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DOE OSTI2023

acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Assessment of Screen-Covered Grooved Sodium Heat Pipes for Microreactor Applications

New nuclear reactor designs that incorporate heat pipes are being investigated for possible near-term deployment in terrestrial applications. Here, this study explores the use of screen-covered axially grooved sodium heat pipes and their applicability for providing heat removal for microreactors. A sodium working fluid is appropriate for microreactors operating in the 5 to 20 MW(thermal) range at approximately 650°C. HTPIPE, a legacy software code, was validated for the case of screen-covered grooves and used to perform steady-state analyses to determine the performance limits of a proposed heat pipe design. The performance limits of a sodium heat pipe with a screen-covered square grooved wick structure is compared to that of an equivalent heat pipe with an annular wick. In a horizontal orientation at an operating temperature of 650°C,the performance limits for the heat pipe with an annular wick configuration are 15% higher than for the screen-covered grooved wick. At operating temperatures below 777°C, the annular wick outperforms the screen-covered grooved wick, and at temperatures above 777°C, the screen-covered grooved wick outperforms the annular wick. However, the marginal performance gain at higher temperatures may not justify the use of heat pipes with a screen-covered grooved wick structure due to increased manufacturing costs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Investigation of the Effect of Gate Oxide Screening with Adjustment Pulse on Commercial SiC Power MOSFETs

This paper presents a method to recover the negative threshold voltage shift during high field gate oxide screening of 1.2 kV 4H-SiC MOSFETs with an additional adjustment gate voltage pulse. To reduce field failure rates of the MOSFETs in operation, manufacturers perform a screening treatment to remove devices with extrinsic defects in the oxide. Current gate oxide screening procedures are limited to oxide fields at or below ~9 MV/cm for short durations (<1 s), which is not enough to remove all the devices with extrinsic defects. The results show that by implementing a lower field gate pulse, the threshold voltage shift can be partially recovered, and therefore the maximum screening field and time can be increased. However, both the initial screening pulse and the adjustment pulse require careful calibration to prevent significant degradation of the device threshold voltage, on-resistance, interface state density, or intrinsic lifetime. With a well calibrated set of pulses, higher screening fields can be utilized without significantly damaging the devices. This leads to an improvement in the overall screening efficiency of the process, reducing the number of devices with extrinsic oxide defects entering the field, and improving the reliability of the SiC MOSFETs in operation.

42 ENGINEERING↗

NASA NTRS2018

A Screening Method Using Pulsed-Power Combined with Infrared Imaging to Detect Pattern Defects in Bulk Metal Foil or Thin Film Resistors

Bulk metal foil and thin film resistors occasionally contain localized defects within the etched resistor pattern. Common defects of this type include in-line constrictions referred to as notches, unremoved resistor material bridges between adjacent pattern lines, and embedded non-conductive particles in the resistor material. Such defects are prone to fracture due to thermomechanical fatigue during powered operation, especially power cycling, resulting in positive resistance change and open circuit failure modes. Common screening methods of optical microscopy, short time overload power tests (e.g., 6.25x rated power for 5 seconds) and burn-in (e.g., 1.5x rated power for 100 hours) are useful, but they are not always effective at removing devices with such defects. An improved method has been developed to screen for localized resistor pattern defects. The method involves the application of brief, high power electrical pulses at a low duty cycle while inspecting the resistor with a high resolution, high speed infrared camera. The following test conditions were found to be suitable for this purpose: 6.25x rated power, 1 to 5 pulses, 50 ms pulse width and 10% duty cycle. During the power pulsing, localized constrictions in the resistor pattern are identifiable as hot spots via the infrared camera. Reject criteria can be established based on observations of hot spots. To assess its effectiveness, a total of two hundred eighty (280) surface mount foil resistors (40 each from 7 different lots) were screened using this infrared technique. The screening identified twenty-nine (29) resistors with significant hot spots in the resistor pattern. All 280 resistors were then subjected to an industry standard 10,000 hour life test at 1x rated power at 70°C with power cycled for 90 minutes on and 30 minutes off. During life testing, three resistors exhibited positive resistance change failure mode. All three failures were due to thermomechanical fatigue failure of localized bridge defects at the locations identified via infrared screening. The results of this evaluation illustrate the benefits of the pulsed-power infrared detection screening technique to identify reliability suspect foil or thin film resistors that may escape common screening methods.

