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Integrative Modeling and Analysis of Fungal Central Carbon Metabolism

Over a thousand fungal genomes have been sequenced, yet manually curated genome-scale metabolic models (GEMs) are available for only a limited number of species. Moreover, these models have often been developed independently, leading to inconsistencies in namespaces, compartment definitions, and pathway representations that hinder comparative analysis, the systematic reuse of prior curation efforts, and the integration of consolidated metabolic knowledge. Here, we present the Consolidated Fungal Core Metabolism Model (CFCMM), constructed by integrating thirteen published fungal models spanning Ascomycota, Mucoromycota, and both Crabtree-positive and Crabtree-negative yeasts. We harmonized metabolites and reactions into a non-redundant shared ModelSEED ontological space, standardized compartmentalization, and refined gene–protein–reaction (GPR) rules. Using pathway-level visualization and systematic gap detection, we further improved the integrated network through literature-guided curation to correct stoichiometry, stereospecificity, and pathway architecture. Orthologous protein family reconstruction and functional annotation workflows were used to validate and inform GPR associations, with particular emphasis on ambiguous enzyme superfamilies and membrane-associated components. Using the resulting CFCMM, we built high-quality central carbon core models for each fungus and performed flux balance analysis to quantify ATP-yield variation under aerobic and anaerobic conditions, explicitly evaluating scenarios driven by differences in electron transport chain (ETC) composition. Simulations reproduced the expected fermentative yield of approximately 2 mmol ATP per mmol glucose under anaerobic conditions and separated the thirteen fungi into two bioenergetic groups under aerobic respiration based on Complex I status, with predicted yields of approximately 30 versus 22 mmol ATP per mmol glucose. Forcing flux through the alternative oxidase bypass further reduced ATP yields to approximately 12 and 4 mmol ATP per mmol glucose in Complex I-containing and Complex I-lacking fungi, respectively. Collectively, this work provides a manually curated, ModelSEED-consistent, and extensible fungal core metabolic template, deployed in DOE KBase as a resource for automated reconstruction of central carbon core models from any sequenced fungal genome. In addition, the CFCMM provides modular components for developing GEMs with more accurate energy predictions and enables robust comparative analyses of fungal bioenergetics and core metabolic diversity

59 BASIC BIOLOGICAL SCIENCES↗

TU-F-BRF-04: Registration of 3D Transesophageal Echocardiography and X-Ray Fluoroscopy Using An Inverse Geometry X-Ray System

Purpose: To develop a method for the fusion of 3D echocardiography and Scanning-Beam Digital X-ray (SBDX) fluoroscopy to assist with catheter device and soft tissue visualization during interventional procedures. Methods: SBDX is a technology for low-dose inverse geometry x-ray fluoroscopy that performs digital tomosynthesis at multiple planes in real time. In this study, transesophageal echocardiography (TEE) images were fused with SBDX images by estimating the 3D position and orientation (the “pose”) of the TEE probe within the x-ray coordinate system and then spatially transforming the TEE image data to match this pose. An initial pose estimate was obtained through tomosynthesis-based 3D localization of points along the probe perimeter. Position and angle estimates were then iteratively refined by comparing simulated projections of a 3D probe model against SBDX x-ray images. Algorithm performance was quantified by imaging a TEE probe in different known orientations and locations within the x-ray field (0-30 degree tilt angle, up to 50 mm translation). Fused 3D TEE/SBDX imaging was demonstrated by imaging a tissue-mimicking polyvinyl alcohol cylindrical cavity as a catheter was navigated along the cavity axis. Results: Detected changes in probe tilt angle agreed with the known changes to within 1.2 degrees. For a 50 mm translation along the source-detector axis, the detected translation was 50.3 mm. Errors for in-plane translations ranged from 0.1 to 0.9 mm. In a fused 3D TEE/SBDX display, the catheter device was well visualized and coincident with the device shadow in the TEE images. The TEE images portrayed phantom boundaries that were not evident under x-ray. Conclusion: Registration of soft tissue anatomy derived from TEE imaging and device imaging from SBDX x-ray fluoroscopy is feasible. The simultaneous 3D visualization of these two modalities may be useful in interventional procedures involving the navigation of devices to soft tissue anatomy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Large-eddy simulation of helical- and straight-bladed vertical-axis wind turbines in boundary layer turbulence

