AndreaBozzo/ceres-open-data-index huggingface dataset:
EV-GHG Mobile Source

The EV-GHG Mobile Source Data asset contains measured mobile source GHG emissions summary compliance information on light-duty vehicles, by model, for certification as required by the 1990 Amendments to the Clean Air Act, and as driven by the 2010 Presidential Memorandum Regarding Fuel Efficiency and the 2005 Supreme Court ruling in Massachusetts v. EPA that supported the regulation of CO2 as a pollutant. Manufacturers submit data on an annual basis, or as needed to document vehicle model changes. This asset will be expanded to include medium and heavy duty vehicles in the future.The EPA performs targeted GHG emissions tests on approximately 15% of vehicles submitted for certification. Confirmatory data on vehicles is associated with its corresponding submission data to verify the accuracy of manufacturer submissions beyond standard business rules.Submitted data comes in XML format or as documents, with the majority of submissions sent in XML, and includes descriptive information on the vehicle itself, emissions information, and the manufacturer's testing approach. This data may contain proprietary information (CBI) such as information on estimated sales or other data elements indicated by the submitter as confidential. CBI data is not publically available; however, CBI data can accessed within EPA under the restrictions of the Office of Transportation and Air Quality (OTAQ) CBI policy [RCS Link]. Pollutants data includes CO2, CH4, N2O. Datasets are divided by vehicle/engine model and/or year with corresponding emission, test, and certification data. Data assets are stored in EPA's Verify system.Coverage began in 2011, with summary light duty data available to the public on request. Raw data is only available to select EPA employees.EV-GHG Mobile Source Data submission documents with metadata, certificate and summary decision information is stored in Verify after it has been quality assured. Where summary data appears inaccurate, OTAQ returns the entries for review to their originator.

Tags: cap, climate-change, emissions, environment, environmental-protection-agency, epa, ev-ghg, ghg, greenhouse, hap, mobile-source, oar, office-of-air-and-radiation, office-of-transportation-and-air-quality, otaq, united-states
Organization: U.S. Environmental Protection Agency
Data for: Direct and indirect effects of floral defoliation on photochemical and non-photochemical chlorophyll fluorescence dynamics of a semiarid bunchgrass

<p dir="ltr">These data were collected in an experimental field study at the USDA-ARS Northern Great Basin Experimental Range, OR, USA, aimed at assessing the effects of floral defoliation on the ability of crested wheatgrass (<i>Agropyron cristatum</i>) florets to dissipate excess light energy over the 2025 plant reproductive period. Basal florets were clipped by 30-50% ca. 3 cm from the distal end of the seed-head, and the chlorophyll fluorescence responses of clipped basal florets and unclipped florets distal to these were compared to those at the same locations on unclipped control seed heads. Chlorophyll fluorescence measurements were made at night to determine dark-adapted baseline (Fo) and maximum fluorescence yields (Fm) and to calculate maximum photosystem II quantum efficiency (Fv/Fm = (Fm-Fo)/Fm). The same florets were then measured again the following morning when exposed to full incident ambient photosynthetic photon flux densities to determine light-adapted steady state fluorescence (Fs), maximum fluorescence yields (Fm') and light-adapted photosystem II quantum efficiency (PhiPSII = (Fm'-Fs)/Fs). Fs, Fm and Fm’ were used to estimate the quantum yield of non-photochemical energy loss (NPQ) in PS II that is physiologically regulated (PhiNPQ = (Fs/Fm’)-(Fs/Fm)) and unregulated (PhiNO = Fs/Fm). Data was collected over two days within each of three reproductive phenological periods (pre-anthesis, anthesis, and post-anthesis), with concurrent average daily volumetric soil moisture at 10 cm soil depth (Vsm) from six Vsm observations made daily.</p>

Tags: chlorophyll-fluorescence, crested-wheatgrass, herbivory, photoprotection, quantum-yield-parameters, reproduction
Organization: Department of Agriculture
Data from: Fungicide efficacy and duration of protection against coffee leaf rust (<i>Hemileia vastatrix</i>) on commercial coffee farms in Hawaii

