cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bj55p
title: Data from: Hydric conditions during incubation influence phenotypes of neonatal reptiles in the field

description: Phenotypic variation is strongly impacted by environmental conditions
 experienced during development. Substantial laboratory research has shown
 that reptiles with flexible-shelled eggs are particularly sensitive to
 hydric conditions, yet research on nests in the wild is sparse. In this
 two-year field experiment, we explore the influence of hydric conditions
 during incubation on phenotypic traits of hatchling painted turtles
 (Chrysemys picta). Using a split-clutch design, we created two artificial
 nests adjacent to each maternally-selected nest site. Half the eggs
 incubated in a nest that received regular supplemental watering, while the
 control nest was exposed to natural precipitation only. Our results
 suggest that the influence of the hydric environment on developing
 reptilian embryos is context dependent. Supplemental water applied to
 nests in a drier than normal season elicited the expected biotic
 responses, based on laboratory experiments. However, when the soil
 surrounding C. picta eggs was already highly moist, the additional water
 from supplemental application effectively stunted embryonic development.
 Our experiment confirms that hydric conditions of the soil during
 incubation in the wild can substantially influence phenotypic variation of
 reptiles with flexible-shelled eggs. Additionally, our experiment
 highlights the importance of complex interactions in the field that are
 often unexplored in laboratory experiments, reiterating the importance of
 validating laboratory work with field experiments.
description: Data from: Hydric
 conditions during incubation influence phenotypes of neonatal reptiles in
 the fieldThis excel spreadsheet
 has four tabs "hydric conditions 12 +13", "temperature
 2012", "temperature 2013", and "phenotypes 12 +
 13". "hydric conditions 12 +13" contains the hydric
 condition data during incubation from 2012 and 2013. "temperature
 2012" contains the temperatures for nests during incubation in 2012.
 "temperature 2013" contains the temperatures for nests during
 incubation in 2013. "phenotypes 12 +13" contains the phenotypic
 data from the eggs and hatchlings in 2012 and 2013.data for
 dryad.xlsx
DOI: 10.5061/dryad.4b115
title: Data from: The trouble with triplets in biodiversity informatics: a data-driven case against current identifier practices

description: The biodiversity informatics community has discussed aspirations and
 approaches for assigning globally unique identifiers (GUIDs) to
 biocollections for nearly a decade. During that time, and despite
 misgivings, the de facto standard identifier has become the “Darwin Core
 Triplet”, which is a concatenation of values for institution code,
 collection code, and catalog number associated with biocollections
 material. Our aim is not to rehash the challenging discussions regarding
 which GUID system in theory best supports the biodiversity informatics use
 case of discovering and linking digital data across the Internet, but how
 well we can link those data together at this moment, utilizing the current
 identifier schemes that have already been deployed. We gathered Darwin
 Core Triplets from a subset of VertNet records, along with vertebrate
 records from GenBank and the Barcode of Life Data System, in order to
 determine how Darwin Core Triplets are deployed “in the wild”. We asked if
 those triplets follow the recommended structure and whether they provide
 an easy and unambiguous means to track from specimen records to genetic
 sequence records. We show that Darwin Core Triplets are often riddled with
 semantic and syntactic errors when deployed and curated in practice,
 despite specifications about how to construct them. Our results strongly
 suggest that Darwin Core Triplets that have not been carefully curated are
 not currently serving a useful role for relinking data. We briefly
 consider needed next steps to overcome current limitations.
description: trouble_w_triples-masterA zip file containing the scripts used to analyze a large dataset of identifiers from different systems - VertNet, BOLD and Genbank. The identifiers are also provided.
DOI: 10.82294/dvniiskie
title: COPUS. Territorio: Caquetá. Sector: Cultura. Año: 2024
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2024 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Caquetá.
DOI: 10.5061/dryad.267d2
title: Data from: Five years of phenology observations from a mixed-grass prairie exposed to warming and elevated CO2