Here, turbulent wake flows behind helical- and straight-bladed vertical axis wind turbines (VAWTs) in boundary layer turbulence are numerically studied using the large-eddy simulation (LES) method combined with the actuator line model. Based on the LES data, systematic statistical analyses are performed to explore the effects of blade geometry on the characteristics of the turbine wake. The time-averaged velocity fields show that the helical-bladed VAWT generates a mean vertical velocity along the center of the turbine wake, which causes a vertical inclination of the turbine wake and alters the vertical gradient of the mean streamwise velocity. Consequently, the intensities of the turbulent fluctuations and Reynolds shear stresses are also affected by the helical-shaped blades when compared with those in the straight-bladed VAWT case. The LES results also show that reversing the twist direction of the helical-bladed VAWT causes the spatial patterns of the turbulent wake flow statistics to be reversed in the vertical direction. Moreover, the mass and kinetic energy transports in the turbine wakes are directly visualized using the transport tube method, and the comparison between the helical- and straight-bladed VAWT cases show significant differences in the downstream evolution of the transport tubes.

17 WIND ENERGY↗

IRAM 30 m large scale survey of {sup 12}CO(2-1) and {sup 13}CO(2-1) emission in the Orion molecular cloud

Using the IRAM 30 m telescope, we have surveyed a 1 × 0.°8 part of the Orion molecular cloud in the {sup 12}CO and {sup 13}CO (2-1) lines with a maximal spatial resolution of ∼11'' and spectral resolution of ∼0.4 km s{sup –1}. The cloud appears filamentary, clumpy, and with a complex kinematical structure. We derive an estimated mass of the cloud of 7700 M {sub ☉} (half of which is found in regions with visual extinctions A{sub V} below ∼10) and a dynamical age for the nebula of the order of 0.2 Myr. The energy balance suggests that magnetic fields play an important role in supporting the cloud, at large and small scales. According to our analysis, the turbulent kinetic energy in the molecular gas due to outflows is comparable to turbulent kinetic energy resulting from the interaction of the cloud with the H II region. This latter feedback appears negative, i.e., the triggering of star formation by the H II region is inefficient in Orion. The reduced data as well as additional products such as the column density map are made available online (http://userpages.irap.omp.eu/∼oberne/Olivier{sub B}erne/Data).

79 ASTRONOMY AND ASTROPHYSICS↗

Potential Demand Reduction from Buildings in a Simulated Utility

The availability of large-area sensing, scalable algorithms, and high-performance computing has enabled the possibility of urban-scale building energy modeling using new methods not limited to the scalability of manual building energy model creation or retrieval of county-by-county tax assessor’s data. Automatic Building detection and Energy Model creation (AutoBEM) has created 178,368 building energy models for the Electric Power Board (EPB) of Chattanooga, TN, and compared simulation performance to 15-minute data from each building. These models leverage several data sources (e.g. imagery, GIS, utility), software tools to extract building properties (e.g. footprint, height, façade type, window-to-wall ratio, occupancy, building type), simulate at scale on two of the world’s #1 fastest supercomputers, and provide web-based visual analytics.Grid-interactive efficient buildings offer the potential to reduce utility and rate-payer energy costs during each calendar month’s hour of critical generation – when the least efficient, most costly, and often dirtiest generation assets must be brought online. In this paper, EnergyPlus is used to simulate over 150,000 buildings to assess the technical potential of utility-controlled smart thermostats. This is analyzed under a couple scenarios leveraging buildings as thermal batteries via pre-conditioning to coast through peak hours. Results are provided in box and whisker plots assessing the distribution of peak demand reduction at the utility-scale along with breakouts of energy and demand savings by building type and vintage.

