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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Comparison of gene expression in the skin tissue of gray, humpback, and fin whales

Analyses of gene expression in the skin of several species of whales identified genes that are differentially expressed in association with environmental factors, suggesting that skin transcriptomics may provide a valuable tool for assessing physiological responses in marine mammals. Previous work exploring differing levels of gene expression has focused on odontocetes with comparatively limited investigation of skin gene expression has been explored in mysticetes. Here, we describe the identity of genes expressed in skin tissue of three species of baleen whales to establish a baseline of gene expression and compare gene identity and expression patterns across species. We also evaluate sex-specific differences in skin gene expression through a comparison of expression levels between males and females in gray and humpback whales. A total of 16 skin tissue samples were collected from free-ranging gray, humpback and fin whales off the central Oregon coast in the eastern North Pacific. Comparison of the expressed genes in the humpback and gray whale skin tissue to the blue whale reference database identified enriched gene ontology terms in the skin tissue of each species, suggesting genes over-represented in the whale skin related to cell epithelial development, regulation of gene expression and cell maintenance . Comparison of gene expression between male and female samples revealed sex-specific differences in gray and humpback whales. A differential gene expression analysis identified several x-linked genes that have been previously identified and show gene expression differences in male and female cetaceans, such as ZFX, DDX3X and USP9X. Establishing baseline skin gene expression profiles for these three baleen whale species sampled off the Oregon coast provides a foundation for linking transcriptome variation with physiological condition and environment.

Sremba, Angela↗
DOE OSTI2021

Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales ): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The differing effects of a dual acting regulator on SIRT1

SIRT1 is an NAD + -dependent protein deacetylase that has been shown to play a significant role in many biological pathways, such as insulin secretion, tumor formation, lipid metabolism, and neurodegeneration. There is great interest in understanding the regulation of SIRT1 to better understand SIRT1-related diseases and to better design therapeutic approaches that target SIRT1. There are many known protein and small molecule activators and inhibitors of SIRT1. One well-studied SIRT1 regulator, resveratrol, has historically been regarded as a SIRT1 activator, however, recent studies have shown that it can also act as an inhibitor depending on the identity of the peptide substrate. The inhibitory nature of resveratrol has yet to be studied in detail. Understanding the mechanism behind this dual behavior is crucial for assessing the potential side effects of STAC-based therapeutics. Here, we investigate the detailed mechanism of substrate-dependent SIRT1 regulation by resveratrol. We demonstrate that resveratrol alters the substrate recognition of SIRT1 by affecting the K M values without significantly impacting the catalytic rate k cat ). Furthermore, resveratrol destabilizes SIRT1 and extends its conformation, but the conformational changes differ between the activation and inhibition scenarios. We propose that resveratrol renders SIRT1 more flexible in the activation scenario, leading to increased activity, while in the inhibition scenario, it unravels the SIRT1 structure, compromising substrate recognition. Our findings highlight the importance of substrate identity in resveratrol-mediated SIRT1 regulation and provide insights into the allosteric control of SIRT1. This knowledge can guide the development of targeted therapeutics for diseases associated with dysregulated SIRT1 activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The saturation mechanism of thermal instability

The literature on thermal instability (TI) reveals that even for a simple homogeneous plasma, the nonlinear outcome ranges from a gentle reconfiguration of the initial state to an explosive one, depending on whether the condensations that form evolve in an isobaric or nonisobaric manner. After summarizing the recent developments on the linear and nonlinear theory of TI, here we derive several general identities from the evolution equation for entropy that reveal the mechanism by which TI saturates; whenever the boundary of the instability region (the Balbus contour) is crossed, a dynamical change is triggered that causes the comoving time derivative of the pressure to change the sign. This event implies that the gas pressure force reverses direction, slowing the continued growth of condensation. For isobaric evolution, this “pressure reversal” occurs nearly simultaneously for every fluid element in condensation and a steady state is quickly reached. For nonisobaric evolution, the condensation is no longer in mechanical equilibrium and the contracting gas rebounds with greater force during the expansion phase that accompanies the gas reaching the equilibrium curve. The cloud then pulsates because the return to mechanical equilibrium becomes wave mediated. We show that both the contraction rebound event and subsequent pulsation behavior follow analytically from an analysis of the new identities. Our analysis also leads to the identification of an isochoric TI zone and makes it clear that unless this zone intersects the equilibrium curve, isochoric modes can only become unstable if the plasma is in a state of thermal non-equilibrium.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Effects of Glymes on the Distribution of Mg(B 10 H 10 ) and Mg(B 12 H 12 ) from the Thermolysis of Mg(BH 4 ) 2

