cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9kd51c5mf
title: Masting is shaped by tree-level attributes and stand structure, more than climate, in a Rocky Mountain conifer species

description: Many tree species mast, meaning seed production is highly variable from
 year to year and synchronous within a stand, but this phenomenon remains
 poorly understood. To better understand how a changing climate, altered
 disturbance regimes, or novel management strategies might affect future
 seed production, we quantified the joint influence of both biotic (tree
 size, age, and neighborhood competition) and abiotic factors (climate and
 weather) on seed production in a widespread conifer species, Rocky
 Mountain ponderosa pine (Pinus ponderosa var. scopulorum). We
 reconstructed individual-level annual cone production across a large
 portion of this species' range using the cone abscission scar method,
 and mixed models were used to test hypotheses related to the causes and
 drivers of masting in this species. Our results suggest that masting in
 ponderosa pine is a process shaped at the individual-level, and this leads
 to high, local-scale variation in annual cone production. The effects of
 weather were strongest at climatically marginal sites, but overall, the
 joint effects of weather and climate only weakly described
 individual-level patterns of annual cone production in ponderosa pine (R2m
 = 1.6%, R2c = 30.1%). Rather, we found that masting was strongly
 influenced by tree- and stand-level factors such as diameter, age, and
 local neighborhood density, all of which were associated with the mean,
 interannual variability, and between-tree synchrony of cone production at
 the individual-level. Larger and older trees produced more cones, more
 frequently, and with less synchrony than smaller and younger trees.
 Open-grown trees experiencing lower levels of neighborhood competition
 also produced more cones with less interannual variability, but with
 higher between-tree synchrony. Because tree- and stand-level traits appear
 to regulate seed production more strongly than climate or weather in this
 species, management interventions targeting these factors could be
 powerful tools to manage future tree recruitment. Thus, current efforts to
 reduce stand density and conserve large trees in some ponderosa pine
 forests may enhance tree-level seed production and reduce variability in
 seed crops among years.
DOI: 10.5061/dryad.2z34tmppz
title: Seascapes and foraging success: movement and resource discovery by a benthic marine herbivore

description: 1. Spatially concentrated resources result in patch-based foraging,
 wherein the detection and choice of patches as well as the process of
 locating and exploiting resource patches involve moving through an
 explicit landscape composed of both resources and barriers to movement. An
 understanding of behavioural responses to resources and barriers is key to
 interpreting observed ecological patterns. 2. We examined the process of
 resource discovery in the context of a heterogeneous seascape using sea
 urchins and drift kelp in urchin barrens as a model system. Under field
 conditions, we manipulated both the presence of a highly valuable resource
 (drift kelp) and a barrier to movement (sandy substratum) to test the
 interacting influence of these two factors on the process of resource
 discovery in barren grounds by urchins. We removed all foraging urchins
 (Strongylocentrotus droebachiensis) from replicate areas and monitored
 urchin recolonization and kelp consumption. We tested two hypotheses: 1)
 unstable substratum is a barrier to urchin movement and 2) the movement
 behaviour of sea urchins is modified by the presence of drift kelp. 3.
 Very few urchins were found on sand, sand was a permeable barrier to
 urchin movement, and the permeability of this barrier varied between
 sites. In general, partial recolonization occurred strikingly rapidly, but
 sand slowed the consumption of drift kelp by limiting the number of
 urchins. Differences in the permeability of sand barriers between sites
 could be driven by differences in the size structure of urchin
 populations, indicating size-specific environmental effects on foraging
 behaviour. 4. We demonstrate the influence of patchy seascapes in
 modulating grazing intensity in barren grounds through modifications of
 foraging behaviour. Behavioural processes modified by environmental
 barriers play an important role in determining grazing pressure, the
 existence of refuges for new algal recruits, and ultimately the dynamics
 of urchin-algal interactions in barren grounds.
description: All data was collected using SCUBA diving, and include in situ
 observations (numbers of urchins present throughout clearing experiments),
 collections measured immediately in the lab (original site densities,
 urchin diameters and biomass, biomass of kelp consumed), or processed and
 then measured later (dry weight lost through dissolution for clod cards).
 See article for details of methods used during data collection.
DOI: 10.5061/dryad.612jm6469
title: Data from: A shared numerical magnitude representation evidenced by the distance effect in frequency-tagging EEG

