OCT correlation maps) were also computed from an OCT image taken before laser irradiation as a base-line to visualize alterations of tissue microstructure induced by laser irradiation. By systematically controlling laser power and exposure times, tissue displacements and structural changes of 200 retinal regions of 10 porcine eyes were characterized. Thermal tissue changes were characterized by B-scan images, OCT correlation maps, and tissue displacement maps. Larger tissue deformation was induced with higher laser power and shorter exposure time, while the same total laser energy (10 mJ) was applied. The measured tissue displacements revealed the complicated dynamics of tissue displacements. Three types of dynamics were observed; lateral expansion, lateral constriction, and a type showing more complicated dynamics. The results demonstrated the ability of this OCT-based method to evaluate retinal changes induced by laser irradiation. This evaluation could lead to further understanding of thermal effects, and increasing reproducibility of photocoagulation therapy.

Combining coherent hard X-ray tomographies with phase retrieval to generate three-dimensional models of forming bone

NASA Astrophysics Data System (ADS)

Bortel, Emely L.; Langer, Max; Rack, Alexander; Forien, Jean-Baptiste; Duda, Georg N.; Fratzl, Peter; Zaslansky, Paul

2017-11-01

Holotomography, a phase sensitive synchrotron-based μCT modality, is a quantitative 3D imaging method. By exploiting partial spatial X-ray coherence, bones can be imaged volumetrically with high resolution coupled with impressive density sensitivity. This tomographic method reveals the main characteristics of the important tissue compartments in forming bones, including the rapidly-changing soft tissue and the partially or fully mineralized bone regions, while revealing subtle density differences in 3D. Here we show typical results observed within the growing femur bone midshafts of healthy mice that are 1, 3, 7, 10 and 14 days old (postpartum). Our results make use of partially-coherent synchrotron radiation employing inline Fresnel-propagation in multiple tomographic datasets obtained in the imaging beamline ID19 of the ESRF. The exquisite detail creates maps of the juxtaposed soft, partially mineralized and highly mineralized bone revealing the environment in which bone cells create and shape the matrix. This high resolution 3D data is a step towards creating realistic computational models that may be used to study the dynamic processes involved in bone tissue formation and adaptation. Such data will enhance our understanding of the important biomechanical interactions directing maturation and shaping of the bone micro- and macro-geometries.

Determining temperature distribution in tissue in the focal plane of the high (>100 W/cm(2)) intensity focused ultrasound beam using phase shift of ultrasound echoes.

PubMed

Karwat, Piotr; Kujawska, Tamara; Lewin, Peter A; Secomski, Wojciech; Gambin, Barbara; Litniewski, Jerzy

2016-02-01

In therapeutic applications of High Intensity Focused Ultrasound (HIFU) the guidance of the HIFU beam and especially its focal plane is of crucial importance. This guidance is needed to appropriately target the focal plane and hence the whole focal volume inside the tumor tissue prior to thermo-ablative treatment and beginning of tissue necrosis. This is currently done using Magnetic Resonance Imaging that is relatively expensive. In this study an ultrasound method, which calculates the variations of speed of sound in the locally heated tissue volume by analyzing the phase shifts of echo-signals received by an ultrasound scanner from this very volume is presented. To improve spatial resolution of B-mode imaging and minimize the uncertainty of temperature estimation the acoustic signals were transmitted and received by 8 MHz linear phased array employing Synthetic Transmit Aperture (STA) technique. Initially, the validity of the algorithm developed was verified experimentally in a tissue-mimicking phantom heated from 20.6 to 48.6 °C. Subsequently, the method was tested using a pork loin sample heated locally by a 2 MHz pulsed HIFU beam with focal intensity ISATA of 129 W/cm(2). The temperature calibration of 2D maps of changes in the sound velocity induced by heating was performed by comparison of the algorithm-determined changes in the sound velocity with the temperatures measured by thermocouples located in the heated tissue volume. The method developed enabled ultrasound temperature imaging of the heated tissue volume from the very inception of heating with the contrast-to-noise ratio of 3.5-12 dB in the temperature range 21-56 °C. Concurrently performed, conventional B-mode imaging revealed CNR close to zero dB until the temperature reached 50 °C causing necrosis. The data presented suggest that the proposed method could offer an alternative to MRI-guided temperature imaging for prediction of the location and extent of the thermal lesion prior to applying the final HIFU treatment. Copyright © 2015 Elsevier B.V. All rights reserved.

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

High-speed spatial frequency domain imaging of rat cortex detects dynamic optical and physiological properties following cardiac arrest and resuscitation.

PubMed

Wilson, Robert H; Crouzet, Christian; Torabzadeh, Mohammad; Bazrafkan, Afsheen; Farahabadi, Maryam H; Jamasian, Babak; Donga, Dishant; Alcocer, Juan; Zaher, Shuhab M; Choi, Bernard; Akbari, Yama; Tromberg, Bruce J

2017-10-01

Quantifying rapidly varying perturbations in cerebral tissue absorption and scattering can potentially help to characterize changes in brain function caused by ischemic trauma. We have developed a platform for rapid intrinsic signal brain optical imaging using macroscopically structured light. The device performs fast, multispectral, spatial frequency domain imaging (SFDI), detecting backscattered light from three-phase binary square-wave projected patterns, which have a much higher refresh rate than sinusoidal patterns used in conventional SFDI. Although not as fast as "single-snapshot" spatial frequency methods that do not require three-phase projection, square-wave patterns allow accurate image demodulation in applications such as small animal imaging where the limited field of view does not allow single-phase demodulation. By using 655, 730, and 850 nm light-emitting diodes, two spatial frequencies ([Formula: see text] and [Formula: see text]), three spatial phases (120 deg, 240 deg, and 360 deg), and an overall camera acquisition rate of 167 Hz, we map changes in tissue absorption and reduced scattering parameters ([Formula: see text] and [Formula: see text]) and oxy- and deoxyhemoglobin concentration at [Formula: see text]. We apply this method to a rat model of cardiac arrest (CA) and cardiopulmonary resuscitation (CPR) to quantify hemodynamics and scattering on temporal scales ([Formula: see text]) ranging from tens of milliseconds to minutes. We observe rapid concurrent spatiotemporal changes in tissue oxygenation and scattering during CA and following CPR, even when the cerebral electrical signal is absent. We conclude that square-wave SFDI provides an effective technical strategy for assessing cortical optical and physiological properties by balancing competing performance demands for fast signal acquisition, small fields of view, and quantitative information content.

Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues.

PubMed

Tremblay, Kimberly D; Zaret, Kenneth S

2005-04-01

The location and movement of mammalian gut tissue progenitors, prior to the expression of tissue-specific genes, has been unknown, but this knowledge is essential to identify transitions that lead to cell type specification. To address this, we used vital dyes to label exposed anterior endoderm cells of early somite stage mouse embryos, cultured the embryos into the tissue bud phase of development, and determined the tissue fate of the dye labeled cells. This approach was performed at three embryonic stages that are prior to, or coincident with, foregut tissue patterning (1-3 somites, 4-6 somites, and 7-10 somites). Short-term labeling experiments tracked the movement of tissue progenitor cells during foregut closure. Surprisingly, we found that two distinct types of endoderm-progenitor cells, lateral and medial, arising from three spatially separated embryonic domains, converge to generate the epithelial cells of the liver bud. Whereas the lateral endoderm-progenitors give rise to descendants that are constrained in tissue fate and position along the anterior-posterior axis of the gut, the medial gut endoderm-progenitors give rise to descendants that stream along the anterior-posterior axis at the ventral midline and contribute to multiple gut tissues. The fate map reveals extensive morphogenetic movement of progenitors prior to tissue specification, it permits a detailed analysis of endoderm tissue patterning, and it illustrates that diverse progenitor domains can give rise to individual tissue cell types.

Parametric mapping of [18F]fluoromisonidazole positron emission tomography using basis functions.

PubMed

Hong, Young T; Beech, John S; Smith, Rob; Baron, Jean-Claude; Fryer, Tim D

2011-02-01

In this study, we show a basis function method (BAFPIC) for voxelwise calculation of kinetic parameters (K(1), k(2), k(3), K(i)) and blood volume using an irreversible two-tissue compartment model. BAFPIC was applied to rat ischaemic stroke micro-positron emission tomography data acquired with the hypoxia tracer [(18)F]fluoromisonidazole because irreversible two-tissue compartmental modelling provided good fits to data from both hypoxic and normoxic tissues. Simulated data show that BAFPIC produces kinetic parameters with significantly lower variability and bias than nonlinear least squares (NLLS) modelling in hypoxic tissue. The advantage of BAFPIC over NLLS is less pronounced in normoxic tissue. K(i) determined from BAFPIC has lower variability than that from the Patlak-Gjedde graphical analysis (PGA) by up to 40% and lower bias, except for normoxic tissue at mid-high noise levels. Consistent with the simulation results, BAFPIC parametric maps of real data suffer less noise-induced variability than do NLLS and PGA. Delineation of hypoxia on BAFPIC k(3) maps is aided by low variability in normoxic tissue, which matches that in K(i) maps. BAFPIC produces K(i) values that correlate well with those from PGA (r(2)=0.93 to 0.97; slope 0.99 to 1.05, absolute intercept <0.00002 mL/g per min). BAFPIC is a computationally efficient method of determining parametric maps with low bias and variance.

3D resolved mapping of optical aberrations in thick tissues

PubMed Central

Zeng, Jun; Mahou, Pierre; Schanne-Klein, Marie-Claire; Beaurepaire, Emmanuel; Débarre, Delphine

2012-01-01

We demonstrate a simple method for mapping optical aberrations with 3D resolution within thick samples. The method relies on the local measurement of the variation in image quality with externally applied aberrations. We discuss the accuracy of the method as a function of the signal strength and of the aberration amplitude and we derive the achievable resolution for the resulting measurements. We then report on measured 3D aberration maps in human skin biopsies and mouse brain slices. From these data, we analyse the consequences of tissue structure and refractive index distribution on aberrations and imaging depth in normal and cleared tissue samples. The aberration maps allow the estimation of the typical aplanetism region size over which aberrations can be uniformly corrected. This method and data pave the way towards efficient correction strategies for tissue imaging applications. PMID:22876353

Improving chemical shift encoding‐based water–fat separation based on a detailed consideration of magnetic field contributions

PubMed Central

Ruschke, Stefan; Eggers, Holger; Meineke, Jakob; Rummeny, Ernst J.; Karampinos, Dimitrios C.

2018-01-01

Purpose To improve the robustness of existing chemical shift encoding‐based water–fat separation methods by incorporating a priori information of the magnetic field distortions in complex‐based water–fat separation. Methods Four major field contributions are considered: inhomogeneities of the scanner magnet, the shim field, an object‐based field map estimate, and a residual field. The former two are completely determined by spherical harmonic expansion coefficients directly available from the magnetic resonance (MR) scanner. The object‐based field map is forward simulated from air–tissue interfaces inside the field of view (FOV). The missing residual field originates from the object outside the FOV and is investigated by magnetic field simulations on a numerical whole body phantom. In vivo the spatially linear first‐order component of the residual field is estimated by measuring echo misalignments after demodulation of other field contributions resulting in a linear residual field. Gradient echo datasets of the cervical and the ankle region without and with shimming were acquired, where all four contributions were incorporated in the water–fat separation with two algorithms from the ISMRM water–fat toolbox and compared to water–fat separation with less incorporated field contributions. Results Incorporating all four field contributions as demodulation steps resulted in reduced temporal and spatial phase wraps leading to almost swap‐free water–fat separation results in all datasets. Conclusion Demodulating estimates of major field contributions reduces the phase evolution to be driven by only small differences in local tissue susceptibility, which supports the field smoothness assumption of existing water–fat separation techniques. PMID:29424458

Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

PubMed Central

Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

2013-01-01

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

Indentation mapping revealed poroelastic, but not viscoelastic, properties spanning native zonal articular cartilage.

PubMed

Wahlquist, Joseph A; DelRio, Frank W; Randolph, Mark A; Aziz, Aaron H; Heveran, Chelsea M; Bryant, Stephanie J; Neu, Corey P; Ferguson, Virginia L

2017-12-01

Osteoarthrosis is a debilitating disease affecting millions, yet engineering materials for cartilage regeneration has proven difficult because of the complex microstructure of this tissue. Articular cartilage, like many biological tissues, produces a time-dependent response to mechanical load that is critical to cell's physiological function in part due to solid and fluid phase interactions and property variations across multiple length scales. Recreating the time-dependent strain and fluid flow may be critical for successfully engineering replacement tissues but thus far has largely been neglected. Here, microindentation is used to accomplish three objectives: (1) quantify a material's time-dependent mechanical response, (2) map material properties at a cellular relevant length scale throughout zonal articular cartilage and (3) elucidate the underlying viscoelastic, poroelastic, and nonlinear poroelastic causes of deformation in articular cartilage. Untreated and trypsin-treated cartilage was sectioned perpendicular to the articular surface and indentation was used to evaluate properties throughout zonal cartilage on the cut surface. The experimental results demonstrated that within all cartilage zones, the mechanical response was well represented by a model assuming nonlinear biphasic behavior and did not follow conventional viscoelastic or linear poroelastic models. Additionally, 10% (w/w) agarose was tested and, as anticipated, behaved as a linear poroelastic material. The approach outlined here provides a method, applicable to many tissues and biomaterials, which reveals and quantifies the underlying causes of time-dependent deformation, elucidates key aspects of material structure and function, and that can be used to provide important inputs for computational models and targets for tissue engineering. Elucidating the time-dependent mechanical behavior of cartilage, and other biological materials, is critical to adequately recapitulate native mechanosensory cues for cells. We used microindentation to map the time-dependent properties of untreated and trypsin treated cartilage throughout each cartilage zone. Unlike conventional approaches that combine viscoelastic and poroelastic behaviors into a single framework, we deconvoluted the mechanical response into separate contributions to time-dependent behavior. Poroelastic effects in all cartilage zones dominated the time-dependent behavior of articular cartilage, and a model that incorporates tension-compression nonlinearity best represented cartilage mechanical behavior. These results can be used to assess the success of regeneration and repair approaches, as design targets for tissue engineering, and for development of accurate computational models. Copyright © 2017 Acta Materialia Inc. All rights reserved.

Cardiac tissue geometry as a determinant of unidirectional conduction block: assessment of microscopic excitation spread by optical mapping in patterned cell cultures and in a computer model.

PubMed

Fast, V G; Kléber, A G

1995-05-01

Unidirectional conduction block (UCB) and reentry may occur as a consequence of an abrupt tissue expansion and a related change in the electrical load. The aim of this study was to evaluate critical dimensions of the tissue necessary for establishing UCB in heart cell culture. Neonatal rat heart cell cultures with cell strands of variable width emerging into a large cell area were grown using a technique of patterned cell growth. Action potential upstrokes were measured using a voltage sensitive dye (RH-237) and a linear array of 10 photodiodes with a 15 microns resolution. A mathematical model was used to relate action potential wave shapes to underlying ionic currents. UCB (block of a single impulse in anterograde direction - from a strand to a large area - and conduction in the retrograde direction) occurred in narrow cell strands with a width of 15(SD 4) microns (1-2 cells in width, n = 7) and there was no conduction block in strands with a width of 31(8) microns (n = 9, P < 0.001) or larger. The analysis of action potential waveshapes indicated that conduction block was either due to geometrical expansion alone (n = 5) or to additional local depression of conduction (n = 2). In wide strands, action potential upstrokes during anterograde conduction were characterised by multiple rising phases. Mathematical modelling showed that two rising phases were caused by electronic current flow, whereas local ionic current did not coincide with the rising portions of the upstrokes. (1) High resolution optical mapping shows multiphasic action potential upstrokes at the region of abrupt expansion. At the site of the maximum decrement in conduction, these peaks were largely determined by the electrotonus and not by the local ionic current. (2) Unidirectional conduction block occurred in strands with a width of 15(4) microns (1-2 cells).

Experimental colitis is exacerbated by concomitant infection with Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Roy, Bishnudeo; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Basler, Tina; Rohde, Manfred; Falk, Christine S; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2014-11-01

Crohn's disease (CD) is a chronic inflammatory disorder of the human gastrointestinal tract. Although genetic, immunological, environmental, and bacterial factors have been implicated, the pathogenesis is incompletely understood. The histopathological appearance of CD strikingly resembles Johne's disease, a ruminant inflammatory bowel disease, caused by Mycobacterium avium ssp. paratuberculosis (MAP), but a causative role of MAP in CD has not been established. In this work, we hypothesized that MAP might exacerbate an already existing intestinal disease. We combined dextran sulfate sodium (DSS)-induced colitis with MAP infection in mice and monitored the immune response and bacterial count in different organs. An increased size of liver and spleen was observed in DSS-treated and MAP-infected animals (DSS + MAP) as compared with DSS-treated uninfected (DSS + PBS) mice. Similarly, DSS treatment increased the number and size of MAP-induced liver granulomas and enhanced the MAP counts in enteric tissue. MAP infection in turn delayed the mucosal healing of DSS-induced tissue damage. Finally, high numbers of MAP were found in mesenteric fat tissue causing large granuloma and necrotic regions. Taken together, we present an in vivo model to study the role of MAP infection in CD. Our results confirm the hypothesis that MAP is able to exacerbate existing intestinal inflammation.

Improving experimental phases for strong reflections prior to density modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Improving experimental phases for strong reflections prior to density modification

DOE PAGES

Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; ...

2013-09-20

Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D 61, 899–902], the impact of identifying optimized phases for a small numbermore » of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Asymptotically stable phase synchronization revealed by autoregressive circle maps

NASA Astrophysics Data System (ADS)

Drepper, F. R.

2000-11-01

A specially designed of nonlinear time series analysis is introduced based on phases, which are defined as polar angles in spaces spanned by a finite number of delayed coordinates. A canonical choice of the polar axis and a related implicit estimation scheme for the potentially underlying autoregressive circle map (next phase map) guarantee the invertibility of reconstructed phase space trajectories to the original coordinates. The resulting Fourier approximated, invertibility enforcing phase space map allows us to detect conditional asymptotic stability of coupled phases. This comparatively general synchronization criterion unites two existing generalizations of the old concept and can successfully be applied, e.g., to phases obtained from electrocardiogram and airflow recordings characterizing cardiorespiratory interaction.

Point-of-care instrument for monitoring tissue health during skin graft repair

NASA Astrophysics Data System (ADS)

Gurjar, R. S.; Seetamraju, M.; Zhang, J.; Feinberg, S. E.; Wolf, D. E.

2011-06-01

We have developed the necessary theoretical framework and the basic instrumental design parameters to enable mapping of subsurface blood dynamics and tissue oxygenation for patients undergoing skin graft procedures. This analysis forms the basis for developing a simple patch geometry, which can be used to map by diffuse optical techniques blood flow velocity and tissue oxygenation as a function of depth in subsurface tissue.skin graft, diffuse correlation analysis, oxygen saturation.

Intraluminal mapping of tissue viscoelastic properties using laser speckle rheology catheter (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wang, Jing; Hosoda, Masaki; Tshikudi, Diane M.; Nadkarni, Seemantini K.

2016-03-01

A number of disease conditions including coronary atherosclerosis, peripheral artery disease and gastro-intestinal malignancies are associated with alterations in tissue mechanical properties. Laser speckle rheology (LSR) has been demonstrated to provide important information on tissue mechanical properties by analyzing the time scale of temporal speckle intensity fluctuations, which serves as an index of tissue viscoelasticity. In order to measure the mechanical properties of luminal organs in vivo, LSR must be conducted via a miniature endoscope or catheter. Here we demonstrate the capability of an omni-directional LSR catheter to quantify tissue mechanical properties over the entire luminal circumference without the need for rotational motion. Retracting the catheter using a motor-drive assembly enables the reconstruction of cylindrical maps of tissue mechanical properties. The performance of the LSR catheter is tested using a luminal phantom with mechanical moduli that vary in both circumferential and longitudinal directions. 2D cylindrical maps of phantom viscoelastic properties are reconstructed over four quadrants of the coronary circumference simultaneously during catheter pullback. The reconstructed cylindrical maps of the decorrelation time constants easily distinguish the different gel components of the phantom with different viscoelastic moduli. The average values of decorrelation times calculated for each gel component of the phantom show a strong correspondence with the viscoelastic moduli measured via standard mechanical rheometry. These results highlight the capability for cylindrical mapping of tissue viscoelastic properties using LSR in luminal organs using a miniature catheter, thus opening the opportunity for improved diagnosis of several disease conditions.

Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

NASA Astrophysics Data System (ADS)

Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

2016-03-01

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and posterior eye segment as well as in skin imaging. The new estimator shows superior performance and also shows clearer image contrast.

Accuracy of MRI-based Magnetic Susceptibility Measurements

NASA Astrophysics Data System (ADS)

Russek, Stephen; Erdevig, Hannah; Keenan, Kathryn; Stupic, Karl

Magnetic Resonance Imaging (MRI) is increasingly used to map tissue susceptibility to identify microbleeds associated with brain injury and pathologic iron deposits associated with neurologic diseases such as Parkinson's and Alzheimer's disease. Field distortions with a resolution of a few parts per billion can be measured using MRI phase maps. The field distortion map can be inverted to obtain a quantitative susceptibility map. To determine the accuracy of MRI-based susceptibility measurements, a set of phantoms with paramagnetic salts and nano-iron gels were fabricated. The shapes and orientations of features were varied. Measured susceptibility of 1.0 mM GdCl3 solution in water as a function of temperature agreed well with the theoretical predictions, assuming Gd+3 is spin 7/2. The MRI susceptibility measurements were compared with SQUID magnetometry. The paramagnetic susceptibility sits on top of the much larger diamagnetic susceptibility of water (-9.04 x 10-6), which leads to errors in the SQUID measurements. To extract out the paramagnetic contribution using standard magnetometry, measurements must be made down to low temperature (2K). MRI-based susceptometry is shown to be as or more accurate than standard magnetometry and susceptometry techniques.

Magnetic mapping of iron in rodent spleen

PubMed Central

Blissett, Angela R.; Ollander, Brooke; Penn, Brittany; McTigue, Dana M.; Agarwal, Gunjan

2016-01-01

Evaluation of iron distribution and density in biological tissues is important to understand the pathogenesis of a variety of diseases and the fate of exogenously administered iron-based carriers and contrast agents. Iron distribution in tissues is typically characterized via histochemical (Perl’s) stains or immunohistochemistry for ferritin, the major iron storage protein. A more accurate mapping of iron can be achieved via ultrastructural transmission electron microscopy (TEM) based techniques, which involve stringent sample preparation conditions. In this study, we elucidate the capability of magnetic force microscopy (MFM) as a label-free technique to map iron at the nanoscale level in rodent spleen tissue. We complemented and compared our MFM results with those obtained using Perl’s staining and TEM. Our results show how MFM mapping corresponded to sizes of iron-rich lysosomes at a resolution comparable to that of TEM. In addition MFM is compatible with tissue sections commonly prepared for routine histology. PMID:27890658

Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

PubMed

Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

2010-09-16

An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

Phase congruency map driven brain tumour segmentation

NASA Astrophysics Data System (ADS)

Szilágyi, Tünde; Brady, Michael; Berényi, Ervin

2015-03-01

Computer Aided Diagnostic (CAD) systems are already of proven value in healthcare, especially for surgical planning, nevertheless much remains to be done. Gliomas are the most common brain tumours (70%) in adults, with a survival time of just 2-3 months if detected at WHO grades III or higher. Such tumours are extremely variable, necessitating multi-modal Magnetic Resonance Images (MRI). The use of Gadolinium-based contrast agents is only relevant at later stages of the disease where it highlights the enhancing rim of the tumour. Currently, there is no single accepted method that can be used as a reference. There are three main challenges with such images: to decide whether there is tumour present and is so localize it; to construct a mask that separates healthy and diseased tissue; and to differentiate between the tumour core and the surrounding oedema. This paper presents two contributions. First, we develop tumour seed selection based on multiscale multi-modal texture feature vectors. Second, we develop a method based on a local phase congruency based feature map to drive level-set segmentation. The segmentations achieved with our method are more accurate than previously presented methods, particularly for challenging low grade tumours.

Frequency Mapping of Rat Spinal Cord at 7T

NASA Astrophysics Data System (ADS)

Chen, Evan; Rauscher, Alexander; Kozlowski, Piotr; Yung, Andrew

2012-10-01

The spinal cord is an integral part of the nervous system responsible for sensory, motor, and reflex control crucial to all bodily function. Due to its non-invasive nature, MRI is well matched for characterizing and imaging of spinal cord, and is used extensively for clinical applications. Recent developments in magnetic resonance imaging (MRI) at high field (7T) using phase represents a new approach of characterizing spinal cord myelin. Theory suggests that microstructure differences in myelinated white matter (WM) and non-myelinated gray matter (GM) affect MR phase, measurable frequency shifts. Data from pilot experiments using a multi-gradient echo (MGE) sequence to image rat spinal cords placed parallel to main magnetic field B0 has shown frequency shifts between not only between WM and GM, but also between specific WM tracts of the dorsal column, including the fasciculus gracilis, fasciculus cuneatus, and corticospinal tract. Using MGE, frequency maps at multiple echo times (TE) between 4ms and 22ms show a non-linear relationship between WM frequency, contrary to what was previously expected. These results demonstrate the effectiveness of MGE in revealing new information about spinal cord tissue microstructure, and lays important groundwork for in-vivo and human studies.

Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping in the Brain

PubMed Central

Liu, Chunlei; Li, Wei; Tong, Karen A.; Yeom, Kristen W.; Kuzminski, Samuel

2015-01-01

Susceptibility-weighted imaging (SWI) is a magnetic resonance imaging (MRI) technique that enhances image contrast by using the susceptibility differences between tissues. It is created by combining both magnitude and phase in the gradient echo data. SWI is sensitive to both paramagnetic and diamagnetic substances which generate different phase shift in MRI data. SWI images can be displayed as a minimum intensity projection that provides high resolution delineation of the cerebral venous architecture, a feature that is not available in other MRI techniques. As such, SWI has been widely applied to diagnose various venous abnormalities. SWI is especially sensitive to deoxygenated blood and intracranial mineral deposition and, for that reason, has been applied to image various pathologies including intracranial hemorrhage, traumatic brain injury, stroke, neoplasm, and multiple sclerosis. SWI, however, does not provide quantitative measures of magnetic susceptibility. This limitation is currently being addressed with the development of quantitative susceptibility mapping (QSM) and susceptibility tensor imaging (STI). While QSM treats susceptibility as isotropic, STI treats susceptibility as generally anisotropic characterized by a tensor quantity. This article reviews the basic principles of SWI, its clinical and research applications, the mechanisms governing brain susceptibility properties, and its practical implementation, with a focus on brain imaging. PMID:25270052

Using a concept map as a tool for strategic planning: The Healthy Brain Initiative.

PubMed

Anderson, Lynda A; Day, Kristine L; Vandenberg, Anna E

2011-09-01

Concept mapping is a tool to assist in strategic planning that allows planners to work through a sequence of phases to produce a conceptual framework. Although several studies describe how concept mapping is applied to various public health problems, the flexibility of the methods used in each phase of the process is often overlooked. If practitioners were more aware of the flexibility, more public health endeavors could benefit from using concept mapping as a tool for strategic planning. The objective of this article is to describe how the 6 concept-mapping phases originally outlined by William Trochim guided our strategic planning process and how we adjusted the specific methods in the first 2 phases to meet the specialized needs and requirements to create The Healthy Brain Initiative: A National Public Health Road Map to Maintaining Cognitive Health. In the first stage (phases 1 and 2 of concept mapping), we formed a steering committee, convened 4 work groups over a period of 3 months, and generated an initial set of 42 action items grounded in science. In the second stage (phases 3 and 4), we engaged stakeholders in sorting and rating the action items and constructed a series of concept maps. In the third and final stage (phases 5 and 6), we examined and refined the action items and generated a final concept map consisting of 44 action items. We then selected the top 10 action items, and in 2007, we published The Healthy Brain Initiative: A National Public Health Road Map to Maintaining Cognitive Health, which represents the strategic plan for The Healthy Brain Initiative.

Mean phase predictor for maximum a posteriori demodulator

NASA Technical Reports Server (NTRS)

Altes, Richard A. (Inventor)

1996-01-01

A system and method for optimal maximum a posteriori (MAP) demodulation using a novel mean phase predictor. The mean phase predictor conducts cumulative averaging over multiple blocks of phase samples to provide accurate prior mean phases, to be input into a MAP phase estimator.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Three-Dimensional Optical Mapping of Nanoparticle Distribution in Intact Tissues.

PubMed

Sindhwani, Shrey; Syed, Abdullah Muhammad; Wilhelm, Stefan; Glancy, Dylan R; Chen, Yih Yang; Dobosz, Michael; Chan, Warren C W

2016-05-24

The role of tissue architecture in mediating nanoparticle transport, targeting, and biological effects is unknown due to the lack of tools for imaging nanomaterials in whole organs. Here, we developed a rapid optical mapping technique to image nanomaterials in intact organs ex vivo and in three-dimensions (3D). We engineered a high-throughput electrophoretic flow device to simultaneously transform up to 48 tissues into optically transparent structures, allowing subcellular imaging of nanomaterials more than 1 mm deep into tissues which is 25-fold greater than current techniques. A key finding is that nanomaterials can be retained in the processed tissue by chemical cross-linking of surface adsorbed serum proteins to the tissue matrix, which enables nanomaterials to be imaged with respect to cells, blood vessels, and other structures. We developed a computational algorithm to analyze and quantitatively map nanomaterial distribution. This method can be universally applied to visualize the distribution and interactions of materials in whole tissues and animals including such applications as the imaging of nanomaterials, tissue engineered constructs, and biosensors within their intact biological environment.

Calculation of susceptibility through multiple orientation sampling (COSMOS): a method for conditioning the inverse problem from measured magnetic field map to susceptibility source image in MRI.

PubMed

Liu, Tian; Spincemaille, Pascal; de Rochefort, Ludovic; Kressler, Bryan; Wang, Yi

2009-01-01

Magnetic susceptibility differs among tissues based on their contents of iron, calcium, contrast agent, and other molecular compositions. Susceptibility modifies the magnetic field detected in the MR signal phase. The determination of an arbitrary susceptibility distribution from the induced field shifts is a challenging, ill-posed inverse problem. A method called "calculation of susceptibility through multiple orientation sampling" (COSMOS) is proposed to stabilize this inverse problem. The field created by the susceptibility distribution is sampled at multiple orientations with respect to the polarization field, B(0), and the susceptibility map is reconstructed by weighted linear least squares to account for field noise and the signal void region. Numerical simulations and phantom and in vitro imaging validations demonstrated that COSMOS is a stable and precise approach to quantify a susceptibility distribution using MRI.

Reconstruction of phase maps from the configuration of phase singularities in two-dimensional manifolds.

PubMed

Herlin, Antoine; Jacquemet, Vincent

2012-05-01

Phase singularity analysis provides a quantitative description of spiral wave patterns observed in chemical or biological excitable media. The configuration of phase singularities (locations and directions of rotation) is easily derived from phase maps in two-dimensional manifolds. The question arises whether one can construct a phase map with a given configuration of phase singularities. The existence of such a phase map is guaranteed provided that the phase singularity configuration satisfies a certain constraint associated with the topology of the supporting medium. This paper presents a constructive mathematical approach to numerically solve this problem in the plane and on the sphere as well as in more general geometries relevant to atrial anatomy including holes and a septal wall. This tool can notably be used to create initial conditions with a controllable spiral wave configuration for cardiac propagation models and thus help in the design of computer experiments in atrial electrophysiology.

Deep-tissue temperature mapping by multi-illumination photoacoustic tomography aided by a diffusion optical model: a numerical study

NASA Astrophysics Data System (ADS)

Zhou, Yuan; Tang, Eric; Luo, Jianwen; Yao, Junjie

2018-01-01

Temperature mapping during thermotherapy can help precisely control the heating process, both temporally and spatially, to efficiently kill the tumor cells and prevent the healthy tissues from heating damage. Photoacoustic tomography (PAT) has been used for noninvasive temperature mapping with high sensitivity, based on the linear correlation between the tissue's Grüneisen parameter and temperature. However, limited by the tissue's unknown optical properties and thus the optical fluence at depths beyond the optical diffusion limit, the reported PAT thermometry usually takes a ratiometric measurement at different temperatures and thus cannot provide absolute measurements. Moreover, ratiometric measurement over time at different temperatures has to assume that the tissue's optical properties do not change with temperatures, which is usually not valid due to the temperature-induced hemodynamic changes. We propose an optical-diffusion-model-enhanced PAT temperature mapping that can obtain the absolute temperature distribution in deep tissue, without the need of multiple measurements at different temperatures. Based on the initial acoustic pressure reconstructed from multi-illumination photoacoustic signals, both the local optical fluence and the optical parameters including absorption and scattering coefficients are first estimated by the optical-diffusion model, then the temperature distribution is obtained from the reconstructed Grüneisen parameters. We have developed a mathematic model for the multi-illumination PAT of absolute temperatures, and our two-dimensional numerical simulations have shown the feasibility of this new method. The proposed absolute temperature mapping method may set the technical foundation for better temperature control in deep tissue in thermotherapy.

The implementation of CMOS sensors within a real time digital mammography intelligent imaging system: The I-ImaS System

NASA Astrophysics Data System (ADS)

Esbrand, C.; Royle, G.; Griffiths, J.; Speller, R.

2009-07-01

The integration of technology with healthcare has undoubtedly propelled the medical imaging sector well into the twenty first century. The concept of digital imaging introduced during the 1970s has since paved the way for established imaging techniques where digital mammography, phase contrast imaging and CT imaging are just a few examples. This paper presents a prototype intelligent digital mammography system designed and developed by a European consortium. The final system, the I-ImaS system, utilises CMOS monolithic active pixel sensor (MAPS) technology promoting on-chip data processing, enabling the acts of data processing and image acquisition to be achieved simultaneously; consequently, statistical analysis of tissue is achievable in real-time for the purpose of x-ray beam modulation via a feedback mechanism during the image acquisition procedure. The imager implements a dual array of twenty 520 pixel × 40 pixel CMOS MAPS sensing devices with a 32μm pixel size, each individually coupled to a 100μm thick thallium doped structured CsI scintillator. This paper presents the first intelligent images of real breast tissue obtained from the prototype system of real excised breast tissue where the x-ray exposure was modulated via the statistical information extracted from the breast tissue itself. Conventional images were experimentally acquired where the statistical analysis of the data was done off-line, resulting in the production of simulated real-time intelligently optimised images. The results obtained indicate real-time image optimisation using the statistical information extracted from the breast as a means of a feedback mechanisms is beneficial and foreseeable in the near future.

Pixel-by-pixel absolute phase retrieval using three phase-shifted fringe patterns without markers

NASA Astrophysics Data System (ADS)

Jiang, Chufan; Li, Beiwen; Zhang, Song

2017-04-01

This paper presents a method that can recover absolute phase pixel by pixel without embedding markers on three phase-shifted fringe patterns, acquiring additional images, or introducing additional hardware component(s). The proposed three-dimensional (3D) absolute shape measurement technique includes the following major steps: (1) segment the measured object into different regions using rough priori knowledge of surface geometry; (2) artificially create phase maps at different z planes using geometric constraints of structured light system; (3) unwrap the phase pixel by pixel for each region by properly referring to the artificially created phase map; and (4) merge unwrapped phases from all regions into a complete absolute phase map for 3D reconstruction. We demonstrate that conventional three-step phase-shifted fringe patterns can be used to create absolute phase map pixel by pixel even for large depth range objects. We have successfully implemented our proposed computational framework to achieve absolute 3D shape measurement at 40 Hz.

Efficient characterization of phase space mapping in axially symmetric optical systems

NASA Astrophysics Data System (ADS)

Barbero, Sergio; Portilla, Javier

2018-01-01

Phase space mapping, typically between an object and image plane, characterizes an optical system within a geometrical optics framework. We propose a novel conceptual frame to characterize the phase mapping in axially symmetric optical systems for arbitrary object locations, not restricted to a specific object plane. The idea is based on decomposing the phase mapping into a set of bivariate equations corresponding to different values of the radial coordinate on a specific object surface (most likely the entrance pupil). These equations are then approximated through bivariate Chebyshev interpolation at Chebyshev nodes, which guarantees uniform convergence. Additionally, we propose the use of a new concept (effective object phase space), defined as the set of points of the phase space at the first optical element (typically the entrance pupil) that are effectively mapped onto the image surface. The effective object phase space provides, by means of an inclusion test, a way to avoid tracing rays that do not reach the image surface.

Is there more valuable information in PWI datasets for a voxel-wise acute ischemic stroke tissue outcome prediction than what is represented by typical perfusion maps?

NASA Astrophysics Data System (ADS)

Forkert, Nils Daniel; Siemonsen, Susanne; Dalski, Michael; Verleger, Tobias; Kemmling, Andre; Fiehler, Jens

2014-03-01

The acute ischemic stroke is a leading cause for death and disability in the industry nations. In case of a present acute ischemic stroke, the prediction of the future tissue outcome is of high interest for the clinicians as it can be used to support therapy decision making. Within this context, it has already been shown that the voxel-wise multi-parametric tissue outcome prediction leads to more promising results compared to single channel perfusion map thresholding. Most previously published multi-parametric predictions employ information from perfusion maps derived from perfusion-weighted MRI together with other image sequences such as diffusion-weighted MRI. However, it remains unclear if the typically calculated perfusion maps used for this purpose really include all valuable information from the PWI dataset for an optimal tissue outcome prediction. To investigate this problem in more detail, two different methods to predict tissue outcome using a k-nearest-neighbor approach were developed in this work and evaluated based on 18 datasets of acute stroke patients with known tissue outcome. The first method integrates apparent diffusion coefficient and perfusion parameter (Tmax, MTT, CBV, CBF) information for the voxel-wise prediction, while the second method employs also apparent diffusion coefficient information but the complete perfusion information in terms of the voxel-wise residue functions instead of the perfusion parameter maps for the voxel-wise prediction. Overall, the comparison of the results of the two prediction methods for the 18 patients using a leave-one-out cross validation revealed no considerable differences. Quantitatively, the parameter-based prediction of tissue outcome led to a mean Dice coefficient of 0.474, while the prediction using the residue functions led to a mean Dice coefficient of 0.461. Thus, it may be concluded from the results of this study that the perfusion parameter maps typically derived from PWI datasets include all valuable perfusion information required for a voxel-based tissue outcome prediction, while the complete analysis of the residue functions does not add further benefits for the voxel-wise tissue outcome prediction and is also computationally more expensive.

Optical coherence microscopy of mouse cortical vasculature surrounding implanted electrodes

NASA Astrophysics Data System (ADS)

Hammer, Daniel X.; Lozzi, Andrea; Abliz, Erkinay; Greenbaum, Noah; Turner, Kevin P.; Pfefer, T. Joshua; Agrawal, Anant; Krauthamer, Victor; Welle, Cristin G.

2014-03-01

Optical coherence microscopy (OCM) provides real-time, in-vivo, three-dimensional, isotropic micron-resolution structural and functional characterization of tissue, cells, and other biological targets. Optical coherence angiography (OCA) also provides visualization and quantification of vascular flow via speckle-based or phase-resolved techniques. Performance assessment of neuroprosthetic systems, which allow direct thought control of limb prostheses, may be aided by OCA. In particular, there is a need to examine the underlying mechanisms of chronic functional degradation of implanted electrodes. Angiogenesis, capillary network remodeling, and changes in flow velocity are potential indicators of tissue changes that may be associated with waning electrode performance. The overall goal of this investigation is to quantify longitudinal changes in vascular morphology and capillary flow around neural electrodes chronically implanted in mice. We built a 1315-nm OCM system to image vessels in neocortical tissue in a cohort of mice. An optical window was implanted on the skull over the primary motor cortex above a penetrating shank-style microelectrode array. The mice were imaged bi-weekly to generate vascular maps of the region surrounding the implanted microelectrode array. Acute effects of window and electrode implantation included vessel dilation and profusion of vessels in the superficial layer of the cortex (0-200 μm). In deeper layers surrounding the electrode, no qualitative differences were seen in this early phase. These measurements establish a baseline vascular tissue response from the cortical window preparation and lay the ground work for future longitudinal studies to test the hypothesis that vascular changes will be associated with chronic electrode degradation.

Real-time and non-invasive measurements of cell mechanical behaviour with optical coherence phase microscopy

NASA Astrophysics Data System (ADS)

Gillies, D.; Gamal, W.; Downes, A.; Reinwald, Y.; Yang, Y.; El Haj, A.; Bagnaninchi, P. O.

2017-02-01

There is an unmet need in tissue engineering for non-invasive, label-free monitoring of cell mechanical behaviour in their physiological environment. Here, we describe a novel optical coherence phase microscopy (OCPM) set-up which can map relative cell mechanical behaviour in monolayers and 3D systems non-invasively, and in real-time. 3T3 and MCF-7 cells were investigated, with MCF-7 demonstrating an increased response to hydrostatic stimulus indicating MCF-7 being softer than 3T3. Thus, OCPM shows the ability to provide qualitative data on cell mechanical behaviour. Quantitative measurements of 6% agarose beads have been taken with commercial Cell Scale Microsquisher system demonstrating that their mechanical properties are in the same order of magnitude of cells, indicating that this is an appropriate test sample for the novel method described.

NIH scientists map gene changes driving tumors in common pediatric soft-tissue cancer

Cancer.gov

Scientists have mapped the genetic changes that drive tumors in rhabdomyosarcoma, a pediatric soft-tissue cancer, and found that the disease is characterized by two distinct genotypes. The genetic alterations identified in this malignancy could be useful

Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

DOE PAGES

Dyck, Ondrej; Hu, Sheng; Das, Sanjib; ...

2015-11-24

Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

Mechanical Characterization of Tissue-Engineered Cartilage Using Microscopic Magnetic Resonance Elastography

PubMed Central

Yin, Ziying; Schmid, Thomas M.; Yasar, Temel K.; Liu, Yifei; Royston, Thomas J.

2014-01-01

Knowledge of mechanical properties of tissue-engineered cartilage is essential for the optimization of cartilage tissue engineering strategies. Microscopic magnetic resonance elastography (μMRE) is a recently developed MR-based technique that can nondestructively visualize shear wave motion. From the observed wave pattern in MR phase images the tissue mechanical properties (e.g., shear modulus or stiffness) can be extracted. For quantification of the dynamic shear properties of small and stiff tissue-engineered cartilage, μMRE needs to be performed at frequencies in the kilohertz range. However, at frequencies greater than 1 kHz shear waves are rapidly attenuated in soft tissues. In this study μMRE, with geometric focusing, was used to overcome the rapid wave attenuation at high frequencies, enabling the measurement of the shear modulus of tissue-engineered cartilage. This methodology was first tested at a frequency of 5 kHz using a model system composed of alginate beads embedded in agarose, and then applied to evaluate extracellular matrix development in a chondrocyte pellet over a 3-week culture period. The shear stiffness in the pellet was found to increase over time (from 6.4 to 16.4 kPa), and the increase was correlated with both the proteoglycan content and the collagen content of the chondrocyte pellets (R2=0.776 and 0.724, respectively). Our study demonstrates that μMRE when performed with geometric focusing can be used to calculate and map the shear properties within tissue-engineered cartilage during its development. PMID:24266395

Mapping tissue oxygen in vivo by photoacoustic lifetime imaging

NASA Astrophysics Data System (ADS)

Shao, Qi; Morgounova, Ekaterina; Choi, Jeung-Hwan; Jiang, Chunlan; Bischof, John; Ashkenazi, Shai

2013-03-01

Oxygen plays a key role in the energy metabolism of living organisms. Any imbalance in the oxygen levels will affect the metabolic homeostasis and lead to pathophysiological diseases. Hypoxia, a status of low tissue oxygen, is a key factor in tumor biology as it is highly prominent in tumor tissues. However, clinical tools for assessing tissue oxygenation are limited. The gold standard is polarographic needle electrode which is invasive and not capable of mapping (imaging) the oxygen content in tissue. We applied the method of photoacoustic lifetime imaging (PALI) of oxygen-sensitive dye to small animal tissue hypoxia research. PALI is new technology for direct, non-invasive imaging of oxygen. The technique is based on mapping the oxygen-dependent transient optical absorption of Methylene Blue (MB) by pump-probe photoacoustic imaging. Our studies show the feasibility of imaging of dissolved oxygen distribution in phantoms. In vivo experiments demonstrate that the hypoxia region is consistent with the site of subcutaneously xenografted prostate tumor in mice with adequate spatial resolution and penetration depth.

Spatial mapping of metals in tissue-sections using combination of mass-spectrometry and histology through image registration

NASA Astrophysics Data System (ADS)

Anyz, Jiri; Vyslouzilova, Lenka; Vaculovic, Tomas; Tvrdonova, Michaela; Kanicky, Viktor; Haase, Hajo; Horak, Vratislav; Stepankova, Olga; Heger, Zbynek; Adam, Vojtech

2017-01-01

We describe a new procedure for the parallel mapping of selected metals in histologically characterized tissue samples. Mapping is achieved via image registration of digital data obtained from two neighbouring cryosections by scanning the first as a histological sample and subjecting the second to laser ablation inductively coupled plasma mass spectrometry. This computer supported procedure enables determination of the distribution and content of metals of interest directly in the chosen histological zones and represents a substantial improvement over the standard approach, which determines these values in tissue homogenates or whole tissue sections. The potential of the described procedure was demonstrated in a pilot study that analysed Zn and Cu levels in successive development stages of pig melanoma tissue using MeLiM (Melanoma-bearing-Libechov-Minipig) model. We anticipate that the procedure could be useful for a complex understanding of the role that the spatial distribution of metals plays within tissues affected by pathological states including cancer.

Spatial mapping of metals in tissue-sections using combination of mass-spectrometry and histology through image registration

PubMed Central

Anyz, Jiri; Vyslouzilova, Lenka; Vaculovic, Tomas; Tvrdonova, Michaela; Kanicky, Viktor; Haase, Hajo; Horak, Vratislav; Stepankova, Olga; Heger, Zbynek; Adam, Vojtech

2017-01-01

We describe a new procedure for the parallel mapping of selected metals in histologically characterized tissue samples. Mapping is achieved via image registration of digital data obtained from two neighbouring cryosections by scanning the first as a histological sample and subjecting the second to laser ablation inductively coupled plasma mass spectrometry. This computer supported procedure enables determination of the distribution and content of metals of interest directly in the chosen histological zones and represents a substantial improvement over the standard approach, which determines these values in tissue homogenates or whole tissue sections. The potential of the described procedure was demonstrated in a pilot study that analysed Zn and Cu levels in successive development stages of pig melanoma tissue using MeLiM (Melanoma-bearing-Libechov-Minipig) model. We anticipate that the procedure could be useful for a complex understanding of the role that the spatial distribution of metals plays within tissues affected by pathological states including cancer. PMID:28071735

Evaluation of specimen preparation techniques for micro-PIXE localisation of elements in hyperaccumulating plants

NASA Astrophysics Data System (ADS)

Kachenko, Anthony G.; Siegele, Rainer; Bhatia, Naveen P.; Singh, Balwant; Ionescu, Mihail

2008-04-01

Hybanthus floribundus subsp. floribundus, a rare Australian Ni-hyperaccumulating shrub and Pityrogramma calomelanos var. austroamericana, an Australian naturalized As-hyperaccumulating fern are promising species for use in phytoremediation of contaminated sites. Micro-proton-induced X-ray emission (μ-PIXE) spectroscopy was used to map the elemental distribution of the accumulated metal(loid)s, Ca and K in leaf or pinnule tissues of the two plant species. Samples were prepared by two contrasting specimen preparation techniques: freeze-substitution in tetrahydrofuran (THF) and freeze-drying. The specimens were analysed to compare the suitability of each technique in preserving (i) the spatial elemental distribution and (ii) the tissue structure of the specimens. Further, the μ-PIXE results were compared with concentration of elements in the bulk tissue obtained by ICP-AES analysis. In H. floribundus subsp. floribundus, μ-PIXE analysis revealed Ni, Ca and K concentrations in freeze-dried leaf tissues were at par with bulk tissue concentrations. Elemental distribution maps illustrated that Ni was preferentially localised in the adaxial epidermal tissues (1% DW) and least concentration was found in spongy mesophyll tissues (0.53% DW). Conversely, elemental distribution maps of THF freeze-substituted tissues indicated significantly lower Ni, Ca and K concentrations than freeze-dried specimens and bulk tissue concentrations. Moreover, Ni concentrations were uniform across the whole specimen and no localisation was observed. In P. calomelanos var. austroamericana freeze-dried pinnule tissues, μ-PIXE revealed statistically similar As, Ca and K concentrations as compared to bulk tissue concentrations. Elemental distribution maps showed that As localisation was relatively uniform across the whole specimen. Once again, THF freeze-substituted tissues revealed a significant loss of As compared to freeze-dried specimens and the concentrations obtained by bulk tissue analysis. The results demonstrate that freeze-drying is a suitable sample preparation technique to study elemental distribution of ions in H. floribundus and P. calomelanos plant tissues using μ-PIXE spectroscopy. Furthermore, cellular structure was preserved in samples prepared using this technique.

The 2007 Feinberg lecture: a new road map for neuroprotection.

PubMed

Donnan, Geoffrey A

2008-01-01

There have now been numerous phase III trials of neuroprotection that have failed to live up to the expectations created by preclinical testing in animal models, the most recent of which was the second pivotal trial of the spin trap agent NXY-059. We have reached a stage at which research in this area should stop altogether or radical new approaches adopted. The purpose of this article is to review how we reached this stage and make recommendations for a new approach to neuroprotection research. The background to neuroprotection research is reviewed and its problems are highlighted based on the research of others and of our own research group. From this, a series of questions are posed that require answers if the field is to progress. A road map for future research is then proposed. The road map involves the following steps for putative neuroprotectants: (1) better proof of efficacy in animal models; (2) in vivo evidence of efficacy in human tissue using cell cultures or brain slices; (3) in vivo studies of their distribution in the normal and ischemic human brain, particularly focusing on the ischemic penumbra; (4) demonstration of efficacy in novel human models of cerebral ischemia; and (5) phase II and III clinical trails with penumbral selection using imaging techniques. The accumulated evidence suggests that neuroprotection failure in clinical trial is due to identifiable preclinical and clinical factors. Neuroprotection research should be pursued but with a very different and more rigorous approach.

Combined passive acoustic mapping and magnetic resonance thermometry for monitoring phase-shift nanoemulsion enhanced focused ultrasound therapy

NASA Astrophysics Data System (ADS)

Crake, Calum; Meral, F. Can; Burgess, Mark T.; Papademetriou, Iason T.; McDannold, Nathan J.; Porter, Tyrone M.

2017-08-01

Focused ultrasound (FUS) has the potential to enable precise, image-guided noninvasive surgery for the treatment of cancer in which tumors are identified and destroyed in a single integrated procedure. However, success of the method in highly vascular organs has been limited due to heat losses to perfusion, requiring development of techniques to locally enhance energy absorption and heating. In addition, FUS procedures are conventionally monitored using MRI, which provides excellent anatomical images and can map temperature, but is not capable of capturing the full gamut of available data such as the acoustic emissions generated during this inherently acoustically-driven procedure. Here, we employed phase-shift nanoemulsions (PSNE) embedded in tissue phantoms to promote cavitation and hence temperature rise induced by FUS. In addition, we incorporated passive acoustic mapping (PAM) alongside simultaneous MR thermometry in order to visualize both acoustic emissions and temperature rise, within the bore of a full scale clinical MRI scanner. Focal cavitation of PSNE could be resolved using PAM and resulted in accelerated heating and increased the maximum elevated temperature measured via MR thermometry compared to experiments without nanoemulsions. Over time, the simultaneously acquired acoustic and temperature maps show translation of the focus of activity towards the FUS transducer, and the magnitude of the increase in cavitation and focal shift both increased with nanoemulsion concentration. PAM results were well correlated with MRI thermometry and demonstrated greater sensitivity, with the ability to detect cavitation before enhanced heating was observed. The results suggest that PSNE could be beneficial for enhancement of thermal focused ultrasound therapies and that PAM could be a critical tool for monitoring this process.

Comparative evaluation of diagnostic tests for the detection of Mycobacterium avium subsp. paratuberculosis in the tissues of sheep affected with distinct pathology of paratuberculosis.

PubMed

Sonawane, Ganesh G; Tripathi, Bhupendra N

2016-12-01

Paratuberculosis or Johne's disease is a chronic infectious granulomatous enteritis, mainly of cattle, sheep, goats, and other domestic and wild animals caused by Mycobacterium avium subsp. paratuberculosis (MAP). Currently, MAP has been recognized as an important animal pathogen with significant zoonotic and public health concerns. The early detection of infected animals using suitable diagnostic methods helps in developing control and preventive strategies for the herd. Therefore, the present study was aimed to determine the comparative efficacy of certain diagnostic methods used in the identification and confirmation of MAP in the ovine tissues with distinct pathology of paratuberculosis. The ileum and mesenteric lymph node (MLN) tissues were collected from 38 sheep infected with paratuberculosis from organized farms of Rajasthan. These animals were further classified as paucibacillary (PB; n=15) or multibacillary (MB; n=23) on the basis of histopathological findings and mycobacterial loads. The ileum and MLN tissues of these animals were subjected to IS900 and 251 gene polymerase chain reaction (PCR) and bacterial culture. The tissue sections from MB, PB, and uninfected control sheep groups were stained using indirect immunoperoxidase technique (IPT) and Ziehl-Neelsen (ZN) method. On bacterial culture examination of the ileum and MLN tissues using Herrold's egg yolk medium, MAP was isolated in 14 (60.9%) MB and 5 (33.3%) PB sheep. Of 38 sheep, IS900 PCR detected 21 (55.2%) positive for MAP, of which 19 (82.6%) were MB and 2 (13.3%) were PB sheep. Similarly, 251 gene PCR detected 25 (65.7%) sheep positive for MAP infection, of which 21 (91.3%) were MB and 4 (27%) were PB sheep. Thus, 251 gene PCR was found superior to IS900 PCR in the detection of MAP from the tissues. In PB sheep, IPT and ZN tests were positive in 87.5% and 50% of ileum sections and 70% and 37.5% in MLN sections, respectively. In MB sheep, IPT and ZN tests detected all animals as positive for MAP organisms or antigen and had equal sensitivity in the detection of MAP. The overall sensitivity of IPT was found superior (95%) to ZN staining (80%) in the demonstration of acid-fast bacteria or its antigen in the tissues. The sensitivity of all the tests in the detection of MAP was lower in PB sheep than in MB sheep. Bacterial culture detected MAP in only 50% of sheep and was found less sensitive than other tests used in the present study. Comparing the overall sensitivity of both the PCR assays, 251 gene PCR was found superior to IS900 gene PCR. The sensitivity of IPT was found superior (95%) to the ZN staining (80%) in the demonstration of acid-fast bacteria in the tissues. In the present study, IPT was found superior in the detection of MAP in PB and MB form of ovine paratuberculosis. This test can be used in the confirmation of post mortem diagnosis and research of paratuberculosis along with histopathology. However, 251 gene PCR assay was found easier to perform than IPT and could be used as paratuberculosis screening test in endemic sheep farms for blood and fecal samples. Copyright © 2016.

Regional Mapping of Gas Uptake by Blood and Tissue in the Human Lung using Hyperpolarized Xenon-129 MRI

PubMed Central

Qing, Kun; Ruppert, Kai; Jiang, Yun; Mata, Jaime F.; Miller, G. Wilson; Shim, Y. Michael; Wang, Chengbo; Ruset, Iulian C.; Hersman, F. William; Altes, Talissa A.; Mugler, John P.

2013-01-01

Purpose To develop a breath-hold acquisition for regional mapping of ventilation and the fractions of hyperpolarized xenon-129 (Xe129) dissolved in tissue (lung parenchyma and plasma) and red blood cells (RBCs), and to perform an exploratory study to characterize data obtained in human subjects. Materials and Methods A three-dimensional, multi-echo, radial-trajectory pulse sequence was developed to obtain ventilation (gaseous Xe129), tissue and RBC images in healthy subjects, smokers and asthmatics. Signal ratios (total dissolved Xe129 to gas, tissue-to-gas, RBC-to-gas and RBC-to-tissue) were calculated from the images for quantitative comparison. Results Healthy subjects demonstrated generally uniform values within coronal slices, and a gradient in values along the anterior-to-posterior direction. In contrast, images and associated ratio maps in smokers and asthmatics were generally heterogeneous and exhibited values mostly lower than those in healthy subjects. Whole-lung values of total dissolved Xe129 to gas, tissue-to-gas, and RBC-to-gas ratios in healthy subjects were significantly larger than those in diseased subjects. Conclusion Regional maps of tissue and RBC fractions of dissolved Xe129 were obtained from a short breath-hold acquisition, well tolerated by healthy volunteers and subjects with obstructive lung disease. Marked differences were observed in spatial distributions and overall amounts of Xe129 dissolved in tissue and RBCs among healthy subjects, smokers and asthmatics. PMID:23681559

Physiological gas exchange mapping of hyperpolarized 129 Xe using spiral-IDEAL and MOXE in a model of regional radiation-induced lung injury.

