Illinois Data Bank Dataset Search Results
Results
published:
2021-10-24
Tillman, Francis E.; Bakken, George S.; O'Keefe, Joy M.
(2021)
This dataset contains daily and hourly temperature measurements in twenty different bat box designs deployed in central Indiana, USA from May to September 2018. Daily and hourly environmental data (temperature, solar radiation, wind speed and direction) are also included for days and hours sampled. Bat box temperature data were reclassified to cool (</= 30°C), permissive (30.1–39.9°C), and stressful (>/= 40°C) categories according to known temperature tolerances of temperate-zone bats.
keywords:
bat box; design; environmental variables; microclimate; temperature
published:
2024-04-11
Margenot, Andrew; Zhou, Shengnan; Xu, Suwei; Condron, Leo; Metson, Geneviève; Haygarth, Philip; Wade, Jordon; Agyeman, Price Chapman
(2024)
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;
keywords:
phosphate rock; biosphere; balances; soil test P; long-term experiment
published:
2025-12-02
Cheng, Ming-Hsun; Maitra, Shraddha; Carr Clennon, Aidan N.; Appell, Michael; Dien, Bruce; Singh, Vijay
(2025)
The recalcitrance of lignocellulosic biomass necessitates an efficient pretreatment protocol for operating a successful cellulosic biorefinery. It is critical to improve cellulose accessibility for hydrolysis and fermentation by altering the plant cell wall’s physical structure and chemical composition. Sequential hydrothermal-mechanical refining pretreatment (HMR) allows efficient recovery of cellulosic sugars without utilizing any hazardous chemicals. HMR has been successfully applied to Liberty switchgrass, a bioenergy cultivar released by the USDA, and now it is being applied to oilcane, a recently developed transgenic sugarcane variety engineered to accumulate lipids in its vegetative tissues. Sugar yields of oilcane bagasse (OCB) and switchgrass (SG) treated with HMR are 96.4% and 75.4%, respectively. This study sought to correlate cellulosic sugar yields with structural changes within the cell wall caused by HMR on two distinct bioenergy crops. Simon’s staining technique for the specific surface area analysis showed that HMR increased the specific surface area of pretreated biomass residues by 80-112%. In addition, ATR-FTIR was performed to determine the effects of HMR on physical structures based on the total crystallinity index (TCI) and hydrogen bonding intensity (HBI). Irrespective of biomass type, HMR decreased the initial crystalline cellulose contents of untreated biomass residues by 3.5% and reduced TCI and HBI by 7-13%. The study found that sugar yields were negatively correlated to reducing values of hydrogen bonding intensity, crystalline cellulose content, and total crystallinity index.
keywords:
Conversion;Biomass Analytics;Economics;Hydrolysate
published:
2025-12-18
Boob, Aashutosh; Zhang, Changyi; Pan, Yuwei; Zaidi, Airah; Whitaker, Rachel; Zhao, Huimin
(2025)
Sulfolobus islandicus, an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.
keywords:
AI/ML; gene editing; genome engineering; metabolic engineering
published:
2019-03-22
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P.
(2019)
This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)
keywords:
songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published:
2019-03-19
Fernandez, Roberto; Parker, Gary; Stark, Colin P.
(2019)
This dataset includes images and extracted centerlines from experiments looking at the formation and evolution of meltwater meandering channels on ice. The laboratory data includes centimeter- and millimeter-scale rivulets. Dataset also includes an image and corresponding centerlines from the Peterman Ice Island.
All centerlines were manually digitized in Matlab but no distributable code was developed for the process. Once digitized, centerlines were smoothed and standardized following methods and routines developed by other authors (Zolezzi and Guneralp, 2016; Guneralp and Rhoads, 2008). Details about the preparation of the centerlines and processing with these methods is included in the dissertation by Fernández (2018) linked to this dataset.
"Millimeter scale and Peterman Ice Island centerlines.pdf": This file includes the images of two mm-scale experimetns and the Peterman Ice Island image. Seventeen centerlines were digitized from the former and seven were digitized from the latter. Those centerlines are shown above the images themselves.
