cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j151bd
title: Data from: Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods

description: Terrestrial arthropods comprise the most species rich communities on
 Earth, and grassland flowers provide resources for hundreds of thousands
 of species. Diverse grassland ecosystems worldwide are threatened by
 various types of environmental change, which has led to decline in
 arthropod diversity, while monitoring grassland arthropod diversity is
 time consuming and strictly dependent on declining taxonomic expertise.
 Environmental DNA (eDNA) metabarcoding of complex samples has demonstrated
 that information on species compositions can be efficiently and
 non-invasively obtained. Here, we test the potential of wild flowers as a
 novel source of arthropod eDNA. We performed eDNA metabarcoding of flowers
 from several different plant species using two sets of generic primers,
 targeting the mitochondrial genes 16S rRNA and COI. Our results show that
 terrestrial arthropod species leave traces of DNA on the flowers that they
 interact with. We obtained eDNA from at least 135 arthropod species in 67
 families and 14 orders, together representing diverse ecological groups
 including pollinators, parasitoids, gall inducers, predators and
 phytophagous species. Arthropod communities clustered together according
 to plant species. Our data also indicate that this experiment was not
 exhaustive, and that an even higher arthropod richness could be obtained
 using this eDNA approach. Overall, our results demonstrate that it is
 possible to obtain information on diverse communities of insects and other
 terrestrial arthropods from eDNA metabarcoding of wild flowers. This novel
 source of eDNA represents a vast potential for addressing fundamental
 research questions in ecology, obtaining data on cryptic and unknown
 species of plant-associated arthropods, as well as applied research on
 pest management or conservation of endangered species such as wild
 pollinators.
description: Arthropod eDNA Illumina
 Nextseq raw dataThis contains the raw
 Illumina Nextseq sequencing files for the studyArthropod_eDNA_flowers.zip
DOI: 10.5061/dryad.48s16
title: Data from: Introducing ORCID

description: ORCID wasn't intended as a massive longitudinal survey of the global
 population of scientists, but with 3 million profiles and growing, it is
 becoming just that. So far a quarter of those researchers have voluntarily
 added personal information to their public ORCID profiles including the
 years, locations, and descriptions of their education and employment
 histories. As this voluntary sampling grows, the demographic and migration
 patterns of the scientific workforce is coming into focus. The biases are
 also apparent: ORCID users skew young, and certain countries are over- and
 underrepresented. The code for processing and analyzing the raw profile
 data are offered here to help researchers explore ORCID, the largest open
 repository of scientific careers. [NOTE: further context for this data
 package is provided in Bohannon (2017) 'Restless Minds' at
 http://dx.doi.org/10.1126/science.356.6339.690].
description: ORCID public
 profilesThis file contains 2.8
 million public profiles from ORCID in both XML and JSON format. You will
 need 300 GB of free space to decompress the data and work with
 it.public_profiles.tarIPython Notebook to process ORCID profilesThis IPython Notebook provides code for processing the data from public_profiles.tar into manageable data files for analysis.Process ORCID profiles.htmlProcess ORCID profiles.ipynbORCID migrationsThis file contains all affiliations (education and employment) and associated data. It is part of the output of the IPython Notebook above.ORCID_migrations_2016_12_16.csvORCID migrations by personThis file is an aggregation of affiliation data for each person. It is part of the output of the IPython Notebook above.ORCID_migrations_2016_12_16_by_person.csvIPython Notebook to analyze migrationsThis IPython Notebook provides analysis of the CSV files above.ORCID data analysis.htmlORCID data analysis.ipynbResearchGate - researcher movements from 2006This file was provided to Science magazine by ResearchGate. It was described as being based on "over one million of our members who display education and employment affiliation on their profiles" with the data representing "percentages of total movements of researchers from country to country since 2006."20170110_Science_Researcher movements from 2006.xlsx
DOI: 10.5061/dryad.pk84p
title: Data from: Use of a rostral appendage during social interactions in the Ecuadorian Anolis proboscis