PubMed

Zanette, Brandon; Stirrat, Elaine; Jelveh, Salomeh; Hope, Andrew; Santyr, Giles

2018-02-01

To map physiological gas exchange parameters using dissolved hyperpolarized (HP) 129 Xe in a rat model of regional radiation-induced lung injury (RILI) with spiral-IDEAL and the model of xenon exchange (MOXE). Results are compared to quantitative histology of pulmonary tissue and red blood cell (RBC) distribution. Two cohorts (n = 6 each) of age-matched rats were used. One was irradiated in the right-medial lung, producing regional injury. Gas exchange was mapped 4 weeks postirradiation by imaging dissolved-phase HP 129 Xe using spiral-IDEAL at five gas exchange timepoints using a clinical 1.5 T scanner. Physiological lung parameters were extracted regionally on a voxel-wise basis using MOXE. Mean gas exchange parameters, specifically air-capillary barrier thickness (δ) and hematocrit (HCT) in the right-medial lung were compared to the contralateral lung as well as nonirradiated control animals. Whole-lung spectroscopic analysis of gas exchange was also performed. δ was significantly increased (1.43 ± 0.12 μm from 1.07 ± 0.09 μm) and HCT was significantly decreased (17.2 ± 1.2% from 23.6 ± 1.9%) in the right-medial lung (i.e., irradiated region) compared to the contralateral lung of the irradiated rats. These changes were not observed in healthy controls. δ and HCT correlated with histologically measured increases in pulmonary tissue heterogeneity (r = 0.77) and decreases in RBC distribution (r = 0.91), respectively. No changes were observed using whole-lung analysis. This work demonstrates the feasibility of mapping gas exchange using HP 129 Xe in an animal model of RILI 4 weeks postirradiation. Spatially resolved gas exchange mapping is sensitive to regional injury between cohorts that was undetected with whole-lung gas exchange analysis, in agreement with histology. Gas exchange mapping holds promise for assessing regional lung function in RILI and other pulmonary diseases. © 2017 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Implementation of the EU environmental noise directive: lessons from the first phase of strategic noise mapping and action planning in Ireland.

PubMed

King, E A; Murphy, E; Rice, H J

2011-03-01

The first phase of noise mapping and action planning in Ireland, in accordance with EU Directive 2002/49/EC, is now complete. In total this included one agglomeration, one airport and approximately 600 km of major roads outside the agglomeration. These noise maps describe the level of noise exposure of approximately 1.25 million people. The first phase of noise mapping was dealt with by five noise mapping bodies while 26 action planning authorities were involved in the development of the associated action plans. The second phase of noise mapping, due to be completed in 2012, sees a reduction in the defined thresholds describing the required agglomerations, roads and railways that have to be mapped. This will have a significant impact on the extent of mapping required. In Ireland this will result in an increased number of local authorities being required to develop strategic noise maps for their area along with the further development of associated action plans. It is appropriate at this point to review the work process and results from the first phase of noise mapping in Ireland in order to establish areas that could be improved, throughout the noise mapping project. In this paper a review of the implementation procedures focussing on (dominant) road traffic noise is presented. It is identified that more standardisation is needed and this could be achieved by the establishment of a national expert steering group. Copyright © 2010 Elsevier Ltd. All rights reserved.

Using global positioning system technology for watershed mapping in Caspar Creek

Treesearch

Norm Henry

1991-01-01

Surveying and mapping work has been an essential and time consuming part of the Caspar Watershed study during the North Fork phase. The cumulative effects study and several other studies being done in this phase require accurate mapping and periodic map updating of watershed features and disturbances.

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation

PubMed Central

Wilke, Marko; Altaye, Mekibib; Holland, Scott K.

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating “unusual” populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php. PMID:28275348

CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

PubMed

Wilke, Marko; Altaye, Mekibib; Holland, Scott K

2017-01-01

Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

PubMed

Avti, Pramod K; Hu, Song; Favazza, Christopher; Mikos, Antonios G; Jansen, John A; Shroyer, Kenneth R; Wang, Lihong V; Sitharaman, Balaji

2012-01-01

In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Optical-resolution (OR) and acoustic-resolution (AR)--Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Observation and correction of transient cavitation-induced PRFS thermometry artifacts during radiofrequency ablation, using simultaneous ultrasound/MR imaging.

PubMed

Viallon, Magalie; Terraz, Sylvain; Roland, Joerg; Dumont, Erik; Becker, Christoph D; Salomir, Rares

2010-04-01

MR thermometry based on the proton resonance frequency shift (PRFS) is the most commonly used method for the monitoring of thermal therapies. As the chemical shift of water protons is temperature dependent, the local temperature variation (relative to an initial baseline) may be calculated from time-dependent phase changes in gradient-echo (GRE) MR images. Dynamic phase shift in GRE images is also produced by time-dependent changes in the magnetic bulk susceptibility of tissue. Gas bubbles (known as "white cavitation") are frequently visualized near the RF electrode in ultrasonography-guided radio frequency ablation (RFA). This study aimed to investigate RFA-induced cavitation's effects by using simultaneous ultrasonography and MRI, to both visualize the cavitation and quantify the subsequent magnetic susceptibility-mediated errors in concurrent PRFS MR-thermometry (MRT) as well as to propose a first-order correction for the latter errors. RF heating in saline gels and in ex vivo tissues was performed with MR-compatible bipolar and monopolar electrodes inside a 1.5 T MR clinical scanner. Ultrasonography simultaneous to PRFS MRT was achieved using a MR-compatible phased-array ultrasonic transducer. PRFS MRT was performed interleaved in three orthogonal planes and compared to measurements from fluoroptic sensors, under low and, respectively, high RFA power levels. Control experiments were performed to isolate the main source of errors in standard PRFS thermometry. Ultrasonography, MRI and digital camera pictures clearly demonstrated generation of bubbles every time when operating the radio frequency equipment at therapeutic powers (> or = 30 W). Simultaneous bimodal (ultrasonography and MRI) monitoring of high power RF heating demonstrated a correlation between the onset of the PRFS-thermometry errors and the appearance of bubbles around the applicator. In an ex vivo study using a bipolar RF electrode under low power level (5 W), the MR measured temperature curves accurately matched the reference fluoroptic data. In similar ex vivo studies when applying higher RFA power levels (30 W), the correlation plots of MR thermometry versus fluoroptic data showed large errors in PRFS-derived temperature (up to 45 degrees C absolute deviation, positive or negative) depending not only on fluoroptic tip position but also on the RF electrode orientation relative to the B0 axis. Regions with apparent decrease in the PRFS-derived temperature maps as much as 30 degrees C below the initial baseline were visualized during RFA high power application. Ex vivo data were corrected assuming a Gaussian dynamic source of susceptibility, centered in the anode/cathode gap of the RF bipolar electrode. After correction, the temperature maps recovered the revolution symmetry pattern predicted by theory and matched the fluoroptic data within 4.5 degrees C mean offset. RFA induces dynamic changes in magnetic bulk susceptibility in biological tissue, resulting in large and spatially dependent errors of phase-subtraction-only PRFS MRT and unexploitable thermal dose maps. These thermometry artifacts were strongly correlated with the appearance of transient cavitation. A first-order dynamic model of susceptibility provided a useful method for minimizing these artifacts in phantom and ex vivo experiments.

Surface wave tomography of North America and the Caribbean using global and regional broad-band networks: Phase velocity maps and limitations of ray theory

USGS Publications Warehouse

Godey, S.; Snieder, R.; Villasenor, A.; Benz, H.M.

2003-01-01

We present phase velocity maps of fundamental mode Rayleigh waves across the North American and Caribbean plates. Our data set consists of 1846 waveforms from 172 events recorded at 91 broad-band stations operating in North America. We compute phase velocity maps in four narrow period bands between 50 and 150 s using a non-linear waveform inversion method that solves for phase velocity perturbations relative to a reference Earth model (PREM). Our results show a strong velocity contrast between high velocities beneath the stable North American craton, and lower velocities in the tectonically active western margin, in agreement with other regional and global surface wave tomography studies. We perform detailed comparisons with global model results, which display good agreement between phase velocity maps in the location and amplitude of the anomalies. However, forward modelling shows that regional maps are more accurate for predicting waveforms. In addition, at long periods, the amplitude of the velocity anomalies imaged in our regional phase velocity maps is three time larger than in global phase velocity models. This amplitude factor is necessary to explain the data accurately, showing that regional models provide a better image of velocity structures. Synthetic tests show that the raypath coverage used in this study enables one to resolve velocity features of the order of 800-1000 km. However, only larger length-scale features are observed in the phase velocity maps. The limitation in resolution of our maps can be attributed to the wave propagation theory used in the inversion. Ray theory does not account for off-great-circle ray propagation effects, such as ray bending or scattering. For wavelengths less than 1000 km, scattering effects are significant and may need to be considered.

Mapping absolute tissue endogenous fluorophore concentrations with chemometric wide-field fluorescence microscopy

NASA Astrophysics Data System (ADS)

Xu, Zhang; Reilley, Michael; Li, Run; Xu, Min

2017-06-01

We report chemometric wide-field fluorescence microscopy for imaging the spatial distribution and concentration of endogenous fluorophores in thin tissue sections. Nonnegative factorization aided by spatial diversity is used to learn both the spectral signature and the spatial distribution of endogenous fluorophores from microscopic fluorescence color images obtained under broadband excitation and detection. The absolute concentration map of individual fluorophores is derived by comparing the fluorescence from "pure" fluorophores under the identical imaging condition following the identification of the fluorescence species by its spectral signature. This method is then demonstrated by characterizing the concentration map of endogenous fluorophores (including tryptophan, elastin, nicotinamide adenine dinucleotide, and flavin adenine dinucleotide) for lung tissue specimens. The absolute concentrations of these fluorophores are all found to decrease significantly from normal, perilesional, to cancerous (squamous cell carcinoma) tissue. Discriminating tissue types using the absolute fluorophore concentration is found to be significantly more accurate than that achievable with the relative fluorescence strength. Quantification of fluorophores in terms of the absolute concentration map is also advantageous in eliminating the uncertainties due to system responses or measurement details, yielding more biologically relevant data, and simplifying the assessment of competing imaging approaches.

In vivo mapping of current density distribution in brain tissues during deep brain stimulation (DBS)

NASA Astrophysics Data System (ADS)

Sajib, Saurav Z. K.; Oh, Tong In; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2017-01-01

New methods for in vivo mapping of brain responses during deep brain stimulation (DBS) are indispensable to secure clinical applications. Assessment of current density distribution, induced by internally injected currents, may provide an alternative method for understanding the therapeutic effects of electrical stimulation. The current flow and pathway are affected by internal conductivity, and can be imaged using magnetic resonance-based conductivity imaging methods. Magnetic resonance electrical impedance tomography (MREIT) is an imaging method that can enable highly resolved mapping of electromagnetic tissue properties such as current density and conductivity of living tissues. In the current study, we experimentally imaged current density distribution of in vivo canine brains by applying MREIT to electrical stimulation. The current density maps of three canine brains were calculated from the measured magnetic flux density data. The absolute current density values of brain tissues, including gray matter, white matter, and cerebrospinal fluid were compared to assess the active regions during DBS. The resulting current density in different tissue types may provide useful information about current pathways and volume activation for adjusting surgical planning and understanding the therapeutic effects of DBS.

Material Properties of Human Ocular Tissue at 7-µm Resolution.

PubMed

Rohrbach, Daniel; Ito, Kazuyo; Lloyd, Harriet O; Silverman, Ronald H; Yoshida, Kenji; Yamaguchi, Tadashi; Mamou, Jonathan

2017-09-01

Quantitative assessment of the material properties of ocular tissues can provide valuable information for investigating several ophthalmic diseases. Quantitative acoustic microscopy (QAM) offers a means of obtaining such information, but few QAM investigations have been conducted on human ocular tissue. We imaged the optic nerve (ON) and iridocorneal angle in 12-µm deparaffinized sections of the human eye using a custom-built acoustic microscope with a 250-MHz transducer (7-µm lateral resolution). The two-dimensional QAM maps of ultrasound attenuation (α), speed of sound ( c), acoustic impedance ( Z), bulk modulus ( K), and mass density (ρ) were generated. Scanned samples were then stained and imaged by light microscopy for comparison with QAM maps. The spatial resolution and contrast of scanning acoustic microscopy (SAM) maps were sufficient to resolve anatomic layers of the retina (Re); anatomic features in SAM maps corresponded to those seen by light microscopy. Significant variations of the acoustic parameters were found. For example, the sclera was 220 MPa stiffer than Re, choroid, and ON tissue. To the authors' knowledge, this is the first systematic study to assess c, Z, K, ρ, and α of human ocular tissue at the high ultrasound frequencies used in this study.

Physics of tissue harmonic imaging by ultrasound

NASA Astrophysics Data System (ADS)

Jing, Yuan

Tissue Harmonic Imaging (THI) is an imaging modality that is currently deployed on diagnostic ultrasound scanners. In THI the amplitude of the ultrasonic pulse that is used to probe the tissue is large enough that the pulse undergoes nonlinear distortion as it propagates into the tissue. One result of the distortion is that as the pulse propagates energy is shifted from the fundamental frequency of the source pulse into its higher harmonics. These harmonics will scatter off objects in the tissue and images formed from the scattered higher harmonics are considered to have superior quality to the images formed from the fundamental frequency. Processes that have been suggested as possibly responsible for the improved imaging in THI include: (1) reduced sensitivity to reverberation, (2) reduced sensitivity to aberration, and (3) reduction in side lobes. By using a combination of controlled experiments and numerical simulations, these three reasons have been investigated. A single element transducer and a clinical ultrasound scanner with a phased array transducer were used to image a commercial tissue-mimicking phantom with calibrated targets. The higher image quality achieved with THI was quantified in terms of spatial resolution and "clutter" signals. A three-dimensional model of the forward propagation of nonlinear sound beams in media with arbitrary spatial properties (a generalized KZK equation) was developed. A time-domain code for solving the KZK equation was validated with measurements of the acoustic field generated by the single element transducer and the phased array transducer. The code was used to investigate the impact of aberration using tissue-like media with three-dimensional variations in all acoustic properties. The three-dimensional maps of tissue properties were derived from the datasets available through the Visible Female project. The experiments and simulations demonstrated that second harmonic imaging (1) suffers less clutter associated with reverberation; (2) is not immune to aberration effects and (3) suffers less clutter due to reduced side-lobe levels. The results indicate that side lobe suppression is the most significant reason for the improvement of second harmonic imaging.

Methods and means of Fourier-Stokes polarimetry and the spatial frequency filtering of phase anisotropy manifestations

NASA Astrophysics Data System (ADS)

Novakovskaya, O. Yu.; Ushenko, A. G.; Dubolazov, A. V.; Ushenko, V. A.; Ushenko, Yu. A.; Sakhnovskiy, M. Yu.; Soltys, I. V.; Zhytaryuk, V. H.; Olar, O. V.; Sidor, M.; Gorsky, M. P.

2016-12-01

The theoretical background of azimuthally stable method of Jones-matrix mapping of histological sections of biopsy of myocardium tissue on the basis of spatial frequency selection of the mechanisms of linear and circular birefringence is presented. The diagnostic application of a new correlation parameter - complex degree of mutual anisotropy - is analytically substantiated. The method of measuring coordinate distributions of complex degree of mutual anisotropy with further spatial filtration of their high- and low-frequency components is developed. The interconnections of such distributions with parameters of linear and circular birefringence of myocardium tissue histological sections are found. The comparative results of measuring the coordinate distributions of complex degree of mutual anisotropy formed by fibrillar networks of myosin fibrils of myocardium tissue of different necrotic states - dead due to coronary heart disease and acute coronary insufficiency are shown. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of complex degree of mutual anisotropy coordinate distributions are studied. The objective criteria of differentiation of cause of death are determined.

Poster - Thurs Eve-43: Verification of dose calculation with tissue inhomogeneity using MapCHECK.

PubMed

Korol, R; Chen, J; Mosalaei, H; Karnas, S

2008-07-01

MapCHECK (Sun Nuclear, Melbourne, FL) with 445 diode detectors has been used widely for routine IMRT quality assurance (QA) 1 . However, routine IMRT QA has not included the verification of inhomogeneity effects. The objective of this study is to use MapCHECK and a phantom to verify dose calculation and IMRT delivery with tissue inhomogeneity. A phantom with tissue inhomogeneities was placed on top of MapCHECK to measure the planar dose for an anterior beam with photon energy 6 MV or 18 MV. The phantom was composed of a 3.5 cm thick block of lung equivalent material and solid water arranged side by side with a 0.5 cm slab of solid water on the top of the phantom. The phantom setup including MapCHECK was CT scanned and imported into Pinnacle 8.0d for dose calculation. Absolute dose distributions were compared with gamma criteria 3% for dose difference and 3 mm for distance-to-agreement. The results are in good agreement between the measured and calculated planar dose with 88% pass rate based on the gamma analysis. The major dose difference was at the lung-water interface. Further investigation will be performed on a custom designed inhomogeneity phantom with inserts of varying densities and effective depth to create various dose gradients at the interface for dose calculation and delivery verification. In conclusion, a phantom with tissue inhomogeneities can be used with MapCHECK for verification of dose calculation and delivery with tissue inhomogeneity. © 2008 American Association of Physicists in Medicine.

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of Neuroradiology.

Brain tissue segmentation based on DTI data

PubMed Central

Liu, Tianming; Li, Hai; Wong, Kelvin; Tarokh, Ashley; Guo, Lei; Wong, Stephen T.C.

2008-01-01

We present a method for automated brain tissue segmentation based on the multi-channel fusion of diffusion tensor imaging (DTI) data. The method is motivated by the evidence that independent tissue segmentation based on DTI parametric images provides complementary information of tissue contrast to the tissue segmentation based on structural MRI data. This has important applications in defining accurate tissue maps when fusing structural data with diffusion data. In the absence of structural data, tissue segmentation based on DTI data provides an alternative means to obtain brain tissue segmentation. Our approach to the tissue segmentation based on DTI data is to classify the brain into two compartments by utilizing the tissue contrast existing in a single channel. Specifically, because the apparent diffusion coefficient (ADC) values in the cerebrospinal fluid (CSF) are more than twice that of gray matter (GM) and white matter (WM), we use ADC images to distinguish CSF and non-CSF tissues. Additionally, fractional anisotropy (FA) images are used to separate WM from non-WM tissues, as highly directional white matter structures have much larger fractional anisotropy values. Moreover, other channels to separate tissue are explored, such as eigenvalues of the tensor, relative anisotropy (RA), and volume ratio (VR). We developed an approach based on the Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm that combines these two-class maps to obtain a complete tissue segmentation map of CSF, GM, and WM. Evaluations are provided to demonstrate the performance of our approach. Experimental results of applying this approach to brain tissue segmentation and deformable registration of DTI data and spoiled gradient-echo (SPGR) data are also provided. PMID:17804258

Segmentation and automated measurement of chronic wound images: probability map approach

NASA Astrophysics Data System (ADS)

Ahmad Fauzi, Mohammad Faizal; Khansa, Ibrahim; Catignani, Karen; Gordillo, Gayle; Sen, Chandan K.; Gurcan, Metin N.

2014-03-01

estimated 6.5 million patients in the United States are affected by chronic wounds, with more than 25 billion US dollars and countless hours spent annually for all aspects of chronic wound care. There is need to develop software tools to analyze wound images that characterize wound tissue composition, measure their size, and monitor changes over time. This process, when done manually, is time-consuming and subject to intra- and inter-reader variability. In this paper, we propose a method that can characterize chronic wounds containing granulation, slough and eschar tissues. First, we generate a Red-Yellow-Black-White (RYKW) probability map, which then guides the region growing segmentation process. The red, yellow and black probability maps are designed to handle the granulation, slough and eschar tissues, respectively found in wound tissues, while the white probability map is designed to detect the white label card for measurement calibration purpose. The innovative aspects of this work include: 1) Definition of a wound characteristics specific probability map for segmentation, 2) Computationally efficient regions growing on 4D map; 3) Auto-calibration of measurements with the content of the image. The method was applied on 30 wound images provided by the Ohio State University Wexner Medical Center, with the ground truth independently generated by the consensus of two clinicians. While the inter-reader agreement between the readers is 85.5%, the computer achieves an accuracy of 80%.

Recursive approach to the moment-based phase unwrapping method.

PubMed

Langley, Jason A; Brice, Robert G; Zhao, Qun

2010-06-01

The moment-based phase unwrapping algorithm approximates the phase map as a product of Gegenbauer polynomials, but the weight function for the Gegenbauer polynomials generates artificial singularities along the edge of the phase map. A method is presented to remove the singularities inherent to the moment-based phase unwrapping algorithm by approximating the phase map as a product of two one-dimensional Legendre polynomials and applying a recursive property of derivatives of Legendre polynomials. The proposed phase unwrapping algorithm is tested on simulated and experimental data sets. The results are then compared to those of PRELUDE 2D, a widely used phase unwrapping algorithm, and a Chebyshev-polynomial-based phase unwrapping algorithm. It was found that the proposed phase unwrapping algorithm provides results that are comparable to those obtained by using PRELUDE 2D and the Chebyshev phase unwrapping algorithm.

Myocardial Tissue Characterization by Magnetic Resonance Imaging

PubMed Central

Ferreira, Vanessa M.; Piechnik, Stefan K.; Robson, Matthew D.; Neubauer, Stefan

2014-01-01

Cardiac magnetic resonance (CMR) imaging is a well-established noninvasive imaging modality in clinical cardiology. Its unsurpassed accuracy in defining cardiac morphology and function and its ability to provide tissue characterization make it well suited for the study of patients with cardiac diseases. Late gadolinium enhancement was a major advancement in the development of tissue characterization techniques, allowing the unique ability of CMR to differentiate ischemic heart disease from nonischemic cardiomyopathies. Using T2-weighted techniques, areas of edema and inflammation can be identified in the myocardium. A new generation of myocardial mapping techniques are emerging, enabling direct quantitative assessment of myocardial tissue properties in absolute terms. This review will summarize recent developments involving T1-mapping and T2-mapping techniques and focus on the clinical applications and future potential of these evolving CMR methodologies. PMID:24576837

Stable learning of functional maps in self-organizing spiking neural networks with continuous synaptic plasticity

PubMed Central

Srinivasa, Narayan; Jiang, Qin

2013-01-01

This study describes a spiking model that self-organizes for stable formation and maintenance of orientation and ocular dominance maps in the visual cortex (V1). This self-organization process simulates three development phases: an early experience-independent phase, a late experience-independent phase and a subsequent refinement phase during which experience acts to shape the map properties. The ocular dominance maps that emerge accommodate the two sets of monocular inputs that arise from the lateral geniculate nucleus (LGN) to layer 4 of V1. The orientation selectivity maps that emerge feature well-developed iso-orientation domains and fractures. During the last two phases of development the orientation preferences at some locations appear to rotate continuously through ±180° along circular paths and referred to as pinwheel-like patterns but without any corresponding point discontinuities in the orientation gradient maps. The formation of these functional maps is driven by balanced excitatory and inhibitory currents that are established via synaptic plasticity based on spike timing for both excitatory and inhibitory synapses. The stability and maintenance of the formed maps with continuous synaptic plasticity is enabled by homeostasis caused by inhibitory plasticity. However, a prolonged exposure to repeated stimuli does alter the formed maps over time due to plasticity. The results from this study suggest that continuous synaptic plasticity in both excitatory neurons and interneurons could play a critical role in the formation, stability, and maintenance of functional maps in the cortex. PMID:23450808

Single grating x-ray imaging for dynamic biological systems

NASA Astrophysics Data System (ADS)

Morgan, Kaye S.; Paganin, David M.; Parsons, David W.; Donnelley, Martin; Yagi, Naoto; Uesugi, Kentaro; Suzuki, Yoshio; Takeuchi, Akihisa; Siu, Karen K. W.

2012-07-01

Biomedical studies are already benefiting from the excellent contrast offered by phase contrast x-ray imaging, but live imaging work presents several challenges. Living samples make it particularly difficult to achieve high resolution, sensitive phase contrast images, as exposures must be short and cannot be repeated. We therefore present a single-exposure, high-flux method of differential phase contrast imaging [1, 2, 3] in the context of imaging live airways for Cystic Fibrosis (CF) treatment assessment [4]. The CF study seeks to non-invasively observe the liquid lining the airways, which should increase in depth in response to effective treatments. Both high spatial resolution and sensitivity are required in order to track micron size changes in a liquid that is not easily differentiated from the tissue on which it lies. Our imaging method achieves these goals by using a single attenuation grating or grid as a reference pattern, and analyzing how the sample deforms the pattern to quantitatively retrieve the phase depth of the sample. The deformations are mapped at each pixel in the image using local cross-correlations comparing each 'sample and pattern' image with a reference 'pattern only' image taken before the sample is introduced. This produces a differential phase image, which may be integrated to give the sample phase depth.

Mapping Magnetic Susceptibility Anisotropies of White Matter in vivo in the Human Brain at 7 Tesla

PubMed Central

Li, Xu; Vikram, Deepti S; Lim, Issel Anne L; Jones, Craig K; Farrell, Jonathan A.D.; van Zijl, Peter C. M.

2012-01-01

High-resolution magnetic resonance phase- or frequency- shift images acquired at high field show contrast related to magnetic susceptibility differences between tissues. Such contrast varies with the orientation of the organ in the field, but the development of quantitative susceptibility mapping (QSM) has made it possible to reproducibly image the intrinsic tissue susceptibility contrast. However, recent studies indicate that magnetic susceptibility is anisotropic in brain white matter and, as such, needs to be described by a symmetric second-rank tensor (χ¯¯). To fully determine the elements of this tensor, it would be necessary to acquire frequency data at six or more orientations. Assuming cylindrical symmetry of the susceptibility tensor in myelinated white matter fibers, we propose a simplified method to reconstruct the susceptibility tensor in terms of a mean magnetic susceptibility, MMS = (χ∥ + 2χ⊥)/3 and a magnetic susceptibility anisotropy, MSA = χ∥ − χ⊥, where χ∥ and χ⊥ are susceptibility parallel and perpendicular to the white matter fiber direction, respectively. Computer simulations show that with a practical head rotation angle of around 20°–30°, four head orientations suffice to reproducibly reconstruct the tensor with good accuracy. We tested this approach on whole brain 1×1×1 mm3 frequency data acquired from five healthy subjects at 7 T. The frequency information from phase images collected at four head orientations was combined with the fiber direction information extracted from diffusion tensor imaging (DTI) to map the white matter susceptibility tensor. The MMS and MSA were quantified for regions in several large white matter fiber structures, including the corona radiata, posterior thalamic radiation and corpus callosum. MMS ranged from −0.037 to −0.053 ppm (referenced to CSF being about zero). MSA values could be quantified without the need for a reference and ranged between 0.004 and 0.029 ppm, in line with the expectation that the susceptibility perpendicular to the fiber is more diamagnetic than the one parallel to it. PMID:22561358

Optical Coherence Tomography for Brain Imaging

NASA Astrophysics Data System (ADS)

Liu, Gangjun; Chen, Zhongping

Recently, there has been growing interest in using OCT for brain imaging. A feasibility study of OCT for guiding deep brain probes has found that OCT can differentiate the white matter and gray matter because the white matter tends to have a higher peak reflectivity and steeper attenuation rate compared to gray matter. In vivo 3D visualization of the layered organization of a rat olfactory bulb with OCT has been demonstrated. OCT has been used for single myelin fiber imaging in living rodents without labeling. The refractive index in the rat somatosensory cortex has also been measured with OCT. In addition, functional extension of OCT, such as Doppler-OCT (D-OCT), polarization sensitive-OCT (PS-OCT), and phase-resolved-OCT (PR-OCT), can image and quantify physiological parameters in addition to the morphological structure image. Based on the scattering changes during neural activity, OCT has been used to measure the functional activation in neuronal tissues. PS-OCT, which combines polarization sensitive detection with OCT to determine tissue birefringence, has been used for the localization of nerve fiber bundles and the mapping of micrometer-scale fiber pathways in the brain. D-OCT, also named optical Doppler tomography (ODT), combines the Doppler principle with OCT to obtain high resolution tomographic images of moving constituents in highly scattering biological tissues. D-OCT has been successfully used to image cortical blood flow and map the blood vessel network for brain research. In this chapter, the principle and technology of OCT and D-OCT are reviewed and examples of potential applications are described.

Benefits of Atrial Substrate Modification Guided by Electrogram Similarity and Phase Mapping Techniques to Eliminate Rotors and Focal Sources Versus Conventional Defragmentation in Persistent Atrial Fibrillation.

PubMed

Lin, Yenn-Jiang; Lo, Men-Tzung; Chang, Shih-Lin; Lo, Li-Wei; Hu, Yu-Feng; Chao, Tze-Fan; Chung, Fa-Po; Liao, Jo-Nan; Lin, Chin-Yu; Kuo, Huan-Yu; Chang, Yi-Chung; Lin, Chen; Tuan, Ta-Chuan; Vincent Young, Hsu-Wen; Suenari, Kazuyoshi; Dan Do, Van Buu; Raharjo, Suunu Budhi; Huang, Norden E; Chen, Shih-Ann

2016-11-01

This prospective study compared the efficacy of atrial substrate modification guided by a nonlinear phase mapping technique with that of conventional substrate ablation. The optimal ablation strategy for persistent atrial fibrillation (AF) was unknown. In phase 1 study, we applied a cellular automation technique to simulate the electrical wave propagation to improve the phase mapping algorithm, involving analysis of high-similarity electrogram regions. In addition, we defined rotors and focal AF sources, using the physical parameters of the divergence and curvature forces. In phase 2 study, we enrolled 68 patients with persistent AF undergoing substrate modification into 2 groups, group-1 (n = 34) underwent similarity index (SI) and phase mapping techniques; group-2 (n = 34) received complex fractionated atrial electrogram ablation with commercially available software. Group-1 received real-time waveform similarity measurements in which a phase mapping algorithm was applied to localize the sources. We evaluated the single-procedure freedom from AF. In group-1, we identified an average of 2.6 ± 0.89 SI regions per chamber. These regions involved rotors and focal sources in 65% and 77% of patients in group-1, respectively. Group-1 patients had shorter ablation procedure times, higher termination rates, and significant reduction in AF recurrence compared to group-2 and a trend toward benefit for all atrial arrhythmias. Multivariate analysis showed that substrate mapping using nonlinear similarity and phase mapping was the independent predictor of freedom from AF recurrence (hazard ratio: 0.26; 95% confidence interval: 0.09 to 0.74; p = 0.01). Our study showed that for persistent AF ablation, a specified substrate modification guided by nonlinear phase mapping could eliminate localized re-entry and non-pulmonary focal sources after pulmonary vein isolation. Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

[Modeling developmental aspects of sensorimotor control of speech production].

PubMed

Kröger, B J; Birkholz, P; Neuschaefer-Rube, C

2007-05-01

Detailed knowledge of the neurophysiology of speech acquisition is important for understanding the developmental aspects of speech perception and production and for understanding developmental disorders of speech perception and production. A computer implemented neural model of sensorimotor control of speech production was developed. The model is capable of demonstrating the neural functions of different cortical areas during speech production in detail. (i) Two sensory and two motor maps or neural representations and the appertaining neural mappings or projections establish the sensorimotor feedback control system. These maps and mappings are already formed and trained during the prelinguistic phase of speech acquisition. (ii) The feedforward sensorimotor control system comprises the lexical map (representations of sounds, syllables, and words of the first language) and the mappings from lexical to sensory and to motor maps. The training of the appertaining mappings form the linguistic phase of speech acquisition. (iii) Three prelinguistic learning phases--i. e. silent mouthing, quasi stationary vocalic articulation, and realisation of articulatory protogestures--can be defined on the basis of our simulation studies using the computational neural model. These learning phases can be associated with temporal phases of prelinguistic speech acquisition obtained from natural data. The neural model illuminates the detailed function of specific cortical areas during speech production. In particular it can be shown that developmental disorders of speech production may result from a delayed or incorrect process within one of the prelinguistic learning phases defined by the neural model.

Novel Passive Clearing Methods for the Rapid Production of Optical Transparency in Whole CNS Tissue.

PubMed

Woo, Jiwon; Lee, Eunice Yoojin; Park, Hyo-Suk; Park, Jeong Yoon; Cho, Yong Eun

2018-05-08

Since the development of CLARITY, a bioelectrochemical clearing technique that allows for three-dimensional phenotype mapping within transparent tissues, a multitude of novel clearing methodologies including CUBIC (clear, unobstructed brain imaging cocktails and computational analysis), SWITCH (system-wide control of interaction time and kinetics of chemicals), MAP (magnified analysis of the proteome), and PACT (passive clarity technique), have been established to further expand the existing toolkit for the microscopic analysis of biological tissues. The present study aims to improve upon and optimize the original PACT procedure for an array of intact rodent tissues, including the whole central nervous system (CNS), kidneys, spleen, and whole mouse embryos. Termed psPACT (process-separate PACT) and mPACT (modified PACT), these novel techniques provide highly efficacious means of mapping cell circuitry and visualizing subcellular structures in intact normal and pathological tissues. In the following protocol, we provide a detailed, step-by-step outline on how to achieve maximal tissue clearance with minimal invasion of their structural integrity via psPACT and mPACT.

Nanoscale quantification of intracellular element concentration by X-ray fluorescence microscopy combined with X-ray phase contrast nanotomography

NASA Astrophysics Data System (ADS)

Gramaccioni, Chiara; Yang, Yang; Procopio, Alessandra; Pacureanu, Alexandra; Bohic, Sylvain; Malucelli, Emil; Iotti, Stefano; Farruggia, Giovanna; Bukreeva, Inna; Notargiacomo, Andrea; Fratini, Michela; Valenti, Piera; Rosa, Luigi; Berlutti, Francesca; Cloetens, Peter; Lagomarsino, Stefano

2018-01-01

We present here a correlative X-ray microscopy approach for quantitative single cell imaging of molar concentrations. By combining the elemental content provided by X-ray fluorescence microscopy and the morphology information extracted from X-ray phase nanotomography, we determine the intracellular molarity distributions. This correlative method was demonstrated on a freeze-dried human phagocytic cell to obtain the absolute elemental concentration maps of K, P, and Fe. The cell morphology results showed a very good agreement with atomic-force microscopy measurements. This work opens the way for non-destructive single cell chemical analysis down to the sub-cellular level using exclusively synchrotron radiation techniques. It will be of high interest in the case where it is difficult to access the morphology using atomic-force microscopy, for example, on frozen-hydrated cells or tissues.

In vivo optical elastography: stress and strain imaging of human skin lesions

NASA Astrophysics Data System (ADS)

Es'haghian, Shaghayegh; Gong, Peijun; Kennedy, Kelsey M.; Wijesinghe, Philip; Sampson, David D.; McLaughlin, Robert A.; Kennedy, Brendan F.

2015-03-01

Probing the mechanical properties of skin at high resolution could aid in the assessment of skin pathologies by, for example, detecting the extent of cancerous skin lesions and assessing pathology in burn scars. Here, we present two elastography techniques based on optical coherence tomography (OCT) to probe the local mechanical properties of skin. The first technique, optical palpation, is a high-resolution tactile imaging technique, which uses a complaint silicone layer positioned on the tissue surface to measure spatially-resolved stress imparted by compressive loading. We assess the performance of optical palpation, using a handheld imaging probe on a skin-mimicking phantom, and demonstrate its use on human skin. The second technique is a strain imaging technique, phase-sensitive compression OCE that maps depth-resolved mechanical variations within skin. We show preliminary results of in vivo phase-sensitive compression OCE on a human skin lesion.

Improving experimental phases for strong reflections prior to density modification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uervirojnangkoorn, Monarin; University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck; Hilgenfeld, Rolf, E-mail: hilgenfeld@biochem.uni-luebeck.de

A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the mapsmore » can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ▶), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

Stiffness mapping prostate biopsy samples using a tactile sensor.

PubMed

Peng, Qiyu; Omata, Sadao; Peehl, Donna M; Constantinou, Chris E

2011-01-01

Previous studies have demonstrated that the stiffness of cancerous cells reflects their pathological stage and progression rates, with increased cancerous cell stiffness associated with increased aggressiveness. Therefore, the elasticity of the cancerous cells has the potential to be used as an indicator of the cancer's aggressiveness. However, the sensitivity and resolution of current palpation and imaging techniques are not sufficient to detect small cancerous tissues. In previous studies, we developed a tactile-based device to map with high resolution the stiffness of a tissue section. The purpose of this study is to evaluate this device using different tissues (BPH, Cancer and PZ) collected from human prostates. The preliminary results show that the tactile device is sensitive enough to tell the differences of the stiffness of different tissues. The results also disclosed the factors (humidity, temperature and tissue degradation) which could dramatically affect the results of stiffness mapping. The tactile technology described in this paper has the potential to help disclose the underlying mechanical mechanisms that lead to increased stiffness in prostate tumors.

Real-Time Vision-Based Stiffness Mapping †.

PubMed

Faragasso, Angela; Bimbo, João; Stilli, Agostino; Wurdemann, Helge Arne; Althoefer, Kaspar; Asama, Hajime

2018-04-26

This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF) Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness.

High-resolution x-ray absorption spectroscopy studies of metal compounds in neurodegenerative brain tissue

NASA Astrophysics Data System (ADS)

Collingwood, J. F.; Mikhaylova, A.; Davidson, M. R.; Batich, C.; Streit, W. J.; Eskin, T.; Terry, J.; Barrea, R.; Underhill, R. S.; Dobson, J.

2005-01-01

Fluorescence mapping and microfocus X-ray absorption spectroscopy are used to detect, locate and identify iron biominerals and other inorganic metal accumulations in neurodegenerative brain tissue at sub-cellular resolution (<5 microns). Recent progress in developing the technique is reviewed. Synchrotron X-rays are used to map tissue sections for metals of interest, and XANES and XAFS are used to characterise anomalous concentrations of the metals in-situ so that they can be correlated with tissue structures and disease pathology. Iron anomalies associated with biogenic magnetite, ferritin and haemoglobin are located and identified in an avian tissue model with a pixel resolution ~5 microns. Subsequent studies include brain tissue sections from transgenic Huntington's mice, and the first high-resolution mapping and identification of iron biominerals in human Alzheimer's and control autopsy brain tissue. Technical developments include use of microfocus diffraction to obtain structural information about biominerals in-situ, and depositing sample location grids by lithography for the location of anomalies by conventional microscopy. The combined techniques provide a breakthrough in the study of both intra- and extra-cellular iron compounds and related metals in tissue. The information to be gained from this approach has implications for future diagnosis and treatment of neurodegeneration, and for our understanding of the mechanisms involved.

Association between increased epicardial adipose tissue volume and coronary plaque composition.

PubMed

Yamashita, Kennosuke; Yamamoto, Myong Hwa; Ebara, Seitarou; Okabe, Toshitaka; Saito, Shigeo; Hoshimoto, Koichi; Yakushiji, Tadayuki; Isomura, Naoei; Araki, Hiroshi; Obara, Chiaki; Ochiai, Masahiko

2014-09-01

To assess the relationship between epicardial adipose tissue volume (EATV) and plaque vulnerability in significant coronary stenosis using a 40-MHz intravascular ultrasound (IVUS) imaging system (iMap-IVUS), we analyzed 130 consecutive patients with coronary stenosis who underwent dual-source computed tomography (CT) and cardiac catheterization. Culprit lesions were imaged by iMap-IVUS before stenting. The iMAP-IVUS system classified coronary plaque components as fibrous, lipid, necrotic, or calcified tissue, based on the radiofrequency spectrum. Epicardial adipose tissue was measured as the tissue ranging from -190 to -30 Hounsfield units. EATV, calculated as the sum of the fat areas on short-axis images, was 85.0 ± 34.0 cm(3). There was a positive correlation between EATV and the percentage of necrotic plaque tissue (R (2) = 0.34, P < 0.01), while there was a negative correlation between EATV and the percentage of fibrous tissue (R (2) = 0.24, P < 0.01). Multivariate analysis revealed that an increased low-density lipoprotein cholesterol level (β = 0.15, P = 0.03) and EATV (β = 0.14, P = 0.02) were independently associated with the percentage of necrotic plaque tissue. An increase in EATV was associated with the development of coronary atherosclerosis and, potentially, with the most dangerous type of plaque.

Atomic resolved phase map of monolayer MoS2 retrieved by spherical aberration-corrected transport of intensity equation.

PubMed

Zhang, Xiaobin; Oshima, Yoshifumi

2016-10-01

An atomic resolution phase map, which enables us to observe charge distribution or magnetic properties at an atomic scale, has been pointed out to be retrieved by transport of intensity equation (TIE) when taking two atomic-resolved transmission electron microscope (TEM) images of small defocus difference. In this work, we firstly obtained the atomic-resolved phase maps of an exfoliated molybdenum disulfide sheet using spherical aberration-corrected transmission electron microscope. We successfully observed 60° grain boundary of mechanically exfoliated monolayer molybdenum disulfide sheet. The relative phase shift of a single molybdenum atomic column to the column consisting of two sulfur atoms was obtained to be about 0.01 rad on average, which was about half lower than the simulated TIE phase map, indicating that the individual atomic sites can be distinguished qualitatively. The appropriate condition for retrieving atomic-resolved TIE phase maps was briefly discussed. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

NASA Astrophysics Data System (ADS)

Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

2016-03-01

The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

Detection, Mapping, and Quantification of Single Walled Carbon Nanotubes in Histological Specimens with Photoacoustic Microscopy

PubMed Central

Mikos, Antonios G.; Jansen, John A.; Shroyer, Kenneth R.; Wang, Lihong V.; Sitharaman, Balaji

2012-01-01

Aims In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Materials and Methods Optical-resolution (OR) and acoustic-resolution (AR) - Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Results Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. Conclusions The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs. PMID:22496892

A multi-frequency sparse hemispherical ultrasound phased array for microbubble-mediated transcranial therapy and simultaneous cavitation mapping

NASA Astrophysics Data System (ADS)

Deng, Lulu; O'Reilly, Meaghan A.; Jones, Ryan M.; An, Ran; Hynynen, Kullervo

2016-12-01

Focused ultrasound (FUS) phased arrays show promise for non-invasive brain therapy. However, the majority of them are limited to a single transmit/receive frequency and therefore lack the versatility to expose and monitor the treatment volume. Multi-frequency arrays could offer variable transmit focal sizes under a fixed aperture, and detect different spectral content on receive for imaging purposes. Here, a three-frequency (306, 612, and 1224 kHz) sparse hemispherical ultrasound phased array (31.8 cm aperture; 128 transducer modules) was constructed and evaluated for microbubble-mediated transcranial therapy and simultaneous cavitation mapping. The array is able to perform effective electronic beam steering over a volume spanning (-40, 40) and (-30, 50) mm in the lateral and axial directions, respectively. The focal size at the geometric center is approximately 0.9 (2.1) mm, 1.7 (3.9) mm, and 3.1 (6.5) mm in lateral (axial) pressure full width at half maximum (FWHM) at 1224, 612, and 306 kHz, respectively. The array was also found capable of dual-frequency excitation and simultaneous multi-foci sonication, which enables the future exploration of more complex exposure strategies. Passive acoustic mapping of dilute microbubble clouds demonstrated that the point spread function of the receive array has a lateral (axial) intensity FWHM between 0.8-3.5 mm (1.7-11.7 mm) over a volume spanning (-25, 25) mm in both the lateral and axial directions, depending on the transmit/receive frequency combination and the imaging location. The device enabled both half and second harmonic imaging through the intact skull, which may be useful for improving the contrast-to-tissue ratio or imaging resolution, respectively. Preliminary in vivo experiments demonstrated the system’s ability to induce blood-brain barrier opening and simultaneously spatially map microbubble cavitation activity in a rat model. This work presents a tool to investigate optimal strategies for non-thermal FUS brain therapy and concurrent microbubble cavitation monitoring through the availability of multiple frequencies.

A multi-frequency sparse hemispherical ultrasound phased array for microbubble-mediated transcranial therapy and simultaneous cavitation mapping

PubMed Central

Deng, Lulu; O'Reilly, Meaghan A.; Jones, Ryan M.; An, Ran; Hynynen, Kullervo

2016-01-01

Focused ultrasound (FUS) phased arrays show promise for non-invasive brain therapy. However, the majority of them are limited to a single transmit/receive frequency and therefore lack the versatility to expose and monitor the treatment volume. Multi-frequency arrays could offer variable transmit focal sizes under a fixed aperture, and detect different spectral content on receive for imaging purposes. Here, a three-frequency (306, 612 and 1224 kHz) sparse hemispherical ultrasound phased array (31.8 cm aperture; 128 transducer modules) was constructed and evaluated for microbubble-mediated transcranial therapy and simultaneous cavitation mapping. The array is able to perform effective electronic beam steering over a volume spanning [−40, 40] and [−30, 50] mm in the lateral and axial directions, respectively. The focal size at the geometric center is approximately 0.9 (2.1) mm, 1.7 (3.9) mm, and 3.1 (6.5) mm in lateral (axial) pressure full width at half maximum (FWHM) at 1224, 612, and 306 kHz, respectively. The array was also found capable of dual-frequency excitation and simultaneous multi–foci sonication, which enables the future exploration of more complex exposure strategies. Passive acoustic mapping of dilute microbubble clouds demonstrated that the point spread function of the receive array has a lateral (axial) intensity FWHM between 0.8-3.5 mm (1.7-11.7 mm) over a volume spanning [−25, 25] mm in both the lateral and axial directions, depending on the transmit/receive frequency combination and the imaging location. The device enabled both half and second harmonic imaging through the intact skull, which may be useful for improving the contrast-to-tissue ratio or imaging resolution, respectively. Preliminary in-vivo experiments demonstrated the system's ability to induce blood-brain barrier opening and simultaneously spatially map microbubble cavitation activity in a rat model. This work presents a tool to investigate optimal strategies for non-thermal FUS brain therapy and concurrent microbubble cavitation monitoring through the availability of multiple frequencies. PMID:27845920

A multi-frequency sparse hemispherical ultrasound phased array for microbubble-mediated transcranial therapy and simultaneous cavitation mapping.

PubMed

Deng, Lulu; O'Reilly, Meaghan A; Jones, Ryan M; An, Ran; Hynynen, Kullervo

2016-12-21

Focused ultrasound (FUS) phased arrays show promise for non-invasive brain therapy. However, the majority of them are limited to a single transmit/receive frequency and therefore lack the versatility to expose and monitor the treatment volume. Multi-frequency arrays could offer variable transmit focal sizes under a fixed aperture, and detect different spectral content on receive for imaging purposes. Here, a three-frequency (306, 612, and 1224 kHz) sparse hemispherical ultrasound phased array (31.8 cm aperture; 128 transducer modules) was constructed and evaluated for microbubble-mediated transcranial therapy and simultaneous cavitation mapping. The array is able to perform effective electronic beam steering over a volume spanning (-40, 40) and (-30, 50) mm in the lateral and axial directions, respectively. The focal size at the geometric center is approximately 0.9 (2.1) mm, 1.7 (3.9) mm, and 3.1 (6.5) mm in lateral (axial) pressure full width at half maximum (FWHM) at 1224, 612, and 306 kHz, respectively. The array was also found capable of dual-frequency excitation and simultaneous multi-foci sonication, which enables the future exploration of more complex exposure strategies. Passive acoustic mapping of dilute microbubble clouds demonstrated that the point spread function of the receive array has a lateral (axial) intensity FWHM between 0.8-3.5 mm (1.7-11.7 mm) over a volume spanning (-25, 25) mm in both the lateral and axial directions, depending on the transmit/receive frequency combination and the imaging location. The device enabled both half and second harmonic imaging through the intact skull, which may be useful for improving the contrast-to-tissue ratio or imaging resolution, respectively. Preliminary in vivo experiments demonstrated the system's ability to induce blood-brain barrier opening and simultaneously spatially map microbubble cavitation activity in a rat model. This work presents a tool to investigate optimal strategies for non-thermal FUS brain therapy and concurrent microbubble cavitation monitoring through the availability of multiple frequencies.

Quantitative evaluation of ischemic myocardial scar tissue by unenhanced T1 mapping using 3.0 Tesla MR scanner

PubMed Central

Okur, Aylin; Kantarcı, Mecit; Kızrak, Yeşim; Yıldız, Sema; Pirimoğlu, Berhan; Karaca, Leyla; Oğul, Hayri; Sevimli, Serdar

2014-01-01

PURPOSE We aimed to use a noninvasive method for quantifying T1 values of chronic myocardial infarction scar by cardiac magnetic resonance imaging (MRI), and determine its diagnostic performance. MATERIALS AND METHODS We performed cardiac MRI on 29 consecutive patients with known coronary artery disease (CAD) on 3.0 Tesla MRI scanner. An unenhanced T1 mapping technique was used to calculate T1 relaxation time of myocardial scar tissue, and its diagnostic performance was evaluated. Chronic scar tissue was identified by delayed contrast-enhancement (DE) MRI and T2-weighted images. Sensitivity, specificity, and accuracy values were calculated for T1 mapping using DE images as the gold standard. RESULTS Four hundred and forty-two segments were analyzed in 26 patients. While myocardial chronic scar was demonstrated in 45 segments on DE images, T1 mapping MRI showed a chronic scar area in 54 segments. T1 relaxation time was higher in chronic scar tissue, compared with remote areas (1314±98 ms vs. 1099±90 ms, P < 0.001). Therefore, increased T1 values were shown in areas of myocardium colocalized with areas of DE and normal signal on T2-weighted images. There was a significant correlation between T1 mapping and DE images in evaluation of myocardial wall injury extent (P < 0.05). We calculated sensitivity, specificity, and accuracy as 95.5%, 97%, and 96%, respectively. CONCLUSION The results of the present study reveal that T1 mapping MRI combined with T2-weighted images might be a feasible imaging modality for detecting chronic myocardial infarction scar tissue. PMID:25010366

Improved UTE-based attenuation correction for cranial PET-MR using dynamic magnetic field monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aitken, A. P.; Giese, D.; Tsoumpas, C.

2014-01-15

Purpose: Ultrashort echo time (UTE) MRI has been proposed as a way to produce segmented attenuation maps for PET, as it provides contrast between bone, air, and soft tissue. However, UTE sequences require samples to be acquired during rapidly changing gradient fields, which makes the resulting images prone to eddy current artifacts. In this work it is demonstrated that this can lead to misclassification of tissues in segmented attenuation maps (AC maps) and that these effects can be corrected for by measuring the true k-space trajectories using a magnetic field camera. Methods: The k-space trajectories during a dual echo UTEmore » sequence were measured using a dynamic magnetic field camera. UTE images were reconstructed using nominal trajectories and again using the measured trajectories. A numerical phantom was used to demonstrate the effect of reconstructing with incorrect trajectories. Images of an ovine leg phantom were reconstructed and segmented and the resulting attenuation maps were compared to a segmented map derived from a CT scan of the same phantom, using the Dice similarity measure. The feasibility of the proposed method was demonstrated inin vivo cranial imaging in five healthy volunteers. Simulated PET data were generated for one volunteer to show the impact of misclassifications on the PET reconstruction. Results: Images of the numerical phantom exhibited blurring and edge artifacts on the bone–tissue and air–tissue interfaces when nominal k-space trajectories were used, leading to misclassification of soft tissue as bone and misclassification of bone as air. Images of the tissue phantom and thein vivo cranial images exhibited the same artifacts. The artifacts were greatly reduced when the measured trajectories were used. For the tissue phantom, the Dice coefficient for bone in MR relative to CT was 0.616 using the nominal trajectories and 0.814 using the measured trajectories. The Dice coefficients for soft tissue were 0.933 and 0.934 for the nominal and measured cases, respectively. For air the corresponding figures were 0.991 and 0.993. Compared to an unattenuated reference image, the mean error in simulated PET uptake in the brain was 9.16% when AC maps derived from nominal trajectories was used, with errors in the SUV{sub max} for simulated lesions in the range of 7.17%–12.19%. Corresponding figures when AC maps derived from measured trajectories were used were 0.34% (mean error) and −0.21% to +1.81% (lesions). Conclusions: Eddy current artifacts in UTE imaging can be corrected for by measuring the true k-space trajectories during a calibration scan and using them in subsequent image reconstructions. This improves the accuracy of segmented PET attenuation maps derived from UTE sequences and subsequent PET reconstruction.« less

Near-infrared voltage-sensitive fluorescent dyes optimized for optical mapping in blood-perfused myocardium.

PubMed

Matiukas, Arvydas; Mitrea, Bogdan G; Qin, Maochun; Pertsov, Arkady M; Shvedko, Alexander G; Warren, Mark D; Zaitsev, Alexey V; Wuskell, Joseph P; Wei, Mei-de; Watras, James; Loew, Leslie M

2007-11-01

Styryl voltage-sensitive dyes (e.g., di-4-ANEPPS) have been used successfully for optical mapping in cardiac cells and tissues. However, their utility for probing electrical activity deep inside the myocardial wall and in blood-perfused myocardium has been limited because of light scattering and high absorption by endogenous chromophores and hemoglobin at blue-green excitation wavelengths. The purpose of this study was to characterize two new styryl dyes--di-4-ANBDQPQ (JPW-6003) and di-4-ANBDQBS (JPW-6033)--optimized for blood-perfused tissue and intramural optical mapping. Voltage-dependent spectra were recorded in a model lipid bilayer. Optical mapping experiments were conducted in four species (mouse, rat, guinea pig, and pig). Hearts were Langendorff perfused using Tyrode's solution and blood (pig). Dyes were loaded via bolus injection into perfusate. Transillumination experiments were conducted in isolated coronary-perfused pig right ventricular wall preparations. The optimal excitation wavelength in cardiac tissues (650 nm) was >70 nm beyond the absorption maximum of hemoglobin. Voltage sensitivity of both dyes was approximately 10% to 20%. Signal decay half-life due to dye internalization was 80 to 210 minutes, which is 5 to 7 times slower than for di-4-ANEPPS. In transillumination mode, DeltaF/F was as high as 20%. In blood-perfused tissues, DeltaF/F reached 5.5% (1.8 times higher than for di-4-ANEPPS). We have synthesized and characterized two new near-infrared dyes with excitation/emission wavelengths shifted >100 nm to the red. They provide both high voltage sensitivity and 5 to 7 times slower internalization rate compared to conventional dyes. The dyes are optimized for deeper tissue probing and optical mapping of blood-perfused tissue, but they also can be used for conventional applications.

Global geologic map of Ganymede

USGS Publications Warehouse

Collins, Geoffrey C.; Patterson, G. Wesley; Head, James W.; Pappalardo, Robert T.; Prockter, Louise M.; Lucchitta, Baerbel K.; Kay, Johnathan P.

2014-01-01

Ganymede is the largest satellite of Jupiter, and its icy surface has been formed through a variety of impact cratering, tectonic, and possibly cryovolcanic processes. The history of Ganymede can be divided into three distinct phases: an early phase dominated by impact cratering and mixing of non-ice materials in the icy crust, a phase in the middle of its history marked by great tectonic upheaval, and a late quiescent phase characterized by a gradual drop in heat flow and further impact cratering. Images of Ganymede suitable for geologic mapping were collected during the flybys of Voyager 1 and Voyager 2 (1979), as well as during the Galileo Mission in orbit around Jupiter (1995–2003). This map represents a synthesis of our understanding of Ganymede geology after the conclusion of the Galileo Mission. We summarize the properties of the imaging dataset used to construct the map, previously published maps of Ganymede, our own mapping rationale, and the geologic history of Ganymede. Additional details on these topics, along with detailed descriptions of the type localities for the material units, may be found in the companion paper to this map (Patterson and others, 2010).

Automated phase mapping with AgileFD and its application to light absorber discovery in the V–Mn–Nb oxide system

DOE PAGES

Suram, Santosh K.; Xue, Yexiang; Bai, Junwen; ...

2016-11-21

Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less

Automated phase mapping with AgileFD and its application to light absorber discovery in the V–Mn–Nb oxide system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suram, Santosh K.; Xue, Yexiang; Bai, Junwen

Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less

'Real angiosome' assessment from peripheral tissue perfusion using tissue oxygen saturation foot-mapping in patients with critical limb ischemia.