screening↗

NASA NTRS2018

A Screening Method Using Pulsed-Power Combined with Infrared Imaging to Detect Pattern Defects in Bulk Metal Foil or Thin Film Resistors

screening↗

DOE OSTI2023

A review of neutronics and thermal hydraulics–based screening methods applied to accelerated nuclear fuel qualification

This paper reviews the state-of-the-art engineering approach for using thermal hydraulic (TH) and neutronics modeling and simulation (M&S) tools to perform rapid screening studies of novel nuclear fuel concepts within the context of accelerated fuel qualification. Global research efforts have introduced nuclear fuel and material concepts that mark a significant departure from traditional reactor materials. The number of new technologies being considered for development for light water reactors and advanced reactor types has created the need for an accelerated fuel qualification procedure. A key component of this procedure is the rapid identification of the most promising fuel concepts using computational screening studies. Advanced TH and neutronic M&S tools should be leveraged to efficiently determine whether the reactor performance and safety characteristics of a given concept warrant additional studies or whether the concept requires modification or elimination. This paper reviews best practices for performing these TH and neutronics screening studies at various stages during a fuel concept's progression through the qualification procedure. The motivation behind standardizing this approach is to minimize time and resources spent on qualification activities for fuel concepts that could be quickly refined or eliminated from consideration based on their reactor physics and TH characteristics. Adoption of this screening procedure—which focuses primarily on nuclear fuels but may be applicable to other reactor materials—will also help accelerate new material qualification by generating boundary conditions crucial to fuel performance evaluations and highlighting needed areas of separate effects experimentation. This article reviews the motivation behind the introduction of novel nuclear fuel concepts, provides incentive for utilizing TH- and neutronics-based screening studies, describes the screening approach and methodology, and includes discussion on how to interpret screening results to provide recommendations for the continued development of a given concept.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets

Identification of metabolic engineering targets is a fundamental challenge in strain development programs. While high-throughput (HTP) genetic engineering methodologies capable of generating vast diversity are being developed at a rapid rate, a majority of industrially interesting molecules cannot be screened at sufficient throughput to leverage these techniques. We propose a workflow that couples HTP screening of common precursors (e.g., amino acids) that can be screened either directly or by artificial biosensors, with low-throughput targeted validation of the molecule of interest to uncover nonintuitive beneficial metabolic engineering targets and combinations hereof. Using this workflow, we identified several nonobvious novel targets for improving p-coumaric acid (p-CA) and L -DOPA production from two large 4k gRNA libraries each deregulating 1000 metabolic genes in the yeast Saccharomyces cerevisiae. We initially screened yeast cells transformed with gRNA library plasmids for individual regulatory targets improving the production of l-tyrosine-derived betaxanthins, identifying 30 targets that increased intracellular betaxanthin content 3.5–5.7 fold. Hereafter, we screened the targets individually in a high-producing p-CA strain, narrowing down the targets to six that increased the secreted titer by up to 15%. To investigate whether any of the six targets could be additively combined to improve p-CA production further, we created a gRNA multiplexing library and subjected it to our proposed coupled workflow. The combination of regulating PYC1 and NTH2 simultaneously resulted in the highest (threefold) improvement of the betaxanthin content, and an additive trend was also observed in the p-CA strain. Lastly, we tested the initial 30 targets in a L -DOPA producing strain, identifying 10 targets that increased the secreted titer by up to 89%, further validating our screening by proxy workflow. This coupled approach is useful for strain development in the absence of direct HTP screening assays for products of interest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗

DOE OSTI2022

Relativistic Coulomb screening in pulsational pair instability supernovae

Pulsational pair-instability supernovae (PPISNe) and pair instability supernovae (PISNe) are the result of a thermonuclear runaway in the presence of a background electron-positron pair plasma. As such, their evolution and resultant black hole masses could possibly be affected by screening corrections due to the electron pair plasma. The sensitivity of PISNe and PPISNe to relativistic weak screening has been explored. In this paper a weak screening model that includes effects from relativistic pair production has been developed and applied at temperatures approaching and exceeding the threshold for pair production. This screening model replaces “classical” screening commonly used in astrophysics. Modifications to the weak screening electron Debye length were incorporated in a computationally tractable analytic form. In PPISNe the BH masses were found to increase somewhat at high temperatures, though this increase is small. The BH collapse is also found to occur at earlier times, and the pulsational morphology also changes. In addition to the resultant BH mass, the sensitivity to the screening model of the pulsational period, the pulse structure, the PPISN-to-PISN transition, and the shift in the BH mass gap has been analyzed. The dependence of the composition of the ejected mass was also examined.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Screening of resonant magnetic perturbation fields assuming various plasma flow models

A recently updated version of the MARS-F code [Y. Q. Liu et al., Phys. Plasmas 7, 3681 (2000); L. Li et al., Phys. Plasmas 25, 082512 (2018); and G. L. Xia et al., Nucl. Fusion 59, 126035 (2019)] is utilized to numerically investigate the plasma screening effect on the applied resonant magnetic perturbation (RMP) field, assuming various equilibrium flow models, including the toroidal flow, the parallel flow and their combinations, and poloidal and toroidal projections of the parallel flow. A parallel equilibrium flow with a uniform radial profile is found to have no effect on plasma screening of the RMP field. A sheared parallel flow, however, does change plasma screening. The poloidal projection of the parallel flow weakens plasma screening in the resistive-inertial regime. The effect on the favorable average curvature regime is found, however, to be non-monotonic. With the increasing flow speed, the poloidal projection first weakens Glasser-Green-Johnson (GGJ)-screening. Further increase in the flow speed results in enhanced GGJ-screening again. This non-monotonic behavior is related to the perturbed parallel shielding current, which appears also off the mode rational surface at fast flow due to additional resonances between the RMP perturbation and the sound wave continuum. These results indicate that flow induced plasma screening to the RMP field can have complicated characteristics, which, in turn, can have implications on the RMP field penetration into the plasma in experiments for controlling the edge localized modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Pre-screening to guide coronary artery calcium scoring for early identification of high-risk individuals in the general population

Abstract Aims To evaluate the ability of Systematic COronary Risk Estimation 2 (SCORE2) and other pre-screening methods to identify individuals with high coronary artery calcium score (CACS) in the general population. Methods and results Computed tomography-based CACS quantification was performed in 6530 individuals aged 45 years or older from the general population. Various pre-screening methods to guide referral for CACS were evaluated. Miss rates for high CACS (CACS ≥300 and ≥100) were evaluated for various pre-screening methods: moderate (≥5%) and high (≥10%) SCORE2 risk, any traditional coronary artery disease (CAD) risk factor, any Risk Or Benefit IN Screening for CArdiovascular Disease (ROBINSCA) risk factor, and moderately (>3 mg/24 h) increased urine albumin excretion (UAE). Out of 6530 participants, 643 (9.8%) had CACS ≥300 and 1236 (18.9%) had CACS ≥100. For CACS ≥300 and CACS ≥100, miss rate was 32 and 41% for pre-screening by moderate (≥5%) SCORE2 risk and 81 and 87% for high (≥10%) SCORE2 risk, respectively. For CACS ≥300 and CACS ≥100, miss rate was 8 and 11% for pre-screening by at least one CAD risk factor, 24 and 25% for at least one ROBINSCA risk factor, and 67 and 67% for moderately increased UAE, respectively. Conclusion Many individuals with high CACS in the general population are left unidentified when only performing CACS in case of at least moderate (≥5%) SCORE2, which closely resembles current clinical practice. Less stringent pre-screening by presence of at least one CAD risk factor to guide CACS identifies more individuals with high CACS and could improve CAD prevention.

