Datasets

This dataset contains all material required to produce the figures found within the manuscript submitted to Geoscientific Model Development entitled “Explicit stochastic advection algorithms for the regional scale particle-resolved atmospheric aerosol model WRF-PartMC (v1.0)”. The dataset consists of Python Jupyter notebooks and any applicable WRF-PartMC output. This dataset covers the three numerical examples of the manuscript, 1D advection by a uniform constant wind, a 2D rotational flow and a 3D time-evolving WRF simulated flow.

Raw data for the results presented in Ferguson et al 2024.

Data for each figure of the article "Greater aperture counteracts effects of reduced stomatal density on WUE: a case study on sugarcane and meta-analysis" published in J. Ex. Bot.

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.

This dataset contains data used to generate figures and tables in the corresponding paper.

This is the dataset that accompanies the paper titled "A Dual-Frequency Radar Retrieval of Snowfall Properties Using a Neural Network", submitted for peer review in August 2020. Please see the github for the most up-to-date data after the revision process: https://github.com/dopplerchase/Chase_et_al_2021_NN Authors: Randy J. Chase, Stephen W. Nesbitt and Greg M. McFarquhar Corresponding author: Randy J. Chase (randyjc2@illinois.edu) Here we have the data used in the manuscript. Please email me if you have specific questions about units etc. 1) DDA/GMM database of scattering properties: base_df_DDA.csv This is the combined dataset from the following papers: Leinonen & Moisseev, 2015; Leinonen & Szyrmer, 2015; Lu et al., 2016; Kuo et al., 2016; Eriksson et al., 2018. The column names are D: Maximum dimension in meters, M: particle mass in grams kg, sigma_ku: backscatter cross-section at ku in m^2, sigma_ka: backscatter cross-section at ka in m^2, sigma_w: backscatter cross-section at w in m^2. The first column is just an index column. 2) Synthetic Data used to train and test the neural network: Unrimed_simulation_wholespecturm_train_V2.nc, Unrimed_simulation_wholespecturm_test_V2.nc This was the result of combining the PSDs and DDA/GMM particles randomly to build the training and test dataset. 3) Notebook for training the network using the synthetic database and Google Colab (tensorflow): Train_Neural_Network_Chase2020.ipynb This is the notebook used to train the neural network. 4)Trained tensorflow neural network: NN_6by8.h5 This is the hdf5 tensorflow model that resulted from the training. You will need this to run the retrieval. 5) Scalers needed to apply the neural network: scaler_X_V2.pkl, scaler_y_V2.pkl These are the sklearn scalers used in training the neural network. You will need these to scale your data if you wish to run the retrieval. 6) <b>New in this version</b> - Example notebook of how to run the trained neural network on Ku- Ka- band observations. We showed this with the 3rd case in the paper: Run_Chase2021_NN.ipynb 7) <b>New in this version</b> - APR data used to show how to run the neural network retrieval: Chase_2021_NN_APR03Dec2015.nc The data for the analysis on the observations are not provided here because of the size of the radar data. Please see the GHRC website (<a href="https://ghrc.nsstc.nasa.gov/home/">https://ghrc.nsstc.nasa.gov/home/</a>) if you wish to download the radar and in-situ data or contact me. We can coordinate transferring the exact datafiles used. The GPM-DPR data are avail. here: <a href="http://dx.doi.org/10.5067/GPM/DPR/GPM/2A/05">http://dx.doi.org/10.5067/GPM/DPR/GPM/2A/05</a>

A set of chemical 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.

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.

The dataset contains trajectories of Pt nanoparticles in 1.98 mM NaBH4 and NaCl, tracked under liquid-phase TEM. The coordinates (x, y) of nanoparticles are provided, together with the conversion factor that translates pixel size to actual distance. In the file, ∆t denotes the time interval and NaN indicates the absence of a value when the nanoparticle has not emerged or been tracked. The labeling of nanoparticles in the paper is also noted in the second row of the file.

This dataset contains records of four years of taxi operations in New York City and includes 697,622,444 trips. Each trip records the pickup and drop-off dates, times, and coordinates, as well as the metered distance reported by the taximeter. The trip data also includes fields such as the taxi medallion number, fare amount, and tip amount. The dataset was obtained through a Freedom of Information Law request from the New York City Taxi and Limousine Commission. The files in this dataset are optimized for use with the ‘decompress.py’ script included in this dataset. This file has additional documentation and contact information that may be of help if you run into trouble accessing the content of the zip files.

Rising global temperatures and urban heat island effects challenge environmental health and energy systems at the city level, particularly in summer. Increased heatwaves raise energy demand for cooling, stressing power facilities, increasing costs, and risking blackouts. Heat impacts vary across cities due to differences in urban morphology, geography, land use, and land cover, highlighting vulnerable areas needing targeted heat mitigation. Urban tree canopies, a nature-based solution, effectively mitigate heat. Trees provide shade and cooling through evaporation, improving thermal comfort, reducing air conditioning energy consumption, and enhancing climate resilience. This report focused on the ComEd service area in the Chicago Metropolitan Region and assessed the impacts of population growth, urbanization, climate change, and an ambitious plan to plant 1 million trees. The report evaluated planting 1 million trees to quantify regional cooling effects projected for the 2030s. Afforestation locations were selected to avoid interference with existing infrastructure. Key findings include (i) extreme hot hours (>95°F) will increase from 30 to 200 per year, adding 420 Cooling Degree Days (CCD) by the 2030s, (ii) greener areas can be up to 10°F cooler than less vegetated neighborhoods in summer, (iii) tree canopies can create localized cooling, reducing temperatures by 0.7°F and lowering annual CCD by 60 to 65, and (iv) afforestation can reduce the region’s temperature by 0.7°F, saving 400 to 1100 Megawatt hours of daily power usage during summer. <b>Note: The data is available upon request from <a href="mailto:dpiclimate@uilliois.edu">dpiclimate@uilliois.edu</br>.

