TH-EF-207A-07: An Integrated X-Ray/bioluminescence Tomography System for Radiation Guidance and Tumor Evaluation

Energy Technology Data Exchange (ETDEWEB)

Shi, J; Udayakumar, T; Wang, Z; Dogan, N; Pollack, A; Yang, Y [University of Miami School of Medicine, Miami, FL (United States)

2016-06-15

Purpose: CT is not able to differentiate tumors from surrounding soft tissue. This study is to develop a bioluminescence tomography (BLT) system that is integrated onto our previously developed CT guided small animal arc radiation treatment system (iSMAART) to guide radiation, monitor tumor growth and evaluate therapeutic response. Methods: The BLT system employs a CCD camera coupled with a high speed lens, and is aligned orthogonally to the x-ray beam central axis. The two imaging modalities, CT and BLT, are physically registered through geometrical calibration. The CT anatomy provides an accurate contour of animal surface which is used to construct 3D mesh for BLT reconstruction. Bioluminescence projections are captured from multiple angles, once every 45 degree rotation. The diffusion equation based on analytical Kirchhoff approximation is adopted to model the photon propagation in tissues. A discrete cosine transform based reweighted L1-norm regularization (DCT-re-L1) algorithm is used for BLT reconstruction. Experiments are conducted on a mouse orthotopic prostate tumor model (n=12) to evaluate the BLT performance, in terms of its robustness and accuracy in locating and quantifying the bioluminescent tumor cells. Iodinated contrast agent was injected intravenously to delineate the tumor in CT. The tumor location and volume obtained from CT also serve as a benchmark against BLT. Results: With our cutting edge reconstruction algorithm, BLT is able to accurately reconstruct the orthotopic prostate tumors. The tumor center of mass in BLT is within 0.5 mm radial distance of that in CT. The tumor volume in BLT is significantly correlated with that in CT (R2 = 0.81). Conclusion: The BLT can differentiate, localize and quantify tumors. Together with CT, BLT will provide precision radiation guidance and reliable treatment assessment in preclinical cancer research.

Iterative Reconstruction Methods for Hybrid Inverse Problems in Impedance Tomography

DEFF Research Database (Denmark)

Hoffmann, Kristoffer; Knudsen, Kim

2014-01-01

For a general formulation of hybrid inverse problems in impedance tomography the Picard and Newton iterative schemes are adapted and four iterative reconstruction algorithms are developed. The general problem formulation includes several existing hybrid imaging modalities such as current density...... impedance imaging, magnetic resonance electrical impedance tomography, and ultrasound modulated electrical impedance tomography, and the unified approach to the reconstruction problem encompasses several algorithms suggested in the literature. The four proposed algorithms are implemented numerically in two...

Inversion methods for fast-ion velocity-space tomography in fusion plasmas

DEFF Research Database (Denmark)

Jacobsen, Asger Schou; Stagner, L.; Salewski, Mirko

2016-01-01

Velocity-space tomography has been used to infer 2D fast-ion velocity distribution functions. Here we compare the performance of five different tomographic inversion methods: truncated singular value decomposition, maximum entropy, minimum Fisher information and zeroth and first-order Tikhonov...... regularization. The inversion methods are applied to fast-ion Dα measurements taken just before and just after a sawtooth crash in the ASDEX Upgrade tokamak as well as to synthetic measurements from different test distributions. We find that the methods regularizing by penalizing steep gradients or maximizing...... entropy perform best. We assess the uncertainty of the calculated inversions taking into account photon noise, uncertainties in the forward model as well as uncertainties introduced by the regularization which allows us to distinguish regions of high and low confidence in the tomographies. In high...

Source inversion in the full-wave tomography; Full wave tomography ni okeru source inversion

Energy Technology Data Exchange (ETDEWEB)

Tsuchiya, T [DIA Consultants Co. Ltd., Tokyo (Japan)

1997-10-22

In order to consider effects of characteristics of a vibration source in the full-wave tomography (FWT), a study has been performed on a method to invert vibration source parameters together with V(p)/V(s) distribution. The study has expanded an analysis method which uses as the basic the gradient method invented by Tarantola and the partial space method invented by Sambridge, and conducted numerical experiments. The experiment No. 1 has performed inversion of only the vibration source parameters, and the experiment No. 2 has executed simultaneous inversion of the V(p)/V(s) distribution and the vibration source parameters. The result of the discussions revealed that and effective analytical procedure would be as follows: in order to predict maximum stress, the average vibration source parameters and the property parameters are first inverted simultaneously; in order to estimate each vibration source parameter at a high accuracy, the property parameters are fixed, and each vibration source parameter is inverted individually; and the derived vibration source parameters are fixed, and the property parameters are again inverted from the initial values. 5 figs., 2 tabs.

SU-E-T-20: A Novel Hybrid CBCT, Bioluminescence and Fluorescence Tomography System for Preclinical Radiation Research

Energy Technology Data Exchange (ETDEWEB)

Zhang, B; Eslami, S; Iordachita, I [Johns Hopkins University, Baltimore, Maryland (United States); Yang, Y [University of Miami School of Medicine, Miami, FL (United States); Patterson, M [Hamilton Regional Cancer Ctr., Hamilton, ON (Canada); Wong, J [Johns Hopkins University, Baltimore, MD (United States); Wang, K [Johns Hopkins Hospital, Baltimore, MD (United States)

2014-06-01

Purpose: A novel standalone bioluminescence and fluorescence tomography (BLT and FT) system equipped with high resolution CBCT has been built in our group. In this work, we present the system calibration method and validate our system in both phantom and in vivo environment. Methods: The CBCT is acquired by rotating the animal stage while keeping the x-ray source and detector panel static. The optical signal is reflected by the 3-mirror system to a multispectral filter set and then delivered to the CCD camera with f/1.4 lens mounted. Nine fibers passing through the stage and in contact with the mouse skin serve as the light sources for diffuse optical tomography (DOT) and FT. The anatomical information and optical properties acquired from the CBCT and DOT, respectively, are used as the priori information to improve the BLT/FT reconstruction accuracy. Flat field correction for the optical system was acquired at multiple wavelengths. A home-built phantom is used to register the optical and CBCT coordinates. An absolute calibration relating the CCD photon counts rate to the light fluence rate emitted at animal surface was developed to quantify the bioluminescence power or fluorophore concentration. Results: An optical inhomogeneous phantom with 2 light sources (3mm separation) imbedded is used to test the system. The optical signal is mapped onto the mesh generated from CBCT for optical reconstruction. Our preliminary results show that the center of mass can be reconstructed within 2.8mm accuracy. A live mouse with the light source imbedded is also used to validate our system. Liver or lung metastatic luminescence tumor model will be used for further testing. Conclusion: This hybrid system transforms preclinical research to a level that even sub-palpable volume of cells can be imaged rapidly and non-invasively, which largely extends the scope of radiobiological research. The research is supported by the NCI grant R01CA158100-01.

A family of inversion formulas in thermoacoustic tomography

KAUST Repository

Nguyen, Linh

2009-10-01

We present a family of closed form inversion formulas in thermoacoustic tomography in the case of a constant sound speed. The formulas are presented in both time-domain and frequency-domain versions. As special cases, they imply most of the previously known filtered backprojection type formulas. © 2009 AMERICAN INSTITUTE OF MATHEMATICAL SCIENCES.

Polarimetry data inversion in conditions of tokamak plasma: Model based tomography concept

International Nuclear Information System (INIS)

Bieg, B.; Chrzanowski, J.; Kravtsov, Yu. A.; Mazon, D.

2015-01-01

Highlights: • Model based plasma tomography is presented. • Minimization procedure for the error function is suggested to be performed using the gradient method. • model based procedure of data inversion in the case of joint polarimetry–interferometry data. - Abstract: Model based plasma tomography is studied which fits a hypothetical multi-parameter plasma model to polarimetry and interferometry experimental data. Fitting procedure implies minimization of the error function, defined as a sum of squared differences between theoretical and empirical values. Minimization procedure for the function is suggested to be performed using the gradient method. Contrary to traditional tomography, which deals exclusively with observational data, model-based tomography (MBT) operates also with reasonable model of inhomogeneous plasma distribution and verifies which profile of a given class better fits experimental data. Model based tomography (MBT) restricts itself by definite class of models for instance power series, Fourier expansion etc. The basic equations of MBT are presented which generalize the equations of model based procedure of polarimetric data inversion in the case of joint polarimetry–interferometry data.

Polarimetry data inversion in conditions of tokamak plasma: Model based tomography concept

Energy Technology Data Exchange (ETDEWEB)

Bieg, B. [Maritime University of Szczecin, Waly Chrobrego 1-2, 70-500 Szczecin (Poland); Chrzanowski, J., E-mail: j.chrzanowski@am.szczecin.pl [Maritime University of Szczecin, Waly Chrobrego 1-2, 70-500 Szczecin (Poland); Kravtsov, Yu. A. [Maritime University of Szczecin, Waly Chrobrego 1-2, 70-500 Szczecin (Poland); Space Research Institute, Profsoyuznaya St. 82/34 Russian Academy of Science, Moscow 117997 (Russian Federation); Mazon, D. [CEA, IRFM, F-13108 Saint Paul-lez-Durance (France)

2015-10-15

Highlights: • Model based plasma tomography is presented. • Minimization procedure for the error function is suggested to be performed using the gradient method. • model based procedure of data inversion in the case of joint polarimetry–interferometry data. - Abstract: Model based plasma tomography is studied which fits a hypothetical multi-parameter plasma model to polarimetry and interferometry experimental data. Fitting procedure implies minimization of the error function, defined as a sum of squared differences between theoretical and empirical values. Minimization procedure for the function is suggested to be performed using the gradient method. Contrary to traditional tomography, which deals exclusively with observational data, model-based tomography (MBT) operates also with reasonable model of inhomogeneous plasma distribution and verifies which profile of a given class better fits experimental data. Model based tomography (MBT) restricts itself by definite class of models for instance power series, Fourier expansion etc. The basic equations of MBT are presented which generalize the equations of model based procedure of polarimetric data inversion in the case of joint polarimetry–interferometry data.

A New Self-Constrained Inversion Method of Potential Fields Based on Probability Tomography

Science.gov (United States)

Sun, S.; Chen, C.; WANG, H.; Wang, Q.

2014-12-01

The self-constrained inversion method of potential fields uses a priori information self-extracted from potential field data. Differing from external a priori information, the self-extracted information are generally parameters derived exclusively from the analysis of the gravity and magnetic data (Paoletti et al., 2013). Here we develop a new self-constrained inversion method based on probability tomography. Probability tomography doesn't need any priori information, as well as large inversion matrix operations. Moreover, its result can describe the sources, especially the distribution of which is complex and irregular, entirely and clearly. Therefore, we attempt to use the a priori information extracted from the probability tomography results to constrain the inversion for physical properties. The magnetic anomaly data was taken as an example in this work. The probability tomography result of magnetic total field anomaly(ΔΤ) shows a smoother distribution than the anomalous source and cannot display the source edges exactly. However, the gradients of ΔΤ are with higher resolution than ΔΤ in their own direction, and this characteristic is also presented in their probability tomography results. So we use some rules to combine the probability tomography results of ∂ΔΤ⁄∂x, ∂ΔΤ⁄∂y and ∂ΔΤ⁄∂z into a new result which is used for extracting a priori information, and then incorporate the information into the model objective function as spatial weighting functions to invert the final magnetic susceptibility. Some magnetic synthetic examples incorporated with and without a priori information extracted from the probability tomography results were made to do comparison, results of which show that the former are more concentrated and with higher resolution of the source body edges. This method is finally applied in an iron mine in China with field measured ΔΤ data and performs well. ReferencesPaoletti, V., Ialongo, S., Florio, G., Fedi, M

Bioluminescence Tomography–Guided Radiation Therapy for Preclinical Research

Energy Technology Data Exchange (ETDEWEB)

Zhang, Bin [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States); Wang, Ken Kang-Hsin, E-mail: kwang27@jhmi.edu [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States); Yu, Jingjing [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States); School of Physics and Information Technology, Shaanxi Normal University, Shaanxi (China); Eslami, Sohrab; Iordachita, Iulian [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, Maryland (United States); Reyes, Juvenal; Malek, Reem [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States); Tran, Phuoc T. [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States); Department of Oncology and Urology, Brady Urological Institute, Johns Hopkins University, Baltimore, Maryland (United States); Patterson, Michael S. [Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario (Canada); Wong, John W. [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland (United States)

2016-04-01

Purpose: In preclinical radiation research, it is challenging to localize soft tissue targets based on cone beam computed tomography (CBCT) guidance. As a more effective method to localize soft tissue targets, we developed an online bioluminescence tomography (BLT) system for small-animal radiation research platform (SARRP). We demonstrated BLT-guided radiation therapy and validated targeting accuracy based on a newly developed reconstruction algorithm. Methods and Materials: The BLT system was designed to dock with the SARRP for image acquisition and to be detached before radiation delivery. A 3-mirror system was devised to reflect the bioluminescence emitted from the subject to a stationary charge-coupled device (CCD) camera. Multispectral BLT and the incomplete variables truncated conjugate gradient method with a permissible region shrinking strategy were used as the optimization scheme to reconstruct bioluminescent source distributions. To validate BLT targeting accuracy, a small cylindrical light source with high CBCT contrast was placed in a phantom and also in the abdomen of a mouse carcass. The center of mass (CoM) of the source was recovered from BLT and used to guide radiation delivery. The accuracy of the BLT-guided targeting was validated with films and compared with the CBCT-guided delivery. In vivo experiments were conducted to demonstrate BLT localization capability for various source geometries. Results: Online BLT was able to recover the CoM of the embedded light source with an average accuracy of 1 mm compared to that with CBCT localization. Differences between BLT- and CBCT-guided irradiation shown on the films were consistent with the source localization revealed in the BLT and CBCT images. In vivo results demonstrated that our BLT system could potentially be applied for multiple targets and tumors. Conclusions: The online BLT/CBCT/SARRP system provides an effective solution for soft tissue targeting, particularly for small, nonpalpable, or

Bioluminescence Tomography–Guided Radiation Therapy for Preclinical Research

International Nuclear Information System (INIS)

Zhang, Bin; Wang, Ken Kang-Hsin; Yu, Jingjing; Eslami, Sohrab; Iordachita, Iulian; Reyes, Juvenal; Malek, Reem; Tran, Phuoc T.; Patterson, Michael S.; Wong, John W.

2016-01-01

Purpose: In preclinical radiation research, it is challenging to localize soft tissue targets based on cone beam computed tomography (CBCT) guidance. As a more effective method to localize soft tissue targets, we developed an online bioluminescence tomography (BLT) system for small-animal radiation research platform (SARRP). We demonstrated BLT-guided radiation therapy and validated targeting accuracy based on a newly developed reconstruction algorithm. Methods and Materials: The BLT system was designed to dock with the SARRP for image acquisition and to be detached before radiation delivery. A 3-mirror system was devised to reflect the bioluminescence emitted from the subject to a stationary charge-coupled device (CCD) camera. Multispectral BLT and the incomplete variables truncated conjugate gradient method with a permissible region shrinking strategy were used as the optimization scheme to reconstruct bioluminescent source distributions. To validate BLT targeting accuracy, a small cylindrical light source with high CBCT contrast was placed in a phantom and also in the abdomen of a mouse carcass. The center of mass (CoM) of the source was recovered from BLT and used to guide radiation delivery. The accuracy of the BLT-guided targeting was validated with films and compared with the CBCT-guided delivery. In vivo experiments were conducted to demonstrate BLT localization capability for various source geometries. Results: Online BLT was able to recover the CoM of the embedded light source with an average accuracy of 1 mm compared to that with CBCT localization. Differences between BLT- and CBCT-guided irradiation shown on the films were consistent with the source localization revealed in the BLT and CBCT images. In vivo results demonstrated that our BLT system could potentially be applied for multiple targets and tumors. Conclusions: The online BLT/CBCT/SARRP system provides an effective solution for soft tissue targeting, particularly for small, nonpalpable, or

Robust inverse scattering full waveform seismic tomography for imaging complex structure

International Nuclear Information System (INIS)

Nurhandoko, Bagus Endar B.; Sukmana, Indriani; Wibowo, Satryo; Deny, Agus; Kurniadi, Rizal; Widowati, Sri; Mubarok, Syahrul; Susilowati; Kaswandhi

2012-01-01

Seismic tomography becomes important tool recently for imaging complex subsurface. It is well known that imaging complex rich fault zone is difficult. In this paper, The application of time domain inverse scattering wave tomography to image the complex fault zone would be shown on this paper, especially an efficient time domain inverse scattering tomography and their run in cluster parallel computer which has been developed. This algorithm is purely based on scattering theory through solving Lippmann Schwienger integral by using Born's approximation. In this paper, it is shown the robustness of this algorithm especially in avoiding the inversion trapped in local minimum to reach global minimum. A large data are solved by windowing and blocking technique of memory as well as computation. Parameter of windowing computation is based on shot gather's aperture. This windowing technique reduces memory as well as computation significantly. This parallel algorithm is done by means cluster system of 120 processors from 20 nodes of AMD Phenom II. Benchmarking of this algorithm is done by means Marmoussi model which can be representative of complex rich fault area. It is shown that the proposed method can image clearly the rich fault and complex zone in Marmoussi model even though the initial model is quite far from the true model. Therefore, this method can be as one of solution to image the very complex mode.

Robust inverse scattering full waveform seismic tomography for imaging complex structure

Energy Technology Data Exchange (ETDEWEB)

Nurhandoko, Bagus Endar B.; Sukmana, Indriani; Wibowo, Satryo; Deny, Agus; Kurniadi, Rizal; Widowati, Sri; Mubarok, Syahrul; Susilowati; Kaswandhi [Wave Inversion and Subsurface Fluid Imaging Research (WISFIR) Lab., Complex System Research Division, Physics Department, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung. and Rock Fluid Imaging Lab., Rock Physics and Cluster C (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung (Indonesia); Physics Department of Institut Teknologi Bandung (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung, Indonesia and Institut Teknologi Telkom, Bandung (Indonesia); Rock Fluid Imaging Lab., Rock Physics and Cluster Computing Center, Bandung (Indonesia)

2012-06-20

Seismic tomography becomes important tool recently for imaging complex subsurface. It is well known that imaging complex rich fault zone is difficult. In this paper, The application of time domain inverse scattering wave tomography to image the complex fault zone would be shown on this paper, especially an efficient time domain inverse scattering tomography and their run in cluster parallel computer which has been developed. This algorithm is purely based on scattering theory through solving Lippmann Schwienger integral by using Born's approximation. In this paper, it is shown the robustness of this algorithm especially in avoiding the inversion trapped in local minimum to reach global minimum. A large data are solved by windowing and blocking technique of memory as well as computation. Parameter of windowing computation is based on shot gather's aperture. This windowing technique reduces memory as well as computation significantly. This parallel algorithm is done by means cluster system of 120 processors from 20 nodes of AMD Phenom II. Benchmarking of this algorithm is done by means Marmoussi model which can be representative of complex rich fault area. It is shown that the proposed method can image clearly the rich fault and complex zone in Marmoussi model even though the initial model is quite far from the true model. Therefore, this method can be as one of solution to image the very complex mode.

Bathyphotometer bioluminescence potential measurements: A framework for characterizing flow agitators and predicting flow-stimulated bioluminescence intensity

Science.gov (United States)

Latz, Michael I.; Rohr, Jim

2013-07-01

Bathyphotometer measurements of bioluminescence are used as a proxy for the abundance of luminescent organisms for studying population dynamics; the interaction of luminescent organisms with physical, chemical, and biological oceanographic processes; and spatial complexity especially in coastal areas. However, the usefulness of bioluminescence measurements has been limited by the inability to compare results from different bathyphotometer designs, or even the same bathyphotometer operating at different volume flow rates. The primary objective of this study was to compare measurements of stimulated bioluminescence of four species of cultured dinoflagellates, the most common source of bioluminescence in coastal waters, using two different bathyphotometer flow agitators as a function of bathyphotometer volume flow rate and dinoflagellate concentration. For both the NOSC and BIOLITE flow agitators and each species of dinoflagellate tested, there was a critical volume flow rate, above which average bioluminescence intensity, designated as bathyphotometer bioluminescence potential (BBP), remained relatively constant and scaled directly with dinoflagellate cell concentration. At supra-critical volume flow rates, the ratio of BIOLITE to NOSC BBP was nearly constant for the same species studied, but varied between species. The spatial pattern and residence time of flash trajectories within the NOSC flow agitator indicated the presence of dominant secondary recirculating flows, where most of the bioluminescence was detected. A secondary objective (appearing in the Appendix) was to study the feasibility of using NOSC BBP to scale flow-stimulated bioluminescence intensity across similar flow fields, where the contributing composition of luminescent species remained the same. Fully developed turbulent pipe flow was chosen because it is hydrodynamically well characterized. Average bioluminescence intensity in a 2.54-cm i.d. pipe was highly correlated with wall shear stress and

Bioluminescent bacteria: lux genes as environmental biosensors

Directory of Open Access Journals (Sweden)

Nunes-Halldorson Vânia da Silva

2003-01-01

Full Text Available Bioluminescent bacteria are widespread in natural environments. Over the years, many researchers have been studying the physiology, biochemistry and genetic control of bacterial bioluminescence. These discoveries have revolutionized the area of Environmental Microbiology through the use of luminescent genes as biosensors for environmental studies. This paper will review the chronology of scientific discoveries on bacterial bioluminescence and the current applications of bioluminescence in environmental studies, with special emphasis on the Microtox toxicity bioassay. Also, the general ecological significance of bioluminescence will be addressed.

Systematic study of target localization for bioluminescence tomography guided radiation therapy

Science.gov (United States)

Yu, Jingjing; Zhang, Bin; Iordachita, Iulian I.; Reyes, Juvenal; Lu, Zhihao; Brock, Malcolm V.; Patterson, Michael S.; Wong, John W.

2016-01-01

Purpose: To overcome the limitation of CT/cone-beam CT (CBCT) in guiding radiation for soft tissue targets, the authors developed a spectrally resolved bioluminescence tomography (BLT) system for the small animal radiation research platform. The authors systematically assessed the performance of the BLT system in terms of target localization and the ability to resolve two neighboring sources in simulations, tissue-mimicking phantom, and in vivo environments. Methods: Multispectral measurements acquired in a single projection were used for the BLT reconstruction. The incomplete variables truncated conjugate gradient algorithm with an iterative permissible region shrinking strategy was employed as the optimization scheme to reconstruct source distributions. Simulation studies were conducted for single spherical sources with sizes from 0.5 to 3 mm radius at depth of 3–12 mm. The same configuration was also applied for the double source simulation with source separations varying from 3 to 9 mm. Experiments were performed in a standalone BLT/CBCT system. Two self-illuminated sources with 3 and 4.7 mm separations placed inside a tissue-mimicking phantom were chosen as the test cases. Live mice implanted with single-source at 6 and 9 mm depth, two sources at 3 and 5 mm separation at depth of 5 mm, or three sources in the abdomen were also used to illustrate the localization capability of the BLT system for multiple targets in vivo. Results: For simulation study, approximate 1 mm accuracy can be achieved at localizing center of mass (CoM) for single-source and grouped CoM for double source cases. For the case of 1.5 mm radius source, a common tumor size used in preclinical study, their simulation shows that for all the source separations considered, except for the 3 mm separation at 9 and 12 mm depth, the two neighboring sources can be resolved at depths from 3 to 12 mm. Phantom experiments illustrated that 2D bioluminescence imaging failed to distinguish two sources

Systematic study of target localization for bioluminescence tomography guided radiation therapy

Energy Technology Data Exchange (ETDEWEB)

Yu, Jingjing [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland 21231 and School of Physics and Information Technology, Shaanxi Normal University, Shaanxi 710119 (China); Zhang, Bin; Reyes, Juvenal; Wong, John W.; Wang, Ken Kang-Hsin, E-mail: kwang27@jhmi.edu [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, Maryland 21231 (United States); Iordachita, Iulian I. [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Lu, Zhihao [Department of Oncology and Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21231 and Key laboratory of Carcinogenesis and Translational Research, Department of GI Oncology, Peking University, Beijing Cancer Hospital and Institute, Beijing 100142 (China); Brock, Malcolm V. [Department of Oncology and Department of Surgery, Johns Hopkins University, Baltimore, Maryland 21231 (United States); Patterson, Michael S. [Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario L8S 4L8 (Canada)

2016-05-15

Purpose: To overcome the limitation of CT/cone-beam CT (CBCT) in guiding radiation for soft tissue targets, the authors developed a spectrally resolved bioluminescence tomography (BLT) system for the small animal radiation research platform. The authors systematically assessed the performance of the BLT system in terms of target localization and the ability to resolve two neighboring sources in simulations, tissue-mimicking phantom, and in vivo environments. Methods: Multispectral measurements acquired in a single projection were used for the BLT reconstruction. The incomplete variables truncated conjugate gradient algorithm with an iterative permissible region shrinking strategy was employed as the optimization scheme to reconstruct source distributions. Simulation studies were conducted for single spherical sources with sizes from 0.5 to 3 mm radius at depth of 3–12 mm. The same configuration was also applied for the double source simulation with source separations varying from 3 to 9 mm. Experiments were performed in a standalone BLT/CBCT system. Two self-illuminated sources with 3 and 4.7 mm separations placed inside a tissue-mimicking phantom were chosen as the test cases. Live mice implanted with single-source at 6 and 9 mm depth, two sources at 3 and 5 mm separation at depth of 5 mm, or three sources in the abdomen were also used to illustrate the localization capability of the BLT system for multiple targets in vivo. Results: For simulation study, approximate 1 mm accuracy can be achieved at localizing center of mass (CoM) for single-source and grouped CoM for double source cases. For the case of 1.5 mm radius source, a common tumor size used in preclinical study, their simulation shows that for all the source separations considered, except for the 3 mm separation at 9 and 12 mm depth, the two neighboring sources can be resolved at depths from 3 to 12 mm. Phantom experiments illustrated that 2D bioluminescence imaging failed to distinguish two sources

Bioluminescent bacteria: lux genes as environmental biosensors

OpenAIRE

Nunes-Halldorson,Vânia da Silva; Duran,Norma Letícia

2003-01-01

Bioluminescent bacteria are widespread in natural environments. Over the years, many researchers have been studying the physiology, biochemistry and genetic control of bacterial bioluminescence. These discoveries have revolutionized the area of Environmental Microbiology through the use of luminescent genes as biosensors for environmental studies. This paper will review the chronology of scientific discoveries on bacterial bioluminescence and the current applications of bioluminescence in env...

Nonlinear inversion of borehole-radar tomography data to reconstruct velocity and attenuation distribution in earth materials

Science.gov (United States)

Zhou, C.; Liu, L.; Lane, J.W.

2001-01-01

A nonlinear tomographic inversion method that uses first-arrival travel-time and amplitude-spectra information from cross-hole radar measurements was developed to simultaneously reconstruct electromagnetic velocity and attenuation distribution in earth materials. Inversion methods were developed to analyze single cross-hole tomography surveys and differential tomography surveys. Assuming the earth behaves as a linear system, the inversion methods do not require estimation of source radiation pattern, receiver coupling, or geometrical spreading. The data analysis and tomographic inversion algorithm were applied to synthetic test data and to cross-hole radar field data provided by the US Geological Survey (USGS). The cross-hole radar field data were acquired at the USGS fractured-rock field research site at Mirror Lake near Thornton, New Hampshire, before and after injection of a saline tracer, to monitor the transport of electrically conductive fluids in the image plane. Results from the synthetic data test demonstrate the algorithm computational efficiency and indicate that the method robustly can reconstruct electromagnetic (EM) wave velocity and attenuation distribution in earth materials. The field test results outline zones of velocity and attenuation anomalies consistent with the finding of previous investigators; however, the tomograms appear to be quite smooth. Further work is needed to effectively find the optimal smoothness criterion in applying the Tikhonov regularization in the nonlinear inversion algorithms for cross-hole radar tomography. ?? 2001 Elsevier Science B.V. All rights reserved.

Repeated and Widespread Evolution of Bioluminescence in Marine Fishes.

Directory of Open Access Journals (Sweden)

Matthew P Davis

Full Text Available Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.

Bioluminescent organs of two deep-sea arrow worms, Eukrohnia fowleri and Caecosagitta macrocephala, with further observations on Bioluminescence in chaetognaths.

Science.gov (United States)

Thuesen, Erik V; Goetz, Freya E; Haddock, Steven H D

2010-10-01

Bioluminescence in the deep-sea chaetognath Eukrohnia fowleri is reported for the first time, and behavioral, morphological, and chemical characteristics of bioluminescence in chaetognaths are examined. Until this study, the only known species of bioluminescent chaetognath was Caecosagitta macrocephala. The luminescent organ of that species is located on the ventral edge of each anterior lateral fin, whereas that of E. fowleri runs across the center of the tail fin on both dorsal and ventral sides. Scanning electron microscopy showed that the bioluminescent organs of both species consist of hexagonal chambers containing elongate ovoid particles-the organelles holding bioluminescent materials. No other luminous organism is known to use hexagonal packing to hold bioluminescent materials. Transmission electron microscopy of particles from C. macrocephala revealed a densely packed paracrystalline matrix punctuated by globular inclusions, which likely correspond to luciferin and luciferase, respectively. Both species use unique luciferases in conjunction with coelenterazine for light emission. Luciferase of C. macrocephala becomes inactive after 30 min, but luciferase of E. fowleri is highly stable. Although C. macrocephala has about 90 times fewer particles than E. fowleri, it has a similar bioluminescent capacity (total particle volume) due to its larger particle size. In situ observations of C. macrocephala from a remotely operated vehicle revealed that the luminous particles are released to form a cloud. The discovery of bioluminescence in a second chaetognath phylogenetically distant from the first highlights the importance of bioluminescence among deep-sea organisms.

The CUBLAS and CULA based GPU acceleration of adaptive finite element framework for bioluminescence tomography.

Science.gov (United States)

Zhang, Bo; Yang, Xiang; Yang, Fei; Yang, Xin; Qin, Chenghu; Han, Dong; Ma, Xibo; Liu, Kai; Tian, Jie

2010-09-13

In molecular imaging (MI), especially the optical molecular imaging, bioluminescence tomography (BLT) emerges as an effective imaging modality for small animal imaging. The finite element methods (FEMs), especially the adaptive finite element (AFE) framework, play an important role in BLT. The processing speed of the FEMs and the AFE framework still needs to be improved, although the multi-thread CPU technology and the multi CPU technology have already been applied. In this paper, we for the first time introduce a new kind of acceleration technology to accelerate the AFE framework for BLT, using the graphics processing unit (GPU). Besides the processing speed, the GPU technology can get a balance between the cost and performance. The CUBLAS and CULA are two main important and powerful libraries for programming on NVIDIA GPUs. With the help of CUBLAS and CULA, it is easy to code on NVIDIA GPU and there is no need to worry about the details about the hardware environment of a specific GPU. The numerical experiments are designed to show the necessity, effect and application of the proposed CUBLAS and CULA based GPU acceleration. From the results of the experiments, we can reach the conclusion that the proposed CUBLAS and CULA based GPU acceleration method can improve the processing speed of the AFE framework very much while getting a balance between cost and performance.

WE-FG-BRA-06: Systematic Study of Target Localization for Bioluminescence Tomography Guided Radiation Therapy for Preclinical Research

Energy Technology Data Exchange (ETDEWEB)

Zhang, B; Reyes, J; Wong, J; Wang, K [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, MD (United States); Yu, J [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, MD (United States); School of Physics and Information Technology, Shaanxi Normal University, Shaanxi (China); Iordachita, I [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, MD (United States); Liu, Z [Department of Oncology, Department of Surgery, Johns Hopkins University, Baltimore, MD (United States); Department of GI Oncology, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing (China); Brock, M [Department of Oncology, Department of Surgery, Johns Hopkins University, Baltimore, MD (United States); Patterson, M [McMaster University, Hamilton, Ontario, CA (Canada)

2016-06-15

Purpose: To overcome the limitation of CT/CBCT in guiding radiation for soft tissue targets, we developed a bioluminescence tomography(BLT) system for preclinical radiation research. We systematically assessed the system performance in target localization and the ability of resolving two sources in simulations, phantom and in vivo environments. Methods: Multispectral images acquired in single projection were used for the BLT reconstruction. Simulation studies were conducted for single spherical source radius from 0.5 to 3 mm at depth of 3 to 12 mm. The same configuration was also applied for the double sources simulation with source separations varying from 3 to 9 mm. Experiments were performed in a standalone BLT/CBCT system. Two sources with 3 and 4.7 mm separations placed inside a tissue-mimicking phantom were chosen as the test cases. Live mice implanted with single source at 6 and 9 mm depth, 2 sources with 3 and 5 mm separation at depth of 5 mm or 3 sources in the abdomen were also used to illustrate the in vivo localization capability of the BLT system. Results: Simulation and phantom results illustrate that our BLT can provide 3D source localization with approximately 1 mm accuracy. The in vivo results are encouraging that 1 and 1.7 mm accuracy can be attained for the single source case at 6 and 9 mm depth, respectively. For the 2 sources study, both sources can be distinguished at 3 and 5 mm separations at approximately 1 mm accuracy using 3D BLT but not 2D bioluminescence image. Conclusion: Our BLT/CBCT system can be potentially applied to localize and resolve targets at a wide range of target sizes, depths and separations. The information provided in this study can be instructive to devise margins for BLT-guided irradiation and suggests that the BLT could guide radiation for multiple targets, such as metastasis. Drs. John W. Wong and Iulian I. Iordachita receive royalty payment from a licensing agreement between Xstrahl Ltd and Johns Hopkins University.

Efficient non-negative constrained model-based inversion in optoacoustic tomography

International Nuclear Information System (INIS)

Ding, Lu; Luís Deán-Ben, X; Lutzweiler, Christian; Razansky, Daniel; Ntziachristos, Vasilis

2015-01-01

The inversion accuracy in optoacoustic tomography depends on a number of parameters, including the number of detectors employed, discrete sampling issues or imperfectness of the forward model. These parameters result in ambiguities on the reconstructed image. A common ambiguity is the appearance of negative values, which have no physical meaning since optical absorption can only be higher or equal than zero. We investigate herein algorithms that impose non-negative constraints in model-based optoacoustic inversion. Several state-of-the-art non-negative constrained algorithms are analyzed. Furthermore, an algorithm based on the conjugate gradient method is introduced in this work. We are particularly interested in investigating whether positive restrictions lead to accurate solutions or drive the appearance of errors and artifacts. It is shown that the computational performance of non-negative constrained inversion is higher for the introduced algorithm than for the other algorithms, while yielding equivalent results. The experimental performance of this inversion procedure is then tested in phantoms and small animals, showing an improvement in image quality and quantitativeness with respect to the unconstrained approach. The study performed validates the use of non-negative constraints for improving image accuracy compared to unconstrained methods, while maintaining computational efficiency. (paper)

Time-dependent stochastic inversion in acoustic tomography of the atmosphere with reciprocal sound transmission

International Nuclear Information System (INIS)

Vecherin, Sergey N; Ostashev, Vladimir E; Wilson, D Keith; Ziemann, A

2008-01-01

Time-dependent stochastic inversion (TDSI) was recently developed for acoustic travel-time tomography of the atmosphere. This type of tomography allows reconstruction of temperature and wind-velocity fields given the location of sound sources and receivers and the travel times between all source–receiver pairs. The quality of reconstruction provided by TDSI depends on the geometry of the transducer array. However, TDSI has not been studied for the geometry with reciprocal sound transmission. This paper is focused on three aspects of TDSI. First, the use of TDSI in reciprocal sound transmission arrays is studied in numerical and physical experiments. Second, efficiency of time-dependent and ordinary stochastic inversion (SI) algorithms is studied in numerical experiments. Third, a new model of noise in the input data for TDSI is developed that accounts for systematic errors in transducer positions. It is shown that (i) a separation of the travel times into temperature and wind-velocity components in tomography with reciprocal transmission does not improve the reconstruction, (ii) TDSI yields a better reconstruction than SI and (iii) the developed model of noise yields an accurate reconstruction of turbulent fields and estimation of errors in the reconstruction

Ray-tracing traveltime tomography versus wave-equation traveltime inversion for near-surface seismic land data

KAUST Repository

Fu, Lei; Hanafy, Sherif M.

2017-01-01

. This initial starting model can be obtained by inverting traveltimes with ray-tracing traveltime tomography (RT) or wave-equation traveltime (WT) inversion. We have found that WT can provide a more accurate tomogram than RT by inverting the first

Image Reconstruction Based on Homotopy Perturbation Inversion Method for Electrical Impedance Tomography

Directory of Open Access Journals (Sweden)

Jing Wang

2013-01-01

Full Text Available The image reconstruction for electrical impedance tomography (EIT mathematically is a typed nonlinear ill-posed inverse problem. In this paper, a novel iteration regularization scheme based on the homotopy perturbation technique, namely, homotopy perturbation inversion method, is applied to investigate the EIT image reconstruction problem. To verify the feasibility and effectiveness, simulations of image reconstruction have been performed in terms of considering different locations, sizes, and numbers of the inclusions, as well as robustness to data noise. Numerical results indicate that this method can overcome the numerical instability and is robust to data noise in the EIT image reconstruction. Moreover, compared with the classical Landweber iteration method, our approach improves the convergence rate. The results are promising.

Direct integration of the inverse Radon equation for X-ray computed tomography.

Science.gov (United States)

Libin, E E; Chakhlov, S V; Trinca, D

2016-11-22

A new mathematical appoach using the inverse Radon equation for restoration of images in problems of linear two-dimensional x-ray tomography is formulated. In this approach, Fourier transformation is not used, and it gives the chance to create the practical computing algorithms having more reliable mathematical substantiation. Results of software implementation show that for especially for low number of projections, the described approach performs better than standard X-ray tomographic reconstruction algorithms.

Bioluminescent bioreporter sensing of foodborne toxins

Science.gov (United States)

Fraley, Amanda C.; Ripp, Steven; Sayler, Gary S.

2004-06-01

Histamine is the primary etiological agent in the foodborne disease scombrotoxicosis, one of the most common food toxicities related to fish consumption. Procedures for detecting histamine in fish products are available, but are often too expensive or too complex for routine use. As an alternative, a bacterial bioluminescent bioreporter has been constructed to develop a biosensor system that autonomously responds to low levels of histamine. The bioreporter contains a promoterless Photorhabdus luminescens lux operon (luxCDABE) fused with the Vibrio anguillarum angR regulatory gene promoter of the anguibactin biosynthetic operon. The bioreporter emitted 1.46 times more bioluminescence than background, 30 minutes after the addition of 100mM histamine. However, specificity was not optimal, as this biosensor generated significant bioluminescence in the presence of L-proline and L-histidine. As a means towards improving histamine specificity, the promoter region of a histamine oxidase gene from Arthrobacter globiformis was cloned upstream of the promotorless lux operon from Photorhabdus luminescens. This recently constructed whole-cell, lux-based bioluminescent bioreporter is currently being tested for optimal performance in the presence of histamine in order to provide a rapid, simple, and inexpensive model sensor for the detection of foodborne toxins.

Effect of electromagnetic fields on the bacteria bioluminescent activity

International Nuclear Information System (INIS)

Berzhanskaya, L.Yu.; Berzhanskij, V.N.; Beloplotova, O.Yu.

1995-01-01

The effect of electromagnetic field with frequency from 36.2 to 55.9 GHz on bioluminescence activity of bacterium were investigated. Electromagnetic field results in decrease of bioluminescence, which depends from frequency. The electromagnetic field adaptation time is higher of intrinsic time parameters of bioluminescence system. The effect has nonthermal nature. It is suggested that electromagnetic field influence connects with structure rearrangements near cell emitter. 8 refs.; 3 figs

An improved exact inversion formula for solenoidal fields in cone beam vector tomography

Science.gov (United States)

Katsevich, Alexander; Rothermel, Dimitri; Schuster, Thomas

2017-06-01

In this paper we present an improved inversion formula for the 3D cone beam transform of vector fields supported in the unit ball which is exact for solenoidal fields. It is well known that only the solenoidal part of a vector field can be determined from the longitudinal ray transform of a vector field in cone beam geometry. The inversion formula, as it was developed in Katsevich and Schuster (2013 An exact inversion formula for cone beam vector tomography Inverse Problems 29 065013), consists of two parts. The first part is of the filtered backprojection type, whereas the second part is a costly 4D integration and very inefficient. In this article we tackle this second term and obtain an improved formula, which is easy to implement and saves one order of integration. We also show that the first part contains all information about the curl of the field, whereas the second part has information about the boundary values. More precisely, the second part vanishes if the solenoidal part of the original field is tangential at the boundary. A number of numerical tests presented in the paper confirm the theoretical results and the exactness of the formula. Also, we obtain an inversion algorithm that works for general convex domains.

Development of a novel preclinical pancreatic cancer research model: bioluminescence image-guided focal irradiation and tumor monitoring of orthotopic xenografts.

Science.gov (United States)

Tuli, Richard; Surmak, Andrew; Reyes, Juvenal; Hacker-Prietz, Amy; Armour, Michael; Leubner, Ashley; Blackford, Amanda; Tryggestad, Erik; Jaffee, Elizabeth M; Wong, John; Deweese, Theodore L; Herman, Joseph M

2012-04-01

We report on a novel preclinical pancreatic cancer research model that uses bioluminescence imaging (BLI)-guided irradiation of orthotopic xenograft tumors, sparing of surrounding normal tissues, and quantitative, noninvasive longitudinal assessment of treatment response. Luciferase-expressing MiaPaCa-2 pancreatic carcinoma cells were orthotopically injected in nude mice. BLI was compared to pathologic tumor volume, and photon emission was assessed over time. BLI was correlated to positron emission tomography (PET)/computed tomography (CT) to estimate tumor dimensions. BLI and cone-beam CT (CBCT) were used to compare tumor centroid location and estimate setup error. BLI and CBCT fusion was performed to guide irradiation of tumors using the small animal radiation research platform (SARRP). DNA damage was assessed by γ-H2Ax staining. BLI was used to longitudinally monitor treatment response. Bioluminescence predicted tumor volume (R = 0.8984) and increased linearly as a function of time up to a 10-fold increase in tumor burden. BLI correlated with PET/CT and necropsy specimen in size (P < .05). Two-dimensional BLI centroid accuracy was 3.5 mm relative to CBCT. BLI-guided irradiated pancreatic tumors stained positively for γ-H2Ax, whereas surrounding normal tissues were spared. Longitudinal assessment of irradiated tumors with BLI revealed significant tumor growth delay of 20 days relative to controls. We have successfully applied the SARRP to a bioluminescent, orthotopic preclinical pancreas cancer model to noninvasively: 1) allow the identification of tumor burden before therapy, 2) facilitate image-guided focal radiation therapy, and 3) allow normalization of tumor burden and longitudinal assessment of treatment response.

Stimulated bioluminescence by fluid shear stress associated with pipe flow

Energy Technology Data Exchange (ETDEWEB)

Cao Jing; Wang Jiangan; Wu Ronghua, E-mail: caojing981@126.com [Col. of Electronic Eng., Naval University of Engineering, Wuhan 430033 (China)

2011-01-01

Dinoflagellate can be stimulated bioluminescence by hydrodynamic agitation. Two typical dinoflagellate (Lingulodinium polyedrum and Pyrocystis noctiluca) was choosed to research stimulated bioluminescence. The bioluminescence intensity and shear stress intensity were measured using fully developed pipe flow. There is shear stress threshold to agitate organism bioluminescence. From these experiment, the response thresholds of the stimulated bioluminscence always occurred in laminar flows at a shear stress level of 0.6-3 dyn/cm{sup 2}. At the same time, the spectral characteristc of dinoflagellate was recorded, the wavelength of them is about 470nm, and the full width at half maximum is approximate 30nm.

Bioluminescence in vivo imaging of autoimmune encephalomyelitis predicts disease

Directory of Open Access Journals (Sweden)

Steinman Lawrence

2008-02-01

Full Text Available Abstract Background Experimental autoimmune encephalomyelitis is a widely used animal model to understand not only multiple sclerosis but also basic principles of immunity. The disease is scored typically by observing signs of paralysis, which do not always correspond with pathological changes. Methods Experimental autoimmune encephalomyelitis was induced in transgenic mice expressing an injury responsive luciferase reporter in astrocytes (GFAP-luc. Bioluminescence in the brain and spinal cord was measured non-invasively in living mice. Mice were sacrificed at different time points to evaluate clinical and pathological changes. The correlation between bioluminescence and clinical and pathological EAE was statistically analyzed by Pearson correlation analysis. Results Bioluminescence from the brain and spinal cord correlates strongly with severity of clinical disease and a number of pathological changes in the brain in EAE. Bioluminescence at early time points also predicts severity of disease. Conclusion These results highlight the potential use of bioluminescence imaging to monitor neuroinflammation for rapid drug screening and immunological studies in EAE and suggest that similar approaches could be applied to other animal models of autoimmune and inflammatory disorders.

In vivo cell tracking with bioluminescence imaging

Energy Technology Data Exchange (ETDEWEB)

Kim, Jung Eun; Kalimuthu, Senthilkumar; Ahn, Byeong Cheol [Dept. of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, Daegu (Korea, Republic of)

2015-03-15

Molecular imaging is a fast growing biomedical research that allows the visual representation, characterization and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In vivo tracking of cells is an indispensable technology for development and optimization of cell therapy for replacement or renewal of damaged or diseased tissue using transplanted cells, often autologous cells. With outstanding advantages of bioluminescence imaging, the imaging approach is most commonly applied for in vivo monitoring of transplanted stem cells or immune cells in order to assess viability of administered cells with therapeutic efficacy in preclinical small animal models. In this review, a general overview of bioluminescence is provided and recent updates of in vivo cell tracking using the bioluminescence signal are discussed.

Bioluminescence lights the way to food safety

Science.gov (United States)

Brovko, Lubov Y.; Griffiths, Mansel W.

2003-07-01

The food industry is increasingly adopting food safety and quality management systems that are more proactive and preventive than those used in the past which have tended to rely on end product testing and visual inspection. The regulatory agencies in many countries are promoting one such management tool, Hazard Analysis Critical Control Point (HACCP), as a way to achieve a safer food supply and as a basis for harmonization of trading standards. Verification that the process is safe must involve microbiological testing but the results need not be generated in real-time. Of all the rapid microbiological tests currently available, the only ones that come close to offering real-time results are bioluminescence-based methods. Recent developments in application of bioluminescence for food safety issues are presented in the paper. These include the use of genetically engineered microorganisms with bioluminescent and fluorescent phenotypes as a real time indicator of physiological state and survival of food-borne pathogens in food and food processing environments as well as novel bioluminescent-based methods for rapid detection of pathogens in food and environmental samples. Advantages and pitfalls of the methods are discussed.

In Vivo Bioluminescence Imaging for Longitudinal Monitoring of Inflammation in Animal Models of Uveitis.

Science.gov (United States)

Gutowski, Michal B; Wilson, Leslie; Van Gelder, Russell N; Pepple, Kathryn L

2017-03-01

We develop a quantitative bioluminescence assay for in vivo longitudinal monitoring of inflammation in animal models of uveitis. Three models of experimental uveitis were induced in C57BL/6 albino mice: primed mycobacterial uveitis (PMU), endotoxin-induced uveitis (EIU), and experimental autoimmune uveitis (EAU). Intraperitoneal injection of luminol sodium salt, which emits light when oxidized, provided the bioluminescence substrate. Bioluminescence images were captured by a PerkinElmer In Vivo Imaging System (IVIS) Spectrum and total bioluminescence was analyzed using Living Image software. Bioluminescence on day zero was compared to bioluminescence on the day of peak inflammation for each model. Longitudinal bioluminescence imaging was performed in EIU and EAU. In the presence of luminol, intraocular inflammation generates detectable bioluminescence in three mouse models of uveitis. Peak bioluminescence in inflamed PMU eyes (1.46 × 105 photons/second [p/s]) was significantly increased over baseline (1.47 × 104 p/s, P = 0.01). Peak bioluminescence in inflamed EIU eyes (3.18 × 104 p/s) also was significantly increased over baseline (1.09 × 104 p/s, P = 0.04), and returned to near baseline levels by 48 hours. In EAU, there was a nonsignificant increase in bioluminescence at peak inflammation. In vivo bioluminescence may be used as a noninvasive, quantitative measure of intraocular inflammation in animal models of uveitis. Primed mycobacterial uveitis and EIU are both acute models with robust anterior inflammation and demonstrated significant changes in bioluminescence corresponding with peak inflammation. Experimental autoimmune uveitis is a more indolent posterior uveitis and generated a more modest bioluminescent signal. In vivo imaging system bioluminescence is a nonlethal, quantifiable assay that can be used for monitoring inflammation in animal models of uveitis.

Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity

Science.gov (United States)

Widder, E. A.

2010-05-01

From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships.

Bioluminescence imaging of Chlamydia muridarum ascending infection in mice.

Directory of Open Access Journals (Sweden)

Jessica Campbell

Full Text Available Chlamydial pathogenicity in the upper genital tract relies on chlamydial ascending from the lower genital tract. To monitor chlamydial ascension, we engineered a luciferase-expressing C. muridarum. In cells infected with the luciferase-expressing C. muridarum, luciferase gene expression and enzymatic activity (measured as bioluminescence intensity correlated well along the infection course, suggesting that bioluminescence can be used for monitoring chlamydial replication. Following an intravaginal inoculation with the luciferase-expressing C. muridarum, 8 of 10 mice displayed bioluminescence signal in the lower with 4 also in the upper genital tracts on day 3 after infection. By day 7, all 10 mice developed bioluminescence signal in the upper genital tracts. The bioluminescence signal was maintained in the upper genital tract in 6 and 2 mice by days 14 and 21, respectively. The bioluminescence signal was no longer detectable in any of the mice by day 28. The whole body imaging approach also revealed an unexpected airway infection following the intravaginal inoculation. Although the concomitant airway infection was transient and did not significantly alter the genital tract infection time courses, caution should be taken during data interpretation. The above observations have demonstrated that C. muridarum can not only achieve rapid ascending infection in the genital tract but also cause airway infection following a genital tract inoculation. These findings have laid a foundation for further optimizing the C. muridarum intravaginal infection murine model for understanding chlamydial pathogenic mechanisms.

Bioluminescence Monitoring of Neuronal Activity in Freely Moving Zebrafish Larvae

Science.gov (United States)

Knafo, Steven; Prendergast, Andrew; Thouvenin, Olivier; Figueiredo, Sophie Nunes; Wyart, Claire

2017-01-01

The proof of concept for bioluminescence monitoring of neural activity in zebrafish with the genetically encoded calcium indicator GFP-aequorin has been previously described (Naumann et al., 2010) but challenges remain. First, bioluminescence signals originating from a single muscle fiber can constitute a major pitfall. Second, bioluminescence signals emanating from neurons only are very small. To improve signals while verifying specificity, we provide an optimized 4 steps protocol achieving: 1) selective expression of a zebrafish codon-optimized GFP-aequorin, 2) efficient soaking of larvae in GFP-aequorin substrate coelenterazine, 3) bioluminescence monitoring of neural activity from motor neurons in free-tailed moving animals performing acoustic escapes and 4) verification of the absence of muscle expression using immunohistochemistry. PMID:29130058

An investigation on the solutions for the linear inverse problem in gamma ray tomography

International Nuclear Information System (INIS)

Araujo, Bruna G.M.; Dantas, Carlos C.; Santos, Valdemir A. dos; Finkler, Christine L.L.; Oliveira, Eric F. de; Melo, Silvio B.; Santos, M. Graca dos

2009-01-01

This paper the results obtained in single beam gamma ray tomography are investigated according to direct problem formulation and the applied solution for the linear system of equations. By image reconstruction based algebraic computational algorithms are used. The sparse under and over-determined linear system of equations was analyzed. Build in functions of Matlab software were applied and optimal solutions were investigate. Experimentally a section of the tube is scanned from various positions and at different angles. The solution, to find the vector of coefficients μ, from the vector of measured p values through the W matrix inversion, constitutes an inverse problem. A industrial tomography process requires a numerical solution of the system of equations. The definition of inverse problem according to Hadmard's is considered and as well the requirement of a well posed problem to find stable solutions. The formulation of the basis function and the computational algorithm to structure the weight matrix W were analyzed. For W full rank matrix the obtained solution is unique as expected. Total Least Squares was implemented which theory and computation algorithm gives adequate treatment for the problems due to non-unique solutions of the system of equations. Stability of the solution was investigating by means of a regularization technique and the comparison shows that it improves the results. An optimal solution as a function of the image quality, computation time and minimum residuals were quantified. The corresponding reconstructed images are shown in 3D graphics in order to compare with the solution. (author)

Chemistry and biology of insect bioluminescence

International Nuclear Information System (INIS)

Colepicolo Neto, P.; Bechara, E.J.H.

1984-01-01

Basic aspects on the Chemistry and Biology of bioluminescence are reviewed, with emphasis on insects. Data from the investigation of Lampyridae (fireflies) are collected from literature. With regard to Elateridae (click beetles) and Phengodidae (rail road worms), the least explored families of luminescent insects, new data are presented on the following aspects: (i) 'in vivo' emission spectra, (ii) chemical nature of the luciferin, (iii) conection between bioluminescence and 'oxygen toxicity' as a result of molecular oxygen storage and (iv) the role of light emission by larvae and pupae. (Author) [pt

Time reversal imaging, Inverse problems and Adjoint Tomography}

Science.gov (United States)

Montagner, J.; Larmat, C. S.; Capdeville, Y.; Kawakatsu, H.; Fink, M.

2010-12-01

With the increasing power of computers and numerical techniques (such as spectral element methods), it is possible to address a new class of seismological problems. The propagation of seismic waves in heterogeneous media is simulated more and more accurately and new applications developed, in particular time reversal methods and adjoint tomography in the three-dimensional Earth. Since the pioneering work of J. Claerbout, theorized by A. Tarantola, many similarities were found between time-reversal methods, cross-correlations techniques, inverse problems and adjoint tomography. By using normal mode theory, we generalize the scalar approach of Draeger and Fink (1999) and Lobkis and Weaver (2001) to the 3D- elastic Earth, for theoretically understanding time-reversal method on global scale. It is shown how to relate time-reversal methods on one hand, with auto-correlations of seismograms for source imaging and on the other hand, with cross-correlations between receivers for structural imaging and retrieving Green function. Time-reversal methods were successfully applied in the past to acoustic waves in many fields such as medical imaging, underwater acoustics, non destructive testing and to seismic waves in seismology for earthquake imaging. In the case of source imaging, time reversal techniques make it possible an automatic location in time and space as well as the retrieval of focal mechanism of earthquakes or unknown environmental sources . We present here some applications at the global scale of these techniques on synthetic tests and on real data, such as Sumatra-Andaman (Dec. 2004), Haiti (Jan. 2010), as well as glacial earthquakes and seismic hum.

Reconstruction for interior region-of-interest inverse geometry computed tomography: preliminary study

Energy Technology Data Exchange (ETDEWEB)

Kim, Dong Su; Kim, Tae Ho; Kim, Kyeong Hyeon; Yoon, Do Kun; Suh, Tae Suk [Dept. of Biomedical Engineering, Research Institute of Biomedical Engineering, College of Medicine, The Catholic University of Korea, Seoul (Korea, Republic of); Kang, Seong Hee [Dept. of Radiation Oncology, Seoul National University Hospital, Seoul (Korea, Republic of); Cho, Min Seok [Dept. of Radiation Oncology, Asan Medical Center, Seoul (Korea, Republic of); Noh, Yu Yoon [Dept. of Radiation Oncology, Eulji University Hospital, Daejeon (Korea, Republic of)

2017-04-15

The inverse geometry computed tomography (IGCT) composed of multiple source and small size detector has several merits such as reduction of scatter effect and large volumetric imaging within one rotation without cone-beam artifact, compared to conventional cone-beam computed tomography (CBCT). By using this multi-source characteristics, we intend to present a selective and multiple interior region-of-interest (ROI) imaging method by using a designed source on-off sequence of IGCT. ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. In this regard, it seems to be useful for diagnostic or image guidance for radiotherapy. ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. Projection of ROI-IGCT is performed by selective irradiation, hence unnecessary imaging dose to non-interest region can be reduced. In this regard, it seems to be useful for diagnostic or image guidance for radiotherapy.

Influence of antibiotic pressure on bacterial bioluminescence, with emphasis on Staphylococcus aureus

NARCIS (Netherlands)

Daghighi, Seyedmojtaba; Sjollema, Jelmer; Harapanahalli, Akshay; Dijkstra, Rene J. B.; van der Mei, Henny C.; Busscher, Henk J.

2015-01-01

Bioluminescence imaging is used for longitudinal evaluation of bacteria in live animals. Clear relations exist between bacterial numbers and their bioluminescence. However, bioluminescence images of Staphylococcus aureus Xen29, S. aureus Xen36 and Escherichia coli Xen14 grown on tryptone soy agar in

Development of a Novel Preclinical Pancreatic Cancer Research Model: Bioluminescence Image-Guided Focal Irradiation and Tumor Monitoring of Orthotopic Xenografts1

Science.gov (United States)

Tuli, Richard; Surmak, Andrew; Reyes, Juvenal; Hacker-Prietz, Amy; Armour, Michael; Leubner, Ashley; Blackford, Amanda; Tryggestad, Erik; Jaffee, Elizabeth M; Wong, John; DeWeese, Theodore L; Herman, Joseph M

2012-01-01

PURPOSE: We report on a novel preclinical pancreatic cancer research model that uses bioluminescence imaging (BLI)-guided irradiation of orthotopic xenograft tumors, sparing of surrounding normal tissues, and quantitative, noninvasive longitudinal assessment of treatment response. MATERIALS AND METHODS: Luciferase-expressing MiaPaCa-2 pancreatic carcinoma cells were orthotopically injected in nude mice. BLI was compared to pathologic tumor volume, and photon emission was assessed over time. BLI was correlated to positron emission tomography (PET)/computed tomography (CT) to estimate tumor dimensions. BLI and cone-beam CT (CBCT) were used to compare tumor centroid location and estimate setup error. BLI and CBCT fusion was performed to guide irradiation of tumors using the small animal radiation research platform (SARRP). DNA damage was assessed by γ-H2Ax staining. BLI was used to longitudinally monitor treatment response. RESULTS: Bioluminescence predicted tumor volume (R = 0.8984) and increased linearly as a function of time up to a 10-fold increase in tumor burden. BLI correlated with PET/CT and necropsy specimen in size (P < .05). Two-dimensional BLI centroid accuracy was 3.5 mm relative to CBCT. BLI-guided irradiated pancreatic tumors stained positively for γ-H2Ax, whereas surrounding normal tissues were spared. Longitudinal assessment of irradiated tumors with BLI revealed significant tumor growth delay of 20 days relative to controls. CONCLUSIONS: We have successfully applied the SARRP to a bioluminescent, orthotopic preclinical pancreas cancer model to noninvasively: 1) allow the identification of tumor burden before therapy, 2) facilitate image-guided focal radiation therapy, and 3) allow normalization of tumor burden and longitudinal assessment of treatment response. PMID:22496923

Optical coherence tomography signal analysis: LIDAR like equation and inverse methods

International Nuclear Information System (INIS)

Amaral, Marcello Magri

2012-01-01

Optical Coherence Tomography (OCT) is based on the media backscattering properties in order to obtain tomographic images. In a similar way, LIDAR (Light Detection and Range) technique uses these properties to determine atmospheric characteristics, specially the signal extinction coefficient. Exploring this similarity allowed the application of signal inversion methods to the OCT images, allowing to construct images based in the extinction coefficient, original result until now. The goal of this work was to study, propose, develop and implement algorithms based on OCT signal inversion methodologies with the aim of determine the extinction coefficient as a function of depth. Three inversion methods were used and implemented in LABView R : slope, boundary point and optical depth. Associated errors were studied and real samples (homogeneous and stratified) were used for two and three dimension analysis. The extinction coefficient images obtained from the optical depth method were capable to differentiate air from the sample. The images were studied applying PCA and cluster analysis that established the methodology strength in determining the sample's extinction coefficient value. Moreover, the optical depth methodology was applied to study the hypothesis that there is some correlation between signal extinction coefficient and the enamel teeth demineralization during a cariogenic process. By applying this methodology, it was possible to observe the variation of the extinction coefficient as depth function and its correlation with microhardness variation, showing that in deeper layers its values tends to a healthy tooth values, behaving as the same way that the microhardness. (author)

BLProt: Prediction of bioluminescent proteins based on support vector machine and relieff feature selection

KAUST Repository

Kandaswamy, Krishna Kumar

2011-08-17

Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.

BLProt: Prediction of bioluminescent proteins based on support vector machine and relieff feature selection

KAUST Repository

Kandaswamy, Krishna Kumar; Pugalenthi, Ganesan; Hazrati, Mehrnaz Khodam; Kalies, Kai-Uwe; Martinetz, Thomas

2011-01-01

Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.

Increased bioassay sensitivity of bioactive molecule discovery using metal-enhanced bioluminescence

International Nuclear Information System (INIS)

Golberg, Karina; Elbaz, Amit; McNeil, Ronald; Kushmaro, Ariel; Geddes, Chris D.; Marks, Robert S.

2014-01-01

We report the use of bioluminescence signal enhancement via proximity to deposited silver nanoparticles for bioactive compound discovery. This approach employs a whole-cell bioreporter harboring a plasmid-borne fusion of a specific promoter incorporated with a bioluminescence reporter gene. The silver deposition process was first optimized to provide optimal nanoparticle size in the reaction time dependence with fluorescein. The use of silver deposition of 350 nm particles enabled the doubling of the bioluminescent signal amplitude by the bacterial bioreporter when compared to an untouched non-silver-deposited microtiter plate surface. This recording is carried out in the less optimal but necessary far-field distance. SEM micrographs provided a visualization of the proximity of the bioreporter to the silver nanoparticles. The electromagnetic field distributions around the nanoparticles were simulated using Finite Difference Time Domain, further suggesting a re-excitation of non-chemically excited bioluminescence in addition to metal-enhanced bioluminescence. The possibility of an antiseptic silver effect caused by such a close proximity was eliminated disregarded by the dynamic growth curves of the bioreporter strains as seen using viability staining. As a highly attractive biotechnology tool, this silver deposition technique, coupled with whole-cell sensing, enables increased bioluminescence sensitivity, making it especially useful for cases in which reporter luminescence signals are very weak

Increased bioassay sensitivity of bioactive molecule discovery using metal-enhanced bioluminescence

Energy Technology Data Exchange (ETDEWEB)

Golberg, Karina, E-mail: karingo@bgu.ac.il; Elbaz, Amit [Ben-Gurion University of the Negev, Avram and Stella Goldstein-Goren Department of Biotechnology Engineering (Israel); McNeil, Ronald [The Institute of Fluorescence, University of Maryland Baltimore County (United States); Kushmaro, Ariel [Ben-Gurion University of the Negev, Avram and Stella Goldstein-Goren Department of Biotechnology Engineering (Israel); Geddes, Chris D. [The Institute of Fluorescence, University of Maryland Baltimore County (United States); Marks, Robert S., E-mail: rsmarks@bgu.ac.il [Ben-Gurion University of the Negev, Avram and Stella Goldstein-Goren Department of Biotechnology Engineering (Israel)

2014-12-15

We report the use of bioluminescence signal enhancement via proximity to deposited silver nanoparticles for bioactive compound discovery. This approach employs a whole-cell bioreporter harboring a plasmid-borne fusion of a specific promoter incorporated with a bioluminescence reporter gene. The silver deposition process was first optimized to provide optimal nanoparticle size in the reaction time dependence with fluorescein. The use of silver deposition of 350 nm particles enabled the doubling of the bioluminescent signal amplitude by the bacterial bioreporter when compared to an untouched non-silver-deposited microtiter plate surface. This recording is carried out in the less optimal but necessary far-field distance. SEM micrographs provided a visualization of the proximity of the bioreporter to the silver nanoparticles. The electromagnetic field distributions around the nanoparticles were simulated using Finite Difference Time Domain, further suggesting a re-excitation of non-chemically excited bioluminescence in addition to metal-enhanced bioluminescence. The possibility of an antiseptic silver effect caused by such a close proximity was eliminated disregarded by the dynamic growth curves of the bioreporter strains as seen using viability staining. As a highly attractive biotechnology tool, this silver deposition technique, coupled with whole-cell sensing, enables increased bioluminescence sensitivity, making it especially useful for cases in which reporter luminescence signals are very weak.

New bioreactor for in situ simultaneous measurement of bioluminescence and cell density

Science.gov (United States)

Picart, Pascal; Bendriaa, Loubna; Daniel, Philippe; Horry, Habib; Durand, Marie-José; Jouvanneau, Laurent; Thouand, Gérald

2004-03-01

This article presents a new device devoted to the simultaneous measurement of bioluminescence and optical density of a bioluminescent bacterial culture. It features an optoelectronic bioreactor with a fully autoclavable module, in which the bioluminescent bacteria are cultivated, a modulated laser diode dedicated to optical density measurement, and a detection head for the acquisition of both bioluminescence and optical density signals. Light is detected through a bifurcated fiber bundle. This setup allows the simultaneous estimation of the bioluminescence and the cell density of the culture medium without any sampling. The bioluminescence is measured through a highly sensitive photomultiplier unit which has been photometrically calibrated to allow light flux measurements. This was achieved by considering the bioluminescence spectrum and the full optical transmission of the device. The instrument makes it possible to measure a very weak light flux of only a few pW. The optical density is determined through the laser diode and a photodiode using numerical synchronous detection which is based on the power spectrum density of the recorded signal. The detection was calibrated to measure optical density up to 2.5. The device was validated using the Vibrio fischeri bacterium which was cultivated under continuous culture conditions. A very good correlation between manual and automatic measurements processed with this instrument has been demonstrated. Furthermore, the optoelectronic bioreactor enables determination of the luminance of the bioluminescent bacteria which is estimated to be 6×10-5 W sr-1 m-2 for optical density=0.3. Experimental results are presented and discussed.

High resolution in vivo bioluminescent imaging for the study of bacterial tumour targeting.

Directory of Open Access Journals (Sweden)

Michelle Cronin

Full Text Available The ability to track microbes in real time in vivo is of enormous value for preclinical investigations in infectious disease or gene therapy research. Bacteria present an attractive class of vector for cancer therapy, possessing a natural ability to grow preferentially within tumours following systemic administration. Bioluminescent Imaging (BLI represents a powerful tool for use with bacteria engineered to express reporter genes such as lux. BLI is traditionally used as a 2D modality resulting in images that are limited in their ability to anatomically locate cell populations. Use of 3D diffuse optical tomography can localize the signals but still need to be combined with an anatomical imaging modality like micro-Computed Tomography (μCT for interpretation.In this study, the non-pathogenic commensal bacteria E. coli K-12 MG1655 and Bifidobacterium breve UCC2003, or Salmonella Typhimurium SL7207 each expressing the luxABCDE operon were intravenously (i.v. administered to mice bearing subcutaneous (s.c FLuc-expressing xenograft tumours. Bacterial lux signal was detected specifically in tumours of mice post i.v.-administration and bioluminescence correlated with the numbers of bacteria recovered from tissue. Through whole body imaging for both lux and FLuc, bacteria and tumour cells were co-localised. 3D BLI and μCT image analysis revealed a pattern of multiple clusters of bacteria within tumours. Investigation of spatial resolution of 3D optical imaging was supported by ex vivo histological analyses. In vivo imaging of orally-administered commensal bacteria in the gastrointestinal tract (GIT was also achieved using 3D BLI. This study demonstrates for the first time the potential to simultaneously image multiple BLI reporter genes three dimensionally in vivo using approaches that provide unique information on spatial locations.

