cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ms3m3n2
title: Data from: Development and validation of a score to detect paroxysmal atrial fibrillation after stroke

description: Objective: Prolonged monitoring times (72h) are recommended to detect
 paroxysmal atrial fibrillation (pAF) after ischemic stroke, but not yet
 clinical practice; therefore, an individual patient selection for
 prolonged ECG monitoring might increase the diagnostic yield of pAF in a
 resource-saving manner. Methods: We used individual patient data from
 three prospective studies (ntotal=1556) performing prolonged Holter ECG
 monitoring (at least 72h) and centralized data evaluation after TIA or
 stroke in patients with sinus rhythm. Based on the TRIPOD guideline, a
 clinical score was developed on one cohort, internally validated by
 bootstrapping and externally validated on two other studies. Results: pAF
 was detected in 77 (4.9%) of 1556 patients during 72h-Holter monitoring.
 After logistic regression analysis with variable selection, age and the
 qualifying stroke event (categorised as stroke severity with NIH-SS≤5 (OR
 2.4 vs. TIA; 95%CI0.8-6.9,p=0.112) or stroke with NIH-SS&gt;5 (OR 7.2
 vs. TIA; 95%CI 2.4-21.8,p&lt;0.001)) were found to be predictive for
 the detection of pAF within 72h-Holter monitoring and included in the
 final score (Age: 0.76 points/year, Stroke Severity NIH-SS≤5 = 9 points,
 NIH-SS&gt;5 = 21 points; to Find AF, AS5F). The high risk group
 defined by AS5F is characterized by a predicted risk between 5.2% and
 40.8% for detection of pAF with a number needed to screen of 3 for the
 highest observed AS5F points within the study population. Regarding the
 low number of outcomes before generalization of AS5F the results need
 replication. Conclusion: The AS5F score can select patients for prolonged
 ECG monitoring after ischemic stroke to detect pAF.
description: Supplemental
 MaterialUphaus_AS5F_rev_suppl_180625.docUphaus_AS5F_rev_suppl_180625.pdf
DOI: 10.57745/jp1gvj
title: balsa_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/gqz1jg
title: Tig_tig_balsa_60kW.dat

description: :unav
DOI: 10.57745/7gng9e
title: poplar_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.5061/dryad.15rs596
title: Data from: Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

description: Genome duplication is widespread in wild and crop plants. However, little
 is known about genome-wide selection in polyploids due to the complexity
 of duplicated genomes. In polyploids, the patterns of purifying selection
 and adaptive substitutions may be affected by masking owing to duplicated
 genes or homeologs as well as effective population size. Here, we
 resequence 25 accessions of the allotetraploid Arabidopsis kamchatica,
 which is derived from the diploid species A. halleri and A. lyrata. We
 observe a reduction in purifying selection compared with the parental
 species. Interestingly, proportions of adaptive non-synonymous
 substitutions are significantly positive in contrast to most plant
 species. A recurrent pattern observed in both frequency and
 divergence–diversity neutrality tests is that the genome-wide
 distributions of both subgenomes are similar, but the correlation between
 homeologous pairs is low. This may increase the opportunity of different
 evolutionary trajectories such as in the HMA4 gene involved in heavy metal
 hyperaccumulation.
description: AT4G12510_ahal_alyr_NGS_SangerHomeolog specific PCRAT3G17360_ahal_alyr_NGS_SangerAT4G36080_ahal_alyr_NGS_SangerAT4G26610_ahal_alyr_NGS_SangerAT3G17611_ahal_alyr_NGS_SangerAT3G10570_ahal_alyr_NGS_SangerAT1G02630_ahal_alyr_NGS_SangerAT1G17770_ahal_alyr_NGS_SangerAT1G02290_ahal_alyr_NGS_SangerAT5G14750_WER_Ahal_Alyr_NGS_sanger_trimmedWHEREWOLF gene (AT5G14750) homeolog specific PCR data from Shimizu-Inatsugi et al. (2009) Molecular EcologyAT1G02180_ahal_alyr_NGS_SangerAT5G13930_CHS_Ahal_Alyr_NGS_sanger_trimmedChalcone synthase (CHS) gene (AT5G13930) homeolog specific PCR from Shimizu-Inatsugi et al. (2009) Molecular EcologyAkam_SNP_validation_report21062017Summary of SNP counts from homeolog specific PCR and NGS alignments included in this submission
DOI: 10.57745/k0a4jv
title: Tig_tig_larch_82kW.dat

