Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “differential analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Kinetics of Pyrolysis and Thermal Evolution of Negev Desert Lithologies

The Negev desert in Israel is home to large quantities of organic-rich, shallow marine sedimentary lithologies that could potentially accommodate the disposal of spent nuclear fuel. Previous thermal analyses of Negev carbonates have focused on industrially relevant considerations such as natural gas and oil extraction or pyrolysis for recovering hydrocarbon fuels. Here, this study addresses thermal evolution of the Negev organic-rich carbonate, siliceous, and phosphorite rocks and associated chemical, mineralogical, and microstructural changes that may occur under prolonged thermal loading in the vicinity of spent nuclear fuel disposal systems. Our employed methods include high-temperature X-ray diffraction, high-temperature infrared spectroscopy, and thermal analysis integrating thermogravimetry, differential scanning calorimetry, and mass spectrometry. Further, we apply iterative iso-conversional model-free methods to derive kinetic parameters for thermal decomposition of the Negev organic-rich carbonate rocks from 200 to 550 °C. Our results have provided mechanistic insights into the thermal evolution encompassing water desorption, decomposition of organic matter, and decarbonation of carbonate phases.

58 GEOSCIENCES↗
DOE OSTI2020

Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermal Dehydration of Aluminum (Oxy)hydroxides on Fuel Cladding Material - 20200

The aluminum cladding of research-reactor fuel undergoes general corrosion with resulting formation of adherent aluminum (oxy)hydroxide films during in-reactor and post-discharge exposure to water under various conditions and temperatures. These (oxy)hydroxides contain chemically-bound water that poses challenges for extended dry storage due to the risk of thermal or radiolytic decomposition releasing free water and/or hydrogen and oxygen gases. This study comprised laboratory experiments of thermal drying behavior of aluminum (oxy)hydroxides to identify approaches for reducing bound water on fuel cladding prior to sealed dry storage. Effective drying strategies for adherent (oxy)hydroxides on fuel cladding will improve the safety of dry storage by mitigating potential avenues for additional corrosion and/or generation of flammable gases inside the storage canister. This work is part of a broader investigation to address knowledge gaps and technical data needs for dry storage of aluminum-clad spent nuclear fuel (ASNF), which included investigation of (oxy)hydroxide formation on aluminum alloy substrates immersed in water, characterization of service-grown films from ASNF, and radiolytic yield of hydrogen from (oxy)hydroxide powders and films. The current work comprises experimental thermal dehydration of aluminum trihydroxides (bayerite and gibbsite) characteristic of low-temperature (<80 deg. C) corrosion in water and aluminum oxyhydroxide (boehmite) characteristic of high temperature (>80 deg. C) corrosion in water. First, commercially produced (oxy)hydroxide powders (boehmite and gibbsite) were tested via thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effort aimed to identify or confirm key temperature ranges/thresholds for the thermal decomposition reactions, as well as impacts of ramp rate and hold times, for drying of isolated, high-surface-area (oxy)hydroxides. The information gleaned from powder tests was used to guide subsequent drying tests on adherent (oxy)hydroxide films grown on aluminum alloy substrates. TGA was used to analyze small samples of the aluminum coupons with adherent (oxy)hydroxide films. Specimens were characterized both pre- and post-drying using X-ray diffraction (XRD) to determine the film composition and scanning electron microscopy (SEM) to determine its morphology. Drying of adherent (oxy)hydroxide films was anticipated to pose additional complications relative to drying of (oxy)hydroxide powders. Anticipated challenges include achieving sufficient drying of the (oxy)hydroxide at low-enough temperature to avoid melting or other undesirable phase changes in the aluminum substrate and overcoming transport limitations of water through the thickness of a dense film or through a tortuous pore structure to reach the outer surface of the film. Inn addition, dehydration of (oxy)hydroxides significantly changes the film density, which may lead to substantial alterations in the morphology, including potential cracking and spalling of the film. TGA/DSC tests of gibbsite powders resulted in successful conversion to boehmite or alumina, depending on the maximum temperature reached. At low ramp rates (≤5 deg. C/min), the conversion to boehmite occurred around 300 deg. C (210-340 deg. C). XRD confirmed that boehmite was the only phase detected after tests reaching 450 deg. C. The transition to alumina occurred around 510 deg. C (470-550 deg. C), with XRD detecting only alumina after tests reaching at least 600 deg. C. Boehmite powders dehydrated to alumina at about 400 deg. C (330-460 deg. C) for coarse (77-μm particle diameter) powder and about 490 deg. C (420-520 deg. C) for fine (0.7-μm particle diameter) powder. For all powders tested, the maximum percent mass loss after drying to high temperature slightly exceeded the theoretical mass loss for complete dehydration of the stoichiometric (oxy)hydroxide to alumina, which is likely attributable to physisorbed water in the powder. Drying of a thick (∼8.6 μm), predominantly bayerite adherent film displayed a dramatic change in film morphology, with the initially continuous trihydroxide film cracking into sections on the order of 50 μm square and partially delaminating. The outermost layer of the film completely faked of in some regions. The layer exposed under the spalled oxide also displayed prominent cracking, with spacing on the order of 10 μm, but this surface layer appeared to remain completely adhered to the aluminum substrate. TGA showed mass losses per unit surface area up to ∼1.0 mg/cm{sup 2}. XRD characterization of the remaining oxide was inconclusive, with no crystalline phases detected. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Understanding the Role of Hydroxyl Functionalization in Linear Poly(Ethylenimine) for Oxidation‐Resistant Direct Air Capture of CO 2