We examined the effects of concentrations and identities of various glymes, from monoglyme up to tetraglyme, on H 2 release from the thermolysis of Mg(BH 4 ) 2 at 160–200 °C for 8 h. 11 B NMR analysis shows major products of Mg(B 10 H 10 ) and Mg(B 12 H 12 ); however, their relative ratio is highly dependent both on the identity and concentration of the glyme to Mg(BH 4 ) 2 . Selective formation of Mg(B 10 H 10 ) was observed with an equivalent of monoglyme and 0.25 equivalent of tetraglyme. However, thermolysis of Mg(BH 4 ) 2 in the presence of stoichiometric or greater equivalent of glymes can lead to unselective formation of Mg(B 10 H 10 ) and Mg(B 12 H 12 ) products or inhibition of H 2 release.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Investigation of Needle Motion Profile Effect on Diesel Spray in Near-Nozzle Field

A variety of needle-motion profiles are used in diesel injectors. However, it is unclear what the underlying mechanism is to determine the needle-motion profiles and how they affect the spray dynamics. It has been of significant interest to examine how the spray dynamics will change if only altering the needle valve opening speed or closing speed while all other parameters are kept the same. The different needle-motion profiles were obtained using a piezo nozzle (Nozzle #P) and a solenoid nozzle (Nozzle #S), which have identical nozzle geometry. By utilizing the X-ray imaging technique, it was observed that the average needle valve speed of Nozzle #P was 51% higher at the opening stage but 17% lower at the closing stage than Nozzle #S. When the needle valve lift is low (approximately 200 μm), the needle valve opening speed has a crucial effect on spray dynamics. The faster needle valve opening of Nozzle #P results in a 42% larger spray spreading angle and 34% lower spray velocity at the downstream field. The spray dynamics may be controllable by properly designing the needle-motion profiles in the scenarios of the low needle lifts. However, when the needle valve is sufficiently open (approximately over 200 μm), almost identical spray characteristics were observed regardless of the needle-motion profiles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Genomic Characterization and Wetland Occurrence of a Novel Campylobacter Isolate from Canada Geese

Populations of resident, non-migratory Canada geese are rapidly increasing. Canada geese are known to transmit viral and bacterial diseases, posing a possible threat to human health. The most prevalent pathogens vectored by geese are Campylobacter species, yet the current understanding of the identity and virulence of these pathogens is limited. In our previous study, we observed a high prevalence of Campylobacter spp. in the Banklick Creek wetland—a constructed treatment wetland (CTW) located in northern KY (USA) used to understand sources of fecal contamination originating from humans and waterfowl frequenting the area. To identify the types of Campylobacter spp. found contaminating the CTW, we performed genetic analyses of Campylobacter 16s ribosomal RNA amplified from CTW water samples and collected fecal material from birds frequenting those areas. Our results showed a high occurrence of a Campylobacter canadensis-like clade from the sampling sites. Whole-genome sequence analyses of an isolate from Canada goose fecal material, called MG1, were used to confirm the identity of the CTW isolates. Further, we examined the phylogenomic position, virulence gene content, and antimicrobial resistance gene profile of MG1. Lastly, we developed an MG1-specific real-time PCR assay and confirmed the presence of MG1 in Canada goose fecal samples surrounding the CTW. Our findings reveal that the Canada goose-vectored Campylobacter sp. MG1 is a novel isolate compared to C. canadensis that possesses possible zoonotic potential, which may be of human health concern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Potentiometric Studies on Ion-Transport Selectivity in Charged Gold Nanotubes

Under ideal conditions, nanotubes with a fixed negative tube-wall charge will reject anions and transport-only cations. Because many proposed nanofluidic devices are optimized in this ideally cation-permselective state, it is important to know the experimental conditions that produce ideal responses. A parameter called Ccrit, the highest salt concentration in a contacting solution that still produces ideal cation permselectivity, is of particular importance. Pioneering potentiometric studies on gold nanotubes were interpreted using an electrostatic model that states that Ccrit should occur when the Debye length in the contacting salt solution becomes equivalent to the tube radius. Since this “double-layer overlap model” (DLOM), treats all same-charge ions as identical point charges, it predicts that all same-charged cations should produce the same Ccrit. However, the effect of cation on Ccrit in gold nanotubes was never investigated. This knowledge gap has become important because recent studies with a polymeric cation-permselective nanopore membrane showed that DLOM failed for every cation studied. To resolve this issue, we conducted potentiometric studies on the effect of salt cation on Ccrit for a 10 nm diameter gold nanotube membrane. Ccrit for all cations studied were, within experimental error, the same and identical, with values predicted by DLOM. The reason DLOM prevailed for the gold nanotubes but failed for the polymeric nanopores stems from the chemical difference between the fixed negative charges of these two membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Spin Quantization in Heavy Ion Collision

