cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13020/d6js3f
title: Transcriptome Meta Data Compilation for Chinese hamster tissues and CHO cell lines

description: Transcriptomics is increasingly being used on Chinese hamster ovary (CHO) cells to unveil physiological insights related to their performance during production processes. The rich transcriptome data can be exploited to provide impetus for systems investigation such as modeling the central carbon metabolism or glycosylation pathways, or even building genome-scale models. To harness the power of transcriptome assays, we assembled and annotated a set of RNA-Seq data from multiple CHO cell lines and Chinese hamster tissues, and constructed a DNA microarray. These tools were used to measure the transcript expression of tissues (liver, brain, ovary), 3 parental cell lines (DG44, DXB11, CHO-K1) and 16 recombinant cell lines. Transcript expression levels for tissues and cell lines have been compiled as an excel spreadsheet to allow for a rapid survey of transcript levels of different genes.
description: The data is organized in the speadsheet file named Transcriptome Meta Data.xlsx and has been color coded for easy visualization. Gene information contains gene description, symbol and orthologous mouse ENSEMBL identifiers. Columns in pink pertaining to 26 different functional pathways can be sorted for the value 1 to quickly assess expression of genes in that pathway. This is followed by RNA sequencing and microarray expression data for tissues and cell lines. The minimum, mean and maximum expression values of each gene for all the cell lines in both microarray and sequencing datasets have also been included.
DOI: 10.13020/d6pc72
title: Duluth 1-Meter Land Cover Classification (Urban Focused)

description: A high-resolution (1-meter) land cover classification raster dataset was completed for three different geographic areas in Minnesota: Duluth, Rochester, and the seven-county Twin Cities Metropolitan area. This classification was created using high-resolution multispectral National Agriculture Imagery Program (NAIP) leaf-on imagery (2015), spring leaf-off imagery (2011- 2014), Multispectral derived indices, LiDAR data, LiDAR derived products, and other thematic ancillary data including the updated National Wetlands Inventory, LiDAR building footprints, airport, OpenStreetMap roads and railroads centerlines. These data sets were integrated using an Object-Based Image Analysis (OBIA) approach to classify 12 land cover classes: Deciduous Tree Canopy, Coniferous Tree Canopy, Buildings, Bare Soil, other Paved surface, Extraction, Row Crop, Grass/Shrub, Lakes, Rivers, Emergent Wetland, Forest and Shrub Wetland. 

We mapped the 12 classes by using an OBIA approach through the creation of customized rule sets for each area. We used the Cognition Network Language (CNL) within the software eCognition Developer to develop the customized rule sets. The eCognition Server was used to execute a batch and parallel processing which greatly reduced the amount of time to produce the classification. The classification results were evaluated for each area using independent stratified randomly generated points. Accuracy assessment estimators included overall accuracies, producers accuracy, users accuracy, and kappa coefficient. The combination of spectral data and LiDAR through an OBIA method helped to improve the overall accuracy results providing more aesthetically pleasing maps of land cover classes with highly accurate results.
DOI: 10.13020/01wt-jg66
title: Combined UMN-MPCA 2014-2017 lake data on Secchi depth, CDOM, Chlorophyll and total suspended solids

description: This file contains approximately 1460 records on four water quality variables measured on near-surface water samples of lakes in Minnesota (primarily) and also in Wisconsin and Michigan collected by our research group from 2014 to 2017 and similar data collected by the Minnesota Pollution Control Agency in its annual lake water quality assessment program from 2015 to 2017. The variables are Secchi depth (SD), colored dissolved organic matter (CDOM) measured as the Napierian light absorption coefficient at 440 nm, chlorophyll-a, and total suspended solids concentrations. The database was used for a published paper to analyze the effects of CDOM on SD and show that high CDOM levels limit light penetration and thus SD in colored lakes.
description: The data are in an Excel spreadsheet with rows representing data for a given lake collected on a specific date. Columns provide lake name or unique lake identifier, sampling date, aquatic ecoregion for the lake, results for CDOM (a440), chlorophyll, Secchi depth, and total suspended solids concentrations, and logarithms of the values for the four water quality variables.
DOI: 10.13020/d6f115
title: Supporting data for Polymeric medical sutures: An exploration of polymers and green chemistry

