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DOE OSTI2023

Defining the Minimal Set of Microbial Genes Required for Valorization of Lignin Biomass (Final Report)

Project Goals: Lignin is the second most abundant biopolymer on earth and represents a critically underutilized biomass resource for hydrocarbon feedstocks. Despite substantial effort, there is still no efficient process to convert lignin to useable carbon-based platform chemicals and materials. The goal of this project is identify a minimal set of microbial enzymes necessary for lignin breakdown and sufficient for the synthesis of valuable chemical intermediates from lignin isolated as a byproduct of lignocellulosic ethanol production. These genes will be then used to engineer functional whole cell biocatalysts for tunable lignin metabolism. To date, although a number of enzymes have been associated with lignin degradation, most have been tested in isolation (as individual enzymes) and on drastically different substrates -- often dyes that are not related to lignin. In contrast, lignin utilization in nature likely occurs by microbial consortia with multiple enzymes acting synergistically. We propose to examine two separate stages of lignin breakdown carried out by the microbes that do it best: (1) early breakdown of native polymeric lignin into soluble fragments by a set of sequenced wood-rotting fungal species, and (2) downstream metabolism of these soluble lignin fragments to useful chemical intermediates by a panel of sequenced soil saprophytes. Our approach involves testing sets of genes that will be assayed combinatorially in the context of a heterologous expression host. The resulting engineered strains will be systematically assayed using soluble lignin fragments, synthetic defined polymeric lignin, and finally lignin directly sourced from lignocellulosic processing streams. In addition to resulting in a functional whole cell biocatalyst for lignin utilization, we anticipate that this approach will allow us to address key unanswered questions about lignin metabolism in nature, including: (1) Why does the Trametes versicolor genome contain 25 different class II peroxidases? (2) What is the role of laccases in lignin metabolism? Why do some aggressive lignin degraders have many laccases (e.g. >7 in T. versicolor) while others have none (e.g. P. chrysosporium)? (3) How is peroxide provided in a controlled manner to drive peroxidase activity without causing the enzyme inhibition that is so often observed in vitro? (4) What strategies do microbial lignin degraders use to avoid the problem of repolymerization during active lignin degradation? and (5) Can microbial lignin metabolism be diverted for high level production of defined aromatics? A final critical question is whether combining key minimal sets of enzymes from a wide range of organisms will result in engineered strains capable of highly efficient, streamlined pathways for lignin utilization that can be tuned for a specific carbon output. This effort will leverage DOE investments in microbial genome sequencing, and secure a critical channel for lignin biomass utilization that will also help to render lignocellulosic a viable feedstock for the production of renewable liquid biofuels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

NOW-23: The 2023 National Offshore Wind Data Set

In this report, we present the latest wind resource data specifically tailored for offshore regions in the United States. The data set, known as the 2023 National Offshore Wind data set (NOW-23), has been developed by the National Renewable Energy Laboratory (NREL) and its partners, and surpasses the previous resource data set, the Wind Integration National Dataset (WIND) Toolkit, which was released approximately ten years ago, in its offshore component. The WIND Toolkit has been widely utilized by stakeholders involved in wind resource assessments across the continental United States. However, with significant advancements in numerical weather prediction modeling over the past decade, the NOW-23 data set incorporates the latest research and development progress to provide stakeholders with an updated and cutting-edge resource for offshore wind analysis.

17 WIND ENERGY↗

DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

An Updated Global Grid Point Surface Air Temperature Anomaly Data Set: 1851-1990 (revised 1991) (NDP-020)

This NDP presents land-based monthly surface-air-temperature anomalies (departures from a 1951-1970 reference period mean) on a 5° latitude by 10° longitude global grid. Monthly surface-air-temperature anomalies (departures from a 1957-1975 reference period mean) for the Antarctic (grid points from 65°S to 85°S) are presented in a similar way as a separate data set. The data were derived primarily from the World Weather Records and from the archives of the United Kingdom Meteorological Office. This long-term record of temperature anomalies may be used in studies addressing possible greenhouse-gas-induced climate changes. To date, the data have been employed in producing regional, hemispheric, and global time series for determining whether recent (i.e., post-1900) warming trends have taken place. The present updated version of this data set is identical to the earlier version for all records from 1851-1978 except for the addition of the Antarctic surface-air-temperature anomalies beginning in 1957. Beginning with the 1979 data, this package differs from the earlier version in several ways. Erroneous data for some sites have been corrected after a review of the actual station temperature data, and inconsistencies in the representation of missing values have been removed. For some grid locations, data have been added from stations that had not contributed to the original set. Data from satellites have also been used to correct station records where large discrepancies were evident. The present package also extends the record by adding monthly surface-air-temperature anomalies for the Northern (grid points from 85°N to 0°) and Southern (grid points from 5°S to 60°S) Hemispheres for 1985-1990. In addition, this updated package presents the monthly-mean-temperature records for the individual stations that were used to produce the set of gridded anomalies. The periods of record vary by station. Northern Hemisphere data have been corrected for inhomogeneities, while Southern Hemisphere data are presented in uncorrected form.For access to the data files, click this link to the CDIAC data transition website: http://cdiac.ess-dive.lbl.gov/ndps/ndp020.html

