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DOE OSTI2018

The intrinsically disordered nature of the peroxisomal protein translocation machinery

Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway.

Barros‐Barbosa, Aurora↗

DOE OSTI2014

SU-D-17A-02: Four-Dimensional CBCT Using Conventional CBCT Dataset and Iterative Subtraction Algorithm of a Lung Patient

Purpose: The Iterative Subtraction Algorithm (ISA) method generates retrospectively a pre-selected motion phase cone-beam CT image from the full motion cone-beam CT acquired at standard rotation speed. This work evaluates ISA method with real lung patient data. Methods: The goal of the ISA algorithm is to extract motion and no- motion components form the full reconstruction CBCT. The workflow consists of subtracting from the full CBCT all of the undesired motion phases and obtain a motion de-blurred single-phase CBCT image, followed by iteration of this subtraction process. ISA is realized as follows: 1) The projections are sorted to various phases, and from all phases, a full reconstruction is performed to generate an image CTM. 2) Generate forward projections of CTM at the desired phase projection angles, the subtraction of projection and the forward projection will reconstruct a CTSub1, which diminishes the desired phase component. 3) By adding back the CTSub1 to CTm, no motion CBCT, CTS1, can be computed. 4) CTS1 still contains residual motion component. 5) This residual motion component can be further reduced by iteration.The ISA 4DCBCT technique was implemented using Varian Trilogy accelerator OBI system. To evaluate the method, a lung patient CBCT dataset was used. The reconstruction algorithm is FDK. Results: The single phase CBCT reconstruction generated via ISA successfully isolates the desired motion phase from the full motion CBCT, effectively reducing motion blur. It also shows improved image quality, with reduced streak artifacts with respect to the reconstructions from unprocessed phase-sorted projections only. Conclusion: A CBCT motion de-blurring algorithm, ISA, has been developed and evaluated with lung patient data. The algorithm allows improved visualization of a single phase motion extracted from a standard CBCT dataset. This study has been supported by National Institute of Health through R01CA133539.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

TH-E-17A-01: Internal Respiratory Surrogate for 4D CT Using Fourier Transform and Anatomical Features

Purpose: To develop a novel algorithm to generate internal respiratory signals for sorting of four-dimensional (4D) computed tomography (CT) images. Methods: The proposed algorithm extracted multiple time resolved features as potential respiratory signals. These features were taken from the 4D CT images and its Fourier transformed space. Several low-frequency locations in the Fourier space and selected anatomical features from the images were used as potential respiratory signals. A clustering algorithm was then used to search for the group of appropriate potential respiratory signals. The chosen signals were then normalized and averaged to form the final internal respiratory signal. Performance of the algorithm was tested in 50 4D CT data sets and results were compared with external signals from the real-time position management (RPM) system. Results: In almost all cases, the proposed algorithm generated internal respiratory signals that visibly matched the external respiratory signals from the RPM system. On average, the end inspiration times calculated by the proposed algorithm were within 0.1 s of those given by the RPM system. Less than 3% of the calculated end inspiration times were more than one time frame away from those given by the RPM system. In 3 out of the 50 cases, the proposed algorithm generated internal respiratory signals that were significantly smoother than the RPM signals. In these cases, images sorted using the internal respiratory signals showed fewer artifacts in locations corresponding to the discrepancy in the internal and external respiratory signals. Conclusion: We developed a robust algorithm that generates internal respiratory signals from 4D CT images. In some cases, it even showed the potential to outperform the RPM system. The proposed algorithm is completely automatic and generally takes less than 2 min to process. It can be easily implemented into the clinic and can potentially replace the use of external surrogates.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

SU-E-J-240: Development of a Novel 4D MRI Sequence for Real-Time Liver Tumor Tracking During Radiotherapy