"Centimeter scale rivulet images.pdf": This file includes images corresponding to all cm-scale centerlines used for the analysis presented in the dissertation by Fernandez (2018). Each image has a short caption indicating the run ID and the time at which it was captured. The images were used to extract centerlines to look at the planform evolution of cm-scale meltwater meandering rivulets on ice. Images include 26 centerlines from four different runs.
"Meltwater meandering channel centerlines.xlsx": This spreadsheet contains the centerline data for all fifty centerlines. The workbook includes 51 sheets. The first 50 are related to each one of the channels. The mm scale and Peterman Ice Island ones are identified using the same IDs shown in "Millimeter scale and Peterman Ice Island centerlines.pdf". The cm-scale centerlines are identified by run ID and a number indicating the time in minutes (with t = 0 min being the time at which water started flowing over the ice block). The naming convention is also associated to the images in "Centimeter scale rivulet images.pdf". The last sheet in the workbook includes a summary of the channel widths measured from every image for each centerline. The 50 sheets with the centerline information have four columns each. The titles of the columns are X, Y, S, and C. X,Y are dimensionless coordinates of the centerline. S is dimensionless streamwise coordinate (location along the centerline). C is dimensionless curvature value. All these values were non-dimensionalized with the channel width. See Fernandez (2018), Zolezzi and Guneralp (2016), and Guneralp and Rhoads (2008) for more details regarding the process of smoothing, standardizing and non-dimensionalization of the centerline coordinates.
keywords:
Meltwater, Meandering, Ice, Supraglacial, Experiments
published:
2025-08-20
Arshad, Muhammad Umer; Archer, David ; Wasonga, Daniel ; Namoi, Nictor; Boe, Arvid ; Rob , Mitchell; Heaton, Emily; Khanna, Madhu; Lee, DoKyoung
(2025)
The compiled datasets include detailed costs for switchgrass production, categorized into establishment, maintenance, and harvesting expenses, along with revenue calculations. Costs were gathered from multiple sources and adjusted for inflation, focusing on farm-gate profitability, excluding fixed costs and transportation. All financial data is provided per hectare. The dataset was used to evaluate the economic performance of forage- and bioenergy-type switchgrass cultivars and their response to nitrogen fertilization across diverse marginal environments in the U.S. Midwest. Data Envelopment Analysis (DEA) and cost-benefit analysis were employed to assess the efficiency and profitability of 23 different cultivar and fertilization rate combinations over five years.
published:
2026-01-08
Dibaeinia, Payam; Sinha, Saurabh
(2026)
CoNSEPT is a tool to predict gene expression in various cis and trans contexts. Inputs to CoNSEPT are enhancer sequence, transcription factor levels in one or many trans conditions, TF motifs (PWMs), and any prior knowledge of TF-TF interactions.
keywords:
software; gene expression
published:
2020-08-18
Althaus, Scott; Berenbaum, May; Jordan, Jenna; Shalmon, Dan
(2020)
These data and code enable replication of the findings and robustness checks in "No buzz for bees: Media coverage of pollinator decline," published in Proceedings of the National Academy of Sciences of the United States of America (2020)". In this paper, we find that although widespread declines in insect biomass and diversity are increasing concern within the scientific community, it remains unclear whether attention to pollinator declines has also increased within information sources serving the general public. Examining patterns of journalistic attention to the pollinator population crisis can also inform efforts to raise awareness about the importance of declines of insect species providing ecosystem services beyond pollination.
