cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6908r
title: Data from: Whole-chloroplast analysis as an approach for fine-tuning the preservation of a highly charismatic but critically endangered species, Wollemia nobilis (Araucariaceae)

description: The critically endangered Wollemia nobilis W.G. Jones, K.D. Hill &
 J.M. Allen is endemic to Wollemi National Park north of Sydney
 (Australia). All known wild individuals are restricted to four sites in a
 single canyon system. W. nobilis can reproduce sexually but at all sites
 individual clumps can be multi-stemmed from a common base. In the first
 genetic study of this species, no genetic variation was found across
 multiple genetic marker types representing hundreds of nuclear loci,
 indicating this species is characterised by very low genetic variation. In
 this study we searched for variation across the chloroplast using shotgun
 sequencing, bioinformatic extraction of chloroplast DNA and variant
 detection. Six chloroplast single nucleotide polymorphisms were detected,
 producing three chlorotypes. Chlorotype 1 is found in every individual
 surveyed at Sites 1 and 3, and in individuals from Sites 2 and 4.
 Chlorotype 2 – the most distinct chlorotype – was found in two individuals
 from Site 4. Chlorotype 3 consists of a single difference from Chlorotype
 1 and may represent a somaclonal mutant. These findings will guide
 management and translocation of this critically endangered species. This
 study provides a practical template that is highly informative and easily
 applicable to other taxa in similar circumstances.
description: Wollemia nobilis
 chloroplast primers and sequencesThe data file contains
 primer sequences designed to verify putative SNPs in the chloroplast DNA
 of Wollemia nobilis. The sequences that contributed to each of the three
 chlorotypes characterised in the paper are included along with the
 position of the variant in the sequence (where one was
 detected).
DOI: 10.15468/dl.pxcbhf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Odonata, Lepidoptera, Orthoptera)",
 "DatasetKey is NABU|naturgucker",
 "Country is Germany",
 "StateProvince is Bayern",
 "HasCoordinate is true",
 "Year is greater than or equal to 1960",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001329-260126135527185/datasets/export for details.
DOI: 10.15468/dl.csvtm8
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Micrurus filiformis"
 ]
}

 The dataset includes 157 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001327-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18384838
title: Unveiling Key Performance Indicators for the Energy Efficiency of Cloud Data Storage (Replication Package)

description: This repository provides the replication package for our study "Unveiling Key Performance Indicators for the Energy Efficiency of Cloud Data Storage", submitted to the GREENS Workshop at ICSA 2024
DOI: 10.5281/zenodo.18384839
title: Unveiling Key Performance Indicators for the Energy Efficiency of Cloud Data Storage (Replication Package)

description: This repository provides the replication package for our study "Unveiling Key Performance Indicators for the Energy Efficiency of Cloud Data Storage", submitted to the GREENS Workshop at ICSA 2024
DOI: 10.5061/dryad.697r480
title: Data from: First-in-human randomized controlled trial of an oral, replicating Adenovirus 26 vector vaccine for HIV-1

description: Background: Live, attenuated viral vectors that express HIV-1 antigens are
 being investigated as an approach to generating durable immune responses
 against HIV-1 in humans. We recently developed a replication-competent,
 highly attenuated Ad26 vector that expresses mosaic HIV-1 Env
 (rcAd26.MOS1.HIV-Env, “rcAd26”). Here we present the results of a
 first-in-human, placebo-controlled clinical trial to test the safety,
 immunogenicity and mucosal shedding of rcAd26 given orally. Methods:
 Healthy adults were randomly assigned to receive a single oral dose of
 vaccine or placebo at 5:1 ratio in a dosage escalation of 10^8 to 10^11
 rcAd26 VP (nominal doses) at University of Rochester Medical Center,
 Rochester, NY, USA. Participants were isolated and monitored for
 reactogenicity for 10 days post-vaccination, and adverse events were
 recorded up to day 112. Rectal and oropharyngeal secretions were evaluated
 for shedding of the vaccine. Humoral and cellular immune responses were
 measured. Household contacts were monitored for secondary vaccine
 transmission. Results: We enrolled 22 participants and 11 household
 contacts between February 7 and June 24, 2015. 18 participants received
 one dose of HIV-1 vaccine and 4 participants received placebo. The vaccine
 caused only mild to moderate adverse events. No vaccine-related SAEs were
 observed. No infectious rcAd26 viral particles were detected in rectal or
 oropharyngeal secretions from any participant. Env-specific ELISA and
 ELISPOT responses were undetectable. No household contacts developed
 vaccine-induced HIV-1 seropositivity or vaccine-associated illness.
 Conclusions: The highly attenuated rcAd26.MOS1.HIV-Env vaccine was well
 tolerated up to 10^11 VP in healthy, HIV-1-uninfected adults, though the
 single dose was poorly immunogenic suggesting the replicative capacity of
 the vector was too attenuated. There was no evidence of shedding of
 infectious virus or secondary vaccine transmission following the isolation
 period. These data suggest the use of less attenuated viral vectors in
 future studies of live, oral HIV-1 vaccines. Clinical Trials Registration:
 NCT02366013
description: Stephenson_PLOS
 ONE_R001This excel file includes
 the safety data, immunologic endpoints, and virologic endpoints collected
 in a clinical trial testing an oral, live HIV vaccine candidate
 (NCT02366013). This was a phase 1 study conducted by Beth Israel Deaconess
 Medical Center and University of Rochester, NY.
DOI: 10.5061/dryad.5n0c3
title: Data from: Species pool functional diversity plays a hidden role in generating β-diversity

