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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗
DOE OSTI2021

Mongooses ( Urva auropunctata ) as reservoir hosts of Leptospira species in the United States Virgin Islands, 2019–2020

During 2019–2020, the Virgin Islands Department of Health investigated potential animal reservoirs of Leptospira spp., the bacteria that cause leptospirosis. In this cross-sectional study, we investigated Leptospira spp. exposure and carriage in the small Indian mongoose (Urva auropunctata, syn: Herpestes auropunctatus), an invasive animal species. This study was conducted across the three main islands of the U.S. Virgin Islands (USVI), which are St. Croix, St. Thomas, and St. John. We used the microscopic agglutination test (MAT), fluorescent antibody test (FAT), real-time polymerase chain reaction (lipl32 rt-PCR), and bacterial culture to evaluate serum and kidney specimens and compared the sensitivity, specificity, positive predictive value, and negative predictive value of these laboratory methods. Mongooses (n = 274) were live-trapped at 31 field sites in ten regions across USVI and humanely euthanized for Leptospira spp. testing. Bacterial isolates were sequenced and evaluated for species and phylogenetic analysis using the ppkgene. Anti-Leptospira spp. antibodies were detected in 34% (87/256) of mongooses. Reactions were observed with the following serogroups: Sejroe, Icterohaemorrhagiae, Pyrogenes, Mini, Cynopteri, Australis, Hebdomadis, Autumnalis, Mankarso, Pomona, and Ballum. Of the kidney specimens examined, 5.8% (16/270) were FAT-positive, 10% (27/274) were culture-positive, and 12.4% (34/274) were positive by rt-PCR. Of the Leptospira spp. isolated from mongooses, 25 were L. borgpetersenii, one was L. interrogans, and one was L. kirschneri. Positive predictive values of FAT and rt-PCR testing for predicting successful isolation of Leptospira by culture were 88% and 65%, respectively. The isolation and identification of Leptospira spp. in mongooses highlights the potential role of mongooses as a wildlife reservoir of leptospirosis; mongooses could be a source of Leptospira spp. infections for other wildlife, domestic animals, and humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Strategy for Safety-Related Digital I&C Qualification

Digital I&C qualification continues to be a major impediment to addressing the reliability and obsolescence issues of the legacy analog I&C systems of the operating LWR fleet. In particular, the issue of digital common cause failure (CCF) has been difficult to address and has been the reason that some nuclear plant licensees have deferred upgrades of these critical plant systems and have rather opted to maintain them with considerable engineering and maintenance efforts. This is getting more and more difficult in the face of declining analog technology suppliers and dwindling supplies of spare parts and support for many critical components. To remain a viable energy source for the nation, the nuclear fleet must reduce its operating costs to a competitive level. Digital technology is the foremost means of implementing performance improvements and cost reductions for this purpose. This has been demonstrated over and over again in other industry sectors, as well as in conventional generation facilities. However, due to the special nature of nuclear energy, these digital I&C qualification barriers remain and must be resolved in order to modernize these plants and transform the business model to one that is competitive. The purpose of this report is to present an assessment of digital I&C qualification issues and address gaps in qualification methods and processes that would potentially benefit from Department of Energy (DOE)-sponsored research and development. Two new qualification methods are described that are recommended for further Department of Energy-sponsored research and development. They are 1) Testability – the exhaustive (100%) testing of certain digital devices addressing all combinations of inputs and internal states, and 2) Elimination of CCF triggers – ensuring that any latent digital defects are not concurrently triggered in redundant and back-up safety systems. In addition this report presents a strategy for full nuclear plant modernization based on four interrelated elements that together address the remaining barriers to prudent implementation. These four elements are 1) End-State Architecture, 2) Cost-Benefit Analysis, 3) Regulatory Approval, and 4) Implementation Sequence Plan.

