cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mw6m909v
title: Phenotypic variation in male Calopteryx splendens damselflies: The role of wing pigmentation and body size in thermoregulation

description: For an ectothermic insect, its color and size are important determinants
 of body temperature: dark colors absorb heat more efficiently, while
 larger bodies require more heat to reach a certain temperature. These dark
 colors are expressed using melanin, which has been intimately linked with
 an insect’s thermoregulatory capabilities. Melanin is also linked with
 immune defense and is often used as a secondary sexual character in
 insects. There is a potential trade-off situation between thermoregulatory
 capabilities, immune defence and secondary sexual characters, all of which
 use melanin. Some Calopteryx damselflies, such as Calopteryx splendens,
 have melanin-based wing pigmentation that is sexually selected and drives
 intra- and interspecific territorial aggressions. Our goal was to
 experimentally study how the wing pigmentation and body size of C.
 splendens males affect their thermoregulation and especially their ability
 to become active after being cooled down. Our results are in line with our
 hypotheses showing that (i) individuals with larger wing spots had
 significantly faster activation times than those with smaller wing spots,
 and (ii) individuals with larger body size had significantly slower
 activation times than those with smaller body size. Both variables showed
 an interaction and thus are important in damselfly warm up and activation.
 We discuss the role wing pigmentation and thermoregulation can have on the
 behavioral patterns observed in Calopteryx species.
description: The dataset was collected by measuring temperatures and
 activation times of damselfies (<em>Calopteryx splendens</em>)
 in laboratory conditions. The wing length and wing spot length were also
 measured. Relative wing spot size was calculated by using following
 formula: 100* wing spot length / wing length.
DOI: 10.5061/dryad.n02v6wwxn
title: Pollen records of Miocene thermal maximum

description: In order to identify the northern latitudinal limit between mangroves
 composed of Avicennia only and diversified mangroves
 during the Cenozoic thermal maxima, a special attention was paid to the
 Middle Miocene Climatic Optimum (MMCO: 17–14 Ma) in the
 Mediterranean s.l. region, including the Mediterranean
 Basin s.s. and its former brackish appendix, the Paratethys
 (Popescu et al., accepted, Journ. Biogeogr.). 
 Pollen data come from forty-five biostratigraphically well-dated marine
 samples from 8 locations belonging to the MMCO. Information on the age and
 stratigraphy of some of the locations can be found in the following
 papers: Jiménez-Moreno et al., 2008, Journ. Biogeogr.,
 35, 1638-1649 (Göllenrsdorf); Jiménez-Moreno & Suc,
 2005, Palaeogeogr. Palaeoclimatol. Palaeoecol., 253, 224-241
 (Alboran A1, Estagel, Bayanne, La Rierussa); Besson et al.,
 2005, C.R. Geoscience, 337, 1045-1054 (Châteauredon). The data
 have been performed and interpreted using a robust botanical background
 for identification of pollen grains and their representativeness in marine
 coastal sediments. Pollen grains have been botanically identified by
 comparison with large modern pollen collections developed from sampling of
 flowers in herbariums, especially on the basis of an accurate
 morphological examination of the pollen grains. Pollen counts are at least
 of 100 to 150 pollen grains per sample, the most abundant taxon,
 usually Pinus in the Mediterranean marine sediments,
 being excluded. These data have been already used for reconstruction of
 vegetation and climate history in the Mediterranean region, particularly
 for past-climate quantification, establishment of the thermal
 palaeo-gradient in Europe during the Miocene and estimate of
 palaeo-elevation of the nearby mountains (e.g., see: Fauquette et al.,
 2007, The Micropalaeontological Soc., Spec. Publ.,The Geological Soc.,
 481-502; Fauquette et al., 2015, Earth Planet. Sci. Lett., 412,
 220-234). They can be reused for any synthesis on the Miocene vegetation
 and climate reconstruction.
DOI: 10.5061/dryad.bnzs7h4bj
title: Data from: Long-term trends in the occupancy of ants revealed through use of multi-sourced datasets

