cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pvmcvdnk7
title: Rumen bacteria, archaea and ciliate protozoa data from animal trial with Nordic Red dairy cows

description: Four multiparous dairy cows fitted with rumen cannula were used in a 4 × 4
 Latin square with 2 × 2 factorial arrangement of treatments to examine how
 starch level and oil mixture impact dry matter (DM) intake and
 digestibility, milk yield and composition, rumen fermentation, ruminal
 methane (CH4) emissions, and microbial diversity. Experimental treatments
 were comprised of high (HS) or low (LS) levels of starch containing 0 or
 30 g of a mixture of sunflower and fish oils (2:1 w/w) per kg diet DM (LSO
 and HSO, respectively). Digestibility was measured by total collection of
 feces and CH4 was measured using SF6 technique. Rumen microbial community
 was assessed by 16S/18S rRNA gene amplicon sequencing.
description: Primers used in this study
 are described in Tapio et al. (2016). Bacteria File containing demultiplexed
 bacteria 16S rRNA gene (V5-6) fasta files for individual animals.
 Barcodes, forward and reverse primer sequences are trimmed. Primer
 sequences and metadata for each sample are provided in the file
 'Sequence metadata.xlsx', that is also part of this Dryad data
 package. Archaea File containing demultiplexed
 archaea 16S rRNA gene (V9) fasta files for individual animals. Barcodes,
 forward and reverse primer sequences are trimmed. Primer sequences and
 metadata for each sample are provided in the file 'Sequence
 metadata.xlsx', that is also part of this Dryad data
 package. Ciliate
 protozoa File
 containing demultiplexed ciliate protozoa 18S rRNA gene fasta files for
 individual animals. Barcodes, forward and reverse primer sequences are
 trimmed. Primer sequences and metadata for each sample are provided in the
 file 'Sequence metadata.xlsx', that is also part of this Dryad
 data package. Reference
 Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR,
 Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. (2016) Oral samples as
 non-invasive proxies for assessing the composition of the rumen microbial
 community. PLoS ONE 11(3): e0151220.
 doi:10.1371/journal.pone.0151220.
DOI: 10.5061/dryad.547d7wm7k
title: Exposing wind stress as a driver of fine-scale variation in plant communities

description: The effects of temperature and precipitation, and the impacts of changes
 in these climatic conditions, on plant communities have been investigated
 extensively. The roles of other climatic factors are, however,
 comparatively poorly understood, despite potentially also strongly
 structuring community patterns. Wind, for example, is seldom considered
 when forecasting species responses to climate change, despite having
 direct physiological and mechanical impacts on plants. It is, therefore,
 important to understand the magnitude of potential impacts of changing
 wind conditions on plant communities, particularly given that wind
 patterns are shifting globally. Here, we examine the relationship between
 wind stress (i.e. a combination of wind exposure and wind speed) and
 species richness, vegetation cover and community composition using
 fine-scale, field-collected data from 1440 quadrats in a windy
 sub-Antarctic environment. Wind stress was consistently a strong predictor
 of all three community characteristics, even after accounting for other
 potentially ecophysiologically important variables, including pH,
 potential direct incident solar radiation, winter and summer soil
 temperature, soil moisture, soil depth, and rock cover. Plant species
 richness peaked at intermediate wind stress, and vegetation cover was
 highest in plots with the greatest wind stress. Community composition was
 also related to wind stress, and, after the influence of soil moisture and
 pH, had a similar strength of effect as winter soil temperature.
 Synthesis: Wind conditions are, therefore, clearly related to plant
 community characteristics in this ecosystem that experiences chronic
 winds. Based on these findings, wind conditions require greater attention
 when examining environment-community relationships, and changing wind
 patterns should be explicitly considered in climate change impact
 predictions.
DOI: 10.5061/dryad.ht76hdrf0
title: Anthropogenic noise alters parental behavior and nestling development, but not fledging condition

