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This data set explores the effect of the cyanobacterial gene ictB on photosynthesis in sorghum, under both normal greenhouse growing temperatures (32 C / 25 C) and during and after an 8 day chilling stress (10 C / 5 C). IctB is a cyanobacterial gene of unknown function, which was initially thought to be involved in inorganic carbon transport into cells. While ictB is known now not to be an independently active carbon transporter in its own right, it may play a role in passive diffusion of metabolites. This transgene was introduced into sorghum by the lab of Thomas Clemente, through Agrobacterium mediated transformation, alone and in combination with the tomato sedoheptulose-1,7-bisphosphatase (SBPase) gene. Eleven events (six double construct and five single construct ictB) were involved in this study. SBPase was included because some previous experiments in C3 species and some previous modeling work, as well as its position at a metabolic branch point, indicates it plays a role as a control point for photosynthesis. A chilling treatment was included because chilling is one of the most serious ecological factors limiting the range of C4 species. Data includes gene expression, metabolomics (at normal growing temperature), SBPase enzyme activity, biomass and photosynthetic traits at both warm temperature and during and after chilling stress. ----------------- EXPLANATORY NOTES FOR ICTB/SBPASE SORGHUM MANUSCRIPT Data are organized into 10 worksheets, representing an expected 10 tables that will serve a supplementary role in the final publication. These include data on gene expression, metabolomics (at normal growing temperature), SBPase enzyme activity, biomass and photosynthetic traits at both warm temperature and during and after chilling stress. <i><b>Tables are as follows:</i></b> 1. Event_Code: for Table S1. Event codes for events and constructs. Two constructs were generated for this study, and numerous transgenic “events” (i.e. independent transformations) were carried out for each construct. A construct represents the actual vector which was introduced into the plants (complete with promoter, gene of interest, marker gene, etc.) while an event represents a single successful introduction of the transgene. Events are uniquely labeled with letter and number strings but also with a four-digit number for ease of reference, this table explains which event corresponds to each four-digit number. 2. Photosynthetic_Data: for Table S2. Photosynthetic data at greenhouse growing temperature, for ictB single construct, ictB/SBPase double construct, and wild type lines. Five ictB and six ictB/SBPase events were included. Greenhouse growing temperature was approximately 32 °C and 25 °C night. Photosynthetic parameters were measured using a Licor 6400-XT, and included parameters related to carbon dioxide uptake, water loss, and chlorophyll fluorescence. 3. Chilling_Treatment: for Table S3. Photosynthetic response to chilling treatment, for ictB single construct, and wild type lines. Four ictB events were included. Chilling treatment lasted approximately 8 days and began either 3.5 or 5.5 weeks after transplanting the plants (chilling was done in two batches). Chilling treatment involved temperatures of 10 °C day / 7 °C night in growth chambers. Photosynthetic parameters were measured at several time points during and after the chilling treatment, were measured using a Licor 6400-XT, and included parameters related to carbon dioxide uptake, water loss, and chlorophyll fluorescence. 4. SBPase_Activity: for Table S4. SBPase activity in double construct plants. These data measure in vitro substrate-saturated activity of SBPase in desalted extracts from leaf tissues, at 25 °C. Units are micromoles of SBP processed per second per m2 of leaf tissue. Five ictB/SBPase events were included. 5. 2014_gene_exp: for Table S5. Gene expression in 2014 experiment (units of cycle times). These data measure cycle times to threshold, relative to reference genes, for expression of ictB and SBPase. Six ictB single construct events and five ictB/SBPase double construct events were included. Cycle times to threshold relative to reference genes (ΔCT) are inversely related to number of transcripts relative to reference genes, as follows: ΔCT = -log2([NictB]/[Nreference])/[1 + log2b] where b = efficiency of replication. 6. 