description: :unav
DOI: 10.57745/zjbrpw
title: beech_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/ipkcfn
title: spruce_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/vw2ybv
title: spruce_auto_tig=f(rho)_55kW.dat

description: :unav
DOI: 10.5061/dryad.rm2n41j
title: Data from: Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories

description: Life history changes may change resource use. Such shifts are not well
 understood in the dung beetles, despite recognized differences in larval
 and adult feeding ability. We use the flightless dung beetle Circellium
 bacchus to explore such shifts, identifying dung sources of adults using
 DNA metabarcoding, and comparing these with published accounts of larval
 dung sources. C. bacchus is traditionally considered to specialise on the
 dung of large herbivores for both larval and adult feeding. We
 successfully extracted mammal DNA from 151 adult C. bacchus fecal samples,
 representing 16 mammal species (ranging from elephants to small rodents),
 many of which are hitherto undescribed in the diet. Adult C. bacchus
 showed clear dung source preferences, especially for large herbivores
 inhabiting dense-cover vegetation. Our approach also confirmed the
 presence of cryptic taxa in the study area, and we propose this may be
 used for biodiversity survey and monitoring purposes. Murid rodent feces
 were the most commonly fed-upon dung source (77.5%) for adult C. bacchus,
 differing markedly from the large and megaherbivore dung sources used for
 larval rearing. These findings support the hypothesis of life
 history-specific shifts in resource use in dung beetles, and reveal a
 hitherto unsuspected, but ecologically important, role of these dung
 beetles in consuming rodent feces. The differences in feeding abilities of
 the larval and adult life history stages have profound consequences for
 their resource use and foraging strategies, and hence the ecological role
 of dung beetles. This principle and its ecological consequences should be
 explored in other scarabaeids.
description: Dereplicated
 sequencesThis fasta file contains
 all different sequences found in the experiments, except sequences that
 occurred only once in the dataset. The sequences have been generated by
 the Illumina technology (HiSeq 2500 sequencing platform, with paired-end
 sequencing, 2 x 125 bp)dungbeetle_dereplicated_data.fastadungbeetle_intermediate_resultsThis file presents filtered data after the OBITools analysis and removing the contaminants, but before the manual inspection. It contains the number of occurrences of each molecular taxonomic units (MOTUs) in the different samples and controls, as well as different columns related to the taxonomic identification of the sequences. The sequences have been generated by the Illumina technology (HiSeq 2500 sequencing platform, with paired-end sequencing, 2 x 125 bp)dungbeetle_final_tableThis file presents the final presence/absence table of the different mammalian species identified in the different dung beetle fecal samples.
DOI: 10.57745/vg3hbc
title: balsa_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/sk0lht
title: poplar_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.5061/dryad.1850
title: Data from: Additional molecular support for the new chordate phylogeny

description: Recent phylogenomic analyses have suggested tunicates instead of
 cephalochordates as the closest living relatives of vertebrates. In direct
 contradiction with the long accepted view of Euchordates, this new
 phylogenetic hypothesis for chordate evolution has been the object of some
 skepticism. We assembled an expanded phylogenomic dataset focused on
 deuterostomes. Maximum-likelihood using standard models and Bayesian
 phylogenetic analyses using the CAT site-heterogeneous mixture model of
 amino-acid replacement both provided unequivocal support for the
 sister-group relationship between tunicates and vertebrates (Olfactores).
 Chordates were recovered as monophyletic with cephalochordates as the most
 basal lineage. These results were robust to both gene sampling and missing
 data. New analyses of ribosomal rRNA also recovered Olfactores when
 compositional bias was alleviated. Despite the inclusion of 25 taxa
 representing all major lineages, the monophyly of deuterostomes remained
 poorly supported. The implications of these phylogenetic results for
 interpreting chordate evolution are discussed in light of recent advances
 from evolutionary developmental biology and genomics.
description: Delsuc2008-Genesis.nex
DOI: 10.57745/lfsdgg
title: oak_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/vzkjox
title: oak_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.15468/dl.d58atq
title: Occurrence Download

description: A dataset containing 13976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tilia europaea"
 ]
}

