cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g1r50k7
title: Data from: Compromised knee internal rotation in total knee arthroplasty patients during stair climbing

description: Due to the significant role of rotational properties for normal knee
 function, this study aimed to investigate transverse plane kinematics and
 kinetics in total knee arthroplasty and unicondylar knee arthroplasty
 patients during activities of daily living compared to a healthy control
 group, including stair ascent and descent. The study participants
 consisted of a total knee arthroplasty group including posterior cruciate
 retaining and posterior stabilized designs as well as a unicondylar knee
 arthroplasty group and a healthy control group. Three-dimensional
 kinematics and kinetics were captured using a Vicon system and two Kistler
 force plates embedded in the floor and another two in a staircase. Inverse
 dynamics of the lower limbs was computed in Anybody™ Modeling System.
 Transverse plane joint angles and joint moments were analyzed utilizing
 the statistical non-parametric mapping approach, considering the entire
 curve shape for statistical analysis. The patients with total knee
 arthroplasty exhibited significantly reduced knee internal rotation of the
 operated knee compared to the control group and the patients’ unimpaired
 limb, especially during the stair climbing tasks. Both unicondylar and
 total knee arthroplasty patients were found to have similar reduced
 internal rotation motion time series in stair descent. In conclusion,
 potential kinematic and kinetic benefits of unicondylar knee arthroplasty
 over total knee arthroplasty could not be proven in the current study.
 Aside from the usually mentioned reasons inducing constrained knee
 internal rotation in total knee arthroplasty patients, future studies
 should investigate to what extent co-contraction may contribute to this
 functional impairment in patients after knee arthroplasty surgery.
description: c3d_dataThis upload contains all relevant c3d-files and subjects' anonymized individual characteristics.
DOI: 10.5061/dryad.3147q
title: Data from: A quantitative test of population genetics using spatio-genetic patterns in bacterial colonies

description: It is widely accepted that population genetics theory is the cornerstone
 of evolutionary analyses. Empirical tests of the theory, however, are
 challenging because of the complex relationships between space, dispersal,
 and evolution. Critically, we lack quantitative validation of the spatial
 models of population genetics. Here we combine analytics, on and
 off-lattice simulations, and experiments with bacteria to perform
 quantitative tests of the theory. We study two bacterial species, the gut
 microbe Escherichia coli and the opportunistic pathogen Pseudomonas
 aeruginosa, and show that spatio-genetic patterns in colony biofilms of
 both species are accurately described by an extension of the
 one-dimensional stepping-stone model. We use one empirical measure,
 genetic diversity at the colony periphery, to parameterize our models and
 show that we can then accurately predict another key variable: the degree
 of short-range cell migration along an edge. Moreover, the model allows us
 to estimate other key parameters including effective population size
 (density) at the expansion frontier. While our experimental system is a
 simplification of natural microbial community, we argue it is a proof of
 principle that the spatial models of population genetics can
 quantitatively capture organismal evolution.
description: images of bacterial
 coloniessubmitted_data.zip
DOI: 10.5061/dryad.hr1f1
title: Data from: Experience-dependent mushroom body plasticity in butterflies: consequences of search complexity and host range

