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DOE OSTI2016

Poster - 32: Atlas Selection for Automated Segmentation of Pelvic CT for Prostate Radiotherapy

Atlas based-segmentation has recently been evaluated for use in prostate radiotherapy. In a typical approach, the essential step is the selection of an atlas from a database that the best matches of the target image. This work proposes an atlas selection strategy and evaluate it impacts on final segmentation accuracy. Several anatomical parameters were measured to indicate the overall prostate and body shape, all of these measurements obtained on CT images. A brute force procedure was first performed for a training dataset of 20 patients using image registration to pair subject with similar contours; each subject was served as a target image to which all reaming 19 images were affinity registered. The overlap between the prostate and femoral heads was quantified for each pair using the Dice Similarity Coefficient (DSC). Finally, an atlas selection procedure was designed; relying on the computation of a similarity score defined as a weighted sum of differences between the target and atlas subject anatomical measurement. The algorithm ability to predict the most similar atlas was excellent, achieving mean DSCs of 0.78 ± 0.07 and 0.90 ± 0.02 for the CTV and either femoral head. The proposed atlas selection yielded 0.72 ± 0.11 and 0.87 ± 0.03 for CTV and either femoral head. The DSC obtained with the proposed selection method were slightly lower than the maximum established using brute force, but this does not include potential improvements expected with deformable registration. The proposed atlas selection method provides reasonable segmentation accuracy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Status of the Atlas of Neutron Resonances [Slides]

The Atlas of Neutron Resonances is the most comprehensive compilation of neutron resonances, thermal cross sections, resonance integrals and Maxwellian averaged cross sections generally available. For decades, the Atlas was carefully curated and maintained by Dr. Said Mughabghab who sadly passed on during the summer of 2018 after publishing the 2018 edition of the Atlas . We are continuing the development of this important compendium. To a large extent, the Atlas book is generated from a series of text files given in a single purpose domain-specific format. Therefore, we developed a software API and began the systematic assessment of the Atlas files. With this work past, we are now focusing on new efforts to expand the quality and scope of the Atlas . Current and recently completed projects include a cross comparison of the Atlas bibliography with Nuclear Science References and the EXFOR data library, a better determination of average resonance parameters, and using machine learning to assess the correctness of the spin group assignments of resonances tabulated in the Atlas .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1991

Planetary atlases

Two kinds of planetary map atlases are in production. Atlases of the first kind contain reduced-scale versions of maps in hard-bound books with dimensions of 11 x 14 inches. These new atlases are intended to: (1) provide concise but comprehensive references to the geography of the planets needed by planetary scientists and others; and (2) allow inexpensive access to the planetary map dataset without requiring acquisition and examination of tens or hundreds of full-size map sheets. Two such atlases have been published and a third is in press. Work was begun of an Atlas of the Satellite of the Outer Planets. The second kind of atlas is a popular or semi-technical version designed for commercial publication and distribution. The first edition, The Atlas of the Solar System, is nearly ready for publication. New funding and contracting constraints now make it unlikely that the atlas can be published in the format originally planned. Currently, the possibility of publishing the maps through the U.S. Geological Survey as a series of folios in the I-map series is being explored. The maps are global views of each solid-surface body of the Solar System. Each map shows airbrushed relief, albedo, and, where available, topography. A set of simplified geologic maps is also included. All of the maps are on equal-area projections. Scales are 1:40,000,000 for the Earth and Venus; 1:2,000,000 for the Saturnian satellites Mimas and Enceladus and the Uranian satellite Miranda; 1:100,000 for the Martian satellites, Phobos and Deimos; and 1:10,000,000 for all other bodies.