 The dataset includes 13976 records from 464 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001542-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/ly9mqi
title: beech_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/fkyuej
title: spruce_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/ag3kmw
title: Tig_tig_spruce_82kW.dat

description: :unav
DOI: 10.57745/rd5swx
title: ipe_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.57745/riu08w
title: spruce_auto_tig=f(rho)_93kW.dat

description: :unav
DOI: 10.57745/lkyq9y
title: Tig_tig_ipe_82kW.dat

description: :unav
DOI: 10.57745/7ym8a7
title: Tig_tig_spruce_55kW.dat

description: :unav
DOI: 10.5061/dryad.8m6n5fs
title: Data from: Harnessing olfactory bulb oscillations to perform fully brain-based sleep-scoring and real-time monitoring of anesthesia depth

description: Real-time tracking of vigilance states related to both sleep or
 anaesthesia has been a goal for over a century. However, sleep scoring
 cannot currently be performed with brain signals alone, despite the deep
 neuromodulatory transformations that accompany sleep state changes.
 Therefore, at heart, the operational distinction between sleep and wake is
 that of immobility and movement, despite numerous situations in which this
 one-to-one mapping fails. Here we demonstrate, using local field potential
 (LFP) recordings in freely moving mice, that gamma (50–70 Hz) power in the
 olfactory bulb (OB) allows for clear classification of sleep and wake,
 thus providing a brain-based criterion to distinguish these two vigilance
 states without relying on motor activity. Coupled with hippocampal theta
 activity, it allows the elaboration of a sleep scoring algorithm that
 relies on brain activity alone. This method reaches over 90% homology with
 classical methods based on muscular activity (electromyography [EMG]) and
 video tracking. Moreover, contrary to EMG, OB gamma power allows correct
 discrimination between sleep and immobility in ambiguous situations such
 as fear-related freezing. We use the instantaneous power of hippocampal
 theta oscillation and OB gamma oscillation to construct a 2D phase space
 that is highly robust throughout time, across individual mice and mouse
 strains, and under classical drug treatment. Dynamic analysis of
 trajectories within this space yields a novel characterisation of
 sleep/wake transitions: whereas waking up is a fast and direct transition
 that can be modelled by a ballistic trajectory, falling asleep is best
 described as a stochastic and gradual state change. Finally, we
 demonstrate that OB oscillations also allow us to track other vigilance
 states. Non-REM (NREM) and rapid eye movement (REM) sleep can be
 distinguished with high accuracy based on beta (10–15 Hz) power. More
 importantly, we show that depth of anaesthesia can be tracked in real time
 using OB gamma power. Indeed, the gamma power predicts and anticipates the
 motor response to stimulation both in the steady state under constant
 anaesthetic and dynamically during the recovery period. Altogether, this
 methodology opens the avenue for multi-timescale characterisation of brain
 states and provides an unprecedented window onto levels of vigilance.
description: Figure1_DataFigure3_DataFigure4_DataFigure5_DataFigure6_DataFigure7_DataFigure8_DataFigure9_DataFigureS1_DataFigureS2_DataFigureS3_Data
DOI: 10.57745/osktw0
title: poplar_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/kxdg6z
title: larch_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/pcbjej
title: Tig_tig_larch_60kW.dat

description: :unav
DOI: 10.57745/dvxweh
title: beech_pilote_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.5061/dryad.dm3hb40
title: Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species