description: The use of sexually selected characters in inter- and intra-sexual
 interactions has long been of interest to evolutionary biologists.
 Recently, a distinction between sexually selected traits as ornaments
 versus weapons has been advanced. We investigated the behaviour of an
 enigmatic lizard with a prominent sexually dimorphic trait in an effort to
 describe whether the trait was the product of sexual selection and further
 whether it functioned as a weapon or an ornament. The subject of our study
 was the Ecuadorian proboscis anole (Anolis proboscis), a slow-moving
 cryptic species endemic to the north-western slopes of the Andes in
 Ecuador. Males, but not females, of this species bear a rostral appendage
 that has been described as an exaggerated trait resulting from sexual
 selection. However, a thorough description of the use of the rostral
 appendage in social interactions is lacking. Here, we describe social
 interactions of this species during 11 male–female courtships and mating
 interactions, as well as three male–male agonistic interactions. We
 describe four types of displays by males, many involving the rostral
 appendage. We found that the rostral appendage is used as an ornament in
 social displays but not as a weapon in combat. We also show that, unlike
 other lizards with rostral appendages, male A. proboscis hatch with this
 structure already developed.
description: VIDEO 1-Anolis proboscis
 displaysDisplays. Four types of
 displays performed by males: proboscis flourishing, alternate up-down head
 bobbing, lowered head bobbing, undulation), and display performed by
 females.VIDEO1.aviVIDEO 2-Anolis proboscis courtship behavior, part IFirst part of the courtship behavior, highlighting the ‘Proboscis flourishing’.VIDEO2.aviVIDEO 3-Anolis proboscis courtship behavior, part IISecond part of the courtship behavior characterized by ‘Chasing’.VIDEO3.aviVIDEO 4-Anolis proboscis courtship behavior: Stimulation and copulationThird and fourth part of the courtship behavior: ‘Stimulation’ and ‘Copulation’. During the stimulation, the male rubs the female’s neck with his snout tip, elevates the rostral appendage and bite the female in the nape. The copula starts, the male stops biting the female nape and low the rostral appendage.VIDEO4.aviVIDEO 5-Agonistic interaction in Anolis proboscis-part IAgonistic Interaction. Bite attempts, rostral appendage lifting, displays with half dewlap extensions and low push-ups. Pushes with the tip of the snout and a bite in the throat of one of the males are observed.VIDEO5.aviVIDEO 6-Agonistic interaction in Anolis proboscis-part IIAgonistic Interaction 2. ‘Agonistic’ display, bite attempts, rostral appendage lifting, tail movements, displays with half dewlap extensions and low push-ups, and jaw locking can be observed.VIDEO6.avi
DOI: 10.5061/dryad.c7c4151
title: Data from: Location of water in fresh sugarcane bagasse observed by synchrotron X-ray microtomography

description: Sugarcane bagasse is a vast lignocellulosic byproduct generated in the
 industry with ~50% humidity (1 kg dry matter associated with 1 kg water).
 Although the presence of water brings deleterious consequences for
 combustion, storage and sugar extraction, the location of water in fresh
 bagasse remains unknown. In this work, we use synchrotron X-ray
 microtomography for non-invasive 3D imaging of fresh bagasse particles,
 which allows the visualization of intraparticle water. The sclerified
 fiber cells in the sheaths surrounding xylem vessels are often found full
 of water. We suggest this can be juice preserved from the native stalks as
 many sclerified fibers seem to keep their structural integrity despite the
 mechanical action during sugarcane crushing. The microtomograms of fresh
 bagasse also shows mineral particles adhered to biomass surfaces, with
 adhesion presumably favored by the presence of water. In summary, this
 work unveils the location of water in fresh bagasse, solving an old
 mystery of sugarcane technology.
description: Compressed
 tomogramsZip file containing 23
 tomograms of fresh (wet) sugarcane bagasse particles encased in Kapton
 tubes. Each tomogram has 1024x1024x1024 voxels and 1.64 um voxel size. The
 images are in 8 bit gray scale and .raw file format. The tomograms were
 generated in the IMX beamline of the UVX lightsource of the Brazilian
 Synchrotron Light Laboratory (LNLS). The tomographic reconstruction was
 performed by the Reconstruction Algorithms for Tomography
 (RAFT).BagasseTomoWet.zipCode for Particle SegmentationPython code used for segmentation of mineral particles in tomograms.Code_ParticleSegmentation.pyCode for Particle MorphometryPython code to determine morphometric parameters of segmented particles.Code_ParticleMorphometry.pyResult of Particle MorphometryExcel file containing the results of particle morphometry.Result_ParticleMorphometry.xlsx
DOI: 10.5281/zenodo.17591636
title: DATASETS of : Insights into the Crystal Packing Interactions of a 960 nm–Emissive DNA-Stabilized Silver Nanocluster