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2015

Meta gene set enrichment analyses link miR-137-regulated pathways with schizophrenia risk

Background: A single nucleotide polymorphism (SNP) within MIR137, the host gene for miR-137, has been identified repeatedly as a risk factor for schizophrenia. Previous genetic pathway analyses suggest that potential targets of this microRNA (miRNA) are also highly enriched in schizophrenia-relevant biological pathways, including those involved in nervous system development and function. Methods: In this study, we evaluated the schizophrenia risk of miR-137 target genes within these pathways. Gene set enrichment analysis of pathway-specific miR-137 targets was performed using the stage 1 (21,856 subjects) schizophrenia genome wide association study data from the Psychiatric Genomics Consortium and a small independent replication cohort (244 subjects) from the Mind Clinical Imaging Consortium and Northwestern University. Results: Gene sets of potential miR-137 targets were enriched with variants associated with schizophrenia risk, including target sets involved in axonal guidance signaling, Ephrin receptor signaling, long-term potentiation, PKA signaling, and Sertoli cell junction signaling. The schizophrenia-risk association of SNPs in PKA signaling targets was replicated in the second independent cohort. Conclusions: These results suggest that these biological pathways may be involved in the mechanisms by which this MIR137 variant enhances schizophrenia risk. SNPs in targets and the miRNA host gene may collectively lead to dysregulation of target expression and aberrant functioning of such implicated pathways. Pathway-guided gene set enrichment analyses should be useful in evaluating the impact of other miRNAs and target genes in different diseases.

Genetics & Heredity↗

DOE OSTI2021

Primary Velocity and Orbital Phase Effects on Planetary Detectability from Small Epoch Number Data Sets

Cross-correlation analyses of high-resolution spectroscopic data have recently shown great success in directly detecting planetary signals and enabling the characterization of their atmospheres. One such technique aims to observe a system at multiple epochs and combine the measured planetary radial velocities from each epoch into a measurement of the planetary Keplerian orbital velocity K {sub p}, constituting a direct detection of the planetary signal. Recent work has shown that in few-epoch (∼5) data sets, unintended structure can arise at a high level, obscuring the planetary detection. In this work, we look to simulations to examine whether there are ways to reduce this structured noise in few-epoch data sets by careful planning of observations. The choice of observation date allows observers to select the primary (stellar) velocity through a set systemic velocity and chosen barycentric velocity and the planetary orbital phase so we focus on the effects of these two parameters. We find that epochs taken when the primary velocity is near zero and the stellar lines remain relatively fixed to the telluric rest-frame greatly reduce the level of structured noise and allow for much stronger planetary detections, on average more than twice the significance of detections made with epochs using randomly selected primary velocities. Following these results, we recommend that observers looking to build up high-resolution multi-epoch data sets target nights when their system has a near-zero primary velocity.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

The 2023 National Offshore Wind data set (NOW-23)

Abstract. This article introduces the 2023 National Offshore Wind data set (NOW-23), which offers the latest wind resource information for offshore regions in the United States. NOW-23 supersedes, for its offshore component, the Wind Integration National Dataset (WIND) Toolkit, which was published a decade ago and is currently a primary resource for wind resource assessments and grid integration studies in the contiguous United States. By incorporating advancements in the Weather Research and Forecasting (WRF) model, NOW-23 delivers an updated and cutting-edge product to stakeholders. In this article, we present the new data set which underwent regional tuning and performance validation against available observations and has data available from 2000 through, depending on the region, 2019–2022. We also provide a summary of the uncertainty quantification in NOW-23, along with NOW-WAKES, a 1-year post-construction data set that quantifies expected offshore wake effects in the US Mid-Atlantic lease areas. Stakeholders can access the NOW-23 data set at https://doi.org/10.25984/1821404 (Bodini et al., 2020).