Bioluminescence of beetle luciferases with 6'-amino-D-luciferin analogues reveals excited keto-oxyluciferin as the emitter and phenolate/luciferin binding site interactions modulate bioluminescence colors.

Science.gov (United States)

Viviani, Vadim R; Neves, Deimison Rodrigues; Amaral, Danilo Trabuco; Prado, Rogilene A; Matsuhashi, Takuto; Hirano, Takashi

2014-08-19

Beetle luciferases produce different bioluminescence colors from green to red using the same d-luciferin substrate. Despite many studies of the mechanisms and structural determinants of bioluminescence colors with firefly luciferases, the identity of the emitters and the specific active site interactions responsible for bioluminescence color modulation remain elusive. To address these questions, we analyzed the bioluminescence spectra with 6'-amino-D-luciferin (aminoluciferin) and its 5,5-dimethyl analogue using a set of recombinant beetle luciferases that naturally elicit different colors and different pH sensitivities (pH-sensitive, Amydetes vivianii λmax=538 nm, Macrolampis sp2 λmax=564 nm; pH-insensitive, Phrixotrix hirtus λmax=623 nm, Phrixotrix vivianii λmax=546 nm, and Pyrearinus termitilluminans λmax=534 nm), a luciferase-like enzyme (Tenebrionidae, Zophobas morio λmax=613 nm), and mutants of C311 (S314). The green-yellow-emitting luciferases display red-shifted bioluminescence spectra with aminoluciferin in relation to those with D-luciferin, whereas the red-emitting luciferases displayed blue-shifted spectra. Bioluminescence spectra with 5,5-dimethylaminoluciferin, in which enolization is blocked, were almost identical to those of aminoluciferin. Fluorescence probing using 2-(4-toluidino)naphthalene-6-sulfonate and inference with aminoluciferin confirm that the luciferin binding site of the red-shifted luciferases is more polar than in the case of the green-yellow-emitting luciferases. Altogether, the results show that the keto form of excited oxyluciferin is the emitter in beetle bioluminescence and that bioluminescence colors are essentially modulated by interactions of the 6'-hydroxy group of oxyluciferin and basic moieties under the influence of the microenvironment polarity of the active site: a strong interaction between a base moiety and oxyluciferin phenol in a hydrophobic microenvironment promotes green-yellow emission, whereas a more polar

Far red bioluminescence from two deep-sea fishes.

Science.gov (United States)

Widder, E A; Latz, M I; Herring, P J; Case, J F

1984-08-03

Spectral measurements of red bioluminescence were obtained from the deep-sea stomiatoid fishes Aristostomias scintillans (Gilbert) and Malacosteus niger (Ayres). Red luminescence from suborbital light organs extends to the near infrared, with peak emission at approximately 705 nanometers in the far red. These fishes also have postorbital light organs that emit blue luminescence with maxima between 470 and 480 nanometers. The red bioluminescence may be due to an energy transfer system and wavelength-selective filtering.

Filtering and deconvolution for bioluminescence imaging of small animals; Filtrage et deconvolution en imagerie de bioluminescence chez le petit animal

Energy Technology Data Exchange (ETDEWEB)

Akkoul, S.

2010-06-22

This thesis is devoted to analysis of bioluminescence images applied to the small animal. This kind of imaging modality is used in cancerology studies. Nevertheless, some problems are related to the diffusion and the absorption of the tissues of the light of internal bioluminescent sources. In addition, system noise and the cosmic rays noise are present. This influences the quality of the images and makes it difficult to analyze. The purpose of this thesis is to overcome these disturbing effects. We first have proposed an image formation model for the bioluminescence images. The processing chain is constituted by a filtering stage followed by a deconvolution stage. We have proposed a new median filter to suppress the random value impulsive noise which corrupts the acquired images; this filter represents the first block of the proposed chain. For the deconvolution stage, we have performed a comparative study of various deconvolution algorithms. It allowed us to choose a blind deconvolution algorithm initialized with the estimated point spread function of the acquisition system. At first, we have validated our global approach by comparing our obtained results with the ground truth. Through various clinical tests, we have shown that the processing chain allows a significant improvement of the spatial resolution and a better distinction of very close tumor sources, what represents considerable contribution for the users of bioluminescence images. (author)

Methodological problems of direct bioluminescent ATP assay in platelets and erythrocytes.

Science.gov (United States)

Girotti, S; Ferri, E; Cascione, M L; Comuzio, S; Mazzuca, A; Orlandini, A; Breccia, A

1989-07-01

Direct bioluminescent ATP determination in platelets and erythrocytes involves the study of different parameters which are discussed here. Some parameters are linked to the bioluminescent reaction and to the analyte (ATP); others have regard to the biological matrix. The composition of bioluminescent reagents and the preparation and conservation of the ATP standard, also in the presence of excipients, are among the first given. Matrix problems involve cell characteristics related to age and form, lysis resistance and the possible formation of aggregates (platelets) that may inhibit the complete release of ATP. For these reasons we used the most efficient ATP release agent with the lowest inhibitory effect on luciferase. The data obtained correlate well with a bioluminescent method requiring extraction with ethanol/EDTA, and therefore more time, for ATP determination in platelets and erythrocytes.

Uptake kinetics and biodistribution of C-14-D-luciferin-a radiolabeled substrate for the firefly luciferase catalyzed bioluminescence reaction : impact on bioluminescence based reporter gene imaging

NARCIS (Netherlands)

Berger, Frank; Paulmurugan, Ramasamy; Bhaumik, Srabani; Gambhir, Sanjiv Sam

2008-01-01

Purpose Firefly luciferase catalyzes the oxidative decarboxylation of D-luciferin to oxyluciferin in the presence of cofactors, producing bioluminescence. This reaction is used in optical bioluminescence-based molecular imaging approaches to detect the expression of the firefly luciferase reporter

Symplectin evolved from multiple duplications in bioluminescent squid

DEFF Research Database (Denmark)

Francis, Warren R.; Christianson, Lynne M.; Haddock, Steven H.D.

2017-01-01

The squid Sthenoteuthis oualaniensis, formerly Symplectoteuthis oualaniensis, generates light using the luciferin coelenterazine and a unique enzyme, symplectin. Genetic information is limited for bioluminescent cephalopod species, so many proteins, including symplectin, occur in public databases...... functioning is conserved across essentially all members of the protein family, even those unlikely to be used for bioluminescence. Conversely, active site residues involved in pantetheinase catalysis are also conserved across essentially all of these proteins, suggesting that symplectin may have multiple...

REVIEW ARTICLE: Bioluminescent signals and the role of reflectors

Science.gov (United States)

Herring, Peter J.

2000-11-01

Organisms in a well lit environment use optical signals derived from the selective reflection of ambient light. In a dim or dark environment it is very difficult (because of low photon numbers) to detect the contrast between light reflected from the organism and that from the background, and many organisms use bioluminescent signals instead. The use of such signals on land is largely restricted to sexual signalling by the luminous beetles, but in the deep ocean their use is widespread, involving both many different organisms and a range of uses which parallel those of reflective signals on land. Some bioluminescent signals rely almost entirely on an optically unmodified light source (e.g. a secretion) but others depend upon complex optical structures, particularly reflectors, in the light-emitting organs. Reflectors in the light organs of many shrimp, squid and fish are based on constructive interference systems but employ different biological materials. They and other structures modify the angular, spectral and intensity distributions of bioluminescent signals. The ready availability of highly efficient biological reflectors has been a formative influence in the evolution of bioluminescent signalling in the sea.

From tomography to full-waveform inversion with a single objective function

KAUST Repository

Alkhalifah, Tariq Ali

2014-02-17

In full-waveform inversion (FWI), a gradient-based update of the velocity model requires an initial velocity that produces synthetic data that are within a half-cycle, everywhere, from the field data. Such initial velocity models are usually extracted from migration velocity analysis or traveltime tomography, among other means, and are not guaranteed to adhere to the FWI requirements for an initial velocity model. As such, we evaluated an objective function based on the misfit in the instantaneous traveltime between the observed and modeled data. This phase-based attribute of the wavefield, along with its phase unwrapping characteristics, provided a frequency-dependent traveltime function that was easy to use and quantify, especially compared to conventional phase representation. With a strong Laplace damping of the modeled, potentially low-frequency, data along the time axis, this attribute admitted a first-arrival traveltime that could be compared with picked ones from the observed data, such as in wave equation tomography (WET). As we relax the damping on the synthetic and observed data, the objective function measures the misfit in the phase, however unwrapped. It, thus, provided a single objective function for a natural transition from WET to FWI. A Marmousi example demonstrated the effectiveness of the approach.

Action of γ-radiation on bioluminescence of Noctiluca miliaris

International Nuclear Information System (INIS)

Tokarev, Yu.N.

1976-01-01

Results of the study in the action of various doses of irradiation on the bioluminescence of Noctiluca miliaris are presented. The doses are found that stimulate the bioluminescence and the dose - effect curves are obtained. It has been shown that stimulation of Noctiluca luminescence by γ-radiation is not of a constant character and extinguishes after a period of time determined by a dose rate

Circular polarization observed in bioluminescence

NARCIS (Netherlands)

Wijnberg, Hans; Meijer, E.W.; Hummelen, J.C.; Dekkers, H.P.J.M.; Schippers, P.H.; Carlson, A.D.

1980-01-01

While investigating circular polarization in luminescence, and having found it in chemiluminescence, we have studied bioluminescence because it is such a widespread and dramatic natural phenomenon. We report here that left and right lanterns of live larvae of the fireflies, Photuris lucicrescens and

Reconstruction Methods for Inverse Problems with Partial Data

DEFF Research Database (Denmark)

Hoffmann, Kristoffer

This thesis presents a theoretical and numerical analysis of a general mathematical formulation of hybrid inverse problems in impedance tomography. This includes problems from several existing hybrid imaging modalities such as Current Density Impedance Imaging, Magnetic Resonance Electrical...... Impedance Tomography, and Ultrasound Modulated Electrical Impedance Tomography. After giving an introduction to hybrid inverse problems in impedance tomography and the mathematical tools that facilitate the related analysis, we explain in detail the stability properties associated with the classification...... of a linearised hybrid inverse problem. This is done using pseudo-differential calculus and theory for overdetermined boundary value problem. Using microlocal analysis we then present novel results on the propagation of singularities, which give a precise description of the distinct features of solutions...

Bioluminescent system for dynamic imaging of cell and animal behavior

Energy Technology Data Exchange (ETDEWEB)

Hara-Miyauchi, Chikako [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama 351-0198 (Japan); Department of Biophysics and Biochemistry, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8510 (Japan); Tsuji, Osahiko [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Hanyu, Aki [Division of Biochemistry, The Cancer Institute of the Japanese Foundation for Cancer Research, Tokyo 135-8550 (Japan); Okada, Seiji [Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582 (Japan); Yasuda, Akimasa [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Fukano, Takashi [Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama 351-0198 (Japan); Akazawa, Chihiro [Department of Biophysics and Biochemistry, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8510 (Japan); Nakamura, Masaya [Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Imamura, Takeshi [Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295 (Japan); Core Research for Evolutional Science and Technology, The Japan Science and Technology Corporation, Tokyo 135-8550 (Japan); Matsuzaki, Yumi [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Okano, Hirotaka James, E-mail: hjokano@jikei.ac.jp [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Division of Regenerative Medicine Jikei University School of Medicine, Tokyo 150-8461 (Japan); and others

2012-03-09

Highlights: Black-Right-Pointing-Pointer We combined a yellow variant of GFP and firefly luciferase to make ffLuc-cp156. Black-Right-Pointing-Pointer ffLuc-cp156 showed improved photon yield in cultured cells and transgenic mice. Black-Right-Pointing-Pointer ffLuc-cp156 enabled video-rate bioluminescence imaging of freely-moving animals. Black-Right-Pointing-Pointer ffLuc-cp156 mice enabled tracking real-time drug delivery in conscious animals. -- Abstract: The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over three orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.

Bioluminescent system for dynamic imaging of cell and animal behavior

International Nuclear Information System (INIS)

Hara-Miyauchi, Chikako; Tsuji, Osahiko; Hanyu, Aki; Okada, Seiji; Yasuda, Akimasa; Fukano, Takashi; Akazawa, Chihiro; Nakamura, Masaya; Imamura, Takeshi; Matsuzaki, Yumi; Okano, Hirotaka James

2012-01-01

Highlights: ► We combined a yellow variant of GFP and firefly luciferase to make ffLuc-cp156. ► ffLuc-cp156 showed improved photon yield in cultured cells and transgenic mice. ► ffLuc-cp156 enabled video-rate bioluminescence imaging of freely-moving animals. ► ffLuc-cp156 mice enabled tracking real-time drug delivery in conscious animals. -- Abstract: The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over three orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.

Rapid Analysis of Eukaryotic Bioluminescence to Assess Potential Groundwater Contamination Events

Directory of Open Access Journals (Sweden)

Zacariah L. Hildenbrand

2015-01-01

Full Text Available Here we present data using a bioluminescent dinoflagellate, Pyrocystis lunula, in a toxicological bioassay to rapidly assess potential instances of groundwater contamination associated with natural gas extraction. P. lunula bioluminescence can be quantified using spectrophotometry as a measurement of organismal viability, with normal bioluminescent output declining with increasing concentration(s of aqueous toxicants. Glutaraldehyde and hydrochloric acid (HCl, components used in hydraulic fracturing and shale acidization, triggered significant toxicological responses in as little as 4 h. Conversely, P. lunula was not affected by the presence of arsenic, selenium, barium, and strontium, naturally occurring heavy metal ions potentially associated with unconventional drilling activities. If exogenous compounds, such as glutaraldehyde and HCl, are thought to have been introduced into groundwater, quantification of P. lunula bioluminescence after exposure to water samples can serve as a cost-effective detection and risk assessment tool to rapidly assess the impact of putative contamination events attributed to unconventional drilling activity.

Unwrapped phase inversion for near surface seismic data

KAUST Repository

Choi, Yun Seok

2012-11-04

The Phase-wrapping is one of the main obstacles of waveform inversion. We use an inversion algorithm based on the instantaneous-traveltime that overcomes the phase-wrapping problem. With a high damping factor, the frequency-dependent instantaneous-traveltime inversion provides the stability of refraction tomography, with higher resolution results, and no arrival picking involved. We apply the instantaneous-traveltime inversion to the synthetic data generated by the elastic time-domain modeling. The synthetic data is a representative of the near surface seismic data. Although the inversion algorithm is based on the acoustic wave equation, the numerical examples show that the instantaneous-traveltime inversion generates a convergent velocity model, very similar to what we see from traveltime tomography.

Filtering and deconvolution for bioluminescence imaging of small animals

International Nuclear Information System (INIS)

Akkoul, S.

2010-01-01

This thesis is devoted to analysis of bioluminescence images applied to the small animal. This kind of imaging modality is used in cancerology studies. Nevertheless, some problems are related to the diffusion and the absorption of the tissues of the light of internal bioluminescent sources. In addition, system noise and the cosmic rays noise are present. This influences the quality of the images and makes it difficult to analyze. The purpose of this thesis is to overcome these disturbing effects. We first have proposed an image formation model for the bioluminescence images. The processing chain is constituted by a filtering stage followed by a deconvolution stage. We have proposed a new median filter to suppress the random value impulsive noise which corrupts the acquired images; this filter represents the first block of the proposed chain. For the deconvolution stage, we have performed a comparative study of various deconvolution algorithms. It allowed us to choose a blind deconvolution algorithm initialized with the estimated point spread function of the acquisition system. At first, we have validated our global approach by comparing our obtained results with the ground truth. Through various clinical tests, we have shown that the processing chain allows a significant improvement of the spatial resolution and a better distinction of very close tumor sources, what represents considerable contribution for the users of bioluminescence images. (author)

Hv 1 Proton Channels in Dinoflagellates: Not Just for Bioluminescence?

Science.gov (United States)

Kigundu, Gabriel; Cooper, Jennifer L; Smith, Susan M E

2018-04-26

Bioluminescence in dinoflagellates is controlled by H V 1 proton channels. Database searches of dinoflagellate transcriptomes and genomes yielded hits with sequence features diagnostic of all confirmed H V 1, and show that H V 1 is widely distributed in the dinoflagellate phylogeny including the basal species Oxyrrhis marina. Multiple sequence alignments followed by phylogenetic analysis revealed three major subfamilies of H V 1 that do not correlate with presence of theca, autotrophy, geographic location, or bioluminescence. These data suggest that most dinoflagellates express a H V 1 which has a function separate from bioluminescence. Sequence evidence also suggests that dinoflagellates can contain more than one H V 1 gene. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Validating Bioluminescence Imaging as a High-Throughput, Quantitative Modality for Assessing Tumor Burden

Directory of Open Access Journals (Sweden)

Zain Paroo

2004-04-01

Full Text Available Bioluminescence imaging (BLI is a highly sensitive tool for visualizing tumors, neoplastic development, metastatic spread, and response to therapy. Although BLI has engendered much excitement due to its apparent simplicity and ease of implementation, few rigorous studies have been presented to validate the measurements. Here, we characterize the nature of bioluminescence output from mice bearing subcutaneous luciferase-expressing tumors over a 4-week period. Following intraperitoneal or direct intratumoral administration of luciferin substrate, there was a highly dynamic kinetic profile of light emission. Although bioluminescence was subject to variability, strong correlations (r > .8, p < .001 between caliper measured tumor volumes and peak light signal, area under light signal curve and light emission at specific time points were determined. Moreover, the profile of tumor growth, as monitored with bioluminescence, closely resembled that for caliper measurements. The study shows that despite the dynamic and variable nature of bioluminescence, where appropriate experimental precautions are taken, single time point BLI may be useful for noninvasive, high-throughput, quantitative assessment of tumor burden.

Biological water quality monitoring using chemiluminescent and bioluminescent techniques

Science.gov (United States)

Thomas, R. R.

1978-01-01

Automated chemiluminescence and bioluminescence sensors were developed for the continuous monitoring of microbial levels in water supplies. The optimal chemical procedures were determined for the chemiluminescence system to achieve maximum sensitivity. By using hydrogen peroxide, reaction rate differentiation, ethylene diamine tetraacetic acid (EDTA), and carbon monoxide pretreatments, factors which cause interference were eliminated and specificity of the reaction for living and dead bacteria was greatly increased. By employing existing technology with some modifications, a sensitive and specific bioluminescent system was developed.

Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion.

Science.gov (United States)

Wollenberg, M S; Preheim, S P; Polz, M F; Ruby, E G

2012-03-01

This study reports the first description and molecular characterization of naturally occurring, non-bioluminescent strains of Vibrio fischeri. These 'dark' V. fischeri strains remained non-bioluminescent even after treatment with both autoinducer and aldehyde, substrate additions that typically maximize light production in dim strains of luminous bacteria. Surprisingly, the entire lux locus (eight genes) was absent in over 97% of these dark V. fischeri strains. Although these strains were all collected from a Massachusetts (USA) estuary in 2007, phylogenetic reconstructions allowed us to reject the hypothesis that these newly described non-bioluminescent strains exhibit monophyly within the V. fischeri clade. These dark strains exhibited a competitive disadvantage against native bioluminescent strains when colonizing the light organ of the model V. fischeri host, the Hawaiian bobtail squid Euprymna scolopes. Significantly, we believe that the data collected in this study may suggest the first observation of a functional, parallel locus-deletion event among independent lineages of a non-pathogenic bacterial species. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

A two-hour antibiotic susceptibility test by ATP-bioluminescence.

Science.gov (United States)

March Rosselló, Gabriel Alberto; García-Loygorri Jordán de Urries, María Cristina; Gutiérrez Rodríguez, María Purificación; Simarro Grande, María; Orduña Domingo, Antonio; Bratos Pérez, Miguel Ángel

2016-01-01

The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

In vitro validation of bioluminescent monitoring of disease progression and therapeutic response in leukaemia model animals

International Nuclear Information System (INIS)

Inoue, Yusuke; Okubo, Toshiyuki; Tojo, Arinobu; Sekine, Rieko; Soda, Yasushi; Kobayashi, Seiichiro; Nomura, Akiko; Izawa, Kiyoko; Kitamura, Toshio; Ohtomo, Kuni

2006-01-01

The application of in vivo bioluminescence imaging to non-invasive, quantitative monitoring of tumour models relies on a positive correlation between the intensity of bioluminescence and the tumour burden. We conducted cell culture studies to investigate the relationship between bioluminescent signal intensity and viable cell numbers in murine leukaemia model cells. Interleukin-3 (IL-3)-dependent murine pro-B cell line Ba/F3 was transduced with firefly luciferase to generate cells expressing luciferase stably under the control of a retroviral long terminal repeat. The luciferase-expressing cells were transduced with p190 BCR-ABL to give factor-independent proliferation. The cells were cultured under various conditions, and bioluminescent signal intensity was compared with viable cell numbers and the cell cycle stage. The Ba/F3 cells showed autonomous growth as well as stable luciferase expression following transduction with both luciferase and p190 BCR-ABL, and in vivo bioluminescence imaging permitted external detection of these cells implanted into mice. The bioluminescence intensities tended to reflect cell proliferation and responses to imatinib in cell culture studies. However, the luminescence per viable cell was influenced by the IL-3 concentration in factor-dependent cells and by the stage of proliferation and imatinib concentration in factor-independent cells, thereby impairing the proportionality between viable cell number and bioluminescent signal intensity. Luminescence per cell tended to vary in association with the fraction of proliferating cells. Although in vivo bioluminescence imaging would allow non-invasive monitoring of leukaemia model animals, environmental factors and therapeutic interventions may cause some discrepancies between tumour burden and bioluminescence intensity. (orig.)

Inverse logarithmic potential problem

CERN Document Server

Cherednichenko, V G

1996-01-01

The Inverse and Ill-Posed Problems Series is a series of monographs publishing postgraduate level information on inverse and ill-posed problems for an international readership of professional scientists and researchers. The series aims to publish works which involve both theory and applications in, e.g., physics, medicine, geophysics, acoustics, electrodynamics, tomography, and ecology.

Multimodal Imaging of Integrin Receptor-Positive Tumors by Bioluminescence, Fluorescence, Gamma Scintigraphy, and Single-Photon Emission Computed Tomography Using a Cyclic RGD Peptide Labeled with a Near-Infrared Fluorescent Dye and a Radionuclide

Directory of Open Access Journals (Sweden)

W. Barry Edwards

2009-03-01

Full Text Available Integrins, particularly the αvβ3 heterodimers, play important roles in tumor-induced angiogenesis and invasiveness. To image the expression pattern of the αvβ3 integrin in tumors through a multimodality imaging paradigm, we prepared a cyclic RGDyK peptide analogue (LS308 bearing a tetraazamacrocycle 1,4,7,10-tetraazacyclododecane-N, N′, N″, N‴-tetraacetic acid (DOTA and a lipophilic near-infrared (NIR fluorescent dye cypate. The αvβ3 integrin binding affinity and the internalization properties of LS308 mediated by the αvβ3 integrin in 4t1luc cells were investigated by receptor binding assay and fluorescence microscopy, respectively. The in vivo distribution of 111In-labeled LS308 in a 4t1luc tumor-bearing mouse model was studied by fluorescence, bioluminescence, planar gamma, and single-photon emission computed tomography (SPECT. The results show that LS308 has high affinity for αvβ3 integrin and internalized preferentially via the αvβ3 integrin-mediated endocytosis in 4t1luc cells. We also found that LS308 selectively accumulated in αvβ3-positve tumors in a receptor-specific manner and was visualized by the four imaging methods. Whereas the endogenous bioluminescence imaging identified the ensemble of the tumor tissue, the fluorescence and SPECT methods with the exogenous contrast agent LS308 reported the local expression of αvβ3 integrin. Thus, the multimodal imaging approach could provide important complementary diagnostic information for monitoring the efficacy of new antiangiogenic drugs.

Systematic calibration of an integrated x-ray and optical tomography system for preclinical radiation research

Energy Technology Data Exchange (ETDEWEB)

Yang, Yidong, E-mail: yidongyang@med.miami.edu [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231 and Department of Radiation Oncology, University of Miami School of Medicine, Miami, Florida 33136 (United States); Wang, Ken Kang-Hsin; Wong, John W. [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231 (United States); Eslami, Sohrab; Iordachita, Iulian I. [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Patterson, Michael S. [Juravinski Cancer Centre and Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Ontario L8S4K1 (Canada)

2015-04-15

Purpose: The cone beam computed tomography (CBCT) guided small animal radiation research platform (SARRP) has been developed for focal tumor irradiation, allowing laboratory researchers to test basic biological hypotheses that can modify radiotherapy outcomes in ways that were not feasible previously. CBCT provides excellent bone to soft tissue contrast, but is incapable of differentiating tumors from surrounding soft tissue. Bioluminescence tomography (BLT), in contrast, allows direct visualization of even subpalpable tumors and quantitative evaluation of tumor response. Integration of BLT with CBCT offers complementary image information, with CBCT delineating anatomic structures and BLT differentiating luminescent tumors. This study is to develop a systematic method to calibrate an integrated CBCT and BLT imaging system which can be adopted onboard the SARRP to guide focal tumor irradiation. Methods: The integrated imaging system consists of CBCT, diffuse optical tomography (DOT), and BLT. The anatomy acquired from CBCT and optical properties acquired from DOT serve as a priori information for the subsequent BLT reconstruction. Phantoms were designed and procedures were developed to calibrate the CBCT, DOT/BLT, and the entire integrated system. Geometrical calibration was performed to calibrate the CBCT system. Flat field correction was performed to correct the nonuniform response of the optical imaging system. Absolute emittance calibration was performed to convert the camera readout to the emittance at the phantom or animal surface, which enabled the direct reconstruction of the bioluminescence source strength. Phantom and mouse imaging were performed to validate the calibration. Results: All calibration procedures were successfully performed. Both CBCT of a thin wire and a euthanized mouse revealed no spatial artifact, validating the accuracy of the CBCT calibration. The absolute emittance calibration was validated with a 650 nm laser source, resulting in a 3

Systematic calibration of an integrated x-ray and optical tomography system for preclinical radiation research

International Nuclear Information System (INIS)

Yang, Yidong; Wang, Ken Kang-Hsin; Wong, John W.; Eslami, Sohrab; Iordachita, Iulian I.; Patterson, Michael S.

2015-01-01

Purpose: The cone beam computed tomography (CBCT) guided small animal radiation research platform (SARRP) has been developed for focal tumor irradiation, allowing laboratory researchers to test basic biological hypotheses that can modify radiotherapy outcomes in ways that were not feasible previously. CBCT provides excellent bone to soft tissue contrast, but is incapable of differentiating tumors from surrounding soft tissue. Bioluminescence tomography (BLT), in contrast, allows direct visualization of even subpalpable tumors and quantitative evaluation of tumor response. Integration of BLT with CBCT offers complementary image information, with CBCT delineating anatomic structures and BLT differentiating luminescent tumors. This study is to develop a systematic method to calibrate an integrated CBCT and BLT imaging system which can be adopted onboard the SARRP to guide focal tumor irradiation. Methods: The integrated imaging system consists of CBCT, diffuse optical tomography (DOT), and BLT. The anatomy acquired from CBCT and optical properties acquired from DOT serve as a priori information for the subsequent BLT reconstruction. Phantoms were designed and procedures were developed to calibrate the CBCT, DOT/BLT, and the entire integrated system. Geometrical calibration was performed to calibrate the CBCT system. Flat field correction was performed to correct the nonuniform response of the optical imaging system. Absolute emittance calibration was performed to convert the camera readout to the emittance at the phantom or animal surface, which enabled the direct reconstruction of the bioluminescence source strength. Phantom and mouse imaging were performed to validate the calibration. Results: All calibration procedures were successfully performed. Both CBCT of a thin wire and a euthanized mouse revealed no spatial artifact, validating the accuracy of the CBCT calibration. The absolute emittance calibration was validated with a 650 nm laser source, resulting in a 3

Quantitative and Functional Requirements for Bioluminescent Cancer Models.

Science.gov (United States)

Feys, Lynn; Descamps, Benedicte; Vanhove, Christian; Vermeulen, Stefan; Vandesompele, J O; Vanderheyden, Katrien; Messens, Kathy; Bracke, Marc; De Wever, Olivier

2016-01-01

Bioluminescent cancer models are widely used but detailed quantification of the luciferase signal and functional comparison with a non-transfected control cell line are generally lacking. In the present study, we provide quantitative and functional tests for luciferase-transfected cells. We quantified the luciferase expression in BLM and HCT8/E11 transfected cancer cells, and examined the effect of long-term luciferin exposure. The present study also investigated functional differences between parental and transfected cancer cells. Our results showed that quantification of different single-cell-derived populations are superior with droplet digital polymerase chain reaction. Quantification of luciferase protein level and luciferase bioluminescent activity is only useful when there is a significant difference in copy number. Continuous exposure of cell cultures to luciferin leads to inhibitory effects on mitochondrial activity, cell growth and bioluminescence. These inhibitory effects correlate with luciferase copy number. Cell culture and mouse xenograft assays showed no significant functional differences between luciferase-transfected and parental cells. Luciferase-transfected cells should be validated by quantitative and functional assays before starting large-scale experiments. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Quorum sensing influences Vibrio harveyi growth rates in a manner not fully accounted for by the marker effect of bioluminescence.

Science.gov (United States)

Nackerdien, Zeena E; Keynan, Alexander; Bassler, Bonnie L; Lederberg, Joshua; Thaler, David S

2008-02-27

The light-emitting Vibrios provide excellent material for studying the interaction of cellular communication with growth rate because bioluminescence is a convenient marker for quorum sensing. However, the use of bioluminescence as a marker is complicated because bioluminescence itself may affect growth rate, e.g. by diverting energy. The marker effect was explored via growth rate studies in isogenic Vibrio harveyi (Vh) strains altered in quorum sensing on the one hand, and bioluminescence on the other. By hypothesis, growth rate is energy limited: mutants deficient in quorum sensing grow faster because wild type quorum sensing unleashes bioluminescence and bioluminescence diverts energy. Findings reported here confirm a role for bioluminescence in limiting Vh growth rate, at least under the conditions tested. However, the results argue that the bioluminescence is insufficient to explain the relationship of growth rate and quorum sensing in Vh. A Vh mutant null for all genes encoding the bioluminescence pathway grew faster than wild type but not as fast as null mutants in quorum sensing. Vh quorum sensing mutants showed altered growth rates that do not always rank with their relative increase or decrease in bioluminescence. In addition, the cell-free culture fluids of a rapidly growing Vibrio parahaemolyticus (Vp) strain increased the growth rate of wild type Vh without significantly altering Vh's bioluminescence. The same cell-free culture fluid increased the bioluminescence of Vh quorum mutants. The effect of quorum sensing on Vh growth rate can be either positive or negative and includes both bioluminescence-dependent and independent components. Bioluminescence tends to slow growth rate but not enough to account for the effects of quorum sensing on growth rate.

Quorum sensing influences Vibrio harveyi growth rates in a manner not fully accounted for by the marker effect of bioluminescence.

Directory of Open Access Journals (Sweden)

Zeena E Nackerdien

2008-02-01

Full Text Available The light-emitting Vibrios provide excellent material for studying the interaction of cellular communication with growth rate because bioluminescence is a convenient marker for quorum sensing. However, the use of bioluminescence as a marker is complicated because bioluminescence itself may affect growth rate, e.g. by diverting energy.The marker effect was explored via growth rate studies in isogenic Vibrio harveyi (Vh strains altered in quorum sensing on the one hand, and bioluminescence on the other. By hypothesis, growth rate is energy limited: mutants deficient in quorum sensing grow faster because wild type quorum sensing unleashes bioluminescence and bioluminescence diverts energy. Findings reported here confirm a role for bioluminescence in limiting Vh growth rate, at least under the conditions tested. However, the results argue that the bioluminescence is insufficient to explain the relationship of growth rate and quorum sensing in Vh. A Vh mutant null for all genes encoding the bioluminescence pathway grew faster than wild type but not as fast as null mutants in quorum sensing. Vh quorum sensing mutants showed altered growth rates that do not always rank with their relative increase or decrease in bioluminescence. In addition, the cell-free culture fluids of a rapidly growing Vibrio parahaemolyticus (Vp strain increased the growth rate of wild type Vh without significantly altering Vh's bioluminescence. The same cell-free culture fluid increased the bioluminescence of Vh quorum mutants.The effect of quorum sensing on Vh growth rate can be either positive or negative and includes both bioluminescence-dependent and independent components. Bioluminescence tends to slow growth rate but not enough to account for the effects of quorum sensing on growth rate.

Bioorthogonal chemistry in bioluminescence imaging.

Science.gov (United States)

Godinat, Aurélien; Bazhin, Arkadiy A; Goun, Elena A

2018-05-18

Bioorthogonal chemistry has developed significant over the past few decades, to the particular benefit of molecular imaging. Bioluminescence imaging (BLI) along with other imaging modalities have significantly benefitted from this chemistry. Here, we review bioorthogonal reactions that have been used to signific antly broaden the application range of BLI. Copyright © 2018. Published by Elsevier Ltd.

Wavefront picking for 3D tomography and full-waveform inversion

KAUST Repository

AlTheyab, Abdullah

2016-09-08

We have developed an efficient approach for picking firstbreak wavefronts on coarsely sampled time slices of 3D shot gathers. Our objective was to compute a smooth initial velocity model for multiscale full-waveform inversion (FWI). Using interactive software, first-break wavefronts were geometrically modeled on time slices with a minimal number of picks. We picked sparse time slices, performed traveltime tomography, and then compared the predicted traveltimes with the data in-between the picked slices. The picking interval was refined with iterations until the errors in traveltime predictions fell within the limits necessary to avoid cycle skipping in early arrivals FWI. This approach was applied to a 3D ocean-bottom-station data set. Our results indicate that wavefront picking has 28% fewer data slices to pick compared with picking traveltimes in shot gathers. In addition, by using sparse time samples for picking, data storage is reduced by 88%, and therefore allows for a faster visualization and quality control of the picks. Our final traveltime tomogram is sufficient as a starting model for early arrival FWI. © 2016 Society of Exploration Geophysicists.

Multi-GPU parallel algorithm design and analysis for improved inversion of probability tomography with gravity gradiometry data

Science.gov (United States)

Hou, Zhenlong; Huang, Danian

2017-09-01

In this paper, we make a study on the inversion of probability tomography (IPT) with gravity gradiometry data at first. The space resolution of the results is improved by multi-tensor joint inversion, depth weighting matrix and the other methods. Aiming at solving the problems brought by the big data in the exploration, we present the parallel algorithm and the performance analysis combining Compute Unified Device Architecture (CUDA) with Open Multi-Processing (OpenMP) based on Graphics Processing Unit (GPU) accelerating. In the test of the synthetic model and real data from Vinton Dome, we get the improved results. It is also proved that the improved inversion algorithm is effective and feasible. The performance of parallel algorithm we designed is better than the other ones with CUDA. The maximum speedup could be more than 200. In the performance analysis, multi-GPU speedup and multi-GPU efficiency are applied to analyze the scalability of the multi-GPU programs. The designed parallel algorithm is demonstrated to be able to process larger scale of data and the new analysis method is practical.

a Study of the Bioluminescence of Larger Zooplankton and the Effects of Low-Level Light Changes on Their Behavior.

Science.gov (United States)

van Keuren, Jeffrey Robert

A bio-optical study was undertaken to quantify the relationships which exist between counter-illuminating organisms and the downwelling spectral light field in which they exist. The basic hypothesis behind counter-illumination is that the animal emits light using ventrally-oriented photophores to disrupt or eliminate the shadowed area on ventral surfaces. An organism lacking photophores sharply silhouettes against the highly directional downwelling irradiance, whereas by distributing photophores over the ventral surface of the body and closely matching the spectral and intensity characteristics of the downwelling light, this silhouette is obscured. Analysis carried out on changes in vertical distribution patterns in response to low-level intensity changes in ambient surface light suggested that diel migrating organisms begin to shift vertically in the water column when surface scalar irradiance decreased below or increased above 1.0 times10^{-2} muEin m^{-2} sec^ {-1}. Maximum aggregations of organisms, as defined by MOCNESS net sampling or single-frequency acoustic backscatter, appeared to remain within definable in situ blue-green isolume ranges varying less than a factor of ten throughout each night. Comparisons made between organism counter-illumination capacity and modeled in situ downwelling irradiance levels suggested that euphausiids, decapods and myctophids use between 1-10 percent of their maximum counter-illumination capacity to match the ambient downwelling light conditions. Modeling also suggested that up to 40 percent of the maximum measured bioluminescence output is required to match ambient irradiance in the shallower surface zones where aggregations of copepods, potential food sources, were commonly found at night. An optical study to quantify the radiative transfer of bioluminescence from a point source revealed that non -isotropic point sources produce radiance patterns that cannot be simply explained by inverse square losses. Therefore simple

Bioluminescent Antibodies for Point-of-Care Diagnostics.

Science.gov (United States)

Xue, Lin; Yu, Qiuliyang; Griss, Rudolf; Schena, Alberto; Johnsson, Kai

2017-06-12

We introduce a general method to transform antibodies into ratiometric, bioluminescent sensor proteins for the no-wash quantification of analytes. Our approach is based on the genetic fusion of antibody fragments to NanoLuc luciferase and SNAP-tag, the latter being labeled with a synthetic fluorescent competitor of the antigen. Binding of the antigen, here synthetic drugs, by the sensor displaces the tethered fluorescent competitor from the antibody and disrupts bioluminescent resonance energy transfer (BRET) between the luciferase and fluorophore. The semisynthetic sensors display a tunable response range (submicromolar to submillimolar) and large dynamic range (ΔR max >500 %), and they permit the quantification of analytes through spotting of the samples onto paper followed by analysis with a digital camera. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Numerical modeling of the dynamic response of a bioluminescent bacterial biosensor.

Science.gov (United States)

Affi, Mahmoud; Solliec, Camille; Legentilhomme, Patrick; Comiti, Jacques; Legrand, Jack; Jouanneau, Sulivan; Thouand, Gérald

2016-12-01

Water quality and water management are worldwide issues. The analysis of pollutants and in particular, heavy metals, is generally conducted by sensitive but expensive physicochemical methods. Other alternative methods of analysis, such as microbial biosensors, have been developed for their potential simplicity and expected moderate cost. Using a biosensor for a long time generates many changes in the growth of the immobilized bacteria and consequently alters the robustness of the detection. This work simulated the operation of a biosensor for the long-term detection of cadmium and improved our understanding of the bioluminescence reaction dynamics of bioreporter bacteria inside an agarose matrix. The choice of the numerical tools is justified by the difficulty to measure experimentally in every condition the biosensor functioning during a long time (several days). The numerical simulation of a biomass profile is made by coupling the diffusion equation and the consumption/reaction of the nutrients by the bacteria. The numerical results show very good agreement with the experimental profiles. The growth model verified that the bacterial growth is conditioned by both the diffusion and the consumption of the nutrients. Thus, there is a high bacterial density in the first millimeter of the immobilization matrix. The growth model has been very useful for the development of the bioluminescence model inside the gel and shows that a concentration of oxygen greater than or equal to 22 % of saturation is required to maintain a significant level of bioluminescence. A continuous feeding of nutrients during the process of detection of cadmium leads to a biofilm which reduces the diffusion of nutrients and restricts the presence of oxygen from the first layer of the agarose (1 mm) and affects the intensity of the bioluminescent reaction. The main advantage of this work is to link experimental works with numerical models of growth and bioluminescence in order to provide a

Photon hunting in the twilight zone: visual features of mesopelagic bioluminescent sharks.

Directory of Open Access Journals (Sweden)

Julien M Claes

Full Text Available The mesopelagic zone is a visual scene continuum in which organisms have developed various strategies to optimize photon capture. Here, we used light microscopy, stereology-assisted retinal topographic mapping, spectrophotometry and microspectrophotometry to investigate the visual ecology of deep-sea bioluminescent sharks [four etmopterid species (Etmopterus lucifer, E. splendidus, E. spinax and Trigonognathus kabeyai and one dalatiid species (Squaliolus aliae]. We highlighted a novel structure, a translucent area present in the upper eye orbit of Etmopteridae, which might be part of a reference system for counterillumination adjustment or acts as a spectral filter for camouflage breaking, as well as several ocular specialisations such as aphakic gaps and semicircular tapeta previously unknown in elasmobranchs. All species showed pure rod hexagonal mosaics with a high topographic diversity. Retinal specialisations, formed by shallow cell density gradients, may aid in prey detection and reflect lifestyle differences; pelagic species display areae centrales while benthopelagic and benthic species display wide and narrow horizontal streaks, respectively. One species (E. lucifer displays two areae within its horizontal streak that likely allows detection of conspecifics' elongated bioluminescent flank markings. Ganglion cell topography reveals less variation with all species showing a temporal area for acute frontal binocular vision. This area is dorsally extended in T. kabeyai, allowing this species to adjust the strike of its peculiar jaws in the ventro-frontal visual field. Etmopterus lucifer showed an additional nasal area matching a high rod density area. Peak spectral sensitivities of the rod visual pigments (λmax fall within the range 484-491 nm, allowing these sharks to detect a high proportion of photons present in their habitat. Comparisons with previously published data reveal ocular differences between bioluminescent and non-bioluminescent

Photon hunting in the twilight zone: visual features of mesopelagic bioluminescent sharks.

Science.gov (United States)

Claes, Julien M; Partridge, Julian C; Hart, Nathan S; Garza-Gisholt, Eduardo; Ho, Hsuan-Ching; Mallefet, Jérôme; Collin, Shaun P

2014-01-01

The mesopelagic zone is a visual scene continuum in which organisms have developed various strategies to optimize photon capture. Here, we used light microscopy, stereology-assisted retinal topographic mapping, spectrophotometry and microspectrophotometry to investigate the visual ecology of deep-sea bioluminescent sharks [four etmopterid species (Etmopterus lucifer, E. splendidus, E. spinax and Trigonognathus kabeyai) and one dalatiid species (Squaliolus aliae)]. We highlighted a novel structure, a translucent area present in the upper eye orbit of Etmopteridae, which might be part of a reference system for counterillumination adjustment or acts as a spectral filter for camouflage breaking, as well as several ocular specialisations such as aphakic gaps and semicircular tapeta previously unknown in elasmobranchs. All species showed pure rod hexagonal mosaics with a high topographic diversity. Retinal specialisations, formed by shallow cell density gradients, may aid in prey detection and reflect lifestyle differences; pelagic species display areae centrales while benthopelagic and benthic species display wide and narrow horizontal streaks, respectively. One species (E. lucifer) displays two areae within its horizontal streak that likely allows detection of conspecifics' elongated bioluminescent flank markings. Ganglion cell topography reveals less variation with all species showing a temporal area for acute frontal binocular vision. This area is dorsally extended in T. kabeyai, allowing this species to adjust the strike of its peculiar jaws in the ventro-frontal visual field. Etmopterus lucifer showed an additional nasal area matching a high rod density area. Peak spectral sensitivities of the rod visual pigments (λmax) fall within the range 484-491 nm, allowing these sharks to detect a high proportion of photons present in their habitat. Comparisons with previously published data reveal ocular differences between bioluminescent and non-bioluminescent deep

Isotropic-resolution linear-array-based photoacoustic computed tomography through inverse Radon transform

Science.gov (United States)

Li, Guo; Xia, Jun; Li, Lei; Wang, Lidai; Wang, Lihong V.

2015-03-01

Linear transducer arrays are readily available for ultrasonic detection in photoacoustic computed tomography. They offer low cost, hand-held convenience, and conventional ultrasonic imaging. However, the elevational resolution of linear transducer arrays, which is usually determined by the weak focus of the cylindrical acoustic lens, is about one order of magnitude worse than the in-plane axial and lateral spatial resolutions. Therefore, conventional linear scanning along the elevational direction cannot provide high-quality three-dimensional photoacoustic images due to the anisotropic spatial resolutions. Here we propose an innovative method to achieve isotropic resolutions for three-dimensional photoacoustic images through combined linear and rotational scanning. In each scan step, we first elevationally scan the linear transducer array, and then rotate the linear transducer array along its center in small steps, and scan again until 180 degrees have been covered. To reconstruct isotropic three-dimensional images from the multiple-directional scanning dataset, we use the standard inverse Radon transform originating from X-ray CT. We acquired a three-dimensional microsphere phantom image through the inverse Radon transform method and compared it with a single-elevational-scan three-dimensional image. The comparison shows that our method improves the elevational resolution by up to one order of magnitude, approaching the in-plane lateral-direction resolution. In vivo rat images were also acquired.

Specific storage and hydraulic conductivity tomography through the joint inversion of hydraulic heads and self-potential data

Science.gov (United States)

Ahmed, A. Soueid; Jardani, A.; Revil, A.; Dupont, J. P.

2016-03-01

Transient hydraulic tomography is used to image the heterogeneous hydraulic conductivity and specific storage fields of shallow aquifers using time series of hydraulic head data. Such ill-posed and non-unique inverse problem can be regularized using some spatial geostatistical characteristic of the two fields. In addition to hydraulic heads changes, the flow of water, during pumping tests, generates an electrical field of electrokinetic nature. These electrical field fluctuations can be passively recorded at the ground surface using a network of non-polarizing electrodes connected to a high impedance (> 10 MOhm) and sensitive (0.1 mV) voltmeter, a method known in geophysics as the self-potential method. We perform a joint inversion of the self-potential and hydraulic head data to image the hydraulic conductivity and specific storage fields. We work on a 3D synthetic confined aquifer and we use the adjoint state method to compute the sensitivities of the hydraulic parameters to the hydraulic head and self-potential data in both steady-state and transient conditions. The inverse problem is solved using the geostatistical quasi-linear algorithm framework of Kitanidis. When the number of piezometers is small, the record of the transient self-potential signals provides useful information to characterize the hydraulic conductivity and specific storage fields. These results show that the self-potential method reveals the heterogeneities of some areas of the aquifer, which could not been captured by the tomography based on the hydraulic heads alone. In our analysis, the improvement on the hydraulic conductivity and specific storage estimations were based on perfect knowledge of electrical resistivity field. This implies that electrical resistivity will need to be jointly inverted with the hydraulic parameters in future studies and the impact of its uncertainty assessed with respect to the final tomograms of the hydraulic parameters.

EDITORIAL: Inverse Problems in Engineering

Science.gov (United States)

West, Robert M.; Lesnic, Daniel

2007-01-01

Presented here are 11 noteworthy papers selected from the Fifth International Conference on Inverse Problems in Engineering: Theory and Practice held in Cambridge, UK during 11-15 July 2005. The papers have been peer-reviewed to the usual high standards of this journal and the contributions of reviewers are much appreciated. The conference featured a good balance of the fundamental mathematical concepts of inverse problems with a diverse range of important and interesting applications, which are represented here by the selected papers. Aspects of finite-element modelling and the performance of inverse algorithms are investigated by Autrique et al and Leduc et al. Statistical aspects are considered by Emery et al and Watzenig et al with regard to Bayesian parameter estimation and inversion using particle filters. Electrostatic applications are demonstrated by van Berkel and Lionheart and also Nakatani et al. Contributions to the applications of electrical techniques and specifically electrical tomographies are provided by Wakatsuki and Kagawa, Kim et al and Kortschak et al. Aspects of inversion in optical tomography are investigated by Wright et al and Douiri et al. The authors are representative of the worldwide interest in inverse problems relating to engineering applications and their efforts in producing these excellent papers will be appreciated by many readers of this journal.

The origins of marine bioluminescence: turning oxygen defence mechanisms into deep-sea communication tools.

Science.gov (United States)

Rees, J F; de Wergifosse, B; Noiset, O; Dubuisson, M; Janssens, B; Thompson, E M

1998-04-01

Bioluminescence, the emission of ecologically functional light by living organisms, emerged independently on several occasions, yet the evolutionary origins of most bioluminescent systems remain obscure. We propose that the luminescent substrates of the luminous reactions (luciferins) are the evolutionary core of most systems, while luciferases, the enzymes catalysing the photogenic oxidation of the luciferin, serve to optimise the expression of the endogenous chemiluminescent properties of the luciferin. Coelenterazine, a luciferin occurring in many marine bioluminescent groups, has strong antioxidative properties as it is highly reactive with reactive oxygen species such as the superoxide anion or peroxides. We suggest that the primary function of coelenterazine was originally the detoxification of the deleterious oxygen derivatives. The functional shift from its antioxidative to its light-emitting function might have occurred when the strength of selection for antioxidative defence mechanisms decreased. This might have been made possible when marine organisms began colonising deeper layers of the oceans, where exposure to oxidative stress is considerably reduced because of reduced light irradiance and lower oxygen levels. A reduction in metabolic activity with increasing depth would also have decreased the endogenous production of reactive oxygen species. Therefore, in these organisms, mechanisms for harnessing the chemiluminescence of coelenterazine in specialised organs could have developed, while the beneficial antioxidative properties were maintained in other tissues. The full range of graded irradiance in the mesopelagic zone, where the majority of organisms are bioluminescent, would have provided a continuum for the selection and improvement of proto-bioluminescence. Although the requirement for oxygen or reactive oxygen species observed in bioluminescent systems reflects the high energy required to produce visible light, it may suggest that oxygen

Effect of irradiation on detection of bacteria in dehydrated vegetables with ATP bioluminescence assay

International Nuclear Information System (INIS)

Xiao Huan; Luo Shishi; Wang Zegang; Feng Min; Zhu Jiating; Chen Xiulan; Zhai Jianqing

2011-01-01

ATP bioluminescence intensity of 4 kinds of irradiated dehydrated vegetables was inconsistent with the bacteria number, the reasons were investigated in this paper. Results showed that irradiation had little effect on background luminescence, and there was no effect on luciferase-luminous system. When irradiation killed the bacteria, the ATPase activity also decreased. As a result, the ATP content in bacteria didn't decreased with the killed of bacteria, which contributed to the increase of free ATP in ATP extract and finally led to the disagreement between the bioluminescence intensity and the actual number of bacteria. When the free ATP in the dehydrated vegetable was removed, the bioluminescence intensity of ATP extract was consistent with the actual number of bacteria in irradiated dehydrated vegetable and ATP bioluminescence technology could be used in bacteria detection of irradiated samples. (authors)

Inverse problems for Maxwell's equations

CERN Document Server

Romanov, V G

1994-01-01

The Inverse and Ill-Posed Problems Series is a series of monographs publishing postgraduate level information on inverse and ill-posed problems for an international readership of professional scientists and researchers. The series aims to publish works which involve both theory and applications in, e.g., physics, medicine, geophysics, acoustics, electrodynamics, tomography, and ecology.

Characterization of an anthraquinone fluor from the bioluminescent, pelagic polychaete Tomopteris

Science.gov (United States)

Francis, Warren R; Powers, Meghan L; Haddock, Steven H D

2014-01-01

Tomopteris is a cosmopolitan genus of polychaetes. Many species produce yellow luminescence in the parapodia when stimulated. Yellow bioluminescence is rare in the ocean, and the components of this luminescent reaction have not been identified. Only a brief description, half a century ago, noted fluorescence in the parapodia with a remarkably similar spectrum to the bioluminescence, which suggested that it may be the luciferin or terminal light-emitter. Here, we report the isolation of the fluorescent yellow–orange pigment found in the luminous exudate and in the body of the animals. Liquid chromatography-mass spectrometry revealed the mass to be 270 m/z with a molecular formula of C15H10O5, which ultimately was shown to be aloe-emodin, an anthraquinone previously found in plants. We speculate that aloe-emodin could be a factor for resonant-energy transfer or the oxyluciferin for Tomopteris bioluminescence. PMID:24760626

Total evidence phylogeny and the evolution of adult bioluminescence in fireflies (Coleoptera: Lampyridae).

Science.gov (United States)

Martin, Gavin J; Branham, Marc A; Whiting, Michael F; Bybee, Seth M

2017-02-01

Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade. The ancestral state of adult bioluminescence is recovered as non-bioluminescent with one to six gains and five to ten subsequent losses. The monophyly of the family, as well as the subfamilies is also tested. Ototretinae, Cyphonocerinae, Luciolinae (incl. Pristolycus), Amydetinae, "cheguevarinae" sensu Jeng 2008, and Photurinae are highly supported as monophyletic. With the exception of four taxa, Lampyrinae is also recovered as monophyletic with high support. Based on phylogenetic and morphological data Lamprohiza, Phausis, and Lamprigera are transferred to Lampyridae incertae sedis. Copyright © 2016 Elsevier Inc. All rights reserved.

Bioluminescent imaging: a critical tool in pre-clinical oncology research.

LENUS (Irish Health Repository)

O'Neill, Karen

2010-02-01

Bioluminescent imaging (BLI) is a non-invasive imaging modality widely used in the field of pre-clinical oncology research. Imaging of small animal tumour models using BLI involves the generation of light by luciferase-expressing cells in the animal following administration of substrate. This light may be imaged using an external detector. The technique allows a variety of tumour-associated properties to be visualized dynamically in living models. The increasing use of BLI as a small-animal imaging modality has led to advances in the development of xenogeneic, orthotopic, and genetically engineered animal models expressing luciferase genes. This review aims to provide insight into the principles of BLI and its applications in cancer research. Many studies to assess tumour growth and development, as well as efficacy of candidate therapeutics, have been performed using BLI. More recently, advances have also been made using bioluminescent imaging in studies of protein-protein interactions, genetic screening, cell-cycle regulators, and spontaneous cancer development. Such novel studies highlight the versatility and potential of bioluminescent imaging in future oncological research.

Surface waves tomography and non-linear inversion in the southeast Carpathians

International Nuclear Information System (INIS)

Raykova, R.B.; Panza, G.F.

2005-11-01

A set of shear-wave velocity models of the lithosphere-asthenosphere system in the southeast Carpathians is determined by the non-linear inversion of surface wave group velocity data, obtained from a tomographic analysis. The local dispersion curves are assembled for the period range 7 s - 150 s, combining regional group velocity measurements and published global Rayleigh wave dispersion data. The lithosphere-asthenosphere velocity structure is reliably reconstructed to depths of about 250 km. The thickness of the lithosphere in the region varies from about 120 km to 250 km and the depth of the asthenosphere between 150 km and 250 km. Mantle seismicity concentrates where the high velocity lid is detected just below the Moho. The obtained results are in agreement with recent seismic refraction, receiver function, and travel time P-wave tomography investigations in the region. The similarity among the results obtained from different kinds of structural investigations (including the present work) highlights some new features of the lithosphere-asthenosphere system in southeast Carpathians, as the relatively thin crust under Transylvania basin and Vrancea zone. (author)

Proximal methods for the resolution of inverse problems: application to positron emission tomography

International Nuclear Information System (INIS)

Pustelnik, N.

2010-12-01

The objective of this work is to propose reliable, efficient and fast methods for minimizing convex criteria, that are found in inverse problems for imagery. We focus on restoration/reconstruction problems when data is degraded with both a linear operator and noise, where the latter is not assumed to be necessarily additive.The reliability of the method is ensured through the use of proximal algorithms, the convergence of which is guaranteed when a convex criterion is considered. Efficiency is sought through the choice of criteria adapted to the noise characteristics, the linear operators and the image specificities. Of particular interest are regularization terms based on total variation and/or sparsity of signal frame coefficients. As a consequence of the use of frames, two approaches are investigated, depending on whether the analysis or the synthesis formulation is chosen. Fast processing requirements lead us to consider proximal algorithms with a parallel structure. Theoretical results are illustrated on several large size inverse problems arising in image restoration, stereoscopy, multi-spectral imagery and decomposition into texture and geometry components. We focus on a particular application, namely Positron Emission Tomography (PET), which is particularly difficult because of the presence of a projection operator combined with Poisson noise, leading to highly corrupted data. To optimize the quality of the reconstruction, we make use of the spatio-temporal characteristics of brain tissue activity. (author)

Dynamic Inversion for Hydrological Process Monitoring with Electrical Resistance Tomography Under Model Uncertainty

Energy Technology Data Exchange (ETDEWEB)

Lehikoinen, A.; Huttunen, J.M.J.; Finsterle, S.; Kowalsky, M.B.; Kaipio, J.P.

2009-08-01

We propose an approach for imaging the dynamics of complex hydrological processes. The evolution of electrically conductive fluids in porous media is imaged using time-lapse electrical resistance tomography. The related dynamic inversion problem is solved using Bayesian filtering techniques, that is, it is formulated as a sequential state estimation problem in which the target is an evolving posterior probability density of the system state. The dynamical inversion framework is based on the state space representation of the system, which involves the construction of a stochastic evolution model and an observation model. The observation model used in this paper consists of the complete electrode model for ERT, with Archie's law relating saturations to electrical conductivity. The evolution model is an approximate model for simulating flow through partially saturated porous media. Unavoidable modeling and approximation errors in both the observation and evolution models are considered by computing approximate statistics for these errors. These models are then included in the construction of the posterior probability density of the estimated system state. This approximation error method allows the use of approximate - and therefore computationally efficient - observation and evolution models in the Bayesian filtering. We consider a synthetic example and show that the incorporation of an explicit model for the model uncertainties in the state space representation can yield better estimates than a frame-by-frame imaging approach.

Comparison of Acute Toxicity of Algal Metabolites Using Bioluminescence Inhibition Assay

Directory of Open Access Journals (Sweden)

Hansa Jeswani

2015-01-01

Full Text Available Microalgae are reported to degrade hazardous compounds. However, algae, especially cyanobacteria are known to produce secondary metabolites which may be toxic to flora, fauna and human beings. The aim of this study was selection of an appropriate algal culture for biological treatment of biomass gasification wastewater based on acute toxicity considerations. The three algae that were selected were Spirulina sp., Scenedesmus abundans and a fresh water algal consortium. Acute toxicity of the metabolites produced by these algal cultures was tested at the end of log phase using the standard bioluminescence inhibition assay based on Vibrio fischeri NRRLB 11174. Scenedesmus abundans and a fresh water algal consortium dominated by cyanobacteria such as Phormidium, Chroococcus and Oscillatoria did not release much toxic metabolites at the end of log phase and caused only about 20% inhibition in bioluminescence. In comparison, Spirulina sp. released toxic metabolites and caused 50% bioluminescence inhibition at 3/5 times dilution of the culture supernatant (EC50.

A robust probabilistic approach for variational inversion in shallow water acoustic tomography

International Nuclear Information System (INIS)

Berrada, M; Badran, F; Crépon, M; Thiria, S; Hermand, J-P

2009-01-01

This paper presents a variational methodology for inverting shallow water acoustic tomography (SWAT) measurements. The aim is to determine the vertical profile of the speed of sound c(z), knowing the acoustic pressures generated by a frequency source and collected by a sparse vertical hydrophone array (VRA). A variational approach that minimizes a cost function measuring the distance between observations and their modeled equivalents is used. A regularization term in the form of a quadratic restoring term to a background is also added. To avoid inverting the variance–covariance matrix associated with the above-weighted quadratic background, this work proposes to model the sound speed vector using probabilistic principal component analysis (PPCA). The PPCA introduces an optimum reduced number of non-correlated latent variables η, which determine a new control vector and a new regularization term, expressed as η T η. The PPCA represents a rigorous formalism for the use of a priori information and allows an efficient implementation of the variational inverse method

SU-C-303-04: Evaluation of On- and Off-Line Bioluminescence Tomography System for Focal Irradiation Guidance

Energy Technology Data Exchange (ETDEWEB)

Zhang, B; Wang, K; Reyes, J; Tran, P; Wong, J [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, MD (United States); Iordachita, I [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, MD (United States)

2015-06-15

Purpose: We have developed offline and on-board bioluminescence tomography(BLT) systems for the small animal radiation research platform(SARRP) for radiation guidance of soft tissue targets. We investigated the effectiveness of offline BLT guidance. Methods: CBCT is equipped on both the offline BLT system and SARRP that are 10 ft. apart. To evaluate the setup error during animal transport between the two systems, we implanted a luminescence source in the abdomen of anesthetized mice. Five mice were studied. After CBCT was acquired on both systems, source centers and correlation coefficients were calculated. CBCT was also used to generate object mesh for BLT reconstruction. To assess target localization, we compared the localization of the luminescence source based on (1)on-board SARRP BLT and CBCT, (2)offline BLT and CBCT, and (3)offline BLT and SARRP CBCT. The 3rd comparison examines if an offline BLT system can be used to guide radiation when there is minimal target contrast in CBCT. Results: Our CBCT results show the offset of the light source center can be maintained within 0.2 mm during animal transport. The center of mass(CoM) of the light source reconstructed by the offline BLT has an offset of 1.0 ± 0.4 mm from the ‘true’ CoM as derived from the SARRP CBCT. The results compare well with the offset of 1.0 ± 0.2 mm using on-line BLT. Conclusion: With CBCT information provided by the SARRP and effective animal immobilization during transport, these findings support the use of offline BLT in close vicinity for accurate soft tissue target localization for irradiation. However, the disadvantage of the off-line system is reduced efficiency as care is required to maintain stable animal transport. We envisage a dual use system where the on-board arrangement allows convenient access to CBCT and avoids disturbance of animal setup. The off-line capability would support standalone longitudinal imaging studies. The work is supported by NIH R01CA158100 and Xstrahl

Bioluminescent hydrocarbonclastic bacteria of the Niger Delta ...

African Journals Online (AJOL)

Utilization of three petroleum hydrocarbons (Mobil SAE 40 Engine Oil, Diesel and Bonny light Crude Oil) by four bioluminescent bacteria (Vibrio harveyi, V. fisheri, Photobacterium leiognathi and P. Phosphoreum isolated from the Bonny estuary in the Niger Delta, Nigeria was investigated. Microbial utilization was monitored ...

In vivo quantitative imaging of point-like bioluminescent and fluorescent sources: Validation studies in phantoms and small animals post mortem

Science.gov (United States)

Comsa, Daria Craita

2008-10-01

There is a real need for improved small animal imaging techniques to enhance the development of therapies in which animal models of disease are used. Optical methods for imaging have been extensively studied in recent years, due to their high sensitivity and specificity. Methods like bioluminescence and fluorescence tomography report promising results for 3D reconstructions of source distributions in vivo. However, no standard methodology exists for optical tomography, and various groups are pursuing different approaches. In a number of studies on small animals, the bioluminescent or fluorescent sources can be reasonably approximated as point or line sources. Examples include images of bone metastases confined to the bone marrow. Starting with this premise, we propose a simpler, faster, and inexpensive technique to quantify optical images of point-like sources. The technique avoids the computational burden of a tomographic method by using planar images and a mathematical model based on diffusion theory. The model employs in situ optical properties estimated from video reflectometry measurements. Modeled and measured images are compared iteratively using a Levenberg-Marquardt algorithm to improve estimates of the depth and strength of the bioluminescent or fluorescent inclusion. The performance of the technique to quantify bioluminescence images was first evaluated on Monte Carlo simulated data. Simulated data also facilitated a methodical investigation of the effect of errors in tissue optical properties on the retrieved source depth and strength. It was found that, for example, an error of 4 % in the effective attenuation coefficient led to 4 % error in the retrieved depth for source depths of up to 12mm, while the error in the retrieved source strength increased from 5.5 % at 2mm depth, to 18 % at 12mm depth. Experiments conducted on images from homogeneous tissue-simulating phantoms showed that depths up to 10mm could be estimated within 8 %, and the relative

Ray-tracing traveltime tomography versus wave-equation traveltime inversion for near-surface seismic land data

KAUST Repository

Fu, Lei

2017-05-11

Full-waveform inversion of land seismic data tends to get stuck in a local minimum associated with the waveform misfit function. This problem can be partly mitigated by using an initial velocity model that is close to the true velocity model. This initial starting model can be obtained by inverting traveltimes with ray-tracing traveltime tomography (RT) or wave-equation traveltime (WT) inversion. We have found that WT can provide a more accurate tomogram than RT by inverting the first-arrival traveltimes, and empirical tests suggest that RT is more sensitive to the additive noise in the input data than WT. We present two examples of applying WT and RT to land seismic data acquired in western Saudi Arabia. One of the seismic experiments investigated the water-table depth, and the other one attempted to detect the location of a buried fault. The seismic land data were inverted by WT and RT to generate the P-velocity tomograms, from which we can clearly identify the water table depth along the seismic survey line in the first example and the fault location in the second example.

Autonomous bioluminescent expression of the bacterial luciferase gene cassette (lux in a mammalian cell line.

Directory of Open Access Journals (Sweden)

Dan M Close

Full Text Available The bacterial luciferase (lux gene cassette consists of five genes (luxCDABE whose protein products synergistically generate bioluminescent light signals exclusive of supplementary substrate additions or exogenous manipulations. Historically expressible only in prokaryotes, the lux operon was re-synthesized through a process of multi-bicistronic, codon-optimization to demonstrate for the first time self-directed bioluminescence emission in a mammalian HEK293 cell line in vitro and in vivo.Autonomous in vitro light production was shown to be 12-fold greater than the observable background associated with untransfected control cells. The availability of reduced riboflavin phosphate (FMNH(2 was identified as the limiting bioluminescence substrate in the mammalian cell environment even after the addition of a constitutively expressed flavin reductase gene (frp from Vibrio harveyi. FMNH(2 supplementation led to a 151-fold increase in bioluminescence in cells expressing mammalian codon-optimized luxCDE and frp genes. When injected subcutaneously into nude mice, in vivo optical imaging permitted near instantaneous light detection that persisted independently for the 60 min length of the assay with negligible background.The speed, longevity, and self-sufficiency of lux expression in the mammalian cellular environment provides a viable and powerful alternative for real-time target visualization not currently offered by existing bioluminescent and fluorescent imaging technologies.

Continuous, real-time bioimaging of chemical bioavailability and toxicology using autonomously bioluminescent human cell lines

Science.gov (United States)

Xu, Tingting; Close, Dan M.; Webb, James D.; Price, Sarah L.; Ripp, Steven A.; Sayler, Gary S.

2013-05-01

Bioluminescent imaging is an emerging biomedical surveillance strategy that uses external cameras to detect in vivo light generated in small animal models of human physiology or in vitro light generated in tissue culture or tissue scaffold mimics of human anatomy. The most widely utilized of reporters is the firefly luciferase (luc) gene; however, it generates light only upon addition of a chemical substrate, thus only generating intermittent single time point data snapshots. To overcome this disadvantage, we have demonstrated substrate-independent bioluminescent imaging using an optimized bacterial bioluminescence (lux) system. The lux reporter produces bioluminescence autonomously using components found naturally within the cell, thereby allowing imaging to occur continuously and in real-time over the lifetime of the host. We have validated this technology in human cells with demonstrated chemical toxicological profiling against exotoxin exposures at signal strengths comparable to existing luc systems (~1.33 × 107 photons/second). As a proof-in-principle demonstration, we have engineered breast carcinoma cells to express bioluminescence for real-time screening of endocrine disrupting chemicals and validated detection of 17β-estradiol (EC50 = ~ 10 pM). These and other applications of this new reporter technology will be discussed as potential new pathways towards improved models of target chemical bioavailability, toxicology, efficacy, and human safety.

Image analyzing method to evaluate in situ bioluminescence from an obligate anaerobe cultivated under various dissolved oxygen concentrations.