PubMed

Kagaya, Y; Ohura, N; Suga, H; Eto, H; Takushima, A; Harii, K

2014-04-01

The "tissue oxygen saturation (StO2) foot-mapping" method was developed using a non-invasive near-infrared tissue oximeter monitor to classify the foot regions as ischemic and non-ischemic areas. The purpose of this study was to evaluate StO2 foot-mapping as a reliable method to detect ischemic areas in the feet of patients with critical limb ischemia (CLI), and to compare the results with assessments from the angiosome model. The foot areas of 20 CLI patients and 20 healthy controls were classified into four regions: (1) 0 ≤ StO2 < 30%, (2) 30 ≤ StO2 < 50%, (3) 50 ≤ StO2 < 70%, and (4) 70 ≤ StO2 ≤ 100% to perform StO2 foot-mapping. Each area occupancy rate was compared between the two groups, and the threshold StO2 value for detecting ischemia was set. Next, the locations of ulcers (in 16 patients) were compared to the predicted ischemic regions by the StO2 foot-mapping and by the angiosome model and angiography. In regions (1) and (2) (StO2 < 50%), the area occupancy rate was significantly higher in the CLI group and almost zero in the control group, so that the threshold StO2 value for detecting ischemia was set at 50%. The locations of ulcers were compatible with StO2 foot-mapping in 87.5% of the cases (14/16), while they were compatible with the assessment from the angiosome model in 68.8% of the cases (11/16). This study suggests that StO2 foot-mapping can successfully and non-invasively detect ischemic areas in the peripheral tissue of the foot, and also more appropriately than the assessment provided by the angiosome model. StO2 foot-mapping can be used to evaluate the real angiosome: the real distribution of the peripheral tissue perfusion in the CLI patient's foot, which is determined by the peripheral microvascular blood flow, rather than the main arterial blood flow. Copyright © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

The Acoustic Lens Design and in Vivo Use of a Multifunctional Catheter Combining Intracardiac Ultrasound Imaging and Electrophysiology Sensing

PubMed Central

Stephens, Douglas N.; Cannata, Jonathan; Liu, Ruibin; Zhao, Jian Zhong; Shung, K. Kirk; Nguyen, Hien; Chia, Raymond; Dentinger, Aaron; Wildes, Douglas; Thomenius, Kai E.; Mahajan, Aman; Shivkumar, Kalyanam; Kim, Kang; O’Donnell, Matthew; Sahn, David

2009-01-01

A multifunctional 9F intracardiac imaging and electrophysiology mapping catheter was developed and tested to help guide diagnostic and therapeutic intracardiac electrophysiology (EP) procedures. The catheter tip includes a 7.25-MHz, 64-element, side-looking phased array for high resolution sector scanning. Multiple electrophysiology mapping sensors were mounted as ring electrodes near the array for electrocardiographic synchronization of ultrasound images. The catheter array elevation beam performance in particular was investigated. An acoustic lens for the distal tip array designed with a round cross section can produce an acceptable elevation beam shape; however, the velocity of sound in the lens material should be approximately 155 m/s slower than in tissue for the best beam shape and wide bandwidth performance. To help establish the catheter’s unique ability for integration with electrophysiology interventional procedures, it was used in vivo in a porcine animal model, and demonstrated both useful intracardiac echocardiographic visualization and simultaneous 3-D positional information using integrated electroanatomical mapping techniques. The catheter also performed well in high frame rate imaging, color flow imaging, and strain rate imaging of atrial and ventricular structures. PMID:18407850

Depth map generation using a single image sensor with phase masks.

PubMed

Jang, Jinbeum; Park, Sangwoo; Jo, Jieun; Paik, Joonki

2016-06-13

Conventional stereo matching systems generate a depth map using two or more digital imaging sensors. It is difficult to use the small camera system because of their high costs and bulky sizes. In order to solve this problem, this paper presents a stereo matching system using a single image sensor with phase masks for the phase difference auto-focusing. A novel pattern of phase mask array is proposed to simultaneously acquire two pairs of stereo images. Furthermore, a noise-invariant depth map is generated from the raw format sensor output. The proposed method consists of four steps to compute the depth map: (i) acquisition of stereo images using the proposed mask array, (ii) variational segmentation using merging criteria to simplify the input image, (iii) disparity map generation using the hierarchical block matching for disparity measurement, and (iv) image matting to fill holes to generate the dense depth map. The proposed system can be used in small digital cameras without additional lenses or sensors.

Phase-Contrast Hounsfield Units of Fixated and Non-Fixated Soft-Tissue Samples

PubMed Central

Willner, Marian; Fior, Gabriel; Marschner, Mathias; Birnbacher, Lorenz; Schock, Jonathan; Braun, Christian; Fingerle, Alexander A.; Noël, Peter B.; Rummeny, Ernst J.; Pfeiffer, Franz; Herzen, Julia

2015-01-01

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissue specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. Furthermore, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results. PMID:26322638

Quantitative analysis of tissue deformation dynamics reveals three characteristic growth modes and globally aligned anisotropic tissue deformation during chick limb development.

PubMed

Morishita, Yoshihiro; Kuroiwa, Atsushi; Suzuki, Takayuki

2015-05-01

Tissue-level characterization of deformation dynamics is crucial for understanding organ morphogenetic mechanisms, especially the interhierarchical links among molecular activities, cellular behaviors and tissue/organ morphogenetic processes. Limb development is a well-studied topic in vertebrate organogenesis. Nevertheless, there is still little understanding of tissue-level deformation relative to molecular and cellular dynamics. This is mainly because live recording of detailed cell behaviors in whole tissues is technically difficult. To overcome this limitation, by applying a recently developed Bayesian approach, we here constructed tissue deformation maps for chick limb development with high precision, based on snapshot lineage tracing using dye injection. The precision of the constructed maps was validated with a clear statistical criterion. From the geometrical analysis of the map, we identified three characteristic tissue growth modes in the limb and showed that they are consistent with local growth factor activity and cell cycle length. In particular, we report that SHH signaling activity changes dynamically with developmental stage and strongly correlates with the dynamic shift in the tissue growth mode. We also found anisotropic tissue deformation along the proximal-distal axis. Morphogenetic simulation and experimental studies suggested that this directional tissue elongation, and not local growth, has the greatest impact on limb shaping. This result was supported by the novel finding that anisotropic tissue elongation along the proximal-distal axis occurs independently of cell proliferation. Our study marks a pivotal point for multi-scale system understanding in vertebrate development. © 2015. Published by The Company of Biologists Ltd.

Tactile mapping system: a novel imaging technology for surface topography and elasticity of tissues or organs.

PubMed

Oie, Tomonori; Suzuki, Hisato; Fukuda, Toru; Murayama, Yoshinobu; Omata, Sadao; Kanda, Keiichi; Nakayama, Yasuhide

2009-11-01

: We demonstrated that the tactile mapping system (TMS) has a high degree of spatial precision in the distribution mapping of surface elasticity of tissues or organs. : Samples used were a circumferential section of a small-caliber porcine artery (diameter: ∼3 mm) and an elasticity test pattern with a line and space configuration for the distribution mapping of elasticity, prepared by regional micropatterning of a 14-μm thick gelatin hydrogel coating on a polyurethane sheet. Surface topography and elasticity in normal saline were simultaneously investigated by TMS using a probe with a diameter of 5 or 12 μm, a spatial interval of 1 to 5 μm, and an indentation depth of 4 μm. : In the test pattern, a spatial resolution in TMS of <5 μm was acquired under water with a minimal probe diameter and spatial interval of the probe movement. TMS was used for the distribution mapping of surface elasticity in a flat, circumferential section (thickness: ∼0.5 mm) of a porcine artery, and the concentric layers of the vascular wall, including the collagen-rich and elastin-rich layers, could be clearly differentiated in terms of surface elasticity at the spatial resolution of <2 μm. : TMS is a simple and inexpensive technique for the distribution mapping of the surface elasticity in vascular tissues at the spatial resolution <2 μm. TMS has the ability to analyze a complex structure of the tissue samples under normal saline.

Phase Aberration and Attenuation Effects on Acoustic Radiation Force-Based Shear Wave Generation.

PubMed

Carrascal, Carolina Amador; Aristizabal, Sara; Greenleaf, James F; Urban, Matthew W

2016-02-01

Elasticity is measured by shear wave elasticity imaging (SWEI) methods using acoustic radiation force to create the shear waves. Phase aberration and tissue attenuation can hamper the generation of shear waves for in vivo applications. In this study, the effects of phase aberration and attenuation in ultrasound focusing for creating shear waves were explored. This includes the effects of phase shifts and amplitude attenuation on shear wave characteristics such as shear wave amplitude, shear wave speed, shear wave center frequency, and bandwidth. Two samples of swine belly tissue were used to create phase aberration and attenuation experimentally. To explore the phase aberration and attenuation effects individually, tissue experiments were complemented with ultrasound beam simulations using fast object-oriented C++ ultrasound simulator (FOCUS) and shear wave simulations using finite-element-model (FEM) analysis. The ultrasound frequency used to generate shear waves was varied from 3.0 to 4.5 MHz. Results: The measured acoustic pressure and resulting shear wave amplitude decreased approximately 40%-90% with the introduction of the tissue samples. Acoustic intensity and shear wave displacement were correlated for both tissue samples, and the resulting Pearson's correlation coefficients were 0.99 and 0.97. Analysis of shear wave generation with tissue samples (phase aberration and attenuation case), measured phase screen, (only phase aberration case), and FOCUS/FEM model (only attenuation case) showed that tissue attenuation affected the shear wave generation more than tissue aberration. Decreasing the ultrasound frequency helped maintain a focused beam for creation of shear waves in the presence of both phase aberration and attenuation.

Applications of Mass Spectrometry Imaging for Safety Evaluation.

PubMed

Bonnel, David; Stauber, Jonathan

2017-01-01

Mass spectrometry imaging (MSI) was first derived from techniques used in physics, which were then incorporated into chemistry followed by application in biology. Developed over 50 years ago, and with different principles to detect and map compounds on a sample surface, MSI supports modern biology questions by detecting biological compounds within tissue sections. MALDI (matrix-assisted laser desorption/ionization) imaging trend analysis in this field shows an important increase in the number of publications since 2005, especially with the development of the MALDI imaging technique and its applications in biomarker discovery and drug distribution. With recent improvements of statistical tools, absolute and relative quantification protocols, as well as quality and reproducibility evaluations, MALDI imaging has become one of the most reliable MSI techniques to support drug discovery and development phases. MSI allows to potentially address important questions in drug development such as "What is the localization of the drug and its metabolites in the tissues?", "What is the pharmacological effect of the drug in this particular region of interest?", or "Is the drug and its metabolites related to an atypical finding?" However, prior to addressing these questions using MSI techniques, expertise needs to be developed to become proficient at histological procedures (tissue preparation with frozen of fixed tissues), analytical chemistry, matrix application, instrumentation, informatics, and mathematics for data analysis and interpretation.

Connective tissue regeneration in skeletal muscle after eccentric contraction-induced injury.

PubMed

Mackey, Abigail L; Kjaer, Michael

2017-03-01

Human skeletal muscle has the potential to regenerate completely after injury induced under controlled experimental conditions. The events inside the myofibers as they undergo necrosis, followed closely by satellite cell-mediated myogenesis, have been mapped in detail. Much less is known about the adaptation throughout this process of both the connective tissue structures surrounding the myofibers and the fibroblasts, the cells responsible for synthesizing this connective tissue. However, the few studies investigating muscle connective tissue remodeling demonstrate a strong response that appears to be sustained for a long time after the major myofiber responses have subsided. While the use of electrical stimulation to induce eccentric contractions vs. voluntary eccentric contractions appears to lead to a greater extent of myofiber necrosis and regenerative response, this difference is not apparent when the muscle connective tissue responses are compared, although further work is required to confirm this. Pharmacological agents (growth hormone and angiotensin II type I receptor blockers) are considered in the context of accelerating the muscle connective tissue adaptation to loading. Cautioning against this, however, is the association between muscle matrix protein remodeling and protection against reinjury, which suggests that a (so far undefined) period of vulnerability to reinjury may exist during the remodeling phases. The role of individual muscle matrix components and their spatial interaction during adaptation to eccentric contractions is an unexplored field in human skeletal muscle and may provide insight into the optimal timing of rest vs. return to activity after muscle injury. Copyright © 2017 the American Physiological Society.

Pulse Oximeter Derived Blood Pressure Measurement in Patients With a Continuous Flow Left Ventricular Assist Device.

PubMed

Hellman, Yaron; Malik, Adnan S; Lane, Kathleen A; Shen, Changyu; Wang, I-Wen; Wozniak, Thomas C; Hashmi, Zubair A; Munson, Sarah D; Pickrell, Jeanette; Caccamo, Marco A; Gradus-Pizlo, Irmina; Hadi, Azam

2017-05-01

Currently, blood pressure (BP) measurement is obtained noninvasively in patients with continuous flow left ventricular assist device (LVAD) by placing a Doppler probe over the brachial or radial artery with inflation and deflation of a manual BP cuff. We hypothesized that replacing the Doppler probe with a finger-based pulse oximeter can yield BP measurements similar to the Doppler derived mean arterial pressure (MAP). We conducted a prospective study consisting of patients with contemporary continuous flow LVADs. In a small pilot phase I inpatient study, we compared direct arterial line measurements with an automated blood pressure (ABP) cuff, Doppler and pulse oximeter derived MAP. Our main phase II study included LVAD outpatients with a comparison between Doppler, ABP, and pulse oximeter derived MAP. A total of five phase I and 36 phase II patients were recruited during February-June 2014. In phase I, the average MAP measured by pulse oximeter was closer to arterial line MAP rather than Doppler (P = 0.06) or ABP (P < 0.01). In phase II, pulse oximeter MAP (96.6 mm Hg) was significantly closer to Doppler MAP (96.5 mm Hg) when compared to ABP (82.1 mm Hg) (P = 0.0001). Pulse oximeter derived blood pressure measurement may be as reliable as Doppler in patients with continuous flow LVADs. © 2016 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

A Study of Early Afterdepolarizations in a Model for Human Ventricular Tissue

PubMed Central

Vandersickel, Nele; Kazbanov, Ivan V.; Nuitermans, Anita; Weise, Louis D.; Pandit, Rahul; Panfilov, Alexander V.

2014-01-01

Sudden cardiac death is often caused by cardiac arrhythmias. Recently, special attention has been given to a certain arrhythmogenic condition, the long-QT syndrome, which occurs as a result of genetic mutations or drug toxicity. The underlying mechanisms of arrhythmias, caused by the long-QT syndrome, are not fully understood. However, arrhythmias are often connected to special excitations of cardiac cells, called early afterdepolarizations (EADs), which are depolarizations during the repolarizing phase of the action potential. So far, EADs have been studied mainly in isolated cardiac cells. However, the question on how EADs at the single-cell level can result in fibrillation at the tissue level, especially in human cell models, has not been widely studied yet. In this paper, we study wave patterns that result from single-cell EAD dynamics in a mathematical model for human ventricular cardiac tissue. We induce EADs by modeling experimental conditions which have been shown to evoke EADs at a single-cell level: by an increase of L-type Ca currents and a decrease of the delayed rectifier potassium currents. We show that, at the tissue level and depending on these parameters, three types of abnormal wave patterns emerge. We classify them into two types of spiral fibrillation and one type of oscillatory dynamics. Moreover, we find that the emergent wave patterns can be driven by calcium or sodium currents and we find phase waves in the oscillatory excitation regime. From our simulations we predict that arrhythmias caused by EADs can occur during normal wave propagation and do not require tissue heterogeneities. Experimental verification of our results is possible for experiments at the cell-culture level, where EADs can be induced by an increase of the L-type calcium conductance and by the application of I blockers, and the properties of the emergent patterns can be studied by optical mapping of the voltage and calcium. PMID:24427289

A simultaneous multichannel monophasic action potential electrode array for in vivo epicardial repolarization mapping.

PubMed

Sahakian, A V; Peterson, M S; Shkurovich, S; Hamer, M; Votapka, T; Ji, T; Swiryn, S

2001-03-01

While the recording of extracellular monophasic action potentials (MAPs) from single epicardial or endocardial sites has been performed for over a century, we are unaware of any previous successful attempt to record MAPs simultaneously from a large number of sites in vivo. We report here the design and validation of an array of MAP electrodes which records both depolarization and repolarization simultaneously at up to 16 epicardial sites in a square array on the heart in vivo. The array consists of 16 sintered Ag-AgCl electrodes mounted in a common housing with individual suspensions allowing each electrode to exert a controlled pressure on the epicardial surface. The electrodes are arranged in a square array, with each quadrant of four having an additional recessed sintered Ag-AgCl reference electrode at its center. A saline-soaked sponge establishes ionic contact between the reference electrodes and the tissue. The array was tested on six anesthetized open-chested pigs. Simultaneous diagnostic-quality MAP recordings were obtained from up to 13 out of 16 ventricular sites. Ventricular MAPs had amplitudes of 10-40 mV with uniform morphologies and stable baselines for up to 30 min. MAP duration at 90% repolarization was measured and shown to vary as expected with cycle length during sustained pacing. The relationship between MAP duration and effective refractory period was also confirmed. The ability of the array to detect local differences in repolarization was tested in two ways. Placement of the array straddling the atrioventricular (AV) junction yielded simultaneous atrial or ventricular recordings at corresponding sites during 1:1 and 2:1 AV conduction. Localized ischemia via constriction of a coronary artery branch resulted in shortening of the repolarization phase at the ischemic, but not the nonischemic, sites. In conclusion, these results indicate that the simultaneous multichannel MAP electrode array is a viable method for in vivo epicardial repolarization mapping. The array has the potential to be expanded to increase the number of sites and spatial resolution.

Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

2014-04-01

X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

Coupling between arterial pressure, cerebral blood velocity, and cerebral tissue oxygenation with spontaneous and forced oscillations.

PubMed

Rickards, Caroline A; Sprick, Justin D; Colby, Hannah B; Kay, Victoria L; Tzeng, Yu-Chieh

2015-04-01

We tested the hypothesis that transmission of arterial pressure to brain tissue oxygenation is low under conditions of arterial pressure instability. Two experimental models of hemodynamic instability were used in healthy human volunteers; (1) oscillatory lower body negative pressure (OLBNP) (N = 8; 5 male, 3 female), and; (2) maximal LBNP to presyncope (N = 21; 13 male, 8 female). Mean arterial pressure (MAP), middle cerebral artery velocity (MCAv), and cerebral tissue oxygen saturation (ScO2) were measured non-invasively. For the OLBNP protocol, between 0 and -60 mmHg negative pressure was applied for 20 cycles at 0.05 Hz, then 20 cycles at 0.1 Hz. For the maximal LBNP protocol, progressive 5 min stages of chamber decompression were applied until the onset of presyncope. Spectral power of MAP, mean MCAv, and ScO2 were calculated within the VLF (0.04-0.07 Hz), and LF (0.07-0.2 Hz) ranges, and cross-spectral coherence was calculated for MAP-mean MCAv, MAP-ScO2, and mean MCAv-ScO2 at baseline, during each OLBNP protocol, and at the level prior to pre-syncope during maximal LBNP (sub-max). The key findings are (1) both 0.1 Hz OLBNP and sub-max LBNP elicited increases in LF power for MAP, mean MCAv, and ScO2 (p ≤ 0.08); (2) 0.05 Hz OLBNP increased VLF power in MAP and ScO2 only (p ≤ 0.06); (3) coherence between MAP-mean MCAv was consistently higher (≥0.71) compared with MAP-ScO2, and mean MCAv-ScO2 (≤0.43) during both OLBNP protocols, and sub-max LBNP (p ≤ 0.04). These data indicate high linearity between pressure and cerebral blood flow variations, but reduced linearity between cerebral tissue oxygenation and both arterial pressure and cerebral blood flow. Measuring arterial pressure variability may not always provide adequate information about the downstream effects on cerebral tissue oxygenation, the key end-point of interest for neuronal viability.

An electrical impedance tomography (EIT) multi-electrode needle-probe device for local assessment of heterogeneous tissue impeditivity.

PubMed

Meroni, Davide; Maglioli, Camilla Carpano; Bovio, Dario; Greco, Francesco G; Aliverti, Andrea

2017-07-01

Electrical Impedance Tomography (EIT) is an image reconstruction technique applied in medicine for the electrical imaging of living tissues. In literature there is the evidence that a large resistivity variation related to the differences of the human tissues exists. As a result of this interest for the electrical characterization of the biological samples, recently the attention is also focused on the identification and characterization of the human tissue, by studying the homogeneity of its structure. An 8 electrodes needle-probe device has been developed with the intent of identifying the structural inhomogeneities under the surface layers. Ex-vivo impeditivity measurements, by placing the needle-probe in 5 different patterns of fat and lean porcine tissue, were performed, and impeditivity maps were obtained by EIDORS open source software for image reconstruction in electrical impedance. The values composing the maps have been analyzed, pointing out a good tissue discrimination, and the conformity with the real images. We conclude that this device is able to perform impeditivity maps matching to reality for position and orientation. In all the five patterns presented is possible to identify and replicate correctly the heterogeneous tissue under test. This new procedure can be helpful to the medical staff to completely characterize the biological sample, in different unclear situations.

Mapping of thermal injury in biologic tissues using quantitative pathologic techniques

NASA Astrophysics Data System (ADS)

Thomsen, Sharon L.

1999-05-01

Qualitative and quantitative pathologic techniques can be used for (1) mapping of thermal injury, (2) comparisons lesion sizes and configurations for different instruments or heating sources and (3) comparisons of treatment effects. Concentric zones of thermal damage form around a single volume heat source. The boundaries between some of these zones are distinct and measurable. Depending on the energy deposition, heating times and tissue type, the zones can include the following beginning at the hotter center and progressing to the cooler periphery: (1) tissue ablation, (2) carbonization, (3) tissue water vaporization, (4) structural protein denaturation (thermal coagulation), (5) vital enzyme protein denaturation, (6) cell membrane disruption, (7) hemorrhage, hemostasis and hyperhemia, (8) tissue necrosis and (9) wound organization and healing.

Route planning with transportation network maps: an eye-tracking study.

PubMed

Grison, Elise; Gyselinck, Valérie; Burkhardt, Jean-Marie; Wiener, Jan Malte

2017-09-01

Planning routes using transportation network maps is a common task that has received little attention in the literature. Here, we present a novel eye-tracking paradigm to investigate psychological processes and mechanisms involved in such a route planning. In the experiment, participants were first presented with an origin and destination pair before we presented them with fictitious public transportation maps. Their task was to find the connecting route that required the minimum number of transfers. Based on participants' gaze behaviour, each trial was split into two phases: (1) the search for origin and destination phase, i.e., the initial phase of the trial until participants gazed at both origin and destination at least once and (2) the route planning and selection phase. Comparisons of other eye-tracking measures between these phases and the time to complete them, which depended on the complexity of the planning task, suggest that these two phases are indeed distinct and supported by different cognitive processes. For example, participants spent more time attending the centre of the map during the initial search phase, before directing their attention to connecting stations, where transitions between lines were possible. Our results provide novel insights into the psychological processes involved in route planning from maps. The findings are discussed in relation to the current theories of route planning.

Spatial cluster analysis of nanoscopically mapped serotonin receptors for classification of fixed brain tissue

NASA Astrophysics Data System (ADS)

Sams, Michael; Silye, Rene; Göhring, Janett; Muresan, Leila; Schilcher, Kurt; Jacak, Jaroslaw

2014-01-01

We present a cluster spatial analysis method using nanoscopic dSTORM images to determine changes in protein cluster distributions within brain tissue. Such methods are suitable to investigate human brain tissue and will help to achieve a deeper understanding of brain disease along with aiding drug development. Human brain tissue samples are usually treated postmortem via standard fixation protocols, which are established in clinical laboratories. Therefore, our localization microscopy-based method was adapted to characterize protein density and protein cluster localization in samples fixed using different protocols followed by common fluorescent immunohistochemistry techniques. The localization microscopy allows nanoscopic mapping of serotonin 5-HT1A receptor groups within a two-dimensional image of a brain tissue slice. These nanoscopically mapped proteins can be confined to clusters by applying the proposed statistical spatial analysis. Selected features of such clusters were subsequently used to characterize and classify the tissue. Samples were obtained from different types of patients, fixed with different preparation methods, and finally stored in a human tissue bank. To verify the proposed method, samples of a cryopreserved healthy brain have been compared with epitope-retrieved and paraffin-fixed tissues. Furthermore, samples of healthy brain tissues were compared with data obtained from patients suffering from mental illnesses (e.g., major depressive disorder). Our work demonstrates the applicability of localization microscopy and image analysis methods for comparison and classification of human brain tissues at a nanoscopic level. Furthermore, the presented workflow marks a unique technological advance in the characterization of protein distributions in brain tissue sections.

Untargeted UPLC-MS Profiling Pipeline to Expand Tissue Metabolome Coverage: Application to Cardiovascular Disease

PubMed Central

2015-01-01

Metabolic profiling studies aim to achieve broad metabolome coverage in specific biological samples. However, wide metabolome coverage has proven difficult to achieve, mostly because of the diverse physicochemical properties of small molecules, obligating analysts to seek multiplatform and multimethod approaches. Challenges are even greater when it comes to applications to tissue samples, where tissue lysis and metabolite extraction can induce significant systematic variation in composition. We have developed a pipeline for obtaining the aqueous and organic compounds from diseased arterial tissue using two consecutive extractions, followed by a different untargeted UPLC-MS analysis method for each extract. Methods were rationally chosen and optimized to address the different physicochemical properties of each extract: hydrophilic interaction liquid chromatography (HILIC) for the aqueous extract and reversed-phase chromatography for the organic. This pipeline can be generic for tissue analysis as demonstrated by applications to different tissue types. The experimental setup and fast turnaround time of the two methods contributed toward obtaining highly reproducible features with exceptional chromatographic performance (CV % < 0.5%), making this pipeline suitable for metabolic profiling applications. We structurally assigned 226 metabolites from a range of chemical classes (e.g., carnitines, α-amino acids, purines, pyrimidines, phospholipids, sphingolipids, free fatty acids, and glycerolipids) which were mapped to their corresponding pathways, biological functions and known disease mechanisms. The combination of the two untargeted UPLC-MS methods showed high metabolite complementarity. We demonstrate the application of this pipeline to cardiovascular disease, where we show that the analyzed diseased groups (n = 120) of arterial tissue could be distinguished based on their metabolic profiles. PMID:25664760

Non-Fourier thermal transport induced structural hierarchy and damage to collagen ultrastructure subjected to laser irradiation.

PubMed

Sahoo, Nilamani; Narasimhan, Arunn; Dhar, Purbarun; Das, Sarit K

2018-05-01

Comprehending the mechanism of thermal transport through biological tissues is an important factor for optimal ablation of cancerous tissues and minimising collateral tissue damage. The present study reports detailed mapping of the rise in internal temperature within the tissue mimics due to NIR (1064 nm) laser irradiation, both for bare mimics and with gold nanostructures infused. Gold nanostructures such as mesoflowers and nanospheres have been synthesised and used as photothermal converters to enhance the temperature rise, resulting in achieving the desired degradation of malignant tissue in targeted region. Thermal history was observed experimentally and simulated considering non-Fourier dual phase lag (DPL) model incorporated Pennes bio-heat transfer equation using COMSOL Multiphysics software. The gross deviation in temperature i.e. rise from the classical Fourier model for bio-heat conduction suggests additional effects of temperature rise on the secondary structures and morphological and physico-chemical changes to the collagen ultrastructures building the tissue mass. The observed thermal denaturation in the collagen fibril morphologies have been explained based on the physico-chemical structure of collagen and its response to thermal radiation. The large shift in frequency of amides A and B is pronounced at a depth of maximum temperature rise compared with other positions in tissue phantom. Observations for change in band of amide I, amide II, and amide III are found to be responsible for damage to collagen ultra-structure. Variation in the concentration of gold nanostructures shows the potentiality of localised hyperthermia treatment subjected to NIR radiation through a proposed free radical mechanism.

[Application of diffusion tensor imaging in judging infarction time of acute ischemic cerebral infarction].

PubMed

Dai, Zhenyu; Chen, Fei; Yao, Lizheng; Dong, Congsong; Liu, Yang; Shi, Haicun; Zhang, Zhiping; Yang, Naizhong; Zhang, Mingsheng; Dai, Yinggui

2015-08-18

To evaluate the clinical application value of diffusion tensor imaging (DTI) and diffusion tensor tractography (DTT) in judging infarction time phase of acute ischemic cerebral infarction. To retrospective analysis DTI images of 52 patients with unilateral acute ischemic cerebral infarction (hyper-acute, acute and sub-acute) from the Affiliated Yancheng Hospital of Southeast University Medical College, which diagnosed by clinic and magnetic resonance imaging. Set the regions of interest (ROIs) of infarction lesions, brain tissue close to infarction lesions and corresponding contra (contralateral normal brain tissue) on DTI parameters mapping of fractional anisotropy (FA), volume ratio anisotropy (VRA), average diffusion coefficient (DCavg) and exponential attenuation (Exat), record the parameters values of ROIs and calculate the relative parameters value of infarction lesion to contra. Meanwhile, reconstruct the DTT images based on the seed points (infarction lesion and contra). The study compared each parameter value of infarction lesions, brain tissue close to infarction lesions and corresponding contra, also analysed the differences of relative parameters values in different infarction time phases. The DTT images of acute ischemic cerebral infarction in each time phase could show the manifestation of fasciculi damaged. The DCavg value of cerebral infarction lesions was lower and the Exat value was higher than contra in each infarction time phase (P<0.05). The FA and VRA value of cerebral infarction lesions were reduced than contra only in acute and sub-acute infarction (P<0.05). The FA, VRA and Exat value of brain tissue close to infarction lesions were increased and DCavg value was decreased than contra in hyper-acute infarction (P<0.05). There were no statistic differences of FA, VRA, DCavg and Exat value of brain tissue close to infarction lesions in acute and sub-acute infarction. The relative FA and VRA value of infarction lesion to contra gradually decreased from hyper-acute to sub-acute cerebral infarction (P<0.05), but there were no difference of the relative VRA value between acute and sub-acute cerebral infarction. The relative DCavg value of infarction lesion to contra in hyper-acute infarction than that in acute and sub-acute infarction (P<0.05), however there was also no difference between acute and sub-acute infarction. ROC curve showed the best diagnosis cut off value of relative FA, VRA and DCavg of infarction lesions to contra were 0.852, 0.886 and 0.541 between hyper-acute and acute cerebral infarction, the best diagnosis cut off value of relative FA was 0.595 between acute and sub-acute cerebral infarction, respectively. The FA, VRA, DCavg and Exat value have specific change mode in acute ischemic cerebral infarction of different infarction time phases, which can be combine used in judging infarction time phase of acute ischemic cerebral infarction without clear onset time, thus to help selecting the reasonable treatment protocols.

Simulation of ultrasonic pulse propagation, distortion, and attenuation in the human chest wall.

PubMed

Mast, T D; Hinkelman, L M; Metlay, L A; Orr, M J; Waag, R C

1999-12-01

A finite-difference time-domain model for ultrasonic pulse propagation through soft tissue has been extended to incorporate absorption effects as well as longitudinal-wave propagation in cartilage and bone. This extended model has been used to simulate ultrasonic propagation through anatomically detailed representations of chest wall structure. The inhomogeneous chest wall tissue is represented by two-dimensional maps determined by staining chest wall cross sections to distinguish between tissue types, digitally scanning the stained cross sections, and mapping each pixel of the scanned images to fat, muscle, connective tissue, cartilage, or bone. Each pixel of the tissue map is then assigned a sound speed, density, and absorption value determined from published measurements and assumed to be representative of the local tissue type. Computational results for energy level fluctuations and arrival time fluctuations show qualitative agreement with measurements performed on the same specimens, but show significantly less waveform distortion than measurements. Visualization of simulated tissue-ultrasound interactions in the chest wall shows possible mechanisms for image aberration in echocardiography, including effects associated with reflection and diffraction caused by rib structures. A comparison of distortion effects for varying pulse center frequencies shows that, for soft tissue paths through the chest wall, energy level and waveform distortion increase markedly with rising ultrasonic frequency and that arrival-time fluctuations increase to a lesser degree.

Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets.

PubMed

Zhu, Ying; Dou, Maowei; Piehowski, Paul D; Liang, Yiran; Wang, Fangjun; Chu, Rosalie K; Chrisler, Will; Smith, Jordan N; Schwarz, Kaitlynn C; Shen, Yufeng; Shukla, Anil K; Moore, Ronald J; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T

2018-06-24

Current mass spectrometry (MS)-based proteomics approaches are ineffective for mapping protein expression in tissue sections with high spatial resolution due to the limited overall sensitivity of conventional workflows. Here we report an integrated and automated method to advance spatially resolved proteomics by seamlessly coupling laser capture microdissection (LCM) with a recently developed nanoliter-scale sample preparation system termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples). The workflow is enabled by prepopulating nanowells with DMSO, which serves as a sacrificial capture liquid for microdissected tissues. The DMSO droplets efficiently collect laser-pressure catapulted LCM tissues as small as 20 µm in diameter with success rates >87%. We also demonstrate that tissue treatment with DMSO can significantly improve proteome coverage, likely due to its ability to dissolve lipids from tissue and enhance protein extraction efficiency. The LCM-nanoPOTS platform was able to identify 180, 695, and 1827 protein groups on average from 12-µm-thick rat brain cortex tissue sections with diameters of 50, 100, and 200 µm, respectively. We also analyzed 100-µm-diameter sections corresponding to 10-18 cells from three different regions of rat brain and comparatively quantified ~1000 proteins, demonstrating the potential utility for high-resolution spatially resolved mapping of protein expression in tissues. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

A systematical analysis of in vivo contact forces on virtual catheter tip/tissue surface contact during cardiac mapping and intervention.

PubMed

Okumura, Yasuo; Johnson, Susan B; Bunch, T Jared; Henz, Benhur D; O'Brien, Christine J; Packer, Douglas L

2008-06-01

While catheter tip/tissue contact has been shown to be an important determinant of ablative lesions in in vitro studies, the impact of contact on the outcomes of mapping and ablation in the intact heart has not been evaluated. Twelve dogs underwent atrial ablation guided by the Senesitrade mark robotic catheter remote control system. After intracardiac ultrasound (ICE) validation of contact force measured by an in-line mechanical sensor, the relationship between contact force and individual lesion formation was established during irrigated-tipped ablation (flow 17 mL/sec) at 15 watts for 30 seconds. Minimal contact by ICE correlated with force of 4.7 +/- 5.8 grams, consistent contact 9.9 +/- 8.6 grams and tissue tenting produced 25.0 +/- 14.0 grams. Conversely, catheter tip/tissue contact by ICE was predicted by contact force. A contact force of 10-20 and > or =20 grams generated full-thickness, larger volume ablative lesions than that created with <10 grams (98 +/- 69 and 89 +/- 70 mm(3) vs 40 +/- 42 mm(3), P < 0.05). Moderate (10 grams) and marked contact (15-20 grams) application produced 1.5 X greater electroanatomic map volumes that were seen with minimal contact (5 grams) (26 +/- 3 cm(3) vs 33 +/- 6, 39 +/- 3 cm(3), P < 0.05). The electroanatomic map/CT merge process was also more distorted when mapping was generated at moderate to marked contact force. This study shows that mapping and ablation using a robotic sheath guidance system are critically dependent on generated force. These findings suggest that ablative lesion size is optimized by the application of 10-20 grams of contact force, although mapping requires lower-force application to avoid image distortions.

Impact of time-of-flight PET on quantification errors in MR imaging-based attenuation correction.

PubMed

Mehranian, Abolfazl; Zaidi, Habib

2015-04-01

Time-of-flight (TOF) PET/MR imaging is an emerging imaging technology with great capabilities offered by TOF to improve image quality and lesion detectability. We assessed, for the first time, the impact of TOF image reconstruction on PET quantification errors induced by MR imaging-based attenuation correction (MRAC) using simulation and clinical PET/CT studies. Standard 4-class attenuation maps were derived by segmentation of CT images of 27 patients undergoing PET/CT examinations into background air, lung, soft-tissue, and fat tissue classes, followed by the assignment of predefined attenuation coefficients to each class. For each patient, 4 PET images were reconstructed: non-TOF and TOF both corrected for attenuation using reference CT-based attenuation correction and the resulting 4-class MRAC maps. The relative errors between non-TOF and TOF MRAC reconstructions were compared with their reference CT-based attenuation correction reconstructions. The bias was locally and globally evaluated using volumes of interest (VOIs) defined on lesions and normal tissues and CT-derived tissue classes containing all voxels in a given tissue, respectively. The impact of TOF on reducing the errors induced by metal-susceptibility and respiratory-phase mismatch artifacts was also evaluated using clinical and simulation studies. Our results show that TOF PET can remarkably reduce attenuation correction artifacts and quantification errors in the lungs and bone tissues. Using classwise analysis, it was found that the non-TOF MRAC method results in an error of -3.4% ± 11.5% in the lungs and -21.8% ± 2.9% in bones, whereas its TOF counterpart reduced the errors to -2.9% ± 7.1% and -15.3% ± 2.3%, respectively. The VOI-based analysis revealed that the non-TOF and TOF methods resulted in an average overestimation of 7.5% and 3.9% in or near lung lesions (n = 23) and underestimation of less than 5% for soft tissue and in or near bone lesions (n = 91). Simulation results showed that as TOF resolution improves, artifacts and quantification errors are substantially reduced. TOF PET substantially reduces artifacts and improves significantly the quantitative accuracy of standard MRAC methods. Therefore, MRAC should be less of a concern on future TOF PET/MR scanners with improved timing resolution. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Real-Time Vision-Based Stiffness Mapping †

PubMed Central

Althoefer, Kaspar; Asama, Hajime

2018-01-01

This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF) Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness. PMID:29701704

Use of an Annular Silicon Drift Detector (SDD) Versus a Conventional SDD Makes Phase Mapping a Practical Solution for Rare Earth Mineral Characterization.

PubMed

Teng, Chaoyi; Demers, Hendrix; Brodusch, Nicolas; Waters, Kristian; Gauvin, Raynald

2018-06-04

A number of techniques for the characterization of rare earth minerals (REM) have been developed and are widely applied in the mining industry. However, most of them are limited to a global analysis due to their low spatial resolution. In this work, phase map analyses were performed on REM with an annular silicon drift detector (aSDD) attached to a field emission scanning electron microscope. The optimal conditions for the aSDD were explored, and the high-resolution phase maps generated at a low accelerating voltage identify phases at the micron scale. In comparisons between an annular and a conventional SDD, the aSDD performed at optimized conditions, making the phase map a practical solution for choosing an appropriate grinding size, judging the efficiency of different separation processes, and optimizing a REM beneficiation flowsheet.

A single bout of exhaustive exercise affects integrated baroreflex function after 16 days of head-down tilt

NASA Technical Reports Server (NTRS)

Engelke, K. A.; Doerr, D. F.; Convertino, V. A.

1995-01-01

We tested the hypothesis that one bout of maximal exercise performed 24 h before reambulation from 16 days of 6 degrees head-down tilt (HDT) could increase integrated baroreflex sensitivity. Isolated carotid-cardiac and integrated baroreflex function was assessed in seven subjects before and after two periods of HDT separated by 11 mo. On the last day of one HDT period, subjects performed a single bout of maximal cycle ergometry (exercise). Subjects did not exercise after the other HDT period (control). Carotid-cardiac baroreflex sensitivity was evaluated using a neck collar device. Integrated baroreflex function was assessed by recording heart rate (HR) and blood pressure (MAP) during a 15-s Valsalva maneuver (VM) at a controlled expiratory pressure of 30 mmHg. The ratio of change in HR to change in MAP (delta HR/ delta MAP) during phases II and IV of the VM was used as an index of cardiac baroreflex sensitivity. Baroreflex-mediated vasoconstriction was assessed by measuring the late phase II rise in MAP. Following HDT, carotid-cardiac baroreflex sensitivity was reduced (2.8 to 2.0 ms/mmHg; P = 0.05) as was delta HR/ delta MAP during phase II (-1.5 to -0.8 beats/mmHg; P = 0.002). After exercise, isolated carotid baroreflex activity and phase II delta HR/ delta MAP returned to pre-HDT levels but remained attenuated in the control condition. Phase IV delta HR/ delta MAP was not altered by HDT or exercise. The late phase II increase of MAP was 71% greater after exercise compared with control (7 vs. 2 mmHg; P = 0.041).(ABSTRACT TRUNCATED AT 250 WORDS).

Chesapeake Bay Low Freshwater Inflow Study. Phase II. MAP FOLIO. Biota Assessment.

DTIC Science & Technology

1982-05-01

conditions. These were: 1) Base Average -- average freshwater inflow conditions. by increased water consumption projected for the year 2020. 3) Base Drought...RESOLUTION TEST CHART NATIONAL BUREAU OF STANDARDS. 1963- A TAI m - ii J May 1982 Chesapeake Bay Low Freshwater Inflow Study Phase II Biota Assessment Map...A PERIOD ZOVERED change was found to CIESAPEAKE BAY LOW FRESHWATER INFLOW STUDY FINAL BIOTA ASSESSMENT PHASE II: FINAL REPORT MAP FOLIO s PERFORMING

Phase-contrast Hounsfield units of fixated and non-fixated soft-tissue samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willner, Marian; Fior, Gabriel; Marschner, Mathias

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissuemore » specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. In addition, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results.« less

Phase-contrast Hounsfield units of fixated and non-fixated soft-tissue samples

DOE PAGES

Willner, Marian; Fior, Gabriel; Marschner, Mathias; ...

2015-08-31

X-ray phase-contrast imaging is a novel technology that achieves high soft-tissue contrast. Although its clinical impact is still under investigation, the technique may potentially improve clinical diagnostics. In conventional attenuation-based X-ray computed tomography, radiological diagnostics are quantified by Hounsfield units. Corresponding Hounsfield units for phase-contrast imaging have been recently introduced, enabling a setup-independent comparison and standardized interpretation of imaging results. Thus far, the experimental values of few tissue types have been reported; these values have been determined from fixated tissue samples. This study presents phase-contrast Hounsfield units for various types of non-fixated human soft tissues. A large variety of tissuemore » specimens ranging from adipose, muscle and connective tissues to liver, kidney and pancreas tissues were imaged by a grating interferometer with a rotating-anode X-ray tube and a photon-counting detector. In addition, we investigated the effects of formalin fixation on the quantitative phase-contrast imaging results.« less

Covariance and correlation estimation in electron-density maps.

PubMed

Altomare, Angela; Cuocci, Corrado; Giacovazzo, Carmelo; Moliterni, Anna; Rizzi, Rosanna

2012-03-01

Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.

3D mapping of breast surface using digital fringe projection

NASA Astrophysics Data System (ADS)

Vairavan, Rajendaran; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Leng, Lai Siang; Wan Norhaimi, Wan Mokhzani; Marimuthu, Rajeswaran; Abdullah, Othman; Kirtsaeng, Supap

2017-02-01

Optical sensing technique has inherited non-contact nature for generating 3D surface mapping where its application ranges from MEMS component characterization, corrosion analysis, and vibration analysis. In particular, the digital fringe projection is utilized for 3D mapping of objects through the illumination of structured light for medical application extending from oral dental measurements, lower back deformation analysis, monitoring of scoliosis and 3D face reconstruction for biometric identification. However, the usage of digital fringe projection for 3D mapping of human breast is very minimal. Thus, this paper addresses the application of digital fringe projection for 3D mapping of breast surface based on total non-contact nature. In this work, phase shift method is utilized to perform the 3D mapping. The phase shifted fringe pattern are displayed through a digital projector onto the breast surface, and the distorted fringe patterns are captured by a CCD camera. A phase map is produced, and phase unwrapping was executed to obtain the 3D surface mapping of the breast. The surface height profile from 3D fringe projection was compared with the surface height measured by a direct method using electronic digital vernier caliper. Preliminary results showed the feasibility of digital fringe projection in providing a 3D mapping of breast and its application could be further extended for breast carcinoma detection.

Expression of SNCG, MAP2, SDF-1 and CXCR4 in gastric adenocarcinoma and their clinical significance

PubMed Central

Zheng, Shufang; Shi, Lifang; Zhang, Yi; He, Tao

2014-01-01

Objectives: The purpose of the study was to detect the expression of SNCG, MAP2, SDF-1 and CXCR4 in gastric adenocarcinoma, and to evaluate their roles in the carcinogenesis of gastric adenocarcinoma, development, invasion and metastasis as well as their clinical significance. Methods: The expression of SNCG, MAP2, SDF-1 and CXCR4 was detected by SP immunohistochemical method in 225 cases of gastric adenocarcinoma and 105 cases of nonneoplastic adjacent gastric tissue. The expression of SNCG, MAP2, SDF-1 and CXCR4 mRNA was also detected by RT-PCR method in 50 cases of gastric adenocarcinoma and 30 cases of nonneoplastic adjacent gastric tissue. Results: The expression of SNCG, MAP2, SDF-1 and CXCR4 in the gastric adenocarcinoma was remarkably higher than those in the nonneoplastic adjacent gastric tissue (P < 0.01); The positive expression of SNCG and MAP2 was correlated with the depth of tumor invasion and the metastasis of lymph nodes (P < 0.05), and that of SDF-1 and CXCR4 was correlated with the metastasis of lymph nodes (P < 0.05). Conclusions: SNCG, MAP2, SDF-1 and CXCR4 may play an important role in the carcinogenesis, progression, invasion and metastasis of gastric adenocarcinoma. However, it still needs more exploration whether they can serve as promising therapeutic targets of gastric adenocarcinoma. PMID:25400739

Determination of skeleton and sign map for phase obtaining from a single ESPI image

NASA Astrophysics Data System (ADS)

Yang, Xia; Yu, Qifeng; Fu, Sihua

2009-06-01

A robust method of determining the sign map and skeletons for ESPI images is introduced in this paper. ESPI images have high speckle noise which makes it difficult to obtain the fringe information, especially from a single image. To overcome the effects of high speckle noise, local directional computing windows are designed according to the fringe directions. Then by calculating the gradients from the filtered image in directional windows, sign map and good skeletons can be determined robustly. Based on the sign map, single image phase-extracting methods such as quadrature transform can be improved. And based on skeletons, fringe phases can be obtained directly by normalization methods. Experiments show that this new method is robust and effective for extracting phase from a single ESPI fringe image.

Systematized water content calculation in cartilage using T1-mapping MR estimations: design and validation of a mathematical model.

PubMed

Shiguetomi-Medina, J M; Ramirez-Gl, J L; Stødkilde-Jørgensen, H; Møller-Madsen, B

2017-09-01

Up to 80 % of cartilage is water; the rest is collagen fibers and proteoglycans. Magnetic resonance (MR) T1-weighted measurements can be employed to calculate the water content of a tissue using T1 mapping. In this study, a method that translates T1 values into water content data was tested statistically. To develop a predictive equation, T1 values were obtained for tissue-mimicking gelatin samples. 1.5 T MRI was performed using inverse angle phase and an inverse sequence at 37 (±0.5) °C. Regions of interest were manually delineated and the mean T1 value was estimated in arbitrary units. Data were collected and modeled using linear regression. To validate the method, articular cartilage from six healthy pigs was used. The experiment was conducted in accordance with the Danish Animal Experiment Committee. Double measurements were performed for each animal. Ex vivo, all water in the tissue was extracted by lyophilization, thus allowing the volume of water to be measured. This was then compared with the predicted water content via Lin's concordance correlation coefficient at the 95 % confidence level. The mathematical model was highly significant when compared to a null model (p < 0.0001). 97.3 % of the variation in water content can be explained by absolute T1 values. Percentage water content could be predicted as 0.476 + (T1 value) × 0.000193 × 100 %. We found that there was 98 % concordance between the actual and predicted water contents. The results of this study demonstrate that MR data can be used to predict percentage water contents of cartilage samples. 3 (case-control study).

In-vitro Thermal Maps to Characterize Human Dental Enamel and Dentin.

PubMed

Lancaster, Paula; Brettle, David; Carmichael, Fiona; Clerehugh, Val

2017-01-01

The crown of a human tooth has an outer layer of highly-mineralized tissue called enamel, beneath which is dentin, a less-mineralized tissue which forms the bulk of the tooth-crown and root. The composition and structure of enamel and dentin are different, resulting in different thermal properties. This gives an opportunity to characterize enamel and dentin from their thermal properties and to visually present the findings as a thermal map. The thermal properties of demineralized enamel and dentin may also be sufficiently different from sound tissue to be seen on a thermal map, underpinning future thermal assessment of caries. The primary aim of this novel study was to produce a thermal map of a sound, human tooth-slice to visually characterize enamel and dentin. The secondary aim was to map a human tooth-slice with demineralized enamel and dentin to consider future diagnostic potential of thermal maps for caries-detection. Two human slices of teeth, one sound and one demineralized from a natural carious lesion, were cooled on ice, then transferred to a hotplate at 30°C where the rewarming-sequence was captured by an infra-red thermal camera. Calculation of thermal diffusivity and thermal conductivity was undertaken, and two methods of data-processing used customized software to produce thermal maps from the thermal characteristic-time-to-relaxation and heat-exchange. The two types of thermal maps characterized enamel and dentin. In addition, sound and demineralized enamel and dentin were distinguishable within both maps. This supports thermal assessment of caries and requires further investigation on a whole tooth.

The monophasic action potential upstroke: a means of characterizing local conduction.

PubMed

Levine, J H; Moore, E N; Kadish, A H; Guarnieri, T; Spear, J F

1986-11-01

The upstrokes of monophasic action potentials (MAPs) recorded with an extracellular pressure electrode were characterized in isolated canine tissue preparations in vitro. The characteristics of the MAP upstroke were compared with those of the local action potential foot as well as with the characteristics of approaching electrical activation during uniform and asynchronous conduction. The upstroke of the MAP was exponential during uniform conduction. The time constant of rise of the MAP upstroke (TMAP) correlated with that of the action potential foot (Tfoot): TMAP + 1.01 Tfoot + 0.50; r2 = .80. Furthermore, changes in Tfoot with alterations in cycle length were associated with similar changes in TMAP: Tfoot = 1.06 TMAP - 0.11; r2 = .78. In addition, TMAP and Tfoot both deviated from exponential during asynchronous activation; the inflections that developed in the MAP upstroke correlated in time with intracellular action potential upstrokes that were asynchronous in onset in these tissues. Finally, the field of view of the MAP was determined and was found to be dependent in part on tissue architecture and the space constant. Specifically, the field of view of the MAP was found to be greater parallel compared with transverse to fiber orientation (6.02 +/- 1.74 vs 3.03 +/- 1.10 mm; p less than .01). These data suggest that the MAP upstroke may be used to define and characterize local electrical activation. The relatively large field of view of the MAP suggests that this technique may be a sensitive means to record focal membrane phenomena in vivo.

Using an ultrasound elasticity microscope to map three-dimensional strain in a porcine cornea.

PubMed

Hollman, Kyle W; Shtein, Roni M; Tripathy, Sakya; Kim, Kang

2013-08-01

An ultrasound elasticity microscope was used to map 3-D strain volume in an ex vivo porcine cornea to illustrate its ability to measure the mechanical properties of this tissue. Mechanical properties of the cornea play an important role in its function and, therefore, also in ophthalmic diseases such as kerataconus and corneal ectasia. The ultrasound elasticity microscope combines a tightly focused high-frequency transducer with confocal scanning to produce high-quality speckle over the entire volume of tissue. This system and the analysis were able to generate volume maps of compressional strain in all three directions for porcine corneal tissue, more information than any previous study has reported. Strain volume maps indicated features of the cornea and mechanical behavior as expected. These results constitute a step toward better understanding of corneal mechanics and better treatment of corneal diseases. Copyright © 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Mapping of information and identification of construction waste at project life cycle

NASA Astrophysics Data System (ADS)

Wibowo, Mochamad Agung; Handayani, Naniek Utami; Nurdiana, Asri; Sholeh, Moh Nur; Pamungkas, Gita Silvia

2018-03-01

The development of construction project towards green construction is needed in order to improve the efficiency of construction projects. One that needs to be minimized is construction waste. Construction waste is waste generated from construction project activities, both solid waste and non solid waste. More specifically, the waste happens at every phase of the project life cycle. Project life cycle are the stage of idea, design, construction, and operation/maintenance. Each phase is managed by different stakeholders. Therefore it requires special handling from the involved stakeholders. The objective of the study is to map the information and identify the waste at each phase of the project life cycle. The purpose of mapping is to figure out the process of information and product flow and with its timeline. This mapping used Value Stream Mapping (VSM). Identification of waste was done by distributing questionnaire to respondents to know the waste according to owner, consultant planner, contractor, and supervisory consultant. The result of the study is the mapping of information flow and product flow at the phases of idea, design, construction, and operation/ maintenance.

Rotation number of integrable symplectic mappings of the plane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zolkin, Timofey; Nagaitsev, Sergei; Danilov, Viatcheslav

2017-04-11

Symplectic mappings are discrete-time analogs of Hamiltonian systems. They appear in many areas of physics, including, for example, accelerators, plasma, and fluids. Integrable mappings, a subclass of symplectic mappings, are equivalent to a Twist map, with a rotation number, constant along the phase trajectory. In this letter, we propose a succinct expression to determine the rotation number and present two examples. Similar to the period of the bounded motion in Hamiltonian systems, the rotation number is the most fundamental property of integrable maps and it provides a way to analyze the phase-space dynamics.

Comparison of prevalence estimation of Mycobacterium avium subsp. paratuberculosis infection by sampling slaughtered cattle with macroscopic lesions vs. systematic sampling.

PubMed

Elze, J; Liebler-Tenorio, E; Ziller, M; Köhler, H

2013-07-01

The objective of this study was to identify the most reliable approach for prevalence estimation of Mycobacterium avium ssp. paratuberculosis (MAP) infection in clinically healthy slaughtered cattle. Sampling of macroscopically suspect tissue was compared to systematic sampling. Specimens of ileum, jejunum, mesenteric and caecal lymph nodes were examined for MAP infection using bacterial microscopy, culture, histopathology and immunohistochemistry. MAP was found most frequently in caecal lymph nodes, but sampling more tissues optimized the detection rate. Examination by culture was most efficient while combination with histopathology increased the detection rate slightly. MAP was detected in 49/50 animals with macroscopic lesions representing 1.35% of the slaughtered cattle examined. Of 150 systematically sampled macroscopically non-suspect cows, 28.7% were infected with MAP. This indicates that the majority of MAP-positive cattle are slaughtered without evidence of macroscopic lesions and before clinical signs occur. For reliable prevalence estimation of MAP infection in slaughtered cattle, systematic random sampling is essential.

Phase mapping of radionuclide gated biventriculograms in patients with sustained ventricular tachycardia or Wolff-Parkinson-White syndrome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le Guludec, D.; Bourguignon, M.; Sebag, C.

1987-01-01

Accuracy of Fourier phase mapping of radionuclide gated biventriculograms in detecting the origin of abnormal ventricular activation was studied during ventricular tachycardia or preexcitation. Group I included six patients suffering from clinical recurrent VT; 3 gated blood pool studies were acquired for each patient: during sinus rhythm, right ventricular pacing, and induced sustained VT-Group II included seven patients with Wolff-Parkinson-White syndrome and recurrent paroxysmal tachycardia; 3 gated blood pool studies were acquired for each patient: during sinus rhythm, right atrial pacing and orthodromic reciprocating tachycardia. Each acquisition lasted 5 min, in 30 degrees-40 degrees left anterior oblique projection. In Groupmore » I, the Fourier phase mapping was consistent with QRS morphology and axis during VT (5/6), except in one patient with LV aneurysm and LBBB electrical pattern during VT. Origin of VT on phase mapping was located in the right ventricle (n = 2) or in left ventricle (n = 4), at the border of wall motion abnormalities each time they existed (5/6). In Group II, the phase advance correlated with the location of the accessory pathway determined by ECG and endocardial mapping (n = 6) and per-operative epicardial mapping (n = 1). Discrimination between anterior and posterior localization of paraseptal pathways and location of intermittent preexcitation was not possible. We conclude that Fourier phase mapping is an accurate method for locating the origin of VT and determining its etiology. It can help locate the site of ventricular preexcitation in patients with only one accessory pathway; its accuracy in locating multiple accessory pathways remains unknown.« less

On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners.

PubMed

Chen, Kevin T; Izquierdo-Garcia, David; Poynton, Clare B; Chonde, Daniel B; Catana, Ciprian

2017-03-01

To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps ("μ-maps") were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map ("PAC-map") generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soerensen, M.P.; Davidson, A.; Pedersen, N.F.