Aminopolymer-based adsorbents are a prominent class of materials being used for direct air capture of CO 2 at the industrial scale. However, improving their working lifetime, specifically by increasing their resilience to oxidative degradation, remains an ongoing challenge. Toward this end, functionalization of aminopolymers with non-amine functionalities such as hydroxyls has emerged in recent years as a promising strategy toward improving adsorbent lifetime. Although there is a growing body of work demonstrating the effectiveness of this approach and investigating the origin of this improved stability, studies to date have primarily focused on branched aminopolymer systems such as branched poly(ethylenimine). In this work, hydroxyl-functionalized linear poly(ethylenimine) is used to continue to probe the underlying protective mechanism of this strategy. A combination of thermogravimetric analysis, NMR relaxometry, differential scanning calorimetry, and computational simulations is used to better understand the relationship between the extent of chemical functionalization, physical properties, and adsorbent performance.

amine-based adsorbent↗
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
DOE OSTI2022

Utilization of the Critic Subnetwork of a Generative Adversarial Network as Detector of Morphological Material Change in Image Data

The resolution of computed tomography (CT) has become high enough to monitor morphological changes due to aging in materials in long-term applications. For this work, we explored the utility of the critic of a generative adversarial network (GAN) to automatically detect such changes. The GAN was trained with images of pristine Pharmatose, which is used as a surrogate energetic material. It is important to note that images of the material with altered morphology were only used during the test phase. The GAN-generated images reproduced the microstructure of Pharmatose well, although some unrealistic particle fusion was seen. Calculated morphological metrics (volume fraction, interfacial line length, and local thickness) for the synthetic images also showed good agreement with the training data, albeit with signs of mode collapse in the interfacial line length. While the critic exposed changes in particle size, it showed limited ability to distinguish images by particle shape. The detection of shape differences was also a more challenging task for the selected morphological metrics that related to energetic material performance. We further tested the critic with images of aged Pharmatose. Subtle changes due to aging are difficult for the human analyst to detect; but both critic and morphological metrics analysis showed image differentiation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

From phase decomposition to evaporation: A multi-modal evaluation of thermally degraded model lightweight high-entropy alloy