We used the Global News Index developed by the Cline Center for Advanced Social Research at the University of Illinois at Urbana-Champaign to track news attention to pollinator topics in nearly 25 million news items published by two American national newspapers and four international wire services over the past four decades. We provide a link to documentation of the Global News Index in the "relationships with articles, code, o. We found vanishingly low levels of attention to pollinator population topics relative to coverage of climate change, which we use as a comparison topic. In the most recent subset of ~10 million stories published from 2007 to 2019, 1.39% (137,086 stories) refer to climate change/global warming, while only 0.02% (1,780) refer to pollinator populations in all contexts and just 0.007% (679) refer to pollinator declines. Substantial increases in news attention were detectable only in U.S. national newspapers. We also find that while climate change stories appear primarily in newspaper “front sections”, pollinator population stories remain largely marginalized in “science” and “back section” reports. At the same time, news reports about pollinator populations increasingly link the issue to climate change, which might ultimately help raise public awareness to effect needed policy changes.
keywords:
News Coverage; Text Analytics; Insects; Pollinator; Cline Center; Cline Center for Advanced Social Research; political; social; political science; Global News Index; Archer; news; mass communication; journalism
published:
2022-06-20
Jiang, Ming; Dubnicek, Ryan; Worthey, Glen; Underwood, Ted; Downie, J. Stephen
(2022)
This is a sentence-level parallel corpus in support of research on OCR quality. The source data comes from: (1) Project Gutenberg for human-proofread "clean" sentences; and, (2) HathiTrust Digital Library for the paired sentences with OCR errors. In total, this corpus contains 167,079 sentence pairs from 189 sampled books in four domains (i.e., agriculture, fiction, social science, world war history) published from 1793 to 1984. There are 36,337 sentences that have two OCR views paired with each clean version. In addition to sentence texts, this corpus also provides the location (i.e., sentence and chapter index) of each sentence in its belonging Gutenberg volume.
keywords:
sentence-level parallel corpus; optical character recognition; OCR errors; Project Gutenberg; HathiTrust Digital Library; digital libraries; digital humanities;
published:
2022-04-29
Wedell, Eleanor; Warnow, Tandy
(2022)
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.
keywords:
Phylogenetic Placement; Phylogenetics; Maximum Likelihood; pplacer; EPA-ng
published:
2025-08-27
Jang, Chunhwa; Namoi, Nictor; Lee, Jung Woo; Becker, Talon; Rooney, William; Lee, DoKyoung
(2025)
Data were collected from agronomy fields in Urbana and Ewing, IL, during the 2022 and 2023 growing seasons. The dataset includes dry biomass yield, nitrogen, phosphorus, and potassium concentrations and removals, and chemical composition elements (cellulose, hemicellulose, lignin, and soluble fractions) for 13 high-biomass sorghum hybrids.
data_sharing.xlsx contains 20 columns and 104 rows. Below is the explanation of all variables in the file:
Year: 2022; 2023
Location: Urbana, IL; Ewing, IL
N rate (kg-N/ha): 0; 112
Hybrid #: H1-H13
Pedigree: Pedigree for 13 hybrids
Dry biomass yield (Mg/ha): Aboveground dry biomass yield
N (g/kg): Nitrogen concentration in plant tissue
P (g/kg): Phosphorus concentration in plant tissue
K (g/kg): Potassium concentration in plant tissue
N (kg/ha): Nitrogen removal by aboveground biomass
P (kg/ha): Phosphorus removal by aboveground biomass
K (kg/ha): Potassium removal by aboveground biomass
Cellulose (g/kg): Cellulose concentration in plant tissue
Hemicellulose (g/kg): Hemicellulose concentration in plant tissue
Lignin (g/kg): Lignin concentration in plant tissue
Soluble (g/kg): Soluble concentration in plant tissue
Cellulose (Mg/ha): Cellulose content in aboveground biomass
Hemicellulose (Mg/ha): Hemicellulose content in aboveground biomass
Lignin (Mg/ha): Lignin content in aboveground biomass
Soluble (Mg/ha): Soluble content in aboveground biomass
keywords:
high-biomass sorghum hybrids; yield potential; environmental adaptability; feedstock quality; nutrient removal; N fertilization
published:
2025-09-26
Arora, Amit; Singh, Vijay
(2025)
In this study, different process schemes were designed and evaluated for biodiesel production from engineered cane lipids with uncertain fatty acid compositions. Four different process schemes were compared under (i) thermal glycerolysis and (ii) enzymatic glycerolysis approaches. These schemes were based on the biodiesel yield and economic indicators such as the net present value (NPV) and the minimum selling price (MSP) of biodiesel. A scheme with polar lipid separation under thermal glycerolysis resulted in the maximum NPV ($96.5 million) and minimum MSP ($1107/ton biodiesel), respectively. Through local sensitivity analysis, it was concluded that the cane lipid percentage is the most significant factor influencing process economics. A conjoint analysis of the lipid procurement price and cane lipid percent suggested that 15% cane lipids with a low lipid procurement price ($0.536/kg) results in a positive NPV. When the cane lipid price is higher (>$0.80/kg), a 20% lipid content should be considered to achieve a positive NPV. At 20% cane lipids, the worst-case and best-case scenarios were evaluated by analyzing the interplay of the three most important parameters, The best-case scenario revealed that the minimum NPV under any process scheme could yield more than $100 million (or MSP: $0.80/L), and the worst-case analysis showed that losses incurred by the plant could be as high as $80 million (MSP: $1.36/L). A Monte Carlo simulation indicated that there is a 70% chance of the plant being profitable (NPV > 0).
