633 Works

Data for Quantifying transportation energy vulnerability and its spatial patterns in the United States.

Shanshan Liu & Eleftheria Kontou
This data set contains all the map data used for "Quantifying transportation energy vulnerability and its spatial patterns in the United States". The multiple dimensions (i.e., exposure, sensitivity, adaptive capacity) of transportation energy vulnerability (TEV) at the census tract level in the United States, the changes in TEV with electric vehicles adoption, and the detailed data for Chicago, Los Angeles, and New York are in the dataset.

Dataset for Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)

Yanghui Cao, Christopher H. Dietrich, James N. Zahniser & Dmitry A. Dmitriev
The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. 1) taxon_sampling.csv: contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. 2)concatenated_nt.phy: concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429...

Timescale reverses the relationship between host density and infection risk

Tara Stewart Merrill, Carla Cáceres, Samantha Gray, Veronika Laird, Zoe Schnitzler & Julia Buck
Host density shapes infection risk through two opposing phenomena. First, when infective stages are subdivided among multiple hosts, greater host densities decrease infection risk through “safety in numbers”. Hosts, however, represent resources for parasites, and greater host availability also fuels parasite reproduction. Hence, host density increases infection risk through “density-dependent transmission”. Theory proposes that these phenomena are not disparate outcomes but occur over different timescales. That is, higher host densities may reduce short-term infection risk,...

Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States

Anastasia Rahlin, Sarah Saunders & Stephanie Beilke
Dataset for "Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States" manuscript contains occupancy data for ten wetland bird species used in single-species occupancy models at four spatial scales and four wetland habitat types. Data were collected from 2017-2019 in NE Illinois and NW Indiana. Dataset includes wetland bird occupancy data, habitat parameter values for each survey location, and R code used to run analyses.

Effect of Micro-patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress

Dharmeshkumar Parmar, Jin Jia, Joshua Shrout, Jonathan Sweedler & Paul Bohn
#### Details of Pseudomonas aeruginosa biofilm dataset #### ----------------*Folder Structure*------------------------------------- This dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in "MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip", each folder contains 3 sub-folders as listed below. 1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]: (1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h 2. StaticBiofilms [Static biofilms grown on mucin surface]:...

Biological and Simulated datasets for testing the SCAMPP framework for phylogenetic placement methods

Eleanor Wedell & Tandy Warnow
Thank you for using these datasets! These files contain trees and reference alignments, as well as the selected query sequences for testing phylogenetic placement methods against and within the SCAMPP framework. There are four datasets from three different sources, each containing their source alignment and "true" tree, any estimated trees that may have been generated, and any re-estimated branch lengths that were created to be used with their requisite phylogenetic placement method. Three biological datasets...

Data for Evaluating bat boxes: Design and placement alter bioenergetic costs and overheating risk

Reed D. Crawford, Luke E. Dodd, Frank E. Tillman & Joy M. O'Keefe
This dataset contains our bi-hourly temperature recordings from 40 rocket box style artificial roosts of 5 designs deployed in Indiana and Kentucky, USA from April through September 2019. This dataset also includes our endothermic and faculatively heterothermic daily energy expenditure datasets used in our bioenergetic analysis, which were calculated from the bi-hourly rocket box temperature data. Lastly, we include our overheating counts dataset which summarizes daily overheating events (i.e., temperatures > 40 Celsius) in each...

SBKS - Celllines Raw Entity Mentions

Jacob Jett
A set of cell-line entity mentions derived from an NERC dataset analyzing 900 synthetic biology articles published by the ACS. This data is associated with the Synthetic Biology Knowledge System repository (https://web.synbioks.org/). The data in this dataset are raw mentions from the NERC data.

Data for Institutional Data Repository Development, a Moving Target

Colleen Fallaw
This dataset contains data used in publication "Institutional Data Repository Development, a Moving Target" submitted to Code4Lib Journal. It is a tabular data file describing attributes of data files in datasets published in Illinois Data Bank 2016-04-01 to 2021-04-01.

SBKS - Chemical Ambiguous Entity Mentions

Jacob Jett
Related to the raw entity mentions (https://doi.org/10.13012/B2IDB-4163883_V1), this dataset represents the effects of the data cleaning process and collates all of the entity mentions which were too ambiguous to successfully link to the ChEBI ontology.

SBKS - Species Ambiguous Entity Mentions

Jacob Jett
Related to the raw entity mentions, this dataset represents the effects of the data cleaning process and collates all of the entity mentions which were too ambiguous to successfully link to the NCBI's taxonomy identifier system.

An Assessment of the Impacts of Climate Change in Illinois

D Wuebbles, J Angel, K Petersen & A.M. Lemke
Please cite as: Wuebbles, D., J. Angel, K. Petersen, and A.M. Lemke, (Eds.), 2021: An Assessment of the Impacts of Climate Change in Illinois. The Nature Conservancy, Illinois, USA. https://doi.org/10.13012/B2IDB-1260194_V1 Climate change is a major environmental challenge that is likely to affect many aspects of life in Illinois, ranging from human and environmental health to the economy. Illinois is already experiencing impacts from the changing climate and, as climate change progresses and temperatures continue to...

Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Andrew D. Sweet, Bret M. Boyd, Julie M. Allen, Scott M. Villa, Michel P. Valim, Jose L. Rivera-Parra, Robert E. Wilson & Kevin P. Johnson
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly...