description: Anthropogenic noise is a ubiquitous feature of the American landscape, and
 is a known stressor for many bird species, leading to negative effects in
 behavior, physiology, reproduction, and ultimately fitness. While a number
 of studies have examined how anthropogenic noise affects avian fitness,
 there are few that simultaneously examine how anthropogenic noise impacts
 the relationship between parental care behavior and nestling fitness. We
 conducted Brownian noise playbacks for six hours a day during the nesting
 cycle on Eastern Bluebird (Sialia sialis) nest boxes to investigate if
 experimentally elevated noise affected parental care behavior, nestling
 body conditions, and nestling stress indices. We documented nest
 attendance by adult females using radio frequency identification (RFID),
 and we assessed nestling stress by measuring baseline corticosterone
 levels and telomere lengths. Based on the RFID data collected during
 individual brood cycles, adult bluebirds exposed to noise had
 significantly higher feeding rates earlier in the brood cycle than adults
 in the control group, but reduced feeding rates later in the cycle.
 Nestlings exposed to noise had higher body conditions than the control
 nestlings at eleven days of age, but conditions equalized between
 treatments by day fourteen. We found no differences in nestling baseline
 corticosterone levels or nestling telomere lengths between the two
 treatment groups. Our results revealed that noise altered adult behavior,
 which corresponded with altered nestling body condition. However, the
 absence of indicators of longer-term effects of noise on offspring
 suggests adult behavior may have been a short-term response.
description: See Pandit et al. 2021. Anthropogenic noise alters parental
 behavior and nestling development patterns, but not fledging condition.
 Behavioral Ecology. In press.
description: The data uploaded to Dryad is the clean version. The R scripts on
 summarizing the radio frequency identification (RFID) data have been
 commented out, and the rest of the code focuses on creating and analyzing
 linear mixed models on the RFID data. The adult and
 nestling CORT data has excluded individuals that took longer than 3 min to
 bleed due to CORT levels increasing after this time period.
 The telomere dataset excludes individuals that had degraded DNA
 samples.
DOI: 10.5061/dryad.k3j9kd567
title: Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

description: Denisova Cave in southern Siberia is the type locality of the Denisovans,
 an archaic hominin group related to Neanderthals. The dozen hominin
 remains recovered from the deposits also include Neanderthals and
 the child of a Neanderthal and a Denisovan, suggesting that Denisova Cave
 was a contact zone between these archaic hominins. Uncertainties persist,
 however, about the order in which they appeared at the site, the timing
 and environmental context of hominin occupation, and their association
 with archaeological assemblages. Here we report the analysis of
 DNA from 728 sediment samples, collected in a grid-like manner from the
 Pleistocene layers. Ancient faunal and hominin mitochondrial (mt) DNA was
 retrieved from 685 and 175 samples, respectively.
description: Multiple sequence alignment file This
 submission contains a multiple sequence alignment file with consensus
 sequences for the 13 protein coding genes (11.3kb) of the mitochondrial
 genome of DNA recovered from four sediment samples.
DOI: 10.5061/dryad.866t1g1pz
title: Data from: Land cover, individual’s age and spatial sorting shape landscape resistance in the invasive frog Xenopus laevis

description: 1. The description of functional connectivity is based on the
 quantification of landscape resistance, which represents species-specific
 movement costs across landscape features. Connectivity models use these
 costs to identify movement corridors at both individual and population
 levels and provide management recommendations for populations of
 conservation interest. Typically, resistance costs assigned to specific
 land cover types are assumed to be valid for all individuals of the
 population. Little attention has been paid to intraspecific variation in
 resistance costs due to age or dispersal syndrome, which may significantly
 affect model predictions. 2. We quantified resistance costs in an
 expanding invasive population of the African clawed frog Xenopus laevis in
 Western France. In this principally aquatic amphibian, juveniles,
 sub-adults and adults disperse overland. The enhancement of dispersal
 traits via spatial sorting has been also observed at the range periphery
 of the population. Resistance costs, and thus connectivity, might vary as
 a function of life stage and position within the invaded range. 3. We
 assessed multiple dimensions of functional connectivity. On various land
 cover types, we measured locomotion, as crossing speed, in different
 post-metamorphic age classes, and dehydration, sensitivity of locomotion
 to dehydration, and substrate preference in juveniles. We also tested the
 effect of the position in the invaded range (core vs. periphery)
 on individual performances. 4. In juveniles, general trends toward higher
 resistance costs on grass and lower resistance costs on bare soil and
 asphalt were observed, although not all experiments provided the same cost
 configurations. Resistance to locomotion varied between age classes, with
 adults and subadults facing lower costs than juveniles, particularly when
 crossing structurally complex land cover types like grass and leaf litter.
 The position in the range had a minor effect on landscape resistance, and
 only in the dehydration experiment, where water loss in juveniles was
 lower at the range periphery. 5. Depicting functional connectivity
 requires: i) assessing multiple dimensions of behavioural and
 physiological challenges faced by animals during movement; ii) considering
 factors, such as age and dispersal syndrome, that may affect movement at
 both individual and population level. Ignoring this complexity might
 generate unreliable connectivity models and provide unsupported management
 recommendations for conservation.
DOI: 10.15468/dl.wu7p4z
title: Occurrence Download

description: A dataset containing 866 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dendrolobium triangulare",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 866 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002772-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3r2280gfd
title: Environmental robustness of the global yeast genetic interaction network