description: An ovipositing insect experiences many sensory challenges during her
 search for a suitable host plant. These sensory challenges become
 exceedingly pronounced when host range increases, as larger varieties of
 sensory inputs have to be perceived and processed in the brain. Neural
 capacities can be exceeded upon information overload, inflicting costs on
 oviposition accuracy. One presumed generalist strategy to diminish
 information overload is the acquisition of a focused search during its
 lifetime based on experiences within the current environment, a strategy
 opposed to a more genetically determined focus expected to be seen in
 relative specialists. We hypothesized that a broader host range is
 positively correlated with mushroom body (MB) plasticity, a brain
 structure related to learning and memory. To test this hypothesis,
 butterflies with diverging host ranges (Polygonia c-album, Aglais io and
 Aglais urticae) were subjected to differential environmental complexities
 for oviposition, after which ontogenetic MB calyx volume differences were
 compared among species. We found that the relative generalist species
 exhibited remarkable plasticity in ontogenetic MB volumes; MB growth was
 differentially stimulated based on the complexity of the experienced
 environment. For relative specialists, MB volume was more canalized. All
 in all, this study strongly suggests an impact of host range on brain
 plasticity in Nymphalid butterflies.
description: LSM stack. Polygonia
 c-album (Swedish strain)The file shows a stack
 of optical sections obtained by LSM scanning of anti-synapsid stained
 central brain of a female Polygonia c-album.Sw P tr 5
 v9.lsmRaw data of Central
 brain, Mushroom body calyx and Antennal lobe volumesThis file contains the
 raw data for central brain, mushroom body calyx and antennal lobe volumes
 for Aglais urticae, Aglais io and Swedish/English Polygonia c-album. The
 first column specifies the treatment the butterfly female underwent (i.e.
 Newly eclosed, Unmated, Simple or Complex). The second column specifies
 the species identity. In the 3rd-5th column the central brain volume,
 mushroom body calyx volume and antennal lobe volume are given
 respectively. The 6th and 7th column describe the relative mushroom body
 calyx volume and relative antennal lobe volume respectively, both
 corrected for central brain size.Raw data CBR, MB and AL
 volumes.xlsx
DOI: 10.5061/dryad.8hv0k
title: Data from: The evolutionary history of plant T2/S-type ribonucleases

description: A growing number of T2/S-RNases are being discovered in plant genomes.
 Members of this protein family have a variety of known functions, but the
 vast majority are still uncharacterized. We present data and analyses of
 phylogenetic relationships among T2/S-RNases, and pay special attention to
 the group that contains the female component of the most widespread system
 of self-incompatibility in flowering plants. The returned emphasis on the
 initially identified component of this mechanism yields important
 conjectures about its evolutionary context. First, we find that the clade
 involved in self-rejection (class III) is found exclusively in core
 eudicots, while the remaining clades contain members from other vascular
 plants. Second, certain features, such as intron patterns, isoelectric
 point, and conserved amino acid regions, help differentiate S-RNases,
 which are necessary for expression of self-incompatibility, from other
 T2/S-RNase family members. Third, we devise and present a set of
 approaches to clarify new S-RNase candidates from existing genome
 assemblies. We use genomic features to identify putative functional and
 relictual S-loci in genomes of plants with unknown mechanisms of
 self-incompatibility. The widespread occurrence of possible relicts
 suggests that the loss of functional self-incompatibility may leave traces
 long after the fact, and that this manner of molecular fossil-like data
 could be an important source of information about the history and
 distribution of both RNase-based and other mechanisms of
 self-incompatibility. Finally, we release a public resource intended to
 aid the search for S-locus RNases, and help provide increasingly detailed
 information about their taxonomic distribution.
description: MrBayes samples and
 summary topologies using nucleotide alignmentMrBayes version
 3.2.2t2_aln_v02_mb_nt_gtr_resampled_780M_580M_BURN.tar.gzMrBayes samples and summary topologies using amino acid alignmentMrBayes version 3.2.2t2_aln_v02_mb_aa_gtr_resampled_200M_150M_BURN.tar.gzt2_aln_v02_nt.fasta NT alignment of T2/S-RNasest2_aln_v02_nt.fastat2_aln_v02_aa.fasta AA alignment of T2/S-RNasest2_aln_v02_aa.fastaUnrooted best NT/GTR RAxML tree with posterior support values from MrBayes analysisunrooted_tree.newickRooted best NT/GTR RAxML tree with posterior support values from MrBayes analysisrooted_tree.newick
DOI: 10.15468/dl.zcuwd7
title: Occurrence Download

description: A dataset containing 1479 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera onca"
 ]
}

 The dataset includes 1479 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000387-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k5g9fw
title: Occurrence Download

description: A dataset containing 987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, Guatemala)",
 "OccurrenceStatus is Present",
 "TaxonKey is Abies guatemalensis"
 ]
}