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Brazilian sugarcane ethanol as an expandable green alternative to crude oil use

Deepak Jaiswal, Amanda P. De Souza, Søren Larsen, David S. LeBauer, Fernando E. Miguez, Gerd Sparovek, Germán Bollero, Marcos S. Buckeridge & Stephen P. Long
Reduction of CO2 emissions will require a transition from fossil fuels to alternative energy sources. Expansion of Brazilian sugarcane ethanol1, 2 provides one near-term scalable solution to reduce CO2 emissions from the global transport sector. In contrast to corn ethanol, the Brazilian sugarcane ethanol system may offset 86% of CO2 emissions compared to oil use, and emissions resulting from land-use change to sugarcane are paid back in just 2–8 years3, 4. But, it has been...

Data from: Root volume distribution of maturing perennial grasses revealed by correcting for minirhizotron surface effects

Christopher K. Black, Michael D. Masters, David S. LeBauer, Kristina J. Anderson-Teixeira & Evan H. DeLucia
Aims: Root architecture drives plant ecology and physiology, but current detection methods limit understanding of root placement within soil profiles. We developed a statistical model of root volume along depth gradients and used it to infer carbon storage potential of land-use changes from conventional agriculture to perennial bioenergy grasses. Methods: We estimated root volume of maize-soybean rotation and three perennial grass systems (Miscanthus × giganteus, Panicum virgatum, tallgrass prairie mix) by Bayesian modeling from minirhizotron...

Data from: Genomic basis of life history evolution in Drosophila melanogaster

Silvia C. Remolina, Peter L. Chang, Jeff Leips, Sergey V. Nuzhdin & Kimberly A. Hughes
Natural diversity in aging and other life history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and...

Data from: Anthropogenic ecosystem disturbance and the recovery debt

David Moreno Mateos, Edward B. Barbier, Peter C. Jones, Holly P. Jones, James Aronson, Jose A. Lopez-Lopez, Michelle L. McCrackin, Paula Meli, Daniel Montoya & José Rey Benayas
Ecosystem recovery from anthropogenic disturbances, either without human intervention or assisted by ecological restoration, is increasingly occurring worldwide. As ecosystems progress through recovery, it is important to estimate any resulting deficit in biodiversity and functions. Here we use data from 3,035 sampling plots worldwide, to quantify the interim reduction of biodiversity and functions occurring during the recovery process (that is, the ‘recovery debt’). Compared with reference levels, recovering ecosystems run annual deficits of 46–51% for...

Data from: Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

Jaeyun Sung, Seunghyeon Kim, Josephine Jill T. Cabatbat, Sungho Jang, Yong-Su Jin, Gyoo Yeol Jung, Nicholas Chia & Pan-Jun Kim
A system-level framework of complex microbe–microbe and host–microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach...

Data from: Identification of species in the angiosperm family Apiaceae using DNA barcodes

Jinxin Liu, Linchun Shi, Jianping Han, Geng Li, Heng Lu, Fanyun Meng, Stephen R. Downie, Jingyi Hou & Xiaoteng Zhou
Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The...

Data from: The effects of age, sex, and habitat on body size and shape of the blackstripe topminnow, Fundulus notatus

Daniel P. Welsh, Muchu Zhou, Steven M. Mussmann, Lauren G. Fields, Claire L. Thomas, Simon P. Pearish, Stephanie L. Kilburn, Jerrod L. Parker, Laura R. Stein, Jennifer A. Bartlett, Christopher R. Bertram, Thomas J. Bland, Kate L. Laskowski, Brett C. Mommer, Xuan Zhuang & Rebecca C. Fuller
Lake and stream habitats pose a variety of challenges to fishes due to differences in variables such as water velocity, habitat structure, prey community, and predator community. These differences can cause divergent selection on body size and/or shape. Here, we measured sex, age, length, and eight different morphological traits of the blackstripe topminnow, Fundulus notatus, from 19 lake and stream populations across four river drainages in central Illinois. Our goal was to determine whether size...

Data from: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms

Brandon L. Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwarq, , Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, , Muhammad G. Kibriya, Lin S. Chen & Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as methylation QTLs (cis-meQTLs), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing...

Data from: Elevated CO2 and temperature increase soil C losses from a soybean-maize ecosystem

Christopher K. Black, Sarah C. Davis, Tara W. Hudiburg, Carl J. Bernacchi & Evan H. DeLucia
Warming temperatures and increasing CO2 are likely to have large effects on the amount of carbon stored in soil, but predictions of these effects are poorly constrained. We elevated temperature (canopy: +2.8 °C; soil growing season: +1.8 °C; soil fallow: +2.3 °C) for 3 years within the 9th–11th years of an elevated CO2 (+200 ppm) experiment on a maize–soybean agroecosystem, measured respiration by roots and soil microbes, and then used a process-based ecosystem model (DayCent)...

Data from: Undocumented beetle diversity in the Southeastern United States: a case study of the minute clubbed beetles (Coleoptera: Monotomidae)

Thomas C. McElrath & Joseph V. McHugh
Studies of the saproxylic and predatory beetle family Monotomidae (Coleoptera: Cucujoidea) in the southeastern USA increased the known diversity for the family in the state of Georgia by one genus and nine species. Online records of Monotomidae from Georgia increased from 0 to 885. This work highlights the lack of basic diversity information about small beetles that inhabit wood, leaf litter, and other decaying plant matter in this region.

Data from: Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation

Christopher J. Holmes, Jelena H. Pantel, Kimberly L. Schulz & Carla E. Cáceres
When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex...

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