Purpose: To develop a Novel 4D MRI Technique that is feasible for realtime liver tumor tracking during radiotherapy. Methods: A volunteer underwent an abdominal 2D fast EPI coronal scan on a 3.0T MRI scanner (Siemens Inc., Germany). An optimal set of parameters was determined based on image quality and scan time. A total of 23 slices were scanned to cover the whole liver in the test scan. For each scan position, the 2D images were retrospectively sorted into multiple phases based on breathing signal extracted from the images. Consequently the 2D slices with same phase numbers were stacked to form one 3D image. Multiple phases of 3D images formed the 4D MRI sequence representing one breathing cycle. Results: The optimal set of scan parameters were: TR= 57ms, TE= 19ms, FOV read= 320mm and flip angle= 30°, which resulted in a total scan time of 14s for 200 frames (FMs) per slice and image resolution of (2.5mm,2.5mm,5.0mm) in three directions. Ten phases of 3D images were generated, each of which had 23 slices. Based on our test scan, only 100FMs were necessary for the phase sorting process which may lower the scan time to 7s/100FMs/slice. For example, only 5 slices/35s are necessary for a 4D MRI scan to cover liver tumor size ≤ 2cm leading to the possibility of tumor trajectory tracking every 35s during treatment. Conclusion: The novel 4D MRI technique we developed can reconstruct a 4D liver MRI sequence representing one breathing cycle (7s/ slice) without an external monitor. This technique can potentially be used for real-time liver tumor tracking during radiotherapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

SU-F-303-13: Initial Evaluation of Four Dimensional Diffusion- Weighted MRI (4D-DWI) and Its Effect On Apparent Diffusion Coefficient (ADC) Measurement

Purpose: Diffusion-weighted imaging(DWI) has been shown to have superior tumor-to-tissue contrast for cancer detection.This study aims at developing and evaluating a four dimensional DWI(4D-DWI) technique using retrospective sorting method for imaging respiratory motion for radiotherapy planning,and evaluate its effect on Apparent Diffusion Coefficient(ADC) measurement. Materials/Methods: Image acquisition was performed by repeatedly imaging a volume of interest using a multi-slice single-shot 2D-DWI sequence in the axial planes and cine MRI(served as reference) using FIESTA sequence.Each 2D-DWI image were acquired in xyz-diffusion-directions with a high b-value(b=500s/mm2).The respiratory motion was simultaneously recorded using bellows.Retrospective sorting was applied in each direction to reconstruct 4D-DWI.The technique was evaluated using a computer simulated 4D-digital human phantom(XCAT),a motion phantom and a healthy volunteer under an IRB-approved study.Motion trajectories of regions-of-interests(ROI) were extracted from 4D-DWI and compared with reference.The mean motion trajectory amplitude differences(D) between the two was calculated.To quantitatively analyze the motion artifacts,XCAT were controlled to simulate regular motion and the motions of 10 liver cancer patients.4D-DWI,free-breathing DWI(FB- DWI) were reconstructed.Tumor volume difference(VD) of each phase of 4D-DWI and FB-DWI from the input static tumor were calculated.Furthermore, ADC was measured for each phase of 4D-DWI and FB-DWI data,and mean tumor ADC values(M-ADC) were calculated.Mean M-ADC over all 4D-DWI phases was compared with M-ADC calculated from FB-DWI. Results: 4D-DWI of XCAT,the motion phantom and the healthy volunteer demonstrated the respiratory motion clearly.ROI D values were 1.9mm,1.7mm and 2.0mm,respectively.For motion artifacts analysis,XCAT 4D-DWI images show much less motion artifacts compare to FB-DWI.Mean VD for 4D-WDI and FB-DWI were 8.5±1.4% and 108±15%,respectively.Mean M-ADC for ADC measured from 4D-DWI and M-ADC measured from FB-DWI were (2.29±0.04)*0.001*mm2/s and (3.80±0.01)*0.001*mm2/s,respectively.ADC value ground-truth is 2.24*0.001*mm2/s from the input of the simulation. Conclusion: A respiratory correlated 4D-DWI technique has been initially evaluated in phantoms and a human subject.Comparing to free breathing DWI,4D-DWI can lead to more accurate measurement of ADC.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

