C++ Utility Library V4.0
A C++ utility library that provides abstractions for common data types with debugging features, support for I/O redirection and support for portability.
Hart, William↗
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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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Simulation Utility Library for HPC codes
SimUtil contains various small utility functions used in multiple HPC simulation codes here at LLNL, such as: simulation parameter input parsing, parallel file-IO, memory allocation, unit parsing, and helper functions for using MPI.
Fattebert, Jean-Luc↗
Application Reporting and Termination Utility for Windows
The Application Reporting and Termination Utility for Windows (terminate.exe) is a simple diagnostics and recovery tool designed to help LANDesk system administrators manage hung client applications on Windows systems. Terminate can either report on (tag) or stop (kill) a specified process on computers on which it is run. If KILL is specified, all processes that match the specified name and have a start time older than the specified minutes will be force stopped. If TAG is specified, all processes that match the name and have a start time older than the specified minutes will be reported to LANDesk inventory via the miniscan LANDesk client component.
Frye, DavidJ.↗
flask_socket_util
This is a small utility for using websockets from within Flask for PSDM web services. It consists of a Flask blueprint for web sockets and some client Javascript.
Shankar, Murali↗
RadSim: Math, Utility & RTK
This package includes three parts, (1) gov.llnl.math, (2)gov.llnl.utility and (3)gov.llnl.rtk, which are utilized in the development of Radiation Detector Simulator (RadSim) project. RadSim is being developed to provide the capability to: (1) simulate radiation source emissions, (2) interpolate results from radiation transport tools into a common format to prepare incident flux, and (3) model radiation detector response to rapidly produce synthetic radiation measurement templates. RadSim is targeted for open-source release, which will enable researchers and industry partners to model gamma-ray detectors response to simulated flux from the transport tool of their choice. The techniques and implementation will be entirely transparent, which will allow for improvements and boutique modifications by future researchers beyond the lifespan of this specific project. The first tool of the package, gov.llnl.math, includes classes and functions to define and perform basic math operations. Some of the example features available in the package include defining statistical distributions and performing algebra and matrix operations, all of which are already accessible on publicly available software packages such as MATLAB and ROOT. The second package gov.llnl.utility includes tools commonly used to enable optimization and readability of various data structures such as Java lists and external xml files. Lastly, the gov.llnl.rtk package includes classes and functions to implement methods commonly used in radiation physics, such as data structures to represent and characterize photon spectra and tools to apply well-defined and published methods to calibrate a given spectra.
Cheung, Hoi Sing↗
cloud_fs (Cloud File System Utilities) [SWR-21-83]
cloud-fs (Cloud File System Utilities) is a generalized file-system handler that will dynamically determine if files are local or on the cloud (currently AWS) and perform basic file-system operations.
Rossol, Michael↗
cloud_fs (Cloud File System Utilities) 10.6.2021 [SWR-21-83]
cloud-fs (Cloud File System Utilities) is a generalized file-system handler that will dynamically determine if files are local or on the cloud (currently AWS) and perform basic file-system operations.
Rossol, Michael↗
nfs-utility-suite
NFS Utility Suite is a collection of code libraries that provide convenience features for working with network filesystems.
Bertschinger, Thomas↗
A survey of numerical linear algebra methods utilizing mixed-precision arithmetic
The efficient utilization of mixed-precision numerical linear algebra algorithms can offer attractive acceleration to scientific computing applications. Especially with the hardware integration of low-precision special-function units designed for machine learning applications, the traditional numerical algorithms community urgently needs to reconsider the floating point formats used in the distinct operations to efficiently leverage the available compute power. In this study, we provide a comprehensive survey of mixed-precision numerical linear algebra routines, including the underlying concepts, theoretical background, and experimental results for both dense and sparse linear algebra problems.