description: Atmospheric CO2 concentrations have been steadily increasing since the
 Industrial Era and contribute to concurrent increases in global
 temperatures. Many observational studies suggest climate warming alone
 contributes to a longer growing season. To determine the relative effect
 of warming on plant phenology, we investigated the individual and joint
 effects of warming and CO2 enrichment on a mixed-grass prairie plant
 community by following the development of six common grassland species and
 recording four major life history events. Our data support that, in a
 semi-arid system, while warming advances leaf emergence and flower
 production, it also expedites seed maturation and senescence at the
 species level. However, the additive effect can be an overall lengthening
 of the growing and reproductive seasons since CO2 enrichment, particularly
 when combined with warming, contributed to a longer growing season by
 delaying plant maturation and senescence. Fostering synthesis across
 multiple phenology datasets and identifying key factors affecting plant
 phenology will be vital for understanding regional plant community
 responses to climate change.
description: PHACEphenology_database_final_forSDWeekly phenology observations exposed to CO2 enrichment and warming over course of the growing season years 2007-2011 in a mixed-grass prairie, Cheyenne WY.PHACEclimate_database_final_forSDAnnual site-specific climate data for years 2007-2011, Cheyenne WY.PHACEswc_database_final_forSDVolumetric soil water content data from primary rooting depth (5-25cm) in a mixed-grass prairie exposed to CO2 enrichment and warming, years 2007-2011, Cheyenne WY.PHACEphenology_summary_final_forSDMean timing of life cycle events (in DOY) for all species in all treatments in all years. Treatment designation are as follows: ct are the ambient CO2, ambient temperature treatments (i.e. control); cT are the ambient CO2, warmed treatments; Ct are the CO2 enriched, ambient temperature treatments; and CT are the CO2 enriched, warmed treatments. Marked (*) cells designate those species that initiated leaf emergence and flower production earliest, and seed maturation and senescence latest in the season within a treatment within a year. Standard errors (SE) are included in parenthesis where applicable. Where SE is blank, there was no variation in induction dates for that particular species or the sample size was not more than one individual per treatment per year. Number of plots (n) where species did occur per treatment is also included (maximum possible n is 5).
DOI: 10.5061/dryad.dd84g
title: Data from: Exposure to mitochondrial genotoxins and dopaminergic neurodegeneration in Caenorhabditis elegans

description: [No abstract entered]
description: Figure1DataFigure2DataFigure4DataFigure5DataFigureS1DataFigureS3DataFigureS4DataTable1DataTable2DataTableS1DataTableS2Data
DOI: 10.5061/dryad.5230v
title: Data from: The prevalence of c.2268dup and detection of two novel alterations, c.670_672del and c.1186C&gt;T, in the TPO gene in a cohort of Malaysian-Chinese with thyroid dyshormonogenesis

