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At least 91 records · Page 5

Protocol for engineering poly(ethylene terephthalate) hydrolases via directed evolution using a high-throughput screening assay

Poly(ethylene terephthalate) (PET) hydrolases, which depolymerize PET to its monomers, have gained attention for their potential to facilitate bio-industrial recycling of this waste plastic. Here, we present a protocol for screening large, random mutagenesis enzyme libraries simultaneously for enhanced activity, solubility, and stability. We outline steps for library construction, screening using plate-based split GFP and model substrate assays, and determination of enzyme thermostability. We then detail procedures for validation assays on PET substrates and characterization of final variants.

59 BASIC BIOLOGICAL SCIENCES↗

In Silico Guidance for In Vitro Androgen and Glucocorticoid Receptor ToxCast Assays

Molecular initiating events (MIEs) are key events in adverse outcome pathways (AOPs) that link molecular chemistry to target biology. As they are based in chemistry, these interactions are excellent targets for computational chemistry approaches to in silico modelling. In this work, we aim to link ligand chemical structure to MIEs for androgen receptor (AR) and glucocorticoid receptor (GR) binding using ToxCast data. This has been done using an automated computational algorithm to perform maximal common substructure searches on chemical binders for each target from the ToxCast dataset. The models developed show a high level of accuracy, correctly assigning 87.20% of AR binders and 96.81% of GR binders in a 25% test set using holdout cross-validation. The 2D structural alerts developed can be used as in silico models to predict these MIEs, and as guidance for in vitro ToxCast assays to confirm hits. These models can target such experimental work, reducing the number of assays to be performed to gain required toxicological insight. Development of these models has also allowed some structural alerts to be identified as predictors for agonist or antagonist behavior at the receptor target. This work represents a first step in using computational methods to guide and target experimental approaches.

Allen, Timothy H.↗

SFCOMPO Database of Spent Nuclear Fuel Assay Data – the Next Frontier

SFCOMPO is the world’s largest database for measured spent nuclear fuel assay data. An international effort coordinated by the Nuclear Energy Agency (NEA) resulted in a significant expansion of the database and its release online in 2017 as a downloadable application. The SFCOMPO Technical Review Group (TRG) was recently formed under the direction of NEA’s Nuclear Science Committee/Working Party on Nuclear Criticality Safety and was mandated to maintain and further coordinate the development of SFCOMPO. This TRG is currently focused on (1) critical evaluation of the experimental assay data by independent experts and (2) development of benchmarks and benchmark models that can be applied to validate burnup codes. This will improve the quality and documentation of the experimental datasets and enable their use by the international community to support code validation for design and safety analysis of spent nuclear fuel transportation, storage, and repository applications. It follows the precedent and draws on the experience gained from similar NEA efforts in the International Reactor Physics Experiment Evaluation Project and the International Criticality Safety Benchmark Experiment Project. Ongoing SFCOMPO evaluations have served as a test bed to develop templates for documenting evaluations, develop review guidance, improve approaches for a global uncertainty analysis, and devise a strategy focused on providing practical information of highest value to the user community. The current effort, status, and associated challenges are discussed.

Ilas, Germina↗

An in vitro BRAF activation assay elucidates molecular mechanisms driving disassembly of the autoinhibited BRAF state

The RAF kinases (ARAF, BRAF, and CRAF) are essential components of the RAS-ERK signaling pathway, which controls vital cellular processes and is frequently dysregulated in human disease. Notably, mutations that alter BRAF function are prominent drivers of human cancer and certain RASopathy disorders, making BRAF an important target for therapeutic intervention. Despite extensive research, several aspects of BRAF regulation remain unclear. In this study, we developed an in vitro BRAF activation assay using purified autoinhibited BRAF:14-3-3 2 :MEK complexes. Our results show that fully processed, active-state KRAS alone can promote dimer-dependent BRAF activation. Moreover, we found that phosphatidylserine (PS)-containing liposomes synergized with KRAS to promote BRAF activation, achieving activity levels comparable to those observed with BRAF proteins that constitutively dimerize. In contrast, the SMP phosphatase complex had only a minimal effect on BRAF catalytic activity in this system but mediated the dephosphorylation of the negative regulatory pS365 14-3-3 binding site in a manner that was accelerated by the presence of KRAS alone or KRAS and 30% PS liposomes. Finally, we show that inhibitors blocking the BRAF RBD:KRAS interaction were able to suppress the in vitro activation of BRAF, underscoring the critical role of RAS binding in initiating the disassembly of the BRAF autoinhibited state. Thus, this assay provides valuable insights into the steps required for BRAF activation and can serve as an effective screening tool for identifying compounds that may inhibit this process and have therapeutic potential.

