The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource
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Eloe-Fadrosh, Emiley A↗
SEARCH · Engineering Papers
Results for “resource selection functions”
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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Design and implementation of I/O performance prediction scheme on HPC systems through large-scale log analysis
Abstract Large-scale high performance computing (HPC) systems typically consist of many thousands of CPUs and storage units used by hundreds to thousands of users simultaneously. Applications from large numbers of users have diverse characteristics, such as varying computation, communication, memory, and I/O intensity. A good understanding of the performance characteristics of each user application is important for job scheduling and resource provisioning. Among these performance characteristics, I/O performance is becoming increasingly important as data sizes rapidly increase and large-scale applications, such as simulation and model training, are widely adopted. However, predicting I/O performance is difficult because I/O systems are shared among all users and involve many layers of software and hardware stack, including the application, network interconnect, operating system, file system, and storage devices. Furthermore, updates to these layers and changes in system management policy can significantly alter the I/O behavior of applications and the entire system. To improve the prediction of the I/O performance on HPC systems, we propose integrating information from several different system logs and developing a regression-based approach to predict the I/O performance. Our proposed scheme can dynamically select the most relevant features from the log entries using various feature selection algorithms and scoring functions, and can automatically select the regression algorithm with the best accuracy for the prediction task. The evaluation results show that our proposed scheme can predict the write performance with up to 90% prediction accuracy and the read performance with up to 99% prediction accuracy using the real logs from the Cori supercomputer system at NERSC.
97 MATHEMATICS AND COMPUTING↗
Institute for Catalysis in Energy Processes (ICEP) (Final Report)
The Institute for Catalysis in Energy Processes (ICEP) was a multi-PI program located at the Northwestern University Center for Catalysis and Surface Science from 2006-2024. Over several renewal cycles and several organizing themes, ICEP addressed fundamental questions in catalysis science. In turn, the scientific questions addressed were directly relevant to the efficient use of the nation’s resources to produce fuels and commodity chemicals, harness alternate energy sources for chemical reactions such as light or electricity, reduce emissions and waste, and minimize the impact of our use of plastics. Selective oxidation, (oxidative) dehydrogenation, deNOx, CO 2 reduction, hydrogen release, polymer decomposition / depolymerization, and many other reactions of intense interest to the US Department of Energy were studied in the center. Major ICEP strengths were in catalyst synthesis, in measurements that elucidated catalyst properties, in reaction mechanisms and kinetics, and in predictive theory and modeling. ICEP researchers were often the inventors or developers of materials and methods that were brought to bear on the Institute’s catalytic systems. Key characterization tools advanced through this project included resonance Raman and related techniques, sum frequency generation, and X-ray standing wave spectroscopy. Center members relied extensively on computational tools such as density functional theory and microkinetic modeling to fully investigate catalyst structures and catalytic mechanisms. ICEP researchers were early developers of atomic layer deposition (ALD) for catalyst synthesis and were early pioneers of metal organic frameworks for catalysis. ICEP innovations are found in areas of intense research such as single-atom catalysts, catalytic deconstruction of plastics, and catalytic MOFs, to name a few. Research areas initiated by ICEP indirectly led to DOE EFRCs, startup companies, and other achievements. Over its 18 years of existence, ICEP involved two different PIs (Stair and Notestein) and 24 senior investigators across several academic disciplines at Northwestern University. There were tight collaborations with Argonne National Laboratory, including specialized equipment and experiments permanently located there. The center supported ~400 person-years of effort by graduate students and postdocs, either directly through DOE support or indirectly by leveraging independent support provided to the trainees, e.g. through the NSF GRFP or internal fellowships. The project resulted in 328 manuscripts and numerous conference presentations.