Batson, R. M.↗

NASA NTRS2007

A Photographic Atlas of Rock Breakdown Features in Geomorphic Environments

A primary goal of geomorphological enquiry is to make genetic associations between process and form. In rock breakdown studies, the links between process, inheritance and lithology are not well constrained. In particular, there is a need to establish an understanding of feature persistence. That is, to determine the extent to which in situ rock breakdown (e.g., aeolian abrasion or salt weathering) masks signatures of earlier geomorphic transport processes (e.g., fluvial transport or crater ejecta). Equally important is the extent to which breakdown during geomorphic transport masks the imprint of past weathering. The use of rock features in this way raises the important question: Can features on the surface of a rock reliably indicate its geomorphic history? This has not been determined for rock surfaces on Earth or other planets. A first step towards constraining the links between process, inheritance, and morphology is to identify pristine features produced by different process regimes. The purpose of this atlas is to provide a comprehensive image collection of breakdown features commonly observed on boulders in different geomorphic environments. The atlas is intended as a tool for planetary geoscientists and their students to assist in identifying features found on rocks on planetary surfaces. In compiling this atlas, we have attempted to include features that have formed 'recently' and where the potential for modification by another geomorphic process is low. However, we acknowledge that this is, in fact, difficult to achieve when selecting rocks in their natural environment. We group breakdown features according to their formative environment and process. In selecting images for inclusion in the atlas we were mindful to cover a wide range of climatic zones. For example, in the weathering chapter, clast features are shown from locations such as the hyper-arid polar desert of Antarctica and the semi-arid canyons of central Australia. This is important as some features (e.g., alveoli) occur across climate regimes. We have drawn on the published geomorphological literature and our own field experience. We use, where possible, images of extrusive igneous rocks as the data returned from Mars, Venus and the Moon indicates that this is the predominant rock type. One of the purposes of this atlas is to expand the range of surface features that are known to indicate a particular geomorphic environment or process history. The surface features on boulders in some environments such as aeolian and weathering are well understood. In contrast, those in fluvial or ejecta environments are not. Therefore we have presented a comprehensive assemblage of features that are likely to be produced in each of the geomorphic environments. We hope that this atlas will trigger more research on diagnostic features, particularly their morphometry and detailed morphology, their persistence and rates of formation. In this first edition of the atlas we detail the features found on clasts in three geomorphic environments: aeolian, fluvial and weathering. Future editions of the atlas will include chapters on ejecta, micro-impacts, coastal, colluvial, glacial and structural features.

Bourke, Mary C.↗

DOE OSTI2014

Evaluation of atlas-based auto-segmentation software in prostate cancer patients

The performance and limitations of an atlas-based auto-segmentation software package (ABAS; Elekta Inc.) was evaluated using male pelvic anatomy as the area of interest. Contours from 10 prostate patients were selected to create atlases in ABAS. The contoured regions of interest were created manually to align with published guidelines and included the prostate, bladder, rectum, femoral heads and external patient contour. Twenty-four clinically treated prostate patients were auto-contoured using a randomised selection of two, four, six, eight or ten atlases. The concordance between the manually drawn and computer-generated contours were evaluated statistically using Pearson's product–moment correlation coefficient (r) and clinically in a validated qualitative evaluation. In the latter evaluation, six radiation therapists classified the degree of agreement for each structure using seven clinically appropriate categories. The ABAS software generated clinically acceptable contours for the bladder, rectum, femoral heads and external patient contour. For these structures, ABAS-generated volumes were highly correlated with ‘as treated’ volumes, manually drawn; for four atlases, for example, bladder r = 0.988 (P < 0.001), rectum r = 0.739 (P < 0.001) and left femoral head r = 0.560 (P < 0.001). Poorest results were seen for the prostate (r = 0.401, P < 0.05) (four atlases); however this was attributed to the comparison prostate volume being contoured on magnetic resonance imaging (MRI) rather than computed tomography (CT) data. For all structures, increasing the number of atlases did not consistently improve accuracy. ABAS-generated contours are clinically useful for a range of structures in the male pelvis. Clinically appropriate volumes were created, but editing of some contours was inevitably required. The ideal number of atlases to improve generated automatic contours is yet to be determined.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

