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DOE OSTI2014

Low-dose phase contrast tomography with conventional x-ray sources

Purpose: The edge illumination (EI) x-ray phase contrast imaging (XPCi) method has been recently further developed to perform tomographic and, thus, volumetric imaging. In this paper, the first tomographic EI XPCi images acquired with a conventional x-ray source at dose levels below that used for preclinical small animal imaging are presented. Methods: Two test objects, a biological sample and a custom-built phantom, were imaged with a laboratory-based EI XPCi setup in tomography mode. Tomographic maps that show the phase shift and attenuating properties of the object were reconstructed, and analyzed in terms of signal-to-noise ratio and quantitative accuracy. Dose measurements using thermoluminescence devices were performed. Results: The obtained images demonstrate that phase based imaging methods can provide superior results compared to attenuation based modalities for weakly attenuating samples also in 3D. Moreover, and, most importantly, they demonstrate the feasibility of low-dose imaging. In addition, the experimental results can be considered quantitative within the constraints imposed by polychromaticity. Conclusions: The results, together with the method's dose efficiency and compatibility with conventional x-ray sources, indicate that tomographic EI XPCi can become an important tool for the routine imaging of biomedical samples.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Three-dimensional texture analysis of contrast enhanced CT images for treatment response assessment in Hodgkin lymphoma: Comparison with F-18-FDG PET

Purpose: To determine the diagnostic performance of three-dimensional (3D) texture analysis (TA) of contrast-enhanced computed tomography (CE-CT) images for treatment response assessment in patients with Hodgkin lymphoma (HL), compared with F-18-fludeoxyglucose (FDG) positron emission tomography/CT. Methods: 3D TA of 48 lymph nodes in 29 patients was performed on venous-phase CE-CT images before and after chemotherapy. All lymph nodes showed pathologically elevated FDG uptake at baseline. A stepwise logistic regression with forward selection was performed to identify classic CT parameters and texture features (TF) that enable the separation of complete response (CR) and persistent disease. Results: The TF fraction of image in runs, calculated for the 45° direction, was able to correctly identify CR with an accuracy of 75%, a sensitivity of 79.3%, and a specificity of 68.4%. Classical CT features achieved an accuracy of 75%, a sensitivity of 86.2%, and a specificity of 57.9%, whereas the combination of TF and CT imaging achieved an accuracy of 83.3%, a sensitivity of 86.2%, and a specificity of 78.9%. Conclusions: 3D TA of CE-CT images is potentially useful to identify nodal residual disease in HL, with a performance comparable to that of classical CT parameters. Best results are achieved when TA and classical CT features are combined.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-D-303-03: Impact of Uncertainty in T1 Measurements On Quantification of Dynamic Contrast Enhanced MRI

Purpose: Quantification of dynamic contrast enhanced (DCE) MRI requires native longitudinal relaxation time (T1) measurement. This study aimed to assess uncertainty in T1 measurements using two different methods. Methods and Materials: Brain MRI scans were performed on a 3T scanner in 9 patients who had low grade/benign tumors and partial brain radiotherapy without chemotherapy at pre-RT, week-3 during RT (wk-3), end-RT, and 1, 6 and 18 months after RT. T1-weighted images were acquired using gradient echo sequences with 1) 2 different flip angles (50 and 150), and 2) 5 variable TRs (100–2000ms). After creating quantitative T1 maps, average T1 was calculated in regions of interest (ROI), which were distant from tumors and received a total of accumulated radiation doses < 5 Gy at wk-3. ROIs included left and right normal Putamen and Thalamus (gray matter: GM), and frontal and parietal white matter (WM). Since there were no significant or even a trend of T1 changes from pre-RT to wk-3 in these ROIs, a relative repeatability coefficient (RC) of T1 as a measure of uncertainty was estimated in each ROI using the data pre-RT and at wk-3. The individual T1 changes at later time points were evaluated compared to the estimated RCs. Results: The 2-flip angle method produced small RCs in GM (9.7–11.7%) but large RCs in WM (12.2–13.6%) compared to the saturation-recovery (SR) method (11.0–17.7% for GM and 7.5–11.2% for WM). More than 81% of individual T1 changes were within T1 uncertainty ranges defined by RCs. Conclusion: Our study suggests that the impact of T1 uncertainty on physiological parameters derived from DCE MRI is not negligible. A short scan with 2 flip angles is able to achieve repeatability of T1 estimates similar to a long scan with 5 different TRs, and is desirable to be integrated in the DCE protocol. Present study was supported by National Institute of Health (NIH) under grant numbers; UO1 CA183848 and RO1 NS064973.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-I-19: Optimization of Low Contrast Detectability Across Two CT Manufacturers