BRAF↗

Extending the Nuclide Inventory Validation Basis for High-Burnup Fuel with New Radiochemical Assay Data

Efforts are underway at Oak Ridge National Laboratory to improve the nuclide inventory validation basis for spent nuclear fuel at high burnups. Recently conducted radiochemical assay experiments provided new measurement data for nine samples of fuel irradiated in a pressurized water reactor, with estimated sample burnups in the 30 to 70 GWd/t range. This type of destructive assay data is essential for validating computational methods, tools, and nuclear data applied in nuclear safety analyses and for improving our understanding of the bias and uncertainty in code predictions. The measurement data include key actinides and fission products that span a gamut of needs and interests for nuclear science and engineering applications in criticality safety, reactor physics, nuclide inventory, decay heat, and radiation shielding. The SCALE 6.3 code system with ENDF/B-VII.1 cross-section libraries was used to simulate the irradiation histories of the measured fuel samples. The calculated nuclide concentrations are compared to corresponding measurement data. The significance of the comparisons is discussed, emphasizing how the addition of the new measurement data fills gaps in the validation basis at high burnups and contributes to the decrease in bias and uncertainty for predicted nuclide concentrations. The discussion addresses the effect of the sample burnup used in the simulation—which is based on reactor operator records or on calibration to measured data for burnup indicator fission products—on the validation results.

Nuclide inventory↗

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗

A mixture parameterized biologically based dosimetry model to predict body burdens of polycyclic aromatic hydrocarbons in developmental zebrafish toxicity assays

Polycyclic aromatic hydrocarbons (PAHs) are a group of environmental toxicants found ubiquitously as complex mixtures in human-impacted environments. Developmental zebrafish exposures have been used widely to study PAH toxicity, but most studies report nominal exposure concentrations. Nominal exposure concentrations can be unreliable dose metrics due to differences in toxicant bioavailability resulting from disparate exposure methodologies and chemical properties. Toxicokinetic modeling can predict toxicant tissue doses to facilitate comparison between exposures of different chemicals, methodologies, and biological models. We parameterize a biologically based dosimetry model for developmental zebrafish toxicity assays for 9 PAHs. The model was optimized with measurements from media, tissue, and plastic plate walls throughout a static developmental exposure to a mixture of 10 PAHs of high abundance within the Portland Harbor Superfund Site. Plate binding, volatilization, zebrafish permeability, and tissue—media partitioning coefficients vary widely between PAHs. Model predictions accounted for 83% and 54% of 48 hpf body burdens within a factor of 2 resulting from exposures to mixtures and individual PAHs, respectively. Accounting for solubility significantly improves model performance. Competition for active sites in metabolizing enzymes may change biotransformation kinetics between individual PAH and mixture exposures. Area under the curve estimations of concentrations in zebrafish resulted in altered hazard rankings from nominal exposure concentrations. Future work will be oriented to generalizing the model to other PAHs. This PAH dosimetry model improves the interpretability of developmental zebrafish toxicity assays by providing time-resolved body burdens from nominal exposure concentrations.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Passive and active neutron signatures of 233 U for nondestructive assay

