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Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool.

59 BASIC BIOLOGICAL SCIENCES↗

PLEXOS Inputs for Voisin et al. 2020 [Data set]

These data files provide MOSART-WM monthly flows at hydropower dam and HUC4 outlet locations. The flows are transformed into monthly generation constraints scenarios for hydro (generation potential) and thermal power plants (derated capacity) for input to the PLEXOS model. Contact: Sean Turner , Nathalie Voisin Authors: Nathalie Voisin, Ana Dyreson, Tao Fu, Matt O'Connell, Sean Turner, Tian Zhou, Jordan Macknick

13 HYDRO ENERGY↗

Results for Voisin et al. 2020 [Data set]

These data files provide contemporary (2010) bulk electricity grid operations and transmission flow as simulated by PLEXOS and informed by historical and future generation constraints scenarios as informed by historical and future water availability at hydro and thermoelectric plants. Contact: Ana Dyreson , Nathalie Voisin Authors: Nathalie Voisin, Ana Dyreson, Tao Fu, Matt O'Connell, Sean Turner, Tian Zhou, Jordan Macknick

13 HYDRO ENERGY↗

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. The NOW-23 data set is created using the Weather Research and Forecasting (WRF) model and its output is available, as for its predecessor, at 5-minute time resolution and 2-kilometer horizontal spatial resolution. However, the NOW-23 data set improves upon the WIND Toolkit through: 1. A modeling period of at least 20 years (and as long as 23 years in selected regions), starting in 2000 (compared to the 7-year 2007–2013 modeling period in the WIND Toolkit). 2. For several offshore regions, a region-specific sensitivity analysis, driven by an ensemble of WRF simulations, to assess the most adequate region-specific WRF setup. 3. An updated WRF model, from Version 3.4 used in the WIND Toolkit to Version 4.2.1 used for the NOW-23 data set, which incorporates significant research advancements. 4. The use of the state-of-the-art reanalysis product ERA5 (which supersedes the older ERA-Interim used in the WIND Toolkit) to provide atmospheric forcing at the WRF domain boundaries. Figure 1 shows the NOW-23 mean wind speed at 160 m above sea level (asl), which we use as proxy for hub-height of a commercial offshore wind turbine in this report across all regions.

17 WIND ENERGY↗

2023 National Offshore Wind data set (NOW-23)

The 2023 National Offshore Wind data set (NOW-23) is the latest wind resource data set for offshore regions in the United States, which supersedes, for its offshore component, the Wind Integration National Dataset (WIND) Toolkit, which was published about a decade ago and is currently one of the primary resources for stakeholders conducting wind resource assessments in the continental United States. The NOW-23 data set was produced using the Weather Research and Forecasting Model (WRF) version 4.2.1. A regional approach was used: for each offshore region, the WRF setup was selected based on validation against available observations. The WRF model was initialized with the European Centre for Medium Range Weather Forecasts 5 Reanalysis (ERA-5) data set, using a 6-hour refresh rate. The model is configured with an initial horizontal grid spacing of 6 km and an internal nested domain that refined the spatial resolution to 2 km. The model is run with 61 vertical levels, with 12 levels in the lower 300m of the atmosphere, stretching from 5 m to 45 m in height. The MYNN planetary boundary layer and surface layer schemes were used the North Atlantic, Mid Atlantic, Great Lakes, Hawaii, and North Pacific regions. On the other hand, using the YSU planetary boundary layer and MM5 surface layer schemes resulted in a better skill in the South Atlantic, Gulf of Mexico, and South Pacific regions. A more detailed description of the WRF model setup can be found in the WRF namelist files linked at the bottom of this page. For all regions, the NOW-23 data set coverage starts on January 1, 2000. For Hawaii and the North Pacific regions, NOW-23 goes until December 31, 2019. For the South Pacific region, the model goes until 31 December, 2022. For all other regions, the model covers until December 31, 2020. Outputs are available at 5 minute resolution, and for all regions we have also included output files at hourly resolution. The NOW-23 data are provided here as HDF5 files. Examples of how to use the HSDS Service to Access the NOW-23 files are linked below. A list of the variables included in the NOW-23 files is also linked below. No filters have been applied to the raw WRF output.

Array↗

Global digital data sets of soil type, soil texture, surface slope and other properties: Documentation of archived data tape

The file structure and coding of four soils data sets derived from the Zobler (1986) world soil file is described. The data were digitized on a one-degree square grid. They are suitable for large-area studies such as climate research with general circulation models, as well as in forestry, agriculture, soils, and hydrology. The first file is a data set of codes for soil unit, land-ice, or water, for all the one-degree square cells on Earth. The second file is a data set of codes for texture, land-ice, or water, for the same soil units. The third file is a data set of codes for slope, land-ice, or water for the same units. The fourth file is the SOILWRLD data set, containing information on soil properties of land cells of both Matthews' and Food and Agriculture Organization (FAO) sources. The fourth file reconciles land-classification differences between the two and has missing data filled in.