We analyzed recent experimental data on the disassembly of 28Si into 7α in terms of a hybrid α-cluster model. We calculated the probability of breaking into several α-like fragments for high l-spin values for identical and non-identical spin zero nuclei. Resonant energies were found for each l-value and compared to the data and other theoretical models. Toroidal-like structures were revealed in coordinate and momentum space when averaging over many events at high l. The transition from quantum to classical mechanics is highlighted.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Constraints on the Correlation of IceCube Neutrinos with a Tracer of Nearby Large-scale Structure

The IceCube Neutrino Observatory has observed extragalactic astrophysical neutrinos with an apparently isotropic distribution. Only a small fraction of the observed astrophysical neutrinos can be explained by known sources. Neutrino production is thought to occur in energetic environments that are ultimately powered by the gravitational collapse of dense regions of the large-scale mass distribution in the universe. Whatever their identity, neutrino sources likely trace this large-scale mass distribution. The clustering of neutrinos with a tracer of the large-scale structure may provide insight into the distribution of neutrino sources with respect to redshift and the identity of neutrino sources. We implement a two-point angular cross correlation of the Northern sky track events with an infrared galaxy catalog derived from the Wide-field Infrared Survey Explorer (WISE) and Two Micron All Sky Survey (2MASS) source catalogs, which trace the nearby large-scale structure. No statistically significant correlation is found between the neutrinos and this infrared galaxy catalog. We find that ≤54% of the diffuse muon neutrino flux can be attributed to sources correlated with the galaxy catalog with 90% confidence. Additionally, when assuming that the neutrino source comoving density evolves following a power law in redshift, dN s /dV ∝ (1 + z) k , we find that sources with negative evolution, in particular k < −1.75, are disfavored at the 90% confidence level.

Abbasi, R. [Loyola University, Chicago, IL (United↗
DOE OSTI2022

Cloud adjustments from large-scale smoke–circulation interactions strongly modulate the southeastern Atlantic stratocumulus-to-cumulus transition

Smoke from southern Africa blankets the southeastern Atlantic Ocean from June to October, producing strong and competing aerosol radiative effects. Smoke effects on the transition between overcast stratocumulus and scattered cumulus clouds are investigated along a Lagrangian (air-mass-following) trajectory in regional climate and large eddy simulation models. Results are compared with observations from three recent field campaigns that took place in August 2017: ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES), CLouds and Aerosol Radiative Impacts and Forcing: Year 2017 (CLARIFY), and Layered Atlantic Smoke Interactions with Clouds (LASIC). The case study is set up around the joint ORACLES–CLARIFY flight that took place near Ascension Island on 18 August 2017. Smoke sampled upstream on an ORACLES flight on 15 August 2017 likely entrained into the marine boundary layer later sampled during the joint flight. The case is first simulated with the WRF-CAM5 regional climate model in three distinct setups: (1) FireOn, in which smoke emissions and any resulting smoke–cloud–radiation interactions are included; (2) FireOff, in which no smoke emissions are included; (3) RadOff, in which smoke emissions and their microphysical effects are included but aerosol does not interact directly with radiation. Over the course of the Lagrangian trajectory, differences in free tropospheric thermodynamic properties between FireOn and FireOff are nearly identical to those between FireOn and RadOff, showing that aerosol–radiation interactions are primarily responsible for the free tropospheric effects. These effects are non-intuitive: in addition to the expected heating within the core of the smoke plume, there is also a “banding” effect of cooler temperature (~1–2 K) and greatly enhanced moisture (>2 g kg -1 ) at the plume top. This banding effect is caused by a vertical displacement of the former continental boundary layer in the free troposphere in the FireOn simulation resulting from anomalous diabatic heating due to smoke absorption of sunlight that manifests primarily as a few hundred meters per day reduction in large-scale subsidence over the ocean. A large eddy simulation (LES) is then forced with free tropospheric fields taken from the outputs for the WRF-CAM5 FireOn and FireOff runs. Cases are run by selectively perturbing one variable (e.g., aerosol number concentration, temperature, moisture, vertical velocity) at a time to better understand the contributions from different indirect (microphysical), “large-scale” semi-direct (above-cloud thermodynamic and subsidence changes), and “local” semi-direct (below-cloud smoke absorption) effects. Despite a more than 5-fold increase in cloud droplet number concentration when including smoke aerosol concentrations, minimal differences in cloud fraction evolution are simulated by the LES when comparing the base case with a perturbed aerosol case with identical thermodynamic and dynamic forcings. A factor of 2 decrease in background free tropospheric aerosol concentrations from the FireOff simulation shifts the cloud evolution from a classical entrainment-driven “deepening–warming” transition to trade cumulus to a precipitation-driven “drizzle-depletion” transition to open cells, however. The thermodynamic and dynamic changes caused by the WRF-simulated large-scale adjustments to smoke diabatic heating strongly influence cloud evolution in terms of both the rate of deepening (especially for changes in the inversion temperature jump and in subsidence) and in cloud fraction on the final day of the simulation (especially for the moisture “banding” effect). Such large-scale semi-direct effects would not have been possible to simulate using a small-domain LES model alone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Electric Field Data from the North Slope of Alaska