description: Humans can effortlessly abstract numerical information from various codes
 and contexts. However, whether the access to the underlying magnitude
 information relies on common or distinct brain representations remains
 highly debated. Here, we recorded electrophysiological responses to
 periodic variation of numerosity (every five items) occurring in rapid
 streams of numbers presented at 6Hz in randomly varying codes – Arabic
 digits, number words, canonical dot patterns and finger configurations.
 Results demonstrated that numerical information was abstracted and
 generalized over the different representation codes by revealing clear
 discrimination responses (at 1.2 Hz) of the deviant numerosity from the
 base numerosity, recorded over parieto-occipital electrodes. Crucially,
 and supporting the claim that discrimination responses reflected magnitude
 processing, the presentation of a deviant numerosity distant from the base
 (e.g., base “2” and deviant “8”) elicited larger right-hemispheric
 responses than the presentation of a close deviant numerosity (e.g., base
 “2” and deviant “3”). This finding nicely represents the neural signature
 of the distance effect, an interpretation further reinforced by the clear
 correlation with individuals’ behavioral performance in an independent
 numerical comparison task. Our results, therefore, provide for the first
 time unambiguously a reliable and specific neural marker of a magnitude
 representation that is shared among several numerical codes.
description: Complete data set for the electrophysiological and behavioral
 experiments (see README).
DOI: 10.5061/dryad.z612jm6fj
title: Data for: Wild bee communities benefit from temporal complementarity of hedges and flower strips in apple orchards

description: 1. Wild bees importantly pollinate both crop and wild plants. Yet, in
 intensive agricultural landscapes, wild bees are rare due to resource
 limitations of nectar and pollen. Flower strips and hedges are often used
 as resource enhancements for wild bees to overcome this shortage, but
 provide floral resources only during specific time periods. To sustain
 diverse and stable bee communities, bee-attractive flowers need to be
 available during the entire growing season. This may be achieved by
 combining flower strips and hedges to complement each other and provide
 continuous floral resources. 2. Over three subsequent years, we compared
 the phenology of flower and wild bee communities in perennial flower
 strips, hedges and improved hedges (complemented with a sown herb layer)
 in conventional apple orchards in Southern Germany, a
 pollination-dependent crop-system. 3. Hedges provided floral resources in
 the early season while the flower strips took over later in the season. 4.
 Bees visited the hedges mostly from March to June, whereas they visited
 the flower strips from June to August (first year), and in the second year
 already from April onwards. Flower strips were visited with an overall
 higher abundance and species richness than the improved and not modified
 hedges. 5. Synthesis and application: For enhancing wild bees in intensive
 apple orchards, hedges and perennial flower strips are complementary in
 providing flower resources. Yet, flower strips bloom more constantly and
 during periods of flower scarcity, and thus attract more bees than hedges.
 Perennial flower strips of different age classes should be preferred over
 annual strips, at best in a network with some well-maintained hedges, as
 perennial flower strips of different age attract different bee communities
 and thus potentially a higher bee diversity on the landscape level.
DOI: 10.6084/m9.figshare.31168501
title: <b>Feasibility of </b><b>c</b><b>ardiac </b><b>m</b><b>agnetic </b><b>r</b><b>esonance for </b><b>a</b><b>ssessing </b><b>a</b><b>trioventricular </b><b>b</b><b>lock in </b><b>a</b><b>cute </b><b>m</b><b>yocarditis</b>

