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At least 109 records · Page 6

Quantitative modeling of carcinogenesis induced by single beams or mixtures of space radiations using targeted and non-targeted effects

Abstract Ionizing radiations encountered by astronauts on deep space missions produce biological damage by two main mechanisms: (1) Targeted effects (TE) due to direct traversals of cells by ionizing tracks. (2) Non-targeted effects (NTE) caused by release of signals from directly hit cells. The combination of these mechanisms generates non-linear dose response shapes, which need to be modeled quantitatively to predict health risks from space exploration. Here we used a TE + NTE model to analyze data on APC (1638N/+) mouse tumorigenesis induced by space-relevant doses of protons, 4 He, 12 C, 16 O, 28 Si or 56 Fe ions, or γ rays. A customized weighted Negative Binomial distribution was used to describe the radiation type- and dose-dependent data variability. This approach allowed detailed quantification of dose–response shapes, NTE- and TE-related model parameters, and radiation quality metrics (relative biological effectiveness, RBE, and radiation effects ratio, RER, relative to γ rays) for each radiation type. Based on the modeled responses for each radiation type, we predicted the tumor yield for a Mars-mission-relevant mixture of these radiations, using the recently-developed incremental effect additivity (IEA) synergy theory. The proposed modeling approach can enhance current knowledge about quantification of space radiation quality effects, dose response shapes, and ultimately the health risks for astronauts.

60 APPLIED LIFE SCIENCES↗

Characterization of robotics parallel algorithms and mapping onto a reconfigurable SIMD machine

The kinematics, dynamics, Jacobian, and their corresponding inverse computations are six essential problems in the control of robot manipulators. Efficient parallel algorithms for these computations are discussed and analyzed. Their characteristics are identified and a scheme on the mapping of these algorithms to a reconfigurable parallel architecture is presented. Based on the characteristics including type of parallelism, degree of parallelism, uniformity of the operations, fundamental operations, data dependencies, and communication requirement, it is shown that most of the algorithms for robotic computations possess highly regular properties and some common structures, especially the linear recursive structure. Moreover, they are well-suited to be implemented on a single-instruction-stream multiple-data-stream (SIMD) computer with reconfigurable interconnection network. The model of a reconfigurable dual network SIMD machine with internal direct feedback is introduced. A systematic procedure internal direct feedback is introduced. A systematic procedure to map these computations to the proposed machine is presented. A new scheduling problem for SIMD machines is investigated and a heuristic algorithm, called neighborhood scheduling, that reorders the processing sequence of subtasks to reduce the communication time is described. Mapping results of a benchmark algorithm are illustrated and discussed.

Lee, C. S. G.↗

Detection of Moving Targets Using Soliton Resonance Effect

The objective of this research was to develop a fundamentally new method for detecting hidden moving targets within noisy and cluttered data-streams using a novel "soliton resonance" effect in nonlinear dynamical systems. The technique uses an inhomogeneous Korteweg de Vries (KdV) equation containing moving-target information. Solution of the KdV equation will describe a soliton propagating with the same kinematic characteristics as the target. The approach uses the time-dependent data stream obtained with a sensor in form of the "forcing function," which is incorporated in an inhomogeneous KdV equation. When a hidden moving target (which in many ways resembles a soliton) encounters the natural "probe" soliton solution of the KdV equation, a strong resonance phenomenon results that makes the location and motion of the target apparent. Soliton resonance method will amplify the moving target signal, suppressing the noise. The method will be a very effective tool for locating and identifying diverse, highly dynamic targets with ill-defined characteristics in a noisy environment. The soliton resonance method for the detection of moving targets was developed in one and two dimensions. Computer simulations proved that the method could be used for detection of singe point-like targets moving with constant velocities and accelerations in 1D and along straight lines or curved trajectories in 2D. The method also allows estimation of the kinematic characteristics of moving targets, and reconstruction of target trajectories in 2D. The method could be very effective for target detection in the presence of clutter and for the case of target obscurations.