description: These files contain data along with associated output from instrumentation supporting all results reported in Knutson, C. M.; Schneiderman, D. K.; Yu, M.; Javner, C. H.; Distefano, M. D.; Wissinger, J. E. Polymeric medical sutures: An exploration of polymers and green chemistry.  J. Chem. Educ. 2017, 94, 1761–1765. In Knutson, et. al. it was found that with new K–12 national science standards emerging, there is an increased need for experiments that integrate engineering into the context of society. Here we describe a chemistry experiment that combines science and engineering principles while introducing basic polymer and green chemistry concepts. Using medical sutures as a platform for investigating polymers, students explore the physical and mechanical properties of threads drawn from poly(ε-caprolactone) samples of different molecular masses and actual purchased absorbable and nonabsorbable medical sutures. An inquiry-based part of the experiment tasks students with designing their own experiment to probe the potential of melt blending poly(ε-caprolactone) with commercially available polylactide products in order to modify the properties of the “sutures” drawn. Through these lessons students gain an appreciation for the importance of plastics in our society and how scientists are working to develop more sustainable alternatives. Overall, this laboratory experiment provides a feasible, versatile, sophisticated laboratory experience that engages students in a relatable topic and meets many of the Next Generation Science Standards.
description: Full description in Readme file.
DOI: 10.13020/p2ze-1y93
title: Gonzalez 2021 tagged CO model archive 

description: This archive contains model code, input files, and simulation results for atmospheric carbon monoxide (CO) posted in association with the referenced paper.
description: Please see README file for a detailed description of the data.
DOI: 10.13020/0dpe-ec23
title: Data from: Auditory enhancement under forward masking in normal-hearing and hearing-impaired listeners

description: A target within a spectrally notched masker can be enhanced by a preceding copy of the masker. Enhancement can also increase the effectiveness of the target as a forward masker. Enhancement has been reported in hearing-impaired listeners under simultaneous but not forward masking. However, previous studies of enhancement under forward masking did not fully assess the potential effect of differences in sensation level or spectral resolution between the normal-hearing and hearing-impaired listeners. This study measured enhancement via forward masking in hearing-impaired and age-matched normal-hearing listeners with different spectral notches in the masker, to account for potential differences in frequency selectivity, and with levels equated by adding a background masking noise to equate both sensation level and sound pressure level or by reducing the sound pressure level of the stimuli to equate sensation level.
description: Two files are included: ReadMe.txt (general layout of the data in the Excel Workbook) and DRUM_HIENH.xls (Excel document with 40 sheets that contain individual data for each participant and condition). The archival copy of the DRUM_HIENH file is a zip folder containing .csv, .txt., and .html files of the relevant data, formulas, and formatting in the excel document.
DOI: 10.13020/d64m64
title: Sampling of St. Louis Estuary and Lake Superior surface water after the Superior Refinery Fire in 2018

description: On April 26, 2018, there were multiple explosions and a fire at the Husky Refinery in Superior, WI. Safety measures worked well, with no loss of life and few injuries; however, significant smoke and soot emissions from the fire itself did impact the local airways and may also have impacted local watersheds, the Twin Ports harbor and far western Lake Superior.  Thus, we measured water quality in the St. Louis estuary and far-western Lake Superior in an attempt to determine if residual petroleum products and/or black carbon (soot) associated with the refinery fire entered Lake Superior or the Saint Louis estuary in measurable amounts. There were indications of very localized impact in total organic carbon and dissolved organic carbon data and aerial deposition of soot in some black carbon samples from surface waters.  We did not find measurable petroleum hydrocarbon in our samples.
description: File List:
   A. Filename: post-refinery report_082918.pdf       
      Short description:  Final project report      
"SeaGrant Funding Summary: Rapid Response to the Superior Refinery Fire"
        