Ties, Daan (ORCID:0000000164729886)↗

DOE OSTI2020

Benefits of colorectal cancer screening using fecal immunochemical testing with varying positivity thresholds by age and sex

Background Fecal immunochemical test (FIT) performance for colorectal cancer screening varies by age and sex, yet most FIT-based screening programs use uniform positivity thresholds. This study assessed the potential benefits of stratifying FIT thresholds based on age and sex. Methods We conducted a meta-analysis of FIT sensitivity and specificity at various positivity thresholds by age and sex. We then used these estimates in 2 microsimulation models of colorectal cancer and projected lifetime clinical outcomes, incremental costs, and quality-adjusted life-years (QALYs) gained from age- and sex-stratified FIT strategies. FIT thresholds ranged from 10 to 50 µg hemoglobin per gram of feces. Results For current uniform FIT screening (20 µg hemoglobin/gram of feces), models projected 85.67 to 122.15 QALYs gained at incremental costs of ‒$982 to $504 per 1000 individuals compared with no screening. At equivalent costs to current uniform screening, only 1 model found stratified FIT approaches cost-effective, yielding a marginal increase of 1.04 and 1.10 QALYs gained/1000 female and male individuals, respectively. At a willingness-to-pay threshold of $100 000/QALYs gained, both models found stratified FIT cutoffs to be the best strategy, with cutoffs being equal to or higher for males and lowest at older ages (70-75 years). Uniform strategies showed comparable effectiveness, falling within 1 quality-adjusted life-day per person of efficient strategies at up to $112 more per person. Results were sensitive to FIT test performance characteristics and 1-time setup costs. Conclusion Stratifying FIT thresholds by age and sex may be cost-effective compared to current screening. The gain in expected health benefits with stratified FIT screening, however, is likely small.

Harlass, Matthias↗

DOE OSTI2023

Laboratory electron screening in nuclear resonance reactions

Both nonresonant and resonance reaction data are subject to laboratory electron screening effects. For non resonant reactions, such effects are well documented and the measured cross sections can be corrected to find the unscreened ones. Frequently, the procedure and expression to calculate laboratory electron screening factors for nonresonant reactions are also applied to isolated narrow resonances, without much theoretical support or experimental evidence. Here, a simple model is applied to estimate electron screening factors, lengths, and potentials for narrow resonances. The corrections to the measured data result in an enhancement of the unscreened resonance strengths by less than 0.2%, contrary to published narrow-resonance screening correction factors, which predict a reduction of the unscreened strengths by up to 25%. Unless it can be proven otherwise, it is recommended that measured strengths of isolated narrow resonances not be corrected for laboratory electron screening. The prospects of investigating laboratory electron screening effects by measuring almost negligible differences in resonance strengths are not promising. Instead, the difference of the resonance energy for the unscreened and screened situation may be measurable. As an example, the case of the E r = 956-keV resonance in the 27 Al(p,γ) 28 Si reaction is discussed. It is also demonstrated that the claim of a previously reported detection of a resonance near 800 keV in the 176 Lu(p,n) 176 Hf reaction is incorrect.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) User’s Manual: Python_V4.1

This user’s manual guides the use of the National Energy Technology Laboratory’s (NETL) CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) tool, which was developed to aid users in screening geologic formations for prospective CO 2 storage resources. This manual is specific to the CO 2 -SCREEN 4.1 version which is based in Python. The 4.1 version of CO 2 -SCREEN adds in newly updated storage efficiency factors for saline formations. CO 2 -SCREEN applies U.S. Department of Energy (DOE) methods and equations for estimating prospective CO 2 storage resources for saline formations, shale formations, and residual oil zones (ROZ). CO 2 -SCREEN was developed to be substantive and user-friendly and provide a consistent method for calculating prospective CO 2 storage resources. CO 2 -SCREEN uses a Java- based graphical user interface (GUI) for data inputs and uses Python to calculate prospective CO 2 storage resources.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Impurity screening behavior of the high-field side scrape-off layer in near-double-null configurations: prospect for mitigating plasma-material interactions on RF actuators and first-wall components