NASA NTRS1994

ATLAS solar pointing operations

The ATLAS-series of Spacelab missions are comprised of a diverse group of scientific instruments including instruments for studying the sun and how the sun's energy changes across an eleven-year solar cycle. The ATLAS solar instruments are located on one or more pallets in the Orbiter payload bay and use the Orbiter as a pointing platform for their examinations of the sun. One of the ATLAS instruments contained a sun sensor which allowed scientists and engineers on the ground to see the pointing error of the sun with respect to the instrument and correct for the error based upon the information coming from the ATLAS 1 and ATLAS 2 missions with particular attention given to identifying the sources of pointing discrepancies of the solar instruments and to describe the crew and ground controller procedures that were developed to correct for these discrepancies. The Orbiter pointing behavior from the ATLAS 1 and ATLAS 2 flights presented in this paper can be applied to future flights which use the Orbiter as a pointing platform.

Tyler, C. A.↗

NASA NTRS2013

Thermal Performance of ATLAS Laser Thermal Control System Demonstration Unit

The second Ice, Cloud, and Land Elevation Satellite mission currently planned by National Aeronautics and Space Administration will measure global ice topography and canopy height using the Advanced Topographic Laser Altimeter System {ATLAS). The ATLAS comprises two lasers; but only one will be used at a time. Each laser will generate between 125 watts and 250 watts of heat, and each laser has its own optimal operating temperature that must be maintained within plus or minus 1 degree Centigrade accuracy by the Laser Thermal Control System (LTCS) consisting of a constant conductance heat pipe (CCHP), a loop heat pipe (LHP) and a radiator. The heat generated by the laser is acquired by the CCHP and transferred to the LHP, which delivers the heat to the radiator for ultimate rejection. The radiator can be exposed to temperatures between minus 71 degrees Centigrade and minus 93 degrees Centigrade. The two lasers can have different operating temperatures varying between plus 15 degrees Centigrade and plus 30 degrees Centigrade, and their operating temperatures are not known while the LTCS is being designed and built. Major challenges of the LTCS include: 1) A single thermal control system must maintain the ATLAS at 15 degrees Centigrade with 250 watts heat load and minus 71 degrees Centigrade radiator sink temperature, and maintain the ATLAS at plus 30 degrees Centigrade with 125 watts heat load and minus 93 degrees Centigrade radiator sink temperature. Furthermore, the LTCS must be qualification tested to maintain the ATLAS between plus 10 degrees Centigrade and plus 35 degrees Centigrade. 2) The LTCS must be shut down to ensure that the ATLAS can be maintained above its lowest desirable temperature of minus 2 degrees Centigrade during the survival mode. No software control algorithm for LTCS can be activated during survival and only thermostats can be used. 3) The radiator must be kept above minus 65 degrees Centigrade to prevent ammonia from freezing using no more than 135 watts of heater power. 4) The LHP reservoir control heater power is limited to 15 watts with a 70 percent duty cycle. 5) The voltage of the power supply can vary between 26 volts direct current and 34 volts direct current during the spacecraft lifetime. A design analysis shows that a single LTCS can satisfy these requirements. However, shutdown of· the LHP is particularly challenging and the shutdown heater must be wired in series with two reservoir thermostats and two CCHP thermostats at different set points. An LTCS demonstration unit has been tested to verify these performance characteristics experimentally prior to proceeding to the final LTCS design and fabrication. Test results showed that the LHP shutdown scheme would be able to shut down the LHP as designed and the reservoir control heater can maintain the ATLAS mass simulator within the plus or minus 1 degrees Centigrade accuracy under various combinations of the heat load, sink temperature, and power supply voltage.