17 WIND ENERGY↗

DOE OSTI2017

The compression–error trade-off for large gridded data sets

The netCDF-4 format is widely used for large gridded scientific data sets and includes several compression methods: lossy linear scaling and the non-lossy deflate and shuffle algorithms. Many multidimensional geoscientific data sets exhibit considerable variation over one or several spatial dimensions (e.g., vertically) with less variation in the remaining dimensions (e.g., horizontally). On such data sets, linear scaling with a single pair of scale and offset parameters often entails considerable loss of precision. We introduce an alternative compression method called "layer-packing" that simultaneously exploits lossy linear scaling and lossless compression. Layer-packing stores arrays (instead of a scalar pair) of scale and offset parameters. An implementation of this method is compared with lossless compression, storing data at fixed relative precision (bit-grooming) and scalar linear packing in terms of compression ratio, accuracy and speed. When viewed as a trade-off between compression and error, layer-packing yields similar results to bit-grooming (storing between 3 and 4 significant figures). Bit-grooming and layer-packing offer significantly better control of precision than scalar linear packing. Relative performance, in terms of compression and errors, of bit-groomed and layer-packed data were strongly predicted by the entropy of the exponent array, and lossless compression was well predicted by entropy of the original data array. Layer-packed data files must be "unpacked" to be readily usable. The compression and precision characteristics make layer-packing a competitive archive format for many scientific data sets.

58 GEOSCIENCES↗

NASA NTRS1975

Life analysis of helical gear sets using Lundberg-Palmgren theory

A mathematical model is developed for surface fatigue life of helical gears. The expected fatigue life of a pinion, gear, or gear set may be calculated from the model. An equation for the dynamic capacity of a gear set was also derived. Dynamic capacity is the transmitted tangential load which gives a 90 percent probability of survival of the gear set for one million pinion revolutions. The equations, when simplified by setting the helix angle to zero, reduce to the results which were previously developed for spur gears. A sample calculation is given which illustrates the use of the new fatigue life model.

Coy, J. J.↗

NASA NTRS1975

The geometric approach to sets of ordinary differential equations and Hamiltonian dynamics

The calculus of differential forms is used to discuss the local integration theory of a general set of autonomous first order ordinary differential equations. Geometrically, such a set is a vector field V in the space of dependent variables. Integration consists of seeking associated geometric structures invariant along V: scalar fields, forms, vectors, and integrals over subspaces. It is shown that to any field V can be associated a Hamiltonian structure of forms if, when dealing with an odd number of dependent variables, an arbitrary equation of constraint is also added. Families of integral invariants are an immediate consequence. Poisson brackets are isomorphic to Lie products of associated CT-generating vector fields. Hamilton's variational principle follows from the fact that the maximal regular integral manifolds of a closed set of forms must include the characteristics of the set.

Estabrook, F. B.↗

NASA NTRS1980

Geometric representation methods for multi-type self-defining remote sensing data sets

Efficient and convenient representation of remote sensing data is highly important for an effective utilization. The task of merging different data types is currently dealt with by treating each case as an individual problem. A description is provided of work which is carried out to standardize the multidata merging process. The basic concept of the new approach is that of the self-defining data set (SDDS). The creation of a standard is proposed. This standard would be such that data which may be of interest in a large number of earth resources remote sensing applications would be in a format which allows convenient and automatic merging. Attention is given to details regarding the multidata merging problem, a geometric description of multitype data sets, image reconstruction from track-type data, a data set generation system, and an example multitype data set.

Anuta, P. E.↗

NASA NTRS1981

SPAR data set contents

The contents of the stored data sets of the SPAR (space processing applications rocket) finite element structural analysis system are documented. The data generated by each of the system's processors are stored in a data file organized as a library. Each data set, containing a two-dimensional table or matrix, is identified by a four-word name listed in a table of contents. The creating SPAR processor, number of rows and columns, and definitions of each of the data items are listed for each data set. An example SPAR problem using these data sets is also presented.