MO-FG-204-08: Optimization-Based Image Reconstruction From Unevenly Distributed Sparse Projection Views

Purpose: Optimization-based reconstruction has been proposed and investigated for reconstructing CT images from sparse views, as such the radiation dose can be substantially reduced while maintaining acceptable image quality. The investigation has so far focused on reconstruction from evenly distributed sparse views. Recognizing the clinical situations wherein only unevenly sparse views are available, e.g., image guided radiation therapy, CT perfusion and multi-cycle cardiovascular imaging, we investigate the performance of optimization-based image reconstruction from unevenly sparse projection views in this work. Methods: The investigation is carried out using the FORBILD and an anthropomorphic head phantoms. In the study, 82 views, which are evenly sorted out from a full (360°) axial CT scan consisting of 984 views, form sub-scan I. Another 82 views are sorted out in a similar manner to form sub-scan II. As such, a CT scan with sparse (164) views at 1:6 ratio are formed. By shifting the two sub-scans relatively in view angulation, a CT scan with unevenly distributed sparse (164) views at 1:6 ratio are formed. An optimization-based method is implemented to reconstruct images from the unevenly distributed views. By taking the FBP reconstruction from the full scan (984 views) as the reference, the root mean square (RMS) between the reference and the optimization-based reconstruction is used to evaluate the performance quantitatively. Results: In visual inspection, the optimization-based method outperforms the FBP substantially in the reconstruction from unevenly distributed, which are quantitatively verified by the RMS gauged globally and in ROIs in both the FORBILD and anthropomorphic head phantoms. The RMS increases with increasing severity in the uneven angular distribution, especially in the case of anthropomorphic head phantom. Conclusion: The optimization-based image reconstruction can save radiation dose up to 12-fold while providing acceptable image quality for advanced clinical applications wherein only unevenly distributed sparse views are available. Research Grants: W81XWH-12-1-0138 (DoD), Sinovision Technologies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-F-T-243: Major Risks in Radiotherapy. A Review Based On Risk Analysis Literature

Purpose: We present a literature review of risk analyses in radiotherapy to highlight the most reported risks and facilitate the spread of this valuable information so that professionals can be aware of these major threats before performing their own studies. Methods: We considered studies with at least an estimation of the probability of occurrence of an adverse event (O) and its associated severity (S). They cover external beam radiotherapy, brachytherapy, intraoperative radiotherapy, and stereotactic techniques. We selected only the works containing a detailed ranked series of elements or failure modes and focused on the first fully reported quartile as much. Afterward, we sorted the risk elements according to a regular radiotherapy procedure so that the resulting groups were cited in several works and be ranked in this way. Results: 29 references published between 2007 and February 2016 were studied. Publication trend has been generally rising. The most employed analysis has been the Failure mode and effect analysis (FMEA). Among references, we selected 20 works listing 258 ranked risk elements. They were sorted into 31 groups appearing at least in two different works. 11 groups appeared in at least 5 references and 5 groups did it in 7 or more papers. These last sets of risks where choosing another set of images or plan for planning or treating, errors related with contours, errors in patient positioning for treatment, human mistakes when programming treatments, and planning errors. Conclusion: There is a sufficient amount and variety of references for identifying which failure modes or elements should be addressed in a radiotherapy department before attempting a specific analysis. FMEA prevailed, but other studies such as “risk matrix” or “occurrence × severity” analyses can also lead professionals’ efforts. Risk associated with human actions ranks very high; therefore, they should be automated or at least peer-reviewed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-CD-207A-06: Optimizing Four-Dimensional Digital Tomosynthesis Acquisition Based On Respiratory Guidance