36 MATERIALS SCIENCE↗
NREM sleep as a novel protective cognitive reserve factor in the face of Alzheimer's disease pathology
Alzheimer’s disease (AD) pathology impairs cognitive function. Yet some individuals with high amounts of AD pathology suffer marked memory impairment, while others with the same degree of pathology burden show little impairment. Why is this? One proposed explanation is cognitive reserve i.e., factors that confer resilience against, or compensation for the effects of AD pathology. Deep NREM slow wave sleep (SWS) is recognized to enhance functions of learning and memory in healthy older adults. However, that the quality of NREM SWS (NREM slow wave activity, SWA) represents a novel cognitive reserve factor in older adults with AD pathology, thereby providing compensation against memory dysfunction otherwise caused by high AD pathology burden, remains unknown. Here, we tested this hypothesis in cognitively normal older adults (N = 62) by combining 11 C-PiB (Pittsburgh compound B) positron emission tomography (PET) scanning for the quantification of β-amyloid (Aβ) with sleep electroencephalography (EEG) recordings to quantify NREM SWA and a hippocampal-dependent face-name learning task. We demonstrated that NREM SWA significantly moderates the effect of Aβ status on memory function. Specifically, NREM SWA selectively supported superior memory function in individuals suffering high Aβ burden, i.e., those most in need of cognitive reserve (B = 2.694, p = 0.019). In contrast, those without significant Aβ pathological burden, and thus without the same need for cognitive reserve, did not similarly benefit from the presence of NREM SWA (B = -0.115, p = 0.876). This interaction between NREM SWA and Aβ status predicting memory function was significant after correcting for age, sex, Body Mass Index, gray matter atrophy, and previously identified cognitive reserve factors, such as education and physical activity (p = 0.042). These findings indicate that NREM SWA is a novel cognitive reserve factor providing resilience against the memory impairment otherwise caused by high AD pathology burden. Furthermore, this cognitive reserve function of NREM SWA remained significant when accounting both for covariates, and factors previously linked to resilience, suggesting that sleep might be an independent cognitive reserve resource. Beyond such mechanistic insights are potential therapeutic implications. Unlike many other cognitive reserve factors (e.g., years of education, prior job complexity), sleep is a modifiable factor. As such, it represents an intervention possibility that may aid the preservation of cognitive function in the face of AD pathology, both present moment and longitudinally.
60 APPLIED LIFE SCIENCES↗
The Near-Gapless Penicillium fuscoglaucum Genome Enables the Discovery of Lifestyle Features as an Emerging Post-Harvest Phytopathogen
Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.
59 BASIC BIOLOGICAL SCIENCES↗
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.
59 BASIC BIOLOGICAL SCIENCES↗
Developing Advanced Genetic and Synthetic Biology Tools for Improved Algae Productivity
Under the UCSD-led Productivity Enhanced Algae and ToolKits (PEAK) project we sought to develop tools to enable the production of valuable co-products, as well as strategies to decrease the cost of cultivation, with an intended outcome of enabling the economic production of algae-based biofuel. We have developed new genetic tools and high throughput selection methods for eukaryotic green algae and used them to express a high value recombinant protein; a growth factor known as Osteopontin (OPN). Recombinant OPN protein expression levels were improved through a newly developed rapid breeding and mutagenesis strain improvement method to generate a robust strain capable of growing in outdoors raceway conditions in brackish water that tolerated high pH and large temperature swings. We further applied the new genetic tools to express recombinant protein in a recently bioprospected strain with even more robust growth characteristics. In response to the COVID-19 pandemic we used our improved workflow to rapidly express, purify, and characterize a recombinant SARS-CoV-2 spike protein Receptor Binding Domain (RBD) and demonstrate that it functionally interacts with its cognate human host receptor ACE2. The newly identified extremophile strain Chlamydomonas sp (402), both mating type (mt+) and mating type (mt-), have been deposited in the Chlamydomonas Resource Center (https://www.chlamycollection.org/), making them available world-wide with no restrictions. In addition, all of genetic tools are also deposited at this site and are also available world-wide with no restrictions.
