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Data associated with the Inorganic Chemistry publication (DOI: 10.1021/acs.inorgchem.4c03924) was made publicly available in a FigShare repository (DOI: 10.6084/m9.figshare.28195664) to ensure reproducibility and support the PI's commitment to open-science that was included in the data management plan of the project.
Focal Area(s): Focal Area 2: AI for predictive modeling, including AI-derived model components, and AI-enabled applications including parameter optimization, data assimilation, and uncertainty quantification. Focal Area 1: AI-assisted data assimilation using numerical Earth system models. Science Challenge: Earth system models have structural biases that lead to uncertain predictions, and their complexity and expense makes it difficult constraining the models with data or improved physical understanding.
The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.
Data associated with the Journal of the American Chemical Society publication (DOI: 10.1021/jacs.4c09888 ) was made publicly available in a FigShare repository (DOI: 10.6084/m9.figshare.26997388) to ensure reproducibility and support the PI's commitment to open-science that was included in the data management plan of the project
As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra, lattice theory, and topology. They are able to represent complex systems interactions more faithfully than graphs and networks, while also being some of the simplest classes of systems representing topological structures as collections of multidimensional objects connected in a particular pattern. In this paper we discuss the role of (undirected) hypergraphs in the science of complex networks, and provide a mathematical overview of the core concepts needed for hypernetwork modeling, including duality and the relationship to bicolored graphs, quantitative adjacency and incidence, the nature of walks in hypergraphs, and available topological relationships and properties. We close with a brief discussion of two example applications: biomedical databases for disease analysis, and domain-name system (DNS) analysis of cyber data.
We report the use of streaming data interfaces to perform fully online data processing for serial crystallography experiments, without storing intermediate data on disk. The system produces Bragg reflection intensity measurements suitable for scaling and merging, with a latency of less than 1 s per frame. Our system uses the CrystFEL software in combination with the ASAP::O data framework. In a series of user experiments at PETRA III, frames from a 16 megapixel Dectris EIGER2 X detector were searched for peaks, indexed and integrated at the maximum full-frame readout speed of 133 frames per second. The computational resources required depend on various factors, most significantly the fraction of non-blank frames ('hits'). The average single-thread processing time per frame was 242 ms for blank frames and 455 ms for hits, meaning that a single 96-core computing node was sufficient to keep up with the data, with ample headroom for unexpected throughput reductions. Further significant improvements are expected, for example by binning pixel intensities together to reduce the pixel count. We discuss the implications of real-time data processing on the `data deluge' problem from recent and future photon-science experiments, in particular on calibration requirements, computing access patterns and the need for the preservation of raw data.
A significant gap exists in our understanding and ability to predict the spatial occurrence and extent of rare earth elements (REE) and certain critical minerals (CM) in sedimentary strata. This is largely due to a lack of existing, systematic, and well-distributed REE and CM samples and analyses in United States sedimentary basins. In addition, the type of sampling and characterization performed to date has generally lacked the resolution and approach required to constrain geologic and geographic heterogeneities typical of subsurface, mineral resources. Here, we describe a robust and systematic method for collecting core scale characterization data that can be applied to studies on the contextual and spatial attributes, the geologic history, and lithostratigraphy of sedimentary basins. The methods were developed using drilled cores from coal bearing sedimentary strata in the Powder River Basin, Wyoming (PRB). The goal of this effort is to create a unified core characterization methodology to guide systematic collection of key data to achieve a foundation of spatially and geologically constrained REEs and CMs. This guidance covers a range of measurement types and methods that are each useful either individually or in combination to support characterization and delineation of REE and CM occurrences. The methods herein, whether used in part or in full, establish a framework to guide consistent acquisition of geological, geochemical, and geospatial datasets that are key to assessing and validating REE and CM occurrences from geologic sources to support future exploration, assessment, and techno-economic related models and analyses.
Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.
Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information available for inquiry. Synthesizing these data is challenging, especially considering the legacy of soil data that have already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last access: 22 December 2020), a flexible database designed to harmonize diverse SOM datasets from multiple research networks. SoDaH is built on several network science efforts in the United States, but the tools built for SoDaH aim to provide an open-access resource to facilitate synthesis of soil carbon data. Moreover, SoDaH allows for individual locations to contribute results from experimental manipulations, repeated measurements from long-term studies, and local- to regional-scale gradients across ecosystems or landscapes. Finally, we also provide data visualization and analysis tools that can be used to query and analyze the aggregated database. The SoDaH v1.0 dataset is archived and available at https://doi.org/10.6073/pasta/9733f6b6d2ffd12bf126dc36a763e0b4 (Wieder et al., 2020).
Variation in the electrical conductivity (EC) of water can reveal environmental disturbance and natural dynamics, including factors such as anthropogenic salinization. Broader application of open source (OS) EC sensors could provide an inexpensive method to measure water quality. While studies show that other water quality parameters can be robustly measured with sensors, a similar effort is needed to evaluate the performance of OS EC sensors. To address this need, we evaluated the accuracy (mean error, %) and precision (sample standard deviation) of OS EC sensors in the laboratory via comparison to EC calibration standards using three different OS and OS/commercial-hybrid (OS/C) EC sensors and data logger configurations and two commercial (C) EC sensors and data logger configurations. We also evaluated the effect of cable length (7.5 m and 30 m) and sensor calibration on OS sensor accuracy and precision. We found a significant difference between OS sensor mean accuracy (3.08%) and all other sensors combined (9.23%). Our study also found that EC sensor precision decreased across all sensor configurations with increasing calibration standard EC. There was also a significant difference between OS sensor mean precision (2.85 μS/cm) and the mean precision of all other sensors combined (9.12 μS/cm). Cable length did not affect OS sensor precision. Furthermore, our results suggest that future research should include evaluating how performance is impacted by combining OS sensors with commercial data loggers as this study found significantly decreased performance in OS/commercial-hybrid sensor configurations. To increase confidence in the reliability of OS sensor data, more studies such as ours are needed to further quantify OS sensor performance in terms of accuracy and precision across different settings and OS sensor and data collection platform configurations.
