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CC BY (203)
Lu, Yiyang; Bohn-Wippert, Kathrin; Pazerunas, Patrick J.; Moy, Jennifer M.; Singh, Harpal; Dar, Roy D. (2022): Time-lapse Fluorescence Microscopy Images and Gene Expression Data of Single T-Cells Infected with a Minimal HIV Feedback Circuit under 1,806 Drug Treatments. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8103861_V1
Upon treatment removal, spontaneous and random reactivation of latently infected T cells remains a major barrier toward curing HIV. Due to its stochastic nature, fluctuations in gene expression (or “noise”) can bias HIV reactivation from latency, and conventional drug screens for mean gene expression neglect compounds that modulate noise. Here we present a time-lapse fluorescence microscopy image set obtained from a Jurkat T-cell line, infected with a minimal HIV gene circuit, treated with 1,806 small molecule compounds, and imaged for 48 hours. In addition, the single-cell time-dependent reporter dynamics (single-cell gene expression intensity and noise trajectories) extracted from the image dataset are included. Based on this dataset, a total of 5 latency promoting agents of HIV was found through further experimentation in Lu et al., PNAS 2021 (doi: 10.1073/pnas.2012191118). For a detailed description of the dataset, please refer to the readme file.
HIV; latency; drug screen; fluorescence microscopy; time-lapse; microscopy; single-cell data; noise; gene expression fluctuation;
Hoang, Khanh Linh; Schneider, Jodi; Kansara, Yogeshwar (2022): Error Analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3407079_V3
The data contains a list of articles given low score by the RCT Tagger and an error analysis of them, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews". Change made in this V3 is that the data is divided into two parts: - Error Analysis of 44 Low Scoring Articles with MEDLINE RCT Publication Type. - Error Analysis of 244 Low Scoring Articles without MEDLINE RCT Publication Type.
Cochrane reviews; automation; randomized controlled trial; RCT; systematic reviews
Sharma, Bijay P.; Zhang, Na; DoKyoung, Lee; Heaton, Emily; Delucia, Evan H.; Sacks, Erik J.; Kantola, Ilsa B.; Boersma, Nicholas N.; Long, Stephen P.; Voigt, Thomas B.; Khanna, Madhu (2022): Data for Responsiveness of Miscanthus and Switchgrass Yields to Stand Age and Nitrogen Fertilization: A Meta-regression Analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3580461_V1
The compiled datasets include plot level observations of energy crops (miscanthus and switchgrass) from recent experimental field trials in the US including dry biomass yield, location, state, region, harvest year, growing season degree days (GDD), winter season heating degree days (HDD), growing season cumulative precipitation, annual nitrogen application rate, age of the pant when harvested, National Commodity Crop Productivity Index (NCCPI) values, and cultivar type (switchgrass) from various published and unpublished sources. The stata codes include estimation procedures for four different specifications, i.e., Model A includes deterministic effect without interaction terms; Model B includes deterministic effect with interaction terms (N2, age2, N × age, GDD2, precip2, N × NCCPI); Model C includes deterministic effect with interaction terms, study, and location random effect; Model D includes deterministic effect with interaction terms, harvest year augmented study, and location random effect.
Age; Miscanthus; Nitrogen; Switchgrass; Yield; Center for Advanced Bioenergy and Bioproducts Innovation
Kansara, Yogeshwar; Hoang, Khanh Linh (2022): Articles With PubMed Identifiers. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4623305_V3
The data file contains a list of articles with PMIDs information, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews".
Cochrane reviews; Randomized controlled trials; RCT; Automation; Systematic reviews
Kansara, Yogeshwar; Hoang, Khanh Linh (2022): RCT Tagger Results. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6773581_V3
The data file contains a list of articles and their RCT Tagger prediction scores, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews".
