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At least 433 records · Page 24

TU-AB-201-02: An Automated Treatment Plan Quality Assurance Program for Tandem and Ovoid High Dose-Rate Brachytherapy

Purpose: For tandem and ovoid (T&O) HDR brachytherapy in our clinic, it is required that the planning physicist manually capture ∼10 images during planning, perform a secondary dose calculation and generate a report, combine them into a single PDF document, and upload it to a record- and-verify system to prove to an independent plan checker that the case was planned correctly. Not only does this slow down the already time-consuming clinical workflow, the PDF document also limits the number of parameters that can be checked. To solve these problems, we have developed a web-based automatic quality assurance (QA) program. Methods: We set up a QA server accessible through a web- interface. A T&O plan and CT images are exported as DICOMRT files and uploaded to the server. The software checks 13 geometric features, e.g. if the dwell positions are reasonable, and 10 dosimetric features, e.g. secondary dose calculations via TG43 formalism and D2cc to critical structures. A PDF report is automatically generated with errors and potential issues highlighted. It also contains images showing important geometric and dosimetric aspects to prove the plan was created following standard guidelines. Results: The program has been clinically implemented in our clinic. In each of the 58 T&O plans we tested, a 14- page QA report was automatically generated. It took ∼45 sec to export the plan and CT images and ∼30 sec to perform the QA tests and generate the report. In contrast, our manual QA document preparation tooks on average ∼7 minutes under optimal conditions and up to 20 minutes when mistakes were made during the document assembly. Conclusion: We have tested the efficiency and effectiveness of an automated process for treatment plan QA of HDR T&O cases. This software was shown to improve the workflow compared to our conventional manual approach.

60 APPLIED LIFE SCIENCES↗

SU-F-T-94: Plan2pdf - a Software Tool for Automatic Plan Report for Philips Pinnacle TPS

Purpose: To implement an automatic electronic PDF plan reporting tool for Philips Pinnacle treatment planning system (TPS) Methods: An electronic treatment plan reporting software is developed by us to enable fully automatic PDF report from Pinnacle TPS to external EMR programs such as MOSAIQ. The tool is named “plan2pdf”. plan2pdf is implemented using Pinnacle scripts, Java and UNIX shell scripts, without any external program needed. plan2pdf supports full auto-mode and manual mode reporting. In full auto-mode, with a single mouse click, plan2pdf will generate a detailed Pinnacle plan report in PDF format, which includes customizable cover page, Pinnacle plan summary, orthogonal views through each plan POI and maximum dose point, DRR for each beam, serial transverse views captured throughout the dose grid at a user specified interval, DVH and scorecard windows. The final PDF report is also automatically bookmarked for each section above for convenient plan review. The final PDF report can either be saved on a user specified folder on Pinnacle, or it can be automatically exported to an EMR import folder via a user configured FTP service. In manual capture mode, plan2pdf allows users to capture any Pinnacle plan by full screen, individual window or rectangular ROI drawn on screen. Furthermore, to avoid possible patients’ plan mix-up during auto-mode reporting, a user conflict check feature is included in plan2pdf: it prompts user to wait if another patient is being exported by plan2pdf by another user. Results: plan2pdf is tested extensively and successfully at our institution consists of 5 centers, 15 dosimetrists and 10 physicists, running Pinnacle version 9.10 on Enterprise servers. Conclusion: plan2pdf provides a highly efficient, user friendly and clinical proven platform for all Philips Pinnacle users, to generate a detailed plan report in PDF format for external EMR systems.

60 APPLIED LIFE SCIENCES↗

Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough

ABSTRACT Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered. IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm.