Purpose: Our goal was to evaluate low contrast detectability (LCD) for abdominal CT protocols across two CT scanner manufacturers, while producing a similar noise texture and CTDIvol for acquired images. Methods: A CIRS tissue equivalent LCD phantom containing three columns of 7 spherical targets, ranging from 10 mm to 2.4 mm, that are 5, 10, and 20 HU below the background matrix (HUBB) was scanned using two a GE HD750 64 slice scanner and a Siemens Somatom Definition AS 64 slice scanner. Protocols were designed to deliver a CTDIvol of 12.26 mGy and images were reconstructed with FBP, ASIR and Sapphire. Comparisons were made with those algorithms that had matching noise power spectrum peaks (NPS). NPS information was extracted from a previously published article that matched NPS peak frequencies across manufacturers by calculating the NPS from uniform phantom images reconstructed with several IR algorithms. Results: The minimum detectable lesion size in the 20 HUBB and 10 HUBB column was 6.3 mm, and 10 mm in the 5 HUBB column for the GE HD 750 scanner. The minimum detectable lesion size in the 20 HUBB column was 4.8 mm, in the 10 HUBB column, 9.5 mm, and the 5 HUBB column, 10 mm for the Siemens Somatom Definition AS. Conclusion: Reducing radiation dose while improving or maintaining LCD is possible with application of IR. However, there are several different IR algorithms, with each generating a different resolution and noise texture. In multi-manufacturer settings, matching only the CTDIvol between manufacturers may Result in a loss of clinically relevant information.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-F-207-14: Low Contrast Detectability (LCD) at Different Diagnostic Reference Levels for Adult Abdominal CT Procedures

Purpose Using diagnostic reference levels (DRL) to optimize CT protocols has potential to reduce radiation dose and meet regulatory requirements. However, DRL’s tend to be misconstrued as dose limits, are typically designed for specific patient populations, and are assumed to have acceptable image quality (AIQ) associated with them. To determine the image quality that is associated with established DRL’s for adult abdominal CT studies, a LCD phantom study was employed. Methods: A CT phantom (CIRS) containing three columns of 7 spherical targets, ranging from 10mm to 2.4 mm, that are 5, 10, and 20 HU below the background (HUBB) matrix was scanned with a GE HD750 64 slice scanner. The phantom was scanned at the NEXT 2006 25th CTDIvol of 12 mGy, the NCRP 172 achievable dose (AD) CTDIvol of 17 mGy and 75th CTDIvol of 25 mGy and at the ACR recommended CTDIvol of 25 mGy. It was also scanned at a CTDIvol 20% greater than the AD at 20 mGy and the ACR maximum threshold of 30 mGy. Results: At the NEXT 2006 25th percentile CTDIvol of 12 mGy, a 6.3 mm low contrast lesion was detectable in the 20 HUBB; 6.3 mm in the 10 HUBB and 10 mm in the 5 HUBB column. Increasing the CTDIvol to the NCRP 172 AD of 17 mGy, an additional 4.8 mm lesion was visualized in the 20 HUBB column. At 20 mGy, an additional 4.8 mm lesion was detectable in the 10 HUBB column. No further lesions were visible between 20 and 30 mGy. However, conspicuity of all lesions increased with each additional step up in CTDI. Conclusion: Optimizing radiation dose to achieve AIQ is a critical aspect of any dose optimization committee. Hence, judicious monitoring of radiation exposure to patients has to be balanced with diagnostic image quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarsely sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

Penalized maximum likelihood reconstruction for x-ray differential phase-contrast tomography

