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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain: Periplasmic Ligand Binding Protein Dret_0059

We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.

Wu, R.↗
DOE OSTI2014

Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

Lu, Jun↗
DOE OSTI2016

Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes

Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms.Moreover, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Prenatal planning of placenta previa: diagnostic accuracy of a novel MRI-based prediction model for placenta accreta spectrum (PAS) and clinical outcome

Purpose: To investigate the diagnostic accuracy of MRI for placenta accreta spectrum (PAS) and clinical outcome prediction in women with placenta previa, using a novel MRI-based predictive model. Methods: Thirty-eight placental MRI exams performed on a 1.5T scanner were retrospectively reviewed by two radiologists in consensus. The presence of T2 dark bands, myometrial thinning, abnormal vascularity, uterine bulging, placental heterogeneity, placental protrusion sign, placental recess, and percretism signs was scored using a 5-point scale. Pathology and clinical intrapartum findings were the standard of reference for PAS, while intrapartum/peripartum bleeding and emergency hysterectomy defined the clinical outcome. Receiver-operating characteristic (ROC) analysis and discriminant function analysis were performed to test the predictive power of MRI findings for both PAS and clinical outcome prediction. Results: Abnormal vascularity and percretism signs were the two most predictive MRI features of PAS. The area under the curve (AUC) of the predictive function was 0.833 (cutoff 0.39, 67% sensitivity, 100% specificity, p = 0.001). Percretism signs and myometrial thinning were the two most predictive MRI features of poor outcome. AUC of the predictive function was 0.971 (cutoff − 0.55, 100% sensitivity, 77% specificity, p < 0.001). Conclusion: The diagnostic accuracy of MRI, especially considering the combination of the most predictive MRI findings, is higher when the target of the prediction is the clinical outcome rather than the PAS.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors

Here, the neuronal PAS domain proteins NPAS1 and NPAS3 are members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family, and their genetic deficiencies are linked to a variety of human psychiatric disorders including schizophrenia, autism spectrum disorders and bipolar disease. NPAS1 and NPAS3 must each heterodimerize with the aryl hydrocarbon receptor nuclear translocator (ARNT), to form functional transcription complexes capable of DNA binding and gene regulation. Here we examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT-DNA complexes, discovering each to contain four putative ligand-binding pockets. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT, HIF-2α-ARNT and CLOCK-BMAL1, we show the wider mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

AmeriFlux FLUXNET-1F US-PAS Florida, Paspalum notatum pasture

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-PAS Florida, Paspalum notatum pasture. This is the FLUXNET version of the carbon flux data for the site US-PAS Florida, Paspalum notatum pasture produced by applying the standard ONEFlux (1F) software. Site Description - Florida cultivated grass (Paspalum notatum) pasture rotationally stocked year-round. Soils are predominatly spodosols, subject to periodoc flooding.

Bracho, Rosvel [University of Florida]↗
DOE OSTI2018

PAS-histidine kinases PHK1 and PHK2 exert oxygen-dependent dual and opposite effects on gametophore formation in the moss Physcomitrella patens

Highlights: • Two unique histidine kinases repress a developmental process in a moss plant. • These kinases promote the same process when submerged under water. • Similarly, they promote the process in artificial hypoxic condition. • Thus, these kinases have dual and opposite functions depending on oxygen condition. • This study adds insight into flexibility and evolution of two-component systems. Two-component systems, versatile signaling mechanisms based on phosphate transfer between component proteins, must have played important roles in adaptation and diversification processes in land plant evolution. We previously demonstrated that two Per-Arnt-Sim (PAS)-histidine kinases, PHK1 and PHK2, repress gametophore formation in the moss Physcomitrella patens under aerobic conditions, and that, in eukaryotes, the presence of their homologs is restricted to early-diverging streptophyte linages. We assessed here whether or not PHKs play a role in oxygen signaling. When submerged under water, the double disruption line for PHK1 and PHK2 formed fewer gametophores than the wild-type line (WT) both under light-dark cycles or continuous light, indicating that PHKs promote gametophore formation under an aquatic environment, in contrast to aerobic conditions. Similarly, in an artificial low-oxygen condition, the double disruption line formed fewer gametophores than WT. These results indicate that PHKs exert dual and opposite effects on gametophore formation depending on oxygen status. This study adds important insight into functional versatility and evolutionary significance of two-component systems in land plants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

pas

PAS: Prelim Attention Score for Detecting Object Hallucinations in Large Vision-Language Models

Bhattarai, Manish↗
DOE OSTI2022

AmeriFlux US-PAS Florida, Paspalum notatum pasture

This is the AmeriFlux version of the carbon flux data for the site US-PAS Florida, Paspalum notatum pasture. Site Description - Florida cultivated grass (Paspalum notatum) pasture rotationally stocked year-round. Soils are predominatly spodosols, subject to periodoc flooding.