59 BASIC BIOLOGICAL SCIENCES↗

Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport

ATP-binding cassette (ABC) transporters constitute a large family of proteins present in all domains of life. They are powered by dynamic ATPases that harness energy from binding and hydrolyzing ATP through a cycle that involves the closing and reopening of their two ATP-binding domains. The LptB 2 FGC exporter is an essential ABC transporter that assembles lipopolysaccharides (LPS) on the surface of Gram-negative bacteria to form a permeability barrier against many antibiotics. LptB 2 FGC extracts newly synthesized LPS molecules from the inner membrane and powers their transport across the periplasm and through the outer membrane. How LptB 2 FGC functions remains poorly understood. Here, we show that the C-terminal domain of the dimeric LptB ATPase is essential for LPS transport in Escherichia coli. Specific changes in the C-terminal domain of LptB cause LPS transport defects that can be repaired by intragenic suppressors altering the ATP-binding domains. Surprisingly, we found that each of two lethal changes in the ATP-binding and C-terminal domains of LptB, when present in combined form, suppressed the defects associated with the other to restore LPS transport to wild-type levels both in vivo and in vitro. We present biochemical evidence explaining the effect that each of these mutations has on LptB function and how the observed cosuppression results from the opposing lethal effects these changes have on the dimerization state of the LptB ATPase. We therefore propose that these sites modulate the closing and reopening of the LptB dimer, providing insight into how the LptB2FGC transporter cycles to export LPS to the cell surface and how to inhibit this essential envelope biogenesis process.

59 BASIC BIOLOGICAL SCIENCES↗

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological рН value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the role of fusion neutron source with thorium blanket in forming the nuclide composition of the nuclear fuel cycle of the Russian Federation

The possible role of available thorium resources of the Russian Federation in utilization of thorium in the closed (U–Pu)-fuel cycle of nuclear power is considered. The efficiency of application of fusion neutron sources with thorium blanket for economical use of available thorium resources is demonstrated. The objective of this study is the search for a solution of such major tasks of nuclear power as reduction of the amount of front-end operations in the nuclear fuel cycle and enhancement of its protection against uncontrolled proliferation of fissile materials with the smallest possible alterations in the fuel cycle. The earlier results are analyzed, new information on the amount of thorium resources of the Russian Federation is used, and additional estimates are made. The following basic results obtained on the basis of the assumption of involving fusion reactors with Th-blanket in future nuclear power for generation of the light uranium fraction {sup 232+233+234}U and {sup 231}Pa are formulated. (1) The fuel cycle would shift from fissile {sup 235}U to {sup 233}U, which is more attractive for thermal power reactors. (2) The light uranium fraction is the most “protected” in the uranium fuel component, and being mixed with regenerated uranium, it would become reduced-enrichment uranium fuel, which would relieve the problem of nonproliferation of the fissile material. (3) The addition of {sup 231}Pa into the fuel would stabilize its neutron-multiplying properties, thus making it possible to implement a long fuel residence time and, as a consequence, increase the export potential of the whole nuclear power technology. (4) The available thorium resource in the vicinity of Krasnoufimsk is sufficient for operation of the large-scale nuclear power industry of the Russian Federation with an electric power of 70 GW for more than one quarter of a century. The general conclusion is that involvement of a small number of fusion reactors with Th-blanket in the future nuclear power industry of the Russian Federation would to a large extent solve its problems and increase its export potential.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

eCounter: Inline Per-IP Network Monitoring at Millisecond Resolution via eBPF

Scientific data acquisition (SciDAQ) systems are shifting from archive-based workflows to streaming paradigms, where real-time, fine-grained network monitoring becomes essential. While P4-enabled devices offer per-packet in-band observability, they require specialized switches and routers. Host-side tools like Prometheus exporters lack sufficient temporal granularity. To bridge this gap, we present eCounter, a lightweight, hardware-agnostic, inline telemetry agent built on extended Berkeley Packet Filter (eBPF). eCounter captures per-interface ingress and egress traffic, categorized by IP address and protocol, at millisecond to sub-millisecond resolution. In a 100 Gbps environment, it continuously exports up to 3,257 time-series bins per second with only 4% CPU utilization at a 35¿KiB/s data rate. We evaluate eCounter across diverse NIC MTU settings, hook types, CPU architectures and operating systems, and observed negligible impact on concurrent high-throughput streaming applications. Complexity analysis confirms that it can be readily scaled to distributed SciDAQ deployments.