Purpose: The purpose of this work is to propose a cost function with regularization to iteratively reconstruct attenuation, phase, and scatter images simultaneously from differential phase contrast (DPC) acquisitions, without the need of phase retrieval, and examine its properties. Furthermore this reconstruction method is applied to an acquisition pattern that is suitable for a DPC tomographic system with continuously rotating gantry (sliding window acquisition), overcoming the severe smearing in noniterative reconstruction. Methods: We derive a penalized maximum likelihood reconstruction algorithm to directly reconstruct attenuation, phase, and scatter image from the measured detector values of a DPC acquisition. The proposed penalty comprises, for each of the three images, an independent smoothing prior. Image quality of the proposed reconstruction is compared to images generated with FBP and iterative reconstruction after phase retrieval. Furthermore, the influence between the priors is analyzed. Finally, the proposed reconstruction algorithm is applied to experimental sliding window data acquired at a synchrotron and results are compared to reconstructions based on phase retrieval. Results: The results show that the proposed algorithm significantly increases image quality in comparison to reconstructions based on phase retrieval. No significant mutual influence between the proposed independent priors could be observed. Further it could be illustrated that the iterative reconstruction of a sliding window acquisition results in images with substantially reduced smearing artifacts. Conclusions: Although the proposed cost function is inherently nonconvex, it can be used to reconstruct images with less aliasing artifacts and less streak artifacts than reconstruction methods based on phase retrieval. Furthermore, the proposed method can be used to reconstruct images of sliding window acquisitions with negligible smearing artifacts.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

SU-D-207A-02: Possible Characterization of the Brain Tumor Vascular Environment by a Novel Strategy of Quantitative Analysis in Dynamic Contrast Enhanced MR Imaging: A Combination of Both Patlak and Logan Analyses

Purpose: The majority of quantitative analyses involving dynamic contrast enhanced (DCE) MRI have been performed to obtain kinetic parameters such as Ktrans and ve. Such analyses are generally performed assuming a “reversible” tissue compartment, where the tracer is assumed to be rapidly equilibrated between the plasma and tissue compartments. However, some tumor vascular environments may be more suited for a “non-reversible” tissue compartment, where, as with FDG PET imaging, the tracer is continuously deposited into the tissue compartment (or the return back to the plasma compartment is very slow in the imaging time scale). Therefore, Patlak and Logan analyses, which represent tools for the “non-reversible” and “reversible” modeling, respectively, were performed to better characterize the brain tumor vascular environment. Methods: A voxel-by-voxel analysis was performed to generate both Patlak and Logan plots in two brain tumor patients, one with grade III astrocytoma and the other with grade IV astrocytoma or glioblastoma. The slopes of plots and the r-square were then obtained by linear fitting and compared for each voxel. Results: The 2-dimensional scatter plots of Logan (Y-axis) vs. Patlak slopes (X-axis) clearly showed increased Logan slopes for glioblastoma (Figure 3A). The scatter plots of goodness-of-fit (Figure 3B) also suggested glioblastoma, relative to grade III astrocytoma, might consist of more voxels that are kinetically Logan-like (i.e. rapidly equilibrated extravascular space and active vascular environment). Therefore, the enhanced Logan-like behavior (and the Logan slope) in glioblastoma may imply an increased fraction of active vascular environment, while the enhanced Patlak-like behavior implies the vascular environment permitting a relatively slower washout of the tracer. Conclusion: Although further verification is required, the combination of Patlak and Logan analyses in DCE MRI may be useful in characterizing the tumor vascular environment, and thus, may have implications in tumor grading and monitoring response to anti-vascular therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-D-207A-04: Use of Gradient Echo Plural Contrast Imaging (GEPCI) in MR-Guided Radiation Therapy: A Feasibility Study Targeting Brain Treatment

Purpose: To implement the Gradient Echo Plural Contrast Imaging(GEPCI) technique in MRI-simulation for radiation therapy and assess the feasibility of using GEPCI images with advanced inhomogeneity correction in MRI-guided radiotherapy for brain treatment. Methods: An optimized multigradient-echo GRE sequence (TR=50ms;TE1=4ms;delta-TE=4ms;flip angle=300,11 Echoes) was developed to generate both structural (T1w and T2*w) and functional MRIs (field and susceptibility maps) from a single acquisition. One healthy subject (Subject1) and one post-surgical brain cancer patient (Subject2) were scanned on a Philips Ingenia 1.5T MRI used for radiation therapy simulation. Another healthy subject (Subject3) was scanned on a 0.35T MRI-guided radiotherapy (MR-IGRT) system (ViewRay). A voxel spread function (VSF) was used to correct the B0 inhomogeneities caused by surgical cavities and edema for Subject2. GEPCI images and standard radiotherapy planning MRIs for this patient were compared focusing the delineation of radiotherapy target region. Results: GEPCI brain images were successfully derived from all three subjects with scan times of <7 minutes. The images derived for Subjects1&2 demonstrated that GEPCI can be applied and combined into radiotherapy MRI simulation. Despite low field, T1-weighted and R2* images were successfully reconstructed for Subject3 and were satisfactory for contour and target delineation. The R2* distribution of grey matter (center=12,FWHM=4.5) and white matter (center=14.6, FWHM=2) demonstrated the feasibility for tissue segmentation and quantification. The voxel spread function(VSF) corrected surgical site related inhomogeneities for Subject2. R2* and quantitative susceptibility map(QSM) images for Subject2 can be used to quantitatively assess the brain structure response to radiation over the treatment course. Conclusion: We implemented the GEPCI technique in MRI-simulation and in MR-IGRT system for radiation therapy. The images demonstrated that it is feasible to adopt this technique in radiotherapy for structural delineation. The preliminary data also enable the opportunity for quantitative assessment of radiation response of the target region and normal tissue.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-FG-CAMPUS-IeP1-02: Dose Reduction in Contrast-Enhanced Digital Mammography Using a Photon-Counting Detector