<p dir="ltr">These data are from a study that characterized fungicide efficacy and duration of protection against coffee leaf rust (CLR, <i>Hemileia vastatrix</i>) on Hawaii Island. Field trials were conducted on three commercial coffee farms in 2022 and five commercial farms in 2023. We included four commercially available fungicides approved for coffee in Hawaii in 2022, and six fungicides in 2023. The preventative fungicides (two copper-based, two <i>Bacillus</i>-based, and one botanical-based fungicide) were applied twice during the field trial, at week 0 and week 5. The translaminar fungicide was applied once (week 0) or twice (week 0 and week 6) in combination with a copper fungicide (week 3) during the field trial. Data was collected on CLR incidence (presence of infection) and leaf retention (leaves per branch) for 12 (2022) to 15 (2023) trees per treatment on a weekly (2022) or bi-weekly (2023) basis. The cost of application was also estimated based on labor (USD$/hour), gas and oil used for the sprayer, and product cost (USD$/pound or Fl oz) and rate (amount of product/acre). Our results suggest that conventional coffee farms can control CLR by alternating applications of translaminar and copper-based fungicides, aiming to apply a total of 4-6 sprays between flowering and harvest to reduce impacts on leaf retention and yield. Without the option to use translaminar fungicides, organic farms will need to aim for 5-8 sprays, alternating between copper and biological fungicides to control CLR.</p>

Tags: agroecosystems, coffea-arabica, disease-incidence, preventative, spray-application, translaminar
Organization: Department of Agriculture
Data from: Block-stumping as an effective and cost-efficient style of pruning to reduce coffee berry borer (Hypothenemus hampei Ferrari) infestation and damage in Hawaiian coffee farms

<p dir="ltr">These data are from a study that assessed the impact of different pruning styles on the regulation of coffee berry borer (CBB, Hypothenemus hampei), widely considered the most damaging insect pest of coffee worldwide. For each pruning system (block-stumping, Kona style, topping, and Beaumont-Fukunaga), 3–4 coffee lots were selected on Hawaii Island and CBB infestation, bean damage, and harvesting efficacy was evaluated in 2023 and 2024. Yields, sale price, and pruning costs were also recorded to calculate the benefit cost ratio of each pruning style. Block-stumping resulted in significantly lower CBB infestation (0.6 % and 2.6 %, year one and two of harvest) relative to Beaumont-Fukunaga (6.3 %), topping (8.6 %) and Kona style (10.0 %). Block-stumping also resulted in significantly lower bean damage (2.6 %) compared to topping (24.3 %) and Kona style (25.6 %). The most effective harvesting was done in lots that were block-stumped (=6.7 berries left per tree), while Beaumont-Fukunaga (10.9), topping (14.5), and Kona style (15.7) resulted in low harvesting efficacy. While there was no significant difference among pruning styles, the benefit cost ratio was higher in lots that employed block-stumping (2.29) or Beaumont-Fukunaga (2.29) compared to topping (2.18) and the traditional Kona style (2.04). Our findings suggest that block-stumping is the optimal pruning style for reducing CBB infestation and bean damage, and results in improved harvesting efficacy and a higher benefit cost ratio relative to other pruning styles that are commonly used in Hawaii.</p>

Tags: benefit-cost-ratio, coffea-arabica, cultural-control, harvesting-efficacy, hawaii, integrated-pest-management
Organization: Department of Agriculture
Genotype variant files for: Harnessing citizen science to contextualize adaptation mechanism discovery

<p dir="ltr">Summary: Genome-wide polymorphisms called from publicly-available switchgrass genotype data. These variants are used in a publication under review, Harnessing citizen science to contextualize adaptation mechanism discovery by Tibbs-Cortes et al. The source genotype data was described in Lovell et al. 2021 (https://doi.org/10.1038/s41586-020-03127-1) and is available at <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568" target="_blank">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA622568</a>.</p><p dir="ltr">Genotype data collection: See Lovell et al. 2021 for full description. Briefly, rhizome plug samples from 789 diverse tetraploid switchgrass accessions were sequenced using Illumina HiSeq X10 and Illumina NovaSeq 6000 paired-end sequencing (2 × 150 bp) at HudsonAlpha Institute for Biotechnology and the Joint Genome Institute.</p><p dir="ltr">Variant calling: The paired-end sequence reads were downloaded from the NCBI SRA. Reads were aligned to the AP13 v5 reference genome with BWA-mem and biallelic polymorphisms were called with bcftools. Polymorphisms with minor allele frequency above 0.05 and missing rate below 20% were retained.</p><p dir="ltr">Funding acknowledgement: This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.</p>