 The dataset includes 987 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000388-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18380665
title: Microwave-assisted extraction of Ulva spp. including a stage of selective coagulation of ulvan stimulated by a bio-ionic liquid
DOI: 10.15468/dl.p92yrb
title: Occurrence Download

description: A dataset containing 2895 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tryngites subruficollis"
 ]
}

 The dataset includes 2895 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000386-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18380664
title: Microwave-assisted extraction of Ulva spp. including a stage of selective coagulation of ulvan stimulated by a bio-ionic liquid
DOI: 10.5061/dryad.rs7bm
title: Data from: Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum)

description: Sexual reproduction is widespread among eukaryotes, and the
 sex-determining processes vary greatly among species. While genetic sex
 determination (GSD) has been intensively described in bilaterian species,
 no example has yet been recorded among non-bilaterians. However, the
 quasi-ubiquitous repartition of GSD among multicellular species suggests
 that similar evolutionary forces can promote this system, and that these
 forces could occur also in non-bilaterians. Studying sex determination
 across the range of Metazoan diversity is indeed important to understand
 better the evolution of this mechanism and its lability. We tested the
 existence of sex-linked genes in the gonochoric red coral (Corallium
 rubrum, Cnidaria) using restriction site-associated DNA sequencing. We
 analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals
 from 12 populations including 53 that were morphologically sexed. We found
 a strong association between the allele frequencies of 472 SNPs and the
 sex of individuals, suggesting an XX/XY sex-determination system. This
 result was confirmed by the identification of 435 male-specific loci. An
 independent test confirmed that the amplification of these loci enabled us
 to identify males with absolute certainty. This is the first demonstration
 of a GSD system among non-bilaterian species and a new example of its
 convergence in multicellular eukaryotes.
description: RAD-Seq_CoralliumRubrum_FilteredData
DOI: 10.5061/dryad.8cr05
title: Data from: Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress-response and developmental genes when exposed to a biologically realistic heat stress

description: Oviparous reptile embryos are expected to breach their critical thermal
 maxima if temperatures reach those predicted under current climate change
 models due to the lack the maternal buffering processes and parental care.
 Heat shock proteins (HSPs) are integral in the molecular response to
 thermal stress, and their expression is heritable, but the roles of other
 candidate families such as the heat shock factors (HSFs) have not been
 determined in reptiles. Here we subject embryonic sea turtles (Caretta
 caretta) to a biologically realistic thermal stress and employ de novo
 transcriptomic profiling of brain tissue to investigate the underlying
 molecular response. From a reference transcriptome of 302,293 transcripts,
 179 were identified as differentially expressed between treatments. As
 anticipated, genes enriched in the heat shock treatment were primarily
 associated with the Hsp families, or were genes whose products play
 similar protein editing and chaperone functions (e.g. bag3, MYOC and
 serpinh1). Unexpectedly, genes encoding the HSFs were not significantly
 upregulated under thermal stress, indicating their presence in unstressed
 cells in an inactive state. Genes that were downregulated under thermal
 stress were less well functionally defined but were associated with stress
 response, development, and cellular organization, suggesting that
 developmental processes may be compromised at realistically high
 temperatures. These results confirm that genes from the Hsp families play
 vital roles in the thermal tolerance of developing reptile embryos, and in
 addition with a number of other genes, should be targets for evaluating
 the capacity of oviparous reptiles to respond adaptively to the effects of
 climate change.
description: caretta_trinotate_annotation_report_FINALTriontate annotation report for Caretta caretta (brain tissue) de novo assembled transcriptome by Trinity. Wild collected eggs from Dirk Hartog Island, Shark Bay, Western Australia. Reared at the University of Western Australia. 50% of individuals were subjected to a biologically relevant thermal stress (36C for 3hrs; HS1-3). BLASTs were against Swissprot and NCBI nr Testudine databases, hmmscan against Pfam. Minimum E-value of -5.
DOI: 10.21223/ov8fue
title: Dataset for: Characterization database of 68 genotypes of native potatoes of the Phurejas group from the Cumbal Indigenous Reservation - 2024