Kulikov, Igor K.↗

The Impact of Sampling Strategy on the Cloud Droplet Number Concentration Estimated From Satellite Data

Cloud droplet number concentration (Nd) is of central importance to observation-based estimates of aerosol indirect effects, being used to quantify both the cloud sensitivity to aerosol and the base state of the cloud. However, the derivation of Nd from satellite data depends on a number of assumptions about the cloud and the accuracy of the retrievals of the cloud properties from which it is derived, making it prone to systematic biases. A number of sampling strategies have been proposed to address these biases by selecting the most accurate Nd retrievals in the satellite data. This work compares the impact of these strategies on the accuracy of the satellite retrieved Nd, using a selection of in situ measurements. In stratocumulus regions, the MODIS Nd retrieval is able to achieve a high precision (r2 of 0.5–0.8). This is lower in other cloud regimes but can be increased by appropriate sampling choices. Although the Nd sampling can have significant effects on the Nd climatology, it produces only a 20 % variation in the implied radiative forcing from aerosol–cloud interactions, with the choice of aerosol proxy driving the overall uncertainty. The results are summarised into recommendations for using MODIS Nd products and appropriate sampling.

Edward Gryspeerdt↗

Heavy-Ion-Induced Lung Tumors: Dose- & LET-Dependence

There is a limited published literature reporting dose-dependent data for in vivo tumorigenesis prevalence in different organs of various rodent models after exposure to low, single doses of charged particle beams. The goal of this study is to reduce uncertainties in estimating particle-radiation-induced risk of lung tumorigenesis for manned travel into deep space by improving our understanding of the high-LET-dependent dose-response from exposure to individual ion beams after low particle doses (0.03 - 0.80 Gy). Female CB6F1 mice were irradiated with low single doses of either oxygen, silicon, titanium, or iron ions at various energies to cover a range of dose-averaged LET values from 0.2 - 193 keV/µm, using 137Cs γ-rays as the reference radiation. Sham-treated controls were included in each individual experiment totally 398 animals across the 5 studies reported. Based on power calculations, between 40 - 156 mice were included in each of the treatment groups. Tumor prevalence at 16 months after radiation exposure was determined and compared to the age-matched, sham-treated animals. Results indicate that lung tumor prevalence is non-linear as a function of dose with suggestions of threshold doses depending on the LET of the beams. Histopathological evaluations of the tumors showed that the majority of tumors were benign bronchioloalveolar adenomas with occasional carcinomas or lymphosarcomas which may have resulted from metastases from other sites.

60 APPLIED LIFE SCIENCES↗

Towards developing robust algorithms for solving partial differential equations on MIMD machines

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

Saltz, J. H.↗

Towards developing robust algorithms for solving partial differential equations on MIMD machines

Methods for efficient computation of numerical algorithms on a wide variety of MIMD machines are proposed. These techniques reorganize the data dependency patterns to improve the processor utilization. The model problem finds the time-accurate solution to a parabolic partial differential equation discretized in space and implicitly marched forward in time. The algorithms are extensions of Jacobi and SOR. The extensions consist of iterating over a window of several timesteps, allowing efficient overlap of computation with communication. The methods increase the degree to which work can be performed while data are communicated between processors. The effect of the window size and of domain partitioning on the system performance is examined both by implementing the algorithm on a simulated multiprocessor system.

Saltz, Joel H.↗

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis

Cross-kingdom microbial symbioses, such as those between algae and bacteria, are key players in biogeochemical cycles. The molecular changes during initiation and establishment of symbiosis are of great interest, but quantitatively monitoring such changes can be challenging, particularly when the microorganisms differ greatly in size or are intimately associated. Here, we analyze output from label-free, data-dependent acquisition (DDA) LC-MS/MS proteomics experiments investigating the well-studied interaction between the alga Chlamydomonas reinhardtii and the heterotrophic bacterium Mesorhizobium japonicum. We found that detection of bacterial proteins decreased in coculture by 50% proteome-wide due to the abundance of algal proteins. As a result, standard differential expression analysis led to numerous false-positive reports of significantly downregulated proteins, where it was not possible to distinguish meaningful biological responses to symbiosis from artifacts of the reduced protein detection in coculture relative to monoculture. We show that data normalization alone does not eliminate the impact of altered detection on differential expression analysis of the cross-kingdom symbiosis. We assessed two additional strategies to overcome this methodological artifact inherent to DDA proteomics. In the first, we combined algal and bacterial monocultures at a relative abundance that mimicked the coculture, creating a “mono-mix” control to which the coculture could be compared. This approach enabled comparable detection of bacterial proteins in the coculture and the monoculture control. In the second strategy, we enhanced detection of lowly abundant bacterial proteins by using sample fractionation upstream of LC-MS/MS analysis. When these simple approaches were combined, they allowed for meaningful comparisons of nearly 10,000 algal proteins and over 4,000 bacterial proteins in response to symbiosis by DDA. They successfully recovered expected changes in the bacterial proteome in response to algal coculture, including upregulation of sugar-binding proteins and transporters. They also revealed novel proteomic responses to coculture that guide hypotheses about algal-bacterial interactions.