keywords:
Conversion;Economics;Feedstock Bioprocessing;Modeling
published:
2025-10-21
Trieu, Anthony; Belaffif, Mohammad B.; Hirannaiah, Pradeepa; Manjunatha, Shilpa; Wood, Rebekah; Bathula, Yokshitha; Billingsley, Rebecca L.; Arpan, Anjali; Sacks, Erik; Clemente, Tom; Moose, Stephen; Reichert, Nancy A.; swaminathan, kankshita
(2025)
Miscanthus, a C4 member of the family Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies Miscanthus x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites.
keywords:
Feedstock Production;Biomass Analytics;Genomics
published:
2023-07-14
Punyasena, Surangi W.; Urban, Michael A.; Adaime, Marc-Elie; Romero, Ingrid; Jaramillo, Carlos
(2023)
This dataset includes a total of 300 images of 45 extant species of Podocarpus (Podocarpaceae) and nine images of fossil specimens of the morphogenus Podocarpidites. The goal of this dataset is to capture the diversity of morphology within the genus and create an image database for training machine learning models.
The images were taken using Airyscan confocal superresolution microscopy at 630x magnification (63x/NA 1.4 oil DIC). The images are in the CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or open microscopy software, such as ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/software/zeiss-zen/czi-image-file-format.html]
Please cite this dataset and listed publications when using these images.
keywords:
optical superresolution microscopy; Zeiss Airyscan; CZI images; conifer; saccate pollen; Podocarpus; Podocarpidites; Smithsonian Tropical Research Institute
published:
2019-05-31
The data are provided to illustrate methods in evaluating systematic transactional data reuse in machine learning. A library account-based recommender system was developed using machine learning processing over transactional data of 383,828 transactions (or check-outs) sourced from a large multi-unit research library. The machine learning process utilized the FP-growth algorithm over the subject metadata associated with physical items that were checked-out together in the library. The purpose of this research is to evaluate the results of systematic transactional data reuse in machine learning. The analysis herein contains a large-scale network visualization of 180,441 subject association rules and corresponding node metrics.
keywords:
evaluating machine learning; network science; FP-growth; WEKA; Gephi; personalization; recommender systems
published:
2020-06-26
Gasparik, Jessica T.; Ye, Qing; Curtis, Jeffrey H.; Presto, Albert A.; Donahue, Neil M.; Sullivan, Ryan C.; West, Matthew; Riemer, Nicole
(2020)
This dataset contains the PartMC-MOSAIC simulations used in the article "Quantifying Errors in the Aerosol Mixing-State Index Based on Limited Particle Sample Size". The 1000 simulations of output data is organized into a series of archived folders, each containing 100 scenarios. Within each scenario directory are 25 NetCDF files, which are the hourly output of a PartMC-MOSAIC simulation containing all information regarding the environment, particle and gas state. This dataset was used to investigate the impact of sample size on determining aerosol mixing state. This data may be useful as a data set for applying different types of estimators.
keywords:
Atmospheric aerosols; single-particle measurements; sampling uncertainty; NetCDF
published:
2022-07-19
Parmar, Dharmeshkumar; Jia, Jin; Shrout, Joshua; Sweedler, Jonathan; Bohn, Paul
(2022)
#### 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]:
(1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones
----------------*File name*----------------------------------------------
Sample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below.