The impurity screening response of the high-field side (HFS) scrape-off layer (SOL) to localized nitrogen injection is investigated on Alcator C-Mod for magnetic equilibria spanning lower-single null, double-null and upper single null configurations under otherwise identical plasma conditions. L-mode, EDA H-mode and I-mode discharges are investigated. HFS impurity screening is found to depend on magnetic flux balance and the direction of B×?B relative to the most active divertor. Impurity ‘plume’ emission patterns indicate that both parallel and perpendicular (E×B) flows in the SOL contribute to the ‘flushing’ of impurities towards the active divertor, thereby affecting the overall impurity screening behavior. Despite the fact that the HFS scrape-off layer is extremely narrow in near-double-null configurations, this SOL is able to screen locally injected nitrogen at least as effectively as the low-field side (LFS) SOL – up to a factor of 10 more effective, depending on specific plasma conditions and whether the magnetic geometry produces parallel flows that work with or against E×B flows. For situations in which the E×B drift of the impurity ions opposes parallel flow toward the primary divertor, HFS impurity screening is found to be least effective. When E×B drifts assist parallel flow toward the primary divertor, HFS impurity screening is found to be very effective. These data support the idea of placing RF actuators and close-fitting wall components on the high-field side of the tokamak. With this configuration, near-double-null magnetic topologies may be used for active control of plasma parameters at the antenna/plasma interface for optimal RF coupling, mitigate the generation of local impurities from plasma-material interactions and, taking advantage of favorable plasma flows and good screening properties of the HFS SOL, further minimize the impact of wall-born impurity sources on the plasma core.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1972

Improvements in solid state radiographic converter screens.

Description of two different kinds of solid-state radiographic converter screens which have been developed. After briefly reviewing the working principles of the solid-state image converter - a sandwich type structure consisting of a photoconductive layer and an electroluminescent layer with a semiconductive layer and a black layer between them, two different kinds of radiographic converter screens are described - a radiographic amplifier screen that can be used as a substitute for the fluoroscopic screen, and a radiographic storage screen that can be used instead of radiographic films. The construction of both kinds of converters is fundamentally the same, the only difference being in the sensing photoconductive material. The radiographic amplifier screen has a moderately fast response, while the radiographic storage screen displays the image long after the irradiation is stopped.

Szepesi, Z.↗

NASA NTRS1990

Flow-induced resonance of screen-covered cavities

An experimental study of screen-covered cavities exposed to airflow tangent to the screen is described. The term screen refers to a thin metal plate perforated with a repetitive pattern of round holes. The purpose was to find the detailed aerodynamic and acoustic mechanisms responsible for screen-covered cavity resonance and to find ways to control the pressure oscillations. Results indicate that strong cavity acoustic resonances are created by screen orifices that shed vortices which couple resonance by choosing hole spacings such that shed vortices do not arrive at a downstream orifice in synchronization with cavity pressure oscillations. The proper hole pattern is effective at all airspeeds. It was also discovered that a reduction of orifice size tended to weaken the screen/cavity interaction regardless of hole pattern, probably because of viscous flow losses at the orifices. The screened cavities that resonated did so at much higher frequencies than the equivalent open cavity. The classical large eddy phenomenon occurs at the relatively small scale of the orifices (the excitation is typically of high frequency). The wind tunnel study was made at airspeeds from 0 to 100m/sec. The 457-mm-long by 1.09-m-high rectangular cavities had length-to-depth ratios greater than one, which is indicative of shallow cavities. The cavity screens were perforated in straight rows and columns with hole diameters ranging from 1.59 to 6.35 mm and with porosities from 2.6 to 19.6 percent.

Soderman, Paul T.↗

NASA NTRS2002

Display screen and method of manufacture therefor

A screen assembly that combines an angle re-distributing prescreen with a conventional diffusion screen. The prescreen minimizes or eliminates the sensitivity of the screen assembly to projector location. The diffusion screen provides other desirable screen characteristics. Compatible screen structures, along with methods for fabricating high resolution prescreens and methods and devices for maintaining the desired relationship between the prescreen and the diffusion screen are contemplated.

Dubin, Matthew B.↗