Cochrane reviews; automation; randomized controlled trial; RCT; systematic reviews
Shen, Chengze; Park, Minhyuk; Warnow, Tandy (2021): Seven ROSE datasets in high and low fragmentation conditions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6128941_V1
This is a general description of the datasets included in this upload; details of each dataset can be found in the individual README.txt in each compressed folder. We have: 1. ROSE-HF.tar.gz 2. ROSE-LF.tar.gz HF (high fragmentary): 50% of the sequences are made fragmentary, which have average lengths of 25% of the original lengths with a standard deviation of 60 bp. LF (low fragmentary): 25% of the sequences are made fragmentary, which have average lengths of 50% of the original lengths with a standard deviation of 60 bp. The seven ROSE datasets made fragmentary are: 1000L1, 1000L3, 1000L4, 1000M3, 1000S1, 1000S2 and 1000S4. "ROSE-HF.tar.gz" contains HF versions of the seven ROSE datasets. "ROSE-LF.tar.gz" contains LF versions of the seven ROSE datasets.
ROSE; simulation; fragmentary
Bakken, George; Tillman, Francis; O'Keefe, Joy (2022): Data for "Methods for assessing artificial thermal refuges: spatiotemporal analysis more informative than averages". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9980397_V1
This dataset contains temperature measurements in four different bat box designs deployed in central Indiana, USA from May to September 2018. Hourly environmental data (temperature, solar radiation, and wind speed) are also included for days and hours sampled. Bat box temperature data were used as inputs in a free program, GNU Octave, to assess design performance with respect to suitability indices for endothermic metabolism and pup development. Scripts are included in the dataset.
bats;thermal refuge;reproduction;conservation;bat box;microclimate
Karakoc, Deniz Berfin; Wang, Junren; Konar, Megan (2022): Data for: Food flows between counties in the Unites States from 2007 to 2017. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9585947_V1
This dataset provides estimates of agricultural and food commodity flows [kg] between all county pairs within the United States for the years 2007, 2012, and 2017. The database provides 206.3 million data points, since pairwise information is provided between 3134 counties, for 7 commodity categories, and 3 time periods. The commodity categories correspond to the Standardized Classification of Transported Goods and are: - SCTG 1: Iive animals and fish - SCTG 2: cereal grains - SCTG 3: agricultural products (except for animal feed, cereal grains, and forage products) - SCTG 4: animal feed, eggs, honey, and other products of animal origin - SCTG 5: meat, poultry, fish, seafood, and their preparations - SCTG 6: milled grain products and preparations, and bakery products - SCTG 7: other prepared foodstuffs, fats and oils For additional information, please see the related paper by Karakoc et al. (2022) in Environmental Research Letters.
food flows; high-resolution; county-scale; time-series; United States
Addepalli, Amulya; Ann Subin, Karen; Schneider, Jodi (2022): Dataset for Testing the Keystone Framework by Analyzing Positive Citations to Wakefield's 1998 Paper. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2532850_V1
retracted papers; knowledge maintenance; keystone citations, Wakefield; misinformation in science; Information Quality Lab
has sharing link
Dominguez, Francina (2022): Data for The Orinoco Low-level Jet and the Cross-Equatorial Moisture Transport over tropical South America: Lessons from seasonal WRF simulations. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9924420_V1
This dataset contains results from WRF simulations over northern South America. The Orinoco Low-Level Jet (OLLJ) and the Cross-Equatorial Moisture Transport are important circulation structures of the climate of tropical South America. We explore the sensitivity of the OLLJ and cross-equatorial transport to the representation of surface fluxes and turbulence by using two different Land Surface Model (LSM) schemes (Noah and CLM) and three Planetary Boundary Layer (PBL) schemes (YSU, QNSE and MYNN).
WRF; Orinoco LLJ; preicpitation
Li, Shuai; Moller, Christopher A.; Mitchell, Noah G.; Lee, DoKyoung; Sacks, Erik J.; Ainsworth, Elizabeth A. (2022): Testing unified theories for ozone response in C4 species. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9373041_V1
Twenty-two genotypes of C4 species grown under ambient and elevated O3 concentration were studied at the SoyFACE (40°02’N, 88°14’W) in 2019. This dataset contains leaf morphology, photosynthesis and nutrient contents measured at three time points. The results of CO2 response curves are also included.