description: The incidence of conduction block in acute myocarditis (AM) is 10% and atrioventricular block (AVB) is generally associated with LV dysfunction and HF.Patients presenting with symptoms of HF have worse prognosis compared with those presenting with chest pain.High-grade atrioventricular block is recognized as a critical criterion for identifying high-risk or complicated myocarditis.However, research specifically focusing on myocardial tissue characteristics identified by CMR in myocarditis patients with AVB remains limited.Therefore,the objectives of the present study are to investigate the performance of CMR tissue characterization parameters in patients with AM and AVB, and to evaluate their diagnostic utility in differentiating these patient groups.Furthermore, it aims to analyze the association between CMR tissue parameters and clinical outcomes to provide an imaging basis for the early identification of poor clinical outcome.We demonstrated that the advanced AVB group had considerably elevated ECV values across multiple segments ,while other tissue parameters had no significant differences. Additionally,the ECV of the basal superior ventricular septum effectively discriminated between non-advanced AVB and advanced AVB.Notably,adverse clinical outcomes occurred exclusively in three patients from the advanced group who had elevated ECV of the basal superior ventricular septum.
DOI: 10.6084/m9.figshare.31168501.v1
title: <b>Feasibility of </b><b>c</b><b>ardiac </b><b>m</b><b>agnetic </b><b>r</b><b>esonance for </b><b>a</b><b>ssessing </b><b>a</b><b>trioventricular </b><b>b</b><b>lock in </b><b>a</b><b>cute </b><b>m</b><b>yocarditis</b>

description: The incidence of conduction block in acute myocarditis (AM) is 10% and atrioventricular block (AVB) is generally associated with LV dysfunction and HF.Patients presenting with symptoms of HF have worse prognosis compared with those presenting with chest pain.High-grade atrioventricular block is recognized as a critical criterion for identifying high-risk or complicated myocarditis.However, research specifically focusing on myocardial tissue characteristics identified by CMR in myocarditis patients with AVB remains limited.Therefore,the objectives of the present study are to investigate the performance of CMR tissue characterization parameters in patients with AM and AVB, and to evaluate their diagnostic utility in differentiating these patient groups.Furthermore, it aims to analyze the association between CMR tissue parameters and clinical outcomes to provide an imaging basis for the early identification of poor clinical outcome.We demonstrated that the advanced AVB group had considerably elevated ECV values across multiple segments ,while other tissue parameters had no significant differences. Additionally,the ECV of the basal superior ventricular septum effectively discriminated between non-advanced AVB and advanced AVB.Notably,adverse clinical outcomes occurred exclusively in three patients from the advanced group who had elevated ECV of the basal superior ventricular septum.
DOI: 10.15468/dl.j7s9cr
title: Occurrence Download

description: A dataset containing 711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hyalosphenia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 711 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003208-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cc2fqz68w
title: Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

description: Long-read sequencing technologies have improved significantly since their
 emergence. Their read lengths, potentially spanning entire transcripts, is
 advantageous for reconstructing transcriptomes. Existing long-read
 transcriptome assembly methods are primarily reference-based and to date,
 there is little focus on reference-free transcriptome assembly. We
 introduce RNA-Bloom2, a reference-free assembly method for long-read
 transcriptome sequencing data. RNA-Bloom2 is available on GitHub
 at: https://github.com/bcgsc/RNA-Bloom. We benchmarked the
 assembly quality and the computational performance of RNA-Bloom2 on
 simulated data. We prepared two mouse simulated datasets with
 Trans-NanoSim for the cDNA and dRNA sequencing protocols model on
 experimental ONT data. The datasets were simulated based on the
 mouse ENSEMBL annotation for GRCm39. To investigate the effect of
 sequencing depth, we subsampled each dataset to 2, 10, and 18 million
 reads, resulting in a total of six sets of reads for our benchmarking
 experiments. Using the simulated data, we showed that the transcriptome
 assembly quality of RNA-Bloom2 is competitive to those of reference-based
 methods.
description: The reads were simulated with Trans-NanoSim version 3.1.0: https://github.com/bcgsc/NanoSim
description: Decompress the tarballs: <pre>tar -zcf
 mouse_cdna.tar.gz<br>tar -zcf mouse_drna.tar.gz</pre>
 Extract the sample read files: <pre>cd
 mouse_cdna<br>bash extract_reads.sh<br><br>cd
 mouse_drna<br>bash extract_reads.sh</pre>
DOI: 10.5061/dryad.6m905qg2w
title: Data from: A comprehensive evaluation of flowering plant diversity and conservation priority for national park planning in China

