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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. Furthermore, these findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Systematic approach for simultaneously correcting the band-gap and p - d separation errors of common cation III-V or II-VI binaries in density functional theory calculations within a local density approximation

We propose a systematic approach that can empirically correct three major errors typically found in a density functional theory (DFT) calculation within the local density approximation (LDA) simultaneously for a set of common cation binary semiconductors, such as III-V compounds, (Ga or In)X with X = N,P,As,Sb, and II-VI compounds, (Zn or Cd)X, with X = O,S,Se,Te. By correcting (1) the binary band gaps at high-symmetry points , L, X, (2) the separation of p-and d-orbital-derived valence bands, and (3) conduction band effective masses to experimental values and doing so simultaneously for common cation binaries, the resulting DFT-LDA-based quasi-first-principles method can be used to predict the electronic structure of complex materials involving multiple binaries with comparable accuracy but much less computational cost than a GW level theory. This approach provides an efficient way to evaluate the electronic structures and other material properties of complex systems, much needed for material discovery and design.

Wang, Jianwei↗
DOE OSTI2015

Purification, crystallization and preliminary X-ray diffraction analysis of the Escherichia coli common pilus chaperone EcpB

In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher pathway that plays a major role in both early biofilm formation and host-cell adhesion. Initial attempts at crystallizing the chaperone EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. This is the first time that this refolding strategy has been used to purify CU chaperones. Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space group P3{sub 1}21 or P3{sub 2}21, with unit-cell parameters a = b = 62.65, c = 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Investigation of Fourth-leg for Common-mode Noise Reduction in Three-level Neutral Point Clamped Inverter Fed Motor Drive

The four-leg topology has been applied to two-level inverters for common-mode (CM) noise elimination. To achieve zero common-mode voltage (CMV), the zero vector typically used in the two-level inverter is not allowed. As a result, the reference cannot be synthesized by nearest three vectors, which introduces a penalty in dc voltage utilization and current THD. This paper applies the fourth-leg to three-level neutral point clamped (NPC) inverter fed motor drives. Unlike the case in the two-level inverter, the reference can be synthesized by the nearest three vectors while zero CMV can be achieved at the same time in a three-level inverter with the fourth-leg. The topology and modulation are presented. The fourth-leg filter structures are investigated, and a fourth-leg filter structure which decouples the fourth-leg from the main circuit power level is proposed for high power applications. The experiment results on a three-level NPC inverter show that with the fourth-leg and presented modulation applied, the CM noise has been significantly reduced, and around 25 dB attenuation can be observed at the first noise peak in the electromagnetic interference (EMI) frequency range.

Chen, Ruirui↗
DOE OSTI2025

Skipper-CCD Output Sensitivity Improvement with a Common Source Cascode Amplifier

A Skipper-CCD output has been traditionally readout in a source follower configuration, also known as common drain, mainly because in this configuration a good compromise between sensitivity, noise and speed is achieved. In this work a different approach is presented: the output transistor is connected in a common source configuration and an external cascode device is added in series, obtaining a voltage gain higher than unity without increasing significantly the parasitic capacitance due to Miller effect and thus increasing the obtained voltage per electron of charge. The proposed output stage improves the sensitivity 3.4 times when compared with the traditionally used stage while keeping almost the same equivalent noise charge.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Comparative Visualization of Vector Field Ensembles Based on Longest Common Subsequence

We propose a longest common subsequence (LCS) based approach to compute the distance among vector field ensembles. By measuring how many common blocks the ensemble pathlines passing through, the LCS distance defines the similarity among vector field ensembles by counting the number of sharing domain data blocks. Compared to the traditional methods (e.g. point-wise Euclidean distance or dynamic time warping distance), the proposed approach is robust to outlier, data missing, and sampling rate of pathline timestep. Taking the advantages of smaller and reusable intermediate output, visualization based on the proposed LCS approach revealing temporal trends in the data at low storage cost, and avoiding tracing pathlines repeatedly. Finally, we evaluate our method on both synthetic data and simulation data, which demonstrate the robustness of the proposed approach.