C4, O3, photosynthesis
Layser, Michelle (2022): Multi-State Survey of State Enterprise Zone Laws (Last Updated Jan. 20, 2022). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8986969_V1
This dataset provides a 50-state (and DC) survey of state-level enterprise zone laws, including summaries and analyses of zone eligibility criteria, eligible investments, incentives to invest in human capital and affordable housing, and taxpayer eligibility.
Enterprise Zones; tax incentives; state law
Layser, Michelle (2022): Multi-State Survey of State New Markets Tax Credit Laws (Last Updated Jan. 19, 2022). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6263002_V1
This dataset provides a 50-state (and DC) survey of state-level tax credits modeled after the federal New Markets Tax Credit program, including summaries of the tax credit amount and credit periods, key definitions, eligibility criteria, application process, and degree of conformity to federal law.
New Markets Tax Credits; NMTC; tax incentives; state law
Layser, Michelle (2022): Multi-State Survey of State Opportunity Zones Laws (Last Updated Jan. 14, 2022). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4303513_V1
This dataset provides a 50-state (and DC) survey of state-level Opportunity Zones laws, including summaries of states' Opportunity Zone tax preferences, supplemental tax preferences, and approach to Opportunity Zones conformity. Data was last updated on January 14, 2022.
Opportunity Zones; tax incentives; state law
Cao, Yanghui; Dietrich, Christopher H. (2022): Datasets for "Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for the phylogeny of their hosts". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7486289_V1
The file “Fla.fasta”, comprising 10526 positions, is the concatenated amino acid alignments of 51 orthologues of 182 bacterial strains. It was used for the maximum likelihood and maximum parsimony analyses of Flavobacteriales. Bacterial species names and strains were used as the sequence names, host names of insect endosymbionts were shown in brackets. The file “16S.fasta” is the alignment of 233 bacterial 16S rRNA sequences. It contains 1455 positions and was used for the maximum likelihood analysis of flavobacterial insect endosymbionts. The names of endosymbiont strains were replaced by the name of their hosts. In addition to the species names, National Center for Biotechnology Information (NCBI) accession numbers were also indicated in the sequence names (e.g., sequence “Cicadellidae_Deltocephalinae_Macrostelini_Macrosteles_striifrons_AB795320” is the 16S rRNA of Macrosteles striifrons (Cicadellidae: Deltocephalinae: Macrostelini) with a NCBI accession number AB795320). The file “Sulcia_pep.fasta” is the concatenated amino acid alignments of 131 orthologues of “Candidatus Sulcia muelleri” (Sulcia). It contains 41970 positions and presents 101 Sulcia strains and 3 Blattabacterium strains. This file was used for the maximum likelihood analysis of Sulcia. The file “Sulcia_nucleotide.fasta” is the concatenated nucleotide alignment corresponding to the sequences in “Sulcia_pep.fasta” but also comprises the alignment of 16S rRNA. It has 127339 positions and was used for the maximum likelihood and maximum parsimony analyses of Sulcia. Individual gene alignments (16S rRNA and 131 orthologues of Sulcia and Blattabacterium) are deposited in the compressed file “individual_gene_alignments.zip”, which were used to construct gene trees for multispecies coalescent analysis. The names of Sulcia strains were replaced by the name of their hosts in “Sulcia_pep.fasta”, “Sulcia_nucleotide.fasta” and the files in “individual_gene_alignments.zip”. In all the alignment files, gaps are indicated by “-”.
endosymbiont, “Candidatus Sulcia muelleri”, Auchenorrhyncha, coevolution
Lyons, Lee Ann; Mateus-Pinilla, Nohra; Smith, Rebecca (2021): Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6268941_V1
We developed and delivered in-person training at local health department offices in six of the seven Illinois Department of Public Health “health regions” between April-May of 2019. Pre-, post-, and six-month follow-up questionnaires on knowledge, attitudes, and practices with regards to tick surveillance were administered to training participants.