Bass, Brett↗

Assessing Cognitive Impacts of Errors from Machine Learning and Deep Learning Models: Final Report

Due to their recent increases in performance, machine learning and deep learning models are being increasingly adopted across many domains for visual processing tasks. One such domain is international nuclear safeguards, which seeks to verify the peaceful use of commercial nuclear energy across the globe. Despite recent impressive performance results from machine learning and deep learning algorithms, there is always at least some small level of error. Given the significant consequences of international nuclear safeguards conclusions, we sought to characterize how incorrect responses from a machine or deep learning-assisted visual search task would cognitively impact users. We found that not only do some types of model errors have larger negative impacts on human performance than other errors, the scale of those impacts change depending on the accuracy of the model with which they are presented and they persist in scenarios of evenly distributed errors and single-error presentations. Further, we found that experiments conducted using a common visual search dataset from the psychology community has similar implications to a safeguards- relevant dataset of images containing hyperboloid cooling towers when the cooling tower images are presented to expert participants. While novice performance was considerably different (and worse) on the cooling tower task, we saw increased novice reliance on the most challenging cooling tower images compared to experts. These findings are relevant not just to the cognitive science community, but also for developers of machine and deep learning that will be implemented in multiple domains. For safeguards, this research provides key insights into how machine and deep learning projects should be implemented considering their special requirements that information not be missed.

97 MATHEMATICS AND COMPUTING↗

DFTT report for Signal Analysis (2023)

The Detection Framework Testbed and Toolkit (DFTT) is a database and associated java programs intended to facilitate the development and testing of algorithms for operating suites of correlation and subspace detectors. This framework is a generalization of the system described in Harris and Dodge (2011) and Dodge and Harris (2016). DFTT allows retrospective processing of sequences of data using various system configurations. Results are saved in a database, so it is easy to compare the results obtained using different configurations of the system. The principal software components of DFTT are the ConfigCreator, the framework_runner and the Builder program. ConfigCreator assembles the files necessary to define a particular configuration used for processing. The framework_runner operates suites of detectors and saves the results in an Oracle™ database. Builder allows visual examination of templates and detected signals and allows editing and creation of detectors. In addition, there are tools for importing continuous data into the database. DFTT is licensed under the MIT license and has LLNL release number LLNL-CODE-801881. In the current fiscal year DFTT has been used in two different projects. The first (NTL-funded) project investigates the feasibility of screening nuisance detections using correlation detectors. The second (GNEM-funded) project seeks to extend the results of Harris and Dodge (2021) to 3- D sources and multiple stations. Each of these efforts required that additional functionality be added to DFTT. In this report I will summarize the enhancements to DFTT in the context of the relevant research effort.

58 GEOSCIENCES↗

WE-FG-207A-00: Advances in Dedicated Breast CT

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

WE-FG-207A-01: Introduction to Dedicated Breast CT - Early Studies

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

WE-FG-207A-02: Why We Need Breast CT? - Clinical Perspective

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

WE-FG-207A-03: Low-Dose Cone-Beam Breast CT: Physics and Technology Development

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

WE-FG-207A-04: Performance Characteristics of Photon-Counting Breast CT

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

WE-FG-207A-05: Dedicated Breast CT as a Diagnostic Imaging Tool: Physics and Clinical Feasibility

