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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.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Identification and characterization of a novel calmodulin binding site in Drosophila TRP C-terminus

Highlights: • Drosophila TRP 783–862 is a novel calmodulin binding site. • The shortest Ca{sup 2+}-CaM interaction region and core CaM binding sequences in TRP 783–862 were dissected. • Ca{sup 2+}-CaM binding induces helical structure formation of Drosophila TRP 783–862. Transient receptor potential (TRP) channels are a group of essential cation channels involved in many important sensory signal transduction processes, such as light, temperature, tastes and pressure sensing. Drosophila TRP channel is the first discovered family member and plays important roles in photo-transduction in Drosophila. Calmodulin (CaM), an important downstream effector of Ca{sup 2+} signal, was considered as a vital regulator of TRP activities. In this study, we discovered a novel Ca{sup 2+} dependent CaM binding site (TRP 783–862) in between the previously reported two calmodulin binding sites (CBSs). The isothermal titration calorimetry (ITC) and the size exclusion chromatography coupled with multi-angle static light scattering (SEC-MALS) results showed that the dissociation constant (Kd) between TRP 783–862 and Ca{sup 2+}-CaM is 0.10 ± 0.04 μM and their binding stoichiometry is 1:1. In addition, the shortest Ca{sup 2+}-CaM interaction region and core CaM binding sequences in TRP 783–862 were dissected by the boundary mapping and mutagenesis experiments. More interestingly, by comparing the circular dichroism (CD) spectra before and after Ca{sup 2+}-CaM binding, the TRP 783–862 fragment showed Ca{sup 2+}-CaM binding dependent secondary structure changes, indicating that the interaction between CaM and Drosophila TRP channel may have a conformational impact on TRP structure. In summary, by identifying and characterizing a novel CaM binding site in TRP C-terminus, our findings provided a biochemical and structural basis for further in vivo functional studies of Ca{sup 2+}-mediated TRP channel regulation through CaM/TRP interaction.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

New insights into the shock tube ignition of H 2 /O 2 at low to moderate temperatures using high-speed end-wall imaging

In this study, the effects of pre-ignition energy releases on H 2 —O 2 mixtures were explored in a shock tube with the aid of high-speed imaging and conventional pressure and emission diagnostics. Ignition delay times and time-resolved camera image sequences were taken behind the reflected shockwaves for two hydrogen mixtures. High concentration experiments spanned temperatures between 858 and 1035 K and pressures between 2.74 and 3.91 atm for a 15% H 2 \18% O 2 \Ar mixture. Low concentration data were also taken at temperatures between 960 and 1131 K and pressures between 3.09 and 5.44 atm for a 4% H 2 \2% O 2 \Ar mixture. These two model mixtures were chosen as they were the focus of recent shock tube work conducted in the literature. Experiments were performed in both a clean and dirty shock tube facility; however, no deviations in ignition delay times between the two types of tests were apparent. The high-concentration mixture (15%H 2 \18%O 2 \Ar) experienced energy releases in the form of deflagration flames followed by local detonations at temperatures < 1000 K. Measured ignition delay times were compared to predictions by three chemical kinetic mechanisms: GRI-Mech 3.0, AramcoMech 2.0, and Burke's et al. (2012) mechanisms. It was found that when proper thermodynamic assumptions are used, all mechanisms were able to accurately predict the experiments with superior performance from the well-validated AramcoMech 2.0 and Burke et al. mechanisms. Current work provides better guidance in using available literature hydrogen shock tube measurements, which spanned more than 50 years but were conducted without the aid of high-speed visualization of the ignition process, and their modeling using combustion kinetic mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure

Altered expression of tumor suppressor genes and oncogenes, which is regulated in part at the level of DNA methylation, is an important event involved in non-genotoxic carcinogenesis. This may serve as a marker for early detection of non-genotoxic carcinogens. Therefore, we evaluated the effects of non-genotoxic hepatocarcinogens, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), hexachlorobenzene (HCB), methapyrilene (MPY) and male rat kidney carcinogens, d-limonene, p-dichlorobenzene (DCB), chloroform and ochratoxin A (OTA) on global and CpG island promoter methylation in their respective target tissues in rats. No significant dose-related effects on global DNA hypomethylation were observed in tissues of rats compared to vehicle controls using LC–MS/MS in response to short-term non-genotoxic carcinogen exposure. Initial experiments investigating gene-specific methylation using methylation-specific PCR and bisulfite sequencing, revealed partial methylation of p16 in the liver of rats treated with HCB and TCDD. However, no treatment related effects on the methylation status of Cx32, e-cadherin, VHL, c-myc, Igfbp2, and p15 were observed. We therefore applied genome-wide DNA methylation analysis using methylated DNA immunoprecipitation combined with microarrays to identify alterations in gene-specific methylation. Under the conditions of our study, some genes were differentially methylated in response to MPY and TCDD, whereas d-limonene, DCB and chloroform did not induce any methylation changes. 90-day OTA treatment revealed enrichment of several categories of genes important in protein kinase activity and mTOR cell signaling process which are related to OTA nephrocarcinogenicity. - Highlights: • Studied non-genotoxic carcinogens caused no change on global DNA hypomethylation. • d-Limonene, DCB and chloroform did not show any genome-wide methylation changes. • Some genes were differentially methylated in response to MPY, TCDD and OTA. • Protein kinase activity and mTOR cell signaling are involved in OTA carcinogenicity. • Our data highlight Cpne4 may be a potential biomarker for non-genotoxic carcinogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) has the potential to produce enzymes, therapeutic agents, and other proteins, while circumventing difficulties associated with in vivo heterologous expression. However, the contents of the cell-free extracts used to carry out synthesis are generally not characterized, which hampers progress toward enhancing yield or functional activity of the target protein. Here we explored the utility of mass spectrometry (MS)-based proteomics for characterizing the bacterial extracts used for transcribing and translating gene sequences into proteins as well as the products of CFPS reactions. Full proteome experiments identified over 1000 proteins per reaction. The complete set of proteins necessary for transcription and translation were found, demonstrating the ability to define potential metabolic capabilities of the extract. Further, MS-based techniques allowed characterization of the CFPS product and provided insight into the synthesis reaction and potential functional activity of the product. These capabilities were demonstrated using two different CFPS products, the commonly used standard green fluorescent protein (GFP, 27 kDa) and the polyketide synthase DEBS1 (394 kDa). For the large, multidomain DEBS1, substantial premature termination of protein translation was observed. Additionally, MS/MS analysis, as part of a conventional full proteomics workflow, identified post-translational modifications, including the chromophore in GFP, as well as the three phosphopantetheinylation sites in DEBS1. A hypothesis-driven approach focused on these three sites identified that all were correctly modified for DEBS1 expressed in vivo but with less complete coverage for protein expressed in CFPS reactions. These post-translational modifications are essential for functional activity, and the ability to identify them with mass spectrometry is valuable for judging the success of the CFPS reaction. Collectively, the use of MS-based proteomics will prove advantageous for advancing the application of CFPS and related techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Disc dichotomy signature in the vertical distribution of [Mg/Fe] and the delayed gas infall scenario