2016_gene_exp: for Table S5. Gene expression in 2016 experiment (units of cycle times). These data measure cycle times to threshold, relative to reference genes, for expression of ictB and SBPase. Six ictB single construct events and five ictB/SBPase double construct events were included. Cycle times to threshold relative to reference genes (ΔCT) are inversely related to number of transcripts relative to reference genes, as follows: ΔCT = -log2([NictB]/[Nreference])/[1 + log2b] where b = efficiency of replication. 7. Metabolites: for Table S7. Levels of 267 metabolites in leaf tissue. Four ictB single construct events and four ictB/SBPase double construct events were included in these analyses. Metabolites were measured in methanol-extracted samples, either by liquid chromatography / mass spectrometry or by gas chromatography / mass spectrometry, and were compared between events on a relative basis. As quantification was relative to wild type rather than on an absolute basis, no units are included. 8. Metabolite_F_values: for Table S8. F values for effects of ictB, SBPase (in cases where the model was better with a SBPase effect) and event. These analyses are done for each metabolite included in Table S7, and show effects of the explanatory variables ictB, SBPase, and individual event. 9. Biomass_2020: for Table S9. Biomass and grain yield at harvest, for ictB, ictB/SBPase and wild type sorghum plants in spring 2020. Four ictb/SBPase double construct and four ictB single construct events were included. 10. Biomass_2017: for Table S10. Biomass and grain yield at harvest, in chilled and non-chilled sorghum plants containing the ictB transgene (along with wild type controls) in fall 2017. Four ictB single construct events were included. Chilling treatment involved temperatures of 10 °C day / 7 °C night in growth chambers. <i><b>All the variables in the file are explained as below:</i></b> o Type (IctB-SBPase and IctB). This refers to whether a plant is wild type, single construct (contains only the ictB transgene) or double construct (contains both the ictB and SBPase transgenes). o Code: these codes are shorter labels to refer to each transgene event for the sake of convenience. o Alternate_Code: these codes are shorter labels to refer to each transgene event for the sake of convenience. o Event Number: these are unique labels for each transgenic events. o Construct Number: these are labels for each transgenic construct (either the ictB single construct or the ictB/SBPase double construct). o year (i): this refers to the year in which the study was conducted (2014, 2016, 2017, or 2020) o transgene or Transgenic: whether the transgene was present o construct or Type : whether the ictB or the ictB/SBPase construct was present (double, single, wildtype): o temp: leaf temperature during the measurement o A: carbon assimilation rate, in μmol m-2 s-1 o gs: stomatal conductance, in mol m-2 s-1 o CI: intercellular carbon dioxide concentration, in parts per million or μL L-1 o fvfm:FV’/FM’ (maximal potential photosystem II quantum yield under light adapted conditions), dimensionless ratio o phipsill: ΦPSII (maximal potential photosystem II quantum yield under light adapted conditions), dimensionless ratio o qP: photochemical quenching, i.e. ratio of ΦPSII to FV’/FM’ , dimensionless ratio o iwue: intrinsic water use efficiency, i.e. ratio of carbon assimilation rate to stomatal conductance, in units of μmol mol-1 o event: individual transgenic / transformation event o Vmax: substrate-saturated in vitro activity of the SBPase enzyme, in μmol m-2 s-1 o ID: identification number of sample o ΔCT1: difference in cycle times to threshold during gene expression (quantitative PCR) assay, between ictB and the reference gene GAPDH, in units of cycles o ΔCT2: cycle times to threshold during gene expression (quantitative PCR) assay, between SBPase and the reference gene GAPDH, in units of cycles o GAPDH: cycle times to threshold for the reference gene GAPDH (glyceraldehyde phosphate dehydrogenase) o IctB: cycle times to threshold for the gene of interest ictB o SBPase: cycle times to threshold for the gene of interest SBPase o v1 to v267 represent individual metabolite (see the heading immediately above the labels v1, v2, etc.). Variables v268-v272 refer to total (summed) metabolite levels for particular pathways of interest. o leaf: Leaf and stem dry biomass (in grams) o seed: Seedhead dry biomass (in grams) o biomass: Total (leaf, stem + seed head) dry biomass (in grams) o harvind: ratio of seed head dry biomass to total dry biomass o treatment (chilled and nonchilled): “Chilled” plants were grown under warm greenhouse conditions (32 °C day / 25 °C night) for 6 or 8 weeks, then switched to chilling temperatures under growth chamber conditions (10 °C / 7 °C night) for 8 days, and were then returned to greenhouse growing conditions. -----------------