Dupuis, Sunnyjoy [University of California, Berkel↗

The Stellar decomposition: A compact representation for simplicial complexes and beyond

Here, we introduce the Stellar decomposition, a model for efficient topological data structures over a broad range of simplicial and cell complexes. A Stellar decomposition of a complex is a collection of regions indexing the complex’s vertices and cells such that each region has sufficient information to locally reconstruct the star of its vertices, i.e., the cells incident in the region’s vertices. Stellar decompositions are general in that they can compactly represent and efficiently traverse arbitrary complexes with a manifold or non-manifold domain. They are scalable to complexes in high dimension and of large size, and they enable users to easily construct tailored application-dependent data structures using a fraction of the memory required by a corresponding global topological data structure on the complex. As a concrete realization of this model for spatially embedded complexes, we introduce the Stellar tree, which combines a nested spatial tree with a simple tuning parameter to control the number of vertices in a region. Stellar trees exploit the complex’s spatial locality by reordering vertex and cell indices according to the spatial decomposition and by compressing sequential ranges of indices. Stellar trees are competitive with state-of-the-art topological data structures for manifold simplicial complexes and offer significant improvements for cell complexes and non-manifold simplicial complexes. We conclude with a high-level description of several mesh processing and analysis applications that utilize Stellar trees to process large datasets.

97 MATHEMATICS AND COMPUTING↗

Emission spectra of selected SSME elements and materials

Stennis Space Center (SSC) is pursuing the advancement of experimental techniques and theoretical developments in the field of plume spectroscopy for application to rocket development testing programs and engine health monitoring. Exhaust plume spectral data for the Space Shuttle Main Engine (SSME) are routinely acquired. The usefulness of this data depends upon qualitative and quantitative interpretation of spectral features and their correlation with the engine performance. A knowledge of the emission spectral characteristics of effluent materials in the exhaust plume is essential. A study of SSME critical components and their materials identified 30 elements and 53 materials whose engine exhaust plume spectral might be required. The most important were evaluated using SSC's Diagnostic Testbed Facility Thruster (DTFT), a 1200-lbf, liquid oxygen/gaseous hydrogen rocket engine which very nearly replicates the temperature and pressure conditions of the SSME exhaust plume in the first Mach diamond. This report presents the spectral data for the 10 most important elements and 27 most important materials which are strongly to moderately emitting in the DTFT exhaust plume. The covered spectral range is 300 to 426 nm and the spectral resolution is 0.25 nm. Spectral line identification information is provided and line interference effects are considered.

Tejwani, Gopal D.↗

Mean thermal and albedo behavior of the Mars surface and atmosphere over a Martian year

A Mars average data set (MADS) has been constructed from thermal and albedo measurements of the Viking Infrared Thermal Mapper; by merging information from all longitudes, and ensuring reasonably complete longitudinal sampling, a representation of mean Mars behavior is obtained. Brightness temperatures at 7, 9, 11, 15, and 20 microns and albedo information in the band 0.3-3.0 microns have been binned using 2 deg latitude strips, 24 times of day, 3 emission angle intervals, and 23 nonoverlapping solar longitude periods covering 1.43 Mars years starting at a solar longitude of 84 deg. The MADS is ideally suited to parametric study of latitudinal, diurnal, angular, and seasonal dependences. Data are presented for surface thermal and albedo behavior in clear and dusty atmospheric conditions; the thermal response of the atmospheric temperature to a major dust storm is found to be consistent with Mariner 9 data from the 1971 storm. Examples of use of the MADS, which is available through the Mars Consortium, indicate how averaged data reveal specific surface and atmospheric phenomena.