Mammography-based screening has been a valuable imaging tool for the early detection of non-palpable lesions and has contributed to significant reduction in breast cancer associated mortality. However, the breast imaging community recognizes that mammography is not ideal, and in particular is inferior for women with dense breasts. Also, the 2-D projection of a 3-D organ results in tissue superposition contributing to false-positives. The sensitivity of mammography is breast-density dependent. Its sensitivity, especially in dense breasts, is low due to overlapping tissue and the fact that normal breast tissue, benign lesions and breast cancers all have similar “densities”, making lesion detection more difficult. We ideally need 3-D imaging for imaging the 3-D breast. MRI is 3-D, whole breast ultrasound is 3-D, digital breast tomosynthesis is called 3-D but is really “pseudo 3-D” due to poor resolution along the depth-direction. Also, and importantly, we need to be able to administer intravenous contrast agents for optimal imaging, similar to other organ systems in the body. Dedicated breast CT allows for 3-D imaging of the uncompressed breast. In current designs, the patient is positioned prone on the table and the breast is pendant through an aperture and the scan takes approximately 10 seconds [O’Connell et al., AJR 195: 496–509, 2010]. Almost on the heels of the invention of CT itself, work began on the development of dedicated breast CT. These early breast CT systems were used in clinical trials and the results from comparative performance evaluation of breast CT and mammography for 1625 subjects were reported in 1980 [Chang et al., Cancer 46: 939–46, 1980]. However, the technological limitations at that time stymied clinical translation for decades. Subsequent to the landmark article in 2001 [Boone et al., Radiology 221: 657–67, 2001] that demonstrated the potential feasibility in terms of radiation dose, multiple research groups are actively investigating dedicated breast CT. The development of large-area flat-panel detectors with field-of-view sufficient to image the entire breast in each projection enabled development of flat-panel cone-beam breast CT. More recently, the availability of complimentary metal-oxide semiconductor (CMOS) detectors with lower system noise and finer pixel pitch, combined with the development of x-ray tubes with focal spot dimensions similar to mammography systems, has shown improved spatial resolution and could improve visualization of microcalcifications. These technological developments promise clinical translation of low-dose cone-beam breast CT. Dedicated photon-counting breast CT (pcBCT) systems represent a novel detector design, which provide high spatial resolution (∼ 100µm) and low mean glandular dose (MGD). The CdTe-based direct conversion detector technology was previously evaluated and confirmed by simulations and basic experiments on laboratory setups [Kalender et al., Eur Radiol 22: 1–8, 2012]. Measurements of dose, technical image quality parameters, and surgical specimens on a pcBCT scanner have been completed. Comparative evaluation of surgical specimens showed that pcBCT outperformed mammography and digital breast tomosynthesis with respect to 3D spatial resolution, detectability of calcifications, and soft tissue delineation. Major barriers to widespread clinical use of BCT relate to radiation dose, imaging of microcalcifications, and adequate coverage of breast tissue near the chest wall. Adequate chest wall coverage is also technically challenging but recent progress in x-ray tube, detector and table design now enables full breast coverage in the majority of patients. At this time, BCT has been deemed to be suitable for diagnostic imaging but not yet for screening. The mean glandular dose (MGD) from BCT has been reported to be between 5.7 to 27.8 mGy, and this range is comparable to, and within the range of, the MGD of 2.6 to 31.6 mGy in diagnostic mammography. In diagnostic studies, the median MGD from BCT and mammography were 12.6 and 11.1 mGy, respectively [Vedantham et al., Phys Med Biol. 58: 7921–36, 2013]. Moreover, in diagnostic imaging of the breast the location of the lesion is known and therefore characterization and not detection is by far the primary consideration. The role of bCT is particularly compelling for diagnostic imaging of the breast because it may replace in part the multiple mammographic views of the breast under vigorous compression. Other non-screening potential applications of bCT include the assessment of response to neoadjuvant therapy [Vedantham et al., J Clin Imaging Sci 4, 64, 2014] and pre-surgical evaluation. Learning Objectives: To understand the metrics used to evaluate screening and diagnostic imaging To understand the benefits and limitations of current clinical modalities To understand how breast CT can improve over current clinical modalities To note the early attempts to translate breast CT to the clinic in 1970s-1990s To understand the recent developments in low-dose cone-beam breast CT To understand the recent developments in photon-counting breast CT To understand the radiation dose, clinical translation, and recent developments in diagnostic imaging with breast CT Supported in part by NIH grants R21 CA134128, R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH or the NCI.; S. Vedantham, Funding sources: Supported in part by NIH/NCI grants R01 CA128906 and R01 CA195512. The contents are solely the responsibility of the authors and do not reflect the official views of the NIH/NCI. Disclosures: Research collaboration with Koning Corporation, West Henrietta, NY. Conflicts of Interest: J. Boone, This research was supported in part by NIH grant R01CA181081; W. Kalender, WK is founder and CEO of CT Imaging GmbH Erlangen, Germany.; A. Karellas, NIH R21 CA134128, R01 CA128906, and R01 CA195512 and Research collaboration with Koning Corporation.

