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This dataset contains the pregnancy status of wild, white-tailed deer (Odocoileus virginianus) from northern Illinois culled as part of the Illinois Department of Natural Resources' chronic wasting disease (CWD) surveillance program. Fiscal years 2005 through 2024 are included. A fiscal year is the time between July 1st of one calendar year and June 30th of the next. Variables in this dataset include the pregnancy status, CWD infection status, age, weight, and day of mortality for each female deer, as well as the deer land cover utility (LCU) score for the TRS, township, or county from which the deer was culled. The deer population density of the county is also included. Data have been anonymized for landowner privacy reasons so that the location and year are not identifiable, but will give the same modeling results by maintaining how the data are grouped. The R code used to conduct the regression modeling is also included.

This dataset includes image stacks, annotated counts, and ground-truth masks from two high-resolution sediment cores extracted from Laguna Pallcacocha, in El Cajas National Park, Ecuadorian Andes by Moy et al. (2002) and Hagemans et al. (2021). The first core (PAL 1999, from Moy et al. (2002)) extends through the Holocene (11,600 cal. yr. BP - present). There are a total of 900 annotated image stacks and masks in the PAL 1999 domain. The second core (PAL IV, from Hagemans et al. (2021)) captures the 20th century. There are 2986 annotated image stacks and masks in the PAL IV domain. Different microscopes and annotations tools were used to image and annotate each core and there are corresponding differences in naming conventions and file formats. Thus, we organized our data separately for the PAL 1999 and the PAL IV domains. The three letter codes used to label our pollen annotations are in the file: “Pollen_Identification_Codes.xlsx”. Both domain directories contain: • Image stacks organized by subdirectory • Annotations within each image stack directory, containing specimen identifications using a three letter code and coordinates defining bounding boxes or circles • Ground-truth distance-transform masks for each image stack The zip file "bestValModel_encoder.paramOnly.zip" is the trained pollen detection model produced from the images and annotations in this dataset. Please cite this dataset as: Feng, Jennifer T.; van den Berg, Thya; Donders, Timme H.; Kong, Shu; Puthanveetil Satheesan, Sandeep; Punyasena, Surangi W. (2025): Slide scans, annotated pollen counts, and trained pollen detection models for fossil pollen samples from Laguna Pallcacocha, El Cajas National Park, Ecuador . University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-4207757_V1 Please also include citations of the original publications from which these data are taken: Feng, Jennifer T., Sandeep Puthanveetil Satheesan, Shu Kong, Timme H. Donders, and Surangi W. Punyasena. “Addressing the ‘Open World’: Detecting and Segmenting Pollen on Palynological Slides with Deep Learning.” bioRxiv, January 1, 2025. https://doi.org/10.1101/2025.01.05.631390. Feng, Jennifer T., Sandeep Puthanveetil Satheesan, Shu Kong, Timme H. Donders, and Surangi W. Punyasena. “Addressing the ‘Open World’: Detecting and Segmenting Pollen on Palynological Slides with Deep Learning.” Paleobiology, 2025 [in press]. Feng, J. T. (2023). Open-world deep learning applied to pollen detection (MS thesis, University of Illinois at Urbana-Champaign). https://hdl.handle.net/2142/120168

This page contains the data for the manuscript "Vacuolating cytotoxin A interactions with the host cell surface". This manuscript is currently in prep.

This supporting information file contains codes related to pending publication Ge et al. Proc. Nat. Acad. Sci. USA, (revisions in review). The contents include a Mathematica code that solves the Laplace transformed equations and generates figures from the paper. A python code is included for generation of Figure 5 in the main text.

