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Wedell, Eleanor; Warnow, Tandy (2022): Biological and Simulated datasets for testing the SCAMPP framework for phylogenetic placement methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9257957_V1
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 (16S.B.ALL, PEWO/LTP_s128_SSU, and PEWO/green85) and one simulated dataset (nt78) is contained. See README.txt in each file for more information.
Phylogenetic Placement; Phylogenetics; Maximum Likelihood; pplacer; EPA-ng
Yan, Bin; Dietrich, Christopher; Yu, Xiaofei; Dai, Renhuai; Maofa, Yang (2022): Data files for phylogenetic analysis of Typhlocybinae (Hemiptera: Cicadellidae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8761342_V1
The files are plain text and contain the original data used in phylogenetic analyses of of Typhlocybinae (Bin, Dietrich, Yu, Meng, Dai and Yang 2022: Ecology & Evolution, in press). The three files with extension .phy are text files with aligned DNA sequences in the standard PHYLIP format and correspond to Matrix 1 (amino acid alignment), Matrix 2 (nucleotide alignment of first two codon positions of protein-coding genes) and Matrix 3 (nucleotide alignment of protein-coding genes plus 2 ribosomal genes) described in the Methods section. An additional text file in NEXUS format (.nex extension) contains the morphological character data used in the ancestral state reconstruction (ASCR) analysis described in the Methods. NEXUS is a standard format used by various phylogenetic analysis software. For more information on data file content, see the included "readme" files.
Hemiptera; phylogeny; mitochondrial genome; morphology; leafhopper
Trivellone, Valeria; Cao, Yanghui; Dietrich, Christopher (2022): Alternative approaches for uncovering phytoplasma biodiversity and vector associations. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9804959_V1
This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.
anchored hybrid enrichment; biodiversity, biorepository; nested PCR; Sanger sequencing
has sharing link
Wong, Tony; Oudshoorn, Luuk; Sofovich, Eliyahu; Green, Alex; Shah, Charmi; Indebetouw, Remy; Meixner, Margaret; Hacar, Alvaro; Nayak, Omnarayani; Tokuda, Kazuki; Bolatto, Alberto D.; Chevance, Melanie; De Marchi, Guido; Fukui, Yasuo; Hirschauer, Alec S.; Jameson, K. E.; Kalari, Venu; Lebouteiller, Vianney; Looney, Leslie W.; Madden, Suzanne C.; Onishi, Toshikazu; Roman-Duval, Julia; Rubio, Monica; Tielens, A. G. G. M. (2022): Data for: The 30 Doradus Molecular Cloud at 0.4 pc Resolution with ALMA: Physical Properties and the Boundedness of CO-emitting Structures. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1671495_V1
12CO and 13CO emission maps of the 30 Doradus molecular cloud in the Large Magellanic Cloud, obtained with the Atacama Large Millimeter/submillimeter Array (ALMA) during Cycle 7. See the associated article in the Astrophysical Journal, and README file, for details. Please cite the article if you use these data.
Xia, Yushu; Wander, Michelle; Kwon, Hoyoung (2021): County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3112432_V1
This dataset includes five files developed using the procedures described in the article 'Developing County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States' and Supplemental Information published in the Journal of Cleaner Production in 2021. Citation: Xia, Yushu, Hoyoung Kwon, and Michelle Wander. "Developing county-level data of nitrogen fertilizer and manure inputs for corn production in the United States." Journal of Cleaner Production 309 (2021): e126957. Brief method: The fertilizer and manure inputs for corn were generated with a top-down approach by assigning county-level total N inputs reported by USGS to different crops using state- and county-level survey data. The corn N needs were estimated using empirical extension-based equations coupled with soil and environmental covariates. The estimates of fertilizer N inputs were further refined for corn grain and silage production at the county level and gap-filling (using state-level averages) was carried out to generate final files for U.S. county-level N inputs. The dataset is provided in an alternative format in Google Earth Engine: https://code.earthengine.google.com/13a0078e7ee727bc001e045ad0e8c6fc
Corn; Nitrogen Fertilizer; Manure; Conterminous U.S.
Chu, Gillian; Warnow, Tandy (2022): RNASim-VS2. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8812049_V1
Provides RNASim-VS2 datasets used in Gillian's Master's thesis.