We use the method of cell-to-cell mapping to locate attractors, basins, and saddle nodes in the phase plane of a driven Josephson junction. The cell-mapping method is discussed in some detail, emphasizing its ability to provide a global view of the phase plane. Our computations confirm the existence of a previously reported interior crisis. In addition, we observe a boundary crisis for a small shift in one parameter. The cell-mapping method allows us to show both crises explicitly in the phase plane, at low computational cost.

MRI Estimates of Brain Iron Concentration in Normal Aging Using Quantitative Susceptibility Mapping

PubMed Central

Bilgic, Berkin; Pfefferbaum, Adolf; Rohlfing, Torsten; Sullivan, Edith V.; Adalsteinsson, Elfar

2011-01-01

Quantifying tissue iron concentration in vivo is instrumental for understanding the role of iron in physiology and in neurological diseases associated with abnormal iron distribution. Herein, we use recently-developed Quantitative Susceptibility Mapping (QSM) methodology to estimate the tissue magnetic susceptibility based on MRI signal phase. To investigate the effect of different regularization choices, we implement and compare ℓ1 and ℓ2 norm regularized QSM algorithms. These regularized approaches solve for the underlying magnetic susceptibility distribution, a sensitive measure of the tissue iron concentration, that gives rise to the observed signal phase. Regularized QSM methodology also involves a pre-processing step that removes, by dipole fitting, unwanted background phase effects due to bulk susceptibility variations between air and tissue and requires data acquisition only at a single field strength. For validation, performances of the two QSM methods were measured against published estimates of regional brain iron from postmortem and in vivo data. The in vivo comparison was based on data previously acquired using Field-Dependent Relaxation Rate Increase (FDRI), an estimate of MRI relaxivity enhancement due to increased main magnetic field strength, requiring data acquired at two different field strengths. The QSM analysis was based on susceptibility-weighted images acquired at 1.5T, whereas FDRI analysis used Multi-Shot Echo-Planar Spin Echo images collected at 1.5T and 3.0T. Both datasets were collected in the same healthy young and elderly adults. The in vivo estimates of regional iron concentration comported well with published postmortem measurements; both QSM approaches yielded the same rank ordering of iron concentration by brain structure, with the lowest in white matter and the highest in globus pallidus. Further validation was provided by comparison of the in vivo measurements, ℓ1-regularized QSM versus FDRI and ℓ2-regularized QSM versus FDRI, which again yielded perfect rank ordering of iron by brain structure. The final means of validation was to assess how well each in vivo method detected known age-related differences in regional iron concentrations measured in the same young and elderly healthy adults. Both QSM methods and FDRI were consistent in identifying higher iron concentrations in striatal and brain stem ROIs (i.e., caudate nucleus, putamen, globus pallidus, red nucleus, and substantia nigra) in the older than in the young group. The two QSM methods appeared more sensitive in detecting age differences in brain stem structures as they revealed differences of much higher statistical significance between the young and elderly groups than did FDRI. However, QSM values are influenced by factors such as the myelin content, whereas FDRI is a more specific indicator of iron content. Hence, FDRI demonstrated higher specificity to iron yet yielded noisier data despite longer scan times and lower spatial resolution than QSM. The robustness, practicality, and demonstrated ability of predicting the change in iron deposition in adult aging suggest that regularized QSM algorithms using single-field-strength data are possible alternatives to tissue iron estimation requiring two field strengths. PMID:21925274

Fluorescence spectroscopy using indocyanine green for lymph node mapping

NASA Astrophysics Data System (ADS)

Haj-Hosseini, Neda; Behm, Pascal; Shabo, Ivan; Wârdell, Karin

2014-02-01

The principles of cancer treatment has for years been radical resection of the primary tumor. In the oncologic surgeries where the affected cancer site is close to the lymphatic system, it is as important to detect the draining lymph nodes for metastasis (lymph node mapping). As a replacement for conventional radioactive labeling, indocyanine green (ICG) has shown successful results in lymph node mapping; however, most of the ICG fluorescence detection techniques developed are based on camera imaging. In this work, fluorescence spectroscopy using a fiber-optical probe was evaluated on a tissue-like ICG phantom with ICG concentrations of 6-64 μM and on breast tissue from five patients. Fiber-optical based spectroscopy was able to detect ICG fluorescence at low intensities; therefore, it is expected to increase the detection threshold of the conventional imaging systems when used intraoperatively. The probe allows spectral characterization of the fluorescence and navigation in the tissue as opposed to camera imaging which is limited to the view on the surface of the tissue.

Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure.

PubMed

Avram, Alexandru V; Sarlls, Joelle E; Barnett, Alan S; Özarslan, Evren; Thomas, Cibu; Irfanoglu, M Okan; Hutchinson, Elizabeth; Pierpaoli, Carlo; Basser, Peter J

2016-02-15

Diffusion tensor imaging (DTI) is the most widely used method for characterizing noninvasively structural and architectural features of brain tissues. However, the assumption of a Gaussian spin displacement distribution intrinsic to DTI weakens its ability to describe intricate tissue microanatomy. Consequently, the biological interpretation of microstructural parameters, such as fractional anisotropy or mean diffusivity, is often equivocal. We evaluate the clinical feasibility of assessing brain tissue microstructure with mean apparent propagator (MAP) MRI, a powerful analytical framework that efficiently measures the probability density function (PDF) of spin displacements and quantifies useful metrics of this PDF indicative of diffusion in complex microstructure (e.g., restrictions, multiple compartments). Rotation invariant and scalar parameters computed from the MAP show consistent variation across neuroanatomical brain regions and increased ability to differentiate tissues with distinct structural and architectural features compared with DTI-derived parameters. The return-to-origin probability (RTOP) appears to reflect cellularity and restrictions better than MD, while the non-Gaussianity (NG) measures diffusion heterogeneity by comprehensively quantifying the deviation between the spin displacement PDF and its Gaussian approximation. Both RTOP and NG can be decomposed in the local anatomical frame for reference determined by the orientation of the diffusion tensor and reveal additional information complementary to DTI. The propagator anisotropy (PA) shows high tissue contrast even in deep brain nuclei and cortical gray matter and is more uniform in white matter than the FA, which drops significantly in regions containing crossing fibers. Orientational profiles of the propagator computed analytically from the MAP MRI series coefficients allow separation of different fiber populations in regions of crossing white matter pathways, which in turn improves our ability to perform whole-brain fiber tractography. Reconstructions from subsampled data sets suggest that MAP MRI parameters can be computed from a relatively small number of DWIs acquired with high b-value and good signal-to-noise ratio in clinically achievable scan durations of less than 10min. The neuroanatomical consistency across healthy subjects and reproducibility in test-retest experiments of MAP MRI microstructural parameters further substantiate the robustness and clinical feasibility of this technique. The MAP MRI metrics could potentially provide more sensitive clinical biomarkers with increased pathophysiological specificity compared to microstructural measures derived using conventional diffusion MRI techniques. Published by Elsevier Inc.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation.

PubMed

Sekiguchi, Yuki; Hashimoto, Saki; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi

2017-09-01

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

Towards a minimally invasive sampling tool for high resolution tissue analytical mapping

NASA Astrophysics Data System (ADS)

Gottardi, R.

2015-09-01

Multiple spatial mapping techniques of biological tissues have been proposed over the years, but all present limitations either in terms of resolution, analytical capacity or invasiveness. Ren et al (2015 Nanotechnology 26 284001) propose in their most recent work the use of a picosecond infrared laser (PIRL) under conditions of ultrafast desorption by impulsive vibrational excitation (DIVE) to extract small amounts of cellular and molecular components, conserving their viability, structure and activity. The PIRL DIVE technique would then work as a nanobiopsy with minimal damage to the surrounding tissues, which could potentially be applied for high resolution local structural characterization of tissues in health and disease with the spatial limit determined by the laser focus.

Hybrid diversity method utilizing adaptive diversity function for recovering unknown aberrations in an optical system

NASA Technical Reports Server (NTRS)

Dean, Bruce H. (Inventor)

2009-01-01

A method of recovering unknown aberrations in an optical system includes collecting intensity data produced by the optical system, generating an initial estimate of a phase of the optical system, iteratively performing a phase retrieval on the intensity data to generate a phase estimate using an initial diversity function corresponding to the intensity data, generating a phase map from the phase retrieval phase estimate, decomposing the phase map to generate a decomposition vector, generating an updated diversity function by combining the initial diversity function with the decomposition vector, generating an updated estimate of the phase of the optical system by removing the initial diversity function from the phase map. The method may further include repeating the process beginning with iteratively performing a phase retrieval on the intensity data using the updated estimate of the phase of the optical system in place of the initial estimate of the phase of the optical system, and using the updated diversity function in place of the initial diversity function, until a predetermined convergence is achieved.

The Use of Concept Map as a Consolidation Phase Based STAD to Enhance Students’ Comprehension about Environmental Pollution

NASA Astrophysics Data System (ADS)

Nugroho, O. F.; Chandra, D. T.; Sanjaya, Y.; Pendidikan Indonesia, Universitas

2017-02-01

The purpose of this study was to improve students’ concept comprehension using concept map as a consolidation phase based STAD. This study was conducted by randomized control group pretest-posttest. Data was collected by using an instrument test to evaluate the effect of concept map as a consolidation phase based STAD on students’understanding about environmental pollution. Data was analyzed using normalized gain (n-gain) and independent t-test. The n-gain analysis shows the increased of students’s understanding about environmental pollution at experimental group arehigher than at the control group. The result of this study showed that students’ comprehension at the experimental class (0,53) higher compared to the control group (0,23). Whilst the t-test analysis shows that there is a significant effect of mapping concept as a consolidation phase based STAD towards students’ concept comprehension. It can be concluded that the implementation of mapping concept based STAD may improve the students’s understanding on science concept.

Radiofrequency Ablation, MR Thermometry, and High-Spatial-Resolution MR Parametric Imaging with a Single, Minimally Invasive Device.

PubMed

Ertürk, M Arcan; Sathyanarayana Hegde, Shashank; Bottomley, Paul A

2016-12-01

Purpose To develop and demonstrate in vitro and in vivo a single interventional magnetic resonance (MR)-active device that integrates the functions of precise identification of a tissue site with the delivery of radiofrequency (RF) energy for ablation, high-spatial-resolution thermal mapping to monitor thermal dose, and quantitative MR imaging relaxometry to document ablation-induced tissue changes for characterizing ablated tissue. Materials and Methods All animal studies were approved by the institutional animal care and use committee. A loopless MR imaging antenna composed of a tuned microcable either 0.8 or 2.2 mm in diameter with an extended central conductor was switched between a 3-T MR imaging unit and an RF power source to monitor and perform RF ablation in bovine muscle and human artery samples in vitro and in rabbits in vivo. High-spatial-resolution (250-300-μm) proton resonance frequency shift MR thermometry was interleaved with ablations. Quantitative spin-lattice (T1) and spin-spin (T2) relaxation time MR imaging mapping was performed before and after ablation. These maps were compared with findings from gross tissue examination of the region of ablated tissue after MR imaging. Results High-spatial-resolution MR imaging afforded temperature mapping in less than 8 seconds for monitoring ablation temperatures in excess of 85°C delivered by the same device. This produced irreversible thermal injury and necrosis. Quantitative MR imaging relaxation time maps demonstrated up to a twofold variation in mean regional T1 and T2 after ablation versus before ablation. Conclusion A simple, integrated, minimally invasive interventional probe that provides image-guided therapy delivery, thermal mapping of dose, and detection of ablation-associated MR imaging parametric changes was developed and demonstrated. With this single-device approach, coupling-related safety concerns associated with multiple conductor approaches were avoided. © RSNA, 2016 Online supplemental material is available for this article.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-01

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

Structure-Preserving Color Normalization and Sparse Stain Separation for Histological Images.

PubMed

Vahadane, Abhishek; Peng, Tingying; Sethi, Amit; Albarqouni, Shadi; Wang, Lichao; Baust, Maximilian; Steiger, Katja; Schlitter, Anna Melissa; Esposito, Irene; Navab, Nassir

2016-08-01

Staining and scanning of tissue samples for microscopic examination is fraught with undesirable color variations arising from differences in raw materials and manufacturing techniques of stain vendors, staining protocols of labs, and color responses of digital scanners. When comparing tissue samples, color normalization and stain separation of the tissue images can be helpful for both pathologists and software. Techniques that are used for natural images fail to utilize structural properties of stained tissue samples and produce undesirable color distortions. The stain concentration cannot be negative. Tissue samples are stained with only a few stains and most tissue regions are characterized by at most one effective stain. We model these physical phenomena that define the tissue structure by first decomposing images in an unsupervised manner into stain density maps that are sparse and non-negative. For a given image, we combine its stain density maps with stain color basis of a pathologist-preferred target image, thus altering only its color while preserving its structure described by the maps. Stain density correlation with ground truth and preference by pathologists were higher for images normalized using our method when compared to other alternatives. We also propose a computationally faster extension of this technique for large whole-slide images that selects an appropriate patch sample instead of using the entire image to compute the stain color basis.

18F-FLT uptake kinetics in head and neck squamous cell carcinoma: a PET imaging study.

PubMed

Liu, Dan; Chalkidou, Anastasia; Landau, David B; Marsden, Paul K; Fenwick, John D

2014-04-01

To analyze the kinetics of 3(')-deoxy-3(')-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels. Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k3-2tiss and k5 of the two- and three-tissue models were studied alongside the flux parameters KFLT- 2tiss and KFLT of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion ("EM-BIC clustering") was used to distil the information from noisy parametric images. Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps of KFLT and KFLT- 2tiss are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for KFLT- 2tiss, 0.64 for KFLT). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k3-2tiss vs KFLT- 2tiss and r = 0.68 for k5 vs KFLT); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels--on average 5.8, 3.5, 3.4, and 1.4 for KFLT- 2tiss, KFLT, k3-2tiss, and k5. This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk5 and k3-2tiss, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust-either by constraining other model parameters or modifying dynamic imaging protocols. © 2014 American Association of Physicists in Medicine.

Elasticity mapping of murine abdominal organs in vivo using harmonic motion imaging (HMI)

NASA Astrophysics Data System (ADS)

Payen, Thomas; Palermo, Carmine F.; Sastra, Stephen A.; Chen, Hong; Han, Yang; Olive, Kenneth P.; Konofagou, Elisa E.

2016-08-01

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5 MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50 Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8 MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young’s moduli measured by rheometry compression testing. HMI was capable of providing reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. The HMI displacement amplitude was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo, thus providing a potentially critical tool to assess pathologies affecting organ elasticity.

Towards optical spectroscopic anatomical mapping (OSAM) for lesion validation in cardiac tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Singh-Moon, Rajinder P.; Zaryab, Mohammad; Hendon, Christine P.

2017-02-01

Electroanatomical mapping (EAM) is an invaluable tool for guiding cardiac radiofrequency ablation (RFA) therapy. The principle roles of EAM is the identification of candidate ablation sites by detecting regions of abnormal electrogram activity and lesion validation subsequent to RF energy delivery. However, incomplete lesions may present interim electrical inactivity similar to effective treatment in the acute setting, despite efforts to reveal them with pacing or drugs, such as adenosine. Studies report that the misidentification and recovery of such lesions is a leading cause of arrhythmia recurrence and repeat procedures. In previous work, we demonstrated spectroscopic characterization of cardiac tissues using a fiber optic-integrated RF ablation catheter. In this work, we introduce OSAM (optical spectroscopic anatomical mapping), the application of this spectroscopic technique to obtain 2-dimensional biodistribution maps. We demonstrate its diagnostic potential as an auxiliary method for lesion validation in treated swine preparations. Endocardial lesion sets were created on fresh swine cardiac samples using a commercial RFA system. An optically-integrated catheter console fabricated in-house was used for measurement of tissue optical spectra between 600-1000nm. Three dimensional, Spatio-spectral datasets were generated by raster scanning of the optical catheter across the treated sample surface in the presence of whole blood. Tissue optical parameters were recovered at each spatial position using an inverse Monte Carlo method. OSAM biodistribution maps showed stark correspondence with gross examination of tetrazolium chloride stained tissue specimens. Specifically, we demonstrate the ability of OSAM to readily distinguish between shallow and deeper lesions, a limitation faced by current EAM techniques. These results showcase the OSAMs potential for lesion validation strategies for the treatment of cardiac arrhythmias.

Elasticity mapping of murine abdominal organs in vivo using Harmonic Motion Imaging (HMI)

PubMed Central

Payen, Thomas; Palermo, Carmine F.; Sastra, Steve; Chen, Hong; Han, Yang; Olive, Kenneth P.; Konofagou, Elisa E.

2016-01-01

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5-MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50-Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8-MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young’s moduli measured by rheometry compression tests. HMI was able to provide reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. HMI displacement was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo providing a crucial tool to understand pathologies affecting organ elasticity. PMID:27401609

Elasticity mapping of murine abdominal organs in vivo using harmonic motion imaging (HMI).

PubMed

Payen, Thomas; Palermo, Carmine F; Sastra, Stephen A; Chen, Hong; Han, Yang; Olive, Kenneth P; Konofagou, Elisa E

2016-08-07

Recently, ultrasonic imaging of soft tissue mechanics has been increasingly studied to image otherwise undetectable pathologies. However, many underlying mechanisms of tissue stiffening remain unknown, requiring small animal studies and adapted elasticity mapping techniques. Harmonic motion imaging (HMI) assesses tissue viscoelasticity by inducing localized oscillation from a periodic acoustic radiation force. The objective of this study was to evaluate the feasibility of HMI for in vivo elasticity mapping of abdominal organs in small animals. Pathological cases, i.e. chronic pancreatitis and pancreatic cancer, were also studied in vivo to assess the capability of HMI for detection of the change in mechanical properties. A 4.5 MHz focused ultrasound transducer (FUS) generated an amplitude-modulated beam resulting in 50 Hz harmonic tissue oscillations at its focus. Axial tissue displacement was estimated using 1D-cross-correlation of RF signals acquired with a 7.8 MHz diagnostic transducer confocally aligned with the FUS. In vitro results in canine liver and kidney showed the correlation between HMI displacement and Young's moduli measured by rheometry compression testing. HMI was capable of providing reproducible elasticity maps of the mouse abdominal region in vivo allowing the identification of, from stiffest to softest, the murine kidney, pancreas, liver, and spleen. Finally, pancreata affected by pancreatitis and pancreatic cancer showed HMI displacements 1.7 and 2.2 times lower than in the control case, respectively, indicating higher stiffness. The HMI displacement amplitude was correlated with the extent of fibrosis as well as detecting the very onset of stiffening even before fibrosis could be detected on H&E. This work shows that HMI can produce reliable elasticity maps of mouse abdominal region in vivo, thus providing a potentially critical tool to assess pathologies affecting organ elasticity.

Phased Array Ultrasonic Sound Field Mapping in Cast Austenitic Stainless Steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Susan L.; Prowant, Matthew S.; Cinson, Anthony D.

2014-05-31

This study maps the phased array-generated acoustic sound fields through three types of CASS microstructure in four specimens to quantitatively assess the beam formation effectiveness in these materials.

Concomitant administration of nitrous oxide and remifentanil reduces oral tissue blood flow without decreasing blood pressure during sevoflurane anesthesia in rabbits.

PubMed

Kasahara, Masataka; Ichinohe, Tatsuya; Okamoto, Sota; Okada, Reina; Kanbe, Hiroaki; Matsuura, Nobuyuki

2015-06-01

To determine whether continuous administration of nitrous oxide and remifentanil—either alone or together—alters blood flow in oral tissues during sevoflurane anesthesia. Eight male tracheotomized Japanese white rabbits were anesthetized with sevoflurane under mechanical ventilation. Heart rate (HR), systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP), common carotid arterial blood flow (CCBF), tongue mucosal blood flow (TMBF), mandibular bone marrow blood flow (BBF), masseter muscle blood flow (MBF), upper alveolar tissue blood flow (UBF), and lower alveolar tissue blood flow (LBF) were recorded in the absence of all test agents and after administration of the test agents (50 % nitrous oxide, 0.4 μg/kg/min remifentanil, and their combination) for 20 min. Nitrous oxide increased SBP, DBP, MAP, CCBF, BBF, MBF, UBF, and LBF relative to baseline values but did not affect HR or TMBF. Remifentanil decreased all hemodynamic variables except DBP. Combined administration of nitrous oxide and remifentanil recovered SBP, DBP, MAP, and CCBF to baseline levels, but HR and oral tissue blood flow remained lower than control values. Our findings suggest that concomitant administration of nitrous oxide and remifentanil reduces blood flow in oral tissues without decreasing blood pressure during sevoflurane anesthesia in rabbits.

Three-dimensional nanomechanical mapping of amorphous and crystalline phase transitions in phase-change materials.

PubMed

Grishin, Ilja; Huey, Bryan D; Kolosov, Oleg V

2013-11-13

The nanostructure of micrometer-sized domains (bits) in phase-change materials (PCM) that undergo switching between amorphous and crystalline phases plays a key role in the performance of optical PCM-based memories. Here, we explore the dynamics of such phase transitions by mapping PCM nanostructures in three dimensions with nanoscale resolution by combining precision Ar ion beam cross-sectional polishing and nanomechanical ultrasonic force microscopy (UFM) mapping. Surface and bulk phase changes of laser written submicrometer to micrometer sized amorphous-to-crystalline (SET) and crystalline-to-amorphous (RESET) bits in chalcogenide Ge2Sb2Te5 PCM are observed with 10-20 nm lateral and 4 nm depth resolution. UFM mapping shows that the Young's moduli of crystalline SET bits exceed the moduli of amorphous areas by 11 ± 2%, with crystalline content extending from a few nanometers to 50 nm in depth depending on the energy of the switching pulses. The RESET bits written with 50 ps pulses reveal shallower depth penetration and show 30-50 nm lateral and few nanometer vertical wavelike topography that is anticorrelated with the elastic modulus distribution. Reverse switching of amorphous RESET bits results in the full recovery of subsurface nanomechanical properties accompanied with only partial topography recovery, resulting in surface corrugations attributed to quenching. This precision sectioning and nanomechanical mapping approach could be applicable to a wide range of amorphous, nanocrystalline, and glass-forming materials for 3D nanomechanical mapping of amorphous-crystalline transitions.

A model-based 3D phase unwrapping algorithm using Gegenbauer polynomials.

PubMed

Langley, Jason; Zhao, Qun

2009-09-07

The application of a two-dimensional (2D) phase unwrapping algorithm to a three-dimensional (3D) phase map may result in an unwrapped phase map that is discontinuous in the direction normal to the unwrapped plane. This work investigates the problem of phase unwrapping for 3D phase maps. The phase map is modeled as a product of three one-dimensional Gegenbauer polynomials. The orthogonality of Gegenbauer polynomials and their derivatives on the interval [-1, 1] are exploited to calculate the expansion coefficients. The algorithm was implemented using two well-known Gegenbauer polynomials: Chebyshev polynomials of the first kind and Legendre polynomials. Both implementations of the phase unwrapping algorithm were tested on 3D datasets acquired from a magnetic resonance imaging (MRI) scanner. The first dataset was acquired from a homogeneous spherical phantom. The second dataset was acquired using the same spherical phantom but magnetic field inhomogeneities were introduced by an external coil placed adjacent to the phantom, which provided an additional burden to the phase unwrapping algorithm. Then Gaussian noise was added to generate a low signal-to-noise ratio dataset. The third dataset was acquired from the brain of a human volunteer. The results showed that Chebyshev implementation and the Legendre implementation of the phase unwrapping algorithm give similar results on the 3D datasets. Both implementations of the phase unwrapping algorithm compare well to PRELUDE 3D, 3D phase unwrapping software well recognized for functional MRI.

Vibration of the organ of Corti within the cochlear apex in mice

PubMed Central

Gao, Simon S.; Wang, Rosalie; Raphael, Patrick D.; Moayedi, Yalda; Groves, Andrew K.; Zuo, Jian; Applegate, Brian E.

2014-01-01

The tonotopic map of the mammalian cochlea is commonly thought to be determined by the passive mechanical properties of the basilar membrane. The other tissues and cells that make up the organ of Corti also have passive mechanical properties; however, their roles are less well understood. In addition, active forces produced by outer hair cells (OHCs) enhance the vibration of the basilar membrane, termed cochlear amplification. Here, we studied how these biomechanical components interact using optical coherence tomography, which permits vibratory measurements within tissue. We measured not only classical basilar membrane tuning curves, but also vibratory responses from the rest of the organ of Corti within the mouse cochlear apex in vivo. As expected, basilar membrane tuning was sharp in live mice and broad in dead mice. Interestingly, the vibratory response of the region lateral to the OHCs, the “lateral compartment,” demonstrated frequency-dependent phase differences relative to the basilar membrane. This was sharply tuned in both live and dead mice. We then measured basilar membrane and lateral compartment vibration in transgenic mice with targeted alterations in cochlear mechanics. Prestin499/499, Prestin−/−, and TectaC1509G/C1509G mice demonstrated no cochlear amplification but maintained the lateral compartment phase difference. In contrast, SfswapTg/Tg mice maintained cochlear amplification but did not demonstrate the lateral compartment phase difference. These data indicate that the organ of Corti has complex micromechanical vibratory characteristics, with passive, yet sharply tuned, vibratory characteristics associated with the supporting cells. These characteristics may tune OHC force generation to produce the sharp frequency selectivity of mammalian hearing. PMID:24920025

Population differences in the rate of proliferation of international HapMap cell lines.

PubMed

Stark, Amy L; Zhang, Wei; Zhou, Tong; O'Donnell, Peter H; Beiswanger, Christine M; Huang, R Stephanie; Cox, Nancy J; Dolan, M Eileen

2010-12-10

The International HapMap Project is a resource for researchers containing genotype, sequencing, and expression information for EBV-transformed lymphoblastoid cell lines derived from populations across the world. The expansion of the HapMap beyond the four initial populations of Phase 2, referred to as Phase 3, has increased the sample number and ethnic diversity available for investigation. However, differences in the rate of cellular proliferation between the populations can serve as confounders in phenotype-genotype studies using these cell lines. Within the Phase 2 populations, the JPT and CHB cell lines grow faster (p < 0.0001) than the CEU or YRI cell lines. Phase 3 YRI cell lines grow significantly slower than Phase 2 YRI lines (p < 0.0001), with no widespread genetic differences based on common SNPs. In addition, we found significant growth differences between the cell lines in the Phase 2 ASN populations and the Han Chinese from the Denver metropolitan area panel in Phase 3 (p < 0.0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration. Copyright © 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Phase gradient imaging for positive contrast generation to superparamagnetic iron oxide nanoparticle-labeled targets in magnetic resonance imaging.

PubMed

Zhu, Haitao; Demachi, Kazuyuki; Sekino, Masaki

2011-09-01

Positive contrast imaging methods produce enhanced signal at large magnetic field gradient in magnetic resonance imaging. Several postprocessing algorithms, such as susceptibility gradient mapping and phase gradient mapping methods, have been applied for positive contrast generation to detect the cells targeted by superparamagnetic iron oxide nanoparticles. In the phase gradient mapping methods, smoothness condition has to be satisfied to keep the phase gradient unwrapped. Moreover, there has been no discussion about the truncation artifact associated with the algorithm of differentiation that is performed in k-space by the multiplication with frequency value. In this work, phase gradient methods are discussed by considering the wrapping problem when the smoothness condition is not satisfied. A region-growing unwrapping algorithm is used in the phase gradient image to solve the problem. In order to reduce the truncation artifact, a cosine function is multiplied in the k-space to eliminate the abrupt change at the boundaries. Simulation, phantom and in vivo experimental results demonstrate that the modified phase gradient mapping methods may produce improved positive contrast effects by reducing truncation or wrapping artifacts. Copyright © 2011 Elsevier Inc. All rights reserved.

Energy content of stormtime ring current from phase space mapping simulations

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, Larry R.

1993-01-01

We perform a phase space mapping study to estimate the enhancement in energy content that results from stormtime particle transport in the equatorial magnetosphere. Our pre-storm phase space distribution is based on a steady-state transport model. Using results from guiding-center simulations of ion transport during model storms having main phases of 3 hr, 6 hr, and 12 hr, we map phase space distributions of ring current protons from the pre-storm distribution in accordance with Liouville's theorem. We find that transport can account for the entire ten to twenty-fold increase in magnetospheric particle energy content typical of a major storm if a realistic stormtime enhancement of the phase space density f is imposed at the nightside tail plasma sheet (represented by an enhancement of f at the neutral line in our model).

Analysis of a new phase and height algorithm in phase measurement profilometry

NASA Astrophysics Data System (ADS)

Bian, Xintian; Zuo, Fen; Cheng, Ju

2018-04-01

Traditional phase measurement profilometry adopts divergent illumination to obtain the height distribution of a measured object accurately. However, the mapping relation between reference plane coordinates and phase distribution must be calculated before measurement. Data are then stored in a computer in the form of a data sheet for standby applications. This study improved the distribution of projected fringes and deducted the phase-height mapping algorithm when the two pupils of the projection and imaging systems are of unequal heights and when the projection and imaging axes are on different planes. With the algorithm, calculating the mapping relation between reference plane coordinates and phase distribution prior to measurement is unnecessary. Thus, the measurement process is simplified, and the construction of an experimental system is made easy. Computer simulation and experimental results confirm the effectiveness of the method.

Improved Topographic Mapping Through Multi-Baseline SAR Interferometry with MAP Estimation

NASA Astrophysics Data System (ADS)

Dong, Yuting; Jiang, Houjun; Zhang, Lu; Liao, Mingsheng; Shi, Xuguo

2015-05-01

There is an inherent contradiction between the sensitivity of height measurement and the accuracy of phase unwrapping for SAR interferometry (InSAR) over rough terrain. This contradiction can be resolved by multi-baseline InSAR analysis, which exploits multiple phase observations with different normal baselines to improve phase unwrapping accuracy, or even avoid phase unwrapping. In this paper we propose a maximum a posteriori (MAP) estimation method assisted by SRTM DEM data for multi-baseline InSAR topographic mapping. Based on our method, a data processing flow is established and applied in processing multi-baseline ALOS/PALSAR dataset. The accuracy of resultant DEMs is evaluated by using a standard Chinese national DEM of scale 1:10,000 as reference. The results show that multi-baseline InSAR can improve DEM accuracy compared with single-baseline case. It is noteworthy that phase unwrapping is avoided and the quality of multi-baseline InSAR DEM can meet the DTED-2 standard.

Qualitative and quantitative mass spectrometry imaging of drugs and metabolites in tissue at therapeutic levels.

PubMed

Sun, Na; Walch, Axel

2013-08-01

Mass spectrometry imaging (MSI) is a rapidly evolving technology that yields qualitative and quantitative distribution maps of small pharmaceutical-active molecules and their metabolites in tissue sections in situ. The simplicity, high sensitivity and ability to provide comprehensive spatial distribution maps of different classes of biomolecules make MSI a valuable tool to complement histopathology for diagnostics and biomarker discovery. In this review, qualitative and quantitative MSI of drugs and metabolites in tissue at therapeutic levels are discussed and the impact of this technique in drug discovery and clinical research is highlighted.

Prostate tissue ablation with MRI guided transurethral therapeutic ultrasound and intraoperative assessment of the integrity of the neurovascular bundle

NASA Astrophysics Data System (ADS)

Sammet, Steffen; Partanen, Ari; Yousuf, Ambereen; Wardrip, Craig; Niekrasz, Marek; Antic, Tatjana; Razmaria, Aria; Sokka, Sham; Karczmar, Gregory; Oto, Aytekin

2017-03-01

OBJECTIVES: Evaluation of the precision of prostate tissue ablation with MRI guided therapeuticultrasound by intraoperative objective assessment of the neurovascular bundle in canines in-vivo. METHODS: In this ongoing IACUC approved study, eight male canines were scanned in a clinical 3T Achieva MRI scanner (Philips) before, during, and after ultrasound therapy with a prototype MR-guided ultrasound therapy system (Philips). The system includes a therapy console to plan treatment, to calculate real-time temperature maps, and to control ultrasound exposures with temperature feedback. Atransurethral ultrasound applicator with eight transducer elements was used to ablate canine prostate tissue in-vivo. Ablated prostate tissue volumes were compared to the prescribed target volumes to evaluate technical effectiveness. The ablated volumes determined by MRI (T1, T2, diffusion, dynamic contrast enhanced and 240 CEM43 thermal dose maps) were compared to H&E stained histological slides afterprostatectomy. Potential nerve damage of the neurovascular bundle was objectively assessed intraoperativelyduring prostatectomy with a CaverMap Surgical Aid nerve stimulator (Blue Torch Medical Technologies). RESULTS: Transurethral MRI -guided ultrasound therapy can effectively ablate canine prostate tissue invivo. Coronal MR-imaging confirmed the correct placement of the HIFU transducer. MRI temperature maps were acquired during HIFU treatment, and subsequently used for calculating thermal dose. Prescribed target volumes corresponded to the 240 CEM43 thermal dose maps during HIFU treatment in all canines. Ablated volumes on high resolution anatomical, diffusion weighted, and contrast enhanced MR images matched corresponding histological slides after prostatectomy. MRI guidance with realtime temperature monitoring showed no damage to surrounding tissues, especially to the neurovascular bundle (assessed intra-operatively with a nerve stimulator) or to the rectum wall. CONCLUSIONS: Our study demonstrates the effectiveness and precision of transurethral ultrasound ablation of prostatic tissue in canines with MRI monitoring and guidance. The canine prostate is an excellent model for the human prostate with similar anatomical characteristics and diseases. MRI guidance with real-time, intraoperative temperature monitoring reduces the risk of damaging critical surrounding anatomical structures in ultrasound therapy of the prostate.

Tissue Cancellation in Dual Energy Mammography Using a Calibration Phantom Customized for Direct Mapping.

PubMed

Han, Seokmin; Kang, Dong-Goo

2014-01-01

An easily implementable tissue cancellation method for dual energy mammography is proposed to reduce anatomical noise and enhance lesion visibility. For dual energy calibration, the images of an imaging object are directly mapped onto the images of a customized calibration phantom. Each pixel pair of the low and high energy images of the imaging object was compared to pixel pairs of the low and high energy images of the calibration phantom. The correspondence was measured by absolute difference between the pixel values of imaged object and those of the calibration phantom. Then the closest pixel pair of the calibration phantom images is marked and selected. After the calibration using direct mapping, the regions with lesion yielded different thickness from the background tissues. Taking advantage of the different thickness, the visibility of cancerous lesions was enhanced with increased contrast-to-noise ratio, depending on the size of lesion and breast thickness. However, some tissues near the edge of imaged object still remained after tissue cancellation. These remaining residuals seem to occur due to the heel effect, scattering, nonparallel X-ray beam geometry and Poisson distribution of photons. To improve its performance further, scattering and the heel effect should be compensated.

Mapping the vascular anatomy of free transplanted soft tissue flaps with computed tomographic angiography.

PubMed

Rozen, Warren M; Chubb, Daniel; Ashton, Mark W; Webster, Howard R

2012-05-01

The use of advanced imaging technologies such as computed tomographic angiography (CTA) has opened the door to the analysis of microvascular anatomy not previously demonstrable with prior imaging techniques. While CTA has been used to evaluate the vascular anatomy of donor body regions in the planning of harvest of tissue for free flap transfer, the use of CTA to evaluate tissues after tissue transplantation has not been demonstrated. The current study aimed to explore whether vascular anatomy was able to highlight CTA within transferred flaps. The arterial and venous anatomy of a transferred deep inferior epigastric artery (DIEA) perforator (DIEP) flap was explored postoperatively with the use of CTA. Intra-flap vasculature was mapped and recorded qualitatively. Postoperative CTA is able to highlight the vascular pedicle of a transferred free flap, highlight the course of individual perforators supplying the flap, and map the zones of lesser perfusion by the source pedicle. The current study has demonstrated that CTA may be of value in identifying vascular anatomy within transferred tissue, as a guide to evaluate flap perfusion and planning further surgery involving the flap. © Springer-Verlag 2011

MAP3K19 Is a Novel Regulator of TGF-β Signaling That Impacts Bleomycin-Induced Lung Injury and Pulmonary Fibrosis

PubMed Central

Franz-Bacon, Karin; DiTirro, Danielle N.; Ly, Tai Wei; Bacon, Kevin B.

2016-01-01

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating disease for which two medications, pirfenidone and nintedanib, have only recently been approved for treatment. The cytokine TGF-β has been shown to be a central mediator in the disease process. We investigated the role of a novel kinase, MAP3K19, upregulated in IPF tissue, in TGF-β-induced signal transduction and in bleomycin-induced pulmonary fibrosis. MAP3K19 has a very limited tissue expression, restricted primarily to the lungs and trachea. In pulmonary tissue, expression was predominantly localized to alveolar and interstitial macrophages, bronchial epithelial cells and type II pneumocytes of the epithelium. MAP3K19 was also found to be overexpressed in bronchoalveolar lavage macrophages from IPF patients compared to normal patients. Treatment of A549 or THP-1 cells with either MAP3K19 siRNA or a highly potent and specific inhibitor reduced phospho-Smad2 & 3 nuclear translocation following TGF-β stimulation. TGF-β-induced gene transcription was also strongly inhibited by both the MAP3K19 inhibitor and nintedanib, whereas pirfenidone had a much less pronounced effect. In combination, the MAP3K19 inhibitor appeared to act synergistically with either pirfenidone or nintedanib, at the level of target gene transcription or protein production. Finally, in an animal model of IPF, inhibition of MAP3K19 strongly attenuated bleomycin-induced pulmonary fibrosis when administered either prophylactically ortherapeutically. In summary, these results strongly suggest that inhibition of MAP3K19 may have a beneficial therapeutic effect in the treatment of IPF and represents a novel strategy to target this disease. PMID:27144281

MAP3K19 Is a Novel Regulator of TGF-β Signaling That Impacts Bleomycin-Induced Lung Injury and Pulmonary Fibrosis.

PubMed

Boehme, Stefen A; Franz-Bacon, Karin; DiTirro, Danielle N; Ly, Tai Wei; Bacon, Kevin B

2016-01-01

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating disease for which two medications, pirfenidone and nintedanib, have only recently been approved for treatment. The cytokine TGF-β has been shown to be a central mediator in the disease process. We investigated the role of a novel kinase, MAP3K19, upregulated in IPF tissue, in TGF-β-induced signal transduction and in bleomycin-induced pulmonary fibrosis. MAP3K19 has a very limited tissue expression, restricted primarily to the lungs and trachea. In pulmonary tissue, expression was predominantly localized to alveolar and interstitial macrophages, bronchial epithelial cells and type II pneumocytes of the epithelium. MAP3K19 was also found to be overexpressed in bronchoalveolar lavage macrophages from IPF patients compared to normal patients. Treatment of A549 or THP-1 cells with either MAP3K19 siRNA or a highly potent and specific inhibitor reduced phospho-Smad2 & 3 nuclear translocation following TGF-β stimulation. TGF-β-induced gene transcription was also strongly inhibited by both the MAP3K19 inhibitor and nintedanib, whereas pirfenidone had a much less pronounced effect. In combination, the MAP3K19 inhibitor appeared to act synergistically with either pirfenidone or nintedanib, at the level of target gene transcription or protein production. Finally, in an animal model of IPF, inhibition of MAP3K19 strongly attenuated bleomycin-induced pulmonary fibrosis when administered either prophylactically ortherapeutically. In summary, these results strongly suggest that inhibition of MAP3K19 may have a beneficial therapeutic effect in the treatment of IPF and represents a novel strategy to target this disease.

Determination of the Elasticity of Breast Tissue during the Menstrual Cycle Using Real-Time Shear Wave Elastography.

PubMed

Li, Xiang; Wang, Jian-Nan; Fan, Zhi-Ying; Kang, Shu; Liu, Yan-Jun; Zhang, Yi-Xia; Wang, Xue-Mei

2015-12-01

We examined breast tissue elasticity during the menstrual cycle using real-time shear wave elastography (RT-SWE), a recent technique developed for soft tissue imaging. Written informed consent for RT-SWE was obtained from all eligible patients, who were healthy women aged between 19 and 52 y. Young's moduli of the breast tissue in the early follicular, late phase and luteal phase were compared. There were no significant differences in the mean, maximum and minimum elasticity values (Emean, Emax and Emin) and standard deviation (ESD). RT-SWE of glandular tissue revealed that ESD was increased in the early follicular phase compared with the luteal phase. Means ± SD of Emin, Emax and Emean in glandular tissue were 5.174 ± 2.138, 8.308 ± 3.166 and 6.593 ± 2.510, respectively, and in adipose tissue, 3.589 ± 2.083, 6.733 ± 3.522 and 4.857 ± 2.564, respectively. There were no significant differences in stiffness between glandular and adipose tissues throughout the menstrual cycle, but glandular tissue stiffness was lower in the luteal phase than in the early follicular phase. On the basis of these observations in normal healthy women, we believe we have obtained sufficient information to establish the baseline changes in human breast elasticity during the menstrual cycle. In the future, we intend to compare the elasticity values of healthy breast tissue with those of breast tissue affected by various pathologies. Our results reveal the significant potential of RT-SWE in the rapid and non-invasive clinical diagnosis of breast diseases, such as breast cancers. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Mechanical perturbation control of cardiac alternans

NASA Astrophysics Data System (ADS)

Hazim, Azzam; Belhamadia, Youssef; Dubljevic, Stevan

2018-05-01

Cardiac alternans is a disturbance in heart rhythm that is linked to the onset of lethal cardiac arrhythmias. Mechanical perturbation control has been recently used to suppress alternans in cardiac tissue of relevant size. In this control strategy, cardiac tissue mechanics are perturbed via active tension generated by the heart's electrical activity, which alters the tissue's electric wave profile through mechanoelectric coupling. We analyze the effects of mechanical perturbation on the dynamics of a map model that couples the membrane voltage and active tension systems at the cellular level. Therefore, a two-dimensional iterative map of the heart beat-to-beat dynamics is introduced, and a stability analysis of the system of coupled maps is performed in the presence of a mechanical perturbation algorithm. To this end, a bidirectional coupling between the membrane voltage and active tension systems in a single cardiac cell is provided, and a discrete form of the proposed control algorithm, that can be incorporated in the coupled maps, is derived. In addition, a realistic electromechanical model of cardiac tissue is employed to explore the feasibility of suppressing alternans at cellular and tissue levels. Electrical activity is represented in two detailed ionic models, the Luo-Rudy 1 and the Fox models, while two active contractile tension models, namely a smooth variant of the Nash-Panfilov model and the Niederer-Hunter-Smith model, are used to represent mechanical activity in the heart. The Mooney-Rivlin passive elasticity model is employed to describe passive mechanical behavior of the myocardium.

Enhanced Positive-Contrast Visualization of Paramagnetic Contrast Agents Using Phase Images

PubMed Central

Mills, Parker H.; Ahrens, Eric T.

2009-01-01

Iron oxide–based MRI contrast agents are increasingly being used to noninvasively track cells, target molecular epitopes, and monitor gene expression in vivo. Detecting regions of contrast agent accumulation can be challenging if resulting contrast is subtle relative to endogenous tissue hypointensities. A postprocessing method is presented that yields enhanced positive-contrast images from the phase map associated with T2*-weighted MRI data. As examples, the method was applied to an agarose gel phantom doped with superparamagnetic iron-oxide nanoparticles and in vivo and ex vivo mouse brains inoculated with recombinant viruses delivering transgenes that induce overexpression of paramagnetic ferritin. Overall, this approach generates images that exhibit a 1- to 8-fold improvement in contrast-to-noise ratio in regions where paramagnetic agents are present compared to conventional magnitude images. This approach can be used in conjunction with conventional T2* pulse sequences, requires no prescans or increased scan time, and can be applied retrospectively to previously acquired data. PMID:19780169

Multiscale biomechanical responses of adapted bone-periodontal ligament-tooth fibrous joints

PubMed Central

Jang, Andrew T.; Merkle, Arno; Fahey, Kevin; Gansky, Stuart A.; Ho, Sunita P.

2015-01-01

Reduced functional loads cause adaptations in organs. In this study, temporal adaptations of bone-ligament-tooth fibrous joints to reduced functional loads were mapped using a holistic approach. Systematic studies were performed to evaluate organ-level and tissue-level adaptations in specimens harvested periodically from rats given powder food for 6 months (N = 60 over 8,12,16,20, and 24 weeks). Bone-periodontal ligament (PDL)-tooth fibrous joint adaptation was evaluated by comparing changes in joint stiffness with changes in functional space between the tooth and alveolar bony socket. Adaptations in tissues included mapping changes in the PDL and bone architecture as observed from collagen birefringence, bone hardness and volume fraction in rats fed soft foods (soft diet, SD) compared to those fed hard pellets as a routine diet (hard diet, HD). In situ biomechanical testing on harvested fibrous joints revealed increased stiffness in SD groups (SD:239-605 N/mm) (p<0.05) at 8 and 12 weeks. Increased joint stiffness in early development phase was due to decreased functional space (at 8wks change in functional space was −33 µm, at 12wks change in functional space was −30 µm) and shifts in tissue quality as highlighted by birefringence, architecture and hardness. These physical changes were not observed in joints that were well into function, that is, in rodents older than 12 weeks of age. Significant adaptations in older groups were highlighted by shifts in bone growth (bone volume fraction 24wks: Δ-0.06) and bone hardness (8wks: Δ−0.04 GPa, 16 wks: Δ−0.07 GPa, 24wks: Δ−0.06 GPa). The response rate (N/s) of joints to mechanical loads decreased in SD groups. Results from the study showed that joint adaptation depended on age. The initial form-related adaptation (observed change in functional space) can challenge strain-adaptive nature of tissues to meet functional demands with increasing age into adulthood. The coupled effect between functional space in the bone-PDLtooth complex and strain-adaptive nature of tissues is necessary to accommodate functional demands, and is temporally sensitive despite joint malfunction. From an applied science perspective, we propose that adaptations are registered as functional history in tissues and joints. PMID:26151121

Dynamic and Inherent B0 Correction for DTI Using Stimulated Echo Spiral Imaging

PubMed Central

Avram, Alexandru V.; Guidon, Arnaud; Truong, Trong-Kha; Liu, Chunlei; Song, Allen W.

2013-01-01

Purpose To present a novel technique for high-resolution stimulated echo (STE) diffusion tensor imaging (DTI) with self-navigated interleaved spirals (SNAILS) readout trajectories that can inherently and dynamically correct for image artifacts due to spatial and temporal variations in the static magnetic field (B0) resulting from eddy currents, tissue susceptibilities, subject/physiological motion, and hardware instabilities. Methods The Hahn spin echo formed by the first two 90° radio-frequency pulses is balanced to consecutively acquire two additional images with different echo times (TE) and generate an inherent field map, while the diffusion-prepared STE signal remains unaffected. For every diffusion-encoding direction, an intrinsically registered field map is estimated dynamically and used to effectively and inherently correct for off-resonance artifacts in the reconstruction of the corresponding diffusion-weighted image (DWI). Results After correction with the dynamically acquired field maps, local blurring artifacts are specifically removed from individual STE DWIs and the estimated diffusion tensors have significantly improved spatial accuracy and larger fractional anisotropy. Conclusion Combined with the SNAILS acquisition scheme, our new method provides an integrated high-resolution short-TE DTI solution with inherent and dynamic correction for both motion-induced phase errors and off-resonance effects. PMID:23630029

Development of Maps of Simple and Complex Cells in the Primary Visual Cortex

PubMed Central

Antolík, Ján; Bednar, James A.

2011-01-01

Hubel and Wiesel (1962) classified primary visual cortex (V1) neurons as either simple, with responses modulated by the spatial phase of a sine grating, or complex, i.e., largely phase invariant. Much progress has been made in understanding how simple-cells develop, and there are now detailed computational models establishing how they can form topographic maps ordered by orientation preference. There are also models of how complex cells can develop using outputs from simple cells with different phase preferences, but no model of how a topographic orientation map of complex cells could be formed based on the actual connectivity patterns found in V1. Addressing this question is important, because the majority of existing developmental models of simple-cell maps group neurons selective to similar spatial phases together, which is contrary to experimental evidence, and makes it difficult to construct complex cells. Overcoming this limitation is not trivial, because mechanisms responsible for map development drive receptive fields (RF) of nearby neurons to be highly correlated, while co-oriented RFs of opposite phases are anti-correlated. In this work, we model V1 as two topographically organized sheets representing cortical layer 4 and 2/3. Only layer 4 receives direct thalamic input. Both sheets are connected with narrow feed-forward and feedback connectivity. Only layer 2/3 contains strong long-range lateral connectivity, in line with current anatomical findings. Initially all weights in the model are random, and each is modified via a Hebbian learning rule. The model develops smooth, matching, orientation preference maps in both sheets. Layer 4 units become simple cells, with phase preference arranged randomly, while those in layer 2/3 are primarily complex cells. To our knowledge this model is the first explaining how simple cells can develop with random phase preference, and how maps of complex cells can develop, using only realistic patterns of connectivity. PMID:21559067

Phase contrast imaging of cochlear soft tissue.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, S.; Hwang, M.; Rau, C.

A noninvasive technique to image soft tissue could expedite diagnosis and disease management in the auditory system. We propose inline phase contrast imaging with hard X-rays as a novel method that overcomes the limitations of conventional absorption radiography for imaging soft tissue. In this study, phase contrast imaging of mouse cochleae was performed at the Argonne National Laboratory Advanced Photon Source. The phase contrast tomographic reconstructions show soft tissue structures of the cochlea, including the inner pillar cells, the inner spiral sulcus, the tectorial membrane, the basilar membrane, and the Reissner's membrane. The results suggest that phase contrast X-ray imagingmore » and tomographic techniques hold promise to noninvasively image cochlear structures at an unprecedented cellular level.« less

Influence of Intramyocardial Adipose Tissue on the Accuracy of Endocardial Contact Mapping of the Chronic Myocardial Infarction Substrate.

PubMed

Samanta, Rahul; Kumar, Saurabh; Chik, William; Qian, Pierre; Barry, Michael A; Al Raisi, Sara; Bhaskaran, Abhishek; Farraha, Melad; Nadri, Fazlur; Kizana, Eddy; Thiagalingam, Aravinda; Kovoor, Pramesh; Pouliopoulos, Jim

2017-10-01

Recent studies have demonstrated that intramyocardial adipose tissue (IMAT) may contribute to ventricular electrophysiological remodeling in patients with chronic myocardial infarction. Using an ovine model of myocardial infarction, we aimed to determine the influence of IMAT on scar tissue identification during endocardial contact mapping and optimal voltage-based mapping criteria for defining IMAT dense regions. In 7 sheep, left ventricular endocardial and transmural mapping was performed 84 weeks (15-111 weeks) post-myocardial infarction. Spearman rank correlation coefficient was used to assess the relationship between endocardial contact electrogram amplitude and histological composition of myocardium. Receiver operator characteristic curves were used to derive optimal electrogram thresholds for IMAT delineation during endocardial mapping and to describe the use of endocardial mapping for delineation of IMAT dense regions within scar. Endocardial electrogram amplitude correlated significantly with IMAT (unipolar r =-0.48±0.12, P <0.001; bipolar r =-0.45±0.22, P =0.04) but not collagen (unipolar r =-0.36±0.24, P =0.13; bipolar r =-0.43±0.31, P =0.16). IMAT dense regions of myocardium reliably identified using endocardial mapping with thresholds of <3.7 and <0.6 mV, respectively, for unipolar, bipolar, and combined modalities (single modality area under the curve=0.80, P <0.001; combined modality area under the curve=0.84, P <0.001). Unipolar mapping using optimal thresholding remained significantly reliable (area under the curve=0.76, P <0.001) during mapping of IMAT, confined to putative scar border zones (bipolar amplitude, 0.5-1.5 mV). These novel findings enhance our understanding of the confounding influence of IMAT on endocardial scar mapping. Combined bipolar and unipolar voltage mapping using optimal thresholds may be useful for delineating IMAT dense regions of myocardium, in postinfarct cardiomyopathy. © 2017 American Heart Association, Inc.

Subject-specific bone attenuation correction for brain PET/MR: can ZTE-MRI substitute CT scan accurately?

PubMed

Khalifé, Maya; Fernandez, Brice; Jaubert, Olivier; Soussan, Michael; Brulon, Vincent; Buvat, Irène; Comtat, Claude

2017-09-21

In brain PET/MR applications, accurate attenuation maps are required for accurate PET image quantification. An implemented attenuation correction (AC) method for brain imaging is the single-atlas approach that estimates an AC map from an averaged CT template. As an alternative, we propose to use a zero echo time (ZTE) pulse sequence to segment bone, air and soft tissue. A linear relationship between histogram normalized ZTE intensity and measured CT density in Hounsfield units ([Formula: see text]) in bone has been established thanks to a CT-MR database of 16 patients. Continuous AC maps were computed based on the segmented ZTE by setting a fixed linear attenuation coefficient (LAC) to air and soft tissue and by using the linear relationship to generate continuous μ values for the bone. Additionally, for the purpose of comparison, four other AC maps were generated: a ZTE derived AC map with a fixed LAC for the bone, an AC map based on the single-atlas approach as provided by the PET/MR manufacturer, a soft-tissue only AC map and, finally, the CT derived attenuation map used as the gold standard (CTAC). All these AC maps were used with different levels of smoothing for PET image reconstruction with and without time-of-flight (TOF). The subject-specific AC map generated by combining ZTE-based segmentation and linear scaling of the normalized ZTE signal into [Formula: see text] was found to be a good substitute for the measured CTAC map in brain PET/MR when used with a Gaussian smoothing kernel of [Formula: see text] corresponding to the PET scanner intrinsic resolution. As expected TOF reduces AC error regardless of the AC method. The continuous ZTE-AC performed better than the other alternative MR derived AC methods, reducing the quantification error between the MRAC corrected PET image and the reference CTAC corrected PET image.

Subject-specific bone attenuation correction for brain PET/MR: can ZTE-MRI substitute CT scan accurately?

NASA Astrophysics Data System (ADS)

Khalifé, Maya; Fernandez, Brice; Jaubert, Olivier; Soussan, Michael; Brulon, Vincent; Buvat, Irène; Comtat, Claude

2017-10-01

In brain PET/MR applications, accurate attenuation maps are required for accurate PET image quantification. An implemented attenuation correction (AC) method for brain imaging is the single-atlas approach that estimates an AC map from an averaged CT template. As an alternative, we propose to use a zero echo time (ZTE) pulse sequence to segment bone, air and soft tissue. A linear relationship between histogram normalized ZTE intensity and measured CT density in Hounsfield units (HU ) in bone has been established thanks to a CT-MR database of 16 patients. Continuous AC maps were computed based on the segmented ZTE by setting a fixed linear attenuation coefficient (LAC) to air and soft tissue and by using the linear relationship to generate continuous μ values for the bone. Additionally, for the purpose of comparison, four other AC maps were generated: a ZTE derived AC map with a fixed LAC for the bone, an AC map based on the single-atlas approach as provided by the PET/MR manufacturer, a soft-tissue only AC map and, finally, the CT derived attenuation map used as the gold standard (CTAC). All these AC maps were used with different levels of smoothing for PET image reconstruction with and without time-of-flight (TOF). The subject-specific AC map generated by combining ZTE-based segmentation and linear scaling of the normalized ZTE signal into HU was found to be a good substitute for the measured CTAC map in brain PET/MR when used with a Gaussian smoothing kernel of 4~mm corresponding to the PET scanner intrinsic resolution. As expected TOF reduces AC error regardless of the AC method. The continuous ZTE-AC performed better than the other alternative MR derived AC methods, reducing the quantification error between the MRAC corrected PET image and the reference CTAC corrected PET image.

Monitoring corneal crosslinking using phase-decorrelation OCT (Conference Presentation)

NASA Astrophysics Data System (ADS)

Blackburn, Brecken J.; Gu, Shi; Jenkins, Michael W.; Rollins, Andrew M.

2017-02-01

Viscosity is often a critical characteristic of biological fluids such as blood and mucus. However, traditional rheology is often inadequate when only small quantities of sample are available. A robust method to measure viscosity of microquantities of biological samples could lead to a better understanding and diagnosis of diseases. Here, we present a method to measure viscosity by observing particle Brownian motion within a sample. M-mode optical coherence tomography (OCT) imaging, obtained with a phase-sensitive 47 kHz spectral domain system, yields a viscosity measurement from multiple 200-1000 microsecond frames. This very short period of continuous acquisition, as compared to laser speckle decorrelation, decreases sensitivity to bulk motion, thereby potentially enabling in vivo and in situ applications. The theory linking g(1) first-order image autocorrelation to viscosity is derived from first principles of Brownian motion and the Stokes-Einstein relation. To improve precision, multiple windows acquired over 500 milliseconds are analyzed and the resulting linear fit parameters are averaged. Verification experiments were performed with 200 µL samples of glycerol and water with polystyrene microbeads. Lateral bulk motion up to 2 mm/s was tolerated and accurate viscosity measurements were obtained to a depth of 400 µm or more. Additionally, the method measured a significant decrease of the apparent diffusion constant of soft tissue after formalin fixation, suggesting potential for mapping tissue stiffness over a volume.