Purpose: Photon-counting detectors (PCDs) allow multi-energy X-ray imaging without additional exposures and spectral overlap. This capability results in the improvement of accuracy of material decomposition for dual-energy X-ray imaging and the reduction of radiation dose. In this study, the PCD-based contrast-enhanced dual-energy mammography (CEDM) was compared with the conventional CDEM in terms of radiation dose, image quality and accuracy of material decomposition. Methods: A dual-energy model was designed by using Beer-Lambert’s law and rational inverse fitting function for decomposing materials from a polychromatic X-ray source. A cadmium zinc telluride (CZT)-based PCD, which has five energy thresholds, and iodine solutions included in a 3D half-cylindrical phantom, which composed of 50% glandular and 50% adipose tissues, were simulated by using a Monte Carlo simulation tool. The low- and high-energy images were obtained in accordance with the clinical exposure conditions for the conventional CDEM. Energy bins of 20–33 and 34–50 keV were defined from X-ray energy spectra simulated at 50 kVp with different dose levels for implementing the PCD-based CDEM. The dual-energy mammographic techniques were compared by means of absorbed dose, noise property and normalized root-mean-square error (NRMSE). Results: Comparing to the conventional CEDM, the iodine solutions were clearly decomposed for the PCD-based CEDM. Although the radiation dose for the PCD-based CDEM was lower than that for the conventional CEDM, the PCD-based CDEM improved the noise property and accuracy of decomposition images. Conclusion: This study demonstrates that the PCD-based CDEM allows the quantitative material decomposition, and reduces radiation dose in comparison with the conventional CDEM. Therefore, the PCD-based CDEM is able to provide useful information for detecting breast tumor and enhancing diagnostic accuracy in mammography.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-H-BRA-09: Relationship Between B0 and the Contrast-To-Noise Ratio (CNR) of Tumour to Background for MRI/Radiotherapy Hybrids

Purpose: To investigate the relationship in MRI between B{sub 0} and the contrast-to-noise ratio (CNR) of various tumour/normal tissue pairs. This study is motivated by the current interest in MRI/radiotherapy hybrids, for which multiple magnetic field strengths have been proposed. CNR is the single most important parameter governing the ability of a system to identify a tumour in real time for treatment guidance. The MRI community has long since recognized that the SNR of a well-designed MR system is roughly proportional to B{sub 0}, the polarizing magnetic field. However, the CNR between two tissues is much more complicated - dependent not only on this signal behavior, but also on the different relaxation properties of the tissues. Methods: Experimentally-based models of B{sub 0}-dependant relaxation for various tumour and normal tissues from the literature were used in conjunction with signal equations for MR sequences suitable for rapid realtime imaging to develop field-dependent predictions for CNR. These CNR models were developed for liver, lung, breast, glioma, and kidney tumours for spoiled-gradient echo (SGE) and balanced steady-state free precession (bSSFP) sequences. Results: In all cases there was an improved CNR at lower fields compared to linear dependency. Further, in some tumour sites, the CNR at lower fields was found to be comparable to, or sometimes higher than those at higher fields (i.e. bSSFP CNR for glioma, kidney and liver tumours). Conclusion: Due to the variation of tissue relaxation parameters with field, lower B{sub 0} fields have been shown to perform as well or better (in terms of CNR) than higher fields for some tumour sites. In other sites this effect was less pronounced. It is the complex relationship between CNR and B{sub 0} that leads to greater CNR at 0.5 T for certain tumour types studied here for fast imaging. B. Gino Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-DE-BRA-08: A Linear Accelerator Target Allowing Rapid Switching Between Treatment and High-Contrast Imaging Modes