description: Phenotypes associated with genetic variants can be altered by interactions
 with other genetic variants (GxG), with the environment (GxE), or both
 (GxGxE). Yeast genetic interactions have been mapped on a global scale,
 but the environmental influence on the plasticity of genetic networks has
 not been examined systematically. To assess environmental rewiring of
 genetic networks, we examined 14 diverse conditions and scored 30,000
 functionally representative yeast gene pairs for dynamic, differential
 interactions. Different conditions revealed novel differential
 interactions, which often uncovered new functional connections between
 distantly related gene pairs. However, the majority of observed genetic
 interactions remained unchanged in different conditions, suggesting that
 the global yeast genetic interaction network is robust to environmental
 perturbation and captures the fundamental functional architecture of a
 eukaryotic cell.
DOI: 10.5281/zenodo.18365614
title: All the source codes and data needed to evaluate the conclusions of the manuscript 'Iron-catalyzed active lipid peroxides drive ultrafast collective cell death in blooming algae' (Under Review)
DOI: 10.5061/dryad.31zcrjdk3
title: Bill size, bill shape, and body size constrain bird song evolution on a macroevolutionary scale

description: Studying macroevolutionary patterns of phenotypic variation and their
 driving forces in large radiations can shed light on how biodiversity is
 generated across broad spatiotemporal scales. In this study, we integrated
 song and morphological variation across more than 300 species representing
 the largest family of songbirds, the tanagers (Thraupidae), to uncover how
 morphological variables of the vocal tract combine to shape vocal
 evolution on a macroevolutionary scale. We found that body size correlated
 with multiple frequency parameters, concurring with past studies that show
 how body size constrains vocal evolution. Furthermore, bill size predicted
 multiple frequency and temporal song characters while bill shape was
 strongly associated with trill rates, suggesting that bill size and shape
 both constrain distinct elements of avian song independently of body size
 covariation. Our results demonstrate that the relationship between
 morphology and song exhibits modular variation when expanded to a
 macroevolutionary scale. Furthermore, our study emphasizes the need to
 consider multiple components of the avian vocal tract when exploring the
 macroevolutionary interplay of morphological traits and acoustic signals.
description: The dataset is a comma-separated file. Each species name follows
 the Clements 2016 checklist. "n.song" and "n.morph"
 show the sample sizes used for each species average. Each column,
 excluding "n.song" and "n.morph", are averages of
 measurements taken from multiple individuals of that species; furthermore,
 these averages have not been transformed. Song data (columns C:M) from
 left to right: average note length, average pause length, low (i.e.,
 minimum) frequency, high (i.e., maximum) frequency, peak frequency,
 average note bandwidth, song bandwidth, frequency shift rate, maximum
 frequency shift, note rate, and trill rate. Morphology data (columns O:Q)
 from left to right: length of the left tarsus, Bill PCA 1 (bill size),
 Bill PCA 2 (bill shape). Additional details regarding song measurements
 and descriptions of each parameter are available in Supplementary Material
 Table S1. Morphological measurements were taken following the measurement
 practices described in Baldwin et al. (1931). Song data was quantified
 from spectrograms taken from the Macauley Library and xeno-canto.
  "tarsus" denotes tarsus length. "PC1" and
 "PC2" denote the bill morphology principal components.
description: Missing values are denoted with an NA.
DOI: 10.25338/b8ss5f
title: Phylogenomics and biogeography of leptonetid spiders (Araneae : Leptonetidae)

description: Leptonetidae are rarely encountered spiders, usually associated with caves
 and mesic habitats, and are disjunctly distributed across the Holarctic.
 Data from ultraconserved elements (UCEs) were used in concatenated and
 coalescent-based analyses to estimate the phylogenetic history of the
 family. Our taxon sample included close outgroups, and 90% of described
 leptonetid genera, with denser sampling in North America and Mediterranean
 Europe. Two data matrices were assembled and analysed; the first ‘relaxed’
 matrix includes the maximum number of loci and the second ‘strict’ matrix
 is limited to the same set of core orthologs but with flanking introns
 mostly removed. A molecular dating analysis incorporating fossil and
 geological calibration points was used to estimate divergence times, and
 dispersal–extinction–cladogenesis analysis (DEC) was used to infer
 ancestral distributions. Analysis of both data matrices using maximum
 likelihood and coalescent-based methods supports the monophyly of
 Archoleptonetinae and Leptonetinae. However, relationships among
 Archoleptonetinae, Leptonetinae, and Austrochiloidea are poorly supported
 and remain unresolved. Archoleptonetinae is elevated to family rank
 Archoleptonetidae (new rank) and Leptonetidae (new status) is restricted
 to include only members of the subfamily Leptonetinae; a taxonomic review
 with morphological diagnoses is provided for both families. Four well
 supported lineages within Leptonetidae (new status) are recovered: (1) the
 Calileptoneta group, (2) the Leptoneta group, (3) the Paraleptoneta group,
 and (4) the Protoleptoneta group. Most genera within Leptonetidae are
 monophyletic, although Barusia, Cataleptoneta, and Leptoneta include
 misplaced species and require taxonomic revision. The origin of
 Archoleptonetidae (new rank), Leptonetidae, and the four main lineages
 within Leptonetidae date to the Cretaceous. DEC analysis infers the
 Leptoneta and Paraleptoneta groups to have ancestral distributions
 restricted to Mediterranean Europe, whereas the Calileptoneta and
 Protoleptoneta groups include genera with ancestral distributions spanning
 eastern and western North America, Mediterranean Europe, and east Asia.
 Based on a combination of biology, estimated divergence times, and
 inferred ancestral distributions we hypothesise that Leptonetidae was once
 widespread across the Holarctic and their present distributions are
 largely the result of vicariance. Given the wide disjunctions between
 taxa, we broadly interpret the family as a Holarctic relict fauna and
 hypothesise that they were once part of the Boreotropical forest
 ecosystem.
DOI: 10.5061/dryad.3n5tb2rgf
title: Repurposing Domperidone in Secondary Progressive MS - A Simon 2-Stage Phase 2 Futility Trial - Table e1: Results of the binary logistic regression model