Phase-locking and bistability in neuronal networks with synaptic depression

NASA Astrophysics Data System (ADS)

Akcay, Zeynep; Huang, Xinxian; Nadim, Farzan; Bose, Amitabha

2018-02-01

We consider a recurrent network of two oscillatory neurons that are coupled with inhibitory synapses. We use the phase response curves of the neurons and the properties of short-term synaptic depression to define Poincaré maps for the activity of the network. The fixed points of these maps correspond to phase-locked modes of the network. Using these maps, we analyze the conditions that allow short-term synaptic depression to lead to the existence of bistable phase-locked, periodic solutions. We show that bistability arises when either the phase response curve of the neuron or the short-term depression profile changes steeply enough. The results apply to any Type I oscillator and we illustrate our findings using the Quadratic Integrate-and-Fire and Morris-Lecar neuron models.

Determination of tylosin and tilmicosin residues in animal tissues by reversed-phase liquid chromatography.

PubMed

Chan, W; Gerhardt, G C; Salisbury, C D

1994-01-01

A method for the simultaneous determination of tylosin and tilmicosin residues in animal tissues is reported. Solid-phase extraction columns are used to isolate the drugs from tissue extracts. Determination is accomplished by reversed-phase liquid chromatography with UV detection at 287 nm. Mean recoveries from spiked tissues were 79.9% (coefficient of variation [CV], 8.1%) for tylosin and 92.6% (CV, 8.7%) for tilmicosin. Detection limits for tylosin and tilmicosin were 0.020 and 0.010 ppm, respectively.

Transient Rotor Activity During Prolonged 3-Dimensional Phase Mapping in Human Persistent Atrial Fibrillation.

PubMed

Pathik, Bhupesh; Kalman, Jonathan M; Walters, Tomos; Kuklik, Pawel; Zhao, Jichao; Madry, Andrew; Prabhu, Sandeep; Nalliah, Chrishan; Kistler, Peter; Lee, Geoffrey

2018-01-01

This study sought to validate a 3-dimensional (3D) phase mapping system and determine the distribution of dominant propagation patterns in persistent atrial fibrillation (AF). Currently available systems display phase as simplified 2-dimensional maps. We developed a novel 3D phase mapping system that uses the 3D location of basket catheter electrodes and the patient's 3D left atrial surface geometry to interpolate phase and create a 3D representation of phase progression. Six-min AF recordings from the left atrium were obtained in 14 patients using the Constellation basket catheter and analyzed offline. Exported signals underwent both phase and traditional activation analysis and were then visualized using a novel 3D mapping system. Analysis involved: 1) validation of phase analysis by comparing beat-to-beat AF cycle length calculated using phase inversion with that determined from activation timing in the same 20-s segment; 2) validation of 3D phase by comparing propagation patterns observed using 3D phase with 3D activation in the same 1-min segment; and 3) determining the distribution of dominant propagation patterns in 6-min recordings using 3D phase. There was strong agreement of beat-to-beat AF cycle length between activation analysis and phase inversion (R 2  = 0.91). There was no significant difference between 3D activation and 3D phase in mean percentage of propagation patterns classified as single wavefronts (p = 0.99), focal activations (p = 0.26), disorganized activity (p = 0.76), or multiple wavefronts (p = 0.70). During prolonged 3D phase, single wavefronts were the most common propagation pattern (50.2%). A total of 34 rotors were seen in 9 of 14 patients. All rotors were transient with mean duration of 1.0 ± 0.6 s. Rotors were only observed in areas of high electrode density where the interelectrode distance was significantly shorter than nonrotor sites (7.4 [interquartile range: 6.3 to 14.6] vs. 15.3 mm [interquartile range: 10.1 to 22.2]; p < 0.001). During prolonged 3D phase mapping, transient rotors were observed in 64% of patients and reformed at the same anatomic location in 44% of patients. The electrode density of the basket catheter may limit the detection of rotors. Copyright © 2018 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations.

PubMed

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-05

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure.

PubMed

Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M; Komlosh, Michal E; İrfanoğlu, M Okan; Pierpaoli, Carlo; Basser, Peter J

2013-09-01

Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in "q-space," and the corresponding "mean apparent propagator (MAP)" describing molecular displacements in "r-space." We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit "displacement" sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions-the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP-MRI provides several novel, quantifiable parameters that capture previously obscured intrinsic features of nervous tissue microstructure. This should prove helpful for investigating the functional organization of normal and pathologic nervous tissue. Copyright © 2013 Elsevier Inc. All rights reserved.

Adaptive DSPI phase denoising using mutual information and 2D variational mode decomposition

NASA Astrophysics Data System (ADS)

Xiao, Qiyang; Li, Jian; Wu, Sijin; Li, Weixian; Yang, Lianxiang; Dong, Mingli; Zeng, Zhoumo

2018-04-01

In digital speckle pattern interferometry (DSPI), noise interference leads to a low peak signal-to-noise ratio (PSNR) and measurement errors in the phase map. This paper proposes an adaptive DSPI phase denoising method based on two-dimensional variational mode decomposition (2D-VMD) and mutual information. Firstly, the DSPI phase map is subjected to 2D-VMD in order to obtain a series of band-limited intrinsic mode functions (BLIMFs). Then, on the basis of characteristics of the BLIMFs and in combination with mutual information, a self-adaptive denoising method is proposed to obtain noise-free components containing the primary phase information. The noise-free components are reconstructed to obtain the denoising DSPI phase map. Simulation and experimental results show that the proposed method can effectively reduce noise interference, giving a PSNR that is higher than that of two-dimensional empirical mode decomposition methods.

Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

PubMed Central

Leemreize, Hanna; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

2013-01-01

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular. PMID:23804437

Phase transitions in coupled map lattices and in associated probabilistic cellular automata.

PubMed

Just, Wolfram

2006-10-01

Analytical tools are applied to investigate piecewise linear coupled map lattices in terms of probabilistic cellular automata. The so-called disorder condition of probabilistic cellular automata is closely related with attracting sets in coupled map lattices. The importance of this condition for the suppression of phase transitions is illustrated by spatially one-dimensional systems. Invariant densities and temporal correlations are calculated explicitly. Ising type phase transitions are found for one-dimensional coupled map lattices acting on repelling sets and for a spatially two-dimensional Miller-Huse-like system with stable long time dynamics. Critical exponents are calculated within a finite size scaling approach. The relevance of detailed balance of the resulting probabilistic cellular automaton for the critical behavior is pointed out.

Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework

PubMed Central

Antonopoulos, Georgios C.; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

2015-01-01

A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available. PMID:26599984

Tile-Based Two-Dimensional Phase Unwrapping for Digital Holography Using a Modular Framework.

PubMed

Antonopoulos, Georgios C; Steltner, Benjamin; Heisterkamp, Alexander; Ripken, Tammo; Meyer, Heiko

2015-01-01

A variety of physical and biomedical imaging techniques, such as digital holography, interferometric synthetic aperture radar (InSAR), or magnetic resonance imaging (MRI) enable measurement of the phase of a physical quantity additionally to its amplitude. However, the phase can commonly only be measured modulo 2π, as a so called wrapped phase map. Phase unwrapping is the process of obtaining the underlying physical phase map from the wrapped phase. Tile-based phase unwrapping algorithms operate by first tessellating the phase map, then unwrapping individual tiles, and finally merging them to a continuous phase map. They can be implemented computationally efficiently and are robust to noise. However, they are prone to failure in the presence of phase residues or erroneous unwraps of single tiles. We tried to overcome these shortcomings by creating novel tile unwrapping and merging algorithms as well as creating a framework that allows to combine them in modular fashion. To increase the robustness of the tile unwrapping step, we implemented a model-based algorithm that makes efficient use of linear algebra to unwrap individual tiles. Furthermore, we adapted an established pixel-based unwrapping algorithm to create a quality guided tile merger. These original algorithms as well as previously existing ones were implemented in a modular phase unwrapping C++ framework. By examining different combinations of unwrapping and merging algorithms we compared our method to existing approaches. We could show that the appropriate choice of unwrapping and merging algorithms can significantly improve the unwrapped result in the presence of phase residues and noise. Beyond that, our modular framework allows for efficient design and test of new tile-based phase unwrapping algorithms. The software developed in this study is freely available.

Scattering properties of normal and cancerous tissues from human stomach based on phase-contrast microscope

NASA Astrophysics Data System (ADS)

Zhang, Hui; Li, Zhifang; Li, Hui

2012-12-01

In order to study scattering properties of normal and cancerous tissues from human stomach, we collect images for human gastric specimens by using phase-contrast microscope. The images were processed by the way of mathematics morphology. The equivalent particle size distribution of tissues can be obtained. Combining with Mie scattering theory, the scattering properties of tissues can be calculated. Assume scattering of light in biological tissue can be seen as separate scattering events by different particles, total scattering properties can be equivalent to as scattering sum of particles with different diameters. The results suggest that scattering coefficient of the cancerous tissue is significantly higher than that of normal tissue. The scattering phase function is different especially in the backscattering area. Those are significant clinical benefits to diagnosis cancerous tissue

Noninvasive Spatially Offset and Transmission Raman Mapping of Breast Tissue: A Multimodal Approach Towards the In Vivo Assessment of Tissue Pathology

DTIC Science & Technology

2013-06-01

spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased breast tissue. Observed spectral changes are compared to infrared...capabilities and performance. Additionally, we conduct spectroscopy on tissue biopsies to correlate spectral bands with healthy and diseased ... disease states, ie hyperplasia, dysplasia, malignant, benign. The instrumentation has been built and characterized using archived tissue that was

Phase Contrast Microscopy Analysis of Breast Tissue

PubMed Central

Wells, Wendy A.; Wang, Xin; Daghlian, Charles P.; Paulsen, Keith D.; Pogue, Brian W.

2010-01-01

OBJECTIVE To assess how optical scatter properties in breast tissue, as measured by phase contrast microscopy and interpreted pathophysiologically, might be exploited as a diagnostic tool to differentiate cancer from benign tissue. STUDY DESIGN We evaluated frozen human breast tissue sections of adipose tissue, normal breast parenchyma, benign fibroadenoma tumors and noninvasive and invasive malignant cancers by phase contrast microscopy through quantification of grayscale values, using multiple regions of interest (ROI). Student’s t tests were performed on phase contrast measures across diagnostic categories testing data from individual cases; all ROI data were used as separate measures. RESULTS Stroma demonstrated significantly higher scatter intensity than did epithelium, with lower scattering in tumor-associated stroma as compared with normal or benign-associated stroma. Measures were comparable for invasive and noninvasive malignant tumors but were higher than those found in benign tumors and were lowest in adipose tissue. CONCLUSION Significant differences were found in scatter coefficient properties of epithelium and stroma across diagnostic categories of breast tissue, particularly between benign and malignant-associated stroma. Improved understanding of how scatter properties correlate with morphologic criteria used in routine pathologic diagnoses could have a significant clinical impact as developing optical technology allows macroscopic in situ phase contrast imaging. PMID:19736867

Dual-energy X-ray absorptiometry: analysis of pediatric fat estimate errors due to tissue hydration effects.

PubMed

Testolin, C G; Gore, R; Rivkin, T; Horlick, M; Arbo, J; Wang, Z; Chiumello, G; Heymsfield, S B

2000-12-01

Dual-energy X-ray absorptiometry (DXA) percent (%) fat estimates may be inaccurate in young children, who typically have high tissue hydration levels. This study was designed to provide a comprehensive analysis of pediatric tissue hydration effects on DXA %fat estimates. Phase 1 was experimental and included three in vitro studies to establish the physical basis of DXA %fat-estimation models. Phase 2 extended phase 1 models and consisted of theoretical calculations to estimate the %fat errors emanating from previously reported pediatric hydration effects. Phase 1 experiments supported the two-compartment DXA soft tissue model and established that pixel ratio of low to high energy (R values) are a predictable function of tissue elemental content. In phase 2, modeling of reference body composition values from birth to age 120 mo revealed that %fat errors will arise if a "constant" adult lean soft tissue R value is applied to the pediatric population; the maximum %fat error, approximately 0.8%, would be present at birth. High tissue hydration, as observed in infants and young children, leads to errors in DXA %fat estimates. The magnitude of these errors based on theoretical calculations is small and may not be of clinical or research significance.

Soft-tissue and phase-contrast imaging at the Swiss Light Source

NASA Astrophysics Data System (ADS)

Schneider, Philipp; Mohan, Nishant; Stampanoni, Marco; Muller, Ralph

2004-05-01

Recent results show that bone vasculature is a major contributor to local tissue porosity, and therefore can be directly linked to the mechanical properties of bone tissue. With the advent of third generation synchrotron radiation (SR) sources, micro-computed tomography (μCT) with resolutions in the order of 1 μm and better has become feasible. This technique has been employed frequently to analyze trabecular architecture and local bone tissue properties, i.e. the hard or mineralized bone tissue. Nevertheless, less is known about the soft tissues in bone, mainly due to inadequate imaging capabilities. Here, we discuss three different methods and applications to visualize soft tissues. The first approach is referred to as negative imaging. In this case the material around the soft tissue provides the absorption contrast necessary for X-ray based tomography. Bone vasculature from two different mouse strains was investigated and compared qualitatively. Differences were observed in terms of local vessel number and vessel orientation. The second technique represents corrosion casting, which is principally adapted for imaging of vascular systems. The technique of corrosion casting has already been applied successfully at the Swiss Light Source. Using the technology we were able to show that pathological features reminiscent of Alzheimer"s disease could be distinguished in the brain vasculature of APP transgenic mice. The third technique discussed here is phase contrast imaging exploiting the high degree of coherence of third generation synchrotron light sources, which provide the necessary physical conditions for phase contrast. The in-line approach followed here for phase contrast retrieval is a modification of the Gerchberg-Saxton-Fienup type. Several measurements and theoretical thoughts concerning phase contrast imaging are presented, including mathematical phase retrieval. Although up-to-now only phase images have been computed, the approach is now ready to retrieve the phase for a large number of angular positions of the specimen allowing application of holotomography, which is the three-dimensional reconstruction of phase images.

Refractive index variance of cells and tissues measured by quantitative phase imaging.

PubMed

Shan, Mingguang; Kandel, Mikhail E; Popescu, Gabriel

2017-01-23

The refractive index distribution of cells and tissues governs their interaction with light and can report on morphological modifications associated with disease. Through intensity-based measurements, refractive index information can be extracted only via scattering models that approximate light propagation. As a result, current knowledge of refractive index distributions across various tissues and cell types remains limited. Here we use quantitative phase imaging and the statistical dispersion relation (SDR) to extract information about the refractive index variance in a variety of specimens. Due to the phase-resolved measurement in three-dimensions, our approach yields refractive index results without prior knowledge about the tissue thickness. With the recent progress in quantitative phase imaging systems, we anticipate that using SDR will become routine in assessing tissue optical properties.

Susceptibility-based functional brain mapping by 3D deconvolution of an MR-phase activation map.

PubMed

Chen, Zikuan; Liu, Jingyu; Calhoun, Vince D

2013-05-30

The underlying source of T2*-weighted magnetic resonance imaging (T2*MRI) for brain imaging is magnetic susceptibility (denoted by χ). T2*MRI outputs a complex-valued MR image consisting of magnitude and phase information. Recent research has shown that both the magnitude and the phase images are morphologically different from the source χ, primarily due to 3D convolution, and that the source χ can be reconstructed from complex MR images by computed inverse MRI (CIMRI). Thus, we can obtain a 4D χ dataset from a complex 4D MR dataset acquired from a brain functional MRI study by repeating CIMRI to reconstruct 3D χ volumes at each timepoint. Because the reconstructed χ is a more direct representation of neuronal activity than the MR image, we propose a method for χ-based functional brain mapping, which is numerically characterised by a temporal correlation map of χ responses to a stimulant task. Under the linear imaging conditions used for T2*MRI, we show that the χ activation map can be calculated from the MR phase map by CIMRI. We validate our approach using numerical simulations and Gd-phantom experiments. We also analyse real data from a finger-tapping visuomotor experiment and show that the χ-based functional mapping provides additional activation details (in the form of positive and negative correlation patterns) beyond those generated by conventional MR-magnitude-based mapping. Copyright © 2013 Elsevier B.V. All rights reserved.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Automated adipose study for assessing cancerous human breast tissue using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gan, Yu; Yao, Xinwen; Chang, Ernest W.; Bin Amir, Syed A.; Hibshoosh, Hanina; Feldman, Sheldon; Hendon, Christine P.

2017-02-01

Breast cancer is the third leading cause of death in women in the United States. In human breast tissue, adipose cells are infiltrated or replaced by cancer cells during the development of breast tumor. Therefore, an adipose map can be an indicator of identifying cancerous region. We developed an automated classification method to generate adipose map within human breast. To facilitate the automated classification, we first mask the B-scans from OCT volumes by comparing the signal noise ratio with a threshold. Then, the image was divided into multiple blocks with a size of 30 pixels by 30 pixels. In each block, we extracted texture features such as local standard deviation, entropy, homogeneity, and coarseness. The features of each block were input to a probabilistic model, relevance vector machine (RVM), which was trained prior to the experiment, to classify tissue types. For each block within the B-scan, RVM identified the region with adipose tissue. We calculated the adipose ratio as the number of blocks identified as adipose over the total number of blocks within the B-scan. We obtained OCT images from patients (n = 19) in Columbia medical center. We automatically generated the adipose maps from 24 B-scans including normal samples (n = 16) and cancerous samples (n = 8). We found the adipose regions show an isolated pattern that in cancerous tissue while a clustered pattern in normal tissue. Moreover, the adipose ratio (52.30 ± 29.42%) in normal tissue was higher than the that in cancerous tissue (12.41 ± 10.07%).

SU-D-18C-05: Variable Bolus Arterial Spin Labeling MRI for Accurate Cerebral Blood Flow and Arterial Transit Time Mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, M; Jung, Y

2014-06-01

Purpose: Arterial spin labeling (ASL) is an MRI perfusion imaging method from which quantitative cerebral blood flow (CBF) maps can be calculated. Acquisition with variable post-labeling delays (PLD) and variable TRs allows for arterial transit time (ATT) mapping and leads to more accurate CBF quantification with a scan time saving of 48%. In addition, T1 and M0 maps can be obtained without a separate scan. In order to accurately estimate ATT and T1 of brain tissue from the ASL data, variable labeling durations were invented, entitled variable-bolus ASL. Methods: All images were collected on a healthy subject with a 3Tmore » Siemens Skyra scanner. Variable-bolus Psuedo-continuous ASL (PCASL) images were collected with 7 TI times ranging 100-4300ms in increments of 700ms with TR ranging 1000-5200ms. All boluses were 1600ms when the TI allowed, otherwise the bolus duration was 100ms shorter than the TI. All TI times were interleaved to reduce sensitivity to motion. Voxel-wise T1 and M0 maps were estimated using a linear least squares fitting routine from the average singal from each TI time. Then pairwise subtraction of each label/control pair and averaging for each TI time was performed. CBF and ATT maps were created using the standard model by Buxton et al. with a nonlinear fitting routine using the T1 tissue map. Results: CBF maps insensitive to ATT were produced along with ATT maps. Both maps show patterns and averages consistent with literature. The T1 map also shows typical T1 contrast. Conclusion: It has been demonstrated that variablebolus ASL produces CBF maps free from the errors due to ATT and tissue T1 variations and provides M0, T1, and ATT maps which have potential utility. This is accomplished with a single scan in a feasible scan time (under 6 minutes) with low sensivity to motion.« less

Spatial-area selective retrieval of multiple object-place associations in a hierarchical cognitive map formed by theta phase coding.

PubMed

Sato, Naoyuki; Yamaguchi, Yoko

2009-06-01

The human cognitive map is known to be hierarchically organized consisting of a set of perceptually clustered landmarks. Patient studies have demonstrated that these cognitive maps are maintained by the hippocampus, while the neural dynamics are still poorly understood. The authors have shown that the neural dynamic "theta phase precession" observed in the rodent hippocampus may be capable of forming hierarchical cognitive maps in humans. In the model, a visual input sequence consisting of object and scene features in the central and peripheral visual fields, respectively, results in the formation of a hierarchical cognitive map for object-place associations. Surprisingly, it is possible for such a complex memory structure to be formed in a few seconds. In this paper, we evaluate the memory retrieval of object-place associations in the hierarchical network formed by theta phase precession. The results show that multiple object-place associations can be retrieved with the initial cue of a scene input. Importantly, according to the wide-to-narrow unidirectional connections among scene units, the spatial area for object-place retrieval can be controlled by the spatial area of the initial cue input. These results indicate that the hierarchical cognitive maps have computational advantages on a spatial-area selective retrieval of multiple object-place associations. Theta phase precession dynamics is suggested as a fundamental neural mechanism of the human cognitive map.

High-spatial-resolution mapping of the oxygen concentration in cortical tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jaswal, Rajeshwer S.; Yaseen, Mohammad A.; Fu, Buyin; Boas, David A.; Sakadžic, Sava

2016-03-01

Due to a lack of imaging tools for high-resolution imaging of cortical tissue oxygenation, the detailed maps of the oxygen partial pressure (PO2) around arterioles, venules, and capillaries remain largely unknown. Therefore, we have limited knowledge about the mechanisms that secure sufficient oxygen delivery in microvascular domains during brain activation, and provide some metabolic reserve capacity in diseases that affect either microvascular networks or the regulation of cerebral blood flow (CBF). To address this challenge, we applied a Two-Photon PO2 Microscopy to map PO2 at different depths in mice cortices. Measurements were performed through the cranial window in the anesthetized healthy mice as well as in the mouse models of microvascular dysfunctions. In addition, microvascular morphology was recorded by the two-photon microscopy at the end of each experiment and subsequently segmented. Co-registration of the PO2 measurements and exact microvascular morphology enabled quantification of the tissue PO2 dependence on distance from the arterioles, capillaries, and venules at various depths. Our measurements reveal significant spatial heterogeneity of the cortical tissue PO2 distribution that is dominated by the high oxygenation in periarteriolar spaces. In cases of impaired oxygen delivery due to microvascular dysfunction, significant reduction in tissue oxygenation away from the arterioles was observed. These tissue domains may be the initial sites of cortical injury that can further exacerbate the progression of the disease.

Tissue Probability Map Constrained 4-D Clustering Algorithm for Increased Accuracy and Robustness in Serial MR Brain Image Segmentation

PubMed Central

Xue, Zhong; Shen, Dinggang; Li, Hai; Wong, Stephen

2010-01-01

The traditional fuzzy clustering algorithm and its extensions have been successfully applied in medical image segmentation. However, because of the variability of tissues and anatomical structures, the clustering results might be biased by the tissue population and intensity differences. For example, clustering-based algorithms tend to over-segment white matter tissues of MR brain images. To solve this problem, we introduce a tissue probability map constrained clustering algorithm and apply it to serial MR brain image segmentation, i.e., a series of 3-D MR brain images of the same subject at different time points. Using the new serial image segmentation algorithm in the framework of the CLASSIC framework, which iteratively segments the images and estimates the longitudinal deformations, we improved both accuracy and robustness for serial image computing, and at the mean time produced longitudinally consistent segmentation and stable measures. In the algorithm, the tissue probability maps consist of both the population-based and subject-specific segmentation priors. Experimental study using both simulated longitudinal MR brain data and the Alzheimer’s Disease Neuroimaging Initiative (ADNI) data confirmed that using both priors more accurate and robust segmentation results can be obtained. The proposed algorithm can be applied in longitudinal follow up studies of MR brain imaging with subtle morphological changes for neurological disorders. PMID:26566399

Encoding methods for B1+ mapping in parallel transmit systems at ultra high field

NASA Astrophysics Data System (ADS)

Tse, Desmond H. Y.; Poole, Michael S.; Magill, Arthur W.; Felder, Jörg; Brenner, Daniel; Jon Shah, N.

2014-08-01

Parallel radiofrequency (RF) transmission, either in the form of RF shimming or pulse design, has been proposed as a solution to the B1+ inhomogeneity problem in ultra high field magnetic resonance imaging. As a prerequisite, accurate B1+ maps from each of the available transmit channels are required. In this work, four different encoding methods for B1+ mapping, namely 1-channel-on, all-channels-on-except-1, all-channels-on-1-inverted and Fourier phase encoding, were evaluated using dual refocusing acquisition mode (DREAM) at 9.4 T. Fourier phase encoding was demonstrated in both phantom and in vivo to be the least susceptible to artefacts caused by destructive RF interference at 9.4 T. Unlike the other two interferometric encoding schemes, Fourier phase encoding showed negligible dependency on the initial RF phase setting and therefore no prior B1+ knowledge is required. Fourier phase encoding also provides a flexible way to increase the number of measurements to increase SNR, and to allow further reduction of artefacts by weighted decoding. These advantages of Fourier phase encoding suggest that it is a good choice for B1+ mapping in parallel transmit systems at ultra high field.

Parametric response mapping cut-off values that predict survival of hepatocellular carcinoma patients after TACE.

PubMed

Nörthen, Aventinus; Asendorf, Thomas; Shin, Hoen-Oh; Hinrichs, Jan B; Werncke, Thomas; Vogel, Arndt; Kirstein, Martha M; Wacker, Frank K; Rodt, Thomas

2018-04-21

Parametric response mapping (PRM) is a novel image-analysis technique applicable to assess tumor viability and predict intrahepatic recurrence of hepatocellular carcinoma (HCC) patients treated with transarterial chemoembolization (TACE). However, to date, the prognostic value of PRM for prediction of overall survival in HCC patients undergoing TACE is unclear. The objective of this explorative, single-center study was to identify cut-off values for voxel-specific PRM parameters that predict the post TACE overall survival in HCC patients. PRM was applied to biphasic CT data obtained at baseline and following 3 TACE treatments of 20 patients with HCC tumors ≥ 2 cm. The individual portal venous phases were registered to the arterial phases followed by segmentation of the largest lesion, i.e., the region of interest (ROI). Segmented voxels with their respective arterial and portal venous phase density values were displayed as a scatter plot. Voxel-specific PRM parameters were calculated and compared to patients' survival at 1, 2, and 3 years post treatment to identify the maximal predictive parameters. The hypervascularized tissue portion of the ROI was found to represent an independent predictor of the post TACE overall survival. For this parameter, cut-off values of 3650, 2057, and 2057 voxels, respectively, were determined to be optimal to predict overall survival at 1, 2, and 3 years after TACE. Using these cut points, patients were correctly classified as having died with a sensitivity of 80, 92, and 86% and as still being alive with a specificity of 60, 75, and 83%, respectively. The prognostic accuracy measured by area under the curve (AUC) values ranged from 0.73 to 0.87. PRM may have prognostic value to predict post TACE overall survival in HCC patients.

Radiosensitivity of different tissues from carrot root at different phases of growth in culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degani, N.; Pickholtz, D.

1980-09-01

The present work compares the effect of ..gamma..-radiation dose and time in culture on the growth of cambium and phloem carrot (Daucus carota) root explants. It was found that the phloem is more radiosensitive than the cambium and that both tissues were more radiosensitive when irradiated on excision at the G/sub 1/ phase rather than at the end of the lag phase on the ninth day of growth in culture when cells were predominantly at the G/sub 2/ phase. The nuclear volumes of cells from both tissues were similar but were larger at the end of the more radioresistant lagmore » phase than those of the G/sub 1/ phase on excision. However, nuclear volume could not account for the differences in radiosensitivity between either the tissues or irradiation times in culture.« less

Quantitative assessment of cancer cell morphology and motility using telecentric digital holographic microscopy and machine learning.

PubMed

Lam, Van K; Nguyen, Thanh C; Chung, Byung M; Nehmetallah, George; Raub, Christopher B

2018-03-01

The noninvasive, fast acquisition of quantitative phase maps using digital holographic microscopy (DHM) allows tracking of rapid cellular motility on transparent substrates. On two-dimensional surfaces in vitro, MDA-MB-231 cancer cells assume several morphologies related to the mode of migration and substrate stiffness, relevant to mechanisms of cancer invasiveness in vivo. The quantitative phase information from DHM may accurately classify adhesive cancer cell subpopulations with clinical relevance. To test this, cells from the invasive breast cancer MDA-MB-231 cell line were cultured on glass, tissue-culture treated polystyrene, and collagen hydrogels, and imaged with DHM followed by epifluorescence microscopy after staining F-actin and nuclei. Trends in cell phase parameters were tracked on the different substrates, during cell division, and during matrix adhesion, relating them to F-actin features. Support vector machine learning algorithms were trained and tested using parameters from holographic phase reconstructions and cell geometric features from conventional phase images, and used to distinguish between elongated and rounded cell morphologies. DHM was able to distinguish between elongated and rounded morphologies of MDA-MB-231 cells with 94% accuracy, compared to 83% accuracy using cell geometric features from conventional brightfield microscopy. This finding indicates the potential of DHM to detect and monitor cancer cell morphologies relevant to cell cycle phase status, substrate adhesion, and motility. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K; Basler, Tina; Falk, Christine S; Seidler, Ursula; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4 + T cell infiltration into the colonic lamina propria . Functional analysis identified a critical role of CD4 + T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis

PubMed Central

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C.; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K.; Basler, Tina; Falk, Christine S.; Seidler, Ursula; Hornef, Mathias W.; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4+ T cell infiltration into the colonic lamina propria. Functional analysis identified a critical role of CD4+ T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD. PMID:28361039

The National Geographic Names Data Base: Phase II instructions

USGS Publications Warehouse

Orth, Donald J.; Payne, Roger L.

1987-01-01

not recorded on topographic maps be added. The systematic collection of names from other sources, including maps, charts, and texts, is termed Phase II. In addition, specific types of features not compiled during Phase I are encoded and added to the data base. Other names of importance to researchers and users, such as historical and variant names, are also included. The rules and procedures for Phase II research, compilation, and encoding are contained in this publication.

Endogenous isoflavone methylation correlates with the in vitro rooting phases of Spartium junceum L. (Leguminosae).

PubMed

Clematis, Francesca; Viglione, Serena; Beruto, Margherita; Lanzotti, Virginia; Dolci, Paola; Poncet, Christine; Curir, Paolo

2014-09-01

Spartium junceum L. (Leguminosae) is a perennial shrub, native to the Mediterranean region in southern Europe, widespread in all the Italian regions and, as a leguminous species, it has a high isoflavone content. An in vitro culture protocol was developed for this species starting from stem nodal sections of in vivo plants, and isoflavone components of the in vitro cultured tissues were studied by means of High Performance Liquid Chromatography (HPLC) analytical techniques. Two main isoflavones were detected in the S. junceum tissues during the in vitro propagation phases: Genistein (4',5,7-Trihydroxyisoflavone), already reported in this species, and its methylated form 4',5,7-Trimethoxyisoflavone, detected for the first time in this plant species (0.750 ± 0.02 mg g(-1) dry tissue). The presence of both of these compounds in S. junceum tissues was consistently detected during the in vitro multiplication phase. The absence of the methylated form within plant tissues in the early phases of the in vitro adventitious root formation was correlated with its negative effect displayed on root induction and initiation phases, while its presence in the final "root manifestation" phase influenced positively the rooting process. The unmethylated form, although detectable in tissues in the precocious rooting phases, was no longer present in the final rooting phase. Its effect on rooting, however, proved always to be beneficial. Copyright © 2014 Elsevier GmbH. All rights reserved.

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues.

PubMed

Ku, Taeyun; Swaney, Justin; Park, Jeong-Yoon; Albanese, Alexandre; Murray, Evan; Cho, Jae Hun; Park, Young-Gyun; Mangena, Vamsi; Chen, Jiapei; Chung, Kwanghun

2016-09-01

The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnified analysis of the proteome (MAP), linearly expands entire organs fourfold while preserving their overall architecture and three-dimensional proteome organization. MAP is based on the observation that preventing crosslinking within and between endogenous proteins during hydrogel-tissue hybridization allows for natural expansion upon protein denaturation and dissociation. The expanded tissue preserves its protein content, its fine subcellular details, and its organ-scale intercellular connectivity. We use off-the-shelf antibodies for multiple rounds of immunolabeling and imaging of a tissue's magnified proteome, and our experiments demonstrate a success rate of 82% (100/122 antibodies tested). We show that specimen size can be reversibly modulated to image both inter-regional connections and fine synaptic architectures in the mouse brain.

Oceanic tide maps and spherical harmonic coefficients from Geosat altimetry

NASA Technical Reports Server (NTRS)

Cartwright, D. E.; Ray, R. D.; Sanchez, B. V.

1991-01-01

Maps and tables for the global ocean tides, 69 degree N to 68 degree S, derived from two years of Geosat altimetry are presented. Global maps of local and Greenwich admittance of the (altimetric) ocean tide, and maps of amplitude and Greenwich phase lag of the ocean tide are shown for M(sub 2), S(sub 2), N(sub 2), O(sub 1), and K(sub 1). Larger scale maps of amplitude and phases are also shown for regional areas of special interest. Spherical harmonic coefficients of the ocean tide through degree and order 8 are tabulated for the six major constituents.

Concomitant bidirectional transport during peritoneal dialysis can be explained by a structured interstitium

PubMed Central

Waniewski, Jacek; Flessner, Michael F.; Lindholm, Bengt

2016-01-01

Clinical and animal studies suggest that peritoneal absorption of fluid and protein from dialysate to peritoneal tissue, and to blood and lymph circulation, occurs concomitantly with opposite flows of fluid and protein, i.e., from blood to dialysate. However, until now a theoretical explanation of this phenomenon has been lacking. A two-phase distributed model is proposed to explain the bidirectional, concomitant transport of fluid, albumin and glucose through the peritoneal transport system (PTS) during peritoneal dialysis. The interstitium of this tissue is described as an expandable two-phase structure with phase F (water-rich, colloid-poor region) and phase C (water-poor, colloid-rich region) with fluid and solute exchange between them. A low fraction of phase F is assumed in the intact tissue, which can be significantly increased under the influence of hydrostatic pressure and tissue hydration. The capillary wall is described using the three-pore model, and the conditions in the peritoneal cavity are assumed commencing 3 min after the infusion of glucose 3.86% dialysis fluid. Computer simulations demonstrate that peritoneal absorption of fluid into the tissue, which occurs via phase F at the rate of 1.8 ml/min, increases substantially the interstitial pressure and tissue hydration in both phases close to the peritoneal cavity, whereas the glucose-induced ultrafiltration from blood occurs via phase C at the rate of 15 ml/min. The proposed model delineating the phenomenon of concomitant bidirectional transport through PTS is based on a two-phase structure of the interstitium and provides results in agreement with clinical and experimental data. PMID:26945084

Landsat maps (phase V, deliverable 60), ASTER maps (phase V, deliverable 62), ASTER_DEM maps (phase V, deliverable 63), and spectral remote sensing in support of PRISM-II mineral resource assessment project, Islamic Republic of Mauritania (phase V, deliverables 61 and 64): Chapter E in Second projet de renforcement institutionnel du secteur minier de la République Islamique de Mauritanie (PRISM-II)

USGS Publications Warehouse

Rockwell, Barnaby W.; Knepper, Daniel H.; Horton, John D.

2015-01-01

The image products derived from Landsat TM and ASTER data enable the delineation of mineral groups across wide areas based on color response. Guides are provided that allow users to interpret these colors as to mineral group occurrence over lithologic units and known deposits. This information can be extrapolated to other geologically permissive tracts for various deposit types in the search for similar mineralogic responses that may be indicative of concealed deposits.

Differential phase optical coherence probe for depth-resolved detection of photothermal response in tissue.

PubMed

Telenkov, Sergey A; Dave, Digant P; Sethuraman, Shriram; Akkin, Taner; Milner, Thomas E

2004-01-07

We describe a differential phase low-coherence interferometric probe for non-invasive, quantitative imaging of photothermal phenomena in biological materials. Our detection method utilizes principles of optical coherence tomography with differential phase measurement of interference fringe signals. A dual-channel optical low-coherence probe is used to analyse laser-induced thermoelastic and thermorefractive effects in tissue with micrometre axial resolution and nanometre sensitivity. We demonstrate an application of the technique using tissue phantoms and ex-vivo tissue specimens of rodent dorsal skin.

Imaging Electric Properties of Biological Tissues by RF Field Mapping in MRI

PubMed Central

Zhang, Xiaotong; Zhu, Shanan; He, Bin

2010-01-01

The electric properties (EPs) of biological tissue, i.e., the electric conductivity and permittivity, can provide important information in the diagnosis of various diseases. The EPs also play an important role in specific absorption rate (SAR) calculation, a major concern in high-field Magnetic Resonance Imaging (MRI), as well as in non-medical areas such as wireless-telecommunications. The high-field MRI system is accompanied by significant wave propagation effects, and the radio frequency (RF) radiation is dependent on the EPs of biological tissue. Based on the measurement of the active transverse magnetic component of the applied RF field (known as B1-mapping technique), we propose a dual-excitation algorithm, which uses two sets of measured B1 data to noninvasively reconstruct the electric properties of biological tissues. The Finite Element Method (FEM) was utilized in three-dimensional (3D) modeling and B1 field calculation. A series of computer simulations were conducted to evaluate the feasibility and performance of the proposed method on a 3D head model within a transverse electromagnetic (TEM) coil and a birdcage (BC) coil. Using a TEM coil, when noise free, the reconstructed EP distribution of tissues in the brain has relative errors of 12% ∼ 28% and correlated coefficients of greater than 0.91. Compared with other B1-mapping based reconstruction algorithms, our approach provides superior performance without the need for iterative computations. The present simulation results suggest that good reconstruction of electric properties from B1 mapping can be achieved. PMID:20129847

Plenoptic mapping for imaging and retrieval of the complex field amplitude of a laser beam.

PubMed

Wu, Chensheng; Ko, Jonathan; Davis, Christopher C

2016-12-26

The plenoptic sensor has been developed to sample complicated beam distortions produced by turbulence in the low atmosphere (deep turbulence or strong turbulence) with high density data samples. In contrast with the conventional Shack-Hartmann wavefront sensor, which utilizes all the pixels under each lenslet of a micro-lens array (MLA) to obtain one data sample indicating sub-aperture phase gradient and photon intensity, the plenoptic sensor uses each illuminated pixel (with significant pixel value) under each MLA lenslet as a data point for local phase gradient and intensity. To characterize the working principle of a plenoptic sensor, we propose the concept of plenoptic mapping and its inverse mapping to describe the imaging and reconstruction process respectively. As a result, we show that the plenoptic mapping is an efficient method to image and reconstruct the complex field amplitude of an incident beam with just one image. With a proof of concept experiment, we show that adaptive optics (AO) phase correction can be instantaneously achieved without going through a phase reconstruction process under the concept of plenoptic mapping. The plenoptic mapping technology has high potential for applications in imaging, free space optical (FSO) communication and directed energy (DE) where atmospheric turbulence distortion needs to be compensated.

Investigating mechanically induced phase response of the tissue by using high-speed phase-resolved optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ling, Yuye; Hendon, Christine P.

2017-02-01

Phase-resolved optical coherence tomography (OCT), a functional extension of OCT, provides depth-resolved phase information with extra contrast. In cardiology, changes in the mechanical properties have been associated with tissue remodeling and disease progression. Here we present the capability of profiling structural deformation of the sample in vivo by using a highly stable swept source OCT system The system, operating at 1300 nm, has an A-line acquisition rate of 200 kHz. We measured the phase noise floor to be 6.5 pm±3.2 pm by placing a cover slip in the sample arm, while blocking the reference arm. We then conducted a vibrational frequency test by measuring the phase response from a polymer membrane stimulated by a pure tone acoustic wave from 10 kHz to 80 kHz. The measured frequency response agreed with the known stimulation frequency with an error < 0.005%. We further measured the phase response of 7 fresh swine hearts obtained from Green Village Packing Company through a mechanical stretching test, within 24 hours of sacrifice. The heart tissue was cut into a 1 mm slices and fixed on two motorized stages. We acquired 100,000 consecutive M-scans, while the sample is stretched at a constant velocity of 10 um/s. The depth-resolved phase image presents linear phase response over time at each depth, but the slope varies among tissue types. Our future work includes refining our experiment protocol to quantitatively measured the elastic modulus of the tissue in vivo and building a tissue classifier based on depth-resolved phase information.

Analysis of neoplastic lesions in magnetic resonance imaging using self-organizing maps.

PubMed

Mei, Paulo Afonso; de Carvalho Carneiro, Cleyton; Fraser, Stephen J; Min, Li Li; Reis, Fabiano

2015-12-15

To provide an improved method for the identification and analysis of brain tumors in MRI scans using a semi-automated computational approach, that has the potential to provide a more objective, precise and quantitatively rigorous analysis, compared to human visual analysis. Self-Organizing Maps (SOM) is an unsupervised, exploratory data analysis tool, which can automatically domain an image into selfsimilar regions or clusters, based on measures of similarity. It can be used to perform image-domain of brain tissue on MR images, without prior knowledge. We used SOM to analyze T1, T2 and FLAIR acquisitions from two MRI machines in our service from 14 patients with brain tumors confirmed by biopsies--three lymphomas, six glioblastomas, one meningioma, one ganglioglioma, two oligoastrocytomas and one astrocytoma. The SOM software was used to analyze the data from the three image acquisitions from each patient and generated a self-organized map for each containing 25 clusters. Damaged tissue was separated from the normal tissue using the SOM technique. Furthermore, in some cases it allowed to separate different areas from within the tumor--like edema/peritumoral infiltration and necrosis. In lesions with less precise boundaries in FLAIR, the estimated damaged tissue area in the resulting map appears bigger. Our results showed that SOM has the potential to be a powerful MR imaging analysis technique for the assessment of brain tumors. Copyright © 2015. Published by Elsevier B.V.

The lipid-reactive oxygen species phenotype of breast cancer. Raman spectroscopy and mapping, PCA and PLSDA for invasive ductal carcinoma and invasive lobular carcinoma. Molecular tumorigenic mechanisms beyond Warburg effect.

PubMed

Surmacki, Jakub; Brozek-Pluska, Beata; Kordek, Radzislaw; Abramczyk, Halina

2015-04-07

Vibrational signatures of human breast tissue (invasive ductal carcinoma and invasive lobular carcinoma) were used to identify, characterize and discriminate structures in normal (noncancerous) and cancerous tissues by confocal Raman imaging, Raman spectroscopy and IR spectroscopy. The most important differences between normal and cancerous tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives. K-means clustering and basis analysis followed by PCA and PLSDA is employed to analyze Raman spectroscopic maps of human breast tissue and for a statistical analysis of the samples (82 patients, 164 samples). Raman maps successfully identify regions of carotenoids, fatty acids, and proteins. The intensities, frequencies and profiles of the average Raman spectra differentiate the biochemical composition of normal and cancerous tissues. The paper demonstrates that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The sensitivity and specificity obtained directly from PLSLD and cross validation are equal to 90.5% and 84.8% for calibration and 84.7% and 71.9% for cross-validation respectively.

A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis[W

PubMed Central

Geng, Yu; Wu, Rui; Wee, Choon Wei; Xie, Fei; Wei, Xueliang; Chan, Penny Mei Yeen; Tham, Cliff; Duan, Lina; Dinneny, José R.

2013-01-01

Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point–specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment. PMID:23898029

Earth Shadows and the SEV Angle of MAP's Lissajous Orbit At L2

NASA Technical Reports Server (NTRS)

Edery, Ariel

2002-01-01

The Microwave Anisotropy Probe (MAP) launched successfully on June 30, 2001 and is presently in a Lissajous orbit about the Sun-Earth libration point L2. To avoid Earth shadows at L2, the Sun-Earth-Vehicle (SEV) angle of MAP has to be greater than 0.5 deg for an extended mission of four years. An equation is derived for the SEV angle in terms of the phase angle, frequencies and amplitudes of the Lissajous. The SEV angle is shown to oscillate with a period of 90.4 days within an amplitude envelope of period 13.9 years. A range of phase angles that avoids shadows is identified. MAP'S present phase angle is within this range and will avoid shadows for approximately 5.8 years.

Tissue refractometry using Hilbert phase microscopy.

PubMed

Lue, Niyom; Bewersdorf, Joerg; Lessard, Mark D; Badizadegan, Kamran; Dasari, Ramachandra R; Feld, Michael S; Popescu, Gabriel

2007-12-15

We present, for the first time to our knowledge, quantitative phase images associated with unstained 5 mum thick tissue slices of mouse brain, spleen, and liver. The refractive properties of the tissue are retrieved in terms of the average refractive index and its spatial variation. We find that the average refractive index varies significantly with tissue type, such that the brain is characterized by the lowest value and the liver by the highest. The spatial power spectra of the phase images reveal power law behavior with different exponents for each tissue type. This approach opens a new possibility for stain-free characterization of tissues, where the diagnostic power is provided by the intrinsic refractive properties of the biological structure. We present results obtained for liver tissue affected by a lysosomal storage disease and show that our technique can quantify structural changes during this disease development.

Fostering clinical reasoning in physiotherapy: comparing the effects of concept map study and concept map completion after example study in novice and advanced learners.

PubMed

Montpetit-Tourangeau, Katherine; Dyer, Joseph-Omer; Hudon, Anne; Windsor, Monica; Charlin, Bernard; Mamede, Sílvia; van Gog, Tamara

2017-12-01

Health profession learners can foster clinical reasoning by studying worked examples presenting fully worked out solutions to a clinical problem. It is possible to improve the learning effect of these worked examples by combining them with other learning activities based on concept maps. This study investigated which combinaison of activities, worked examples study with concept map completion or worked examples study with concept map study, fosters more meaningful learning of intervention knowledge in physiotherapy students. Moreover, this study compared the learning effects of these learning activity combinations between novice and advanced learners. Sixty-one second-year physiotherapy students participated in the study which included a pre-test phase, a 130-min guided-learning phase and a four-week self-study phase. During the guided and self-study learning sessions, participants had to study three written worked examples presenting the clinical reasoning for selecting electrotherapeutic currents to treat patients with motor deficits. After each example, participants engaged in either concept map completion or concept map study depending on which learning condition they were randomly allocated to. Students participated in an immediate post-test at the end of the guided-learning phase and a delayed post-test at the end of the self-study phase. Post-tests assessed the understanding of principles governing the domain of knowledge to be learned (conceptual knowledge) and the ability to solve new problems that have similar (i.e., near transfer) or different (i.e., far transfer) solution rationales as problems previously studied in the examples. Learners engaged in concept map completion outperformed those engaged in concept map study on near transfer (p = .010) and far transfer (p < .001) performance. There was a significant interaction effect of learners' prior ability and learning condition on conceptual knowledge but not on near and far transfer performance. Worked examples study combined with concept map completion led to greater transfer performance than worked examples study combined with concept map study for both novice and advanced learners. Concept map completion might give learners better insight into what they have and have not yet learned, allowing them to focus on those aspects during subsequent example study.

Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling.

PubMed

Basse, Astrid L; Dixen, Karen; Yadav, Rachita; Tygesen, Malin P; Qvortrup, Klaus; Kristiansen, Karsten; Quistorff, Bjørn; Gupta, Ramneek; Wang, Jun; Hansen, Jacob B

2015-03-19

Large mammals are capable of thermoregulation shortly after birth due to the presence of brown adipose tissue (BAT). The majority of BAT disappears after birth and is replaced by white adipose tissue (WAT). We analyzed the postnatal transformation of adipose in sheep with a time course study of the perirenal adipose depot. We observed changes in tissue morphology, gene expression and metabolism within the first two weeks of postnatal life consistent with the expected transition from BAT to WAT. The transformation was characterized by massively decreased mitochondrial abundance and down-regulation of gene expression related to mitochondrial function and oxidative phosphorylation. Global gene expression profiling demonstrated that the time points grouped into three phases: a brown adipose phase, a transition phase and a white adipose phase. Between the brown adipose and the transition phase 170 genes were differentially expressed, and 717 genes were differentially expressed between the transition and the white adipose phase. Thirty-eight genes were shared among the two sets of differentially expressed genes. We identified a number of regulated transcription factors, including NR1H3, MYC, KLF4, ESR1, RELA and BCL6, which were linked to the overall changes in gene expression during the adipose tissue remodeling. Finally, the perirenal adipose tissue expressed both brown and brite/beige adipocyte marker genes at birth, the expression of which changed substantially over time. Using global gene expression profiling of the postnatal BAT to WAT transformation in sheep, we provide novel insight into adipose tissue plasticity in a large mammal, including identification of novel transcriptional components linked to adipose tissue remodeling. Moreover, our data set provides a useful resource for further studies in adipose tissue plasticity.

Development of novel force-limiting grasping forceps with a simple mechanism.

PubMed

Sakaguchi, Yasuto; Sato, Toshihiko; Yutaka, Yojiro; Muranishi, Yusuke; Komatsu, Teruya; Yoshizawa, Akihiko; Nakajima, Naoki; Nakamura, Tatsuo; Date, Hiroshi

2018-06-06

In endoscopic surgery, fragile tissues may be damaged by the application of excessive force. Thus, we developed novel endoscopic forceps with a simple force-limiting mechanism. The novel forceps were constructed with a leaf spring, and the spring thickness determines grasping pressure. We established an evaluation system (maximum score is 11 points) for lung tissue damage leading to complications. We tested the conventional forceps (186.8 kPa) and 3 novel spring forceps with the following thicknesses: 1.3 mm (53.0 kPa), 2.2 mm (187.7 kPa) and 2.8 mm (369.2 kPa). After grasping, peripheral canine lung tissues were microscopically examined for acute- and late-phase damages. In the acute phase (20 sites), the novel forceps caused capillary congestion and haemorrhage in the subpleural tissue, whereas the conventional forceps caused deep tissue and pleural damages. In the late phase (30 sites), both forceps caused fibroblast formation and interstitial thickening, which progressed to the deeper tissues as grasping pressure increased. In the acute phase, the median scores were 2.0 and 6.0 for the novel and conventional forceps, respectively (P = 0.003). In the late phase, the median scores were 2.0, 2.5 and 5.0 for 1.3-, 2.2- and 2.8-mm thick forceps, respectively, and 5.0 for the conventional forceps (P < 0.001). In both phases, the novel forceps with grasping pressure set below 187.7 kPa (2.2 mm) caused significantly less lung tissue damage than the conventional forceps. The novel endoscopic forceps are able to regulate the tissue-grasping pressure and induce less damage in lung tissues than conventional forceps.

Probability mapping of scarred myocardium using texture and intensity features in CMR images

PubMed Central

2013-01-01

Background The myocardium exhibits heterogeneous nature due to scarring after Myocardial Infarction (MI). In Cardiac Magnetic Resonance (CMR) imaging, Late Gadolinium (LG) contrast agent enhances the intensity of scarred area in the myocardium. Methods In this paper, we propose a probability mapping technique using Texture and Intensity features to describe heterogeneous nature of the scarred myocardium in Cardiac Magnetic Resonance (CMR) images after Myocardial Infarction (MI). Scarred tissue and non-scarred tissue are represented with high and low probabilities, respectively. Intermediate values possibly indicate areas where the scarred and healthy tissues are interwoven. The probability map of scarred myocardium is calculated by using a probability function based on Bayes rule. Any set of features can be used in the probability function. Results In the present study, we demonstrate the use of two different types of features. One is based on the mean intensity of pixel and the other on underlying texture information of the scarred and non-scarred myocardium. Examples of probability maps computed using the mean intensity of pixel and the underlying texture information are presented. We hypothesize that the probability mapping of myocardium offers alternate visualization, possibly showing the details with physiological significance difficult to detect visually in the original CMR image. Conclusion The probability mapping obtained from the two features provides a way to define different cardiac segments which offer a way to identify areas in the myocardium of diagnostic importance (like core and border areas in scarred myocardium). PMID:24053280

Maximum a posteriori decoder for digital communications

NASA Technical Reports Server (NTRS)

Altes, Richard A. (Inventor)

1997-01-01

A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.

Effects of digital phase-conjugate light intensity on time-reversal imaging through animal tissue.

PubMed

Toda, Sogo; Kato, Yuji; Kudo, Nobuki; Shimizu, Koichi

2018-04-01

For transillumination imaging of animal tissues, we have attempted to suppress the scattering effect in a turbid medium using the time-reversal principle of phase-conjugate light. We constructed a digital phase-conjugate system to enable intensity modulation and phase modulation. Using this system, we clarified the effectiveness of the intensity information for restoration of the original light distribution through a turbid medium. By varying the scattering coefficient of the medium, we clarified the limit of time-reversal ability with intensity information of the phase-conjugate light. Experiment results demonstrated the applicability of the proposed technique to animal tissue.

Imaging of cochlear tissue with a grating interferometer and hard X-rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richter, Claus-Peter; Shintani-Smith, Stephanie; Fishman, Andrew

This article addresses an important current development in medical and biological imaging: the possibility of imaging soft tissue at resolutions in the micron range using hard X-rays. Challenging environments, including the cochlea, require the imaging of soft tissue structure surrounded by bone. We demonstrate that cochlear soft tissue structures can be imaged with hard X-ray phase contrast. Furthermore, we show that only a thin slice of the tissue is required to introduce a large phase shift. It is likely that the phase contrast image of the soft tissue structures is sufficient to image the structures even if surrounded by bone.more » For the present set of experiments, structures with low-absorption contrast have been visualized using in-line phase contrast imaging and a grating interferometer. The experiments have been performed at the Advanced Photon Source at Argonne National Laboratories, a third generation source of synchrotron radiation. The source provides highly coherent X-ray radiation with high-photon flux (>10{sup 12} photons/s) at high-photon energies (5-70 keV). Radiographic and light microscopy images of the gerbil cochlear slice samples were compared. It has been determined that a 20-{micro}m thick tissue slice induces a phase shift between 1/3{pi} and 2/3{pi}.« less

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern.

PubMed

Tao, Xuelian; Chen, Jianning; Jiang, Yanzhi; Wei, Yingying; Chen, Yan; Xu, Huaming; Zhu, Li; Tang, Guoqing; Li, Mingzhou; Jiang, Anan; Shuai, Surong; Bai, Lin; Liu, Haifeng; Ma, Jideng; Jin, Long; Wen, Anxiang; Wang, Qin; Zhu, Guangxiang; Xie, Meng; Wu, Jiayun; He, Tao; Huang, Chunyu; Gao, Xiang; Li, Xuewei

2017-04-28

N 6 -methyladenosine (m 6 A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m 6 A methylation on mRNA have been revealed by mapping of m 6 A methylomes in several species. m 6 A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m 6 A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m 6 A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. Our findings show that there were 5,872 and 2,826 m 6 A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for m 6 A peaks. Gene ontology analysis revealed that common m 6 A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m 6 A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m 6 A methylation extent and the transcript level, suggesting a regulatory role for m 6 A in gene expression. This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m 6 A modification in adipose deposition and muscle growth.

Labeling single cell for in-vivo study of cell fate mapping and lineage tracing

NASA Astrophysics Data System (ADS)

He, Sicong; Xu, Jin; Wu, Yi; Tian, Ye; Sun, Qiqi; Wen, Zilong; Qu, Jianan Y.

2018-02-01

Cell fate mapping and lineage tracing are significant ways to understanding the developmental origins of biological tissues. It requires labeling individual cells and tracing the development of their progeny. We develop an infrared laser-evoked gene operator heat-shock microscope system to achieve single-cell labeling in zebrafish. With a fluorescent thermometry technique, we measure the temperature increase in zebrafish tissues induced by infrared laser and identify the optimal heat shock conditions for single-cell gene induction in different types of zebrafish cells. We use this technique to study the fate mapping of T lymphocytes and discover the distinct waves of lymphopoiesis during the zebrafish development.