   B. Filename:    post-refineryTOC&DOC_archive.csv    
      Short description:   Total organic carbon (TOC) and dissolved organic carbon (DOC) data from Shimadzu TOC-Vcsh Analyzer, 
samples from 1 to 3 days after refinery fire in Superior, WI (April 26, 2018)     

        
   C. Filename:      post-refineryPOC_archive.csv  
      Short description: Particulate organic carbon (POC) data from Finnegan Delta PLus XP IRMS with Conflo interface
coupled to a Costech ECS 4010 EA, samples from 1 to 3 days after refinery fire in Superior, WI (April 26, 2018)
	
   D. Filename: post-refinery_BCSAMPLES2_archive.csv
      Short description: Black carbon (BC) data from Finnegan Delta PLus XP IRMS with Conflo interface
coupled to a Costech ECS 4010 EA, samples from 1 to 3 days after refinery fire in Superior, WI (April 26, 2018).
BC isolated following Zigah et al 2012.

  E. Filename: Collated data_refinery sampling_archive.csv
	Short description: TOC, DOC, POC, BC, and sampling location data collated into one spreadsheet.


2. Relationship between files:    Files A and E are summary files; A is a report while E is a spreadsheet of data. 
Files B, C, and D are the data work-up, including blanks and calibrations, for the data summarized in A and E.
DOI: 10.13020/d6md51
title: Phylogenetic character matrix for Mortoniella (Trichoptera: Glossomatidae)

description: Phylogenetic character matrix for the caddisfly (Trichoptera) genus Mortoniella.
description: Text file. Convert to .nex file format and open in PAUP (Phylogenetic Analysis Using PAUP), Mesquite, or other phylogenetic analysis application.
DOI: 10.13020/f0cn-mm13
title:  Data for: Implications of seasonal and annual heat accumulation for population dynamics of an invasive defoliator
DOI: 10.13020/bd01-3547
title: R code and data for "Comparing multiple survey and recruitment-mortality models to assess growth rates and population projections"

description: This collection of files provides data and R code supporting the publication "Comparing survey and multiple recruitment-mortality models to assess growth rates and population projections" in Ecology and Evolution. We provide all necessary data not included in the manuscript to reproduce the analysis of growth rates and population projections of moose in northeastern Minnesota.
description: This collection of files provides data and R code supporting the publication "Comparing survey and multiple recruitment-mortality models to assess growth rates and population projections" in Ecology and Evolution.  We provide all necessary data not included in the manuscript to reproduce the analysis of growth rates and population projections of moose in northeastern Minnesota.
description: See ReadMe text file for a comprehensive description of all uploaded data files.
DOI: 10.13020/v959-dr15
title: Global isoprene measurements from CrIS

description: This archive contains global measurements of atmospheric isoprene columns from the CrIS satellite sensor. Isoprene columns were derived using an artificial neural network approach as described in the citation below. Data are archived in association with that manuscript.
description: Please see README file and citation for a description of the data.
DOI: 10.13020/d6f59k
title: Supporting Data Analysis for "An Integrated Analysis of Phenotypic Selection on Insect Body Size and Development Time"

description: This technical report (TR) gives details of the data analysis backing up a paper having the same authors as this TR and having the title that is quoted in the title of this TR.  It uses the R package knitr to process its source file (Rnw file) containing LaTex and R, so that all R that appears in this document is not cut-and-pasted but actually run and actually produces the results that it appears to produce.  This document reproduces all tables and figures from the paper and hence the entire data analysis reported in the paper.
description: The data for the analysis are in the R object hornworm in the R package aster2, which is a CRAN package. This dataset was created from Msexta.Aster.csv, originally collected by Kingsolver, Diamond, Seiter, & Higgins (2012). Metadata for the hornworm and Msexta.Aster.csv datafiles can be found in documentation for the package; help(hornworm, package="aster2��). Instructions for compiling the source file to produce the technical report can be found in the README.txt file.  An appendix of this technical report shows how this R object of class "asterdata" was created from the raw data, a comma separated values (CSV) file. In the aster2 hornworm data: The "id" variable gives the identification number of the Manduca sexta; this variable is unimportant in the analysis. The ���resp�� variable is short for response vector and it contains all of the realized response variables for every node in the aster graph for every individual. We obtain estimates of parameters using "resp" and compare different aster models using "resp".
DOI: 10.13020/eqra-hp74
title: Materials to re-create results of Austin et al Zooplankton Migration paper 