Lightweight high-entropy alloys (LHEAs) have the potential to replace conventional lightweight materials due to their superior mechanical properties and thermal stability. However, the thermal degradation pattern of LHEAs from phase decomposition to evaporation is not clear. We develop a new Al-based dual phase (FCC + HCP) LHEA—AlTi 0.45 CuZn, and further investigate its thermal degradation behavior for potential high-temperature structural applications. Using multimodal advanced characterization techniques such as differential scanning calorimetry/thermogravimetric analysis, scanning/transmission electron microscopy, and synchrotron X-ray diffraction/pair distribution function (XRD/PDF), a sequence of thermal degradation events beyond the thermal phase stability limit—between 250 and 360 °C—is observed. These include phase decomposition at ~360 °C, Zn evaporation at ~750 °C, and LHEA melting at 880 °C which results in ~25% cumulative weight loss. The formation of Al-Ti phase off the AlTi 0.45 CuZn matrix is due to the largest negative mixing enthalpy for Al-Ti than other binary pairs. Similarly, Zn evaporation from AlTi 0.45 CuZn LHEA is due to its faster evaporation rate than other constituent elements. The high-resolution synchrotron XRD and PDF results support the aforementioned observations; in addition, they reveal local atomic arrangements, local strain, and sluggish grain growth in the LHEA. Among other LHEAs of close density range (5.55 ≤ ρ ≤ 5.85 g/cc), the investigated LHEA exhibits outstanding nano-indentation hardness values due to the coupled grain size effect and HCP phase strengthening of the FCC matrix. As the search for LHEAs for lightweight applications grows, this study shows the potential use of AlTi 0.45 CuZn LHEA for structural applications even at elevated temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Signature of 0 + excited state and shape coexistence in 94 Kr through 93 Kr(d,p) 94 Kr reaction

A measurement of the excitation spectrum of 94 Kr via one-neutron transfer to the ground state of 93 Kr using the 93 Kr(d,p) 94 Kr reaction at 8A MeV, observing the outgoing protons, performed with the IRIS facility at TRIUMF is reported. Two states in 94 Kr, at 1.50±0.14 MeV and 2.20±0.14 MeV, were observed. An adiabatic-wave approximation analysis of the differential cross sections leads us to identify the lower energy state as being populated with neutron transfer to the 3 s1/2 orbital. This leads to the first observation of the lowest 0 + excited state in 94 Kr, hence signaling shape co-existence. Theoretical calculations performed within the in-medium similarity renormalization group framework are presented that also show the existence of a low-energy 0 + state, aligning qualitatively with the observation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Connecting radiation-driven changes in structural, thermal, and mechanical properties in several medical device polymers

Stemming from security threats and shortages in supply, a recent push has emerged to develop alternatives to radioisotope Cobalt-60 gamma radiation for sterilization of polymeric medical products, including electron beam (e-beam) and X-ray machine-based sources. However, before large-scale implementation, the effects of these non-isotope-based methods must be thoroughly investigated from several perspectives, involving their potential detrimental effects on the structural, thermal, and mechanical properties of polymers in medical devices. This paper investigates such effects in commonly used medical device polymers, including polypropylene homopolymer (PPH), polyolefin elastomer (POE), low-density polyethylene (LDPE), acrylonitrile butadiene styrene (ABS), and chlorobutyl rubber (CIIR). To connect radiation-driven changes in polymer structural and thermal properties and corresponding changes in mechanical properties, several characterization techniques were utilized, including gel permeation chromatography (GPC), Fourier transform infrared spectroscopy (FTIR), dynamic mechanical analysis (DMA) and differential scanning calorimetry (DSC). We found that the tensile strength of X-ray irradiated PPH, as well as X-ray, e-beam, and gamma irradiated CIIR decreases due to chain scission, which is corroborated by GPC and DMA. The GPC results of LDPE suggest chain scission, but interestingly without a corresponding decline in tensile strength. By comparison, POE and ABS appear to undergo further crosslinking with increasing irradiation dose, which generally strengthens them. Importantly, in the vast majority of the cases, there were small to no changes in properties upon changing radiation technologies (at a given dose), i.e., no radiation source dependence. However, in a few specific cases, radiation method dependencies did arise, for instance, in terms of the molecular weight of PPH being significantly increased upon X-ray irradiation, while the melting temperature, glass transition temperature, and elongation at break reduced compared to gamma. Overall, this study provides valuable insight into radiation-driven chemical and structural changes in polymers that produce changes in physical and functional properties.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High-Temperature Thermodynamics of Cerium Silicates, A-Ce 2 Si 2 O 7 , and Ce 4.67 (SiO 4 ) 3 O