File contains raw as well as calibrated electric field values (V/m) from two CS110 electric field meters. The file also contains raw 2-m U and V winds at the same site. The sampling rate is 1Hz. All files contain raw electric field data, as well as calibrated values to a one week ground-based calibration setup. During this week, simultaneous upward-facing ground based electric field measurements were taken alongside the two downward facing instruments on the pole (CS110-3 at 2m and CS110-2 at 5m). Slopes and intercepts were calculated and applied to the values influenced by the pole to convert the raw data to calibrated values. These calibrated values are absolute electric field measurements. There are no missing data codes. The missong data is not included in the files, and thus any files with missing data will be shorter than the normal 86,400 values. In July 2023, the CS110-3 was replaced with an identical instrument named CS110-8, and the CS110-2 was replaced with an identical instrument called CS110-9. All the variable names remained consistent and the same.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A Systematic Framework for Tuning Open-Source Multifunctional IBR Models To Emulate OEM Black-Box Fault Dynamics

This paper presents a systematic framework to tune a generic IBR EMT model to match with an OEM provided balckbox inverter model based on the fault current responses. The key learnings and findings are summarized as follows: The tunable key parameters include inner control loops and current limiters to align the fault current magnitude, sequence content, and phase trajectories with the OEM models across diverse fault type and locations. The tuned model's fidelity is validated through comparative analysis with an OEM blackbox model, assessing both the fault current response and the responses of multiple relay elements. The results demonstrate the tuned generic model can trigger relay decision logic that is identical or near identical to that of the OEM model, thus generating very good match model for fault studies.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC transcriptomic type identity is not specified at mitotic exit, but acquired by gradual, asynchronous restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity emerges. Optimal transport inference identifies groups of RGC precursors with largely nonoverlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando↗
DOE OSTI2020

In vitro recombination method

The present invention relates, e.g., to in vitro method, using isolated protein reagents, for joining two double stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity, comprising contacting the two DNA molecules in a reaction mixture with (a) a non-processive 5′ exonuclease; (b) a single stranded DNA binding protein (SSB) which accelerates nucleic acid annealing; (c) a non strand-displacing DNA polymerase; and (d) a ligase, under conditions effective to join the two DNA molecules to form an intact double stranded DNA molecule, in which a single copy of the region of sequence identity is retained. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A Step Towards the Final Frontier: Lessons Learned from Acceptance Testing of the First HPE/Cray EX 3000 System at ORNL

In this paper, we summarize the deployment of the Air Force Weather (AFW) HPC11 system at Oak Ridge National Laboratory (ORNL) including the process followed to successfully complete acceptance testing of the system. HPC11 is the first HPE/Cray EX 3000 system that has been successfully released to its user community in a federal facility. HPC11 consists of two identical 800-node supercomputers, Fawbush and Miller, with access to two independent and identical Lustre parallel file systems. HPC11 is equipped with Slingshot 10 interconnect technology and relies on the HPE Performance Cluster Manager (HPCM) software for system configuration. ORNL has a clearly defined acceptance testing process used to ensure that every new system deployed can provide the necessary capabilities to support user workloads. We worked closely with HPE and AFW to develop a set of tests that used the United Kingdom’s Meteorological Office’s Unified Model (UM) and 4DVAR. We also included benchmarks and applications from the Oak Ridge Leadership Computing Facility (OLCF) portfolio to fully exercise the HPE/Cray programming environment and evaluate the functionality and performance of the system. Acceptance testing of HPC11 required parallel execution of each element on Fawbush and Miller. In addition, careful coordination was needed to ensure successful acceptance of the newly deployed Lustre file systems alongside the compute resources. In this work, we present test results from specific system components and provide an overview of the issues identified, challenges encountered, and the lessons learned along the way.

Melesse Vergara, Veronica↗
DOE OSTI2021

Host cells and methods for producing toluene biochemically

The present invention provides for a genetically modified host cell comprising a first polypeptide comprising a sequence having at least 70% amino acid sequence identity with a phenylacetate decarboxylase, and having an enzymatic activity to decarboxylate a phenylacetic acid into a toluene and a carbon dioxide, and a second polypeptide comprising a sequence having at least 70% amino acid sequence identity with a phenylacetate decarboxylase activating enzyme, and having an enzymatic activity to cleave a S-adenosylmethionine (SAM) to form a methionine and a 5′-deoxyadenosyl radical.

Beller, Harry R.↗