cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13020/qxtc-sc36
title: Data to accompany evaluation of the first U.S. staple foods ordinance: Impact on nutritional quality of food retailer offerings, customer purchases and home food environments

description: Many lower-income and racially diverse communities in the U.S. have limited access to
healthy foods, with few supermarkets and many small convenience stores, which tend
to stock limited quantities and varieties of healthy foods. To address food access, in
2015 the Minneapolis Staple Foods Ordinance became the first policy requiring food
stores to stock minimum quantities and varieties of 10 categories of healthy
foods/beverages, including fruits, vegetables, whole grains and other staples, through
licensing. This study examined whether: (a) stores complied, (b) overall healthfulness
of store environments improved, (c) healthy customer purchases increased, and (d)
healthfulness of home food environments improved among frequent small store
shoppers. Data for this natural (or quasi) experiment were collected at four times: pre-policy
(2014), implementation only (no enforcement, 2015), enforcement initiation (2016) and
continued monitoring (2017). In-person store assessments were conducted to evaluate
food availability, price, quality, marketing and placement in randomly sampled food
retailers in Minneapolis (n=84) and compared to those in a nearby control city, St. Paul,
Minnesota (n=71). Stores were excluded that were: supermarkets, authorized through
WIC (Special Supplemental Nutrition Program for Women, Infants, and Children), and
specialty stores (e.g., spice shops). Customer intercept interviews were conducted
with 3,039 customers exiting stores. Home visits, including administration of home food
inventories, were conducted with a sub-sample of frequent shoppers (n=88). 
Overall, findings indicated significant improvements in healthy food offerings by
retailers over time in both Minneapolis and St. Paul, with no significant differences in
change between the two cities. Compliance was low; in 2017 only 10% of Minneapolis
retailers in the sample were fully compliant, and 51% of participating Minneapolis
retailers met at least 8 of the 10 required standards. Few changes were observed in
the healthfulness of customer purchases or the healthfulness of home food
environments among frequent shoppers, and changes were not different between
cities. This study is the first evaluation of a local staple foods ordinance in the U.S. and reflects
the challenges and time required for implementing such policies.
description: The same data are provided in both .sas7bdat and .csv formats.
DOI: 10.13020/x0qn-y082
title: Trash-ICRA19: A bounding box labeled dataset of underwater trash

description: This data was sourced from the J-EDI dataset of marine debris. The videos that comprise that dataset vary greatly in quality, depth, objects in scenes, and the cameras used. They contain images of many different types of marine debris, captured from real-world environments, providing a variety of objects in different states of decay, occlusion, and overgrowth. Additionally, the clarity of the water and quality of the light vary significantly from video to video. These videos were processed to extract 5,700 images, which comprise this dataset, all labeled with bounding boxes on instances of trash, biological objects such as plants and animals, and ROVs. The eventual goal is to develop efficient and accurate trash detection methods suitable for onboard robot deployment. It is our hope that the release of this dataset will facilitate further research on this challenging problem, bringing the marine robotics community closer to a solution for the urgent problem of autonomous trash detection and removal.
description: This dataset is available for download as a .zip file named Trash_ICRA19.zip. Within the compressed folder are both the dataset  and configurations for testing the datset with deep learning algorithms. There is a README in the top directory, and in most lower directories, explaining the files and directories in its directory.
DOI: 10.13020/0p2p-j920
title: Code, data, and metadata for the manuscript 'Territoriality drives preemptive habitat selection in recovering wolves: implications for carnivore conservation'