Purpose: Patient breathing-related sorting method of projections in 4D digital tomosythesis (DTS) can be suffered from severe artifacts due to non-uniform angle distribution of projections and noncoplanar reconstructed images for each phase. In this study, we propose a method for optimally acquiring projection images in 4D DTS. Methods: In this method every pair of projections at x-ray tube’s gantry angles symmetrical with respect to the center of the range of gantry rotation is obtained at the same respiration amplitude. This process is challenging but becomes feasible with visual-biofeedback using a patient specific respiration guide wave which is in sinusoidal shape (i.e., smooth and symmetrical enough). Depending on scan parameters such as the number of acquisition points per cycle, total scan angle and projections per acquisition amplitude, acquisition sequence is pre-determined. A simulation study for feasibility test was performed. To mimic actual situation closely, a group of volunteers were recruited and breathing data were acquired both with/without biofeedback. Then, x-ray projections for a humanoid phantom were virtually performed following (1) the breathing data from volunteers without guide, (2) the breathing data with guide and (3) the planned breathing data (i.e., ideal situation). Images from all of 3 scenarios were compared. Results: Scenario #2 showed significant artifact reduction compared to #1 while did minimal increase from the ideal situation (i.e., scenario #3). We verified the performance of the method with regard to the degree of inaccuracy during respiratory guiding. Also, the scan angle dependence-related differences in the DTS images could reduce between using the proposed method and the established patient breathing-related sorting method. Conclusion: Through the proposed 4D DTS method, it is possible to improve the accuracy of image guidance between intra/inter fractions with relatively low imaging dose. This research was supported by the Mid-career Researcher Program through NRF funded by the Ministry of Science, ICT & Future Planning of Korea (NRF-2014R1A2A1A10050270) and by the Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Ultrastructural and Single-Cell-Level Characterization Reveals Metabolic Versatility in a Microbial Eukaryote Community from an Ice-Covered Antarctic Lake

The McMurdo Dry Valleys (MCM) of southern Victoria Land, Antarctica, harbor numerous ice-covered bodies of water that provide year-round liquid water oases for isolated food webs dominated by the microbial loop. Single-cell microbial eukaryotes (protists) occupy major trophic positions within this truncated food web, ranging from primary producers (e.g., chlorophytes, haptophytes, and cryptophytes) to tertiary predators (e.g., ciliates, dinoflagellates, and choanoflagellates). To advance the understanding of MCM protist ecology and the roles of MCM protists in nutrient and energy cycling, we investigated potential metabolic strategies and microbial interactions of key MCM protists isolated from a well-described lake (Lake Bonney). Fluorescence-activated cell sorting (FACS) of enrichment cultures, combined with single amplified genome/amplicon sequencing and fluorescence microscopy, revealed that MCM protists possess diverse potential metabolic capabilities and interactions. Two metabolically distinct bacterial clades ( Flavobacteria and Methylobacteriaceae ) were independently associated with two key MCM lake microalgae ( Isochrysis and Chlamydomonas , respectively). We also report on the discovery of two heterotrophic nanoflagellates belonging to the Stramenopila supergroup, one of which lives as a parasite of Chlamydomonas , a dominate primary producer in the shallow, nutrient-poor layers of the lake. Single-cell eukaryotes called protists play critical roles in the cycling of organic matter in aquatic environments. In the ice-covered lakes of Antarctica, protists play key roles in the aquatic food web, providing the majority of organic carbon to the rest of the food web (photosynthetic protists) and acting as the major consumers at the top of the food web (predatory protists). In this study, we utilized a combination of techniques (microscopy, cell sorting, and genomic analysis) to describe the trophic abilities of Antarctic lake protists and their potential interactions with other microbes. Ultimately, our work reveals that Antarctic lake protists rely on metabolic versatility for their energy and nutrient requirements in this unique and isolated environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A