description: Objectives: The c.2268dup mutation in the thyroid peroxidase (TPO) gene is
 the most common TPO alteration reported in Taiwanese patients with thyroid
 dyshormonogenesis. The ancestors of these patients are believed to
 originate from the southern province of China. Our previous study showed
 that this mutation leads to reduced abundance of the TPO protein and loss
 of TPO enzyme activity in a Malaysian-Chinese family with goitrous
 hypothyroidism. The aim of our study was to provide further data on the
 incidence of the c.2268dup mutation in a cohort of Malaysian-Chinese and
 its possible phenotypic effects. Setting: Cohort study. Participants:
 Twelve biologically unrelated Malaysian-Chinese patients with congenital
 hypothyroidism were recruited in this study. All patients showed high TSH
 and low fT4 levels at the time of diagnosis with proven presence of
 thyroid gland Primary outcome measure: Screening of the c.2268dup mutation
 in the TPO gene in all patients was carried out using PCR-direct DNA
 sequencing method. Secondary outcome measure: Further screening for
 mutations in other exonic regions of the TPO gene was carried out if the
 patient is a carrier for the c.2268dup mutation Results: The c.2268dup
 mutation was detected in 4 out of the 12 patients. Apart from the
 c.2268dup and a previously documented mutation, c.2647C&gt;T, two
 novel TPO alterations namely c.670_672del and c.1186C&gt;T were also
 detected in our patients. In silico analyses predicted that the novel
 alteration affect the structure/function of the TPO protein. Conclusion:
 The c.2268dup was detected in approximately one third of the
 Malaysian-Chinese with thyroid dyshormonogenesis. The detection of the
 novel c.670_672del and c.1186C&gt;T alterations expand the mutation
 spectrum of TPO associated with thyroid dyshormonogenesis.
description: Forward sequence
 (c.670_672 del)Chromatogram profile -
 Forward sequence (c.670_672 del)Forward.ab1Forward sequence (c.670_672del)FASTA sequence file - Forward sequence (c.670_672del)Forward.seqReverse sequence (c.670_672del)Chromatogram profile - Reverse sequence (c.670_672del)Reverse.ab1Reverse sequence (c.670_672del)FASTA sequence format - Reverse sequence (c.670_672del)Reverse.seqForward sequence (c.1186CT)Chromatogram - Forward sequence (c.1186CT)Forward.ab1Forward sequence (c.1186CT)FASTA format - Forward sequence (c.1186CT)Forward.seqReverse sequence (c.1186CT)Chromatogram - Reverse sequence (c.1186CT)Reverse.ab1Reverse sequence (c.1186CT)FASTA format - Reverse sequence (c.1186CT)Reverse.seqwt-lowest-energy-structureWild-type pdb file to be opened/viewed using Accelrys Discovery Studio or DeepView-Swiss Pdb ViewerASP224-md-10nsASP224-md-10ns pdb file to be opened/viewed using Accelrys Discovery Studio or DeepView-Swiss Pdb ViewerARG396-md-10nsARG396-md-10ns file to be opened/viewed using Accelrys Discovery Studio or DeepView-Swiss Pdb Viewer
DOI: 10.5061/dryad.sm227
title: Data from: Designer self-assembling hydrogel scaffolds can impact skin cell proliferation and migration

description: There is a need to develop economical, efficient and widely available
 therapeutic approaches to enhance the rate of skin wound healing. The
 optimal outcome of wound healing is restoration to the pre-wound quality
 of health. In this study we investigate the cellular response to
 biological stimuli using functionalized nanofibers from the
 self-assembling peptide, RADA16. We demonstrate that adding different
 functional motifs to the RADA16 base peptide can influence the rate of
 proliferation and migration of keratinocytes and dermal fibroblasts.
 Relative to unmodified RADA16; the Collagen I motif significantly promotes
 cell migration, and reduces proliferation.
description: Keratinocytes on
 RADA16-Collagen I (1% wt)Live cell tracking
 migration assay with keratinocytes on RADA16-Collagen I (1%
 wt).Col1-K.aviFibroblasts on RADA16-Collagen I (1% wt)Live cell tracking migration assay with fibroblasts on RADA16-Collagen I (1% wt).Coll1-F.aviFibroblasts on RADA16-Fibronectin (1% wt)Live cell tracking migration assay with fibroblasts on RADA16-Fibronectin (1% wt).Fibronectin-F.aviKeratinocytes on RADA16-Fibronectin (1% wt)Live cell tracking migration assay with keratinocytes on RADA16-Fibronectin (1% wt).Fibronectin-K.aviFibroblasts on RADA16 (1% wt)Live cell tracking migration assay with fibroblasts on RADA16 (1% wt).rada16-f.aviKeratinocytes on RADA16 (1% wt)Live cell tracking migration assay with keratinocytes on RADA16 (1% wt).rada16-k.avi
DOI: 10.5061/dryad.vr4b0
title: Data from: Pervasive early 21st-century vegetation changes across Danish semi-natural ecosystems – more losers than winners and a shift towards competitive, tall-growing species