Science.gov (United States)

Ninomiya, Kazuaki; Yamada, Ryuji; Matsumoto, Masami; Fukiya, Satoru; Katayama, Takane; Ogino, Chiaki; Shimizu, Nobuaki

2013-02-01

An image analyzing method was developed to evaluate in situ bioluminescence expression, without exposing the culture sample to the ambient oxygen atmosphere. Using this method, we investigated the effect of dissolved oxygen concentration on bioluminescence from an obligate anaerobe Bifidobacterium longum expressing bacterial luciferase which catalyzes an oxygen-requiring bioluminescent reaction. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Effect of number of of projections on inverse radon transform based image reconstruction by using filtered back-projection for parallel beam transmission tomography

International Nuclear Information System (INIS)

Qureshi, S.A.; Mirza, S.M.; Arif, M.

2007-01-01

This paper present the effect of number of projections on inverse Radon transform (IRT) estimation using filtered back-projection (FBP) technique for parallel beam transmission tomography. The head phantom and the lung phantom have been used in this work. Various filters used in this study include Ram-Lak, Shepp-Logan, Cosin, Hamming and Hanning filters. The slices have been reconstructed by increasing the number of projections through parallel beam transmission tomography keeping the projections uniformly distributed. The Euclidean and Mean Squared errors and peak signal-to-noise ratio (PSNR) have been analyzed for their sensitiveness as functions of number of projections. It has found that image quality improves with the number of projections but at the cost of the computer time. The error has been minimized to get the best approximation of inverse Radon transform (IRT) as the number of projections is enhanced. The value of PSNR has been found to increase from 8.20 to 24.53 dB as the number of projections is raised from 5 to 180 for head phantom. (author)

The Use of Stimulable Bioluminescence From Dinoflagellates as a Means of Detecting Toxicity in the Marine Environment

Science.gov (United States)

1993-03-01

AND SSTýTL FUNDINCG NUMI)) W, TIHE USE OF STIMt LABILE BIOLUMINESCENCE FROM DI NOIFLAGELLATk. PH: M1E69 AS A MEAN’S OF DETrECTING ToxicITY IN THE...bioluminescence dinoflagellates for asseossmnent of toxic effects when exposed to a single tox~icant or mixture. Successful use of this type of bioassav... tributyltin chloride (TFITCI), Copper (11) Sulfate (CuSO 4 I. zinc sulfate (ZnSO4 ), or storm drain effluent. Stimulable bioluminescence was measured at

Detection of organic compounds with whole-cell bioluminescent bioassays.

Science.gov (United States)

Xu, Tingting; Close, Dan; Smartt, Abby; Ripp, Steven; Sayler, Gary

2014-01-01

Natural and manmade organic chemicals are widely deposited across a diverse range of ecosystems including air, surface water, groundwater, wastewater, soil, sediment, and marine environments. Some organic compounds, despite their industrial values, are toxic to living organisms and pose significant health risks to humans and wildlife. Detection and monitoring of these organic pollutants in environmental matrices therefore is of great interest and need for remediation and health risk assessment. Although these detections have traditionally been performed using analytical chemical approaches that offer highly sensitive and specific identification of target compounds, these methods require specialized equipment and trained operators, and fail to describe potential bioavailable effects on living organisms. Alternatively, the integration of bioluminescent systems into whole-cell bioreporters presents a new capacity for organic compound detection. These bioreporters are constructed by incorporating reporter genes into catabolic or signaling pathways that are present within living cells and emit a bioluminescent signal that can be detected upon exposure to target chemicals. Although relatively less specific compared to analytical methods, bioluminescent bioassays are more cost-effective, more rapid, can be scaled to higher throughput, and can be designed to report not only the presence but also the bioavailability of target substances. This chapter reviews available bacterial and eukaryotic whole-cell bioreporters for sensing organic pollutants and their applications in a variety of sample matrices.

Smartphone-based low light detection for bioluminescence application

Science.gov (United States)

We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation ...

Molecular phylogeny of Neotropical bioluminescent beetles (Coleoptera: Elateroidea) in southern and central Brazil.

Science.gov (United States)

Amaral, D T; Arnoldi, F G C; Rosa, S P; Viviani, V R

2014-08-01

Bioluminescence in beetles is found mainly in the Elateroidea superfamily (Elateridae, Lampyridae and Phengodidae). The Neotropical region accounts for the richest diversity of bioluminescent species in the world with about 500 described species, most occurring in the Amazon, Atlantic rainforest and Cerrado (savanna) ecosystems in Brazil. The origin and evolution of bioluminescence, as well as the taxonomic status of several Neotropical taxa in these families remains unclear. In order to contribute to a better understanding of the phylogeny and evolution of bioluminescent Elateroidea we sequenced and analyzed sequences of mitochondrial NADH2 and the nuclear 28S genes and of the cloned luciferase sequences of Brazilian species belonging to the following genera: (Lampyridae) Macrolampis, Photuris, Amydetes, Bicellonycha, Aspisoma, Lucidota, Cratomorphus; (Elateridae) Conoderus, Pyrophorus, Hapsodrilus, Pyrearinus, Fulgeochlizus; and (Phengodidae) Pseudophengodes, Phrixothrix, Euryopa and Brasilocerus. Our study supports a closer phylogenetic relationship between Elateridae and Phengodidae as other molecular studies, in contrast with previous morphologic and molecular studies that clustered Lampyridae/Phengodidae. Molecular data also supported division of the Phengodinae subfamily into the tribes Phengodini and Mastinocerini. The position of the genus Amydetes supports the status of the Amydetinae as a subfamily. The genus Euryopa is included in the Mastinocerini tribe within the Phengodinae/Phengodidae. Copyright © 2013 John Wiley & Sons, Ltd.

Triple Bioluminescence Imaging for In Vivo Monitoring of Cellular Processes

Directory of Open Access Journals (Sweden)

Casey A Maguire

2013-01-01

Full Text Available Bioluminescence imaging (BLI has shown to be crucial for monitoring in vivo biological processes. So far, only dual bioluminescence imaging using firefly (Fluc and Renilla or Gaussia (Gluc luciferase has been achieved due to the lack of availability of other efficiently expressed luciferases using different substrates. Here, we characterized a codon-optimized luciferase from Vargula hilgendorfii (Vluc as a reporter for mammalian gene expression. We showed that Vluc can be multiplexed with Gluc and Fluc for sequential imaging of three distinct cellular phenomena in the same biological system using vargulin, coelenterazine, and D-luciferin substrates, respectively. We applied this triple imaging system to monitor the effect of soluble tumor necrosis factor-related apoptosis-inducing ligand (sTRAIL delivered using an adeno-associated viral vector (AAV on brain tumors in mice. Vluc imaging showed efficient sTRAIL gene delivery to the brain, while Fluc imaging revealed a robust antiglioma therapy. Further, nuclear factor-κB (NF-κB activation in response to sTRAIL binding to glioma cells death receptors was monitored by Gluc imaging. This work is the first demonstration of trimodal in vivo bioluminescence imaging and will have a broad applicability in many different fields including immunology, oncology, virology, and neuroscience.

Bacteria as part of bioluminescence emission at the deep ANTARES station (North-Western Mediterranean Sea) during a one-year survey

Science.gov (United States)

Martini, S.; Michotey, V.; Casalot, L.; Bonin, P.; Guasco, S.; Garel, M.; Tamburini, C.

2016-10-01

Bioluminescent bacteria have been studied during a one-year survey in 2011 at the deep ANTARES site (Northwestern Mediterranean Sea, 2000 m depth). The neutrino underwater telescope ANTARES, located at this station, has been used to record the bioluminescence at the same depth. Together with these data, environmental variables (potential temperature, salinity, nutrients, dissolved organic carbon and oxygen) have been characterized in water samples. The year 2011 was characterized by relatively stable conditions, as revealed by minor variability in the monitored oceanographic variables, by low bioluminescence and low current speed. This suggests weak eukaryote participation and mainly non-stimulated light emission. Hence, no processes of dense water have affected the ANTARES station during this survey. Abundance of bioluminescent bacteria belonging to Photobacterium genus, measured by qPCR of the luxF gene, ranged from 1.4×102 to 7.2×102 genes mL-1. Their effective activity was confirmed through mRNA luxF quantification. Our results reveal that bioluminescent bacteria appeared more active than the total counterpart of bacteria, suggesting an ecological benefit of this feature such as favoring interaction with macro-organisms. Moreover, these results show that part of the bioluminescence, recorded at 2000 m depth over one year, could be due to bioluminescent bacteria in stable hydrological conditions.

Formulas in inverse and ill-posed problems

CERN Document Server

Anikonov, Yu E

1997-01-01

The Inverse and Ill-Posed Problems Series is a series of monographs publishing postgraduate level information on inverse and ill-posed problems for an international readership of professional scientists and researchers. The series aims to publish works which involve both theory and applications in, e.g., physics, medicine, geophysics, acoustics, electrodynamics, tomography, and ecology.

Time-reversal and Bayesian inversion

Science.gov (United States)

Debski, Wojciech

2017-04-01

Probabilistic inversion technique is superior to the classical optimization-based approach in all but one aspects. It requires quite exhaustive computations which prohibit its use in huge size inverse problems like global seismic tomography or waveform inversion to name a few. The advantages of the approach are, however, so appealing that there is an ongoing continuous afford to make the large inverse task as mentioned above manageable with the probabilistic inverse approach. One of the perspective possibility to achieve this goal relays on exploring the internal symmetry of the seismological modeling problems in hand - a time reversal and reciprocity invariance. This two basic properties of the elastic wave equation when incorporating into the probabilistic inversion schemata open a new horizons for Bayesian inversion. In this presentation we discuss the time reversal symmetry property, its mathematical aspects and propose how to combine it with the probabilistic inverse theory into a compact, fast inversion algorithm. We illustrate the proposed idea with the newly developed location algorithm TRMLOC and discuss its efficiency when applied to mining induced seismic data.

Autonomously bioluminescent mammalian cells for continuous and real-time monitoring of cytotoxicity.

Science.gov (United States)

Xu, Tingting; Close, Dan M; Webb, James D; Ripp, Steven A; Sayler, Gary S

2013-10-28

Mammalian cell-based in vitro assays have been widely employed as alternatives to animal testing for toxicological studies but have been limited due to the high monetary and time costs of parallel sample preparation that are necessitated due to the destructive nature of firefly luciferase-based screening methods. This video describes the utilization of autonomously bioluminescent mammalian cells, which do not require the destructive addition of a luciferin substrate, as an inexpensive and facile method for monitoring the cytotoxic effects of a compound of interest. Mammalian cells stably expressing the full bacterial bioluminescence (luxCDABEfrp) gene cassette autonomously produce an optical signal that peaks at 490 nm without the addition of an expensive and possibly interfering luciferin substrate, excitation by an external energy source, or destruction of the sample that is traditionally performed during optical imaging procedures. This independence from external stimulation places the burden for maintaining the bioluminescent reaction solely on the cell, meaning that the resultant signal is only detected during active metabolism. This characteristic makes the lux-expressing cell line an excellent candidate for use as a biosentinel against cytotoxic effects because changes in bioluminescent production are indicative of adverse effects on cellular growth and metabolism. Similarly, the autonomous nature and lack of required sample destruction permits repeated imaging of the same sample in real-time throughout the period of toxicant exposure and can be performed across multiple samples using existing imaging equipment in an automated fashion.

Near-Infrared Diffuse Optical Tomography

Directory of Open Access Journals (Sweden)

A. H. Hielscher

2002-01-01

Full Text Available Diffuse optical tomography (DOT is emerging as a viable new biomedical imaging modality. Using near-infrared (NIR light, this technique probes absorption as well as scattering properties of biological tissues. First commercial instruments are now available that allow users to obtain cross-sectional and volumetric views of various body parts. Currently, the main applications are brain, breast, limb, joint, and fluorescence/bioluminescence imaging. Although the spatial resolution is limited when compared with other imaging modalities, such as magnetic resonance imaging (MRI or X-ray computerized tomography (CT, DOT provides access to a variety of physiological parameters that otherwise are not accessible, including sub-second imaging of hemodynamics and other fast-changing processes. Furthermore, DOT can be realized in compact, portable instrumentation that allows for bedside monitoring at relatively low cost. In this paper, we present an overview of current state-of-the -art technology, including hardware and image-reconstruction algorithms, and focus on applications in brain and joint imaging. In addition, we present recent results of work on optical tomographic imaging in small animals.

Efficient generalized Golub-Kahan based methods for dynamic inverse problems

Science.gov (United States)

Chung, Julianne; Saibaba, Arvind K.; Brown, Matthew; Westman, Erik

2018-02-01

We consider efficient methods for computing solutions to and estimating uncertainties in dynamic inverse problems, where the parameters of interest may change during the measurement procedure. Compared to static inverse problems, incorporating prior information in both space and time in a Bayesian framework can become computationally intensive, in part, due to the large number of unknown parameters. In these problems, explicit computation of the square root and/or inverse of the prior covariance matrix is not possible, so we consider efficient, iterative, matrix-free methods based on the generalized Golub-Kahan bidiagonalization that allow automatic regularization parameter and variance estimation. We demonstrate that these methods for dynamic inversion can be more flexible than standard methods and develop efficient implementations that can exploit structure in the prior, as well as possible structure in the forward model. Numerical examples from photoacoustic tomography, space-time deblurring, and passive seismic tomography demonstrate the range of applicability and effectiveness of the described approaches. Specifically, in passive seismic tomography, we demonstrate our approach on both synthetic and real data. To demonstrate the scalability of our algorithm, we solve a dynamic inverse problem with approximately 43 000 measurements and 7.8 million unknowns in under 40 s on a standard desktop.

Assessing the bioavailability of organic contaminants using a novel bioluminescent biosensor

International Nuclear Information System (INIS)

Keane, A.; Phoenix, P.; Lau, P.C.K.; Ghoshal, S.

2002-01-01

The limited rate and extent of biodegradation in contaminated soils is often attributed to a lack of bioavailability of hydrophobic organic compounds. To date, the majority of studies aimed at assessing bioavailability and modes of bacterial uptake have relied upon quantification of microbial degradation rates in comparison to rates of dissolution or desorption in corresponding abiotic systems. Several studies have indicated the possibility of a direct uptake mechanism for sorbed or separate phase compounds. However, there is a lack of direct evidence to support these claims. To address the need for a direct measurement technique for microbial bioavailability, we have constructed a whole-cell bioluminescent biosensor, Pseudomonas putida F1G4 (PpF1G4), by fusing lux genes that encode for bioluminescence to the solvent efflux pump (sep) promoter element in PpF1G4, which is induced by the presence of target organic compounds. When the biosensor microorganism is exposed to an inducing compound, the bioluminescence system is activated and the cell produces an intensity of visible light (λ = 495 nm) that is directly related to the level of exposure to the contaminant. Batch experiments were carried out to assess whether the biosensor is able to sense the presence of toluene, a representative target compound, contained in a NAPL. Preliminary results show that while PpF1G4 responds to toluene in the aqueous phase, the biosensor does not appear to emit a significant bioluminescence signal in response to the toluene present in the NAPL. Ongoing research is focusing on optimizing the experimental procedure to fully explore this issue. (author)

The application of superweak bioluminescence on freshness degree of chicken egg

International Nuclear Information System (INIS)

Zhao Hongxia; Li Guochen; Li Qiangzheng; Li Juan

2007-01-01

The luminescence of chicken egg in storage is studied by a detection system of superweak bioluminescence. The results show that egg has the strongest vigour on the third day after it is laid, subsequently the luminescence presents decay with oscillation. These eggs, which have been stored for 3 days, are most suitable for hatching. Different eggs have different luminescence intensities depending on the vigour of the egg. The stronger the vigour of the egg is, the more intensive the luminescence is. Superweak bioluminescence as a comprehensive index of biology and biochemistry response can be used for inspecting the freshness degree of the egg, and the test is nondestructive and sensitive

The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium

Directory of Open Access Journals (Sweden)

Hannah M. Read

2016-06-01

Full Text Available Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC and enterohaemorrhagic E. coli (EHEC infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169 in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments.

Forward transformation for high resolution eddy current tomography using whitney elements

International Nuclear Information System (INIS)

Szewczyk, R.; Salach, J.; Nowicki, M.; Ruokolainen, J.; Raback, P.

2014-01-01

Tomographic methods are intensively developed field of non-destructive testing. The main advantage of this type of NDT method is 3D information concerning the shape of the discontinuities in investigated material. On the other hand, the most common tomography method utilizing X-rays creates the significant risks typical to X-ray technique. As a result, Xray tomography is difficult to use in industry. Introduced to the industry in 2007, the eddy current tomography is safe and cost effective. However, in opposite to X-ray tomography, eddy current tomography requires sophisticated and time consuming inverse transformation creating 2D or 3D view of discontinuities. For this reason solutions presented previously are focused on 2D inverse transformation and exhibit limited resolution. For eddy current tomography, the forward tomographic transformation is most important, which is the base of inverse transformation. This paper presents the novel, fast and cost-effective solution utilizing Whitney elements method for such forward transformation. As a result, new possibilities of development in the area of high resolution 3D eddy current tomography are created. (authors)

Bacterial bioluminescence onset and quenching: a dynamical model for a quorum sensing-mediated property

OpenAIRE

Side, Domenico Delle; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Di Salvo, Marco; Talà, Adelfia; Chechkin, Aleksei; Seno, Flavio; Trovato, Antonio

2017-01-01

We present an effective dynamical model for the onset of bacterial bioluminescence, one of the most studied quorum sensing-mediated traits. Our model is built upon simple equations that describe the growth of the bacterial colony, the production and accumulation of autoinducer signal molecules, their sensing within bacterial cells, and the ensuing quorum activation mechanism that triggers bioluminescent emission. The model is directly tested to quantitatively reproduce the experimental distri...

Effect of Naphthalene and Salicylate Analogues on the Bioluminescence of Bioreporter Pseudomonas Fluorescens HK44.

Czech Academy of Sciences Publication Activity Database

Trögl, Josef; Kuncová, Gabriela; Kubicová, L.; Pařík, P.; Hálová, Jaroslava; Demnerová, K.; Ripp, S.; Sayler, G. S.

2007-01-01

Roč. 52, 1 (2007) , s. 3-14 ISSN 0015-5632 R&D Projects: GA ČR(CZ) GA104/05/2637; GA ČR(CZ) GA203/06/1244 Institutional research plan: CEZ:AV0Z40720504; CEZ:AV0Z40320502 Keywords : pseudomonas fluorescens HK44 * bioluminescence * bioluminescence Subject RIV: CE - Biochemistry Impact factor: 0.989, year: 2007

An ebCMOS camera system for marine bioluminescence observation: The LuSEApher prototype

Energy Technology Data Exchange (ETDEWEB)

Dominjon, A., E-mail: a.dominjon@ipnl.in2p3.fr [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France); Ageron, M. [CNRS/IN2P3, Centre de Physique des Particules de Marseille, Marseille, F-13288 (France); Barbier, R. [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France); Universite de Lyon, Universite Lyon 1, Lyon F-69003 (France); Billault, M.; Brunner, J. [CNRS/IN2P3, Centre de Physique des Particules de Marseille, Marseille, F-13288 (France); Cajgfinger, T. [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France); Universite de Lyon, Universite Lyon 1, Lyon F-69003 (France); Calabria, P. [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France); Chabanat, E. [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France); Universite de Lyon, Universite Lyon 1, Lyon F-69003 (France); Chaize, D.; Doan, Q.T.; Guerin, C.; Houles, J.; Vagneron, L. [CNRS/IN2P3, Institut de Physique Nucleaire de Lyon, Villeurbanne F-69622 (France)

2012-12-11

The ebCMOS camera, called LuSEApher, is a marine bioluminescence recorder device adapted to extreme low light level. This prototype is based on the skeleton of the LUSIPHER camera system originally developed for fluorescence imaging. It has been installed at 2500 m depth off the Mediterranean shore on the site of the ANTARES neutrino telescope. The LuSEApher camera is mounted on the Instrumented Interface Module connected to the ANTARES network for environmental science purposes (European Seas Observatory Network). The LuSEApher is a self-triggered photo detection system with photon counting ability. The presentation of the device is given and its performances such as the single photon reconstruction, noise performances and trigger strategy are presented. The first recorded movies of bioluminescence are analyzed. To our knowledge, those types of events have never been obtained with such a sensitivity and such a frame rate. We believe that this camera concept could open a new window on bioluminescence studies in the deep sea.

Deep-sea bioluminescence blooms after dense water formation at the ocean surface.

Directory of Open Access Journals (Sweden)

Christian Tamburini

Full Text Available The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as "open-sea convection". It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms. Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts.

Deep-sea bioluminescence blooms after dense water formation at the ocean surface.

Science.gov (United States)

Tamburini, Christian; Canals, Miquel; Durrieu de Madron, Xavier; Houpert, Loïc; Lefèvre, Dominique; Martini, Séverine; D'Ortenzio, Fabrizio; Robert, Anne; Testor, Pierre; Aguilar, Juan Antonio; Samarai, Imen Al; Albert, Arnaud; André, Michel; Anghinolfi, Marco; Anton, Gisela; Anvar, Shebli; Ardid, Miguel; Jesus, Ana Carolina Assis; Astraatmadja, Tri L; Aubert, Jean-Jacques; Baret, Bruny; Basa, Stéphane; Bertin, Vincent; Biagi, Simone; Bigi, Armando; Bigongiari, Ciro; Bogazzi, Claudio; Bou-Cabo, Manuel; Bouhou, Boutayeb; Bouwhuis, Mieke C; Brunner, Jurgen; Busto, José; Camarena, Francisco; Capone, Antonio; Cârloganu, Christina; Carminati, Giada; Carr, John; Cecchini, Stefano; Charif, Ziad; Charvis, Philippe; Chiarusi, Tommaso; Circella, Marco; Coniglione, Rosa; Costantini, Heide; Coyle, Paschal; Curtil, Christian; Decowski, Patrick; Dekeyser, Ivan; Deschamps, Anne; Donzaud, Corinne; Dornic, Damien; Dorosti, Hasankiadeh Q; Drouhin, Doriane; Eberl, Thomas; Emanuele, Umberto; Ernenwein, Jean-Pierre; Escoffier, Stéphanie; Fermani, Paolo; Ferri, Marcelino; Flaminio, Vincenzo; Folger, Florian; Fritsch, Ulf; Fuda, Jean-Luc; Galatà, Salvatore; Gay, Pascal; Giacomelli, Giorgio; Giordano, Valentina; Gómez-González, Juan-Pablo; Graf, Kay; Guillard, Goulven; Halladjian, Garadeb; Hallewell, Gregory; van Haren, Hans; Hartman, Joris; Heijboer, Aart J; Hello, Yann; Hernández-Rey, Juan Jose; Herold, Bjoern; Hößl, Jurgen; Hsu, Ching-Cheng; de Jong, Marteen; Kadler, Matthias; Kalekin, Oleg; Kappes, Alexander; Katz, Uli; Kavatsyuk, Oksana; Kooijman, Paul; Kopper, Claudio; Kouchner, Antoine; Kreykenbohm, Ingo; Kulikovskiy, Vladimir; Lahmann, Robert; Lamare, Patrick; Larosa, Giuseppina; Lattuada, Dario; Lim, Gordon; Presti, Domenico Lo; Loehner, Herbert; Loucatos, Sotiris; Mangano, Salvatore; Marcelin, Michel; Margiotta, Annarita; Martinez-Mora, Juan Antonio; Meli, Athina; Montaruli, Teresa; Moscoso, Luciano; Motz, Holger; Neff, Max; Nezri, Emma Nuel; Palioselitis, Dimitris; Păvălaş, Gabriela E; Payet, Kevin; Payre, Patrice; Petrovic, Jelena; Piattelli, Paolo; Picot-Clemente, Nicolas; Popa, Vlad; Pradier, Thierry; Presani, Eleonora; Racca, Chantal; Reed, Corey; Riccobene, Giorgio; Richardt, Carsten; Richter, Roland; Rivière, Colas; Roensch, Kathrin; Rostovtsev, Andrei; Ruiz-Rivas, Joaquin; Rujoiu, Marius; Russo, Valerio G; Salesa, Francisco; Sánchez-Losa, Augustin; Sapienza, Piera; Schöck, Friederike; Schuller, Jean-Pierre; Schussler, Fabian; Shanidze, Rezo; Simeone, Francesco; Spies, Andreas; Spurio, Maurizio; Steijger, Jos J M; Stolarczyk, Thierry; Taiuti, Mauro G F; Toscano, Simona; Vallage, Bertrand; Van Elewyck, Véronique; Vannoni, Giulia; Vecchi, Manuela; Vernin, Pascal; Wijnker, Guus; Wilms, Jorn; de Wolf, Els; Yepes, Harold; Zaborov, Dmitry; De Dios Zornoza, Juan; Zúñiga, Juan

2013-01-01

The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as "open-sea convection". It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms. Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts.

Inverse problems in vision and 3D tomography

CERN Document Server

Mohamad-Djafari, Ali

2013-01-01

The concept of an inverse problem is a familiar one to most scientists and engineers, particularly in the field of signal and image processing, imaging systems (medical, geophysical, industrial non-destructive testing, etc.) and computer vision. In imaging systems, the aim is not just to estimate unobserved images, but also their geometric characteristics from observed quantities that are linked to these unobserved quantities through the forward problem. This book focuses on imagery and vision problems that can be clearly written in terms of an inverse problem where an estimate for the image a

Inverse transport theory and applications

International Nuclear Information System (INIS)

Bal, Guillaume

2009-01-01

Inverse transport consists of reconstructing the optical properties of a domain from measurements performed at the domain's boundary. This review concerns several types of measurements: time-dependent, time-independent, angularly resolved and angularly averaged measurements. We review recent results on the reconstruction of the optical parameters from such measurements and the stability of such reconstructions. Inverse transport finds applications e.g. in medical imaging (optical tomography, optical molecular imaging) and in geophysical imaging (remote sensing in the Earth's atmosphere). (topical review)

Statistical perspectives on inverse problems

DEFF Research Database (Denmark)

Andersen, Kim Emil

of the interior of an object from electrical boundary measurements. One part of this thesis concerns statistical approaches for solving, possibly non-linear, inverse problems. Thus inverse problems are recasted in a form suitable for statistical inference. In particular, a Bayesian approach for regularisation...... problem is given in terms of probability distributions. Posterior inference is obtained by Markov chain Monte Carlo methods and new, powerful simulation techniques based on e.g. coupled Markov chains and simulated tempering is developed to improve the computational efficiency of the overall simulation......Inverse problems arise in many scientific disciplines and pertain to situations where inference is to be made about a particular phenomenon from indirect measurements. A typical example, arising in diffusion tomography, is the inverse boundary value problem for non-invasive reconstruction...

Disposable bioluminescence-based biosensor for detection of bacterial count in food.

Science.gov (United States)

Luo, Jinping; Liu, Xiaohong; Tian, Qing; Yue, Weiwei; Zeng, Jing; Chen, Guangquan; Cai, Xinxia

2009-11-01

A biosensor for rapid detection of bacterial count based on adenosine 5'-triphosphate (ATP) bioluminescence has been developed. The biosensor is composed of a key sensitive element and a photomultiplier tube used as a detector element. The disposable sensitive element consists of a sampler, a cartridge where intracellular ATP is chemically extracted from bacteria, and a microtube where the extracted ATP reacts with the luciferin-luciferase reagent to produce bioluminescence. The bioluminescence signal is transformed into relevant electrical signal by the detector and further measured with a homemade luminometer. Parameters affecting the amount of the extracted ATP, including the types of ATP extractants, the concentrations of ATP extractant, and the relevant neutralizing reagent, were optimized. Under the optimal experimental conditions, the biosensor showed a linear response to standard bacteria in a concentration range from 10(3) to 10(8) colony-forming units (CFU) per milliliter with a correlation coefficient of 0.925 (n=22) within 5min. Moreover, the bacterial count of real food samples obtained by the biosensor correlated well with those by the conventional plate count method. The proposed biosensor, with characteristics of low cost, easy operation, and fast response, provides potential application to rapid evaluation of bacterial contamination in the food industry, environment monitoring, and other fields.

Scattered Neutron Tomography Based on A Neutron Transport Inverse Problem

International Nuclear Information System (INIS)

William Charlton

2007-01-01

Neutron radiography and computed tomography are commonly used techniques to non-destructively examine materials. Tomography refers to the cross-sectional imaging of an object from either transmission or reflection data collected by illuminating the object from many different directions

Smartphone-based low light detection for bioluminescence application

Science.gov (United States)

Kim, Huisung; Jung, Youngkee; Doh, Iyll-Joon; Lozano-Mahecha, Roxana Andrea; Applegate, Bruce; Bae, Euiwon

2017-01-01

We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation by smartphone (BAQS), provides an opportunity for onsite analysis and quantitation of luminescent signals from biological and non-biological sensing elements which emit photons in response to an analyte. A simple cradle that houses the smartphone, sample tube, and collection lens supports the measuring platform, while noise reduction by ensemble averaging simultaneously lowers the background and enhances the signal from emitted photons. Five different types of smartphones, both Android and iOS devices, were tested, and the top two candidates were used to evaluate luminescence from the bioluminescent reporter Pseudomonas fluorescens M3A. The best results were achieved by OnePlus One (android), which was able to detect luminescence from ~106 CFU/mL of the bio-reporter, which corresponds to ~107 photons/s with 180 seconds of integration time.

Mathematics of Computed Tomography

Science.gov (United States)

Hawkins, William Grant

A review of the applications of the Radon transform is presented, with emphasis on emission computed tomography and transmission computed tomography. The theory of the 2D and 3D Radon transforms, and the effects of attenuation for emission computed tomography are presented. The algebraic iterative methods, their importance and limitations are reviewed. Analytic solutions of the 2D problem the convolution and frequency filtering methods based on linear shift invariant theory, and the solution of the circular harmonic decomposition by integral transform theory--are reviewed. The relation between the invisible kernels, the inverse circular harmonic transform, and the consistency conditions are demonstrated. The discussion and review are extended to the 3D problem-convolution, frequency filtering, spherical harmonic transform solutions, and consistency conditions. The Cormack algorithm based on reconstruction with Zernike polynomials is reviewed. An analogous algorithm and set of reconstruction polynomials is developed for the spherical harmonic transform. The relations between the consistency conditions, boundary conditions and orthogonal basis functions for the 2D projection harmonics are delineated and extended to the 3D case. The equivalence of the inverse circular harmonic transform, the inverse Radon transform, and the inverse Cormack transform is presented. The use of the number of nodes of a projection harmonic as a filter is discussed. Numerical methods for the efficient implementation of angular harmonic algorithms based on orthogonal functions and stable recursion are presented. The derivation of a lower bound for the signal-to-noise ratio of the Cormack algorithm is derived.

Melatonin Entrains PER2::LUC Bioluminescence Circadian Rhythm in the Mouse Cornea

Science.gov (United States)

Baba, Kenkichi; Davidson, Alec J.; Tosini, Gianluca

2015-01-01

Purpose Previous studies have reported the presence of a circadian rhythm in PERIOD2::LUCIFERASE (PER2::LUC) bioluminescence in mouse photoreceptors, retina, RPE, and cornea. Melatonin (MLT) modulates many physiological functions in the eye and it is believed to be one of the key circadian signals within the eye. The aim of the present study was to investigate the regulation of the PER2::LUC circadian rhythm in mouse cornea and to determine the role played by MLT. Methods Corneas were obtained from PER2::LUC mice and cultured to measure bioluminescence rhythmicity in isolated tissue using a Lumicycle or CCD camera. To determine the time-dependent resetting of the corneal circadian clocks in response to MLT or IIK7 (a melatonin type 2 receptor, MT2, agonist) was added to the cultured corneas at different times of the day. We also defined the location of the MT2 receptor within different corneal layers using immunohistochemistry. Results A long-lasting bioluminescence rhythm was recorded from cultured PER2::LUC cornea and PER2::LUC signal was localized to the corneal epithelium and endothelium. MLT administration in the early night delayed the cornea rhythm, whereas administration of MLT at late night to early morning advanced the cornea rhythm. Treatment with IIK7 mimicked the MLT phase-shifting effect. Consistent with these results, MT2 immunoreactivity was localized to the corneal epithelium and endothelium. Conclusions Our work demonstrates that MLT entrains the PER2::LUC bioluminescence rhythm in the cornea. Our data indicate that the cornea may represent a model to study the molecular mechanisms by which MLT affects the circadian clock. PMID:26207312

Seismic tomography inversion in the case that sources and receivers are distributed out of a 2-D plane; Shingen jushinten ga nijigen heimennai ni nai baai no danseiha tomography kaiseki ni kansuru kosatsu

Energy Technology Data Exchange (ETDEWEB)

Yokota, T; Miyazaki, T [Geological Survey of Japan, Tsukuba (Japan); Rokugawa, S; Matsushima, J [The University of Tokyo, Tokyo (Japan). Faculty of Engineering; Ashida, Y [Kyoto University, Kyoto (Japan). Faculty of Engineering

1996-10-01

In the case where sources and receivers are not distributed on a 2-D plane, seismic tomography inversion was studied. In tomography experiments, the existing wells are generally used. In such case, sources and receivers are frequently not distributed on a 2-D plane. The 2.5-D analysis method including 2-D structure and 3-D ray-tracing was thus developed. This method is featured by less memory necessary for ray-tracing calculation, and the same algorithm for velocity determination as 2-D analysis method. In previous methods, since analysis is generally carried out by projecting sources and receivers on a certain assumed 2-D plane, it can derive correct results in the case of constant velocity and straight ray, however, in the other case, it derives incorrect results. Application of 3-D tomography requires a large amount of memory, and falls into poor convergence because of various parameters. The 2.5-D analysis method can avoid these demerits. This analysis method was applied to the data obtained in Ogiri area, Kagoshima prefecture. 5 refs., 3 figs., 2 tabs.

Dive Activities for Bioluminescence 2009 - Office of Ocean Exploration and Research

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Information about dive activities were recorded by personnel during the "Bioluminescence 2009" expedition, July 20 through 31, 2009. Additional information was...

Attenuated Bioluminescent Brucella melitensis Mutants GR019 (virB4), GR024 (galE), and GR026 (BMEI1090-BMEI1091) Confer Protection in Mice

OpenAIRE

Rajashekara, Gireesh; Glover, David A.; Banai, Menachem; O'Callaghan, David; Splitter, Gary A.

2006-01-01

In vivo bioluminescence imaging is a persuasive approach to investigate a number of issues in microbial pathogenesis. Previously, we have applied bioluminescence imaging to gain greater insight into Brucella melitensis pathogenesis. Endowing Brucella with bioluminescence allowed direct visualization of bacterial dissemination, pattern of tissue localization, and the contribution of Brucella genes to virulence. In this report, we describe the pathogenicity of three attenuated bioluminescent B....

Bioluminescent bacteria have potential as a marker of drowning in seawater: two immersed cadavers retrieved near estuaries.

Science.gov (United States)

Kakizaki, Eiji; Kozawa, Shuji; Sakai, Masahiro; Yukawa, Nobuhiro

2009-03-01

We detected numerous bioluminescent bacteria in blood samples from two cadavers that had been immersed in estuarine environments. Autopsy, diatomaceous and toxicological findings indicated death by drowning, which agreed with environmental aspects and the findings of police investigations. Bioluminescent bacteria appeared in blood samples cultured on selective agar containing 2%, 3% and 4% NaCl after about 18h. Blood from the left side of the heart, the right side of the heart and the femoral vein generated 7.0 x 10(2), 2.0 x 10(4) and 8.0 x 10(2) cfu/ml of blood (case 1), and 1.8 x 10(4), 1.1 x 10(3) and 2.5 x 10(1) cfu/ml (case 2) of bioluminescent colonies, respectively, in agar containing 4% NaCl. Homologous analysis based on the 16S rRNA gene also identified the bioluminescent colonies as Vibrio fischeri and V. harveyi, which normally inhabit seawater. This simple assay might serve as an additional indicator to support a conclusion of death by drowning together with the diatom test.

Frozen Gaussian approximation for 3D seismic tomography

Science.gov (United States)

Chai, Lihui; Tong, Ping; Yang, Xu

2018-05-01

Three-dimensional (3D) wave-equation-based seismic tomography is computationally challenging in large scales and high-frequency regime. In this paper, we apply the frozen Gaussian approximation (FGA) method to compute 3D sensitivity kernels and seismic tomography of high-frequency. Rather than standard ray theory used in seismic inversion (e.g. Kirchhoff migration and Gaussian beam migration), FGA is used to compute the 3D high-frequency sensitivity kernels for travel-time or full waveform inversions. Specifically, we reformulate the equations of the forward and adjoint wavefields for the purpose of convenience to apply FGA, and with this reformulation, one can efficiently compute the Green’s functions whose convolutions with source time function produce wavefields needed for the construction of 3D kernels. Moreover, a fast summation method is proposed based on local fast Fourier transform which greatly improves the speed of reconstruction as the last step of FGA algorithm. We apply FGA to both the travel-time adjoint tomography and full waveform inversion (FWI) on synthetic crosswell seismic data with dominant frequencies as high as those of real crosswell data, and confirm again that FWI requires a more sophisticated initial velocity model for the convergence than travel-time adjoint tomography. We also numerically test the accuracy of applying FGA to local earthquake tomography. This study paves the way to directly apply wave-equation-based seismic tomography methods into real data around their dominant frequencies.

3D first-arrival traveltime tomography with modified total variation regularization

Science.gov (United States)

Jiang, Wenbin; Zhang, Jie

2018-02-01

Three-dimensional (3D) seismic surveys have become a major tool in the exploration and exploitation of hydrocarbons. 3D seismic first-arrival traveltime tomography is a robust method for near-surface velocity estimation. A common approach for stabilizing the ill-posed inverse problem is to apply Tikhonov regularization to the inversion. However, the Tikhonov regularization method recovers smooth local structures while blurring the sharp features in the model solution. We present a 3D first-arrival traveltime tomography method with modified total variation (MTV) regularization to preserve sharp velocity contrasts and improve the accuracy of velocity inversion. To solve the minimization problem of the new traveltime tomography method, we decouple the original optimization problem into two following subproblems: a standard traveltime tomography problem with the traditional Tikhonov regularization and a L2 total variation problem. We apply the conjugate gradient method and split-Bregman iterative method to solve these two subproblems, respectively. Our synthetic examples show that the new method produces higher resolution models than the conventional traveltime tomography with Tikhonov regularization. We apply the technique to field data. The stacking section shows significant improvements with static corrections from the MTV traveltime tomography.

Ship track for Bioluminescence 2009 - Office of Ocean Exploration and Research

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Ship track of the R/V Seward Johnson during the "Bioluminescence 2009" expedition sponsored by the National Oceanic and Atmospheric Administration (NOAA) Office of...

Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca

NARCIS (Netherlands)

Eremeeva, Elena V.; Bartsev, Sergey I.; Berkel, van Willem J.H.; Vysotski, Eugene S.

2017-01-01

Upon binding their metal ion cofactors, Ca2+-regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca2+-regulated

Bioluminescence imaging: a shining future for cardiac regeneration

Science.gov (United States)

Roura, Santiago; Gálvez-Montón, Carolina; Bayes-Genis, Antoni

2013-01-01

Advances in bioanalytical techniques have become crucial for both basic research and medical practice. One example, bioluminescence imaging (BLI), is based on the application of natural reactants with light-emitting capabilities (photoproteins and luciferases) isolated from a widespread group of organisms. The main challenges in cardiac regeneration remain unresolved, but a vast number of studies have harnessed BLI with the discovery of aequorin and green fluorescent proteins. First described in the luminous hydromedusan Aequorea victoria in the early 1960s, bioluminescent proteins have greatly contributed to the design and initiation of ongoing cell-based clinical trials on cardiovascular diseases. In conjunction with advances in reporter gene technology, BLI provides valuable information about the location and functional status of regenerative cells implanted into numerous animal models of disease. The purpose of this review was to present the great potential of BLI, among other existing imaging modalities, to refine effectiveness and underlying mechanisms of cardiac cell therapy. We recount the first discovery of natural primary compounds with light-emitting capabilities, and follow their applications to bioanalysis. We also illustrate insights and perspectives on BLI to illuminate current efforts in cardiac regeneration, where the future is bright. PMID:23402217

Inversion of the star transform

International Nuclear Information System (INIS)

Zhao, Fan; Schotland, John C; Markel, Vadim A

2014-01-01

We define the star transform as a generalization of the broken ray transform introduced by us in previous work. The advantages of using the star transform include the possibility to reconstruct the absorption and the scattering coefficients of the medium separately and simultaneously (from the same data) and the possibility to utilize scattered radiation which, in the case of conventional x-ray tomography, is discarded. In this paper, we derive the star transform from physical principles, discuss its mathematical properties and analyze numerical stability of inversion. In particular, it is shown that stable inversion of the star transform can be obtained only for configurations involving odd number of rays. Several computationally-efficient inversion algorithms are derived and tested numerically. (paper)

Propagation of singularities for linearised hybrid data impedance tomography

DEFF Research Database (Denmark)

Bal, Guillaume; Hoffmann, Kristoffer; Knudsen, Kim

2017-01-01

For a general formulation of linearised hybrid inverse problems in impedance tomography, the qualitative properties of the solutions are analysed. Using an appropriate scalar pseudo-differential formulation, the problems are shown to permit propagating singularities under certain non-elliptic con......For a general formulation of linearised hybrid inverse problems in impedance tomography, the qualitative properties of the solutions are analysed. Using an appropriate scalar pseudo-differential formulation, the problems are shown to permit propagating singularities under certain non...

Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

Science.gov (United States)

Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

2010-05-01

The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

Fast monitoring of indoor bioaerosol concentrations with ATP bioluminescence assay using an electrostatic rod-type sampler.

Directory of Open Access Journals (Sweden)

Ji-Woon Park

Full Text Available A culture-based colony counting method is the most widely used analytical technique for monitoring bioaerosols in both indoor and outdoor environments. However, this method requires several days for colony formation. In this study, our goal was fast monitoring (Sampling: 3 min, Detection: < 1 min of indoor bioaerosol concentrations with ATP bioluminescence assay using a bioaerosol sampler. For this purpose, a novel hand-held electrostatic rod-type sampler (110 mm wide, 115 mm long, and 200 mm tall was developed and used with a commercial luminometer, which employs the Adenosine triphosphate (ATP bioluminescence method. The sampler consisted of a wire-rod type charger and a cylindrical collector, and was operated with an applied voltage of 4.5 kV and a sampling flow rate of 150.7 lpm. Its performance was tested using Staphylococcus epidermidis which was aerosolized with an atomizer. Bioaerosol concentrations were measured using ATP bioluminescence method with our sampler and compared with the culture-based method using Andersen cascade impactor under controlled laboratory conditions. Indoor bioaerosol concentrations were also measured using both methods in various indoor environments. A linear correlation was obtained between both methods in lab-tests and field-tests. Our proposed sampler with ATP bioluminescence method may be effective for fast monitoring of indoor bioaerosol concentrations.

An Experimental-Numerical Study of Small Scale Flow Interaction with Bioluminescent Plankton

National Research Council Canada - National Science Library

Latz, Michael

1998-01-01

Numerical and experimental approaches were used to investigate the effects of quantified flow stimuli on bioluminescence sUmulatidn at the small length and time scales appropriate for individual plankton...

Assessment of tumor energy and oxygenation status by bioluminescence, nuclear magnetic resonance spectroscopy, and cryospectrophotometry.

Science.gov (United States)

Mueller-Klieser, W; Schaefer, C; Walenta, S; Rofstad, E K; Fenton, B M; Sutherland, R M

1990-03-15

The energy and oxygenation status of tumors from two murine sarcoma lines (KHT, RIF-1) and two human ovarian carcinoma xenograft lines (MLS, OWI) were assessed using three independent techniques. Tumor energy metabolism was investigated in vivo by 31P nuclear magnetic resonance spectroscopy. After nuclear magnetic resonance measurements, tumors were frozen in liquid nitrogen to determine the tissue ATP concentration by imaging bioluminescence and to register the intracapillary oxyhemoglobin (HbO2) saturation using the cryospectrophotometric method. There was a positive correlation between the nucleoside triphosphate beta/total resonance ratio or a negative correlation between the Pi/total resonance ratio and the model ATP concentration obtained by bioluminescence, respectively. This was true for small tumors with no extended necrosis irrespective of tumor type. Moreover, a positive correlation was obtained between the HbO2 saturations and the ATP concentration measured with bioluminescence. The results demonstrate the potential of combined studies using noninvasive, integrating methods and high-resolution imaging techniques for characterizing the metabolic milieu in tumors.

Monitoring Bloom Dynamics of a Common Coastal Bioluminescent Ctenophore

Science.gov (United States)

2010-09-30

photodiode array are simultaneously burst sampled through integrating transimpedance amplifiers with an integration period of 0.1 s. 64-bursts are...clear acrylic test section to reduce the optical path length and reducing integrator capacitance to increase transimpedance gain. A later improvement...gain, higher resolution analog to digital conversion, and greater transimpedance gain. Figure 5 Bioluminescence intensities from Pyrocystis

ATP bioluminescence: Surface hygiene monitoring in milk preparation room of neonatal intensive care unit

Science.gov (United States)

Mohamad, Mahirah; Ishak, Shareena; Jaafar, Rohana; Sani, Norrakiah Abdullah

2018-04-01

ATP Bioluminescence application and standard microbiological analyses were used to evaluate the cleanliness of milk contact surfaces and non-milk contact surfaces in milk preparation room of neonatal intensive care unit (NICU) of Universiti Kebangsaan Malaysia Medical Centre (UKMMC). A total of 44 samples including the breast pump, milk bottle, milk bottle screw top and screw ring, teats, measuring cups, waterless warmer, refrigerator, dishwasher and pasteurizer inner wall were tested on May 2017. 3M Clean and Trace Hygiene Monitoring (UXL100 ATP Test swabs) and the bioluminescence reader Clean-Trace NG Luminometer (3M) were used to measure the Relative Light Unit (RLU) and microbiological analysis using 3M Quick Swab and 3MTM PetrifilmTM for enumeration of aerobic count, Staphylococcus aureus, Enterobacteriaceae, coliform and detection of Escherichia coli (CFU /100cm2 or utensil/item). The RLU values were from 11 to 194 and passed the ATP benchmark for intensive care unit (ICU), < 250 RLU as recommended. Aerobic colony count was only found in waterless warmer (0.05±0.01 mean log CFU/warmer). None of S. aureus, Enterobacteriaceae, E. coli and coliform was detected in all samples. A weak correlation was found between bioluminescence measurements RLU and the microbiological analysis (CFU). However, the use of ATP bioluminescence in monitoring milk preparation room cleanliness can be a useful method for assessing rapidly the surface hygiene as well as to verify the Sanitation Standard Operating Procedure (SSOP) prior to implementation of Hazard Analysis and Critical Control Points (HACCP) in milk preparation room.

Expression of a humanized viral 2A-mediated lux operon efficiently generates autonomous bioluminescence in human cells.

Directory of Open Access Journals (Sweden)

Tingting Xu

Full Text Available Expression of autonomous bioluminescence from human cells was previously reported to be impossible, suggesting that all bioluminescent-based mammalian reporter systems must therefore require application of a potentially influential chemical substrate. While this was disproven when the bacterial luciferase (lux cassette was demonstrated to function in a human cell, its expression required multiple genetic constructs, was functional in only a single cell type, and generated a significantly reduced signal compared to substrate-requiring systems. Here we investigate the use of a humanized, viral 2A-linked lux genetic architecture for the efficient introduction of an autobioluminescent phenotype across a variety of human cell lines.The lux cassette was codon optimized and assembled into a synthetic human expression operon using viral 2A elements as linker regions. Human kidney, breast cancer, and colorectal cancer cell lines were both transiently and stably transfected with the humanized operon and the resulting autobioluminescent phenotype was evaluated using common imaging instrumentation. Autobioluminescent cells were screened for cytotoxic effects resulting from lux expression and their utility as bioreporters was evaluated through the demonstration of repeated monitoring of single populations over a prolonged period using both a modified E-SCREEN assay for estrogen detection and a classical cytotoxic compound detection assay for the antibiotic Zeocin. Furthermore, the use of self-directed bioluminescent initiation in response to target detection was assessed to determine its amenability towards deployment as fully autonomous sensors. In all cases, bioluminescent measurements were supported with traditional genetic and transcriptomic evaluations.Our results demonstrate that the viral 2A-linked, humanized lux genetic architecture successfully produced autobioluminescent phenotypes in all cell lines tested without the induction of cytotoxicity

Light and vision in the deep-sea benthos: I. Bioluminescence at 500-1000 m depth in the Bahamian islands.

Science.gov (United States)

Johnsen, Sönke; Frank, Tamara M; Haddock, Steven H D; Widder, Edith A; Messing, Charles G

2012-10-01

Bioluminescence is common and well studied in mesopelagic species. However, the extent of bioluminescence in benthic sites of similar depths is far less studied, although the relatively large eyes of benthic fish, crustaceans and cephalopods at bathyal depths suggest the presence of significant biogenic light. Using the Johnson-Sea-Link submersible, we collected numerous species of cnidarians, echinoderms, crustaceans, cephalopods and sponges, as well as one annelid from three sites in the northern Bahamas (500-1000 m depth). Using mechanical and chemical stimulation, we tested the collected species for light emission, and photographed and measured the spectra of the emitted light. In addition, in situ intensified video and still photos were taken of different benthic habitats. Surprisingly, bioluminescence in benthic animals at these sites was far less common than in mesopelagic animals from similar depths, with less than 20% of the collected species emitting light. Bioluminescent taxa comprised two species of anemone (Actinaria), a new genus and species of flabellate Parazoanthidae (formerly Gerardia sp.) (Zoanthidea), three sea pens (Pennatulacea), three bamboo corals (Alcyonacea), the chrysogorgiid coral Chrysogorgia desbonni (Alcyonacea), the caridean shrimp Parapandalus sp. and Heterocarpus ensifer (Decapoda), two holothuroids (Elasipodida and Aspidochirota) and the ophiuroid Ophiochiton ternispinus (Ophiurida). Except for the ophiuroid and the two shrimp, which emitted blue light (peak wavelengths 470 and 455 nm), all the species produced greener light than that measured in most mesopelagic taxa, with the emissions of the pennatulaceans being strongly shifted towards longer wavelengths. In situ observations suggested that bioluminescence associated with these sites was due primarily to light emitted by bioluminescent planktonic species as they struck filter feeders that extended into the water column.

Full traveltime inversion in source domain

KAUST Repository

Liu, Lu

2017-06-01

This paper presents a new method of source-domain full traveltime inversion (FTI). The objective of this study is automatically building near-surface velocity using the early arrivals of seismic data. This method can generate the inverted velocity that can kinetically best match the reconstructed plane-wave source of early arrivals with true source in source domain. It does not require picking first arrivals for tomography, which is one of the most challenging aspects of ray-based tomographic inversion. Besides, this method does not need estimate the source wavelet, which is a necessity for receiver-domain wave-equation velocity inversion. Furthermore, we applied our method on one synthetic dataset; the results show our method could generate a reasonable background velocity even when shingling first arrivals exist and could provide a good initial velocity for the conventional full waveform inversion (FWI).

Integrated visualization of multi-angle bioluminescence imaging and micro CT

NARCIS (Netherlands)

Kok, P.; Dijkstra, J.; Botha, C.P.; Post, F.H.; Kaijzel, E.; Que, I.; Löwik, C.W.G.M.; Reiber, J.H.C.; Lelieveldt, B.P.F.

2007-01-01

This paper explores new methods to visualize and fuse multi-2D bioluminescence imaging (BLI) data with structural imaging modalities such as micro CT and MR. A geometric, back-projection-based 3D reconstruction for superficial lesions from multi-2D BLI data is presented, enabling a coarse estimate

Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control

Energy Technology Data Exchange (ETDEWEB)

Ripp, S.; Nivens, D.E.; Ahn, Y.; Werner, C.; Jarrell, J. IV; Easter, J.P.; Cox, C.D.; Burlage, R.S.; Sayler, G.S.

2000-03-01

Pseudomonas fluorescens HK44 represents the first genetically engineered microorganism approved for field testing in the United States for bioremediation purposes. Strain HK44 harbors an introduced lux gene fused within a naphthalene degradative pathway, thereby allowing this recombinant microbe to bioluminescent as it degrades specific polyaromatic hydrocarbons such as naphthalene. The bioremediation process can therefore be monitored by the detection of light. P. fluorescens HK44 was inoculated into the vadose zone of intermediate-scale, semicontained soil lysimeters contaminated with naphthalene, anthracene, and phenanthrene, and the population dynamics were followed over an approximate 2-year period in order to assess the long-term efficacy of using strain HK44 for monitoring and controlling bioremediation processes. Results showed that P. fluorescens HK44 was capable of surviving initial inoculation into both hydrocarbon contaminated and uncontaminated soils and was recoverable from these soils 660 days post inoculation. It was also demonstrated that strain HK44 was capable of generating bioluminescence in response to soil hydrocarbon bioavailability. Bioluminescence approaching 166,000 counts/s was detected in fiber optic-based biosensor devices responding to volatile polyaromatic hydrocarbons, while a portable photomultiplier module detected bioluminescence at an average of 4300 counts/s directly from soil-borne HK44 cells within localized treatment areas. The utilization of lux-based bioreporter microorganisms therefore promises to be a viable option for in situ determination of environmental contaminant bioavailability and biodegradation process monitoring and control.

A 2.5-D Diffraction Tomography Inversion Scheme for Ground Penetrating Radar

DEFF Research Database (Denmark)

Meincke, Peter

1999-01-01

A new 2.5-D inversion scheme is derived for ground penetrating radar (GPR) that applies to a monostatic fixed-offset measurement configuration. The inversion scheme, which is based upon the first Born approximation and the pseudo-inverse operator, takes rigorously into account the planar air...

Ship Sensor Observations for Bioluminescence 2009 - Office of Ocean Exploration and Research

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Hourly measurements made by selected ship sensors on the R/V Seward Johnson during the "Bioluminescence 2009" expedition sponsored by the National Oceanic and...

[Determination of minimal concentrations of biocorrosion inhibitors by a bioluminescence method in relation to bacteria, participating in biocorrosion].

Science.gov (United States)

Efremenko, E N; Azizov, R E; Makhlis, T A; Abbasov, V M; Varfolomeev, S D

2005-01-01

By using a bioluminescence ATP assay, we have determined the minimal concentrations of some biocorrosion inhibitors (Katon, Khazar, VFIKS-82, Nitro-1, Kaspii-2, and Kaspii-4) suppressing most common microbial corrosion agents: Desulfovibrio desulfuricans, Desulfovibrio vulgaris, Pseudomonas putida, Pseudomonas fluorescens, and Acidithiobacillus ferrooxidans. The cell titers determined by the bioluminescence method, including not only dividing cells but also their dormant living counterparts, are two- to sixfold greater than the values determined microbiologically. It is shown that the bioluminescence method can be applied to determination of cell titers in samples of oil-field waters in the presence of iron ions (up to 260 mM) and iron sulfide (to 186 mg/l) and in the absence or presence of biocidal corrosion inhibitors.

Smartphone-based low light detection for bioluminescence application

OpenAIRE

Kim, Huisung; Jung, Youngkee; Doh, Iyll-Joon; Lozano-Mahecha, Roxana Andrea; Applegate, Bruce; Bae, Euiwon

2017-01-01

We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation by smartphone (BAQS), provides an opportunity for onsite analysis and quantitation of luminescent signals from biological and non-biological sensing elements which emit photons in response to an an...

Inverse planning and optimization: a comparison of solutions

Energy Technology Data Exchange (ETDEWEB)

Ringor, Michael [School of Health Sciences, Purdue University, West Lafayette, IN (United States); Papiez, Lech [Department of Radiation Oncology, Indiana University, Indianapolis, IN (United States)

1998-09-01

The basic problem in radiation therapy treatment planning is to determine an appropriate set of treatment parameters that would induce an effective dose distribution inside a patient. One can approach this task as an inverse problem, or as an optimization problem. In this presentation, we compare both approaches. The inverse problem is presented as a dose reconstruction problem similar to tomography reconstruction. We formulate the optimization problem as linear and quadratic programs. Explicit comparisons are made between the solutions obtained by inversion and those obtained by optimization for the case in which scatter and attenuation are ignored (the NS-NA approximation)

Sensitive in situ monitoring of a recombinant bioluminescent Yersinia enterocolitica reporter mutant in real time on Camembert cheese.

Science.gov (United States)

Maoz, Ariel; Mayr, Ralf; Bresolin, Geraldine; Neuhaus, Klaus; Francis, Kevin P; Scherer, Siegfried

2002-11-01

Bioluminescent mutants of Yersinia enterocolitica were generated by transposon mutagenesis using a promoterless, complete lux operon (luxCDABE) derived from Photorhabdus luminescens, and their production of light in the cheese environment was monitored. Mutant B94, which had the lux cassette inserted into an open reading frame of unknown function was used for direct monitoring of Y. enterocolitica cells on cheeses stored at 10 degrees C by quantifying bioluminescence using a photon-counting, intensified charge-coupled device camera. The detection limit on cheese was 200 CFU/cm(2). Bioluminescence of the reporter mutant was significantly regulated by its environment (NaCl, temperature, and cheese), as well as by growth phase, via the promoter the lux operon had acquired upon transposition. At low temperatures, mutant B94 did not exhibit the often-reported decrease of photon emission in older cells. It was not necessary to include either antibiotics or aldehyde in the food matrix in order to gain quantitative, reproducible bioluminescence data. As far as we know, this is the first time a pathogen has been monitored in situ, in real time, in a "real-product" status, and at a low temperature.

Mathematical Methods in Tomography

CERN Document Server

Louis, Alfred; Natterer, Frank

1991-01-01

The conference was devoted to the discussion of present and future techniques in medical imaging, including 3D x-ray CT, ultrasound and diffraction tomography, and biomagnetic ima- ging. The mathematical models, their theoretical aspects and the development of algorithms were treated. The proceedings contains surveys on reconstruction in inverse obstacle scat- tering, inversion in 3D, and constrained least squares pro- blems.Research papers include besides the mentioned imaging techniques presentations on image reconstruction in Hilbert spaces, singular value decompositions, 3D cone beam recon- struction, diffuse tomography, regularization of ill-posed problems, evaluation reconstruction algorithms and applica- tions in non-medical fields. Contents: Theoretical Aspects: J.Boman: Helgason' s support theorem for Radon transforms-a newproof and a generalization -P.Maass: Singular value de- compositions for Radon transforms- W.R.Madych: Image recon- struction in Hilbert space -R.G.Mukhometov: A problem of in- teg...

Visualization of local Ca2+ dynamics with genetically encoded bioluminescent reporters.

Science.gov (United States)

Rogers, Kelly L; Stinnakre, Jacques; Agulhon, Cendra; Jublot, Delphine; Shorte, Spencer L; Kremer, Eric J; Brûlet, Philippe

2005-02-01

Measurements of local Ca2+ signalling at different developmental stages and/or in specific cell types is important for understanding aspects of brain functioning. The use of light excitation in fluorescence imaging can cause phototoxicity, photobleaching and auto-fluorescence. In contrast, bioluminescence does not require the input of radiative energy and can therefore be measured over long periods, with very high temporal resolution. Aequorin is a genetically encoded Ca(2+)-sensitive bioluminescent protein, however, its low quantum yield prevents dynamic measurements of Ca2+ responses in single cells. To overcome this limitation, we recently reported the bi-functional Ca2+ reporter gene, GFP-aequorin (GA), which was developed specifically to improve the light output and stability of aequorin chimeras [V. Baubet, et al., (2000) PNAS, 97, 7260-7265]. In the current study, we have genetically targeted GA to different microdomains important in synaptic transmission, including to the mitochondrial matrix, endoplasmic reticulum, synaptic vesicles and to the postsynaptic density. We demonstrate that these reporters enable 'real-time' measurements of subcellular Ca2+ changes in single mammalian neurons using bioluminescence. The high signal-to-noise ratio of these reporters is also important in that it affords the visualization of Ca2+ dynamics in cell-cell communication in neuronal cultures and tissue slices. Further, we demonstrate the utility of this approach in ex-vivo preparations of mammalian retina, a paradigm in which external light input should be controlled. This represents a novel molecular imaging approach for non-invasive monitoring of local Ca2+ dynamics and cellular communication in tissue or whole animal studies.

Aequorin fusion proteins as bioluminescent tracers for competitive immunoassays

Science.gov (United States)

Mirasoli, Mara; Michelini, Elisa; Deo, Sapna K.; Dikici, Emre; Roda, Aldo; Daunert, Sylvia

2004-06-01

The use of bio- and chemiluminescence for the development of quantitative binding assays offers undoubted advantages over other detection systems, such as spectrophotometry, fluorescence, or radioactivity. Indeed, bio- and chemiluminescence detection provides similar, or even better, sensitivity and detectability than radioisotopes, while avoiding the problems of health hazards, waste disposal, and instability associated with the use of radioisotopes. Among bioluminescent labels, the calcium-activated photoprotein aequorin, originally isolated from Aequorea victoria and today available as a recombinant product, is characterized by very high detectability, down to attomole levels. It has been used as a bioluminescent label for developing a variety of highly sensitive immunoassays, using various analyte-aequorin conjugation strategies. When the analyte is a protein or a peptide, genetic engineering techniques can be used to produce protein fusions where the analyte is in-frame fused with aequorin, thus producing homogeneous one-to-one conjugation products, available in virtually unlimited amount. Various assays were developed using this strategy: a short review of the most interesting applications is presented, as well as the cloning, purification and initial characterization of an endothelin-1-aequorin conjugate suitable for developing a competitive immunoassay for endothelin-1, a potent vasoconstrictor peptide, involved in hypertension.

An inverse method for radiation transport

Energy Technology Data Exchange (ETDEWEB)

Favorite, J. A. (Jeffrey A.); Sanchez, R. (Richard)

2004-01-01

Adjoint functions have been used with forward functions to compute gradients in implicit (iterative) solution methods for inverse problems in optical tomography, geoscience, thermal science, and other fields, but only once has this approach been used for inverse solutions to the Boltzmann transport equation. In this paper, this approach is used to develop an inverse method that requires only angle-independent flux measurements, rather than angle-dependent measurements as was done previously. The method is applied to a simplified form of the transport equation that does not include scattering. The resulting procedure uses measured values of gamma-ray fluxes of discrete, characteristic energies to determine interface locations in a multilayer shield. The method was implemented with a Newton-Raphson optimization algorithm, and it worked very well in numerical one-dimensional spherical test cases. A more sophisticated optimization method would better exploit the potential of the inverse method.

A genetic screen for bioluminescence genes in the fungus Armillaria mellea, through the use of Agrobacterium tumefaciens-mediated random insertional mutagenesis

Science.gov (United States)

Bioluminescence is reported from 71 saprobic species of fungi from four, distant lineages in the order Agaricales. Analyses of the fungal luminescent chemistry shows that all four lineages share a functionally conserved substrate and luciferase, indicating that the bioluminescent pathway is likely c...

Riemann–Hilbert problem approach for two-dimensional flow inverse scattering

Energy Technology Data Exchange (ETDEWEB)

Agaltsov, A. D., E-mail: agalets@gmail.com [Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Novikov, R. G., E-mail: novikov@cmap.polytechnique.fr [CNRS (UMR 7641), Centre de Mathématiques Appliquées, Ecole Polytechnique, 91128 Palaiseau (France); IEPT RAS, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology, Dolgoprudny (Russian Federation)

2014-10-15

We consider inverse scattering for the time-harmonic wave equation with first-order perturbation in two dimensions. This problem arises in particular in the acoustic tomography of moving fluid. We consider linearized and nonlinearized reconstruction algorithms for this problem of inverse scattering. Our nonlinearized reconstruction algorithm is based on the non-local Riemann–Hilbert problem approach. Comparisons with preceding results are given.

Riemann–Hilbert problem approach for two-dimensional flow inverse scattering

International Nuclear Information System (INIS)

Agaltsov, A. D.; Novikov, R. G.

2014-01-01

We consider inverse scattering for the time-harmonic wave equation with first-order perturbation in two dimensions. This problem arises in particular in the acoustic tomography of moving fluid. We consider linearized and nonlinearized reconstruction algorithms for this problem of inverse scattering. Our nonlinearized reconstruction algorithm is based on the non-local Riemann–Hilbert problem approach. Comparisons with preceding results are given

Wave-equation dispersion inversion

KAUST Repository

Li, Jing

2016-12-08

We present the theory for wave-equation inversion of dispersion curves, where the misfit function is the sum of the squared differences between the wavenumbers along the predicted and observed dispersion curves. The dispersion curves are obtained from Rayleigh waves recorded by vertical-component geophones. Similar to wave-equation traveltime tomography, the complicated surface wave arrivals in traces are skeletonized as simpler data, namely the picked dispersion curves in the phase-velocity and frequency domains. Solutions to the elastic wave equation and an iterative optimization method are then used to invert these curves for 2-D or 3-D S-wave velocity models. This procedure, denoted as wave-equation dispersion inversion (WD), does not require the assumption of a layered model and is significantly less prone to the cycle-skipping problems of full waveform inversion. The synthetic and field data examples demonstrate that WD can approximately reconstruct the S-wave velocity distributions in laterally heterogeneous media if the dispersion curves can be identified and picked. The WD method is easily extended to anisotropic data and the inversion of dispersion curves associated with Love waves.

From tomography to FWI with a single objective function

KAUST Repository

Alkhalifah, Tariq Ali

2013-06-10

Reflections in our seismic data induce serious nonlinear behavior in the objective function of full waveform inversion (FWI). Thus, without a good initial velocity model, that can produce the reflections within a cycle of the frequency used in the inversion, convergence to the solution becomes hard. Such velocity models are usually extracted from migration velocity analysis or traveltime tomography, among other means, that are not guaranteed to adhere to the FWI requirements. As such, we promote an objective function based on the misfit in the instantaneous traveltime between the observed and modeled data. This phase based attribute of the wavefield, along with its phase unwrapping features, provide a frequency dependent traveltime function. With strong damping of the of the synthetic, potentially low frequency, data, this attribute admits first arrival traveltime that could be compared with picked ones from the observed data, like in wave equation tomography. As we relax the damping on the synthetic and observed data, the objective function measures the misfit in the phase, however unwrapped in an FWI type inversion. It, thus, provides a single objective function and a natural transition from traveltime tomography to full waveform inversion. A Marmousi example demonstrates the effectiveness of the approach.

Photon Counting System for High-Sensitivity Detection of Bioluminescence at Optical Fiber End.

Science.gov (United States)

Iinuma, Masataka; Kadoya, Yutaka; Kuroda, Akio

2016-01-01

The technique of photon counting is widely used for various fields and also applicable to a high-sensitivity detection of luminescence. Thanks to recent development of single photon detectors with avalanche photodiodes (APDs), the photon counting system with an optical fiber has become powerful for a detection of bioluminescence at an optical fiber end, because it allows us to fully use the merits of compactness, simple operation, highly quantum efficiency of the APD detectors. This optical fiber-based system also has a possibility of improving the sensitivity to a local detection of Adenosine triphosphate (ATP) by high-sensitivity detection of the bioluminescence. In this chapter, we are introducing a basic concept of the optical fiber-based system and explaining how to construct and use this system.

Improving attenuation tomography by novel inversions for t* and Q: application to Parkfield, California and Okmok volcano, Alaska

Science.gov (United States)

Pesicek, J. D.; Bennington, N. L.; Thurber, C. H.; Zhang, H.