Southey, Bruce; Rodriguez-Zas, Sandra L. (2022): Data for changes in neuropeptide prohormone genes among Cetartio-dactyla livestock and wild species associated with evolution and domestication. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2071917_V1
This dataset contain information for the paper "Changes in neuropeptide prohormone genes among Cetartio-dactyla livestock and wild species associated with evolution and domestication" Veterinary Sciences, MDPI. Protein sequences were predicted using GeneWise for 98 neuropeptide prohormone genes from publicly available genomes of 118 Cetartiodactyla species. All predictions (CetartiodactylaSequences2022.zip) were manually verified. Sequences were aligned within each prohormone using MAFFT (MDPImultalign2022.zip includes multiple sequence alignment of all species available for each prohormone). Phylogenetic gene trees were constructed using PhyML and the species tree was constructed using ASTRAL (MDPItree2022.zip). The data is released under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).
prohormone; neuropeptide; Cetartiodactyla; Cetartiodactyla; phylogenetics; gene tree; species tree
Madhavan, Vidya; Aishwarya, Anuva (2022): Data for Long-lifetime spin excitations near domain walls in 1T-TaS2. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0883774_V1
The data files are for the paper entitled: Long-lifetime spin excitations near domain walls in 1T-TaS2 to be published in PNAS. The data was obtained on a 300 mK custom designed Unisoku scanning tunneling microscope using the Nanonis module. All the data files have been named based on the Figure numbers that they represent.
Mott Insulator; Spins; Charge Density Wave; Domain walls; Long lifetime
Clem, Scott; Hobson, Keith; Harmon-Threatt, Alexandra (2022): Raw data and code for the paper: Do Nearctic hover flies (Diptera: Syrphidae) engage in long-distance migration? An assessment of evidence and mechanisms. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6560908_V1
This dataset is for the publication "Do Nearctic hover flies (Diptera: Syrphidae) engage in long-distance migration? An assessment of evidence and mechanisms." It consists of 11 Excel spreadsheets and 4 R scripts which correspond to the analyses which were conducted. Paper abstract: Long-distance insect migration is poorly understood despite its tremendous ecological and economic importance. As a group, Nearctic hover flies (Diptera: Syrphidae: Syrphinae), which are crucial pollinators as adults and biological control agents as larvae, are almost entirely unrecognized as migratory despite examples of highly migratory behavior among several Palearctic species. Here, we examined evidence and mechanisms of migration for four hover fly species (Allograpta obliqua, Eupeodes americanus, Syrphus rectus, and Syrphus ribesii) common throughout eastern North America using stable hydrogen isotope (δ2H) measurements of chitinous tissue, morphological assessments, abundance estimations, and cold-tolerance assays. While further studies are needed, non-local isotopic values obtained from hover fly specimens collected in central Illinois support the existence of long-distance fall migratory behavior in Eu. americanus, and to a lesser extent S. ribesii and S. rectus. Elevated abundance of Eu. americanus during the expected autumn migratory period further supports the existence of such behavior. Moreover, high phenotypic plasticity of morphology associated with dispersal coupled with significant differences between local and non-local specimens suggest that Eu. americanus exhibits a unique suite of morphological traits that decrease costs associated with long-distance flight. Finally, compared to the ostensibly non-migratory A. obliqua, Eu. americanus was less cold tolerant, a factor that may be associated with migratory behavior. Collectively, our findings imply that fall migration occurs in Nearctic hover flies, but we consider methodological limitations of our study in addition to potential ecological and economic consequences of these novel findings.
Insect migration; hover fly; Syrphidae; stable isotopes; deuterium; morphometrics; cold tolerance
Getahun, Elias; Zavelle, Atticus; Keefer, Laura (2022): Illinois Coastal Zone Water Quality Database (ICoastalDB) . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7799136_V1
ICoastalDB, which was developed using Microsoft structured query language (SQL) Server, consists of water quality and related data in the Illinois coastal zone that were collected by various organizations. The information in the dataset includes, but is not limited to, sample data type, method of data sampling, location, time and date of sampling and data units.