Staphylococcus aureus causes reiterative and chronic persistent infections. This can be explained by the formidable ability of this pathogen to escape immune surveillance mechanisms. Cells of S. aureus display the abundant staphylococcal protein A (SpA). SpA binds to immunoglobulin (Ig) molecules and coats the bacterial surface to prevent phagocytic uptake. SpA also binds and cross-links variable heavy 3 (V H 3) idiotype (IgM) B cell receptors, promoting B cell expansion and the secretion of nonspecific V H 3-IgM via a mechanism requiring CD4 + T cell help. SpA binding to antibodies is mediated by the N-terminal Ig-binding domains (IgBDs). The so-called region X, uncharacterized LysM domain, and C-terminal LPXTG sorting signal for peptidoglycan attachment complete the linear structure of the protein. Here, we report that both the LysM domain and the LPXTG motif sorting signal are required for the B cell superantigen activity of SpA in a mouse model of infection. SpA molecules purified from staphylococcal cultures are sufficient to exert B cell superantigen activity and promote immunoglobulin secretion as long as they carry intact LysM and LPXTG motif domains with bound peptidoglycan fragments. The LysM domain binds the glycan chains of peptidoglycan fragments, whereas the LPXTG motif is covalently linked to wall peptides lacking glycan. These findings emphasize the complexity of SpA interactions with B cell receptors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Modern status of photonuclear data

The reliability of experimental cross sections obtained for (γ, 1n), (γ, 2n), and (γ, 3n) partial photoneutron reactions using beams of quasimonoenergetic annihilation photons and bremsstrahlung is analyzed by employing data for a large number of medium-heavy and heavy nuclei, including those of {sup 63,65}Cu, {sup 80}Se, {sup 90,91,94}Zr, {sup 115}In, {sup 112−124}Sn, {sup 133}Cs, {sup 138}Ba, {sup 159}Tb, {sup 181}Ta, {sup 186−192}Os, {sup 197}Au, {sup 208}Pb, and {sup 209}Bi. The ratios of the cross sections of definite partial reactions to the cross section of the neutron-yield reaction, F{sub i} = σ(γ, in)/σ(γ, xn), are used as criteria of experimental-data reliability. By definition, positive values of these ratios should not exceed the upper limits of 1.00, 0.50, 0.33,... for i = 1, 2, 3,..., respectively. For many nuclei, unreliable values of the above ratios were found to correlate clearly in various photon-energy regions F{sub i} with physically forbidden negative values of cross sections of partial reactions. On this basis, one can conclude that correspondent experimental data are unreliable. Significant systematic uncertainties of the methods used to determine photoneutron multiplicity are shown to be the main reason for this. New partial-reaction cross sections that satisfy the above data-reliability criteria were evaluated within an experimental–theoretical method [σ{sup eval}(γ, in) = F{sub i}{sup theor} (γ, in) × σ{sup expt}(γ, xn)] by employing the ratios F{sub i}{sup theor} (γ, in) calculated on the basis of a combined photonuclear-reaction model. It was obtained that cross sections evaluated in this way deviate substantially from the results of many experiments performed via neutron-multiplicity sorting, but, at the same time, agree with the results of alternative activation experiments. Prospects of employing methods that would provide, without recourse to photoneutron-multiplicity sorting, reliable data on cross sections of partial photoneutron reactions are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Detection of UV Radiation from Extensive Air Showers: Prospects for Cherenkov Gamma-Ray Astronomy

Cherenkov emission of extensive air showers (EAS) from cosmic gamma rays and cosmic-ray protons has been modelled. Spectral density of such emission in the 240–700 nm band has been determined for 3 GeV–10 TeV primaries of both sorts. It has been shown that the ratio of EAS Cherenkov emission fluxes in the optical and ultraviolet (UV) bands substantially depends on the sort of the primary, so the ratio can be employed to select gamma-ray events from the background produced by cosmic rays. Detection of EAS Cherenkov emission with specialized silicon photomultipliers sensitive in the UV band would allow one to substantially extend the duty cycle of a Cherenkov gamma-ray telescope, as it would be possible to observe the showers during moonlit nights. The UV-sensitive silicon photomultipliers developed at the Ioffe Institute would allow to detect gamma-ray-induced EAS at the Cherenkov gamma-ray observatory ALEGRO over a threshold of about 40 GeV at 5 km above sea level and about 80 GeV at 2 km above sea level.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