description: Genome-wide assessments allow for fuller characterization of genetic
 diversity, finer-scale population delineation, and better detection of
 demographically significant units to guide conservation compared to those
 based on “traditional” markers. Galapagos giant tortoises (Chelonoidis
 spp.) have long provided a case study for how evolutionary genetics may be
 applied to advance species conservation. Ongoing efforts to bolster
 tortoise populations, which have declined by 90%, have been informed by
 analyses of mitochondrial DNA sequence and microsatellite genotypic data,
 but could benefit from genome-wide markers. Taking this next step, we used
 double-digest restriction-site associated DNA sequencing to collect
 genotypic data at &gt;26,000 single nucleotide polymorphisms (SNPs)
 for 117 individuals representing all recognized extant Galapagos giant
 tortoise species. We then quantified genetic diversity, population
 structure, and compared results to estimates from mitochondrial DNA and
 microsatellite loci. Our analyses detected 12 genetic lineages concordant
 with the 11 named species as well as previously described structure within
 one species, C. becki. Furthermore, the SNPs provided increased
 resolution, detecting admixture in four individuals. SNP-based estimates
 of diversity and differentiation were significantly correlated with those
 derived from nuclear microsatellite loci and mitochondrial DNA sequences.
 The SNP toolkit presented here will serve as a resource for advancing
 efforts to understand tortoise evolution, species radiations, and aid
 conservation of the Galapagos tortoise species complex.
description: Miller_et_al_Tortoise_SNPsVCF file containing ddRAD derived SNP genotypes for 117 Galapagos tortoises.Miller_et_al_Tortoise_SNP_PairedMinCov10.vcf.zip
DOI: 10.57745/ri12h2
title: Tig_tig_spruce_49kW.dat

description: :unav
DOI: 10.57745/woufp9
title: poplar_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.5061/dryad.3vk16fq
title: Data from: Resisting annihilation: relationships between functional trait dissimilarity, assemblage competitive power and allelopathy

description: Allelopathic species can alter biodiversity. Using simulated assemblages
 that are characterised by neutrality, lumpy coexistence and
 intransitivity, we explore relationships between within-assemblage
 competitive dissimilarities and resistance to allelopathic species. An
 emergent behaviour from our models is that assemblages are more resistant
 to allelopathy when members strongly compete exploitatively (high
 competitive power). We found that neutral assemblages were the most
 vulnerable to allelopathic species, followed by lumpy and then by
 intransitive assemblages. We find support for our modeling in real-world
 time-series data from eight lakes of varied morphometry and trophic state.
 Our analysis of this data shows that a lake’s history of allelopathic
 phytoplankton species biovolume density and dominance is related to the
 number of species clusters occurring in the plankton assemblages of those
 lakes, an emergent trend similar to that of our modeling. We suggest that
 an assemblage’s competitive power determines its allelopathy resistance
description: Assemblage_HAB_resistanceThis is the master program (Matlab) that is used to determine an assemblages sensitivity to allelopathyAssemblage_HAB_resistance_funcThis is the function called by the main program.for Dryad - Lake KoroniaThis is the time-series phytoplankton data for Lake Koronia, Greecefor Dryad - Lake Mikri PrespaThis is the time-series phytoplankton data for Lake Mikri Prespa, Greecefor Dryad - Lake VolviThis is the time-series phytoplankton data for Lake Volvi, Greecefor Dryad - Lake Constancetime series data for Lake Constance, Germanyfor Dryad - Lake Mezeshegyitime series data for Lake Mezeshegyi, Hungaryfor Dryad - Lake Fancsika1time series data for Lake Fancsika1, Hungaryfor Dryad - Lake Fancsika2time series data for Lake Fancsika2, Hungaryfor Dryad - Lake Kinnerettime series data for Lake Kinneret, Israel
DOI: 10.57745/enmwlk
title: Tig_tig_oak_60kW.dat

description: :unav
DOI: 10.57745/0fcw5x
title: Tig_tig_poplar_60kW.dat

description: :unav
DOI: 10.57745/vmadvn
title: spruce_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/e5iudv
title: larch_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.5061/dryad.14717cs
title: Data from: Clade-age-dependent diversification under high species turnover shapes species richness disparities among tropical rainforest lineages of Bulbophyllum (Orchidaceae)