Illinois Coastal Zone; Water Quality Data
Andrade, Flavia (2022): Data for A biopsychosocial examination of chronic back pain, limitations on usual activities, and treatment in Brazil, 2019. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2309514_V1
This dataset was created based on the publicly available microdata from PNS-2019, a national health survey conducted by the Instituto Brasileiro de Geografia e Estatistica (IBGE, Brazilian Institute of Geography and Statistics). IBGE is a federal agency responsible for the official collection of statistical information in Brazil – essentially, the Brazilian census bureau. Data on selected variables focusing on biopsychosocial domains related to pain prevalence, limitations and treatment are available. The Fundação Instituto Oswaldo Cruz has detailed information about the PNS, including questionnaires, survey design, and datasets (www.pns.fiocruz.br). The microdata can be found on the IBGE website (https://www.ibge.gov.br/estatisticas/downloads-estatisticas.html?caminho=PNS/2019/Microdados/Dados).
back pain; health status disparities; biopsychosocial; Brazil
Zinnen, Jack (2022): Data for: Functional traits and responses to nutrient and mycorrhizal addition are inconsistently related to wetland plant species’ coefficients of conservatism. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6489931_V1
This is the core data for Zinnen et al., "Functional traits and responses to nutrient and mycorrhizal addition are inconsistently related to wetland plant species’ coefficients of conservatism." This is submitted to Wetlands Ecology and Management. Two datasets are submitted here. The first is greenhouse-collected data of 9 plant traits and concurrent treatment responses of Illinois wetland plant species. The second are field-collected leaf trait data of Illinois wetland plant species. These data are analyzed in the paper. Please refer to the main manuscript to see how these data were produced and specific analyses.
ecological indicators; Floristic Quality Assessment; Floristic Quality Index; wetland degradation
Saleh, Ehsan; Ghaffari, Saba; Forsyth, David; Yu-Xiong, Wang (2022): Dataset for On the Importance of Firth Bias Reduction in Few-Shot Classification. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1016367_V1
This data repository includes the features and the trained backbone parameters used in the ICLR 2022 Paper "On the Importance of Firth Bias Reduction in Few-Shot Classification". The code accompanying this data is open-source and available at https://github.com/ehsansaleh/firth_bias_reduction The code and the data have three modules: 1. The "code_firth" module (10 files) relates to the basic ResNet backbones and logistic classifiers (e.g., Figures 2 and 3 in the main paper). 2. The "code_s2m2rf" module (2 files) relates to the S2M2R feature backbones and cosine classifiers (e.g., Figure 4 in the main paper). 3. The "code_dcf" module (3 files) relates to the few-shot Distribution Calibration (DC) method (e.g., Table 1 in the main paper). The relevant files for each module have the module name as a prefix in their name. 1. For instance, the "code_dcf_features.tar" file should be placed at the "features" directory of the "code_dcf" module. 2. As another example, "code_firth_features_cifarfs_novel.tar" should be placed in the "features" directory of the "code_firth" module, and it includes the features extracted from the novel split of mini-ImageNet dataset. Each tar-ball should be extracted in its relevant directory, and the md5 check-sums of the extracted files are also provided in the open-source code repository for verification. Please note that the actual datasets of images are not included here (since we do not own those datasets). However, helper scripts for automatically downloading the original datasets are also provided in the every module and sub-directory of the GitHub code repository.