97 MATHEMATICS AND COMPUTING↗
Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae
Abstract Background Branched-chain higher alcohols (BCHAs), including isobutanol and 2-methyl-1-butanol, are promising advanced biofuels, superior to ethanol due to their higher energy density and better compatibility with existing gasoline infrastructure. Compartmentalizing the isobutanol biosynthetic pathway in yeast mitochondria is an effective way to produce BCHAs from glucose. However, to improve the sustainability of biofuel production, there is great interest in developing strains and processes to utilize lignocellulosic biomass, including its hemicellulose component, which is mostly composed of the pentose xylose. Results In this work, we rewired the xylose isomerase assimilation and mitochondrial isobutanol production pathways in the budding yeast Saccharomyces cerevisiae . We then increased the flux through these pathways by making gene deletions of BAT1 , ALD6 , and PHO13 , to develop a strain (YZy197) that produces as much as 4 g/L of BCHAs (3.10 ± 0.18 g isobutanol/L and 0.91 ± 0.02 g 2-methyl-1-butanol/L) from xylose. This represents approximately a 28-fold improvement on the highest isobutanol titers obtained from xylose previously reported in yeast and the first report of 2-methyl-1-butanol produced from xylose. The yield of total BCHAs is 57.2 ± 5.2 mg/g xylose, corresponding to ~ 14% of the maximum theoretical yield. Respirometry experiments show that xylose increases mitochondrial activity by as much as 7.3-fold compared to glucose. Conclusions The enhanced levels of mitochondrial BCHA production achieved, even without disrupting ethanol byproduct formation, arise mostly from xylose activation of mitochondrial activity and are correlated with slow rates of sugar consumption.
09 BIOMASS FUELS↗
Towards sustainable production and utilization of plant-biomass-based nanomaterials: a review and analysis of recent developments
Abstract Plant-biomass-based nanomaterials have attracted great interest recently for their potential to replace petroleum-sourced polymeric materials for sustained economic development. However, challenges associated with sustainable production of lignocellulosic nanoscale polymeric materials (NPMs) need to be addressed. Producing materials from lignocellulosic biomass is a value-added proposition compared with fuel-centric approach. This report focuses on recent progress made in understanding NPMs—specifically lignin nanoparticles (LNPs) and cellulosic nanomaterials (CNMs)—and their sustainable production. Special attention is focused on understanding key issues in nano-level deconstruction of cell walls and utilization of key properties of the resultant NPMs to allow flexibility in production to promote sustainability. Specifically, suitable processes for producing LNPs and their potential for scaled-up production, along with the resultant LNP properties and prospective applications, are discussed. In the case of CNMs, terminologies such as cellulose nanocrystals (CNCs) and cellulose nanofibrils (CNFs) used in the literature are examined. The term cellulose nano-whiskers (CNWs) is used here to describe a class of CNMs that has a morphology similar to CNCs but without specifying its crystallinity, because most applications of CNCs do not need its crystalline characteristic. Additionally, progress in enzymatic processing and drying of NPMs is also summarized. Finally, the report provides some perspective of future research that is likely to result in commercialization of plant-based NPMs.