09 BIOMASS FUELS↗
Multilevel Analysis, Design, and Modeling of Coupling Advanced Nuclear Reactors and Thermal Energy Storage in an Integrated Energy System
This report discusses the different options for coupling thermal energy storage (TES) systems to advanced nuclear power plants (A-NPPs) in order to enable flexible and hybrid plant operation. An advanced light-water reactor (A LWR), a high-temperature gas-cooled reactor (HTGR) and a liquid-metal fast reactor (LMFR) were selected as the initial use cases for demonstrating a thermally balanced energy storage coupling design for thermal power extraction. The models presented herein showcase several design considerations, focusing on optimal deployment methodologies for achieving steady-state and transient-state operation with minimum disruption to the nuclear power cycle. This first part of the study presents steady-state models developed using Aspen HYSYS®, with the thermal energy bypass for NPP-TES coupling being varied at up to 50%. The various components were sized using the Aspen Process Economic Analyzer (APEA) and Aspen Exchanger Design and Rating (EDR), when applicable. Cost functions from these models were developed using the latest publicly available data obtained from APEA V11. The TES-coupled A-NPP steady-state models and cost functions then provided a baseline for dynamic operation and process optimization by using Idaho National Laboratory (INL)’s Framework for Optimization of Resources and Economics (FORCE) tools. A stochastic optimization of the various energy storage systems coupled to the A-NPPs was then performed using the Risk Analysis Virtual Environment (RAVEN) and its dispatch optimization plugin, the Holistic Energy Resource Optimization Network (HERON). The signal processing and synthetic history capabilities of RAVEN were used to account for the unpredictable behavior of electricity markets. An autoregressive moving average (ARMA) model was used to analyze price signals from the Pennsylvania-New Jersey-Maryland (PJM) market and were applied to the HERON analysis in order to optimize a system with the best economics. Transient modeling evaluation was then performed using Modelica models within the HYBRID repository, which was developed at INL for the Department of Energy Integrated Energy Systems program for the characterization of dynamic integrated system behavior and feedback. This includes evaluation of the TES-coupled A-LWR systems’ impact on physical and thermal system response during imposed system demands. Additional TES-coupled reactor types, coupling approaches, markets, and TES technologies will be evaluated in future work.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Phenotypically anchored transcriptomics across diverse agrichemicals reveals conserved pathways and unique gene expression signatures in zebrafish
Agrichemicals such as herbicides, fungicides, insecticides, and biocides are widely used in agriculture, yet some are associated with adverse effects in humans and the environment. While many of these chemicals have been extensively studied in vitro and are included in the EPA’s ToxCast program, comprehensive in vivo comparisons using RNA sequencing across structurally diverse agrichemicals, in a single screening platform, are lacking. In this study, we examined structurally diverse agrichemicals found in the U.S. Environmental Protection Agency’s (EPA) Toxcast Phase I and II library by statically exposing early life stage zebrafish at 6 h post fertilization (hpf) until 120 hpf at concentrations ranging from 0.25 to 100 µM. Morphological outcomes were assessed at 120 hpf across 10 endpoints, including yolk sac edema, craniofacial malformations, and axis abnormalities. Chemicals that produced robust concentration-response relationships were selected for transcriptomic profiling. For transcriptomic analysis, zebrafish were statically exposed to each chemical and sampled at 48 hpf, prior to the onset of morphological effects observed at 120 hpf. Differential expression analysis identified between 0 and 4,538 differentially expressed genes (DEGs) per chemical, with no clear correlation to morphological severity. Both DEG and co-expression network analyses revealed chemical-specific expression patterns that converged on shared biological pathways, including neurodevelopment and cytoskeletal organization. Key regulatory genes such as mylpfa and krt4 were identified within co-expression modules, suggesting their potential role in conserved toxicity mechanisms. Semantic similarity analysis of enriched gene ontology (GO) terms, when compared to existing datasets, highlighted gaps in the annotation of neurodevelopmental processes, indicating that some in vivo effects may not be fully captured by current curated resources. The results provide new insights into the modes of action of diverse agrichemicals and establish a framework for understanding how agrichemical structure relates to biological function in a vertebrate model.
agrichemical↗
Scalable Fabrication of a Fibrous Amine-functionalized Matrix (FAM) Sorbent for Critical Mineral Recovery
We report a novel flat sheet Fibrous Amine-functionalized Matrix (FAM) sorbent platform designed for efficient and selective capture of CM from dilute solutions. The FAM sorbent features crosslinked amine microfilms coated onto/within a glass fiber matrix, providing fast mass transfer and excellent mechanical stability. Systematic batch and flow-through tests with FAM revealed rapid metal uptake kinetics and high capacity for representative species, achieving ~90 mg/g of Gallium, ~100 mg/g of Cobalt, and ~90 mg/g for Neodymium. Moreover, multiple eluents, including mineral acids and complexing agents, enabled highly effective desorption of adsorbed metals, demonstrating the feasibility of regenerating FAM sorbents. Importantly, tests with authentic coal ash leachate demonstrated strong selectivity toward U.S. Department of Energy (DOE)-listed CM and rare earth elements over abundant base cations, confirming the robustness of FAM in realistic complex solutions. The flat sheet geometry was amenable to scaling into durable spiral wound modules, highlighting the potential for future regeneration and reuse. This work establishes FAM sorbents as a promising platform for the recovery of CM from wastewaters, advancing both resource sustainability and environmental stewardship.