description: Since 2023, a participatory process with the Indigenous Pasto People in Cumbal (Nariño, Colombia) has supported the conservation of Phureja native potato landraces (“chauchas”). Through Five-Cell workshops and Red Listing exercises, 68 local varieties were identified and collected. Seed multiplication plots were established in early 2024, followed by three morphological characterization plots during 2024–2025 with local custodians and the Cumbe Indigenous Agricultural School. Using CIP standardized descriptors (Gómez, 2000), the dataset records 20 morphological traits related to plant, stem, flower, and tuber characteristics, supported by a systematic photographic record for the local variety catalogue.
DOI: 10.5061/dryad.22c867m
title: Data from: Hierarchical Bayesian model reveals the distributional shifts of Arctic marine mammals

description: Aim: Our aim involved developing a method to analyze spatiotemporal
 distributions of Arctic marine mammals (AMMs) using heterogeneous open
 source data, such as scientific papers and open repositories. Another aim
 was to quantitatively estimate the effects of environmental covariates on
 AMMs’ distributions and to analyze whether their distributions have
 shifted along with environmental changes. Location: Arctic shelf area. The
 Kara Sea. Methods: Our literature search focused on survey data regarding
 polar bears (Ursus maritimus), Atlantic walruses (Odobenus rosmarus
 rosmarus) and ringed seals (Phoca hispida). We mapped the data on a grid
 and built a hierarchical Poisson point process model to analyze species’
 densities. The heterogeneous data lacked information on survey intensity
 and we could model only the relative density of each species. We explained
 relative densities with environmental covariates and random effects
 reflecting excess spatiotemporal variation and the unknown, varying
 sampling effort. The relative density of polar bears was explained also by
 the relative density of seals. Results: The most important covariates
 explaining AMMs’ relative densities were ice concentration and distance to
 the coast, and regarding polar bears, also the relative density of seals.
 The results suggest that due to the decrease in the average ice
 concentration, the relative densities of polar bears and walruses slightly
 decreased or stayed constant during the 17-yearlong study period, whereas
 seals shifted their distribution from the Eastern to the Western Kara Sea.
 Main conclusions: Point process modelling is a robust methodology to
 estimate distributions from heterogeneous observations, providing
 spatially explicit information about ecosystems and thus serves advances
 for conservation efforts in the Arctic. In a simple trophic system, a
 distribution model of a top predator benefits from utilizing prey species’
 distributions compared to a solely environmental model. The decreasing ice
 cover seems to have led to changes in AMMs’ distributions in the marginal
 Arctic region.
description: Raster layers and
 species observations from the Kara SeaThis folder contains all
 raster layers and species observations that were used for model
 calibration and predictions in our study.GIS_species_data.zip
DOI: 10.5061/dryad.284tf
title: Data from: Single nucleotide polymorphism (SNP) variation of wolves (Canis lupus) in Southeast Alaska and comparison with wolves, dogs, and coyotes in North America

description: There is considerable interest in the genetics of wolves (Canis lupus)
 because of their close relationship to domestic dogs (C. familiaris) and
 the need for informed conservation and management. This includes wolf
 populations in Southeast Alaska for which we determined genotypes of 305
 wolves at 173662 single nucleotide polymorphism (SNP) loci. After removal
 of invariant and linked SNP, 123801 SNP were used to quantify genetic
 differentiation of wolves in Southeast Alaska and wolves, coyotes (C.
 latrans), and dogs from other areas in North America. There is
 differentiation of SNP allele frequencies between the species (wolves,
 coyotes, and dogs), although differentiation is relatively low between
 some wolf and coyote populations. There are varying levels of
 differentiation among populations of wolves, including low differentiation
 of wolves in interior Alaska, British Columbia, and the northern US Rocky
 Mountains. There is considerable differentiation of SNP allele frequencies
 of wolves in Southeast Alaska from wolves in other areas. However, wolves
 in Southeast Alaska are not a genetically homogeneous group and there are
 comparable levels of genetic differentiation among areas within Southeast
 Alaska and between Southeast Alaska and other geographic areas. SNP
 variation and other genetic data are discussed regarding taxonomy and
 management.
description: data_123801SNP
DOI: 10.5061/dryad.370nq
title: Data from: Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