description: In a recent manuscript, zooplankton are shown to change their migratory behavior due to a change in stratification regime. This submission includes data and MATLAB scripts sufficient to recreate the four figures in the paper.
description: There are four data files: Two CTD (Conductivity-temperature-depth) profiles; one file containing backscatter data from an acoustic Doppler current profiler; and one containing temperature data from nine precision thermistors. There are also four MATLAB scripts which call this data to create the figures in the referenced manuscript.
DOI: 10.13020/d6bs3k
title: Full simulation data and worked examples from Specht et al. Conditional Occupancy Manuscript

description: Occupancy models are widely used to describe the distribution of rare and cryptic species— those that occur on only a portion of the landscape and cannot be detected reliably during a single survey. However, occupancy models often provide inaccurate estimates of occupancy (ψ ̂) and detection probabilities (p ̂) under these circumstances. We developed a new "conditional" occupancy design that more accurately estimates occupancy for rare species. Here we provide the full simulation dataset used to compare estimation properties of standard, removal and conditional designs.  Data were simulated in R and analyzed using MCMC methods in package R2jags. See Specht et al. (in review) for description of methods. Please cite Specht et al. in further use of this data set.
description: To accompany publication of the conditional design for occupancy analysis, we provide the full simulation dataset used to compare the performance of standard, removal and conditional designs in common occupancy analysis programs: R package unmarked, Program MARK and PRESENCE.  
Specht_etal_AS3_CondOcc_SimulationCode.R is an R script that was used to generate the simulation data in AS4_Specht_etal_SimulationData.csv. AS4_Specht_etal_SimDataSet_metadata.csv contains variable labels for columns in AS4_Specht_etal_SimulationData.csv, including additional calculated variables not generated from the simulations. PRESENCE_files_for_Specht_etal.zip, ProgramMARK_files_for_Specht_etal.zip and Unmarked_example_for_Specht_etal.R provide files to work through examples of conditional, standard and removal occupancy designs for the same case in Program MARK, Program PRESENCE and R package unmarked, respectively. These files allow users to compare estimation by each method in a case where true occupancy probability is 0.2 and true detection probability is 0.5, and provide examples of formatted data input files. See Readme_Specht_etal.txt for more details.
DOI: 10.13020/yrva-zr31
title: Cryopreservation of Pancreatic Islets Experimental Data Repository 2022

description: These are the raw data used to generate each figure for our paper under review in Nature Medicine
description: These are the raw data used to generate each figure for our paper under review in Nature Medicine
DOI: 10.13020/d69x0h
title: Maize bisulfite coupled sequence capture (SeqCap-Epi-v2) probe design

description: Table detailing the design and genomic coordinates (v2 and v4) for the maize bisulfite coupled sequence capture (SeqCap-Epi-v2) probe design for profiling of the maize methylome. Released to accompany our publication on DNA methylation changes induced by tissue culture (Han et al 2017) as a supporting supplemental methods file.
description: Maize bisulfite coupled sequence capture (SeqCap-Epi-v2) probe design. Contained in the dataset are descriptions of the "target” regions, which are the bait regions corresponding to the sequence capture probes. Also contained are the coordinates of the target region in the B73 v4 maize genome build (Jiao et al. 2017); the strand orientation of the target; the original “target” probe capture region for the maize v2 genome build. This submission also describes the “specific” regions of interest within the captured “target” bait regions; the coordinates of the specific region in the B73 v4 maize genome build (Jiao et al. 2017); and the original “specific” region of interest for the maize v2 genome build.
DOI: 10.13020/r6af-pj55
title: Data from: Individual Magnetoencephalography Response Profiles to Short-Duration L-Dopa in Parkinson’s Disease