Computer Vision; Few-Shot Classification; Few-Shot Learning; Firth Bias Reduction
Nowak, Romana; Yang, Shuhong; Li, Kailiang; Bi, Jiajia; Drnevich, Jenny (2022): List of differentially expressed genes for "Basigin is necessary for normal decidualization of human uterine stromal cells". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5457341_V1
List of differentially expressed genes in human endometrial stromal cells with knockdown of Basigin (BSG) gene expression during decidualization. The BSG siRNA or negative scrambled control siRNA were transfected into human endometrial stromal cells (HESCs) following the protocol of siLentFect™ Lipid (Bio-Rad, Hercules, CA. Following complete knock down of BSG in HESCs (72 hours after adding siRNA), HESCs were treated with medium containing estrogen, progesterone and cAMP to induce decidualization. BSG siRNA and negative control scrambled siRNA were added to the cells every four days (day 0, 4) over the course of the decidualization protocol. Total RNA was harvested at day 6 of the decidualization protocol for microarray analysis. Microarray analysis was performed at the University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center. Briefly, 0.2 micrograms of total RNA were labeled using the Agilent two color QuickAmp labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. The optional spike-in controls were not used. Samples were hybridized to Human Gene Expression 4x44K v2 Microarray (Agilent Technologies, Santa Clara, CA) in an Agilent Hybridization Cassette according to standard protocols. The arrays were then scanned on an Axon GenePix 4000B scanner and the images were quantified using Axon GenePix 6.1. Microarray data pre-processing and statistical analyses were done in R (v3.6.2) using the limma package (3.42.0 (Ritchie et al., 2015). Median foreground and median background values from the 4 arrays were read into R and any spots that had been manually flagged (-100 values) were given a weight of zero. The background values were ignored because investigations showed that trying to use them to adjust for background fluorescence added more noise to the data; background was low and even for all arrays, therefore no background correction was done. The individual Cy5 and Cy3 fluorescence for each array were normalized together using the quantile method 3 (Yang and Thorne, 2003). Agilent's Human Gene Expression 4x44K v2 Microarray has a total of 45,220 probes: 1224 probes for positive controls, 153 negative control, 823 labeled “ignore” and 43,118 labeled “cDNA”. The pos+neg+ignore probes were used to ascertain the background level of fluorescence (6, on the log2 scale) then discarded. The cDNA probes comprise 34,127 unique 60mer probes, of which 999 probes are spotted 10 times each and the rest one time each. We averaged the replicate probes for those spotted 10 times and then fit a mixed model that had treatment and dye as fixed effects and array pairing as a random effect (Phipson et al., 2016; Smyth et al., 2005). After fitting the model but before False Discovery Rate (FDR) correction (Benjamini and Hochberg, 1995), probes were filtered out by the following criteria: 1) did not have at least 4/8 samples with expression values > 6 (14,105 probes removed), 2) no longer had an assigned Entrez Gene ID in Bioconductor’s HsAgilentDesign026652.db annotation package (v3.2.3; 2,152 probes removed) (Huber et al., 2015), 3) mapped to the same Entrez Gene ID as another probe but had a larger p-value for treatment effect (4,141 probes removed). This left 13,729 probes representing 13,729 unique genes. <b>*Please note: that there is a discrepancy between the file and the readme as this plain text is the actual data file of this dataset.</b>
Basigin; endometrium; decidualization; human
Liu, Shanshan; Kontou, Eleftheria (2022): Data for Quantifying transportation energy vulnerability and its spatial patterns in the United States.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9337369_V2
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.
Transport energy; Vulnerability; Fuel costs; Electric vehicles
Kudeki, Erhan; Reyes, Pablo (2022): EVEX Campaign Ground Based Radar Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8835972_V1
Ground based radar data sets collected during the 2013 NASA EVEX Campaign conducted in Roi-Namur island of the Kwajalein Atoll in the Republic of Marshall Islands are deposited in this databank. Radar data were collected with IRIS VHF and ALTAIR VHF/UHF systems.
Wang, Junren; Karakoc, Deniz Berfin; Konar, Megan (2022): Data for: The Carbon Footprint of Cold Chain Food Flows in the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8455093_V1
This dataset is a estimation of county-to-county commodity delivery through cold chain in 2017. For each county pair, the weight[kg] and value[$] of the cold chain flow between origin and destination for SCTG 5 and SCTG 7 commodities are estimated by our model. - SCTG 5 - Meat, poultry, fish, seafood, and their preparations - SCTG 7 - Other prepared foodstuffs, fats, and oils
food flows; cold chain; county-scale; United States; carbon footprint
McCoy, Annette; Secor, Erica; Roady, Patrick; Gray, Sarah; Klein, Julie; Gutierrez-Nibeyro, Santiago (2022): Plantar osteochondral fragments in young Standardbreds are associated with minimal joint inflammation at the time of surgical removal. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3414496_V1
Raw arthroscopic scores, histologic scores, cytokine measurements, and performance data for the study cohort described in the accompanying publication.
horse; metatarsophalangeal joint; arthroscopy; exercise; developmental orthopedic disease
Kantola, Ilsa; Masters, Michael; Blanc-Betes, Elena; Gomez-Casanovas, Nuria; DeLucia, Evan (2022): Data from: Long-term yields in annual and perennial bioenergy crops in the Midwestern USA. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0142760_V1
Data sets relating to the manuscript “Long-term yields in annual and perennial bioenergy crops in the Midwestern USA” published in Global Change Biology Bioenergy. Field data, including annual peak biomass and harvest yields from maize/soy, miscanthus, switchgrass, and prairie field trials from 2008-2018 are included. Peak and harvest biomass for fertilized and unfertilized miscanthus are included from 2014-2018.