Mei, Xinxin [Computational Sciences and Technology↗

OSTI Semantic Thesaurus v1

The OSTI Semantic Thesaurus is a reference for scientific and technical terms and relationships. The term data is used to implement keyword-to-concept mapping in OSTI.GOV searches, where searched term(s) will be mapped to related scientific concepts, allowing the end user to retrieve results related to their search terms and also explore narrower and similar concepts. The OSTI Semantic Thesaurus originally inherited data and structure from the INIS/ETDE Thesaurus (https://www.etde.org/edb/IAEA-INIS-ETDE-01-2013-08.pdf), which was a controlled terminology for indexing information within the subject scopes of the International Nuclear Information System (INIS) and the Energy Technology Data Exchange (ETDE). The data has been expanded upon since that time with the inclusion of scientific concepts from sources like Wikidata, and through manual curation. This dataset is an export from the OSTI Semantic Thesaurus in RDF/SKOS format, which is specifically suited for representation of controlled vocabularies like thesauri. While the full thesaurus includes additional relation types which may be included in future revisions, this export is limited to broader, narrower, and related term relations. Definitions and scope notes are included where available.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

SimulatorToFMU v0.1

SimulatorToFMU is a software package written in Python which allows users to export a memoryless Python-driven simulation program or script as a Functional Mock-up Unit (FMU) for model exchange or co-simulation.In CyDER (Cyber Physical Co-simulation Platform for Distributed Energy Resources in Smart Grids), SimulatorToFMU will allow exporting OPAL-RT as an FMU. This will enable OPAL-RT to be linked to CYMDIST and GridDyn FMUs through a standardized open source interface.

Nouidui, Thierry↗

Floorspace.js

Floorspace.js is a 2D geometry editor. Users can define an explicit floor plan for each story of a building. A story-by-story interface makes it easy to develop space geometry and assign properties. Referencing satellite imagery or floor plan images, when available, speeds up geometry entry. Conversion of 2D to 3D geometry is currently out of scope for Floorspace.js, a reference implementation is available in the OpenStudio® SDK. Explicit floor plans allow more building-specific information than parameterized shoe-boxes but less information than a full 3D BIM model. Sloped walls, complex roofs, detailed shading structures, and other complex 3D structures are out of FloorspaceJS's scope. In general, if users have a 3D BIM model in a tool that can export a useful BEM representation then it is better to use that export than to recreate a new model using FloorspaceJS. Re-usability and minimal dependencies were key design considerations for software developers. Web technologies can be used in both online and desktop applications. The editor was written in pure JavaScript for maximum portability and re-usability. A custom JavaScript Object Notation (JSON) file format was developed to ease integration with other applications. Custom JSON schema design was a key part of FloorspaceJS development.

Noland, Katie↗

T.Rex

T.Rex is used to explore tabular data sets containing up to ten million records to help rapidly understand a previously unknown data set. Analysis can quickly identify patterns of interest and the records and fields that capture those patterns. T.Rex contains a growing set of deep analytical tools and supports robust export capabilities that selected data can be incorporated into to other specialized tools for further analysis. T.Rex is flexible in ingesting different types and formats of data, allowing the user to interactively experiment and perform trial and error guesses on the structure of the data; and also has a variety of linked visual analytic tools that enable exploration of the data to find relevant content, relationships among content, trends within the content, and capture knowledge about the content. Finally, T.Rex has a rich export capability, to extract relevant subsets of a larger data source, to further analyze their data in other analytic tools.

Source record↗

ctrl-flow v0.0.1

ctrl-flow is a software that assists users in selecting a building control sequence from a library of control sequences that are implemented in the Modelica Buildings Library. The software allows selecting, configuring and editing the control sequences. It also allows exporting the sequence for use in building project design documents in Modelica-based simulations. The export will be in a json intermediate format, in the Modelica Language, in the Control Description Language and in English language format, such as in a Word document. The software functions as a web based application that includes a graphical user interface.