2011-12-01

Standard methods for mapping variations in seismic attenuation (Q) structure using local earthquake data involve a two-step process. First, values of the whole path attenuation operator t* are determined from earthquake data recorded on a seismic array by inverting observed spectra for source and attenuation parameters. Then, these t* data are used to invert tomographically for frequency-independent Q models. The observed earthquake amplitude spectra depend on both source parameters and site effects. However, quantification of site effects is often neglected. Bennington et al. [2008] determined site response jointly with source parameters for small groups of events and then computed each station's site response as the average over all groups. Building on this work, we have adapted the method to model all events simultaneously to more accurately determine site response from the earthquake spectra. This in turn allows us to more accurately determine t*. However, resolution analysis of the results shows that some parameters are not well resolved in the joint inversion. Thus, an alternating inversion scheme is tested and adapted to alleviate poor resolution and parameter trade-offs. The new scheme produces better fits to the earthquake spectra than previous methods, and the resulting t* data should allow for more accurate determination of the Q structure. Because the equation relating t* to Q is nonlinear, the typical approach to determining Q is to solve for changes to a starting model iteratively, similar to methods commonly used in travel time tomography. However, if we instead solve for the inverse of Q, the equation becomes linear and the solution no longer depends on the starting model. This simple modification may allow us to more accurately determine Q. We test these new t* and Q methods using earthquake data from Parkfield, California and Okmok volcano, Alaska. We present the results for real and synthetic data and compare and contrast these results to more

VECTOR TOMOGRAPHY FOR THE CORONAL MAGNETIC FIELD. II. HANLE EFFECT MEASUREMENTS

International Nuclear Information System (INIS)

Kramar, M.; Inhester, B.; Lin, H.; Davila, J.

2013-01-01

In this paper, we investigate the feasibility of saturated coronal Hanle effect vector tomography or the application of vector tomographic inversion techniques to reconstruct the three-dimensional magnetic field configuration of the solar corona using linear polarization measurements of coronal emission lines. We applied Hanle effect vector tomographic inversion to artificial data produced from analytical coronal magnetic field models with equatorial and meridional currents and global coronal magnetic field models constructed by extrapolation of real photospheric magnetic field measurements. We tested tomographic inversion with only Stokes Q, U, electron density, and temperature inputs to simulate observations over large limb distances where the Stokes I parameters are difficult to obtain with ground-based coronagraphs. We synthesized the coronal linear polarization maps by inputting realistic noise appropriate for ground-based observations over a period of two weeks into the inversion algorithm. We found that our Hanle effect vector tomographic inversion can partially recover the coronal field with a poloidal field configuration, but that it is insensitive to a corona with a toroidal field. This result demonstrates that Hanle effect vector tomography is an effective tool for studying the solar corona and that it is complementary to Zeeman effect vector tomography for the reconstruction of the coronal magnetic field

Passive seismic tomography application for cave monitoring in DOZ underground mine PT. Freeport Indonesia

International Nuclear Information System (INIS)

Nurhandoko, Bagus Endar B.; Wely, Woen; Setiadi, Herlan; Riyanto, Erwin

2015-01-01

It is already known that tomography has a great impact for analyzing and mapping unknown objects based on inversion, travel time as well as waveform inversion. Therefore, tomography has used in wide area, not only in medical but also in petroleum as well as mining. Recently, tomography method is being applied in several mining industries. A case study of tomography imaging has been carried out in DOZ ( Deep Ore Zone ) block caving mine, Tembagapura, Papua. Many researchers are undergoing to investigate the properties of DOZ cave not only outside but also inside which is unknown. Tomography takes a part for determining this objective.The sources are natural from the seismic events that caused by mining induced seismicity and rocks deformation activity, therefore it is called as passive seismic. These microseismic travel time data are processed by Simultaneous Iterative Reconstruction Technique (SIRT). The result of the inversion can be used for DOZ cave monitoring. These information must be used for identifying weak zone inside the cave. In addition, these results of tomography can be used to determine DOZ and cave information to support mine activity in PT. Freeport Indonesia

Passive seismic tomography application for cave monitoring in DOZ underground mine PT. Freeport Indonesia

Energy Technology Data Exchange (ETDEWEB)

Nurhandoko, Bagus Endar B.; Wely, Woen; Setiadi, Herlan [WISFIR Laboratory, Earth Physics and Complex System Division, Physics Department, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung (Indonesia); Riyanto, Erwin [Geotechnical and Hydrology PT. Freeport Indonesia wonbin-ww@hotmail.com (Indonesia)

2015-04-16

It is already known that tomography has a great impact for analyzing and mapping unknown objects based on inversion, travel time as well as waveform inversion. Therefore, tomography has used in wide area, not only in medical but also in petroleum as well as mining. Recently, tomography method is being applied in several mining industries. A case study of tomography imaging has been carried out in DOZ ( Deep Ore Zone ) block caving mine, Tembagapura, Papua. Many researchers are undergoing to investigate the properties of DOZ cave not only outside but also inside which is unknown. Tomography takes a part for determining this objective.The sources are natural from the seismic events that caused by mining induced seismicity and rocks deformation activity, therefore it is called as passive seismic. These microseismic travel time data are processed by Simultaneous Iterative Reconstruction Technique (SIRT). The result of the inversion can be used for DOZ cave monitoring. These information must be used for identifying weak zone inside the cave. In addition, these results of tomography can be used to determine DOZ and cave information to support mine activity in PT. Freeport Indonesia.

Bioluminescence determination of active caspase-3 in single apoptotic cells

Czech Academy of Sciences Publication Activity Database

Lišková, Marcela; Klepárník, Karel; Matalová, Eva; Hegrová, Jitka; Přikryl, Jan; Švandová, Eva; Foret, František

2013-01-01

Roč. 34, č. 12 (2013), s. 1772-1777 ISSN 0173-0835 R&D Projects: GA ČR GAP206/11/2377 Grant - others:GA ČR(CZ) GAP502/12/1285 Program:GA Institutional support: RVO:68081715 ; RVO:67985904 Keywords : apoptosis * bioluminescence * caspase-3 Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.161, year: 2013

Auroral Tomography Workshop, Proceedings

International Nuclear Information System (INIS)

Steen, Aa.

1993-08-01

In ionospheric and atmospheric physics the importance of multi-station imaging has grown as a consequence of the availability of scientific grade CCD cameras with digital output and affordable massive computing power. Tomographic inversion techniques are used in many different areas, e.g. medicine, plasma research and space physics. The tomography workshop was announced to gather a limited group of people interested in auroral tomography or tomographic inversion methods in general. ALIS (Auroral Large Imaging System) is a multi-station ground-based system developed primarily for three-dimensional auroral imaging, however other non-auroral objects can be studied with ALIS, e.g. stratospheric clouds. Several of the contributions in the workshop dealt with problems related to geometries similar to the ALIS-configuration. The Proceedings contain written contributions received either in abstract form or as full papers. The Proceedings also contain contributions intended for the Workshop but not presented due to the absence of the speaker. Separate abstracts have been prepared for 15 of the 17 papers

Wave equation tomography using the unwrapped phase - Analysis of the traveltime sensitivity kernels

KAUST Repository

Djebbi, Ramzi

2013-01-01

Full waveform inversion suffers from the high non-linearity in the misfit function, which causes the convergence to a local minimum. In the other hand, traveltime tomography has a quasi-linear misfit function but yields low- resolution models. Wave equation tomography (WET) tries to improve on traveltime tomography, by better adhering to the requirements of our finite-frequency data. However, conventional (WET), based on the crosscorelaion lag, yields the popular hallow banana sensitivity kernel indicating that the measured wavefield at a point is insensitive to perturbations along the ray theoretical path at certain finite frequencies. Using the instantaneous traveltime, the sensitivity kernel reflects more the model-data dependency we grown accustom to in seismic inversion (even phase inversion). Demonstrations on synthetic and the Mamousi model support such assertions.

BarTeL, a Genetically Versatile, Bioluminescent and Granule Neuron Precursor-Targeted Mouse Model for Medulloblastoma.

Directory of Open Access Journals (Sweden)

Gregory M Shackleford

Full Text Available Medulloblastomas are the most common malignant pediatric brain tumor and have been divided into four major molecular subgroups. Animal models that mimic the principal molecular aberrations of these subgroups will be important tools for preclinical studies and allow greater understanding of medulloblastoma biology. We report a new transgenic model of medulloblastoma that possesses a unique combination of desirable characteristics including, among others, the ability to incorporate multiple and variable genes of choice and to produce bioluminescent tumors from a limited number of somatic cells within a normal cellular environment. This model, termed BarTeL, utilizes a Barhl1 homeobox gene promoter to target expression of a bicistronic transgene encoding both the avian retroviral receptor TVA and an eGFP-Luciferase fusion protein to neonatal cerebellar granule neuron precursor (cGNP cells, which are cells of origin for the sonic hedgehog (SHH subgroup of human medulloblastomas. The Barhl1 promoter-driven transgene is expressed strongly in mammalian cGNPs and weakly or not at all in mature granule neurons. We efficiently induced bioluminescent medulloblastomas expressing eGFP-luciferase in BarTeL mice by infection of a limited number of somatic cGNPs with avian retroviral vectors encoding the active N-terminal fragment of SHH and a stabilized MYCN mutant. Detection and quantification of the increasing bioluminescence of growing tumors in young BarTeL mice was facilitated by the declining bioluminescence of their uninfected maturing cGNPs. Inclusion of eGFP in the transgene allowed enriched sorting of cGNPs from neonatal cerebella. Use of a single bicistronic avian vector simultaneously expressing both Shh and Mycn oncogenes increased the medulloblastoma incidence and aggressiveness compared to mixed virus infections. Bioluminescent tumors could also be produced by ex vivo transduction of neonatal BarTeL cerebellar cells by avian retroviruses and

Dual-color bioluminescent sensor proteins for therapeutic drug monitoring of antitumor antibodies

NARCIS (Netherlands)

van Rosmalen, M.; Ni, Y.; Vervoort, D.F.M.; Arts, R.; Ludwig, S.K.J.; Merkx, M.

2018-01-01

Monitoring the levels of therapeutic antibodies in individual patients would allow patient-specific dose optimization, with the potential for major therapeutic and financial benefits. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor)

Submersible Data (Dive Waypoints) for Bioluminescence 2009 - Office of Ocean Exploration and Research

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Data and information collected by the submersible Johnson Sea-Link II at waypoints along its track during seventeen dives of the 2009 "Bioluminescence" expedition...

Near-surface traveltime tomographic inversion using multiple first break picks

KAUST Repository

Saragiotis, Christos; Choi, Yun Seok; Keho, T.; Alkhalifah, Tariq Ali

2013-01-01

The input data for refraction traveltime tomography are the traveltimes of the first breaks, which are picked using automatic pickers. Although automatic pickers perform satisfactorily overall, no one automatic picker can be characterized as the best one; one picker might fail for traces for which other pickers are accurate and vice versa for other traces. We introduce an iterative method for traveltime tomography, which takes as input traveltimes from a number of pickers. During the inversion scheme inconsistent traveltimes are replaced with more meaningful ones to obtain a smooth near-surface velocity model. The scheme is easily parallelizable and a byproduct of the inversion scheme is a set of consistent traveltimes which is close to the actual traveltimes of the first breaks.

Double-Difference Global Adjoint Tomography

Science.gov (United States)

Orsvuran, R.; Bozdag, E.; Lei, W.; Tromp, J.

2017-12-01

The adjoint method allows us to incorporate full waveform simulations in inverse problems. Misfit functions play an important role in extracting the relevant information from seismic waveforms. In this study, our goal is to apply the Double-Difference (DD) methodology proposed by Yuan et al. (2016) to global adjoint tomography. Dense seismic networks, such as USArray, lead to higher-resolution seismic images underneath continents. However, the imbalanced distribution of stations and sources poses challenges in global ray coverage. We adapt double-difference multitaper measurements to global adjoint tomography. We normalize each DD measurement by its number of pairs, and if a measurement has no pair, as may frequently happen for data recorded at oceanic stations, classical multitaper measurements are used. As a result, the differential measurements and pair-wise weighting strategy help balance uneven global kernel coverage. Our initial experiments with minor- and major-arc surface waves show promising results, revealing more pronounced structure near dense networks while reducing the prominence of paths towards cluster of stations. We have started using this new measurement in global adjoint inversions, addressing azimuthal anisotropy in upper mantle. Meanwhile, we are working on combining the double-difference approach with instantaneous phase measurements to emphasize contributions of scattered waves in global inversions and extending it to body waves. We will present our results and discuss challenges and future directions in the context of global tomographic inversions.

A multi-channel bioluminescent bacterial biosensor for the on-line detection of metals and toxicity. Part I: design and optimization of bioluminescent bacterial strains

Energy Technology Data Exchange (ETDEWEB)

Charrier, Thomas; Durand, Marie-Jose; Jouanneau, Sulivan; Thouand, Gerald [UMR CNRS 6144 GEPEA, CBAC, Nantes University, PRES UNAM, Campus de la Courtaisiere-IUT, La Roche-sur-Yon cedex (France); Dion, Michel [UMR CNRS 6204, Nantes University, PRES UNAM, Biotechnologie, Biocatalyse, Bioregulation, 2, Rue de la Houssiniere, BP 92208, Nantes cedex 3 (France); Pernetti, Mimma; Poncelet, Denis [ONIRIS-ENITIAA, UMR CNRS GEPEA, Rue de la Geraudiere, BP 82225, Nantes cedex 3 (France)

2011-05-15

This study describes the construction of inducible bioluminescent strains via genetic engineering along with their characterization and optimization in the detection of heavy metals. Firstly, a preliminary comparative study enabled us to select a suitable carbon substrate from pyruvate, glucose, citrate, diluted Luria-Bertani, and acetate. The latter carbon source provided the best induction ratios for comparison. Results showed that the three constructed inducible strains, Escherichia coli DH1 pBzntlux, pBarslux, and pBcoplux, were usable when conducting a bioassay after a 14-h overnight culture at 30 C. Utilizing these sensors gave a range of 12 detected heavy metals including several cross-detections. Detection limits for each metal were often close to and sometimes lower than the European standards for water pollution. Finally, in order to maintain sensitive bacteria within the future biosensor-measuring cell, the agarose immobilization matrix was compared to polyvinyl alcohol (PVA). Agarose was selected because the detection limits of the bioluminescent strains were not affected, in contrast to PVA. Specific detection and cross-detection ranges determined in this study will form the basis of a multiple metals detection system by the new multi-channel Lumisens3 biosensor. (orig.)

Adjoint-state inversion of electric resistivity tomography data of seawater intrusion at the Argentona coastal aquifer (Spain)

Science.gov (United States)

Fernández-López, Sheila; Carrera, Jesús; Ledo, Juanjo; Queralt, Pilar; Luquot, Linda; Martínez, Laura; Bellmunt, Fabián

2016-04-01

Seawater intrusion in aquifers is a complex phenomenon that can be characterized with the help of electric resistivity tomography (ERT) because of the low resistivity of seawater, which underlies the freshwater floating on top. The problem is complex because of the need for joint inversion of electrical and hydraulic (density dependent flow) data. Here we present an adjoint-state algorithm to treat electrical data. This method is a common technique to obtain derivatives of an objective function, depending on potentials with respect to model parameters. The main advantages of it are its simplicity in stationary problems and the reduction of computational cost respect others methodologies. The relationship between the concentration of chlorides and the resistivity values of the field is well known. Also, these resistivities are related to the values of potentials measured using ERT. Taking this into account, it will be possible to define the different resistivities zones from the field data of potential distribution using the basis of inverse problem. In this case, the studied zone is situated in Argentona (Baix Maresme, Catalonia), where the values of chlorides obtained in some wells of the zone are too high. The adjoint-state method will be used to invert the measured data using a new finite element code in C ++ language developed in an open-source framework called Kratos. Finally, the information obtained numerically with our code will be checked with the information obtained with other codes.

Heterogeneity in quorum sensing-regulated bioluminescence of Vibrio harveyi.

Science.gov (United States)

Anetzberger, Claudia; Pirch, Torsten; Jung, Kirsten

2009-07-01

Quorum sensing (QS) refers to the ability of bacterial populations to read out the local environment for cell density and to collectively activate gene expression. Vibrio harveyi, one of the best characterized model organisms in QS, was used to address the question how single cells behave within a QS-activated community in a homogeneous environment. Analysis of the QS-regulated bioluminescence of a wild type strain revealed that even at high cell densities only 69% of the cells of the population produced bioluminescence, 25% remained dark and 6% were dead. Moreover, light intensities greatly varied from cell to cell at high population density. Addition of autoinducer to a bright liquid culture of V. harveyi increased the percentage of luminescent cells up to 98%, suggesting that V. harveyi produces and/or keeps the autoinducers at non-saturating concentrations. In contrast, all living cells of a constitutive QS-active mutant (DeltaluxO) produced light. We also found that QS affects biofilm formation in V. harveyi. Our data provide first evidence that a heterogeneous population produces more biofilm than a homogeneous one. It is suggested that even a QS-committed population of V. harveyi takes advantage of heterogeneity, which extends the current view of QS-regulated uniformity.

Structure of fungal oxyluciferin, the product of the bioluminescence reaction.

Science.gov (United States)

Purtov, K V; Osipova, Z M; Petushkov, V N; Rodionova, N S; Tsarkova, A S; Kotlobay, A A; Chepurnykh, T V; Gorokhovatsky, A Yu; Yampolsky, I V; Gitelson, J I

2017-11-01

The structure of fungal oxyluciferin was determined, the enzymatic bioluminescence reaction under substrate saturation conditions with discrete monitoring of formed products was conducted, and the structures of the end products of the reaction were established. On the basis of these studies, the scheme of oxyluciferin degradation to the end products was developed. The structure of fungal oxyluciferin was confirmed by counter synthesis.

Local inversions in ultrasound-modulated optical tomography

International Nuclear Information System (INIS)

Bal, Guillaume; Moskow, Shari

2014-01-01

Ultrasound-modulated optical tomography is a hybrid imaging modality that aims to combine the high contrast of optical waves with the high resolution of ultrasound. We follow the model of the influence of ultrasound modulation on the light intensity measurements developed in Bal and Schotland (2010 Phys. Rev. Lett. 104 043902). We present sufficient conditions ensuring that the absorption and diffusion coefficients modeling light propagation can locally be uniquely and stably reconstructed from the corresponding available information. We present an iterative procedure to solve such a problem based on the analysis of linear elliptic systems of redundant partial differential equations. (paper)

Doppler Tomography

Science.gov (United States)

Marsh, T. R.

I review the method of Doppler tomography which translates binary-star line profiles taken at a series of orbital phases into a distribution of emission over the binary. I begin with a discussion of the basic principles behind Doppler tomography, including a comparison of the relative merits of maximum entropy regularisation versus filtered back-projection for implementing the inversion. Following this I discuss the issue of noise in Doppler images and possible methods for coping with it. Then I move on to look at the results of Doppler Tomography applied to cataclysmic variable stars. Outstanding successes to date are the discovery of two-arm spiral shocks in cataclysmic variable accretion discs and the probing of the stream/magnetospheric interaction in magnetic cataclysmic variable stars. Doppler tomography has also told us much about the stream/disc interaction in non-magnetic systems and the irradiation of the secondary star in all systems. The latter indirectly reveals such effects as shadowing by the accretion disc or stream. I discuss all of these and finish with some musings on possible future directions for the method. At the end I include a tabulation of Doppler maps published in refereed journals.

Observations and Measurements of Planktonic Bioluminescence in and Around a Milky Sea

Science.gov (United States)

1988-03-01

malticharnel analysers operating in the multiscaler mode. The details of both the onboard underway system and the LPTC systems have been published (Lapota...the Arabian Sea during the southwest monsoon. No nutrient data was collected during our study, yet phosphates, nitrates , and trace BIOLUMINESCENCE IN

Preliminary results of local earthquake tomography around Bali, Lombok, and Sumbawa regions

Energy Technology Data Exchange (ETDEWEB)

Nugraha, Andri Dian, E-mail: nugraha@gf.itb.ac.id; Puspito, Nanang T; Yudistira, Tedi [Global Geophysical Reserach Group, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, JlGanesa 10, Bandung, 40132 (Indonesia); Kusnandar, Ridwan; Sakti, Artadi Pria [Meteorological, Climatological, and Geophysical Agency (MCGA) of Indonesian, Jakarta (Indonesia)

2015-04-24

Bali, Sumbawa, and Lombok regions are located in active tectonic influence by Indo-Australia plate subducts beneath Sunda plate in southern part and local back-arc thrust in northern part the region. Some active volcanoes also lie from eastern part of Java, Bali, Lombok and Sumbawa regions. Previous studies have conducted subsurface seismic velocity imaging using regional and global earthquake data around the region. In this study, we used P-arrival time from local earthquake networks compiled by MCGA, Indonesia within time periods of 2009 up to 2013 to determine seismic velocity structure and simultaneously hypocenter adjustment by applying seismic tomography inversion method. For the tomographic inversion procedure, we started from 1-D initial velocity structure. We evaluated the resolution of tomography inversion results through checkerboard test and calculating derivative weigh sum. The preliminary results of tomography inversion show fairly clearly high seismic velocity subducting Indo-Australian and low velocity anomaly around volcano regions. The relocated hypocenters seem to cluster around the local fault system such as back-arc thrust fault in northern part of the region and around local fault in Sumbawa regions. Our local earthquake tomography results demonstrated consistent with previous studies and improved the resolution. For future works, we will determine S-wave velocity structure using S-wave arrival time to enhance our understanding of geological processes and for much better interpretation.

Recent Advances and Field Trial Results Integrating Cosmic Ray Muon Tomography with Other Data Sources for Mineral Exploration

Science.gov (United States)

Schouten, D.

2015-12-01

CRM GeoTomography Technologies, Inc. is leading the way in applying muon tomography to discovery and definition of dense ore bodies for mineral exploration and resource estimation. We have successfully imaged volcanogenic massive sulfide (VMS) deposits at mines in North America using our suite of field-proven muon tracking detectors, and are at various stages of development for other applications. Recently we developed in-house inversion software that integrates data from assays, surface and borehole gravity, and underground muon flux measurements. We have found that the differing geophysical data sources provide complementary information and that dramatic improvements in inversion results are attained using various inversion performance metrics related to the excess tonnage of the mineral deposits, as well as their spatial extents and locations. This presentation will outline field tests of muon tomography performed by CRM Geotomography in some real world examples, and will demonstrate the effectiveness of joint muon tomography, assay and gravity inversion techniques in field tests (where data are available) and in simulations.

Luciferin Amides Enable in Vivo Bioluminescence Detection of Endogenous Fatty Acid Amide Hydrolase Activity.

Science.gov (United States)

Mofford, David M; Adams, Spencer T; Reddy, G S Kiran Kumar; Reddy, Gadarla Randheer; Miller, Stephen C

2015-07-15

Firefly luciferase is homologous to fatty acyl-CoA synthetases. We hypothesized that the firefly luciferase substrate d-luciferin and its analogs are fatty acid mimics that are ideally suited to probe the chemistry of enzymes that release fatty acid products. Here, we synthesized luciferin amides and found that these molecules are hydrolyzed to substrates for firefly luciferase by the enzyme fatty acid amide hydrolase (FAAH). In the presence of luciferase, these molecules enable highly sensitive and selective bioluminescent detection of FAAH activity in vitro, in live cells, and in vivo. The potency and tissue distribution of FAAH inhibitors can be imaged in live mice, and luciferin amides serve as exemplary reagents for greatly improved bioluminescence imaging in FAAH-expressing tissues such as the brain.

Uninterrupted monitoring of drug effects in human-induced pluripotent stem cell-derived cardiomyocytes with bioluminescence Ca2+ microscopy.

Science.gov (United States)

Suzuki, Kazushi; Onishi, Takahito; Nakada, Chieko; Takei, Shunsuke; Daniels, Matthew J; Nakano, Masahiro; Matsuda, Tomoki; Nagai, Takeharu

2018-05-18

Cardiomyocytes derived from human-induced pluripotent stem cells are a powerful platform for high-throughput drug screening in vitro. However, current modalities for drug testing, such as electrophysiology and fluorescence imaging have inherent drawbacks. To circumvent these problems, we report the development of a bioluminescent Ca 2+ indicator GmNL(Ca 2+ ), and its application in a customized microscope for high-throughput drug screening. GmNL(Ca 2+ ) gives a 140% signal change with Ca 2+ , and can image drug-induced changes of Ca 2+ dynamics in cultured cells. Since bioluminescence requires application of a chemical substrate, which is consumed over ~ 30 min we made a dedicated microscope with automated drug dispensing inside a light-tight box, to control drug addition. To overcome thermal instability of the luminescent substrate, or small molecule, dual climate control enables distinct temperature settings in the drug reservoir and the biological sample. By combining GmNL(Ca 2+ ) with this adaptation, we could image spontaneous Ca 2+ transients in cultured cardiomyocytes and phenotype their response to well-known drugs without accessing the sample directly. In addition, the bioluminescent strategy demonstrates minimal perturbation of contractile parameters and long-term observation attributable to lack of phototoxicity and photobleaching. Overall, bioluminescence may enable more accurate drug screening in a high-throughput manner.

Reflection tomography from pre-stack migrated images; Tomographie de reflexion a partir des images migrees avant addition

Energy Technology Data Exchange (ETDEWEB)

Adler, F

1996-10-29

The application of reflection tomography to data from complex geological structures is very interesting in the hydrocarbons exploration. Indeed, it contributes to localize the hydrocarbons potential traps. The used reflection tomography method is faced with two major difficulties. Travel time picking is difficult or impossible in seismic time sections. The processing of multiple arrival travel times needs an adequate formulation of reflection tomography. In order to solve the first problem, we adopt the approach of the SMART (Sequential Migration Aided Reflection Tomography) method which is an original method for the implementation of migration velocity analysis. The velocity model is automatically calculated by reflection tomography. The kinematic data set for reflection tomography is constructed from pre-stack depth-migrated images that are interpreted in the chosen migration configuration. For the implementation of the SMART method in the common-offset domain, we propose an original formulation of reflection tomography that takes multiple arrival travel times, which are calculated from common-offset migrated images, into account. In this new formulation, we look for a model such that a modelling, which consists in shooting in this model from the source locations with some ray parameters at the source, matches some emergence conditions: for each offset, the rays emerge at the receiver locations (given by the offset) with the same travel times and the same travel time slopes as observed in the associated common-offset section. These conditions constitute the kinematic data set for tomographic inversion. The common-offset travel time slope is the difference between the ray parameter at the receiver and the ray parameter at the source. Therefore, the ray parameter at the source is an unknown and has to be determined together with the model parameters during inversion. (author)

Bioluminescence imaging of β cells and intrahepatic insulin gene activity under normal and pathological conditions.

Directory of Open Access Journals (Sweden)

Tokio Katsumata

Full Text Available In diabetes research, bioluminescence imaging (BLI has been applied in studies of β-cell impairment, development, and islet transplantation. To develop a mouse model that enables noninvasive imaging of β cells, we generated a bacterial artificial chromosome (BAC transgenic mouse in which a mouse 200-kbp genomic fragment comprising the insulin I gene drives luciferase expression (Ins1-luc BAC transgenic mouse. BLI of mice was performed using the IVIS Spectrum system after intraperitoneal injection of luciferin, and the bioluminescence signal from the pancreatic region analyzed. When compared with MIP-Luc-VU mice [FVB/N-Tg(Ins1-lucVUPwrs/J] expressing luciferase under the control of the 9.2-kbp mouse insulin I promoter (MIP, the bioluminescence emission from Ins1-luc BAC transgenic mice was enhanced approximately 4-fold. Streptozotocin-treated Ins1-luc BAC transgenic mice developed severe diabetes concomitant with a sharp decline in the BLI signal intensity in the pancreas. Conversely, mice fed a high-fat diet for 8 weeks showed an increase in the signal, reflecting a decrease or increase in the β-cell mass. Although the bioluminescence intensity of the islets correlated well with the number of isolated islets in vitro, the intensity obtained from a living mouse in vivo did not necessarily reflect an absolute quantification of the β-cell mass under pathological conditions. On the other hand, adenovirus-mediated gene transduction of β-cell-related transcription factors in Ins1-luc BAC transgenic mice generated luminescence from the hepatic region for more than 1 week. These results demonstrate that BLI in Ins1-luc BAC transgenic mice provides a noninvasive method of imaging islet β cells and extrapancreatic activity of the insulin gene in the liver under normal and pathological conditions.

Dual monitoring using 124I-FIAU and bioluminescence for HSV1-tk suicide gene therapy

International Nuclear Information System (INIS)

Lee, T. S.; Kim, J. H.; Kwon, H. C.

2007-01-01

Herpes simplex virus type I thymidine kinase (HSV-tk) is the most common reporter gene and is used in cancer gene therapy with a prodrug nucleoside analog, ganciclovir (GCV). The aim of this study is to evaluate therapeutic efficacy of suicide gene therapy with 2'-fluoro-2'-deoxy-1-D-arabinofuranosyl-5-[ 124 I] iodouracil ( 124 I - FIAU) and bioluminescence in retrovirally HSV -tk and firefly luciferase transduced hepatoma model. The HSV -tk and firefly luciferase (Luc) was retrovirally transduced and expressed in MCA rat Morris hepatoma cells. Nude mice with subcutaneous tumors, MCA and MCA-TK-Luc, were subjected to GCV treatment (50mg/Kg/d intraperitoneally) for 5 day. PET imaging and biodistribution with ( 124 I-FIAU) were performed at before and after initiation of therapy with GCV. Bioluminescent signal was also measured during GCV treatment. Before GCV treatment, no significant difference in tumor volume was found in tumors between MCA and MCA-TK-Luc. After GCV treatment, tumor volume of MCA-TK-Luc markedly reduced compared to that of MCA. In biodistribution study, 124 I-FIAU uptake after GCV therapy significantly decreased compared with pretreatment levels (34.8 13.67 %ID/g vs 7.6 2.59 %ID/g) and bioluminescent signal was also significantly decreased compared with pretreatment levels. In small animal PET imaging, 124 I-FIAU selectively localized in HSV -tk expressing tumor and the therapeutic efficacy of GCV treatment was evaluated by 124 I-FIAU PET imaging. 124 I-FIAU PET and bioluminescence imaging in HSV-tk suicide gene therapy were effective to evaluate the therapeutic response. 124 I-FIAU may serve as an efficient and selective agent for monitoring of transduced HSV1-tk gene expression in vivo in clinical trials

Nucleic acid detection using BRET-beacons based on bioluminescent protein-DNA hybrids

NARCIS (Netherlands)

Engelen, W.; van de Wiel, K.M.; Meijer, L.H.H.; Saha, B.; Merkx, M.

2017-01-01

Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM

Investigation of Processes and Factors Regulating the Generation, Maintenance and Breakdown of Bioluminescent Thin Layers

National Research Council Canada - National Science Library

Widder, Edith

2001-01-01

.... Katz's submersible holographic camera mounted on the upper work platform. Thin layers were located using real-time sensor feedback from intensified video recordings of stimulated bioluminescence...

Development of Optical Molecular Imaging System for the Acquisition of Bioluminescence Signals from Small Animals

International Nuclear Information System (INIS)

Lee, Byeong Il; Kim, Hyeon Sik; Jeong, Hye Jin; Lee, Hyung Jae; Moon, Seung Min; Kwon, Seung Young; Jeong, Shin Young; Bom, Hee Seung; Min, Jung Joon; Choi, Eun Seo

2009-01-01

Optical imaging is providing great advance and improvement in genetic and molecular imaging of animals and humans. Optical imaging system consists of optical imaging devices, which carry out major function for monitoring, tracing, and imaging in most of molecular in-vivo researches. In bio-luminescent imaging, small animals containing luciferase gene locally irradiate light, and emitted photons transmitted through skin of the small animals are imaged by using a high sensitive charged coupled device (CCD) camera. In this paper, we introduced optical imaging system for the image acquisition of bio-luminescent signals emitted from small animals. In the system, Nikon lens and four LED light sources were mounted at the inside of a dark box. A cooled CCD camera equipped with a control module was used. We tested the performance of the optical imaging system using effendorf tube and light emitting bacteria which injected intravenously into CT26 tumor bearing nude mouse. The performance of implemented optical imaging system for bio-luminescence imaging was demonstrated and the feasibility of the system in small animal imaging application was proved. We anticipate this system could be a useful tool for the molecular imaging of small animals adaptable for various experimental conditions in future

Brazilian Bioluminescent Beetles: Reflections on Catching Glimpses of Light in the Atlantic Forest and Cerrado

Directory of Open Access Journals (Sweden)

ETELVINO J.H. BECHARA

Full Text Available ABSTRACT Bioluminescence - visible and cold light emission by living organisms - is a worldwide phenomenon, reported in terrestrial and marine environments since ancient times. Light emission from microorganisms, fungi, plants and animals may have arisen as an evolutionary response against oxygen toxicity and was appropriated for sexual attraction, predation, aposematism, and camouflage. Light emission results from the oxidation of a substrate, luciferin, by molecular oxygen, catalyzed by a luciferase, producing oxyluciferin in the excited singlet state, which decays to the ground state by fluorescence emission. Brazilian Atlantic forests and Cerrados are rich in luminescent beetles, which produce the same luciferin but slightly mutated luciferases, which result in distinct color emissions from green to red depending on the species. This review focuses on chemical and biological aspects of Brazilian luminescent beetles (Coleoptera belonging to the Lampyridae (fireflies, Elateridae (click-beetles, and Phengodidae (railroad-worms families. The ATP-dependent mechanism of bioluminescence, the role of luciferase tuning the color of light emission, the “luminous termite mounds” in Central Brazil, the cooperative roles of luciferase and superoxide dismutase against oxygen toxicity, and the hypothesis on the evolutionary origin of luciferases are highlighted. Finally, we point out analytical uses of beetle bioluminescence for biological, clinical, environmental, and industrial samples.

Factors Influencing Quantification of in Vivo Bioluminescence Imaging: Application to Assessment of Pancreatic Islet Transplants

Directory of Open Access Journals (Sweden)

John Virostko

2004-10-01

Full Text Available The aim of this study is to determine and characterize factors influencing in vivo bioluminescence imaging (BLI and apply them to the specific application of imaging transplanted pancreatic islets. Noninvasive quantitative assessment of transplanted pancreatic islets poses a formidable challenge. Murine pancreatic islets expressing firefly luciferase were transplanted under the renal capsule or into the portal vein of nonobese diabetic–severe combined immunodeficiency mice and the bioluminescence was quantified with a cooled charge coupled device camera and digital photon image analysis. The important, but often neglected, effects of wound healing, mouse positioning, and transplantation site on bioluminescence measurements were investigated by imaging a constant emission, isotropic light-emitting bead (λ = 600 implanted at the renal or hepatic site. The renal beads emitted nearly four times more light than hepatic beads with a smaller spot size, indicating that light absorption and scatter are greatly influenced by the transplant site and must be accounted for in BLI measurements. Detected luminescence decreased with increasing angle between the mouse surface normal and optical axis. By defining imaging parameters such as postsurgical effects, animal positioning, and light attenuation as a function of transplant site, this study develops BLI as a useful imaging modality for quantitative assessment of islets post-transplantation.

Brazilian Bioluminescent Beetles: Reflections on Catching Glimpses of Light in the Atlantic Forest and Cerrado.

Science.gov (United States)

Bechara, Etelvino J H; Stevani, Cassius V

2018-01-01

Bioluminescence - visible and cold light emission by living organisms - is a worldwide phenomenon, reported in terrestrial and marine environments since ancient times. Light emission from microorganisms, fungi, plants and animals may have arisen as an evolutionary response against oxygen toxicity and was appropriated for sexual attraction, predation, aposematism, and camouflage. Light emission results from the oxidation of a substrate, luciferin, by molecular oxygen, catalyzed by a luciferase, producing oxyluciferin in the excited singlet state, which decays to the ground state by fluorescence emission. Brazilian Atlantic forests and Cerrados are rich in luminescent beetles, which produce the same luciferin but slightly mutated luciferases, which result in distinct color emissions from green to red depending on the species. This review focuses on chemical and biological aspects of Brazilian luminescent beetles (Coleoptera) belonging to the Lampyridae (fireflies), Elateridae (click-beetles), and Phengodidae (railroad-worms) families. The ATP-dependent mechanism of bioluminescence, the role of luciferase tuning the color of light emission, the "luminous termite mounds" in Central Brazil, the cooperative roles of luciferase and superoxide dismutase against oxygen toxicity, and the hypothesis on the evolutionary origin of luciferases are highlighted. Finally, we point out analytical uses of beetle bioluminescence for biological, clinical, environmental, and industrial samples.

Flexible Measurement of Bioluminescent Reporters Using an Automated Longitudinal Luciferase Imaging Gas- and Temperature-optimized Recorder (ALLIGATOR).

Science.gov (United States)

Crosby, Priya; Hoyle, Nathaniel P; O'Neill, John S

2017-12-13

Luciferase-based reporters of cellular gene expression are in widespread use for both longitudinal and end-point assays of biological activity. In circadian rhythms research, for example, clock gene fusions with firefly luciferase give rise to robust rhythms in cellular bioluminescence that persist over many days. Technical limitations associated with photomultiplier tubes (PMT) or conventional microscopy-based methods for bioluminescence quantification have typically demanded that cells and tissues be maintained under quite non-physiological conditions during recording, with a trade-off between sensitivity and throughput. Here, we report a refinement of prior methods that allows long-term bioluminescence imaging with high sensitivity and throughput which supports a broad range of culture conditions, including variable gas and humidity control, and that accepts many different tissue culture plates and dishes. This automated longitudinal luciferase imaging gas- and temperature-optimized recorder (ALLIGATOR) also allows the observation of spatial variations in luciferase expression across a cell monolayer or tissue, which cannot readily be observed by traditional methods. We highlight how the ALLIGATOR provides vastly increased flexibility for the detection of luciferase activity when compared with existing methods.

Use of a highly sensitive two-dimensional luminescence imaging system to monitor endogenous bioluminescence in plant leaves

Directory of Open Access Journals (Sweden)

Flor-Henry Michel

2004-11-01

Full Text Available Abstract Background All living organisms emit spontaneous low-level bioluminescence, which can be increased in response to stress. Methods for imaging this ultra-weak luminescence have previously been limited by the sensitivity of the detection systems used. Results We developed a novel configuration of a cooled charge-coupled device (CCD for 2-dimensional imaging of light emission from biological material. In this study, we imaged photon emission from plant leaves. The equipment allowed short integration times for image acquisition, providing high resolution spatial and temporal information on bioluminescence. We were able to carry out time course imaging of both delayed chlorophyll fluorescence from whole leaves, and of low level wound-induced luminescence that we showed to be localised to sites of tissue damage. We found that wound-induced luminescence was chlorophyll-dependent and was enhanced at higher temperatures. Conclusions The data gathered on plant bioluminescence illustrate that the equipment described here represents an improvement in 2-dimensional luminescence imaging technology. Using this system, we identify chlorophyll as the origin of wound-induced luminescence from leaves.

Direct observations of surface water-groundwater interaction using electrical resistivity tomography

NARCIS (Netherlands)

Noell, Ursula; Wießner, Claudia; Ganz, Christina; Westhoff, Martijn

2011-01-01

Electrical resistivity tomography is a helpful tool to observe the infiltration process in and through the soil. Array 3-D measurements and 3-D inversion schemes are required for reliable interpretation of heterogeneous subsurface structures. Smoothing of the inversion can be minimized by using

Multi-frequency accelerating strategy for the contrast source inversion method of ultrasound waveform tomography using pulse data

Science.gov (United States)

Lin, Hongxiang; Azuma, Takashi; Qu, Xiaolei; Takagi, Shu

2017-03-01

In this work, we construct a multi-frequency accelerating strategy for the contrast source inversion (CSI) method using pulse data in the time domain. CSI is a frequency-domain inversion method for ultrasound waveform tomography that does not require the forward solver through the process of reconstruction. Several prior researches show that the CSI method has a good performance of convergence and accuracy in the low-center-frequency situation. In contrast, utilizing the high-center-frequency data leads to a high-resolution reconstruction but slow convergence on large numbers of grid. Our objective is to take full advantage of all low frequency components from pulse data with the high-center-frequency data measured by the diagnostic device. First we process the raw data in the frequency domain. Then multi-frequency accelerating strategy helps restart CSI in the current frequency using the last iteration result obtained from the lower frequency component. The merit of multi- frequency accelerating strategy is that computational burden decreases at the first few iterations. Because the low frequency component of dataset computes on the coarse grid with assuming a fixed number of points per wavelength. In the numerical test, the pulse data were generated by the K-wave simulator and have been processed to meet the computation of the CSI method. We investigate the performance of the multi-frequency and single-frequency reconstructions and conclude that the multi-frequency accelerating strategy significantly enhances the quality of the reconstructed image and simultaneously reduces the average computational time for any iteration step.

Muons tomography applied to geosciences and volcanology

Energy Technology Data Exchange (ETDEWEB)

Marteau, J., E-mail: marteau@ipnl.in2p3.fr [Institut de Physique Nucleaire de Lyon (UMR CNRS-IN2P3 5822), Universite Lyon 1, Lyon (France); Gibert, D.; Lesparre, N. [Institut de Physique du Globe de Paris (UMR CNRS 7154), Sorbonne Paris Cite, Paris (France); Nicollin, F. [Geosciences Rennes (CNRS UMR 6118), Universite Rennes 1, Bat. 15 Campus de Beaulieu, 35042 Rennes cedex (France); Noli, P. [Universita degli studi di Napoli Federico II and INFN sez. Napoli (Italy); Giacoppo, F. [Laboratory for High Energy Physics, University of Bern, SidlerStrasse 5, CH-3012 Bern (Switzerland)

2012-12-11

Imaging the inner part of large geological targets is an important issue in geosciences with various applications. Different approaches already exist (e.g. gravimetry, electrical tomography) that give access to a wide range of information but with identified limitations or drawbacks (e.g. intrinsic ambiguity of the inverse problem, time consuming deployment of sensors over large distances). Here we present an alternative and complementary tomography method based on the measurement of the cosmic muons flux attenuation through the geological structures. We detail the basics of this muon tomography with a special emphasis on the photo-active detectors.

Identification of different geologic units using fuzzy constrained resistivity tomography

Science.gov (United States)

Singh, Anand; Sharma, S. P.

2018-01-01

Different geophysical inversion strategies are utilized as a component of an interpretation process that tries to separate geologic units based on the resistivity distribution. In the present study, we present the results of separating different geologic units using fuzzy constrained resistivity tomography. This was accomplished using fuzzy c means, a clustering procedure to improve the 2D resistivity image and geologic separation within the iterative minimization through inversion. First, we developed a Matlab-based inversion technique to obtain a reliable resistivity image using different geophysical data sets (electrical resistivity and electromagnetic data). Following this, the recovered resistivity model was converted into a fuzzy constrained resistivity model by assigning the highest probability value of each model cell to the cluster utilizing fuzzy c means clustering procedure during the iterative process. The efficacy of the algorithm is demonstrated using three synthetic plane wave electromagnetic data sets and one electrical resistivity field dataset. The presented approach shows improvement on the conventional inversion approach to differentiate between different geologic units if the correct number of geologic units will be identified. Further, fuzzy constrained resistivity tomography was performed to examine the augmentation of uranium mineralization in the Beldih open cast mine as a case study. We also compared geologic units identified by fuzzy constrained resistivity tomography with geologic units interpreted from the borehole information.

Detection of antibodies in blood plasma using bioluminescent sensor proteins and a smartphone

NARCIS (Netherlands)

Arts, R.; den Hartog, I.; Zijlema, S.E.; Thijssen, V.; van der Beelen, S.H.E.; Merkx, M.

2016-01-01

Antibody detection is of fundamental importance in many diagnostic and bioanalytical assays, yet current detection techniques tend to be laborious and/or expensive. We present a new sensor platform (LUMABS) based on bioluminescence resonance energy transfer (BRET) that allows detection of antibodies

Toxicity assessment of Hanford Site wastes by bacterial bioluminescence

International Nuclear Information System (INIS)

Rebagay, T.V.; Dodd, D.A.; Voogd, J.A.

1991-09-01

This paper examines the toxicity of the nonradioactive component of low-level wastes stored in tanks on the Hanford reservation. The use of a faster, cheaper bioassay to replace the 96 hour fish acute toxicity test is examined. The new bioassay is based on loss of bioluminescence of Photobacter phosphoreum (commonly called Microtox) following exposure to toxic materials. This bioassay is calibrated and compares well to the standard fish acute toxicity test for characterization of Hanford Wastes. 4 refs., 11 figs., 11 tabs

Revealing the ability of a novel polysaccharide bioflocculant in bioremediation of heavy metals sensed in a Vibrio bioluminescence reporter assay.

Science.gov (United States)

Sajayan, Arya; Seghal Kiran, G; Priyadharshini, S; Poulose, Navya; Selvin, Joseph

2017-09-01

A bioflocculant-producing bacterial strain, designated MSI021, was isolated from the marine sponge Dendrilla nigra and demonstrated 94% flocculation activity in a kaolin clay suspension. MSI021 was identified as Bacillus cereus based on phylogenetic affiliation and biochemical characteristics. The purified extra-cellular bioflocculant was chemically elucidated as a polysaccharide molecule. The polysaccharide bioflocculant was stable under both acidic and alkaline conditions (pH 2.0-10.0) and temperatures up to 100 °C. The purified bioflocculant efficiently nucleated the formation of silver nanoparticles which showed broad spectrum antibacterial activity. The ability of the bioflocculant to remediate heavy metal toxicity was evaluated by measuring the inhibition of bioluminescence expression in Vibrio harveyi. Enrichment of heavy metals such as zinc, mercury and copper at concentrations of 1, 2 and 3 mM in culture media showed significant reduction of bioluminescence in Vibrio, whereas media enriched with heavy metals and bioflocculant showed dose dependent improvement in the expression of bioluminescence. The assay results demonstrated that the polysaccharide bioflocculant effectively mitigates heavy metal toxicity, thereby improving the expression of bioluminescence in Vibrio. This bioluminescence reporter assay can be developed into a high-throughput format to monitor and evaluate of heavy metal toxicity. The findings of this study revealed that a novel polysaccharide bioflocculant produced by a marine B. cereus demonstrated strong flocculating performance and was effective in nucleating the formation antibacterial silver nanoparticles and removing heavy metals. These results suggest that the MSI021 polysaccharide bioflocculant can be used to develop greener waste water treatment systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Inversion of Ionospheric/plasmaspheric Electron Density From GPS Beacon Observations

Science.gov (United States)

Zou, Y. H.; Xu, J. S.; Ma, S. Y.

It is a space-time 4-D tomography to reconstruct ionospheric/ plasmaspheric elec- tron density, Ne, from ground-based GPS beacon measurements. The mathematical foundation of such inversion is studied in this paper and some simulation results of reconstruction for GPS network observation are presented. Assuming reasonably a power law dependence of NE on time with an index number of 1-3 during one ob- servational time of GPS (60-90min.), 4-D inversion in consideration is reduced to a 3-D cone-beam tomography with incomplete projections. To see clearly the effects of the incompleteness on the quality of reconstruction for 3-D condition, we deduced theoretically the formulae of 3-D parallel-beam tomography. After establishing the mathematical basis, we adopt linear temporal dependence of NE and voxel elemental functions to perform simulation of NE reconstruction with the help of IRI90 model. Reasonable time-dependent 3-D images of ionosphere/ plasmasphere electron density distributions are obtained when taking proper layout of the GPS network and allowing variable resolutions in vertical.

TH-C-17A-12: Integrated CBCT and Optical Tomography System On-Board a Small Animal Radiation Research Platform (SARRP)

Energy Technology Data Exchange (ETDEWEB)

Wang, K; Zhang, B; Eslami, S; Iordachita, I; Wong, J [Johns Hopkins University, Baltimore, MD (United States); Patterson, M [Hamilton Regional Cancer Ctr., Hamilton, ON (Canada)

2014-06-15

Purpose: We present a newly developed on-board optical tomography system for SARRP. Innovative features include the compact design and fast acquisition optical method to perform 3D soft tissue radiation guidance. Because of the on-board feature and the combination of the CBCT, diffusive optical tomography (DOT), bioluminescence and fluorescence tomography (BLT and FT), this integrated system is expected to provide more accurate soft tissue guidance than an off-line system as well as highly sensitive functional imaging in preclinical research. Methods: Images are acquired in the order of CBCT, DOT and then BLT/FT, where the SARRP CBCT and DOT are used to provide the anatomical and optical properties information to enhance the subsequent BLT/FT optical reconstruction. The SARRP stage is redesigned to include 9 imbedded optical fibers in contact with the animal's skin. These fibers, connected to a white light lamp or laser, serve as the light sources for the DOT or FT, respectively. A CCD camera with f/1.4 lens and multi-spectral filter set is used as the optical detector and is mounted on a portable cart ready to dock into the SARRP. No radiation is delivered during optical image acquisition. A 3-way mirror system capable of 180 degree rotation around the animal reflects the optical signal to the camera at multiple projection angles. A special black-painted dome covers the stage and provides the light shielding. Results: Spontaneous metastatic bioluminescent liver and lung tumor models will be used to validate the 3D BLT reconstruction. To demonstrate the capability of our FT system, GastroSense750 fluorescence agent will be used to imaging the mouse stomach and intestinal region in 3D. Conclusion: We expect that this integrated CBCT and optical tomography on-board a SARRP will present new research opportunities for pre-clinical radiation research. Supported by NCI RO1-CA 158100.

TH-C-17A-12: Integrated CBCT and Optical Tomography System On-Board a Small Animal Radiation Research Platform (SARRP)

International Nuclear Information System (INIS)

Wang, K; Zhang, B; Eslami, S; Iordachita, I; Wong, J; Patterson, M

2014-01-01

Purpose: We present a newly developed on-board optical tomography system for SARRP. Innovative features include the compact design and fast acquisition optical method to perform 3D soft tissue radiation guidance. Because of the on-board feature and the combination of the CBCT, diffusive optical tomography (DOT), bioluminescence and fluorescence tomography (BLT and FT), this integrated system is expected to provide more accurate soft tissue guidance than an off-line system as well as highly sensitive functional imaging in preclinical research. Methods: Images are acquired in the order of CBCT, DOT and then BLT/FT, where the SARRP CBCT and DOT are used to provide the anatomical and optical properties information to enhance the subsequent BLT/FT optical reconstruction. The SARRP stage is redesigned to include 9 imbedded optical fibers in contact with the animal's skin. These fibers, connected to a white light lamp or laser, serve as the light sources for the DOT or FT, respectively. A CCD camera with f/1.4 lens and multi-spectral filter set is used as the optical detector and is mounted on a portable cart ready to dock into the SARRP. No radiation is delivered during optical image acquisition. A 3-way mirror system capable of 180 degree rotation around the animal reflects the optical signal to the camera at multiple projection angles. A special black-painted dome covers the stage and provides the light shielding. Results: Spontaneous metastatic bioluminescent liver and lung tumor models will be used to validate the 3D BLT reconstruction. To demonstrate the capability of our FT system, GastroSense750 fluorescence agent will be used to imaging the mouse stomach and intestinal region in 3D. Conclusion: We expect that this integrated CBCT and optical tomography on-board a SARRP will present new research opportunities for pre-clinical radiation research. Supported by NCI RO1-CA 158100

BIOLUMINESCENCE: TEACHING BIOCHEMISTRY BEYOND THE UNIVERSITY WALLS

Directory of Open Access Journals (Sweden)

Ana Paula Jesus de Almeida

2016-11-01

Full Text Available INTRODUCTION: The use of video in teaching and learning processes provides a challenging environment, able to stimulate the intellect and facilitate understanding in life science studies. Videos can be of extraordinary importance in education and dissemination of knowledge, contributing to greater learning, but is rarely used and exploited properly, especially for teaching biochemistry. Biochemistry is considered complex because it involves many molecular structures and processes, especially considering the number of events and molecules involved in the metabolism. OBJECTIVES: This study aimed to introduce biochemistry for the students of basic education using the theme "Light, Science and Life" in a playful and fun way. MATERIALS AND METHODS: A video about bioluminescence was designed and prepared aiming to use it as a support for learning biochemistry by students of basic education of public schools located in Salvador, Bahia. In order to prepare the video, undergraduate students initially revised the literature in order to acquire proper knowledge, and along with their teacher advisor worked the elaboration of texts, textbook and questionnaire and applied at school. DISCUSSION AND RESULTS: Analysis the qualitative results of the experiment on the preparation and use of the video about "Bioluminescence" focused mainly on the content of biochemistry linked to theme Light, Science and Life, and demonstrated the importance of such work in the teaching-learning process. The dynamics used allowed greater interaction between students and teacher, and the teaching of biochemistry in a fun way beyond the university walls. CONCLUSION: The teaching through recreational resources, e.g. videos and other educational strategies that foster learning should be encouraged from basic education, always bearing in order to transmit through these teaching methods the main concepts covered in biochemistry.

Fast automatic segmentation of anatomical structures in x-ray computed tomography images to improve fluorescence molecular tomography reconstruction.

Science.gov (United States)

Freyer, Marcus; Ale, Angelique; Schulz, Ralf B; Zientkowska, Marta; Ntziachristos, Vasilis; Englmeier, Karl-Hans

2010-01-01

The recent development of hybrid imaging scanners that integrate fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) allows the utilization of x-ray information as image priors for improving optical tomography reconstruction. To fully capitalize on this capacity, we consider a framework for the automatic and fast detection of different anatomic structures in murine XCT images. To accurately differentiate between different structures such as bone, lung, and heart, a combination of image processing steps including thresholding, seed growing, and signal detection are found to offer optimal segmentation performance. The algorithm and its utilization in an inverse FMT scheme that uses priors is demonstrated on mouse images.

Dual monitoring using {sup 124}I-FIAU and bioluminescence for HSV1-tk suicide gene therapy

Energy Technology Data Exchange (ETDEWEB)

Lee, T. S.; Kim, J. H.; Kwon, H. C. [Korea Institute of Radiological and Medical Sciences, Seoul (Korea, Republic of)] (and others)

2007-07-01

Herpes simplex virus type I thymidine kinase (HSV-tk) is the most common reporter gene and is used in cancer gene therapy with a prodrug nucleoside analog, ganciclovir (GCV). The aim of this study is to evaluate therapeutic efficacy of suicide gene therapy with 2'-fluoro-2'-deoxy-1-D-arabinofuranosyl-5-[{sup 124}I] iodouracil ({sup 124}I - FIAU) and bioluminescence in retrovirally HSV -tk and firefly luciferase transduced hepatoma model. The HSV -tk and firefly luciferase (Luc) was retrovirally transduced and expressed in MCA rat Morris hepatoma cells. Nude mice with subcutaneous tumors, MCA and MCA-TK-Luc, were subjected to GCV treatment (50mg/Kg/d intraperitoneally) for 5 day. PET imaging and biodistribution with ({sup 124}I-FIAU) were performed at before and after initiation of therapy with GCV. Bioluminescent signal was also measured during GCV treatment. Before GCV treatment, no significant difference in tumor volume was found in tumors between MCA and MCA-TK-Luc. After GCV treatment, tumor volume of MCA-TK-Luc markedly reduced compared to that of MCA. In biodistribution study, {sup 124}I-FIAU uptake after GCV therapy significantly decreased compared with pretreatment levels (34.8 13.67 %ID/g vs 7.6 2.59 %ID/g) and bioluminescent signal was also significantly decreased compared with pretreatment levels. In small animal PET imaging, {sup 124}I-FIAU selectively localized in HSV -tk expressing tumor and the therapeutic efficacy of GCV treatment was evaluated by {sup 124}I-FIAU PET imaging. {sup 124}I-FIAU PET and bioluminescence imaging in HSV-tk suicide gene therapy were effective to evaluate the therapeutic response. {sup 124}I-FIAU may serve as an efficient and selective agent for monitoring of transduced HSV1-tk gene expression in vivo in clinical trials.

What Orthopaedic Operating Room Surfaces Are Contaminated With Bioburden? A Study Using the ATP Bioluminescence Assay.

Science.gov (United States)

Richard, Raveesh Daniel; Bowen, Thomas R

2017-07-01

Contaminated operating room surfaces can increase the risk of orthopaedic infections, particularly after procedures in which hardware implantation and instrumentation are used. The question arises as to how surgeons can measure surface cleanliness to detect increased levels of bioburden. This study aims to highlight the utility of adenosine triphosphate (ATP) bioluminescence technology as a novel technique in detecting the degree of contamination within the sterile operating room environment. What orthopaedic operating room surfaces are contaminated with bioburden? When energy is required for cellular work, ATP breaks down into adenosine biphosphate (ADP) and phosphate (P) and in that process releases energy. This process is inherent to all living things and can be detected as light emission with the use of bioluminescence assays. On a given day, six different orthopaedic surgery operating rooms (two adult reconstruction, two trauma, two spine) were tested before surgery with an ATP bioluminescence assay kit. All of the cases were considered clean surgery without infection, and this included the previously performed cases in each sampled room. These rooms had been cleaned and prepped for surgery but the patients had not been physically brought into the room. A total of 13 different surfaces were sampled once in each room: the operating room (OR) preparation table (both pre- and postdraping), OR light handles, Bovie machine buttons, supply closet countertops, the inside of the Bair Hugger™ hose, Bair Hugger™ buttons, right side of the OR table headboard, tourniquet machine buttons, the Clark-socket attachment, and patient positioners used for total hip and spine positioning. The relative light units (RLUs) obtained from each sample were recorded and data were compiled and averaged for analysis. These values were compared with previously published ATP benchmark values of 250 to 500 RLUs to define cleanliness in both the hospital and restaurant industries. All

Optimal experiment design for quantum state tomography: Fair, precise, and minimal tomography

International Nuclear Information System (INIS)

Nunn, J.; Smith, B. J.; Puentes, G.; Walmsley, I. A.; Lundeen, J. S.

2010-01-01

Given an experimental setup and a fixed number of measurements, how should one take data to optimally reconstruct the state of a quantum system? The problem of optimal experiment design (OED) for quantum state tomography was first broached by Kosut et al.[R. Kosut, I. Walmsley, and H. Rabitz, e-print arXiv:quant-ph/0411093 (2004)]. Here we provide efficient numerical algorithms for finding the optimal design, and analytic results for the case of 'minimal tomography'. We also introduce the average OED, which is independent of the state to be reconstructed, and the optimal design for tomography (ODT), which minimizes tomographic bias. Monte Carlo simulations confirm the utility of our results for qubits. Finally, we adapt our approach to deal with constrained techniques such as maximum-likelihood estimation. We find that these are less amenable to optimization than cruder reconstruction methods, such as linear inversion.

SeisFlows-Flexible waveform inversion software

Science.gov (United States)

Modrak, Ryan T.; Borisov, Dmitry; Lefebvre, Matthieu; Tromp, Jeroen

2018-06-01

SeisFlows is an open source Python package that provides a customizable waveform inversion workflow and framework for research in oil and gas exploration, earthquake tomography, medical imaging, and other areas. New methods can be rapidly prototyped in SeisFlows by inheriting from default inversion or migration classes, and code can be tested on 2D examples before application to more expensive 3D problems. Wave simulations must be performed using an external software package such as SPECFEM3D. The ability to interface with external solvers lends flexibility, and the choice of SPECFEM3D as a default option provides optional GPU acceleration and other useful capabilities. Through support for massively parallel solvers and interfaces for high-performance computing (HPC) systems, inversions with thousands of seismic traces and billions of model parameters can be performed. So far, SeisFlows has run on clusters managed by the Department of Defense, Chevron Corp., Total S.A., Princeton University, and the University of Alaska, Fairbanks.

Inversion of seismic data: how to take the correlated nature of noise into account; Inversion de donnees sismiques: prise en compte de la nature correlee du bruit

Energy Technology Data Exchange (ETDEWEB)

Renard, F.

2003-01-01

The goal of seismic inversion is to recover an Earth model that best fits some observed data. To reach that goal, we have to minimize an objective function that measures the amplitude of the misfits according to a norm to be chosen in data space. In general, the used norm is the L2 norm. Unfortunately, such a norm is not adapted to data corrupted by correlated noise: the noise is in that case inverted as signal and the inversion results are unacceptable. The goal of this thesis is to obtain satisfactory results to the inverse problem in that situation. For this purpose, we study two inverse problems: reflection tomography and waveform inversion. In reflection tomography, we propose a new formulation of the continuum inverse problem which relies on a H1 norm in data space. This allows us to account for the correlated nature of the noise that corrupts the kinematic information. However, this norm does not give more satisfactory results than the ones obtained with the classical formalism. This is why, for sake of simplicity, we recommend to use this classical formalism. Then we try to understand how to properly sample the kinematic information so as to obtain an accurate approximation of the continuum inverse problem. In waveform inversion, we propose to directly invert data corrupted by some correlated noise. A first idea consists in rejecting the noise in the residues. In that goal, we can use a semi-norm to formulate the inverse problem. This technique gives very good results, except when the data are corrupted by random noise. Thus we propose a second method which consists in retrieving, by solving an inverse problem, the signal and the noise whose sum best fits the data. This technique gives very satisfactory results, even if some random noise pollutes the data, and is moreover solved, thanks to an original algorithm, in a very efficient way. (author)

Plasma diagnostics by Abel inversion in hyperbolic geometry

International Nuclear Information System (INIS)

Alhasi, A.S.; Elliott, J.A.

1992-01-01

Plasma confined in the UMIST linear quadrupole adopts a configuration with approximately hyperbolic symmetry. The normal diagnostic is a Langmuir probe, but we have developed an alternative method using optical emission tomography based upon an analytic Abel inversion. Plasma radiance is obtained as a function of a parameter identifying magnetic flux surfaces. The inversion algorithm has been tested using artificial data. Experimentally, the results show that ionizing collisions cause the confined plasma distribution to broaden as the plasma travels through the confining field. This is shown to be a consequence of the approximate incompressibility of the E x B flow. (author)

Tomographic inversion of prismatic reflections for the delineation of steeply dipping structures; Inversion tomographique des reflexions prismatiques en vue de la delineation des structures tres pentees

Energy Technology Data Exchange (ETDEWEB)

Cavalca, M.

2005-11-15

Seismic imaging of salt flanks still remains a challenge for oil exploration. We propose here to exploit the kinematic information contained in prismatic reflections for the delineation of steeply dipping structures, such as faults or overhangs of salt bodies. This double reflection (on a steeply dipping structure and on a sedimentary interface) contains in fact precious information on the geometry of such structures, information that we try to exploit in travel-time tomography. We first carry out a precise kinematic analysis of these unusual reflections, to better understand under which conditions prismatic reflections can be observed in surface data; and we propose some interpretative guidelines, of great help for identifying such reflections in seismic data. We then study the tomographic inversion of prismatic reflections. Our first attempts at inverting prismatic reflections by standard travel-time tomography reveal a major difficulty due to the possible non definition of the standard forward map. We thus propose a new formulation of travel-time tomography which ensures the definition of the forward map and therefore a robust inversion of prismatic reflections. This approach shows its efficiency for delineating steeply dipping (and/or overhanging) structures on different synthetic experiments. We finally illustrate the benefit of jointly using the information contained in prismatic reflections and in primary events for the velocity model building (simultaneous determination of velocities and interface geometries), through the joint inversion of events interpreted and picked on a realistic synthetic dataset (BP-AIT 2004). (author)

Ambient noise adjoint tomography for a linear array in North China

Science.gov (United States)

Zhang, C.; Yao, H.; Liu, Q.; Yuan, Y. O.; Zhang, P.; Feng, J.; Fang, L.

2017-12-01

Ambient noise tomography based on dispersion data and ray theory has been widely utilized for imaging crustal structures. In order to improve the inversion accuracy, ambient noise tomography based on the 3D adjoint approach or full waveform inversion has been developed recently, however, the computational cost is tremendous. In this study we present 2D ambient noise adjoint tomography for a linear array in north China with significant computational efficiency compared to 3D ambient noise adjoint tomography. During the preprocessing, we first convert the observed data in 3D media, i.e., surface-wave empirical Green's functions (EGFs) from ambient noise cross-correlation, to the reconstructed EGFs in 2D media using a 3D/2D transformation scheme. Different from the conventional steps of measuring phase dispersion, the 2D adjoint tomography refines 2D shear wave speeds along the profile directly from the reconstructed Rayleigh wave EGFs in the period band 6-35s. With the 2D initial model extracted from the 3D model from traditional ambient noise tomography, adjoint tomography updates the model by minimizing the frequency-dependent Rayleigh wave traveltime misfits between the reconstructed EGFs and synthetic Green function (SGFs) in 2D media generated by the spectral-element method (SEM), with a preconditioned conjugate gradient method. The multitaper traveltime difference measurement is applied in four period bands during the inversion: 20-35s, 15-30s, 10-20s and 6-15s. The recovered model shows more detailed crustal structures with pronounced low velocity anomaly in the mid-lower crust beneath the junction of Taihang Mountains and Yin-Yan Mountains compared with the initial model. This low velocity structure may imply the possible intense crust-mantle interactions, probably associated with the magmatic underplating during the Mesozoic to Cenozoic evolution of the region. To our knowledge, it's first time that ambient noise adjoint tomography is implemented in 2D media

Rapid susceptibility testing of Mycobacterium tuberculosis by bioluminescence assay of mycobacterial ATP

International Nuclear Information System (INIS)

Nilsson, L.E.; Hoffner, S.E.; Ansehn, S.

1988-01-01

Mycobacterial growth was monitored by bioluminescence assay of mycobacterial ATP. Cultures of Mycobacterium tuberculosis H37Rv and of 25 clinical isolates of the same species were exposed to serial dilutions of ethambutol, isoniazid, rifampin, and streptomycin. A suppression of ATP, indicating growth inhibition, occurred for susceptible but not resistant strains within 5 to 7 days of incubation. Breakpoint concentrations between susceptibility and resistance were determined by comparing these results with those obtained by reference techniques. Full agreement was found in 99% of the assays with the resistance ratio method on Lowenstein-Jensen medium, and 98% of the assays were in full agreement with the radiometric system (BACTEC). A main advantage of the bioluminescence method is its rapidity, with results available as fast as with the radiometric system but at a lower cost and without the need for radioactive culture medium. The method provides kinetic data concerning drug effects within available in vivo drug concentrations and has great potential for both rapid routine susceptibility testing and research applications in studies of drug effects on mycobacteria

Inverse Monte Carlo: a unified reconstruction algorithm for SPECT

International Nuclear Information System (INIS)

Floyd, C.E.; Coleman, R.E.; Jaszczak, R.J.