Liu, Richen↗
DOE OSTI2023

Prototype Design of Global Common Module for ATLAS Experiment’s Phase-II Upgrade

A new Global Trigger subsystem will be installed in the Level-0 Trigger as part of HL-LHC Upgrade of ATLAS during the upcoming Long-Shutdown 3. It will feature new and improved trigger hardware and algorithms, and an increased maximum output rate of 1 MHz. The Global Trigger will run offline-like trigger algorithms on full-granularity data, gathered from several sub-detectors and trigger-processing subsystems. A single Global Common Module (GCM) hardware is implemented across the Global Trigger system to be used as Multiplexer Processor, Global Event Processor and CTP Interface (gCTPi). This common hardware platform method will minimize the complexity of the firmware and simplify the system design and long-term maintenance. The GCM prototype is an ATCA front form factor board with two Xilinx Virtex UltraScale+ FPGA VU13P and one ZYNQ UltraScale+ FPGA ZU19EG and seventeen 25.78125 Gb/s FireFly duplex optical modules on it. The total power consumption of this board must be less than 350 W, and the temperature of the optical modules should be less than 70 °C in the worst case. The VU13Ps serve as algorithms processor nodes such as MUX, GEP and gCTPi, and the ZU19EG with Peta Linux OS running on it, is used as Command/Control/Readout Unit to configure and monitor the board and communicate with the ATLAS Detector Control System (DCS). The development of an ATCA blade with three large FPGAs and about 200 optical links running at 25Gb/s is a very challenging task, and the successful test results have demonstrated this GCM prototype as an advancement of state-of-the-art electronics module design in HEP experiments. This paper presents the hardware design considerations, functionalities, and performance test results of this GCM prototype.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Hidden diversity: Transcriptomic and photosynthetic variation among common ‘wild type’ Chlamydomonas strains

The unicellular green alga Chlamydomonas reinhardtii is a widely studied reference organism, particularly in photosynthesis research. It employs photoprotective mechanisms, such as state transitions (ST) and non-photochemical quenching (NPQ), to cope with rapid light changes. Most widely used strains share a recent common ancestor yet differ by up to ~50 000 nuclear variants—genetic diversity that is often overlooked. Even among ‘wild type’ strains, we document significant phenotypic differences, such as pigment accumulation, and nutrient utilization. To elucidate the basis for this variation, we compared transcriptomes and physiological traits of seven commonly used laboratory strains, including the reference strain and the CLiP mutant library parental strain. Despite identical growth conditions, ~40% of genes were differentially expressed between strains. Most of these differences are attributable to changes that have accrued during laboratory propagation, and adverse conditions may have driven transcriptomic drift. At the physiological level, we catalog the range of strain-dependent responses related to photosynthesis and high light (HL) acclimation. Specifically, (i) all strains develop NPQ upon HL exposure, but to various degrees, (ii) they show a substantial variation in ST capacity, and (iii) they regulate the composition of the photosynthetic apparatus differently. We find that NPQ levels do not correlate with LHCSR3 expression, suggesting an additional layer of NPQ regulation. STs are constantly activated and independent of growth light intensities. Overall, our findings highlight significant strain-to-strain differences in virtually all photosynthetic parameters, emphasizing the importance of careful strain selection in future research endeavors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SU-E-P-24: Simplified EDW Profile Measurements Using Two Commonly Available Detector Arrays