Tags: adaptation, citizen-science, flowering-time, panicum-virgatum-switchgrass, phenotypic-plasticity
Organization: Department of Agriculture
Data and Code From: AI-Based bread quality assessment using image processing techniques and the developed BQe-CNN

<p dir="ltr">Ensuring consistent bread quality is vital for maintaining industry standards, reducing waste, and keeping consumer satisfaction. Traditional methods of bread quality analysis which rely on manual inspection, are often subjective, time-consuming, and prone to inconsistencies, while modern analysis techniques, though available, tend to be prohibitively expensive. This study introduces an AI-driven approach that leverages advanced image processing techniques to automate and enhance the accuracy of bread quality assessment. By extracting key features such as porosity, texture, and air cell structure, the proposed Bread Quality Enhanced Convolutional Neural Network (BQe-CNN) offers a more precise analysis of bread parameters. The model achieved classification accuracies of 92% for bread colors and 88% for quality levels, significantly outperforming manual methods. By leveraging enhanced layers like residual connections and attention mechanisms, the model efficiently captured fine details in bread images, making it highly effective at detecting subtle variations in texture and air cell distribution. While the model demonstrates high performance in quantitative analysis, it is important to note that artisan scoring—characterized by detailed aesthetic evaluations integral to traditional bread-making—remains a challenging domain for automation. This limitation presents an opportunity to further enhance the model's capabilities by integrating advanced algorithms or hybrid approaches, bridging the gap between precise computational analysis and the specific requirements of artisan scoring. Nevertheless, the BQe-CNN's ability to provide real-time, automated quality control is a dependable and transformative tool, optimizing production, reducing waste, and complementing human expertise in a cost-effective manner. These image processing techniques allow for real-time, automated quality control, optimizing production and reducing waste. This novel approach, rooted in visual analysis of product characteristics, represents a significant leap forward in achieving consistency and scalability in bread quality control for the baking industry.</p><p dir="ltr">Included is a subsample of images of bread of different color and porosity, examples of the processed images, a data descriptor README, metadata for the bread images, porosity values for the bread images, and MatLab code.</p>

Tags: ai, bread-quality, image-processing, neural-network, porosity, source-code
Organization: Department of Agriculture
Data from: Tracking Individual <i>Bactrocera tryoni </i>(Diptera: Tephritidae): Wind Effects and Natural Movement

<p dir="ltr">Determining the natural movement parameters of pest insects, such as tephritid fruit flies, is critical to developing models that can be used to increase the effectiveness of control and surveillance strategies. In this study, two experiments were conducted using harmonic radar to track wild-caught male Queensland fruit flies (Qflies), <i>Bactrocera tryoni</i>, a major horticultural pest in Australia. Experiment 1 continuously tracked individual flies which were prodded to induce movement in a high-density papaya field. Experiment 2 was conducted in a field with lower papaya density and tracked flies were allowed to move without disturbance. This latter natural movement experiment showed that Qfly move at a rate of 19 ± 3 m/h. In both experiments, overall and between-tree flight directions were found to be correlated with wind direction while within-tree movement directions were not. Further, the effect of wind direction on fly trajectories varied by step-distance but not strongly with wind speed while step-distance distributions were consistent with Lévy walks. Qfly movements were well fitted by two-state hidden Markov models further supporting the observation that Qflies move differently within (short steps with random direction) and between (longer more directional steps) trees. Data on flight directionality, step-distances, and movement speed determined in this study provide parameters that may help enhance current surveillance, control, and eradication methods, such as optimizing trap placements and pesticide applications, determining release sites for parasitoids, and setting quarantine boundaries after incursions.</p>

Tags: directional-movements, dispersion, field-tracking, harmonic-radar, step-distance, turning-angle, wind
Organization: Department of Agriculture
Data from: Enhanced survival of mass reared Mediterranean fruit flies via regular diurnal temperature oscillations