description: This repository contains the full set of experimental data associated with the manuscript. All datasets are provided as CSV files, and each filename corresponds directly to the mutant names reported in the paper. The dataset includes mass spectrometry data, chromatograms, optical/crystallographic spectroscopic data, quantum yield measurements, and images of the crystals shown in the Supporting Information.
DOI: 10.5281/zenodo.17591637
title: DATASETS of : Insights into the Crystal Packing Interactions of a 960 nm–Emissive DNA-Stabilized Silver Nanocluster

description: This repository contains the full set of experimental data associated with the manuscript. All datasets are provided as CSV files, and each filename corresponds directly to the mutant names reported in the paper. The dataset includes mass spectrometry data, chromatograms, optical/crystallographic spectroscopic data, quantum yield measurements, and images of the crystals shown in the Supporting Information.
DOI: 10.5061/dryad.3rq8q88
title: Data from: Comprehensive experimental fitness landscape and evolutionary network for small RNA

description: The origin of life is believed to have progressed through an RNA world, in
 which RNA acted as both genetic material and functional molecules. The
 structure of the evolutionary fitness landscape of RNA would determine
 natural selection for the first functional sequences. Fitness landscapes
 are the subject of much speculation, but their structure is essentially
 unknown. Here we describe a comprehensive map of a fitness landscape,
 exploring nearly all of sequence space, for short RNAs surviving selection
 in vitro. With the exception of a small evolutionary network, we find that
 fitness peaks are largely isolated from one another, highlighting the
 importance of historical contingency and indicating that natural selection
 would be constrained to local exploration in the RNA world.
description: Replicate 'm';
 FASTQ data for selection rounds 0-4This archive holds
 FASTQ-formatted sequencing data from replicate 'm' (from May,
 repl. 1 of 2) of a selection for GTP-binding aptamers; it contains 3
 files, each with sequences from 1 or 2 rounds of the selection. See
 README.txt for more information.may-fastq.tar.bz2Replicate 'j'; FASTQ data for selection rounds 0-4This archive holds FASTQ-formatted sequencing data from replicate 'j' (from July, repl. 2 of 2) of a selection for GTP-binding aptamers; it contains 2 files, each with sequences from 2 or 3 rounds of the selection. See README.txt for more information.july-fastq.tar.bz2Selection Pool StatisticsThis archive includes 6 files which contain statistics regarding the first (May) and second (July) replicate selection pools, including transition probabilities (used to model the selection pools) and the frequency of 5’ and 3’ hexamers (used to correct ligation bias). See README.txt for more information.r0-stats.tarFitness LandscapesThis MS Excel document includes two spreadsheets, each containing the fitness landscape from one of the two replicate selections (May and July). In each landscape, fitness peaks are collections of related sequences and their associated fitness values. Fitness is derived from sequence abundance after correcting for: sequencing errors, bias introduced by sequencing adapter ligation, and non-uniform sequence distribution in the initial pool. Each sequence is listed along with the following information: peak rank, sequence rank (within its peak), label (indicating that peak's rank in both replicates), fitness value (with standard deviation), and edit distance from the peak center. Alignments for each peak are also given. Fitness peaks are presented in descending order of fitness (measured at the peak center), as are sequences within each peak.MayJuly_FitnessLandscapes.xlsx
DOI: 10.5061/dryad.9js92
title: Data from: "Transcriptome sequence identity between Lyme disease tick vectors, Ixodes scapularis and Ixodes ricinus" in Genomic Resources Notes accepted 1 April 2014 to 31 May 2014