Purpose: Enhanced dynamic wedge (EDW) profiles are needed as part of the commissioning of a treatment planning system. This work compares the acquisition of EDW profiles using a linear diode array (LDA) with two commonly used detector arrays available in the clinics, with the goal of identifying the simplest approach for these measurements. Methods: The measurements of EDW profiles were performed on a Varian TrueBeam linear accelerator for 6, 10, and 18 MV photon beams for all seven wedge angles at four depths. The measurements were done using the LDA 99 in Blue Phantom2 (IBA Dosimetry), and IC Profiler and MapCHECK2 (Sun Nuclear) in solid water phantoms. The water phantom was set up at 100 cm SSD, whereas the two other devices were set up at 75 cm due to the size limitations of the devices. The largest possible field size was used. The average and maximum percentage differences were examined within the central 90% of the field and in the penumbra. Results: Dose profiles measured with IC Profiler were in a good agreement with LDA 99 data. The average percentage difference within the field did not exceed 0.5% for all energies. MapCHECK2 measurements matched well with LDA 99 for 10 and 18 MV (within 0.3%) with discrepancies of up to 1.4% observed for the 6 MV beam. The maximum percentage differences for both devices in the penumbra exhibited larger variations than LDA 99 results due to differences in detector spacing and high dose gradient, as expected. Conclusion: Common linac QA devices such as IC Profiler or MapCHECK2 provide EDW beam profile data of reasonable accuracy as compared to measurements performed using a linear diode array in a water phantom, saving the expense and time involved in acquiring and setting up a LDA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Common femtoscopic hadron-emission source in pp collisions at the LHC

The femtoscopic study of pairs of identical pions is particularly suited to investigate the effective source function of particle emission, due to the resulting Bose–Einstein correlation signal. In small collision systems at the LHC, pp in particular, the majority of the pions are produced in resonance decays, which significantly affect the profile and size of the source. In this work, we explicitly model this effect in order to extract the primordial source in pp collisions at $\sqrt{s}$ = 13 TeV from charged π–π correlations measured by ALICE. We demonstrate that the assumption of a Gaussian primordial source is compatible with the data and that the effective source, resulting from modifications due to resonances, is approximately exponential, as found in previous measurements at the LHC. The universality of hadron emission in pp collisions is further investigated by applying the same methodology to characterize the primordial source of K–p pairs. The size of the primordial source is evaluated as a function of the transverse mass (m T ) of the pairs, leading to the observation of a common scaling for both π–π and K–p, suggesting a collective effect. Further, the present results are compatible with the m T scaling of the p–p and p–Λ primordial source measured by ALICE in high multiplicity pp collisions, providing additional evidence for the presence of a common emission source for all hadrons in small collision systems at the LHC. This will allow the determination of the source function for any hadron–hadron pairs with high precision, granting access to the properties of the possible final-state interaction among pairs of less abundantly produced hadrons, such as strange or charmed particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

QCI Common

There are many common software patterns and utilities for the ORNL Quantum Computing Institute that can and should be shared across projects. Otherwise we find duplication of code which adds unwanted complexity. This is a software product seeks to alleviate this by providing common utilities such as object factories, graph data structures, parameter input mechanisms, etc., for other software products within the ORNL Quantum Computing Institute. This work enables pure basic research, has no export controlled utilities, and has no real commercial value.

McCaskey, AlexanderJ.↗
DOE OSTI2015

CPSW: Common Platform Software

The “Common Platform Software” is a package which facilitates communication with common platform firmware. It is intended to provide basic access to firmware features while hiding details of the communication protocols involved. CPSW implements abstractions for entities like registers and devices and hides low-level details such as addressing or routing information, byte-order etc.

Vasquez, Jesus↗
DOE OSTI2026

HPC ODA Commons [SWR-26-003]

HPC ODA Commons is a community-driven platform for standardizing HPC operational data analytics. HPC sites generate enormous volumes of operational data - scheduler logs, accounting records, monitoring streams - but turning that data into actionable insight is needlessly hard. Each site builds bespoke parsers, schemas, and evaluation pipelines. Results can't be compared across institutions. Promising analytics ideas stay siloed because there's no shared language for describing the data, the experiments, or the outcomes. HPC ODA Commons fixes this by establishing community-governed contracts - versioned schemas, canonical artifacts, and benchmark recipes - that make ODA workflows discoverable, reproducible, and comparable. It pairs these standards with a practical, CLI-first toolkit that lets operators and researchers go from raw logs to standardized results without sending data off-cluster.