description: 1.	According to the ideal-free distribution (IFD), individuals within a population are free to select habitats that maximize their chances of success. Assuming knowledge of habitat quality, the IFD predicts that average fitness will be approximately equal among individuals and between habitats, while density varies (density-dependent habitat selection). Populations are often assumed to follow an IFD, although this assumption is rarely tested with empirical data, and may be incorrect when territoriality indicates habitat selection tactics that deviate from the IFD (e.g. ideal despotic distribution or ideal preemptive distribution).
2.	When territoriality influences habitat selection, species’ density will not directly reflect components of fitness such as reproductive success or survival. In such cases, assuming an IFD can lead to false conclusions about habitat quality. We tested theoretical models of density-dependent habitat selection on a species known to exhibit territorial behavior in order to determine whether commonly applied habitat models are appropriate under these circumstances.  
3.	We combined long-term radio telemetry and census data from gray wolves (Canis lupus) in the Upper Peninsula of Michigan, USA to relate spatiotemporal variability in wolf density to underlying classifications of habitat within a hierarchical state-space modeling framework. We then iteratively applied isodar analysis to evaluate which distribution of habitat selection best described this recolonizing wolf population. 
4.	The wolf population in our study expanded by >1000% during our study (~ 50 to > 600 individuals), and density-dependent habitat selection was most consistent with the ideal preemptive distribution, as opposed to the ideal-free or ideal-despotic alternatives.
5.	Population density of terrestrial carnivores may not be positively correlated with the fitness value of their habitats, and density-dependent habitat selection patterns may help to explain complex predator-prey dynamics and cascading indirect effects. Source-sink population dynamics appear likely when species exhibit rapid growth and occupy interspersed habitats of contrasting quality. These conditions are likely and have implications for large carnivores in many systems, such as areas in North America and Europe where large predator species are currently recolonizing their former ranges.
DOI: 10.13020/mkez-rd57
title: CT radiomic features for canine primary lung tumors

description: Quantitative analysis of computed tomography (CT) radiomic features is an indirect measure of tumor heterogeneity, which has been associated with prognosis in human lung carcinoma. Canine lung tumors share similar features to human lung tumors and may serve as a model in which to investigate the utility of radiomic features in differentiating tumor type and prognostication. The purpose of this study was to correlate first-order radiomic features from canine primary lung tumors to histopathologic characteristics and outcome. Sixty-seven tumors from 65 dogs were evaluated in this study.
description: Datasets used for statistical analyses from the 65 dogs included in the study are available for review. Data include clinical data, CT review, histopathologic review, and first order radiomic features extracted from postcontrast thoracic CT images.
DOI: 10.13020/z341-jg60
title: Supporting data for "4-Carboalkoxylated Polyvalerolactones from Malic Acid: Tough and Degradable Polyesters"

description: Eight 4-carboalkoxyvalerolactones (CRVLs), varying in the composition of their alkyl (R) side chains, were synthesized from malic acid and subjected to ring-opening transesterification polymerization (ROTEP) using diphenyl phosphate [DPP, (PhO)2PO2H] as a catalyst. Each CRVL produced a semicrystalline poly(4-carboalkoxyvalerolactone) (PCRVL), and the nature of the R group impacted the thermal transitions of these polyesters. Bulk polymerizations at 70 °C allowed for preparation of high molar mass samples that contained small amounts of branching, as evidenced by 1H NMR spectroscopy, MALDI spectrometry, size-exclusion chromatography, and eliminative degradation. Tensile testing of these lightly branched, high molar mass samples revealed that these polyesters are tough (tensile toughness values up to 88 ± 33 MJ•m–3) and have Young’s moduli (E) up to 186 ± 13 MPa. The acid- and base-catalyzed hydrolytic degradation of the PCRVLs was quantitatively monitored using total organic carbon analysis, and effect of the alkyl chain length on PCRVL hydrolysis rate was determined. Finally, the methyl ester variant of these malic acid-derived thermoplastics is known to be chemically recyclable.
description: Each type of data is collected in a single master folder (e.g., NMR spectra, SEC chromatograms, etc.) and then segregated into separate folders.
DOI: 10.13020/xpa3-w249
title: Supporting Information for Ligand effects on Decarbonylation of Palladium-acyl Complexes