Martin, T. Z.↗

Elemental Composition of 433 Eros: New Calibration of the NEAR-Shoemaker XRS Data

We present relative elemental abundances for six elements (Mg, Al, Si, S, Ca, Fe) in the surface layer of 433 Eros, derived from a new analysis of the solar induced fluorescence measured by the NEARShoemaker X ray Spectrometer (XRS).XRS derived elemental abundances have been presented before. However, calibration of XRS data depends critically on knowledge of the incident solar spectrum, which varies greatly on time scales of seconds to minutes. Unfortunately, the gas solar monitor carried by NEAR was inadequately calibrated prior to launch. The previously published XRS results were based partly on broadband measurements by the Earthorbiting GOES8 (Geostationary Operational Environmental Satellites) Xray detectors and partly on a preliminary solar monitor calibration carried out by the present authors. The new solar monitor calibration is based on a more recent set of physical models of the solar spectrum at various temperatures, an improved fitting procedure, analysis of a large number of flight spectra, and comparison with concurrent data from the GOES Xray detectors. In addition, the new analysis includes data from three solar flares not considered in earlier papers.

Lim, L. F.↗

Data-flow parallelism for high-energy and nuclear physics frameworks

The processing tasks of an event-processing workflow in high-energy and nuclear physics (HENP) can typically be represented as a directed acyclic graph formed according to the data flow—i.e. the data dependencies among algorithms executed as part of the workflow. With this representation, an HENP framework can optimally execute a workflow, exploiting the parallelism inherent among independent tasks. Despite such a natural description of a workflow, most HENP frameworks do not make use of technologies that provide concurrent execution of graph-based tasking structures. In this talk, we describe Fermilab efforts to adopt a graph-based technology (specifically Intel’s oneTBB flow graph) for meeting the framework needs of its experiments, notably DUNE. Building on the Meld project as presented at CHEP2023, we demonstrate that all common processing idioms supported by current frameworks can naturally be supported by oneTBB’s data-flow technology, optimally leveraging the concurrent capabilities of the machine. In addition, we discuss collaborative efforts between Fermilab and the Intel oneTBB development team, who is considering improvements to the flow-graph technology to better support HENP use cases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ejecta patterns of Meteor Crater, Arizona derived from the linear un-mixing of TIMS data and laboratory thermal emission spectra

Accurate interpretation of thermal infrared data depends upon the understanding and removal of complicating effects. These effects may include physical mixing of various mineralogies and particle sizes, atmospheric absorption and emission, surficial coatings, geometry effects, and differential surface temperatures. The focus is the examination of the linear spectral mixing of individual mineral or endmember spectra. Linear addition of spectra, for particles larger than the wavelength, allows for a straight-forward method of deconvolving the observed spectra, predicting a volume percent of each endmember. The 'forward analysis' of linear mixing (comparing the spectra of physical mixtures to numerical mixtures) has received much attention. The reverse approach of un-mixing thermal emission spectra was examined with remotely sensed data, but no laboratory verification exists. Understanding of the effects of spectral mixing on high resolution laboratory spectra allows for the extrapolation to lower resolution, and often more complicated, remotely gathered data. Thermal Infrared Multispectral Scanner (TIMS) data for Meteor Crater, Arizona were acquired in Sep. 1987. The spectral un-mixing of these data gives a unique test of the laboratory results. Meteor Crater (1.2 km in diameter and 180 m deep) is located in north-central Arizona, west of Canyon Diablo. The arid environment, paucity of vegetation, and low relief make the region ideal for remote data acquisition. Within the horizontal sedimentary sequence that forms the upper Colorado Plateau, the oldest unit sampled by the impact crater was the Permian Coconino Sandstone. A thin bed of the Toroweap Formation, also of Permian age, conformably overlays the Coconino. Above the Toroweap lies the Permian Kiabab Limestone which, in turn, is covered by a thin veneer of the Moenkopi Formation. The Moenkopi is Triassic in age and has two distinct sub-units in the vicinity of the crater. The lower Wupatki member is a fine-grained sandstone, while the upper Moqui member is a fissile siltstone. Ejecta from these units are preserved as inverted stratigraphy up to 2 crater radii from the rim. The mineralogical contrast between the units, relative lack of post-emplacement erosion and ejecta mixing provide a unique site to apply the un-mixing model. Selection of the aforementioned units as endmembers reveals distinct patterns in the ejecta of the crater.