*Example file name "Rep1-Stat-FRD1-mPat-48-FS"*
~ Each unit of information is separated by "-"
~Unit 1 - "Rep1" - Biological replicate ( Rep1, Rep2, and Rep3)
~Unit 2 - "Stat" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant)
~Unit 3 - "FRD1" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain)
~Unit 4 - "mPat" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface)
~Unit 5 - "48" - Sample time point (hours = 48, 72, 96)
~Unit 6 - "FS" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288))
----------------*File structure*------------------------------------------
All MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix.
----------------*End of Information*--------------------------------------
keywords:
mass spectrometry imaging (MSI); biofilm; antibiotic resistance; Pseudomonas aeruginosa; quorum sensing; rhamnolipids
published:
2025-07-09
Kim, Ahyoung; Kim, Chansong; Waltmann, Tommy; Vo, Thi; Kim, Eun Mi; Kim, Junseok; Shao, Yu-Tsun; Michelson, Aaron; Crockett, John R.; Kalutantirige, Falon C.; Yang, Eric; Yao, Lehan; Hwang, Chu-Yun; Zhang, Yugang; Liu, Yu-Shen; An, Hyosung; Gao, Zirui; Kim, Jiyeon; Mandal, Sohini; Muller, David; Fichthorn, Kristen; Glotzer, Sharon; Chen, Qian
(2025)
This dataset contains the raw transmission electron microscopy (TEM) and scanning electron microscopy (SEM) images used to calculate the synthesis yield of patchy nanoparticles (NPs), as described in Supplementary Table 1 of the paper “Patchy Nanoparticles by Atomic “Stencilling” (2025).” All the images were taken at the Materials Research Laboratory, University of Illinois at Urbana-Champaign by Qian Chen group.
1. We have 21 subfolders, each with a name corresponding to one of the 21 patchy NPs listed in Supplementary Table 1 of the paper “Patchy Nanoparticles by Atomic “Stencilling” (2025)."
2. In TEM images, the bright and dark regions indicate the polymer patches and NP cores, respectively.
3. In SEM images, the bright and dark regions indicate the NP cores and polymer patches, respectively.
4. Each subfolder contains a “readme (subfolder name).txt” file with more detailed information about each sample.
keywords:
Patchy nanoparticle; polymer; synthesis; self-assembly
published:
2025-10-10
Field, John L.; Richard, Tom; Smithwick, Erica A. H.; Cai, Hao; Laser, Mark; LeBauer, David; Long, Stephen; Paustian, Keith; Qin, Zhangcai; Sheehan, John; Smith, Pete; Wang, Michael Q.; Lynd, Lee
(2025)
This zip file contains a UNIX-format DayCent model executable, input files, automation code, and associated directory structure necessary to re-produce the DayCent analysis underlying the manuscript. The main script “autodaycent.py” (written for Python 2.7) opens an interactive command line routine that facilitates: Calibrating the DayCent pine growth model; Initializing DayCent for a set of case studies sites; Executing an ensemble of model runs representing case study site reforestation, grassland restoration, or conversion to switchgrass cultivation; and Results analysis & generation of manuscript Fig. 3. Note that the interactive analysis code requires that all input files to be contained in the directory structure as uploaded, without modification. Executable versions of the DayCent model compatible with other operating systems are available upon request.
keywords:
Feedstock Production;Modeling
published:
2018-01-03
Sweet, Andrew; Bush, Sarah; Gustafsson, Daniel; Allen, Julie; DiBlasi, Emily; Skeen, Heather; Weckstein, Jason; Johnson, Kevin
(2018)
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis.
1) Files from the MrBayes analyses:
a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre
b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre
c) a maximum clade credibility tree - mcc_tree_brueelia.tre
The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication.