description: Ixodes scapularis and I. ricinus transmit the Lyme disease agent Borrelia
 burgdorferi in the U.S. and Europe, respectively. The only tick genome
 sequence available is that of I. scapularis, which constitutes a
 limitation for tick research. Recent evidences suggest that I. ricinus and
 I. scapularis transcriptomes share some degree of sequence identity.
 However, only the global transcriptome comparison reported here
 demonstrated that I. ricinus and I. scapularis share a 99.232±0.005
 percent sequence identity with a very low frequency of INDELs. However,
 due to limitations of the current I. scapularis genome assembly, the
 number of aligned reads was only 26-27%. These results support the use of
 I. scapularis genome sequence as a reference for the analysis of I.
 ricinus transcriptomics and proteomics data, but addressing the
 limitations associated with the I. scapularis genome assembly.
description: IL_accepted_hits.bam.baiBAI file corresponding to the BAM file of the Larvae samples Tophat accepted hits.IG_accepted_hits.bam.baiBAI file corresponding to the BAM file with the Glands samples Tophat accepted hitsSample_Larvas_Ixo_all_samples.fastqFASTQ file with reads from Larvae samplesSample_Glandulas_Ixo_all_samples.fastqFASTQ file with the reads from Glands samplesIG_accepted_hits.bamBAM file containing the Tophat accepted hits of the Glands samplesIL_accepted_hits.bamBAM file containing the Tophat accepted hits of the Larvae samplesIG-tophat-runCommands run to map the reads to the reference genome, glads sampleIL-tophat-runCommands used to map the reads to the reference genome, Larvae sample
DOI: 10.5061/dryad.d6736c7
title: Data from: Accounting for heteroscedasticity and censoring in chromosome partitioning analyses

description: A fundamental assumption in quantitative genetics is that traits are
 controlled by many loci of small effect. Using genomic data, this
 assumption can be tested using chromosome partitioning analyses, where the
 proportion of genetic variance for a trait explained by each chromosome
 (h2c), is regressed on its size. However, as h2c-estimates are necessarily
 positive (censoring) and the variance increases with chromosome size
 (heteroscedasticity), two fundamental assumptions of ordinary least
 squares (OLS) regression are violated. Using simulated and empirical data
 we demonstrate that these violations lead to incorrect inference of
 genetic architecture. The degree of bias depend mainly on the number of
 chromosomes and their size distribution and are therefore specific to the
 species; using published data across many different species we estimate
 that not accounting for this effect overall resulted in 28% false
 positives. We introduce a new and computationally efficient resampling
 method that corrects for inflation caused by heteroscedasticity and
 censoring and that works under a large range of data set sizes and genetic
 architectures in empirical data sets. Our new method substantially
 improves the robustness of inferences from chromosome partitioning
 analyses.
description: R_project_folder.tarContains the complete R.project and necessary files for all analyses and figures, including code to perform the simulations. The raw data from simulations are available from separate data files, but summaries of this data are available as ".rds" files in this folder. A readme.txt file is also available in this folder with further instructions.data_NG_100-replaceRaw data for comparing permutation against HC-correction (100 replicates)data_NG_100.tar.gzdata_NG_1000_2-replaceContains raw data from simulations under the null hypothesis where P-value inflation was investigated (1000 replicates).data_NG_1000_2.tar.gzdata_NG_pop_struct-replaceContains raw data from simulations with population structure.data_NG_pop_struct.tar.gzdata_sim_vs_emp-replaceContains raw simulated data for comparing empirical data versus simulated data.data_sim_vs_emp.tar.gz
DOI: 10.5061/dryad.k4d0q
title: Data from: Bone-eating Osedax worms lived on Mesozoic marine reptile deadfalls