Purpose: During radiotherapy treatment, lung tumors can display substantial respiratory motion. This motion usually necessitates enlarged treatment margins to provide full tumour coverage. Unfortunately, these margins limit the dose that can be prescribed for tumour control and cause complications to normal tissue. Options for real-time methods of direct detection of tumour position, and particularly those that obviate the need for inserted fiducial markers, are limited. We propose a method of tumor tracking without implanted fiducial markers using a novel fast switching-target that toggles between a FFF copper/tungsten therapy mode and a FFF low-Z target mode for imaging. In this work we demonstrate proof-of-concept of this new technology. Methods: The prototype includes two targets: i) a FFF copper/tungsten target equivalent to that in the Varian 2100 EX 6 MV, and ii) a low-Z (carbon) target with a thickness of 110% of continuous slowing down approximation range (CSDA) at 7 MeV. The two targets can be exchanged with a custom made linear slide and motor-driven actuator. The usefulness of the switching-target concept is demonstrated through experimental BEV Planar images acquired with continual treatment and imaging at a user-defined period. Results: The prototype switching-target demonstrates that two recent advances in linac technology (FFF target for therapy and low-Z target) can be combined with synergy. The switching-target approach offers the capacity for rapid switching between treatment and high-contrast imaging modes, allowing intrafractional tracking, as demonstrated in this work with dynamic breathing phantom. By using a single beam-line, the design is streamlined and may obviate the need for an auxiliary imaging system (e.g., kV OBI.) Conclusion: This switching-target approach is a feasible combination of two current advances in linac technology (FFF target for therapy and a FFF low-Z target) allowing new options in on-line IGRT.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass–based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

09 BIOMASS FUELS↗
DOE OSTI2019

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages. IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Theoretical analysis of the possibilities of Zernike phase contrast method in hard X rays for nondestructive imaging of micropipes in a silicon carbide single crystal

The possibilities of using Zernike phase contrast in hard X rays for imaging micropipes in a silicon carbide single crystal are analyzed by numerical simulation. Calculations are performed for the experimental conditions characteristic of third-generation synchrotron radiation sources. A scheme is considered where the focusing element is a parabolic refracting lens and the phase-shifting element is mounted at the point of the source image. It is shown that micropipe cross sections by a beam with a longitudinal diameter reaching 10 {mu}m are imaged by the lens without distortions. At the same time, the lens makes it possible to magnify the image several tens of times. The cross sections that are significantly elongated along the beam are imaged with artifacts; however, their structure can also be recovered. It is shown that polychromaticity of radiation does not significantly affect the object imaging.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Two strongly contrasting Λ-systems in the D{sub 1} line of {sup 87}Rb in a transverse magnetic field

Four different types of spectroscopic cells that cover all possible existing versions of sealed-off cells (containing alkali atomic vapor) characterized by drastically different relaxation rates γ{sub rel} are used to study the electromagnetically induced transparency spectra of two Λ-systems in the D{sub 1} line of {sup 87}Rb in the presence of transverse magnetic field. Two cw narrowband diode-lasers are used to form the coupling laser radiation (with a fixed frequency) and the probe radiation with a tunable frequency. Two strongly contrasting Λ-systems are found: the first shows resonances that are transformed from dark resonances to bright resonances in all cases apart from nanocells, whereas the second shows four dark resonances in all four different types of cell. The theoretical simulations are in good agreement with the experimental results.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00 , derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Algorithms for Forward and Inverse Problem Solutions in Phase Contrast Tomography

PhaseTorch is a python package that implements algorithms for forward and inverse problem solutions in X-ray phase contrast tomography (XPCT). XPCT is useful to reconstruct the 3D distribution of the refractive index decrement and absorption index of an imaged object. PhaseTorch implements algorithms for simulation, reconstruction, and analysis of XPCT data. PhaseTorch provides algorithms for simulation of XPCT data of an object with known refractive and absorption indices. It contains algorithms for reconstructing the projections of the absorption index and refractive index decrement.

Sridhar, Venkatesh↗