description: Objective: To assess whether treatment with the generic drug domperidone
 can reduce the progression of disability in secondary progressive multiple
 sclerosis (SPMS), we conducted a phase 2 futility trial following the
 Simon two-stage design. Methods: We enrolled patients in an open-label,
 Simon two-stage, single-center, phase 2, single-arm futility trial at the
 Calgary MS Clinic if they met the following criteria: age 18 to 60 years,
 SPMS, screening EDSS score of 4.0 to 6.5 and screening T25FW of 9 seconds
 or more. Patients received domperidone 10mg QID for one year. The primary
 outcome was worsening of disability, defined as worsening of the T25FW
 performance by 20% or more at 12 months compared to at baseline. This
 trial is registered with ClinicalTrials.gov, number NCT02308137. Results:
 Between February 13th, 2015 and January 3rd, 2020, 110 patients were
 screened, 81 received treatment, 64 completed follow-up, of whom 62 were
 analysed. The study did not meet its primary endpoint: 22 of 62 (35%)
 patients experienced significant worsening of disability, which is close
 to the expected proportion of 40%, and above the pre-defined futility
 threshold. Patients with higher prolactin levels during the study had a
 significantly lower risk of disability progression, which may warrant
 further investigation. Domperidone treatment was reasonably well
 tolerated, but adverse events occurred in 84% and serious adverse events
 in 15% of patients. Conclusions: Domperidone treatment could not reject
 futility in reducing disability progression in SPMS. The Simon two-stage
 trial model may be a useful model for phase 2 studies in progressive MS.
 Classification of Evidence: This study provides Class III evidence that in
 individuals with secondary progressive multiple sclerosis participating in
 a futility trial, domperidone treatment could not reject futility in
 reducing disability progression at 12 months.
DOI: 10.5061/dryad.zcrjdfn9t
title: Adjunctive intraarterial thrombolysis in endovascular thrombectomy: a systematic review and meta-analysis

description: Objective To evaluate the safety and efficacy of intra-arterial
 thrombolysis (IAT) as an adjunct to endovascular thrombectomy (EVT) in
 ischemic stroke, we performed a systematic review and meta-analysis of the
 literature. Methods Searches were performed using Medline, Embase, and
 Cochrane databases for studies that compared EVT to EVT with adjunctive
 IAT (EVT+IAT). Safety outcomes included symptomatic intracerebral
 hemorrhage (sICH) and mortality at three months. Efficacy outcomes
 included successful reperfusion (Thrombolysis in Cerebral Infarction score
 of 2b to 3), and functional independence, defined as a modified Rankin
 Scale score of 0 to 2 at three months. Results Five studies were
 identified that compared combined EVT+IAT with alteplase or urokinase
 to EVT-only, and were included in the random effects
 meta-analysis. There were 1693 EVT patients, including 269 patients
 treated with combined EVT+IAT and 1424 patients receiving EVT-only. Pooled
 analysis did not demonstrate any differences between EVT+IAT and EVT-only
 in rates of sICH (OR: 0.61, 95% CI: 0.20-1.85; P=0.78), mortality (OR:
 0.77, 95% CI: 0.54-1.10; P=0.15), or successful reperfusion (OR: 1.05, 95%
 CI: 0.52-2.15; P=0.89). There was a higher rate of functional independence
 in patients treated with EVT+IAT, although this was not statistically
 significant (OR: 1.34, 95% CI: 1.00-1.80; P=0.053). Conclusions Adjunctive
 IAT appears to be safe. In specific situations, neurointerventionists may
 be justified in administering small doses of intraarterial alteplase or
 urokinase as rescue therapy during EVT.