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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Validation of Spawn Checks and Saltwater Age Assignments Based on Scales from Known Repeat-Spawning Steelhead

Abstract It is critical to resolve the effects of regeneration, false annuli, and resorption on interpretation of scale patterns. We used scales collected from known repeat-spawning steelhead Oncorhynchus mykiss from the Snake River to (1) determine the accuracy of spawn check identification and (2) investigate errors in assignment of saltwater ages before and after spawn checks. Scale readers (n = 4) accurately identified over 96% of known repeat spawners (n = 107) and did not identify spawn checks in known first-time spawners (n = 197). Scale resorption associated with the spawn check caused an obscured or lost saltwater annulus in 66% of samples, most frequently in fish that spent 2 years versus 1 year in saltwater. Presence or absence of an annulus after the spawn check was accurately assigned in 86% of samples (n = 100). The potential for scale resorption to affect interpretation of the life history of iteroparous anadromous salmonids is significant. We supply two examples of how circulus counts can provide guidance to scale readers, but this analysis should be customized to the growth characteristics of each stock of interest.

Copeland, Timothy↗
DOE OSTI2010

Amyloid formation and disaggregation of {alpha}-synuclein and its tandem repeat ({alpha}-TR)

Research highlights: {yields} Formation of the {alpha}-synuclein amyloid fibrils by [BIMbF{sub 3}Im]. {yields} Disaggregation of amyloid fibrils by epigallocatechin gallate (EGCG) and baicalein. {yields} Amyloid formation of {alpha}-synuclein tandem repeat ({alpha}-TR). -- Abstract: The aggregation of {alpha}-synuclein is clearly related to the pathogenesis of Parkinson's disease. Therefore, detailed understanding of the mechanism of fibril formation is highly valuable for the development of clinical treatment and also of the diagnostic tools. Here, we have investigated the interaction of {alpha}-synuclein with ionic liquids by using several biochemical techniques including Thioflavin T assays and transmission electron microscopy (TEM). Our data shows a rapid formation of {alpha}-synuclein amyloid fibrils was stimulated by 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [BIMbF{sub 3}Im], and these fibrils could be disaggregated by polyphenols such as epigallocatechin gallate (EGCG) and baicalein. Furthermore, the effect of [BIMbF{sub 3}Im] on the {alpha}-synuclein tandem repeat ({alpha}-TR) in the aggregation process was studied.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Confirmation of a Low {alpha}/{beta} Ratio for Prostate Cancer Treated by External Beam Radiation Therapy Alone Using a Post-Treatment Repeated-Measures Model for PSA Dynamics

Purpose: To estimate the {alpha}/{beta} ratio of prostate cancer treated with external beam radiation only by use of a model of long-term prostate-specific antigen (PSA) dynamics. Methods and Materials: Repeated measures of PSA from 5,093 patients from 6 institutions treated for localized prostate cancer by external beam radiation therapy (EBRT) without planned androgen deprivation were analyzed. A biphasic linear mixed model described the post-treatment evolution of PSA, rather than a conventional model of time to biochemical recurrence. The model was adjusted for standard prognostic factors (T stage, initial PSA level, and Gleason score) and cohort-specific effects. The radiation dose fractionation effect was estimated from the long-term rate of rise of PSA level. Results: Adjusted for other factors, total dose of EBRT and sum of squared doses per fraction were associated with long-term rate of change of PSA level (p = 0.0017 and p = 0.0003, respectively), an increase of each being associated with a lower rate of rise. The {alpha}/{beta} ratio was estimated at 1.55 Gy (95% confidence band, 0.46-4.52 Gy). This estimate was robust to adjustment of the linear mixed model. Conclusions: By analysis of a large EBRT-only cohort along with a method that uses all the repeated measures of PSA after the end of treatment, a low and precise {alpha}/{beta} was estimated. These data support the use of hypofractionation at fractional doses up to 2.8 Gy but cannot presently be assumed to accurately represent higher doses per fraction.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Relative plan robustness of step-and-shoot vs rotational intensity–modulated radiotherapy on repeat computed tomographic simulation for weight loss in head and neck cancer