Ku, Jentung↗

DOE OSTI2023

Energy Community Atlas

The Energy Community Atlas provides efficient access to authoritative, curated, and relevant data that is vital to supporting energy planning, development, and economic growth across the U.S. In this effort, researchers at the National Energy Technology Laboratory (NETL) are utilizing advanced data visualization and transformation capabilities to develop an integrated, data atlas and resource focused on supporting energy community transitions to new manufacturing opportunities. Specifically, this project is working to find, acquire, integrate, and virtually host in a user-friendly, public and private solution from available resources, relevant to understanding and characterizing fossil energy communities themselves and inform energy planning, development, and economic growth opportunities, including opportunities for co-development to support manufacturing, critical materials, and more. This Atlas when complete is to offer a one-stop-shop for stakeholders to derive new insights to accelerate energy investments and strategic decision support needs. These are following datasets that are available as part of this ongoing project • Energy Community Atlas Map Package - This is ArcPro Map package and it contains all of the symbolized layers along with ArcPro map and geodatabase • Energy Community Atlas ArcGIS REST service - https://www.arcgis.com/apps/mapviewer/index.html?panel=gallery&suggestField=true&layers=537ced69bd88440380a62c2ec8aca30c • README Energy Community Atlas - Read me word document that has details about feature classes in Map package, ArcPro map and ArcGIS Rest Service

Bipartisan Infrastructure Law↗

DOE OSTI2016

Integration Of PanDA Workload Management System With Supercomputers for ATLAS and Data Intensive Science

The.LHC, operating at CERN, is leading Big Data driven scientific explorations. Experiments at the LHC explore the fundamental nature of matter and the basic forces that shape our universe. ATLAS, one of the largest collaborations ever assembled in the sciences, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. The ATLAS experiment uses PanDA (Production and Data Analysis) Workload Management System for managing the workflow for all data processing on over 150 data centers. Through PanDA, ATLAS physicists see a single computing facility that enables rapid scientific breakthroughs for the experiment, even though the data centers are physically scattered all over the world. While PanDA currently uses more than 250,000 cores with a peak performance of 0.3 petaFLOPS, LHC data taking runs require more resources than grid can possibly provide. To alleviate these challenges, LHC experiments are engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. We will describe a project aimed at integration of PanDA WMS with supercomputers in United States, in particular with Titan supercomputer at Oak Ridge Leadership Computing Facility. Current approach utilizes modified PanDA pilot framework for job submission to the supercomputers batch queues and local data management, with light-weight MPI wrappers to run single threaded workloads in parallel on LCFs multi-core worker nodes. This implementation was tested with a variety of Monte-Carlo workloads on several supercomputing platforms for ALICE and ATLAS experiments and it is in full pro duction for the ATLAS since September 2015. We will present our current accomplishments with running PanDA at supercomputers and demonstrate our ability to use PanDA as a portal independent of the computing facilities infrastructure for High Energy and Nuclear Physics as well as other data-intensive science applications, such as bioinformatics and astro-particle physics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

The ATLAS multi-user upgrade and potential applications

With the recent integration of the CARIBU-EBIS charge breeder into the ATLAS accelerator system to provide for more pure and efficient charge breeding of radioactive beams, a multi-user upgrade of the ATLAS facility is being proposed to serve multiple users simultaneously. ATLAS was the first superconducting ion linac in the world and is the US DOE low-energy Nuclear Physics National User Facility. The proposed upgrade will take advantage of the continuous-wave nature of ATLAS and the pulsed nature of the EBIS charge breeder in order to simultaneously accelerate two beams with very close mass-to-charge ratios; one stable from the existing ECR ion source and one radioactive from the newly commissioned EBIS charge breeder. In addition to enhancing the nuclear physics program, beam extraction at different points along the linac will open up the opportunity for other potential applications; for instance, material irradiation studies at ~ 1 MeV/u and isotope production at ~ 6 MeV/u or at the full ATLAS energy of ~ 15 MeV/u. Furthermore, the concept and proposed implementation of the ATLAS multi-user upgrade will be presented. Future plans to enhance the flexibility of this upgrade will also be presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