Menear, Kevin [National Laboratory of the Rockies ↗
DOE OSTI2020

A new mud shrimp of the genus Pugnatrypaea from outer continental shelf waters of the northern Gulf of Mexico, commonly associated with hydrocarbon seeps (Crustacea: Decapoda: Callianassidae)

A new species of callianassid mud shrimp is described from outer continental shelf waters of the northwestern Gulf of Mexico, where it appears to commonly live in close association with sediments on or near natural hydrocarbon seeps. Recent genus-level taxonomic revisions of the Callianassidae, based on gene sequence analyses and comparative morphological studies, included specimens representing this new species, assigning it with strong support to the genus Pugnatrypaea Poore et al., 2019. The other known species of this genus are also typically found in offshore waters of continental shelves, but are all restricted in distribution to the Indo-West Pacific and are known from relatively few specimens. Collections of this new Gulf of Mexico representative of the genus are all from slightly deeper waters than for other known congeners, and commonly occur near hydrocarbon seeps, on some occasions being directly associated with sulfidic substrates that include waxy crude oil globules.

Zoology↗
DOE OSTI2014

Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7

Background: Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases. Results: We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced STEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a common lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 10 EHEC strains. Of the 4,192 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains. Conclusions: Our data provide evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a distinctive evolutionary path between the two outbreak strains. The distinct methylome between the two EcO145 strains is likely due to the presence of a BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic alteration in the evolution of individual EHEC strains.

DNA methylation↗
DOE OSTI2017

Quantifying engineered nanomaterial toxicity: comparison of common cytotoxicity and gene expression measurements

When evaluating the toxicity of engineered nanomaterials (ENMS) it is important to use multiple bioassays based on different mechanisms of action. In this regard we evaluated the use of gene expression and common cytotoxicity measurements using as test materials, two selected nanoparticles with known differences in toxicity, 5 nm mercaptoundecanoic acid (MUA)-capped InP and CdSe quantum dots (QDs). We tested the effects of these QDs at concentrations ranging from 0.5 to 160 µg/mL on cultured normal human bronchial epithelial (NHBE) cells using four common cytotoxicity assays: the dichlorofluorescein assay for reactive oxygen species (ROS), the lactate dehydrogenase assay for membrane viability (LDH), the mitochondrial dehydrogenase assay for mitochondrial function, and the Comet assay for DNA strand breaks.

Biomarkers↗
DOE OSTI2018

Density characterization of discharged gas-filled capillaries through common-path two-color spectral-domain interferometry

Electrically discharged plasma structures, typically several centimeters in length and sub-millimeter in diameter, have been applied to guide laser pulses in laser plasma accelerators and to focus ion and relativistic electron beams in compact, radially symmetric transport configurations. Knowledge of the on-axis plasma density is critical. Traditional density interferometry has been ineffective for these laser-machined structures, while group velocity delay (GVD) techniques involve combining two laser paths with corresponding alignment complexities and stability sensitivities. Here the GVD technique is advanced to a common-path two-color interferometer configuration performed in the spectral domain of a broad-bandwidth femtosecond laser. Multi-shot tracking of the phase is not required, and the common path assures improved stability. Here, this in situ technique was validated on 15 mm long plasma structures, measuring electron densities of 10 17 -10 18 cm -3 for various fill pressures.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Dual-wavelength channel GHz repetition rate mode-locked VECSEL cavities sourced from a common gain medium

Mode-locked vertical external cavity semiconductor lasers are a unique class of nonlinear dynamical systems driven far from equilibrium. We present a novel, to the best of our knowledge, experimental result, supported by rigorous microscopic simulations, of two coexisting mode-locked V-cavity configurations sourced by a common gain medium and operating as independent channels at angle controlled separated wavelengths. Microscopic simulations support pulses coincident on the common gain chip extracting photons from a nearby pair of coexisting kinetic holes burned in the carrier distributions.

47 OTHER INSTRUMENTATION↗