Staub, B.↗

Statistical Validation of Multiple Related Data Sets—Case Study Using Interstellar Boundary Explorer Satellite Data

Abstract Space scientists often face the question of whether data collected by different instruments are measurements of the same source population. This paper proposes a statistical validation method for evaluating the agreement between such related data sets. It offers a detailed case study focused on validating a new data set from the Interstellar Boundary Explorer (IBEX) mission, which serves as a practical how-to guide for similar analyses. Since 2008, the IBEX satellite has been gathering data on heliospheric energetic neutral atoms (ENAs) while being exposed to various sources of background noise, such as cosmic rays and solar energetic particles. The IBEX mission initially released only a qualified triple-coincidence (qABC) data product, which was designed to provide observations of ENAs free of background contamination. Further measurements revealed that the qABC data were in fact susceptible to contamination, having relatively low ENA counts and high background rates. To mitigate this issue, the mission team recently considered releasing a certain qualified double-coincidence (qBC) data product, which has roughly twice the detection rate of the qABC data product. This paper presents a simulation-based validation of the new qBC data product against the already-released qABC data product. The results show that the qBCs can plausibly be said to be measuring the same source population as the qABCs up to an average absolute deviation of 3.6%. Visual diagnostics provide additional confirmation of source rate coherence across data products. The framework introduced here is general and can be applied to other validation problems both within and outside the field of space physics.

79 ASTRONOMY AND ASTROPHYSICS↗

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.↗

User's guide to the Nimbus-4 backscatter ultraviolet experiment data sets

The first year's data from the Nimbus 4 backscatter ultraviolet (BUV) experiment have been archived in the National Space Science Data Center (NSSDC). Backscattered radiances in the ultraviolet measured by the satellite were used to compute the global total ozone for the period April 1970 - April 1971. The data sets now in the NSSDC are the results obtained by the Ozone Processing Team, which has processed the data with the purpose of determining the best quality of the data. There are four basic sets of data available in the NSSDC representing various stages in processing. The primary data base contains organized and cleaned data in telemetry units. The radiance data has had most of the engineering calibrations performed. The detailed total ozone data is the result of computations to obtain the total ozone; the Compressed Total Ozone data is a convenient condensation of the detailed total ozone. Product data sets are also included.

Lowrey, B. E.↗

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.↗

Tests of a Semi-Analytical Case 1 and Gelbstoff Case 2 SeaWiFS Algorithm with a Global Data Set

A semi-analytical algorithm was tested with a total of 733 points of either unpackaged or packaged-pigment data, with corresponding algorithm parameters for each data type. The 'unpackaged' type consisted of data sets that were generally consistent with the Case 1 CZCS algorithm and other well calibrated data sets. The 'packaged' type consisted of data sets apparently containing somewhat more packaged pigments, requiring modification of the absorption parameters of the model consistent with the CalCOFI study area. This resulted in two equally divided data sets. A more thorough scrutiny of these and other data sets using a semianalytical model requires improved knowledge of the phytoplankton and gelbstoff of the specific environment studied. Since the semi-analytical algorithm is dependent upon 4 spectral channels including the 412 nm channel, while most other algorithms are not, a means of testing data sets for consistency was sought. A numerical filter was developed to classify data sets into the above classes. The filter uses reflectance ratios, which can be determined from space. The sensitivity of such numerical filters to measurement resulting from atmospheric correction and sensor noise errors requires further study. The semi-analytical algorithm performed superbly on each of the data sets after classification, resulting in RMS1 errors of 0.107 and 0.121, respectively, for the unpackaged and packaged data-set classes, with little bias and slopes near 1.0. In combination, the RMS1 performance was 0.114. While these numbers appear rather sterling, one must bear in mind what mis-classification does to the results. Using an average or compromise parameterization on the modified global data set yielded an RMS1 error of 0.171, while using the unpackaged parameterization on the global evaluation data set yielded an RMS1 error of 0.284. So, without classification, the algorithm performs better globally using the average parameters than it does using the unpackaged parameters. Finally, the effects of even more extreme pigment packaging must be examined in order to improve algorithm performance at high latitudes. Note, however, that the North Sea and Mississippi River plume studies contributed data to the packaged and unpackaged classess, respectively, with little effect on algorithm performance. This suggests that gelbstoff-rich Case 2 waters do not seriously degrade performance of the semi-analytical algorithm.

Carder, Kendall L.↗

The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules

Abstract Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Latest developments in the display of large-scale ionospheric and thermospheric data sets

Over the past decade, data base sizes have continually increased and will continue to do so in the future. This problem of size is further compounded because the trend in present-day studies is to use data from many different locations and different instruments and then compare it with data from global scale physical models. The latter produce data bases of comparable if not even larger size. Much of the data can be viewed as 'image' time sequences and is most readily viewed on color display terminals. These data sets reside in national or owner-generated data bases linked together by computer networks. As the size increases, just moving this data around, taking 'quick-looks' at the data, or even storing it locally become severe problems compromising the scientific return from the data. Is the present-day technology with these analysis techniques being used in the best way? What are the prospects for reducing the storage and transmission size of the data sets? Examples of such problems and potential solutions are described in this paper.