critical mineral recovery↗
Simulation of PV Variability as a Function of PV Generation and Plant Size: Preprint
The deployment of photovoltaic (PV) systems continues to show significant expansion; however, this growth has brought added attention to issues around the variability of the solar resource. Both spatial and temporal variability exist. Temporal scales can range from the sub-second to multiyear, whereas spatial scales can range from a few meters to tens of kilometers. There are multiple methods described in the literature to quantify PV variability at various spatial and temporal scales. This study focuses on short-term temporal variability and uses similar approaches with the addition of PV plant size a parameter to quantify variability. The method employed here incorporates the normalization of clear- and cloudy-sky conditions and PV plant size to quantify nominal variability metrics. The distribution and fluctuations of these metrics provide relevant information that is useful for system operations. The National Solar Radiation Database (NSRDB) is used to simulate PV variability as a function of PV generation and plant size. Hypothetical but realistic system information at 33 locations is used to model PV generation by feeding NSRDB solar irradiance data to the National Renewable Energy Laboratory’s System Advisor Model (SAM). Over the selected region, it is found that the aggregated ramp rates for the 1-minute data are associated with standard deviations ranging from 0.002–0.055 on a daily basis; however, hourly intervals induce higher aggregated ramp rates than the other timescales. Even though minute-to-minute variations are significant for the 1-minute timescale, the standard deviation aggregated into a daily metric is smaller because of the cancellation of values.
41 EE - Solar Energy Technologies Office (EE-4S)↗
Simulation of PV Variability as a Function of PV Generation and Plant Size
The deployment of photovoltaic (PV) systems continues to show significant expansion; however, this growth has brought added attention to issues around the variability of the solar resource. Both spatial and temporal variability exist. Temporal scales can range from the sub-second to multiyear, whereas spatial scales can range from a few meters to tens of kilometers. There are multiple methods described in the literature to quantify PV variability at various spatial and temporal scales. This study focuses on short-term temporal variability and uses similar approaches with the addition of PV plant size a parameter to quantify variability. The method employed here incorporates the normalization of clear-and cloudy-sky conditions and PV plant size to quantify nominal variability metrics. The distribution and fluctuations of these metrics provide relevant information that is useful for system operations. The National Solar Radiation Database (NSRDB) is used to simulate PV variability as a function of PV generation and plant size. Hypothetical but realistic system information at 33 locations is used to model PV generation by feeding NSRDB solar irradiance data to the National Renewable Energy Laboratory’s System Advisor Model (SAM). Over the selected region, it is found that the aggregated ramp rates for the 1-minute data are associated with standard deviations ranging from 0.002–0.055 on a daily basis; however, hourly intervals induce higher aggregated ramp rates than the other timescales. Even though minute-to-minute variations are significant for the 1-minute time-scale, the standard deviation aggregated into a daily metric is smaller because of the cancellation of values.
irradiance↗
Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize
Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.
59 BASIC BIOLOGICAL SCIENCES↗
WELLS Interactive Application
The Wellbore Exploration and Location Logistic System (WELLS) Interactive Application is an interactive tool to enable easy exploration and visualization of the living national wellbore database (WELLS Database (https://edx.netl.doe.gov/dataset/wells_database)). The tool and underlying database were created and are maintained by the National Energy Technology Laboratory (NETL), providing visualization of the more than six million public wellbore records from more than 65 authoritative state, federal, and tribal resources. The WELLS Interactive Application serves up wellbore data from oil, gas, underground injection, research, geothermal, geotechnical, groundwater, and other types of wells in a single, standardized, unified system. In addition to the surface location of these wells, the underlying database combines select key attributes for features such as well age, depth, and operating status. The system also provides users with references back to the original sources used in this unified platform. The underlying data can be accessed through the WELLS Database: https://edx.netl.doe.gov/dataset/wells_database Additional Information: The WELLS Interactive Application (formerly titled CO2-Locate) enables visualization and access to the public wellbore records through an intuitive web-based mapping tool. The WELLS Interactive Application was designed to help users visualize, query, analyze, and download wellbore records. Public wellbore points are included as a layer in the Map page, called Public Wells. Additionally, a multivariate hexagon grid summarizing well density from proprietary well data, called Well Density, is included to identify data gaps between the public and proprietary well data. Filtering functionalities in the tool allow these two layers to be spatially filtered by state, county, or basin as well as by status, type, true vertical depth, and spud year. The WELLS Interactive Application also contains a Near Me tool can be used to search and explore wellbore data within a user-defined distance of a specified location on the map, which can also be downloaded. The Query tool allows users to query the selected or filtered wells in the Public Wells layer and export the data. For additional information on these tool functionalities, see the help documentation on the About page of the tool. Notes for Consideration: The Well Density layer provided in this application is derived from proprietary wellbore data, the records of which do not always contain values for key features (status, type, true vertical depth, or spud year). Therefore, data might not be available when layers are queried for all filter combinations. Additionally, visualizing layers and applying filters may take additional time to load (i.e., draw on the map) due to the large size of the data.