Context. Analysis of the Apache Point Observatory Galactic Evolution Experiment project (APOGEE) data suggests the existence of a clear distinction between two sequences of disc stars in the [α/Fe] versus [Fe/H] abundance ratio space, known as the high- and low-α sequence, respectively. This dichotomy also emerges from an analysis of the vertical distribution of the [α/Fe] abundance ratio. Aims. We aim to test whether the revised two-infall chemical evolution models designed to reproduce the low- and high-α sequences in the [α/Fe] versus [Fe/H] ratios in the solar neighbourhood are also capable of predicting the disc bimodality observed in the vertical distribution of [Mg/Fe] in APOGEE DR16 data. Methods. Along with the chemical composition of the simple stellar populations born at different Galactic times predicted by our reference chemical evolution models in the solar vicinity, we provide their maximum vertical height above the Galactic plane |zmax| computed assuming the relation between the vertical action and stellar age in APOGEE thin-disc stars. Result. The vertical distribution of the [Mg/Fe] abundance ratio predicted by the reference chemical evolution models is in agreement with that observed when combining the APOGEE DR16 data (chemical abundances) with the astroNN catalogue (stellar ages, orbital parameters) for stars younger than 8 Gyr (only low-α sequence stars). Including the high-α disc component, the dichotomy in the vertical [Mg/Fe] abundance distribution is reproduced considering the observational cut in the Galactic height of |z|< 2 kpc. However, our model predicts an overly flat (almost constant) growth of the maximum vertical height |zmax| quantity as a function of [Mg/Fe] for high-α objects in contrast with the median values from APOGEE data. Possible explanations for such a tension are that: (i) the APOGEE sample with |z|< 2 kpc is more likely than ours to be contaminated by halo stars, causing the median values to be kinematically hotter, and (ii) external perturbations – such as minor mergers – that the Milky Way experienced in the past could have heated up the disc, and the heating of the orbits cannot be modeled by only scattering processes. Assuming a disc dissection based on chemistry for APOGEE-DR16 stars (|z|< 2 kpc), the observed |zmax| distributions for high-α and low-α sequences are in good agreement with our model predictions if we consider the errors in the vertical action estimates in the calculation. Moreover, a better agreement between predicted and observed stellar distributions at different Galactic vertical heights is achieved if asteroseismic ages are included as a constraint in the best-fit model calculations. Conclusions. The signature of a delayed gas infall episode, which gives rise to a hiatus in the star formation history of the Galaxy, are imprinted both in the [Mg/Fe] versus [Fe/H] relation and in vertical distribution of [Mg/Fe] abundances in the solar vicinity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Syncopated dynamical decoupling to suppress crosstalk in quantum circuits

Theoretically understanding and experimentally characterizing and modifying the underlying Hamiltonian of a quantum system is of utmost importance in achieving high-fidelity quantum gates for quantum computing. Here, in this work, we explore the use of dynamical decoupling (DD) in characterizing and suppressing undesired two-qubit couplings as well as the underlying single-qubit decoherence, both significant hurdles to achieving precise quantum control and realizing quantum computing on many hardware prototypes. Through discrete search of DD sequences, we identify sequences that protect against decoherence and selectively target unwanted two-qubit interactions of general form. On a transmon-qubit-based superconducting quantum device, we identify separate white and 1/𝑓 noise components underlying the single-qubit decoherence and a static ZZ coupling between pairs of qubits. A family of syncopated DD sequences is found and their efficiency is demonstrated in two-qubit benchmarking experiments. The syncopated decoupling technique significantly boosts performance in a realistic algorithmic quantum circuit.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor

Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [ Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F 3:4 and F 4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. In addition, genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus

Here, a greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of PdIQD10 , a Populus gene belonging to the IQ67-Domain1 family of IQD genes, in impacting biomass formation and chemistry. Expression studies showed that PdIQD10 has enhanced expression in developing xylem and tension-stressed tissues in Populus deltoides . Molecular dynamics simulation and yeast two-hybrid interaction experiments suggest interactions with two calmodulin proteins, CaM247 and CaM014, supporting the sequence-predicted functional role of the PdIQD10 as a calmodulin-binding protein. PdIQD10 was found to interact with specific Populus isoforms of the Kinesin Light Chain protein family, shown previously to function as microtubule-guided, cargo binding and delivery proteins in Arabidopsis . Subcellular localization studies showed that PdIQD10 localizes in the nucleus and plasma membrane regions. Promoter-binding assays suggest that a known master transcriptional regulator of secondary cell wall biosynthesis (PdWND1B) may be upstream of an HD-ZIP III gene that is in turn upstream of PdIQD10 gene in the transcriptional network. RNAi-mediated downregulation of PdIQD10 expression resulted in plants with altered biomass properties including higher cellulose, wall glucose content and greater biomass quantity. Furthermore, these results present evidence in support of a new functional role for an IQD gene family member, PdIQD10 , in secondary cell wall biosynthesis and biomass formation in Populus.