1985-01-01

Inverse Monte Carlo (IMOC) is presented as a unified reconstruction algorithm for Emission Computed Tomography (ECT) providing simultaneous compensation for scatter, attenuation, and the variation of collimator resolution with depth. The technique of inverse Monte Carlo is used to find an inverse solution to the photon transport equation (an integral equation for photon flux from a specified source) for a parameterized source and specific boundary conditions. The system of linear equations so formed is solved to yield the source activity distribution for a set of acquired projections. For the studies presented here, the equations are solved using the EM (Maximum Likelihood) algorithm although other solution algorithms, such as Least Squares, could be employed. While the present results specifically consider the reconstruction of camera-based Single Photon Emission Computed Tomographic (SPECT) images, the technique is equally valid for Positron Emission Tomography (PET) if a Monte Carlo model of such a system is used. As a preliminary evaluation, experimentally acquired SPECT phantom studies for imaging Tc-99m (140 keV) are presented which demonstrate the quantitative compensation for scatter and attenuation for a two dimensional (single slice) reconstruction. The algorithm may be expanded in a straight forward manner to full three dimensional reconstruction including compensation for out of plane scatter

Bioanalytical Applications of Real-Time ATP Imaging Via Bioluminescence

Energy Technology Data Exchange (ETDEWEB)

Gruenhagen, Jason Alan [Iowa State Univ., Ames, IA (United States)

2003-01-01

The research discussed within involves the development of novel applications of real-time imaging of adenosine 5'-triphosphate (ATP). ATP was detected via bioluminescence and the firefly luciferase-catalyzed reaction of ATP and luciferin. The use of a microscope and an imaging detector allowed for spatially resolved quantitation of ATP release. Employing this method, applications in both biological and chemical systems were developed. First, the mechanism by which the compound 48/80 induces release of ATP from human umbilical vein endothelial cells (HUVECs) was investigated. Numerous enzyme activators and inhibitors were utilized to probe the second messenger systems involved in release. Compound 48/80 activated a G{sub q}-type protein to initiate ATP release from HUVECs. Ca²⁺ imaging along with ATP imaging revealed that activation of phospholipase C and induction of intracellular Ca²⁺ signaling were necessary for release of ATP. Furthermore, activation of protein kinase C inhibited the activity of phospholipase C and thus decreased the magnitude of ATP release. This novel release mechanism was compared to the existing theories of extracellular release of ATP. Bioluminescence imaging was also employed to examine the role of ATP in the field of neuroscience. The central nervous system (CNS) was dissected from the freshwater snail Lymnaea stagnalis. Electrophysiological experiments demonstrated that the neurons of the Lymnaea were not damaged by any of the components of the imaging solution. ATP was continuously released by the ganglia of the CNS for over eight hours and varied from ganglion to ganglion and within individual ganglia. Addition of the neurotransmitters K⁺ and serotonin increased release of ATP in certain regions of the Lymnaea CNS. Finally, the ATP imaging technique was investigated for the study of drug release systems. MCM-41-type mesoporous nanospheres were loaded with ATP and end-capped with mercaptoethanol

Characterization of G-protein coupled receptor kinase interaction with the neurokinin-1 receptor using bioluminescence resonance energy transfer

DEFF Research Database (Denmark)

Jorgensen, Rasmus; Holliday, Nicholas D; Hansen, Jakob L

2007-01-01

To analyze the interaction between the neurokinin-1 (NK-1) receptor and G-protein coupled receptor kinases (GRKs), we performed bioluminescence resonance energy transfer(2) (BRET(2)) measurements between the family A NK-1 receptor and GRK2 and GRK5 as well as their respective kinase-inactive muta......To analyze the interaction between the neurokinin-1 (NK-1) receptor and G-protein coupled receptor kinases (GRKs), we performed bioluminescence resonance energy transfer(2) (BRET(2)) measurements between the family A NK-1 receptor and GRK2 and GRK5 as well as their respective kinase...

Bioluminescence imaging in a medium-sized animal by local injection of d-luciferin

Energy Technology Data Exchange (ETDEWEB)

Moon, Sung Min; Min, Jung Joon; Kim, Sung Mi; Bom, Hee Seung [Chonnam National University Medical School, Gwangju (Korea, Republic of); Oh, Suk Jung; Kang, Han Saem; Kim, Kwang Yoon [ECOBIO INC., Gwangju (Korea, Republic of); Kim, Young Ho [Chosun University, Gwangju (Korea, Republic of)

2005-07-01

Luciferase is one of the most commonly used reporter enzymes in the field of molecular imaging. D-luciferin is known as the substrate for luciferase enzyme and its cost is very expensive. Therefore, the bioluminescence molecular imaging study has been allowed in small animals such as mice and rats. In this current study, we validated local injection of D-luciferin in articular capsule for bioluminescence imaging in rabbits. Chondrocytes were cultured and infected by replication-defective adenoviral vector encoding firefly luciferase. And then was performed different method of chondrocyte cell injection and transplantation into the knee of rabbits. The rabbits underwent imaging by cooled CCD camera after local injection of D-luciferin (3mg) into experimental knee joint as well as contralateral normal knee joint on days 1, 5, 7, 9. We sought whether optimal imaging signal was acquired by using cooled CCD camera after local injection of D-luciferin. We successfully visualized injected or transplanted cells in knee joint by local injection of D-luciferin. Total photon flux (7.86E+08 p/s/cm{sup 2}/sr) from the knee joint transplanted with cells approximately increased 10-fold more than (9.43E+07p/s/cm{sup 2}/sr) that from injected knee joints until 7 day. Imaging signal was observed in transplanted joints until day 9 after surgery while signal from injected knee was observed by day 7 after injection. We successfully carried out bioluminescence imaging study with medium sized animal by local injection of small amount of D-luciferin. Survival of chondrocytes were prolonged when surgically transplanted in joints than when directly injected in joint space.

Wavefront picking for 3D tomography and full-waveform inversion

KAUST Repository

AlTheyab, Abdullah; Schuster, Gerard T.

2016-01-01

We have developed an efficient approach for picking firstbreak wavefronts on coarsely sampled time slices of 3D shot gathers. Our objective was to compute a smooth initial velocity model for multiscale full-waveform inversion (FWI). Using

Variational constraints for electrical-impedance tomography

International Nuclear Information System (INIS)

Berryman, J.G.; Kohn, R.V.

1990-01-01

The task of electrical-impedance tomography is to invert boundary measurements for the conductivity distribution of a body. This inverse problem can be formulated so the primary data are the measured powers dissipated across injection electrodes. Then, since these powers are minima of the pertinent (dual) variational principles, feasibility constraints can be found for the nonlinear inversion problem. When power may be measured accurately, the existence of these dual variational principles implies that any exact solution must lie at a point of intersection of the two feasibility boundaries

Distributed RF Tomography for Tunnel Detection: Suitable Inversion Schemes

Science.gov (United States)

2009-01-01

methods, ranging from seismic to electromagnetic waves, or from gravity to optics, from impedance tomography to magnetotellurics, no technique...unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Borehole GPR, which may...one manner to different targets (when targets are well-resolved). In particular, the wavefront generated by the array , when excited by one of these

Basic methodology of tomographic imaging by filtered inverse projection at a turbo-pump. Project report; Methodische Grundlagen fuer die Tomographie durch gefilterte Rueckprojektion an einer Axialpumpe. Projektbericht

Energy Technology Data Exchange (ETDEWEB)

Hoppe, D.

2000-11-01

A two-phase medium consisting of a fluid containing gas is transported in a turbo-pump via an impeller. The interaction between the gaseous phase and the impeller is to be examined by tomography with gamma rays. Reconstruction of the image of the object is to be made by way of filtered inverse projection. The methodology of using this principle in the given system (geometry and measuring conditions) is explained. (orig./CB) [German] Ein zweiphasiges, aus einer gashaltigen Fluessigkeit bestehendes Medium wird in einer Axialpumpe von einem propellerartigen Laufrad senkrecht zur Drehachse dieses Laufrades transportiert. Die Wechselwirkung zwischen der Gasphase und dem Laufrad soll unter Verwendung von Gamma-Strahlung mittels Tomographie untersucht werden. Dabei ist fuer die Rekonstruktion des Objektbildes das Prinzip der sogenannten gefilterten Rueckprojektion vorgesehen. Die methodischen Grundlagen fuer die Nutzung dieses Prinzips unter von vorgesehenen geometrischen und messtechnischen Bedingungen sind Gegenstand dieser Arbeit. (orig.)

X-ray micro-modulated luminescence tomography (XMLT)

Science.gov (United States)

Cong, Wenxiang; Liu, Fenglin; Wang, Chao; Wang, Ge

2014-01-01

Imaging depth of optical microscopy has been fundamentally limited to millimeter or sub-millimeter due to strong scattering of light in a biological sample. X-ray microscopy can resolve spatial details of few microns deep inside a sample but contrast resolution is inadequate to depict heterogeneous features at cellular or sub-cellular levels. To enhance and enrich biological contrast at large imaging depth, various nanoparticles are introduced and become essential to basic research and molecular medicine. Nanoparticles can be functionalized as imaging probes, similar to fluorescent and bioluminescent proteins. LiGa5O8:Cr3+ nanoparticles were recently synthesized to facilitate luminescence energy storage with x-ray pre-excitation and subsequently stimulated luminescence emission by visible/near-infrared (NIR) light. In this paper, we propose an x-ray micro-modulated luminescence tomography (XMLT, or MLT to be more general) approach to quantify a nanophosphor distribution in a thick biological sample with high resolution. Our numerical simulation studies demonstrate the feasibility of the proposed approach. PMID:24663898

A look at some systemic properties of self-bioluminescent emission

Science.gov (United States)

Creath, Katherine

2008-08-01

Self-bioluminescent emission (SBE) is a type of biological chemiluminescence where photons are emitted as part of chemical reactions occurring during metabolic processes. This emission is also known as biophoton emission, ultraweak photon emission and ultraweak bioluminescence. This paper outlines research over the past century on some systemic properties of SBE as measured with biological detectors, photomultiplier detectors and ultra-sensitive imaging arrays. There is an apparent consensus in the literature that emission in the deep blue and ultraviolet (150-450nm) is related to DNA / RNA processes while emission in the red and near infrared (600-1000nm) is related to mitochondria and oxidative metabolisms involving reactive oxygen species, singlet oxygen and free radicals in plant, animal and human cells along with chlorophyll fluorescent decay in plants. Additionally, there are trends showing that healthy, unstressed and uninjured samples have less emission than samples that are unhealthy, stressed or injured. Mechanisms producing this emission can be narrowed down by isolating the wavelength region of interest and waiting for short-term fluorescence to decay leaving the ultraweak long-term metabolic emission. Examples of imaging this emission in healthy versus unhealthy, stressed versus unstressed, and injured versus uninjured plant parts are shown. Further discussion poses questions still to be answered related to properties such as coherence, photon statistics, and methodological means of isolating mechanisms.

Crosshole Tomography, Waveform Inversion, and Anisotropy: A Combined Approach Using Simulated Annealing

Science.gov (United States)

Afanasiev, M.; Pratt, R. G.; Kamei, R.; McDowell, G.

2012-12-01

Crosshole seismic tomography has been used by Vale to provide geophysical images of mineralized massive sulfides in the Eastern Deeps deposit at Voisey's Bay, Labrador, Canada. To date, these data have been processed using traveltime tomography, and we seek to improve the resolution of these images by applying acoustic Waveform Tomography. Due to the computational cost of acoustic waveform modelling, local descent algorithms are employed in Waveform Tomography; due to non-linearity an initial model is required which predicts first-arrival traveltimes to within a half-cycle of the lowest frequency used. Because seismic velocity anisotropy can be significant in hardrock settings, the initial model must quantify the anisotropy in order to meet the half-cycle criterion. In our case study, significant velocity contrasts between the target massive sulfides and the surrounding country rock led to difficulties in generating an accurate anisotropy model through traveltime tomography, and our starting model for Waveform Tomography failed the half-cycle criterion at large offsets. We formulate a new, semi-global approach for finding the best-fit 1-D elliptical anisotropy model using simulated annealing. Through random perturbations to Thompson's ɛ parameter, we explore the L2 norm of the frequency-domain phase residuals in the space of potential anisotropy models: If a perturbation decreases the residuals, it is always accepted, but if a perturbation increases the residuals, it is accepted with the probability P = exp(-(Ei-E)/T). This is the Metropolis criterion, where Ei is the value of the residuals at the current iteration, E is the value of the residuals for the previously accepted model, and T is a probability control parameter, which is decreased over the course of the simulation via a preselected cooling schedule. Convergence to the global minimum of the residuals is guaranteed only for infinitely slow cooling, but in practice good results are obtained from a variety

Bayesian image reconstruction for improving detection performance of muon tomography.

Science.gov (United States)

Wang, Guobao; Schultz, Larry J; Qi, Jinyi

2009-05-01

Muon tomography is a novel technology that is being developed for detecting high-Z materials in vehicles or cargo containers. Maximum likelihood methods have been developed for reconstructing the scattering density image from muon measurements. However, the instability of maximum likelihood estimation often results in noisy images and low detectability of high-Z targets. In this paper, we propose using regularization to improve the image quality of muon tomography. We formulate the muon reconstruction problem in a Bayesian framework by introducing a prior distribution on scattering density images. An iterative shrinkage algorithm is derived to maximize the log posterior distribution. At each iteration, the algorithm obtains the maximum a posteriori update by shrinking an unregularized maximum likelihood update. Inverse quadratic shrinkage functions are derived for generalized Laplacian priors and inverse cubic shrinkage functions are derived for generalized Gaussian priors. Receiver operating characteristic studies using simulated data demonstrate that the Bayesian reconstruction can greatly improve the detection performance of muon tomography.

Re-Inversion of Surface Electrical Resistivity Tomography Data from the Hanford Site B-Complex

Energy Technology Data Exchange (ETDEWEB)

Johnson, Timothy C.; Wellman, Dawn M.

2013-05-01

This report documents the three-dimensional (3D) inversion results of surface electrical resistivity tomography (ERT) data collected over the Hanford Site B-Complex. The data were collected in order to image the subsurface distribution of electrically conductive vadose zone contamination resulting from both planned releases of contamination into subsurface infiltration galleries (cribs, trenches, and tile fields), as well as unplanned releases from the B, BX, and BY tank farms and/or associated facilities. Electrically conductive contaminants are those which increase the ionic strength of pore fluids compared to native conditions, which comprise most types of solutes released into the subsurface B-Complex. The ERT data were collected and originally inverted as described in detail in report RPP-34690 Rev 0., 2007, which readers should refer to for a detailed description of data collection and waste disposal history. Although the ERT imaging results presented in that report successfully delineated the footprint of vadose zone contamination in areas outside of the tank farms, imaging resolution was not optimized due to the inability of available inversion codes to optimally process the massive ERT data set collected at the site. Recognizing these limitations and the potential for enhanced ERT characterization and time-lapse imaging at contaminated sites, a joint effort was initiated in 2007 by the U.S. Department of Energy – Office of Science (DOE-SC), with later support by the Office of Environmental Management (DOE-EM), and the U.S. Department of Defense (DOD), to develop a high-performance distributed memory parallel 3D ERT inversion code capable of optimally processing large ERT data sets. The culmination of this effort was the development of E4D (Johnson et al., 2010,2012) In 2012, under the Deep Vadose Zone Applied Field Research Initiative (DVZ-AFRI), the U.S. Department of Energy – Richland Operations Office (DOE-RL) and CH2M Hill Plateau Remediation

Phylogenetic relationships of click beetles (Coleoptera: Elateridae) inferred from 28S ribosomal DNA: insights into the evolution of bioluminescence in Elateridae.

Science.gov (United States)

Sagegami-Oba, Reiko; Oba, Yuichi; Ohira, Hitoo

2007-02-01

Although the taxonomy of click beetles (family Elateridae) has been studied extensively, inconsistencies remain. We examine here the relationships between species of Elateridae based on partial sequences of nuclear 28S ribosomal DNA. Specimens were collected primarily from Japan, while luminous click beetles were also sampled from Central and South America to investigate the origins of bioluminescence in Elateridae. Neighbor-joining, maximum-parsimony, and maximum-likelihood analyses produced a consistent basal topology with high statistical support that is partially congruent with the results of previous investigations based on the morphological characteristics of larvae and adults. The most parsimonious reconstruction of the "luminous" and "nonluminous" states, based on the present molecular phylogeny, indicates that the ancestral state of Elateridae was nonluminous. This suggests that the bioluminescence in click beetle evolved independent of that of other luminous beetles, such as Lampyridae, despite their common mechanisms of bioluminescence.

Mitrocomin from the jellyfish Mitrocoma cellularia with deleted C-terminal tyrosine reveals a higher bioluminescence activity compared to wild type photoprotein

Energy Technology Data Exchange (ETDEWEB)

Burakova, Ludmila P.; Natashin, Pavel V.; Markova, Svetlana V.; Eremeeva, Elena V.; Malikova, Natalia P.; Cheng, Chongyun; Liu, Zhi-Jie; Vysotski, Eugene S.

2016-09-01

The full-length cDNA genes encoding five new isoforms of Ca2 +-regulated photoprotein mitrocomin from a small tissue sample of the outer bell margin containing photocytes of only one specimen of the luminous jellyfish Mitrocoma cellularia were cloned, sequenced, and characterized after their expression in Escherichia coli and subsequent purification. The analysis of cDNA nucleotide sequences encoding mitrocomin isoforms allowed suggestion that two isoforms might be the products of two allelic genes differing in one amino acid residue (64R/Q) whereas other isotypes appear as a result of transcriptional mutations. In addition, the crystal structure of mitrocomin was determined at 1.30 Å resolution which expectedly revealed a high similarity with the structures of other hydromedusan photoproteins. Although mitrocomin isoforms reveal a high degree of identity of amino acid sequences, they vary in specific bioluminescence activities. At that, all isotypes displayed the identical bioluminescence spectra (473–474 nm with no shoulder at 400 nm). Fluorescence spectra of Ca2 +-discharged mitrocomins were almost identical to their light emission spectra similar to the case of Ca2 +-discharged aequorin, but different from Ca2 +-discharged obelins and clytin which fluorescence is red-shifted by 25–30 nm from bioluminescence spectra. The main distinction of mitrocomin from other hydromedusan photoproteins is an additional Tyr at the C-terminus. Using site-directed mutagenesis, we showed that this Tyr is not important for bioluminescence because its deletion even increases specific activity and efficiency of apo-mitrocomin conversion into active photoprotein, in contrast to C-terminal Pro of other photoproteins. Since genes in a population generally exist as different isoforms, it makes us anticipate the cloning of even more isoforms of mitrocomin and other hydromedusan photoproteins with different bioluminescence properties.

Distribution of bioluminescent fungi across old-growth and secondary tropical rain forest in Costa Rica

Directory of Open Access Journals (Sweden)

Carolina Seas-Carvajal

2013-06-01

Full Text Available Most research on bioluminescent fungi is concentrated on their taxonomic relationships, while the basics of their natural history and ecological relationships are poorly understood. In this study, we compared the distribution of bioluminescent fungi between old-growth and secondary forest as related to four different soil types at the tropical rainforest of La Selva Biological Station in Costa Rica. The study was conducted during the wet season of 2009. Bioluminescent fungi were sought following eight different transects distributed evenly in old-growth and secondary forests across four different soil types, covering an area of 9 420m². We found fungi in four different substrates: litter, fallen branches, dead trunks, and roots, for a total of 61 samples. Correspondence analysis showed that the occurrence of fungi and soil types were related (inertia=0.21, p=0.071. We found a significant relationship between the presence of fungi and the distribution of soil types (X²=18.89, df=9, p=0.026. We found only three samples with fruiting bodies, two of which had Mycena and the other had one fungus of the order Xylariales (possibly Hypoxylon sp., Kretzschmariella sp., Xylaria sp.. Future work will concentrate on exploring other aspects of their ecology, such as their dispersal and substrate preference. This information will facilitate field identification and will foster more research on the distribution, seasonality, reproductive phenology and ecological requirements of this group of Fungi.

Oculogryphus chenghoiyanae sp. n. (Coleoptera, Lampyridae: a new ototretine firefly from Hong Kong with descriptions of its bioluminescent behavior and ultraviolet-induced fluorescence in females

Directory of Open Access Journals (Sweden)

Vor Yiu

2018-02-01

Full Text Available The first Oculogryphus species with associated males and female was found in Hong Kong and is described as new: O. chenghoiyanae sp. n. Adults of both sexes were collected live in the field and their bioluminescent behavior is reported for the first time in the genus. The captive males emit weak and continuous light from a pair of light spots on abdominal ventrite 6 or do so when disturbed. The larviform (highly paedomorphic females can glow brightly from a pair of light-emitting organs on the abdomen. The females of Oculogryphus and Stenocladius are to date the only documented representatives of paedomorphism in ototretine fireflies. The finding is consistent with the evidence from male morphology and bioluminescent behavior, supporting the close relationship between the two genera. A key to the Oculogryphus species is provided. The Oculogryphus females can fluoresce with a blue-green light through the whole body under ultraviolet illumination, a phenomenon reported in the Lampyridae for the first time. The co-occurrence of bioluminescence and fluorescence is rare in terrestrial ecosystems, previously known only in some millipedes (Diplopoda. The fluorescence and bioluminescence abilities of Oculogryphus females are functionally independent: abdominal light-emitting organs producing bright yellowish green light while the body wall fluoresces with blue-green light. In contrast, fluorescence and bioluminescence in millipedes are biochemically linked, like in some jellyfish (Cnidaria: Medusozoa.

Computerized Tomography and its Applications : a Guided Tour

NARCIS (Netherlands)

Roerdink, J.B.T.M.

1992-01-01

We present a review of the mathematical principles of computerized tomography. Topics treated include the role of the Radon transform and related transforms, inversion formulas, uniqueness, ill-posedness and stability, practical reconstruction algorithms, and various generalizations such as

Inverse problems basics, theory and applications in geophysics

CERN Document Server

Richter, Mathias

2016-01-01

The overall goal of the book is to provide access to the regularized solution of inverse problems relevant in geophysics without requiring more mathematical knowledge than is taught in undergraduate math courses for scientists and engineers. From abstract analysis only the concept of functions as vectors is needed. Function spaces are introduced informally in the course of the text, when needed. Additionally, a more detailed, but still condensed introduction is given in Appendix B. A second goal is to elaborate the single steps to be taken when solving an inverse problem: discretization, regularization and practical solution of the regularized optimization problem. These steps are shown in detail for model problems from the fields of inverse gravimetry and seismic tomography. The intended audience is mathematicians, physicists and engineers having a good working knowledge of linear algebra and analysis at the upper undergraduate level.

Assessment of chitosan-affected metabolic response by peroxisome proliferator-activated receptor bioluminescent imaging-guided transcriptomic analysis.

Directory of Open Access Journals (Sweden)

Chia-Hung Kao

Full Text Available Chitosan has been widely used in food industry as a weight-loss aid and a cholesterol-lowering agent. Previous studies have shown that chitosan affects metabolic responses and contributes to anti-diabetic, hypocholesteremic, and blood glucose-lowering effects; however, the in vivo targeting sites and mechanisms of chitosan remain to be clarified. In this study, we constructed transgenic mice, which carried the luciferase genes driven by peroxisome proliferator-activated receptor (PPAR, a key regulator of fatty acid and glucose metabolism. Bioluminescent imaging of PPAR transgenic mice was applied to report the organs that chitosan acted on, and gene expression profiles of chitosan-targeted organs were further analyzed to elucidate the mechanisms of chitosan. Bioluminescent imaging showed that constitutive PPAR activities were detected in brain and gastrointestinal tract. Administration of chitosan significantly activated the PPAR activities in brain and stomach. Microarray analysis of brain and stomach showed that several pathways involved in lipid and glucose metabolism were regulated by chitosan. Moreover, the expression levels of metabolism-associated genes like apolipoprotein B (apoB and ghrelin genes were down-regulated by chitosan. In conclusion, these findings suggested the feasibility of PPAR bioluminescent imaging-guided transcriptomic analysis on the evaluation of chitosan-affected metabolic responses in vivo. Moreover, we newly identified that downregulated expression of apoB and ghrelin genes were novel mechanisms for chitosan-affected metabolic responses in vivo.

Uncertainty analysis in seismic tomography

Science.gov (United States)

Owoc, Bartosz; Majdański, Mariusz

2017-04-01

Velocity field from seismic travel time tomography depends on several factors like regularization, inversion path, model parameterization etc. The result also strongly depends on an initial velocity model and precision of travel times picking. In this research we test dependence on starting model in layered tomography and compare it with effect of picking precision. Moreover, in our analysis for manual travel times picking the uncertainty distribution is asymmetric. This effect is shifting the results toward faster velocities. For calculation we are using JIVE3D travel time tomographic code. We used data from geo-engineering and industrial scale investigations, which were collected by our team from IG PAS.

Comparison of the spectral emission of lux recombinant and bioluminescent marine bacteria.

Science.gov (United States)

Thouand, Gérald; Daniel, Philippe; Horry, Habib; Picart, Pascal; Durand, Marie José; Killham, Ken; Knox, Oliver G G; DuBow, Michael S; Rousseau, Michel

2003-01-01

The purpose of the present paper was to study the influence of bacteria harbouring the luciferase-encoding Vibrio harveyi luxAB genes upon the spectral emission during growth in batch-culture conditions. In vivo bioluminescence spectra were compared from several bioluminescent strains, either naturally luminescent (Vibrio fischeri and Vibrio harveyi) or in recombinant strains (two Gram-negative Escherichia coli::luxAB strains and a Gram-positive Bacillus subtilis::luxAB strain). Spectral emission was recorded from 400 nm to 750 nm using a highly sensitive spectrometer initially devoted to Raman scattering. Two peaks were clearly identified, one at 491-500 nm (+/- 5 nm) and a second peak at 585-595 (+/- 5 nm) with the Raman CCD. The former peak was the only one detected with traditional spectrometers with a photomultiplier detector commonly used for spectral emission measurement, due to their lack of sensitivity and low resolution in the 550-650 nm window. When spectra were compared between all the studied bacteria, no difference was observed between natural or recombinant cells, between Gram-positive and Gram-negative strains, and growth conditions and growth medium were not found to modify the spectrum of light emission. Copyright 2003 John Wiley & Sons, Ltd.

Enlightening the malaria parasite life cycle: bioluminescent Plasmodium in fundamental and applied research

Directory of Open Access Journals (Sweden)

Giulia eSiciliano

2015-05-01

Full Text Available The unicellular protozoan parasites of the genus Plasmodium impose on human health worldwide the enormous burden of malaria. The possibility to genetically modify several species of malaria parasites represented a major advance in the possibility to elucidate their biology and is now turning laboratory lines of transgenic Plasmodium into precious weapons to fight malaria. Amongst the various genetically modified plasmodia, transgenic parasite lines expressing bioluminescent reporters have been essential to unveil mechanisms of parasite gene expression and to develop in vivo imaging approaches in mouse malaria models. Mainly the human malaria parasite Plasmodium falciparum and the rodent parasite Plasmodium berghei have been engineered to express bioluminescent reporters in almost all the developmental stages of the parasite along its complex life cycle between the insect and the vertebrate hosts. Plasmodium lines expressing conventional and improved luciferase reporters are now gaining a central role to develop cell based assays in the much needed search of new antimalarial drugs and to open innovative approaches for both fundamental and applied research in malaria.

Enlightening the malaria parasite life cycle: bioluminescent Plasmodium in fundamental and applied research.

Science.gov (United States)

Siciliano, Giulia; Alano, Pietro

2015-01-01

The unicellular protozoan parasites of the genus Plasmodium impose on human health worldwide the enormous burden of malaria. The possibility to genetically modify several species of malaria parasites represented a major advance in the possibility to elucidate their biology and is now turning laboratory lines of transgenic Plasmodium into precious weapons to fight malaria. Amongst the various genetically modified plasmodia, transgenic parasite lines expressing bioluminescent reporters have been essential to unveil mechanisms of parasite gene expression and to develop in vivo imaging approaches in mouse malaria models. Mainly the human malaria parasite Plasmodium falciparum and the rodent parasite P. berghei have been engineered to express bioluminescent reporters in almost all the developmental stages of the parasite along its complex life cycle between the insect and the vertebrate hosts. Plasmodium lines expressing conventional and improved luciferase reporters are now gaining a central role to develop cell based assays in the much needed search of new antimalarial drugs and to open innovative approaches for both fundamental and applied research in malaria.

Waveform tomography in geophysics and helioseismology

NARCIS (Netherlands)

Cobden, L.J.; Fichtner, A.; Tong, Vincent

2015-01-01

Seismic tomography – in which we construct images of a body's interior using seismic waves – is an inverse problem; that is, our goal is to find a model that fits a set of existing data observations. This is much less straightforward than the reverse, forward problem (i.e., generating synthetic data

Iterative Reconstruction Methods for Inverse Problems in Tomography with Hybrid Data

DEFF Research Database (Denmark)

Sherina, Ekaterina

. The goal of these modalities is to quantify physical parameters of materials or tissues inside an object from given interior data, which is measured everywhere inside the object. The advantage of these modalities is that large variations in physical parameters can be resolved and therefore, they have...... data is precisely the reason why reconstructions with a high contrast and a high resolution can be expected. The main contributions of this thesis consist in formulating the underlying mathematical problems with interior data as nonlinear operator equations, theoretically analysing them within...... iteration and the Levenberg-Marquardt method are employed for solving the problems. The first problem considered in this thesis is a problem of conductivity estimation from interior measurements of the power density, known as Acousto-Electrical Tomography. A special case of limited angle tomography...

A Reduced-Order Successive Linear Estimator for Geostatistical Inversion and its Application in Hydraulic Tomography

Science.gov (United States)

Zha, Yuanyuan; Yeh, Tian-Chyi J.; Illman, Walter A.; Zeng, Wenzhi; Zhang, Yonggen; Sun, Fangqiang; Shi, Liangsheng

2018-03-01

Hydraulic tomography (HT) is a recently developed technology for characterizing high-resolution, site-specific heterogeneity using hydraulic data (nd) from a series of cross-hole pumping tests. To properly account for the subsurface heterogeneity and to flexibly incorporate additional information, geostatistical inverse models, which permit a large number of spatially correlated unknowns (ny), are frequently used to interpret the collected data. However, the memory storage requirements for the covariance of the unknowns (ny × ny) in these models are prodigious for large-scale 3-D problems. Moreover, the sensitivity evaluation is often computationally intensive using traditional difference method (ny forward runs). Although employment of the adjoint method can reduce the cost to nd forward runs, the adjoint model requires intrusive coding effort. In order to resolve these issues, this paper presents a Reduced-Order Successive Linear Estimator (ROSLE) for analyzing HT data. This new estimator approximates the covariance of the unknowns using Karhunen-Loeve Expansion (KLE) truncated to nkl order, and it calculates the directional sensitivities (in the directions of nkl eigenvectors) to form the covariance and cross-covariance used in the Successive Linear Estimator (SLE). In addition, the covariance of unknowns is updated every iteration by updating the eigenvalues and eigenfunctions. The computational advantages of the proposed algorithm are demonstrated through numerical experiments and a 3-D transient HT analysis of data from a highly heterogeneous field site.

A fast sparse reconstruction algorithm for electrical tomography

International Nuclear Information System (INIS)

Zhao, Jia; Xu, Yanbin; Tan, Chao; Dong, Feng

2014-01-01

Electrical tomography (ET) has been widely investigated due to its advantages of being non-radiative, low-cost and high-speed. However, the image reconstruction of ET is a nonlinear and ill-posed inverse problem and the imaging results are easily affected by measurement noise. A sparse reconstruction algorithm based on L 1 regularization is robust to noise and consequently provides a high quality of reconstructed images. In this paper, a sparse reconstruction by separable approximation algorithm (SpaRSA) is extended to solve the ET inverse problem. The algorithm is competitive with the fastest state-of-the-art algorithms in solving the standard L 2 −L 1 problem. However, it is computationally expensive when the dimension of the matrix is large. To further improve the calculation speed of solving inverse problems, a projection method based on the Krylov subspace is employed and combined with the SpaRSA algorithm. The proposed algorithm is tested with image reconstruction of electrical resistance tomography (ERT). Both simulation and experimental results demonstrate that the proposed method can reduce the computational time and improve the noise robustness for the image reconstruction. (paper)

Inversion gradients for acoustic VTI wavefield tomography

KAUST Repository

Li, Vladimir; Wang, Hui; Tsvankin, Ilya; Dí az, Esteban; Alkhalifah, Tariq Ali

2017-01-01

Wavefield tomography can handle complex subsurface geology better than ray-based techniques and, ultimately, provide a higher resolution. Here, we implement forward and adjoint wavefield extrapolation for VTI (transversely isotropic with a vertical symmetry axis) media using a generalized pseudospectral operator based on a separable approximation for the P-wave dispersion relation. This operator is employed to derive the gradients of the differential semblance optimization (DSO) and modified image-power objective functions. We also obtain the gradient expressions for a data-domain objective function that can more easily incorporate borehole information necessary for stable VTI velocity analysis. These gradients are similar to the ones obtained with a space-time finite-difference (FD) scheme for a system of coupled wave equations but the pseudospectral method is not hampered by the imprint of the shear-wave artifact. Numerical examples also show the potential advantages of the modified image-power objective function in estimating the anellipticity parameter η.

Inversion gradients for acoustic VTI wavefield tomography

KAUST Repository

Li, Vladimir

2017-03-21

Wavefield tomography can handle complex subsurface geology better than ray-based techniques and, ultimately, provide a higher resolution. Here, we implement forward and adjoint wavefield extrapolation for VTI (transversely isotropic with a vertical symmetry axis) media using a generalized pseudospectral operator based on a separable approximation for the P-wave dispersion relation. This operator is employed to derive the gradients of the differential semblance optimization (DSO) and modified image-power objective functions. We also obtain the gradient expressions for a data-domain objective function that can more easily incorporate borehole information necessary for stable VTI velocity analysis. These gradients are similar to the ones obtained with a space-time finite-difference (FD) scheme for a system of coupled wave equations but the pseudospectral method is not hampered by the imprint of the shear-wave artifact. Numerical examples also show the potential advantages of the modified image-power objective function in estimating the anellipticity parameter η.

Laboratory scale tests of electrical impedence tomography

International Nuclear Information System (INIS)

Binley, A; Daily, W; LaBredcque, D; Ramirez, A.

1998-01-01

Electrical impedance tomographs (magnitude and phase) of known, laboratory-scale targets are reported. Three methods are used to invert electrical impedance data and their tomographs compared. The first method uses an electrical resistance tomography (ERT) algonthm (designed for DC resistivity inversion) to perform impedance magnitude inversion and a linearized perturbation approach (PA) to invert the imaginary part. The second approximate method compares ERT magnitude inversions at two frequencies and uses the frequency effect (FE) to compute phase tomographs. The third approach, electrrcal impedance tomography (EIT), employs fully complex algebra to account for the real and imaginary components of electrical impedance data. The EIT approach provided useful magnitude and phase images for the frequency range of 0.0625 to 64 Hz; images for higher frequencies were not reliable. Comparisons of the ERT and EIT magnitude images show that both methods provided equivalent results for the water blank, copper rod and PVC rod targets. The EIT magnitude images showed better spatial resolutron for a sand-lead mixture target. Phase images located anomalies of both high and low contrast IP and provided better spatial resolution than the magnitude images. When IP was absent from the data, the EIT algorithm reconstructed phase values consistent with the data noise levels

Semi-local inversion of the geodesic ray transform in the hyperbolic plane

International Nuclear Information System (INIS)

Courdurier, Matias; Saez, Mariel

2013-01-01

The inversion of the ray transform on the hyperbolic plane has applications in geophysical exploration and in medical imaging techniques (such as electrical impedance tomography). The geodesic ray transform has been studied in more general geometries and including attenuation, but all of the available inversion formulas require knowledge of the ray transform for all the geodesics. In this paper we present a different inversion formula for the ray transform on the hyperbolic plane, which has the advantage of only requiring knowledge of the ray transform in a reduced family of geodesics. The required family of geodesics is directly related to the set where the original function is to be recovered. (paper)

Validity of bioluminescence measurements for noninvasive in vivo imaging of tumor load in small animals

NARCIS (Netherlands)

Klerk, Clara P. W.; Overmeer, Renée M.; Niers, Tatjana M. H.; Versteeg, Henri H.; Richel, Dick J.; Buckle, Tessa; van Noorden, Cornelis J. F.; van Tellingen, Olaf

2007-01-01

A relatively new strategy to longitudinally monitor tumor load in intact animals and the effects of therapy is noninvasive bioluminescence imaging (BLI). The validity of BLI for quantitative assessment of tumor load in small animals is critically evaluated in the present review. Cancer cells are

SU-F-J-183: Interior Region-Of-Interest Tomography by Using Inverse Geometry System

Energy Technology Data Exchange (ETDEWEB)

Kim, K; Kim, D; Kang, S; Kim, T; Shin, D; Cho, M; Noh, Y; Suh, T [Department of Biomedical Engineering and Research Institute of Biomedical Engineering, College of Medicine, The Catholic University of Korea, Seoul (Korea, Republic of)

2016-06-15

Purpose: The inverse geometry computed tomography (IGCT) composed of multiple source and small size detector has several merits such as reduction of scatter effect and large volumetric imaging within one rotation without cone-beam artifact, compared to conventional cone-beam computed tomography (CBCT). By using this multi-source characteristics, we intend to present a selective and multiple interior region-of-interest (ROI) imaging method by using a designed source on-off sequence of IGCT. Methods: All of the IGCT sources are operated one by one sequentially, and each projection in the shape of narrow cone-beam covers its own partial volume of full field of view (FOV) determined from system geometry. Thus, through controlling multi source operation, limited irradiation within ROI is possible and selective radon space data for ROI imaging can be acquired without additional X-ray filtration. With this feature, we designed a source on-off sequence for multi ROI-IGCT imaging, and projections of ROI-IGCT were generated by using the on-off sequence. Multi ROI-IGCT images were reconstructed by using filtered back-projection algorithm. All these imaging process of our study has been performed by utilizing digital phantom and patient CT data. ROI-IGCT images of the phantom were compared to CBCT image and the phantom data for the image quality evaluation. Results: Image quality of ROI-IGCT was comparable to that of CBCT. However, the distal axial-plane from the FOV center, large cone-angle region, ROI-IGCT showed uniform image quality without significant cone-beam artifact contrary to CBCT. Conclusion: ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. Projection of ROI-IGCT is performed by selective irradiation, hence unnecessary imaging dose to non-interest region can be reduced. In this regard, it seems to be useful for diagnostic or image guidance purpose in radiotherapy such as low dose target localization and

SU-F-J-183: Interior Region-Of-Interest Tomography by Using Inverse Geometry System

International Nuclear Information System (INIS)

Kim, K; Kim, D; Kang, S; Kim, T; Shin, D; Cho, M; Noh, Y; Suh, T

2016-01-01

Purpose: The inverse geometry computed tomography (IGCT) composed of multiple source and small size detector has several merits such as reduction of scatter effect and large volumetric imaging within one rotation without cone-beam artifact, compared to conventional cone-beam computed tomography (CBCT). By using this multi-source characteristics, we intend to present a selective and multiple interior region-of-interest (ROI) imaging method by using a designed source on-off sequence of IGCT. Methods: All of the IGCT sources are operated one by one sequentially, and each projection in the shape of narrow cone-beam covers its own partial volume of full field of view (FOV) determined from system geometry. Thus, through controlling multi source operation, limited irradiation within ROI is possible and selective radon space data for ROI imaging can be acquired without additional X-ray filtration. With this feature, we designed a source on-off sequence for multi ROI-IGCT imaging, and projections of ROI-IGCT were generated by using the on-off sequence. Multi ROI-IGCT images were reconstructed by using filtered back-projection algorithm. All these imaging process of our study has been performed by utilizing digital phantom and patient CT data. ROI-IGCT images of the phantom were compared to CBCT image and the phantom data for the image quality evaluation. Results: Image quality of ROI-IGCT was comparable to that of CBCT. However, the distal axial-plane from the FOV center, large cone-angle region, ROI-IGCT showed uniform image quality without significant cone-beam artifact contrary to CBCT. Conclusion: ROI-IGCT showed comparable image quality and has the capability to provide multi ROI image within a rotation. Projection of ROI-IGCT is performed by selective irradiation, hence unnecessary imaging dose to non-interest region can be reduced. In this regard, it seems to be useful for diagnostic or image guidance purpose in radiotherapy such as low dose target localization and

Refraction traveltime tomography with irregular topography using the unwrapped phase inversion

KAUST Repository

Choi, Yun Seok; Alkhalifah, Tariq Ali

2013-01-01

inversion zones and ray shadow regions. We develop a tomographic approach based on traveltime solutions obtained by tracking the phase (instantaneous traveltime) of the wavefield solution of the Helmholtz wave equation. Since the instantaneous

Accurate Antenna Models in Ground Penetrating Radar Diffraction Tomography

DEFF Research Database (Denmark)

Meincke, Peter; Kim, Oleksiy S.

2002-01-01

are modeled by their plane-wave receiving and transmitting spectra. We find these spectra numerically for a resistively loaded dipole using the method of moments. Also, we illustrate, through a numerical example, the importance of taking into account the correct antenna pattern in GPR diffraction tomography.......Linear inversion schemes based on the concept of diffraction tomography have proven successful for ground penetrating radar (GPR) imaging. In many GPR surveys, the antennas of the GPR are located close to the air-soil interface and, therefore, it is important to incorporate the presence...... of this interface in the inversion scheme (see Hansen, T.B. and Meincke Johansen, P., IEEE Trans. Geoscience and Remote Sensing, vol.38, p.496-506, 2000). Hansen and Meincke Johansen modeled the antennas as ideal (Hertzian) electric dipoles. Since practical GPR antennas are not ideal, it is of interest...

Adenosina trifosfato bioluminescência para avaliação da limpeza de superfícies: uma revisão integrativa

OpenAIRE

Oliveira, Adriana Cristina de; Viana, Roberta El Hariri

2014-01-01

Objetivo: Identificar na literatura indicações e controvérsias do ATP bioluminescência para avaliação da efetividade da limpeza de superfícies em estabelecimentos de saúde. Método: Revisão integrativa da literatura, entre 2000 e 2012, nas bases de dados MEDLINE, LILACS, Science Direct, SCOPUS e Isi Web of Knowledge. Resultados: Selecionou-se para esta revisão 15 artigos. O ATP bioluminescência foi apontado como importante recurso educacional e método complementar à inspeção visual e às anális...

Ship track for Islands in the Stream 2002 - Pharmaceutical Discovery, Vision, and Bioluminescence - Office of Ocean Exploration

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Ship track of the R/V Seward Johnson during the 2002 "Islands in the Stream - Pharmaceutical Discovery, Vision, and Bioluminescence" expedition sponsored by the...

Renormalized nonlinear sensitivity kernel and inverse thin-slab propagator in T-matrix formalism for wave-equation tomography

International Nuclear Information System (INIS)

Wu, Ru-Shan; Wang, Benfeng; Hu, Chunhua

2015-01-01

We derived the renormalized nonlinear sensitivity operator and the related inverse thin-slab propagator (ITSP) for nonlinear tomographic waveform inversion based on the theory of nonlinear partial derivative operator and its De Wolf approximation. The inverse propagator is based on a renormalization procedure to the forward and inverse transition matrix scattering series. The ITSP eliminates the divergence of the inverse Born series for strong perturbations by stepwise partial summation (renormalization). Numerical tests showed that the inverse Born T-series starts to diverge at moderate perturbation (20% for the given model of Gaussian ball with a radius of 5 wavelength), while the ITSP has no divergence problem for any strong perturbations (up to 100% perturbation for test model). In addition, the ITSP is a non-iterative, marching algorithm with only one sweep, and therefore very efficient in comparison with the iterative inversion based on the inverse-Born scattering series. This convergence and efficiency improvement has potential applications to the iterative procedure of waveform inversion. (paper)

Regularized inversion of controlled source and earthquake data

International Nuclear Information System (INIS)

Ramachandran, Kumar

2012-01-01

Estimation of the seismic velocity structure of the Earth's crust and upper mantle from travel-time data has advanced greatly in recent years. Forward modelling trial-and-error methods have been superseded by tomographic methods which allow more objective analysis of large two-dimensional and three-dimensional refraction and/or reflection data sets. The fundamental purpose of travel-time tomography is to determine the velocity structure of a medium by analysing the time it takes for a wave generated at a source point within the medium to arrive at a distribution of receiver points. Tomographic inversion of first-arrival travel-time data is a nonlinear problem since both the velocity of the medium and ray paths in the medium are unknown. The solution for such a problem is typically obtained by repeated application of linearized inversion. Regularization of the nonlinear problem reduces the ill posedness inherent in the tomographic inversion due to the under-determined nature of the problem and the inconsistencies in the observed data. This paper discusses the theory of regularized inversion for joint inversion of controlled source and earthquake data, and results from synthetic data testing and application to real data. The results obtained from tomographic inversion of synthetic data and real data from the northern Cascadia subduction zone show that the velocity model and hypocentral parameters can be efficiently estimated using this approach. (paper)

Wave-equation reflection traveltime inversion

KAUST Repository

Zhang, Sanzong

2011-01-01

The main difficulty with iterative waveform inversion using a gradient optimization method is that it tends to get stuck in local minima associated within the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in the velocity model. To reduce this nonlinearity, we present a reflection traveltime tomography method based on the wave equation which enjoys a more quasi-linear relationship between the model and the data. A local crosscorrelation of the windowed downgoing direct wave and the upgoing reflection wave at the image point yields the lag time that maximizes the correlation. This lag time represents the reflection traveltime residual that is back-projected into the earth model to update the velocity in the same way as wave-equation transmission traveltime inversion. No travel-time picking is needed and no high-frequency approximation is assumed. The mathematical derivation and the numerical examples are presented to partly demonstrate its efficiency and robustness. © 2011 Society of Exploration Geophysicists.

Accounting for imperfect forward modeling in geophysical inverse problems — Exemplified for crosshole tomography

DEFF Research Database (Denmark)

Hansen, Thomas Mejer; Cordua, Knud Skou; Holm Jacobsen, Bo

2014-01-01

forward models, can be more than an order of magnitude larger than the measurement uncertainty. We also found that the modeling error is strongly linked to the spatial variability of the assumed velocity field, i.e., the a priori velocity model.We discovered some general tools by which the modeling error...... synthetic ground-penetrating radar crosshole tomographic inverse problems. Ignoring the modeling error can lead to severe artifacts, which erroneously appear to be well resolved in the solution of the inverse problem. Accounting for the modeling error leads to a solution of the inverse problem consistent...

Feasibility study for mega-electron-volt electron beam tomography.

Science.gov (United States)

Hampel, U; Bärtling, Y; Hoppe, D; Kuksanov, N; Fadeev, S; Salimov, R

2012-09-01

Electron beam tomography is a promising imaging modality for the study of fast technical processes. But for many technical objects of interest x rays of several hundreds of keV energy are required to achieve sufficient material penetration. In this article we report on a feasibility study for fast electron beam computed tomography with a 1 MeV electron beam. The experimental setup comprises an electrostatic accelerator with beam optics, transmission target, and a single x-ray detector. We employed an inverse fan-beam tomography approach with radiographic projections being generated from the linearly moving x-ray source. Angular projections were obtained by rotating the object.

Global Seismic Imaging Based on Adjoint Tomography

Science.gov (United States)

Bozdag, E.; Lefebvre, M.; Lei, W.; Peter, D. B.; Smith, J. A.; Zhu, H.; Komatitsch, D.; Tromp, J.

2013-12-01

Our aim is to perform adjoint tomography at the scale of globe to image the entire planet. We have started elastic inversions with a global data set of 253 CMT earthquakes with moment magnitudes in the range 5.8 ≤ Mw ≤ 7 and used GSN stations as well as some local networks such as USArray, European stations, etc. Using an iterative pre-conditioned conjugate gradient scheme, we initially set the aim to obtain a global crustal and mantle model with confined transverse isotropy in the upper mantle. Global adjoint tomography has so far remained a challenge mainly due to computational limitations. Recent improvements in our 3D solvers (e.g., a GPU version) and access to high-performance computational centers (e.g., ORNL's Cray XK7 "Titan" system) now enable us to perform iterations with higher-resolution (T > 9 s) and longer-duration (200 min) simulations to accommodate high-frequency body waves and major-arc surface waves, respectively, which help improve data coverage. The remaining challenge is the heavy I/O traffic caused by the numerous files generated during the forward/adjoint simulations and the pre- and post-processing stages of our workflow. We improve the global adjoint tomography workflow by adopting the ADIOS file format for our seismic data as well as models, kernels, etc., to improve efficiency on high-performance clusters. Our ultimate aim is to use data from all available networks and earthquakes within the magnitude range of our interest (5.5 ≤ Mw ≤ 7) which requires a solid framework to manage big data in our global adjoint tomography workflow. We discuss the current status and future of global adjoint tomography based on our initial results as well as practical issues such as handling big data in inversions and on high-performance computing systems.

Sequential and joint hydrogeophysical inversion using a field-scale groundwater model with ERT and TDEM data

DEFF Research Database (Denmark)

Herckenrath, Daan; Fiandaca, G.; Auken, Esben

2013-01-01

hydrogeophysical inversion approaches to inform a field-scale groundwater model with time domain electromagnetic (TDEM) and electrical resistivity tomography (ERT) data. In a sequential hydrogeophysical inversion (SHI) a groundwater model is calibrated with geophysical data by coupling groundwater model parameters...... with the inverted geophysical models. We subsequently compare the SHI with a joint hydrogeophysical inversion (JHI). In the JHI, a geophysical model is simultaneously inverted with a groundwater model by coupling the groundwater and geophysical parameters to explicitly account for an established petrophysical...

Sequential and joint hydrogeophysical inversion using a field-scale groundwater model with ERT and TDEM data

DEFF Research Database (Denmark)

Herckenrath, Daan; Fiandaca, G.; Auken, Esben

2013-01-01

with the inverted geophysical models. We subsequently compare the SHI with a joint hydrogeophysical inversion (JHI). In the JHI, a geophysical model is simultaneously inverted with a groundwater model by coupling the groundwater and geophysical parameters to explicitly account for an established petrophysical...... hydrogeophysical inversion approaches to inform a field-scale groundwater model with time domain electromagnetic (TDEM) and electrical resistivity tomography (ERT) data. In a sequential hydrogeophysical inversion (SHI) a groundwater model is calibrated with geophysical data by coupling groundwater model parameters...

DIRECT OBSERVATION OF SOLAR CORONAL MAGNETIC FIELDS BY VECTOR TOMOGRAPHY OF THE CORONAL EMISSION LINE POLARIZATIONS

International Nuclear Information System (INIS)

Kramar, M.; Lin, H.; Tomczyk, S.

2016-01-01

We present the first direct “observation” of the global-scale, 3D coronal magnetic fields of Carrington Rotation (CR) Cycle 2112 using vector tomographic inversion techniques. The vector tomographic inversion uses measurements of the Fe xiii 10747 Å Hanle effect polarization signals by the Coronal Multichannel Polarimeter (CoMP) and 3D coronal density and temperature derived from scalar tomographic inversion of Solar Terrestrial Relations Observatory (STEREO)/Extreme Ultraviolet Imager (EUVI) coronal emission lines (CELs) intensity images as inputs to derive a coronal magnetic field model that best reproduces the observed polarization signals. While independent verifications of the vector tomography results cannot be performed, we compared the tomography inverted coronal magnetic fields with those constructed by magnetohydrodynamic (MHD) simulations based on observed photospheric magnetic fields of CR 2112 and 2113. We found that the MHD model for CR 2112 is qualitatively consistent with the tomography inverted result for most of the reconstruction domain except for several regions. Particularly, for one of the most noticeable regions, we found that the MHD simulation for CR 2113 predicted a model that more closely resembles the vector tomography inverted magnetic fields. In another case, our tomographic reconstruction predicted an open magnetic field at a region where a coronal hole can be seen directly from a STEREO-B/EUVI image. We discuss the utilities and limitations of the tomographic inversion technique, and present ideas for future developments

Attenuated bioluminescent Brucella melitensis mutants GR019 (virB4), GR024 (galE), and GR026 (BMEI1090-BMEI1091) confer protection in mice.

Science.gov (United States)

Rajashekara, Gireesh; Glover, David A; Banai, Menachem; O'Callaghan, David; Splitter, Gary A

2006-05-01

In vivo bioluminescence imaging is a persuasive approach to investigate a number of issues in microbial pathogenesis. Previously, we have applied bioluminescence imaging to gain greater insight into Brucella melitensis pathogenesis. Endowing Brucella with bioluminescence allowed direct visualization of bacterial dissemination, pattern of tissue localization, and the contribution of Brucella genes to virulence. In this report, we describe the pathogenicity of three attenuated bioluminescent B. melitensis mutants, GR019 (virB4), GR024 (galE), and GR026 (BMEI1090-BMEI1091), and the dynamics of bioluminescent virulent bacterial infection following vaccination with these mutants. The virB4, galE, and BMEI1090-BMEI1091 mutants were attenuated in interferon regulatory factor 1-deficient (IRF-1(-/-)) mice; however, only the GR019 (virB4) mutant was attenuated in cultured macrophages. Therefore, in vivo imaging provides a comprehensive approach to identify virulence genes that are relevant to in vivo pathogenesis. Our results provide greater insights into the role of galE in virulence and also suggest that BMEI1090 and downstream genes constitute a novel set of genes involved in Brucella virulence. Survival of the vaccine strain in the host for a critical period is important for effective Brucella vaccines. The galE mutant induced no changes in liver and spleen but localized chronically in the tail and protected IRF-1(-/-) and wild-type mice from virulent challenge, implying that this mutant may serve as a potential vaccine candidate in future studies and that the direct visualization of Brucella may provide insight into selection of improved vaccine candidates.

Bioluminescence in a complex coastal environment: 1. Temporal dynamics of nighttime water-leaving radiance

Science.gov (United States)

Moline, Mark A.; Oliver, Matthew J.; Mobley, Curtis D.; Sundman, Lydia; Bensky, Thomas; Bergmann, Trisha; Bissett, W. Paul; Case, James; Raymond, Erika H.; Schofield, Oscar M. E.

2007-11-01

Nighttime water-leaving radiance is a function of the depth-dependent distribution of both the in situ bioluminescence emissions and the absorption and scattering properties of the water. The vertical distributions of these parameters were used as inputs for a modified one-dimensional radiative transfer model to solve for spectral bioluminescence water-leaving radiance from prescribed depths of the water column. Variation in the water-leaving radiance was consistent with local episodic physical forcing events, with tidal forcing, terrestrial runoff, particulate accumulation, and biological responses influencing the shorter timescale dynamics. There was a >90 nm shift in the peak water-leaving radiance from blue (˜474 nm) to green as light propagated to the surface. In addition to clues in ecosystem responses to physical forcing, the temporal dynamics in intensity and spectral quality of water-leaving radiance provide suitable ranges for assessing detection. This may provide the information needed to estimate the depth of internal light sources in the ocean, which is discussed in part 2 of this paper.

Imaging of bioluminescent LNCaP-luc-M6 tumors: a new animal model for the study of metastatic human prostate cancer.

Science.gov (United States)

Scatena, Caroline D; Hepner, Mischa A; Oei, Yoko A; Dusich, Joan M; Yu, Shang-Fan; Purchio, Tony; Contag, Pamela R; Jenkins, Darlene E

2004-05-15

Animal experiments examining hormone-sensitive metastatic prostate cancer using the human LNCaP cell line have been limited to endpoint analyses. To permit longitudinal studies, we generated a luciferase-expressing cell line and used bioluminescent imaging (BLI) to non-invasively monitor the in vivo growth of primary LNCaP tumors and metastasis. LNCaP.FGC cells were transfected to constitutively express firefly luciferase. LNCaP-luc-M6 cells were tested for bioluminescent signal intensity and hormone responsiveness in vitro. The cells were implanted in subcutaneous and orthotopic sites in SCID-bg mice and imaged over time. The LNCaP-luc-M6 cells formed subcutaneous and orthotopic tumors in SCID-bg mice, and nearly all tumor-bearing animals developed pulmonary metastases. Early detection and temporal growth of primary tumors and metastatic lesions was successfully monitored by BLI. The LNCaP-luc-M6 cell line is a bioluminescent, hormone-sensitive prostate cancer cell line applicable for BLI studies to non-invasively monitor subcutaneous and orthotopic prostate tumor growth and metastasis in vivo. Copyright 2004 Wiley-Liss, Inc.

Bioluminescence : the potential of a non-invasive bio-optical imaging technique and improvement of animal research

NARCIS (Netherlands)

Hesselink, J. W.; van Dam, G. M.

2007-01-01

Bioluminescence is an optical imaging technique that exploits the emission of photons at specific wavelengths based on energy-dependent reactions catalysed by luciferases. The technique makes it possible to monitor measure, and track biological processes in living animals. A short review is

Effect of fluid-filled boreholes on resistivity tomography; Hiteiko tomography ni okeru konaisui no eikyo

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, Y [DIA Consultants Co. Ltd., Tokyo (Japan)

1997-10-22

Theoretical discussions were given on the effect of fluid-filled boreholes on resistivity tomography. The discussions performed incorporation of earth resistance as a method to consider borehole diameters in an FEM calculation using wire elements. The numerical experiment conducted a simulation on the following two objects: resistivity tomography in a horizontal multi-layer structure consisted of layers with resistivity ranging from 10 to 10000 ohm-m, and a model with a slanted low resistivity band existing in a background of 5000 ohm-m. As a result of the discussions, it was made clear that the effect of the boreholes can be corrected by giving earth resistance between the wire elements and natural ground. An improved potential calculating program indicated that the effect of the fluid-filled boreholes in the resistivity tomography generates false images with high resistivity along the bores if the resistivity has high contrast. Incorporating the wire elements into an inverse analysis model reduces the false images and improves the accuracy. 1 ref., 12 figs.

FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography.

Science.gov (United States)

Ale, Angelique; Ermolayev, Vladimir; Herzog, Eva; Cohrs, Christian; de Angelis, Martin Hrabé; Ntziachristos, Vasilis

2012-06-01

The development of hybrid optical tomography methods to improve imaging performance has been suggested over a decade ago and has been experimentally demonstrated in animals and humans. Here we examined in vivo performance of a camera-based hybrid fluorescence molecular tomography (FMT) system for 360° imaging combined with X-ray computed tomography (XCT). Offering an accurately co-registered, information-rich hybrid data set, FMT-XCT has new imaging possibilities compared to stand-alone FMT and XCT. We applied FMT-XCT to a subcutaneous 4T1 tumor mouse model, an Aga2 osteogenesis imperfecta model and a Kras lung cancer mouse model, using XCT information during FMT inversion. We validated in vivo imaging results against post-mortem planar fluorescence images of cryoslices and histology data. Besides offering concurrent anatomical and functional information, FMT-XCT resulted in the most accurate FMT performance to date. These findings indicate that addition of FMT optics into the XCT gantry may be a potent upgrade for small-animal XCT systems.

Numerical experiment for nonlinear full-wave tomography. 3; Hisenkei full wave tomography no suchi jikken

Energy Technology Data Exchange (ETDEWEB)

Tsuchiya, T [Dia Consultants Company, Tokyo (Japan)

1996-10-01

Nonlinear full-wave tomography (FWT) is under investigation to improve the estimation accuracy of Vp/Vs distributions. Full-wave tomography is one of the underground structure exploration methods mainly using Tarantola`s nonlinear local optimization method (LOM). Numerical experiment for FWT was carried out assuming relatively weak nonlinear underground structure. In the case of inversion by local optimization method, adequate preconditioning is important. Utilization of geological information is also effective in estimating low-frequency components of a model. As far as data are obtained under proper observation arrangement, even in actual field, precise estimation of Vp/Vs distributions is possible by FWT using explosion in a hole as wave source. In full-wave tomography, selection of observation arrangement is essential for both Vp and Vs. However, the proper arrangement is different between Vp and Vs. Approach to different analyses for Vp and Vs is also necessary by using only proper data for Vp and Vs among obtained data sets. 4 figs.

In vivo bioluminescence imaging using orthotopic xenografts towards patient's derived-xenograft Medulloblastoma models.

Science.gov (United States)

Asadzadeh, Fatemeh; Ferrucci, Veronica; DE Antonellis, Pasqualino; Zollo, Massimo

2017-03-01

Medulloblastoma is a cerebellar neoplasia of the central nervous system. Four molecular subgrups have been identified (MBWNT, MBSHH, MBgroup3 and MBgroup4) with distinct genetics and clinical outcome. Among these, MBgroup3-4 are highly metastatic with the worst prognosis. The current standard therapy includes surgery, radiation and chemotherapy. Thus, specific treatments adapted to cure those different molecular subgroups are needed. The use of orthotopic xenograft models, together with the non-invasive in vivo biolumiscence imaging (BLI) technology, is emerging during preclinical studies to test novel therapeutics for medulloblastoma treatment. Orthotopic MB xenografts were performed by injection of Daoy-luc cells, that had been previously infected with lentiviral particles to stably express luciferase gene, into the fourth right ventricle of the cerebellum of ten nude mice. For the implantation, specific stereotactic coordinates were used. Seven days after the implantation the mice were imaged by acquisitions of bioluminescence imaging (BLI) using IVIS 3D Illumina Imaging System (Xenogen). Tumor growth was evaluated by quantifying the bioluminescence signals using the integrated fluxes of photons within each area of interest using the Living Images Software Package 3.2 (Xenogen-Perkin Elmer). Finally, histological analysis using hematoxylin-eosin staining was performed to confirm the presence of tumorigenic cells into the cerebellum of the mice. We describe a method to use the in vivo bioluminescent imaging (BLI) showing the potential to be used to investigate the potential antitumorigenic effects of a drug for in vivo medulloblastoma treatment. We also discuss other studies in which this technology has been applied to obtain a more comprehensive knowledge of medulloblastoma using orthotopic xenograft mouse models. There is a need to develop patient's derived-xenograft (PDX) model systems to test novel drugs for medulloblastoma treatment within each molecular sub

Performance dependence of hybrid x-ray computed tomography/fluorescence molecular tomography on the optical forward problem.

Science.gov (United States)

Hyde, Damon; Schulz, Ralf; Brooks, Dana; Miller, Eric; Ntziachristos, Vasilis

2009-04-01

Hybrid imaging systems combining x-ray computed tomography (CT) and fluorescence tomography can improve fluorescence imaging performance by incorporating anatomical x-ray CT information into the optical inversion problem. While the use of image priors has been investigated in the past, little is known about the optimal use of forward photon propagation models in hybrid optical systems. In this paper, we explore the impact on reconstruction accuracy of the use of propagation models of varying complexity, specifically in the context of these hybrid imaging systems where significant structural information is known a priori. Our results demonstrate that the use of generically known parameters provides near optimal performance, even when parameter mismatch remains.

Development of axial tomography technique for the study of steam explosion

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae Young; Seo, S. W.; You, S. [Handong Golbal Univ., Pohang (Korea, Republic of)

2006-05-15

In this report, axial tomography applying to steam explosion is implemented. When steam explosion experiment is performed, we have seen the difficulty with physical modeling due to the complex phenomena of generated steam, propagation of shock wave and bubble breakup and coalescence. Hence, the uncertainty due to these phenomena is occurred. The fast and global measurement of the steam distribution is imperative to understand the complex phenomena performed during the steam explosion, KAERI have developed the fast and global measuring instrument to monitor such phenomena of axial steam distribution. Generally, X-ray is used as measuring method, but this method is very expensive and has limited measurement area. So we need new method that can substitute X-ray method and in this research, ECT method is replaced. The research is performed dividing within two parts: Software and Hardware. In the software part, the electric field analysis code and algorithm for inverse projection were developed. And, in the hardware part, capacitance measurement circuit is developed to measure up to fF level. Operable axial tomography was analyzed with concept design of axial tomography appropriate to steam explosion accident and analysis code for axial electric field analysis and inverse algorithm were developed, moreover, designing signal analysis system for axial tomography was performed.

Diffuse optical tomography with physiological and spatial a priori constraints

International Nuclear Information System (INIS)

Intes, Xavier; Maloux, Clemence; Guven, Murat; Yazici, Birzen; Chance, Britton

2004-01-01

Diffuse optical tomography is a typical inverse problem plagued by ill-condition. To overcome this drawback, regularization or constraining techniques are incorporated in the inverse formulation. In this work, we investigate the enhancement in recovering functional parameters by using physiological and spatial a priori constraints. More accurate recovery of the two main functional parameters that are the blood volume and the relative saturation is demonstrated through simulations by using our method compared to actual techniques. (note)

On the use of sensitivity tests in seismic tomography

NARCIS (Netherlands)

Rawlinson, N.; Spakman, W.

2016-01-01

Sensitivity analysis with synthetic models is widely used in seismic tomography as a means for assessing the spatial resolution of solutions produced by, in most cases, linear or iterative nonlinear inversion schemes. The most common type of synthetic reconstruction test is the so-called

Hybrid inverse problems for a system of Maxwell’s equations

International Nuclear Information System (INIS)

Bal, Guillaume; Zhou, Ting

2014-01-01

This paper concerns the quantitative step of the medical imaging modality thermo-acoustic tomography (TAT). We model the radiation propagation by a system of Maxwell’s equations. We show that the index of refraction of light and the absorption coefficient (conductivity) can be uniquely and stably reconstructed from a sufficiently large number of TAT measurements. Our method is based on verifying that the linearization of the inverse problem forms a redundant elliptic system of equations. We also observe that the reconstructions are qualitatively quite different from the setting where radiation is modeled by a scalar Helmholtz equation as in Bal G et al (2011 Inverse Problems 27 055007). (paper)

X-ray tomography on TCV

International Nuclear Information System (INIS)

Anton, M.; Weisen, H.; Dutch, M.J.; Buhlmann, F.; Chavan, R.; Marletaz, B.; Marmillod, P.; Paris, P.

1996-04-01

The TCV Tokamak offers an outstanding variability of the plasma shape. Using X-ray tomography, the shape of the inner flux surfaces of a poloidal cross section of the plasma can be reconstructed, including fast variations due to MHD activity. The hardware as well as the software of the 200 channel system developed for TCV is described. A new, 'dynamical' calibration is used. The actual plasma temperature and some global profile parameters serve to determine the spectrum-dependent efficiency of the photodiodes. Compared to a 'static' calibration with constant calibration factors, an enhanced quality of the reconstructed images is observed. The tomographic inversion is performed using a variety of methods such as Maximum Entropy, linear Regularisation and a new method making use of the Fisher information of the emissivity distribution. The merits of the different algorithms which have been implemented as MATLAB functions are compared. The tomographic inversion results are analysed with the help of the biorthogonal decomposition, allowing e.g. identification of MHD modes without using any a priori information on the poloidal mode structure. Recent results on the dependence of sawtooth activity on the plasma triangularity are presented to demonstrate the performance of the soft X-ray tomography system. (author) 14 figs., 2 tabs., 26 refs

[Activation of the bioluminescence of the sensor Escherichia coli strains used for detecting N-acyl-homoserine lactones in the presence of nitrofurans and NO generators].

Science.gov (United States)

Zaĭtseva, Iu V; Granik, V G; Belik, A S; Koksharova, O A; Khmel', I A

2010-01-01

Nitrofurans (nitrofurazone, nitrofurantoin, furazidin, nifuroxazide), and nitric oxide generators (sodium nitroprusside and isosorbide mononitrate) in subinhibitory concentrations were shown to significantly increase the bioluminescence of the sensor Escherichia coli strains used for detecting N-acyl-homoserine lactones, signaling molecules of Quorum Sensing (QS) regulatory systems. The highest activation of bioluminescence (up to 250-400 fold) was observed in the presence of nitrofurazone on E. coli DH5alpha biosensors containing lux-reporter plasmids pSB401 or pSB536. However, this activation was not specifically associated with the functioning of QS systems. We suggest that the effect observed results from a direct action of nitrofurans and NO donors on the process of bioluminescence. The data indicate the necessity of using the biosensors that make it possible to detect specific effects of substances tested on QS regulation.