The use of atlas registration and graph cuts for prostate segmentation in magnetic resonance images

Purpose: An automatic method for 3D prostate segmentation in magnetic resonance (MR) images is presented for planning image-guided radiotherapy treatment of prostate cancer. Methods: A spatial prior based on intersubject atlas registration is combined with organ-specific intensity information in a graph cut segmentation framework. The segmentation is tested on 67 axial T{sub 2}-weighted MR images in a leave-one-out cross validation experiment and compared with both manual reference segmentations and with multiatlas-based segmentations using majority voting atlas fusion. The impact of atlas selection is investigated in both the traditional atlas-based segmentation and the new graph cut method that combines atlas and intensity information in order to improve the segmentation accuracy. Best results were achieved using the method that combines intensity information, shape information, and atlas selection in the graph cut framework. Results: A mean Dice similarity coefficient (DSC) of 0.88 and a mean surface distance (MSD) of 1.45 mm with respect to the manual delineation were achieved. Conclusions: This approaches the interobserver DSC of 0.90 and interobserver MSD 0f 1.15 mm and is comparable to other studies performing prostate segmentation in MR.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

SU-E-I-71: Quality Assessment of Surrogate Metrics in Multi-Atlas-Based Image Segmentation

Purpose: With the ever-growing data of heterogeneous quality, relevance assessment of atlases becomes increasingly critical for multi-atlas-based image segmentation. However, there is no universally recognized best relevance metric and even a standard to compare amongst candidates remains elusive. This study, for the first time, designs a quantification to assess relevance metrics’ quality, based on a novel perspective of the metric as surrogate for inferring the inaccessible oracle geometric agreement. Methods: We first develop an inference model to relate surrogate metrics in image space to the underlying oracle relevance metric in segmentation label space, with a monotonically non-decreasing function subject to random perturbations. Subsequently, we investigate model parameters to reveal key contributing factors to surrogates’ ability in prognosticating the oracle relevance value, for the specific task of atlas selection. Finally, we design an effective contract-to-noise ratio (eCNR) to quantify surrogates’ quality based on insights from these analyses and empirical observations. Results: The inference model was specialized to a linear function with normally distributed perturbations, with surrogate metric exemplified by several widely-used image similarity metrics, i.e., MSD/NCC/(N)MI. Surrogates’ behaviors in selecting the most relevant atlases were assessed under varying eCNR, showing that surrogates with high eCNR dominated those with low eCNR in retaining the most relevant atlases. In an end-to-end validation, NCC/(N)MI with eCNR of 0.12 compared to MSD with eCNR of 0.10 resulted in statistically better segmentation with mean DSC of about 0.85 and the first and third quartiles of (0.83, 0.89), compared to MSD with mean DSC of 0.84 and the first and third quartiles of (0.81, 0.89). Conclusion: The designed eCNR is capable of characterizing surrogate metrics’ quality in prognosticating the oracle relevance value. It has been demonstrated to be correlated with the performance of relevant atlas selection and ultimate label fusion.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-C-BRA-04: Automated Segmentation of Head-And-Neck CT Images for Radiotherapy Treatment Planning Via Multi-Atlas Machine Learning (MAML)