60 APPLIED LIFE SCIENCES↗

Utilizing a Novel Acoustic Backscatter Array to Characterize Waste Consolidation and Settling in a Horizontal Flow Clarifier - 16051

As part of a collaboration between the University of Leeds, Sellafield Ltd and MMI Engineering Ltd, bespoke acoustic instrumentation and numerical simulation methods have been established to optimize nuclear legacy waste transfers. Specifically, a new ultrasonic measurement system has been developed, allowing suspended particle concentration and consolidation to be measured remotely. This technology has been combined with computational fluid dynamics (CFD) modelling of settling particulate systems, permitting full characterization, simulation and prediction of sludge separation processes. Presented here are experimental and numerical results on the transport and settling behavior of non-active nuclear-analogue suspensions in two flow geometries: gravitational settling of glass dispersions in a 250-liter column; and transport and sedimentation of flocculated calcite in a close-to-full-scale clarifier (9 m{sup 3} total volume and 4.8 m{sup 2} length). In addition, details of the design, construction and calibration of a custom-built Ultrasonic Array Research Platform (UARP) are described. Settling column results suggested that particle concentration changes could be simulated with good accuracy by a CFD model (developed using the open source OpenFOAM framework) when compared to measured samples. Large-scale clarifier trials were used to assess the effectiveness of the UARP controller with an attached in situ acoustic backscatter array (ABA). The ABA consisted of 8 transducers angled down at 20 deg. to the vertical, pulsing at 2-2.5 MHz in cycles (covering 1.8 m total depth). In comparison to a range of sampled concentrations across the length of the clarifier, results confirmed that the UARP-ABA system was highly successful at characterizing these complex flows over several hours of operation, allowing visualization of depth-wise bulk density changes and bed build-up over time. Collectively, this work highlights the capability of these tools to monitor and optimize a number of current waste transfer operations at Sellafield, with further potential applications for solid-liquid separations across waste, water treatment and minerals engineering industries. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state

Neutron crystallography provides direct visual evidence of the atomic positions of deuterium-exchanged H atoms, enabling the accurate determination of the protonation/deuteration state of hydrated biomolecules. Comparison of two neutron structures of hemoglobins, human deoxyhemoglobin (T state) and equine cyanomethemoglobin (R state), offers a direct observation of histidine residues that are likely to contribute to the Bohr effect. Previous studies have shown that the T-state N-terminal and C-terminal salt bridges appear to have a partial instead of a primary overall contribution. Four conserved histidine residues [αHis72(EF1), αHis103(G10), αHis89(FG1), αHis112(G19) and βHis97(FG4)] can become protonated/deuterated from the R to the T state, while two histidine residues [αHis20(B1) and βHis117(G19)] can lose a proton/deuteron. αHis103(G10), located in the α 1 :β 1 dimer interface, appears to be a Bohr group that undergoes structural changes: in the R state it is singly protonated/deuterated and hydrogen-bonded through a water network to βAsn108(G10) and in the T state it is doubly protonated/deuterated with the network uncoupled. The very long-term H/D exchange of the amide protons identifies regions that are accessible to exchange as well as regions that are impermeable to exchange. The liganded relaxed state (R state) has comparable levels of exchange (17.1% non-exchanged) compared with the deoxy tense state (T state; 11.8% non-exchanged). Interestingly, the regions of non-exchanged protons shift from the tetramer interfaces in the T-state interface (α 1 :β 2 and α 2 :β 1 ) to the cores of the individual monomers and to the dimer interfaces (α 1 :β 1 and α 2 :β 2 ) in the R state. The comparison of regions of stability in the two states allows a visualization of the conservation of fold energy necessary for ligand binding and release.