09 BIOMASS FUELS↗
DOE OSTI2019

Membrane Binding of Soluble Enzymes, Explored Through Simulation of Bacterial P450s

Members of the P450 enzyme family catalyze the oxidation of many different, but primarily lipophillic, substrates. In eukaryotic P450s, a membrane-anchored N-terminal helix tethers the enzyme to the membrane. However, in bacterial P450s, no N-terminal helix is present in the sequence, and the proteins are found to be soluble and amenable to solution experiments. Through unbiased classical molecular dynamics simulations, we demonstrate that these soluble enzymes bind to lipid membranes in the same orientation as tethered P450s. We postulate that the observed membrane binding improves the turnover of the enzyme by co-locating the enzyme at regions of high substrate concentration. Through mathematical modeling, we determine that the small cellular volume in prokaryotes is the primary reason that no N-terminal helix is found in these enzymes, as fewer enzymes are mistargeted into the small cytoplasmic space.

09 BIOMASS FUELS↗
DOE OSTI2022

Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer

Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic experiments, and with accelerators like GPUs and TPUs making inference using large models rapid, genome-level structure prediction becomes an obvious aim. Leadership-class computing resources can be used to perform genome-scale protein structure prediction using state-of-the-art deep learning models, providing a wealth of new data for systems biology applications. Here we describe our efforts to efficiently deploy the AlphaFold v.2 program, for full-proteome structure prediction, at scale on the Oak Ridge Leadership Computing Facility's resources, including the Summit supercomputer. We performed inference to produce the predicted structures for 40,526 protein sequences, corresponding to four prokaryotic proteomes and one plant proteome, using under 4,400 total Summit node hours, equivalent to using the majority of the supercomputer for a little over one hour. We also designed an optimized structure refinement that reduced the time for the relaxation stage of the AlphaFold pipeline by over 10X for longer sequences. We demonstrate the types of analyses that can be performed on proteome-scale collections of sequences, including a search for novel quaternary structures and implications for functional annotation.

Gao, Mu↗
DOE OSTI2017

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Here, the first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro , with CpII capturing excess reducing equivalents under nitrogen fixation conditions. Comparison of the primary sequences of CpI and CpII and their homologs provides an initial basis for identifying key structural determinants that modulate hydrogen production and hydrogen oxidation activities.

09 BIOMASS FUELS↗
DOE OSTI2018

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A Possible Mechanism for Driving Oscillations in Hot Giant Planets

The κ -mechanism has been successful in explaining the origin of observed oscillations of many types of “classical” pulsating variable stars. Here we examine quantitatively if that same process is prominent enough to excite the potential global oscillations within Jupiter, whose energy flux is powered by gravitational collapse rather than nuclear fusion. Additionally, we examine whether external radiative forcing, i.e., starlight, could be a driver for global oscillations in hot Jupiters orbiting various main-sequence stars at defined orbital semimajor axes. Using planetary models generated by the Modules for Experiments in Stellar Astrophysics and nonadiabatic oscillation calculations, we confirm that Jovian oscillations cannot be driven via the κ -mechanism. However, we do show that, in hot Jupiters, oscillations can likely be excited via the suppression of radiative cooling due to external radiation given a large enough stellar flux and the absence of a significant oscillatory damping zone within the planet. This trend does not seem to be dependent on the planetary mass. In future observations, we can thus expect that such planets may be pulsating, thereby giving greater insight into the internal structure of these bodies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Prime factorization using magnonic holographic devices