The thorium fuel cycle is emerging as an attractive alternative to conventional nuclear fuel cycles, as it does not require the enrichment of uranium for long-term sustainability. The operating principle of this fuel cycle is the irradiation of 232 Th to produce 233 U, which is fissile and sustains the fission chain reaction. 233 U poses unique challenges for nuclear safeguards, as it is associated with a uniquely extreme γ-ray environment from 232 U contamination, which limits the feasibility of the γ-ray-based assay, as well as more conservative accountability requirements than for 235 U set by the International Atomic Energy Agency. Consequently, instrumentation used for safeguarding 235 U in traditional fuel cycles may be inapplicable. It is essential that the nondestructive signatures of 233 U be characterized so that nuclear safeguards can be applied to thorium fuel-cycle facilities as they come online. In this work, a set of 233 U 3 O 8 plates, containing 984 g 233 U, was measured at the National Criticality Experiments Research Center. A high-pressure 4 He gaseous scintillation detector, which is insensitive to γ-rays, was used to perform a passive fast neutron spectral signature measurement of 233 U 3 O 8 , and was used in conjunction with a pulsed deuterium-tritium neutron generator to demonstrate the differential die-away signature of this material. Furthermore, an array of 3 He detectors was used in conjunction with the same neutron generator to measure the delayed neutron time profile of 233 U, which is unique to this nuclide. These measurements provide a benchmark for future nondestructive assay instrumentation development, and demonstrate a set of key neutron signatures to be leveraged for nuclear safeguards in the thorium fuel cycle.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Data-Driven Optimization of Pixelated CdZnTe Spectrometers for Uranium Enrichment Assay

Here, in recent work [Vavrek et al. (2025)], we developed the performance optimization framework spectre-ml for gamma spectrometers with variable performance across many readout channels. The framework uses non-negative matrix factorization (NMF) and clustering to learn groups of similarly-performing channels and sweep through various learned channel combinations to optimize the performance tradeoff of including worse-performing channels for better total efficiency. In this work, we integrate the pyGEM uranium enrichment assay code with our spectre-ml framework, and show that the U-235 enrichment relative uncertainty can be directly used as an optimization target. We find that this optimization reduces relative uncertainties after a 30 -minute measurement by an average of 20%, as tested on six different H3D M400 CdZnTe spectrometers, which can significantly improve uranium non-destructive assay measurement times in nuclear safeguards contexts. Additionally, this work demonstrates that the spect re-ml optimization framework can accommodate arbitrary end-user spectroscopic analysis code and performance metrics, enabling future optimizations for complex Pu spectra.

Gamma-ray detection↗

Improved Zika virus plaque assay using Vero/TMPRSS2 cell line

Plaque assay is the gold standard for the quantification of viable cytopathic viruses like Zika virus (ZIKV). Some strains of ZIKV produce plaques that are very difficult to accurately visualize and count on the commonly used Vero cell line. From data generated in our lab, we became curious if Vero/TMPRSS2 cells may be a better alternative; therefore, we compared the plaque forming units of two strains of ZIKV on Vero/TMPRSS2 cells to those produced by Vero cells. We also compared the virus stock titer generated on Vero/TMPRSS2 cells to that generated by the Vero cell line. Although the Vero cells generated higher quantity of ZIKV stocks, the Vero/TMPRSS2 cells produced plaques with significantly improved morphology and visibility and may, therefore, be a better alternative to use for performing plaque assays for strains of ZIKV that are more difficult to titer on regular Vero cells.

60 APPLIED LIFE SCIENCES↗

A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are a continuous threat to human life. An urgent need remains for simple and fast tests that reliably detect active infections with SARS-CoV-2 and its variants in the early stage of infection. Here we introduce a simple and rapid activity-based diagnostic (ABDx) test that identifies SARS-CoV-2 infections by measuring the activity of a viral enzyme, Papain-Like protease (PLpro). The test system consists of a peptide that fluoresces when cleaved by SARS PLpro that is active in crude, unprocessed lysates from human tongue scrapes and saliva. Test results are obtained in 30 minutes or less using widely available fluorescence plate readers, or a battery-operated portable instrument for on-site testing. Proof-of-concept was obtained in a study on clinical specimens collected from patients with COVID-19 like symptoms who tested positive (n = 10) or negative (n = 10) with LIAT RT-PCR using nasal mid turbinate swabs. When saliva from these patients was tested with in-house endpoint RT-PCR, 17 were positive and only 5 specimens were negative, of which 2 became positive when tested 5 days later. PLpro activity correlated in 17 of these cases (3 out of 3 negatives and 14 out of 16 positives, with one invalid specimen). Despite the small number of samples, the agreement was significant (p value = 0.01). Two false negatives were detected, one from a sample with a late Ct value of 35 in diagnostic RT-PCR, indicating that an active infection was no longer present. The PLpro assay is easily scalable and expected to detect all viable SARS-CoV-2 variants, making it attractive as a screening and surveillance tool. Additionally, we show feasibility of the platform as a new homogeneous phenotypic assay for rapid screening of SARS-CoV-2 antiviral drugs and neutralizing antibodies.