Lanthanide disilicates and oxyapatites have potential roles in high temperature applications as thermal (TBC) and environmental barrier coatings (EBC), or possible alteration phases in geological nuclear waste repositories. However, those Ce 3+ -bearing silicates have only been limitedly studied. In this work, we performed detailed structural and thermodynamic investigations on A-Ce 2 Si 2 O 7 (tetragonal, P4 1 ) and Ce 4.67 (SiO 4 ) 3 O (hexagonal, P6 3 /m). The high temperature structural behaviors and coefficients of thermal expansion were determined by in situ high temperature synchrotron X-ray diffraction (HT-XRD) implemented with Rietveld analysis and thermogravimetric analysis coupled with differential scanning calorimetry (TGA-DSC). A-Ce 2 Si 2 O 7 was found to be stable in N 2 and air up to ~1483 K with anisotropic thermal expansion along the a and c axes (α a = 12.3 × 10 -6 K -1 and α c = 12.4 × 10 -6 K -1 ). Ce 4.67 (SiO 4 ) 3 O had a slow partial oxidation between 533 K and 873 K to a new nonstoichiometric phase Ce 3+ 1.67- xCe4 + x Ce 3+ 3 (SiO 4 ) 3 O 1+0.5x , followed by a thermal decomposition to CeO 2 and SiO 2 at ~1000 K in air. By using high temperature oxide melt solution calorimetry at 973 K with lead borate as the solvent, the standard enthalpy of formation was determined for A-Ce 2 Si 2 O 7 (-3825.1 ± 6.0 kJ/mol) and Ce 4.67 (SiO 4 ) 3 O (-7391.3 ± 9.5 kJ/mol). Finally, these thermodynamic parameters were compared with those of CeO 2 , CeSiO 4 , and other silicate oxyapatites for examining their chemical stability in high temperature environments relevant for aeronautical applications, mineral formation, and nuclear fuel cycle.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal Chemistry and Thermodynamics of HREE (Er, Yb) Mixing in a Xenotime Solid Solution

Rare earth elements (REEs), the 15 naturally occurring lanthanides plus yttrium and scandium, are ubiquitously used in modern life as they are critical components of many advanced devices and technologies. However, the demand for REEs is not equal, with the heavy rare earth elements (HREEs) having a higher demand. Xenotime (HREEPO 4 ) is an important HREE ore mineral and globally is an economical source of HREE. Most of the crystallographic and thermodynamic properties of xenotime endmembers have been elucidated by calorimetric, solubility, and high-pressure studies. Yet, in natural systems, endmembers are rarely encountered, and instead, REE solid solutions are more commonly observed. Here, we characterize the crystal chemistry, thermodynamics of HREE mixing, and high-temperature material behaviors and thermochemistry of a synthetic erbium (Er)-ytterbium (Yb) binary xenotime solid solution (Er (x) Yb (1-x) PO 4 ) using a suite of experimental techniques, including X-ray fluorescence spectroscopy, synchrotron X-ray powder diffraction implemented with Rietveld analysis, Fourier transform infrared spectroscopy coupled with attenuated total reflectance, Raman spectroscopy, thermogravimetric analysis coupled with differential scanning calorimetry, and high-temperature oxide melt drop solution calorimetry. Our results shed light on the formation of natural xenotimes and lay the foundation for their industrial applications as thermal coating materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Correlation-based network analysis combined with machine learning techniques highlight the role of the GABA shunt in Brachypodium sylvaticum freezing tolerance

