cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60790/lqxwvd
title: Nutritional Nudges Study - NNS: Nutritional nudges at restaurants: Establishments´ adoption and perceptions by consumers

description: The Nutritional Nudges Study - NNS- aimed to identify key nutritional nudges to promote healthy eating in restaurants. Based on the Nutritional Nudges Inventory at Restaurants - NNIR-, during this research, nutritional nudges were examined in two comparative studies conducted in Colombia and the U.S. to identify the restaurant industry's prevalence of nutritional nudges adoption in health-focused and other-focused restaurants and consumers' perceived importance of those nudges. The attached databases contain data from both studies. Restaurant data was collected through observations made by two independently trained data collectors, followed by a final assessment from an expert reviewer, resulting in a comprehensive profile for each restaurant being included in the database. Consumer data was gathered through an online survey targeting individuals over 18 years old who dined in any restaurant at least once a week. This data may be of interest to those working on the ecology of restaurant food choices and policies related to restaurant food environments.
DOI: 10.60790/dzwxco
title: Periodic Table of Food Initiative (PTFI) - Pulses
title: Nutritional and Biochemical Diversity in Bean Accessions from Three Phaseolus Species Using Multi-Omics Characterization

description: Molecular characterization of 46 bean accessions selected based on morphological diversity and representing maximum variability in phaseolin, lectins, and alpha-amylase inhibitors as well as a range of seed coat colors. Seeds were obtained from the Future Seeds genebank collection (44 accessions) and two P. vulgaris cultivars chosen by CIAT Bean Program located in Palmira, Colombia. Accessions were distributed among three species as follows: 35 accessions of Phaseolus vulgaris (Common bean) from the core collection (Tohme et al., 1995), 7 accessions of Phaseolus lunatus (Lima bean), and 4 accessions of Phaseolus acutifolius (Tepary bean). Between 30-50g of seeds were obtained from each accession according to the genebank availability. Bean accessions metadata was extracted from the Genesys web portal (https://www.genesys-pgr.org/) and is included in the data repository for this article. 
The plant material was obtained in compliance with all relevant international and national regulations, following the International Treaty on Plant Genetic Resources for Food and Agriculture, and transferred under a Standard Material Transfer Agreement (SMTA). For the three Colombian accessions (G26506, G4691, and G7309), we subscribed Addendum No. 17 to Contract No. 212 of 2018 under the Framework Agreement for Access to Genetic Resources and Their Derived Products, granted by the Colombian Ministry of Environment and Sustainable Development (MADS).
The dataset includes raw data from the different omics platforms, including metabolomics, proteomics, ionomics, FAMEs, and macronutrients.
DOI: 10.34894/sjcjf1
title: Supplementary materials edited volume 'Connecting deliberation and voting in democratic innovations'

description: This dataset contains the supplementary materials for various chapters in the Edited Volume 'Connecting deliberation and voting in hybrid democratic innovations: variations and perspectives on hybrid designs'.
&lt;br&gt;&lt;br&gt;
Supplementary file Chapter 9: Citizen support for hybrid democratic innovations. Results of a survey experiment.
&lt;br&gt;&lt;br&gt;
Supplementary file Chapter 12: Perceived inclusion amongst participants of hybrid democratic innovations.
&lt;br&gt;&lt;br&gt;
Supplementary file Chapter 13: Politicians and hybrid democratic innovations: an uneasy fit or a matchmade in heaven?
&lt;br&gt;&lt;br&gt;
Supplemental Materials Chapter 14: Civil servants and the administrative shaping of hybrid democratic innovations through the lens of public administration logics.
DOI: 10.25519/6q9c-jv42
title: Observation of contrail formation and evolution over Clermont-Ferrand on June 2, 2023