B-Trees and Cache-Oblivious B-Trees with Different-Sized Atomic Keys

Most B-tree articles assume that all $\textit{N}$ keys have the same size $\textit{K}$, that $\textit{f = B/K}$ keys fit in a disk block, and therefore that the search cost is $O(\text{log}_{f+1}N) $ block transfers. When keys have variable size, B-tree operations have no nontrivial performance guarantees, however. This article provides B-tree-like performance guarantees on dictionaries that contain keys of different sizes in a model in which keys must be stored and compared as opaque objects. The resulting atomic-key dictionaries exhibit performance bounds in terms of the average key size and match the bounds when all keys are the same size. Atomic-key dictionaries can be built with minimal modification to the B-tree structure, simply by choosing the pivot keys properly. Further, this article describes both static and dynamic atomic-key dictionaries. In the static case, if there are $\textit{N}$ keys with average size $\textit{K}$, the search cost is $O(\lceil K/B\rceil \text{log}_{1 + \lceil K/B\rceil} N)$ expected transfers. It is not possible to transform these expected bounds into worst-case bounds. The cost to build the tree is $\textit{O(NK)}$ operations and $\textit{O(NK/B)}$ transfers if all keys are presented in sorted order. If not, the cost is the sorting cost. For the dynamic dictionaries, the amortized cost to insert a key $\textit{κ}$ of arbitrary length at an arbitrary rank is dominated by the cost to search for $\textit{κ}$. Specifically, the amortized cost to insert a key $\textit{κ}$ of arbitrary length and random rank is $O(\lceil K/B\rceil log_{1+ \lceil B/K\rceil } N + |κ|/B)$ transfers. A dynamic-programming algorithm is shown for constructing a search tree with minimal expected cost. This article also gives a cache-oblivious static atomic-key B-tree, which achieves the same asymptotic performance as the static B-tree dictionary, mentioned previously. A cache-oblivious data structure or algorithm is not parameterized by the block size $\textit{B}$ or memory size $\textit{M}$ in the memory hierarchy; rather, it is universal, working simultaneously for all possible values of $\textit{B}$ or $\textit{M}$. On a machine with block size $\textit{B}$, if there are $\textit{N}$ keys with average size $\textit{K}$, search operations costs $O(\lceil K/B \rceil log_{1+ \lceil B/K \rceil} N)$ block transfers in expectation. This cache-oblivious layout can be built in $\textit{O(N}\text{log}\textit{(NK))}$ processor operations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Computational Complexity of Neuromorphic Algorithms

Neuromorphic computing has several characteristics that make it an extremely compelling computing paradigm for post Moore computation. Some of these characteristics include intrinsic parallelism, inherent scalability, collocated processing and memory, and event-driven computation. While these characteristics impart energy efficiency to neuromorphic systems, they do come with their own set of challenges. One of the biggest challenges in neuromorphic computing is to establish the theoretical underpinnings of the computational complexity of neuromorphic algorithms. In this paper, we take the first steps towards defining the space and time complexity of neuromorphic algorithms. Specifically, we describe a model of neuromorphic computation and state the assumptions that govern the computational complexity of neuromorphic algorithms. Next, we present a theoretical framework to define the computational complexity of a neuromorphic algorithm. We explicitly define what space and time complexities mean in the context of neuromorphic algorithms based on our model of neuromorphic computation. Finally, we leverage our approach and define the computational complexities of six neuromorphic algorithms: constant function, successor function, predecessor function, projection function, neuromorphic sorting algorithm and neighborhood subgraph extraction algorithm.