Perennial grasses will account for approximately 16 billion gallons of renewable fuels by the year 2022, contributing significantly to carbon and nitrogen sequestration. However, perennial grasses productivity can be limited by severe freezing conditions in some geographical areas, although these risks could decrease with the advance of climate warming, the possibility of unpredictable early cold events cannot be discarded. We conducted a study on the model perennial grass Brachypodium sylvaticum to investigate the molecular mechanisms that contribute to cold and freezing adaption. The study was performed on two different B. sylvaticum accessions, Ain1 and Osl1, typical to warm and cold climates, respectively. Both accessions were grown under controlled conditions with subsequent cold acclimation followed by freezing stress. For each treatment a set of morphological parameters, transcription, metabolite, and lipid profiles were measured. State-of-the-art algorithms were employed to analyze cross-component relationships. Phenotypic analysis revealed higher adaption of Osl1 to freezing stress. Our analysis highlighted the differential regulation of the TCA cycle and the GABA shunt between Ain1 and Osl1. Osl1 adapted to freezing stress by repressing the GABA shunt activity, avoiding the detrimental reduction in fatty acid biosynthesis and the concomitant detrimental effects on membrane integrity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Oligomerization of Pr55 Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55 Gag . However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55 Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18–33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles’ membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain’s 2D layers during assembly and budding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Parametric study of an acid baking process for rare earth element recovery from a bituminous-coal source

Acid baking treatment is widely used to extract rare earth elements (REEs) from refractory rare earth bearing minerals such as monazite and xenotime. Since these REE minerals have been identified in coal-based sources, a parametric study was conducted to evaluate the impact and optimize the parametric values associated with the acid-baking process when treating a bituminous coal source. The parameters studied using a three-level statistical experimental program were acid baking time, acid solution concentration, baking temperature, and acid solution-to-solids ratio and each were found to significantly impact REE and contaminant element recovery. An increase in baking temperature up to around 250°C improved the light and heavy REE recovery values by more than 50 absolute percentage points relative to performances achieved when direct leaching. Acid baking was needed to dehydroxylate the clays and liberate the REE minerals, which allowed access for the acid to solubilize the REEs. Acid concentration of the solution used for acid baking was studied as a means of minimizing the amount of acid needed to achieve a target REE recovery. However, thermo-gravimetric and differential scanning calorimetry analysis (TGA-DSC) of sulfuric acid under oxidizing atmosphere revealed that the addition of water decreased the evaporation temperature, which explains the lower REE recovery values obtained when using lower acid concentrations. Using pure sulfuric acid at an acid-to-solid ratio of 0.8:1 resulted in recovery values of around 70% for both LREEs and HREEs. The decomposition reaction time was relatively quick with 65% of the TREEs recovered within the first 10 minutes. Water leaching experiments performed on the acid-baked products under a temperature of 25°C instead of 75°C revealed an increase in REE recovery by 10 absolute percentage points, which was likely due to the high solubility of REE-sulfates at room temperatures.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Artificial intelligence-empowered cellular morphometric risk score improves prognostic stratification of cutaneous squamous cell carcinoma

Abstract Background Risk stratification of cutaneous squamous cell carcinoma (cSCC) is essential for managing patients. Objectives To determine if artificial intelligence and machine learning might help to stratify patients with cSCC by risk using more than solely clinical and histopathological factors. Methods We retrieved a retrospective cohort of 104 patients whose cSCCs had been excised with clear margins. Clinical and histopathological risk factors were evaluated. Haematoxylin and eosin-stained slides were scanned and analysed by an algorithm based on the stacked predictive sparse decomposition technique. Cellular morphometric biomarkers (CMBs) were identified via machine learning and used to derive a cellular morphometric risk score (CMRS) that classified cSCCs into clusters of differential prognoses. Concordance analysis, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were calculated and compared with results obtained with the Brigham and Women’s Hospital (BWH) staging system. The performance of the combination of the BWH staging system and the CMBs was also analysed. Results There were no differences among the CMRS groups in terms of clinical and histopathological risk factors and T-stage assignment, but there were significant differences in prognosis. Combining the CMRS with BWH staging systems increased distinctiveness and improved prognostic performance. C-indices were 0.91 local recurrence and 0.91 for nodal metastasis when combining the two approaches. The NPV was 94.41% and 96.00%, the PPV was 36.36% and 41.67%, and accuracy reached 86.75% and 89.16%, respectively, with the combined approach. Conclusions CMRS is helpful for cSCC risk stratification beyond classic clinical and histopathological risk features. Combining the information from the CMRS and the BWH staging system offers outstanding prognostic performance for patients with high-risk cSCC.

Pérez-Baena, Manuel J.↗