Active tectonics in Central Italy: Constraint from surface wave tomography and source moment tensor inversion

International Nuclear Information System (INIS)

Chimera, G.; Aoudia, A.; Panza, G.F.; Sarao, A.

2002-06-01

We make a multiscale investigation of the lithosphere-asthenosphere structure and of the active tectonics along a stripe from the Tyrrhenian to the Adriatic coast, with emphasis on the Umbria-Marche area, by means of surface-wave tomography and inversion experiments for structure and seismic moment tensor retrieval. The data include: a large number of new local and regional group velocity measurements sampling the Umbria-Marche Apennines and the Adria margin respectively; new and published phase velocity measurements sampling Italy and surroundings; deep seismic soundings which, crossing the whole Peninsula from the Tyrrhenian to the Adriatic coasts, go through the Umbria-Marche area. The local group velocity maps cover the area reactivated by the 1997-1998 Umbria-Marche earthquake sequence. These maps suggest an intimate relation between the lateral variations and distribution of the active fault systems and related sedimentary basins. Such relation is confirmed by the non-linear inversion of the local dispersion curves. To image the structure of the lithosphere-asthenosphere system from the Tyrrhenian to the Adriatic coast, we fix the upper crust parameters consistently with our Umbria-Marche models and with pertinent deep seismic sounding data and invert the regional long period dispersion measurements. At a local scale, in the Umbria-Marche area, the retrieved models for the upper crust reveal the importance of the inherited compressional tectonics on the ongoing extensional deformation and related seismic activity. The lateral and in-depth structural changes in the upper crust are likely controlling fault segmentation and seismogenesis. Source inversion studies of the large crustal events of the 1997 earthquake sequence show the dominance of normal faulting mechanisms, whereas selected aftershocks between the fault segments reveal that the prevailing deformation at the step-over is of strike-slip faulting type and may control the lateral fault extent. At the

Enlightening the malaria parasite life cycle: bioluminescent Plasmodium in fundamental and applied research

OpenAIRE

Siciliano, Giulia; Alano, Pietro

2015-01-01

The unicellular protozoan parasites of the genus Plasmodium impose on human health worldwide the enormous burden of malaria. The possibility to genetically modify several species of malaria parasites represented a major advance in the possibility to elucidate their biology and is now turning laboratory lines of transgenic Plasmodium into precious weapons to fight malaria. Amongst the various genetically modified plasmodia, transgenic parasite lines expressing bioluminescent reporters have bee...

Application de la bioluminescence au dénombrement des microorganismes vivants dans les vins

Directory of Open Access Journals (Sweden)

Aline Lonvaud-Funel

1982-12-01

Bioluminescence was applied to enumerate the microorganisms present in wine. An excellent correlation is obtained by counting colonies grown in Petri dishes. The simplicity of the manipulations and the rapid obtention of results are the principal benefits of this method. Research is still necessary both in the differentiation of yeasts and bacteria and the reduction of the threshold of detection.

A Bone Metastasis Nude Mouse Model Created by Ultrasound Guided Intracardiac Injection of Breast Cancer Cells: the Micro-CT, MRI and Bioluminescence Imaging Analysis

Energy Technology Data Exchange (ETDEWEB)

Park, Young Jin; Song, Eun Hye; Kim, Seol Hwa; Song, Ho Taek; Suh, Jin Suck [Yonsei University College of Medicine, Seoul (Korea, Republic of); Choi, Sang Hyun [Korean Minjok Leadership Academy, Heongsung (Korea, Republic of)

2011-01-15

The purpose of this study was to develop a nude mouse model of bone metastasis by performing intracardiac injection of breast cancer cells under ultrasonography guidance and we wanted to evaluate the development and the distribution of metastasis in vivo using micro-CT, MRI and bioluminescence imaging. Animal experiments were performed in 6-week-old female nude mice. The animals underwent left ventricular injection of 2x105 MDA-MB-231Bo-Luc cells. After injection of the tumor cells, serial bioluminescence imaging was performed for 7 weeks. The findings of micro-CT, MRI and the histology were correlated with the 'hot' lesions seen on the bioluminescence imaging. Metastasis was found in 62.3% of the animals. Two weeks after intracardiac injection, metastasis to the brain, spine and femur was detected with bioluminescence imaging with an increasing intensity by week 7. Micro-CT scan confirmed multiple osteolytic lesions at the femur, spine and skull. MRI and the histology were able to show metastasis in the brain and extraskeletal metastasis around the femur. The intracardiac injection of cancer cells under ultrasonography guidance is a safe and highly reproducible method to produce bone metastasis in nude mice. This bone metastasis nude mouse model will be useful to study the mechanism of bone metastasis and to validate new therapeutics

3D and 4D magnetic susceptibility tomography based on complex MR images

Science.gov (United States)

Chen, Zikuan; Calhoun, Vince D

2014-11-11

Magnetic susceptibility is the physical property for T2*-weighted magnetic resonance imaging (T2*MRI). The invention relates to methods for reconstructing an internal distribution (3D map) of magnetic susceptibility values, .chi. (x,y,z), of an object, from 3D T2*MRI phase images, by using Computed Inverse Magnetic Resonance Imaging (CIMRI) tomography. The CIMRI technique solves the inverse problem of the 3D convolution by executing a 3D Total Variation (TV) regularized iterative convolution scheme, using a split Bregman iteration algorithm. The reconstruction of .chi. (x,y,z) can be designed for low-pass, band-pass, and high-pass features by using a convolution kernel that is modified from the standard dipole kernel. Multiple reconstructions can be implemented in parallel, and averaging the reconstructions can suppress noise. 4D dynamic magnetic susceptibility tomography can be implemented by reconstructing a 3D susceptibility volume from a 3D phase volume by performing 3D CIMRI magnetic susceptibility tomography at each snapshot time.

Inversion of full acoustic wavefield in local helioseismology: A study with synthetic data

NARCIS (Netherlands)

Cobden, L.J.; Tong, C.H.; Warner, M.R.

We present the first results from the inversion of full acoustic wavefield in the helioseismic context. In contrast to time-distance helioseismology, which involves analyzing the travel times of seismic waves propagating into the solar interior, wavefield tomography models both the travel times and

Stabilizing inverse problems by internal data. II: non-local internal data and generic linearized uniqueness

KAUST Repository

Kuchment, Peter

2015-05-10

© 2015, Springer Basel. In the previous paper (Kuchment and Steinhauer in Inverse Probl 28(8):084007, 2012), the authors introduced a simple procedure that allows one to detect whether and explain why internal information arising in several novel coupled physics (hybrid) imaging modalities could turn extremely unstable techniques, such as optical tomography or electrical impedance tomography, into stable, good-resolution procedures. It was shown that in all cases of interest, the Fréchet derivative of the forward mapping is a pseudo-differential operator with an explicitly computable principal symbol. If one can set up the imaging procedure in such a way that the symbol is elliptic, this would indicate that the problem was stabilized. In the cases when the symbol is not elliptic, the technique suggests how to change the procedure (e.g., by adding extra measurements) to achieve ellipticity. In this article, we consider the situation arising in acousto-optical tomography (also called ultrasound modulated optical tomography), where the internal data available involves the Green’s function, and thus depends globally on the unknown parameter(s) of the equation and its solution. It is shown that the technique of (Kuchment and Steinhauer in Inverse Probl 28(8):084007, 2012) can be successfully adopted to this situation as well. A significant part of the article is devoted to results on generic uniqueness for the linearized problem in a variety of situations, including those arising in acousto-electric and quantitative photoacoustic tomography.

Estimation of Material Distribution at the Premixing Stage in the Steam Explosion Event using the Electric Tomography

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae Young; Seo, S. W.; Lee, C. H. [Handong Global Univ., Pohang (Korea, Republic of)

2008-02-15

Axixal tomography code which is developed in 2005-06, is improved through the present research. In the first year, the objects of project are the measurement of water level and measurement of bubble distribution that are significant measurement factor used in axial tomography. To improve the previous axial tomography code, we gave attention to inverse algorithm. Inverse algorithm is the method to solve a system of equations that has many unknowns than the number of equations. The system of equations is not solved exactly. To find a more exact approximated solution of the system of equations, it is proposed to the number of equations increasing. If the number of electrode is increased, image reconstruction results are better than the previous one, because of the number of equations corresponded to the number of independent measurement. Therefore, the axial tomography code was changed by increase in the number of electrode. And phase distribution was reconstructed by new axial tomography code. As the results, image reconstruction performance is improved. The water level and bubble distribution is measured more precisely than the previous study.

Dispersion free full range spectral intensity optical coherence tomography

DEFF Research Database (Denmark)

Jensen, Mikkel; Israelsen, Niels Møller; Maria, Michael

2017-01-01

Optical coherence tomography (OCT) is a non-invasive imaging technique with many applications and widespread use in ophthalmology [1]. The axial resolution in OCT is inversely proportional to the bandwidth of the optical source used, but the improved axial resolution comes at the price of more...

Forward and Inverse Modeling of Self-potential. A Tomography of Groundwater Flow and Comparison Between Deterministic and Stochastic Inversion Methods

Science.gov (United States)

Quintero-Chavarria, E.; Ochoa Gutierrez, L. H.

2016-12-01

Applications of the Self-potential Method in the fields of Hydrogeology and Environmental Sciences have had significant developments during the last two decades with a strong use on groundwater flows identification. Although only few authors deal with the forward problem's solution -especially in geophysics literature- different inversion procedures are currently being developed but in most cases they are compared with unconventional groundwater velocity fields and restricted to structured meshes. This research solves the forward problem based on the finite element method using the St. Venant's Principle to transform a point dipole, which is the field generated by a single vector, into a distribution of electrical monopoles. Then, two simple aquifer models were generated with specific boundary conditions and head potentials, velocity fields and electric potentials in the medium were computed. With the model's surface electric potential, the inverse problem is solved to retrieve the source of electric potential (vector field associated to groundwater flow) using deterministic and stochastic approaches. The first approach was carried out by implementing a Tikhonov regularization with a stabilized operator adapted to the finite element mesh while for the second a hierarchical Bayesian model based on Markov chain Monte Carlo (McMC) and Markov Random Fields (MRF) was constructed. For all implemented methods, the result between the direct and inverse models was contrasted in two ways: 1) shape and distribution of the vector field, and 2) magnitude's histogram. Finally, it was concluded that inversion procedures are improved when the velocity field's behavior is considered, thus, the deterministic method is more suitable for unconfined aquifers than confined ones. McMC has restricted applications and requires a lot of information (particularly in potentials fields) while MRF has a remarkable response especially when dealing with confined aquifers.

Detection of Antibodies in Blood Plasma Using Bioluminescent Sensor Proteins and a Smartphone.

Science.gov (United States)

Arts, Remco; den Hartog, Ilona; Zijlema, Stefan E; Thijssen, Vito; van der Beelen, Stan H E; Merkx, Maarten

2016-04-19

Antibody detection is of fundamental importance in many diagnostic and bioanalytical assays, yet current detection techniques tend to be laborious and/or expensive. We present a new sensor platform (LUMABS) based on bioluminescence resonance energy transfer (BRET) that allows detection of antibodies directly in solution using a smartphone as the sole piece of equipment. LUMABS are single-protein sensors that consist of the blue-light emitting luciferase NanoLuc connected via a semiflexible linker to the green fluorescent acceptor protein mNeonGreen, which are kept close together using helper domains. Binding of an antibody to epitope sequences flanking the linker disrupts the interaction between the helper domains, resulting in a large decrease in BRET efficiency. The resulting change in color of the emitted light from green-blue to blue can be detected directly in blood plasma, even at picomolar concentrations of antibody. Moreover, the modular architecture of LUMABS allows changing of target specificity by simple exchange of epitope sequences, as demonstrated here for antibodies against HIV1-p17, hemagglutinin (HA), and dengue virus type I. The combination of sensitive ratiometric bioluminescent detection and the intrinsic modularity of the LUMABS design provides an attractive generic platform for point-of-care antibody detection that avoids the complex liquid handling steps associated with conventional immunoassays.

Optical coherence tomography signal analysis: LIDAR like equation and inverse methods; Analise de sinais de tomografia por coerencia optica: equacao LIDAR e metodos de inversao

Energy Technology Data Exchange (ETDEWEB)

Amaral, Marcello Magri

2012-07-01

Optical Coherence Tomography (OCT) is based on the media backscattering properties in order to obtain tomographic images. In a similar way, LIDAR (Light Detection and Range) technique uses these properties to determine atmospheric characteristics, specially the signal extinction coefficient. Exploring this similarity allowed the application of signal inversion methods to the OCT images, allowing to construct images based in the extinction coefficient, original result until now. The goal of this work was to study, propose, develop and implement algorithms based on OCT signal inversion methodologies with the aim of determine the extinction coefficient as a function of depth. Three inversion methods were used and implemented in LABView{sup R}: slope, boundary point and optical depth. Associated errors were studied and real samples (homogeneous and stratified) were used for two and three dimension analysis. The extinction coefficient images obtained from the optical depth method were capable to differentiate air from the sample. The images were studied applying PCA and cluster analysis that established the methodology strength in determining the sample's extinction coefficient value. Moreover, the optical depth methodology was applied to study the hypothesis that there is some correlation between signal extinction coefficient and the enamel teeth demineralization during a cariogenic process. By applying this methodology, it was possible to observe the variation of the extinction coefficient as depth function and its correlation with microhardness variation, showing that in deeper layers its values tends to a healthy tooth values, behaving as the same way that the microhardness. (author)

Rapid detection of E. Coli O157:H7 by IFAST and ATP bioluminescence assay for water analysis

CSIR Research Space (South Africa)

Ngamsom, B

2016-10-01

Full Text Available The present investigation reports isolation and detection of E. coli O157:H7 employing a simple and portable microfluidic device based on immiscible filtration assisted by surface tension (IFAST) and adenosine triphosphate (ATP) bioluminescence...

Infection routes of Aeromonas salmonicida in rainbow trout monitored in vivo by real-time bioluminescence imaging

DEFF Research Database (Denmark)

Bartkova, Simona; Kokotovic, Branko; Dalsgaard, Inger

2017-01-01

Recent development of imaging tools has facilitated studies of pathogen infections in vivo in real time. This trend can be exemplified by advances in bioluminescence imaging (BLI), an approach that helps to visualize dissemination of pathogens within the same animal over several time points. Here...

A miniaturized device for bioluminescence analysis of caspase-3/7 5 activity in a single apoptotic cell

Czech Academy of Sciences Publication Activity Database

Adamová, Eva; Lišková, Marcela; Matalová, E.; Klepárník, Karel

Roč. 406 , č. 22 (2014), s. 5389-5394 ISSN 1618-2642 R&D Projects: GA ČR(CZ) GA14-28254S Institutional support: RVO:68081715 Keywords : apoptosis * bioluminescence * single-cell analysis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.436, year: 2014

A miniaturized device for bioluminescence analysis of caspase-3/7 5 activity in a single apoptotic cell

Czech Academy of Sciences Publication Activity Database

Adamová, Eva; Lišková, Marcela; Matalová, E.; Klepárník, Karel

2014-01-01

Roč. 406, č. 22 (2014), s. 5389-5394 ISSN 1618-2642 R&D Projects: GA ČR(CZ) GA14-28254S Institutional support: RVO:68081715 Keywords : apoptosis * bioluminescence * single-cell analysis Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.436, year: 2014

Muon tomography: Plans for observations in the Lesser Antilles

International Nuclear Information System (INIS)

Gibert, Dominique; Beauducel, Francois; Lesparre, Nolwenn; Tarantola, Albert; Declais, Yves; Marteau, Jacques; Nicollin, Florence

2010-01-01

The application of muon tomography to monitor and image the internal structure of volcanoes in the Lesser Antilles is discussed. Particular focus is directed towards the three volcanoes that fall under the responsibility of the Institut de Physique du Globe of Paris, namely La Montagne Pelee in Martinique, La Soufriere in Guadeloupe, and the Soufriere Hills in Montserrat. The technological criteria for the design of portable muon telescopes are presented in detail for both their mechanical and electronic aspects. The detector matrices are constructed with scintillator strips, and their detection characteristics are discussed. The tomography inversion is presented, and its distinctive characteristics are briefly discussed. Details are given on the implementation of muon tomography experiments on La Soufriere in Guadeloupe. (author)

INVERSION OF FULL ACOUSTIC WAVEFIELD IN LOCAL HELIOSEISMOLOGY: A STUDY WITH SYNTHETIC DATA

International Nuclear Information System (INIS)

Cobden, L. J.; Warner, M. R.; Tong, C. H.

2011-01-01

We present the first results from the inversion of full acoustic wavefield in the helioseismic context. In contrast to time-distance helioseismology, which involves analyzing the travel times of seismic waves propagating into the solar interior, wavefield tomography models both the travel times and amplitude variations present in the entire seismic record. Unlike the use of ray-based, Fresnel-zone, Born, or Rytov approximations in previous time-distance studies, this method does not require any simplifications to be made to the sensitivity kernel in the inversion. In this study, the acoustic wavefield is simulated for all iterations in the inversion. The sensitivity kernel is therefore updated while lateral variations in sound-speed structure in the model emerge during the course of the inversion. Our results demonstrate that the amplitude-based inversion approach is capable of resolving sound-speed structures defined by relatively sharp vertical and horizontal boundaries. This study therefore provides the foundation for a new type of subsurface imaging in local helioseismology that is based on the inversion of the entire seismic wavefield.

Acoustic propagational characteristics and tomography studies of the northern Indian Ocean

Digital Repository Service at National Institute of Oceanography (India)

PrasannaKumar, S.; Somayajulu, Y.K.; Murty, T.V.R.

, is dealt with in section 2, followed by the simulation results in section 3, using a ray acoustic model and reference sound speed profile to delineate the acoustic waveguide characteristics in the context of tomography. The generalised inversion model...

Bayesian inversion of refraction seismic traveltime data

Science.gov (United States)

Ryberg, T.; Haberland, Ch

2018-03-01

We apply a Bayesian Markov chain Monte Carlo (McMC) formalism to the inversion of refraction seismic, traveltime data sets to derive 2-D velocity models below linear arrays (i.e. profiles) of sources and seismic receivers. Typical refraction data sets, especially when using the far-offset observations, are known as having experimental geometries which are very poor, highly ill-posed and far from being ideal. As a consequence, the structural resolution quickly degrades with depth. Conventional inversion techniques, based on regularization, potentially suffer from the choice of appropriate inversion parameters (i.e. number and distribution of cells, starting velocity models, damping and smoothing constraints, data noise level, etc.) and only local model space exploration. McMC techniques are used for exhaustive sampling of the model space without the need of prior knowledge (or assumptions) of inversion parameters, resulting in a large number of models fitting the observations. Statistical analysis of these models allows to derive an average (reference) solution and its standard deviation, thus providing uncertainty estimates of the inversion result. The highly non-linear character of the inversion problem, mainly caused by the experiment geometry, does not allow to derive a reference solution and error map by a simply averaging procedure. We present a modified averaging technique, which excludes parts of the prior distribution in the posterior values due to poor ray coverage, thus providing reliable estimates of inversion model properties even in those parts of the models. The model is discretized by a set of Voronoi polygons (with constant slowness cells) or a triangulated mesh (with interpolation within the triangles). Forward traveltime calculations are performed by a fast, finite-difference-based eikonal solver. The method is applied to a data set from a refraction seismic survey from Northern Namibia and compared to conventional tomography. An inversion test

Spatially-Variant Tikhonov Regularization for Double-Difference Waveform Inversion

Energy Technology Data Exchange (ETDEWEB)

Lin, Youzuo [Los Alamos National Laboratory; Huang, Lianjie [Los Alamos National Laboratory; Zhang, Zhigang [Los Alamos National Laboratory

2011-01-01

Double-difference waveform inversion is a potential tool for quantitative monitoring for geologic carbon storage. It jointly inverts time-lapse seismic data for changes in reservoir geophysical properties. Due to the ill-posedness of waveform inversion, it is a great challenge to obtain reservoir changes accurately and efficiently, particularly when using time-lapse seismic reflection data. Regularization techniques can be utilized to address the issue of ill-posedness. The regularization parameter controls the smoothness of inversion results. A constant regularization parameter is normally used in waveform inversion, and an optimal regularization parameter has to be selected. The resulting inversion results are a trade off among regions with different smoothness or noise levels; therefore the images are either over regularized in some regions while under regularized in the others. In this paper, we employ a spatially-variant parameter in the Tikhonov regularization scheme used in double-difference waveform tomography to improve the inversion accuracy and robustness. We compare the results obtained using a spatially-variant parameter with those obtained using a constant regularization parameter and those produced without any regularization. We observe that, utilizing a spatially-variant regularization scheme, the target regions are well reconstructed while the noise is reduced in the other regions. We show that the spatially-variant regularization scheme provides the flexibility to regularize local regions based on the a priori information without increasing computational costs and the computer memory requirement.

Engineering the metal sensitive sites in Macrolampis sp2 firefly luciferase and use as a novel bioluminescent ratiometric biosensor for heavy metals.

Science.gov (United States)

Gabriel, Gabriele V M; Viviani, Vadim R

2016-12-01

Most luminescent biosensors for heavy metals are fluorescent and rely on intensity measurements, whereas a few are ratiometric and rely on spectral changes. Bioluminescent biosensors for heavy metals are less common. Firefly luciferases have been coupled to responsive promoters for mercury and arsenium, and used as light on biosensors. Firefly luciferase bioluminescence spectrum is naturally sensitive to heavy metal cations such as zinc and mercury and to pH. Although pH sensitivity of firefly luciferases was shown to be useful for ratiometric estimation of intracellular pH, its potential use for ratiometric estimation of heavy metals was never considered. Using the yellow-emitting Macrolampis sp2 firefly luciferase and site-directed mutagenesis, we show that the residues H310 and E354 constitute two critical sites for metal sensitivity that can be engineered to increase sensitivity to zinc, nickel, and mercury. A linear relationship between cation concentration and the ratio of bioluminescence intensities at 550 and 610 nm allowed, for the first time, the ratiometric estimation of heavy metals concentrations down to 0.10 mM, demonstrating the potential applicability of firefly luciferases as enzymatic and intracellular ratiometric metal biosensors.

Joint inversion of lake-floor electrical resistivity tomography and boat-towed radio-magnetotelluric data illustrated on synthetic data and an application from the Äspö Hard Rock Laboratory site, Sweden

Science.gov (United States)

Wang, Shunguo; Kalscheuer, Thomas; Bastani, Mehrdad; Malehmir, Alireza; Pedersen, Laust B.; Dahlin, Torleif; Meqbel, Naser

2018-04-01

The electrical resistivity tomography (ERT) method provides moderately good constraints for both conductive and resistive structures, while the radio-magnetotelluric (RMT) method is well suited to constrain conductive structures. Additionally, RMT and ERT data may have different target coverage and are differently affected by various types of noise. Hence, joint inversion of RMT and ERT data sets may provide a better constrained model as compared to individual inversions. In this study, joint inversion of boat-towed RMT and lake-floor ERT data has for the first time been formulated and implemented. The implementation was tested on both synthetic and field data sets incorporating RMT transverse electrical mode and ERT data. Results from synthetic data demonstrate that the joint inversion yields models with better resolution compared with individual inversions. A case study from an area adjacent to the Äspö Hard Rock Laboratory (HRL) in southeastern Sweden was used to demonstrate the implementation of the method. A 790-m-long profile comprising lake-floor ERT and boat-towed RMT data combined with partial land data was used for this purpose. Joint inversions with and without weighting (applied to different data sets, vertical and horizontal model smoothness) as well as constrained joint inversions incorporating bathymetry data and water resistivity measurements were performed. The resulting models delineate subsurface structures such as a major northeasterly directed fracture system, which is observed in the HRL facility underground and confirmed by boreholes. A previously uncertain weakness zone, likely a fracture system in the northern part of the profile, is inferred in this study. The fractures are highly saturated with saline water, which make them good targets of resistivity-based geophysical methods. Nevertheless, conductive sediments overlain by the lake water add further difficulty to resolve these deep fracture zones. Therefore, the joint inversion of RMT

Geostatistical regularization operators for geophysical inverse problems on irregular meshes

Science.gov (United States)

Jordi, C.; Doetsch, J.; Günther, T.; Schmelzbach, C.; Robertsson, J. OA

2018-05-01

Irregular meshes allow to include complicated subsurface structures into geophysical modelling and inverse problems. The non-uniqueness of these inverse problems requires appropriate regularization that can incorporate a priori information. However, defining regularization operators for irregular discretizations is not trivial. Different schemes for calculating smoothness operators on irregular meshes have been proposed. In contrast to classical regularization constraints that are only defined using the nearest neighbours of a cell, geostatistical operators include a larger neighbourhood around a particular cell. A correlation model defines the extent of the neighbourhood and allows to incorporate information about geological structures. We propose an approach to calculate geostatistical operators for inverse problems on irregular meshes by eigendecomposition of a covariance matrix that contains the a priori geological information. Using our approach, the calculation of the operator matrix becomes tractable for 3-D inverse problems on irregular meshes. We tested the performance of the geostatistical regularization operators and compared them against the results of anisotropic smoothing in inversions of 2-D surface synthetic electrical resistivity tomography (ERT) data as well as in the inversion of a realistic 3-D cross-well synthetic ERT scenario. The inversions of 2-D ERT and seismic traveltime field data with geostatistical regularization provide results that are in good accordance with the expected geology and thus facilitate their interpretation. In particular, for layered structures the geostatistical regularization provides geologically more plausible results compared to the anisotropic smoothness constraints.

Monitoring and quantitative assessment of tumor burden using in vivo bioluminescence imaging

Energy Technology Data Exchange (ETDEWEB)

Chen, C.-C. [Cancer Research Division, National Health Research Institute, Miaoli 350, Taiwan (China); Hwang, Jeng-Jong [Institute of Radiological Sciences, National Yang-Ming University, Taipei 112, Taiwan (China)]. E-mail: jjhwang@ym.edu.tw; Ting, G. [Cancer Research Division, National Health Research Institute, Miaoli 350, Taiwan (China); Tseng, Y.-L. [Taiwan Liposome Company, Taipei 115, Taiwan (China); Wang, S.-J. [Department of Nuclear Medicine, Veterans General Hospital, Taipei 112, Taiwan (China); Whang-Peng, J. [Cancer Research Division, National Health Research Institute, Miaoli 350, Taiwan (China)

2007-02-01

In vivo bioluminescence imaging (BLI) is a sensitive imaging modality that is rapid and accessible, and may comprise an ideal tool for evaluating tumor growth. In this study, the kinetic of tumor growth has been assessed in C26 colon carcinoma bearing BALB/c mouse model. The ability of BLI to noninvasively quantitate the growth of subcutaneous tumors transplanted with C26 cells genetically engineered to stably express firefly luciferase and herpes simplex virus type-1 thymidine kinase (C26/tk-luc). A good correlation (R {sup 2}=0.998) of photon emission to the cell number was found in vitro. Tumor burden and tumor volume were monitored in vivo over time by quantitation of photon emission using Xenogen IVIS 50 and standard external caliper measurement, respectively. At various time intervals, tumor-bearing mice were imaged to determine the correlation of in vivo BLI to tumor volume. However, a correlation of BLI to tumor volume was observed when tumor volume was smaller than 1000 mm{sup 3} (R {sup 2}=0.907). {gamma} Scintigraphy combined with [{sup 131}I]FIAU was another imaging modality used for verifying the previous results. In conclusion, this study showed that bioluminescence imaging is a powerful and quantitative tool for the direct assay to monitor tumor growth in vivo. The dual reporter genes transfected tumor-bearing animal model can be applied in the evaluation of the efficacy of new developed anti-cancer drugs.

Monitoring and quantitative assessment of tumor burden using in vivo bioluminescence imaging

International Nuclear Information System (INIS)

Chen, C.-C.; Hwang, Jeng-Jong; Ting, G.; Tseng, Y.-L.; Wang, S.-J.; Whang-Peng, J.

2007-01-01

In vivo bioluminescence imaging (BLI) is a sensitive imaging modality that is rapid and accessible, and may comprise an ideal tool for evaluating tumor growth. In this study, the kinetic of tumor growth has been assessed in C26 colon carcinoma bearing BALB/c mouse model. The ability of BLI to noninvasively quantitate the growth of subcutaneous tumors transplanted with C26 cells genetically engineered to stably express firefly luciferase and herpes simplex virus type-1 thymidine kinase (C26/tk-luc). A good correlation (R 2 =0.998) of photon emission to the cell number was found in vitro. Tumor burden and tumor volume were monitored in vivo over time by quantitation of photon emission using Xenogen IVIS 50 and standard external caliper measurement, respectively. At various time intervals, tumor-bearing mice were imaged to determine the correlation of in vivo BLI to tumor volume. However, a correlation of BLI to tumor volume was observed when tumor volume was smaller than 1000 mm 3 (R 2 =0.907). γ Scintigraphy combined with [ 131 I]FIAU was another imaging modality used for verifying the previous results. In conclusion, this study showed that bioluminescence imaging is a powerful and quantitative tool for the direct assay to monitor tumor growth in vivo. The dual reporter genes transfected tumor-bearing animal model can be applied in the evaluation of the efficacy of new developed anti-cancer drugs

Advances in Global Adjoint Tomography -- Massive Data Assimilation

Science.gov (United States)

Ruan, Y.; Lei, W.; Bozdag, E.; Lefebvre, M. P.; Smith, J. A.; Krischer, L.; Tromp, J.

2015-12-01

Azimuthal anisotropy and anelasticity are key to understanding a myriad of processes in Earth's interior. Resolving these properties requires accurate simulations of seismic wave propagation in complex 3-D Earth models and an iterative inversion strategy. In the wake of successes in regional studies(e.g., Chen et al., 2007; Tape et al., 2009, 2010; Fichtner et al., 2009, 2010; Chen et al.,2010; Zhu et al., 2012, 2013; Chen et al., 2015), we are employing adjoint tomography based on a spectral-element method (Komatitsch & Tromp 1999, 2002) on a global scale using the supercomputer ''Titan'' at Oak Ridge National Laboratory. After 15 iterations, we have obtained a high-resolution transversely isotropic Earth model (M15) using traveltime data from 253 earthquakes. To obtain higher resolution images of the emerging new features and to prepare the inversion for azimuthal anisotropy and anelasticity, we expanded the original dataset with approximately 4,220 additional global earthquakes (Mw5.5-7.0) --occurring between 1995 and 2014-- and downloaded 300-minute-long time series for all available data archived at the IRIS Data Management Center, ORFEUS, and F-net. Ocean Bottom Seismograph data from the last decade are also included to maximize data coverage. In order to handle the huge dataset and solve the I/O bottleneck in global adjoint tomography, we implemented a python-based parallel data processing workflow based on the newly developed Adaptable Seismic Data Format (ASDF). With the help of the data selection tool MUSTANG developed by IRIS, we cleaned our dataset and assembled event-based ASDF files for parallel processing. We have started Centroid Moment Tensors (CMT) inversions for all 4,220 earthquakes with the latest model M15, and selected high-quality data for measurement. We will statistically investigate each channel using synthetic seismograms calculated in M15 for updated CMTs and identify problematic channels. In addition to data screening, we also modified

The Repetitive Detection of Toluene with Bioluminescence Bioreporter Pseudomonas putida TVA8 Encapsulated in Silica Hydrogel on an Optical Fiber.

Czech Academy of Sciences Publication Activity Database

Kuncová, Gabriela; Ishizaki, Takayuki; Solovyev, Andrey; Trögl, J.; Ripp, S.

2016-01-01

Roč. 9, č. 6 (2016), s. 467 ISSN 1996-1944 Institutional support: RVO:67985858 Keywords : bioluminescent biosensor * silica gel * encapsulation Subject RIV: CC - Organic Chemistry Impact factor: 2.654, year: 2016

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.

Science.gov (United States)

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-01-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Modelling chemical reactions by QM/MM calculations: the case of the tautomerization in fireflies bioluminescent systems

Science.gov (United States)

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-04-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modelling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

The effect of radiation on bioluminescent bacteria: possible use of luminescent bacteria as a biological dosemeter

International Nuclear Information System (INIS)

Mantel, J.; Freidin, M.; Perry, H.

1983-01-01

The purpose of the study was to investigate the response of the bioluminescent Photobacterium phosphoreum to radiation, and the possible use of the bacteria as a biological radiation dosemeter, i.e. a water-equivalent biological system that will compare beams not merely on the basis of absorbed dose, but also have intrinsic RBE values for different radiation beams. Samples were irradiated by a 12 MeV electron beam at a dose rate of 3.0 Gy min -1 , by 60 Co gamma rays at 2.85 Gy min -1 , and by 100 kVsub(p) x-rays at a dose rate of 2.13 Gy min -1 . To study dose-rate dependence, the survival fraction was obtained for a 12 MeV electron beam at 0.50 and 12 Gy min -1 for 20.0 Gy. The survival fraction proved to be independent of dose rate in this range. The results presented in this work indicate that by using bioluminescent bacteria, RBE measurements can be markedly simplified and the results interpreted unequivocally. (U.K.)

Optimal Tikhonov Regularization in Finite-Frequency Tomography

Science.gov (United States)

Fang, Y.; Yao, Z.; Zhou, Y.

2017-12-01

The last decade has witnessed a progressive transition in seismic tomography from ray theory to finite-frequency theory which overcomes the resolution limit of the high-frequency approximation in ray theory. In addition to approximations in wave propagation physics, a main difference between ray-theoretical tomography and finite-frequency tomography is the sparseness of the associated sensitivity matrix. It is well known that seismic tomographic problems are ill-posed and regularizations such as damping and smoothing are often applied to analyze the tradeoff between data misfit and model uncertainty. The regularizations depend on the structure of the matrix as well as noise level of the data. Cross-validation has been used to constrain data uncertainties in body-wave finite-frequency inversions when measurements at multiple frequencies are available to invert for a common structure. In this study, we explore an optimal Tikhonov regularization in surface-wave phase-velocity tomography based on minimization of an empirical Bayes risk function using theoretical training datasets. We exploit the structure of the sensitivity matrix in the framework of singular value decomposition (SVD) which also allows for the calculation of complete resolution matrix. We compare the optimal Tikhonov regularization in finite-frequency tomography with traditional tradeo-off analysis using surface wave dispersion measurements from global as well as regional studies.

Fourier rebinning algorithm for inverse geometry CT.

Science.gov (United States)

Mazin, Samuel R; Pele, Norbert J

2008-11-01

Inverse geometry computed tomography (IGCT) is a new type of volumetric CT geometry that employs a large array of x-ray sources opposite a smaller detector array. Volumetric coverage and high isotropic resolution produce very large data sets and therefore require a computationally efficient three-dimensional reconstruction algorithm. The purpose of this work was to adapt and evaluate a fast algorithm based on Defrise's Fourier rebinning (FORE), originally developed for positron emission tomography. The results were compared with the average of FDK reconstructions from each source row. The FORE algorithm is an order of magnitude faster than the FDK-type method for the case of 11 source rows. In the center of the field-of-view both algorithms exhibited the same resolution and noise performance. FORE exhibited some resolution loss (and less noise) in the periphery of the field-of-view. FORE appears to be a fast and reasonably accurate reconstruction method for IGCT.

Fourier-based magnetic induction tomography for mapping resistivity

International Nuclear Information System (INIS)

Puwal, Steffan; Roth, Bradley J.

2011-01-01

Magnetic induction tomography is used as an experimental tool for mapping the passive electromagnetic properties of conductors, with the potential for imaging biological tissues. Our numerical approach to solving the inverse problem is to obtain a Fourier expansion of the resistivity and the stream functions of the magnetic fields and eddy current density. Thus, we are able to solve the inverse problem of determining the resistivity from the applied and measured magnetic fields for a two-dimensional conducting plane. When we add noise to the measured magnetic field, we find the fidelity of the measured to the true resistivity is quite robust for increasing levels of noise and increasing distances of the applied and measured field coils from the conducting plane, when properly filtered. We conclude that Fourier methods provide a reliable alternative for solving the inverse problem.

A novel mouse model of soft-tissue infection using bioluminescence imaging allows noninvasive, real-time monitoring of bacterial growth.

Science.gov (United States)

Yoshioka, Kenji; Ishii, Ken; Kuramoto, Tetsuya; Nagai, Shigenori; Funao, Haruki; Ishihama, Hiroko; Shiono, Yuta; Sasaki, Aya; Aizawa, Mamoru; Okada, Yasunori; Koyasu, Shigeo; Toyama, Yoshiaki; Matsumoto, Morio

2014-01-01

Musculoskeletal infections, including surgical-site and implant-associated infections, often cause progressive inflammation and destroy areas of the soft tissue. Treating infections, especially those caused by multi-antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) remains a challenge. Although there are a few animal models that enable the quantitative evaluation of infection in soft tissues, these models are not always reproducible or sustainable. Here, we successfully established a real-time, in vivo, quantitative mouse model of soft-tissue infection in the superficial gluteus muscle (SGM) using bioluminescence imaging. A bioluminescent strain of MRSA was inoculated into the SGM of BALB/c adult male mice, followed by sequential measurement of bacterial photon intensity and serological and histological analyses of the mice. The mean photon intensity in the mice peaked immediately after inoculation and remained stable until day 28. The serum levels of interleukin-6, interleukin-1 and C-reactive protein at 12 hours after inoculation were significantly higher than those prior to inoculation, and the C-reactive protein remained significantly elevated until day 21. Histological analyses showed marked neutrophil infiltration and abscesses containing necrotic and fibrous tissues in the SGM. With this SGM mouse model, we successfully visualized and quantified stable bacterial growth over an extended period of time with bioluminescence imaging, which allowed us to monitor the process of infection without euthanizing the experimental animals. This model is applicable to in vivo evaluations of the long-term efficacy of novel antibiotics or antibacterial implants.

Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

DEFF Research Database (Denmark)

Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

2002-01-01

-induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

Support Minimized Inversion of Acoustic and Elastic Wave Scattering

Science.gov (United States)

Safaeinili, Ali

Inversion of limited data is common in many areas of NDE such as X-ray Computed Tomography (CT), Ultrasonic and eddy current flaw characterization and imaging. In many applications, it is common to have a bias toward a solution with minimum (L^2)^2 norm without any physical justification. When it is a priori known that objects are compact as, say, with cracks and voids, by choosing "Minimum Support" functional instead of the minimum (L^2)^2 norm, an image can be obtained that is equally in agreement with the available data, while it is more consistent with what is most probably seen in the real world. We have utilized a minimum support functional to find a solution with the smallest volume. This inversion algorithm is most successful in reconstructing objects that are compact like voids and cracks. To verify this idea, we first performed a variational nonlinear inversion of acoustic backscatter data using minimum support objective function. A full nonlinear forward model was used to accurately study the effectiveness of the minimized support inversion without error due to the linear (Born) approximation. After successful inversions using a full nonlinear forward model, a linearized acoustic inversion was developed to increase speed and efficiency in imaging process. The results indicate that by using minimum support functional, we can accurately size and characterize voids and/or cracks which otherwise might be uncharacterizable. An extremely important feature of support minimized inversion is its ability to compensate for unknown absolute phase (zero-of-time). Zero-of-time ambiguity is a serious problem in the inversion of the pulse-echo data. The minimum support inversion was successfully used for the inversion of acoustic backscatter data due to compact scatterers without the knowledge of the zero-of-time. The main drawback to this type of inversion is its computer intensiveness. In order to make this type of constrained inversion available for common use, work

Duality reconstruction algorithm for use in electrical impedance tomography

International Nuclear Information System (INIS)

Abdullah, M.Z.; Dickin, F.J.

1996-01-01

A duality reconstruction algorithm for solving the inverse problem in electrical impedance tomography (EIT) is described. In this method, an algorithm based on the Geselowitz compensation (GC) theorem is used first to reconstruct an approximate version of the image. It is then fed as a first guessed data to the modified Newton-Raphson (MNR) algorithm which iteratively correct the image until a final acceptable solution is reached. The implementation of the GC and MNR based algorithms using the finite element method will be discussed. Reconstructed images produced by the algorithm will also be presented. Consideration is also given to the most computationally intensive aspects of the algorithm, namely the inversion of the large and sparse matrices. The methods taken to approximately compute the inverse ot those matrices will be outlined. (author)

Advances in Global Full Waveform Inversion

Science.gov (United States)

Tromp, J.; Bozdag, E.; Lei, W.; Ruan, Y.; Lefebvre, M. P.; Modrak, R. T.; Orsvuran, R.; Smith, J. A.; Komatitsch, D.; Peter, D. B.

2017-12-01

Information about Earth's interior comes from seismograms recorded at its surface. Seismic imaging based on spectral-element and adjoint methods has enabled assimilation of this information for the construction of 3D (an)elastic Earth models. These methods account for the physics of wave excitation and propagation by numerically solving the equations of motion, and require the execution of complex computational procedures that challenge the most advanced high-performance computing systems. Current research is petascale; future research will require exascale capabilities. The inverse problem consists of reconstructing the characteristics of the medium from -often noisy- observations. A nonlinear functional is minimized, which involves both the misfit to the measurements and a Tikhonov-type regularization term to tackle inherent ill-posedness. Achieving scalability for the inversion process on tens of thousands of multicore processors is a task that offers many research challenges. We initiated global "adjoint tomography" using 253 earthquakes and produced the first-generation model named GLAD-M15, with a transversely isotropic model parameterization. We are currently running iterations for a second-generation anisotropic model based on the same 253 events. In parallel, we continue iterations for a transversely isotropic model with a larger dataset of 1,040 events to determine higher-resolution plume and slab images. A significant part of our research has focused on eliminating I/O bottlenecks in the adjoint tomography workflow. This has led to the development of a new Adaptable Seismic Data Format based on HDF5, and post-processing tools based on the ADIOS library developed by Oak Ridge National Laboratory. We use the Ensemble Toolkit for workflow stabilization & management to automate the workflow with minimal human interaction.

Spatiotemporal expression of heme oxygenase-1 detected by in vivo bioluminescence after hepatic ischemia in HO-1/luc mice

NARCIS (Netherlands)

Su, Huawei; van Dam, Gooitzen M.; Buis, Carlijn I.; Visser, Dorien S.; Hesselink, Jan Willem; Schuurs, Theo A.; Leuvenink, Henri G. D.; Contag, Christopher H.; Porte, Robert J.

Upregulation of heme oxygenase-1 (HO-1) has been proposed as a critical mechanism protecting against cellular stress during liver transplantation, providing a potential target for new therapeutic interventions. We investigated the feasibility of in vivo bioluminescence imaging (BLI) to noninvasively

Suppression of intensity transition artifacts in statistical x-ray computer tomography reconstruction through Radon inversion initialization

International Nuclear Information System (INIS)

Zbijewski, Wojciech; Beekman, Freek J.

2004-01-01

Statistical reconstruction (SR) methods provide a general and flexible framework for obtaining tomographic images from projections. For several applications SR has been shown to outperform analytical algorithms in terms of resolution-noise trade-off achieved in the reconstructions. A disadvantage of SR is the long computational time required to obtain the reconstructions, in particular when large data sets characteristic for x-ray computer tomography (CT) are involved. As was shown recently, by combining statistical methods with block iterative acceleration schemes [e.g., like in the ordered subsets convex (OSC) algorithm], the reconstruction time for x-ray CT applications can be reduced by about two orders of magnitude. There are, however, some factors lengthening the reconstruction process that hamper both accelerated and standard statistical algorithms to similar degree. In this simulation study based on monoenergetic and scatter-free projection data, we demonstrate that one of these factors is the extremely high number of iterations needed to remove artifacts that can appear around high-contrast structures. We also show (using the OSC method) that these artifacts can be adequately suppressed if statistical reconstruction is initialized with images generated by means of Radon inversion algorithms like filtered back projection (FBP). This allows the reconstruction time to be shortened by even as much as one order of magnitude. Although the initialization of the statistical algorithm with FBP image introduces some additional noise into the first iteration of OSC reconstruction, the resolution-noise trade-off and the contrast-to-noise ratio of final images are not markedly compromised

Resolution tests of global geodynamic models by travel-time tomography

Czech Academy of Sciences Publication Activity Database

Běhounková, Marie; Čížková, H.; Matyska, C.

2005-01-01

Roč. 49, č. 3 (2005), s. 343-363 ISSN 0039-3169 R&D Projects: GA ČR GA205/02/1306 Institutional research plan: CEZ:AV0Z30120515 Keywords : seismic tomography * synthetic inversion * resolution tests Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 0.656, year: 2005

Anomaly detection in random heterogeneous media Feynman-Kac formulae, stochastic homogenization and statistical inversion

CERN Document Server

Simon, Martin

2015-01-01

This monograph is concerned with the analysis and numerical solution of a stochastic inverse anomaly detection problem in electrical impedance tomography (EIT). Martin Simon studies the problem of detecting a parameterized anomaly in an isotropic, stationary and ergodic conductivity random field whose realizations are rapidly oscillating. For this purpose, he derives Feynman-Kac formulae to rigorously justify stochastic homogenization in the case of the underlying stochastic boundary value problem. The author combines techniques from the theory of partial differential equations and functional analysis with probabilistic ideas, paving the way to new mathematical theorems which may be fruitfully used in the treatment of the problem at hand. Moreover, the author proposes an efficient numerical method in the framework of Bayesian inversion for the practical solution of the stochastic inverse anomaly detection problem.   Contents Feynman-Kac formulae Stochastic homogenization Statistical inverse problems  Targe...

Visualization of glucagon secretion from pancreatic α cells by bioluminescence video microscopy: Identification of secretion sites in the intercellular contact regions

International Nuclear Information System (INIS)

Yokawa, Satoru; Suzuki, Takahiro; Inouye, Satoshi; Inoh, Yoshikazu; Suzuki, Ryo; Kanamori, Takao; Furuno, Tadahide; Hirashima, Naohide

2017-01-01

We have firstly visualized glucagon secretion using a method of video-rate bioluminescence imaging. The fusion protein of proglucagon and Gaussia luciferase (PGCG-GLase) was used as a reporter to detect glucagon secretion and was efficiently expressed in mouse pancreatic α cells (αTC1.6) using a preferred human codon-optimized gene. In the culture medium of the cells expressing PGCG-GLase, luminescence activity determined with a luminometer was increased with low glucose stimulation and KCl-induced depolarization, as observed for glucagon secretion. From immunochemical analyses, PGCG-GLase stably expressed in clonal αTC1.6 cells was correctly processed and released by secretory granules. Luminescence signals of the secreted PGCG-GLase from the stable cells were visualized by video-rate bioluminescence microscopy. The video images showed an increase in glucagon secretion from clustered cells in response to stimulation by KCl. The secretory events were observed frequently at the intercellular contact regions. Thus, the localization and frequency of glucagon secretion might be regulated by cell-cell adhesion. - Highlights: • The fused protein of proglucagon to Gaussia luciferase was used as a reporter. • The fusion protein was highly expressed using a preferred human-codon optimized gene. • Glucagon secretion stimulated by depolarization was determined by luminescence. • Glucagon secretion in α cells was visualized by bioluminescence imaging. • Glucagon secretion sites were localized in the intercellular contact regions.

Computational study on full-wave inversion based on the acoustic wave-equation; Onkyoha hado hoteishiki full wave inversion no model keisan ni yoru kento

Energy Technology Data Exchange (ETDEWEB)

Watanabe, T; Sassa, K [Kyoto University, Kyoto (Japan); Uesaka, S [Kyoto University, Kyoto (Japan). Faculty of Engineering

1996-10-01

The effect of initial models on full-wave inversion (FWI) analysis based on acoustic wave-equation was studied for elastic wave tomography of underground structures. At present, travel time inversion using initial motion travel time is generally used, and inverse analysis is conducted using the concept `ray,` assuming very high wave frequency. Although this method can derive stable solutions relatively unaffected by initial model, it uses only the data of initial motion travel time. FWI calculates theoretical waveform at each receiver using all of observed waveforms as data by wave equation modeling where 2-D underground structure is calculated by difference calculus under the assumption that wave propagation is described by wave equation of P wave. Although it is a weak point that FWI is easily affected by noises in an initial model and data, it is featured by high resolution of solutions. This method offers very excellent convergence as a proper initial model is used, resulting in sufficient performance, however, it is strongly affected by initial model. 2 refs., 7 figs., 1 tab.

Applications of multiscale waveform inversion to marine data using a flooding technique and dynamic early-arrival windows

KAUST Repository

Boonyasiriwat, Chaiwoot

2010-11-01

A recently developed time-domain multiscale waveform tomography (MWT) method is applied to synthetic and field marine data. Although the MWT method was already applied to synthetic data, the synthetic data application leads to a development of a hybrid method between waveform tomography and the salt flooding technique commonly use in subsalt imaging. This hybrid method can overcome a convergence problem encountered by inversion with a traveltime velocity tomogram and successfully provides an accurate and highly resolved velocity tomogram for the 2D SEG/EAGE salt model. In the application of MWT to the field data, the inversion process is carried out using a multiscale method with a dynamic early-arrival muting window to mitigate the local minima problem of waveform tomography and elastic effects. With the modified MWT method, reasonably accurate results as verified by comparison of migration images and common image gathers were obtained. The hybrid method with the salt flooding technique is not used in this field data example because there is no salt in the subsurface according to our interpretation. However, we believe it is applicable to field data applications. © 2010 Society of Exploration Geophysicists.

Linear GPR Imaging Based on Electromagnetic Plane-Wave Spectra and Diffraction Tomography

DEFF Research Database (Denmark)

Meincke, Peter

2004-01-01

Two linear diffraction-tomography based inversion schemes, referred to as the Fourier transform method (FTM) and the far-field method (FFM), are derived for 3-dimensional fixed-offset GPR imaging of buried objects. The FTM and FFM are obtained by using different asymptotic approximations...

Quantum tomography via equidistant states

International Nuclear Information System (INIS)

Paiva-Sanchez, C.; Burgos-Inostroza, E.; Jimenez, O.; Delgado, A.

2010-01-01

We study the possibility of performing quantum state tomography via equidistant states. This class of states allows us to propose a nonsymmetric informationally complete Positive Operator Valued Measure (POVM) based tomographic scheme. The scheme is defined for odd dimensions N and involves the measurement of N 2 transition probabilities and an inversion, which can be analytically carried out by Fourier transform. The scheme can be modified to allow the reconstruction of states in the case of even dimensions at the expense of increasing the number of measurements to 3N 2 /2.

Bioluminescence-Based Method for Measuring Assimilable Organic Carbon in Pretreatment Water for Reverse Osmosis Membrane Desalination ▿

Science.gov (United States)

Weinrich, Lauren A.; Schneider, Orren D.; LeChevallier, Mark W.

2011-01-01

A bioluminescence-based assimilable organic carbon (AOC) test was developed for determining the biological growth potential of seawater within the reverse osmosis desalination pretreatment process. The test uses Vibrio harveyi, a marine organism that exhibits constitutive luminescence and is nutritionally robust. AOC was measured in both a pilot plant and a full-scale desalination plant pretreatment. PMID:21148685

Survival of bioluminescent Listeria monocytogenes and Escherichia coli O157:H7 in soft cheeses.

Science.gov (United States)

Ramsaran, H; Chen, J; Brunke, B; Hill, A; Griffiths, M W

1998-07-01

Pasteurized and raw milks that had been inoculated at 10(4) cfu/ml with bioluminescent strains of Listeria monocytogenes and Escherichia coli O157:H7 were used in the manufacture of Camembert and Feta cheeses with or without nisin-producing starter culture. Survival of both organisms was determined during the manufacture and storage of Camembert and Feta cheeses at 2 +/- 1 degree C for 65 and 75 d, respectively. Bacterial bioluminescence was used as an indicator to enumerate the colonies plated on selective Listeria agar and on MacConkey agar. Escherichia coli O157:H7 survived the manufacturing process of both cheeses and was present at the end of the storage period in greater numbers than in the initial inoculum. At the end of 75 d of storage, E. coli O157:H7 was found in the brine of Feta cheese. The counts of L. monocytogenes increased as the pH of the Camembert cheese increased, and there were significant differences between the counts from samples taken from the inside and the counts from samples obtained near the surface of the cheese. The Feta cheese that contained nisin was the only cheese in which L. monocytogenes was at the level of the initial inoculum after 75 d of storage.

Variational structure of inverse problems in wave propagation and vibration

Energy Technology Data Exchange (ETDEWEB)

Berryman, J.G.

1995-03-01

Practical algorithms for solving realistic inverse problems may often be viewed as problems in nonlinear programming with the data serving as constraints. Such problems are most easily analyzed when it is possible to segment the solution space into regions that are feasible (satisfying all the known constraints) and infeasible (violating some of the constraints). Then, if the feasible set is convex or at least compact, the solution to the problem will normally lie on the boundary of the feasible set. A nonlinear program may seek the solution by systematically exploring the boundary while satisfying progressively more constraints. Examples of inverse problems in wave propagation (traveltime tomography) and vibration (modal analysis) will be presented to illustrate how the variational structure of these problems may be used to create nonlinear programs using implicit variational constraints.

A neural network image reconstruction technique for electrical impedance tomography

International Nuclear Information System (INIS)

Adler, A.; Guardo, R.

1994-01-01

Reconstruction of Images in Electrical Impedance Tomography requires the solution of a nonlinear inverse problem on noisy data. This problem is typically ill-conditioned and requires either simplifying assumptions or regularization based on a priori knowledge. This paper presents a reconstruction algorithm using neural network techniques which calculates a linear approximation of the inverse problem directly from finite element simulations of the forward problem. This inverse is adapted to the geometry of the medium and the signal-to-noise ratio (SNR) used during network training. Results show good conductivity reconstruction where measurement SNR is similar to the training conditions. The advantages of this method are its conceptual simplicity and ease of implementation, and the ability to control the compromise between the noise performance and resolution of the image reconstruction

Elongation of exogenous fatty acids by the bioluminescent bacterium Vibrio harveyi

Energy Technology Data Exchange (ETDEWEB)

Byers, D.M.

1989-01-01

Bioluminescent bacteria require myristic acid (C14:0) to produce the myristaldehyde substrate of the light-emitting luciferase reaction. Since both endogenous and exogenous C14:0 can be used for this purpose, the metabolism of exogenous fatty acids by luminescent bacteria has been investigated. Both Vibrio harveyi and Vibrio fischeri incorporated label from (1-14C)myristic acid (C14:0) into phospholipid acyl chains as well as into CO2. In contrast, Photobacterium phosphoreum did not exhibit phospholipid acylation or beta-oxidation using exogenous fatty acids. Unlike Escherichia coli, the two Vibrio species can directly elongate fatty acids such as octanoic (C8:0), lauric (C12:0), and myristic acid, as demonstrated by radio-gas liquid chromatography. The induction of bioluminescence in late exponential growth had little effect on the ability of V. harveyi to elongate fatty acids, but it did increase the amount of C14:0 relative to C16:0 labeled from (14C)C8:0. This was not observed in a dark mutant of V. harveyi that is incapable of supplying endogenous C14:0 for luminescence. Cerulenin preferentially decreased the labeling of C16:0 and of unsaturated fatty acids from all 14C-labeled fatty acid precursors as well as from (14C)acetate, suggesting that common mechanisms may be involved in elongation of fatty acids from endogenous and exogenous sources. Fatty acylation of the luminescence-related synthetase and reductase enzymes responsible for aldehyde synthesis exhibited a chain-length preference for C14:0, which also was indicated by reverse-phase thin-layer chromatography of the acyl groups attached to these enzymes. The ability of V. harveyi to activate and elongate exogenous fatty acids may be related to an adaptive requirement to metabolize intracellular C14:0 generated by the luciferase reaction during luminescence development.

Elongation of exogenous fatty acids by the bioluminescent bacterium Vibrio harveyi

International Nuclear Information System (INIS)

Byers, D.M.

1989-01-01

Bioluminescent bacteria require myristic acid (C14:0) to produce the myristaldehyde substrate of the light-emitting luciferase reaction. Since both endogenous and exogenous C14:0 can be used for this purpose, the metabolism of exogenous fatty acids by luminescent bacteria has been investigated. Both Vibrio harveyi and Vibrio fischeri incorporated label from [1-14C]myristic acid (C14:0) into phospholipid acyl chains as well as into CO2. In contrast, Photobacterium phosphoreum did not exhibit phospholipid acylation or beta-oxidation using exogenous fatty acids. Unlike Escherichia coli, the two Vibrio species can directly elongate fatty acids such as octanoic (C8:0), lauric (C12:0), and myristic acid, as demonstrated by radio-gas liquid chromatography. The induction of bioluminescence in late exponential growth had little effect on the ability of V. harveyi to elongate fatty acids, but it did increase the amount of C14:0 relative to C16:0 labeled from [14C]C8:0. This was not observed in a dark mutant of V. harveyi that is incapable of supplying endogenous C14:0 for luminescence. Cerulenin preferentially decreased the labeling of C16:0 and of unsaturated fatty acids from all 14C-labeled fatty acid precursors as well as from [14C]acetate, suggesting that common mechanisms may be involved in elongation of fatty acids from endogenous and exogenous sources. Fatty acylation of the luminescence-related synthetase and reductase enzymes responsible for aldehyde synthesis exhibited a chain-length preference for C14:0, which also was indicated by reverse-phase thin-layer chromatography of the acyl groups attached to these enzymes. The ability of V. harveyi to activate and elongate exogenous fatty acids may be related to an adaptive requirement to metabolize intracellular C14:0 generated by the luciferase reaction during luminescence development

Guided wave tomography in anisotropic media using recursive extrapolation operators

Science.gov (United States)

Volker, Arno

2018-04-01

Guided wave tomography is an advanced technology for quantitative wall thickness mapping to image wall loss due to corrosion or erosion. An inversion approach is used to match the measured phase (time) at a specific frequency to a model. The accuracy of the model determines the sizing accuracy. Particularly for seam welded pipes there is a measurable amount of anisotropy. Moreover, for small defects a ray-tracing based modelling approach is no longer accurate. Both issues are solved by applying a recursive wave field extrapolation operator assuming vertical transverse anisotropy. The inversion scheme is extended by not only estimating the wall loss profile but also the anisotropy, local material changes and transducer ring alignment errors. This makes the approach more robust. The approach will be demonstrated experimentally on different defect sizes, and a comparison will be made between this new approach and an isotropic ray-tracing approach. An example is given in Fig. 1 for a 75 mm wide, 5 mm deep defect. The wave field extrapolation based tomography clearly provides superior results.

Time stamp generation with inverse FIR filters for Positron Emission Tomography

International Nuclear Information System (INIS)

Namias, Mauro

2009-01-01

Photon coincidence detection is the process by which Positron Emission Tomography (PET) works. This requires the determination of the time of impact of each coincident photon at the detector system, also known as time stamp. In this work, the timestamp was generated by means of digital time-domain deconvolution with FIR filters for a INa(Tl) based system. The detector deadtime was reduced from 350 ns to 175 ns while preserving the system's energy resolution and a direct relation between the amount of light collected and the temporal resolution was found.(author)

A bio-electromechanical imaging technique with combined electrical impedance and ultrasound tomography

International Nuclear Information System (INIS)

Steiner, G; Watzenig, D; Soleimani, M

2008-01-01

Electrical impedance tomography (EIT) seeks to image the electrical conductivity of an object using electrical impedance measurement data at its periphery. Ultrasound reflection tomography (URT) is an imaging modality that is able to generate images of mechanical properties of the object in terms of acoustic impedance changes. Both URT and EIT have the potential to be used in various medical applications. In this paper we focus on breast tumour detection. Both URT and EIT belong to soft field tomography and suffer from the small amounts of available data and the inherently ill-posed nature of the inverse problems. These facts result in limited achievable reconstruction accuracy and resolution. A dual bio-electromechanical tomography system using ultrasound and electrical tomography is proposed in this paper to improve the detection of the small-size tumour. Data fusion techniques are implemented to combine the EIT/URT data. Based on simulations, we demonstrate the improvement of detection of small size anomalies and improved depth detection compared to single modality soft field tomography

The Neuroelectromagnetic Inverse Problem and the Zero Dipole Localization Error

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Rolando Grave de Peralta

2009-01-01

Full Text Available A tomography of neural sources could be constructed from EEG/MEG recordings once the neuroelectromagnetic inverse problem (NIP is solved. Unfortunately the NIP lacks a unique solution and therefore additional constraints are needed to achieve uniqueness. Researchers are then confronted with the dilemma of choosing one solution on the basis of the advantages publicized by their authors. This study aims to help researchers to better guide their choices by clarifying what is hidden behind inverse solutions oversold by their apparently optimal properties to localize single sources. Here, we introduce an inverse solution (ANA attaining perfect localization of single sources to illustrate how spurious sources emerge and destroy the reconstruction of simultaneously active sources. Although ANA is probably the simplest and robust alternative for data generated by a single dominant source plus noise, the main contribution of this manuscript is to show that zero localization error of single sources is a trivial and largely uninformative property unable to predict the performance of an inverse solution in presence of simultaneously active sources. We recommend as the most logical strategy for solving the NIP the incorporation of sound additional a priori information about neural generators that supplements the information contained in the data.

3D optical tomography in the presence of void regions

Science.gov (United States)

Riley, J.; Dehghani, Hamid; Schweiger, Martin; Arridge, Simon R.; Ripoll, Jorge; Nieto-Vesperinas, Manuel

2000-12-01

We present an investigation of the effect of a 3D non-scattering gap region on image reconstruction in diffuse optical tomography. The void gap is modelled by the Radiosity-Diffusion method and the inverse problem is solved using the adjoint field method. The case of a sphere with concentric spherical gap is used as an example.

Wavelet-based multiscale adjoint waveform-difference tomography using body and surface waves

Science.gov (United States)

Yuan, Y. O.; Simons, F. J.; Bozdag, E.

2014-12-01

We present a multi-scale scheme for full elastic waveform-difference inversion. Using a wavelet transform proves to be a key factor to mitigate cycle-skipping effects. We start with coarse representations of the seismogram to correct a large-scale background model, and subsequently explain the residuals in the fine scales of the seismogram to map the heterogeneities with great complexity. We have previously applied the multi-scale approach successfully to body waves generated in a standard model from the exploration industry: a modified two-dimensional elastic Marmousi model. With this model we explored the optimal choice of wavelet family, number of vanishing moments and decomposition depth. For this presentation we explore the sensitivity of surface waves in waveform-difference tomography. The incorporation of surface waves is rife with cycle-skipping problems compared to the inversions considering body waves only. We implemented an envelope-based objective function probed via a multi-scale wavelet analysis to measure the distance between predicted and target surface-wave waveforms in a synthetic model of heterogeneous near-surface structure. Our proposed method successfully purges the local minima present in the waveform-difference misfit surface. An elastic shallow model with 100~m in depth is used to test the surface-wave inversion scheme. We also analyzed the sensitivities of surface waves and body waves in full waveform inversions, as well as the effects of incorrect density information on elastic parameter inversions. Based on those numerical experiments, we ultimately formalized a flexible scheme to consider both body and surface waves in adjoint tomography. While our early examples are constructed from exploration-style settings, our procedure will be very valuable for the study of global network data.

3D Hydraulic tomography from joint inversion of the hydraulic heads and self-potential data. (Invited)

Science.gov (United States)

Jardani, A.; Soueid Ahmed, A.; Revil, A.; Dupont, J.

2013-12-01

Pumping tests are usually employed to predict the hydraulic conductivity filed from the inversion of the head measurements. Nevertheless, the inverse problem is strongly underdetermined and a reliable imaging requires a considerable number of wells. We propose to add more information to the inversion of the heads by adding (non-intrusive) streaming potentials (SP) data. The SP corresponds to perturbations in the local electrical field caused directly by the fow of the ground water. These SP are obtained with a set of the non-polarising electrodes installed at the ground surface. We developed a geostatistical method for the estimation of the hydraulic conductivity field from measurements of hydraulic heads and SP during pumping and injection experiments. We use the adjoint state method and a recent petrophysical formulation of the streaming potential problem in which the streaming coupling coefficient is derived from the hydraulic conductivity allowed reducing of the unknown parameters. The geostatistical inverse framework is applied to three synthetic case studies with different number of the wells and electrodes used to measure the hydraulic heads and the streaming potentials. To evaluate the benefits of the incorporating of the streaming potential to the hydraulic data, we compared the cases in which the data are coupled or not to map the hydraulic conductivity. The results of the inversion revealed that a dense distribution of electrodes can be used to infer the heterogeneities in the hydraulic conductivity field. Incorporating the streaming potential information to the hydraulic head data improves the estimate of hydraulic conductivity field especially when the number of piezometers is limited.

Finite frequency shear wave splitting tomography: a model space search approach

Science.gov (United States)

Mondal, P.; Long, M. D.

2017-12-01

Observations of seismic anisotropy provide key constraints on past and present mantle deformation. A common method for upper mantle anisotropy is to measure shear wave splitting parameters (delay time and fast direction). However, the interpretation is not straightforward, because splitting measurements represent an integration of structure along the ray path. A tomographic approach that allows for localization of anisotropy is desirable; however, tomographic inversion for anisotropic structure is a daunting task, since 21 parameters are needed to describe general anisotropy. Such a large parameter space does not allow a straightforward application of tomographic inversion. Building on previous work on finite frequency shear wave splitting tomography, this study aims to develop a framework for SKS splitting tomography with a new parameterization of anisotropy and a model space search approach. We reparameterize the full elastic tensor, reducing the number of parameters to three (a measure of strength based on symmetry considerations for olivine, plus the dip and azimuth of the fast symmetry axis). We compute Born-approximation finite frequency sensitivity kernels relating model perturbations to splitting intensity observations. The strong dependence of the sensitivity kernels on the starting anisotropic model, and thus the strong non-linearity of the inverse problem, makes a linearized inversion infeasible. Therefore, we implement a Markov Chain Monte Carlo technique in the inversion procedure. We have performed tests with synthetic data sets to evaluate computational costs and infer the resolving power of our algorithm for synthetic models with multiple anisotropic layers. Our technique can resolve anisotropic parameters on length scales of ˜50 km for realistic station and event configurations for dense broadband experiments. We are proceeding towards applications to real data sets, with an initial focus on the High Lava Plains of Oregon.

Inherent Limitations of Hydraulic Tomography

Science.gov (United States)

Bohling, Geoffrey C.; Butler, J.J.