These data obtained from the peer-reviewed literature and a public database depict the geographic expansion of the black-legged tick (Ixodes scapularis) and human cases of Lyme disease in the midwestern U.S. <b><i>Note</b></i>: There was an omission from the first version (V1) of the data set that required us to update the data. Specifically, we failed to include the data from the article "Caporale DA, Johnson CM, Millard BJ. 2005 Presence of Borrelia burgdorferi (Spirochaetales: Spirochaetaceae) in Southern Kettle Moraine State Forest, Wisconsin, and characterization of strain W97F51. J. Med. Entomol. 42, 457–472". In the second version (V2) of the data, this omission is corrected.

Dataset includes temperature data (local average April daily temperatures), first egg dates and reproductive output of Prothonotary Warblers breeding in southernmost Illinois, USA. Also included are arrival dates for warblers returning to breeding grounds from wintering grounds, and global temperature anomaly data for comparison with local temperatures. These data were used in the manuscript entitled "Warmer April Temperatures on Breeding Grounds Promote Earlier Nesting in a Long-Distance Migratory Bird, the Prothonotary Warbler" published in Frontiers in Ecology and Evolution. A rich text file is included with explanations of each variable in the dataset.

This dataset contains BEPAM model code and input data to replicate the outcomes for "The Economic and Environmental Costs and Benefits of the Renewable Fuel Standard". The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output.gms. (BEPAM-Social cost model-ERL.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.

A 30 year record of the vegetation in sample plots in a woodland in the Chicago area. The changes in these plots over time show how ecological restoration can yield dramatic results.

Supporting information for "Urinary Phthalate Metabolite Concentrations and Hot Flashes in Pre- and Perimenopausal Women from the Midlife Women’s Health Study." This file contains tables of the results of stratified analyses of the associations of hot flash outcomes with urinary phthalates metabolites by menopause status, race/ethnicity, body mass index, and depressive status. This file also contains supplementary HPLC methods for the analysis of phthalate metabolites.

The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

Raw gas exchange data for photosynthetic induction in 6 rice accession flag leaves. Photosynthetic induction and point measurements were made at ambient [CO2]. Two accessions (AUS 278 and IR64) were selected to screen in greater detail in which photosynthetic induction was measured at six [CO2].

This repository contains the datasets and corresponding results for the paper "MAGUS: Multiple Sequence Alignment using Graph Clustering". The Datasets.zip archive contains the ROSE, balibase, Gutell, and RNASim datasets used in our experiments. The Results.zip archive contains the outputs of running our methods against these datasets. Datasets used: ROSE: 10 simulated nucleotide model conditions from the SATe paper, each with 20 replicates, and with 1000 sequences per replicate. The ROSE datasets were originally taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/sate-i">https://sites.google.com/eng.ucsd.edu/datasets/alignment/sate-i</a> RNASim: This is a collection of simulated nucleotide datasets that were generated under a model of evolution that reflects selection due to RNA structural constraints. We sampled 20 subsets of 1000 sequences each, as well as 10 subsets of 10000 each, by randomly sampling from the original million-sequence RNASim dataset. Gutell: 16S.M, 16S.3, 16S.T, 16S.B.ALL: Four biological nucleotide datasets from the Comparative Ribosomal Website (CRW) with cleaned reference alignments from SATe. Since PASTA is restricted to datasets without sequence length heterogeneity, these were modified to remove sequences that deviate by more than 20% from the median length. The scrubbed datasets range from 740 to 24,246 sequences. The pre-screened 16S datasets were taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/16s23s">https://sites.google.com/eng.ucsd.edu/datasets/alignment/16s23s</a> BAliBASE: We use eight BAliBASE amino acid datasets used in the PASTA paper. As above, we remove outlier sequences, which leaves us with sizes ranging from 195 to 732 sequences. The pre-screened Balibase datasets were taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/pastaupp">https://sites.google.com/eng.ucsd.edu/datasets/alignment/pastaupp</a>