ticks; survey; tick-borne disease; public health
Xia, Yushu; Wander, Michelle (2021): Correlation Between Soil Quality Indictors including β-glucosidase, Fluorescein Diacetate Hydrolysis and Permanganate Oxidizable Carbon, and Ecosystem Functions represented by Crop Productivity and Greenhouse Gas Emissions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4693684_V3
*Updates for this V3: added a few more records and rearranged the sequence of the tables in order to support our new paper "Evaluation of Indirect and Direct Scoring Methods to Relate Biochemical Soil Quality Indicators to Ecosystem Services" accepted by the Soil Science Society of America Journal. We summarize peer reviewed literature reporting associations between for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) and crop yield and greenhouse gas emissions. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, or “fluorescein diacetate hydrolysis”, together with one or more of the following: “crop yield”, “productivity”, “greenhouse gas’, “CO2”, “CH4”, or “N2O”. Meta-data for records include the following descriptor variables and covariates useful for scoring function development: 1) identifying factors for the study site (location, duration of the experiment), 2) soil textural class, pH, and SOC, 3) depth of soil sampling, 4) units used in published works (i.e.: equivalent mass, concentration), 5) SQI abundances and measured ecosystem functions, and 6) summary statistics for correlation between SQIs and functions (yield and greenhouse gas emissions). *Note: Blank values in tables are considered unreported data.
Soil health promoting practices; Soil quality indicators; β-glucosidase; fluorescein diacetate hydrolysis; Permanganate oxidizable carbon; Greenhouse gas emissions; Scoring curves; Soil Management Assessment Framework
Burnham, Mark; Simon, Sandra; Lee, DK; Kent, Angela; DeLucia, Evan; Yang, Wendy (2021): Data for Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3696813_V1
These data were collected in 2018 and 2019 at the University of Illinois Energy Farm (N 40.063607, W 88.206926). During each growing season, bulk and rhizosphere soil were collected from replicate Sorghum bicolor nitrogen use efficiency trial plots at three separate time points (approximately July 1, August 1, and September 1). We measured soil moisture, pH, soil nitrate and ammonium, potential nitrification, potential denitrification, and extracted and sequenced the V4 region of the 16S rRNA gene for microbial community analysis. All microbial sequence data is archived in the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (accession number SRP326979, project number PRJNA741261).
soil nitrogen; nitrification; nitrogen cycle; sorghum; bioenergy; Center for Advanced Bioenergy and Bioproducts Innovation
Crist, Samantha; Kopsco, Heather; Miller, Alexandria; Gronemeyer, Margaret; Mateus-Pinilla, Nohra; Smith, Rebecca (2021): Knowledge, attitudes, and practices of veterinary professionals towards ticks and tick-borne diseases in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9227641_V1
An online knowledge, attitudes, and practices survey on ticks and tick-borne diseases was distributed to veterinary professionals in Southern and Central Illinois during summer and fall 2020. These are the raw data associated with that survey and the survey questions used. * NOTE: "age" and "gender" variables were removed from the data to protect participants.
ticks; veterinary medicine; tick-borne disease; survey
Riemer, Nicole; Yao, Yu; Dawson, Matthew; Dabdub, Donald (2021): Data for: Evaluating the impacts of cloud processing on resuspended aerosol particles after cloud evaporation using a particle-resolved model. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8367769_V2
This dataset contains simulation results from PartMC-MOSAIC-CAPRAM used in the article ”Eval- uating the impacts of cloud processing on resuspended aerosol particles after cloud evaporation using a particle-resolved model”. In this V2, there are eight folders: one for urban plume simulation to provide the initial particle population for cloud processing, the other four folders are for the four cloud cycles simulated and the last two are for the coagulation cases. Within the urban plume simulation, there are 25 NetCDF files hourly output from PartMC-MOSAIC simulations containing the gas and particle information. Within the four cloud cycle folders, there are 25 subdirectories that contain the cloud processing results for aerosol population from urban plume environment. For each subdirectory, there are 31 NetCDF files out- put every minute from PartMC-MOSAIC-CAPRAM simulations containing aerosol and gas information after aqueous chemistry. Another two folders are for the cases considering Brownian coagulation and sedimentation coalescence. Each contained 93 NetCDF files, produced from repeating the 30-minutes simulations for three times to consider the coagulation randomness. The low polluted case folder includes the simulated cloud processing results for 25 urban plume cases with less aerosol number concentration. This dataset was used to investigate the effects of cloud processing on aerosol mixing state and CCN properties.