2010-01-01

We offer a cautionary note in response to an increasing level of enthusiasm regarding high-resolution aquifer characterization with hydraulic tomography. We use synthetic examples based on two recent field experiments to demonstrate that a high degree of nonuniqueness remains in estimates of hydraulic parameter fields even when those estimates are based on simultaneous analysis of a number of carefully controlled hydraulic tests. We must, therefore, be careful not to oversell the technique to the community of practicing hydrogeologists, promising a degree of accuracy and resolution that, in many settings, will remain unattainable, regardless of the amount of effort invested in the field investigation. No practically feasible amount of hydraulic tomography data will ever remove the need to regularize or bias the inverse problem in some fashion in order to obtain a unique solution. Thus, along with improving the resolution of hydraulic tomography techniques, we must also strive to couple those techniques with procedures for experimental design and uncertainty assessment and with other more cost-effective field methods, such as geophysical surveying and, in unconsolidated formations, direct-push profiling, in order to develop methods for subsurface characterization with the resolution and accuracy needed for practical field applications. Copyright ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

Training-Image Based Geostatistical Inversion Using a Spatial Generative Adversarial Neural Network

Science.gov (United States)

Laloy, Eric; Hérault, Romain; Jacques, Diederik; Linde, Niklas

2018-01-01

Probabilistic inversion within a multiple-point statistics framework is often computationally prohibitive for high-dimensional problems. To partly address this, we introduce and evaluate a new training-image based inversion approach for complex geologic media. Our approach relies on a deep neural network of the generative adversarial network (GAN) type. After training using a training image (TI), our proposed spatial GAN (SGAN) can quickly generate 2-D and 3-D unconditional realizations. A key characteristic of our SGAN is that it defines a (very) low-dimensional parameterization, thereby allowing for efficient probabilistic inversion using state-of-the-art Markov chain Monte Carlo (MCMC) methods. In addition, available direct conditioning data can be incorporated within the inversion. Several 2-D and 3-D categorical TIs are first used to analyze the performance of our SGAN for unconditional geostatistical simulation. Training our deep network can take several hours. After training, realizations containing a few millions of pixels/voxels can be produced in a matter of seconds. This makes it especially useful for simulating many thousands of realizations (e.g., for MCMC inversion) as the relative cost of the training per realization diminishes with the considered number of realizations. Synthetic inversion case studies involving 2-D steady state flow and 3-D transient hydraulic tomography with and without direct conditioning data are used to illustrate the effectiveness of our proposed SGAN-based inversion. For the 2-D case, the inversion rapidly explores the posterior model distribution. For the 3-D case, the inversion recovers model realizations that fit the data close to the target level and visually resemble the true model well.

Implementation of Tuy's cone-beam inversion formula

International Nuclear Information System (INIS)

Zeng, G.L.; Clack, R.; Gullberg, G.T.

1994-01-01

Tuy's cone-beam inversion formula was modified to develop a cone-beam reconstruction algorithm. The algorithm was implemented for a cone-beam vertex orbit consisting of a circle and two orthogonal lines. This orbit geometry satisfies the cone-beam data sufficiency condition and is easy to implement on commercial single photon emission computed tomography (SPECT) systems. The algorithm which consists of two derivative steps, one rebinning step, and one three-dimensional backprojection step, was verified by computer simulations and by reconstructing physical phantom data collected on a clinical SPECT system. The proposed algorithm gives equivalent results and is as efficient as other analytical cone-beam reconstruction algorithms. (Author)

Seismic tomography analysis using finite differential calculation of the eikonal equation and reciplocal principle; Eikonal equation no sabunkaiho to sohan genri wo riyoshita danseiha tomography kaiseki

Energy Technology Data Exchange (ETDEWEB)

Fujimoto, M; Ashida, Y; Watanabe, T; Sassa, K [Kyoto University, Kyoto (Japan)

1996-10-01

This paper describes the seismic tomography analysis of underground structures using finite differential calculation (FDC) and a reciprocal principle which points out that a propagation path is constant even if a source and receiver are exchanged with each other. Tomography analysis generally determines a ray length across each underground cell structure by ray tracing method to modify each cell slowness (inverse of velocity). Travel time field was determined by FDC of eikonal equation among ray tracing methods, and a wave propagation path was determined by reciprocity of elastic wave to carry out inversion. In conventional methods, since a wave length is assumed to be infinitesimal by ray theory, false modified slowness structures frequently appears depending on the density of a ray. Wave propagates in a certain width, and is affected by environment. The slowness was thus modified on the basis of the wave propagation path with a certain width by using not ray-tracing but reciprocity. By this modification, false structures were hardly found under a fine grid, and several propagation paths could be considered. 6 refs., 9 figs.

Joint body and surface wave tomography applied to the Toba caldera complex (Indonesia)

Science.gov (United States)

Jaxybulatov, Kairly; Koulakov, Ivan; Shapiro, Nikolai

2016-04-01

We developed a new algorithm for a joint body and surface wave tomography. The algorithm is a modification of the existing LOTOS code (Koulakov, 2009) developed for local earthquake tomography. The input data for the new method are travel times of P and S waves and dispersion curves of Rayleigh and Love waves. The main idea is that the two data types have complementary sensitivities. The body-wave data have good resolution at depth, where we have enough crossing rays between sources and receivers, whereas the surface waves have very good near-surface resolution. The surface wave dispersion curves can be retrieved from the correlations of the ambient seismic noise and in this case the sampled path distribution does not depend on the earthquake sources. The contributions of the two data types to the inversion are controlled by the weighting of the respective equations. One of the clearest cases where such approach may be useful are volcanic systems in subduction zones with their complex magmatic feeding systems that have deep roots in the mantle and intermediate magma chambers in the crust. In these areas, the joint inversion of different types of data helps us to build a comprehensive understanding of the entire system. We apply our algorithm to data collected in the region surrounding the Toba caldera complex (north Sumatra, Indonesia) during two temporary seismic experiments (IRIS, PASSCAL, 1995, GFZ, LAKE TOBA, 2008). We invert 6644 P and 5240 S wave arrivals and ~500 group velocity dispersion curves of Rayleigh and Love waves. We present a series of synthetic tests and real data inversions which show that joint inversion approach gives more reliable results than the separate inversion of two data types. Koulakov, I., LOTOS code for local earthquake tomographic inversion. Benchmarks for testing tomographic algorithms, Bull. seism. Soc. Am., 99(1), 194-214, 2009, doi:10.1785/0120080013

Compressive Phase Contrast Tomography

International Nuclear Information System (INIS)

Maia, Filipe; MacDowell, Alastair; Marchesini, Stefano; Padmore, Howard A.; Parkinson, Dula Y.; Pien, Jack; Schirotzek, Andre; Yang, Chao

2010-01-01

When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher contrast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

Radial reflection diffraction tomography

Science.gov (United States)

Lehman, Sean K.

2012-12-18

A wave-based tomographic imaging method and apparatus based upon one or more rotating radially outward oriented transmitting and receiving elements have been developed for non-destructive evaluation. At successive angular locations at a fixed radius, a predetermined transmitting element can launch a primary field and one or more predetermined receiving elements can collect the backscattered field in a "pitch/catch" operation. A Hilbert space inverse wave (HSIW) algorithm can construct images of the received scattered energy waves using operating modes chosen for a particular application. Applications include, improved intravascular imaging, bore hole tomography, and non-destructive evaluation (NDE) of parts having existing access holes.

Effects of induced stress on seismic forward modelling and inversion

Science.gov (United States)

Tromp, Jeroen; Trampert, Jeannot

2018-05-01

We demonstrate how effects of induced stress may be incorporated in seismic modelling and inversion. Our approach is motivated by the accommodation of pre-stress in global seismology. Induced stress modifies both the equation of motion and the constitutive relationship. The theory predicts that induced pressure linearly affects the unstressed isotropic moduli with a slope determined by their adiabatic pressure derivatives. The induced deviatoric stress produces anisotropic compressional and shear wave speeds; the latter result in shear wave splitting. For forward modelling purposes, we determine the weak form of the equation of motion under induced stress. In the context of the inverse problem, we determine induced stress sensitivity kernels, which may be used for adjoint tomography. The theory is illustrated by considering 2-D propagation of SH waves and related Fréchet derivatives based on a spectral-element method.

Evaluation of biolistic gene transfer methods in vivo using non-invasive bioluminescent imaging techniques

Directory of Open Access Journals (Sweden)

Daniell Henry

2011-06-01

Full Text Available Abstract Background Gene therapy continues to hold great potential for treating many different types of disease and dysfunction. Safe and efficient techniques for gene transfer and expression in vivo are needed to enable gene therapeutic strategies to be effective in patients. Currently, the most commonly used methods employ replication-defective viral vectors for gene transfer, while physical gene transfer methods such as biolistic-mediated ("gene-gun" delivery to target tissues have not been as extensively explored. In the present study, we evaluated the efficacy of biolistic gene transfer techniques in vivo using non-invasive bioluminescent imaging (BLI methods. Results Plasmid DNA carrying the firefly luciferase (LUC reporter gene under the control of the human Cytomegalovirus (CMV promoter/enhancer was transfected into mouse skin and liver using biolistic methods. The plasmids were coupled to gold microspheres (1 μm diameter using different DNA Loading Ratios (DLRs, and "shot" into target tissues using a helium-driven gene gun. The optimal DLR was found to be in the range of 4-10. Bioluminescence was measured using an In Vivo Imaging System (IVIS-50 at various time-points following transfer. Biolistic gene transfer to mouse skin produced peak reporter gene expression one day after transfer. Expression remained detectable through four days, but declined to undetectable levels by six days following gene transfer. Maximum depth of tissue penetration following biolistic transfer to abdominal skin was 200-300 μm. Similarly, biolistic gene transfer to mouse liver in vivo also produced peak early expression followed by a decline over time. In contrast to skin, however, liver expression of the reporter gene was relatively stable 4-8 days post-biolistic gene transfer, and remained detectable for nearly two weeks. Conclusions The use of bioluminescence imaging techniques enabled efficient evaluation of reporter gene expression in vivo. Our results

Bioluminescent human breast cancer cell lines that permit rapid and sensitive in vivo detection of mammary tumors and multiple metastases in immune deficient mice

International Nuclear Information System (INIS)

Jenkins, Darlene E; Hornig, Yvette S; Oei, Yoko; Dusich, Joan; Purchio, Tony

2005-01-01

Our goal was to generate xenograft mouse models of human breast cancer based on luciferase-expressing MDA-MB-231 tumor cells that would provide rapid mammary tumor growth; produce metastasis to clinically relevant tissues such as lymph nodes, lung, and bone; and permit sensitive in vivo detection of both primary and secondary tumor sites by bioluminescent imaging. Two clonal cell sublines of human MDA-MB-231 cells that stably expressed firefly luciferase were isolated following transfection of the parental cells with luciferase cDNA. Each subline was passaged once or twice in vivo to enhance primary tumor growth and to increase metastasis. The resulting luciferase-expressing D3H1 and D3H2LN cells were analyzed for long-term bioluminescent stability, primary tumor growth, and distal metastasis to lymph nodes, lungs, bone and soft tissues by bioluminescent imaging. Cells were injected into the mammary fat pad of nude and nude-beige mice or were delivered systemically via intracardiac injection. Metastasis was also evaluated by ex vivo imaging and histologic analysis postmortem. The D3H1 and D3H2LN cell lines exhibited long-term stable luciferase expression for up to 4–6 months of accumulative tumor growth time in vivo. Bioluminescent imaging quantified primary mammary fat pad tumor development and detected early spontaneous lymph node metastasis in vivo. Increased frequency of spontaneous lymph node metastasis was observed with D3H2LN tumors as compared with D3H1 tumors. With postmortem ex vivo imaging, we detected additional lung micrometastasis in mice with D3H2LN mammary tumors. Subsequent histologic evaluation of tissue sections from lymph nodes and lung lobes confirmed spontaneous tumor metastasis at these sites. Following intracardiac injection of the MDA-MB-231-luc tumor cells, early metastasis to skeletal tissues, lymph nodes, brain and various visceral organs was detected. Weekly in vivo imaging data permitted longitudinal analysis of metastasis at

Tomography of the ionospheric electron density with geostatistical inversion

Directory of Open Access Journals (Sweden)

D. Minkwitz

2015-08-01

Full Text Available In relation to satellite applications like global navigation satellite systems (GNSS and remote sensing, the electron density distribution of the ionosphere has significant influence on trans-ionospheric radio signal propagation. In this paper, we develop a novel ionospheric tomography approach providing the estimation of the electron density's spatial covariance and based on a best linear unbiased estimator of the 3-D electron density. Therefore a non-stationary and anisotropic covariance model is set up and its parameters are determined within a maximum-likelihood approach incorporating GNSS total electron content measurements and the NeQuick model as background. As a first assessment this 3-D simple kriging approach is applied to a part of Europe. We illustrate the estimated covariance model revealing the different correlation lengths in latitude and longitude direction and its non-stationarity. Furthermore, we show promising improvements of the reconstructed electron densities compared to the background model through the validation of the ionosondes Rome, Italy (RO041, and Dourbes, Belgium (DB049, with electron density profiles for 1 day.

Image reconstruction in electrostatic tomography using a priori knowledge from ECT

International Nuclear Information System (INIS)

Zhou Bin; Zhang Jianyong; Xu Chuanlong; Wang Shimin

2011-01-01

Research highlights: → A dual-mode sensor technique based on ECT and EST is proposed. → The interference of the charged particles to ECT can be eliminated. → A priori knowledge from ECT improves the inversion accuracy. - Abstract: In gas-solid two-phase flow, the charge distribution is a very important process parameter which is useful to the study of electrostatic adhesion. Electrostatic tomography (EST) is a relatively new non-intrusive technique which can be used to acquire charge distribution. However, due to limited measurements, the quality of image reconstruction is poor. In this paper, a dual-mode sensor technique based on electrical capacitance tomography (ECT) and EST is proposed. The theoretical analysis and the numerical simulation results reveal that the permittivity distribution obtained from ECT can provide a priori knowledge for the inversion calculation of EST, so that the accuracy of spatial sensitivity calculation in EST can be improved. This proposed technique is expected to be prospective in industrial applications and will also be beneficial to the research on the fluid dynamics of gas-solid two-phase flow.

Seismic transmission tomography: determination of the elastic properties of building structures (some examples

Directory of Open Access Journals (Sweden)

E. Cardarelli

2000-06-01

Full Text Available This paper is a general review on seismic transmission tomography considering data acquisition and processing. Some questions on linear and non linear inversions are tackled, and advice given on the choice of the best damping factor. Taking into account prediction matrices we show that it is possible to point out the best distribution of sensors and shot points in terms of resolution and stability of system. Then two examples in which seismic tomography was used are described concerning the determination of elastic characteristics of building structures.

The cAMP-dependent protein kinase inhibitor H-89 attenuates the bioluminescence signal produced by Renilla Luciferase.

Directory of Open Access Journals (Sweden)

Katie J Herbst

2009-05-01

Full Text Available Investigations into the regulation and functional roles of kinases such as cAMP-dependent protein kinase (PKA increasingly rely on cellular assays. Currently, there are a number of bioluminescence-based assays, for example reporter gene assays, that allow the study of the regulation, activity, and functional effects of PKA in the cellular context. Additionally there are continuing efforts to engineer improved biosensors that are capable of detecting real-time PKA signaling dynamics in cells. These cell-based assays are often utilized to test the involvement of PKA-dependent processes by using H-89, a reversible competitive inhibitor of PKA.We present here data to show that H-89, in addition to being a competitive PKA inhibitor, attenuates the bioluminescence signal produced by Renilla luciferase (RLuc variants in a population of cells and also in single cells. Using 10 microM of luciferase substrate and 10 microM H-89, we observed that the signal from RLuc and RLuc8, an eight-point mutation variant of RLuc, in cells was reduced to 50% (+/-15% and 54% (+/-14% of controls exposed to the vehicle alone, respectively. In vitro, we showed that H-89 decreased the RLuc8 bioluminescence signal but did not compete with coelenterazine-h for the RLuc8 active site, and also did not affect the activity of Firefly luciferase. By contrast, another competitive inhibitor of PKA, KT5720, did not affect the activity of RLuc8.The identification and characterization of the adverse effect of H-89 on RLuc signal will help deconvolute data previously generated from RLuc-based assays looking at the functional effects of PKA signaling. In addition, for the current application and future development of bioluminscence assays, KT5720 is identified as a more suitable PKA inhibitor to be used in conjunction with RLuc-based assays. These principal findings also provide an important lesson to fully consider all of the potential effects of experimental conditions on a cell

Pulsed excitation terahertz tomography - multiparametric approach

Science.gov (United States)

Lopato, Przemyslaw

2018-04-01

This article deals with pulsed excitation terahertz computed tomography (THz CT). Opposite to x-ray CT, where just a single value (pixel) is obtained, in case of pulsed THz CT the time signal is acquired for each position. Recorded waveform can be parametrized - many features carrying various information about examined structure can be calculated. Based on this, multiparametric reconstruction algorithm was proposed: inverse Radon transform based reconstruction is applied for each parameter and then fusion of results is utilized. Performance of the proposed imaging scheme was experimentally verified using dielectric phantoms.

Angle-domain Migration Velocity Analysis using Wave-equation Reflection Traveltime Inversion

KAUST Repository

Zhang, Sanzong

2012-11-04

The main difficulty with an iterative waveform inversion is that it tends to get stuck in a local minima associated with the waveform misfit function. This is because the waveform misfit function is highly non-linear with respect to changes in the velocity model. To reduce this nonlinearity, we present a reflection traveltime tomography method based on the wave equation which enjoys a more quasi-linear relationship between the model and the data. A local crosscorrelation of the windowed downgoing direct wave and the upgoing reflection wave at the image point yields the lag time that maximizes the correlation. This lag time represents the reflection traveltime residual that is back-projected into the earth model to update the velocity in the same way as wave-equation transmission traveltime inversion. The residual movemout analysis in the angle-domain common image gathers provides a robust estimate of the depth residual which is converted to the reflection traveltime residual for the velocity inversion. We present numerical examples to demonstrate its efficiency in inverting seismic data for complex velocity model.

Seismic traveltime tomography by use of gridpoints discritization; Koshitenho ni yoru danseiha tomography kaiseki

Energy Technology Data Exchange (ETDEWEB)

Hirai, T; Watanabe, T; Sassa, K [Kyoto University, Kyoto (Japan). Faculty of Engineering

1996-05-01

Efforts were made to enhance analytical precision and stabilize the results in seismic traveltime tomography by use of a method wherein the velocity distribution is expressed as a continuous function interpolated by parameters respectively assigned to the gridpoints. In this method, the slowness data are regarded as the parameters respectively assigned to the gridpoints, and the slowness value at a given point is determined after interpolation by the gridpoints surrounding the said point. A method based on the variation principle was used for ray tracing. As the result, it was confirmed that this method determines the ray path and traveltime with high precision. A method of least squares using Lagrange`s multiplier was applied for inversion. Comparison was made between the use of cells and the use of gridpoints in the results of inversions performed for an inclined 4-layer structure model, when it was found that the values involving the boundaries between layers, inclinations of the layers, and velocities of seismic waves are ambiguous with the cells while those with the gridpoints are reconstructed roughly correctly. 5 refs., 7 figs., 1 tab.

Image reconstruction of single photon emission computed tomography (SPECT) on a pebble bed reactor (PBR) using expectation maximization and exact inversion algorithms: Comparison study by means of numerical phantom

Energy Technology Data Exchange (ETDEWEB)

Razali, Azhani Mohd, E-mail: azhani@nuclearmalaysia.gov.my; Abdullah, Jaafar, E-mail: jaafar@nuclearmalaysia.gov.my [Plant Assessment Technology (PAT) Group, Industrial Technology Division, Malaysian Nuclear Agency, Bangi, 43000 Kajang (Malaysia)

2015-04-29

Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm.

Image reconstruction of single photon emission computed tomography (SPECT) on a pebble bed reactor (PBR) using expectation maximization and exact inversion algorithms: Comparison study by means of numerical phantom

International Nuclear Information System (INIS)

Razali, Azhani Mohd; Abdullah, Jaafar

2015-01-01

Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm

Image reconstruction of single photon emission computed tomography (SPECT) on a pebble bed reactor (PBR) using expectation maximization and exact inversion algorithms: Comparison study by means of numerical phantom

Science.gov (United States)

Razali, Azhani Mohd; Abdullah, Jaafar

2015-04-01

Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm.

Fully probabilistic seismic source inversion – Part 1: Efficient parameterisation

Directory of Open Access Journals (Sweden)

S. C. Stähler

2014-11-01

Full Text Available Seismic source inversion is a non-linear problem in seismology where not just the earthquake parameters themselves but also estimates of their uncertainties are of great practical importance. Probabilistic source inversion (Bayesian inference is very adapted to this challenge, provided that the parameter space can be chosen small enough to make Bayesian sampling computationally feasible. We propose a framework for PRobabilistic Inference of Seismic source Mechanisms (PRISM that parameterises and samples earthquake depth, moment tensor, and source time function efficiently by using information from previous non-Bayesian inversions. The source time function is expressed as a weighted sum of a small number of empirical orthogonal functions, which were derived from a catalogue of >1000 source time functions (STFs by a principal component analysis. We use a likelihood model based on the cross-correlation misfit between observed and predicted waveforms. The resulting ensemble of solutions provides full uncertainty and covariance information for the source parameters, and permits propagating these source uncertainties into travel time estimates used for seismic tomography. The computational effort is such that routine, global estimation of earthquake mechanisms and source time functions from teleseismic broadband waveforms is feasible.

Multi-dimensional Inversion Modeling of Surface Nuclear Magnetic Resonance (SNMR Data for Groundwater Exploration

Directory of Open Access Journals (Sweden)

Warsa

2014-07-01

Full Text Available Groundwater is an important economic source of water supply for drinking water and irrigation water for agriculture. Surface nuclear magnetic resonance (SNMR sounding is a relatively new geophysical method that can be used to determine the presence of culturally and economically important substances, such as subsurface water or hydrocarbon distribution. SNMR sounding allows the determination of water content and pore size distribution directly from the surface. The SNMR method is performed by stimulating an alternating current pulse through an antenna at the surface in order to confirm the existence of water in the subsurface. This paper reports the development of a 3-D forward modeling code for SNMR amplitudes and decay times, after which an improved 2-D and 3-D inversion algorithm is investigated, consisting of schemes for regularizing model parameterization. After briefly reviewing inversion schemes generally used in geophysics, the special properties of SNMR or magnetic resonance sounding (MRS inversion are evaluated. We present an extension of MRS to magnetic resonance tomography (MRT, i.e. an extension for 2-D and 3-D investigation, and the appropriate inversions.

ODTbrain: a Python library for full-view, dense diffraction tomography.

Science.gov (United States)

Müller, Paul; Schürmann, Mirjam; Guck, Jochen

2015-11-04

Analyzing the three-dimensional (3D) refractive index distribution of a single cell makes it possible to describe and characterize its inner structure in a marker-free manner. A dense, full-view tomographic data set is a set of images of a cell acquired for multiple rotational positions, densely distributed from 0 to 360 degrees. The reconstruction is commonly realized by projection tomography, which is based on the inversion of the Radon transform. The reconstruction quality of projection tomography is greatly improved when first order scattering, which becomes relevant when the imaging wavelength is comparable to the characteristic object size, is taken into account. This advanced reconstruction technique is called diffraction tomography. While many implementations of projection tomography are available today, there is no publicly available implementation of diffraction tomography so far. We present a Python library that implements the backpropagation algorithm for diffraction tomography in 3D. By establishing benchmarks based on finite-difference time-domain (FDTD) simulations, we showcase the superiority of the backpropagation algorithm over the backprojection algorithm. Furthermore, we discuss how measurment parameters influence the reconstructed refractive index distribution and we also give insights into the applicability of diffraction tomography to biological cells. The present software library contains a robust implementation of the backpropagation algorithm. The algorithm is ideally suited for the application to biological cells. Furthermore, the implementation is a drop-in replacement for the classical backprojection algorithm and is made available to the large user community of the Python programming language.

Joint inversion of hydraulic head and self-potential data associated with harmonic pumping tests

Science.gov (United States)

Soueid Ahmed, A.; Jardani, A.; Revil, A.; Dupont, J. P.

2016-09-01

Harmonic pumping tests consist in stimulating an aquifer by the means of hydraulic stimulations at some discrete frequencies. The inverse problem consisting in retrieving the hydraulic properties is inherently ill posed and is usually underdetermined when considering the number of well head data available in field conditions. To better constrain this inverse problem, we add self-potential data recorded at the ground surface to the head data. The self-potential method is a passive geophysical method. Its signals are generated by the groundwater flow through an electrokinetic coupling. We showed using a 3-D saturated unconfined synthetic aquifer that the self-potential method significantly improves the results of the harmonic hydraulic tomography. The hydroelectric forward problem is obtained by solving first the Richards equation, describing the groundwater flow, and then using the result in an electrical Poisson equation describing the self-potential problem. The joint inversion problem is solved using a reduction model based on the principal component geostatistical approach. In this method, the large prior covariance matrix is truncated and replaced by its low-rank approximation, allowing thus for notable computational time and storage savings. Three test cases are studied, to assess the validity of our approach. In the first test, we show that when the number of harmonic stimulations is low, combining the harmonic hydraulic and self-potential data does not improve the inversion results. In the second test where enough harmonic stimulations are performed, a significant improvement of the hydraulic parameters is observed. In the last synthetic test, we show that the electrical conductivity field required to invert the self-potential data can be determined with enough accuracy using an electrical resistivity tomography survey using the same electrodes configuration as used for the self-potential investigation.

Full-waveform inversion of GPR data acquired between boreholes in Rustrel carbonates

Directory of Open Access Journals (Sweden)

Pinard Hugo

2016-01-01

Full Text Available Full waveform inversion (FWI of seismic or Ground Penetrating Radar data provides high-resolution quantitative images of the constitutive parameters of the rock/soil which control seismic/GPR wave propagation. We developed a 2D inversion tool in the frequency domain adapted to the multi-parameter physics controlling GPR propagation in isotropic non dispersive media, i.e. dielectric permittivity and electrical conductivity. This inversion engine was previously tested using synthetic 2D data to mitigate the trade-off between the two parameter classes. In this paper, we present the required processing techniques and first inversion results obtained on a real GPR dataset acquired in carbonates with a cross-hole configuration. The presence of the 2 m diameter underground gallery at depth constitutes a nice target to test the robustness, efficiency and resolution of the inversion in such high-contrasts context. Starting from a time tomographic image for the dielectric permittivity and from a homogeneous conductivity, we show that FWI is efficient to retrieve high resolution images of dielectric permittivity but struggles with electrical conductivity. As a quality control, we compare real and synthetic radargrams computed from the tomography and final images, showing the efficiency of the process to reconstruct some events but also underlying some issues, particularly on large incidence angles amplitude traces.

Refraction traveltime tomography based on damped wave equation for irregular topographic model

Science.gov (United States)

Park, Yunhui; Pyun, Sukjoon

2018-03-01

Land seismic data generally have time-static issues due to irregular topography and weathered layers at shallow depths. Unless the time static is handled appropriately, interpretation of the subsurface structures can be easily distorted. Therefore, static corrections are commonly applied to land seismic data. The near-surface velocity, which is required for static corrections, can be inferred from first-arrival traveltime tomography, which must consider the irregular topography, as the land seismic data are generally obtained in irregular topography. This paper proposes a refraction traveltime tomography technique that is applicable to an irregular topographic model. This technique uses unstructured meshes to express an irregular topography, and traveltimes calculated from the frequency-domain damped wavefields using the finite element method. The diagonal elements of the approximate Hessian matrix were adopted for preconditioning, and the principle of reciprocity was introduced to efficiently calculate the Fréchet derivative. We also included regularization to resolve the ill-posed inverse problem, and used the nonlinear conjugate gradient method to solve the inverse problem. As the damped wavefields were used, there were no issues associated with artificial reflections caused by unstructured meshes. In addition, the shadow zone problem could be circumvented because this method is based on the exact wave equation, which does not require a high-frequency assumption. Furthermore, the proposed method was both robust to an initial velocity model and efficient compared to full wavefield inversions. Through synthetic and field data examples, our method was shown to successfully reconstruct shallow velocity structures. To verify our method, static corrections were roughly applied to the field data using the estimated near-surface velocity. By comparing common shot gathers and stack sections with and without static corrections, we confirmed that the proposed tomography

Study of structural change in volcanic and geothermal areas using seismic tomography

Science.gov (United States)

Mhana, Najwa; Foulger, Gillian; Julian, Bruce; peirce, Christine

2014-05-01

Long Valley caldera is a large silicic volcano. It has been in a state of volcanic and seismic unrest since 1978. Farther escalation of this unrest could pose a threat to the 5,000 residents and the tens of thousands of tourists who visit the area. We have studied the crustal structure beneath 28 km X 16 km area using seismic tomography. We performed tomographic inversions for the years 2009 and 2010 with a view to differencing it with the 1997 result to look for structural changes with time and whether repeat tomography is a capable of determining the changes in structure in volcanic and geothermal reservoirs. Thus, it might provide a useful tool to monitoring physical changes in volcanoes and exploited geothermal reservoirs. Up to 600 earthquakes, selected from the best-quality events, were used for the inversion. The inversions were performed using program simulps12 [Thurber, 1983]. Our initial results show that changes in both V p and V s were consistent with the migration of CO2 into the upper 2 km or so. Our ongoing work will also invert pairs of years simultaneously using a new program, tomo4d [Julian and Foulger, 2010]. This program inverts for the differences in structure between two epochs so it can provide a more reliable measure of structural change than simply differencing the results of individual years.

Multisource inverse-geometry CT. Part II. X-ray source design and prototype

Energy Technology Data Exchange (ETDEWEB)

Neculaes, V. Bogdan, E-mail: neculaes@ge.com; Caiafa, Antonio; Cao, Yang; De Man, Bruno; Edic, Peter M.; Frutschy, Kristopher; Gunturi, Satish; Inzinna, Lou; Reynolds, Joseph; Vermilyea, Mark; Wagner, David; Zhang, Xi; Zou, Yun [GE Global Research, Niskayuna, New York 12309 (United States); Pelc, Norbert J. [Department of Radiology, Stanford University, Stanford, California 94305 (United States); Lounsberry, Brian [Healthcare Science Technology, GE Healthcare, West Milwaukee, Wisconsin 53219 (United States)

2016-08-15

Purpose: This paper summarizes the development of a high-power distributed x-ray source, or “multisource,” designed for inverse-geometry computed tomography (CT) applications [see B. De Man et al., “Multisource inverse-geometry CT. Part I. System concept and development,” Med. Phys. 43, 4607–4616 (2016)]. The paper presents the evolution of the source architecture, component design (anode, emitter, beam optics, control electronics, high voltage insulator), and experimental validation. Methods: Dispenser cathode emitters were chosen as electron sources. A modular design was adopted, with eight electron emitters (two rows of four emitters) per module, wherein tungsten targets were brazed onto copper anode blocks—one anode block per module. A specialized ceramic connector provided high voltage standoff capability and cooling oil flow to the anode. A matrix topology and low-noise electronic controls provided switching of the emitters. Results: Four modules (32 x-ray sources in two rows of 16) have been successfully integrated into a single vacuum vessel and operated on an inverse-geometry computed tomography system. Dispenser cathodes provided high beam current (>1000 mA) in pulse mode, and the electrostatic lenses focused the current beam to a small optical focal spot size (0.5 × 1.4 mm). Controlled emitter grid voltage allowed the beam current to be varied for each source, providing the ability to modulate beam current across the fan of the x-ray beam, denoted as a virtual bowtie filter. The custom designed controls achieved x-ray source switching in <1 μs. The cathode-grounded source was operated successfully up to 120 kV. Conclusions: A high-power, distributed x-ray source for inverse-geometry CT applications was successfully designed, fabricated, and operated. Future embodiments may increase the number of spots and utilize fast read out detectors to increase the x-ray flux magnitude further, while still staying within the stationary target inherent

Skeletonized wave-equation Qs tomography using surface waves

KAUST Repository

Li, Jing

2017-08-17

We present a skeletonized inversion method that inverts surface-wave data for the Qs quality factor. Similar to the inversion of dispersion curves for the S-wave velocity model, the complicated surface-wave arrivals are skeletonized as simpler data, namely the amplitude spectra of the windowed Rayleigh-wave arrivals. The optimal Qs model is then found that minimizes the difference in the peak frequencies of the predicted and observed Rayleigh wave arrivals using a gradient-based wave-equation optimization method. Solutions to the viscoelastic wave-equation are used to compute the predicted Rayleigh-wave arrivals and the misfit gradient at every iteration. This procedure, denoted as wave-equation Qs tomography (WQs), does not require the assumption of a layered model and tends to have fast and robust convergence compared to Q full waveform inversion (Q-FWI). Numerical examples with synthetic and field data demonstrate that the WQs method can accurately invert for a smoothed approximation to the subsur-face Qs distribution as long as the Vs model is known with sufficient accuracy.

Prestack first-break traveltime tomography using the double-square-root eikonal equation

KAUST Repository

Li, Siwei

2012-09-01

Traveltime tomography with shot-based eikonal equation fixes shot positions then relies on inversion to resolve any contradicting information between independent shots and achieve a possible cost-function minimum. On the other hand, the double-square-root (DSR) eikonal equation that describes the whole survey, while providing the same first-arrival travel-times, allows not only the receivers but also the shots to change position and therefore leads to faster convergence in tomo-graphic inversion. The DSR eikonal equation can be solved by a version of the fast-marching method (FMM) with special treatment for its singularity at horizontally traveling waves. For inversion, we use an upwind finite-difference scheme and the adjoint-state method to avoid explicit calculation of Fréchet derivatives. The proposed method generalizes to the 3D case straightforwardly.

Detection of the onset of ischemia and carcinogenesis by hypoxia-inducible transcription factor-based in vivo bioluminescence imaging.

Directory of Open Access Journals (Sweden)

Tetsuya Kadonosono

Full Text Available An animal model for the early detection of common fatal diseases such as ischemic diseases and cancer is desirable for the development of new drugs and treatment strategies. Hypoxia-inducible factor 1 (HIF-1 is a transcription factor that regulates oxygen homeostasis and plays key roles in a number of diseases, including cancer. Here, we established transgenic (Tg mice that carry HRE/ODD-luciferase (HOL gene, which generates bioluminescence in an HIF-1-dependent manner and was successfully used in this study to monitor HIF-1 activity in ischemic tissues. To monitor carcinogenesis in vivo, we mated HOL mice with rasH2 Tg mice, which are highly sensitive to carcinogens and are used for short-term carcinogenicity assessments. After rasH2-HOL Tg mice were treated with N-methyl-N-nitrosourea, bioluminescence was detected noninvasively as early as 9 weeks in tissues that contained papillomas and malignant lesions. These results suggest that the Tg mouse lines we established hold significant potential for monitoring the early onset of both ischemia and carcinogenesis and that these lines will be useful for screening chemicals for carcinogenic potential.

Offset-electrode profile acquisition strategy for electrical resistivity tomography

Science.gov (United States)

Robbins, Austin R.; Plattner, Alain

2018-04-01

We present an electrode layout strategy that allows electrical resistivity profiles to image the third dimension close to the profile plane. This "offset-electrode profile" approach involves laterally displacing electrodes away from the profile line in an alternating fashion and then inverting the resulting data using three-dimensional electrical resistivity tomography software. In our synthetic and field surveys, the offset-electrode method succeeds in revealing three-dimensional structures in the vicinity of the profile plane, which we could not achieve using three-dimensional inversions of linear profiles. We confirm and explain the limits of linear electrode profiles through a discussion of the three-dimensional sensitivity patterns: For a homogeneous starting model together with a linear electrode layout, all sensitivities remain symmetric with respect to the profile plane through each inversion step. This limitation can be overcome with offset-electrode layouts by breaking the symmetry pattern among the sensitivities. Thanks to freely available powerful three-dimensional resistivity tomography software and cheap modern computing power, the requirement for full three-dimensional calculations does not create a significant burden and renders the offset-electrode approach a cost-effective method. By offsetting the electrodes in an alternating pattern, as opposed to laying the profile out in a U-shape, we minimize shortening the profile length.

A multi-channel bioluminescent bacterial biosensor for the on-line detection of metals and toxicity. Part II: technical development and proof of concept of the biosensor

Energy Technology Data Exchange (ETDEWEB)

Charrier, Thomas; Thouand, Gerald [UMR CNRS 6144 GEPEA, CBAC, Nantes University, PRES UNAM, Campus de la Courtaisiere-IUT, La Roche-sur-Yon cedex (France); Chapeau, Cyrille [Biolumine, Biokar Diagnostic, Rue des Quarante Mines ZAC de Ther-Allonne, Beauvais Cedex (France); Bendria, Loubna; Daniel, Philippe [UMR CNRS 6087 LPEC, Universite du Maine, Av Olivier Messiaen, Le Mans cedex 9 (France); Picart, Pascal [UMR CNRS 6613 IAM-LAUM, Ecole Nationale des Ingenieurs du Mans, Universite du Maine, Le Mans Cedex 9 (France)

2011-05-15

This research study deals with the on-line detection of heavy metals and toxicity within the context of environmental pollution monitoring. It describes the construction and the proof of concept of a multi-channel bioluminescent bacterial biosensor in immobilized phase: Lumisens3. This new versatile device, designed for the non-stop analysis of water pollution, enables the insertion of any bioluminescent strains (inducible or constitutive), immobilized in a multi-well removable card. The technical design of Lumisens3 has benefited from both a classical and a robust approach and includes four main parts: (1) a dedicated removable card contains 64 wells, 3 mm in depth, arranged in eight grooves within which bacteria are immobilized, (2) this card is incubated on a Pelletier block with a CCD cooled camera on top for bioluminescence monitoring, (3) a fluidic network feeds the card with the sample to be analyzed and finally (4) a dedicated computer interface, BIOLUX 1.0, controls all the elements of the biosensor, allowing it to operate autonomously. The proof of concept of this biosensor was performed using a set of four bioluminescent bacteria (Escherichia coli DH1 pBzntlux, pBarslux, pBcoplux, and E. coli XL1 pBfiluxCDABE) in the on-line detection of CdCl{sub 2} 0.5 {mu}M and As{sub 2}O{sub 3} 5 {mu}M from an influent. When considering metals individually, the ''fingerprints'' from the biosensor were as expected. However, when metals were mixed together, cross reaction and synergistic effects were detected. This biosensor allowed us to demonstrate the simultaneous on-line cross detection of one or several heavy metals as well as the measurement of the overall toxicity of the sample. (orig.)

Optical diffraction tomography in an inhomogeneous background medium

International Nuclear Information System (INIS)

Devaney, A; Cheng, J

2008-01-01

The filtered back-propagation algorithm (FBP algorithm) is a computationally fast and efficient inversion algorithm for reconstructing the 3D index of refraction distribution of weak scattering samples in free space from scattered field data collected in a set of coherent optical scattering experiments. This algorithm is readily derived using classical Fourier analysis applied to the Born or Rytov weak scattering models appropriate to scatterers embedded in a non-attenuating uniform background. In this paper, the inverse scattering problem for optical diffraction tomography (ODT) is formulated using the so-called distorted wave Born and Rytov approximations and a generalized version of the FBP algorithm is derived that applies to weakly scattering samples that are embedded in realistic, multiple scattering ODT experimental configurations. The new algorithms are based on the generalized linear inverse of the linear transformation relating the scattered field data to the complex index of refraction distribution of the scattering samples and are in the form of a superposition of filtered data, computationally back propagated into the ODT experimental configuration. The paper includes a computer simulation comparing the generalized Born and Rytov based FBP inversion algorithms as well as reconstructions generated using the generalized Born based FBP algorithm of a step index optical fiber from experimental ODT data

Full-waveform Inversion of Crosshole GPR Data Collected in Strongly Heterogeneous Chalk

DEFF Research Database (Denmark)

Keskinen, Johanna; Zibar, Majken Caroline Looms; Nielsen, Lars

2015-01-01

Chalk is an important reservoir rock for hydrocarbons and for groundwater resources for many major cities. Therefore, this rock type has been extensively investigated using both geological and geophysical methods. Many applications of crosshole GPR tomography rely on the ray approximation...... and corresponding inversions of first break traveltimes and/or maximum first-cycle amplitudes. Due to the inherent limitations associated with such approaches, the resulting models tend to be overly smooth and cannot adequately capture the small-scale heterogeneities. In contrast, the full-waveform inversion uses...... address the importance of (i) adequate starting models, both in terms of the dielectric permittivity and the electrical conductivity, (ii) the estimation of the source wavelet, (iii) and the effects of data sampling density when imaging this rock type. Moreover, we discuss the resolution of the bedding...

Tomography of a simply magnetized toroidal plasma

Science.gov (United States)

Ruggero, BARNI; Stefano, CALDIROLA; Luca, FATTORINI; Claudia, RICCARDI

2018-02-01

Optical emission spectroscopy is a passive diagnostic technique, which does not perturb the plasma state. In particular, in a hydrogen plasma, Balmer-alpha (H α ) emission can be easily measured in the visible range along a line of sight from outside the plasma vessel. Other emission lines in the visible spectral range from hydrogen atoms and molecules can be exploited too, in order to gather complementary pieces of information on the plasma state. Tomography allows us to capture bi-dimensional structures. We propose to adopt an emission spectroscopy tomography for studying the transverse profiles of magnetized plasmas when Abel inversion is not exploitable. An experimental campaign was carried out at the Thorello device, a simple magnetized torus. The characteristics of the profile extraction method, which we implemented for this purpose are discussed, together with a few results concerning the plasma profiles in a simply magnetized torus configuration.

Using ATP-driven bioluminescence assay to monitor microbial safety in a contemporary human cadaver laboratory.

Science.gov (United States)

Benninger, Brion; Maier, Thomas

2015-03-01

The objective of this study was to utilize a cost-effective method for assessing the levels of bacterial, yeast, and mold activity during a human dissection laboratory course. Nowadays, compliance with safety regulations is policed by institutions at higher standards than ever before. Fear of acquiring an unknown infection is one of the top concerns of professional healthcare students, and it provokes anti-laboratory anxiety. Human cadavers are not routinely tested for bacteria and viruses prior to embalming. Human anatomy dissecting rooms that house embalmed cadavers are normally cleaned after the dissected cadavers have been removed. There is no evidence that investigators have ever assessed bacterial and fungal activities using adenosine triphosphate (ATP)-driven bioluminescence assays. A literature search was conducted on texts, journals, and websites regarding bacterial, yeast, and mold activities in an active cadaver laboratory. Midway into a clinical anatomy course, ATP bioluminescence assays were used to swab various sites within the dissection room, including entrance and exiting door handles, water taps, cadaver tables, counter tops, imaging material, X-ray box switches, and the cadaver surfaces. The results demonstrated very low activities on cadaver tables, washing up areas, and exiting door handles. There was low activity on counter tops and X-ray boxes. There was medium activity on the entrance door handles. These findings suggest an inexpensive and accurate method for monitoring safety compliance and microbial activity. Students can feel confident and safe in the environment in which they work. © 2014 Wiley Periodicals, Inc.

Filtered Bessel functions in computerized tomography

International Nuclear Information System (INIS)

Rathore, R.K.S.; Munshi, P.; Bhatia, V.K.; Pandimani, S.

1988-01-01

Computer Aided Tomography (CAT) is widely used in the medical imaging area for the detection of cancerous tissues. It has also proved to be a good technique for measuring point-density (void-fraction) in two-phase flow systems. The present day CAT-scanners employ alogorithms which are essentially a discrete implementation of the Radon Inversion Formulae. These methods of reconstructing density distributions are fast and easy to implement. The present work is an attempt to simplify (and consequently to speed-up) the existing algorithms for the cases of radially symmetric density distribution. The method uses Radon Inversion Formulae and involves Bessels's Function of Fourier frequency. The algorithm was tested on some known distributions and the reconstruction is excellent. Data for bubbly-flow was also processed to obtain a point density distribution. The range of investigation was 0.6 ≤ ≤ 0.9 g/cm 3 , where ' ' denotes average cross-sectional value. The values of CT > are within ±0.03 g/cm 3 of the true values , for the data sets considered. The results are comparable with another simple method involving radial polynominals. It is observed that the simplified Radon Inversion Formulae for the radially symmetric case gives good results and can be implemented with ease. (orig.)

BOOK REVIEW: Inverse Problems. Activities for Undergraduates

Science.gov (United States)

Yamamoto, Masahiro

2003-06-01

into the nature of inverse problems and the appropriate mode of thought, chapter 1 offers historical vignettes, most of which have played an essential role in the development of natural science. These vignettes cover the first successful application of `non-destructive testing' by Archimedes (page 4) via Newton's laws of motion up to literary tomography, and readers will be able to enjoy a wide overview of inverse problems. Therefore, as the author asks, the reader should not skip this chapter. This may not be hard to do, since the headings of the sections are quite intriguing (`Archimedes' Bath', `Another World', `Got the Time?', `Head Games', etc). The author embarks on the technical approach to inverse problems in chapter 2. He has elegantly designed each section with a guide specifying course level, objective, mathematical and scientifical background and appropriate technology (e.g. types of calculators required). The guides are designed such that teachers may be able to construct effective and attractive courses by themselves. The book is not intended to offer one rigidly determined course, but should be used flexibly and independently according to the situation. Moreover, every section closes with activities which can be chosen according to the students' interests and levels of ability. Some of these exercises do not have ready solutions, but require long-term study, so readers are not required to solve all of them. After chapter 5, which contains discrete inverse problems such as the algebraic reconstruction technique and the Backus - Gilbert method, there are answers and commentaries to the activities. Finally, scripts in MATLAB are attached, although they can also be downloaded from the author's web page (http://math.uc.edu/~groetsch/). This book is aimed at students but it will be very valuable to researchers wishing to retain a wide overview of inverse problems in the midst of busy research activities. A Japanese version was published in 2002.

Bioluminescence and the Actin Cytoskeleton in the Dinoflagellate Pyrocystis fusiformis: An Examination of Organelle Transport and Mechanotransduction

OpenAIRE

McDougall, Carrie A.

2002-01-01

Bioluminescence (BL), light produced by organisms, is a diverse and widespread marine phenomenon. yet little studied by researchers. Major contributors to sea surface BL displays are dinoflagellates, which produce rapid BL flashes upon fluid motion; mechanical stimulation triggers a 200-ms flash within 20 ms, representing one of the most rapid sensor-effector transduction systems described. In some dinoflagellate species the sensor-effector link is not constant throughout a 24-hour period. Me...

An adaptive phase space method with application to reflection traveltime tomography

International Nuclear Information System (INIS)

Chung, Eric; Qian, Jianliang; Uhlmann, Gunther; Zhao, Hongkai

2011-01-01

In this work, an adaptive strategy for the phase space method for traveltime tomography (Chung et al 2007 Inverse Problems 23 309–29) is developed. The method first uses those geodesics/rays that produce smaller mismatch with the measurements and continues on in the spirit of layer stripping without defining the layers explicitly. The adaptive approach improves stability, efficiency and accuracy. We then extend our method to reflection traveltime tomography by incorporating broken geodesics/rays for which a jump condition has to be imposed at the broken point for the geodesic flow. In particular, we show that our method can distinguish non-broken and broken geodesics in the measurement and utilize them accordingly in reflection traveltime tomography. We demonstrate that our method can recover the convex hull (with respect to the underlying metric) of unknown obstacles as well as the metric outside the convex hull. (paper)

Inverse photoemission

International Nuclear Information System (INIS)

Namatame, Hirofumi; Taniguchi, Masaki

1994-01-01

Photoelectron spectroscopy is regarded as the most powerful means since it can measure almost perfectly the occupied electron state. On the other hand, inverse photoelectron spectroscopy is the technique for measuring unoccupied electron state by using the inverse process of photoelectron spectroscopy, and in principle, the similar experiment to photoelectron spectroscopy becomes feasible. The development of the experimental technology for inverse photoelectron spectroscopy has been carried out energetically by many research groups so far. At present, the heightening of resolution of inverse photoelectron spectroscopy, the development of inverse photoelectron spectroscope in which light energy is variable and so on are carried out. But the inverse photoelectron spectroscope for vacuum ultraviolet region is not on the market. In this report, the principle of inverse photoelectron spectroscopy and the present state of the spectroscope are described, and the direction of the development hereafter is groped. As the experimental equipment, electron guns, light detectors and so on are explained. As the examples of the experiment, the inverse photoelectron spectroscopy of semimagnetic semiconductors and resonance inverse photoelectron spectroscopy are reported. (K.I.)

Effect of Iron Fe (II and Fe (III in a Binary System Evaluated Bioluminescent Method

Directory of Open Access Journals (Sweden)

Elena Sorokina

2013-01-01

Full Text Available The effect of iron ions Fe2+ and Fe3+ on the bioluminescent recombinant strain of Escherichia coli in a single-component and binary system. Found that for the bacteria E. coli Fe3+ ions are more toxic than Fe2+. Under the combined effect of iron toxicity increases, the percentage of luminescence quenching increases, but the value is much less than the sum of the indicator for the Fe2+ and Fe3+. The biological effect of insertion of iron is not proportional to their content in the mixture.

Adenylate kinase amplification of ATP bioluminescence for hygiene monitoring in the food and beverage industry.

Science.gov (United States)

Corbitt, A J; Bennion, N; Forsythe, S J

2000-06-01

Fourteen food residues, Escherichia coli O157:H7 and Staphylococcus aureus on stainless steel surfaces were detected using a combined assay with adenylate kinase as a cellular marker and ATP bioluminescence. The limit of sensitivity ranged from 0.02 to 708 microg for minced meat and broccoli, respectively. Both methods gave the same detection limit (105 cfu) for E. coli and Staph. aureus on stainless steel surfaces. The combined adenylate kinase-ATP assay is applicable to monitor the hygiene of work surfaces, especially those prone to contamination by meat and vegetable residues.

Engraftment and bone mass are enhanced by PTHrP 1-34 in ectopically transplanted vertebrae (vossicle model) and can be non-invasively monitored with bioluminescence and fluorescence imaging.

Science.gov (United States)

Hildreth, Blake Eason; Williams, Michelle M; Dembek, Katarzyna A; Hernon, Krista M; Rosol, Thomas J; Toribio, Ramiro E

2015-12-01

Evidence exists that parathyroid hormone-related protein (PTHrP) 1-34 may be more anabolic in bone than parathyroid hormone 1-34. While optical imaging is growing in popularity, scant information exists on the relationships between traditional bone imaging and histology and bioluminescence (BLI) and fluorescence (FLI) imaging. We aimed to evaluate the effects of PTHrP 1-34 on bone mass and determine if relationships existed between radiographic and histologic findings in bone and BLI and FLI indices. Vertebrae (vossicles) from mice coexpressing luciferase and green fluorescent protein were implanted subcutaneously into allogenic nude mice. Transplant recipients were treated daily with saline or PTHrP 1-34 for 4 weeks. BLI, FLI, radiography, histology, and µCT of the vossicles were performed over time. PTHrP 1-34 increased bioluminescence the most after 2 weeks, fluorescence at all time points, and decreased the time to peak bioluminescence at 4 weeks (P ≤ 0.027), the latter of which suggesting enhanced engraftment. PTHrP 1-34 maximized vertebral body volume at 4 weeks (P bone observed histologically increased in both groups at 2 and 4 weeks (P ≤ 0.002); however, PTHrP 1-34 exceeded time-matched controls (P ≤ 0.044). A positive linear relationship existed between the percentage of trabecular bone and (1) total bioluminescence (r = 0.595; P = 0.019); (2) total fluorescence (r = 0.474; P = 0.074); and (3) max fluorescence (r = 0.587; P = 0.021). In conclusion, PTHrP 1-34 enhances engraftment and bone mass, which can be monitored non-invasively by BLI and FLI.

Quantitative imaging of magnetic nanoparticles by magneto-relaxometric tomography for biomedical applications; Quantitative Bildgebung magnetischer Nanopartikel mittels magnetrelaxometrischer Tomographie fuer biomedizinische Anwendungen

Energy Technology Data Exchange (ETDEWEB)

Liebl, Maik

2016-11-18

Current biomedical research focuses on the development of novel biomedical applications based on magnetic nanoparticles (MNPs), e.g. for local cancer treatment. These therapy approaches employ MNPs as remotely controlled drug carriers or local heat generators. Since location and quantity of MNPs determine drug enrichment and heat production, quantitative knowledge of the MNP distribution inside a body is essential for the development and success of these therapies. Magnetorelaxometry (MRX) is capable to provide such quantitative information based on the specific response of the MNPs after switching-off an applied magnetic field. Applying a uniform (homogeneous) magnetic field to a MNP distribution and measuring the MNP response by multiple sensors at different locations allows for spatially resolved MNP quantification. However, to reconstruct the MNP distribution from this spatially resolved MRX data, an ill posed inverse problem has to be solved. So far, the solution of this problem was stabilized incorporating a-priori knowledge in the forward model, e.g. by setting priors on the vertical position of the distribution using a 2D reconstruction grid or setting priors on the number and geometry of the MNP sources inside the body. MRX tomography represents a novel approach for quantitative 3D imaging of MNPs, where the inverse solution is stabilized by a series of MRX measurements. In MRX tomography, only parts of the MNP distribution are sequentially magnetized by the use of inhomogeneous magnetic fields. Each magnetizing is followed by detection of the response of the corresponding part of the distribution by multiple sensors. The 3D reconstruction of the MNP distribution is then accomplished by a common evaluation of the distinct MRX measurement series. In this thesis the first experimental setup for MRX tomography was developed for quantitative 3D imaging of biomedical MNP distributions. It is based on a multi-channel magnetizing unit which has been engineered to

Near-Field Resonance Microwave Tomography and Holography

Science.gov (United States)

Gaikovich, K. P.; Smirnov, A. I.; Yanin, D. V.

2018-02-01

We develop the methods of electromagnetic computer near-field microwave tomography of distributed subsurface inhomogeneities of complex dielectric permittivity and of holography (shape retrieval) of internally homogeneous subsurface objects. The methods are based on the solution of the near-field inverse scattering problem from measurements of the resonance-parameter variations of microwave probes above the medium surface. The capabilities of the proposed diagnostic technique are demonstrated in the numerical simulation for sensors with a cylindrical capacitor as a probe element, the edge capacitance of which is sensitive to subsurface inhomogeneities.

Cone Beam Micro-CT System for Small Animal Imaging and Performance Evaluation

Directory of Open Access Journals (Sweden)

Shouping Zhu

2009-01-01

in this paper. Experimental results show that the system is suitable for small animal imaging and is adequate to provide high-resolution anatomic information for bioluminescence tomography to build a dual modality system.

Imaging of Bubonic Plague Dynamics by In Vivo Tracking of Bioluminescent Yersinia pestis

Science.gov (United States)

Nham, Toan; Filali, Sofia; Danne, Camille; Derbise, Anne; Carniel, Elisabeth

2012-01-01

Yersinia pestis dissemination in a host is usually studied by enumerating bacteria in the tissues of animals sacrificed at different times. This laborious methodology gives only snapshots of the infection, as the infectious process is not synchronized. In this work we used in vivo bioluminescence imaging (BLI) to follow Y. pestis dissemination during bubonic plague. We first demonstrated that Y. pestis CO92 transformed with pGEN-luxCDABE stably emitted bioluminescence in vitro and in vivo, while retaining full virulence. The light produced from live animals allowed to delineate the infected organs and correlated with bacterial loads, thus validating the BLI tool. We then showed that the first step of the infectious process is a bacterial multiplication at the injection site (linea alba), followed by a colonization of the draining inguinal lymph node(s), and subsequently of the ipsilateral axillary lymph node through a direct connection between the two nodes. A mild bacteremia and an effective filtering of the blood stream by the liver and spleen probably accounted for the early bacterial blood clearance and the simultaneous development of bacterial foci within these organs. The saturation of the filtering capacity of the spleen and liver subsequently led to terminal septicemia. Our results also indicate that secondary lymphoid tissues are the main targets of Y. pestis multiplication and that colonization of other organs occurs essentially at the terminal phase of the disease. Finally, our analysis reveals that the high variability in the kinetics of infection is attributable to the time the bacteria remain confined at the injection site. However, once Y. pestis has reached the draining lymph nodes, the disease progresses extremely rapidly, leading to the invasion of the entire body within two days and to death of the animals. This highlights the extraordinary capacity of Y. pestis to annihilate the host innate immune response. PMID:22496846

Imaging of bubonic plague dynamics by in vivo tracking of bioluminescent Yersinia pestis.

Directory of Open Access Journals (Sweden)

Toan Nham

Full Text Available Yersinia pestis dissemination in a host is usually studied by enumerating bacteria in the tissues of animals sacrificed at different times. This laborious methodology gives only snapshots of the infection, as the infectious process is not synchronized. In this work we used in vivo bioluminescence imaging (BLI to follow Y. pestis dissemination during bubonic plague. We first demonstrated that Y. pestis CO92 transformed with pGEN-luxCDABE stably emitted bioluminescence in vitro and in vivo, while retaining full virulence. The light produced from live animals allowed to delineate the infected organs and correlated with bacterial loads, thus validating the BLI tool. We then showed that the first step of the infectious process is a bacterial multiplication at the injection site (linea alba, followed by a colonization of the draining inguinal lymph node(s, and subsequently of the ipsilateral axillary lymph node through a direct connection between the two nodes. A mild bacteremia and an effective filtering of the blood stream by the liver and spleen probably accounted for the early bacterial blood clearance and the simultaneous development of bacterial foci within these organs. The saturation of the filtering capacity of the spleen and liver subsequently led to terminal septicemia. Our results also indicate that secondary lymphoid tissues are the main targets of Y. pestis multiplication and that colonization of other organs occurs essentially at the terminal phase of the disease. Finally, our analysis reveals that the high variability in the kinetics of infection is attributable to the time the bacteria remain confined at the injection site. However, once Y. pestis has reached the draining lymph nodes, the disease progresses extremely rapidly, leading to the invasion of the entire body within two days and to death of the animals. This highlights the extraordinary capacity of Y. pestis to annihilate the host innate immune response.

Volcano deformation source parameters estimated from InSAR: Sensitivities to uncertainties in seismic tomography

Science.gov (United States)

Masterlark, Timothy; Donovan, Theodore; Feigl, Kurt L.; Haney, Matt; Thurber, Clifford H.; Tung, Sui

2016-01-01

The eruption cycle of a volcano is controlled in part by the upward migration of magma. The characteristics of the magma flux produce a deformation signature at the Earth's surface. Inverse analyses use geodetic data to estimate strategic controlling parameters that describe the position and pressurization of a magma chamber at depth. The specific distribution of material properties controls how observed surface deformation translates to source parameter estimates. Seismic tomography models describe the spatial distributions of material properties that are necessary for accurate models of volcano deformation. This study investigates how uncertainties in seismic tomography models propagate into variations in the estimates of volcano deformation source parameters inverted from geodetic data. We conduct finite element model-based nonlinear inverse analyses of interferometric synthetic aperture radar (InSAR) data for Okmok volcano, Alaska, as an example. We then analyze the estimated parameters and their uncertainties to characterize the magma chamber. Analyses are performed separately for models simulating a pressurized chamber embedded in a homogeneous domain as well as for a domain having a heterogeneous distribution of material properties according to seismic tomography. The estimated depth of the source is sensitive to the distribution of material properties. The estimated depths for the homogeneous and heterogeneous domains are 2666 ± 42 and 3527 ± 56 m below mean sea level, respectively (99% confidence). A Monte Carlo analysis indicates that uncertainties of the seismic tomography cannot account for this discrepancy at the 99% confidence level. Accounting for the spatial distribution of elastic properties according to seismic tomography significantly improves the fit of the deformation model predictions and significantly influences estimates for parameters that describe the location of a pressurized magma chamber.

Seasonal variation of deep-sea bioluminescence in the Ionian Sea

International Nuclear Information System (INIS)

Craig, Jessica; Jamieson, Alan J.; Bagley, Philip M.; Priede, Imants G.

2011-01-01

The ICDeep (Image Intensified Charge Coupled Device for Deep sea research) profiler was used to measure the density of deep bioluminescent animals (BL) through the water column in the east, west and mid-Ionian Sea and in the Algerian Basin. A west to east decrease in BL density was found. Generalized additive modelling was used to investigate seasonal variation in the east and west Ionian Sea (NESTOR and NEMO neutrino telescope sites, respectively) from BL measurements in autumn 2008 and spring 2009. A significant seasonal effect was found in the west Ionian Sea (p<0.001), where a deep autumnal peak in BL density occurred between 500 and 2400 m. No significant seasonal variation in BL density was found in the east Ionian Sea (p=0.07). In both spring and autumn, significant differences in BL density were found through the water column between the east and west Ionian Sea (p<0.001).

Seasonal variation of deep-sea bioluminescence in the Ionian Sea

Energy Technology Data Exchange (ETDEWEB)

Craig, Jessica, E-mail: j.craig@abdn.ac.u [University of Aberdeen, Oceanlab, Main Street, Newburgh, Aberdeenshire, AB41 6AA (United Kingdom); Jamieson, Alan J.; Bagley, Philip M.; Priede, Imants G. [University of Aberdeen, Oceanlab, Main Street, Newburgh, Aberdeenshire, AB41 6AA (United Kingdom)

2011-01-21

The ICDeep (Image Intensified Charge Coupled Device for Deep sea research) profiler was used to measure the density of deep bioluminescent animals (BL) through the water column in the east, west and mid-Ionian Sea and in the Algerian Basin. A west to east decrease in BL density was found. Generalized additive modelling was used to investigate seasonal variation in the east and west Ionian Sea (NESTOR and NEMO neutrino telescope sites, respectively) from BL measurements in autumn 2008 and spring 2009. A significant seasonal effect was found in the west Ionian Sea (p<0.001), where a deep autumnal peak in BL density occurred between 500 and 2400 m. No significant seasonal variation in BL density was found in the east Ionian Sea (p=0.07). In both spring and autumn, significant differences in BL density were found through the water column between the east and west Ionian Sea (p<0.001).

Inversion of travel times obtained during active seismic refraction experiments CELEBRATION 2000, ALP 2002 and SUDETES 2003

Czech Academy of Sciences Publication Activity Database

Růžek, Bohuslav; Hrubcová, Pavla; Novotný, Miroslav; Špičák, Aleš; Karousová, Olga

2007-01-01

Roč. 51, č. 1 (2007), s. 141-164 ISSN 0039-3169 R&D Projects: GA MŽP SB/630/3/02; GA ČR GA205/03/0999 Institutional research plan: CEZ:AV0Z30120515 Keywords : seismic tomography * kinematic velocity inversion * Bohemian Massif Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 0.733, year: 2007

Time-dependent seismic tomography

Science.gov (United States)

Julian, B.R.; Foulger, G.R.

2010-01-01

Of methods for measuring temporal changes in seismic-wave speeds in the Earth, seismic tomography is among those that offer the highest spatial resolution. 3-D tomographic methods are commonly applied in this context by inverting seismic wave arrival time data sets from different epochs independently and assuming that differences in the derived structures represent real temporal variations. This assumption is dangerous because the results of independent inversions would differ even if the structure in the Earth did not change, due to observational errors and differences in the seismic ray distributions. The latter effect may be especially severe when data sets include earthquake swarms or aftershock sequences, and may produce the appearance of correlation between structural changes and seismicity when the wave speeds are actually temporally invariant. A better approach, which makes it possible to assess what changes are truly required by the data, is to invert multiple data sets simultaneously, minimizing the difference between models for different epochs as well as the rms arrival-time residuals. This problem leads, in the case of two epochs, to a system of normal equations whose order is twice as great as for a single epoch. The direct solution of this system would require twice as much memory and four times as much computational effort as would independent inversions. We present an algorithm, tomo4d, that takes advantage of the structure and sparseness of the system to obtain the solution with essentially no more effort than independent inversions require. No claim to original US government works Journal compilation ?? 2010 RAS.

Calculation of the inverse data space via sparse inversion

KAUST Repository

Saragiotis, Christos

2011-01-01

The inverse data space provides a natural separation of primaries and surface-related multiples, as the surface multiples map onto the area around the origin while the primaries map elsewhere. However, the calculation of the inverse data is far from trivial as theory requires infinite time and offset recording. Furthermore regularization issues arise during inversion. We perform the inversion by minimizing the least-squares norm of the misfit function by constraining the $ell_1$ norm of the solution, being the inverse data space. In this way a sparse inversion approach is obtained. We show results on field data with an application to surface multiple removal.

Pyramidal resistor networks for electrical impedance tomography with partial boundary measurements

International Nuclear Information System (INIS)

Borcea, L; Mamonov, A V; Druskin, V; Vasquez, F Guevara

2010-01-01

We introduce an inversion algorithm for electrical impedance tomography (EIT) with partial boundary measurements in two dimensions. It gives stable and fast reconstructions using sparse parameterizations of the unknown conductivity on optimal grids that are computed as part of the inversion. We follow the approach in Borcea et al (2008 Inverse Problems 24 035013) and Vasquez (2006 PhD thesis Rice University, Houston, TX, USA) that connects inverse discrete problems for resistor networks to continuum EIT problems, using optimal grids. The algorithm in Borcea et al (2008 Inverse Problems 24 035013) and Vasquez (2006 PhD Thesis Rice University, Houston, TX, USA) is based on circular resistor networks, and solves the EIT problem with full boundary measurements. It is extended in Borcea et al (2010 Inverse Problems 26 045010) to EIT with partial boundary measurements, using extremal quasi-conformal mappings that transform the problem to one with full boundary measurements. Here we introduce a different class of optimal grids, based on resistor networks with pyramidal topology, that is better suited for the partial measurements setup. We prove the unique solvability of the discrete inverse problem for these networks and develop an algorithm for finding them from the measurements of the Dirichlet to Neumann map. Then, we show how to use the networks to define the optimal grids and to approximate the unknown conductivity. We assess the performance of our approach with numerical simulations and compare the results with those in Borcea et al (2010)

Matrix-based image reconstruction methods for tomography

International Nuclear Information System (INIS)

Llacer, J.; Meng, J.D.

1984-10-01

Matrix methods of image reconstruction have not been used, in general, because of the large size of practical matrices, ill condition upon inversion and the success of Fourier-based techniques. An exception is the work that has been done at the Lawrence Berkeley Laboratory for imaging with accelerated radioactive ions. An extension of that work into more general imaging problems shows that, with a correct formulation of the problem, positron tomography with ring geometries results in well behaved matrices which can be used for image reconstruction with no distortion of the point response in the field of view and flexibility in the design of the instrument. Maximum Likelihood Estimator methods of reconstruction, which use the system matrices tailored to specific instruments and do not need matrix inversion, are shown to result in good preliminary images. A parallel processing computer structure based on multiple inexpensive microprocessors is proposed as a system to implement the matrix-MLE methods. 14 references, 7 figures

Anisotropic magnetotelluric inversion using a mutual information constraint

Science.gov (United States)

Mandolesi, E.; Jones, A. G.

2012-12-01

In recent years, several authors pointed that the electrical conductivity of many subsurface structures cannot be described properly by a scalar field. With the development of field devices and techniques, data quality improved to the point that the anisotropy in conductivity of rocks (microscopic anisotropy) and tectonic structures (macroscopic anisotropy) cannot be neglected. Therefore a correct use of high quality data has to include electrical anisotropy and a correct interpretation of anisotropic data characterizes directly a non-negligible part of the subsurface. In this work we test an inversion routine that takes advantage of the classic Levenberg-Marquardt (LM) algorithm to invert magnetotelluric (MT) data generated from a bi-dimensional (2D) anisotropic domain. The LM method is routinely used in inverse problems due its performance and robustness. In non-linear inverse problems -such the MT problem- the LM method provides a spectacular compromise betwee quick and secure convergence at the price of the explicit computation and storage of the sensitivity matrix. Regularization in inverse MT problems has been used extensively, due to the necessity to constrain model space and to reduce the ill-posedness of the anisotropic MT problem, which makes MT inversions extremely challenging. In order to reduce non-uniqueness of the MT problem and to reach a model compatible with other different tomographic results from the same target region, we used a mutual information (MI) based constraint. MI is a basic quantity in information theory that can be used to define a metric between images, and it is routinely used in fields as computer vision, image registration and medical tomography, to cite some applications. We -thus- inverted for the model that best fits the anisotropic data and that is the closest -in a MI sense- to a tomographic model of the target area. The advantage of this technique is that the tomographic model of the studied region may be produced by any

pyGIMLi: An open-source library for modelling and inversion in geophysics

Science.gov (United States)

Rücker, Carsten; Günther, Thomas; Wagner, Florian M.