miscanthus; switchgrass; yield; drought; crop; perennial; bioenergy
Cao, Yanghui; Dietrich, Christopher H.; Zahniser, James N.; Dmitriev, Dmitry A. (2022): Dataset for Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8842653_V2
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. <b>1) taxon_sampling.csv:</b> 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. <b>2)concatenated_nt.phy:</b> 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 genes in 730 samples. Hyphens are used to represent gaps. <b>3) concatenated_nt_partition.nex:</b> the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set. <b>4) concatenated_aa.phy:</b> concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps. <b>5) concatenated_aa_partition.nex:</b> the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set. <b>6) concatenated_nt_106taxa.phy:</b> a reduced concatenated nucleotide alignment representing 107 samples x 86 genes. This alignment is used to estimate the divergence times of Deltocephalinae using MCMCTree in PAML v4.9. The file lists the sequences of 79,239 nucleotide positions from 86 genes in 107 samples. Hyphens are used to represent gaps. <b>7) concatenated_nt_106taxa_partition.nex:</b> the partitions for the nucleotide alignment concatenated_nt_106taxa.phy. The file partitions the 79,239 nucleotide characters into 86 character sets, and defines the best substitution model for each character set. <b>8) individual_gene_alignment.zip:</b> contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12, followed by multispecies coalescent analysis using ASTRAL v 4.10.5.
Proescholdt, Randi; Hsiao, Tzu-Kun; Schneider, Jodi; Cohen, Aaron; McDonagh, Marian; Smalheiser, Neil (2022): Data from Testing a filtering strategy for systematic reviews: Evaluating work savings and recall. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9257002_V1
This dataset contains the files used to perform the work savings and recall evaluation in the study titled "Data from Testing a filtering strategy for systematic reviews: Evaluating work savings and recall."
systematic reviews; machine learning; work savings; recall; search results filtering
Allen, Maximilian (2022): PumaCaching. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5816195_V1
Dataset associated with Allen et al. (In Review): Food caching by a solitary large carnivore supports optimal foraging theory If using this dataset, please cite this manuscript.
Yao, Yu; Curtis, Jeffrey; Ching, Joseph; Zheng, Zhonghua; Riemer, Nicole (2022): Data for: Quantifying the effects of mixing state on aerosol optical properties. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8157303_V1
This dataset contains simulation results from numerical model PartMC-MOSAIC used in the article "Quantifying the effects of mixing state on aerosol optical properties". This article is submitted to the journal Atmospheric Physics and Chemistry. There are total 100 scenario directories in this dataset, denoted from 00-99. Each scenario contains 25 NetCDF files hourly output from PartMC-MOSAIC simulations containing the simulated gas and particle information. The data was produced using version 2.5.0 of PartMC-MOSAIC. Instructions to compile and run PartMC-MOSAIC are available at https://github.com/compdyn/partmc. The chemistry code MOSAIC is available by request from Rahul.Zaveri@pnl.gov. For more details of reproducing the cases, please contact email@example.com and firstname.lastname@example.org.
Aerosol mixing state; Aerosol optical properties; Mie calculation; Black Carbon
Trivellone, Valeria; Cao, Yanghui; Blackshear, Millon; Kim, Chang-Hyun; Stone, Christopher (2022): Trivellone, Valeria; Cao, Yanghui; Blackshear, Millon ; Kim, Chang-Hyun ; Stone, Christopher (2022): FASTA file of the final sequence alignment used in the haplotype analyses of Culex pipiens complex populations collected in south-eastern Illinois (2016-2017). University of Illinois at Urbana-Champaign. . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5032907_V1
The Culex_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the haplotype analyses of Trivellone et al. (Frontiers in Public Health, under review). The 492 sequences (from specimens of Culex pipiens complex collected in different habitat types using a BG-sentinel traps) were aligned using PASTA v1.8.5 under default settings. The final dataset contains 686 positions of the cytochrome c oxidase subunit I (COI) mitochondrial gene. The data analyses are further described in the cited original paper.
Culex; Culicidae; COI; mosquito surveillance, species assemblages
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;