description: Establishment of a national park protection system in China, including the
 latest target proposed to protect at least 30% of the land area, calls for
 a comprehensive exploration of conservation priorities incorporating
 multiple diversity facets. We herein evaluate the spatial distribution of
 Chinese flowering plants from the perspectives of richness, uniqueness,
 vulnerability, and evolutionary history, by integrating three
 mega-phylogenies and comprehensive distribution data. We detect
 significantly high consistency among hotspots of different diversity
 measures for Chinese flowering plants, suggesting that multiple facets of
 evolutionary diversity are concentrically distributed in China. Affording
 legal protection to these areas is expected to maximize positive
 conservation outcomes. We propose two integrative diversity indices by
 incorporating three richness-based and three phylogeny-based measures,
 respectively. Both methods identify areas with high species richness, but
 the integrative phylogeny-based index also locates key areas with ancient
 and unique evolutionary histories (e.g., Ailao-Wuliang Mts, Dabie Mts,
 Hainan rainforest, Karst area of Yunnan-Guizhou-Guangxi, Nanling Mts, and
 southeast coastal regions). Of all the diversity indices explored,
 phylogenetic endemism maximizes the incidental protection of other indices
 in most cases, emphasizing its significance for conservation planning.
 Finally, 42 priority areas are identified by combining the 5%-criterion
 hotspots of two integrative indices and the minimum area to protect all
 threatened species analyzed. These priorities cover only 13.3% of China’s
 land area but host 97.1% of species richness (23,394/24,095), 96.5% of
 endemic species (11,841/12,274), 100% of threatened species (2,613/2,613),
 and 99.3% of phylogenetic diversity for flowering plants involved in this
 study. These frameworks provide a solid scientific basis for national park
 planning in China.
description: The dataset contains: (1) The time tree of
 13,663 species estimated using treePL (Tactual);
 <em>time_tree_13663sp.tre</em> (2)
 The complete-species tree of 27,185 species generated by inserting species
 without sequence data into the basal node of its corresponding genus or
 family using “scenario 1” in “V.PhyloMaker” package of R
 (Tbasal);
 <em>species_tree_27,185sp_s1.tre</em>
 (3) Ten complete-species trees of 27,185 species generated by
 randomly inserting species without sequence data at or below the basal
 node of its corresponding genus or family using “scenario 2” in
 “V.PhyloMaker” package of R (Trandom).
 <em>10_species_trees_27,185sp_s2.tre</em>
DOI: 10.5061/dryad.wm37pvmqv
title: Nitrogen and water availability control plant carbon storage with warming

description: Plants may slow global warming through enhanced growth, because increased
 levels of photosynthesis stimulate the land carbon (C) sink. However, how
 climate warming affects plant C storage globally and key drivers
 that determining the response of plant C storage to climate warming
 remains unclear, causing uncertainty in climate projections. We performed
 a comprehensive meta-analysis, compiling 393 observations from 99 warming
 studies to examine the global patterns of plant C storage responses to
 climate warming and explore the key drivers. Warming significantly
 increased total biomass (+8.4%), aboveground biomass (+12.6%) and
 belowground biomass (+10.1%). The effect of experimental warming on plant
 biomass was best explained by the availability of soil nitrogen
 (N) and water. Across the entire dataset, warming-induced changes
 in total, aboveground and belowground biomass all positively
 correlated with soil C:N ratio, an indicator of soil N
 availability. In addition, warming stimulated plant biomass more strongly
 in humid than in dry ecosystems, and warming tended to decrease root:shoot
 ratios at high soil C:N ratios. Together, these results suggest dual
 controls of warming effects on plant C storage; warming increases plant
 growth in ecosystems where N is limiting plant growth, but it reduces
 plant growth where water availability is limiting plant growth. Together,
 these findings suggested that warming effects on plant C storage largely
 depend on soil N and water status, which should be considered into
  Earth system models to improve the future prediction of
 C-climate change feedbacks.
DOI: 10.5061/dryad.k6djh9w9b
title: Urbanization shapes the relation between density and melanin-based colouration in bird communities