Bracho, Rosvel↗
DOE OSTI2017

Impacts of Updated GSA Groundwater Flow Models on the FTF, HTF and SDF PAs

Savannah River Remediation (SRR) requested that the Savannah River National Laboratory (SRNL) evaluate the impacts of an updated General Separations Area (GSA) groundwater flow model on the F-Area Tank Farm (FTF), H-Area Tank Farm (HTF) and Saltstone Disposal Facility (SDF) Performance Assessments (PAs)1. For each facility, PORFLOW simulations were performed using both the 2004 GSA/PORFLOW (i.e., GSA_2004) and GSA2016 (i.e., GSA_2016) flow models. Overall, GSA_2004 and “_reference” (i.e., the archived data) results are practically identical, indicating GSA_2004 simulations reproduce the archived data very well. Compared with GSA_2004 data, the PEST.47 GSA_2016 results (with PORFLOW harmonic averaging at cell faces and diagonal terms in the dispersion tensor) support the following findings.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

PAS: Privacy Algorithms in Systems

Today we face an explosion of data generation, ranging from health monitoring to national security infrastructure systems. More and more systems are connected to the Internet that collects data at regular time intervals. These systems share data and use machine learning methods for intelligent decisions, which resulted in numerous real-world applications (e.g., autonomous vehicles, recommendation systems, and heart-rate monitoring) that have benefited from it. However, these approaches are prone to identity thief and other privacy related cyber-security attacks. So, how can data privacy be protected efficiently in these scenarios? More dedicated efforts are needed to propose the integration of privacy techniques into existing systems and develop more advanced privacy techniques to address the complex challenges of multi-system connectivity and data fusion. Therefore, we have introduced Privacy Algorithms in Systems (PAS) at CIKM which provides a venue to gather academic researchers and industry researchers/practitioners to present their research in an effort to advance the frontier of this critical direction of privacy algorithms in systems.

Kotevska, Olivera↗
DOE OSTI2023

Ceci N’est Pas Une Bombe: Lessons from a Field Experiment Using Neutron and Gamma Measurements to Confirm the Absence of Nuclear Weapons

In March 2023, the UN Institute for Disarmament Research held a verification experiment that included a mockup onsite inspection at a former military facility in the municipality of Menzingen, Switzerland. The experiment included a visit to the site by an inspection team, accompanied by the host team. Among other activities, radiation measurements were used to confirm the non-nuclear nature of selected items stored onsite. In this paper, we discuss the neutron and gamma measurement systems used during the experiment and the inspection protocols followed to confirm the absence of nuclear weapons. Furthermore, results from the experiment and a laboratory reproduction are presented, before concluding with lessons learned for how absence-confirmation measurements can help support verification of future arms control agreements.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2014

Ceci N'est Pas a globular cluster: the metallicity distribution of the stellar system Terzan 5

We present new determinations of the iron abundance for 220 stars belonging to the stellar system Terzan 5 in the Galactic bulge. The spectra have been acquired with FLAMES at the Very Large Telescope of the European Southern Observatory and DEIMOS at the Keck II Telescope. This is by far the largest spectroscopic sample of stars ever observed in this stellar system. From this data set, a subsample of targets with spectra unaffected by TiO bands was extracted and statistically decontaminated from field stars. Once combined with 34 additional stars previously published by our group, a total sample of 135 member stars covering the entire radial extent of the system has been used to determine the metallicity distribution function of Terzan 5. The iron distribution clearly shows three peaks: a super-solar component at [Fe/H] ≅ 0.25 dex, accounting for ∼29% of the sample, a dominant sub-solar population at [Fe/H] ≅ –0.30 dex, corresponding to ∼62% of the total, and a minor (6%) metal-poor component at [Fe/H] ≅ –0.8 dex. Such a broad, multi-modal metallicity distribution demonstrates that Terzan 5 is not a genuine globular cluster but the remnant of a much more complex stellar system.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Texture analysis of placental MRI: can it aid in the prenatal diagnosis of placenta accreta spectrum?

Purpose: To determine if texture analysis can differentiate placenta accreta spectrum (PAS) from normal placenta on MRI. Methods: We performed retrospective image analysis of 80 patients, comprised of 46 patients with PAS and 34 patients without PAS. Histopathology was used as the reference standard. Sagittal single shot fast spin echo T2-weighted MRI sequences acquired from a single institution were analyzed. Placental heterogeneity was quantified using in-house software on a Matlab platform, including the standard deviation of pixel intensity, coefficient of variation, gray-level co-occurrence matrices (GLCM), histogram-oriented gradients (HOG), and fractal analysis with box sizes from 2 to 512. Two-tailed unpaired Student’s t test was used with statistical significance of p < 0.05. Results: PAS was associated with higher values for standard deviation of pixel intensity and fractal analysis at every box size. Fractal analysis at box sizes 256 (p = 0.011) and 32 (p = 0.021), and standard deviation of pixel intensity (p = 0.023) were the most statistically significant. Fractal values at box size 256 for PAS was 0.13 versus 0.090 for patients without PAS, while standard deviation of pixel intensity was 3.7 for PAS versus 2.5 for patients without PAS. No statistically significant association between PAS and GLCM, coefficient of variation, and HOG was found. Conclusion: Statistically significant differences were found between normal and abnormal groups using standard deviation of pixel intensity and fractal analysis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