<p dir="ltr">Effectively mass rearing insects is critical for research, for environmentally friendly technologies like Sterile Insect Technique (SIT), producing biological control agents, and enabling novel methods such as those based on genetics or symbionts.  While constant temperature conditions are typically used in mass rearing, based on the idea that there is an optimum value that produces the most fit insects, homeostatic conditions do not reflect the real world, potentially impacting insect performance in the field. We investigated the performance of mass-reared adult Mediterranean fruit flies (Medflies) under constant (Const24: 24 °C) and oscillating (Osc2: 24 ± 2 °C, Osc5: 24 ± 5 °C) temperature regimes. Male and female survivorship, flight ability, and female fecundity were assessed across the temperature regimes. Additionally, we compared adult medfly performance under environmental chamber and outdoor conditions to determine if temperature and humidity as simulated in the chambers resulted in similar performance outcomes for the insects as being outdoors. Male medflies under the Osc 5 treatment had higher survival probability at 55 days post-emergence compared to the constant temperature regime, while females showed no significant differences in survivorship among temperature regimes. Flight ability and fecundity were not significantly affected by temperature regimes, though the Osc 5 group showed the highest fecundity. Comparisons between environmental chamber and outdoor conditions revealed minimal differences in performance metrics. Our findings suggest that the performance of mass reared male adult medflies under temperature variance in the field can be improved by oscillating temperature regimes in mass-rearing facilities. </p>

Tags: entomology-data, invasive-insect, mass-rearing, sterile-insect-technique-sit, tephritidae
Organization: Department of Agriculture
Data from: Genetic variations and accelerated growth at low temperatures in a <i>Listeria monocytogenes </i>isolate

<p dir="ltr"><i>Listeria monocytogenes </i>contamination of fresh-cut produce poses a threat to consumers due to its high mortality rate. Because it is widespread in the environment, as well as able to grow and survive in harsh conditions, such as low temperatures, it is difficult to control. A strain of <i>L. monocytogenes</i>, L008, with significantly faster growth than other strains was identified in our laboratory during experiments with fresh-cut produce. The L008 strain had a significantly shorter lag phase and reached maximum spectrophotometric absorbance (optical density) faster than three other <i>L. monocytogenes </i>strains during growth curve studies at 4 and 8°C. The lag phase was also shorter, when compared with two of the three strains at 12°C. A genetic comparison between L008 and the other three strains identified missense mutations in the <i>fapR, mngB, pfkB, </i>and <i>uvrC</i> genes of L008 that may account for the faster growth. These genes are involved in metabolism, cell membrane maintenance, and stress tolerance, which may allow L008 to adapt to lower temperatures better than the other strains. Accelerated growth at low temperatures may elevate the risk associated with this isolate and other <i>L. monocytogenes </i>strains with similar genetic variants.</p>

Tags: fresh-cut-produce, genetic-variant, listeria-monocytogenes, low-temperature, missense-mutation, rapid-growth
Organization: Department of Agriculture
Data from: Genotypic variation in lead (Pb) accumulation dataset in sweetpotato flesh for 10 accessions from the United States of America

<p dir="ltr">The goal of this research is to reduce the lead content in sweetpotato through development of varieties that have concentrations below the action levels for lead in processed food intended for babies and young children in guidance for industry set forth by the Food and Drug Administration (FDA-2022-D-0278) in January 2025. This dataset provides the concentration of lead (ppb) accumulation in sweetpotato root tissue (flesh) for 10 genotypes that were grown in sand and treated with a nutrient solution containing 10 ppm of lead. For determination of lead concentration in the flesh, the skins were removed prior to elemental analyses with a single quadrupole inductively coupled plasma mass spectrometer (Agilent 7900 ICP-MS). All experiments were arranged in a randomized complete block design (RCBD) with three replications. This research demonstrates that genotype-specific variability of lead accumulation exists in U.S. sweetpotato germplasm and can be used for development of new varieties that have low levels of lead to ensure a safe source of food for human consumption.</p>

Tags: food-safety, heavy-metals, ipomoea-batatas, lead-accumulation
Organization: Department of Agriculture
Data from: Using harmonic radar to compare movement behavior between <i>Bactrocera dorsalis</i> and <i>Ceratitis capitata</i> (Diptera: Tephritidae)