description: BECOM (Better Contrail Mitigation) is a project proposing to develop strategies to mitigate the formation and impact of contrails. By combining advanced atmospheric modelling with real-world flight data, it aims to identify optimal flight paths and operational practices that minimize contrail formation (https://becom-project.eu/).
We documented the observation and formation conditions of contrails on June 2, 2023, over Clermont-Ferrand, France.
This study is part of the work package Operational and new measurements and characterization of the project BECOM. 
This DOI contadins the dataset allowing to support observations regarding this case study.
DOI: 10.15468/dl.nxa2m3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.795388 23.833714, 88.71862 23.828137, 88.643761 23.811545, 88.572672 23.78435, 88.50711699999999 23.747229, 88.448719 23.701103, 88.39891799999999 23.647116, 88.35893799999999 23.586608, 88.329753 23.521074, 88.31206899999999 23.452135, 88.306304 23.381492, 88.31258099999999 23.310886, 88.330727 23.242054, 88.36027799999999 23.176687, 88.40049399999999 23.116387, 88.45037600000001 23.062633, 88.50869299999999 23.01674, 88.57401299999999 22.979828, 88.644735 22.9528, 88.719132 22.936314, 88.795388 22.930774, 88.871644 22.936314, 88.94604099999999 22.9528, 89.016763 22.979828, 89.082083 23.01674, 89.1404 23.062633, 89.190282 23.116387, 89.230498 23.176687, 89.260049 23.242054, 89.278195 23.310886, 89.28447199999999 23.381492, 89.278707 23.452135, 89.26102299999999 23.521074, 89.231838 23.586608, 89.191858 23.647116, 89.14205699999999 23.701103, 89.083659 23.747229, 89.01810399999999 23.78435, 88.94701499999999 23.811545, 88.872156 23.828137, 88.795388 23.833714))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007404-260120142942310/datasets/export for details.
DOI: 10.15468/dl.u29xtj
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Crotalus totonacus",
 "Year 1960-2026"
 ]
}

 The dataset includes 61 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007405-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epv7kd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((88.833538 24.094689, 88.756615 24.089112, 88.681606 24.07252, 88.61037399999999 24.045326, 88.54468900000001 24.008204, 88.486175 23.962078, 88.43627600000001 23.908092, 88.396218 23.847584, 88.366979 23.782052, 88.34926299999999 23.713114, 88.34348900000001 23.642474, 88.349782 23.57187, 88.36796699999999 23.503041, 88.397578 23.437677, 88.43787500000001 23.377381, 88.48785599999999 23.32363, 88.54628700000001 23.277739, 88.611734 23.24083, 88.68259399999999 23.213804, 88.75713500000001 23.19732, 88.833538 23.19178, 88.909941 23.19732, 88.984482 23.213804, 89.055342 23.24083, 89.120789 23.277739, 89.17922 23.32363, 89.229201 23.377381, 89.269498 23.437677, 89.299109 23.503041, 89.317294 23.57187, 89.323587 23.642474, 89.317813 23.713114, 89.30009699999999 23.782052, 89.270858 23.847584, 89.2308 23.908092, 89.18090100000001 23.962078, 89.122387 24.008204, 89.056702 24.045326, 88.98547000000001 24.07252, 88.910461 24.089112, 88.833538 24.094689))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007408-260120142942310/datasets/export for details.
DOI: 10.15468/dl.ajvwsd
title: Occurrence Download

description: A dataset containing 4244675 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d', "year", "month") yearmonth,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, PRINTF('%04d-%02d', "year", "month"))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, PRINTF('%04d-%02d', "year", "month"))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '797', TRUE)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 PRINTF('%04d-%02d', "year", "month")

 The dataset's 4244675 records were derived from 10100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007324-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mcvdncjx9
title: Error, noise and bias in de novo transcriptome assemblies

