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This document is a short summary of the steps required for MicroCT evaluation of a specimen. This includes data acquisition through image analysis, for the Explosives Threat Assessment (ETA) program. Expected outputs for each stage are outlined. Information and data shall be shipped to LLNL as described herein.
Background: Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored. Results: Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability. Conclusions: We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.
This paper details speckle observations of binary stars taken at the Lowell Discovery Telescope, the WIYN telescope, and the Gemini telescopes between 2016 January and 2019 September. The observations taken at Gemini and Lowell were done with the Differential Speckle Survey Instrument (DSSI), and those done at WIYN were taken with the successor instrument to DSSI at that site, the NN-EXPLORE Exoplanet Star and Speckle Imager (NESSI). In total, we present 378 observations of 178 systems, and we show that the uncertainty in the measurement precision for the combined data set is ∼2 mas in separation, ∼1°–2° in position angle depending on the separation, and ∼0.1 mag in magnitude difference. Together with data already in the literature, these new results permit 25 visual orbits and one spectroscopic-visual orbit to be calculated for the first time. In the case of the spectroscopic-visual analysis, which is done on the ternary star HD 173093, we calculate masses with a precision of better than 1% for all three stars in that system. Twenty-one of the visual orbits calculated have a K dwarf as the primary star; we add these to the known orbits of K-dwarf primary stars and discuss the basic orbital properties of these stars at this stage. Although incomplete, the data that exist so far indicate that binaries with K-dwarf primaries tend not to have low-eccentricity orbits at separations of one to a few tens of astronomical units, that is, on solar system scales.
Analytical and semi–analytical models for stream depletion with transient stream stage drawdown induced by groundwater pumping are developed to address a deficiency in existing models, namely, the use of a fixed stream stage condition at the stream–aquifer interface. Here field data are presented to demonstrate that stream stage drawdown does indeed occur in response to groundwater pumping near aquifer–connected streams. A model that predicts stream depletion with transient stream drawdown is developed based on stream channel mass conservation and finite stream channel storage. The resulting models are shown to reduce to existing fixed–stage models in the limit as stream channel storage becomes infinitely large, and to the confined aquifer flow with a no–flow boundary at the streambed in the limit as stream storage becomes vanishingly small. The model is applied to field measurements of aquifer and stream drawdown, giving estimates of aquifer hydraulic parameters, streambed conductance, and a measure of stream channel storage. The results of the modeling and data analysis presented herein have implications for sustainable groundwater management.
FOILPOLARS (Grassmannian Foil Shape Sweeps for Polar Generation): Multifidelity aerodynamic polar data generation for hydrofoil/tidal-turbine airfoil sections. Foilpolars ties together three pieces: *AeroSandbox supplies the baseline airfoil coordinates (UIUC database). *G2Aero parameterizes those shapes on a Grassmannian manifold (Karcher mean + PGA basis) and samples new perturbed shapes around that basis. *XFoil (panel method) and NeuralFoil (neural-network surrogate, shipped with AeroSandbox) each solve the resulting shapes for lift, drag, moment, and pressure at the swept angles of attack, Reynolds numbers, and n_crit values. Design optimization of foil shapes in a computationally efficient way requires polars data across many candidate shapes, not just a handful of baseline foils. However, high-fidelity CFD at that scale is too costly, and naive shape perturbation strays from realistic geometries. FOILPOLARS addresses this by loading baseline airfoils (via AeroSandbox) and mapping them onto a Grassmannian manifold (via G2Aero), computing a Karcher mean and principal geodesic analysis (PGA) basis. New shapes are sampled by perturbing PGA coefficients, keeping them close to the manifold of realistic foils. Each sampled shape is evaluated across a configurable sweep of angle of attack, Reynolds number, and critical amplification factor using two solvers: XFoil (panel method) and NeuralFoil (neural-network surrogate), producing a paired dataset of lift, drag, moment, pressure, convergence, and confidence, indexed alongside each shape's PGA coefficients and shared Grassmannian basis in a single xarray dataset. From this, FOILPOLARS produces convergence summaries and comparison plots per shape, Reynolds number, and n_crit. A command-line interface exposes each pipeline stage independently, supporting data-driven design, optimization, and machine-learning workflows for foils.