description: Clinical responses to dopamine replacement therapy for individuals with Parkinson’s disease (PD) are often difficult to predict. We characterized changes in MDS-UPDRS motor factor scores resulting from a short-duration L-Dopa response (SDR), and investigated how the inter-subject clinical differences could be predicted from motor cortical magnetoencephalography (MEG). MDS-UPDRS motor factor scores and resting-state MEG recordings were collected during SDR from twenty individuals with a PD diagnosis. We used a novel subject-specific strategy based on linear support vector machines to quantify motor cortical oscillatory frequency profiles that best predicted medication state. Motor cortical profiles differed substantially across individuals and showed consistency across multiple data folds. There was a linear relationship between classification accuracy and SDR of lower limb bradykinesia, although this relationship did not persist after multiple comparison correction, suggesting that combinations of spectral power features alone are insufficient to predict clinical state. Factor score analysis of therapeutic response and novel subject-specific machine learning approaches based on subject-specific neuroimaging provide tools to predict outcomes of therapies for PD.
description: The .csv files contain all the motor factor scores, cross-validated feature weights, and cross-validated accuracy for figures 1, 2A, and 2B from the publication entitled "Individual Magnetoencephalography Response Profiles to Short- Duration L-Dopa in Parkinson's Disease" (Peña et al 2021 Frontiers in Human Neuroscience, DOI: 10.3389/fnhum.2021.640591).
DOI: 10.13020/sm2d-fk79
title: Data and R code supporting "A hidden Markov model for ecosystems exhibiting alternative stable states" 

description: This repository contains the data and R code used to conduct the analyses in the article "Using hidden Markov models to inform conservation and management strategies in ecosystems exhibiting alternative stable states" in Journal of Applied Ecology.
description: Detailed descriptions for each of the files can be found in README.txt. We recommend using RStudio to run the code. Once all files are downloaded to a single directory, double-click on 'HMM.Rproj' to open up a new RStudio window, and the working directory will automatically be set to the folder where the project files are located.
DOI: 10.13020/d6xs3v
title: Greater Blue Earth River Basin sediment budget shapefiles

description: These are the extents of landforms used in the construction of suspended sediment budgets for the LeSueur, Blue Earth and Watonwan Rivers. The extents of bluffs, ravines, lakes, and subwatersheds in 2010 are included, as well as riverbanks from 2008 and 1938.
DOI: 10.13020/d6nh40
title: Leaf-level trade-offs between drought avoidance and desiccation recovery drive elevation stratification in arid oaks: site environmental data, individual tree stem and leaf physiological data, and analyses

description: This dataset and RStudio project includes all processed data, most raw data, and R scripts needed for analysis and figure construction included in the manuscript Fallon and J. Cavender-Bares 2018 (Fallon B. and J. Cavender-Bares. 2018. Leaf-level trade-offs between drought avoidance and desiccation recovery drive elevation stratification in arid oaks. Ecosphere. in press). We investigated whether oak species in the Chiricahua Mountains were 1) elevationally stratified, 2) whether that stratification was correlated with temperature minima, maxima, and water availability, 3) if physiological tolerances to freezing or drought stress correlated with elevation ranges, and 4) if traits important to local (elevation) distributions were correlated with climatic values of the wider species ranges. Data were collected at field sites from wild, adult trees in the Chiricahua Mountains, Arizona, USA from 2014-2015.This research was done with funding to B. Fallon from the Southwestern Research Station (SWRS, American Museum of Natural History), the University of Minnesota Charles J. Brand, Carolyn Crosby, and Dayton Bell Fellowships, and the Department of Plant and Microbial Biology. Additional funding was provided by NSF Award 1146380 (J. Cavender-Bares PI). We performed all data collection under permit with the Coronado National Forest, Douglas Ranger District, managed by the United States Forest Service (USDA).
description: The zip file contains folders, scripts, and data necessary to reproduce the analysis and figures. Once unzipped, all scripts and data can be opened and run in RStudio with the "RStudio Project Leaf-level tradeoffs oaks AZ.Rproj" file.  All folders with data (folders proceeded by “input_”, the “gen_data” folder, and the “hipp_etal” folder) contain separate readme files that document the individual files in that folder. See the primary README.txt for more information.