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At least 1,171 records · Page 65

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DOE OSTI2016

TU-FG-201-07: Development of SRS Conical Collimator Collision Prediction Software for Radiation Treatment Safety

Purpose: Stereotactic radiosurgery (SRS) treatments using conical collimators can potentially result in gantry collision with treatment table due to limited collision-clear spaces. An in-house software was developed to help the SRS treatment planner mitigate potential SRS conical collimator (Varian Medical System, Palo Alto, CA) collisions with the treatment table. This software was designed to remove treatment re-planning secondary to unexpected collisions. Methods: A BrainLAB SRS ICT Frameless Extension used for SRS treatments in our clinic was mathematically modelled using surface points registered to the 3D co-ordinate space of the couch extension. The surface points are transformed based on the treatment isocenter point and potential collisions are determined in 3D space for couch and gantry angle combinations. The distance between the SRS conical collimators and LINAC isocenter is known. The collision detection model was programmed in MATLAB (Mathwork, Natick, MA) to display graphical plots of the calculations, and the plotted data is used to avoid the gantry and couch angle combinations that would likely result in a collision. We have utilized the cone collision tool for 23 SRS cone treatment plans (8 retrospective and 15 prospective for 10 patients). Results: Twenty one plans strongly agreed with the software tool prediction for collision. However, in two plans, a collision was observed with a 0.5 cm margin when the software predicted no collision. Therefore, additional margins were added to the clearance criteria in the program to achieve a lower risk of actual collisions. Conclusion: Our in-house developed collision check software successfully avoided SRS cone re-planning by 91.3% due to a reduction in cone collisions with the treatment table. Future developments to our software will include a CT image data set based collision prediction model as well as a beam angle optimization tool to avoid normal critical tissues as well as previously treated lesions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-CD-207A-10: Using the Gamma Index to Flag Changes in Anatomy During Radiation Therapy of Head and Neck Cancer

Purpose: This article presents a fast algorithm for comparing 3-D anatomy from Cone-Beam CT (CBCT) imaging using the gamma comparison index and to demonstrate how this can be used to flag patients for possible re-planning of treatment. Methods: CBCT scans acquired on a Varian linear accelerator during treatment were used as input to the gamma comparator using thresholds of 5 mm distance to agreement and 30 Hounsfield Unit CT number difference. The fraction 1 CBCT study was initially used as the reference. Should there be a re-plan during treatment, the reference resets to the CBCT study acquired on the day 1 of the re-plan. Histograms of failing pixels (γ > 1) were generated from each 3-D gamma map. An indicator of anatomy congruence, the match quality parameter (MQP), was derived from failed pixel histograms using the 90th percentile gamma value. The MQP was plotted versus fraction number and related to actual repeat computed tomography (re-CT) order dates as decided by a radiation oncologist. From this, decision criteria were derived for the algorithm to “trigger” re-CT consideration and predictive power was scored using receiver-operator characteristic (ROC) analysis. Results: The MQP plot generally showed that the on-line match from CBCT image guidance deteriorated as the treatment progressed due to weight loss and tumor regression. The optimized MQP criteria for triggering re-CT consideration demonstrated high sensitivity and specificity, consistent with actual re-CT order dates within ± 3 fractions. Out of 20 patients that were actually re-planned, the algorithm failed to trigger a re-CT recommendation only twice and this was caused by CBCT ring artifacts. Conclusion: We have demonstrated that gamma comparisons can be used to evaluate CBCT-acquired anatomy pairs and, from this, an algorithm can be “trained” to flag patients for possible re-planning in a manner consistent with local radiation oncology practice.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

An experimental extrapolation technique using the Gafchromic EBT3 film for relative output factor measurements in small x-ray fields

Purpose: An experimental extrapolation technique is presented, which can be used to determine the relative output factors for very small x-ray fields using the Gafchromic EBT3 film. Methods: Relative output factors were measured for the Brainlab SRS cones ranging in diameters from 4 to 30 mm{sup 2} on a Novalis Trilogy linear accelerator with 6 MV SRS x-rays. The relative output factor was determined from an experimental reducing circular region of interest (ROI) extrapolation technique developed to remove the effects of volume averaging. This was achieved by scanning the EBT3 film measurements with a high scanning resolution of 1200 dpi. From the high resolution scans, the size of the circular regions of interest was varied to produce a plot of relative output factors versus area of analysis. The plot was then extrapolated to zero to determine the relative output factor corresponding to zero volume. Results: Results have shown that for a 4 mm field size, the extrapolated relative output factor was measured as a value of 0.651 ± 0.018 as compared to 0.639 ± 0.019 and 0.633 ± 0.021 for 0.5 and 1.0 mm diameter of analysis values, respectively. This showed a change in the relative output factors of 1.8% and 2.8% at these comparative regions of interest sizes. In comparison, the 25 mm cone had negligible differences in the measured output factor between zero extrapolation, 0.5 and 1.0 mm diameter ROIs, respectively. Conclusions: This work shows that for very small fields such as 4.0 mm cone sizes, a measureable difference can be seen in the relative output factor based on the circular ROI and the size of the area of analysis using radiochromic film dosimetry. The authors recommend to scan the Gafchromic EBT3 film at a resolution of 1200 dpi for cone sizes less than 7.5 mm and to utilize an extrapolation technique for the output factor measurements of very small field dosimetry.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Designing and defining dynamic protein cage nanoassemblies in solution

Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

ABSTRACT As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world. IMPORTANCE The massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Multidecadal shifts in forest plant diversity and community composition across glacial landforms in northern lower Michigan, USA

Understanding how plant community assemblage is affected by spatial and temporal patterns is crucial to understanding forest ecosystem responses to disturbance, including future climate change. In this article, we tracked how diversity and composition are distributed through space and time in a midsuccessional mixed hardwood forest in northern lower Michigan, United States. This region’s geographically and abiotically distinct glacial landforms influence both the spatial and temporal dynamics of its forest communities. Vegetation sampling plots (n = 87) were established at the University of Michigan Biological Station in 1990 and resampled in 2015. Vegetation in the overstory, sapling, and groundcover layers was censused. Abiotic variables, including elevation, pH, and soil nutrients, were measured in a subset of plots (n = 40). There were strong differences in diversity and community composition among glacial landforms, with the moraine having a 31% greater species richness in the groundcover layer compared with those of the other glacial landforms. Surprisingly, plant communities across all three vegetation layers showed little change over the 25-year period, and we found no evidence of differences in successional rates among glacial landforms. Our findings indicate that glacial landforms have a large influence on the production and maintenance of local plant diversity and community composition in this area and suggest that successional dynamics may manifest themselves over much longer time periods in these northern biomes.

Forestry↗

DOE OSTI2015

Erratum to: Search for production of WW / WZ resonances decaying to a lepton, neutrino and jets in pp collisions at $\sqrt{s}=8$ TeV with the ATLAS detector

It has been found that the bulk RS graviton (G*)(G*) exclusion limits were erroneously expressed as a function of σ(pp→G*)×BR(G*→WW)σ(pp→G*)×BR(G*→WW) . The corrected version of the top plot in Fig. 2 of the paper is presented below. With this correction, resonance masses below 760 GeV are excluded at 95 % confidence level for this model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

η ′ → η π π decays in unitarized resonance chiral theory

We study the hadronic $η^{\prime}\toηππ$ decays within the framework of $U(3)_{L}\otimes U(3)_{R}$ Chiral Perturbation Theory including resonance states and the complete one-loop corrections. The amplitude is projected in partial waves and unitarized by means of the $N/D$ method resumming both the important $S$-and $D$-wave $ππ$ and the subleading $S$-wave $πη$ final-state interactions. The participating scalar multiplet mass and coupling strengths are determined from fits to the Dalitz plot experimental data recently released by the A2 collaboration. As a byproduct of our analysis, the associated Dalitz-plot slope parameters are found to be $a=-0.072(7)_{\rm{stat}}(8)_{\rm{syst}}\,, b=-0.052(1)_{\rm{stat}}(2)_{\rm{syst}}\,, d=-0.051(8)_{\rm{stat}}(6)_{\rm{syst}}$, which lie in the ballpark of the current experimental and theoretical determinations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Radiative three-body D -meson decays in and beyond the standard model

We study radiative charm decays D → P 1 P 2γ , P 1,2 = π, K in QCD factorization at leading order and within heavy hadron chiral perturbation theory. Branching ratios including resonance contributions are around ~10 –3 for the Cabibbo-favored modes into Kπγ and ~10 –5 for the singly Cabibbo-suppressed modes into π + π – γ,K + K – γ, and thus in reach of the flavor factories BES III and Belle II. Dalitz plots and forward–backward asymmetries reveal significant differences between the two QCD frameworks; such observables are therefore ideally suited for a data-driven identification of relevant decay mechanisms in the standard-model dominated D → Kπγ decays. This increases the potential to probe new physics with the D → π + π – γ and D → K + K – γ decays, which are sensitive to enhanced dipole operators. CP asymmetries are useful to test the SM and look for new physics in neutral |ΔC| = 1 transitions. Cuts in the Dalitz plot enhance the sensitivity to new physics due to the presence of both s- and t, u-channel intermediate resonances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Toward extracting $$\gamma $$ from $$B\rightarrow DK$$ without binning