Connective Tissue Mineralization in Abcc6−/− Mice, a Model for Pseudoxanthoma Elasticum

PubMed Central

Kavukcuoglu, N. Beril; Li, Qiaoli; Pleshko, Nancy; Uitto, Jouni

2012-01-01

Pseudoxanthoma elasticum (PXE) is a heritable multisystem disorder characterized by ectopic mineralization. However, the structure of the mineral deposits, their interactions with the connective tissue matrix, and the details of the progressive maturation of the mineral crystals are currently unknown. In this study, we examined the mineralization processes in Abcc6−/− mice, a model system for PXE, by energy dispersive X-ray, and Fourier transform infrared imaging spectroscopy (FT-IRIS). The results indicated that the principal components of the mineral deposits were calcium and phosphate which co-localized within the histologically demonstrable lesions determined by topographic mapping. The Ca/P ratio increased in samples with progressive mineralization reaching the value comparable to that in endochondral bone. A progressive increase in mineralization was also reflected by increased mineral-to-matrix ratio determined by FT-IRIS. Determination of the mineral phases by FT-IRIS suggested progressive maturation of the mineral deposits from amorphous calcium phosphate to hydroxyapatite. These results provide critical information of the mechanisms of mineralization in PXE, with potential pharmacologic implications. PMID:22421595

Wide field and highly sensitive angiography based on optical coherence tomography with akinetic swept source.

PubMed

Xu, Jingjiang; Song, Shaozhen; Wei, Wei; Wang, Ruikang K

2017-01-01

Wide-field vascular visualization in bulk tissue that is of uneven surface is challenging due to the relatively short ranging distance and significant sensitivity fall-off for most current optical coherence tomography angiography (OCTA) systems. We report a long ranging and ultra-wide-field OCTA (UW-OCTA) system based on an akinetic swept laser. The narrow instantaneous linewidth of the swept source with its high phase stability, combined with high-speed detection in the system enable us to achieve long ranging (up to 46 mm) and almost negligible system sensitivity fall-off. To illustrate these advantages, we compare the basic system performances between conventional spectral domain OCTA and UW-OCTA systems and their functional imaging of microvascular networks in living tissues. In addition, we show that the UW-OCTA is capable of different depth-ranging of cerebral blood flow within entire brain in mice, and providing unprecedented blood perfusion map of human finger in vivo . We believe that the UW-OCTA system has promises to augment the existing clinical practice and explore new biomedical applications for OCT imaging.

Wide field and highly sensitive angiography based on optical coherence tomography with akinetic swept source

PubMed Central

Xu, Jingjiang; Song, Shaozhen; Wei, Wei; Wang, Ruikang K.

2016-01-01

Wide-field vascular visualization in bulk tissue that is of uneven surface is challenging due to the relatively short ranging distance and significant sensitivity fall-off for most current optical coherence tomography angiography (OCTA) systems. We report a long ranging and ultra-wide-field OCTA (UW-OCTA) system based on an akinetic swept laser. The narrow instantaneous linewidth of the swept source with its high phase stability, combined with high-speed detection in the system enable us to achieve long ranging (up to 46 mm) and almost negligible system sensitivity fall-off. To illustrate these advantages, we compare the basic system performances between conventional spectral domain OCTA and UW-OCTA systems and their functional imaging of microvascular networks in living tissues. In addition, we show that the UW-OCTA is capable of different depth-ranging of cerebral blood flow within entire brain in mice, and providing unprecedented blood perfusion map of human finger in vivo. We believe that the UW-OCTA system has promises to augment the existing clinical practice and explore new biomedical applications for OCT imaging. PMID:28101428

Synchrotron radiation CT from the micro to nanoscale for the investigation of bone tissue

NASA Astrophysics Data System (ADS)

Peyrin, Francoise; Dong, Pei; Pacureanu, Alexandra; Zuluaga, Maria; Olivier, Cécile; Langer, Max; Cloetens, Peter

2012-10-01

During the last decade, X-ray micro Computerized Tomography (CT) has become a conventional technique for the three-dimensional (3D) investigation of trabecular bone micro-architecture. Coupling micro-CT to synchrotron sources possesses significant advantages in terms of image quality and gives access to information on bone mineralization which is an important factor of bone quality. We present an overview of the investigation of bone using Synchrotron Radiation (SR) CT from the micro to the nano scale. We introduce two synchrotron CT systems developed at the ESRF based on SR parallel-beam micro-CT and magnified phase CT respectively, achieving down to submicrometric and nanometric spatial resolution. In the latter, by using phase retrieval prior to tomographic reconstruction, the system provides maps of the 3D refractive index distribution. Parallel-beam SR micro-CT has extensively been used for the analysis of trabecular or cortical bone in human or small animals with spatial resolution in the range [3-10] μm. However, the characterization of the bone properties at the cellular scale is also of major interest. At the micrometric scale, the shape, density and morphology of osteocyte lacunae can be studied on statistically representative volumes. At the nanometric scale, unprecedented 3D displays of the canaliculi network have been obtained on fields of views including a large number of interconnected osteocyte lacunae. Finally SR magnified phase CT provides a detailed analysis of the lacuno-canalicular network and in addition information on the organization of the collagen fibers. These findings open new perspectives for three-dimensional quantitative assessment of bone tissue at the cellular scale.

SU-E-J-90: Lobar-Level Lung Ventilation Analysis Using 4DCT and Deformable Image Registration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, K; Bayouth, J; Patton, T

2015-06-15

Purpose: To assess regional changes in human lung ventilation and mechanics using four-dimensional computed tomography (4DCT) and deformable image registration. This work extends our prior analysis of the entire lung to a lobe-based analysis. Methods: 4DCT images acquired from 20 patients prior to radiation therapy (RT) were used for this analysis. Jacobian ventilation and motion maps were computed from the displacement field after deformable image registration between the end of expiration breathing phase and the end of inspiration breathing phase. The lobes were manually segmented on the reference phase by a medical physicist expert. The voxel-by-voxel ventilation and motion magnitudemore » for all subjects were grouped by lobes and plotted into cumulative voxel frequency curves respectively. In addition, to eliminate the effect of different breathing efforts across subjects, we applied the inter-subject equivalent lung volume (ELV) method on a subset of the cohort and reevaluated the lobar ventilation. Results: 95% of voxels in the lung are expanding during inspiration. However, some local regions of lung tissue show far more expansion than others. The greatest expansion with respiration occurs within the lower lobes; between exhale and inhale the median expansion in lower lobes is approximately 15%, while the median expansion in upper lobes is 10%. This appears to be driven by a subset of lung tissues within the lobe that have greater expansion; twice the number of voxels in the lower lobes (20%) expand by > 30% when compared to the upper lobes (10%). Conclusion: Lung ventilation and motion show significant difference on the lobar level. There are different lobar fractions of driving voxels that contribute to the major expansion of the lung. This work was supported by NIH grant CA166703.« less

Quantitative micro-elastography: imaging of tissue elasticity using compression optical coherence elastography

PubMed Central

Kennedy, Kelsey M.; Chin, Lixin; McLaughlin, Robert A.; Latham, Bruce; Saunders, Christobel M.; Sampson, David D.; Kennedy, Brendan F.

2015-01-01

Probing the mechanical properties of tissue on the microscale could aid in the identification of diseased tissues that are inadequately detected using palpation or current clinical imaging modalities, with potential to guide medical procedures such as the excision of breast tumours. Compression optical coherence elastography (OCE) maps tissue strain with microscale spatial resolution and can delineate microstructural features within breast tissues. However, without a measure of the locally applied stress, strain provides only a qualitative indication of mechanical properties. To overcome this limitation, we present quantitative micro-elastography, which combines compression OCE with a compliant stress sensor to image tissue elasticity. The sensor consists of a layer of translucent silicone with well-characterized stress-strain behaviour. The measured strain in the sensor is used to estimate the two-dimensional stress distribution applied to the sample surface. Elasticity is determined by dividing the stress by the strain in the sample. We show that quantification of elasticity can improve the ability of compression OCE to distinguish between tissues, thereby extending the potential for inter-sample comparison and longitudinal studies of tissue elasticity. We validate the technique using tissue-mimicking phantoms and demonstrate the ability to map elasticity of freshly excised malignant and benign human breast tissues. PMID:26503225

OpenStreetMap Collaborative Prototype, Phase 1

USGS Publications Warehouse

Wolf, Eric B.; Matthews, Greg D.; McNinch, Kevin; Poore, Barbara S.

2011-01-01

Phase One of the OpenStreetMap Collaborative Prototype (OSMCP) attempts to determine if the open source software developed for the OpenStreetMap (OSM, http://www.openstreetmap.org) can be used for data contributions and improvements that meet or exceed the requirements for integration into The National Map (http://www.nationalmap.gov). OpenStreetMap Collaborative Prototype Phase One focused on road data aggregated at the state level by the Kansas Data Access and Support Center (DASC). Road data from the DASC were loaded into a system hosted by the U.S. Geological Survey (USGS) National Geospatial Technical Operations Center (NGTOC) in Rolla, Missouri. U.S. Geological Survey editing specifications were developed by NGTOC personnel (J. Walters and G. Matthews, USGS, unpub. report, 2010). Interstate and U.S. Highways in the dataset were edited to the specifications by NGTOC personnel while State roads were edited by DASC personnel. Resulting data were successfully improved to meet standards for The National Map once the system and specifications were in place. The OSM software proved effective in providing a usable platform for collaborative data editing

Novel cardiac magnetic resonance biomarkers: native T1 and extracellular volume myocardial mapping.

PubMed

Cannaò, Paola Maria; Altabella, Luisa; Petrini, Marcello; Alì, Marco; Secchi, Francesco; Sardanelli, Francesco

2016-04-28

Cardiac magnetic resonance (CMR) is a non-invasive diagnostic tool playing a key role in the assessment of cardiac morphology and function as well as in tissue characterization. Late gadolinium enhancement is a fundamental CMR technique for detecting focal or regional abnormalities such as scar tissue, replacement fibrosis, or inflammation using qualitative, semi-quantitative, or quantitative methods, but not allowing for evaluating the whole myocardium in the presence of diffuse disease. The novel T1 mapping approach permits a quantitative assessment of the entire myocardium providing a voxel-by-voxel map of native T1 relaxation time, obtained before the intravenous administration of gadolinium-based contrast material. Combining T1 data obtained before and after contrast injection, it is also possible to calculate the voxel-by-voxel extracellular volume (ECV), resulting in another myocardial parametric map. This article describes technical challenges and clinical perspectives of these two novel CMR biomarkers: myocardial native T1 and ECV mapping.

An automated method for mapping human tissue permittivities by MRI in hyperthermia treatment planning.

PubMed

Farace, P; Pontalti, R; Cristoforetti, L; Antolini, R; Scarpa, M

1997-11-01

This paper presents an automatic method to obtain tissue complex permittivity values to be used as input data in the computer modelling for hyperthermia treatment planning. Magnetic resonance (MR) images were acquired and the tissue water content was calculated from the signal intensity of the image pixels. The tissue water content was converted into complex permittivity values by monotonic functions based on mixture theory. To obtain a water content map by MR imaging a gradient-echo pulse sequence was used and an experimental procedure was set up to correct for relaxation and radiofrequency field inhomogeneity effects on signal intensity. Two approaches were followed to assign the permittivity values to fat-rich tissues: (i) fat-rich tissue localization by a segmentation procedure followed by assignment of tabulated permittivity values; (ii) water content evaluation by chemical shift imaging followed by permittivity calculation. Tests were performed on phantoms of known water content to establish the reliability of the proposed method. MRI data were acquired and processed pixel-by-pixel according to the outlined procedure. The signal intensity in the phantom images correlated well with water content. Experiments were performed on volunteers' healthy tissue. In particular two anatomical structures were chosen to calculate permittivity maps: the head and the thigh. The water content and electric permittivity values were obtained from the MRI data and compared to others in the literature. A good agreement was found for muscle, cerebrospinal fluid (CSF) and white and grey matter. The advantages of the reported method are discussed in the light of possible application in hyperthermia treatment planning.

{sup 18}F-FLT uptake kinetics in head and neck squamous cell carcinoma: A PET imaging study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Dan, E-mail: dan.liu@oncology.ox.ac.uk; Fenwick, John D.; Chalkidou, Anastasia

2014-04-15

Purpose: To analyze the kinetics of 3{sup ′}-deoxy-3{sup ′}-[F-18]-fluorothymidine (18F-FLT) uptake by head and neck squamous cell carcinomas and involved nodes imaged using positron emission tomography (PET). Methods: Two- and three-tissue compartment models were fitted to 12 tumor time-activity-curves (TACs) obtained for 6 structures (tumors or involved nodes) imaged in ten dynamic PET studies of 1 h duration, carried out for five patients. The ability of the models to describe the data was assessed using a runs test, the Akaike information criterion (AIC) and leave-one-out cross-validation. To generate parametric maps the models were also fitted to TACs of individual voxels.more » Correlations between maps of different parameters were characterized using Pearson'sr coefficient; in particular the phosphorylation rate-constants k{sub 3-2tiss} and k{sub 5} of the two- and three-tissue models were studied alongside the flux parameters K{sub FLT-2tiss} and K{sub FLT} of these models, and standardized uptake values (SUV). A methodology based on expectation-maximization clustering and the Bayesian information criterion (“EM-BIC clustering”) was used to distil the information from noisy parametric images. Results: Fits of two-tissue models 2C3K and 2C4K and three-tissue models 3C5K and 3C6K comprising three, four, five, and six rate-constants, respectively, pass the runs test for 4, 8, 10, and 11 of 12 tumor TACs. The three-tissue models have lower AIC and cross-validation scores for nine of the 12 tumors. Overall the 3C6K model has the lowest AIC and cross-validation scores and its fitted parameter values are of the same orders of magnitude as literature estimates. Maps ofK{sub FLT} and K{sub FLT-2tiss} are strongly correlated (r = 0.85) and also correlate closely with SUV maps (r = 0.72 for K{sub FLT-2tiss}, 0.64 for K{sub FLT}). Phosphorylation rate-constant maps are moderately correlated with flux maps (r = 0.48 for k{sub 3-2tiss} vs K{sub FLT-2tiss} and r = 0.68 for k{sub 5} vs K{sub FLT}); however, neither phosphorylation rate-constant correlates significantly with SUV. EM-BIC clustering reduces the parametric maps to a small number of levels—on average 5.8, 3.5, 3.4, and 1.4 for K{sub FLT-2tiss}, K{sub FLT}, k{sub 3-2tiss}, and k{sub 5.} This large simplification is potentially useful for radiotherapy dose-painting, but demonstrates the high noise in some maps. Statistical simulations show that voxel level noise degrades TACs generated from the 3C6K model sufficiently that the average AIC score, parameter bias, and total uncertainty of 2C4K model fits are similar to those of 3C6K fits, whereas at the whole tumor level the scores are lower for 3C6K fits. Conclusions: For the patients studied here, whole tumor FLT uptake time-courses are represented better overall by a three-tissue than by a two-tissue model. EM-BIC clustering simplifies noisy parametric maps, providing the best description of the underlying information they contain and is potentially useful for radiotherapy dose-painting. However, the clustering highlights the large degree of noise present in maps of the phosphorylation rate-constantsk{sub 5} and k{sub 3-2tiss}, which are conceptually tightly linked to cellular proliferation. Methods must be found to make these maps more robust—either by constraining other model parameters or modifying dynamic imaging protocols.« less

Stem Cell Therapy to Improve Burn Wound Healing

DTIC Science & Technology

2017-03-01

Aim(s) • Perform Phase 1 Trial of Allogeneic MSCs in Burns • Perform Phase 2 Trial of Allogeneic MSCs in Burns • Collect Tissue Repository for...for safety/dose studies CY15 Goal – Continue Phase 1 and, Start Tissue Repository  Continue donors recruitment, screening and Bone Marrow Aspiration...1 Trial and Collect Tissue Repository  Continue donors recruitment, screening and Bone Marrow Aspiration as needed.  Continue patients screening

Color image encryption based on gyrator transform and Arnold transform

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Gao, Bo

2013-06-01

A color image encryption scheme using gyrator transform and Arnold transform is proposed, which has two security levels. In the first level, the color image is separated into three components: red, green and blue, which are normalized and scrambled using the Arnold transform. The green component is combined with the first random phase mask and transformed to an interim using the gyrator transform. The first random phase mask is generated with the sum of the blue component and a logistic map. Similarly, the red component is combined with the second random phase mask and transformed to three-channel-related data. The second random phase mask is generated with the sum of the phase of the interim and an asymmetrical tent map. In the second level, the three-channel-related data are scrambled again and combined with the third random phase mask generated with the sum of the previous chaotic maps, and then encrypted into a gray scale ciphertext. The encryption result has stationary white noise distribution and camouflage property to some extent. In the process of encryption and decryption, the rotation angle of gyrator transform, the iterative numbers of Arnold transform, the parameters of the chaotic map and generated accompanied phase function serve as encryption keys, and hence enhance the security of the system. Simulation results and security analysis are presented to confirm the security, validity and feasibility of the proposed scheme.

Combinatorial materials synthesis and high-throughput screening: an integrated materials chip approach to mapping phase diagrams and discovery and optimization of functional materials.

PubMed

Xiang, X D

Combinatorial materials synthesis methods and high-throughput evaluation techniques have been developed to accelerate the process of materials discovery and optimization and phase-diagram mapping. Analogous to integrated circuit chips, integrated materials chips containing thousands of discrete different compositions or continuous phase diagrams, often in the form of high-quality epitaxial thin films, can be fabricated and screened for interesting properties. Microspot x-ray method, various optical measurement techniques, and a novel evanescent microwave microscope have been used to characterize the structural, optical, magnetic, and electrical properties of samples on the materials chips. These techniques are routinely used to discover/optimize and map phase diagrams of ferroelectric, dielectric, optical, magnetic, and superconducting materials.

Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

NASA Astrophysics Data System (ADS)

Yarnykh, V.; Korostyshevskaya, A.

2017-08-01

Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

Tissue refractometry using Hilbert phase microscopy

PubMed Central

Lue, Niyom; Bewersdorf, Joerg; Lessard, Mark D.; Badizadegan, Kamran; Dasari, Ramachandra R.; Feld, Michael S.; Popescu, Gabriel

2009-01-01

We present, for the first time to our knowledge, quantitative phase images associated with unstained 5 μm thick tissue slices of mouse brain, spleen, and liver. The refractive properties of the tissue are retrieved in terms of the average refractive index and its spatial variation. We find that the average refractive index varies significantly with tissue type, such that the brain is characterized by the lowest value and the liver by the highest. The spatial power spectra of the phase images reveal power law behavior with different exponents for each tissue type. This approach opens a new possibility for stain-free characterization of tissues, where the diagnostic power is provided by the intrinsic refractive properties of the biological structure. We present results obtained for liver tissue affected by a lysosomal storage disease and show that our technique can quantify structural changes during this disease development. PMID:18087529

Real-time three-dimensional temperature mapping in photothermal therapy with optoacoustic tomography

NASA Astrophysics Data System (ADS)

Oyaga Landa, Francisco Javier; Deán-Ben, Xosé Luís.; Sroka, Ronald; Razansky, Daniel

2017-07-01

Ablation and photothermal therapy are widely employed medical protocols where the selective destruction of tissue is a necessity as in cancerous tissue removal or vascular and brain abnormalities. Tissue denaturation takes place when the temperature reaches a threshold value while the time of exposure determines the lesion size. Therefore, the spatio-temporal distribution of temperature plays a crucial role in the outcome of these clinical interventions. We demonstrate fast volumetric temperature mapping with optoacoustic tomography based on real-time optoacoustic readings from the treated region. The performance of the method was investigated in tissue-mimicking phantom experiments. The new ability to non-invasively measure temperature volumetrically in an entire treated region with high spatial and temporal resolutions holds potential for improving safety and efficacy of thermal ablation and to advance the general applicability of laser-based therapy.

Hyperspectral Stimulated Raman Scattering Microscopy Unravels Aberrant Accumulation of Saturated Fat in Human Liver Cancer.

PubMed

Yan, Shuai; Cui, Sishan; Ke, Kun; Zhao, Bixing; Liu, Xiaolong; Yue, Shuhua; Wang, Ping

2018-06-05

Lipid metabolism is dysregulated in human cancers. The analytical tools that could identify and quantitatively map metabolites in unprocessed human tissues with submicrometer resolution are highly desired. Here, we implemented analytical hyperspectral stimulated Raman scattering microscopy to map the lipid metabolites in situ in normal and cancerous liver tissues from 24 patients. In contrast to the conventional wisdom that unsaturated lipid accumulation enhances tumor cell survival and proliferation, we unexpectedly visualized substantial amount of saturated fat accumulated in cancerous liver tissues, which was not seen in majority of their adjacent normal tissues. Further analysis by mass spectrometry confirmed significant high levels of glyceryl tripalmitate specifically in cancerous liver. These findings suggest that the aberrantly accumulated saturated fat may have great potential to be a metabolic biomarker for liver cancer.

Spatial analysis of biomineralization associated gene expression from the mantle organ of the pearl oyster Pinctada maxima

PubMed Central

2011-01-01

Background Biomineralization is a process encompassing all mineral containing tissues produced within an organism. One of the most dynamic examples of this process is the formation of the mollusk shell, comprising a variety of crystal phases and microstructures. The organic component incorporated within the shell is said to dictate this architecture. However general understanding of how this process is achieved remains ambiguous. The mantle is a conserved organ involved in shell formation throughout molluscs. Specifically the mantle is thought to be responsible for secreting the protein component of the shell. This study employs molecular approaches to determine the spatial expression of genes within the mantle tissue to further the elucidation of the shell biomineralization. Results A microarray platform was custom generated (PmaxArray 1.0) from the pearl oyster Pinctada maxima. PmaxArray 1.0 consists of 4992 expressed sequence tags (ESTs) originating from mantle tissue. This microarray was used to analyze the spatial expression of ESTs throughout the mantle organ. The mantle was dissected into five discrete regions and analyzed for differential gene expression with PmaxArray 1.0. Over 2000 ESTs were determined to be differentially expressed among the tissue sections, identifying five major expression regions. In situ hybridization validated and further localized the expression for a subset of these ESTs. Comparative sequence similarity analysis of these ESTs revealed a number of the transcripts were novel while others showed significant sequence similarities to previously characterized shell related genes. Conclusions This investigation has mapped the spatial distribution for over 2000 ESTs present on PmaxArray 1.0 with reference to specific locations of the mantle. Expression profile clusters have indicated at least five unique functioning zones in the mantle. Three of these zones are likely involved in shell related activities including formation of nacre, periostracum and calcitic prismatic microstructure. A number of novel and known transcripts have been identified from these clusters. The development of PmaxArray 1.0, and the spatial map of its ESTs expression in the mantle has begun characterizing the molecular mechanisms linking the organics and inorganics of the molluscan shell. PMID:21936921

Exploring the Nuclear Phase Diagram with Beam Energy Scans

NASA Astrophysics Data System (ADS)

Horvat, Stephen

2017-04-01

The nuclear phase diagram is mapped using beam energy scans of relativistic heavy-ion collisions. This mapping is possible because different collision energies develop along different trajectories through the phase diagram. High energy collisions will evolve though a crossover phase transition according to lattice QCD, but lower collision energies may traverse a first order phase transition. There are hints for this first order phase transition and its critical endpoint, but further measurements and theoretical guidance is needed. In addition to mapping the phase transition, beam energy scans allow us to see if we can turn off the signatures of deconfinement. If an observable is a real signature for the formation of the deconfined state called quark-gluon plasma, then it should turn off at sufficiently low collision energies. In this summary talk I will show the current state of the field using beam energy scan results from RHIC and SPS, I will show where precise theoretical guidance is needed for understanding recent measurements, and I will motivate the need for more data and new measurements from FAIR, NICA, RHIC, and the SPS.

Serial analysis of gene expression (SAGE) in normal human trabecular meshwork.

PubMed

Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Allingham, R Rand; Hauser, Michael A

2011-04-08

To identify the genes expressed in normal human trabecular meshwork tissue, a tissue critical to the pathogenesis of glaucoma. Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

Dual-energy CT iodine maps as an alternative quantitative imaging biomarker to abdominal CT perfusion: determination of appropriate trigger delays for acquisition using bolus tracking.

PubMed

Skornitzke, Stephan; Fritz, Franziska; Mayer, Philipp; Koell, Marco; Hansen, Jens; Pahn, Gregor; Hackert, Thilo; Kauczor, Hans-Ulrich; Stiller, Wolfram

2018-05-01

Quantitative evaluation of different bolus tracking trigger delays for acquisition of dual energy (DE) CT iodine maps as an alternative to CT perfusion. Prior to this retrospective analysis of prospectively acquired data, DECT perfusion sequences were dynamically acquired in 22 patients with pancreatic carcinoma using dual source CT at 80/140 kV p with tin filtration. After deformable motion-correction, perfusion maps of blood flow (BF) were calculated from 80 kV p image series of DECT, and iodine maps were calculated for each of the 34 DECT acquisitions per patient. BF and iodine concentrations were measured in healthy pancreatic tissue and carcinoma. To evaluate potential DECT acquisition triggered by bolus tracking, measured iodine concentrations from the 34 DECT acquisitions per patient corresponding to different trigger delays were assessed for correlation to BF and intergroup differences between tissue types depending on acquisition time. Average BF measured in healthy pancreatic tissue and carcinoma was 87.6 ± 28.4 and 38.6 ± 22.2 ml/100 ml min -1 , respectively. Correlation between iodine concentrations and BF was statistically significant for bolus tracking with trigger delay greater than 0 s (r max = 0.89; p < 0.05). Differences in iodine concentrations between healthy pancreatic tissue and carcinoma were statistically significant for DECT acquisitions corresponding to trigger delays of 15-21 s (p < 0.05). An acquisition window between 15 and 21 s after exceeding bolus tracking threshold shows promising results for acquisition of DECT iodine maps as an alternative to CT perfusion measurements of BF. Advances in knowledge: After clinical validation, DECT iodine maps of pancreas acquired using bolus tracking with appropriate trigger delay as determined in this study could offer an alternative quantitative imaging biomarker providing functional information for tumor assessment at reduced patient radiation exposure compared to CT perfusion measurements of BF.

MO-A-BRD-05: Evaluation of Composed Lung Ventilation with 4DCT and Image Registration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, K; Bayouth, J; Reinhardt, J

Purpose: Regional pulmonary function can be derived using fourdimensional computed tomography (4DCT) combined with deformable image registration. However, only peak inhale and exhale phases have been used thus far while the lung ventilation during intermediate phases is not considered. In our previous work, we have investigated the spatiotemporal heterogeneity of lung ventilation and its dependence on respiration effort. In this study, composed ventilation is introduced using all inspiration phases and compared to direct ventilation. Both methods are evaluated against Xe-CT derived ventilation. Methods: Using an in-house tissue volume preserving deformable image registration, unlike the direct ventilation method, which computes frommore » end expiration to end inspiration, Jacobian ventilation maps were computed from one inhale phase to the next and then composed from all inspiration steps. The two methods were compared in both patients prior to RT and mechanically ventilated sheep subjects. In addition, they wereassessed for the correlation with Xe-CT derived ventilation in sheep subjects. Annotated lung landmarks were used to evaluate the accuracy of original and composed deformation field. Results: After registration, the landmark distance for composed deformation field was always higher than that for direct deformation field (0IN to 100IN average in human: 1.03 vs 1.53, p=0.001, and in sheep: 0.80 vs0.94, p=0.009), and both increased with longer phase interval. Direct and composed ventilation maps were similar in both sheep (gamma pass rate 87.6) and human subjects (gamma pass rate 71.9),and showed consistent pattern from ventral to dorsal when compared to Xe-CT derived ventilation. Correlation coefficient between Xe-CT and composed ventilation was slightly better than the direct method but not significant (average 0.89 vs 0.85, p=0.135). Conclusion: More strict breathing control in sheep subjects may explain higher similarity between direct and composed ventilation. When compared to Xe-CT ventilation, no significant difference was found for the composed method. NIH Grant: R01 CA166703.« less

Optical sensor nanoparticles in artificial sediments--a new tool to visualize O2 dynamics around the rhizome and roots of seagrasses.

PubMed

Koren, Klaus; Brodersen, Kasper E; Jakobsen, Sofie L; Kühl, Michael

2015-02-17

Seagrass communities provide important ecosystems services in coastal environments but are threatened by anthropogenic impacts. Especially the ability of seagrasses to aerate their below-ground tissue and immediate rhizosphere to prevent sulfide intrusion from the surrounding sediment is critical for their resilience to environmental disturbance. There is a need for chemical techniques that can map the O2 distribution and dynamics in the seagrass rhizosphere upon environmental changes and thereby identify critical stress thresholds of e.g. water flow, turbidity, and O2 conditions in the water phase. In a novel experimental approach, we incorporated optical O2 sensor nanoparticles into a transparent artificial sediment matrix consisting of pH-buffered deoxygenated sulfidic agar. Seagrass growth and photosynthesis was not inhibited in the experimental setup when the below-ground biomass was immobilized in the artificial sulfidic sediment with nanoparticles and showed root growth rates (∼ 5 mm day(-1)) and photosynthetic quantum yields (∼ 0.7) comparable to healthy seagrasses in their natural habitat. We mapped the real-time below ground O2 distribution and dynamics in the whole seagrass rhizosphere during experimental manipulation of light exposure and O2 content in the overlaying water. Those manipulations showed that oxygen release from the belowground tissue is much higher in light as compared to darkness and that water column hypoxia leads to diminished oxygen levels around the rhizome/roots. Oxygen release was visualized and analyzed on a whole rhizosphere level, which is a substantial improvement to existing methods relying on point measurements with O2 microsensors or partial mapping of the rhizosphere in close contact with a planar O2 optode. The combined use of optical nanoparticle-based sensors with artificial sediments enables imaging of chemical microenvironments in the rhizosphere of aquatic plants at high spatiotemporal resolution with a relatively simple experimental setup and thus represents a significant methodological advancement for studies of environmental impacts on aquatic plant ecophysiology.

Variable Sampling Mapping

NASA Technical Reports Server (NTRS)

Smith, Jeffrey, S.; Aronstein, David L.; Dean, Bruce H.; Lyon, Richard G.

2012-01-01

The performance of an optical system (for example, a telescope) is limited by the misalignments and manufacturing imperfections of the optical elements in the system. The impact of these misalignments and imperfections can be quantified by the phase variations imparted on light traveling through the system. Phase retrieval is a methodology for determining these variations. Phase retrieval uses images taken with the optical system and using a light source of known shape and characteristics. Unlike interferometric methods, which require an optical reference for comparison, and unlike Shack-Hartmann wavefront sensors that require special optical hardware at the optical system's exit pupil, phase retrieval is an in situ, image-based method for determining the phase variations of light at the system s exit pupil. Phase retrieval can be used both as an optical metrology tool (during fabrication of optical surfaces and assembly of optical systems) and as a sensor used in active, closed-loop control of an optical system, to optimize performance. One class of phase-retrieval algorithms is the iterative transform algorithm (ITA). ITAs estimate the phase variations by iteratively enforcing known constraints in the exit pupil and at the detector, determined from modeled or measured data. The Variable Sampling Mapping (VSM) technique is a new method for enforcing these constraints in ITAs. VSM is an open framework for addressing a wide range of issues that have previously been considered detrimental to high-accuracy phase retrieval, including undersampled images, broadband illumination, images taken at or near best focus, chromatic aberrations, jitter or vibration of the optical system or detector, and dead or noisy detector pixels. The VSM is a model-to-data mapping procedure. In VSM, fully sampled electric fields at multiple wavelengths are modeled inside the phase-retrieval algorithm, and then these fields are mapped to intensities on the light detector, using the properties of the detector and optical system, for comparison with measured data. Ultimately, this model-to-data mapping procedure enables a more robust and accurate way of incorporating the exit-pupil and image detector constraints, which are fundamental to the general class of ITA phase retrieval algorithms.

Using NIR spatial illumination for detection and mapping chromophore changes during cerebral edema

NASA Astrophysics Data System (ADS)

Abookasis, David; Mathews, Marlon S.; Owen, Christopher M.; Binder, Devin K.; Linskey, Mark E.; Frostig, Ron D.; Tromberg, Bruce J.

2008-02-01

We used spatially modulated near-infrared (NIR) light to detect and map chromophore changes during cerebral edema in the rat neocortex. Cerebral edema was induced by intraperitoneal injections of free water (35% of body weight). Intracranial pressure (ICP) was measured with an optical fiber based Fabry-Perot interferometer sensor inserted into the parenchyma of the right frontal lobe during water administration. Increase in ICP from a baseline value of 10 cm-water to 145 cm-water was observed. Following induction of cerebral edema, there was a 26+/-1.7% increase in tissue concentration of deoxyhemoglobin and a 47+/-4.7%, 17+/-3% and 37+/-3.7% decrease in oxyhemoglobin, total hemoglobin concentration and cerebral tissue oxygen saturation levels, respectively. To the best of our knowledge, this is the first report describing the use of NIR spatial modulation of light for detecting and mapping changes in tissue concentrations of physiologic chromophores over time in response to cerebral edema.

CT Perfusion in Acute Stroke: "Black Holes" on Time-to-Peak Image Maps Indicate Unsalvageable Brain.

PubMed

Meagher, Ruairi; Shankar, Jai Jai Shiva

2016-11-01

CT perfusion is becoming important in acute stroke imaging to determine optimal patient-management strategies. The purpose of this study was to examine the predictive value of time-to-peak image maps and, specifically, a phenomenon coined a "black hole" for assessing infarcted brain tissue at the time of scan. Acute stroke patients were screened for the presence of black holes and their follow-up imaging (noncontrast CT or MR) was reviewed to assess for infarcted brain tissue. Of the 23 patients with signs of acute ischemia on CT perfusion, all had black holes. The black holes corresponded with areas of infarcted brain on follow-up imaging (specificity 100%). Black holes demonstrated significantly lower cerebral blood volumes (P < .001) and cerebral blood flow (P < .001) compared to immediately adjacent tissue. Black holes on time-to-peak image maps represent areas of unsalvageable brain. Copyright © 2016 by the American Society of Neuroimaging.

Automated cell-type classification in intact tissues by single-cell molecular profiling

PubMed Central

2018-01-01

A major challenge in biology is identifying distinct cell classes and mapping their interactions in vivo. Tissue-dissociative technologies enable deep single cell molecular profiling but do not provide spatial information. We developed a proximity ligation in situ hybridization technology (PLISH) with exceptional signal strength, specificity, and sensitivity in tissue. Multiplexed data sets can be acquired using barcoded probes and rapid label-image-erase cycles, with automated calculation of single cell profiles, enabling clustering and anatomical re-mapping of cells. We apply PLISH to expression profile ~2900 cells in intact mouse lung, which identifies and localizes known cell types, including rare ones. Unsupervised classification of the cells indicates differential expression of ‘housekeeping’ genes between cell types, and re-mapping of two sub-classes of Club cells highlights their segregated spatial domains in terminal airways. By enabling single cell profiling of various RNA species in situ, PLISH can impact many areas of basic and medical research. PMID:29319504

Color image encryption by using Yang-Gu mixture amplitude-phase retrieval algorithm in gyrator transform domain and two-dimensional Sine logistic modulation map

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Liu, Benqing; Wang, Qiang; Li, Ye; Liang, Junli

2015-12-01

A color image encryption scheme is proposed based on Yang-Gu mixture amplitude-phase retrieval algorithm and two-coupled logistic map in gyrator transform domain. First, the color plaintext image is decomposed into red, green and blue components, which are scrambled individually by three random sequences generated by using the two-dimensional Sine logistic modulation map. Second, each scrambled component is encrypted into a real-valued function with stationary white noise distribution in the iterative amplitude-phase retrieval process in the gyrator transform domain, and then three obtained functions are considered as red, green and blue channels to form the color ciphertext image. Obviously, the ciphertext image is real-valued function and more convenient for storing and transmitting. In the encryption and decryption processes, the chaotic random phase mask generated based on logistic map is employed as the phase key, which means that only the initial values are used as private key and the cryptosystem has high convenience on key management. Meanwhile, the security of the cryptosystem is enhanced greatly because of high sensitivity of the private keys. Simulation results are presented to prove the security and robustness of the proposed scheme.

Crust structure beneath Jilin Province and Liaoning Province in China based on seismic ambient noise tomography

NASA Astrophysics Data System (ADS)

Pang, Guanghua; Feng, Jikun; Lin, Jun

2016-11-01

We imaged the crust structure beneath Jilin Province and Liaoning Province in China with fundamental mode Rayleigh waves recorded by 60 broadband stations deployed in the region. Surface-wave empirical Green's functions were retrieved from cross-correlations of inter-station data and phase velocity dispersions were measured using a frequency-time analysis method. Dispersion measurements were then utilized to construct 2D phase velocity maps for periods between 5 and 35 s. Subsequently, the phase-dispersion curves extracted from each cell of the 2D phase velocity maps were inverted to determine the 3D shear wave velocity structures of the crust. The phase velocity maps at different periods reflected the average velocity structures corresponding to different depth ranges. The maps in short periods, in particular, were in excellent agreement with known geological features of the surface. In addition to imaging shear wave velocity structures of the volcanoes, we show that obvious low-velocity anomalies imaged in the Changbaishan-Tianchi Volcano, the Longgang-Jinlongdingzi Volcano, and the system of the Dunmi Fault crossing the Jingbohu Volcano, all of which may be due to geothermal anomalies.

Phased-array ultrasonic surface contour mapping system and method for solids hoppers and the like

DOEpatents

Fasching, George E.; Smith, Jr., Nelson S.

1994-01-01

A real time ultrasonic surface contour mapping system is provided including a digitally controlled phased-array of transmitter/receiver (T/R) elements located in a fixed position above the surface to be mapped. The surface is divided into a predetermined number of pixels which are separately scanned by an arrangement of T/R elements by applying phase delayed signals thereto that produce ultrasonic tone bursts from each T/R that arrive at a point X in phase and at the same time relative to the leading edge of the tone burst pulse so that the acoustic energies from each T/R combine in a reinforcing manner at point X. The signals produced by the reception of the echo signals reflected from point X back to the T/Rs are also delayed appropriately so that they add in phase at the input of a signal combiner. This combined signal is then processed to determine the range to the point X using density-corrected sound velocity values. An autofocusing signal is developed from the computed average range for a complete scan of the surface pixels. A surface contour map is generated in real time form the range signals on a video monitor.

Two-dimensional ice mapping of molecular cores

NASA Astrophysics Data System (ADS)

Noble, J. A.; Fraser, H. J.; Pontoppidan, K. M.; Craigon, A. M.

2017-06-01

We present maps of the column densities of H2O, CO2 and CO ices towards the molecular cores B 35A, DC 274.2-00.4, BHR 59 and DC 300.7-01.0. These ice maps, probing spatial distances in molecular cores as low as 2200 au, challenge the traditional hypothesis that the denser the region observed, the more ice is present, providing evidence that the relationships between solid molecular species are more varied than the generic picture we often adopt to model gas-grain chemical processes and explain feedback between solid phase processes and gas phase abundances. We present the first combined solid-gas maps of a single molecular species, based upon observations of both CO ice and gas phase C18O towards B 35A, a star-forming dense core in Orion. We conclude that molecular species in the solid phase are powerful tracers of 'small-scale' chemical diversity, prior to the onset of star formation. With a component analysis approach, we can probe the solid phase chemistry of a region at a level of detail greater than that provided by statistical analyses or generic conclusions drawn from single pointing line-of-sight observations alone.

Correlation characteristics of phase and amplitude chimeras in an ensemble of nonlocally coupled maps

NASA Astrophysics Data System (ADS)

Vadivasova, T. E.; Strelkova, G. I.; Bogomolov, S. A.; Anishchenko, V. S.

2017-01-01

Correlation characteristics of chimera states have been calculated using the coefficient of mutual correlation of elements in a closed-ring ensemble of nonlocally coupled chaotic maps. Quantitative differences between the coefficients of mutual correlation for phase and amplitude chimeras are established for the first time.

Development and Implementation of High-Throughput SNP Genotyping in Barley

USDA-ARS?s Scientific Manuscript database

Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Pilot phase data from three barley doubled haploid mapping populations supported the production of an initial consensus map, ...

Association of intraoperative tissue oxygenation with suspected risk factors for tissue hypoxia.

PubMed

Spruit, R J; Schwarte, L A; Hakenberg, O W; Scheeren, T W L

2013-10-01

Tissue hypoxia may cause organ dysfunction, but not much is known about tissue oxygenation in the intraoperative setting. We studied microcirculatory tissue oxygen saturation (StO₂) to determine representative values for anesthetized patients undergoing urological surgery and to test the hypothesis that StO₂ is associated with known perioperative risk factors for morbidity and mortality, conventionally monitored variables, and hypotension requiring norepinephrine. Using near-infrared spectroscopy, we measured StO₂ on the thenar eminence in 160 patients undergoing open urological surgery under general anesthesia (FiO2 0.35-0.4), and calculated its correlations with age, risk level for general perioperative complications and mortality (high if age ≥70 and procedure is radical cystectomy), mean arterial pressure (MAP), hemoglobin concentration (Hb), central venous oxygen saturation (ScvO₂), and norepinephrine use. The time averaged StO₂ was 86 ± 6 % (mean ± SD). In the multivariate analysis, Hb [standardized coefficient (SC) 0.21, p = 0.003], ScvO₂ (SC 0.53, p < 0.001) and high risk level (SC 0.06, p = 0.03) were significant independent variables correlated with StO₂. SStO₂ was partly dependent on MAP only when this was below 65 mmHg (lowest MAP SC 0.20, p = 0.006, MAP area under the curve <65 mmHg SC 0.03, p = 0.02). Finally, StO₂ was slightly lower in patients requiring norepinephrine (85 ± 6 vs. 89 ± 6 %, p = 0.001). Intraoperative StO₂ in urological patients was comparable to that of healthy volunteers breathing room air as reported in the literature and correlated with known perioperative risk factors. Further research should investigate its association with outcome and the effect of interventions aimed at optimizing StO₂.

Evaluation of linear discriminant analysis for automated Raman histological mapping of esophageal high-grade dysplasia

NASA Astrophysics Data System (ADS)

Hutchings, Joanne; Kendall, Catherine; Shepherd, Neil; Barr, Hugh; Stone, Nicholas

2010-11-01

Rapid Raman mapping has the potential to be used for automated histopathology diagnosis, providing an adjunct technique to histology diagnosis. The aim of this work is to evaluate the feasibility of automated and objective pathology classification of Raman maps using linear discriminant analysis. Raman maps of esophageal tissue sections are acquired. Principal component (PC)-fed linear discriminant analysis (LDA) is carried out using subsets of the Raman map data (6483 spectra). An overall (validated) training classification model performance of 97.7% (sensitivity 95.0 to 100% and specificity 98.6 to 100%) is obtained. The remainder of the map spectra (131,672 spectra) are projected onto the classification model resulting in Raman images, demonstrating good correlation with contiguous hematoxylin and eosin (HE) sections. Initial results suggest that LDA has the potential to automate pathology diagnosis of esophageal Raman images, but since the classification of test spectra is forced into existing training groups, further work is required to optimize the training model. A small pixel size is advantageous for developing the training datasets using mapping data, despite lengthy mapping times, due to additional morphological information gained, and could facilitate differentiation of further tissue groups, such as the basal cells/lamina propria, in the future, but larger pixels sizes (and faster mapping) may be more feasible for clinical application.

The role of necrosis, acute hypoxia and chronic hypoxia in 18F-FMISO PET image contrast: a computational modelling study

NASA Astrophysics Data System (ADS)

Warren, Daniel R.; Partridge, Mike

2016-12-01

Positron emission tomography (PET) using 18F-fluoromisonidazole (FMISO) is a promising technique for imaging tumour hypoxia, and a potential target for radiotherapy dose-painting. However, the relationship between FMISO uptake and oxygen partial pressure ({{P}{{\\text{O}2}}} ) is yet to be quantified fully. Tissue oxygenation varies over distances much smaller than clinical PET resolution (<100 μm versus  ˜4 mm), and cyclic variations in tumour perfusion have been observed on timescales shorter than typical FMISO PET studies (˜20 min versus a few hours). Furthermore, tracer uptake may be decreased in voxels containing some degree of necrosis. This work develops a computational model of FMISO uptake in millimetre-scale tumour regions. Coupled partial differential equations govern the evolution of oxygen and FMISO distributions, and a dynamic vascular source map represents temporal variations in perfusion. Local FMISO binding capacity is modulated by the necrotic fraction. Outputs include spatiotemporal maps of {{P}{{\\text{O}2}}} and tracer accumulation, enabling calculation of tissue-to-blood ratios (TBRs) and time-activity curves (TACs) as a function of mean tissue oxygenation. The model is characterised using experimental data, finding half-maximal FMISO binding at local {{P}{{\\text{O}2}}} of 1.4 mmHg (95% CI: 0.3-2.6 mmHg) and half-maximal necrosis at 1.2 mmHg (0.1-4.9 mmHg). Simulations predict a non-linear non-monotonic relationship between FMISO activity (4 hr post-injection) and mean tissue {{P}{{\\text{O}2}}} : tracer uptake rises sharply from negligible levels in avascular tissue, peaking at  ˜5 mmHg and declining towards blood activity in well-oxygenated conditions. Greater temporal variation in perfusion increases peak TBRs (range 2.20-5.27) as a result of smaller predicted necrotic fraction, rather than fundamental differences in FMISO accumulation under acute hypoxia. Identical late FMISO uptake can occur in regions with differing {{P}{{\\text{O}2}}} and necrotic fraction, but simulated TACs indicate that additional early-phase information may allow discrimination of hypoxic and necrotic signals. We conclude that a robust approach to FMISO interpretation (and dose-painting prescription) is likely to be based on dynamic PET analysis.

The role of necrosis, acute hypoxia and chronic hypoxia in 18F-FMISO PET image contrast: a computational modelling study.

PubMed

Warren, Daniel R; Partridge, Mike

2016-12-21

Positron emission tomography (PET) using 18 F-fluoromisonidazole (FMISO) is a promising technique for imaging tumour hypoxia, and a potential target for radiotherapy dose-painting. However, the relationship between FMISO uptake and oxygen partial pressure ([Formula: see text]) is yet to be quantified fully. Tissue oxygenation varies over distances much smaller than clinical PET resolution (<100 μm versus  ∼4 mm), and cyclic variations in tumour perfusion have been observed on timescales shorter than typical FMISO PET studies (∼20 min versus a few hours). Furthermore, tracer uptake may be decreased in voxels containing some degree of necrosis. This work develops a computational model of FMISO uptake in millimetre-scale tumour regions. Coupled partial differential equations govern the evolution of oxygen and FMISO distributions, and a dynamic vascular source map represents temporal variations in perfusion. Local FMISO binding capacity is modulated by the necrotic fraction. Outputs include spatiotemporal maps of [Formula: see text] and tracer accumulation, enabling calculation of tissue-to-blood ratios (TBRs) and time-activity curves (TACs) as a function of mean tissue oxygenation. The model is characterised using experimental data, finding half-maximal FMISO binding at local [Formula: see text] of 1.4 mmHg (95% CI: 0.3-2.6 mmHg) and half-maximal necrosis at 1.2 mmHg (0.1-4.9 mmHg). Simulations predict a non-linear non-monotonic relationship between FMISO activity (4 hr post-injection) and mean tissue [Formula: see text] : tracer uptake rises sharply from negligible levels in avascular tissue, peaking at  ∼5 mmHg and declining towards blood activity in well-oxygenated conditions. Greater temporal variation in perfusion increases peak TBRs (range 2.20-5.27) as a result of smaller predicted necrotic fraction, rather than fundamental differences in FMISO accumulation under acute hypoxia. Identical late FMISO uptake can occur in regions with differing [Formula: see text] and necrotic fraction, but simulated TACs indicate that additional early-phase information may allow discrimination of hypoxic and necrotic signals. We conclude that a robust approach to FMISO interpretation (and dose-painting prescription) is likely to be based on dynamic PET analysis.

Butterflies' wings deformations using high speed digital holographic interferometry

NASA Astrophysics Data System (ADS)

Mendoza Santoyo, Fernando; Aguayo, Daniel D.; de La Torre-Ibarra, Manuel H.; Salas-Araiza, Manuel D.

2011-08-01

A variety of efforts in different scientific disciplines have tried to mimic the insect's in-flight complex system. The gained knowledge has been applied to improve the performance of different flying artifacts. In this research report it is presented a displacement measurement on butterflies' wings using the optical noninvasive Digital Holographic Interferometry technique with out of plane sensitivity, using a high power cw laser and a high speed CMOS camera to record the unrepeatable displacement movements on these organic tissues. A series of digital holographic interferograms were recorded and the experimental results for several butterflies during flapping events. The relative unwrapped phase maps micro-displacements over the whole wing surface are shown in a wire-mesh representation. The difference between flying modes is remarkably depicted among them.

Imaging acoustic vibrations in an ear model using spectrally encoded interferometry

NASA Astrophysics Data System (ADS)

Grechin, Sveta; Yelin, Dvir

2018-01-01

Imaging vibrational patterns of the tympanic membrane would allow an accurate measurement of its mechanical properties and provide early diagnosis of various hearing disorders. Various optical technologies have been suggested to address this challenge and demonstrated in vitro using point scanning and full-field interferometry. Spectrally encoded imaging has been previously demonstrated capable of imaging tissue acoustic vibrations with high spatial resolution, including two-dimensional phase and amplitude mapping. In this work, we demonstrate a compact optical apparatus for imaging acoustic vibrations that could be incorporated into a commercially available digital otoscope. By transmitting harmonic sound waves through the otoscope insufflation port and analyzing the spectral interferograms using custom-built software, we demonstrate high-resolution vibration imaging of a circular rubber membrane within an ear model.

Spatial reconstruction of single-cell gene expression data.

PubMed

Satija, Rahul; Farrell, Jeffrey A; Gennert, David; Schier, Alexander F; Regev, Aviv

2015-05-01

Spatial localization is a key determinant of cellular fate and behavior, but methods for spatially resolved, transcriptome-wide gene expression profiling across complex tissues are lacking. RNA staining methods assay only a small number of transcripts, whereas single-cell RNA-seq, which measures global gene expression, separates cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos and generated a transcriptome-wide map of spatial patterning. We confirmed Seurat's accuracy using several experimental approaches, then used the strategy to identify a set of archetypal expression patterns and spatial markers. Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems.

Application of Monte-Carlo Analyses for the Microwave Anisotropy Probe (MAP) Mission

NASA Technical Reports Server (NTRS)

Mesarch, Michael A.; Rohrbaugh, David; Schiff, Conrad; Bauer, Frank H. (Technical Monitor)

2001-01-01

The Microwave Anisotropy Probe (MAP) is the third launch in the National Aeronautics and Space Administration's (NASA's) a Medium Class Explorers (MIDEX) program. MAP will measure, in greater detail, the cosmic microwave background radiation from an orbit about the Sun-Earth-Moon L2 Lagrangian point. Maneuvers will be required to transition MAP from it's initial highly elliptical orbit to a lunar encounter which will provide the remaining energy to send MAP out to a lissajous orbit about L2. Monte-Carlo analysis methods were used to evaluate the potential maneuver error sources and determine their effect of the fixed MAP propellant budget. This paper will discuss the results of the analyses on three separate phases of the MAP mission - recovering from launch vehicle errors, responding to phasing loop maneuver errors, and evaluating the effect of maneuver execution errors and orbit determination errors on stationkeeping maneuvers at L2.

Molecular deletion mapping of the Y chromosome in males with idiopathic azoospermia reveals a new class of microdeletions located in middle Yq11

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farah, S.B.; Ramos, C.F.; Bortoletto, R.K.

1994-09-01

Microdeletions in proximal and distal Yq11 found {open_quotes}de novo{close_quotes} in males with idiopathic azoospermia or a severe oligospermia suggested that these Y mutations interrupt the gene structure(s) of a spermatogenesis function located in Yq11 and defined earlier as AZF. Using an extended interval map, dividing Yq11 into 22 subintervals (D1-D22) a third class of microdeletions could now be mapped in middle Yq11. It was found {open_quotes}de novo{close_quotes} in two sterile males with idiopathic azoospermia. Histological analysis of testes tissue sections of both males reveals arrest of spermatogenesis during the pachytene stage. Y-mutations in proximal Yq11 were usually associated to anmore » arrest of spermatogenesis before the proliferation phase of spermatogonia; the corresponding Y gene was defined as {open_quotes}AZFa{close_quotes}. It is, therefore, assumed that the new class of microdeletions, observed now in the middle of Yq11, disrupt another Y spermatogenesis gene expressed during the spermatocyte stage and defined earlier as {open_quotes}AZFb{close_quotes}. Experimental evidence presented during the meeting will try to confirm this view discussing a series of Y genes (AZFa,b,c,...) in Yq11 functioning at different stages during human spermatogenesis.« less

Phase transitions in oleic acid and in human breast tissue as studied by Raman spectroscopy and Raman imaging.

PubMed

Brozek-Pluska, Beata; Jablonska-Gajewicz, Joanna; Kordek, Radzislaw; Abramczyk, Halina

2011-05-12

We present the results of differential scanning calorimetry (DSC) and Raman studies in the temperature range of 293-77 K on vibrational properties of the oleic acid and the human breast tissue as a function of temperature. We have found that vibrational properties are very sensitive indicators to specify phases and phase transitions at the molecular level. We have found that water content confined in the cancerous tissue is markedly different from that in the noncancerous tissue. The OH stretching vibrations of water are useful as potential Raman biomarkers to distinguish between the cancerous and the noncancerous human breast tissues. Our results provide experimental evidence on the role of lipid profile and cell hydration as factors of particular significance in differentiation of the noncancerous and cancerous breast tissues.

MRI-guided attenuation correction in whole-body PET/MR: assessment of the effect of bone attenuation.

PubMed

Akbarzadeh, A; Ay, M R; Ahmadian, A; Alam, N Riahi; Zaidi, H

2013-02-01

Hybrid PET/MRI presents many advantages in comparison with its counterpart PET/CT in terms of improved soft-tissue contrast, decrease in radiation exposure, and truly simultaneous and multi-parametric imaging capabilities. However, the lack of well-established methodology for MR-based attenuation correction is hampering further development and wider acceptance of this technology. We assess the impact of ignoring bone attenuation and using different tissue classes for generation of the attenuation map on the accuracy of attenuation correction of PET data. This work was performed using simulation studies based on the XCAT phantom and clinical input data. For the latter, PET and CT images of patients were used as input for the analytic simulation model using realistic activity distributions where CT-based attenuation correction was utilized as reference for comparison. For both phantom and clinical studies, the reference attenuation map was classified into various numbers of tissue classes to produce three (air, soft tissue and lung), four (air, lungs, soft tissue and cortical bones) and five (air, lungs, soft tissue, cortical bones and spongeous bones) class attenuation maps. The phantom studies demonstrated that ignoring bone increases the relative error by up to 6.8% in the body and up to 31.0% for bony regions. Likewise, the simulated clinical studies showed that the mean relative error reached 15% for lesions located in the body and 30.7% for lesions located in bones, when neglecting bones. These results demonstrate an underestimation of about 30% of tracer uptake when neglecting bone, which in turn imposes substantial loss of quantitative accuracy for PET images produced by hybrid PET/MRI systems. Considering bones in the attenuation map will considerably improve the accuracy of MR-guided attenuation correction in hybrid PET/MR to enable quantitative PET imaging on hybrid PET/MR technologies.

Using deconvolution to improve the metrological performance of the grid method

NASA Astrophysics Data System (ADS)

Grédiac, Michel; Sur, Frédéric; Badulescu, Claudiu; Mathias, Jean-Denis

2013-06-01

The use of various deconvolution techniques to enhance strain maps obtained with the grid method is addressed in this study. Since phase derivative maps obtained with the grid method can be approximated by their actual counterparts convolved by the envelope of the kernel used to extract phases and phase derivatives, non-blind restoration techniques can be used to perform deconvolution. Six deconvolution techniques are presented and employed to restore a synthetic phase derivative map, namely direct deconvolution, regularized deconvolution, the Richardson-Lucy algorithm and Wiener filtering, the last two with two variants concerning their practical implementations. Obtained results show that the noise that corrupts the grid images must be thoroughly taken into account to limit its effect on the deconvolved strain maps. The difficulty here is that the noise on the grid image yields a spatially correlated noise on the strain maps. In particular, numerical experiments on synthetic data show that direct and regularized deconvolutions are unstable when noisy data are processed. The same remark holds when Wiener filtering is employed without taking into account noise autocorrelation. On the other hand, the Richardson-Lucy algorithm and Wiener filtering with noise autocorrelation provide deconvolved maps where the impact of noise remains controlled within a certain limit. It is also observed that the last technique outperforms the Richardson-Lucy algorithm. Two short examples of actual strain fields restoration are finally shown. They deal with asphalt and shape memory alloy specimens. The benefits and limitations of deconvolution are presented and discussed in these two cases. The main conclusion is that strain maps are correctly deconvolved when the signal-to-noise ratio is high and that actual noise in the actual strain maps must be more specifically characterized than in the current study to address higher noise levels with Wiener filtering.

Comprehensive analysis of TEM methods for LiFePO4/FePO4 phase mapping: spectroscopic techniques (EFTEM, STEM-EELS) and STEM diffraction techniques (ACOM-TEM).