Data extracted from Text, Tables and Figures of publications in summarizing crop responses to Free-Air CO2 Elevation (FACE)

Data are from a long-term fire manipulation experiment in the Missouri Ozarks, USA. Data include the raw, annual ring-width increment (rwl), basal area increment (BAI), population-level annual growth resistance (Drs) and resilience (Drl) to drought, intrinsic water use efficiency values (WUEi) and oxygen isotopic composition of individual radial growth rings (δ18O) from southern red oak (Quercus falcata) and post oak (Q. stellata) trees. ---------------------- TITLE: Data for "Sixty-five years of fire manipulation reveals climate and fire interact to determine growth rates of Quercus spp." ---------------------- FILE OVERVIEW: This dataset contains four (4) CSV files as described below: Refsland_et_al_ECS20-0465_BAI.csv: annual basal area increment between 1948-2015 for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_DroughtIndices.csv: population-level drought resistance and resilience of trees during each target drought period Refsland_et_al_ECS20-0465_WUEi.csv: carbon isotope indicators of drought stress for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_d18Or.csv: oxygen isotope indicators of drought stress for trees across the fire manipulation experiment ---------------------- VARIABLE EXPLANATION: All the variables in those four files are explained as below: treeID: unique character string that identifies subject tree block: integer (1, 2) that identifies the study block plot: integer (1-12) that identifies the plot nested within each study block trt: character string (Annual, Control, Periodic) that identifies the fire treatment of a given plot species: character string (Quercus falcata, Quercus stellata) that identifies species of subject tree year: integer (1948-2015) that identifies the dated year of each tree ring rwl_mm: numerical value representing the annual tree ring-width, in mm bai_cm2: numerical value representing the annual basal area increment, in cm2 timeperiod: integer value (1953, 1964, 2007, 2012) representing the periods encompassing target dry and wet years Drs_2yr: numerical value representing the drought resistance, defined as the population-level annual growth of trees during drought years relative to pre-drought years for a given time period Drl_2yr: numerical value representing the drought resilience, defined as the population-level annual growth of trees following drought years relative to pre-drought years for a given time period stand_ba_m2ha: numerical value representing the total basal area of a given plot, in m2 per ha stand_density_stems_ha: numerical value representing the total stem density of a given plot, in stems per ha pool: numerical value (1-40) identifying the set of tree ring samples pooled for analysis. Samples were pooled by block, plot, year and species period: integer value (1953, 1964, 1980, 2007, 2012) representing the periods encompassing target dry and wet years type: character string (Dry, Wet) indicating the water availability of a given year d13C: numerical value representing the carbon isotopic composition of radial growth rings within a given sample pool, in per mil WUEi: numerical value representing the annual intrinsic water use efficiency of radial growth rings within a given sample pool d18O: numerical value representing the oxygen isotopic composition of radial growth rings within a given sample pool, in per mil

This file contains 13 unique case studies that were created for the One health: Infectious diseases course offered at the University of Illinois at Urbana-Champaign campus. The case studies are being made available as educational resources for other One health courses. Each case study is focused on a theme/topic which is associated with One health. These case studies were created using publicly available information and references have been provided for each case study.

These data are from an observational study and small experiment investigating reproductive biology and hybridization between two plants, Celastrus scandens L. and Celastrus orbiculatus Thunb. (Celastraceae). These data were collected during the 2008 growing season from the Indiana Dunes National Park (formerly Indiana Dunes National Lakeshore), just east of the municipality of Ogden Dunes, Indiana, USA. The five data files provide information on floral output of the two species, fertilization rate, fruit set rate, hybridization rate at two scales (individual flowers in both species, individual maternal plants in C. scandens), and the results of a hand-pollination experiment that exchanged pollen between the two species. There are six data files associated with this submission, five data files in comma-separated values format and one text file (‘readme.txt’) that includes detailed explanations of the data files.