This dataset includes a total of 16 images of 2 extant species of Podocarpus (Podocarpaceae) and 23 images of fossil specimens of the morphogenus Podocarpidites. The images were taken using a Zeiss LSM 880 microscope with Airyscan confocal superresolution at 630x magnification (63x/NA 1.4 oil DIC). The images are in the original CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or open microscopy software, such as ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/software/zeiss-zen/czi-image-file-format.html] For Podocarpus (modern specimens): Each folder is labelled by genus and contain all images corresponding to that genus. Detailed information about the folders, files, and specimens can be found in the Excel file "METADATA_Podocarpus_extant.csv". This file includes metadata on: species, slide ID, collection, folder name file name and notes. Images are of pollen grains from slides in the Florida Museum of Natural History collections. For Podocarpidites (fossil specimens): Each image is named after the sample from which it was derived. Detailed information about the specimens can be found in the Excel file "METADATA_ Podocarpidites_fossil.csv". This file includes metadata: the fossil type (Taxon), the slide and sample name (Slide Info), the location of the sample locality (Country, Latitude, Longitude), the age of the sample (Min age, Max age), the location of the specimen on the sample slide (England Finder coordinates), and the image file name. Images are of fossil pollen from slides in Smithsonian Tropical Research Institute collections. Please cite this dataset and listed publications when using these images.

This dataset contains Raman spectra, each acquired from an individual, living, cell entrapped within a soft or stiff gelatin methacrylate hydrogel or from a cell-free region of the hydrogel sample. Spectra were acquired from the following cell types: Madin-Darby Canine Kidney cell (MDCK); Chinese hamster ovary cell (CHO-K1); transfected CHO-K1 cell that expressed the SNAP-tag and HaloTag reporter proteins fused to an organelle-specific protein (CHO-T); human monocyte-like cell (THP-1); inactive macrophage-like (M0-like); active anti-inflammatory macrophage-like (M2-like), pro/anti-inflammatory macrophage-like (M1/M2-like). These spectra are useful for identifying whether the hydrogel matrix obscures the Raman spectral signatures that are characteristic of each of these cell types.

This dataset represents the results of targeted eDNA assays via quantitative PCR for two imperiled freshwater species.

Biometric, and ground-based and eddy covariance flux data to investigate the impact of sugarcane expansion across subtropical Florida on the carbon (C) budget over a three-year rotation. Dataset includes: three-year record of daily fluxes, NPP and SOC input measurements, and estimates of carbon use efficiency and net ecosystem carbon balance in sugarcane and improved and semi-native pastures following pasture conversion to sugarcane.

Over the past 15 years, soybean seed yield response to season-long elevated O3 concentrations [O3] and to year-to-year weather conditions was studied using free-air O3 concentration enrichment (O3-FACE) in the field at the SoyFACE facility in Central Illinois. Elevated [O3] significantly reduced seed yield across cultivars and years. However, our results quantitatively demonstrate that weather conditions, including soil water availability and air temperature, did not alter yield sensitivity to elevated [O3] in soybean.

BEPAM, Biofuel and Environmental Policy Analysis Model, models the agricultural sector and determines economically optimal land-use and feedstock mix at the US scale by maximizing the sum of agricultural sector consumers’ and producers’ surplus subject to various resource balances, land availability, and technological constraints under a range of biomass prices, from zero to $140 Mg-1 over the 2016-2030 period. Here BEPAM is used to model SAF production using energy crops and crop residues. BEPAM uses the GAMS format and uses yield and GHG balance projections from the biogeochemical model, DayCent.

Dataset of the standing dead trees at Trelease Woods in 2022. Dataset contains volume, biomass, decay class, and GPS coordinates for each standing dead tree.

Downed woody debris census data for Trelease Woods collected in the summer of 2022. Dataset contains volume, biomass, decay class, and GPS coordinates for each downed woody debris piece.

Soil data for ten soil cores collected at Trelease Woods in 2022. Soil samples were analyzed with an elemental analyzer via combustion to obtain total carbon (C) and nitrogen. A subset of these samples were analyzed using the Walkley-Black method to obtain organic C. A calibration curve relating organic C and total C was created using these data.