PubMed

Mu, X; Kobler, A; Wang, D; Chakravadhanula, V S K; Schlabach, S; Szabó, D V; Norby, P; Kübel, C

2016-11-01

Transmission electron microscopy (TEM) has been used intensively in investigating battery materials, e.g. to obtain phase maps of partially (dis)charged (lithium) iron phosphate (LFP/FP), which is one of the most promising cathode material for next generation lithium ion (Li-ion) batteries. Due to the weak interaction between Li atoms and fast electrons, mapping of the Li distribution is not straightforward. In this work, we revisited the issue of TEM measurements of Li distribution maps for LFP/FP. Different TEM techniques, including spectroscopic techniques (energy filtered (EF)TEM in the energy range from low-loss to core-loss) and a STEM diffraction technique (automated crystal orientation mapping (ACOM)), were applied to map the lithiation of the same location in the same sample. This enabled a direct comparison of the results. The maps obtained by all methods showed excellent agreement with each other. Because of the strong difference in the imaging mechanisms, it proves the reliability of both the spectroscopic and STEM diffraction phase mapping. A comprehensive comparison of all methods is given in terms of information content, dose level, acquisition time and signal quality. The latter three are crucial for the design of in-situ experiments with beam sensitive Li-ion battery materials. Furthermore, we demonstrated the power of STEM diffraction (ACOM-STEM) providing additional crystallographic information, which can be analyzed to gain a deeper understanding of the LFP/FP interface properties such as statistical information on phase boundary orientation and misorientation between domains. Copyright © 2016 Elsevier B.V. All rights reserved.

An image encryption algorithm based on 3D cellular automata and chaotic maps

NASA Astrophysics Data System (ADS)

Del Rey, A. Martín; Sánchez, G. Rodríguez

2015-05-01

A novel encryption algorithm to cipher digital images is presented in this work. The digital image is rendering into a three-dimensional (3D) lattice and the protocol consists of two phases: the confusion phase where 24 chaotic Cat maps are applied and the diffusion phase where a 3D cellular automata is evolved. The encryption method is shown to be secure against the most important cryptanalytic attacks.

Referenceless MR thermometry-a comparison of five methods.

PubMed

Zou, Chao; Tie, Changjun; Pan, Min; Wan, Qian; Liang, Changhong; Liu, Xin; Chung, Yiu-Cho

2017-01-07

Proton resonance frequency shift (PRFS) MR thermometry is commonly used to measure temperature in thermotherapy. The method requires a baseline temperature map and is therefore motion sensitive. Several referenceless MR thermometry methods were proposed to address this problem but their performances have never been compared. This study compared the performance of five referenceless methods through simulation, heating of ex vivo tissues and in vivo imaging of the brain and liver of healthy volunteers. Mean, standard deviation, root mean square, 2/98 percentiles of error were used as performance metrics. Probability density functions (PDF) of the error distribution for these methods in the different tests were also compared. The results showed that the phase gradient method (PG) exhibited largest error in all scenarios. The original method (ORG) and the complex field estimation method (CFE) had similar performance in all experiments. The phase finite difference method (PFD) and the near harmonic method (NH) were better than other methods, especially in the lower signal-to-noise ratio (SNR) and fast changing field cases. Except for PG, the PDFs of each method were very similar among the different experiments. Since phase unwrapping in ORG and NH is computationally demanding and subject to image SNR, PFD and CFE would be good choices as they do not need phase unwrapping. The results here would facilitate the choice of appropriate referenceless methods in various MR thermometry applications.

Referenceless MR thermometry—a comparison of five methods

NASA Astrophysics Data System (ADS)

Zou, Chao; Tie, Changjun; Pan, Min; Wan, Qian; Liang, Changhong; Liu, Xin; Chung, Yiu-Cho

2017-01-01

Proton resonance frequency shift (PRFS) MR thermometry is commonly used to measure temperature in thermotherapy. The method requires a baseline temperature map and is therefore motion sensitive. Several referenceless MR thermometry methods were proposed to address this problem but their performances have never been compared. This study compared the performance of five referenceless methods through simulation, heating of ex vivo tissues and in vivo imaging of the brain and liver of healthy volunteers. Mean, standard deviation, root mean square, 2/98 percentiles of error were used as performance metrics. Probability density functions (PDF) of the error distribution for these methods in the different tests were also compared. The results showed that the phase gradient method (PG) exhibited largest error in all scenarios. The original method (ORG) and the complex field estimation method (CFE) had similar performance in all experiments. The phase finite difference method (PFD) and the near harmonic method (NH) were better than other methods, especially in the lower signal-to-noise ratio (SNR) and fast changing field cases. Except for PG, the PDFs of each method were very similar among the different experiments. Since phase unwrapping in ORG and NH is computationally demanding and subject to image SNR, PFD and CFE would be good choices as they do not need phase unwrapping. The results here would facilitate the choice of appropriate referenceless methods in various MR thermometry applications.

A 32-Channel Phased-Array Receive with Asymmetric Birdcage Transmit RF Coil for Hyperpolarized Xenon-129 Lung Imaging

PubMed Central

Dregely, Isabel; Ruset, Iulian C.; Wiggins, Graham; Mareyam, Azma; Mugler, John P.; Altes, Talissa A.; Meyer, Craig; Ruppert, Kai; Wald, Lawrence L.; Hersman, F. William

2012-01-01

Hyperpolarized xenon-129 (HP Xe) has the potential to become a non-invasive contrast agent for lung MRI. In addition to its utility for imaging of ventilated airspaces, the property of xenon to dissolve in lung tissue and blood upon inhalation provides the opportunity to study gas exchange. Implementations of imaging protocols for obtaining regional parameters that exploit the dissolved phase are limited by the available signal-to-noise ratio (SNR), excitation homogeneity, and length of acquisition times. To address these challenges, a 32-channel receive-array coil complemented by an asymmetric birdcage transmit coil tuned to the HP Xe resonance at 3T was developed. First results of spin-density imaging in healthy subjects and subjects with obstructive lung disease demonstrated the improvements in image quality by high resolution ventilation images with high SNR. Parallel imaging performance of the phased-array coil was demonstrated by acceleration factors up to three in 2D acquisitions and up to six in 3D acquisitions. Transmit-field maps showed a regional variation of only 8% across the whole lung. The newly developed phased-array receive coil with the birdcage transmit coil will lead to an improvement in existing imaging protocols, but moreover enable the development of new, functional lung imaging protocols based on the improvements in excitation homogeneity, SNR, and acquisition speed. PMID:23132336

Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

2014-10-01

Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

Computed inverse resonance imaging for magnetic susceptibility map reconstruction.

PubMed

Chen, Zikuan; Calhoun, Vince

2012-01-01

This article reports a computed inverse magnetic resonance imaging (CIMRI) model for reconstructing the magnetic susceptibility source from MRI data using a 2-step computational approach. The forward T2*-weighted MRI (T2*MRI) process is broken down into 2 steps: (1) from magnetic susceptibility source to field map establishment via magnetization in the main field and (2) from field map to MR image formation by intravoxel dephasing average. The proposed CIMRI model includes 2 inverse steps to reverse the T2*MRI procedure: field map calculation from MR-phase image and susceptibility source calculation from the field map. The inverse step from field map to susceptibility map is a 3-dimensional ill-posed deconvolution problem, which can be solved with 3 kinds of approaches: the Tikhonov-regularized matrix inverse, inverse filtering with a truncated filter, and total variation (TV) iteration. By numerical simulation, we validate the CIMRI model by comparing the reconstructed susceptibility maps for a predefined susceptibility source. Numerical simulations of CIMRI show that the split Bregman TV iteration solver can reconstruct the susceptibility map from an MR-phase image with high fidelity (spatial correlation ≈ 0.99). The split Bregman TV iteration solver includes noise reduction, edge preservation, and image energy conservation. For applications to brain susceptibility reconstruction, it is important to calibrate the TV iteration program by selecting suitable values of the regularization parameter. The proposed CIMRI model can reconstruct the magnetic susceptibility source of T2*MRI by 2 computational steps: calculating the field map from the phase image and reconstructing the susceptibility map from the field map. The crux of CIMRI lies in an ill-posed 3-dimensional deconvolution problem, which can be effectively solved by the split Bregman TV iteration algorithm.

High Resolution X-ray Phase Contrast Imaging with Acoustic Tissue-Selective Contrast Enhancement

DTIC Science & Technology

2008-06-01

Imaging with Acoustic Tissue-Selective Contrast Enhancement PRINCIPAL INVESTIGATOR: Gerald J. Diebold, Ph.D. CONTRACTING... Contrast Imaging with Acoustic Tissue-Selective Contrast Enhancement 5b. GRANT NUMBER W81XWH-04-1-0481 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...additional phase contrast features are visible at the interfaces of soft tissues as slight contrast enhancements . The image sequence in Fig. 2 shows an image

High-speed multislice T1 mapping using inversion-recovery echo-planar imaging.

PubMed

Ordidge, R J; Gibbs, P; Chapman, B; Stehling, M K; Mansfield, P

1990-11-01

Tissue contrast in MR images is a strong function of spin-lattice (T1) and spin-spin (T2) relaxation times. However, the T1 relaxation time is rarely quantified because of the long scan time required to produce an accurate T1 map of the subject. In a standard 2D FT technique, this procedure may take up to 30 min. Modifications of the echo-planar imaging (EPI) technique which incorporate the principle of inversion recovery (IR) enable multislice T1 maps to be produced in total scan times varying from a few seconds up to a minute. Using IR-EPI, rapid quantification of T1 values may thus lead to better discrimination between tissue types in an acceptable scan time.

Four-dimensional optoacoustic temperature mapping in laser-induced thermotherapy

NASA Astrophysics Data System (ADS)

Oyaga Landa, Francisco Javier; Deán-Ben, Xosé Luís.; Sroka, Ronald; Razansky, Daniel

2018-02-01

Photoablative laser therapy is in common use for selective destruction of malignant masses, vascular and brain abnormalities. Tissue ablation and coagulation are irreversible processes occurring shortly after crossing a certain thermal exposure threshold. As a result, accurate mapping of the temperature field is essential for optimizing the outcome of these clinical interventions. Here we demonstrate four-dimensional optoacoustic temperature mapping of the entire photoablated region. Accuracy of the method is investigated in tissue-mimicking phantom experiments. Deviations of the volumetric optoacoustic temperature readings provided at 40ms intervals remained below 10% for temperature elevations above 3°C, as validated by simultaneous thermocouple measurements. The excellent spatio-temporal resolution of the new temperature monitoring approach aims at improving safety and efficacy of laser-based photothermal procedures.

Choice of surrogate tissue influences neonatal EWAS findings.

PubMed

Lin, Xinyi; Teh, Ai Ling; Chen, Li; Lim, Ives Yubin; Tan, Pei Fang; MacIsaac, Julia L; Morin, Alexander M; Yap, Fabian; Tan, Kok Hian; Saw, Seang Mei; Lee, Yung Seng; Holbrook, Joanna D; Godfrey, Keith M; Meaney, Michael J; Kobor, Michael S; Chong, Yap Seng; Gluckman, Peter D; Karnani, Neerja

2017-12-05

Epigenomes are tissue specific and thus the choice of surrogate tissue can play a critical role in interpreting neonatal epigenome-wide association studies (EWAS) and in their extrapolation to target tissue. To develop a better understanding of the link between tissue specificity and neonatal EWAS, and the contributions of genotype and prenatal factors, we compared genome-wide DNA methylation of cord tissue and cord blood, two of the most accessible surrogate tissues at birth. In 295 neonates, DNA methylation was profiled using Infinium HumanMethylation450 beadchip arrays. Sites of inter-individual variability in DNA methylation were mapped and compared across the two surrogate tissues at birth, i.e., cord tissue and cord blood. To ascertain the similarity to target tissues, DNA methylation profiles of surrogate tissues were compared to 25 primary tissues/cell types mapped under the Epigenome Roadmap project. Tissue-specific influences of genotype on the variable CpGs were also analyzed. Finally, to interrogate the impact of the in utero environment, EWAS on 45 prenatal factors were performed and compared across the surrogate tissues. Neonatal EWAS results were tissue specific. In comparison to cord blood, cord tissue showed higher inter-individual variability in the epigenome, with a lower proportion of CpGs influenced by genotype. Both neonatal tissues were good surrogates for target tissues of mesodermal origin. They also showed distinct phenotypic associations, with effect sizes of the overlapping CpGs being in the same order of magnitude. The inter-relationship between genetics, prenatal factors and epigenetics is tissue specific, and requires careful consideration in designing and interpreting future neonatal EWAS. This birth cohort is a prospective observational study, designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .

Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients.

PubMed

Bezrukov, Ilja; Schmidt, Holger; Gatidis, Sergios; Mantlik, Frédéric; Schäfer, Jürgen F; Schwenzer, Nina; Pichler, Bernd J

2015-07-01

Pediatric imaging is regarded as a key application for combined PET/MR imaging systems. Because existing MR-based attenuation-correction methods were not designed specifically for pediatric patients, we assessed the impact of 2 potentially influential factors: inter- and intrapatient variability of attenuation coefficients and anatomic variability. Furthermore, we evaluated the quantification accuracy of 3 methods for MR-based attenuation correction without (SEGbase) and with bone prediction using an adult and a pediatric atlas (SEGwBONEad and SEGwBONEpe, respectively) on PET data of pediatric patients. The variability of attenuation coefficients between and within pediatric (5-17 y, n = 17) and adult (27-66 y, n = 16) patient collectives was assessed on volumes of interest (VOIs) in CT datasets for different tissue types. Anatomic variability was assessed on SEGwBONEad/pe attenuation maps by computing mean differences to CT-based attenuation maps for regions of bone tissue, lungs, and soft tissue. PET quantification was evaluated on VOIs with physiologic uptake and on 80% isocontour VOIs with elevated uptake in the thorax and abdomen/pelvis. Inter- and intrapatient variability of the bias was assessed for each VOI group and method. Statistically significant differences in mean VOI Hounsfield unit values and linear attenuation coefficients between adult and pediatric collectives were found in the lungs and femur. The prediction of attenuation maps using the pediatric atlas showed a reduced error in bone tissue and better delineation of bone structure. Evaluation of PET quantification accuracy showed statistically significant mean errors in mean standardized uptake values of -14% ± 5% and -23% ± 6% in bone marrow and femur-adjacent VOIs with physiologic uptake for SEGbase, which could be reduced to 0% ± 4% and -1% ± 5% using SEGwBONEpe attenuation maps. Bias in soft-tissue VOIs was less than 5% for all methods. Lung VOIs showed high SDs in the range of 15% for all methods. For VOIs with elevated uptake, mean and SD were less than 5% except in the thorax. The use of a dedicated atlas for the pediatric patient collective resulted in improved attenuation map prediction in osseous regions and reduced interpatient bias variation in femur-adjacent VOIs. For the lungs, in which intrapatient variation was higher for the pediatric collective, a patient- or group-specific attenuation coefficient might improve attenuation map accuracy. Mean errors of -14% and -23% in bone marrow and femur-adjacent VOIs can affect PET quantification in these regions when bone tissue is ignored. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

77 FR 15369 - Mobility Fund Phase I Auction GIS Data of Potentially Eligible Census Blocks

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-15

....fcc.gov/auctions/901/ , are the following: Downloadable shapefile Web mapping service MapBox map tiles... GIS software allows you to add this service as a layer to your session or project. 6. MapBox map tiles are cached map tiles of the data. With this open source software approach, these image tiles can be...

Comparison of rapid diagnostic tests to detect Mycobacterium avium subsp. paratuberculosis disseminated infection in bovine liver.

PubMed

Zarei, Mehdi; Ghorbanpour, Masoud; Tajbakhsh, Samaneh; Mosavari, Nader

2017-08-01

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, a chronic enteritis in cattle and other domestic and wild ruminants. The presence of MAP in tissues other than intestines and associated lymph nodes, such as meat and liver, is a potential public health concern. In the present study, the relationship between the results of rapid diagnostic tests of the Johne's disease, such as serum ELISA, rectal scraping PCR, and acid-fast staining, and the presence of MAP in liver was evaluated. Blood, liver, and rectal scraping samples were collected from 200 slaughtered cattle with unknown Johne's disease status. ELISA was performed to determine the MAP antibody activity in the serum. Acid-fast staining was performed on rectal scraping samples, and PCR was performed on rectal scraping and liver samples. PCR-positive liver samples were used for mycobacterial culture. Overall, the results of this study demonstrated that MAP can be detected and cultured from liver of slaughtered cattle and rapid diagnostic tests of Johne's disease have limited value in detecting cattle with MAP infection in liver. These findings show that the presence of MAP in liver tissue may occur in cows with negative results for rapid diagnostic tests and vice versa. Hence, liver might represent another possible risk of human exposure to MAP. Given concerns about a potential zoonotic role for MAP, these results show the necessity to find new methods for detecting cattle with MAP disseminated infection.

A population-based tissue probability map-driven level set method for fully automated mammographic density estimations.

PubMed

Kim, Youngwoo; Hong, Byung Woo; Kim, Seung Ja; Kim, Jong Hyo

2014-07-01

A major challenge when distinguishing glandular tissues on mammograms, especially for area-based estimations, lies in determining a boundary on a hazy transition zone from adipose to glandular tissues. This stems from the nature of mammography, which is a projection of superimposed tissues consisting of different structures. In this paper, the authors present a novel segmentation scheme which incorporates the learned prior knowledge of experts into a level set framework for fully automated mammographic density estimations. The authors modeled the learned knowledge as a population-based tissue probability map (PTPM) that was designed to capture the classification of experts' visual systems. The PTPM was constructed using an image database of a selected population consisting of 297 cases. Three mammogram experts extracted regions for dense and fatty tissues on digital mammograms, which was an independent subset used to create a tissue probability map for each ROI based on its local statistics. This tissue class probability was taken as a prior in the Bayesian formulation and was incorporated into a level set framework as an additional term to control the evolution and followed the energy surface designed to reflect experts' knowledge as well as the regional statistics inside and outside of the evolving contour. A subset of 100 digital mammograms, which was not used in constructing the PTPM, was used to validate the performance. The energy was minimized when the initial contour reached the boundary of the dense and fatty tissues, as defined by experts. The correlation coefficient between mammographic density measurements made by experts and measurements by the proposed method was 0.93, while that with the conventional level set was 0.47. The proposed method showed a marked improvement over the conventional level set method in terms of accuracy and reliability. This result suggests that the proposed method successfully incorporated the learned knowledge of the experts' visual systems and has potential to be used as an automated and quantitative tool for estimations of mammographic breast density levels.

A two-phase model of plantar tissue: a step toward prediction of diabetic foot ulceration.

PubMed

Sciumè, G; Boso, D P; Gray, W G; Cobelli, C; Schrefler, B A

2014-11-01

A new computational model, based on the thermodynamically constrained averaging theory, has been recently proposed to predict tumor initiation and proliferation. A similar mathematical approach is proposed here as an aid in diabetic ulcer prevention. The common aspects at the continuum level are the macroscopic balance equations governing the flow of the fluid phase, diffusion of chemical species, tissue mechanics, and some of the constitutive equations. The soft plantar tissue is modeled as a two-phase system: a solid phase consisting of the tissue cells and their extracellular matrix, and a fluid one (interstitial fluid and dissolved chemical species). The solid phase may become necrotic depending on the stress level and on the oxygen availability in the tissue. Actually, in diabetic patients, peripheral vascular disease impacts tissue necrosis; this is considered in the model via the introduction of an effective diffusion coefficient that governs transport of nutrients within the microvasculature. The governing equations of the mathematical model are discretized in space by the finite element method and in time domain using the θ-Wilson Method. While the full mathematical model is developed in this paper, the example is limited to the simulation of several gait cycles of a healthy foot. Copyright © 2014 John Wiley & Sons, Ltd.

Fringe pattern demodulation with a two-frame digital phase-locked loop algorithm.

PubMed

Gdeisat, Munther A; Burton, David R; Lalor, Michael J

2002-09-10

A novel technique called a two-frame digital phase-locked loop for fringe pattern demodulation is presented. In this scheme, two fringe patterns with different spatial carrier frequencies are grabbed for an object. A digital phase-locked loop algorithm tracks and demodulates the phase difference between both fringe patterns by employing the wrapped phase components of one of the fringe patterns as a reference to demodulate the second fringe pattern. The desired phase information can be extracted from the demodulated phase difference. We tested the algorithm experimentally using real fringe patterns. The technique is shown to be suitable for noncontact measurement of objects with rapid surface variations, and it outperforms the Fourier fringe analysis technique in this aspect. Phase maps produced withthis algorithm are noisy in comparison with phase maps generated with the Fourier fringe analysis technique.

Rapid computation of the amplitude and phase of tightly focused optical fields distorted by scattering particles

PubMed Central

Ranasinghesagara, Janaka C.; Hayakawa, Carole K.; Davis, Mitchell A.; Dunn, Andrew K.; Potma, Eric O.; Venugopalan, Vasan

2014-01-01

We develop an efficient method for accurately calculating the electric field of tightly focused laser beams in the presence of specific configurations of microscopic scatterers. This Huygens–Fresnel wave-based electric field superposition (HF-WEFS) method computes the amplitude and phase of the scattered electric field in excellent agreement with finite difference time-domain (FDTD) solutions of Maxwell’s equations. Our HF-WEFS implementation is 2–4 orders of magnitude faster than the FDTD method and enables systematic investigations of the effects of scatterer size and configuration on the focal field. We demonstrate the power of the new HF-WEFS approach by mapping several metrics of focal field distortion as a function of scatterer position. This analysis shows that the maximum focal field distortion occurs for single scatterers placed below the focal plane with an offset from the optical axis. The HF-WEFS method represents an important first step toward the development of a computational model of laser-scanning microscopy of thick cellular/tissue specimens. PMID:25121440

Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

PubMed Central

2009-01-01

Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

Azimuthally invariant Mueller-matrix mapping of biological optically anisotropic network

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Grytsyuk, M.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.

2017-09-01

A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular dichroism of histological sections liver tissue of mice with different degrees of severity of diabetes are found. The interconnections between such distributions and parameters of linear and circular dichroism of liver of mice tissue histological sections are defined. The comparative investigations of coordinate distributions of parameters of amplitude anisotropy formed by Liver tissue with varying severity of diabetes (10 days and 24 days) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular dichroism are defined. The objective criteria of cause of the degree of severity of the diabetes differentiation are determined.

Analogous on-axis interference topographic phase microscopy (AOITPM).

PubMed

Xiu, P; Liu, Q; Zhou, X; Xu, Y; Kuang, C; Liu, X

2018-05-01

The refractive index (RI) of a sample as an endogenous contrast agent plays an important role in transparent live cell imaging. In tomographic phase microscopy (TPM), 3D quantitative RI maps can be reconstructed based on the measured projections of the RI in multiple directions. The resolution of the RI maps not only depends on the numerical aperture of the employed objective lens, but also is determined by the accuracy of the quantitative phase of the sample measured at multiple scanning illumination angles. This paper reports an analogous on-axis interference TPM, where the interference angle between the sample and reference beams is kept constant for projections in multiple directions to improve the accuracy of the phase maps and the resolution of RI tomograms. The system has been validated with both silica beads and red blood cells. Compared with conventional TPM, the proposed system acquires quantitative RI maps with higher resolution (420 nm @λ = 633 nm) and signal-to-noise ratio that can be beneficial for live cell imaging in biomedical applications. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Bifurcation and Fractal of the Coupled Logistic Map

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Luo, Chao

The nature of the fixed points of the coupled Logistic map is researched, and the boundary equation of the first bifurcation of the coupled Logistic map in the parameter space is given out. Using the quantitative criterion and rule of system chaos, i.e., phase graph, bifurcation graph, power spectra, the computation of the fractal dimension, and the Lyapunov exponent, the paper reveals the general characteristics of the coupled Logistic map transforming from regularity to chaos, the following conclusions are shown: (1) chaotic patterns of the coupled Logistic map may emerge out of double-periodic bifurcation and Hopf bifurcation, respectively; (2) during the process of double-period bifurcation, the system exhibits self-similarity and scale transform invariability in both the parameter space and the phase space. From the research of the attraction basin and Mandelbrot-Julia set of the coupled Logistic map, the following conclusions are indicated: (1) the boundary between periodic and quasiperiodic regions is fractal, and that indicates the impossibility to predict the moving result of the points in the phase plane; (2) the structures of the Mandelbrot-Julia sets are determined by the control parameters, and their boundaries have the fractal characteristic.

Influence of contact force on voltage mapping: A combined magnetic resonance imaging and electroanatomic mapping study in patients with tetralogy of Fallot.

PubMed

Teijeira-Fernandez, Elvis; Cochet, Hubert; Bourier, Felix; Takigawa, Masateru; Cheniti, Ghassen; Thompson, Nathaniel; Frontera, Antonio; Camaioni, Claudia; Massouille, Gregoire; Jalal, Zakaria; Derval, Nicolas; Iriart, Xavier; Denis, Arnaud; Hocini, Meleze; Haissaguerre, Michel; Jais, Pierre; Thambo, Jean-Benoit; Sacher, Frederic

2018-03-20

Voltage criteria for ventricular mapping have been obtained from small series of patients and prioritizing high specificity. The purpose of this study was to analyse the potential influence of contact force (CF) on voltage mapping and to define voltage cutoff values for right ventricular (RV) scar using the tetralogy of Fallot as a model of transmural RV scar and magnetic resonance imaging (MRI) as reference. Fourteen patients (age 32.6 ± 14.3 years; 5 female) with repaired tetralogy of Fallot underwent high-resolution cardiac MRI (1.25 × 1.25 × 2.5 mm). Scar, defined as pixels with intensity >50% maximum, was mapped over the RV geometry and merged within the CARTO system to RV endocardial voltage maps acquired using a 3.5-mm ablation catheter with CF technology (SmartTouch, Biosense Webster). In total, 2446 points were analyzed, 915 within scars and 1531 in healthy tissue according to MRI. CF correlated to unipolar (ρ = 0.186; P <.001) and bipolar voltage in healthy tissue (ρ = 0.245; P <.001) and in scar tissue. Receiver operating characteristic curve analysis excluding points with very low CF (<5g) identified optimal voltage cutoffs of 5.19 mV for unipolar voltage and 1.76 mV for bipolar voltage, yielding sensitivity/specificity of 0.89/0.85 and 0.9/0.9, respectively. CF is an important factor to be taken into account for voltage mapping. If good CF is applied, unipolar and bipolar voltage cutoffs of 5.19 mV and 1.76 mV are optimal for identifying RV scar on endocardial mapping with the SmartTouch catheter. Data on the diagnostic accuracy of different voltage cutoff values are provided. Copyright © 2018 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Polarization-interference mapping of biological fluids polycrystalline films in differentiation of weak changes of optical anisotropy

NASA Astrophysics Data System (ADS)

Ushenko, V. O.; Vanchuliak, O.; Sakhnovskiy, M. Y.; Dubolazov, O. V.; Grygoryshyn, P.; Soltys, I. V.; Olar, O. V.; Antoniv, A.

2017-09-01

The theoretical background of the azimuthally stable method of polarization-interference mapping of the histological sections of the biopsy of the prostate tissue on the basis of the spatial frequency selection of the mechanisms of linear and circular birefringence is presented. The diagnostic application of a new correlation parameter - complex degree of mutual anisotropy - is analytically substantiated. The method of measuring coordinate distributions of complex degree of mutual anisotropy with further spatial filtration of their high- and low-frequency components is developed. The interconnections of such distributions with parameters of linear and circular birefringence of prostate tissue histological sections are found. The objective criteria of differentiation of benign and malignant conditions of prostate tissue are determined.

High Spatial Resolution and Temporally Resolved T2 * Mapping of Normal Human Myocardium at 7.0 Tesla: An Ultrahigh Field Magnetic Resonance Feasibility Study

PubMed Central

Hezel, Fabian; Thalhammer, Christof; Waiczies, Sonia; Schulz-Menger, Jeanette; Niendorf, Thoralf

2012-01-01

Myocardial tissue characterization using T2 * relaxation mapping techniques is an emerging application of (pre)clinical cardiovascular magnetic resonance imaging. The increase in microscopic susceptibility at higher magnetic field strengths renders myocardial T2 * mapping at ultrahigh magnetic fields conceptually appealing. This work demonstrates the feasibility of myocardial T2 * imaging at 7.0 T and examines the applicability of temporally-resolved and high spatial resolution myocardial T2 * mapping. In phantom experiments single cardiac phase and dynamic (CINE) gradient echo imaging techniques provided similar T2 * maps. In vivo studies showed that the peak-to-peak B0 difference following volume selective shimming was reduced to approximately 80 Hz for the four chamber view and mid-ventricular short axis view of the heart and to 65 Hz for the left ventricle. No severe susceptibility artifacts were detected in the septum and in the lateral wall for T2 * weighting ranging from TE = 2.04 ms to TE = 10.2 ms. For TE >7 ms, a susceptibility weighting induced signal void was observed within the anterior and inferior myocardial segments. The longest T2 * values were found for anterior (T2 * = 14.0 ms), anteroseptal (T2 * = 17.2 ms) and inferoseptal (T2 * = 16.5 ms) myocardial segments. Shorter T2 * values were observed for inferior (T2 * = 10.6 ms) and inferolateral (T2 * = 11.4 ms) segments. A significant difference (p = 0.002) in T2 * values was observed between end-diastole and end-systole with T2 * changes of up to approximately 27% over the cardiac cycle which were pronounced in the septum. To conclude, these results underscore the challenges of myocardial T2 * mapping at 7.0 T but demonstrate that these issues can be offset by using tailored shimming techniques and dedicated acquisition schemes. PMID:23251708

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

A statistical model of false negative and false positive detection of phase singularities.

PubMed

Jacquemet, Vincent

2017-10-01

The complexity of cardiac fibrillation dynamics can be assessed by analyzing the distribution of phase singularities (PSs) observed using mapping systems. Interelectrode distance, however, limits the accuracy of PS detection. To investigate in a theoretical framework the PS false negative and false positive rates in relation to the characteristics of the mapping system and fibrillation dynamics, we propose a statistical model of phase maps with controllable number and locations of PSs. In this model, phase maps are generated from randomly distributed PSs with physiologically-plausible directions of rotation. Noise and distortion of the phase are added. PSs are detected using topological charge contour integrals on regular grids of varying resolutions. Over 100 × 10 6 realizations of the random field process are used to estimate average false negative and false positive rates using a Monte-Carlo approach. The false detection rates are shown to depend on the average distance between neighboring PSs expressed in units of interelectrode distance, following approximately a power law with exponents in the range of 1.14 to 2 for false negatives and around 2.8 for false positives. In the presence of noise or distortion of phase, false detection rates at high resolution tend to a non-zero noise-dependent lower bound. This model provides an easy-to-implement tool for benchmarking PS detection algorithms over a broad range of configurations with multiple PSs.

Reliable two-dimensional phase unwrapping method using region growing and local linear estimation.

PubMed

Zhou, Kun; Zaitsev, Maxim; Bao, Shanglian

2009-10-01

In MRI, phase maps can provide useful information about parameters such as field inhomogeneity, velocity of blood flow, and the chemical shift between water and fat. As phase is defined in the (-pi,pi] range, however, phase wraps often occur, which complicates image analysis and interpretation. This work presents a two-dimensional phase unwrapping algorithm that uses quality-guided region growing and local linear estimation. The quality map employs the variance of the second-order partial derivatives of the phase as the quality criterion. Phase information from unwrapped neighboring pixels is used to predict the correct phase of the current pixel using a linear regression method. The algorithm was tested on both simulated and real data, and is shown to successfully unwrap phase images that are corrupted by noise and have rapidly changing phase. (c) 2009 Wiley-Liss, Inc.

Digital tissue and what it may reveal about the brain.

PubMed

Morgan, Josh L; Lichtman, Jeff W

2017-10-30

Imaging as a means of scientific data storage has evolved rapidly over the past century from hand drawings, to photography, to digital images. Only recently can sufficiently large datasets be acquired, stored, and processed such that tissue digitization can actually reveal more than direct observation of tissue. One field where this transformation is occurring is connectomics: the mapping of neural connections in large volumes of digitized brain tissue.

Citygml Modelling for Singapore 3d National Mapping

NASA Astrophysics Data System (ADS)

Soon, K. H.; Khoo, V. H. S.

2017-10-01

Since 2014, the Land Survey Division of Singapore Land Authority (SLA) has spearheaded a Whole-of-Government (WOG) 3D mapping project to create and maintain a 3D national map for Singapore. The implementation of the project is divided into two phases. The first phase of the project, which was based on airborne data collection, has produced 3D models for Relief, Building, Vegetation and Waterbody. This part of the work was completed in 2016. To complement the first phase, the second phase used mobile imaging and scanning technique. This phase is targeted to be completed by the mid of 2017 and is creating 3D models for Transportation, CityFurniture, Bridge and Tunnel. The project has extensively adopted the Open Geospatial Consortium (OGC)'s CityGML standard. Out of 10 currently supported thematic modules in CityGML 2.0, the project has implemented 8. The paper describes the adoption of CityGML in the project, and discusses challenges, data validations and management of the models.

SU-E-J-233: Effect of Brachytherapy Seed Artifacts in T2 and Proton Density Maps in MR Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mashouf, S; University of Toronto, Dept of Radiation Oncology, Toronto, Ontario; Fatemi-Ardekani, A

Purpose: This study aims at investigating the influence of brachytherapy seeds on T2 and proton density (PD) maps generated from MR images. Proton density maps can be used to extract water content. Since dose absorbed in tissue surrounding low energy brachytherapy seeds are highly influenced by tissue composition, knowing the water content is a first step towards implementing a heterogeneity correction algorithm using MR images. Methods: An LDR brachytherapy (IsoAid Advantage Pd-103) seed was placed in the middle of an agar-based gel phantom and imaged using a 3T Philips MR scanner with a 168-channel head coil. A multiple echo sequencemore » with TE=20, 40, 60, 80, 100 (ms) with large repetition time (TR=6259ms) was used to extract T2 and PD maps. Results: Seed artifacts were considerably reduced on T2 maps compared to PD maps. The variation of PD around the mean was obtained as −97% to 125% (±1%) while for T2 it was recorded as −71% to 24% (±1%). Conclusion: PD maps which are required for heterogeneity corrections are susceptible to artifacts from seeds. Seed artifacts on T2 maps, however, are significantly reduced due to not being sensitive to B0 field variation.« less

Cardiac tissue slices: preparation, handling, and successful optical mapping.

PubMed

Wang, Ken; Lee, Peter; Mirams, Gary R; Sarathchandra, Padmini; Borg, Thomas K; Gavaghan, David J; Kohl, Peter; Bollensdorff, Christian

2015-05-01

Cardiac tissue slices are becoming increasingly popular as a model system for cardiac electrophysiology and pharmacology research and development. Here, we describe in detail the preparation, handling, and optical mapping of transmembrane potential and intracellular free calcium concentration transients (CaT) in ventricular tissue slices from guinea pigs and rabbits. Slices cut in the epicardium-tangential plane contained well-aligned in-slice myocardial cell strands ("fibers") in subepicardial and midmyocardial sections. Cut with a high-precision slow-advancing microtome at a thickness of 350 to 400 μm, tissue slices preserved essential action potential (AP) properties of the precutting Langendorff-perfused heart. We identified the need for a postcutting recovery period of 36 min (guinea pig) and 63 min (rabbit) to reach 97.5% of final steady-state values for AP duration (APD) (identified by exponential fitting). There was no significant difference between the postcutting recovery dynamics in slices obtained using 2,3-butanedione 2-monoxime or blebistatin as electromechanical uncouplers during the cutting process. A rapid increase in APD, seen after cutting, was caused by exposure to ice-cold solution during the slicing procedure, not by tissue injury, differences in uncouplers, or pH-buffers (bicarbonate; HEPES). To characterize intrinsic patterns of CaT, AP, and conduction, a combination of multipoint and field stimulation should be used to avoid misinterpretation based on source-sink effects. In summary, we describe in detail the preparation, mapping, and data analysis approaches for reproducible cardiac tissue slice-based investigations into AP and CaT dynamics. Copyright © 2015 the American Physiological Society.

Cardiac tissue slices: preparation, handling, and successful optical mapping

PubMed Central

Wang, Ken; Lee, Peter; Mirams, Gary R.; Sarathchandra, Padmini; Borg, Thomas K.; Gavaghan, David J.; Kohl, Peter

2015-01-01

Cardiac tissue slices are becoming increasingly popular as a model system for cardiac electrophysiology and pharmacology research and development. Here, we describe in detail the preparation, handling, and optical mapping of transmembrane potential and intracellular free calcium concentration transients (CaT) in ventricular tissue slices from guinea pigs and rabbits. Slices cut in the epicardium-tangential plane contained well-aligned in-slice myocardial cell strands (“fibers”) in subepicardial and midmyocardial sections. Cut with a high-precision slow-advancing microtome at a thickness of 350 to 400 μm, tissue slices preserved essential action potential (AP) properties of the precutting Langendorff-perfused heart. We identified the need for a postcutting recovery period of 36 min (guinea pig) and 63 min (rabbit) to reach 97.5% of final steady-state values for AP duration (APD) (identified by exponential fitting). There was no significant difference between the postcutting recovery dynamics in slices obtained using 2,3-butanedione 2-monoxime or blebistatin as electromechanical uncouplers during the cutting process. A rapid increase in APD, seen after cutting, was caused by exposure to ice-cold solution during the slicing procedure, not by tissue injury, differences in uncouplers, or pH-buffers (bicarbonate; HEPES). To characterize intrinsic patterns of CaT, AP, and conduction, a combination of multipoint and field stimulation should be used to avoid misinterpretation based on source-sink effects. In summary, we describe in detail the preparation, mapping, and data analysis approaches for reproducible cardiac tissue slice-based investigations into AP and CaT dynamics. PMID:25595366

Raman microspectroscopy of noncancerous and cancerous human breast tissues. Identification and phase transitions of linoleic and oleic acids by Raman low-temperature studies.

PubMed

Brozek-Pluska, Beata; Kopec, Monika; Surmacki, Jakub; Abramczyk, Halina

2015-04-07

We present the results of Raman studies in the temperature range of 293-77 K on vibrational properties of linoleic and oleic acids and Raman microspectroscopy of human breast tissues at room temperature. Our results confirmed the significant role of unsaturated fatty acids in differentiation of noncancerous and cancerous breast tissues and the role of vibrational spectroscopy in phase transition identification. We have found that vibrational properties are very sensitive indicators to specify phases and phase transitions typical of unsaturated fatty acids at the molecular level. Using Raman spectroscopy we have identified high-temperature, middle-temperature and low-temperature phases of linoleic acid. Results obtained for linoleic acid were compared with parameters characteristic of α and γ phases of oleic acid - the parent compound of polyunsaturated fatty acids.

Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert.

PubMed

Singh, Gopal; Singh, Gagandeep; Singh, Pradeep; Parmar, Rajni; Paul, Navgeet; Vashist, Radhika; Swarnkar, Mohit Kumar; Kumar, Ashok; Singh, Sanatsujat; Singh, Anil Kumar; Kumar, Sanjay; Sharma, Ram Kumar

2017-09-19

Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.

Single-Shot MR Spectroscopic Imaging with Partial Parallel Imaging

PubMed Central

Posse, Stefan; Otazo, Ricardo; Tsai, Shang-Yueh; Yoshimoto, Akio Ernesto; Lin, Fa-Hsuan

2010-01-01

An MR spectroscopic imaging (MRSI) pulse sequence based on Proton-Echo-Planar-Spectroscopic-Imaging (PEPSI) is introduced that measures 2-dimensional metabolite maps in a single excitation. Echo-planar spatial-spectral encoding was combined with interleaved phase encoding and parallel imaging using SENSE to reconstruct absorption mode spectra. The symmetrical k-space trajectory compensates phase errors due to convolution of spatial and spectral encoding. Single-shot MRSI at short TE was evaluated in phantoms and in vivo on a 3 T whole body scanner equipped with 12-channel array coil. Four-step interleaved phase encoding and 4-fold SENSE acceleration were used to encode a 16×16 spatial matrix with 390 Hz spectral width. Comparison with conventional PEPSI and PEPSI with 4-fold SENSE acceleration demonstrated comparable sensitivity per unit time when taking into account g-factor related noise increases and differences in sampling efficiency. LCModel fitting enabled quantification of Inositol, Choline, Creatine and NAA in vivo with concentration values in the ranges measured with conventional PEPSI and SENSE-accelerated PEPSI. Cramer-Rao lower bounds were comparable to those obtained with conventional SENSE-accelerated PEPSI at the same voxel size and measurement time. This single-shot MRSI method is therefore suitable for applications that require high temporal resolution to monitor temporal dynamics or to reduce sensitivity to tissue movement. PMID:19097245

Direct Evaluation of MR-Derived Attenuation Correction Maps for PET/MR of the Mouse Myocardium

NASA Astrophysics Data System (ADS)

Evans, Eleanor; Buonincontri, Guido; Hawkes, Rob C.; Ansorge, Richard E.; Carpenter, T. Adrian; Sawiak, Stephen J.

2016-02-01

Attenuation correction (AC) must be applied to provide accurate measurements of PET tracer activity concentrations. Due to the limited space available in PET/MR scanners, MR-derived AC (MRAC) is used as a substitute for transmission source scanning. In preclinical PET/MR, there has been limited exploration of MRAC, as the magnitude of AC in murine imaging is much smaller than that required in clinical scans. We investigated if a simple 2 class (air and tissue) segmentation-based MRAC approach could provide adequate AC for mouse PET imaging. To construct the default MRAC μ maps, MR images were thresholded and segmented using ASIPRO software (Siemens Molecular Imaging), which defined the mouse body region as tissue with a uniform linear attenuation coefficient ( μ) of 0.095 cm - 1, and the background and lungs as air, with a μ value of 0 cm - 1. To correct for the misassignment of the lungs as air, two further MRAC μ maps were tested: 1) MRAC (tissue) approach, which changed the lung region designation from air to tissue ( μ = 0.095 cm - 1) and 2) MRAC (lung) approach, which treated the lungs as an additional tissue class, with a μ value of 0.032 cm - 1. All μ maps were then forward projected to create attenuation sinograms for image reconstruction. Standard uptake value (SUV) maps of the myocardium were derived for 10 mice with and without AC applied using gold standard transmission scans (TXAC), the 3 MRAC methods and PET emission scans (EmAC). All AC methods produced significantly different myocardial SUVs to those produced without AC when compared across the mouse group ( ). Similar ( ) SUV were derived with all AC methods, with the best agreement to TXAC achieved using the MRAC (tissue) method, giving a mean difference of 0.9±2.4% in myocardial SUV when compared across all mice. SUV differences of up to 40%, however, were seen in areas adjacent to the RF coil in images produced using all AC methods, except for TXAC. A 2 class MRAC approach can therefore provide acceptable AC for myocardial imaging in mice, although additional CT templates of coils and animals beds would be recommended to further improve image quantification.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion.

PubMed

Malyarenko, Dariya I; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K; Ross, Brian D; Chenevert, Thomas L

2015-12-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b -maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion

PubMed Central

Malyarenko, Dariya I.; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K.; Ross, Brian D.; Chenevert, Thomas L.

2015-01-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b-maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction. PMID:26811845

Mapping the Superconducting Anti-ferromagnetic C4 Phase in Iron-Pnictides

NASA Astrophysics Data System (ADS)

Stadel, Ryan; Taddei, Keith; Bugaris, Dan; Lapidus, Saul; Claus, Helmut; Phelan, Daniel; Chung, Duck Young; Kanatzidis, Mercouri; Osborn, Raymond; Rosenkranz, Stephan; Chmaissem, Omar

Following the discovery of the microscopic coexistence of antifermagnetic spin density waves and superconductivity in Ba1-xKxFe2As2 and the low temperature re-entrance to the novel magnetic C4 tetragonal phase in Ba1-xNaxFe2As2, there has been significant interest in developing an understanding of the properties and formation of these phases and analyzing their dependence on temperature and composition in hole-doped 122 alkaline earth metal/iron-pnictides. We describe the mapping of various Ba, Sr, and Ca 122 phase diagrams with systematically controlled levels of hole-doping of alkaline metal onto the alkaline earth metal site, which was investigated via x-ray and neutron diffraction. Our elaborate synthesis, diffraction work, and analysis maps and firmly establishes the C4 phase space in these ternary diagrams as well as the boundary lines that separate the individual phases, and provides natural clues as well as a framework to investigate the stability and formation of the C4 domes that shift location with doping contents in the phase diagrams. Work at Argonne was supported by US DOE, Office of Science, Materials Sciences and Engineering Division.

Phase contrast MR angiography techniques.

PubMed

Dumoulin, C L

1995-08-01

Phase contrast MR methods encode information from macroscopic motion into the phase of the MR signal. Phase contrast methods can be applied with small and large fields-of-view, can give quantitative measures of velocity, and provide excellent suppression of signals from stationary tissue. Unlike time-of-flight methods, phase contrast methods directly measure flow and thus are not hindered by the artifactual appearance of tissue having short T1. Phase contrast angiograms can be two-dimensional (thin slice or projectile), three-dimensional, and/or time resolved and have applications throughout the body.

Fibronectin is an acute phase reactant in mice.

PubMed

Dyck, R F; Rogers, S L

1985-01-01

Tissue injury and inflammation are potent stimuli for the immediate increased synthesis of several plasma proteins collectively known as acute phase phase reactants. This dramatic phenomenon is thought to play an important role in inflammation and tissue repair. Plasma fibronectin is a normal plasma glycoprotein and a major non-specific opsonin apparently involved in maintaining the integrity of the mononuclear phagocytic system. Because of its ability to mediate clearance of intravascular particulate matter, increased production following tissue injury could be of benefit to the organism. We now report that plasma fibronectin is a significant acute phase reactant in mice with levels increasing from a baseline mean value of 257 ug/ml to 595 ug/ml by 24 hours (p less than 0.01) after a subcutaneous injection of silver nitrate. Similar findings were observed when subcutaneous casein was used as the acute phase stimulus. This data provides further circumstantial evidence that plasma fibronectin is involved in host defence and tissue repair.

Comparison of different numerical treatments for x-ray phase tomography of soft tissue from differential phase projections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pelliccia, Daniele; Vaz, Raquel; Svalbe, Imants

X-ray imaging of soft tissue is made difficult by their low absorbance. The use of x-ray phase imaging and tomography can significantly enhance the detection of these tissues and several approaches have been proposed to this end. Methods such as analyzer-based imaging or grating interferometry produce differential phase projections that can be used to reconstruct the 3D distribution of the sample refractive index. We report on the quantitative comparison of three different methods to obtain x-ray phase tomography with filtered back-projection from differential phase projections in the presence of noise. The three procedures represent different numerical approaches to solve themore » same mathematical problem, namely phase retrieval and filtered back-projection. It is found that obtaining individual phase projections and subsequently applying a conventional filtered back-projection algorithm produces the best results for noisy experimental data, when compared with other procedures based on the Hilbert transform. The algorithms are tested on simulated phantom data with added noise and the predictions are confirmed by experimental data acquired using a grating interferometer. The experiment is performed on unstained adult zebrafish, an important model organism for biomedical studies. The method optimization described here allows resolution of weak soft tissue features, such as muscle fibers.« less

X-ray absorption microtomography (microCT) and small beam diffraction mapping of sea urchin teeth.

PubMed

Stock, S R; Barss, J; Dahl, T; Veis, A; Almer, J D

2002-07-01

Two noninvasive X-ray techniques, laboratory X-ray absorption microtomography (microCT) and X-ray diffraction mapping, were used to study teeth of the sea urchin Lytechinus variegatus. MicroCT revealed low attenuation regions at near the tooth's stone part and along the carinar process-central prism boundary; this latter observation appears to be novel. The expected variation of Mg fraction x in the mineral phase (calcite, Ca(1-x)Mg(x)CO(3)) cannot account for all of the linear attenuation coefficient decrease in the two zones: this suggested that soft tissue is localized there. Transmission diffraction mapping (synchrotron X-radiation, 80.8 keV, 0.1 x 0.1mm(2) beam area, 0.1mm translation grid, image plate area detector) simultaneously probed variations in 3-D and showed that the crystal elements of the "T"-shaped tooth were very highly aligned. Diffraction patterns from the keel (adaxial web) and from the abaxial flange (containing primary plates and the stone part) differed markedly. The flange contained two populations of identically oriented crystal elements with lattice parameters corresponding to x=0.13 and x=0.32. The keel produced one set of diffraction spots corresponding to the lower x. The compositions were more or less equivalent to those determined by others for camarodont teeth, and the high Mg phase is expected to be disks of secondary mineral epitaxially related to the underlying primary mineral element. Lattice parameter gradients were not noted in the keel or flange. Taken together, the microCT and diffraction results indicated that there was a band of relatively high protein content, of up to approximately 0.25 volume fraction, in the central part of the flange and paralleling its adaxial and abaxial faces. X-ray microCT and microdiffraction data used in conjunction with protein distribution data will be crucial for understanding the properties of various biocomposites and their mechanical functions.

Correlation of quantitative dual-energy computed tomography iodine maps and abdominal computed tomography perfusion measurements: are single-acquisition dual-energy computed tomography iodine maps more than a reduced-dose surrogate of conventional computed tomography perfusion?

PubMed

Stiller, Wolfram; Skornitzke, Stephan; Fritz, Franziska; Klauss, Miriam; Hansen, Jens; Pahn, Gregor; Grenacher, Lars; Kauczor, Hans-Ulrich

2015-10-01

Study objectives were the quantitative evaluation of whether conventional abdominal computed tomography (CT) perfusion measurements mathematically correlate with quantitative single-acquisition dual-energy CT (DECT) iodine concentration maps, the determination of the optimum time of acquisition for achieving maximum correlation, and the estimation of the potential for radiation exposure reduction when replacing conventional CT perfusion by single-acquisition DECT iodine concentration maps. Dual-energy CT perfusion sequences were dynamically acquired over 51 seconds (34 acquisitions every 1.5 seconds) in 24 patients with histologically verified pancreatic carcinoma using dual-source DECT at tube potentials of 80 kVp and 140 kVp. Using software developed in-house, perfusion maps were calculated from 80-kVp image series using the maximum slope model after deformable motion correction. In addition, quantitative iodine maps were calculated for each of the 34 DECT acquisitions per patient. Within a manual segmentation of the pancreas, voxel-by-voxel correlation between the perfusion map and each of the iodine maps was calculated for each patient to determine the optimum time of acquisition topt defined as the acquisition time of the iodine map with the highest correlation coefficient. Subsequently, regions of interest were placed inside the tumor and inside healthy pancreatic tissue, and correlation between mean perfusion values and mean iodine concentrations within these regions of interest at topt was calculated for the patient sample. The mean (SD) topt was 31.7 (5.4) seconds after the start of contrast agent injection. The mean (SD) perfusion values for healthy pancreatic and tumor tissues were 67.8 (26.7) mL per 100 mL/min and 43.7 (32.2) mL per 100 mL/min, respectively. At topt, the mean (SD) iodine concentrations were 2.07 (0.71) mg/mL in healthy pancreatic and 1.69 (0.98) mg/mL in tumor tissue, respectively. Overall, the correlation between perfusion values and iodine concentrations was high (0.77), with correlation of 0.89 in tumor and of 0.56 in healthy pancreatic tissue at topt. Comparing radiation exposure associated with a single DECT acquisition at topt (0.18 mSv) to that of an 80 kVp CT perfusion sequence (2.96 mSv) indicates that an average reduction of Deff by 94% could be achieved by replacing conventional CT perfusion with a single-acquisition DECT iodine concentration map. Quantitative iodine concentration maps obtained with DECT correlate well with conventional abdominal CT perfusion measurements, suggesting that quantitative iodine maps calculated from a single DECT acquisition at an organ-specific and patient-specific optimum time of acquisition might be able to replace conventional abdominal CT perfusion measurements if the time of acquisition is carefully calibrated. This could lead to large reductions of radiation exposure to the patients while offering quantitative perfusion data for diagnosis.

Dual-reference digital holographic interferometry for analyzing high-density gradients in fluid mechanics.

PubMed

Desse, Jean-Michel; Olchewsky, François

2018-04-15

This Letter proposes a dual-reference digital holographic interferometer for analyzing the high refractive index encountered in transonic and supersonic flows. For that, a Wollaston prism is inserted in the reference arm in order to simultaneously generate two orthogonally polarized reference waves. As a consequence, recorded interferograms contain two crossed and perpendicular interference patterns that give two orders fully separated in the Fourier spectrum. It is then possible to analyze a transparent object regardless of the orientation of the refractive index gradient using the two phase maps reconstructed with each of the two first interference orders. Fusion of the phase maps yields a single phase map in which the phase singularities are removed. Experimental results demonstrate the suitability of the proposed approach for analyzing shock waves in the unsteady wake flow around a circular cylinder at Mach 0.75.

Correlation matching method for high-precision position detection of optical vortex using Shack-Hartmann wavefront sensor.

PubMed

Huang, Chenxi; Huang, Hongxin; Toyoda, Haruyoshi; Inoue, Takashi; Liu, Huafeng

2012-11-19

We propose a new method for realizing high-spatial-resolution detection of singularity points in optical vortex beams. The method uses a Shack-Hartmann wavefront sensor (SHWS) to record a Hartmanngram. A map of evaluation values related to phase slope is then calculated from the Hartmanngram. The position of an optical vortex is determined by comparing the map with reference maps that are calculated from numerically created spiral phases having various positions. Optical experiments were carried out to verify the method. We displayed various spiral phase distribution patterns on a phase-only spatial light modulator and measured the resulting singularity point using the proposed method. The results showed good linearity in detecting the position of singularity points. The RMS error of the measured position of the singularity point was approximately 0.056, in units normalized to the lens size of the lenslet array used in the SHWS.

Mapping Isobaric Aging onto the Equilibrium Phase Diagram.

PubMed

Niss, Kristine

2017-09-15

The linear volume relaxation and the nonlinear volume aging of a glass-forming liquid are measured, directly compared, and used to extract the out-of-equilibrium relaxation time. This opens a window to investigate how the relaxation time depends on temperature, structure, and volume in parts of phase space that are not accessed by the equilibrium liquid. It is found that the temperature dependence of relaxation time is non-Arrhenius even in the isostructural case-challenging the Adam-Gibbs entropy model. Based on the presented data and the idea that aging happens through quasiequilibrium states, we suggest a mapping of the out-of-equilibrium states during isobaric aging to the equilibrium phase diagram. This mapping implies the existence of isostructural lines in the equilibrium phase diagram. The relaxation time is found to depend on the bath temperature, density, and a just single structural parameter, referred to as an effective temperature.

Single-shot three-dimensional reconstruction based on structured light line pattern

NASA Astrophysics Data System (ADS)

Wang, ZhenZhou; Yang, YongMing

2018-07-01

Reconstruction of the object by single-shot is of great importance in many applications, in which the object is moving or its shape is non-rigid and changes irregularly. In this paper, we propose a single-shot structured light 3D imaging technique that calculates the phase map from the distorted line pattern. This technique makes use of the image processing techniques to segment and cluster the projected structured light line pattern from one single captured image. The coordinates of the clustered lines are extracted to form a low-resolution phase matrix which is then transformed to full-resolution phase map by spline interpolation. The 3D shape of the object is computed from the full-resolution phase map and the 2D camera coordinates. Experimental results show that the proposed method was able to reconstruct the three-dimensional shape of the object robustly from one single image.

A Topographical Atlas of Shiga Toxin 2e Receptor Distribution in the Tissues of Weaned Piglets.

PubMed

Steil, Daniel; Bonse, Robert; Meisen, Iris; Pohlentz, Gottfried; Vallejo, German; Karch, Helge; Müthing, Johannes

2016-11-30

Shiga toxin (Stx) 2e of Stx-producing Escherichia coli (STEC) is the primary virulence factor in the development of pig edema disease shortly after weaning. Stx2e binds to the globo-series glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer, Galα1-4Galβ1-4Glcβ1-1Cer) and globotetraosylceramide (Gb4Cer, GalNAcβ1-3Galα1-4Galβ1-4Glcβ1-1Cer), the latter acting as the preferential Stx2e receptor. We determined Stx receptor profiles of 25 different tissues of a male and a female weaned piglet using immunochemical solid phase binding assays combined with mass spectrometry. All probed tissues harbored GSL receptors, ranging from high (category I) over moderate (category II) to low content (category III). Examples of Gb4Cer expression in category I tissues are small intestinal ileum, kidney pelvis and whole blood, followed by colon, small intestinal duodenum and jejunum belonging to category II, and kidney cortex, cerebrum and cerebellum as members of category III organs holding true for both genders. Dominant Gb3Cer and Gb4Cer lipoforms were those with ceramides carrying constant sphingosine (d18:1) and a variable C16:0, C22:0 or C24:1/C24:0 fatty acid. From the mapping data, we created a topographical atlas for Stx2e receptors in piglet tissues and organs, which might be helpful to further investigations on the molecular and cellular mechanisms that underlie infections of Stx2e-producing STEC in pigs and their zoonotic potential for humans.