description: We combined participatory science data and museum records to
 understand long-term changes in occupancy for 29 ant species in
 Denmark over 119 years. Bayesian occupancy modelling indicated
 change in occupancy for 15 species: five increased, four declined
 and six showed fluctuating trends. We consider how trends may
 have been influenced by life-history and habitat changes. Our
 results build on an emerging picture that biodiversity change in
 insects is more complex than implied by the simple insect decline
 narrative.
description: We used seven sources of data: 1. pinned specimen records from
 the Natural History Museum of Denmark, 2. pinned specimen records from the
 Natural History Museum of Aarhus, 3. specimen records from the Natural
 History Museum of Stavanger, collected by Holger Holgersen, 4. observation
 records from AntWeb collected by Sämi Schär, 5. observation records from
 Christian Skøtt, 6. observation records from the EuroAnts course and 7.
 preserved specimen records from the Ant Hunt. These were manually
 georeferenced and cleaned so that we excluded detections of unidentified
 species, those without collection date or geographic coordinates and
 non-native species. Using ArcGIS, remaining data were binned into 10 x 10
 km grid cells and 10 year time-periods (decades).  The
 raw data sets are available from GBIF: 
 Calabuig I (2014). Danish Ants (Formicidae). Zoological Museum,
 Natural History Museum of Denmark. Occurrence dataset https://doi.org/10.15468/xcwkfb Simonsen T, Sheard J K (2021). Natural History Museum Aarhus Ant Collection. Version 1.2. Natural History Museum Aarhus. Occurrence dataset https://doi.org/10.15468/wp3kzr Fiskå A (2018). MUST, Insecta. Version 9.266. Museum Stavanger. Occurrence dataset https://doi.org/10.15468/zkm8mj Fisher B, Fong J (2021). AntWeb. California Academy of Sciences. Occurrence dataset https://doi.org/10.15468/wqmjjt Sheard J K, Nielsen, M G, Pedersen, J (2020). Skoett Ant Collection. Center for Macroecology, Evolution and Climate, University of Copenhagen. Occurrence dataset https://doi.org/10.15468/2xh5fd Sheard J K, Nash D R (2020). Euroants. Department of Biology, University of Copenhagen. Occurrence dataset https://doi.org/10.15468/jpacce Sheard J K, Sanders N, Dunn R, Rahbek C (2021). The Danish Ant Hunt. Version 1.9. Center for Macroecology, Evolution and Climate, University of Copenhagen. Sampling event dataset https://doi.org/10.15468/dcijnc
description: The combined, cleaned dataset is uploaded as
 Dataset.csv. The scripts zipfile contains the R code
 used to run the analysis. The analysis_outout zipfile
 contains files needed to run the analysis and produce the
 figures. The results zipfile contains the results of
 the occupancy models. The README.pdf contains an
 explanation of all dataset files and scripts uploaded to Dryad.
DOI: 10.5061/dryad.cjsxksn64
title: Preliminary assessment of cavity-nesting Hymenopterans in a low-intensity agricultural landscape in Transylvania

description: In this study our aim was to assess several traits of cavity-nesting
 Hymenopteran taxa in a low-intensity agricultural landscape in
 Transylvania. The study took place between May and August 2018 at eight
 study sites in the hilly-mountainous central part of Romania, where the
 majority of the landscape is used for extensive farming or forestry.
 During the processing of the trap-nest material, we recorded several
 traits regarding the nests of different cavity-nesting Hymenopteran taxa
 and the spider prey found inside the nests of the spider-hunting
 representatives of these taxa. We also evaluated the relationship between
 the edge density and proportion of low-intensity agricultural areas
 surrounding the study sites and some of these traits. The majority of
 nests were built by the solitary wasp genus Trypoxylon, followed by the
 solitary wasp taxa Dipogon and Eumeninae. Solitary bees were much less
 common, with Hylaeus being the most abundant genus. In the nests of
 Trypoxylon, we mostly found spider prey from the family of Araneidae,
 followed by specimens from the families of Linyphiidae and Theridiidae. In
 the nests of Dipogon, we predominantly encountered spider prey from the
 family of Thomisidae. We found significant effects of low-intensity
 agricultural areas for the genera of Auplopus, Megachile, Osmia and the
 Thomisid prey of Dipogon. We also found that the spider prey of Trypoxylon
 was significantly more diverse at study sites with higher proportions of
 low-intensity agricultural areas. Our results indicate that solitary bees
 seem to be more abundant in areas, where the influence of human activities
 is stronger, while solitary wasps seem to rather avoid these areas.
 Therefore, we suggest that future studies not only should put more effort
 into sampling in low-intensity agricultural landscapes, but also focus
 more on solitary wasp taxa, when sampling such an area.
description: These datasets were used in the article 'Preliminary
 assessment of cavity-nesting Hymenopterans in a low-intensity agricultural
 landscape in Transylvania'. The methods used for data collection and
 processing are described in this article.
DOI: 10.15468/dl.72ypat
title: Occurrence Download