The ICARUS-T600 Liquid Argon (LAr) Time Projection Chamber (TPC) is presently taking data in the Short Baseline Neutrino (SBN) program at Fermilab (U.S.A.) to search for a possible LSND-like sterile neutrino signal at Δm 2 ≈ 1 eV 2 with the Booster Neutrino Beam (BNB). A light detection system, based on 360 large area Photo-Multiplier Tubes (PMTs), has been realized for ICARUS-T600 to detect VUV photons produced by the passage of ionizing particles in LAr. This system is fundamental for the TPC operation, providing an efficient trigger and contributing to the 3D reconstruction of events. Moreover, since the detector is exposed to a huge flux of cosmic rays due to its shallow depths installation, the light detection system allows for the time reconstruction of events, contributing to the identification and to the selection of genuine neutrino interactions. The correct time reconstruction of events requires the precise knowledge of the delay of each PMT channel and a good synchronization of recording electronics, this last based on fast sampling digitizers. To achieve a time resolution better than 1 ns, we perform three consecutive timing corrections deployed at different stages of the optical data flow. Results demonstrate the capability of the ICARUS-T600 light detection system to allow a precise reconstruction of the temporal evolution of each event occurring in the detector and the association of neutrino events with the bunched structure of BNB.
This work presents a two-stage adaptive framework for progressively developing deep neural network (DNN) architectures that generalize well for a given training data set. In the first stage, a layerwise training approach is adopted where a new layer is added each time and trained independently by freezing parameters in the previous layers. We impose desirable structures on the DNN by employing manifold regularization, sparsity regularization, and physics-informed terms. We introduce a ε – δ – stability-promoting concept as a desirable property for a learning algorithm and show that employing manifold regularization yields a ε – δ stability-promoting algorithm. Further, we also derive the necessary conditions for the trainability of a newly added layer and investigate the training saturation problem. In the second stage of the algorithm (post-processing), a sequence of shallow networks is employed to extract information from the residual produced in the first stage, thereby improving the prediction accuracy. Numerical investigations on prototype regression and classification problems demonstrate that the proposed approach can outperform fully connected DNNs of the same size. Moreover, by equipping the physics-informed neural network (PINN) with the proposed adaptive architecture strategy to solve partial differential equations, we numerically show that adaptive PINNs not only are superior to standard PINNs but also produce interpretable hidden layers with provable stability. As a result, we also apply our architecture design strategy to solve inverse problems governed by elliptic partial differential equations.
In February 2022, the U.S. Department of Energy and six national laboratories launched the Puerto Rico Grid Resilience and Transitions to 100% Renewable Energy Study (PR100). PR100 aims to provide a comprehensive analysis of possible pathways for Puerto Rico's energy future, with a goal of 100% renewable energy by 2050. As a part of the renewable energy potential assessment in this project, we developed 20 years (2001-2020) of data using a numerical weather prediction (NWP) model for onshore and offshore wind resource assessment for the Puerto Rico. The research steps in developing the long-term wind resource data sets based on the NWP model were: 1. Model wind resource based on the Weather Research and Forecasting (WRF) model. 2. Develop WRF model configurations for Puerto Rico. 3. Test WRF with 11 different physics parameterizations for planetary boundary layer (PBL). 4. Assess WRF output from the different PBL schemes against observations. 5. Select a final model configuration which can produce the modeled wind speed with sufficient accuracy. 6. Produce 20 years wind resource data sets for Puerto Rico region. In the first stage of our framework for developing wind resource data, we developed a WRF model configuration using two nested domains (9 km and 3 km) to cover Puerto Rico and U.S. Virgin Islands and downscale the ERA5 reanalysis data (0.25 degrees x 0.25 degrees; hourly interval) to a 3-km domain. For the second stage, we implemented one-year simulations focused on using 11 different PBL physics parameterizations to find a combination of WRF physics parameterizations that could provide accurately modeled wind speed for Puerto Rico. We also analyzed the sensitivity of the modeled wind speed to PBL schemes for onshore and offshore locations. The WRF output resulting from the 11 WRF experiments using different PBL parameterizations were evaluated against observations obtained from the National Data Buoy Center (NDBC) as well as at hub height for a location for which measurements were available. A final model setup selected through the validation with observational data was used to produce 20 years of data with 3-km spatial and 5-minute temporal resolution. The WRF model output was post-processed to include wind profiles and basic atmospheric variables in a format that can be easily used for downstream modeling. The 20 years of wind resource data will be made available through NREL and support the estimation of wind energy development costs for the PR100 study.
Drugs targeting multiple stages of the Plasmodium vivax life cycle are needed to reduce the health and economic burdens caused by malaria worldwide. N-myristoyltransferase (NMT) is an essential eukaryotic enzyme and a validated drug target for combating malaria. However, previous PvNMT inhibitors have failed due to their low selectivity over human NMTs. Herein, we apply a structure-guided hybridization approach combining chemical moieties of previously reported NMT inhibitors to develop the next generation of PvNMT inhibitors. A high-resolution crystal structure of PvNMT bound to a representative selective hybrid compound reveals a unique binding site architecture that includes a selective conformation of a key tyrosine residue. The hybridized compounds significantly decrease P. falciparum blood-stage parasite load and consistently exhibit dose-dependent inhibition of P. vivax liver stage schizonts and hypnozoites. Our data demonstrate that hybridized NMT inhibitors can be multistage antimalarials, targeting dormant and developing forms of liver and blood stage.