42 ENGINEERING↗
DOE OSTI2026

Microreactor Core Transportation Cask Model Description for Criticality Safety Validation Basis Assessment (Rev. 1)

Criticality safety analyses are completed on transportation casks used for microreactor whole core shipment to provide examples of models and analyses to industry, regulators, and nuclear community at large to be used in verification and validation analyses of similar applications. The microreactors considered are based on a Gas-Cooled Microreactor (GCMR) and a Heat-Pipe Microreactor (HPMR), both utilize HALEU fuel in the form of TRISO particles and various other design options considered in industry microreactor designs. Variant design options of GCMR and HPMR were also investigated to provide a wider application range for each technology. Criticality safety analyses for the GCMR and HPMR packages were performed using the CSAS6 sequence of SCALE 6.3.2 with the ENDF/B-VII.1-based continuous energy neutron libraries. Different scenarios were investigated, including normal operation and water flooded conditions to represent nominal and hypothetical accident scenarios. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE 6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with Intermediate and mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems, together with additional experiments that are sponsored by the DNCSH program. Many experiments were found marginally similar to the GCMR and HPMR models, with similarity index (ck) values greater than 0.8 but less than 0.9. Among all the experiments analyzed, no case has a ck value greater than 0.9, indicating that additional critical experiments might be needed to further validate the criticality safety models for microreactors transport packages.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Microreactor Core Transportation Cask Model Description for Criticality Safety Validation Basis Assessment (Rev. 2)

Criticality safety analyses are completed on transportation casks used for microreactor whole core shipment to provide examples of models and analyses to industry, regulators, and nuclear community at large to be used in verification and validation analyses of similar applications. The microreactors considered are based on a Gas-Cooled Microreactor (GCMR) and a Heat-Pipe Microreactor (HPMR), both utilize HALEU fuel in the form of TRISO particles and various other design options considered in industry microreactor designs. Variant design options of GCMR and HPMR were also investigated to provide a wider application range for each technology. Criticality safety analyses for the GCMR and HPMR packages were performed using the CSAS6 sequence of SCALE 6.3.2 with the ENDF/B-VII.1-based continuous energy neutron libraries. Different scenarios were investigated, including normal operation and water flooded conditions to represent nominal and hypothetical accident scenarios. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE 6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with High Enriched Uranium (HEU), Intermediate and mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems. Many ICSBEP experiments were found marginally similar, with similarity index (ck) values greater than 0.8, to the GCMR and HPMR cask models, especially in flooded conditions that may be more constraining due to reduced reactivity margins. Some experiments using TRISO fuel particles and graphite moderator, including the recent THETA and Deimos experiments from LANL, together with some IRPhEP experiments, were also used for the similarity analyses. These TRISO-fueled and graphite moderated experiments behaved similarly to the GCMR models, with maximum ck value greater than 0.9, but they are less similar to the HPMR models. This observation indicates that additional critical experiments might be needed to further validate the criticality safety models, especially for heat-pipe based microreactor transport packages and for non-flooded transportation configurations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor

There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Furthermore, transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC)

Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol Collector (ABC) for NASA's C-20A that can make collections for microbiological research investigations up to altitudes of 13.7 km. Herein we report results from the first set of science flights—four consecutive missions flown over the United States (US) from 30 October to 2 November, 2017. To ascertain how the concentration of airborne bacteria changed across the tropopause, we collected air during aircraft Ascent/Descent (0.3 to 11 km), as well as sustained Cruise altitudes in the lower stratosphere (~12 km). Bioaerosols were captured on DNA-treated gelatinous filters inside a cascade air sampler, then analyzed with molecular and culture-based characterization. Several viable bacterial isolates were recovered from flight altitudes, including Bacillus sp., Micrococcus sp., Arthrobacter sp., and Staphylococcus sp. from Cruise samples and Brachybacterium sp. from Ascent/Descent samples. Using 16S V4 sequencing methods for a culture-independent analysis of bacteria, the average number of total OTUs was 305 for Cruise samples and 276 for Ascent/Descent samples. Some taxa were more abundant in the flight samples than the ground samples, including OTUs from families Lachnospiraceae , Ruminococcaceae and Erysipelotrichaceae as well as the following genera: Clostridium, Mogibacterium, Corynebacterium, Bacteroides, Prevotella, Pseudomonas, and Parabacteroides . Surprisingly, our results revealed a homogeneous distribution of bacteria in the atmosphere up to 12 km. The observation could be due to atmospheric conditions producing similar background aerosols across the western US, as suggested by modeled back trajectories and satellite measurements. However, the influence of aircraft-associated bacterial contaminants could not be fully eliminated and that background signal was reported throughout our dataset. Furthermore considering the tremendous engineering challenge of collecting biomass at extreme altitudes where contamination from flight hardware remains an ever-present issue, we note the utility of using the stratosphere as a proving ground for planned life detection missions across the solar system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Adaptive Evolution of Sphingobium hydrophobicum C1 T in Electronic Waste Contaminated River Sediment

Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1 T , characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1 T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1 T and other Sphingobium strains, numerous C1 T -unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1 T . Moreover, presence of type IV secretion systems may allow strain C1 T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies.

comparative genomics↗
DOE OSTI2017

VLT/Magellan spectroscopy of 29 strong lensing selected galaxy clusters

We present an extensive spectroscopic follow-up campaign of 29 strong lensing (SL) selected galaxy clusters discovered primarily in the Second Red-Sequence Cluster Survey (RCS-2). Our spectroscopic analysis yields redshifts for 52 gravitational arcs present in the core of our galaxy clusters, which correspond to 35 distinct background sources that are clearly distorted by the gravitational potential of these clusters. These lensed galaxies span a wide redshift range of 0.8 ≤ z ≤ 2.9, with a median redshift of z{sub s} = 1.8 ± 0.1. We also measure reliable redshifts for 1004 cluster members, allowing us to obtain robust velocity dispersion measurements for 23 of these clusters, which we then use to determine their dynamical masses by using a simulation-based σ{sub DM} − M{sub 200} scaling relation. The redshift and mass ranges covered by our SL sample are 0.22 ≤ z ≤ 1.01 and 5×10{sup 13}⩽M{sub 200}/h{sub 70}{sup −1} M{sub ⊙}⩽1.9×10{sup 15}, respectively. We analyze and quantify some possible effects that might bias our mass estimates, such as the presence of substructure, the region where cluster members are selected for spectroscopic follow-up, the final number of confirmed members, and line-of-sight effects. We find that 10 clusters of our sample with N{sub mem} ≳ 20 show signs of dynamical substructure. However, the velocity data of only one system is inconsistent with a uni-modal distribution. We therefore assume that the substructures are only marginal and not of comparable size to the clusters themselves. Consequently, our velocity dispersion and mass estimates can be used as priors for SL mass reconstruction studies and also represent an important step toward a better understanding of the properties of the SL galaxy cluster population.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1966

Dynamic Environment of the Ranger Spacecraft I Through IX (Final Report)

The dynamic environment of the Ranger spacecraft (I through IX)during the launch portion of flight is defined in this Report. Flight data from each of nine spacecraft launches have been reviewed and are included. The environments receiving emphasis herein include liftoff acoustics, liftoff and transonic vibration, and the transient vibrations of the various pyrotechnic and staging events in the launch sequence. The systems for data acquisition and analysis are briefly described. In addition, post-flight comparison of flight data and ground test specification levels is made, and the dynamic test program is briefly discussed.

SHOCK↗
NASA NTRS1971

Techniques for generation of control and guidance signals derived from optical fields, part 2

The development is reported of a high resolution technique for the detection and identification of landmarks from spacecraft optical fields. By making use of nonlinear regression analysis, a method is presented whereby a sequence of synthetic images produced by a digital computer can be automatically adjusted to provide a least squares approximation to a real image. The convergence of the method is demonstrated by means of a computer simulation for both elliptical and rectangular patterns. Statistical simulation studies with elliptical and rectangular patterns show that the computational techniques developed are able to at least match human pattern recognition capabilities, even in the presence of large amounts of noise. Unlike most pattern recognition techniques, this ability is unaffected by arbitrary pattern rotation, translation, and scale change. Further development of the basic approach may eventually allow a spacecraft or robot vehicle to be provided with an ability to very accurately determine its spatial relationship to arbitrary known objects within its optical field of view.

Hemami, H.↗
NASA NTRS1972

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2A: Accident model document, appendix

The detailed abort sequence trees for the reference zirconium hydride (ZrH) reactor power module that have been generated for each phase of the reference Space Base program mission are presented. The trees are graphical representations of causal sequences. Each tree begins with the phase identification and the dichotomy between success and failure. The success branch shows the mission phase objective as being achieved. The failure branch is subdivided, as conditions require, into various primary initiating abort conditions.