The U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) user facility recently deployed its First ARM Mobile Facility (AMF1) to La Jolla, California as part of the Eastern Pacific Cloud Aerosol Precipitation Experiment (EPCAPE) campaign. Some of the goals behind EPCAPE were to characterize the diurnal and seasonal cycles of stratocumulus clouds and to investigate the cloud-aerosol-radiation interactions and feedbacks in the area. The deployment of the AMF1 for a full year from 15 February 2023 to 14 February 2024 aided in addressing these scientific questions. While AMF1 collected data year-round, enhanced measurements were taken during two intensive operational periods (IOPs). The first IOP occurred from April to June and focused on the chemistry of low clouds (EPCAPE_Chem), while the second IOP occurred from July to September and was focused on the radiation of high clouds (EPCAPE_Radiation). Several cloud radars were deployed with AMF1 to collect valuable data on cloud properties that will help users address key science objectives. As in past ARM campaigns, a1-level radar data is extensively analyzed and calibration techniques are performed to generate b1-level data (Matthews et al. 2023, Feng et al. 2024). Radar data at the b1-level are of the highest quality and thus can be used to examine scientific questions. The status of the a1-level data and the a1-to-b1 process for the EPCAPE radars is subsequently detailed in this document.
Summit Darshan Archival Dataset contains 2021 Summit Darshan log data for 25 applications and is grouped into science domains. The dataset is processed, and all the propriety fields are anonymized. The resultant data is converted into a tabular structure and saved in parquet file format. In this notebook, we demonstrate how to access the data. Data Organization: The data is organized into two directories: Darshan total (`darshan_total`): List all the high levels generated by the `darshan-parser --total` command on `.darshan` files. There is one parquet file for each application. Note: `uid` and `exe` field are masked Darshan detail (`darshan_detail`): This data contains detailed job level log information extracted by command `darshan-parser` on the raw `.darshan` files. The data is sorted by directory hierarchy in the order of `year/month/day (2021/12/07)`. For instance, to get the data for a `job_id` 3819766 of application `App11`, which was executed on `2021-12-07`can be accessed as follows. Note:`uid` and `filename` fields are masked
Big Data in nuclear comes in the form of many structures, systems, components, data streams, data types, and more.
For the High-Luminosity Large Hadron Collider, the trigger and data acquisition system of the CMS experiment will be entirely replaced. Novel design choices have been explored, including ATCA prototyping platforms with SoC controllers and newly available interconnect technologies with serial optical links with data rates up to 28 Gb/s. Trigger analyses will be performed through sophisticated algorithms, including widespread use of Machine Learning, in large FPGAs, such as the Xilinx Ultrascale family. The system will process over 50 Tb/s of detector data with an event rate of 750 kHz. Here, we describe system design and prototyping and review trigger algorithm exemplars.
Focal Area 3: Explainable AI Our confidence in the projections made by Earth System Models (ESMs) depends on understanding them to be, in some important respects, faithful representations of the Earth system. Here we present an “explainable Artificial Intelligence (AI)” method that allows us to uncover the dynamical structure of the observed and modeled Earth system, discover hidden links across wide spatiotemporal scales, target model development efforts at poorly-represented dynamics, and optimize observed or modeled data collection to maximize predictive information. Science Challenge: Dynamical system science for the Earth system poses unique challenges given the large degree of internal climate variability. Thus, tools that help us understand how ESMs succeed and fail at representing these dynamics are crucial, particularly in relation to the observed system. Furthermore, the computational and memory constraints on ESM data output motivate in situ analysis of ESM dynamics, including automatic detection of dynamical shifts. Also, of key importance are procedures that leverage ESMs to optimize observational campaigns for improving process representation, reducing structural uncertainty and improving model skill.
We present the first rest-frame optical size–luminosity relation of galaxies at z > 7, using the NIRCam imaging data obtained by the GLASS James Webb Space Telescope Early Release Science (GLASS-JWST-ERS) program, providing the deepest extragalactic data of the ERS campaign. Our sample consists of 19 photometrically selected bright galaxies with m F444W ≤ 27.8 at 7 < z < 9 and m F444W < 28.2 at z ~ 9–15. We measure the size of the galaxies in five bands, from rest-frame optical (~4800 Å) to the UV (~1600 Å) based on the Sérsic model, and analyse the size–luminosity relation as a function of wavelength. Remarkably, the data quality of the NIRCam imaging is sufficient to probe the half-light radius r e down to ~100 pc at z > 7. Given the limited sample size and magnitude range, we first fix the slope to that observed for larger samples in rest-frame UV using Hubble Space Telescope samples. The median size r 0 at the reference luminosity M = –21 decreases slightly from rest-frame optical (600 ± 80 pc) to UV (450 ± 130 pc). We then refit the size–luminosity relation allowing the slope to vary. The slope is consistent with β ~ 0.2 for all bands except F150W, where we find a marginally steeper slope of β = 0.53 ± 0.15. The steep UV slope is mainly driven by the smallest and faintest galaxies. If confirmed by larger samples, it implies that the UV size–luminosity relation breaks toward the faint end, as suggested by lensing studies.
Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.
We have successfully developed the first working version of online ensemble coupled data assimilation (ECDA) on E3SM for both version 1 and version 2. Our schemes have also been tested successfully for assimilating SST data in both synthetic observations and real world observations, laying a foundation for future development.