09 BIOMASS FUELS↗
Utilization of microalgae for agricultural runoff remediation and sustainable biofuel production through an integrated biorefinery approach
Generally wastewater such agricultural runoff is considered a nuisance; however, it could be harnessed as a potential source of nutrients like nitrates and phosphates in integrated biorefinery context. In the current study, microalgae Chlorella sp. S5 was used for bioremediation of agricultural runoff and the leftover algal biomass was used as a potential source for production of biofuels in an integrated biorefinery context. The microalgae Chlorella sp. S5 was cultivated on Blue Green (BG 11) medium and a comprehensive optimization of different parameters including phosphates, nitrates, and pH was carried out to acquire maximum algal biomass enriched with high lipids content. Dry biomass was quantified using the solvent extraction technique, while the identification of nitrates and phosphates in agricultural runoff was carried out using commercial kits. The algal extracted lipids (oils) were employed in enzymatic trans-esterification for biodiesel production using whole-cell biomass of Bacillus subtilis Q4 MZ841642. The resultant fatty acid methyl esters (FAMEs) were analyzed using Fourier transform infrared (FTIR) spectroscopy and gas chromatography coupled with mass spectrometry (GC–MS). Subsequently, both the intact algal biomass and its lipid-depleted algal biomass were used for biogas production within a batch anaerobic digestion setup. Interestingly, Chlorella sp. S5 demonstrated a substantial reduction of 95% in nitrate and 91% in phosphate from agricultural runoff. The biodiesel derived from algal biomass exhibited a noteworthy total FAME content of 98.2%, meeting the quality standards set by American Society for Testing and Materials (ASTM) and European union (EU) standards. Furthermore, the biomethane yields obtained from whole biomass and lipid-depleted biomass were 330.34 NmL/g VS added and 364.34 NmL/g VS added , respectively. In conclusion, the findings underscore the potent utility of Chlorella sp. S5 as a multi-faceted resource, proficiently employed in a sequential cascade for treating agricultural runoff, producing biodiesel, and generating biogas within the integrated biorefinery concept.
09 BIOMASS FUELS↗
Utility of Early Postoperative Unstimulated Thyroglobulin in Influencing Decision Making in Patients with Papillary Thyroid Carcinoma
Background: Serum thyroglobulin is used to screen for disease persistence or recurrence of papillary thyroid carcinoma (PTC). We sought to assess the utility of early postoperative unstimulated thyroglobulin levels (uTg) as a decision-making tool to guide the use of radioactive iodine (RAI) in PTC patients. Methods: We performed a retrospective analysis of a prospectively maintained database of patients surgically treated for PTC from 2015 to 2017. We analyzed uTg approximately 6 weeks postoperatively. Patients undergoing total thyroidectomy or completion thyroidectomy were included in the study, and patients were analyzed according to postoperative uTg and receipt of RAI. Results: A total of 255 patients were analyzed, with 134 patients meeting the inclusion criteria. The median postoperative uTg was 0.3 ng/mL. Overall, 49.3% (66/134) of patients achieved the target uTg of ≤ 0.2 ng/mL at a mean time of 7.9 ± 0.3 weeks postoperatively; 60% (40/66) of patients who achieved uTg ≤ 0.2 ng/mL postoperatively did not receive RAI. A uTg ≤ 0.2 ng/mL was maintained at 6 months in 98.1% of patients, including 100% of patients who received RAI and 96.7% of patients who did not receive RAI (p = 0.8). Of those who did not receive RAI, none demonstrated structural disease recurrence on 6-month ultrasound. Patients with early postoperative uTg > 0.2–2.0 ng/mL showed benefit from RAI, while patients with uTg > 2.0 ng/mL did not achieve the targeted uTg level regardless of receipt of RAI. Conclusions: Postoperative uTg may be used to guide the use of RAI. Achieving near-undetectable uTg within 6 weeks postoperatively could aid providers in assessing disease burden and minimize RAI use for patients with a low-risk of disease recurrence. Continued follow-up is necessary to accurately determine long-term outcomes.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Advancing lightweight mirror design: a paradigm shift in mirror preforms by utilizing design for additive manufacturing
Additive manufacturing is a disruptive technology that can be leveraged by the redesign of components in most engineering fields. Fundamental engineering resources for lightweight mirrors were developed more than 30 years ago with a main design limitation, state of the art manufacturing. In this study, we present two design methodologies for the design of lightweight mirrors. The first method utilizes analytical expressions to design a traditional isogrid mirror, which provided the foundation for most lightweight mirrors to date. The second method employs a combination of topology optimization, lattice infill, and analytical estimation to develop an advanced lightweight mirror designed for additive manufacturing. The advanced mirror design outperforms the traditional design for each functional requirement, including a 94% reduction in predicted surface quilting and a higher specific stiffness. The manufacturing of the advanced mirror is only possible with an additive manufacturing process.