description: A dataset containing 11865 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Amaranthus"
 ]
}

 The dataset includes 11865 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002891-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gtht76hmv
title: Methodological approach to generate reflection and reflective notes

description: The objective of this data note is twofold: 1) to illustrate the
 methodological approach used to generate guided reflections at
 undergraduate level aided by a patient-based vignette portraying an
 individual with a history of substance use and mental health disorders; 2)
 to provide a summary of the raw data set in the form brief educational
 reflections submitted anonymously by undergraduate dental and dental
 hygiene students. These reflections were used in our recent publication
 titled ‘The role of an educational vignette to teach dental students on
 issues of substance use and mental health disorders at the University of
 British Columbia: An exploratory Qualitative study. By offering the reader
 with a road map to generate such reflections, and a summary of the
 reflections themselves, we hope to engage other dental schools in planning
 their educational teaching activities on issues pertaining to mental
 health and substance use for dental and dental hygiene students as we have
 advocated over the years.
description: Data were in the form of
 personal reflections and were obtained by asking undergraduate dental
 students at the University of British Columbia to reflect freely on issues
 of stigma and discrimination towards substance use and mental health
 disorders as a socially responsible provider. These anonymous reflections
 were prompted by an educational vignette posed during a 2,5hrs didactic
 session, and had a maximum of 300 characters.
DOI: 10.5061/dryad.xgxd254h1
title: Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information

description: Dispersal has a crucial role determining eco-evolutionary dynamics through
 both gene flow and population size regulation. However, to study dispersal
 and its consequences, one must distinguish immigrants from residents.
 Dispersers can be identified using telemetry, capture-mark-recapture (CMR)
 methods, or genetic assignment methods. All of these methods have
 disadvantages, such as, high costs and substantial field efforts needed
 for telemetry and CMR surveys, and adequate genetic distance required in
 genetic assignment. In this study, we used genome-wide 200K Single
 Nucleotide Polymorphism data and two different genetic assignment
 approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation)
 to identify the dispersers in a house sparrow (Passer domesticus)
 metapopulation sampled over 16 years. Our results showed higher assignment
 accuracy with BONE. Hence, we proceeded to diagnose potential sources of
 errors in the assignment results from the BONE method due to variation in
 levels of inter-population genetic differentiation, intra-population
 genetic variation and sample size. We show that assignment accuracy is
 high even at low levels of genetic differentiation and that it increases
 with the proportion of a population that has been sampled. Finally, we
 highlight that dispersal studies integrating both ecological and genetic
 data provide robust assessments of the dispersal patterns in natural
 populations.
description: Description of the data and scripts are given in the
 Geneticassignment_README.txt file.
DOI: 10.6076/d1gw20
title: Mapfile and ASV table of whole-body and shell-surface samples from geminate species of gastropods separated by the Isthmus of Panama