Automatic and manual counts of black flies captured in Illinois.

Nest survival and Fledgling production data for Bell's Vireo and Willow Flycatcher nests.

Raw measurement data for umbilical remnants (umbilical vein, umbilical arteries and urachus) in support of Equine Veterinary Journal publication "Normal Regression of the Internal Umbilical Remnant Structures in Standardbred Foals."

Data on bank elevations determined from lidar data for the Upper Sangamon River, Illinois, the Mission River, Texas, and the White River in Indiana

Dataset associated with Hoover et al AUK-19-093 submission: Local conspecific density does not influence reproductive output in a secondary cavity-nesting songbird. Excel CSV with all of the data used in analyses. Description of variables YEARS: year ORDINAL_DATE: number for what day of the year it is with 1 January = 1,……30 December = 365 SITE: acronym for each study site BOX: unique nest box identifier on each study site TREAT: designates whether nest box was in a high- or low- nest box density area within each study site ACTUAL_NO_NEIGHBORS: number of pairs of warblers using a nest box within 200 m of a given pair’s nest box CLUTCH_SIZE: number of warbler eggs in nest at the onset of incubation PROWN: number of warbler nestlings once eggs have hatched PROWF: number of warbler nestlings that fledged out of the nest box HATCH_SUCCESS: proportion of eggs in the nest that hatched FLEDG_SUCCESS: proportion of the nestlings that fledged from the nest box HATCH_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no hatching failure FLEDG_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no nestling failure (i.e. nestling death) BHCO_PARASIT2: binary category where “0” indicates no cowbird parasitism, and “1” indicates there was cowbird parasitism BHCOE: number of cowbird eggs in clutch BHCOF: number of cowbird nestlings that fledged from the nest PAIRID: unique number that identifies a male and female warbler that are together at a nest box and this number is the same in a subsequent nesting attempt or year if the same male and female are together again FEMALE_ID: unique identifier for each female which represents her leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg FEM_AGE: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird FEMALE_BREEDING_ATTEMPT: “1” indicates first, “2” indicates second,……..breeding attempt within a given year SECOND_ATTEMPT: for any female that fledged a brood in a given year, binary category where “0” represents that they did not, and “1” indicates that they did attempt a second brood that year F_TOT_PROWF: total reproductive output (number of warbler fledglings produced) for a given female in a given year MALE_ID: unique identifier for each male which represents his leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg MALE_AGE2: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird Provisioning_rate: total number of food provisions per nestling per hour by male and female warbler combined BROOD_MASS: average nestling mass (g) for the brood BROOD_TARSUS: average nestling tarsus length (mm) for the brood Brood_condition: unit-less index of nestling condition that uses the residuals of the BROOD_MASS/BROOD_TARSUS relationship A period (“.”) represents where data were not collected, not available, or because individual nest or female did not qualify for consideration of a category assignment. An empty cell represents no data available for this particular cell.

This dataset includes two data files that provide the time series (Jul. - Sep. 2017) data of sun-induced chlorophyll fluorescence (SIF_760) collected under sunny conditions at two maize sites (one rainfed and the other irrigated) in Nebraska in 2017. Data contain 392 SIF_760 records at the rainfed site and 707 records at the irrigated site. The timestamp uses local standard time. Data are available for the sunny conditions from 8 am to 5 pm (corresponding to 9 am to 6 pm local time) throughout the study period.

Supporting secondary data used in a manuscript currently in submission regarding the invasion dynamics of the asian tiger mosquito, Aedes albopictus, in the state of Illinois

Software (Matlab .m files) for the article: Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses. The files can be used to reproduce the analysis and figures in the article.

The data set here include data from NMR, LC-MS/MS, MALDI-MS, H/D exchange MS experiments used in paper "A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection".

Simulation data related to the paper "Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study"