Purpose: Accurate image segmentation is a crucial step during image guided radiation therapy. This work proposes multi-atlas machine learning (MAML) algorithm for automated segmentation of head-and-neck CT images. Methods: As the first step, the algorithm utilizes normalized mutual information as similarity metric, affine registration combined with multiresolution B-Spline registration, and then fuses together using the label fusion strategy via Plastimatch. As the second step, the following feature selection strategy is proposed to extract five feature components from reference or atlas images: intensity (I), distance map (D), box (B), center of gravity (C) and stable point (S). The box feature B is novel. It describes a relative position from each point to minimum inscribed rectangle of ROI. The center-of-gravity feature C is the 3D Euclidean distance from a sample point to the ROI center of gravity, and then S is the distance of the sample point to the landmarks. Then, we adopt random forest (RF) in Scikit-learn, a Python module integrating a wide range of state-of-the-art machine learning algorithms as classifier. Different feature and atlas strategies are used for different ROIs for improved performance, such as multi-atlas strategy with reference box for brainstem, and single-atlas strategy with reference landmark for optic chiasm. Results: The algorithm was validated on a set of 33 CT images with manual contours using a leave-one-out cross-validation strategy. Dice similarity coefficients between manual contours and automated contours were calculated: the proposed MAML method had an improvement from 0.79 to 0.83 for brainstem and 0.11 to 0.52 for optic chiasm with respect to multi-atlas segmentation method (MA). Conclusion: A MAML method has been proposed for automated segmentation of head-and-neck CT images with improved performance. It provides the comparable result in brainstem and the improved result in optic chiasm compared with MA. Xuhua Ren and Hao Gao were partially supported by the NSFC (#11405105), the 973 Program (#2015CB856000), and the Shanghai Pujiang Talent Program (#14PJ1404500).

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-F-J-113: Multi-Atlas Based Automatic Organ Segmentation for Lung Radiotherapy Planning

Purpose: Normal organ segmentation is one time-consuming and labor-intensive step for lung radiotherapy treatment planning. The aim of this study is to evaluate the performance of a multi-atlas based segmentation approach for automatic organs at risk (OAR) delineation. Methods: Fifteen Lung stereotactic body radiation therapy patients were randomly selected. Planning CT images and OAR contours of the heart - HT, aorta - AO, vena cava - VC, pulmonary trunk - PT, and esophagus – ES were exported and used as reference and atlas sets. For automatic organ delineation for a given target CT, 1) all atlas sets were deformably warped to the target CT, 2) the deformed sets were accumulated and normalized to produce organ probability density (OPD) maps, and 3) the OPD maps were converted to contours via image thresholding. Optimal threshold for each organ was empirically determined by comparing the auto-segmented contours against their respective reference contours. The delineated results were evaluated by measuring contour similarity metrics: DICE, mean distance (MD), and true detection rate (TD), where DICE=(intersection volume/sum of two volumes) and TD = {1.0 - (false positive + false negative)/2.0}. Diffeomorphic Demons algorithm was employed for CT-CT deformable image registrations. Results: Optimal thresholds were determined to be 0.53 for HT, 0.38 for AO, 0.28 for PT, 0.43 for VC, and 0.31 for ES. The mean similarity metrics (DICE[%], MD[mm], TD[%]) were (88, 3.2, 89) for HT, (79, 3.2, 82) for AO, (75, 2.7, 77) for PT, (68, 3.4, 73) for VC, and (51,2.7, 60) for ES. Conclusion: The investigated multi-atlas based approach produced reliable segmentations for the organs with large and relatively clear boundaries (HT and AO). However, the detection of small and narrow organs with diffused boundaries (ES) were challenging. Sophisticated atlas selection and multi-atlas fusion algorithms may further improve the quality of segmentations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-F-J-171: Robust Atlas Based Segmentation of the Prostate and Peripheral Zone Regions On MRI Utilizing Multiple MRI System Vendors