Introduction: Interfractional anatomical alterations may have a differential effect on the dose delivered by step-and-shoot intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT). The increased degrees of freedom afforded by rotational delivery may increase plan robustness (measured by change in target volume coverage and doses to organs at risk [OARs]). However, this has not been evaluated for head and neck cancer. Materials and methods: A total of 10 patients who required repeat computed tomography (CT) simulation and replanning during head and neck IMRT were included. Step-and-shoot IMRT and VMAT plans were generated from the original planning scan. The initial and second CT simulation scans were fused and targets/OAR contours transferred, reviewed, and modified. The plans were applied to the second CT scan and doses recalculated without repeat optimization. Differences between step-and-shoot IMRT and VMAT for change in target volume coverage and doses to OARs between first and second CT scans were compared by Wilcoxon signed rank test. Results: There were clinically relevant dosimetric changes between the first and the second CT scans for both the techniques (reduction in mean D{sub 95%} for PTV2 and PTV3, D{sub min} for CTV2 and CTV3, and increased mean doses to the parotid glands). However, there were no significant differences between step-and-shoot IMRT and VMAT for change in any target coverage parameter (including D{sub 95%} for PTV2 and PTV3 and D{sub min} for CTV2 and CTV3) or dose to any OARs (including parotid glands) between the first and the second CT scans. Conclusions: For patients with head and neck cancer who required replanning mainly due to weight loss, there were no significant differences in plan robustness between step-and-shoot IMRT and VMAT. This information is useful with increased clinical adoption of VMAT.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2010

FR-like EBNA1 binding repeats in the human genome

Epstein-Barr virus (EBV) is widely spread in the human population. EBV nuclear antigen 1 (EBNA1) is a transcription factor that activates viral genes and is necessary for viral replication and partitioning, which binds the EBV genome cooperatively. We identify similar EBNA1 repeat binding sites in the human genome using a nearest-neighbor positional weight matrix. Previously experimentally verified EBNA1 sites in the human genome are successfully recovered by our approach. Most importantly, 40 novel regions are identified in the human genome, constituted of tandemly repeated binding sites for EBNA1. Genes located in the vicinity of these regions are presented as possible targets for EBNA1-mediated regulation. Among these, four are discussed in more detail: IQCB1, IMPG1, IRF2BP2 and TPO. Incorporating the cooperative actions of EBNA1 is essential when identifying regulatory regions in the human genome and we believe the findings presented here are highly valuable for the understanding of EBV-induced phenotypic changes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

The crystal structure of HIV CRF07 B′/C gp41 reveals a hyper-mutant site in the middle of HR2 heptad repeat

HIV CRF07 B′/C is a strain circulating mainly in northwest region of China. The gp41 region of CRF07 is derived from a clade C virus. In order to compare the difference of CRF07 gp41 with that of typical clade B virus, we solved the crystal structure of the core region of CRF07 gp41. Compared with clade B gp41, CRF07 gp41 evolved more basic and hydrophilic residues on its helix bundle surface. Based on sequence alignment, a hyper-mutant cluster located in the middle of HR2 heptads repeat was identified. The mutational study of these residues revealed that this site is important in HIV mediated cell–cell fusion and plays critical roles in conformational changes during viral invasion. - Highlights: • We solved the crystal structure of HIV CRF07 gp41 core region. • A hyper-mutant cluster in the middle of HR2 heptads repeat was identified. • The hyper-mutant site is important in HIV-cell fusion. • The model will help to understand the HIV fusion process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core

WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. In this paper, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Results of the IEA Round Robin on Viscosity and Aging of Fast Pyrolysis Bio-oils: Long-Term Tests and Repeatability

An international round robin study of the viscosity and aging of fast pyrolysis bio-oil has been undertaken recently and this work is an outgrowth from that effort. Two bio-oil samples were distributed to the laboratories for aging tests and extended viscosity studies. The accelerated aging test was defined as the change in viscosity of a sealed sample of bio-oil held for 24 h at 80 °C. The test was repeated 10 times over consecutive days to determine the repeatability of the method. Other bio-oil samples were placed in storage at three temperatures, 21 °C, 4 °C and -17 °C for a period up to a year to evaluate the change in viscosity. The variation in the results of the aging test was shown to be low within a given laboratory. Storage of bio-oil under refrigeration can minimize the amount of change in viscosity. The accelerated aging test gives a measure of change similar to that of 6-12 months of storage at room temperature. These results can be helpful in setting standards for use of bio-oil, which is just coming into the marketplace.

