cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d1vh5w
title: Data from: Evaluating the tradeoff between offspring number and survivorship across fishes, amphibians, reptiles and mammals

description: Species differ widely in their strategies of resource allocation to
 offspring size and number, ranging from teleost fishes and amphibians that
 produce many tiny offspring to reptiles and mammals that produce
 relatively few large offspring. Trade-offs between offspring survivorship
 and fecundity are thought to limit the success of any particular
 reproductive strategy, but these trade-offs have not been evaluated
 quantitatively across the full range of variability in offspring size and
 number. Here we examine the relationship of offspring size to reproductive
 success (i.e., fitness) within and across teleost fishes, amphibians,
 reptiles and mammals. To do so, we evaluate the relationships of offspring
 size to survivorship (proportion of offspring surviving to maturity) and
 to fecundity (# offspring/time). We show that survivorship tends to
 increase in proportion with relative offspring mass (offspring mass/adult
 mass), whereas fecundity, normalized to offspring biomass production rate,
 tends to decrease in proportion with offspring mass. Consequently, the
 product of survivorship and fecundity – reproductive success – is
 generally independent of offspring mass. Thus, our results show
 quantitatively how survivorship and fecundity trade-off across diverse
 taxa to limit reproductive success.
description: The R code used to produce the results in the manuscript can be
 found here: https://github.com/daan4786/reproductive-success
DOI: 10.5061/dryad.79cnp5htw
title: A tipping-point in carbon storage when forest expands into tundra is related to mycorrhizal recycling of nitrogen

description: Tundra ecosystems are global belowground sinks for atmospheric CO2.
 Ongoing warming-induced encroachment by shrubs and trees risks turning
 this sink into a CO2 source, resulting in a positive feedback on climate
 warming. To advance mechanistic understanding of how shifts in mycorrhizal
 types affect long-term carbon (C) and nitrogen (N) stocks, we studied
 small-scale soil depth profiles of fungal communities and C-N dynamics
 across a subarctic-alpine forest-heath vegetation gradient. Belowground
 organic stocks decreased abruptly at the transition from heath to forest,
 linked to the presence of certain tree-associateds ectomycorrhizal fungi
 that contribute to decomposition when mining N from organic matter. In
 contrast, ericoid mycorrhizal plants and fungi were associated with
 organic matter accumulation and slow decomposition. If climatic controls
 on arctic-alpine forest lines are relaxed, increased decomposition will
 likely outbalance increased plant productivity, decreasing the overall C
 sink capacity of displaced tundra.
description: Soil samples were taken in 24 plots representing four vegetation
 types along a subarctic-alpine birch forest-heath tundra ecotone in
 Northern Sweden. Soil cores were split into fine-scaled layers, which were
 analysed for various biochemical characteristics and for fungal
 communities based on ITS2 meta-barcoding. Please find all details on
 sampling and analyses in the associated paper.
DOI: 10.5061/dryad.m0cfxpp36
title: Supplementary figures for: Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data

description: Stochastic models of character trait evolution have become a cornerstone
 of evolutionary biology in an array of contexts. While probabilistic
 models have been used extensively for statistical inference, they have
 largely been ignored for the purpose of measuring distances between
 phylogeny-aware models. Recent contributions to the problem of
 phylogenetic distance computation have highlighted the importance of
 explicitly considering evolutionary model parameters and their impacts on
 molecular sequence data when quantifying dissimilarity between trees. By
 comparing two phylogenies in terms of their induced probability
 distributions that are functions of many model parameters, these distances
 can be more informative than traditional approaches that rely strictly on
 differences in topology or branch lengths alone. Currently, however, these
 approaches are designed for comparing models of nucleotide substitution
 and gene tree distributions, and thus, are unable to address other classes
 of traits and associated models that may be of interest to evolutionary
 biologists. Here we expand the principles of probabilistic phylogenetic
 distances to compute tree distances under models of continuous trait
 evolution along a phylogeny. By explicitly considering both the degree of
 relatedness among species and the evolutionary processes that collectively
 give rise to character traits, these distances provide a foundation for
 comparing models and their predictions, and for quantifying the impacts of
 assuming one phylogenetic background over another while studying the
 evolution of a particular trait. We demonstrate the properties of these
 approaches using theory, simulations, and several empirical datasets that
 highlight potential uses of probabilistic distances in many scenarios. We
 also introduce an open-source R package named PRDATR for easy application
 by the scientific community for computing phylogenetic distances under
 models of character trait evolution.
DOI: 10.6078/d15m5x
title: Data in support of capturing functional strategies and compositional dynamics in vegetation demographic models