Cunningham, S. W.↗

NASA NTRS1984

A calibration adjustment technique combining ERB parameters from different remote sensing platforms into a long-term data set

Earth-radiation-budget (ERB) experiments on board the Nimbus-6 (ERB 6) and Nimbus-7 (ERB 7) spacecraft have measured wide-field-of-view total (0.2 to 50 micron), shortwave (0.2 to 3.8 micron), and near-infrared (0.7 to 2.8 micron) terrestrial irradiances for a joint lifetime of over 8 years. Though the spectral characteristics of both experiments are nearly identical, instrument degradation and altitude differences introduce discrepancies between the two data sets. ERB parameters from these two observing platforms may be combined into a scientifically meaningful data set only after these discrepancies are eliminated. To facilitate the creation of a long-term ERB data set, comparisons of the ERB 6 experiment irradiances with, and calibration adjustments with respect to, the corresponding ERB 7 irradiances have been performed. Two calibration methods were developed and applied to the irradiance data from 28 pairs of collocated orbits. The differential effects of altitude, illumination, albedo, and scene inhomogeneities were applied. The result is a set of calibration adjustments that adjust the ERB 6 data to match the ERB 7 data.

Ardanuy, P. E.↗

NASA NTRS1985

Comparison of Two Orographical Data Sets for the GLAS Fourth Order GCM

The development of a 2 deg latitude by 2.5 deg longitude version of the GLAS Fourth Order General Circulation Model has necessitated the specification of a correspondingly fine horizontal resolution orographic data set to act as a lower boundary condition for the GCM. The S1 topography attempts to relate the mean areally averaged height of such terrain while the Q3 topography emphasizes the effect of the flow of the tallest peaks in such regions by specifying an exaggerated significant height. In order to assess the relative merits of these two orographic data sets. A series of tests was initiated to evaluate the comparative weather forecasting and climate simulation skills of the GLAS Fourth Order GCM when the S1 and Q3 topographies are applied to the lower boundary. Three sets of Northern Hemispheric winter forecasts at the 2 deg x 2.5 deg resolution indicate that the Q3 topography gives slightly better results over the Northern Hemisphere than does the S1 topography. It is apparent that more forecasts will be necessary at both horizontal resolutions before any definitive conclusions are made regarding the choice of an optimal orographic data set.

Helfand, H. M.↗

NASA NTRS1987

Near Hartree-Fock quality GTO basis sets for the second-row atoms

Energy optimized, near Hartree-Fock quality Gaussian basis sets ranging in size from (17s12p) to (20s15p) are presented for the ground states of the second-row atoms for Na(2P), Na(+), Na(-), Mg(3P), P(-), S(-), and Cl(-). In addition, optimized supplementary functions are given for the ground state basis sets to describe the negative ions, and the excited Na(2P) and Mg(3P) atomic states. The ratios of successive orbital exponents describing the inner part of the 1s and 2p orbitals are found to be nearly independent of both nuclear charge and basis set size. This provides a method of obtaining good starting estimates for other basis set optimizations.

Partridge, Harry↗

NASA NTRS1987

Applications of classical and zero-total-pressure-loss sets of Euler equations to delta wings

Classical and zero-total pressure-loss sets of Euler equations were applied to sharp- and round-edge delta wings. The origin of the total pressure was explained in the classical set. For sharp-edged delta wings, all sets of Euler equations produce the same separated flow solutions. For round-edged delta wings and for coarse grids, the solution depends on the level of dissipation, the accuracy of the surface boundary condition, and the type of Euler equations set. For round-edged delta wings and for fine grids, attached flow solutions are obtained. Also presented were three dimensional flow solutions and asymmetric flow solutions including unsteady flow for sharp-edged delta wings. Euler equations should be restricted to sharp-edged wings for real flow solutions. For roung-edged wings, Navier-Stokes equations must be used.

Kandil, Osama A.↗

NASA NTRS1987

Near Hartree-Fock quality GTO basis sets for the second-row atoms

Partridge, Harry↗

NASA NTRS1986

Software engineering environment tool set integration

Space Transportation System Division (STSD) Engineering has a program to promote excellence within the engineering function. This program resulted in a capital funded facility based on a VAX cluster called the Rockwell Operational Engineering System (ROSES). The second phase of a three phase plan to establish an integrated software engineering environment for ROSES is examined. It discusses briefly phase one which establishes the basic capability for a modern software development environment to include a tool set, training and standards. Phase two is a tool set integration. The tool set is primarily off-the-shelf tools acquired through vendors or government agencies (public domain). These tools were placed into categories of software development. These categories are: requirements, design, and construction support; verification and validation support; and software management support. The integration of the tool set is being performed through concept prototyping and development of tools specifically designed to support the life cycle and provide transition from one phase to the next.

Selfridge, William P.↗