ccs↗
SpecDis: Value Added Distance Catalog for 4 Million Stars from DESI Year-1 Data
We present the SpecDis value-added stellar distance catalog accompanying DESI Data Release 1. SpecDis trains a feed-forward neural network (NN) with Gaia parallaxes and gets the distance estimates. To build up an unbiased training sample, we do not apply selections on parallax error or signal-to-noise (S/N) of the stellar spectra, and instead, we incorporate parallax error into the loss function. Moreover, we employ principal component analysis to reduce the noise and dimensionality of stellar spectra. Validated by independent external samples of member stars with precise distances from globular clusters, dwarf galaxies, stellar streams, combined with blue horizontal branch stars, we demonstrate that our distance measurements show no significant bias up to 100 kpc, and are much more precise than Gaia parallax beyond 7 kpc. The median distance uncertainties are 23%, 19%, 11%, and 7% for S/N < 20, 20 ≤ S/N < 60, 60 ≤ S/N < 100, and S/N ≥ 100. Selecting stars with ${\mathrm{log}}\,g\lt 3.8$ and distance uncertainties smaller than 25%, we have more than 74,000 giant candidates within 50 kpc of the Galactic center and 1500 candidates beyond this distance. Additionally, we develop a Gaussian mixture model to identify unresolvable equal-mass binaries by modeling the discrepancy between the NN-predicted and the geometric absolute magnitudes from Gaia parallaxes and identify 120,000 equal-mass binary candidates. Our final catalog provides distances and distance uncertainties for >4 million stars, offering a valuable resource for Galactic astronomy.
astronomy data analysis↗
LAI, EVI, NDVI, and kNDVI in 23 pantropical forests affected by 21 cyclones
Statement of purpose: Cyclones alter the function and composition of tropical forests, making effects of intensifying cyclones on carbon-rich forests a critical topic of study. Here, we quantified cyclone-induced damage and recovery of 21 cyclone disturbances affecting 23 pantropical forest sites between 1988-2017 utilizing leaf area index (LAI), enhanced vegetation index (EVI), normalized difference vegetation index (NDVI), and transformed NDVI (kNDVI) values from Google Earth Engine. Field observations collected in a meta-analysis (Bomfim et al., 2022, in review) were used to ground-truth and test effects of soil resource availability and disturbance factors on damage and recovery. This meta-analysis also served as the basis to begin vegetation index extraction, utilizing unique site and date combinations, from tropical forests effect by cyclone disturbances. We began collecting NDVI (5km resolution) from the NOAA Climate Data Record (CDR) of AVHRR Normalized Difference Vegetation Index (NDVI), Version 5 data product (Vermote, 2019) for all case studies included, 42. Next, we began extracting Landsat data from Landsat 4, 5, and 8, courtesy of the U.S. Geological Survey, in search of higher resolution data. We selected a 3 by 3 Landsat pixel area, leading to a 90m resolution data extraction. The specific imagery used includes Landsat 4 USGS Landsat 4 TM Collection 1 Tier 1 TOA (top of atmosphere) Reflectance, Landsat 5 USGS Landsat 5 TM (thematic mapper) Collection 1 Tier 1 TOA Reflectance, and Landsat 8 USGS Landsat 8 Collection 1 Tier 1 TOA Reflectance. Within Google Earth Engine, we selected the date and location (latitude and longitude), calculated NDVI, kNDVI, and EVI utilizing Landsat bands (see metadata_NGEE-tropics_cyclones), and extracted post- and pre-cyclone values for each case study to calculate cyclone-induced change in the vegetative index. Due to limited spatial resolution of Landsat remote sensing data, MODIS products were investigated next. First, the MOD13Q1.006 Terra Vegetation Indices 16-Day Global 250m product was used to extract 250m EVI and NDVI (Didan, 2015) and then the MCD15A3H.006 MODIS Leaf Area Index/FPAR 4-Day Global 500m product product was used to extract LAI 500m (Myneni et al., 2015). Pre- and post-cyclone values, change in the vegetative index, and standard deviation for all values are included in the main csv (see case_study_data.csv) for all vegetative indices collected, including LAI 500m, EVI 250m, NDVI 250m, NDVI 90m, kNDVI 90m, EVI 90m, and NDVI 5km. Lastly, recovery values were calculated utilizing a standardization method (see metadata_NGEE-tropics_cyclones) and recovery values for MODIS (see MODIS_recovery.csv) and Landsat (Landsat_recovery.csv) data are included.