2017-12-01

Many tasks in applied geosciences cannot be solved by single measurements, but require the integration of geophysical, geotechnical and hydrological methods. Numerical simulation techniques are essential both for planning and interpretation, as well as for the process understanding of modern geophysical methods. These trends encourage open, simple, and modern software architectures aiming at a uniform interface for interdisciplinary and flexible modelling and inversion approaches. We present pyGIMLi (Python Library for Inversion and Modelling in Geophysics), an open-source framework that provides tools for modelling and inversion of various geophysical but also hydrological methods. The modelling component supplies discretization management and the numerical basis for finite-element and finite-volume solvers in 1D, 2D and 3D on arbitrarily structured meshes. The generalized inversion framework solves the minimization problem with a Gauss-Newton algorithm for any physical forward operator and provides opportunities for uncertainty and resolution analyses. More general requirements, such as flexible regularization strategies, time-lapse processing and different sorts of coupling individual methods are provided independently of the actual methods used. The usage of pyGIMLi is first demonstrated by solving the steady-state heat equation, followed by a demonstration of more complex capabilities for the combination of different geophysical data sets. A fully coupled hydrogeophysical inversion of electrical resistivity tomography (ERT) data of a simulated tracer experiment is presented that allows to directly reconstruct the underlying hydraulic conductivity distribution of the aquifer. Another example demonstrates the improvement of jointly inverting ERT and ultrasonic data with respect to saturation by a new approach that incorporates petrophysical relations in the inversion. Potential applications of the presented framework are manifold and include time

Quantitative study of luminescence optical tomography. Application to sources localisation in molecular imaging

International Nuclear Information System (INIS)

Boffety, Matthieu

2010-01-01

Molecular imaging is a major modality in the field of preclinical research. Among the existing methods, techniques based on optical detection of visible or near infrared radiation are the most recent and are mainly represented by luminescence optical tomography techniques. These methods allow for 3D characterization of a biological medium by reconstructing maps of concentration or localisation of luminescent beacons sensitive to biological and chemical processes at the molecular or cellular scale. Luminescence optical tomography is based on a model of light propagation in tissues, a protocol for acquiring surface signal and a numerical inversion procedure used to reconstruct the parameters of interest. This thesis is structured around these three axes and provides an answer to each problem. The main objective of this study is to introduce and present the tools to evaluate the theoretical performances of optical tomography methods. One of its major outcomes is the realisation of experimental tomographic reconstructions from images acquired by an optical imager designed for 2D planar imaging and developed by the company Quidd. In a first step we develop the theory of transport in scattering medium to establish the concept on which our work will rely. We present two different propagation models as well as resolution methods and theoretical difficulties associated with them. In a second part we introduce the statistical tools used to characterise tomographic systems. We define and apply a procedure to simple situations in luminescence optical tomography. The last part of this work presents the development of an inversion procedure. After introducing the theoretical framework we validate the procedure from numerical data before successfully applying it to experimental measurements. (author) [fr

3D electrical conductivity tomography of volcanoes

Science.gov (United States)

Soueid Ahmed, A.; Revil, A.; Byrdina, S.; Coperey, A.; Gailler, L.; Grobbe, N.; Viveiros, F.; Silva, C.; Jougnot, D.; Ghorbani, A.; Hogg, C.; Kiyan, D.; Rath, V.; Heap, M. J.; Grandis, H.; Humaida, H.

2018-05-01

Electrical conductivity tomography is a well-established galvanometric method for imaging the subsurface electrical conductivity distribution. We characterize the conductivity distribution of a set of volcanic structures that are different in terms of activity and morphology. For that purpose, we developed a large-scale inversion code named ECT-3D aimed at handling complex topographical effects like those encountered in volcanic areas. In addition, ECT-3D offers the possibility of using as input data the two components of the electrical field recorded at independent stations. Without prior information, a Gauss-Newton method with roughness constraints is used to solve the inverse problem. The roughening operator used to impose constraints is computed on unstructured tetrahedral elements to map complex geometries. We first benchmark ECT-3D on two synthetic tests. A first test using the topography of Mt. St Helens volcano (Washington, USA) demonstrates that we can successfully reconstruct the electrical conductivity field of an edifice marked by a strong topography and strong variations in the resistivity distribution. A second case study is used to demonstrate the versatility of the code in using the two components of the electrical field recorded on independent stations along the ground surface. Then, we apply our code to real data sets recorded at (i) a thermally active area of Yellowstone caldera (Wyoming, USA), (ii) a monogenetic dome on Furnas volcano (the Azores, Portugal), and (iii) the upper portion of the caldera of Kīlauea (Hawai'i, USA). The tomographies reveal some of the major structures of these volcanoes as well as identifying alteration associated with high surface conductivities. We also review the petrophysics underlying the interpretation of the electrical conductivity of fresh and altered volcanic rocks and molten rocks to show that electrical conductivity tomography cannot be used as a stand-alone technique due to the non-uniqueness in

GPS Tomography: Water Vapour Monitoring for Germany

Science.gov (United States)

Bender, Michael; Dick, Galina; Wickert, Jens; Raabe, Armin

2010-05-01

Ground based GPS atmosphere sounding provides numerous atmospheric quantities with a high temporal resolution for all weather conditions. The spatial resolution of the GPS observations is mainly given by the number of GNSS satellites and GPS ground stations. The latter could considerably be increased in the last few years leading to more reliable and better resolved GPS products. New techniques such as the GPS water vapour tomography gain increased significance as data from large and dense GPS networks become available. The GPS tomography has the potential to provide spatially resolved fields of different quantities operationally, i. e. the humidity or wet refractivity as required for meteorological applications or the refraction index which is important for several space based observations or for precise positioning. The number of German GPS stations operationally processed by the GFZ in Potsdam was recently enlarged to more than 300. About 28000 IWV observations and more than 1.4 millions of slant total delay data are now available per day with a temporal resolution of 15 min and 2.5 min, respectively. The extended network leads not only to a higher spatial resolution of the tomographically reconstructed 3D fields but also to a much higher stability of the inversion process and with that to an increased quality of the results. Under these improved conditions the GPS tomography can operate continuously over several days or weeks without applying too tight constraints. Time series of tomographically reconstructed humidity fields will be shown and different initialisation strategies will be discussed: Initialisation with a simple exponential profile, with a 3D humidity field extrapolated from synoptic observations and with the result of the preceeding reconstruction. The results are compared to tomographic reconstructions initialised with COSMO-DE analyses and to the corresponding model fields. The inversion can be further stabilised by making use of independent

Detection and quantitation of circulating tumor cell dynamics by bioluminescence imaging in an orthotopic mammary carcinoma model.

Directory of Open Access Journals (Sweden)

Laura Sarah Sasportas

Full Text Available Circulating tumor cells (CTCs have been detected in the bloodstream of both early-stage and advanced cancer patients. However, very little is know about the dynamics of CTCs during cancer progression and the clinical relevance of longitudinal CTC enumeration. To address this, we developed a simple bioluminescence imaging assay to detect CTCs in mouse models of metastasis. In a 4T1 orthotopic metastatic mammary carcinoma mouse model, we demonstrated that this quantitative method offers sensitivity down to 2 CTCs in 0.1-1mL blood samples and high specificity for CTCs originating from the primary tumor, independently of their epithelial status. In this model, we simultaneously monitored blood CTC dynamics, primary tumor growth, and lung metastasis progression over the course of 24 days. Early in tumor development, we observed low numbers of CTCs in blood samples (10-15 cells/100 µL and demonstrated that CTC dynamics correlate with viable primary tumor growth. To our knowledge, these data represent the first reported use of bioluminescence imaging to detect CTCs and quantify their dynamics in any cancer mouse model. This new assay is opening the door to the study of CTC dynamics in a variety of animal models. These studies may inform clinical decision on the appropriate timing of blood sampling and value of longitudinal CTC enumeration in cancer patients.

Electric capacitance tomography and two-phase flow for the nuclear reactor safety analysis

International Nuclear Information System (INIS)

Lee, Jae Young

2008-01-01

Recently electric capacitance tomography has been developed to be used in the analysis of two-phase flow. Although its electric field is not focused as the hard ray tomography such as the X-ray or gamma ray, its convenience of easy access to the system and easy maintenance due to no requirement of radiation shielding benefits us in its application in the two-phase flow study, one of important area in the nuclear safety analysis. In the present paper, the practical technologies in the electric capacitance tomography are represented in both parts of hardware and software. In the software part, both forward problem and inverse problem are discussed and the method of regularization. In the hardware part, the brief discussion of the electronics circuits is made which provides femto farad resolution with a reasonable speed (150 frame/sec for 16 electrodes). Some representative ideal cases are studied to demonstrate its potential capability for the two-phase flow analysis. Also, some variations of the tomography such as axial tomography, and three dimensional tomography are discussed. It was found that the present ECT is expected to become a useful tool to understand the complicated three dimensional two-phase flow which may be an important feature to be equipped by the safety analysis codes. (author)

The Use of Stimulable Bioluminescence from Marine Dinoflagellates as a Means of Detecting Toxicity in the Marine Environment

Science.gov (United States)

1993-04-01

FROM MARINE PR: ME65 DINOFLAGELLATES AS A MEANS OF DETECTING TOXICITY IN THE PE: 060372N MARINE ENVIRONMENT WU: DN288604 6ý AUTHOR(S) Accesion For I...measure the acute and sublethal effects of heavy metals ( tributyltin , copper, and zinc) and storm drain effluent on the light output from marine...Grovhoug 3 THE USE OF STIM1ULABLE BIOLUMINESCENCE FROM MARINE DINOFLAGELLATES AS A MEANS OF DETECTING TOXICITY IN THE MARINE ENVIRONMENT. REFERENCE

Full-waveform inversion of cross-hole GPR data collected in a strongly heterogeneous chalk reservoir analogue with sharp permittivity and conductivity contrasts

DEFF Research Database (Denmark)

Keskinen, Johanna; Zibar, Majken Caroline Looms; Moreau, Julien

2014-01-01

Chalk sediments form an important reservoir for groundwater onshore and for hydrocarbons in the Danish sector of the North Sea. Cross-hole Ground-penetrating radar (GPR) tomography is an efficient method to investigate subtle porosity variations in the chalk. Traditional ray-based inversion...

The Role of Synthetic Reconstruction Tests in Seismic Tomography

Science.gov (United States)

Rawlinson, N.; Spakman, W.

2015-12-01

Synthetic reconstruction tests are widely used in seismic tomography as a means for assessing the robustness of solutions produced by linear or iterative non-linear inversion schemes. The most common test is the so-called checkerboard resolution test, which uses an alternating pattern of high and low wavespeeds (or some other seismic property such as attenuation). However, checkerboard tests have a number of limitations, including that they (1) only provide indirect evidence of quantitative measures of reliability such as resolution and uncertainty; (2) give a potentially misleading impression of the range of scale-lengths that can be resolved; (3) don't give a true picture of the structural distortion or smearing caused by the data coverage; and (4) result in an inverse problem that is biased towards an accurate reconstruction. The widespread use of synthetic reconstruction tests in seismic tomography is likely to continue for some time yet, so it is important to implement best practice where possible. The goal here is to provide a general set of guidelines, derived from the underlying theory and illustrated by a series of numerical experiments, on their implementation in seismic tomography. In particular, we recommend (1) using a sparse distribution of spikes, rather than the more conventional tightly-spaced checkerboard; (2) using the identical data coverage (e.g. geometric rays) for the synthetic model that was computed for the observation-based model; (3) carrying out multiple tests using anomalies of different scale length; (4) exercising caution when analysing synthetic recovery tests that use anomaly patterns that closely mimic the observation-based model; (5) investigating the trade-off between data noise levels and the minimum wavelength of recovered structure; (6) where possible, test the extent to which preconditioning (e.g. identical parameterization for input and output models) influences the recovery of anomalies.

Novel peptide chemistry in terrestrial animals: natural luciferin analogues from the bioluminescent earthworm Fridericia heliota.

Science.gov (United States)

Dubinnyi, Maxim A; Tsarkova, Aleksandra S; Petushkov, Valentin N; Kaskova, Zinaida M; Rodionova, Natalja S; Kovalchuk, Sergey I; Ziganshin, Rustam H; Baranov, Mikhail S; Mineev, Konstantin S; Yampolsky, Ilia V

2015-03-02

We report isolation and structure elucidation of AsLn5, AsLn7, AsLn11 and AsLn12: novel luciferin analogs from the bioluminescent earthworm Fridericia heliota. They were found to be highly unusual modified peptides, comprising either of the two tyrosine-derived chromophores, CompX or CompY and a set of amino acids, including threonine, gamma-aminobutyric acid, homoarginine, and unsymmetrical N,N-dimethylarginine. These natural compounds represent a unique peptide chemistry found in terrestrial animals and rise novel questions concerning their biosynthetic origin. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hyperspectral tomography based on multi-mode absorption spectroscopy (MUMAS)

Science.gov (United States)

Dai, Jinghang; O'Hagan, Seamus; Liu, Hecong; Cai, Weiwei; Ewart, Paul

2017-10-01

This paper demonstrates a hyperspectral tomographic technique that can recover the temperature and concentration field of gas flows based on multi-mode absorption spectroscopy (MUMAS). This method relies on the recently proposed concept of nonlinear tomography, which can take full advantage of the nonlinear dependency of MUMAS signals on temperature and enables 2D spatial resolution of MUMAS which is naturally a line-of-sight technique. The principles of MUMAS and nonlinear tomography, as well as the mathematical formulation of the inversion problem, are introduced. Proof-of-concept numerical demonstrations are presented using representative flame phantoms and assuming typical laser parameters. The results show that faithful reconstruction of temperature distribution is achievable when a signal-to-noise ratio of 20 is assumed. This method can potentially be extended to simultaneously reconstructing distributions of temperature and the concentration of multiple flame species.

Geoelectrical Tomography Investigating and Modeling of Fractures Network around Bittit Spring (Middle Atlas, Morocco

Directory of Open Access Journals (Sweden)

Kh. Qarqori

2012-01-01

Full Text Available Direct current Resistivity (DCR method was carried out to characterize the hydrogeological connection between the Tabular Middle Atlas (TMA and the Saïs Basin. The TMA is one of the most important aquifers in northern Morocco that supplies the deep aquifer of the Saïs Basin. Electrical resistivity tomography (ERT survey was focused on the Bittit area that is one of the most important outlet discharges, and it is representative of the relations between the TMA and the Saïs Basin. The high resolution capabilities of the electrical tomography were used to define the geological draining features in the framework of water paths from the TMA to the karstic springs. The synthetic data were calculated for the similar model expected in field data inversion and inversion result of these synthetic data used as a guide for the interpretation of the inverse data resistivity sections. Joint interpretation of geophysical, geological, structural, and synthetic simulation data allowed identifying a conductive horizontal shallow layer overlying two subvertical families of fractures of NE-SW and NW-SE directions. This result leads to propose hydrological behaviour of water from the Tabular Middle Atlas and the Saïs Basin at the Bittit Spring, which takes into account for both horizontal flows through stratification joints or karst and through subvertical fractures.

Inversion based on computational simulations

International Nuclear Information System (INIS)

Hanson, K.M.; Cunningham, G.S.; Saquib, S.S.

1998-01-01

A standard approach to solving inversion problems that involve many parameters uses gradient-based optimization to find the parameters that best match the data. The authors discuss enabling techniques that facilitate application of this approach to large-scale computational simulations, which are the only way to investigate many complex physical phenomena. Such simulations may not seem to lend themselves to calculation of the gradient with respect to numerous parameters. However, adjoint differentiation allows one to efficiently compute the gradient of an objective function with respect to all the variables of a simulation. When combined with advanced gradient-based optimization algorithms, adjoint differentiation permits one to solve very large problems of optimization or parameter estimation. These techniques will be illustrated through the simulation of the time-dependent diffusion of infrared light through tissue, which has been used to perform optical tomography. The techniques discussed have a wide range of applicability to modeling including the optimization of models to achieve a desired design goal

Inverse problems with Poisson data: statistical regularization theory, applications and algorithms

International Nuclear Information System (INIS)

Hohage, Thorsten; Werner, Frank

2016-01-01

Inverse problems with Poisson data arise in many photonic imaging modalities in medicine, engineering and astronomy. The design of regularization methods and estimators for such problems has been studied intensively over the last two decades. In this review we give an overview of statistical regularization theory for such problems, the most important applications, and the most widely used algorithms. The focus is on variational regularization methods in the form of penalized maximum likelihood estimators, which can be analyzed in a general setup. Complementing a number of recent convergence rate results we will establish consistency results. Moreover, we discuss estimators based on a wavelet-vaguelette decomposition of the (necessarily linear) forward operator. As most prominent applications we briefly introduce Positron emission tomography, inverse problems in fluorescence microscopy, and phase retrieval problems. The computation of a penalized maximum likelihood estimator involves the solution of a (typically convex) minimization problem. We also review several efficient algorithms which have been proposed for such problems over the last five years. (topical review)

Total internal reflection tomography of small objects

International Nuclear Information System (INIS)

Chen Xudong

2008-01-01

The multiple signal classification (MUSIC) imaging method is applied to determine the locations of a collection of small anisotropic spherical scatterers in the framework of the total internal reflection tomography. Multiple scattering between scatterers is considered and the inverse scattering problem is nonlinear, which, however, is solved by the proposed fast analytical approach where no associated forward problem is iteratively evaluated. The paper also discusses the role of the polarization of incidence waves, the incidence angle, the separation of scatterers from the surface of the substrate, and the level of noise on the resolution of imaging.

Developmental and Microbiological Analysis of the Inception of Bioluminescent Symbiosis in the Marine Fish Nuchequula nuchalis (Perciformes: Leiognathidae)▿

OpenAIRE

Dunlap, Paul V.; Davis, Kimberly M.; Tomiyama, Shinichi; Fujino, Misato; Fukui, Atsushi

2008-01-01

Many marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fish Nuchequula nuchalis, a species that harbors Photobacterium leiognathi as ...

Time reversal method with stabilizing boundary conditions for Photoacoustic tomography

International Nuclear Information System (INIS)

Chervova, Olga; Oksanen, Lauri

2016-01-01

We study an inverse initial source problem that models photoacoustic tomography measurements with array detectors, and introduce a method that can be viewed as a modification of the so called back and forth nudging method. We show that the method converges at an exponential rate under a natural visibility condition, with data given only on a part of the boundary of the domain of wave propagation. In this paper we consider the case of noiseless measurements. (paper)

An inversion formula for the exponential Radon transform in spatial domain with variable focal-length fan-beam collimation geometry

International Nuclear Information System (INIS)

Wen Junhai; Liang Zhengrong

2006-01-01

Inverting the exponential Radon transform has a potential use for SPECT (single photon emission computed tomography) imaging in cases where a uniform attenuation can be approximated, such as in brain and abdominal imaging. Tretiak and Metz derived in the frequency domain an explicit inversion formula for the exponential Radon transform in two dimensions for parallel-beam collimator geometry. Progress has been made to extend the inversion formula for fan-beam and varying focal-length fan-beam (VFF) collimator geometries. These previous fan-beam and VFF inversion formulas require a spatially variant filtering operation, which complicates the implementation and imposes a heavy computing burden. In this paper, we present an explicit inversion formula, in which a spatially invariant filter is involved. The formula is derived and implemented in the spatial domain for VFF geometry (where parallel-beam and fan-beam geometries are two special cases). Phantom simulations mimicking SPECT studies demonstrate its accuracy in reconstructing the phantom images and efficiency in computation for the considered collimator geometries

Cone-beam local reconstruction based on a Radon inversion transformation

International Nuclear Information System (INIS)

Wang Xian-Chao; Yan Bin; Li Lei; Hu Guo-En

2012-01-01

The local reconstruction from truncated projection data is one area of interest in image reconstruction for computed tomography (CT), which creates the possibility for dose reduction. In this paper, a filtered-backprojection (FBP) algorithm based on the Radon inversion transform is presented to deal with the three-dimensional (3D) local reconstruction in the circular geometry. The algorithm achieves the data filtering in two steps. The first step is the derivative of projections, which acts locally on the data and can thus be carried out accurately even in the presence of data truncation. The second step is the nonlocal Hilbert filtering. The numerical simulations and the real data reconstructions have been conducted to validate the new reconstruction algorithm. Compared with the approximate truncation resistant algorithm for computed tomography (ATRACT), not only it has a comparable ability to restrain truncation artifacts, but also its reconstruction efficiency is improved. It is about twice as fast as that of the ATRACT. Therefore, this work provides a simple and efficient approach for the approximate reconstruction from truncated projections in the circular cone-beam CT

Review of tomography technique for 3-dimensional fission product distribution determination in irradiated fuel

Energy Technology Data Exchange (ETDEWEB)

Pakr, D G; Hong, K P; Joo, Y S; Lee, H K

2006-04-15

Tomography algorithm is reviewed in order to determine radial 2-dimensional fission product distribution of irradiated fuel rod and to reconstruct it's image using computer. Main contents are Radon transformation, Fourier central slice theorem, inverse Fourier transform, accompanied FBP(Filtered Back Projection) and BPB(Back Projection Filtering). In addition, another tomography reconstruction algorithm, namely, ART(Algebraic Reconstruction Technique) is reviewed briefly. According to reviewed results, we devise equipment for determining of 2-dimensional distribution of irradiated nuclear fuel using existing gamma scanning apparatus. On results of review, It is necessary to develop computer program of reconstruction algorithm for determining of object function and image reconstruction.

Review of tomography technique for 3-dimensional fission product distribution determination in irradiated fuel

International Nuclear Information System (INIS)

Pakr, D. G.; Hong, K. P.; Joo, Y. S.; Lee, H. K.

2006-04-01

Tomography algorithm is reviewed in order to determine radial 2-dimensional fission product distribution of irradiated fuel rod and to reconstruct it's image using computer. Main contents are Radon transformation, Fourier central slice theorem, inverse Fourier transform, accompanied FBP(Filtered Back Projection) and BPB(Back Projection Filtering). In addition, another tomography reconstruction algorithm, namely, ART(Algebraic Reconstruction Technique) is reviewed briefly. According to reviewed results, we devise equipment for determining of 2-dimensional distribution of irradiated nuclear fuel using existing gamma scanning apparatus. On results of review, It is necessary to develop computer program of reconstruction algorithm for determining of object function and image reconstruction

GPS tomography tests for DInSAR applications on Mt. Etna

Directory of Open Access Journals (Sweden)

Massimo Aranzulla

2015-07-01

Full Text Available Tropospheric artifacts of SAR images in a volcanic area like Mt. Etna cause ambiguity in the interpretation of deformations with such technique. It would be useful to measure the delay caused by tropospheric anomalies in synthetic aperture radar (SAR satellite signals (phase of the back-scattered radar wave that could be interpreted as deformation. From the delay estimated through the GPS data processing, the tropospheric tomography of electromagnetic waves refractivity, has been performed using the SIMULps12 software. The aim of this study was to perform software synthetic tests by using SIMULps12 applied to atmospheric tomography and to verify the influence of the different GPS geodetic network configurations on obtaining a reliable tomography. Three different anomalies of increasing complexity have been investigated in order to understand the representative parameters of a correct tomography, the best spatial resolution and the portions of space in which the tomography is reliable. The tests also focused on fixing/establishing the a-priori atmospheric model and the critical values of the main parameters involved in the tomographic inversion. To this end, we made a random choice of two days, necessary to define the tomographic problem. Three different network configurations with 15, 30 and 90 GPS receivers were studied. The results indicate that the well-resolved area of tomographic images increases with the number of GPS receivers not linearly, and that the actual GPS network of 42 receivers is capable of revealing/detecting the atmospheric anomalies.

TOMOGRAPHY OF PLASMA FLOWS IN THE UPPER SOLAR CONVECTION ZONE USING TIME-DISTANCE INVERSION COMBINING RIDGE AND PHASE-SPEED FILTERING

International Nuclear Information System (INIS)

Švanda, Michal

2013-01-01

The consistency of time-distance inversions for horizontal components of the plasma flow on supergranular scales in the upper solar convection zone is checked by comparing the results derived using two k-ω filtering procedures—ridge filtering and phase-speed filtering—commonly used in time-distance helioseismology. I show that both approaches result in similar flow estimates when finite-frequency sensitivity kernels are used. I further demonstrate that the performance of the inversion improves (in terms of a simultaneously better averaging kernel and a lower noise level) when the two approaches are combined together in one inversion. Using the combined inversion, I invert for horizontal flows in the upper 10 Mm of the solar convection zone. The flows connected with supergranulation seem to be coherent only for the top ∼5 Mm; deeper down there is a hint of change of the convection scales toward structures larger than supergranules

Inverse problems for partial differential equations

CERN Document Server

Isakov, Victor

2017-01-01

This third edition expands upon the earlier edition by adding nearly 40 pages of new material reflecting the analytical and numerical progress in inverse problems in last 10 years. As in the second edition, the emphasis is on new ideas and methods rather than technical improvements. These new ideas include use of the stationary phase method in the two-dimensional elliptic problems and of multi frequencies\\temporal data to improve stability and numerical resolution. There are also numerous corrections and improvements of the exposition throughout. This book is intended for mathematicians working with partial differential equations and their applications, physicists, geophysicists, and financial, electrical, and mechanical engineers involved with nondestructive evaluation, seismic exploration, remote sensing, and various kinds of tomography. Review of the second edition: "The first edition of this excellent book appeared in 1998 and became a standard reference for everyone interested in analysis and numerics of...

Rapid drug susceptibility test of mycobacterium tuberculosis by bioluminescence sensor

Science.gov (United States)

Lu, Bin; Xu, Shunqing; Chen, Zifei; Zhou, Yikai

2001-09-01

With the persisting increase of drug-resistant stains of M. Tuberculosis around the world, rapid and sensitive detection of antibiotic of M. Tuberculosis is becoming more and more important. In the present study, drug susceptibility of M. tuberculosis were detected by recombination mycobacteriophage combined with bioluminescence sensor. It is based on the use of recombination mycobacteriophage which can express firefly luciferase when it infects viable mycobacteria, and can effectively produce quantifiable photon. Meanwhile, in mycobacterium cells treated with active antibiotic, no light is observed. The emitted light is recorded by a bioluminscence sensor, so the result of drug-resistant test can be determined by the naked eye. 159 stains of M. tuberculosis were applied to this test on their resistant to rifampin, streptomycin and isoniazid. It is found that the agreement of this assay with Liewenstein- Jensen slat is: rifampin 95.60 percent, isoniazid 91.82 percent, streptomycin 88.68 percent, which showed that it is a fast and practical method to scene and detect drug resistant of mycobacterium stains.

Angle-domain inverse scattering migration/inversion in isotropic media

Science.gov (United States)

Li, Wuqun; Mao, Weijian; Li, Xuelei; Ouyang, Wei; Liang, Quan

2018-07-01

The classical seismic asymptotic inversion can be transformed into a problem of inversion of generalized Radon transform (GRT). In such methods, the combined parameters are linearly attached to the scattered wave-field by Born approximation and recovered by applying an inverse GRT operator to the scattered wave-field data. Typical GRT-style true-amplitude inversion procedure contains an amplitude compensation process after the weighted migration via dividing an illumination associated matrix whose elements are integrals of scattering angles. It is intuitional to some extent that performs the generalized linear inversion and the inversion of GRT together by this process for direct inversion. However, it is imprecise to carry out such operation when the illumination at the image point is limited, which easily leads to the inaccuracy and instability of the matrix. This paper formulates the GRT true-amplitude inversion framework in an angle-domain version, which naturally degrades the external integral term related to the illumination in the conventional case. We solve the linearized integral equation for combined parameters of different fixed scattering angle values. With this step, we obtain high-quality angle-domain common-image gathers (CIGs) in the migration loop which provide correct amplitude-versus-angle (AVA) behavior and reasonable illumination range for subsurface image points. Then we deal with the over-determined problem to solve each parameter in the combination by a standard optimization operation. The angle-domain GRT inversion method keeps away from calculating the inaccurate and unstable illumination matrix. Compared with the conventional method, the angle-domain method can obtain more accurate amplitude information and wider amplitude-preserved range. Several model tests demonstrate the effectiveness and practicability.

Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria.

Science.gov (United States)

Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong; Luo, Zhao-Qing; Shen, Xihui

2014-05-20

Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells

Ultra-thin titanium nanolayers for plasmon-assisted enhancement of bioluminescence of chloroplast in biological light emitting devices

Energy Technology Data Exchange (ETDEWEB)

Hsun Su, Yen [Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan (China); Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan 70101, Taiwan (China); Hsu, Chia-Yun; Chang, Chung-Chien [Science and Technology of Accelerator Light Source, Hsinchu 300, Taiwan (China); Department of Materials Science and Engineering, National Chiao Tung University, Hsinchu 300, Taiwan (China); Tu, Sheng-Lung; Shen, Yun-Hwei [Department of Resource Engineering, National Cheng Kung University, Tainan 70101, Taiwan (China)

2013-08-05

Ultra-thin titanium films were deposited via ultra-high vacuum ion beam sputter deposition. Since the asymmetric electric field of the metal foil plane matches the B-band absorption of chlorophyll a, the ultra-thin titanium nanolayers were able to generate surface plasmon resonance, thus enhancing the photoluminescence of chlorophyll a. Because the density of the states of plasmon resonance increases, the enhancement of photoluminescence also rises. Due to the biocompatibility and inexpensiveness of titanium, it can be utilized to enhance the bioluminescence of chloroplast in biological light emitting devices, bio-laser, and biophotonics.

Hydrologic Process-oriented Optimization of Electrical Resistivity Tomography

Science.gov (United States)

Hinnell, A.; Bechtold, M.; Ferre, T. A.; van der Kruk, J.

2010-12-01

Electrical resistivity tomography (ERT) is commonly used in hydrologic investigations. Advances in joint and coupled hydrogeophysical inversion have enhanced the quantitative use of ERT to construct and condition hydrologic models (i.e. identify hydrologic structure and estimate hydrologic parameters). However the selection of which electrical resistivity data to collect and use is often determined by a combination of data requirements for geophysical analysis, intuition on the part of the hydrogeophysicist and logistical constraints of the laboratory or field site. One of the advantages of coupled hydrogeophysical inversion is the direct link between the hydrologic model and the individual geophysical data used to condition the model. That is, there is no requirement to collect geophysical data suitable for independent geophysical inversion. The geophysical measurements collected can be optimized for estimation of hydrologic model parameters rather than to develop a geophysical model. Using a synthetic model of drip irrigation we evaluate the value of individual resistivity measurements to describe the soil hydraulic properties and then use this information to build a data set optimized for characterizing hydrologic processes. We then compare the information content in the optimized data set with the information content in a data set optimized using a Jacobian sensitivity analysis.

Boundary Element Solution of Geometrical Inverse Heat Conduction Problems for Development of IR CAT Scan

International Nuclear Information System (INIS)

Choi, C. Y.; Park, C. T.; Kim, T. H.; Han, K. N.; Choe, S. H.

1995-01-01

A geometrical inverse heat conduction problem is solved for the development of Infrared Computerized-Axial-Tomography (IR CAT) Scan by using a boundary element method in conjunction with regularization procedure. In this problem, an overspecified temperature condition by infrared scanning is provided on the surface, and is used together with other conditions to solve the position of an unknown boundary (cavity). An auxiliary problem is introduced in the solution of this problem. By defining a hypothetical inner boundary for the auxiliary problem domain, the cavity is located interior to the domain and its position is determined by solving a potential problem. Boundary element method with regularization procedure is used to solve this problem, and the effects of regularization on the inverse solution method are investigated by means of numerical analysis

Brain serotonin 4 receptor binding is inversely associated with verbal memory recall

DEFF Research Database (Denmark)

Stenbæk, Dea S; Fisher, Patrick M; Ozenne, Brice

2017-01-01

the association between cerebral 5-HT 4R binding and affective verbal memory recall. METHODS: Twenty-four healthy volunteers were scanned with the 5-HT 4R radioligand [11C]SB207145 and positron emission tomography, and were tested with the Verbal Affective Memory Test-24. The association between 5-HT 4R binding...... and affective verbal memory was evaluated using a linear latent variable structural equation model. RESULTS: We observed a significant inverse association across all regions between 5-HT 4R binding and affective verbal memory performances for positive (p = 5.5 × 10-4) and neutral (p = .004) word recall......BACKGROUND: We have previously identified an inverse relationship between cerebral serotonin 4 receptor (5-HT 4R) binding and nonaffective episodic memory in healthy individuals. Here, we investigate in a novel sample if the association is related to affective components of memory, by examining...

A novel triple-modality reporter gene for whole-body fluorescent, bioluminescent, and nuclear noninvasive imaging

International Nuclear Information System (INIS)

Ponomarev, Vladimir; Vider, Jelena; Shavrin, Aleksander; Ageyeva, Ludmila; Tourkova, Vilia; Doubrovin, Michael; Serganova, Inna; Beresten, Tatiana; Ivanova, Anna; Blasberg, Ronald; Balatoni, Julius; Bornmann, William; Gelovani Tjuvajev, Juri

2004-01-01

Two genetic reporter systems were developed for multimodality reporter gene imaging of different molecular-genetic processes using fluorescence, bioluminescence (BLI), and nuclear imaging techniques. The eGFP cDNA was fused at the N-terminus with HSV1-tk cDNA bearing a nuclear export signal from MAPKK (NES-HSV1-tk) or with truncation at the N-terminus of the first 45 amino acids (Δ45HSV1-tk) and with firefly luciferase at the C-terminus. A single fusion protein with three functional subunits is formed following transcription and translation from a single open reading frame. The NES-TGL (NES-TGL) or Δ45HSV1-tk/GFP/luciferase (Δ45-TGL) triple-fusion gene cDNAs were cloned into a MoMLV-based retrovirus, which was used for transduction of U87 human glioma cells. The integrity, fluorescence, bioluminescence, and enzymatic activity of the TGL reporter proteins were assessed in vitro. The predicted molecular weight of the fusion proteins (130 kDa) was confirmed by western blot. The U87-NES-TGL and U87-Δ45-TGL cells had cytoplasmic green fluorescence. The in vitro BLI was 7- and 13-fold higher in U87-NES-TGL and U87-Δ45-TGL cells compared to nontransduced control cells. The Ki of 14 C-FIAU was 0.49±0.02, 0.51±0.03, and 0.003±0.001 ml/min/g in U87-NES-TGL, U87-Δ45-TGL, and wild-type U87 cells, respectively. Multimodality in vivo imaging studies were performed in nu/nu mice bearing multiple s.c. xenografts established from U87-NES-TGL, U87-Δ45-TGL, and wild-type U87 cells. BLI was performed after administration of d-luciferin (150 mg/kg i.v.). Gamma camera or PET imaging was conducted at 2 h after i.v. administration of [ 131 I]FIAU (7.4 MBq/animal) or [ 124 I]FIAU (7.4 MBq/animal), respectively. Whole-body fluorescence imaging was performed in parallel with the BLI and radiotracer imaging studies. In vivo BLI and gamma camera imaging showed specific localization of luminescence and radioactivity to the TGL transduced xenografts with background levels of activity

2.5D far-field diffraction tomography inversion scheme for GPR that takes into account the planar air-soil interface

DEFF Research Database (Denmark)

Meincke, Peter

2001-01-01

A new 2.5D inversion scheme is derived for fixed-offset ground penetrating radar (GPR) that takes into account the planar air-soil interface. The inversion scheme is based upon the first Born approximation and a far-field approximation of the dyadic Green function for a two-layer medium....

Wave-equation Q tomography and least-squares migration

KAUST Repository

Dutta, Gaurav

2016-03-01

This thesis designs new methods for Q tomography and Q-compensated prestack depth migration when the recorded seismic data suffer from strong attenuation. A motivation of this work is that the presence of gas clouds or mud channels in overburden structures leads to the distortion of amplitudes and phases in seismic waves propagating inside the earth. If the attenuation parameter Q is very strong, i.e., Q<30, ignoring the anelastic effects in imaging can lead to dimming of migration amplitudes and loss of resolution. This, in turn, adversely affects the ability to accurately predict reservoir properties below such layers. To mitigate this problem, I first develop an anelastic least-squares reverse time migration (Q-LSRTM) technique. I reformulate the conventional acoustic least-squares migration problem as a viscoacoustic linearized inversion problem. Using linearized viscoacoustic modeling and adjoint operators during the least-squares iterations, I show with numerical tests that Q-LSRTM can compensate for the amplitude loss and produce images with better balanced amplitudes than conventional migration. To estimate the background Q model that can be used for any Q-compensating migration algorithm, I then develop a wave-equation based optimization method that inverts for the subsurface Q distribution by minimizing a skeletonized misfit function ε. Here, ε is the sum of the squared differences between the observed and the predicted peak/centroid-frequency shifts of the early-arrivals. Through numerical tests on synthetic and field data, I show that noticeable improvements in the migration image quality can be obtained from Q models inverted using wave-equation Q tomography. A key feature of skeletonized inversion is that it is much less likely to get stuck in a local minimum than a standard waveform inversion method. Finally, I develop a preconditioning technique for least-squares migration using a directional Gabor-based preconditioning approach for isotropic

Inversion of the conical Radon transform with vertices on a surface of revolution arising in an application of a Compton camera

International Nuclear Information System (INIS)

Moon, Sunghwan

2017-01-01

A Compton camera has been introduced for use in single photon emission computed tomography to improve the low efficiency of a conventional gamma camera. In general, a Compton camera brings about the conical Radon transform. Here we consider a conical Radon transform with the vertices on a rotation symmetric set with respect to a coordinate axis. We show that this conical Radon transform can be decomposed into two transforms: the spherical sectional transform and the weighted fan beam transform. After finding inversion formulas for these two transforms, we provide an inversion formula for the conical Radon transform. (paper)

Adenosina trifosfato bioluminescência para avaliação da limpeza de superfícies: uma revisão integrativa

Directory of Open Access Journals (Sweden)

Adriana Cristina de Oliveira

2014-12-01

Full Text Available Objetivo: Identificar na literatura indicações e controvérsias do ATP bioluminescência para avaliação da efetividade da limpeza de superfícies em estabelecimentos de saúde. Método: Revisão integrativa da literatura, entre 2000 e 2012, nas bases de dados MEDLINE, LILACS, Science Direct, SCOPUS e Isi Web of Knowledge. Resultados: Selecionou-se para esta revisão 15 artigos. O ATP bioluminescência foi apontado como importante recurso educacional e método complementar à inspeção visual e às análises microbiológicas na avaliação da efetividade da limpeza. A impossibilidade de indicar a contaminação da superfície por micro-organismos viáveis, a interferência por substâncias químicas e a dificuldade de interpretação dos resultados constituem as principais controvérsias para o uso deste nos serviços de saúde. Conclusão: Apesar de constituir importante recurso na avaliação da limpeza de superfícies, mais estudos são necessários para incorporação efetiva do método nos serviços de saúde.

Inversion Algorithms and PS Detection in SAR Tomography, Case Study of Bucharest City

Directory of Open Access Journals (Sweden)

C. Dănişor

2016-06-01

Full Text Available Synthetic Aperture Radar (SAR tomography can reconstruct the elevation profile of each pixel based on a set of co-registered complex images of a scene. Its main advantage over classical interferometric methods consists in the capability to improve the detection of single persistent scatterers as well as to enable the detection of multiple scatterers interfering within the same pixel. In this paper, three tomographic algorithms are compared and applied to a dataset of 32 images to generate the elevation map of dominant scatterers from a scene. Targets which present stable proprieties over time - Persistent Scatterers (PS are then detected based on reflectivity functions reconstructed with Capon filtering.

Axial tomography

International Nuclear Information System (INIS)

Brueckner, K.A.; Lewis, J.H.

1979-01-01

The invention relates to axial tomography, sometimes referred to as cross-sectional x-ray. The apparatus described may utilize the conventional x-ray or ultrasonic source and detector and scanning mechanism for producing the plurality of sets of radiation detector output signals. It has the means for storing the detector output signals in analog form with the signals of one set overlying the signals of another set so that signals resulting from radiation through a zone of the object being examined are summed at a corresponding zone in the storage device, typically an electronic storage tube. The summed signals are read from the storage device with a radially inversely proportional reader producing a second signal for storage, again typically in an electronic storage tube. These signals stored in the second storage device are read with Laplacian relation, with the resultant sigal being a video signal that may be connected to a TV monitor for display of the sectional image. In alternative embodiments, optical film systems and electrostatic systems are utilized. (JTA)

Generation of a new bioluminescent model for visualisation of mammary tumour development in transgenic mice

Directory of Open Access Journals (Sweden)

Zagozdzon Agnieszka M

2012-05-01

Full Text Available Abstract Background Numerous transgenic models have been generated to study breast cancer. However, despite many advantages, traditional transgenic models for breast cancer are also burdened with difficulties in early detection and longitudinal observation of transgene-induced tumours, which in most cases are randomly located and occur at various time points. Methods such as palpation followed by mechanical measurement of the tumours are of limited value in transgenic models. There is a crucial need for making these previously generated models suitable for modern methods of tumour visualisation and monitoring, e.g. by bioluminescence-based techniques. This approach was successfully used in the current study. Results A new mouse strain (MMTV-Luc2 mice expressing Luc2 luciferase primarily in mammary tissue in females, with low-level background expression in internal organs, was generated and bred to homozygosity. After these mice were intercrossed with MMTV-PyVT mice, all double transgenic females developed mammary tumours by the age of 10 weeks, the localisation and progression of which could be effectively monitored using the luminescence-based in vivo imaging. Luminescence-based readout allowed for early visualisation of the locally overgrown mammary tissue and for longitudinal evaluation of local progression of the tumours. When sampled ex vivo at the age of 10 weeks, all tumours derived from MMTV-Luc2PyVT females displayed robust bioluminescent signal. Conclusions We have created a novel transgenic strain for visualisation and longitudinal monitoring of mammary tumour development in transgenic mice as an addition and/or a new and more advanced alternative to manual methods. Generation of this mouse strain is vital for making many of the existing mammary tumour transgenic models applicable for in vivo imaging techniques.

Generation of a new bioluminescent model for visualisation of mammary tumour development in transgenic mice

LENUS (Irish Health Repository)

Zagozdzon, Agnieszka M

2012-05-30

AbstractBackgroundNumerous transgenic models have been generated to study breast cancer. However, despite many advantages, traditional transgenic models for breast cancer are also burdened with difficulties in early detection and longitudinal observation of transgene-induced tumours, which in most cases are randomly located and occur at various time points. Methods such as palpation followed by mechanical measurement of the tumours are of limited value in transgenic models. There is a crucial need for making these previously generated models suitable for modern methods of tumour visualisation and monitoring, e.g. by bioluminescence-based techniques. This approach was successfully used in the current study.ResultsA new mouse strain (MMTV-Luc2 mice) expressing Luc2 luciferase primarily in mammary tissue in females, with low-level background expression in internal organs, was generated and bred to homozygosity. After these mice were intercrossed with MMTV-PyVT mice, all double transgenic females developed mammary tumours by the age of 10 weeks, the localisation and progression of which could be effectively monitored using the luminescence-based in vivo imaging. Luminescence-based readout allowed for early visualisation of the locally overgrown mammary tissue and for longitudinal evaluation of local progression of the tumours. When sampled ex vivo at the age of 10 weeks, all tumours derived from MMTV-Luc2PyVT females displayed robust bioluminescent signal.ConclusionsWe have created a novel transgenic strain for visualisation and longitudinal monitoring of mammary tumour development in transgenic mice as an addition and\\/or a new and more advanced alternative to manual methods. Generation of this mouse strain is vital for making many of the existing mammary tumour transgenic models applicable for in vivo imaging techniques.

Iterative methods for photoacoustic tomography in attenuating acoustic media

Science.gov (United States)

Haltmeier, Markus; Kowar, Richard; Nguyen, Linh V.

2017-11-01

The development of efficient and accurate reconstruction methods is an important aspect of tomographic imaging. In this article, we address this issue for photoacoustic tomography. To this aim, we use models for acoustic wave propagation accounting for frequency dependent attenuation according to a wide class of attenuation laws that may include memory. We formulate the inverse problem of photoacoustic tomography in attenuating medium as an ill-posed operator equation in a Hilbert space framework that is tackled by iterative regularization methods. Our approach comes with a clear convergence analysis. For that purpose we derive explicit expressions for the adjoint problem that can efficiently be implemented. In contrast to time reversal, the employed adjoint wave equation is again damping and, thus has a stable solution. This stability property can be clearly seen in our numerical results. Moreover, the presented numerical results clearly demonstrate the efficiency and accuracy of the derived iterative reconstruction algorithms in various situations including the limited view case.

The shifting zoom: new possibilities for inverse scattering on electrically large domains

Science.gov (United States)

Persico, Raffaele; Ludeno, Giovanni; Soldovieri, Francesco; De Coster, Alberic; Lambot, Sebastien

2017-04-01

Inverse scattering is a subject of great interest in diagnostic problems, which are in their turn of interest for many applicative problems as investigation of cultural heritage, characterization of foundations or subservices, identification of unexploded ordnances and so on [1-4]. In particular, GPR data are usually focused by means of migration algorithms, essentially based on a linear approximation of the scattering phenomenon. Migration algorithms are popular because they are computationally efficient and do not require the inversion of a matrix, neither the calculation of the elements of a matrix. In fact, they are essentially based on the adjoint of the linearised scattering operator, which allows in the end to write the inversion formula as a suitably weighted integral of the data [5]. In particular, this makes a migration algorithm more suitable than a linear microwave tomography inversion algorithm for the reconstruction of an electrically large investigation domain. However, this computational challenge can be overcome by making use of investigation domains joined side by side, as proposed e.g. in ref. [3]. This allows to apply a microwave tomography algorithm even to large investigation domains. However, the joining side by side of sequential investigation domains introduces a problem of limited (and asymmetric) maximum view angle with regard to the targets occurring close to the edges between two adjacent domains, or possibly crossing these edges. The shifting zoom is a method that allows to overcome this difficulty by means of overlapped investigation and observation domains [6-7]. It requires more sequential inversion with respect to adjacent investigation domains, but the really required extra-time is minimal because the matrix to be inverted is calculated ones and for all, as well as its singular value decomposition: what is repeated more time is only a fast matrix-vector multiplication. References [1] M. Pieraccini, L. Noferini, D. Mecatti, C

Inverse transport theory of photoacoustics

International Nuclear Information System (INIS)

Bal, Guillaume; Jollivet, Alexandre; Jugnon, Vincent

2010-01-01

We consider the reconstruction of optical parameters in a domain of interest from photoacoustic data. Photoacoustic tomography (PAT) radiates high-frequency electromagnetic waves into the domain and measures acoustic signals emitted by the resulting thermal expansion. Acoustic signals are then used to construct the deposited thermal energy map. The latter depends on the constitutive optical parameters in a nontrivial manner. In this paper, we develop and use an inverse transport theory with internal measurements to extract information on the optical coefficients from knowledge of the deposited thermal energy map. We consider the multi-measurement setting in which many electromagnetic radiation patterns are used to probe the domain of interest. By developing an expansion of the measurement operator into singular components, we show that the spatial variations of the intrinsic attenuation and the scattering coefficients may be reconstructed. We also reconstruct coefficients describing anisotropic scattering of photons, such as the anisotropy coefficient g(x) in a Henyey–Greenstein phase function model. Finally, we derive stability estimates for the reconstructions

3-D waveform tomography sensitivity kernels for anisotropic media

KAUST Repository

Djebbi, Ramzi

2014-01-01

The complications in anisotropic multi-parameter inversion lie in the trade-off between the different anisotropy parameters. We compute the tomographic waveform sensitivity kernels for a VTI acoustic medium perturbation as a tool to investigate this ambiguity between the different parameters. We use dynamic ray tracing to efficiently handle the expensive computational cost for 3-D anisotropic models. Ray tracing provides also the ray direction information necessary for conditioning the sensitivity kernels to handle anisotropy. The NMO velocity and η parameter kernels showed a maximum sensitivity for diving waves which results in a relevant choice of those parameters in wave equation tomography. The δ parameter kernel showed zero sensitivity; therefore it can serve as a secondary parameter to fit the amplitude in the acoustic anisotropic inversion. Considering the limited penetration depth of diving waves, migration velocity analysis based kernels are introduced to fix the depth ambiguity with reflections and compute sensitivity maps in the deeper parts of the model.

Inversions

Science.gov (United States)

Brown, Malcolm

2009-01-01

Inversions are fascinating phenomena. They are reversals of the normal or expected order. They occur across a wide variety of contexts. What do inversions have to do with learning spaces? The author suggests that they are a useful metaphor for the process that is unfolding in higher education with respect to education. On the basis of…

Development of a Novel Preclinical Pancreatic Cancer Research Model: Bioluminescence Image-Guided Focal Irradiation and Tumor Monitoring of Orthotopic Xenografts1

OpenAIRE

Tuli, Richard; Surmak, Andrew; Reyes, Juvenal; Hacker-Prietz, Amy; Armour, Michael; Leubner, Ashley; Blackford, Amanda; Tryggestad, Erik; Jaffee, Elizabeth M; Wong, John; DeWeese, Theodore L; Herman, Joseph M

2012-01-01

PURPOSE: We report on a novel preclinical pancreatic cancer research model that uses bioluminescence imaging (BLI)-guided irradiation of orthotopic xenograft tumors, sparing of surrounding normal tissues, and quantitative, noninvasive longitudinal assessment of treatment response. MATERIALS AND METHODS: Luciferase-expressing MiaPaCa-2 pancreatic carcinoma cells were orthotopically injected in nude mice. BLI was compared to pathologic tumor volume, and photon emission was assessed over time. B...

Seismic tomography of Basse-Terre volcanic island, Guadeloupe, Lesser Antilles, using earthquake travel times and noise correlations

Science.gov (United States)

Barnoud, Anne; Coutant, Olivier; Bouligand, Claire; Massin, Frédérick; Stehly, Laurent

2015-04-01

We image the volcanic island of Basse-Terre, Guadeloupe, Lesser Antilles, using both earthquake travel times and noise correlations. (1) A new earthquake catalog was recently compiled for the Lesser Antilles by the CDSA/OVSG/IPGP (Massin et al., EGU General Assembly 2014) and allows us to perform classical travel time tomography to obtain smooth 3D body wave velocity models. The geometrical configuration of the volcanic arc controls the resolution of the model in our zone of interest. (2) Surface wave tomography using noise correlations was successfully applied to volcanoes (Brenguier et al., Geophys. Res. Lett. 2007). We use seismic noise recorded at 16 broad-band stations and 9 short-period stations from Basse-Terre over a period of six years (2007-2012). For each station pair, we extract a dispersion curve from the noise correlation to get surface wave velocity models. The inversion of the dispersion curves produces a 3D S-wave velocity model of the island. The spatial distribution of seismic stations accross the island is highly heterogeneous, leading to higher resolution near the dome of the Soufrière of Guadeloupe volcano. Resulting velocity models are compared with densities obtained by 3D inversion of gravimetric data (Barnoud et al., AGU Fall Meeting 2013). Further work should include simultaneous inversion of seismic and gravimetric datasets to overcome resolution limitations.

Natural killer cell lines preferentially kill clonogenic multiple myeloma cells and decrease myeloma engraftment in a bioluminescent xenograft mouse model.

Science.gov (United States)

Swift, Brenna E; Williams, Brent A; Kosaka, Yoko; Wang, Xing-Hua; Medin, Jeffrey A; Viswanathan, Sowmya; Martinez-Lopez, Joaquin; Keating, Armand

2012-07-01

Novel therapies capable of targeting drug resistant clonogenic MM cells are required for more effective treatment of multiple myeloma. This study investigates the cytotoxicity of natural killer cell lines against bulk and clonogenic multiple myeloma and evaluates the tumor burden after NK cell therapy in a bioluminescent xenograft mouse model. The cytotoxicity of natural killer cell lines was evaluated against bulk multiple myeloma cell lines using chromium release and flow cytometry cytotoxicity assays. Selected activating receptors on natural killer cells were blocked to determine their role in multiple myeloma recognition. Growth inhibition of clonogenic multiple myeloma cells was assessed in a methylcellulose clonogenic assay in combination with secondary replating to evaluate the self-renewal of residual progenitors after natural killer cell treatment. A bioluminescent mouse model was developed using the human U266 cell line transduced to express green fluorescent protein and luciferase (U266eGFPluc) to monitor disease progression in vivo and assess bone marrow engraftment after intravenous NK-92 cell therapy. Three multiple myeloma cell lines were sensitive to NK-92 and KHYG-1 cytotoxicity mediated by NKp30, NKp46, NKG2D and DNAM-1 activating receptors. NK-92 and KHYG-1 demonstrated 2- to 3-fold greater inhibition of clonogenic multiple myeloma growth, compared with killing of the bulk tumor population. In addition, the residual colonies after treatment formed significantly fewer colonies compared to the control in a secondary replating for a cumulative clonogenic inhibition of 89-99% at the 20:1 effector to target ratio. Multiple myeloma tumor burden was reduced by NK-92 in a xenograft mouse model as measured by bioluminescence imaging and reduction in bone marrow engraftment of U266eGFPluc cells by flow cytometry. This study demonstrates that NK-92 and KHYG-1 are capable of killing clonogenic and bulk multiple myeloma cells. In addition, multiple myeloma

Magnetic resonance tomography for focal lesions in the liver using the para-magnetic contrast medium gadolinium DTPA

International Nuclear Information System (INIS)

Hamm, B.; Roemer, T.; Felix, R.; Wolf, K.J.; Klinikum Charlottenburg, Berlin

1986-01-01

The use of the para-magnetic contrast medium gadolinium DTPA for magnetic resonance tomography of focal lesions in the liver was investigated in 31 patients. Two dosage schedules of the contrast medium (0.1 and 0.2 mmol/kg body weight) were used with field strengths of 0.35 and 0.5 Tesla. Using T 1 sequences, gadolinium DTPA showed increased signal intensity in the liver and in tumours, but this was significantly more marked in the tumour. On T 1 spin-echo sequences, previously iso-intense lesions became visible after administration of contrast. On the other hand, contrast-enhanced lesions were less well seen on inversion recovery sequences because of a reduction in the contrast between tumour and liver tissue. The contrast between tumour and liver tissue was not improved by gadolinium DTPA in comparison with precontrast inversion recovery sequences and T 2 spin-echo sequences. The perfusion of intra-hepatic tumours could be elucidated by magnetic resonance tomography after the administration of gadolinium DTPA. (orig.) [de

Upper mantle delay time tomography : with an application to the collision zone of the Eurasian, African, and Arabian plates

NARCIS (Netherlands)

Spakman, W.

1988-01-01

More than a decade ago the method of seismic delay time tomography was introduced in geophysics by Alci et al. (1974, 1977). In the 1977 paper the inverse problem is formulated of retrieving the three-dimensional seismic velocity structure of the Earth's interior from a finite number of data

Quantitative imaging of magnetic nanoparticles by magneto-relaxometric tomography for biomedical applications

International Nuclear Information System (INIS)

Liebl, Maik

2016-01-01

Current biomedical research focuses on the development of novel biomedical applications based on magnetic nanoparticles (MNPs), e.g. for local cancer treatment. These therapy approaches employ MNPs as remotely controlled drug carriers or local heat generators. Since location and quantity of MNPs determine drug enrichment and heat production, quantitative knowledge of the MNP distribution inside a body is essential for the development and success of these therapies. Magnetorelaxometry (MRX) is capable to provide such quantitative information based on the specific response of the MNPs after switching-off an applied magnetic field. Applying a uniform (homogeneous) magnetic field to a MNP distribution and measuring the MNP response by multiple sensors at different locations allows for spatially resolved MNP quantification. However, to reconstruct the MNP distribution from this spatially resolved MRX data, an ill posed inverse problem has to be solved. So far, the solution of this problem was stabilized incorporating a-priori knowledge in the forward model, e.g. by setting priors on the vertical position of the distribution using a 2D reconstruction grid or setting priors on the number and geometry of the MNP sources inside the body. MRX tomography represents a novel approach for quantitative 3D imaging of MNPs, where the inverse solution is stabilized by a series of MRX measurements. In MRX tomography, only parts of the MNP distribution are sequentially magnetized by the use of inhomogeneous magnetic fields. Each magnetizing is followed by detection of the response of the corresponding part of the distribution by multiple sensors. The 3D reconstruction of the MNP distribution is then accomplished by a common evaluation of the distinct MRX measurement series. In this thesis the first experimental setup for MRX tomography was developed for quantitative 3D imaging of biomedical MNP distributions. It is based on a multi-channel magnetizing unit which has been engineered to

Classification of movement intention by spatially filtered electromagnetic inverse solutions

International Nuclear Information System (INIS)

Congedo, M; Lotte, F; Lecuyer, A

2006-01-01

We couple standardized low-resolution electromagnetic tomography, an inverse solution for electroencephalography (EEG) and the common spatial pattern, which is here conceived as a data-driven beamformer, to classify the benchmark BCI (brain-computer interface) competition 2003, data set IV. The data set is from an experiment where a subject performed a self-paced left and right finger tapping task. Available for analysis are 314 training trials whereas 100 unlabelled test trials have to be classified. The EEG data from 28 electrodes comprise the recording of the 500 ms before the actual finger movements, hence represent uniquely the left and right finger movement intention. Despite our use of an untrained classifier, and our extraction of only one attribute per class, our method yields accuracy similar to the winners of the competition for this data set. The distinct advantages of the approach presented here are the use of an untrained classifier and the processing speed, which make the method suitable for actual BCI applications. The proposed method is favourable over existing classification methods based on an EEG inverse solution, which rely either on iterative algorithms for single-trial independent component analysis or on trained classifiers

Thermoacoustic tomography for an integro-differential wave equation modeling attenuation

Science.gov (United States)

Acosta, Sebastián; Palacios, Benjamín

2018-02-01

In this article we study the inverse problem of thermoacoustic tomography (TAT) on a medium with attenuation represented by a time-convolution (or memory) term, and whose consideration is motivated by the modeling of ultrasound waves in heterogeneous tissue via fractional derivatives with spatially dependent parameters. Under the assumption of being able to measure data on the whole boundary, we prove uniqueness and stability, and propose a convergent reconstruction method for a class of smooth variable sound speeds. By a suitable modification of the time reversal technique, we obtain a Neumann series reconstruction formula.

Recent Progress on the Factorization Method for Electrical Impedance Tomography

Directory of Open Access Journals (Sweden)

Bastian Harrach

2013-01-01

method was introduced by Kirsch for inverse scattering problems and extended to electrical impedance tomography (EIT by Brühl and Hanke. Since these pioneering works, substantial progress has been made on the theoretical foundations of the method. The necessary assumptions have been weakened, and the proofs have been considerably simplified. In this work, we aim to summarize this progress and present a state-of-the-art formulation of the Factorization Method for EIT with continuous data. In particular, we formulate the method for general piecewise analytic conductivities and give short and self-contained proofs.

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging.

Science.gov (United States)

Kolehmainen, Ville; Vanne, Antti; Siltanen, Samuli; Järvenpää, Seppo; Kaipio, Jari P; Lassas, Matti; Kalke, Martti

2006-02-01

Diagnostic and operational tasks based on dental radiology often require three-dimensional (3-D) information that is not available in a single X-ray projection image. Comprehensive 3-D information about tissues can be obtained by computerized tomography (CT) imaging. However, in dental imaging a conventional CT scan may not be available or practical because of high radiation dose, low-resolution or the cost of the CT scanner equipment. In this paper, we consider a novel type of 3-D imaging modality for dental radiology. We consider situations in which projection images of the teeth are taken from a few sparsely distributed projection directions using the dentist's regular (digital) X-ray equipment and the 3-D X-ray attenuation function is reconstructed. A complication in these experiments is that the reconstruction of the 3-D structure based on a few projection images becomes an ill-posed inverse problem. Bayesian inversion is a well suited framework for reconstruction from such incomplete data. In Bayesian inversion, the ill-posed reconstruction problem is formulated in a well-posed probabilistic form in which a priori information is used to compensate for the incomplete information of the projection data. In this paper we propose a Bayesian method for 3-D reconstruction in dental radiology. The method is partially based on Kolehmainen et al. 2003. The prior model for dental structures consist of a weighted l1 and total variation (TV)-prior together with the positivity prior. The inverse problem is stated as finding the maximum a posteriori (MAP) estimate. To make the 3-D reconstruction computationally feasible, a parallelized version of an optimization algorithm is implemented for a Beowulf cluster computer. The method is tested with projection data from dental specimens and patient data. Tomosynthetic reconstructions are given as reference for the proposed method.

A new algorithm for three-dimensional joint inversion of body wave and surface wave data and its application to the Southern California plate boundary region

Science.gov (United States)

Fang, Hongjian; Zhang, Haijiang; Yao, Huajian; Allam, Amir; Zigone, Dimitri; Ben-Zion, Yehuda; Thurber, Clifford; van der Hilst, Robert D.

2016-05-01

We introduce a new algorithm for joint inversion of body wave and surface wave data to get better 3-D P wave (Vp) and S wave (Vs) velocity models by taking advantage of the complementary strengths of each data set. Our joint inversion algorithm uses a one-step inversion of surface wave traveltime measurements at different periods for 3-D Vs and Vp models without constructing the intermediate phase or group velocity maps. This allows a more straightforward modeling of surface wave traveltime data with the body wave arrival times. We take into consideration the sensitivity of surface wave data with respect to Vp in addition to its large sensitivity to Vs, which means both models are constrained by two different data types. The method is applied to determine 3-D crustal Vp and Vs models using body wave and Rayleigh wave data in the Southern California plate boundary region, which has previously been studied with both double-difference tomography method using body wave arrival times and ambient noise tomography method with Rayleigh and Love wave group velocity dispersion measurements. Our approach creates self-consistent and unique models with no prominent gaps, with Rayleigh wave data resolving shallow and large-scale features and body wave data constraining relatively deeper structures where their ray coverage is good. The velocity model from the joint inversion is consistent with local geological structures and produces better fits to observed seismic waveforms than the current Southern California Earthquake Center (SCEC) model.

Advancing Molecular Therapies through In Vivo Bioluminescent Imaging

Directory of Open Access Journals (Sweden)

Anton McCaffrey

2003-04-01

Full Text Available Effective development of therapeutics that target the molecular basis of disease is dependent on testing new therapeutic moieties and delivery strategies in animal models of human disease. Accelerating the analyses of these models and improving their predictive value through whole animal imaging methods, which provide data in real time and are sensitive to the subtle changes, are crucial for rapid advancement of these approaches. Modalities based on optics are rapid, sensitive, and accessible methods for in vivo analyses with relatively low instrumentation costs. In vivo bioluminescent imaging (BLI is one of these optically based imaging methods that enable rapid in vivo analyses of a variety of cellular and molecular events with extreme sensitivity. BLI is based on the use of light-emitting enzymes as internal biological light sources that can be detected externally as biological indicators. BLI has been used to test spatio-temporal expression patterns of both target and therapeutic genes in living laboratory animals where the contextual influences of whole biological systems are preserved. BLI has also been used to analyze gene delivery, immune cell therapies, and the in vivo efficacy of inhibitory RNAs. New tools for BLI are being developed that will offer greater flexibility in detection and analyses. BLI can be used to accelerate the evaluation of experimental therapeutic strategies and whole body imaging offers the opportunity of revealing the effects of novel approaches on key steps in disease processes.

Application of tomographic inversion in studying airglow in the mesopause region

Directory of Open Access Journals (Sweden)

T. Nygrén

Full Text Available It is pointed out that observations of periodic nightglow structures give excellent information on atmospheric gravity waves in the mesosphere and lower thermosphere. The periods, the horizontal wavelengths and the phase speeds of the waves can be determined from airglow images and, using several cameras, the approximate altitude of the luminous layer can also be determined by triangulation. In this paper the possibility of applying tomographic methods for reconstructing the airglow structures is investigated using numerical simulations. A ground-based chain of cameras is assumed, two-dimensional airglow models in the vertical plane above the chain are constructed, and simulated data are calculated by integrating the models along a great number of rays with different elevation angles for each camera. After addition of random noise, these data are then inverted to obtain reconstructions of the models. A tomographic analysis package originally designed for satellite radiotomography is used in the inversion. The package is based on a formulation of stochastic inversion which allows the input of a priori information to the solver in terms of regularization variances. The reconstruction is carried out in two stages. In the first inversion, constant regularization variances are used within a wide altitude range. The results are used in determining the approximate altitude range of the airglow structures. Then, in the second inversion, constant non-zero regularization variances are used inside this region and zero variances outside it. With this method reliable reconstructions of the models are obtained. The number of cameras as well as their separations are varied in order to find out the limitations of the method.

Key words. Tomography · Airglow · Mesopause · Gravity waves

Limitations of the acoustic approximation for seismic crosshole tomography

Science.gov (United States)

Marelli, Stefano; Maurer, Hansruedi

2010-05-01

Modelling and inversion of seismic crosshole data is a challenging task in terms of computational resources. Even with the significant increase in power of modern supercomputers, full three-dimensional elastic modelling of high-frequency waveforms generated from hundreds of source positions in several boreholes is still an intractable task. However, it has been recognised that full waveform inversion offers substantially more information compared with traditional travel time tomography. A common strategy to reduce the computational burden for tomographic inversion is to approximate the true elastic wave propagation by acoustic modelling. This approximation assumes that the solid rock units can be treated like fluids (with no shear wave propagation) and is generally considered to be satisfactory so long as only the earliest portions of the recorded seismograms are considered. The main assumption is that most of the energy in the early parts of the recorded seismograms is carried by the faster compressional (P-) waves. Although a limited number of studies exist on the effects of this approximation for surface/marine synthetic reflection seismic data, and show it to be generally acceptable for models with low to moderate impedance contrasts, to our knowledge no comparable studies have been published on the effects for cross-borehole transmission data. An obvious question is whether transmission tomography should be less affected by elastic effects than surface reflection data when only short time windows are applied to primarily capture the first arriving wavetrains. To answer this question we have performed 2D and 3D investigations on the validity of the acoustic approximation for an elastic medium and using crosshole source-receiver configurations. In order to generate consistent acoustic and elastic data sets, we ran the synthetic tests using the same finite-differences time-domain elastic modelling code for both types of simulations. The acoustic approximation was

Sampling of finite elements for sparse recovery in large scale 3D electrical impedance tomography

International Nuclear Information System (INIS)

Javaherian, Ashkan; Moeller, Knut; Soleimani, Manuchehr

2015-01-01

This study proposes a method to improve performance of sparse recovery inverse solvers in 3D electrical impedance tomography (3D EIT), especially when the volume under study contains small-sized inclusions, e.g. 3D imaging of breast tumours. Initially, a quadratic regularized inverse solver is applied in a fast manner with a stopping threshold much greater than the optimum. Based on assuming a fixed level of sparsity for the conductivity field, finite elements are then sampled via applying a compressive sensing (CS) algorithm to the rough blurred estimation previously made by the quadratic solver. Finally, a sparse inverse solver is applied solely to the sampled finite elements, with the solution to the CS as its initial guess. The results show the great potential of the proposed CS-based sparse recovery in improving accuracy of sparse solution to the large-size 3D EIT. (paper)

Analysis of genetically modified organisms by pyrosequencing on a portable photodiode-based bioluminescence sequencer.

Science.gov (United States)

Song, Qinxin; Wei, Guijiang; Zhou, Guohua

2014-07-01

A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

An efficient sequential strategy for realizing cross-gradient joint inversion: method and its application to 2-D cross borehole seismic traveltime and DC resistivity tomography