description: These files contain primary data along with associated output from instrumentation supporting all results reported in "Ligand effects on Decarbonylation of Palladium-acyl Complexes". In this work we found: The influences of perturbations of supporting phosphine ligands on the dehydrative decarbonylation of (Ln)Pd(II)(Cl)-hydrocinnamoyl com-plexes (L = PtBu3, n = 1; L = PPh3, n = 2; L = dppe, n = 1) to yield styrene were studied through combined experiment and theory. Abstraction of chloride from the complexes by silver and zinc salts, as well as sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate, enhanced the efficiency of styrene formation, according to the trend in L: PtBu3 > dppe > PPh3. DFT calculations corroborated the experimental findings and provided insights into the ligand influences on reaction step barriers and transition state structures. Key findings include: a stable intermediate forms after chloride abstraction, from which -hydride elimination is rate-determining, the low coordination number for the PtBu3 case lowers reaction barriers for all steps, and the trans disposition of two ligands for L = PPh3 contributes to low efficiency for styrene production in that case.
description: Each form of data (e.g. NMR, crystallography, etc.) is stored within a single folder, in which they are further sorted out into specific folders (e.g. characterization of complexes, additive reactions, etc.). Computational work is uploaded and sorted within a separate master folder.
DOI: 10.13020/c66z-2z26
title: Electronic structure data for ³A´ and ³A´´ N₂O

description: This dataset constitutes the electronic structure data that was fitted to obtain global reactive potential energy surfaces (PESs) for Born-Oppenheimer collisions of oxygen atoms with nitrogen molecules. In particular it contains data for the lowest-energy ³Α´ and ³A´´ PESs for the high-energy reaction N₂(X ¹Σ) + O(³P) → NO(X ²Π) + N(⁴S); these potential energy surfaces can serve to generate forces for dynamics calculations. The data was obtained by multireference configuration interaction (MRCI) calculations that were improved by a dynamically scaled external correlation (DSEC) term. The MRCI calculations are based on wave functions obtained from state-averaged complete active space self-consistent-field calculations for 2280 geometries for the three lowest ³A´´  states and for 2298 geometries for the three lowest ³A´ states. The lowest-energy ³A´ and ³A´´  state at each of these geometries was then improved by applying the DSEC method to all MRCI points.
DOI: 10.13020/0s9b-p605
title: Fast neutron mutagenesis in soybean creates frameshift mutations

description: The mutagenic effects of ionizing radiation have been used for decades to create novel variants in experimental populations. Fast neutron (FN) bombardment as a mutagen has been especially widespread in plants, with extensive reports describing the induction of large structural variants, i.e., deletions, insertions, inversions, and translocations. However, the full spectrum of FN-induced mutations is poorly understood. We contrast small insertions and deletions (indels) observed in 27 soybean lines subject to FN irradiation with the standing indels identified in 107 diverse soybean lines. We use the same populations to contrast the nature and context (bases flanking a nucleotide change) of single nucleotide variants. The rate of accumulation of new single nucleotide changes in FN lines is marginally higher than expected based on spontaneous mutation. In both FN treated lines and in standing variation, C→T transitions and the corresponding reverse complement G→A transitions are the most abundant and occur most frequently in a CpG local context. These data indicate that most SNPs identified in FN lines are likely derived from spontaneous de novo processes that occurred in subsequent generations following mutagenesis, rather than from the FN irradiation mutagen. However, small indels in FN lines differ from standing variants. Short insertions, from 1 – 6 base pairs, are less abundant than in standing variation, and short deletions are more abundant and more prone to induce frameshift mutations that should disrupt the structure and function of encoded proteins. These findings indicate that FN irradiation generates numerous small indels in the genome, increasing the abundance of loss of function mutations that will impact single genes.
description: Supplemental data from "Wyant SR, Rodriguez MF, Carter CK, Parrott WA, Jackson SA, Stupar RM, Morrell PL (in preparation) The context of genetic variants in standing variation and under fast neutron mutagenesis."
DOI: 10.13020/d6s59p
title: Supplementary Data for Modeling and Conservation of Wildlife Populations in Managed Landscapes: A Trade-Off Between Effort and Results, Ph.D. Dissertation

description: The data included here are supplemental R codes associated with the dissertation "Modeling and Conservation of Wildlife Populations in Managed Landscapes: A Trade-Off Between Effort and Results" by Sergey S. Berg. The dissertation explores the trade-off between effort and the validity or impact of results in a variety of ecological systems. The data are being released with the publication of the dissertation.
description: The two files contain excerpts of codes written in Program R (Version 3.1.1) to determine the accuracy and precision of statistical population reconstruction (Chapter 4) and to explore the effectiveness of localized management on the spread of chronic wasting disease (Chapter 5). The files can be opened by any text editors.  To run the codes, R environment is required.
DOI: 10.13020/cp4r-0v95
title: SNP Genotyping Data for the Barley Population in "Registration of the S2MET Barley Mapping Population for Multi-Environment Genomewide Selection"