description: The rise of the Isthmus of Panama ~3.5 mya separated populations of many
 marine organisms, which then diverged into new geminate sister species
 currently living in the Eastern Pacific Ocean and Caribbean Sea. However,
 we know very little about how such evolutionary divergences of host
 species have shaped their microbiomes. Here, we compared the microbiomes
 of whole-body and shell-surface samples of geminate species of marine
 gastropods in the
 genera Cerithiumand Cerithideopsis to those of
 congeneric outgroups. Our results show that the effects of the Isthmus on
 microbiome composition varied among host genera and between sample types
 within the same hosts. In the whole-body samples, microbiome compositions
 of geminate species pairs in the focal genera tended to be similar, likely
 due to host filtering, although the strength of this relationship varied
 among the two groups and across similarity metrics. Shell-surface
 communities showed contrasting patterns, with co-divergence between the
 host taxa and a small number of microbial clades evident
 in Cerithideopsis, but not Cerithium. These results
 suggest that (i) the rise of the Isthmus of Panama affected microbiomes of
 geminate hosts in a complex and clade-specific manner and (ii)
 host-associated microbial taxa respond differently to vicariance events
 than the hosts themselves. 
description: These data were collected by sequencing the V4 region of the 16S
 rRNA gene from seven species of intertidal gastropods collected from four
 sites across the Isthmus of Panama, as well as environmental samples.
 Three of these hosts are from the genus <em>Cerithium</em>,
 the others are from the genus <em>Cerithideopsis</em>.
 Whole-body tissues and shell-surface swabs from each sample were processed
 using the Qiagen DNeasy Blood and Tissue kit, the 16S rRNA gene region was
 amplified using the 515f-806rb primer pair and amplicons were barcoded
 using the NexTeraXT barcode kit. Sequencing was conducted on an Illumina
 MiSeq (2x250bp, paired end). Sequences were processed via DADA2 and
 assigned taxonomy using the Silva 138 database.
description: The associated mapfile should provide all necessary metadata for
 the usage of the ASV table. Raw sequences are available from the NCBI SRA
 under BioProject accession #PRJNA74415.
DOI: 10.5061/dryad.1zcrjdfsg
title: Genotype data not consistent with clonal transmission of sea turtle fibropapillomatosis or goldfish schwannoma

description: Recent discoveries of transmissible cancers in multiple bivalve species
 suggest that direct transmission of cancer cells within species may be
 more common than previously thought, particularly in aquatic environments.
 Fibropapillomatosis occurs with high prevalence in green sea turtles
 (Chelonia mydas) and the geographic range of disease has increased since
 fibropapillomatosis was first reported in this species. Widespread
 incidence of schwannomas, benign tumours of Schwann cell origin, reported
 in aquarium-bred goldfish (Carassius auratus), suggest an infectious
 aetiology. We investigated the hypothesis that cancers in these species
 arise by clonal transmission of cancer cells. Through analysis of
 polymorphic microsatellite alleles, we demonstrate concordance of host and
 tumour genotypes in diseased animals. These results imply that the tumours
 examined arose from independent oncogenic transformation of host tissue
 and were not clonally transmitted. Further, failure to experimentally
 transmit goldfish schwannoma via water exposure or inoculation suggest
 that this disease is unlikely to have an infectious aetiology.
description: Fragment sequence data files for five loci (A6, B103, B123, C102,
 D108) for tumour (T) and matched normal (N) tissues from six individual
 green sea turtles (GT1-GT6) afflicted with fibropapillomatosis. Two
 tumours (T1,T2) were sampled from individual GT2.
DOI: 10.5061/dryad.7pvmcvdt0
title: FASTA sequences of 6 different proteins of SARS-CoV-2

description: The acute respiratory disease induced by the severe acute respiratory
 syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just
 less than a year by the first half of 2020. The subsequent efficient
 human-to-human transmission of this virus eventually affected millions of
 people worldwide. The virulence of the SARS-CoV-2 is mostly regulated by
 its proteins but very little is known about the protein structures and
 functionalities. Therefore, the main purpose of this study is to learn
 more about these proteins through bioinformatics approaches. In this
 study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope
 protein have been selected from a Bangladeshi Corona-virus strain G039392
 and a number of bioinformatics tools and strategies were implemented for
 multiple sequence alignment and phylogeny analysis with 9 different
 variants, predicting hydropathicity, amino acid compositions,
 protein-binding propensity, protein disorders, 2D and 3D protein modeling.
DOI: 10.5061/dryad.ns1rn8ptd
title: Supplementary information for: A continuous-score occupancy modeling framework for incorporating uncertain machine learning output in autonomous biodiversity surveys