This is the core data for RELIX, a dataset of vascular plant species presence for 353 prairie remnants in the Midwestern United States and associated dataset of prairie remnant metadata. The primary data file contains a list of the vascular plant species observed in the prairie remnants, as well as a metadata table with more information about the prairie remnant in question and the species list itself. The data was compiled from a variety of written sources, private and published, chronicling observations made between the mid-twentieth century and 2021. It also contains a supplementary data table of vascular plant species observed in at least 8 of the prairie remnants in RELIX, as well as a list of acknowledgements for the associated manuscript.

This study acquired publicly available Shell annual reports. Reports were selected for the years since the UN investigation in 2011, resulting in documents from 2012 to 2023.

Historical census data collected at Trelease Woods from 1986 to 2004 with information on tree species, diameter at breast height (DBH), and plot location.

Census data collected at Trelease Woods in 1936 with information on tree species, stem count, diameter at breast height (DBH), and basal area. The plot boundaries from the 1936 census were georeferenced to subset 2018 census data for a direct comparison between the two census years.

A mechanistic functional structural plant model. The .gsz file includes a parameterised maize and soybean to be used in GRoIMP software https://grogra.de/. The current model is parameterised to maize cultivar DKC63-21RIB and soybean cultivar AG36X6 for the 2019 growing season in Champaign, IL USA.

The included files are the alignments of DNA or amino acid sequences used for phylogenetic analyses of Auchenorrhyncha (Insecta: Hemiptera) in the manuscript by Bin et al. submitted to the journal “Systematic Entomology.” The files are plain text in either FASTA (.fa or .fas suffix) or PHYLIP (.phy suffix) format. Matrix0 is the set of all loci after multiple sequence alignment and trimming (hereafter called). Matrix1 consists of loci having 75% average bootstrap support and 80% taxon completeness (hereafter called Matrix1). Matrix2 consists of loci having 75% average bootstrap support and 95% completeness. Matrix2_nt12 is the same as Matrix2 but with third codon positions excluded. More details on how the datasets were compiled is provided in the Methods section of the manuscript file, also included as a PDF. Supplemental figures for the submitted manuscript are also provided as a PDF for additional information.

Data at the lake summary and individual crayfish level that supports the manuscript Sawyer, E.K., Kreps, T. A., Lodge, D. M. and E.R. Larson. “Long-term declines in body size of the invasive rusty crayfish (Faxonius rusticus) in temperate lakes." Includes size measurements of 69,303 individual rusty crayfish (Faxonius rusticus) for 17 lakes of Vilas County, Wisconsin, United States collected between 1980 and 2020.

Dataset used for the paper entitled "Morphological differences between wild and game-farm Mallards in North America". Large-scale releases of domesticated, game-farm Mallards to supplement wild populations have resulted in wide-spread introgressive hybridization that changed the genetic constitution of wild populations in eastern North America. The resulting gene flow is well-documented between game-farm and wild Mallards, but the mechanistic consequences from such interactions remain unknown in North America. We provide the first study to characterize and investigate potential differences in morphology between genetically known, wild and game-farm Mallards in North America. We used nine morphological measurements to discriminate between wild and game-farm Mallards with 96% accuracy. Compared to their wild counterparts, game-farm Mallards had longer bodies and tarsi, shorter heads and wings, and shorter, wider, and taller bills. The nail on the end of the bill of game-farm Mallards was longer, and game-farm Mallard bills had a greater lamellae:bill length ratio than wild Mallards. Differences in body morphologies between wild and game-farm Mallards are consistent with an artificial, terrestrial life whereby game-farm Mallards are fed pelleted foods resulting in artificial selection for a more “goose-like” bill. We posit that 1) game-farm Mallards have diverged from their wild ancestral traits of flying and filter feeding towards becoming optimized to run and peck for food; 2) game-farm morphological traits optimized over the last 400 years in domestic environments are likely to be maladaptive in the wild; and 3) the introgression of such traits into wild populations is likely to reduce fitness. Understanding effects of game-farm Mallard introgression requires analysis of various game-farm × wild hybrid generations to determine how domestically-derived traits persist or diminish with each generation.

Raw data associated with PMID: 38925247

This page contains the data for the publication "The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila" published in the journal Science Advances.