60 APPLIED LIFE SCIENCES↗

Application of FISH based G2-PCC assay for the cytogenetic assessment of high radiation dose exposures: Potential implications for rapid triage biodosimetry

The main goal of this study is to test the utility of calyculin A induced G2-PCC assay as a biodosimetry triage tool for assessing a wide range of low and acute high radiation dose exposures of photons. Towards this initiative, chromosome aberrations induced by low and high doses of x-rays were evaluated and characterized in G2-prematurely condensed chromosomes (G2-PCCs) by fluorescence in situ hybridization (FISH) using human centromere and telomere specific PNA (peptide nucleic acid) probes. A dose dependent increase in the frequency of dicentric chromosomes was observed in the G2-PCCs up to 20 Gy of x-rays. The combined yields of dicentrics and rings in the G2-PCCs showed a clear dose dependency up to 20 Gy from 0.02/cell for 0.1 Gy to 14.98/cell for 20 Gy. Centric rings were observed more frequently than acentric ring chromosomes in the G2-PCCs at all the radiation doses from 1 Gy to 20 Gy. A head-to-head comparison was also performed by FISH on the yields of chromosome aberrations induced by different doses of x-rays (0 Gy -7.5 Gy) in colcemid arrested metaphase chromosomes and calyculin A induced G2-PCCs. In general, the frequencies of dicentrics, rings and acentric fragments were slightly higher in G2-PCCs than in colcemid arrested metaphase chromosomes at all the radiation doses, but the differences were not statistically significant. To reduce the turnaround time for absorbed radiation dose estimation, attempt was made to obtain G2-PCCs by reducing the culture time to 36 hrs. The absorbed doses estimated in x-rays irradiated (0,1,2 and 4 Gy) G2-PCCs after 36 hrs of culture were grossly like that of G2-PCCs and colcemid arrested metaphase chromosomes prepared after 48 hrs of culture. Our study indicates that the shortened version of calyculin A induced G2-PCC assay coupled with the FISH staining technique can serve as an effective triage biodosimetry tool for large-scale radiological/nuclear incidents.

Science & Technology - Other Topics↗

Measurement results for 60Co Assay baskets H5, H9, H14, H15, A4, and B3 (C003, C001, C005, C022, C021, C020, C032, C033, C038, C035, C036, C039, C053, C054, C055, C065, C066, & C067)

Eighteen cobalt targets (C003, C001, C005, C022, C021, C020, C032, C033, C038, C035, C036, C039, C053, C054, C055, C065, C066, & C067) were assayed on July 28-29, 2020, following irradiation in ATR cycle 168A. The average specific activity of each target was determined by using the cobalt assay system located in the ATR canal following procedure ACMM-3610.