description: This collection includes output from simulations of the vegetation
 demographic model CLM-FATES, plot census data from the Soaproot Saddle
 site in the Southern Sierra Critical Zone Observatory, and a database of
 tree trait values synthesized from the literature.  The data were
 used in support of a manuscript in preparation for submission to
 Biogeosciences with the provisional title "Capturing functional
 strategies and compositional dynamics in vegetation demographic
 models".
description: FATES output: All FATES simulations were forced with 4x4 km
 spatial resolution daily climate data from 1979-2009 (Abatzoglou 2013)
 disaggregated to 3-hourly intervals (Rupp and Buotte 2020).  Soil texture
 and organic carbon content were taken from the best available soils data
 for our domain, with citations provided in the submitted manuscript. 
 Simulations were run with pine and incense cedar plant functional types.
 Parameter files used to run the four regional FATES simulations described
 in the submitted manuscritp are provided. Tree census
 data: All trees within 100ha plots were identified to species, recorded as
 live or dead, and diameter at breast height (dbh) measured to the nearest
 0.1 cm. Trait Data: These data were collected from the
 peer-review literature.  Each measurement has a column for the units and
 the citation for the values. Data for Figures: Data
 necessary to recreate all figures in the submitted manuscript, which are
 not publically available elsewhere and cited in the submitted manuscript,
 are provided.  These data take the form of raw vegetation demographic
 model output, and R objects that hold model output, benchmarking data
 available from external sourcces, and trait data.
description: Please see the Data_archive_README.rtf file for a description of
 the data.
DOI: 10.5061/dryad.s7h44j166
title: Data from: Drought then wildfire reveals a compound disturbance in a resprouting forest

description: The frequency and intensity of forest disturbances such as drought and
 fire are increasing globally, with an increased likelihood of multiple
 disturbance events occurring in short succession. Disturbances layered
 over one another may influence the likelihood or intensity of subsequent
 events (a linked disturbance) or impact response and recovery trajectories
 (a compound disturbance), with substantial implications for ecological
 spatiotemporal vulnerability. This study evaluates evidence for
 disturbance interactions of drought followed by wildfire in a resprouting
 eucalypt-dominated forest (the Northern Jarrah Forest) in southwestern
 Australia.  Sites were stratified by drought (high, low) from
 previous modelling and ground validation, and fire severity (high,
 moderate, unburnt) via remote sensing using the relative difference
 normalised burn ratio (RdNBR). Evidence of a linked disturbance was
 assessed via fine fuel consumption and remotely sensed fire severity
 (RdNBR). Compound disturbance effects were quantified at stand scale
 (canopy height, quadratic mean diameter, stem density) and at the stem
 scale (mortality).  There was no evidence of prior drought
 influencing fine fuel consumption or fire severity, hence no evidence of a
 linked disturbance.  However, compound disturbance effects were
 evident; stands previously affected by drought experienced smaller shifts
 in canopy height, quadratic mean diameter, and stem density than stands
 without prior drought impact. At the stem scale, size and fire severity
 were the strongest determinants of stem survival. Proportional resprouting
 height was higher in high drought sites than in low drought sites
 (p&lt;0.01), thus, structurally, the low drought stands decreased in
 height more than the high drought stands. Thus, a legacy of the drought
 was evident after the wildfire. While these resprouting eucalypt forests
 have been regarded as particularly resilient, this study illustrates how
 multiple disturbances can overwhelm the larger tree component and promote
 an abundance of smaller stems. We suggest that this is early evidence of a
 structural destabilisation of these forests under a more fire prone,
 hotter and drier future climate.
DOI: 10.5061/dryad.1c59zw3tx
title: Automated location invariant animal detection in camera trap images using publicly available data sources

description: 1. A time-consuming challenge faced by ecologists is the extraction of
 meaningful data from camera trap images to inform ecological management.
 Automated object detection solutions are increasingly, however, most are
 not sufficiently robust to be deployed on a large scale due to lack of
 location invariance across sites. This prevents optimal use of ecological
 data and results in significant resource expenditure to annotate and
 retrain object detectors. 2. In this study, we aimed to (a) assess the
 value of publicly available image datasets including FlickR and
 iNaturalist (FiN) when training deep learning models for camera trap
 object detection (b) develop a for training location invariant object
 detection models and (c) explore the use of small subsets of camera trap
 images for optimization training. 3. We collected and annotated 3 datasets
 of images of striped hyena, rhinoceros and pig, from FiN, and used
 transfer learning to train 3 object detection models in the task of animal
 detection. We compared the performance of these models to that of 3 models
 trained on the Wildlife Conservation Society and Camera CATalogue
 datasets, when tested on out of sample Snapshot Serengeti datasets.
 Furthermore, optimized the FiN models via infusion of small subsets of
 camera trap images to increase robustness for challenging detection cases.
 4. In all experiments, the mean Average Precision (mAP) of the FiN models
 was significantly higher (82.33-88.59%) than that achieved by the models
 trained only on camera trap datasets (38.5-66.74%). The infusion of camera
 trap images into FiN training further improved mAP, with increases ranging
 from 1.78-32.08%. 5. Ecology researchers can use FiN images for training
 robust, location invariant, out-of-the-box, deep learning object detection
 solutions for camera trap image processing. This would allow AI
 technologies to be deployed on a large scale in ecological applications.
 Datasets and code related to this study are open source and available on
 Dryad (https://doi.org/10.5061/dryad.1c59zw3tx).
DOI: 10.15468/dl.bjy577
title: Occurrence Download