Storage backends of parallel compute clusters are still based mostly on magnetic disks, while newer and faster storage technologies such as flash-based SSDs or non-volatile random access memory (NVRAM) are deployed within compute nodes. Including these new storage technologies into scientific workflows is unfortunately today a mostly manual task, and most scientists therefore do not take advantage of the faster storage media. One approach to systematically include nodelocal SSDs or NVRAMs into scientific workflows is to deploy ad hoc file systems over a set of compute nodes, which serve as temporary storage systems for single applications or longer-running campaigns. This paper presents results from the Dagstuhl Seminar 17202 “Challenges and Opportunities of User-Level File Systems for HPC” and discusses application scenarios as well as design strategies for ad hoc file systems using node-local storage media. The discussion includes open research questions, such as how to couple ad hoc file systems with the batch scheduling environment and how to schedule stage-in and stage-out processes of data between the storage backend and the ad hoc file systems. Also presented are strategies to build ad hoc file systems by using reusable components for networking and how to improve storage device compatibility. Various interfaces and semantics are presented, for example those used by the three ad hoc file systems BeeOND, GekkoFS, and BurstFS. Their presentation covers a range from file systems running in production to cutting-edge research focusing on reaching the performance limits of the underlying devices.
The sources of the magmas that formed the Rustenburg Layered Suite of the Bushveld Complex in South Africa remain debated, despite decades of research. Vertical and lateral variation in bulk rock and mineral separate Sr-Nd isotopic compositions, which generally indicate enriched sources, demonstrate that the layered sequence was formed by the emplacement of multiple batches of magma, crucially resulting in episodes of PGE-Cr-V mineralisation. The Lu-Hf isotope compositions of zircon are, however, at odds with the bulk rock Sr-Nd isotopic heterogeneity as they show near homogeneous compositions throughout the layered sequence (εHf (2.06 Ga) =−8). This lack of variation in Hf isotope composition has been attributed to deep, continental lithospheric mantle-related and/or crustal contamination of plume-derived Bushveld magmas. In this study, we analysed the major, trace element and Sr-Nd isotope geochemistry of apatite in the Rustenburg Layered Suite. Apatite occurs as an intercumulus mineral in the lowermost regions and a cumulus mineral in the uppermost regions of the layered sequence and can therefore be used to test existing models for the isotopic disequilibrium between bulk rock Sr-Nd and zircon Hf isotopic compositions. Apatite is largely chlorapatite in the lowermost regions and fluorapatite in the uppermost regions of the layered sequence. The Merensky Reef is unusual in that it comprises both chlorapatite and fluorapatite. Apatite throughout the layered sequence is generally unzoned and shows no evidence of late-stage alteration. Trace element data show that apatite is enriched in L/HREE, with common negative Eu-Sr anomalies. These trace element signatures are consistent with a magmatic origin for the apatite grains, with prior, or concurrent, plagioclase crystallization from the same melt. Variability in in situ Sr and Nd isotope compositions of apatite is recorded throughout the layered sequence with εNd (2.06 Ga) compositions varying between −2.5 and − 10.2 and initial 87 Sr/ 86 Sr compositions varying between 0.7079 and 0.7103 (for the Marikana dikes only). The variability in Sr-Nd isotope compositions of apatite is consistent with the bulk rock (and mineral separate) variation in Sr-Nd isotope compositions, suggesting apatite preserves primary magmatic compositions in the Rustenburg Layered Suite.
Optical-model potentials (OMPs) are critical ingredients for basic and applied nuclear physics. Present-day computational capabilities allow us to generate data-driven nucleon-nucleus OMPs that are non-local and exactly dispersive (as theoretically required to be), include statistically-sound uncertainty quantification, and are trained on both scattering and bound-state data from a wide area of the nuclear chart. Combined together, these features allow for significant improvement in fidelity and extrapolative power of the model. Here, we present preliminary work toward the development and training of such an OMP. The capability of the model to describe data at this first stage is encouraging.