Determining the prime factors of a given number $N$ is a problem that requires super-polynomial time for conventional digital computers. A polynomial-time algorithm was invented by Shor for quantum computers. In this paper, we present experimental data that demonstrate prime factorization using spin-wave interference but without quantum entanglement. Prime factorization includes three major steps. First, a general-type computer calculates the sequence of numbers m k mod($N$), where $N$ is the number to be factorized, m is a randomly chosen positive integer, and k = 1, 2, 3, 4, 5, 6…. Next, the period of the calculated sequence $r$ is determined by exploiting spin-wave interference. Finally, the general-type computer determines the primes based on the obtained $r$. The experiment for period finding was conducted on a six-terminal Y 3 Fe 2 (FeO 4 ) 3 device. We chose number 15 for testing and determined its primes using a sequence of measurements. The obtained experimental data for a micrometer-sized prototype aimed to demonstrate the benefits of using spin-wave devices to solve complex computational problems. Scalability is one of the major strengths inherent in this type of wave-based device, which may provide a route to nanometer-sized logic circuits. We discuss the physical and technological limitations of this approach, which define the maximum size of N and the computational speed. Although this classical approach cannot compete with the quantum algorithm in terms of efficiency, magnonic holographic devices can potentially be used as complementary logic units aimed at speeding up prime factorization for classical computers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Technical Note: A novel leaf sequencing optimization algorithm which considers previous underdose and overdose events for MLC tracking radiotherapy

Purpose: Multileaf collimator (MLC) tracking radiotherapy is complex as the beam pattern needs to be modified due to the planned intensity modulation as well as the real-time target motion. The target motion cannot be planned; therefore, the modified beam pattern differs from the original plan and the MLC sequence needs to be recomputed online. Current MLC tracking algorithms use a greedy heuristic in that they optimize for a given time, but ignore past errors. To overcome this problem, the authors have developed and improved an algorithm that minimizes large underdose and overdose regions. Additionally, previous underdose and overdose events are taken into account to avoid regions with high quantity of dose events. Methods: The authors improved the existing MLC motion control algorithm by introducing a cumulative underdose/overdose map. This map represents the actual projection of the planned tumor shape and logs occurring dose events at each specific regions. These events have an impact on the dose cost calculation and reduce recurrence of dose events at each region. The authors studied the improvement of the new temporal optimization algorithm in terms of the L1-norm minimization of the sum of overdose and underdose compared to not accounting for previous dose events. For evaluation, the authors simulated the delivery of 5 conformal and 14 intensity-modulated radiotherapy (IMRT)-plans with 7 3D patient measured tumor motion traces. Results: Simulations with conformal shapes showed an improvement of L1-norm up to 8.5% after 100 MLC modification steps. Experiments showed comparable improvements with the same type of treatment plans. Conclusions: A novel leaf sequencing optimization algorithm which considers previous dose events for MLC tracking radiotherapy has been developed and investigated. Reductions in underdose/overdose are observed for conformal and IMRT delivery.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2016

Asperity generation and its relationship to seismicity on a planar fault: A laboratory simulation