description: De novo transcriptome assembly is a powerful tool, widely used over the
 last decade for making evolutionary inferences. However, it relies on two
 implicit assumptions: that the assembled transcriptome is an unbiased
 representation of the underlying expressed transcriptome, and that
 expression estimates from the assembly are good, if noisy approximations
 of the relative abundance of expressed transcripts. Using publicly
 available data for model organisms, we demonstrate that, across assembly
 algorithms and data sets, these assumptions are consistently violated.
 Bias exists at the nucleotide level, with genotyping error rates ranging
 from 30-83%. As a result, diversity is underestimated in transcriptome
 assemblies, with consistent under-estimation of heterozygosity in all but
 the most inbred samples. Even at the gene level, expression estimates show
 wide deviations from map-to-reference estimates, and positive bias at
 lower expression levels. Standard filtering of transcriptome assemblies
 improves the robustness of gene expression estimates but leads to the loss
 of a meaningful number of protein-coding genes, including many that are
 highly expressed. We demonstrate a computational method, length-rescaled
 CPM, to partly alleviate noise and bias in expression estimates.
 Researchers should consider ways to minimize the impact of bias in
 transcriptome assemblies.
description: Publicly available paired-end RNA seq data were used to perform
 de novo transcriptome assemblies using Trinity, Shannon and BinPacker
 assemblers. Gene expression estimates were generated in various ways with
 RSEM and kallisto. SuperTranscripts were assembled from the assemblies,
 and genotyping off of these assemblies was performed with GATK. To
 benchmark these genotypes, we defined "true" genotypes as those
 generated my aligning RNA-seq reads directly to the
 <em>Mus</em> genome. For details concerning analysis
 pipelines, please see the methods section of the manuscript, related
 supplementary information and the github repository documenting methods
 and command lines in detail:
 https://github.com/harvardinformatics/TranscriptomeAssemblyEvaluation
 .
description: For details concerning analysis pipelines, and specifics
 regarding data processing, please see the methods section of the
 manuscript, related supplementary information and the github repository
 documenting methods and command lines in detail:
 https://github.com/harvardinformatics/TranscriptomeAssemblyEvaluation
 .
DOI: 10.5061/dryad.0p2ngf1wq
title: Contrasting altitudinal variation of alpine plant communities along the Swedish mountains

description: Changes in abiotic factors along altitudinal and latitudinal gradients
 cause powerful environmental gradients. The topography of alpine areas
 generates environmental gradients over short distances, and alpine areas
 are expected to experience greater temperature increase compared to the
 global average. In this study, we investigate alpha, beta and gamma
 diversity, as well as community structure, of vascular plant communities
 along altitudinal gradients at three latitudes in the Swedish mountains.
 Species richness and evenness decreased with altitude but the patterns
 within the altitudinal gradient varied between sites, including a sudden
 decrease at high altitude, a monotonic decrease as well as a unimodal
 pattern. However, we did not observe a decline in beta diversity with
 altitude at all sites, and plant communities at all sites were spatially
 nested according to some other factors than altitude, such as the
 availability of water or micro topographic position. Moreover, the
 observed diversity patterns did not follow the latitudinal gradient. We
 observed a spatial modularity according to altitude, which was consistent
 across sites. Our results suggest strong influences of site specific
 factors on plant community composition, and that such factors partly may
 override effects from altitudinal and latitudinal environmental variation.
 Spatial variation of the observed vascular plant communities appear to
 have been caused by a combination of processes at multiple spatial scales.
description: File includes a data table containing plant species richness,
 plant Shannon evenness, and distances to centroids (which have been used
 as measurements of beta diversity), as well as binary presence - absence
 matrix used for community structure calculations.
DOI: 10.15468/dl.ruuymh
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Stigmatopora macropterygia",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 36 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002267-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vhhmgqnqk
title: Implications of life history uncertainty when evaluating status in the Northwest Atlantic population of white shark (Carcharodon carcharias)

description: To effectively protect at-risk sharks, resource managers and conservation
 practitioners must have a good understanding of how fisheries removals
 contribute to changes in abundance and how regulatory restrictions may
 impact a population trajectory. This means they need to know the number of
 animals being removed from a population and whether a given number of
 removals will lead to population increases or declines. For white shark
 (Carcharodon carcharias), theoretical quantities like the intrinsic rate
 of population increase or rebound potential (ability to increase in size
 following decline) are difficult to conceptualize in terms of real-world
 abundance changes, which limits our ability to answer practical management
 questions. To address this shortfall, we designed a simulation model to
 evaluate how our understanding of longevity and life history variability
 of white shark affects our understanding of population trends in the
 Northwest Atlantic. Then, we quantified the magnitude of removals that
 could have caused historical population declines, compared these to
 biologically-based reference points, and explored the removal scenarios
 which would result in population increase. Our results suggest that
 removals on the order of 100s of juveniles per year could have resulted in
 population-level declines in excess of 60% during the 1970s and 1980s.
 Conservation actions implemented since the 1990s would have needed to be
 nearly 100% effective at preventing fishing mortality in order for the
 population to double in abundance over the last 30 years. Total removals
 from all fleets needed to be exceptionally small to keep them below
 biological reference points for white shark in the Northwest Atlantic. The
 population’s inherent vulnerability to fishing pressure reaffirms the need
 for restrictive national and international conservation measures, even
 under a situation of abundance increase.
DOI: 10.5061/dryad.xsj3tx9bk
title: Precipitation gradients, plant biogeography, and the incidence of drip-tips in Cerrado plant species