Wetter, Michael↗

IRMA

IRMA (In)elastic Representation of Materials As S(α,β) evaluations IRMA turns one phonon model into three outputs that usually require three separate tool chains: an evaluated nuclear-data file, predicted neutron-scattering spectra, and scattering kernels for Monte Carlo transport. The three outputs draw on a single, consistent description of the material, so the evaluation, the spectroscopy that can validate it, and the transport that uses it always agree about the physics. Nuclear data. IRMA writes ENDF-6 File 7 thermal scattering evaluations on automatically constructed (α, β) grids. This part reimplements and generalizes NJOY's LEAPR: the classic kernels reproduce freshly generated NJOY2016 tapes digit for digit and published reference tapes to about 1e-4, and the generalized paths add the exact coherent one-phonon term, anisotropic Debye-Waller tensors, coherent elastic for arbitrary crystals, and a per-species partition for polyatomic materials. The tapes feed NJOY, AMPX, FUDGE, and every transport code downstream of them. Neutron spectroscopy. The irma.spectra forward model projects the same physics onto an instrument's kinematics and resolution: INS spectra for VISION and generic indirect geometries, and 2-D S(Q,E) powder maps for direct-geometry spectrometers, from a phonopy model or straight from a phonon DOS. It can be used to predict a proposed measurement before beam time; in analysis, it supplies the calculated single-scattering counterpart of a measured spectrum, from the same material description the evaluation was built from. Monte Carlo transport. The irma.ncrystal exporter writes per-temperature scattering kernels for the companion NCrystal plugin, so McStas, OpenMC, and other NCrystal-aware codes sample the same physics. The exported kernels carry the per-site anisotropic Debye-Waller tensors, keeping directional coherent-elastic physics that NCrystal's standard scalar treatment does not represent. With the same physics inside a transport code, an entire beamline becomes a virtual experiment: IRMA's end-to-end validation ran a custom McStas implementation of the ARCS spectrometer, assembled from the existing McVine and McStas models, against measured data. From a bare crystal structure. The irma mlip front end builds the phonon model itself: a structure file and a choice of potential are enough. Nine pretrained machine-learned interatomic potentials are supported, on a laptop CPU, with no first-principles calculation; an approximate phonon model for a new material costs minutes, not a DFT campaign, and the build emits prefilled inputs for all three outputs. The result is a good starting point rather than a finished evaluation: survey-quality physics with every parameter exposed for review. A converged atomistic calculation enters the same way, as a phonopy model, when higher fidelity is needed.

Ramic, Kemal [Oak Ridge National Laboratory (ORNL)↗

Steric Sea Level Rise and Relationships with Model Drift and Water Mass Representation in GFDL CM4 and ESM4

Abstract Density-driven steric seawater changes are a leading-order contributor to global mean sea level rise. However, intermodel differences in the magnitude and spatial patterns of steric sea level rise exist at regional scales and often emerge during the spinup and preindustrial control integrations of climate models. Steric sea level results from an eddy-permitting climate model, GFDL CM4, are compared with a lower-resolution counterpart, GFDL-ESM4. The results from both models are examined through basin-scale heat budgets and watermass analysis, and we compare the patterns of ocean heat uptake, redistribution, and sea level differ in ocean-only [i.e., Ocean Model Intercomparison Project (OMIP)] and coupled climate configurations. After correcting for model drift, both GFDL CM4 and GFDL-ESM4 simulate nearly equivalent ocean heat content change and global sea level rise during the historical period. However, the GFDL CM4 model exhibits as much as a 40% increase in surface ocean heat uptake in the Southern Ocean and subsequent increases in horizontal export to other ocean basins after bias correction. The results suggest regional differences in the processes governing Southern Ocean heat export, such as the formation of Antarctic Intermediate Water (AAIW), Subpolar Mode Water (SPMW), and gyre transport between the two models, and that sea level changes in these models cannot be fully bias-corrected. Since the process-level differences between the two models are evident in the preindustrial control simulations of both models, these results suggest that the control simulations are important for identifying and correcting sea level–related model biases.