54 ENVIRONMENTAL SCIENCES↗
A large-scale comparison of Artificial Intelligence and Data Mining (AI&DM) techniques in simulating reservoir releases over the Upper Colorado Region
In recent years, the Artificial Intelligence and Data Mining (AI&DM) models have become popular tools in assisting various aspects of reservoir operation. However, the practical uses are still rarely reported. Comparison experiment of many AI&DM models over a large number of reservoir cases is particularly valuable to help reservoir operators first examine the usefulness and transferability of different AI&DM models, and then identify the most stable and reliable AI&DM model in assist of various decision-making processes. In this study, a total of 12 AI&DM models with different parameterizations and simulation scenarios are comprehensively tested out and compared in simulating the controlled reservoir outflows of 33 reservoir cases over the Upper Colorado Region, United States. Results show that the Random Forecast and the Long-Short-Term-Memory model could consistently derive the best statistical performance than other models under the baseline simulation scenario. The employed AI&DM models could obtain satisfactory statistical interquartile ranges (25–75%) between [0.6–0.9], [0.3–0.8], and [0.2–0.8], for CORR, NSE, and KGE measurements, respectively, and [1.5–6.5], [–15 to 20], and [0.5–8.5] for the normalized RMSE, PBIAS and RSR measurements, respectively. Results also show Multi-Layer Perceptron model and Extreme Gradient Boosting Tree Algorithm produced more stable and superior performance than other models under more complex input scenarios. We also found that the performance of different AI&DM models are closely relevant to the reservoir elevations, sizes, and functionalities. Discussions were made about the sensitivity of AI&DM models’ parameterizations and the key advantages of AI&DM models over the rule-based reservoir models. We further identify that the main advantage of AI&DM models is the flexibility in designing input structures, whereas the rule-based simulation model is rather limited. Future studies were suggested regarding the best way reservoir operators and researchers could use, select, and apply different AI&DM models in simulating reservoir releases under different natural and modeling environments. Finally, this comparison study also serves as a reference and a piece of groundwork for further promoting the practical uses of AI&DM models in assisting reservoir operation.
54 ENVIRONMENTAL SCIENCES↗
Exploring drought-responsive crucial genes in Sorghum
Drought severely affects global food production. Sorghum is a typical drought-resistant model crop. Based on RNA-seq data for Sorghum with multiple time points and the gray correlation coefficient, this paper firstly selects candidate genes via mean variance test and constructs weighted gene differential co-expression networks (WGDCNs); then, based on guilt-by-rewiring principle, the WGDCNs and the hidden Markov random field model, drought-responsive crucial genes are identified for five developmental stages respectively. Enrichment and sequence alignment analysis reveal that the screened genes may play critical functional roles in drought responsiveness. A multilayer differential co-expression network for the screened genes reveals that Sorghum is very sensitive to pre-flowering drought. Furthermore, a crucial gene regulatory module is established, which regulates drought responsiveness via plant hormone signal transduction, MAPK cascades, and transcriptional regulations. The proposed method can well excavate crucial genes through RNA-seq data, which have implications in breeding of new varieties with improved drought tolerance.
60 APPLIED LIFE SCIENCES↗