07 ISOTOPE AND RADIATION SOURCES↗

Characteristics of Uranium-Plutonium Mixed Oxide Nondestructive Assay Standards

A set of six well-characterized, homogeneous, mixed HEU-WGPu oxide standards has been manufactured for and are proposed for qualification as NDA working reference standards with SAFE-NMCA. These standards, if approved, will provide the basis for qualifying the FRAM isotopic systems for use in accountability measurements of 235U in the presence of Pu for unknown mixed U-Pu items by nondestructive assay. The U to Pu elemental mass ratios of the six analytical standards are nominally in the proportions 0.1, 0.25, 1.0, 2.5, 10, and 20; these values were chosen to span the U/Pu mass ratios of inventory items that ultimately will be measured by nondestructive assay and which currently reside in long term storage. The measured characteristics, including plutonium and uranium elemental masses and isotopic distribution, of each standard and relevant source documentation are reported here.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Economic Impacts of Irradiated High Assay Low-Enriched Uranium Fuel Management

Commercial nuclear power plants typically use nuclear fuel that is enriched to less than five weight percent in the isotope 235 U. However, recently several vendors have proposed new nuclear power plant designs that would use fuel with 235 U enrichments between five weight percent and 19.75 weight percent. Nuclear fuel with this level of 235 U enrichment is known as “high assay low-enriched uranium.” Once it has been irradiated in a nuclear reactor and becomes used (or spent) nuclear fuel, it will be stored, transported, and disposed of. However, irradiated high assay low-enriched uranium differs from typical irradiated nuclear fuel in several ways, and these differences may have economic effects on its storage, transport, and disposal, compared to typical irradiated nuclear fuel. This report describes those differences and qualitatively discusses their potential economic effects on storage, transport, and disposal.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Smartphone-Based Device for Colorimetric Detection of MicroRNA Biomarkers Using Nanoparticle-Based Assay

The detection of microRNAs (miRNAs) is emerging as a clinically important tool for the non-invasive detection of a wide variety of diseases ranging from cancers and cardiovascular illnesses to infectious diseases. Over the years, miRNA detection schemes have become accessible to clinicians, but they still require sophisticated and bulky laboratory equipment and trained personnel to operate. The exceptional computing ability and ease of use of modern smartphones coupled with fieldable optical detection technologies can provide a useful and portable alternative to these laboratory systems. Herein, we present the development of a smartphone-based device called Krometriks, which is capable of simple and rapid colorimetric detection of microRNA (miRNAs) using a nanoparticle-based assay. The device consists of a smartphone, a 3D printed accessory, and a custom-built dedicated mobile app. We illustrate the utility of Krometriks for the detection of an important miRNA disease biomarker, miR-21, using a nanoplasmonics-based assay developed by our group. We show that Krometriks can detect miRNA down to nanomolar concentrations with detection results comparable to a laboratory-based benchtop spectrophotometer. With slight changes to the accessory design, Krometriks can be made compatible with different types of smartphone models and specifications. Thus, the Krometriks device offers a practical colorimetric platform that has the potential to provide accessible and affordable miRNA diagnostics for point-of-care and field applications in low-resource settings.

Krishnan, Tushar (ORCID:0000000342610336)↗

Microbiologic assay of space hardware.

Review of the procedures used in the microbiological examination of space hardware. The general procedure for enumerating aerobic and anaerobic microorganisms and spores is outlined. Culture media and temperature-time cycles used for incubation are reviewed, along with assay systems designed for the enumeration of aerobic and anaerobic spores. The special problems which are discussed are involved in the precise and accurate enumeration of microorganisms on surfaces and in the neutralization of viable organisms buried inside solid materials that could be released to a planet's surface if the solid should be fractured. Special attention is given to sampling procedures including also the indirect techniques of surface assays of space hardware such as those using detachable or fallout strips. Some data on comparative levels of microbial contamination on lunar and planetary spacecraft are presented.

Favero, M. S.↗

Problem areas in the use of the firefly luciferase assay for bacterial detection

By purifying the firefly luciferase extract and adding all necessary chemicals but ATP in excess, an assay for ATP was performed by measuring the amount of light produced when a sample containing soluble ATP is added to the luciferase reaction mixture. Instrumentation, applications, and basic characteristics of the luciferase assay are presented. Effect of the growth medium and length of time grown in this medium on ATP per viable E. coli values is shown in graphic form, along with an ATP concentration curve showing relative light units versus ATP injected. Reagent functions and concentration methods are explored. Efforts to develop a fast automatable system to detect the presence of bacteria in biological fluids, especially urine, resulted in the optimization of procedures for use with different types of samples.

Picciolo, G. L.↗