A Topographical Atlas of Shiga Toxin 2e Receptor Distribution in the Tissues of Weaned Piglets

PubMed Central

Steil, Daniel; Bonse, Robert; Meisen, Iris; Pohlentz, Gottfried; Vallejo, German; Karch, Helge; Müthing, Johannes

2016-01-01

Shiga toxin (Stx) 2e of Stx-producing Escherichia coli (STEC) is the primary virulence factor in the development of pig edema disease shortly after weaning. Stx2e binds to the globo-series glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer, Galα1-4Galβ1-4Glcβ1-1Cer) and globotetraosylceramide (Gb4Cer, GalNAcβ1-3Galα1-4Galβ1-4Glcβ1-1Cer), the latter acting as the preferential Stx2e receptor. We determined Stx receptor profiles of 25 different tissues of a male and a female weaned piglet using immunochemical solid phase binding assays combined with mass spectrometry. All probed tissues harbored GSL receptors, ranging from high (category I) over moderate (category II) to low content (category III). Examples of Gb4Cer expression in category I tissues are small intestinal ileum, kidney pelvis and whole blood, followed by colon, small intestinal duodenum and jejunum belonging to category II, and kidney cortex, cerebrum and cerebellum as members of category III organs holding true for both genders. Dominant Gb3Cer and Gb4Cer lipoforms were those with ceramides carrying constant sphingosine (d18:1) and a variable C16:0, C22:0 or C24:1/C24:0 fatty acid. From the mapping data, we created a topographical atlas for Stx2e receptors in piglet tissues and organs, which might be helpful to further investigations on the molecular and cellular mechanisms that underlie infections of Stx2e-producing STEC in pigs and their zoonotic potential for humans. PMID:27916888

Broadband hyperspectral coherent anti-Stokes Raman scattering microscopy for stain-free histological imaging with principal component analysis

NASA Astrophysics Data System (ADS)

Xu, Jingjiang; Guo, Baoshan; Wong, Kenneth K. Y.; Tsia, Kevin K.

2014-02-01

Routine procedures in standard histopathology involve laborious steps of tissue processing and staining for final examination. New techniques which can bypass these procedures and thus minimize the tissue handling error would be of great clinical value. Coherent anti-Stokes Raman scattering (CARS) microscopy is an attractive tool for label-free biochemical-specific characterization of biological specimen. However, a vast majority of prior works on CARS (or stimulated Raman scattering (SRS)) bioimaging restricted analyses on a narrowband or well-distinctive Raman spectral signatures. Although hyperspectral SRS/CARS imaging has recently emerged as a better solution to access wider-band spectral information in the image, studies mostly focused on a limited spectral range, e.g. CH-stretching vibration of lipids, or non-biological samples. Hyperspectral image information in the congested fingerprint spectrum generally remains untapped for biological samples. In this regard, we further explore ultrabroadband hyperspectral multiplex (HM-CARS) to perform chemoselective histological imaging with the goal of exploring its utility in stain-free clinical histopathology. Using the supercontinuum Stokes, our system can access the CARS spectral window as wide as >2000cm-1. In order to unravel the congested CARS spectra particularly in the fingerprint region, we first employ a spectral phase-retrieval algorithm based on Kramers-Kronig (KK) transform to minimize the non-resonant background in the CARS spectrum. We then apply principal component analysis (PCA) to identify and map the spatial distribution of different biochemical components in the tissues. We demonstrate chemoselective HM-CARS imaging of a colon tissue section which displays the key cellular structures that correspond well with standard stained-tissue observation.

Design and Validation of a Compressive Tissue Stimulator with High-Throughput Capacity and Real-Time Modulus Measurement Capability

PubMed Central

Salvetti, David J.; Pino, Christopher J.; Manuel, Steven G.; Dallmeyer, Ian; Rangarajan, Sanjeet V.; Meyer, Tobias; Kotov, Misha

2012-01-01

Mechanical stimulation has been shown to impact the properties of engineered hyaline cartilage constructs and is relevant for engineering of cartilage and osteochondral tissues. Most mechanical stimulators developed to date emphasize precision over adaptability to standard tissue culture equipment and protocols. The realization of mechanical characteristics in engineered constructs approaching native cartilage requires the optimization of complex variables (type of stimulus, regimen, and bimolecular signals). We have proposed and validated a stimulator design that focuses on high construct capacity, compatibility with tissue culture plastic ware, and regimen adaptability to maximize throughput. This design utilizes thin force sensors in lieu of a load cell and a linear encoder to verify position. The implementation of an individual force sensor for each sample enables the measurement of Young's modulus while stimulating the sample. Removable and interchangeable Teflon plungers mounted using neodymium magnets contact each sample. Variations in plunger height and design can vary the strain and force type on individual samples. This allows for the evaluation of a myriad of culture conditions and regimens simultaneously. The system was validated using contact accuracy, and Young's modulus measurements range as key parameters. Contact accuracy for the system was excellent within 1.16% error of the construct height in comparison to measurements made with a micrometer. Biomaterials ranging from bioceramics (cancellous bone, 123 MPa) to soft gels (1% agarose, 20 KPa) can be measured without any modification to the device. The accuracy of measurements in conjunction with the wide range of moduli tested demonstrate the unique characteristics of the device and the feasibility of using this device in mapping real-time changes to Young's modulus of tissue constructs (cartilage, bone) through the developmental phases in ex vivo culture conditions. PMID:21988089

Morphology enabled dipole inversion (MEDI) from a single-angle acquisition: comparison with COSMOS in human brain imaging.

PubMed

Liu, Tian; Liu, Jing; de Rochefort, Ludovic; Spincemaille, Pascal; Khalidov, Ildar; Ledoux, James Robert; Wang, Yi

2011-09-01

Magnetic susceptibility varies among brain structures and provides insights into the chemical and molecular composition of brain tissues. However, the determination of an arbitrary susceptibility distribution from the measured MR signal phase is a challenging, ill-conditioned inverse problem. Although a previous method named calculation of susceptibility through multiple orientation sampling (COSMOS) has solved this inverse problem both theoretically and experimentally using multiple angle acquisitions, it is often impractical to carry out on human subjects. Recently, the feasibility of calculating the brain susceptibility distribution from a single-angle acquisition was demonstrated using morphology enabled dipole inversion (MEDI). In this study, we further improved the original MEDI method by sparsifying the edges in the quantitative susceptibility map that do not have a corresponding edge in the magnitude image. Quantitative susceptibility maps generated by the improved MEDI were compared qualitatively and quantitatively with those generated by calculation of susceptibility through multiple orientation sampling. The results show a high degree of agreement between MEDI and calculation of susceptibility through multiple orientation sampling, and the practicality of MEDI allows many potential clinical applications. Copyright © 2011 Wiley-Liss, Inc.

Report: An ex vivo up-take of levamisole molecules by cestode (Monezia expensa) of goat (Capra hirsa) and its detection through RP-HPLC.

PubMed

Ayaz, Muhammad Mazhar; Sajid, Muhammad; Das, Sanjota Nirmal; Hanif, Muhammad

2018-05-01

Detection of various molecules of drugs remained a prime issue especially in tissues of animals, humans and in their target parasites. The cestode/tapeworms pose a dilemma because of their weird body composition and uptake pattern of nutrients and medicines especially through absorption by tegument. We selected levamisole; thought to be potent antiparasitic/ani-cestodal drug. The uptake of levamisole (LEV) through cestodeal tissues is studied through HPCL in this paper. High performance liquid chromatography technique has been utilized to know the uptake of levamisole in tissues of cestodes of Goat (Monezia expensa) in small ruminants. The drug was exposed to M. expensa by in vitro till its death or a parasite ceases its movement. The tissue/ part of proglattids of the M. expensa were homogenized with some modifications and levamisole extraction was performed with liquid phase extraction method. The evaporation of solvent was done and the residual cestodal tissues were cleaned by solid phase. After the solid phase extraction method, the recovery of drug, detection and quantification of levamisole from cestodal tissues was determined through Reverse Phase Column High Performance Liquid Chromatography (RP-HPLC). Levamisole (LEV) molecules assay was obtained on a C18 reverse-phase (20um, 6mm x 150mm) column at flow rate of 1ml/min using acetonitrile and ammonium acetate as mobile phase and UV detection was done at 254nm. The development of method of Levamisole (LEV) detection from cestodal tissues by HPLC in vitro samples has been demonstrated first time in Pakistan, which can provide the solution of parasitic control and provide in sight in to the uptake of anti cestodal drugs either against human or livestock parasites.

A finite element model of remote palpation of breast lesions using radiation force: factors affecting tissue displacement.

PubMed

Nightingale, K R; Nightingale, R W; Palmeri, M L; Trahey, G E

2000-01-01

The early detection of breast cancer reduces patient mortality. The most common method of breast cancer detection is palpation. However, lesions that lie deep within the breast are difficult to palpate when they are small. Thus, a method of remote palpation, which may allow the detection of small lesions lying deep within the breast, is currently under investigation. In this method, acoustic radiation force is used to apply localized forces within tissue (to tissue volumes on the order of 2 mm3) and the resulting tissue displacements are mapped using ultrasonic correlation based methods. A volume of tissue that is stiffer than the surrounding medium (i.e., a lesion) distributes the force throughout the tissue beneath it, resulting in larger regions of displacement, and smaller maximum displacements. The resulting displacement maps may be used to image tissue stiffness. A finite-element-model (FEM) of acoustic remote palpation is presented in this paper. Using this model, a parametric analysis of the affect of varying tissue and acoustic beam characteristics on radiation force induced tissue displacements is performed. The results are used to evaluate the potential of acoustic remote palpation to provide useful diagnostic information in a clinical setting. The potential for using a single diagnostic transducer to both generate radiation force and track the resulting displacements is investigated.

Micro-PIXE mapping of mineral distribution in mature grain of two pearl millet cultivars

NASA Astrophysics Data System (ADS)

Minnis-Ndimba, R.; Kruger, J.; Taylor, J. R. N.; Mtshali, C.; Pineda-Vargas, C. A.

2015-11-01

Micro-proton-induced X-ray emission (micro-PIXE) was used to map the distribution of several nutritionally important minerals found in the grain tissue of two cultivars of pearl millet (Pennisetum glaucum (L.) R. Br.). The distribution maps revealed that the predominant localisation of minerals was within the germ (consisting of the scutellum and embryo) and the outer grain layers (specifically the pericarp and aleurone); whilst the bulk of the endosperm tissue featured relatively low concentrations of the surveyed minerals. Within the germ, the scutellum was revealed as a major storage tissue for P and K, whilst Ca, Mn and Zn were more prominent within the embryo. Fe was revealed to have a distinctive distribution pattern, confined to the dorsal end of the scutellum; but was also highly concentrated in the outer grain layers. Interestingly, the hilar region was also revealed as a site of high accumulation of minerals, particularly for S, Ca, Mn, Fe and Zn, which may be part of a defensive strategy against infection or damage. Differences between the two cultivars, in terms of the bulk Fe and P content obtained via inductively coupled plasma optical emission spectrometry (ICP-OES), concurred with the average concentration data determined from the analysis of micro-PIXE spectra specifically extracted from the endosperm tissue.

Robust dynamic 3-D measurements with motion-compensated phase-shifting profilometry

NASA Astrophysics Data System (ADS)

Feng, Shijie; Zuo, Chao; Tao, Tianyang; Hu, Yan; Zhang, Minliang; Chen, Qian; Gu, Guohua

2018-04-01

Phase-shifting profilometry (PSP) is a widely used approach to high-accuracy three-dimensional shape measurements. However, when it comes to moving objects, phase errors induced by the movement often result in severe artifacts even though a high-speed camera is in use. From our observations, there are three kinds of motion artifacts: motion ripples, motion-induced phase unwrapping errors, and motion outliers. We present a novel motion-compensated PSP to remove the artifacts for dynamic measurements of rigid objects. The phase error of motion ripples is analyzed for the N-step phase-shifting algorithm and is compensated using the statistical nature of the fringes. The phase unwrapping errors are corrected exploiting adjacent reliable pixels, and the outliers are removed by comparing the original phase map with a smoothed phase map. Compared with the three-step PSP, our method can improve the accuracy by more than 95% for objects in motion.

Statistical Image Recovery From Laser Speckle Patterns With Polarization Diversity

DTIC Science & Technology

2010-09-01

Fourier Transform is taken mapping the data to the pupil plane . The computed phase from this operation is multiplied to the amplitude of the pupil...guess generated by a uniform ran- dom number generator (−π to π). The guessed phase is multiplied to the measured amplitude in the image plane and the... plane data. Again, a Fourier transform is performed mapping the manipulated data set back to the image plane . The computed phase in this op- eration is

Color mapping of one specific velocity of a biological fluid flows with complex geometry using optical coherence tomography

NASA Astrophysics Data System (ADS)

Potlov, A. Yu.; Frolov, S. V.; Proskurin, S. G.

2018-04-01

The method of Doppler color mapping of one specific (previously chosen) velocity in a turbulent flow inside biological tissues using optical coherence tomography is described. The key features of the presented method are: the raw data are separated into three parts, corresponding to the unmoving biological tissue, the positively and negatively directed biological fluid flows; the further independent signal processing procedure yields the structure image and two images of the chosen velocity, which are then normalised, encoded and joined. The described method can be used to obtain in real time the anatomical maps of the chosen velocities in normal and pathological states. The described method can be applied not only in optical coherence tomography, but also in endoscopic and Doppler ultrasonic medical imaging systems.

Phase quality map based on local multi-unwrapped results for two-dimensional phase unwrapping.

PubMed

Zhong, Heping; Tang, Jinsong; Zhang, Sen

2015-02-01

The efficiency of a phase unwrapping algorithm and the reliability of the corresponding unwrapped result are two key problems in reconstructing the digital elevation model of a scene from its interferometric synthetic aperture radar (InSAR) or interferometric synthetic aperture sonar (InSAS) data. In this paper, a new phase quality map is designed and implemented in a graphic processing unit (GPU) environment, which greatly accelerates the unwrapping process of the quality-guided algorithm and enhances the correctness of the unwrapped result. In a local wrapped phase window, the center point is selected as the reference point, and then two unwrapped results are computed by integrating in two different simple ways. After the two local unwrapped results are computed, the total difference of the two unwrapped results is regarded as the phase quality value of the center point. In order to accelerate the computing process of the new proposed quality map, we have implemented it in a GPU environment. The wrapped phase data are first uploaded to the memory of a device, and then the kernel function is called in the device to compute the phase quality in parallel by blocks of threads. Unwrapping tests performed on the simulated and real InSAS data confirm the accuracy and efficiency of the proposed method.

A new imaging technique on strength and phase of pulsatile tissue-motion in brightness-mode ultrasonogram

NASA Astrophysics Data System (ADS)

Fukuzawa, Masayuki; Yamada, Masayoshi; Nakamori, Nobuyuki; Kitsunezuka, Yoshiki

2007-03-01

A new imaging technique has been developed for observing both strength and phase of pulsatile tissue-motion in a movie of brightness-mode ultrasonogram. The pulsatile tissue-motion is determined by evaluating the heartbeat-frequency component in Fourier transform of a series of pixel value as a function of time at each pixel in a movie of ultrasonogram (640x480pixels/frame, 8bit/pixel, 33ms/frame) taken by a conventional ultrasonograph apparatus (ATL HDI5000). In order to visualize both the strength and the phase of the pulsatile tissue-motion, we propose a pulsatile-phase image that is obtained by superimposition of color gradation proportional to the motion phase on the original ultrasonogram only at which the motion strength exceeds a proper threshold. The pulsatile-phase image obtained from a cranial ultrasonogram of normal neonate clearly reveals that the motion region gives good agreement with the anatomical shape and position of the middle cerebral artery and the corpus callosum. The motion phase is fluctuated with the shape of arteries revealing local obstruction of blood flow. The pulsatile-phase images in the neonates with asphyxia at birth reveal decreases of the motion region and increases of the phase fluctuation due to the weakness and local disturbance of blood flow, which is useful for pediatric diagnosis.

Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues

PubMed Central

Blazie, Stephen M.; Geissel, Heather C.; Wilky, Henry; Joshi, Rajan; Newbern, Jason; Mangone, Marco

2017-01-01

mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3′untranslated region (3′UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3′UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3′UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis. PMID:28348061

Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Caenorhabditis elegans Somatic Tissues.

PubMed

Blazie, Stephen M; Geissel, Heather C; Wilky, Henry; Joshi, Rajan; Newbern, Jason; Mangone, Marco

2017-06-01

mRNA expression dynamics promote and maintain the identity of somatic tissues in living organisms; however, their impact in post-transcriptional gene regulation in these processes is not fully understood. Here, we applied the PAT-Seq approach to systematically isolate, sequence, and map tissue-specific mRNA from five highly studied Caenorhabditis elegans somatic tissues: GABAergic and NMDA neurons, arcade and intestinal valve cells, seam cells, and hypodermal tissues, and studied their mRNA expression dynamics. The integration of these datasets with previously profiled transcriptomes of intestine, pharynx, and body muscle tissues, precisely assigns tissue-specific expression dynamics for 60% of all annotated C. elegans protein-coding genes, providing an important resource for the scientific community. The mapping of 15,956 unique high-quality tissue-specific polyA sites in all eight somatic tissues reveals extensive tissue-specific 3'untranslated region (3'UTR) isoform switching through alternative polyadenylation (APA) . Almost all ubiquitously transcribed genes use APA and harbor miRNA targets in their 3'UTRs, which are commonly lost in a tissue-specific manner, suggesting widespread usage of post-transcriptional gene regulation modulated through APA to fine tune tissue-specific protein expression. Within this pool, the human disease gene C. elegans orthologs rack-1 and tct-1 use APA to switch to shorter 3'UTR isoforms in order to evade miRNA regulation in the body muscle tissue, resulting in increased protein expression needed for proper body muscle function. Our results highlight a major positive regulatory role for APA, allowing genes to counteract miRNA regulation on a tissue-specific basis. Copyright © 2017 Blazie et al.

Generating Multi-Destination Maps.

PubMed

Zhang, Junsong; Fan, Jiepeng; Luo, Zhenshan

2017-08-01

Multi-destination maps are a kind of navigation maps aimed to guide visitors to multiple destinations within a region, which can be of great help to urban visitors. However, they have not been developed in the current online map service. To address this issue, we introduce a novel layout model designed especially for generating multi-destination maps, which considers the global and local layout of a multi-destination map. We model the layout problem as a graph drawing that satisfies a set of hard and soft constraints. In the global layout phase, we balance the scale factor between ROIs. In the local layout phase, we make all edges have good visibility and optimize the map layout to preserve the relative length and angle of roads. We also propose a perturbation-based optimization method to find an optimal layout in the complex solution space. The multi-destination maps generated by our system are potential feasible on the modern mobile devices and our result can show an overview and a detail view of the whole map at the same time. In addition, we perform a user study to evaluate the effectiveness of our method, and the results prove that the multi-destination maps achieve our goals well.

Quantitative Susceptibility Mapping using Structural Feature based Collaborative Reconstruction (SFCR) in the Human Brain

PubMed Central

Cai, Congbo; Chen, Zhong; van Zijl, Peter C.M.

2017-01-01

The reconstruction of MR quantitative susceptibility mapping (QSM) from local phase measurements is an ill posed inverse problem and different regularization strategies incorporating a priori information extracted from magnitude and phase images have been proposed. However, the anatomy observed in magnitude and phase images does not always coincide spatially with that in susceptibility maps, which could give erroneous estimation in the reconstructed susceptibility map. In this paper, we develop a structural feature based collaborative reconstruction (SFCR) method for QSM including both magnitude and susceptibility based information. The SFCR algorithm is composed of two consecutive steps corresponding to complementary reconstruction models, each with a structural feature based l1 norm constraint and a voxel fidelity based l2 norm constraint, which allows both the structure edges and tiny features to be recovered, whereas the noise and artifacts could be reduced. In the M-step, the initial susceptibility map is reconstructed by employing a k-space based compressed sensing model incorporating magnitude prior. In the S-step, the susceptibility map is fitted in spatial domain using weighted constraints derived from the initial susceptibility map from the M-step. Simulations and in vivo human experiments at 7T MRI show that the SFCR method provides high quality susceptibility maps with improved RMSE and MSSIM. Finally, the susceptibility values of deep gray matter are analyzed in multiple head positions, with the supine position most approximate to the gold standard COSMOS result. PMID:27019480

Observations of two-phase flow patterns in a horizontal circular channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ewing, M.E.; Weinandy, J.J.; Christensen, R.N.

1999-01-01

Horizontal two-phase flow patterns were observed in a transparent circular channel (1.90 cm I.D.) using adiabatic mixtures of air and water. Visual identification of the flow regimes was supplemented with photographic data and the results were plotted on the flow regime map which has been proposed by Breber et al. for condensation applications. The results indicate general consistency between the observations and the predictions of the map, and, by providing data for different fluids and conditions from which the map was developed, support its general applicability.

Phase contrast imaging of buccal mucosa tissues-Feasibility study

NASA Astrophysics Data System (ADS)

Fatima, A.; Tripathi, S.; Shripathi, T.; Kulkarni, V. K.; Banda, N. R.; Agrawal, A. K.; Sarkar, P. S.; Kashyap, Y.; Sinha, A.

2015-06-01

Phase Contrast Imaging (PCI) technique has been used to interpret physical parameters obtained from the image taken on the normal buccal mucosa tissue extracted from cheek of a patient. The advantages of this method over the conventional imaging techniques are discussed. PCI technique uses the X-ray phase shift at the edges differentiated by very minute density differences and the edge enhanced high contrast images reveal details of soft tissues. The contrast in the images produced is related to changes in the X-ray refractive index of the tissues resulting in higher clarity compared with conventional absorption based X-ray imaging. The results show that this type of imaging has better ability to visualize microstructures of biological soft tissues with good contrast, which can lead to the diagnosis of lesions at an early stage of the diseases.

Quantified elasticity mapping of ocular tissue using acoustic radiation force optical coherence elastography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Qu, Yueqiao; He, Youmin; Zhang, Yi; Ma, Teng; Zhu, Jiang; Miao, Yusi; Dai, Cuixia; Silverman, Ronald; Humayun, Mark S.; Zhou, Qifa; Chen, Zhongping

2017-02-01

Age-related macular degeneration and keratoconus are two ocular diseases occurring in the posterior and anterior eye, respectively. In both conditions, the mechanical elasticity of the respective tissues changes during the early onset of disease. It is necessary to detect these differences and treat the diseases in their early stages to provide proper treatment. Acoustic radiation force optical coherence elastography is a method of elasticity mapping using confocal ultrasound waves for excitation and Doppler optical coherence tomography for detection. We report on an ARF-OCE system that uses modulated compression wave based excitation signals, and detects the spatial and frequency responses of the tissue. First, all components of the system is synchronized and triggered such that the signal is consistent between frames. Next, phantom studies are performed to validate and calibrate the relationship between the resonance frequency and the Young's modulus. Then the frequency responses of the anterior and posterior eye are detected for porcine and rabbit eyes, and the results correlated to the elasticity. Finally, spatial elastograms are obtained for a porcine retina. Layer segmentation and analysis is performed and correlated to the histology of the retina, where five distinct layers are recognized. The elasticities of the tissue layers will be quantified according to the mean thickness and displacement response for the locations on the retina. This study is a stepping stone to future in-vivo animal studies, where the elastic modulus of the ocular tissue can be quantified and mapped out accordingly.

Long Read Alignment with Parallel MapReduce Cloud Platform

PubMed Central

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

Long Read Alignment with Parallel MapReduce Cloud Platform.

PubMed

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

Molecular imaging of cannabis leaf tissue with MeV-SIMS method

NASA Astrophysics Data System (ADS)

Jenčič, Boštjan; Jeromel, Luka; Ogrinc Potočnik, Nina; Vogel-Mikuš, Katarina; Kovačec, Eva; Regvar, Marjana; Siketić, Zdravko; Vavpetič, Primož; Rupnik, Zdravko; Bučar, Klemen; Kelemen, Mitja; Kovač, Janez; Pelicon, Primož

2016-03-01

To broaden our analytical capabilities with molecular imaging in addition to the existing elemental imaging with micro-PIXE, a linear Time-Of-Flight mass spectrometer for MeV Secondary Ion Mass Spectrometry (MeV-SIMS) was constructed and added to the existing nuclear microprobe at the Jožef Stefan Institute. We measured absolute molecular yields and damage cross-section of reference materials, without significant alteration of the fragile biological samples during the duration of measurements in the mapping mode. We explored the analytical capability of the MeV-SIMS technique for chemical mapping of the plant tissue of medicinal cannabis leaves. A series of hand-cut plant tissue slices were prepared by standard shock-freezing and freeze-drying protocol and deposited on the Si wafer. We show the measured MeV-SIMS spectra showing a series of peaks in the mass area of cannabinoids, as well as their corresponding maps. The indicated molecular distributions at masses of 345.5 u and 359.4 u may be attributed to the protonated THCA and THCA-C4 acids, and show enhancement in the areas with opened trichome morphology.

Catlas: An magnetic resonance imaging-based three-dimensional cortical atlas and tissue probability maps for the domestic cat (Felis catus).

PubMed

Stolzberg, Daniel; Wong, Carmen; Butler, Blake E; Lomber, Stephen G

2017-10-15

Brain atlases play an important role in effectively communicating results from neuroimaging studies in a standardized coordinate system. Furthermore, brain atlases extend analysis of functional magnetic resonance imaging (MRI) data by delineating regions of interest over which to evaluate the extent of functional activation as well as measures of inter-regional connectivity. Here, we introduce a three-dimensional atlas of the cat cerebral cortex based on established cytoarchitectonic and electrophysiological findings. In total, 71 cerebral areas were mapped onto the gray matter (GM) of an averaged T1-weighted structural MRI acquired at 7 T from eight adult domestic cats. In addition, a nonlinear registration procedure was used to generate a common template brain as well as GM, white matter, and cerebral spinal fluid tissue probability maps to facilitate tissue segmentation as part of the standard preprocessing pipeline for MRI data analysis. The atlas and associated files can also be used for planning stereotaxic surgery and for didactic purposes. © 2017 Wiley Periodicals, Inc.

Mathematical modeling of the malignancy of cancer using graph evolution.

PubMed

Gunduz-Demir, Cigdem

2007-10-01

We report a novel computational method based on graph evolution process to model the malignancy of brain cancer called glioma. In this work, we analyze the phases that a graph passes through during its evolution and demonstrate strong relation between the malignancy of cancer and the phase of its graph. From the photomicrographs of tissues, which are diagnosed as normal, low-grade cancerous and high-grade cancerous, we construct cell-graphs based on the locations of cells; we probabilistically generate an edge between every pair of cells depending on the Euclidean distance between them. For a cell-graph, we extract connectivity information including the properties of its connected components in order to analyze the phase of the cell-graph. Working with brain tissue samples surgically removed from 12 patients, we demonstrate that cell-graphs generated for different tissue types evolve differently and that they exhibit different phase properties, which distinguish a tissue type from another.

Dual-phase 99mTc-MIBI imaging and the expressions of P-gp, GST-π, and MRP1 in hyperparathyroidism.

PubMed

Xue, Jianjun; Liu, Yan; Yang, Danrong; Yu, Yan; Geng, Qianqian; Ji, Ting; Yang, Lulu; Wang, Qi; Wang, Yuanbo; Lu, Xueni; Yang, Aimin

2017-10-01

The aim of this study was to further elucidate the mechanisms of dual-phase technetium-99m methoxyisobutylisonitrile (Tc-MIBI) parathyroid imaging by exploring the association between early uptake results (EUR), delayed uptake results (DUR), and the retention index (RI) in dual-phase Tc-MIBI parathyroid imaging and P glycoprotein (P-gp), multidrug resistance-associated protein 1 (MRP1), and glutathione S-transferase-π (GST-π) expression in hyperparathyroidism (HPT). Preoperative dual-phase (early and delayed) Tc-MIBI imaging was performed on 74 patients undergoing parathyroidectomy for HPT. EUR, DUR, and RI were calculated. P-gp, MRP1, and GST-π expressions were assessed using immunohistochemistry in resected tissue from HPT and control patients. The association between P-gp, MRP1, and GST-π expressions and EUR, DUR, and RI in HPT was evaluated. The positive rate of dual-phase T c-MIBI imaging was 91.89% (68/74) and the false-negative rate was 8.11% (6/74). P-gp and GST-π expressions were higher in tissues resected from control compared with HPT patients (47.37 and 81.5%, P<0.05); there was no difference in MRP1. EUR were associated with P-gp and GST-π expressions, and DUR were associated with MRP1 expression. There was a significant difference in MRP1 expression between RI greater than or equal to 0 and RI less than 0. There was no relationship between the sensitivity of dual-phase Tc-MIBI imaging and P-gp, MRP1, and GST-π expressions in resected parathyroid tissue. The six false-negative HPT cases consisted of three P-gp (-)/MRP1 (-) tissues, three P-gp (-)/GST-π (-) tissues, and four MRP1 (-)/GST-π (-) tissues. As P-gp and GST-π expressions were higher in tissues resected from control compared with HPT patients, Tc-MIBI may wash out faster from normal parathyroid tissue surrounding the lesion compared with the lesion itself, facilitating detection.

Various clinical application of phase contrast X-ray

NASA Astrophysics Data System (ADS)

Oh, Chilhwan; Park, Sangyong; Ha, Seunghan; Park, Gyuman; Lee, Gunwoo; Lee, Onseok; Je, Jungho

2008-02-01

In biomedical application study using phase contrast X-ray, both sample thickness or density and absorption difference are very important factors in aspects of contrast enhancement. We present experimental evidence that synchrotron hard X-ray are suitable for radiological imaging of biological samples down to the cellular level. We investigated the potential of refractive index radiology using un-monochromatized synchrotron hard X-rays for the imaging of cell and tissue in various diseases. Material had been adopted various medical field, such as apoE knockout mouse in cardiologic field, specimen from renal and prostatic carcinoma patient in urology, basal cell epithelioma in dermatology, brain tissue from autosy sample of pakinson's disease, artificially induced artilrtis tissue from rabbits and extracted tooth from patients of crack tooth syndrome. Formalin and paraffin fixed tissue blocks were cut in 3 mm thickness for the X-ray radiographic imaging. From adjacent areas, 4 μm thickness sections were also prepared for hematoxylin-eosin staining. Radiographic images of dissected tissues were obtained using the hard X-rays from the 7B2 beamline of the Pohang Light Source (PLS). The technique used for the study was the phase contrast images were compared with the optical microscopic images of corresponding histological slides. Radiographic images of various diseased tissues showed clear histological details of organelles in normal tissues. Most of cancerous lesions were well differentiated from adjacent normal tissues and detailed histological features of each tumor were clearly identified. Also normal microstructures were identifiable by the phase contrast imaging. Tissue in cancer or other disease showed clearly different findings from those of surrounding normal tissue. For the first time we successfully demonstrated that synchrotron hard X-rays can be used for radiological imaging of relatively thick tissue samples with great histological details.

A Comparison of Phasing Algorithms for Trios and Unrelated Individuals

PubMed Central

Marchini, Jonathan; Cutler, David; Patterson, Nick; Stephens, Matthew; Eskin, Eleazar; Halperin, Eran; Lin, Shin; Qin, Zhaohui S.; Munro, Heather M.; Abecasis, Gonçalo R.; Donnelly, Peter

2006-01-01

Knowledge of haplotype phase is valuable for many analysis methods in the study of disease, population, and evolutionary genetics. Considerable research effort has been devoted to the development of statistical and computational methods that infer haplotype phase from genotype data. Although a substantial number of such methods have been developed, they have focused principally on inference from unrelated individuals, and comparisons between methods have been rather limited. Here, we describe the extension of five leading algorithms for phase inference for handling father-mother-child trios. We performed a comprehensive assessment of the methods applied to both trios and to unrelated individuals, with a focus on genomic-scale problems, using both simulated data and data from the HapMap project. The most accurate algorithm was PHASE (v2.1). For this method, the percentages of genotypes whose phase was incorrectly inferred were 0.12%, 0.05%, and 0.16% for trios from simulated data, HapMap Centre d'Etude du Polymorphisme Humain (CEPH) trios, and HapMap Yoruban trios, respectively, and 5.2% and 5.9% for unrelated individuals in simulated data and the HapMap CEPH data, respectively. The other methods considered in this work had comparable but slightly worse error rates. The error rates for trios are similar to the levels of genotyping error and missing data expected. We thus conclude that all the methods considered will provide highly accurate estimates of haplotypes when applied to trio data sets. Running times differ substantially between methods. Although it is one of the slowest methods, PHASE (v2.1) was used to infer haplotypes for the 1 million–SNP HapMap data set. Finally, we evaluated methods of estimating the value of r2 between a pair of SNPs and concluded that all methods estimated r2 well when the estimated value was ⩾0.8. PMID:16465620

Molecular mechanisms underlying variations in lung function: a systems genetics analysis

PubMed Central

Obeidat, Ma’en; Hao, Ke; Bossé, Yohan; Nickle, David C; Nie, Yunlong; Postma, Dirkje S; Laviolette, Michel; Sandford, Andrew J; Daley, Denise D; Hogg, James C; Elliott, W Mark; Fishbane, Nick; Timens, Wim; Hysi, Pirro G; Kaprio, Jaakko; Wilson, James F; Hui, Jennie; Rawal, Rajesh; Schulz, Holger; Stubbe, Beate; Hayward, Caroline; Polasek, Ozren; Järvelin, Marjo-Riitta; Zhao, Jing Hua; Jarvis, Deborah; Kähönen, Mika; Franceschini, Nora; North, Kari E; Loth, Daan W; Brusselle, Guy G; Smith, Albert Vernon; Gudnason, Vilmundur; Bartz, Traci M; Wilk, Jemma B; O’Connor, George T; Cassano, Patricia A; Tang, Wenbo; Wain, Louise V; Artigas, María Soler; Gharib, Sina A; Strachan, David P; Sin, Don D; Tobin, Martin D; London, Stephanie J; Hall, Ian P; Paré, Peter D

2016-01-01

Summary Background Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48 201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. Methods The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. Findings SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. Interpretation The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. Funding The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS. PMID:26404118

Acoustic methods for cavitation mapping in biomedical applications

NASA Astrophysics Data System (ADS)

Wan, M.; Xu, S.; Ding, T.; Hu, H.; Liu, R.; Bai, C.; Lu, S.

2015-12-01

In recent years, cavitation is increasingly utilized in a wide range of applications in biomedical field. Monitoring the spatial-temporal evolution of cavitation bubbles is of great significance for efficiency and safety in biomedical applications. In this paper, several acoustic methods for cavitation mapping proposed or modified on the basis of existing work will be presented. The proposed novel ultrasound line-by-line/plane-by-plane method can depict cavitation bubbles distribution with high spatial and temporal resolution and may be developed as a potential standard 2D/3D cavitation field mapping method. The modified ultrafast active cavitation mapping based upon plane wave transmission and reception as well as bubble wavelet and pulse inversion technique can apparently enhance the cavitation to tissue ratio in tissue and further assist in monitoring the cavitation mediated therapy with good spatial and temporal resolution. The methods presented in this paper will be a foundation to promote the research and development of cavitation imaging in non-transparent medium.

Tumor tissue characterization using polarization-sensitive second harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Tokarz, Danielle; Cisek, Richard; Golaraei, Ahmad; Krouglov, Serguei; Navab, Roya; Niu, Carolyn; Sakashita, Shingo; Yasufuku, Kazuhiro; Tsao, Ming-Sound; Asa, Sylvia L.; Barzda, Virginijus; Wilson, Brian C.

2015-06-01

Changes in the ultrastructure of collagen in various tumor and non-tumor human tissues including lung, pancreas and thyroid were investigated ex vivo by a polarization-sensitive second harmonic generation (SHG) microscopy technique referred to as polarization-in, polarization-out (PIPO) SHG. This involves measuring the orientation of the linear polarization of outgoing SHG as a function of the linear polarization orientation of incident laser radiation. From the PIPO SHG data, the second-order nonlinear optical susceptibility tensor component ratio, χ(2) ZZZ'/χ(2) ZXX', for each pixel of the SHG image was obtained and presented as color-coded maps. Further, the orientation of collagen fibers in the tissue was deduced. Since the χ(2) ZZZ'/χ(2) ZXX' values represent the organization of collagen in the tissue, theses maps revealed areas of altered collagen structure (not simply concentration) within tissue sections. Statistically-significant differences in χ(2) ZZZ'/χ(2) ZXX' were found between tumor and non-tumor tissues, which varied from organ to organ. Hence, PIPO SHG microscopy could potentially be used to aid pathologists in diagnosing cancer. Additionally, PIPO SHG microscopy could aid in characterizing the structure of collagen in other collagen-related biological processes such as wound repair.

Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

2015-05-01

Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

Comparing phase-sensitive and phase-insensitive echolocation target images using a monaural audible sonar.

PubMed

Kuc, Roman

2018-04-01

This paper describes phase-sensitive and phase-insensitive processing of monaural echolocation waveforms to generate target maps. Composite waveforms containing both the emission and echoes are processed to estimate the target impulse response using an audible sonar. Phase-sensitive processing yields the composite signal envelope, while phase-insensitive processing that starts with the composite waveform power spectrum yields the envelope of the autocorrelation function. Analysis and experimental verification show that multiple echoes form an autocorrelation function that produces near-range phantom-reflector artifacts. These artifacts interfere with true target echoes when the first true echo occurs at a time that is less than the total duration of the target echoes. Initial comparison of phase-sensitive and phase-insensitive maps indicates that both display important target features, indicating that phase is not vital. A closer comparison illustrates the improved resolution of phase-sensitive processing, the near-range phantom-reflectors produced by phase-insensitive processing, and echo interference and multiple reflection artifacts that were independent of the processing.

Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water.

PubMed

Wang, Zhi-Xiang; Duan, Yong

2004-11-15

The effects of solvation on the conformations and energies of alanine dipeptide (AD) have been studied by ab initio calculations up to MP2/cc-pVTZ//MP2/6-31G**, utilizing the polarizable continuum model (PCM) to mimic solvation effects. The energy surfaces in the gas phase, ether, and water bear similar topological features carved by the steric hindrance, but the details differ significantly due to the solvent effects. The gas-phase energy map is qualitatively consistent with the Ramachandran plot showing seven energy minima. With respect to the gas-phase map, the significant changes of the aqueous map include (1) the expanded low-energy regions, (2) the emergence of an energy barrier between C5-beta and alpha(R)-beta(2) regions, (3) a clearly pronounced alpha(R) minimum, a new beta-conformer, and the disappearance of the gas-phase global minimum, and (4) the shift of the dominant region in LEII from the gas-phase C7(ax) region to the alpha(L) region. These changes bring the map in water to be much closer to the Ramachandran plot than the gas-phase map. The solvent effects on the geometries include the elongation of the exposed N-H and C=O bonds, the shortening of the buried HN--CO peptide bonds, and the enhanced planarity of the peptide bonds. The energy surface in ether has features similar to those both in the gas phase and in water. The free energy order computed in the gas phase and in ether is in good agreement with experimental studies that concluded that C5 and C7(eq) are the dominant species in both the gas phase and nonpolar solvents. The free energy order in water is consistent with the experimental observation that the dominant C7(eq) in the nonpolar solvent was largely replaced by P(II)-like (i.e., beta) and alpha(R) in the strong polar solvents. Based on calculations on AD + 4H(2)O and other AD-water clusters, we suggest that explicit water-AD interactions may distort C5 and beta (or alpha(R) and beta) to an intermediate conformation. Our analysis also shows that the PCM calculations at the MP2/cc-pVTZ//MP2/6-31G** level give good descriptions to the bulk solvent polarization effect. The results presented in this article should be of sufficient quality to characterize the peptide bonds in the gas phase and solvents. The energy surfaces may serve as the basis for developing of strategies enabling the inclusion of solvent polarization in the force field.

Towards noninvasive method for the detection of pathological tissue variations by mapping different blood parameters

NASA Astrophysics Data System (ADS)

Abdallah, Omar; Qananwah, Qasem; Abo Alam, Kawther; Bolz, Armin

2010-04-01

This paper describes the development of an early detection method for probing pathological tissue variations. The method could be used for classifying various tissue alteration namely tumors tissue or skin disorders. The used approach is based on light scattering and absorption spectroscopy. Spectral content of the scattered light provides diagnostic information about the tissue contents. The importance of this method is using a safe light that has less power than the used in the imaging methods that will enable the frequent examination of tissue, while the exiting modalities have drawbacks like ionization, high cost, time-consuming, and agents' usage. A modality for mapping the oxygen saturation distribution in tissues noninvasively is new in this area of research, since this study focuses on the oxygen molecule in the tissue which supposed to be homogenously distributed through the tissues. Cancers may cause greater vascularization and greater oxygen consumption than in normal tissue. Therefore, oxygen existence and homogeneity will be alternated depending on the tissue state. In the proposed system, the signal was extracted after illuminating the tissue by light emitting diodes (LED's) that emits light in two wavelengths, red (660 nm) and infrared (880 nm). The absorption in these wavelengths is mainly due to oxyhemoglobin (HbO2) and deoxyhemoglobin (Hb) while other blood and tissue contents nearly have low effect on the signal. The backscattered signal which is received by a photodiodes array (128 PDs) was measured and processed using LabVIEW. Photoplethysmogram (PPG) signals have been measured at different locations. These signals will be used to differentiate between the normal and the pathological tissues. Variations in hemoglobin concentration and blood perfusion will also be used as an important indication feature for this purpose.

STUDIES ON THE PROPAGATION IN VITRO OF POLIOMYELITIS VIRUSES

PubMed Central

Scherer, William F.; Syverton, Jerome T.

1952-01-01

The growth of poliomyelitis virus, Type 2, Yale-SK strain, in cultures of monkey testicular tissue was observed to occur in discrete cycles. Growth curves showed that each cycle was composed of (a) an initial lag phase when little or no virus was released from the cells, (6) a phase of viral production, and (c) a plateau which represented a decrement in the rate of viral production. This pattern of viral multiplication occurred in monkey testicular tissue cultures which have as the liquid phase either ox serum ultrafiltrate or monkey serum-chicken embryonic extract medium. The presence of a solid medium composed of chicken plasma, clotted either with chicken embryonic extract or bovine thrombin, did not alter the pattern of viral multiplication. The shape of the growth curve as established by any of four different techniques for tissue cultivation, was shown to be independent of the cultural technique employed. For cultures of monkey testicular tissue, the amount of virus in the tissue was as much as tenfold greater than that in the liquid of the same cultures. Moreover, viral production was evident earlier and was detectable for a longer period of time in the tissue than in the liquid phase. The rapidly incremental phase of the growth cycle, when large quantities of virus were released into the liquid phase, coincided in time with the destruction of the spindle-shaped cells, which extended from the explants. Although destruction of outgrowth cells was marked, there remained cells within the explants capable of supporting the growth of poliomyelitis virus. PMID:12981221

Probabilistic atlas-based segmentation of combined T1-weighted and DUTE MRI for calculation of head attenuation maps in integrated PET/MRI scanners.

PubMed

Poynton, Clare B; Chen, Kevin T; Chonde, Daniel B; Izquierdo-Garcia, David; Gollub, Randy L; Gerstner, Elizabeth R; Batchelor, Tracy T; Catana, Ciprian

2014-01-01

We present a new MRI-based attenuation correction (AC) approach for integrated PET/MRI systems that combines both segmentation- and atlas-based methods by incorporating dual-echo ultra-short echo-time (DUTE) and T1-weighted (T1w) MRI data and a probabilistic atlas. Segmented atlases were constructed from CT training data using a leave-one-out framework and combined with T1w, DUTE, and CT data to train a classifier that computes the probability of air/soft tissue/bone at each voxel. This classifier was applied to segment the MRI of the subject of interest and attenuation maps (μ-maps) were generated by assigning specific linear attenuation coefficients (LACs) to each tissue class. The μ-maps generated with this "Atlas-T1w-DUTE" approach were compared to those obtained from DUTE data using a previously proposed method. For validation of the segmentation results, segmented CT μ-maps were considered to the "silver standard"; the segmentation accuracy was assessed qualitatively and quantitatively through calculation of the Dice similarity coefficient (DSC). Relative change (RC) maps between the CT and MRI-based attenuation corrected PET volumes were also calculated for a global voxel-wise assessment of the reconstruction results. The μ-maps obtained using the Atlas-T1w-DUTE classifier agreed well with those derived from CT; the mean DSCs for the Atlas-T1w-DUTE-based μ-maps across all subjects were higher than those for DUTE-based μ-maps; the atlas-based μ-maps also showed a lower percentage of misclassified voxels across all subjects. RC maps from the atlas-based technique also demonstrated improvement in the PET data compared to the DUTE method, both globally as well as regionally.

Chaos M-ary modulation and demodulation method based on Hamilton oscillator and its application in communication.

PubMed

Fu, Yongqing; Li, Xingyuan; Li, Yanan; Yang, Wei; Song, Hailiang

2013-03-01

Chaotic communication has aroused general interests in recent years, but its communication effect is not ideal with the restriction of chaos synchronization. In this paper a new chaos M-ary digital modulation and demodulation method is proposed. By using region controllable characteristics of spatiotemporal chaos Hamilton map in phase plane and chaos unique characteristic, which is sensitive to initial value, zone mapping method is proposed. It establishes the map relationship between M-ary digital information and the region of Hamilton map phase plane, thus the M-ary information chaos modulation is realized. In addition, zone partition demodulation method is proposed based on the structure characteristic of Hamilton modulated information, which separates M-ary information from phase trajectory of chaotic Hamilton map, and the theory analysis of zone partition demodulator's boundary range is given. Finally, the communication system based on the two methods is constructed on the personal computer. The simulation shows that in high speed transmission communications and with no chaos synchronization circumstance, the proposed chaotic M-ary modulation and demodulation method has outperformed some conventional M-ary modulation methods, such as quadrature phase shift keying and M-ary pulse amplitude modulation in bit error rate. Besides, it has performance improvement in bandwidth efficiency, transmission efficiency and anti-noise performance, and the system complexity is low and chaos signal is easy to generate.

A real time QRS detection using delay-coordinate mapping for the microcontroller implementation.

PubMed

Lee, Jeong-Whan; Kim, Kyeong-Seop; Lee, Bongsoo; Lee, Byungchae; Lee, Myoung-Ho

2002-01-01

In this article, we propose a new algorithm using the characteristics of reconstructed phase portraits by delay-coordinate mapping utilizing lag rotundity for a real-time detection of QRS complexes in ECG signals. In reconstructing phase portrait the mapping parameters, time delay, and mapping dimension play important roles in shaping of portraits drawn in a new dimensional space. Experimentally, the optimal mapping time delay for detection of QRS complexes turned out to be 20 ms. To explore the meaning of this time delay and the proper mapping dimension, we applied a fill factor, mutual information, and autocorrelation function algorithm that were generally used to analyze the chaotic characteristics of sampled signals. From these results, we could find the fact that the performance of our proposed algorithms relied mainly on the geometrical property such as an area of the reconstructed phase portrait. For the real application, we applied our algorithm for designing a small cardiac event recorder. This system was to record patients' ECG and R-R intervals for 1 h to investigate HRV characteristics of the patients who had vasovagal syncope symptom and for the evaluation, we implemented our algorithm in C language and applied to MIT/BIH arrhythmia database of 48 subjects. Our proposed algorithm achieved a 99.58% detection rate of QRS complexes.

Characterizing optical properties and spatial heterogeneity of human ovarian tissue using spatial frequency domain imaging

NASA Astrophysics Data System (ADS)

Nandy, Sreyankar; Mostafa, Atahar; Kumavor, Patrick D.; Sanders, Melinda; Brewer, Molly; Zhu, Quing

2016-10-01

A spatial frequency domain imaging (SFDI) system was developed for characterizing ex vivo human ovarian tissue using wide-field absorption and scattering properties and their spatial heterogeneities. Based on the observed differences between absorption and scattering images of different ovarian tissue groups, six parameters were quantitatively extracted. These are the mean absorption and scattering, spatial heterogeneities of both absorption and scattering maps measured by a standard deviation, and a fitting error of a Gaussian model fitted to normalized mean Radon transform of the absorption and scattering maps. A logistic regression model was used for classification of malignant and normal ovarian tissues. A sensitivity of 95%, specificity of 100%, and area under the curve of 0.98 were obtained using six parameters extracted from the SFDI images. The preliminary results demonstrate the diagnostic potential of the SFDI method for quantitative characterization of wide-field optical properties and the spatial distribution heterogeneity of human ovarian tissue. SFDI could be an extremely robust and valuable tool for evaluation of the ovary and detection of neoplastic changes of ovarian cancer.

Quantitative real-time optical imaging of the tissue metabolic rate of oxygen consumption

NASA Astrophysics Data System (ADS)

Ghijsen, Michael; Lentsch, Griffin R.; Gioux, Sylvain; Brenner, Matthew; Durkin, Anthony J.; Choi, Bernard; Tromberg, Bruce J.

2018-03-01

The tissue metabolic rate of oxygen consumption (tMRO2) is a clinically relevant marker for a number of pathologies including cancer and arterial occlusive disease. We present and validate a noncontact method for quantitatively mapping tMRO2 over a wide, scalable field of view at 16 frames / s. We achieve this by developing a dual-wavelength, near-infrared coherent spatial frequency-domain imaging (cSFDI) system to calculate tissue optical properties (i.e., absorption, μa, and reduced scattering, μs‧, parameters) as well as the speckle flow index (SFI) at every pixel. Images of tissue oxy- and deoxyhemoglobin concentration ( [ HbO2 ] and [HHb]) are calculated from optical properties and combined with SFI to calculate tMRO2. We validate the system using a series of yeast-hemoglobin tissue-simulating phantoms and conduct in vivo tests in humans using arterial occlusions that demonstrate sensitivity to tissue metabolic oxygen debt and its repayment. Finally, we image the impact of cyanide exposure and toxicity reversal in an in vivo rabbit model showing clear instances of mitochondrial uncoupling and significantly diminished tMRO2. We conclude that dual-wavelength cSFDI provides rapid, quantitative, wide-field mapping of tMRO2 that can reveal unique spatial and temporal dynamics relevant to tissue pathology and viability.

Overexpression of peptide deformylase in breast, colon, and lung cancers.

PubMed

Randhawa, Harsharan; Chikara, Shireen; Gehring, Drew; Yildirim, Tuba; Menon, Jyotsana; Reindl, Katie M

2013-07-01

Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation.

Overexpression of peptide deformylase in breast, colon, and lung cancers

PubMed Central

2013-01-01

Background Human mitochondrial peptide deformylase (PDF) has been proposed as a novel cancer therapeutic target. However, very little is known about its expression and regulation in human tissues. The purpose of this study was to characterize the expression pattern of PDF in cancerous tissues and to identify mechanisms that regulate its expression. Methods The mRNA expression levels of PDF and methionine aminopeptidase 1D (MAP1D), an enzyme involved in a related pathway with PDF, were determined using tissue panels containing cDNA from patients with various types of cancer (breast, colon, kidney, liver, lung, ovarian, prostate, or thyroid) and human cell lines. Protein levels of PDF were also determined in 2 colon cancer patients via western blotting. Colon cancer cells were treated with inhibitors of ERK, Akt, and mTOR signaling pathways and the resulting effects on PDF and MAP1D mRNA levels were determined by qPCR for colon and lung cancer cell lines. Finally, the effects of a PDF inhibitor, actinonin, on the proliferation of breast, colon, and prostate cell lines were determined using the CyQUANT assay. Results PDF and MAP1D mRNA levels were elevated in cancer cell lines compared to non-cancer lines. PDF mRNA levels were significantly increased in breast, colon, and lung cancer samples while MAP1D mRNA levels were increased in just colon cancers. The expression of PDF and MAP1D varied with stage in these cancers. Further, PDF protein expression was elevated in colon cancer tissue samples. Inhibition of the MEK/ERK, but not PI3K or mTOR, pathway reduced the expression of PDF and MAP1D in both colon and lung cancer cell lines. Further, inhibition of PDF with actinonin resulted in greater reduction of breast, colon, and prostate cancer cell proliferation than non-cancer cell lines. Conclusions This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers, and the first evidence that the MEK/ERK pathway plays a role in regulating the expression of PDF and MAP1D. The over-expression of PDF in several cancers and the inhibition of cancer cell growth by a PDF inhibitor suggest this enzyme may act as an oncogene to promote cancer cell proliferation. PMID:23815882

An Approximation to the Temporal Order in Endogenous Circadian Rhythms of Genes Implicated in Human Adipose Tissue Metabolism

PubMed Central

GARAULET, MARTA; ORDOVÁS, JOSÉ M.; GÓMEZ-ABELLÁN, PURIFICACIÓN; MARTÍNEZ, JOSE A.; MADRID, JUAN A.

2015-01-01

Although it is well established that human adipose tissue (AT) shows circadian rhythmicity, published studies have been discussed as if tissues or systems showed only one or few circadian rhythms at a time. To provide an overall view of the internal temporal order of circadian rhythms in human AT including genes implicated in metabolic processes such as energy intake and expenditure, insulin resistance, adipocyte differentiation, dyslipidemia, and body fat distribution. Visceral and subcutaneous abdominal AT biopsies (n = 6) were obtained from morbid obese women (BMI ≥ 40 kg/m2). To investigate rhythmic expression pattern, AT explants were cultured during 24-h and gene expression was analyzed at the following times: 08:00, 14:00, 20:00, 02:00 h using quantitative real-time PCR. Clock genes, glucocorticoid metabolism-related genes, leptin, adiponectin and their receptors were studied. Significant differences were found both in achrophases and relative-amplitude among genes (P <0.05). Amplitude of most genes rhythms was high (>30%). When interpreting the phase map of gene expression in both depots, data indicated that circadian rhythmicity of the genes studied followed a predictable physiological pattern, particularly for subcutaneous AT. Interesting are the relationships between adiponectin, leptin, and glucocorticoid metabolism-related genes circadian profiles. Their metabolic significance is discussed. Visceral AT behaved in a different way than subcutaneous for most of the genes studied. For every gene, protein mRNA levels fluctuated during the day in synchrony with its receptors. We have provided an overall view of the internal temporal order of circadian rhythms in human adipose tissue. PMID:21520059

High speed all optical shear wave imaging optical coherence elastography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Song, Shaozhen; Hsieh, Bao-Yu; Wei, Wei; Shen, Tueng; O'Donnell, Matthew; Wang, Ruikang K.

2016-03-01

Optical Coherence Elastography (OCE) is a non-invasive testing modality that maps the mechanical property of soft tissues with high sensitivity and spatial resolution using phase-sensitive optical coherence tomography (PhS-OCT). Shear wave OCE (SW-OCE) is a leading technique that relies on the speed of propagating shear waves to provide a quantitative elastography. Previous shear wave imaging OCT techniques are based on repeated M-B scans, which have several drawbacks such as long acquisition time and repeated wave stimulations. Recent developments of Fourier domain mode-locked high-speed swept-source OCT system has enabled enough speed to perform KHz B-scan rate OCT imaging. Here we propose ultra-high speed, single shot shear wave imaging to capture single-shot transient shear wave propagation to perform SW-OCE. The frame rate of shear wave imaging is 16 kHz, at A-line rate of ~1.62 MHz, which allows the detection of high-frequency shear wave of up to 8 kHz. The shear wave is generated photothermal-acoustically, by ultra-violet pulsed laser, which requires no contact to OCE subjects, while launching high frequency shear waves that carries rich localized elasticity information. The image acquisition and processing can be performed at video-rate, which enables real-time 3D elastography. SW-OCE measurements are demonstrated on tissue-mimicking phantoms and porcine ocular tissue. This approach opens up the feasibility to perform real-time 3D SW-OCE in clinical applications, to obtain high-resolution localized quantitative measurement of tissue biomechanical property.

PERFORMANCE, RELIABILITY, AND IMPROVEMENT OF A TISSUE-SPECIFIC METABOLIC SIMULATOR

EPA Science Inventory

A methodology is described that has been used to build and enhance a simulator for rat liver metabolism providing reliable predictions within a large chemical domain. The tissue metabolism simulator (TIMES) utilizes a heuristic algorithm to generate plausible metabolic maps using...