Krasting, John P. [a NOAA/OAR/Geophysical Fluid Dy↗

“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

Chemical database searching has become a fxture in many non-targeted identifcation workfows based on highresolution mass spectrometry (HRMS). However, the form of a chemical structure observed in HRMS does not always match the form stored in a database (e.g., the neutral form versus a salt; one component of a mixture rather than the mixture form used in a consumer product). Linking the form of a structure observed via HRMS to its related form(s) within a database will enable the return of all relevant variants of a structure, as well as the related metadata, in a single query. A Konstanz Information Miner (KNIME) workfow has been developed to produce structural representations observed using HRMS (“MS-Ready structures”) and links them to those stored in a database. These MS-Ready structures, and associated mappings to the full chemical representations, are surfaced via the US EPA’s Chemistry Dashboard (https://comptox.epa.gov/dashboard/). This article describes the workfow for the generation and linking of ~700,000 MS-Ready structures (derived from ~760,000 original structures) as well as download, search and export capabilities to serve structure identifcation using HRMS. The importance of this form of structural representation for HRMS is demonstrated with several examples, including integration with the in silico fragmentation software application MetFrag. The structures, search, download and export functionality are all available through the CompTox Chemistry Dashboard, while the MetFrag implementation can be viewed at https://msbi.ipb-halle.de/MetFragBeta/.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sorghum bicolor Core Metabolism Model

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

Feedstock Production↗

Motion Tracking Above and Below Water Dataset

This data set includes one trial of above and under water motion tracking measurements from a Qualysis motion tracking system. The Qualisys native .qtm file can be opened by the Qualisys Track Manager software. Data from this file has been exported to a tab separated value (.tsv) file which is a generic ASCII file format that can be read by a text editor, MATLAB, Excel, etc... Also exported is a native MATLAB formatted file (.mat) which can be loaded directly into MATLAB. The trial is from a three body wave energy converter device, using the underwater system for the central nacelle data, and above water system for the fore and aft floats.

16 TIDAL AND WAVE POWER↗

Stochastic simulations of temporally and spatially variable Fe cycling within a floodplain aquifer

This data package contains model input and output files for local and global sensitivity analysis (SA) of a reactive transport model simulating redox cycling within a floodplain aquifer. The reaction network is implemented in CrunchFlow and focuses on spatially and temporally heterogeneous Fe cycling, though it contains several other species and redox pathways (37 aqueous species and 7 minerals in total). The package contains data from 600 Monte Carlo simulations (for global SA) and 104 one-at-a-time simulations (for local SA). It includes all input files required to run the CrunchFlow model, as well as limited model output – .csv files containing time series of primary species concentrations at 21 grid cells within the domain. These time series files contain the following species: H+, CO32-, SO42-, Cl-, Ca2+, Mg2+, Na+, K+, Fe(II), Fe(III), HS-, CH3COO-, O2(aq), S(aq), and Br-.These data were used to demonstrate the application of a novel form of global SA, distance-based generalized sensitivity analysis (DGSA) to a reactive transport model. The 2D model simulates the export of reduced species from pockets of fine-grained, organic-rich sediments embedded in a coarse sand aquifer. Stochastic simulations jointly varied 17 key model input parameters across several orders of magnitude, including the spatial variability of each parameter. DGSA on the model results reveal that the amplitude and variability of exported Fe(II) are most sensitive to the interaction between sand permeability and individual reaction rates. By contrast, the propagation of reducing conditions downgradient from the fine-grained lenses depends most heavily on the rate of dissolved organic carbon and sulfate release from the fines.

54 ENVIRONMENTAL SCIENCES↗