description: A dataset containing 823416 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "not" : {
 "PublishingCountry" : [
 "is Norway"
 ]
 }
 },
 "Country is Svalbard and Jan Mayen",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is null",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
 },
 {
 "not" : {
 "DatasetKey" : [
 "is EBCC Atlas of European Breeding Birds"
 ]
 }
 },
 {
 "not" : {
 "DatasetKey" : [
 "is (Table 3) Relative abundance of Azolla spp., peridinoid dinocysts, gonyaulacoid dinocysts, non-saccate pollen, bisaccate pollen and spores from the Lomonosov Ridge during different Arctic coring expeditions"
 ]
 }
 }
 ]
}

 The dataset includes 823416 records from 841 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002751-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.34tmpg4jq
title: Aerosol formation due to a dental procedure: Insights leading to the transmission of diseases to the environments

description: As a result of the outbreak and diffusion of SARS-CoV-2, there has been a
 directive to advance medical working conditions. In dentistry, airborne
 particles are produced through aerosolization facilitated by dental
 instruments. To develop methods for reducing risks of infection in
 confined environments, understanding the nature and dynamics of these
 droplets is imperative and timely. This study provides the first evidence
 of aerosol droplet formation from an ultrasonic scalar under simulated
 oral conditions. State-of-the-art optical flow tracking velocimetry and
 shadowgraphy measurements are employed to quantitatively measure the flow
 velocity, trajectories, and size distribution of droplets produced during
 a dental scaling process. The droplet sizes are found to vary from 5 μm to
 300 μm; these correspond to droplet nuclei that could carry viruses. The
 droplet velocities also vary between 1.3 m/s and 2.6 m/s. These
 observations confirm the critical role of aerosols in the transmission of
 disease during dental procedures, providing invaluable knowledge for
 developing protocols and procedures to ensure the safety of both dentists
 and patients.
DOI: 10.5061/dryad.2z34tmpm0
title: Non-linear thresholds in the effects of island area on functional diversity in woody plant communities

description: 1. Threshold non-linearities in the relationship between island
 area and species richness can result in dramatic declines in richness with
 a seemingly small decline in area near the threshold. What is not known,
 is whether threshold declines in richness are also accompanied by
 non-linear changes in functional trait space and non-random shifts of
 trait group composition in response to declining area. 2. Plant
 species richness was recorded, and four functional diversity (FD)
 indices calculated based on 12 traits for 76 tree species in 5082 plots
 (5×5m) on 29 islands in the Thousand Island Lake region, Zhejiang, China.
 We tested for threshold non-linearities in richness and FD relationships
 using segmented regression, with randomized resampling using a null model
 to account for potential sampling artefacts. We clustered tree species
 into trait groupings based on trait dissimilarity, and used multinomial
 segmented models to test whether threshold area effects on FD were
 associated with shifts in trait group composition. 3. Species
 richness and three of the four FD indices showed significant threshold
 non-linearities with declining island area below a threshold of ca
 1.16–6.88 ha. K-means clustering identified two trait groups, reflecting
 species at the ‘fast’ versus ’slow’ ends of the trait spectrum.
 Significant area thresholds in trait group composition were driven by
 increasing relative richness, but decreasing relative abundance, of
 species with resource-conservation traits on islands below the threshold.
 4. Synthesis. We found a threshold collapse in richness on
 islands below ca. 1 ha, resulting in a significant decrease in functional
 trait space (functional richness) and an increase in the degree of niche
 differentiation among species in the community (functional divergence) on
 small islands. Threshold effects were associated with non-random
 re-assembly of trait group composition, favouring the relative richness of
 species at the ‘slow’ resource-conservation end of the trait spectrum, but
 the relative abundance of a few species with ‘fast’ resource-acquisition
 traits. These results suggest that disturbance-driven dynamics potentially
 drive a functional shift in the ecosystem state at a critical threshold.
 We show that a minimum critical habitat area is required to maintain
 functional diversity in woody plant communities
description: The data of functional diversity on the 29 islands in the
 Thousand Island Lake.
DOI: 10.15468/dl.66yhg4
title: Occurrence Download

description: A dataset containing 520 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Erythrina variegata"
 ]
}