The time-resolving magnetic recoil spectrometer (MRSt) is a transformative diagnostic that will be used to measure the time-resolved neutron spectrum from an inertial confinement fusion implosion at the National Ignition Facility (NIF). It uses a CD foil on the outside of the hohlraum to convert fusion neutrons to recoil deuterons. An ion-optical system positioned outside the NIF target chamber energy-disperses and focuses forward-scattered deuterons. A pulse-dilation drift tube (PDDT) subsequently dilates, un-skews, and detects the signal. While the foil and ion-optical system have been designed, the PDDT requires more development before it can be implemented. Therefore, a phased plan is presented that first uses the foil and ion-optical systems with detectors that can be implemented immediately—namely CR-39 and hDISC streak cameras. These detectors will allow the MRSt to be commissioned in an intermediate stage and begin collecting data on a reduced timescale, while the PDDT is developed in parallel. A CR-39 detector will be used in phase 1 for the measurement of the time-integrated neutron spectra with excellent energy-resolution, necessary for the energy calibration of the system. Streak cameras will be used in phase 2 for measurement of the time-resolved spectrum with limited spectral coverage, which is sufficient to diagnose the time-resolved ion temperature. Simulations are presented that predict the performance of the streak camera detector, indicating that it will achieve excellent burn history measurements at current yields, and good time-resolved ion-temperature measurements at yields above 3 × 10 17 . The PDDT will be used for optimal efficiency and resolution in phase 3.
High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as Relion , cryoSPARC , cisTEM , SPHIRE and EMAN2 .
In this paper, a composite scheme is proposed for detecting stealthy data manipulation attacks on distribution system which is unobservable with standard least squares based state estimators. This technique has three stages where the process of data imputation, voltage phasor estimation and the bad data detection are carried out in a systematic manner. The proposed approach is then integrated with moving target defense strategies which perturbs the network parameters to reveal stealthy false data injection attacks. The proposed approach is tested is validated on a three-phase, unbalanced 37-node distribution system and its results are presented. It is shown that the proposed approach has the ability to accurately detect the presence of FDI attacks using limited measurements (i.e., the test system is unobservable).
Here this paper presents a superconducting, magnetically-coupled, shuttle-flux shift register (SF-SR) that stores single flux quantum (SFQ) pulses. This shift register has a DC bias operating margin of ±34% at 10 GHz, with a power dissipation of 3.6 μW and 38% fewer Josephson junctions (JJs) when scaled up to multiple stages compared to a data flip-flop (DFF) based shift register. The clock input is inductively coupled and is independent from the data input. We then present three applications for our SF-SR. In the first application, we add two non-destructive readout (NDRO) cells to construct a buffer that temporarily stores the temporal information of a series of race logic (RL) pulses. The second application is a pseudo-random number generator based on a linear function shift register (LFSR). The third application is N parallel SF-SRs that can act similar to a deserializer or instead can emulate a single SF-SR of N times higher clock frequency. These three applications motivate deep shift registers with many shifting intervals, which our SF-SR can implement with fewer JJs and lower power consumption compared to DFF-based shift registers.
Housing unit level demographic characteristics for SETX counties. Census years 2010 and 2020. These data are in beta testing stage, designed for use with the SETX-UIFL project. Contact Nathanael Rosenheim (nrosenheim@arch.tamu.edu) for more information. Papers using these data should include Nathanael Rosenheim in the development phase and co-authorship discussions.
We report the extensive development of unconventional reservoirs using horizontal drilling and multistage hydraulic fracturing has generated large volumes of reservoir characterization and production data. The analysis of this abundant data using statistical methods and advanced machine-learning (ML) techniques can provide data-driven insights into well performance. Most predictive modeling studies have focused on the impact that different well completion and stimulation strategies have on well production but have not fully exploited the available in situ rock property data to determine its role in reservoir productivity. We have used machine-learning techniques to rank rock mechanical properties, microseismic attributes, and stimulation parameters in the order of their significance for predicting natural gas production from an unconventional reservoir. The data for this study came from a hydraulically fractured well in the Marcellus Shale in Monongalia County, West Virginia. The data classes included measurements aggregated by well completion stage that included (1) gas production, (2) well-log-derived measurements including bulk density, elastic moduli, shear impedance, compressional impedance, brittleness, and gamma measurements, (3) microseismic attributes, (4) long-period long-duration (LPLD) event counts, (5) fracture counts, and (6) stimulation parameters that included the fluid injection volume and average pumping pressure. To identify observable proxies for the drivers of gas production, we evaluated five commonly used ML approaches including multivariate adaptive regression spline, Gaussian mixture model, random forest, gradient boosting, and neural network. We selected five variables including LPLD event count, seismogenic b-value, hydraulic diffusivity, cumulative moment, and fluid volume as the features most likely to impact gas productivity at the stage level in the study area. The data-driven selection of these parameters for their importance in determining gas production can help reservoir engineers design more effective hydraulic-fracture treatments in the Marcellus Shale and other similar unconventional reservoirs. Plain language summary: We use machine-learning methods and data-driven selection of reservoir parameters to rank and better understand their importance in determining gas production, which can help reservoir engineers design more effective hydraulic-fracture treatments in the Marcellus Shale and other similar unconventional reservoirs.