description: We report fossil traces of Osedax, a genus of siboglinid annelids that
 consume the skeletons of sunken vertebrates on the ocean floor, from
 early-Late Cretaceous (approx. 100 Myr) plesiosaur and sea turtle bones.
 Although plesiosaurs went extinct at the end-Cretaceous mass extinction
 (66 Myr), chelonioids survived the event and diversified, and thus
 provided sustenance for Osedax in the 20 Myr gap preceding the radiation
 of cetaceans, their main modern food source. This finding shows that
 marine reptile carcasses, before whales, played a key role in the
 evolution and dispersal of Osedax and confirms that its generalist ability
 of colonizing different vertebrate substrates, like fishes and marine
 birds, besides whale bones, is an ancestral trait. A Cretaceous age for
 unequivocal Osedax trace fossils also dates back to the Mesozoic the
 origin of the entire siboglinid family, which includes chemosynthetic
 tubeworms living at hydrothermal vents and seeps, contrary to phylogenetic
 estimations of a Late Mesozoic–Cenozoic origin (approx. 50–100 Myr).
description: CT scan data - specimen
 B56629CT scan original files
 used to reconstruct Osedax boring in specimen B56629. The bone is a
 plesiosaur humerus from the Cenomanian Cambridge Greensand Member, UK.
 B56629 is curated at the Sedgwick Museum of Earth Sciences, University of
 Cambridge, UKB56629.zipB206000-1CT scan original files used to reconstruct Osedax boring in specimens B206000-1. They are two fragmentary bones (rib and costal plate) belonging to a marine turtle, family Cheloniidae, collected from the Cenomanian Grey Chalk Subgroup (Burham, Kent, UK). The specimens are curated at the Sedgwick Museum of Earth Sciences, University of Cambridge, UK
DOI: 10.5061/dryad.rq583
title: Data from: Quantitative analysis of connectivity in populations of a semi-aquatic mammal using kinship categories and network assortativity

description: Analyzing the impact of anthropogenic and natural river barriers on the
 dispersal of aquatic and semi-aquatic species may be critical for their
 conservation, but no adequate genetic methods have been developed for
 quantifying the effect of specific barriers on current connectivity.
 Knowledge of kinship relationships between individuals and reconstructions
 of pedigrees obtained using genomic data can be extremely useful, not only
 for studying the social organization of animals, but also inferring how
 the last few generations of offspring have dispersed. In this study, we
 used kinship data to analyze connectivity patterns in a small semi-aquatic
 mammal, the Pyrenean desman, in an area comprising two river systems with
 close headwaters and dams of various sizes. Using a large SNP dataset from
 70 specimens, we obtained kinship categories and reconstructed pedigrees.
 To quantify the barrier effect of specific obstacles, we constructed
 kinship networks and devised a method based on the assortativity
 coefficient, which measures the proportion between observed and expected
 kinship relationships across a barrier. The estimation of this parameter
 enabled us to infer that the most important barrier in the area was the
 watershed divide between the rivers, followed by a dam on one of the
 rivers. Other barriers did not significantly reduce the expected number of
 kinship relationships across them. This strategy and the information
 obtained with it may be crucial in determining the most important
 connectivity problems in an area and help develop conservation plans aimed
 at improving genetic exchange between populations of threatened species.
description: ddRAD
 readsQuality-filtered reads
 for each sample in FASTA format.ddRAD_reads.zipGenotype_counts.plPerl script for calculating genotype counts from a PED file to be used in the VCF2LR program.Genotype_counts.zipAssortativity.plPerl script for calculating the assortativity coefficient between two groups or sectors and example file.Assortativity.zipSNP datasetSNP dataset in PED and VCF formats.SNP_dataset.zip
DOI: 10.5281/zenodo.18385772
title: Experimental measurements from the PRIN PNRR 2022 HYDRA project CUP: J53D23013850001(Block 2)

description: This dataset contains Block 2 of 3 experimental data  collected within the HYDRA project PRIN PNRR 2022- ID project number: P2022PY3AC, CUP: J53D23013850001

The dataset includes measurements of PV-derived traits, hydraulics and biomass traits performed during . The files are provided in CSV UTF-8 format**.

Files included:**- `data_block1.csv`: main experimental measurements  - `README.md` and READMe.pdf: detailed documentation

EmbargoThe data in this block are currently **under embargo** and will be publicly released **upon publication of the associated paper**. Access to the dataset prior to this date is restricted.
DOI: 10.5281/zenodo.18385773
title: Experimental measurements from the PRIN PNRR 2022 HYDRA project CUP: J53D23013850001(Block 2)

description: This dataset contains Block 2 of 3 experimental data  collected within the HYDRA project PRIN PNRR 2022- ID project number: P2022PY3AC, CUP: J53D23013850001

The dataset includes measurements of PV-derived traits, hydraulics and biomass traits performed during . The files are provided in CSV UTF-8 format**.

Files included:**- `data_block1.csv`: main experimental measurements  - `README.md` and READMe.pdf: detailed documentation

EmbargoThe data in this block are currently **under embargo** and will be publicly released **upon publication of the associated paper**. Access to the dataset prior to this date is restricted.