Source record↗
NASA NTRS1973

A unified method for analyzing mission reliability for fault tolerant computer systems.

For fault-tolerant computer systems consisting of multiple classes of modules, a unified method for analyzing mission reliability is proposed and evaluated. The analysis proceeds by generalizing the notions of standby and N modular redundancy into a concept called hybrid-degraded redundancy. The probabilistic evaluation of the unified redundancy concept is then developed to yield, for a given modular class, the joint distribution of success and the number of nonfailed modules from that class, at special times. With this information, a Markov chain analysis gives the reliability of an entire sequence of phases (mission profile).

Bricker, J. L.↗
NASA NTRS1975

Design automation techniques for custom LSI arrays

The standard cell design automation technique is described as an approach for generating random logic PMOS, CMOS or CMOS/SOS custom large scale integration arrays with low initial nonrecurring costs and quick turnaround time or design cycle. The system is composed of predesigned circuit functions or cells and computer programs capable of automatic placement and interconnection of the cells in accordance with an input data net list. The program generates a set of instructions to drive an automatic precision artwork generator. A series of support design automation and simulation programs are described, including programs for verifying correctness of the logic on the arrays, performing dc and dynamic analysis of MOS devices, and generating test sequences.

Feller, A.↗
NASA NTRS1975

Centaur propellant acquisition system study

A study was performed to determine the desirability of replacing the hydrogen peroxide settling system on the Centaur D-1S with a capillary acquisition system. A comprehensive screening was performed to select the most promising capillary device fluid acquisition, thermal conditioning, and fabrication techniques. Refillable start baskets and bypass feed start tanks were selected for detailed design. Critical analysis areas were settling and refilling, start sequence development with an initially dry boost pump, and cooling the fluid delivered to the boost pump in order to provide necessary net position suction head (NPSH). Design drawings were prepared for the start basket and start tank concepts for both LO2 and LH2 tanks. System comparisons indicated that the start baskets using wicking for thermal conditioning, and thermal subcooling for boost pump NPSH, are the most desirable systems for future development.

Blatt, M. H.↗
NASA NTRS1975

Centaur propellant acquisition system

The desirability of replacing the hydrogen peroxide settling system of the Centaur D-1S with a capillary acquisition system was evaluated. A comprehensive screening was performed to select the most promising capillary device fluid acquisition, thermal conditioning, and fabrication techniques. Refillable start baskets and bypass feed start tanks were selected for detailed design. Critical analysis areas were settling and refilling, start sequence development with an initially dry boost pump, and cooling the fluid delivered to the boost pump to provide the necessary net positive suction head (NPSH). Design drawings were prepared for start basket and start tank concepts for both the liquid oxygen and liquid hydrogen tanks. System comparisons indicated that the start baskets using wicking flow for thermal conditioning, and thermal subcooling for providing boost pump NPSH, are the most desirable systems for future Centaur acquisition system development.

Blatt, M. H.↗
NASA NTRS1980

Stability optimization of laminated composite plates

The optimum design of plates with orthotropic layers under axial compression and shear is discussed. The plates considered are the laminates of N orthotropic layers whose principal material axes coincide with the plate axes. Each layer is assumed to have the same thickness and an equal number of fibers in the direction of + alpha sub i and - alpha sub i with respect to the plate axis. The fiber directions which give the highest axial buckling stress and the highest shear buckling stress are found by utilizing a mathematical optimization technique for various aspect ratios of the plates. Inhomogeneity in the direction of the plate thickness (stacking sequence) is taken into account in this analysis.

Hirano, Y.↗
NASA NTRS1980

ISSYS: An integrated synergistic Synthesis System

Integrated Synergistic Synthesis System (ISSYS), an integrated system of computer codes in which the sequence of program execution and data flow is controlled by the user, is discussed. The commands available to exert such control, the ISSYS major function and rules, and the computer codes currently available in the system are described. Computational sequences frequently used in the aircraft structural analysis and synthesis are defined. External computer codes utilized by the ISSYS system are documented. A bibliography on the programs is included.

Dovi, A. R.↗