<p dir="ltr">Behavioral differences between related insects may inform how pest management strategies or conservation efforts are tailored to specific species. Movement behavior is particularly important, but few studies have undertaken head-to-head comparisons to evaluate differences in interspecific movement. This study used harmonic radar to simultaneously track 2 agriculturally important tephritid fruit fly species, <i>Bactrocera </i><i>dorsalis</i> (Hendel) and <i>Ceratitis capitata</i> (Wiedemann), in an outdoor cage (experiment 1) and a coffee field (experiments 2 and 3) to assess fly directional movement, distance, and speed parameters. In general, both fly species have similar movement parameters. However, experiment 2 showed <i>B. dorsalis</i> to be more active with fewer induced movements and less time needed to record the target number of movement steps. This was supported by a laboratory bioassay (experiment 4) that confirmed <i>B. dorsalis</i> were more active. Mean step-distances only differed in experiment 2 and were longer for <i>C. capitata</i>. Experiment 3 tracked tagged flies over time with 2 <i>B. dorsalis</i> located after 3 d post-release while no <i>C. capitata</i> were located after 48 h. Both species generally move with the prevailing wind. While this study found some differences in movement behaviors between these 2 fly pests, fly movement parameters were more similar than expected, suggesting that it may be possible to characterize the movement of key insect species and then generalize these findings to related taxa. If this is possible, control and detection strategies optimized with movement data from one species may be transferable to other pests, thereby increasing the impact of movement research.</p>

Tags: flight-direction, fruit-fly, insect-movement, nitinol, speed, step-distance, wind-effects
Organization: Department of Agriculture
Chicken Breast Microwave Detection Data

<p dir="ltr">Testing was conducted with collaboration with the U.S. National Poultry Research Center (Athens, GA) from 08/24-11/24. Chicken breasts were processed and graded by two expert graders for woody breast and other meat myopathies. For woody breast (WB), the scoring consisted of a subjective score indicating no (score of 1), moderate (score of 2), or severe (score of 3) WB, with intermediate scores (i.e. 1.5 or 2.5) indicating a specimen on the margins of the integer values. <br>Following the grading, the chicken breasts were chilled and measured using the Compass Technology Group epsilon measurement probe (eMP) sensor. Each chicken breast was measured at a minimum of 3 locations, with the thickness of each location measured and input into the eMP software to aid in inversion. </p><p dir="ltr">Data was classified by using an ordinary least squares regression on the permittivity data from the eMP sensor and the WB data scored from the graders. Classification accuracy is shown in the attached bar graphs.</p>

Tags: microwave-non-destructive-evaluation, myopathies-prediction
Organization: Department of Agriculture
Data from: Digital morphological data can generate accurate pre-emergence herbicide dose-response curves in <i>Chenopodium album </i>L.

<p dir="ltr">Greenhouse dose-response assays were performed on <i>Chenopodium album</i> L. using pre-emergence treatments of fomesafen and atrazine. Digital collection of data was performed with the Phenospex TraitFinder at 21 days after treatment. This equipment is equipped with two PlantEye scanners that generate 3D models of plants through the laser line triangulation principle, which builds a model of the plants based on the disruptions in the laser line. During the scanning process, the two scanners shine and simultaneously collect reflectance data for the laser, Red, Green, Blue, and Near-Infrared light. Each data point in the resulting 3D model contains not only coordinate information but also spectral data. The Phenospex TraitFinder collects data for 7 spectral parameters and 13 morphological parameters. Spectral data, which often ranges from -1 to 1, is also sorted into bins to detail how many data points fell within a given range. Digitally collected data were compared to manual measurements of fresh biomass and plant height to assess accuracy and determine which Phenospex parameters generate similar dose-response curves and growth reduction 50 estimates. Abbreviations: normalized difference vegetation index, NDVI; green leaf index, GLI; plant senescence reflectance index, PSRI; normalized pigment chlorophyll index, NPCI.</p><p dir="ltr"><br></p>

Tags: chenopodium-album-l, digital-data-collection, herbicide-dose-response, morphological-data, phenotypic-data-files, spectral-data
Organization: Department of Agriculture