description: Background: Tropical rainforests (TRFs) harbour almost half of the world’s
 vascular plant species diversity while covering only about 6–7% of land.
 However, why species richness varies amongst the Earth’s major TRF regions
 remains poorly understood. Here we investigate the evolutionary processes
 shaping continental species richness disparities of the pantropical,
 epiphytic and mostly TRF-dwelling orchid genus Bulbophyllum (c. 1,948 spp.
 in total; Asia-Pacific region: c. 1,564 spp.; Madagascar: 210; Africa: 80;
 Neotropics: 94) using diversification analyses based on a time-calibrated
 molecular phylogeny, coupled with ecological niche modelling (ENM) of
 geographic distributions under present and past (Last Glacial Maximum)
 conditions. Results: Our results suggest an early-to-late Miocene scenario
 of ‘out-of-Asia-Pacific’ origin and progressive, dispersal-mediated
 diversification in Madagascar, Africa and the Neotropics, respectively.
 Species richness disparities amongst these four TRF lineages are best
 explained by a time-for-speciation effect rather than differences in net
 diversification or diversity-dependent diversification due to present or
 past spatial-bioclimatic limits. All four lineages of experienced dramatic
 range expansions during the LGM, which conflicts with the common notion
 that TRFs mostly fragmented/contracted during glacial periods.
 Conclusions: Most species of at least the Madagascan, African and
 Neotropical lineages originated during the Quaternary. Their
 diversification under high species turnover (i.e. high rates of speciation
 and extinction) might relate to climate-induced range fluctuations during
 this time period combined with various intrinsic features commonly invoked
 to foster rapid population turnover in tropical orchids (e.g., epiphytism,
 specialization on pollinators and mycorrhizal fungi, dispersal by wind).
 Further (e.g., phylogenomic and ecological) research within each
 Bulbophyllum lineage but also other pantropical TRF taxa is required to
 provide a better understanding of how evolutionary processes as well as
 past and current environmental conditions drive tropical biodiversity and
 account for regional differences in species richness patterns on a global
 scale.
description: BEAST chronogram of
 BulbophyllumBEAST-derived species
 level maximum clade credibility (MCC) chronogramBEAST
 logfileBulbophyllum
 backbonetreeBulbophyllum backbone
 phylogeny (with each major lineage collapsed into a single terminal unit)
 used for phylogenetic generalised least squares (PGLS)
 regressions.ITS_Bulbophyllum_global_2019ITS AlignmentENMPotential distributions of the four major lineages of Bulbophyllum from the Neotropics, Africa, Madagascar and the Asia-Pacific region at the present (c. 1950–2000) and at the Last Glacial Maximum (CCSM and MIROC)
DOI: 10.57745/ywc9sl
title: oak_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/7icaoj
title: spruce_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/qutbkc
title: balsa_auto_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/ulh5ny
title: balsa_auto_tig=f(rho)_82kW.dat

description: :unav
DOI: 10.5061/dryad.nf45q26
title: Data from: Transgenerational and within-generation plasticity in response to climate change: insights from a manipulative field experiment across an elevational gradient

description: Parental environmental effects, or transgenerational plasticity, can
 influence an individual’s phenotype or fitness, yet remain underexplored
 in the context of global change. Using the perennial self-pollinating
 plant Boechera stricta, we explored the effects of climate change on
 transgenerational and within-generation plasticity in dormancy,
 germination, growth, and survival. We first conducted a snow removal
 experiment in the field, in which we transplanted 16 families of known
 origin into three common gardens at different elevations and exposed half
 of the siblings to contemporary snow dynamics and half to early snow
 removal. We planted the offspring of these individuals in a factorial
 manipulation of temperature and water level in the growth chamber, and
 reciprocally transplanted them across all parental environments in the
 field. The growth chamber experiment revealed that the effects of
 transgenerational plasticity persist in traits expressed after
 establishment, even when accounting for parental effects on seed mass. The
 field experiment showed that transgenerational and within-generation
 plasticity can interact and that plasticity varies clinally in populations
 distributed across elevations. These findings demonstrate that
 transgenerational plasticity can influence fitness-related traits and
 should be incorporated in studies of biological responses to climate
 change.
description: ME_GC_DryadThese are the data from the growth chamber experiment.ME_field_DryadThese are the data from the field experiment.
DOI: 10.57745/gxoyfi
title: oak_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/6acyby
title: ipe_pilote_tig=f(rho)_60kW.dat

description: :unav
DOI: 10.57745/ivuccd
title: spruce_auto_tig=f(rho)_49kW.dat

description: :unav
DOI: 10.57745/oj1qxu
title: beech_pilote_tig=f(rho)_60kW.dat

description: :unav