description: Note: for occupancy model implementations and other R and Python scripts,
 please see the "Software" DOI hosted by Zenodo:
 https://doi.org/10.5281/zenodo.6353948 Ecologists often study biodiversity
 by evaluating species occupancy and the relationship between occupancy and
 other covariates. Occupancy models are now widely used to account for
 false absences in field surveys and to reduce bias in estimates of
 covariate relationships. Existing occupancy models take as inputs binary
 detection/non-detection observations of species at each visit to each
 site. However, autonomous sensing devices and machine learning models are
 increasingly used to survey biodiversity, generating a new type of
 observation record (i.e., continuous-score data) that reflects the model’s
 confidence a species is present in each autonomously sensed file, instead
 of binary detection/non-detection data. These data are not directly
 compatible with traditional binary occupancy modeling methods. Here, we
 develop a new occupancy model that models continuous scores on a visit
 level as a Gaussian mixture, combining a distribution of scores for files
 that do contain the species of interest and a distribution of scores for
 files that do not. The model takes as input continuous scores for each
 autonomously sensed and classified file, along with an optional small
 number of binary, manually verified detection and non-detection
 annotations. We present a simulation study that shows that over a range of
 empirically realistic parameters, our model outperforms traditional
 occupancy models that are based on binary annotation alone. We also apply
 this new model to an empirical case study using data generated from five
 machine learning classifiers applied to autonomous acoustic recordings
 gathered in the eastern United States. Because our occupancy model
 generalizes allowable input data beyond binary observations, it is
 particularly well-suited to the increasing volume of machine learning
 classified data in ecology and conservation.
description: This dataset contains the supplementary information for the
 manuscript "A continuous-score occupancy modeling framework for
 incorporating uncertain machine learning output in autonomous biodiversity
 surveys," including the Supporting Information document, scripts used
 to create and fit occupancy models for three experiments, weights of the
 trained machine learning models used in the manuscript, and scripts used
 to create and apply these machine learning models.
DOI: 10.5061/dryad.zgmsbccbz
title: Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

description: During growth, cells must expand their cell volumes in coordination with
 biomass to control the level of cytoplasmic macromolecular crowding.
 Dry-mass density, the average ratio of dry mass to volume, is roughly
 constant between different nutrient conditions in bacteria, but it remains
 unknown whether cells maintain dry-mass density constant at the
 single-cell level and during non-steady conditions. Furthermore, the
 regulation of dry-mass density is fundamentally not understood in any
 organism. Using quantitative phase microscopy and a new image-analysis
 pipeline, we measured absolute single-cell mass and shape of the model
 organisms Escherichia coli and Caulobacter crescentus with improved
 precision and accuracy. We found that cells control dry-mass density
 indirectly, by expanding their surface, rather than volume, in direct
 proportion to biomass growth – according to a new surface growth law. At
 the same time, cell width is controlled independently. Therefore, cellular
 dry-mass density varies systematically with cell shape, both during the
 cell cycle or after nutrient shifts, while the surface-to-mass ratio
 remains nearly constant on the generation time scale. Transient deviations
 from constancy during nutrient shifts can be reconciled with
 turgor-pressure variations and the resulting elastic changes in surface
 area. Finally, we find that plastic changes of cell width after nutrient
 shifts are likely driven by turgor variations, demonstrating an important
 regulatory role of mechanical forces for width regulation. In conclusion,
 turgor-dependent cell width and a new, slowly varying surface-to-mass
 coupling constant are the independent variables that determine dry-mass
 density.
DOI: 10.25338/b8z04p
title: Saliva protein profiling for subject identification and potential medical applications

description: This study delineates a protocol to obtain a set of proteins from human
 saliva to distinguish objectively among individual donors. A small subset
 of proteins (&lt;10%) of those identified by mass spectrometry from
 wet saliva samples allowed to discriminate among donors supporting the
 notion that most of the salivary proteome is highly conserved across
 subjects. Most of these discriminating proteins were involved with
 immunity, tissue metabolism and regeneration. They were already identified
 in other saliva proteome studies including those performed with dry saliva
 samples indicating the likelihood of using wet or dry saliva samples. The
 differences in the proteomes across subjects likely reflect a combination
 of different lifestyle habits, environmental factors, underlying
 diseases/conditions, among others, but not necessarily age. Application of
 such proteomic analysis has the potential to increase substantially the
 value of saliva as a source of proteins in forensic evidence.
description: See original masnucript for detailed methods.
description: See readme file.