 The dataset includes 520 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002793-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5hqbzkh58
title: Spatial and local environmental factors outweigh geo-climatic gradients in structuring taxonomically and trait-based β-diversity of benthic algae

description: Aim Understanding the variation in biodiversity and its underlying drivers
 and mechanisms is a core task in biogeography and ecology. We examined (a)
 the relative contributions of species replacement (i.e., turnover) and
 richness difference (i.e., nestedness) to taxonomically and
 trait-based β-diversity of stream benthic algae; (b) whether
 these two facets of β-diversity are correlated with each other;
 and (c) the relative contributions of local environmental, geo-climatic
 and spatial factors to the two facets of β-diversity and their
 components. Location Hun-Tai River Basin, northeastern China. Taxon Stream
 benthic algae. Methods A total of 157 sites were sampled. Mantel tests
 were used to examine the complementarities between the two facets
 of β-diversity and their components. Distance-based redundancy
 analysis and variation partitioning were utilized to investigate the
 relative contributions of local environmental, geo-climatic and spatial
 factors to each facet of β-diversity and their components.
 Results Weak correlations between taxonomically and
 trait-based β-diversity and their components were detected, which
 indicated complementarity of ecological information. Taxonomically based
 total β-diversity was largely driven by turnover, whereas
 trait-based total β-diversity was more driven by nestedness.
 Variation partitioning results indicated that local environmental and
 spatial factors contributed more than geo-climatic variables to the total
 explained variation in taxonomically and trait-based β-diversity.
 Main conclusions Different facets of β-diversity and their
 decomposition are important for understanding diversity patterns of
 benthic algae relative to abiotic factors. A high level of trait-based
 convergence among benthic algae communities, despite high taxonomic
 divergence, demonstrated turnover of species with similar biological
 traits across our study region. Our study provides a trait-based insight
 into stream benthic algae communities, which was less documented by
 previous freshwater studies that focused on regions undergoing recovery
 following human disturbances.
DOI: 10.5061/dryad.sbcc2fr60
title: High-value plant metabolite production in synthetic biosystems

description: Ephedra sinica is a high-value medicinal plant that produces important
 phenylpropylamino alkaloids pseudoephedrine and ephedrine. Few genomics
 resources exist for E. sinica, which has been characterized as a
 tetraploid with a monoploid genome size of 8.56 Gb. Here we reported a
 partial genome assembly of E. sinica (12.8 Gb) based on
 Illumina short-read sequencing technology at low coverage.
description: Total genomic DNA was extracted using a standard CTAB modified
 with the addition of RNase A treatment and polysaccharide removal. gDNA of
 greater than &gt;20kb in length was obtained. For shotgun sequencing
 on Illumina HiSeq X, we constructed four PCR-Free libraries with
 insert-size of 550 bp, and obtained 349 million 150 bp pair-ended reads
 (base count of 105.5 Gb). We first filtered the raw Illumina data with
 fastp<sup> </sup>(-q 20 -u 40 -l 51). SOAPdenovo-63mer module
 of the SOAPdenovo2 was used for the contig level assembly with the best
 kmer-size of 25. The same dataset was used for the scaffolding
 step.
DOI: 10.5061/dryad.905qfttk2
title: A case report on concurrent catatonia in a man with COVID-19

description: Introduction: Coronavirus disease 2019, the disease caused by SARS-CoV-2,
 has contributed to considerable morbidity and mortality in 2020. While
 respiratory symptoms are predominant in COVID-19, there have been reports
 of neurologic sequel including central nervous symptoms such as catatonia,
 which is a complex syndrome of bizarre motor behavior, impaired volition,
 and vegetative abnormalities. Here we present a case of catatonia as the
 first symptom in a patient with Covid-19, and his challenging treatment.
 Case: We describe a case of concurrent COVID-19 and catatonia in a 43-year
 old man without any prior psychiatric history, who was hospitalized with
 loss of consciousness. His symptoms of catatonia improved with the
 administration of ECT. Discussion: We highlight the importance of the
 consideration of catatonia as a possible cause of loss of consciousness in
 medically ill patients. we investigate the various possible mechanisms of
 Covid-19 involvement in the development of catatonia and the methods of
 dealing with a patient with Covid-19 and psychological symptoms admitted
 in the ICU. Conclusion: Not only catatonia can co-occur with COVID-19, but
 it may be the first and only Feature presented in the context of this
 infection, so it deserves special attention especially in unconscious
 patients. In medically-ill patients with Covid-19 and catatonia symptoms
 for which benzodiazepines can’t be administered, ETC use can be considered
 as a low-complicated and rapid method.