description: Two barley populations were genotyped for use in studies of genomewide selection: a training population of 183 individuals and a selection candidate population of 1200 individuals.
description: 1383 (1200 + 183) barley individuals were genotyped using genotyping-by-sequencing (GBS). 100 - 150 bp single-end reads were generated from the USDA-ARS Small Grains Genotyping Lab in Fargo, ND. SNPs were called using a custom pipeline (https://github.com/neyhartj/GBarleyS) and were filtered for mapping quality, genotype quality, and read depth (see README). Markers and entries were further processed and filtered on minor allele frequency and missingness using the relevant R script (see README). Missing marker genotypes were imputed using 3 different methods using the relevant R script (see README). Both the unimputed ("discrete") and imputed ("imputed") marker genotypes are available in this repository.
DOI: 10.13020/d6w990
title: Supporting data for The Fate of Deleterious Variants in a Barley Genomic Prediction Population

description: Targeted identification and purging of segregating deleterious genetic variants has been proposed as a novel approach to plant breeding. This approach is motivated in part by the observation that demographic events and strong selection associated with cultivated species pose a “cost of domestication.” This includes an increase in the proportion of genetic variants at phylogenetically-constrained sites where a mutation is likely to reduce fitness. Recent advances in DNA resequencing technology and sequence constraint-based approaches to predict the functional impact of a mutation now permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley 6-row spring breeding lines, we identify 3,855 dSNPs among 497,754 total SNPs. The dSNPs are more frequent in portions of the genome with a higher recombination rate, as measured by cM/Mb, than in pericentromeric regions with lower recombination rate and gene density. Using 5,215 progeny from a genomic prediction experiment, we examine the fate of dSNPs over three breeding cycles. Average derived allele frequency is lower for dSNPs than any other class of variants. Adjusting for frequency, derived alleles at dSNPs reduce in frequency or are lost more frequently than other classes of SNPs. Using a linear mixed model applied to 677 lines phenotyped at 5 year-locations, we find that a genomic region with the strongest association with a fungal disease resistance trait that was selected for in the population also negatively impacts yield. Finally, the highest yielding lines in the experiment, as chosen by standard genomic prediction approaches, carry fewer homozygous dSNPs than randomly selected lines.
DOI: 10.13020/fxwc-np62
title: Perceptions of COVID-19 and Health Survey in the United States, Cross-sectional study April 2020

description: Cross-sectional anonymous online survey among individuals with and without  cancer in the United States during the initial phase of the
COVID-19 pandemic (April 3, 2020 – April 11, 2020). NOTE: To protect the identity of participants, the variables dem_1, dem_3, and dem_17 - which correspond to exact age, transgender status, and state of residence - have been removed from this public data set. Please contact the principal investigator if you require the full data set with these variables included for your research.
DOI: 10.13020/776n-tf21
title: Electronic structure data of singlet N4

description: Calculated electronic structure energies by CASPT2/maug-cc-pVTZ and CCSD(T)/maug-cc-pVTZ for 21406 geometry points of the singlet N₄ system. These points can be used to fit the global potential energy surface of the ground state of singlet N₄.
DOI: 10.13020/wtbm-2258
title: Model file for Ishikawa et al. "Automatic Detection of Occulted Hard X-ray Flares Using Deep-Learning Methods"

description: Deep-learning model for occulted hard X-ray flare detection was published in association with the publication Ishikawa et al. "Automatic Detection of Occulted Hard X-ray Flares Using Deep-Learning Methods" in Sol. Phys. (2021). We checked the model file with the Google Colaboratory environment (Python 3.6.9 and Tensorflow 2.4.0).
description: The file named "model_occulted_flare_classifier.h5" is a Keras model file to detect occulated hard X-ray flares by RHESSI spectrogram data described in Ishikawa et al. 2021. The model file was created with Python 3.6.8, Tensorflow 1.14.0 and Keras 2.2.4.
DOI: 10.13020/gpac-zb41
title:  Supporting Data for "Effects of Electrolytes on Thermodynamics and Structure of Oligo(ethylene oxide)/Salt Solutions and Liquid–Liquid Equilibria of a Squalane/Tetraethylene Glycol Dimethyl Ether Blend" 