36 MATERIALS SCIENCE↗
High x-ray resolving power utilizing asymmetric diffraction from a quartz transmission crystal measured in the 6 keV to 22 keV energy range
We report a Cauchois-type spectrometer utilizing the (203) lattice planes at an oblique angle of 11.53° to the normal to the surface of a quartz transmission crystal recorded the Kα and Kβ spectral lines of six elements from Fe to Ag in the 6–22 keV energy range from a laboratory x-ray source. After deconvolving the natural lifetime widths and the image plate detector broadening from the observed spectral linewidths, the intrinsic crystal resolving power was determined to be 4000 at the lower energies and decreasing to 1000 at the higher energies. Previously, a Si wafer crystal exhibited twice this resolving power when the (331) planes had been used in asymmetric geometry. The investigation of diffraction with this quartz crystal, with a very similar lattice spacing and therefore spectral coverage, was motivated by the larger integrated reflectivity of quartz due to its well-known quasimosaicity upon elastic bending. The measured spectral linewidths were in good agreement with the widths calculated by accounting for various broadening mechanisms, including source size, crystal thickness, crystal height, crystal rocking curve width, geometrical aberrations, and possible spectrometer configuration errors. This is the first, to the best of our knowledge, demonstration of high resolving power achieved by asymmetric diffraction over a wide energy range (6–22 keV) and with detailed comparisons with theoretical broadenings. Finally, based on these results, Cauchois spectrometers employing asymmetric planes of perfect quartz and silicon crystals can be reliably designed and optimized for high-resolution spectroscopy in the >6 keV energy range.
36 MATERIALS SCIENCE↗
Towards a more general understanding of the algorithmic utility of recurrent connections
Lateral and recurrent connections are ubiquitous in biological neural circuits. Yet while the strong computational abilities of feedforward networks have been extensively studied, our understanding of the role and advantages of recurrent computations that might explain their prevalence remains an important open challenge. Foundational studies by Minsky and Roelfsema argued that computations that require propagation of global information for local computation to take place would particularly benefit from the sequential, parallel nature of processing in recurrent networks. Such “tag propagation” algorithms perform repeated, local propagation of information and were originally introduced in the context of detecting connectedness, a task that is challenging for feedforward networks. Here, we advance the understanding of the utility of lateral and recurrent computation by first performing a large-scale empirical study of neural architectures for the computation of connectedness to explore feedforward solutions more fully and establish robustly the importance of recurrent architectures. In addition, we highlight a tradeoff between computation time and performance and construct hybrid feedforward/recurrent models that perform well even in the presence of varying computational time limitations. We then generalize tag propagation architectures to propagating multiple interacting tags and demonstrate that these are efficient computational substrates for more general computations of connectedness by introducing and solving an abstracted biologically inspired decision-making task. Our work thus clarifies and expands the set of computational tasks that can be solved efficiently by recurrent computation, yielding hypotheses for structure in population activity that may be present in such tasks.
59 BASIC BIOLOGICAL SCIENCES↗
UNNT: A novel Utility for comparing Neural Net and Tree-based models
The use of deep learning (DL) is steadily gaining traction in scientific challenges such as cancer research. Advances in enhanced data generation, machine learning algorithms, and compute infrastructure have led to an acceleration in the use of deep learning in various domains of cancer research such as drug response problems. In our study, we explored tree-based models to improve the accuracy of a single drug response model and demonstrate that tree-based models such as XGBoost (eXtreme Gradient Boosting) have advantages over deep learning models, such as a convolutional neural network (CNN), for single drug response problems. However, comparing models is not a trivial task. To make training and comparing CNNs and XGBoost more accessible to users, we developed an open-source library called UNNT (A novel Utility for comparing Neural Net and Tree-based models). The case studies, in this manuscript, focus on cancer drug response datasets however the application can be used on datasets from other domains, such as chemistry.
59 BASIC BIOLOGICAL SCIENCES↗