Abstract $$B^\pm \rightarrow DK^\pm $$ B ± → D K ± transitions are known to provide theoretically clean information about the CKM angle $$\gamma $$ γ , with the most precise available methods exploiting the cascade decay of the neutral D into CP self-conjugate states. Such analyses currently require binning in the D decay Dalitz plot, while a recently proposed method replaces this binning with the truncation of a Fourier series expansion. In this paper, we present a proof of principle of a novel alternative to these two methods, in which no approximations at the level of the data representation are required. In particular, our new strategy makes no assumptions about the amplitude and strong phase variation over the Dalitz plot. This comes at the cost of a degree of ambiguity in the choice of test statistic quantifying the compatibility of the data with a given value of $$\gamma $$ γ , with improved choices of test statistic yielding higher sensitivity. While our current proof-of-principle implementation does not demonstrate optimal sensitivity to $$\gamma $$ γ , its conceptually novel approach opens the door to new strategies for $$\gamma $$ γ extraction. More studies are required to see if these can be competitive with the existing methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗

DOE OSTI2023

ALGEBRA v.1.27

The ALGEBRA program allows the user to manipulate data from a finite element analysis before it is plotted. The finite element output data is in the form of variable values (e.g., stress, strain, and velocity components) in an EXODUS II database. The ALGEBRA program evaluates user-supplied functions of the data and writes the results to an output EXODUS II database that can be read by plot programs.

Sjaardema, Gregory↗

DOE OSTI2017

SimApp 1.8.x

System for converting DESIRE (Direct Executing Simulation in Real Time) simulation models to executable code models (C# / C++). These converted models are used as the basis for 2 products, one of which is the focus of this review: an engineering design interface for Fissile Solution Systems. ModelConverter.exe (C#) converts DESIRE model inputs to a C++ plug-in subclass. SimApp.exe (C# / C++) has a C++ dll that is a numerical integration engine that the Converted models plug into. The engineering design interface is a C# GUI that calls on the C++ dll to execute a particular converted model. The GUI allows the user to specify the length of a simulation, run the simulation, view data plots and data tables. Stability plots may also be produced and manipulated. The engineering design interface will be released as source code and executable; the model converter source is also intended for release.

Determan, JohnC.↗

DOE OSTI2019

CATS v. 2

This program calculates performance characteristics for a split flow recompression closed Brayton cycle. The user defines for the cycle; minimum temperature, minimum pressure, maximum temperature, maximum pressure, pinch temperature at the cold ends of the low temperature and high temperature recuperators, component fractional pressure drop, and efficiencies for each of the two turbines and each of the two compressors. All of these parameters except component fractional pressure drop and turbomachinery efficiencies are varies in separate do loops. In this way, minimum and maximum values for each of these parameters can be set. Results from each iteration are saved to a .csv file. Following completion of the program run, the .csv file can be read into a plotting package and the results can be plotted.

Pasch, James↗

DOE OSTI2019

bokeh streaming [SWR 19-08]

Simple examples of bokeh streaming data. The plots are intended to be generic and able to infer some of the plot data from the structure of the data sent. The receiver accepts zlib compressed pickled python dictionaries.

Simpson, Jeffery↗

DOE OSTI2021

Igor Pro procedures for ARPES analysis (ARPES Igor procedures) v21.0

A suite of non-proprietary C-like procedures (code) that compile and run within the commercial Igor Pro data analysis program (wavemetrics.com) have been developed for the data file loading, plotting and analysis of Angle-Resolved Photoemission Spectroscopy (ARPES) data. The data file loading procedures are more specific to ARPES data acquisition and file formats at Advanced Light Source (ALS) beamlines, while plotting and analysis procedures are more generic to processing of 1D, 2D and higher dimensional dataset arrays with some specific tools tailored to the ARPES technique.

Rotenberg, Eli↗

DOE OSTI2014

Lipid Informed Quantitation and Identification

LIQUID (Lipid Informed Quantitation and Identification) is a software program that has been developed to enable users to conduct both informed and high-throughput global liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics analysis. This newly designed desktop application can quickly identify and quantify lipids from LC-MS/MS datasets while providing a friendly graphical user interface for users to fully explore the data. Informed data analysis simply involves the user specifying an electrospray ionization mode, lipid common name (i.e. PE(16:0/18:2)), and associated charge carrier. A stemplot of the isotopic profile and a line plot of the extracted ion chromatogram are also provided to show the MS-level evidence of the identified lipid. In addition to plots, other information such as intensity, mass measurement error, and elution time are also provided. Typically, a global analysis for 15,000 lipid targets.

Crowell, Kevin↗

DOE OSTI2016

Sensor Fish Communicator

The Sensor Fish collects information that can be used to evaluate conditions encountered by juvenile salmonids and other fish as they pass through hydroelectric dams on their way to the ocean. Sensor Fish are deployed in turbines, spillways, and sluiceways and measure changes in pressure, angular rate of change, and linear acceleration during passage. The software is need to make Sensor Fish fully functional and easy to use. Sensor Fish Communicator (SFC) links to Sensor Fish, allowing users to control data collection settings and download data. It may also be used to convert native raw data (.raw2) files into Comma Separated Variable (.csv) files and plot the results. The multiple capabilities of the SFC allow hardware communication, data conversion, and data plotting with one application.

Source record↗