Earthquake faults, and all frictional surfaces, establish contact through asperities. A detailed knowledge of how asperities form will enable a better understanding of the manner in which they communicate during foreshock failure sequences that are observed, leading to the larger main shock. We present results of experiments where a pressure sensitive film was used to map, size and measure the magnitudes of the normal stresses at asperities along a seismogenic section of a laboratory simulated fault. We measured seismicity acoustically and foreshocks were found to be the result of localized asperity failure during the nucleation phase of gross fault rupture. Since surface roughness plays an important role in how asperities are formed, two Hurst exponents were measured to characterize a highly worn interface using roughness profiles: (i) long wavelength estimates (H ~ 0.45) and (ii) short wavelength estimates (H ~ 0.8-1.2). The short wavelength roughness estimates were computed at the scale of single asperity junction points. Macroscopically, the number of asperities and real contact area increased with additional application of normal force while the mean normal stress remained constant. The ratio of real to nominal contact area was low - ranging from 0.02 < A r /A 0 < 0.05-predicting that the asperities should be elastically independent of each other. Results from the pressure sensitive film showed that asperities were closely spaced and could not be treated as mechanically independent. Larger asperities carried both higher levels of average normal stress and higher levels of normal stress heterogeneity than smaller ones. Using linear stability theorem, the critical slip distance on foreshocking asperities was estimated to be d 0 ~ 0.65-3 μm. The critical slip distance d 0 was ~1.8-11.5 per cent of the premonitory slip needed to initiate gross fault rupture of the interface (20-40 μm) and the overall slip necessary to initiate gross fault rupture was on the order of the average asperity diameter (52 μm). In conclusion, foreshocks may be due to a change in the critical slip distance, at localized sections of the fault, caused by the two distinct roughness profiles measured at short and long length scales.

58 GEOSCIENCES↗
DOE OSTI2023

Desiccation induces varied responses within a soil bacterial genus

Abstract Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation‐induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128‐day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium . We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage‐resistant bacterium, Deinococcus radiodurans . However, within the genus, there were also 10‐fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up‐regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up‐regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB , the chaperone groEL , and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Super-resolution reconstruction in frequency, image, and wavelet domains to reduce through-plane partial voluming in MRI

Purpose: To compare and evaluate the use of super-resolution reconstruction (SRR), in frequency, image, and wavelet domains, to reduce through-plane partial voluming effects in magnetic resonance imaging. Methods: The reconstruction of an isotropic high-resolution image from multiple thick-slice scans has been investigated through techniques in frequency, image, and wavelet domains. Experiments were carried out with thick-slice T2-weighted fast spin echo sequence on the Academic College of Radiology MRI phantom, where the reconstructed images were compared to a reference high-resolution scan using peak signal-to-noise ratio (PSNR), structural similarity image metric (SSIM), mutual information (MI), and the mean absolute error (MAE) of image intensity profiles. The application of super-resolution reconstruction was then examined in retrospective processing of clinical neuroimages of ten pediatric patients with tuberous sclerosis complex (TSC) to reduce through-plane partial voluming for improved 3D delineation and visualization of thin radial bands of white matter abnormalities. Results: Quantitative evaluation results show improvements in all evaluation metrics through super-resolution reconstruction in the frequency, image, and wavelet domains, with the highest values obtained from SRR in the image domain. The metric values for image-domain SRR versus the original axial, coronal, and sagittal images were PSNR = 32.26 vs 32.22, 32.16, 30.65; SSIM = 0.931 vs 0.922, 0.924, 0.918; MI = 0.871 vs 0.842, 0.844, 0.831; and MAE = 5.38 vs 7.34, 7.06, 6.19. All similarity metrics showed high correlations with expert ranking of image resolution with MI showing the highest correlation at 0.943. Qualitative assessment of the neuroimages of ten TSC patients through in-plane and out-of-plane visualization of structures showed the extent of partial voluming effect in a real clinical scenario and its reduction using SRR. Blinded expert evaluation of image resolution in resampled out-of-plane views consistently showed the superiority of SRR compared to original axial and coronal image acquisitions. Conclusions: Thick-slice 2D T2-weighted MRI scans are part of many routine clinical protocols due to their high signal-to-noise ratio, but are often severely affected by through-plane partial voluming effects. This study shows that while radiologic assessment is performed in 2D on thick-slice scans, super-resolution MRI reconstruction techniques can be used to fuse those scans to generate a high-resolution image with reduced partial voluming for improved postacquisition processing. Qualitative and quantitative evaluation showed the efficacy of all SRR techniques with the best results obtained from SRR in the image domain. The limitations of SRR techniques are uncertainties in modeling the slice profile, density compensation, quantization in resampling, and uncompensated motion between scans.

60 APPLIED LIFE SCIENCES↗