Date, Prasanna↗

DOE OSTI2024

Divergence Reduction in Monte Carlo Neutron Transport with On-GPU Asynchronous Scheduling

While Monte Carlo Neutron Transport (MCNT) is near-embarrasingly parallel, the effectively unpredictable lifetime of neutrons can lead to divergence when MCNT is evaluated on GPUs. Divergence is the phenomenon of adjacent threads in a warp executing different control flow paths; on GPUS, it reduces performance because each work group may only execute one path at a time. The process of Thread Data Remapping (TDR) resolves these discrepancies by moving data across hardware such that data in the same warp will be processed through similar paths. A common issue among prior implementations of TDR is the synchronous nature of its remapping and processing cycles, which exhaustively sort data produced by prior processing passes and exhaustively evaluate the sorted data. In another work, we defined a method of remapping data through an asynchronous scheduler which allows for work to be stored in shared memory and deferred arbitrarily until that work is a viable option for low-divergence evaluation. This article surveys a wider set of cases, with the goal of characterizing performance trends across a more comprehensive set of parameters. These parameters include cross sections of scattering/capturing/fission, use of implicit capture, source neutron counts, simulation time spans, and tuned memory allocations. Across these cases, we have recorded minimum and average execution times, as well as a heuristically tuned near-optimal memory allocation size for both synchronous and asynchronous scheduling. Across the collected data, it is shown that the asynchronous method is faster and more memory efficient in the majority of cases, and that it requires less tuning to achieve competitive performance.

Computer Science↗

DOE OSTI2016

PcapDB: Search Optimized Packet Capture, Version 0.1.0.0

PcapDB is a packet capture system designed to optimize the captured data for fast search in the typical (network incident response) use case. The technology involved in this software has been submitted via the IDEAS system and has been filed as a provisional patent. It includes the following primary components: capture: The capture component utilizes existing capture libraries to retrieve packets from network interfaces. Once retrieved the packets are passed to additional threads for sorting into flows and indexing. The sorted flows and indexes are passed to other threads so that they can be written to disk. These components are written in the C programming language. search: The search components provide a means to find relevant flows and the associated packets. A search query is parsed and represented as a search tree. Various search commands, written in C, are then used resolve this tree into a set of search results. The tree generation and search execution management components are written in python. interface: The PcapDB web interface is written in Python on the Django framework. It provides a series of pages, API's, and asynchronous tasks that allow the user to manage the capture system, perform searches, and retrieve results. Web page components are written in HTML,CSS and Javascript.

Ferrell, Paul↗

DOE OSTI2019

Pretty Linter GrumPhP

This software takes JSON and YAML files, and after running them through a linter, sorts the keys of objects alphabetically. This helps prevent the following problems when checking these data/config files into repositories: Problems where the entire file looks like it was removed and added due to Indentation changes Key sorting differences Merging issues when 2 or more people add data to the same or similar locations

Williams, Thom↗

DOE OSTI2024

Cell Population–resolved Multiomics Atlas of the Developing Lung

The lung is a vital organ that undergoes extensive morphological and functional changes during postnatal development. To disambiguate how different cell populations contribute to organ development, we performed proteomic and transcriptomic analyses of four sorted cell populations from the lung of human subjects aged 0 to 8 years-old with a focus on early life. The cell populations analyzed included epithelial, endothelial, mesenchymal, and immune cells. Our results revealed distinct molecular signatures for each of the sorted cell populations that enable the description of molecular shifts occurring in these populations during post-natal development. Here, we confirmed that the proteome of the different cell populations was distinct regardless of age and identified functions specific to each population. We identified a series of cell population protein markers, including those located at the cell surface, that show differential expression and distribution on RNA in situ hybridization and immunofluorescence imaging. We validated the spatial distribution of AT1 and endothelial cell surface markers. Temporal analyses of the proteome of each of the four populations revealed processes modulated during postnatal development and disambiguating results obtained on whole tissue proteome. Finally, the proteome was compared to a transcriptomics survey performed on the same lung samples to evaluate processes under post-transcriptional control.

59 BASIC BIOLOGICAL SCIENCES↗