description: The recent emergence of barcoding approaches coupled to those of Next
 Generation Sequencing (NGS) have raised new perspectives for studying
 environmental communities. In this framework, we tested the possibility to
 derive accurate inventories of diatom communities from pyrosequencing
 outputs with an available DNA reference library. We used three molecular
 markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU
 rDNA, rbcL, and cox1), and three samples of a mock community composed of
 30 known diatom strains belonging to 21 species. In the goal to detect
 methodological biases, one sample was constituted directly from pooled
 cultures, whereas the others consisted of pooled PCR products. The NGS
 reads obtained by pyrosequencing (Roche 454) were compared first to a DNA
 reference library including the sequences of all the species used to
 constitute the mock community, and secondly to a complete DNA reference
 library with a larger taxonomic coverage. A stringent taxonomic
 assignation, gave inventories that were compared to the real one. We
 detected biases due to DNA extraction and to PCR amplification that
 resulted in false-negatives detection. Conversely, pyrosequencing errors
 appeared to generate false-positives, especially in case of closely allied
 species. The taxonomic coverage of DNA reference libraries appears to be
 the most crucial factor, together with marker polymorphism which is
 essential to identify taxa at the species level. RbcL offers a high
 resolving power which, together with its large DNA reference library.
 Though needing further optimization, pyrosequencing is suitable for
 identifying diatom assemblages and may find applications in the field of
 freshwater biomonitoring.
description: PCR1PCR1 mix: Bulk sample
 constituted from 30 diatoms strains corresponding to 12 genera and 21
 species. 30 PCR products were mixed in varying molar proportions ranging
 from 0.1% to 8.8%. Then product of 3 markers (SSU rDNA, rbcL and cox1)
 were pooled in equimolar concentration. Fragmented PCR products were then
 sequenced in one random direction on a Roche GS FLX with Titanium
 chemistry on a GS FLX Titanium PicoTiterPlate 454 (Roche) at the Genomic
 Platform of Genopole Toulouse/Midi-PyreneesPCR2CMix
DOI: 10.5061/dryad.0003s
title: Data from: Vertebral architecture in the earliest stem tetrapods

description: The construction of the vertebral column has been used as a key anatomical
 character in defining and diagnosing early tetrapod groups. Rhachitomous
 vertebrae - in which there is a dorsally placed neural arch and spine, an
 anteroventrally placed intercentrum and paired, posterodorsally placed
 pleurocentra - have long been considered the ancestral morphology for
 tetrapods. Nonetheless, very little is known about vertebral anatomy in
 the earliest stem tetrapods, as most specimens remain trapped in
 surrounding matrix, obscuring important anatomical features. Here we
 describe the three-dimensional vertebral architecture of the Late Devonian
 stem tetrapod Ichthyostega using propagation phase contrast x-ray
 synchrotron microtomography (PPC-SRµCT). Our scans reveal a diverse array
 of new morphological, and associated developmental and functional,
 characteristics, including a possible posterior-to-anterior vertebral
 ossification sequence and the first evolutionary appearance of ossified
 sternal elements. However, one of the most intriguing features relates to
 the positional relationships between the vertebral elements, with the
 pleurocentra being unexpectedly sutured/fused to the intercentra that
 directly succeed them - implying a 'reverse' rhachitomous
 design. Comparison of Ichthyostega with two other stem tetrapods,
 Acanthostega and Pederpes, shows that 'reverse' rhachitomous
 vertebrae may be the ancestral condition for limbed vertebrates. This
 study fundamentally revises our current understanding of vertebral column
 evolution in the earliest tetrapods and raises questions about the
 presumed vertebral architecture of tetrapodomorph fish and later, more
 crownward, tetrapods.
description: Image Stack
 Movies_Pierce et al