description: Growing urbanization increasingly influences ecosystems worldwide. While
 the effects of urban conditions within species (through either plastic or
 evolutionary responses) have been widely studied, their potential
 influences among species (through environmental filter), especially
 concerning their colouration, remain poorly known. Here, we investigated
 whether avian communities breeding inside and outside a major European
 city (Paris) differ with regards to melanin-based plumage colouration.
 Melanins are heritable pigments present in many taxa and have a series of
 unique properties that may allow coping with urban conditions. Using
 melanic-based colouration as an integrative phenotypic marker, we
 predicted (i) that the probability of breeding inside the city should
 increase with the intensity of species melanin-based colouration, (ii)
 that for species breeding both inside and outside the city, density should
 increase with the intensity of dark colouration inside the city, but not
 outside the city, and (iii) that species not breeding inside the city
 should not exhibit this positive relation between density and colouration.
 Our results confirmed these predictions. In addition, the density of
 species not breeding inside the city decreased with the darkness of their
 plumage. Altogether, these results suggest that bird species experience a
 balance between costs and benefits of melanin-based colouration shaped by
 environmental conditions. Both the environmental filtering and the
 urbanisation-shaped relation between density and colouration evidenced
 here are likely a general trend, however possibly modulated by additional
 local environmental conditions. Their importance may even be
 underestimated given the restricted geographical scale and the overall
 urbanization rate of the region studied. Further studies involving regions
 with contrasted environmental conditions should gain insight into the
 consequences of urbanization worldwide on traits associated with
 melanin-based colouration.
DOI: 10.15468/dl.u5svz4
title: Occurrence Download

description: A dataset containing 7826 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euploea mulciber"
 ]
}

 The dataset includes 7826 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003206-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5hqbzkh8k
title: Drivers of Odonata flight timing revealed by natural history collection data

description: Global change may cause widespread phenological shifts. But knowledge of
 the extent and generality of these shifts is limited by the availability
 of phenological records with sufficiently large spatiotemporal extents.
 Using North American odonates (damselflies and dragonflies) as a model
 system, we show how a combination of natural history museum and community
 science collections, beginning in 1901 and extending through 2020, can be
 leveraged to better understand phenology. We begin with an analysis of
 odonate functional traits. Principal coordinate analysis is used to place
 odonate genera within a three-dimensional trait ordination. From this, we
 identify seven distinct functional groups and select a single odonate
 genus to represent each group. Next, we pair the odonate records with a
 list of environmental covariates, including air temperature and degree
 days, photoperiod, precipitation, latitude, and elevation. An iterative
 subsampling process is then used to mitigate spatiotemporal sampling bias
 within the odonate dataset. Finally, we use path analysis to quantify the
 direct effects of degree days, photoperiod, and precipitation on odonate
 emergence timing, while accounting for indirect effects of latitude,
 elevation, and year. Path models showed that degree days, photoperiod, and
 precipitation each have a significant influence on odonate emergence
 timing, but degree days have the largest overall effect. Notably, the
 effect that each covariate has on emergence timing varied among functional
 groups, with positive relationships observed for some group
 representatives and negative relationships observed for others. For
 instance, Calopteryx sp. emerged earlier as degree days increased, while
 Sympetrum sp. emerged later. Previous studies have linked odonate
 emergence timing to temperature, photoperiod, or precipitation. By using
 natural history museum and community science data to simultaneously
 examine all three influences, we show that systems-level understanding of
 odonate phenology may now be possible.
DOI: 10.15468/dl.8pmgmj
title: Occurrence Download

description: A dataset containing 5347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tetrastichium"
 ]
}

 The dataset includes 5347 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003209-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.