Ramsey, Michael S.↗

Data-flow parallelism for high-energy and nuclear physics computing frameworks

The processing tasks of a scientific workflow in high-energy and nuclear physics (HENP) can typically be represented as a directed acyclic graph formed according to the data flow—i.e. the data dependencies among algorithms executed as part of the workflow. With this representation, an HENP computing framework can optimally execute a workflow, exploiting the parallelism inherent among independent tasks. Despite such a natural description of a workflow, most HENP frameworks do not make use of technologies that provide concurrent execution of graph-based tasking structures. In this session, we describe Fermilab efforts to adopt a graph-based technology (specifically Intel’s oneTBB flow graph) for meeting the framework needs of its experiments, notably DUNE. After introducing the physics DUNE intends to explore, we will show that all common processing idioms supported by current HENP frameworks can naturally be supported by oneTBB’s data-flow technology, optimally leveraging the concurrent capabilities of the machine. In addition, we discuss collaborative efforts between Fermilab and the Intel oneTBB development team, who is considering improvements to the flow-graph technology to better support HENP use cases.

43 PARTICLE ACCELERATORS↗

Accuracy Assessments and Validation of an Expanded UV Irradiance Database from Satellite Total Ozone Mapping Spectrometer (TOMS)

The TOMS UV irradiance database (1978 to 2000) has been expanded to include 5 new products (noon irradiance at 305, 310, 324, and 380 nm, and noon erythemal-weighted irradiance), in addition to the existing erythemal daily exposure, which permit direct Comparisons with ground-based measurements from UV spectrometers. Sensitivity studies are conducted to estimate uncertainties of the new TOMS UV irradiance data due to algorithm apriori assumptions. Comparisons with Brewer spectrometers as well as filter radiometers are used to review of the sources of known errors. Inability to distinguish between snow and cloud cover using only TOMS data results in large errors in estimating surface UV using snow climatology. A correction is suggested for the case when the regional snow albedo is known from an independent source. The summer-time positive bias between TOMS UV estimations and Brewer measurements can be seen at all wavelengths. This suggests the difference is not related to ozone absorption effects. We emphasize that uncertainty of boundary layer UV aerosol absorption properties remains a major source of error in modeling UV irradiance in clear sky conditions. Neglecting aerosol absorption by the present TOMS algorithm results in a positive summertime bias in clear-sky UV estimations over many locations. Due to high aerosol variability the bias is strongly site dependent. Data from UV-shadow-band radiometer and well-calibrated CIMEL sun-sky radiometer are used to quantify the bias at NASA/GSFC site in Greenbelt, MD. Recommendations are given to enable potential users to better account for local conditions by combining standard TOMS UV data with ancillary ground measurements.

Krotkov, N. A.↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

Detector Control and Data Acquisition for the Wide-Field Infrared Survey Telescope (WFIRST) with a Custom ASIC

The Wide-Field Infrared Survey Telescope (WFIRST) will have the largest near-IR focal plane ever flown by NASA, a total of 18 4K x 4K devices. The project has adopted a system-level approach to detector control and data acquisition where 1) control and processing intelligence is pushed into components closer to the detector to maximize signal integrity, 2) functions are performed at the highest allowable temperatures, and 3) the electronics are designed to ensure that the intrinsic detector noise is the limiting factor for system performance. For WFIRST, the detector arrays operate at 90 to 100 K, the detector control and data acquisition functions are performed by a custom ASIC at 150 to 180 K, and the main data processing electronics are at the ambient temperature of the spacecraft, notionally approx.300 K. The new ASIC is the main interface between the cryogenic detectors and the warm instrument electronics. Its single-chip design provides basic clocking for most types of hybrid detectors with CMOS ROICs. It includes a flexible but simple-to-program sequencer, with the option of microprocessor control for more elaborate readout schemes that may be data-dependent. All analog biases, digital clocks, and analog-to-digital conversion functions are incorporated and are connected to the nearby detectors with a short cable that can provide thermal isolation. The interface to the warm electronics is simple and robust through multiple LVDS channels. It also includes features that support parallel operation of multiple ASICs to control detectors that may have more capability or requirements than can be supported by a single chip.

data acquisition↗