description: Examining how both climate and species distribution patterns correlate
 with leaf morphology can give insights into the ecological and
 evolutionary patterns that drive adaptive selection of leaf form and
 function. Drip-tips are a common feature of leaves in rain forest tree
 species; they are thought to be an adaptation that aids leaf drying and
 maximizes photosynthesis in areas with high-rainfall climates. We tested
 whether this macroecological pattern holds true across the precipitation
 gradients in a non-rain forest region – the woodland savannas of Brazil
 known as the Cerrado – and compared our results with previous studies from
 Amazonia. Drip-tips were, as expected, less common overall in the drier
 Cerrado than in Amazonia. In addition, within the Cerrado, drip-tips were
 more prevalent in areas with higher rainfall as well as in Cerrado sites
 that were closer to Amazonia. Moreover, species that occurred across both
 the Cerrado and Amazonia had drip-tips more often than species that were
 found only in the Cerrado. These findings support the hypothesis that
 drip-tips are adaptive and that either the cost of retaining drip-tips is
 low or that in drier regions they have other benefits.
description: Data on leaf characteristics were collected
 using online herbarium specimens from Kew (K), New York Botanic Garden
 (NY), the Field Museum (F), and Missouri Botanical Garden (MO), Flora
 Neotropica, and Gottsberger & Gottsberger (2006). Most specimens
 were collected in Brazil; we obtained 1–17 specimens per species (median =
 2). Excluding two leafless tree-like Cactaceae, we found leaf size and tip
 data for 845 of the remaining 846 species. We were unable to locate
 specimens of <i>Mezilaurus mattogrossensis</i> (Lauraceae).
 Leaf tip characteristics vary continuously
 across species (Gentry 1969). Furthermore, intra-specific variation in
 leaf form is common in some species but not others. To ensure consistency
 with previous data from Amazonia, we scored leaf tip type for each species
 as one of five ordinal categories: retuse, rounded, acute, small tip, and
 drip-tip, following Malhado et al. (2012) (Fig. 1 and SI Fig. 1) using the
 most abundant tip type observed in the specimens. To reduce variability
 that could be associated with observer bias, all images were assessed by
 the lead author (MKS). Because leaf tip can vary with leaf size, we
 classified leaf size into one of seven size categories using Webb’s (1959)
 modification of Raunkiaer’s (1934) method (<i>sensu
 </i>Malhado et al.<i>,</i> 2009).
DOI: 10.15468/dl.shfv7v
title: Occurrence Download

description: A dataset containing 2670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus whitneyi"
 ]
}

 The dataset includes 2670 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002268-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.41ns1rnb3
title: Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

description: Microscale processes are critically important to soil ecology and
 biogeochemistry yet are difficult to study due to soil’s opacity and
 complexity. To advance the study of soil processes, we constructed
 transparent soil microcosms that enable the visualization of microbes via
 fluorescence microscopy and the non-destructive measurement of microbial
 activity and carbon uptake in situ via Raman microspectroscopy. We
 assessed the polymer Nafion and the crystal cryolite as optically
 transparent soil substrates. We demonstrated that both substrates enable
 the growth, maintenance, and visualization of microbial cells in three
 dimensions over time, and are compatible with stable isotope probing using
 Raman. We applied this system to ascertain that after a dry-down/rewetting
 cycle, bacteria on and near dead fungal hyphae were more metabolically
 active than those far from hyphae. These data underscore the impact fungi
 have facilitating bacterial survival in fluctuating conditions and how
 these microcosms can yield insights into microscale microbial activities.
description: These data include Raman spectra and confocal fluorescence
 images.