description: 1. Semi-natural open habitats in northwestern Europe are highly
 prioritized for conservation and optimization of management planning is
 essential for continued protection of their diversity. We evaluate whether
 current management practices, which consist mainly of summer grazing by
 livestock, are sufficient to maintain plant species composition in a
 stable state across semi-natural areas in Denmark, or if shifts in
 functional composition are taking place. Further, we investigate important
 drivers of any on-going changes through trait differences between winner
 and loser species. 2. Using a dataset of 6513 annually inventoried
 (2004–2010) vegetation plots from 202 semi-natural NATURA 2000 protected
 areas, we assessed changes in cover of all plant species and, using
 boosted regression trees, whether winners and losers differ in regard to
 autecological characteristics and traits. 3. There were consistent changes
 in cover for 123 out of 603 species across the six-year study period, with
 more species losing than winning (78 versus 45). Winner and loser species
 were strongly differentiated by competition-related traits, but traits
 related to soil nutrients and soil moisture also had some importance.
 Generally, our results indicate a trend towards a species composition
 consisting of taller and more competitive species. 4. Synthesis and
 applications. Despite conservation actions in order to maintain so-called
 favourable conservation status, vegetation in NATURA 2000 protected areas
 is still undergoing compositional changes. Overall, autecological
 characteristics and trait differences between winners and losers match
 expectations given the contemporary anthropogenic pressures, especially
 with reduced livestock grazing. Atmospheric nitrogen deposition and
 increased soil moisture due to reduced drainage might also be involved in
 observed changes. Current management (i.e. summer grazing by livestock) is
 insufficient to preserve the diversity of less-competitive, low-statured
 and stress-tolerant herbaceous species, potentially leading to species
 losses. Such patterns can thus be expected across semi-natural ecosystems
 in northwestern Europe and other places where traditional land use (i.e.
 previous widespread extensive livestock grazing) have been replaced with
 various degrees of conservation management. A greater focus on returning
 large grazing herbivores to conservation areas is recommended for the
 protection of plant species diversity and to counteract on-going changes.
description: Timmermannetal2014JAEdataVegetation data on species cover collected in the field through the Danish National Monitoring and Assessment Programme for the Aquatic and Terrestrial Environments (NOVANA). Columns include a site number (SiteNo), the habitat type (NatureType) according to the definitions of the EU-habitat directive, Year, cover of species, and species.
DOI: 10.5061/dryad.rc917
title: Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

description: Microsatellite loci are ideal for testing hypotheses relating to genetic
 segregation at fine spatio-temporal scales. They are also conserved among
 closely related species, making them potentially useful for clarifying
 interspecific relationships between recently diverged taxa. However,
 mutations at primer binding sites may lead to increased nonamplification,
 or disruptions that may result in decreased polymorphism in nontarget
 species. Furthermore, high mutation rates and constraints on allele size
 may also with evolutionary time, promote an increase in convergently
 evolved allele size classes, biasing measures of interspecific genetic
 differentiation. Here, we used next-generation sequencing to develop
 microsatellite markers from a shotgun genome sequence of the sub-Antarctic
 seabird, the thin-billed prion (Pachyptila belcheri), that we tested for
 cross-species amplification in other Pachyptila and related sub-Antarctic
 species. We found that heterozygosity decreased and the proportion of
 nonamplifying loci increased with phylogenetic distance from the target
 species. Surprisingly, we found that species trees estimated from
 interspecific FST provided better approximations of mtDNA relationships
 among the studied species than those estimated using DC, even though FST
 was more affected by null alleles. We observed a significantly nonlinear
 second order polynomial relationship between microsatellite and mtDNA
 distances. We propose that the loss of linearity with increasing mtDNA
 distance stems from an increasing proportion of homoplastic allele size
 classes that are identical in state, but not identical by descent.
 Therefore, despite high cross-species amplification success and high
 polymorphism among the closely related Pachyptila species, we caution
 against the use of microsatellites in phylogenetic inference among
 distantly related taxa.
description: NGS shotgun data from
 Pachytila belcheriThese are the 454
 sequencing reads generated from two Pachyptila belcheri individuals
 (Kerguelen Archepelago) from which the 26 microsatellite loci used in this
 study were isolated.Prions_Msat_genotypes_by_Species_FinalThese are the genotypes for the 25 unlinked microsatellite loci analysed in this paper. The Excel file is in "Covert" format, divided into species populations for easy conversion into any other data format.Tree files and pairwise distance matricesThese are the MEGA input distance matrices for Fst and DC distances calculated from 25 microsatellite loci. Also included are the newick format tree files for each matric. These are the trees presented in Figure 2A and B.Cytochrome B ALignment and Tree
DOI: 10.5061/dryad.4rr39
title: Data from: Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding

description: Sympatric species are expected to minimize competition by partitioning
 resources, especially when these are limited. Herbivores inhabiting the
 High Arctic in winter are a prime example of a situation where food
 availability is anticipated to be low, and thus reduced diet overlap is
 expected. We present here the first assessment of diet overlap of high
 arctic lemmings during winter based on DNA metabarcoding of feces. In
 contrast to previous analyses based on microhistology, we found that the
 diets of both collared (Dicrostonyx groenlandicus) and brown lemmings
 (Lemmus trimucronatus) on Bylot Island were dominated by Salix while
 mosses, which were significantly consumed only by the brown lemming, were
 a relatively minor food item. The most abundant plant taxon, Cassiope
 tetragona, which alone composes more than 50% of the available plant
 biomass, was not detected in feces and can thus be considered to be
 non-food. Most plant taxa that were identified as food items were consumed
 in proportion to their availability and none were clearly selected for.
 The resulting high diet overlap, together with a lack of habitat
 segregation, indicates a high potential for resource competition between
 the two lemming species. However, Salix is abundant in the winter habitats
 of lemmings on Bylot Island and the non-Salix portion of the diets
 differed between the two species. Also, lemming grazing impact on
 vegetation during winter in the study area is negligible. Hence, it seems
 likely that the high potential for resource competition predicted between
 these two species did not translate into actual competition. This
 illustrates that even in environments with low primary productivity food
 resources do not necessarily generate strong competition among herbivores.
description: Reference library for
 arctic and boreal bryphytesArctic and boreal
 bryophyte reference library, chloroplast P6-loop trnL (UAA) intron, c-h
 primers.references.bryo-ch.txtlemming diet dataDNA metabarcoding diet data on lemming feces samples from Bylot Island. Dataset includes sequence data, environmental variables and validation data for lemming species identification.lemming samples.zip
DOI: 10.5061/dryad.9g5fp
title: Data from: Cophylogeny Reconstruction via an Approximate Bayesian Computation

description: Despite an increasingly vast literature on cophylogenetic reconstructions
 for studying host-parasite associations, understanding the common
 evolutionary history of such systems remains a problem that is far from
 being solved. Most algorithms for host-parasite reconciliation use an
 event-based model, where the events include in general (a subset of)
 cospeciation, duplication, loss, and host switch. All known parsimonious
 event-based methods then assign a cost to each type of event in order to
 find a reconstruction of minimum cost. The main problem with this approach
 is that the cost of the events strongly influences the reconciliation
 obtained. Some earlier approaches attempt to avoid this problem by finding
 a Pareto set of solutions and hence by considering event costs under some
 minimisation constraints. To deal with this problem, we developed an
 algorithm, called \Coala, for estimating the frequency of the events based
 on an approximate Bayesian computation approach. The benefits of this
 method are twofold: (1) it provides more confidence in the set of costs to
 be used in a reconciliation, and (2) it allows estimation of the frequency
 of the events in cases where the dataset consists of trees with a large
 number of taxa. We evaluate our method on simulated and on biological
 datasets. We show that in both cases, for the same pair of host and
 parasite trees, different sets of frequencies for the events lead to
 equally probable solutions. Moreover, often these solutions differ greatly
 in terms of the number of inferred events. It appears crucial to take this
 into account before attempting any further biological interpretation of
 such reconciliations. More generally, we also show that the set of
 frequencies can vary widely depending on the input host and parasite
 trees. Indiscriminately applying a standard vector of costs may thus not
 be a good strategy.
description: Cophylogeny
 reconstruction via an approximate Bayesian computation - Supplementary
 MaterialSupplementary material
 for the work "Cophylogeny reconstruction via an approximate Bayesian
 computation". It brings the description of datasets and additional
 experiments which make part of this work.coala_Supp_Material.pdfCophylogeny reconstruction via an approximate Bayesian computation - Biological datasetsThis file contains the nexus files of the biological datasets which were analysed in this work.PaperDatasets.zip