cloud process; coagulation; aqueous chemistry; aerosol mixing state; CCN
Edmonds, Devin (2021): Data for Poison Frogs in U.S. Collections. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4717502_V1
The dataset shows all poison frogs (superfamily Dendrobatoidea) in private U.S. collections during 1990–2020. For each species and color morph, there is a date of arrival, the way it arrived in U.S. collections, and detailed notes related to its presence in the pet trade.
pet trade; amphibians; Dendrobatidae
Prada, Cecilia M.; Turner, Benjamin L.; Dalling, James W. (2021): Seedling traits in oak and mix stands. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7636863_V1
Data from an a field experiment at El Velo, Chiriqui, Republic of Panama. Data contain information about functional traits of seedlings growing in different treatments including type of forest, nitrogen addition and organic matter.
Mycorrhiza; nitrogen; oak forest; Panama; plant-soil feedbacks, seedling growth
de Jesús Astacio, Luis Miguel ; Prabhakara, Kaumudi Hassan; Li, Zeqian; Mickalide, Harry; Kuehn , Seppe (2021): Closed microbial communities self-organize to persistently cycle carbon -- 16S Sequencing data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8967648_V1
Shared dataset consists of 16S sequencing data of microbial communities. Each community is composed of heterotrophic bacteria derived from one of two soil samples and the model algae Chlamydomonas reinhardtii. Each comunity was placed in a materially closed environment with an initial supply of carbon in the media and subjected to light-dark cycles. The closed microbial ecosystems (CES) survived via carbon cycling. Each CES was subjected to rounds of dilution, after which the community was sequenced (data provided here). The shared dataset allowed us to conclude that CES consistently self-assembled to cycle carbon (data not provided) via conserved metabolic capabilites (data not provided) dispite differences in taxonomic composition (data provided). --------------------------- Naming convention: [soil sample = A or B][CES replicate = 1,2,3, or 4]_[round number = 1,2,3,or 4]_[reverse read = R or forward read = F]_filt.fastq Example -- A1_r1_F_filt.fastq means soil sample A, CES replicate 1, end of round1, forward read
16S seq; .fastq; closed microbial ecosystems; carbon cycling
Liu, Baqiao; Warnow, Tandy (2021): Data from Scalable Species Tree Inference with External Constraints. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2566000_V1
This dataset contains re-estimated gene trees from the ASTRAL-II  simulated datasets. The re-estimated variants of the datasets are called MC6H and MC11H -- they are derived from the MC6 and MC11 conditions from the original data (the MC6 and MC11 names are given by ASTRID ). The uploaded files contain the sequence alignments (half-length their original alignments), and the re-estimated species trees using FastTree2. Note: - "mc6h.tar.gz" and "mc11h.tar.gz" contain the sequence alignments and the re-estimated gene trees for the two conditions - the sequence alignments are in the format "all-genes.phylip.splitted.[i].half" where i means that this alignment is for the i-th alignment of the original dataset, but truncating the alignment halving its length - "g1000.trees" under each replicate contains the newline-separated re-estimated gene trees. The gene trees were estimated from the above described alignments using FastTree2 (version 2.1.11) command "FastTree -nt -gtr" : Mirarab, S., & Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52. : Vachaspati, P., & Warnow, T. (2015). ASTRID: accurate species trees from internode distances. BMC genomics, 16(10), 1-13.
simulated data; ASTRAL; alignments; gene trees
Keralis, Spencer D. C.; Yakin, Syamil (2021): Becoming A Trans Inclusive Library - Library Employee Survey. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0888551_V1
This data set contains survey results from a 2021 survey of University of Illinois University Library employees conducted as part of the Becoming A Trans Inclusive Library Project to evaluate the awareness of University of Illinois faculty, staff, and student employees regarding transgender identities, and to assess the professional development needs of library employees to better serve trans and gender non-conforming patrons. The survey instrument is available in the IDEALS repository: http://hdl.handle.net/2142/110080.
transgender awareness, academic library, gender identity awareness, professional development opportunities