2) Files related to a BEAST analysis with COI data:
a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml
b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre
c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre
3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre
4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
keywords:
bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
published:
2025-11-24
Dubinkina, Veronika; Bhogale, Shounak; Hsieh, Ping-Hung; Dibaeinia, Payam; Nambiar, Ananthan; Maslov, Sergei; Yoshikuni, Yasuo; Sinha, Saurabh
(2025)
Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae. Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.
keywords:
Conversion;Transcriptomics
published:
2022-11-11
Hsiao, Haw-Wen; Zuo, Jian-Min
(2022)
This dataset is for characterizing chemical short-range-ordering in CrCoNi medium entropy alloys. It has three sub-folders: 1. code, 2. sample WQ, 3. sample HT. The software needed to run the files is Gatan Microscopy Suite® (GMS). Please follow the instruction on this page to install the DM3 GMS: <a href="https://www.gatan.com/installation-instructions#Step1">https://www.gatan.com/installation-instructions#Step1</a>
1. Code folder contains three DM scripts to be installed in Gatan DigitalMicrograph software to analyze scanning electron nanobeam diffraction (SEND) dataset:
Cepstrum.s: need [EF-SEND_sampleWQ_cropped_aligned.dm3] in Sample WQ and the average image from [EF-SEND_sampleWQ_cropped_aligned.dm3]. Same for Sample HT folder.
log_BraggRemoval.s: same as above.
Patterson.s: Need refined diffuse patterns in Sample HT folder.
2. Sample WQ and 3. Sample HT folders both contain the SEND data (.ser) and the binned SEND data (.dm3) as well as our calculated strain maps as the strain measurement reference. The Sample WQ folder additionally has atomic resolution STEM images; the Sample HT folder additionally has three refined diffuse patterns as references for diffraction data processing.
* Only .ser file is needed to perform the strain measurement using imToolBox as listed in the manuscript. .emi file contains the meta data of the microscope, which can be opened together with .ser file using FEI TIA software.
keywords:
Medium entropy alloy; CrCoNi; chemical short-range-ordering; CSRO; TEM
published:
2024-02-21
Hartman, Jordan H; Corush, Joel B; Larson, Eric R; Tiemann, Jeremy S; Willink, Philip; Davis, Mark A
(2024)
Data associated with the manuscript "Niche conservatism and spread explain hybridization and introgression between native and invasive fish" by Jordan H. Hartman, Joel B. Corush, Eric R. Larson, Jeremy S. Tiemann, Philip Willink, and Mark A. Davis. For this project, we combined results of ecological niche models (ENMs) and next-generation restriction site-associated DNA sequencing (RADseq) to test theories of niche conservatism and biotic resistance on the success of invasion, hybridization, and extent of introgression between native Western Banded Killifish and non-native Eastern Banded Killifish. This dataset provides the sampling locations and number of Banded Killifish in each population, accession numbers for RADseq from the National Center for Biotechnology Information Sequence Read Archive and the assignment of each Banded Killifish, the habitat associations of each population from the ENMs, and the occurrence points used to build the ENMs.
keywords:
Banded Killifish; ecological niche model; Fundulus diaphanus; hybrid swarm; invasive species; Laurentian Great Lakes
published:
2024-03-28
Zhang, Yue; Zhao, Helin; Huang, Siyuan; Hossain, Mohhamad Abir; van der Zande, Arend
(2024)
Read me file for the data repository
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This repository has raw data for the publication "Enhancing Carrier Mobility In Monolayer MoS2 Transistors With Process Induced Strain". We arrange the data following the figure in which it first appeared. For all electrical transfer measurement, we provide the up-sweep and down-sweep data, with voltage units in V and conductance unit in S. All Raman modes have unit of cm^-1.
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How to use this dataset
All data in this dataset is stored in binary Numpy array format as .npy file.
To read a .npy file: use the Numpy module of the python language, and use np.load() command.
Example: suppose the filename is example_data.npy. To load it into a python program, open a Jupyter notebook, or in the python program, run:
import numpy as np
data = np.load("example_data.npy")
Then the example file is stored in the data object.
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