Purpose: Automatically generated prostate MRI contours can be used to aid in image registration with CT or ultrasound and to reduce the burden of contouring for radiation treatment planning. In addition, prostate and zonal contours can assist to automate quantitative imaging features extraction and the analyses of longitudinal MRI studies. These potential gains are limited if the solutions are not compatible across different MRI vendors. The goal of this study is to characterize an atlas based automatic segmentation procedure of the prostate collected on MRI systems from multiple vendors. Methods: The prostate and peripheral zone (PZ) were manually contoured by an expert radiation oncologist on T2-weighted scans acquired on both GE (n=31) and Siemens (n=33) 3T MRI systems. A leave-one-out approach was utilized where the target subject is removed from the atlas before the segmentation algorithm is initiated. The atlas-segmentation method finds the best nine matched atlas subjects and then performs a normalized intensity-based free-form deformable registration of these subjects to the target subject. These nine contours are then merged into a single contour using Simultaneous Truth and Performance Level Estimation (STAPLE). Contour comparisons were made using Dice similarity coefficients (DSC) and Hausdorff distances. Results: Using the T2 FatSat (FS) GE datasets the atlas generated contours resulted in an average DSC of 0.83±0.06 for prostate, 0.57±0.12 for PZ and 0.75±0.09 for CG. Similar results were found when using the Siemens data with a DSC of 0.79±0.14 for prostate, 0.54±0.16 and 0.70±0.9. Contrast between prostate and surrounding anatomy and between the PZ and CG contours for both vendors demonstrated superior contrast separation; significance was found for all comparisons p-value < 0.0001. Conclusion: Atlas-based segmentation yielded promising results for all contours compared to expertly defined contours in both Siemens and GE 3T systems providing fast and automatic segmentation of the prostate. Funding Support, Disclosures, and Conflict of Interest: AS Nelson is a partial owner of MIM Software, Inc. AS Nelson, and A Swallen are current employees at MIM Software, Inc.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Searches for New Long-Lived Particles and Upgrade to the ATLAS Inner Detector (Final Technical Report)

The search for new fundamental particles is one of the defining goals of the Large Hadron Collider (LHC). The discovery of the Higgs Boson by the ATLAS and CMS collaborations provided the capstone of the Standard Model of particle physics, but outstanding questions remain. Why does the Higgs boson have a mass of 125 GeV when its natural mass would be many orders of magnitude larger? Is there a universal symmetry which unites all three forces described by the Standard Model? Can that symmetry be extended to include gravity? Is dark matter, evidenced by astronomical observations, made of a particle that interacts via Standard Model forces with the rest of matter? Together, these motivations provide compelling arguments that new physical processes await discovery. This project addressed some outstanding questions about the fundamental particles and their interactions with the ATLAS experiment at the Large Hadron Collider. In particular, the project improved the discovery potential for new, long- lived particles produced via electroweak processes in proton-proton collisions and set world-leading limits on their existence for certain values of their potential mass and lifetime. To achieve this, the project developed new data analysis methods, developed new triggers to select events with new long-lived particles during data-taking of the ATLAS experiment, and analyzed the largest proton–proton collision dataset ever produced. The project also supported significant development of the data acquisition software for the upgrade to the ATLAS inner detector, the Inner TracKer (ITk). The upgrade of the ATLAS inner detector is essential to the success of the entire Phase II physics program on ATLAS. Personnel supported by the project provided support for integration, assembly, and testing of the inner two layers of the ITk pixel system during its prototype and pre-production phase. Four PhD students and two post-doctoral scholars were supported by the grant and received invaluable scientific training as part of the research endeavor. The students and postdocs gained essential professional skills in the areas of advanced data analysis techniques, statistical analysis of data and simulation, programming in C++ and Python, hardware and instrumentation development, and presentation and collaboration skills. Additionally, approximately ten undergraduate students supported through other funding sources participated in research activities synergistic with the goals of this project, receiving essential mentorship from the personnel supported by this project.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2017

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

genome binning↗

NASA NTRS1982

The AFGL molecular line Atlases

There are two compilations: the main Atlas and the Trace Gas Atlas. The main Atlas includes the major absorbers in the Earth's atmosphere. The main Atlas includes about 150,000 lines (the Trace Gas Atlas is 30-40,000 at the moment). The information on each Atlas is essentially a card image per line, which includes the frequency (in vacuum wavenumbers) of the transition, the line strength at a standard temperature of 296 Kelvin, and the half width of the line.

Rothman, L. S.↗