This data and code accompany the manuscript "Small population size and possible extirpation of the threatened Malagasy poison frog Mantella cowanii". The data were collected using photograph capture-recapture at three sites in the central highlands of Madagascar. In Part 1, the script implements robust design capture-mark-recapture models in program MARK through the RMark interface to estimate population sizes and annual survival probabilities. In Part 2, it estimates the number of surveys needed to infer absence at sites where we did not detect the frog.

This dataset includes the gas exchange and TDL (tunable diode laser) files between 4 accessions of Glycine soja and 1 elite accession of Glycine max (soybean) during light induction. In this V2, code files for Matlab and R are also included to calculate mesophyll conductance and calculate the limitation on photosynthesis, respectively.

This repository contains the data and computational analysis notebooks that were used in the following manuscript. For more information on the methods and contributing authors, please refer to the original manuscript. "Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Omid Gholamalamdari et al. 2024"

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

This dataset includes the RT-PCR results, RT-LAMP results, and the minutes to positive ROC curve calculations. This dataset includes data for the synthetic gBlock, cell culture, and clinical sample assays (nasal swabs and nasal wipes). Also included is a list of FDA approved point of care tests for influenza A virus to date (2-16-2024). MIQE guidelines are also included.

A defining feature of the Anthropocene is the distortion of the biosphere phosphorus (P) cycle. A relatively sudden acceleration of input fluxes without a concomitant increase in output fluxes has led to net accumulation of P in the terrestrial-aquatic continuum. Over the past century, P has been mined from geological deposits to produce crop fertilizers. When P inputs are not fully removed with harvest of crop biomass, the remaining P accumulates in soils. This residual P is a uniquely anthropogenic pool of P, and its management is critical for agronomic and environmental sustainability. This dataset includes data for us to quantify residual P from different long-term managed systems. The following is the desccription of the dataset. There are 7 sheets in total. 1. P_balance: From Morrow Plots maize-maize rotaiton (1888-2021), L: Low estimation; M: medium estimation; H: high estimation; 2. M3P: From Morrow Plots selected plots (selected years), M3P_sur: Mehlich III P concentration in surface 17cm soils; M3P_sub: Mehlich III P concentration in 17-34cm subsoils; P_balance: the difference between P inputs and P outputs; TP_sur: total P stocks in surface 17cm soils; TP_sub: total P stocks in 17-34cm subsoils; 3. Morrow_Plot_P_pool_all: Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; Fertilized: P stocks in the fertilized plot; Unfertilized: P stocks in the unfertilized plot; F-U: difference between P stocks in ther fertilized and unfertilized plots; dif%: percent difference in total P; 4. Rothamsted_P_pool_all: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 5. L'Acadie_P_pool_all: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 6. Rothamsted_P_pool_duration: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 7. L'Acadie_P_pool_duration: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;

A population genetics study was conducted on three plant taxa in the genus Physaria that are found on the Kaibab Plateau (Arizona, USA). Physaria kingii subsp. kaibabensis is endemic to the Kaibab Plateau, and is of conservation concern because of its rarity, limited range, and potential threats to its long-term persistence. Additionally, the taxon is a candidate for federal protection under the Endangered Species Act. It was not clear how genetically isolated P. k. subsp. kaibabensis was from Physaria kingii subsp. latifolia, which is a widespread subspecies found throughout the southwestern USA, including on the Kaibab Plateau. Additionally, other authors have suggested that P. k. subsp. kaibabensis may hybridize with Physaria arizonica, a different species that is also widespread and found on and off the Kaibab Plateau. We conducted a population genetics study of all three groups to better determine the conservation status of P. k. subsp. kaibabensis. Genetic data are in the form of nuclear DNA microsatellites for 13 loci (all apparently diploid). Additionally, we have included location information for the collection sites. We collected tissue samples from on and off the Kaibab Plateau. The overall findings are shared in a manuscript being submitted for peer-review.

U-2 OS MERFISH data set prepared by the Han lab at UIUC based off of procedures developed in Moffitt et al. Proc. Natl. Acad. Sci. USA 113 (39), 11046–11051. Data is comprised of ~2 million spots from 130 genes with x,y,z location, cell assignment, and correction status.

Supplemental data for the paper titled 'Environmental modulators of algae-bacteria interactions at scale'. Each of the excel workbooks corresponding to datasets 1, 2, and 3 contain a README sheet explaining the reported data. Dataset 4 comprising microscopy data contains a README text file describing the image files.

This page contains the data for the publication "Revisiting bacterial cytolethal distending toxin structure and function" published in Frontiers in Cellular and Infection Microbiology in 2023.

This dataset is associated with the manuscript "Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment" This dataset includes 2 Excel files: 1) raw_data_bioassay.xlsx: this file contains the raw data for waxworm bioassay. There are 2 worksheets within this file: - LC50: raw data for measuring LC50 in the laboratory and field strain of Galleria mellonella. - RGR: Relative Growth Rate, raw data for measuring body weight of field strain of Galleria mellonella . 2) raw-data_RT-qPCR.xlsx: this file contains raw data (Ct value) of RT-qPCR.

This page contains the data for the manuscript "Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis" currently available in preprint on bioRxiv