description: Data including input/output and restart files for all the systems, analysis codes (python, fortran, cpp), and figures in the paper "Effects of Electrolytes on Thermodynamics and Structure of Oligo(ethylene oxide)/Salt Solutions and Liquid–Liquid Equilibria of a Squalane/Tetraethylene Glycol Dimethyl Ether Blend". Sample movie files of the production trajectory are provided.
description: The data consists of four folders (compressed as zips). A. Filename: MCCCS‒MN (Monte Carlo for Complex Chemical Systems‒Minnesota) software, that is under constant development in the Siepmann Group. MCCCS‒MN allows for the simulation of multi-component molecular systems in the canonical, isobaric-isothermal, grand-canonical, semi-grand, and Gibbs ensembles. It uses the configurational-bias Monte Carlo method to efficiently sample phase space for linear, branched and cyclic chain molecules, the adiabatic nuclear and electronic sampling Monte Carlo method to treat many-body polarization effects, and the aggregation-volume-bias Monte Carlo algorithm to efficiently sample the spatial distribution of associating molecules. B. Filename: simulation_data contains the input and output files for MC production cycles (last 50,000 MCC) for all systems (PEO-salt) and (PEP-PEO-salt) simulations. C. Filename: xlink_analysis includes codes (Ipython notebook) and converted configuration files for analyzing and plotting the distribution of cation-oxygen(EO) and cation-anion cross-linking at r = 0.01. D. Filename: manuscript_figures are manuscript figures in pdf format. See readme.txt for more details about each folder.
DOI: 10.13020/c5kj-af95
title: Supporting data for Development of a multi-parent population for genetic mapping and allele discovery in six-row barley

description: Germplasm collections hold valuable allelic diversity for crop improvement and genetic mapping of complex traits. To gain access to the genetic diversity within the USDA National Small Grain Collection (NSGC), we developed the Barley Recombinant Inbred Diverse Germplasm Population (BRIDG6), a six-row spring barley multi-parent population (MPP) with 88 cultivated accessions ranging from landrace to cultivars crossed to a common parent (Rasmusson). The parents were randomly selected from a core subset of the NSGC that represents the genetic diversity of landrace and breeding accessions. In total, we generated 6,160 F5 recombinant inbred lines (RILs) with an average of 69 and a range of 37-168 RILs per family genotyped with 7,773 SNPs. The number of segregating SNPs per family range from 956 to 6,775, with an average of 3,889 SNPs per family. Using BRIDG6, we detected 23 QTL contributing to flowering time. Five QTL were within five megabase pairs of previously described flowering time genes. For the major QTL detected near HvPpd-H1, a flowering time gene that affects photoperiod, we observed both positive and negative allele effects ranging from +4 to –3 days relative to Rasmusson among the 79 families segregating for the SNP. Haplotype-based analysis of HvPpd-H1 identified private alleles to families of Asian origin conferring both positive and negative effects, providing the first observation of flowering time-related alleles private to Asian accessions. We evaluate several subsampling strategies to determine their effect on the power of QTL detection and found that for flowering time in barley, a sample size larger than 50 families or 3,000 individuals results in the highest QTL detection. This MPP will be useful for uncovering large and small effect QTL for traits of interest and identifying and utilizing valuable alleles from the NSGC for barley improvement.
DOI: 10.13020/v7fs-9589
title: Data and R code: Towards sustainable maize production in the U.S. upper Midwest with interseeded cover crops

description: Six cover crop treatments were interseeded into maize at two distinct timings: at the four to six-leaf collar stage and at physiological maturity. The canopy cover and biomass of cover crops, soil moisture at planting maize, and maize biomass and yield were evaluated to determine the potential impacts of interseeded cover crops on maize productivity.
description: The data is saved as .csv files and can be viewed in Microsoft Excel workbook and/or R statistical software. The data was collected at field and entered into master files, from which the data to create the .csv files was taken.
DOI: 10.7910/dvn/nocql9
title: data deposit Mar 9 2022

description: Two studies