aging↗
DOE OSTI2016

Crosstalk between MSH2–MSH3 and polβ promotes trinucleotide repeat expansion during base excision repair

Studies in knockout mice provide evidence that MSH2–MSH3 and the BER machinery promote trinucleotide repeat (TNR) expansion, yet how these two different repair pathways cause the mutation is unknown. Here we report the first molecular crosstalk mechanism, in which MSH2–MSH3 is used as a component of the BER machinery to cause expansion. On its own, pol b fails to copy TNRs during DNA synthesis, and bypasses them on the template strand to cause deletion. Remarkably, MSH2–MSH3 not only stimulates pol b to copy through the repeats but also enhances formation of the flap precursor for expansion. Our results provide direct evidence that MMR and BER, operating together, form a novel hybrid pathway that changes the outcome of TNR instability from deletion to expansion during the removal of oxidized bases. We propose that cells implement crosstalk strategies and share machinery when a canonical pathway is ineffective in removing a difficult lesion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The 27 kDa Trypanosoma brucei Pentatricopeptide Repeat Protein is a G-tract Specific RNA Binding Protein

Pentatricopeptide repeat (PPR) proteins, a helical repeat family of organellar RNA binding proteins, play essential roles in post-transcriptional RNA processing. In Trypanosoma brucei, an expanded family of PPR proteins localize to the parasite’s single mitochondrion, where they are believed to perform important roles in both RNA processing and translation. We studied the RNA binding specificity of the simplest T. brucei PPR protein (KRIPP11) using electrophoretic mobility shift assays, fluorescence anisotropy, circular dichroism spectroscopy, and in vitro selection. We found KRIPP11 to be an RNA binding protein with specificity for sequences of four or more consecutive guanosine residues (G-tracts). Such G-tracts are dramatically enriched in T. brucei mitochondrial transcripts that are destined for extensive uridine insertion/deletion editing but are not present in mRNAs following editing. We further found that the quadruplex oligoguanosine RNA conformation is preferentially recognized by KRIPP11 over other conformational forms, and is bound without disruption of the quadruplex structure. In combination with prior data demonstrating association of KRIPP11 with the small ribosomal subunit, these results suggest possible roles for KRIPP11 in bridging mRNA maturation and translation or in facilitating translation of unusual dual-coded open reading frames.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Repeated interactions in open quantum systems

Analyzing the dynamics of open quantum systems has a long history in mathematics and physics. Depending on the system at hand, basic physical phenomena that one would like to explain are, for example, convergence to equilibrium, the dynamics of quantum coherences (decoherence) and quantum correlations (entanglement), or the emergence of heat and particle fluxes in non-equilibrium situations. From the mathematical physics perspective, one of the main challenges is to derive the irreversible dynamics of the open system, starting from a unitary dynamics of the system and its environment. The repeated interactions systems considered in these notes are models of non-equilibrium quantum statistical mechanics. They are relevant in quantum optics, and more generally, serve as a relatively well treatable approximation of a more difficult quantum dynamics. In particular, the repeated interaction models allow to determine the large time (stationary) asymptotics of quantum systems out of equilibrium.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

A high stability and repeatability electrochemical scanning tunneling microscope

We present a home built electrochemical scanning tunneling microscope (ECSTM) with very high stability and repeatability. Its coarse approach is driven by a closely stacked piezo motor of GeckoDrive type with four rigid clamping points, which enhances the rigidity, compactness, and stability greatly. It can give high clarity atomic resolution images without sound and vibration isolations. Its drifting rates in XY and Z directions in solution are as low as 84 pm/min and 59 pm/min, respectively. In addition, repeatable coarse approaches in solution within 2 mm travel distance show a lateral deviation less than 50 nm. The gas environment can be well controlled to lower the evaporation rate of the cell, thus reducing the contamination and elongating the measurement time. Atomically resolved SO{sub 4}{sup 2−} image on Au (111) work electrode is demonstrated to show the performance of the ECSTM.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models

WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P 7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Analysis of Repeatability and Reproducibility Studies With Ordinal Measurements

A Bayesian inferential approach with a noninformative prior is introduced to analyze ordinal repeatability and reproducibility (R&R) data using the De Mast–Van Wieringen model. This approach is extended with a weakly informative prior and random effects to allow for the consideration of a population of raters and prediction of a new rater. This random-effects approach is also shown to result in partial pooling of estimates across raters. In addition, match-probability-based measures to decompose ordinal R&R study data into contributions due to repeatability and due to reproducibility are defined. All extensions involving Bayesian inference (for fixed or random effects) and measures are illustrated on real and simulated ordinal R&R study data and are applicable in business and industry settings. This methodology can be implemented using the supplemental R package ordinalRR available from CRAN. Additional supplementary material for this article is available online.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

SGR-like behaviour of the repeating FRB 121102

Fast radio bursts (FRBs) are millisecond-duration radio signals occurring at cosmological distances. However the physical model of FRBs is mystery, many models have been proposed. Here we study the frequency distributions of peak flux, fluence, duration and waiting time for the repeating FRB 121102. The cumulative distributions of peak flux, fluence and duration show power-law forms. The waiting time distribution also shows power-law distribution, and is consistent with a non-stationary Poisson process. These distributions are similar as those of soft gamma repeaters (SGRs). We also use the statistical results to test the proposed models for FRBs. These distributions are consistent with the predictions from avalanche models of slowly driven nonlinear dissipative systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2010

FIRST VERY LOW FREQUENCY DETECTION OF SHORT REPEATED BURSTS FROM MAGNETAR SGR J1550-5418

We report on the first detection of ionospheric disturbances caused by short repeated gamma-ray bursts from the magnetar SGR J1550-5418. Very low frequency (VLF) radio wave data obtained in South America clearly show sudden amplitude and phase changes at the corresponding times of eight soft gamma-ray repeater bursts. Maximum amplitude and phase changes of the VLF signals appear to be correlated with the gamma-ray fluence. On the other hand, VLF recovery timescales do not show any significant correlation with the fluence, possibly suggesting that the bursts' spectra are not similar to each other. In summary, Earth's ionosphere can be used as a very large gamma-ray detector and the VLF observations provide us with a new method to monitor high-energy astrophysical phenomena without interruption such as Earth occultation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tetratricopeptide repeat protein SlREC2 positively regulates cold tolerance in tomato

Abstract Cold stress is a key environmental constraint that dramatically affects the growth, productivity, and quality of tomato (Solanum lycopersicum); however, the underlying molecular mechanisms of cold tolerance remain poorly understood. In this study, we identified REDUCED CHLOROPLAST COVERAGE 2 (SlREC2) encoding a tetratricopeptide repeat protein that positively regulates tomato cold tolerance. Disruption of SlREC2 largely reduced abscisic acid (ABA) levels, photoprotection, and the expression of C-REPEAT BINDING FACTOR (CBF)-pathway genes in tomato plants under cold stress. ABA deficiency in the notabilis (not) mutant, which carries a mutation in 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1 (SlNCED1), strongly inhibited the cold tolerance of SlREC2-silenced plants and empty vector control plants and resulted in a similar phenotype. In addition, foliar application of ABA rescued the cold tolerance of SlREC2-silenced plants, which confirms that SlNCED1-mediated ABA accumulation is required for SlREC2-regulated cold tolerance. Strikingly, SlREC2 physically interacted with β-RING CAROTENE HYDROXYLASE 1b (SlBCH1b), a key regulatory enzyme in the xanthophyll cycle. Disruption of SlBCH1b severely impaired photoprotection, ABA accumulation, and CBF-pathway gene expression in tomato plants under cold stress. Taken together, this study reveals that SlREC2 interacts with SlBCH1b to enhance cold tolerance in tomato via integration of SlNCED1-mediated ABA accumulation, photoprotection, and the CBF-pathway, thus providing further genetic knowledge for breeding cold-resistant tomato varieties.

Zhang, Ying (ORCID:0000000169841164)↗