Sojka, J. J.↗

A global data set of soil particle size properties

A standardized global data set of soil horizon thicknesses and textures (particle size distributions) was compiled. This data set will be used by the improved ground hydrology parameterization designed for the Goddard Institute for Space Studies General Circulation Model (GISS GCM) Model 3. The data set specifies the top and bottom depths and the percent abundance of sand, silt, and clay of individual soil horizons in each of the 106 soil types cataloged for nine continental divisions. When combined with the World Soil Data File, the result is a global data set of variations in physical properties throughout the soil profile. These properties are important in the determination of water storage in individual soil horizons and exchange of water with the lower atmosphere. The incorporation of this data set into the GISS GCM should improve model performance by including more realistic variability in land-surface properties.

Webb, Robert S.↗

SeaWiFS technical report series. Volume 15: The simulated SesWiFS data set, version 2

This document describes the second version of the simulated SeaWiFS data set. A realistic simulated data set is essential for mission readiness preparations and can potentially assist in all phases of ground support for a future mission. The second version improves on the first version primarily through additional realism and complexity. This version incorporates a representation of virtually every aspect of the flight mission. Thus, it provides a high-fidelity data set for testing several aspects of the ground system, including data acquisition, data processing, data transfers, calibration and validation, quality control, and mission operations. The data set is constructed for a seven-day period, 25-31 March 1994. Specific features of the data set include Global Area coverage (GAC), recorded Local Area Coverage (LAC), and realtime High Resolution Picture Transmission (HRPT) data for the seven-day period. A realistic orbit, which is propagated using a Brouwer-Lyddane model with drag, is used to simulate orbit positions. The simulated data corresponds to the command schedule based on the orbit for this seven-day period. It includes total (at-satellite) radiances not only for ocean, but for land, clouds, and ice. The simulation also utilizes a high-resolution land-sea mask. It includes the April 1993 SeaWiFS spectral responses and sensor saturation responses. The simulation is formatted according to July 1993 onboard data structures, which include corresponding telemetry (instrument and spacecraft) data. The methods are described and some examples of the output are given. The instrument response functions made available in April 1993 have been used to produce the Version 2 simulated data. These response functions will change as part of the sensor improvements initiated in July-August 1993.

Hooker, Stanford B.↗

MiniWall Tool for Analyzing CFD and Wind Tunnel Large Data Sets

It is challenging to review and assimilate large data sets created by Computational Fluid Dynamics (CFD) simulations and wind tunnel tests. Over the past 10 years, NASA Ames Research Center has developed and refined a software tool dubbed the "MiniWall" to increase productivity in reviewing and understanding large CFD‐generated data sets. Under the recent NASA ERA project, the application of the tool expanded to enable rapid comparison of experimental and computational data. The MiniWall software is browser based so that it runs on any computer or device that can display a web page. It can also be used remotely and securely by using web server software such as the Apache HTTP Server. The MiniWall software has recently been rewritten and enhanced to make it even easier for analysts to review large data sets and extract knowledge and understanding from these data sets. This paper describes the MiniWall software and demonstrates how the different features are used to review and assimilate large data sets.

Data Analysis↗

MiniWall Tool for Analyzing CFD and Wind Tunnel Large Data Sets

It is challenging to review and assimilate large data sets created by Computational Fluid Dynamics (CFD) simulations and wind tunnel tests. Over the past 10 years, NASA Ames Research Center has developed and refined a software tool dubbed the MiniWall to increase productivity in reviewing and understanding large CFD-generated data sets. Under the recent NASA ERA project, the application of the tool expanded to enable rapid comparison of experimental and computational data. The MiniWall software is browser based so that it runs on any computer or device that can display a web page. It can also be used remotely and securely by using web server software such as the Apache HTTP server. The MiniWall software has recently been rewritten and enhanced to make it even easier for analysts to review large data sets and extract knowledge and understanding from these data sets. This paper describes the MiniWall software and demonstrates how the different features are used to review and assimilate large data sets.

Computational Fluid Dyanmics↗

Monthly mean global satellite data sets available in CCM history tape format

Satellite data for climate monitoring have become increasingly important over the past decade, especially with increasing concern for inadvertent antropogenic climate change. Although most satellite based data are of short record, satellites can provide the global coverage that traditional meteorological observations network lack. In addition, satellite data are invaluable for the validation of climate models, and they are useful for many diagnostic studies. Herein, several satellite data sets were processed and transposed into 'history tape' format for use with the Community Climate Model (CCM) modular processor. Only a few of the most widely used and best documented data sets were selected at this point, although future work will expand the number of data sets examined as well as update the archived data sets. An attempt was made to include data of longer record and only monthly averaged data were processed. For studies using satellite data over an extended period, it is important to recognize the impact of changes in instrumentation, drift in instrument calibration, errors introduced by retrieval algorithms and other sources of errors such as those resulting from insufficient space and/or time sampling.

Hurrell, James W.↗