59 BASIC BIOLOGICAL SCIENCES↗

Diabatic visualization shows effects of micro-fins on evaporation of R410A: Smooth, axial micro-fin, and helical micro-fin tubes

A novel approach to visualize the flow boiling inside a clear micro-fin tube under diabatic conditions is presented. Transparent smooth, axial micro-fin, and helical micro-fin tubes are made by 3D printing. The 3D printed tube is placed inside a glass tube and heated by the transparent secondary fluid flowing between the two tubes for providing the evaporation conditions and transparency. R410A flow boiling and the flow patterns in the three geometries captured with a high speed camera are compared. The experimental results show that micro-fin geometry influences flow behavior. Bubbles are mainly generated in the groove region due to a higher superheat than the fin region. Some of the liquid refrigerant is trapped in the grooves of the upper part of the micro-fin tube when the slug flow is present, and bubbles are generated in this thin liquid layer. In addition, the bubbles in the helical micro-fin tube are easier to merge because of the obstacle of the fin geometry for the bubble flowing path. As the two bubble merge, the conversion of surface free energy causes the bubble to travel with a higher velocity.

3D printed↗

Modeling DNP3 Traffic Characteristics of Field Devices in SCADA Systems of the Smart Grid

In the generation, transmission, and distribution sectors of the smart grid, intelligence of field devices is realized by programmable logic controllers (PLCs). Many smart-grid subsystems are essentially cyber-physical energy systems (CPES): For instance, the power system process (i.e., the physical part) within a substation is monitored and controlled by a SCADA network with hosts running miscellaneous applications (i.e., the cyber part). To study the interactions between the cyber and physical components of a CPES, several co-simulation platforms have been proposed. However, the network simulators/emulators of these platforms do not include a detailed traffic model that takes into account the impacts of the execution model of PLCs on traffic characteristics. As a result, network traces generated by co-simulation only reveal the impacts of the physical process on the contents of the traffic generated by SCADA hosts, whereas the distinction between PLCs and computing nodes (e.g., a hardened computer running a process visualization application) has been overlooked. To generate realistic network traces using co-simulation for the design and evaluation of applications relying on accurate traffic profiles, it is necessary to establish a traffic model for PLCs. In this work, we propose a parameterized model for PLCs that can be incorporated into existing co-simulation platforms. We focus on the DNP3 subsystem of slave PLCs, which automates the processing of packets from the DNP3 master. To validate our approach, we extract model parameters from both the configuration and network traces of real PLCs. Simulated network traces are generated and compared against those from PLCs. Our evaluation shows that our proposed model captures the essential traffic characteristics of DNP3 slave PLCs, which can be used to extend existing co-simulation platforms and gain further insights into the behaviors of CPES.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

A new model to study cell-to-cell transfer of αSynuclein in vivo

Highlights: • Parkinson's disease involved the loss of dopaminergic neurons associated with the accumulation of misfolded alpha-synuclein. • The neurodegeneration in Parkinson's disease spread through the brain by the transfer of alpha-synuclein from cell to cell. • The mechanisms involved alpha-synuclein secretion, uptake and spreading are not well understood. • In this study we developed a new model to monitor cell-to-cell transfer of alpha-Synuclein in vivo. Parkinson's disease (PD) compromises motor control due to the loss of dopaminergic neurons in the substantia nigra pars compacta. At the histopathological level, PD is characterized by the accumulation of Lewy bodies, large protein inclusions containing aggregated αSynuclein (αSyn). The progression of PD involves the spreading of αSyn misfolding through the brain mediated by a prion-like mechanism, where the protein is transferred between cells. Here we report that αSyn internalization is a dynamic process, where the protein transits through different sub-cellular compartments. Importantly, cells incorporating αSyn develop larger protein-like inclusions when compared to αSyn producing cells. We developed a new tool to monitor cell-to-cell transfer of αSyn in vivo using an adeno-associated viral (AAV) vector expressing αSyn fused to a red fluorescent protein in addition to soluble EGFP to label donor cells. Intra-nigral delivery of this reporter AAV construct allowed the visualization of αSyn incorporation into surrounding neurons. This work provides a new tool to study αSyn cell-to-cell transfer in vivo and may open new opportunities to study PD pathogenesis.

60 APPLIED LIFE SCIENCES↗