description: Functional trait diversity is used as a way to infer mechanistic processes
 that drive community assembly. While functional diversity within
 communities is often viewed as a response variable, here we present and
 test a framework for how functional diversity among taxa in the regional
 species pool drive the assembly of communities among habitats. We
 predicted that species pool functional diversity should work with
 environmental heterogeneity to drive β-diversity. We tested these
 predictions by modeling empirical patterns in invertebrate communities
 from 570 streams in 52 watersheds. Our analysis of the field data provided
 strong support for the inclusion of both functional diversity and
 environmental heterogeneity in the models, and our predictions were
 supported when the community was analyzed all together. However, analyses
 within individual functional feeding guilds revealed strong context
 dependency in the relative importance of functional diversity, γ-richness,
 and environmental heterogeneity on β-diversity. We interpret the results
 to mean that functional diversity can play an important role in driving
 β-diversity; however, within guilds the nature of interspecific
 interactions and species pool size complicate the relationship. Future
 research should test this conceptual model across different ecosystems and
 in experimental settings using metacommunity mecocosms to enhance our
 understanding the role that functional variation plays in generating
 spatial biodiversity patterns.
description: Watershed Invertebrate
 Diversity Data for 1995 MBSSData accompanying the
 analyses in Patrick & Brown 2017, Species pool functional diversity
 plays a hidden role in generating β-diversity. Eight columns by 266 rows.
 Each row corresponds to a community type in a particular watershed.
 Community type is designated by the "group" column (P= Predator,
 H=Herbivore, F=Filterer, C=Collector-Gatherer, S = Shredder, all = Whole
 Community). Watershed is denoted in the "MDE8Digit" column by a
 code referring to a Maryland 8 Digit watershed code (corresponds to USGS
 HUC12). The average within stream alpha richness for the watershed is in
 the "alpha" column. The total gamma richness for the watershed
 is in the "gamma" column. The functional diversity, expressed as
 RaoQ, for the species pool of the watershed is in the "fdiv"
 column. The beta diversity, expressed as mean bray curtis dissimilarity,
 of the watershed is in the "bdiv" column. The environmental
 dispersion, expressed as multivariate dispersion among environmental
 variables, is in the "envdisp" column. Please see Patrick &
 Brown 2017 for detailed methods.dryad.table.csv
DOI: 10.15468/dl.k4wzzu
title: Occurrence Download

description: A dataset containing 4970 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Dicranopteris linearis"
 ]
}

 The dataset includes 4970 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001326-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h550gp2
title: Data from: Competitive growth in a social fish

description: Many animal societies have dominance hierarchies in which social rank is
 correlated with size. In such societies, the growth and size of
 individuals can be a strategic response to their social environment: in
 fishes, individuals may decrease their growth rate to remain small and
 retain a subordinate position; in mammals, individuals may increase their
 growth rate to become large and attain a dominant position — a strategy
 called competitive growth. Here, we investigate whether the clown
 anemonefish Amphiprion percula exhibits competitive growth also. We show
 that juvenile clownfish paired with a size-matched reproductive rival
 increase their growth rate and size relative to solitary controls.
 Remarkably, paired individuals achieved this despite being provided with
 the same amount of food as solitary controls. Our results demonstrate that
 clownfish are able to increase their growth rate in response to social
 competition. This study adds to the growing body of evidence that the
 growth of social vertebrates can be a fine-tuned plastic response to their
 social environment.
description: Reed_BioLet_Data_20181210Data on growth of clown anemonefish Amphiprion percula collected in the lab at Boston University in 2016 and 2017. Two years of data, reflecting two slightly different experiments, on two separate pages. 'Final length' is the length of the fish at the end of the experiment (mm); 'Individual' is the type of individual at the end of the experiment (P1 = pair-rank-1; P2 = pair-rank-2; S = solitary); 'Treatment' is the experimental treatment (P = paired; S = solitary); 'Replicate' is the replicate ID: in both years the fish were housed in size-matched replicates at the start of the experiment.
DOI: 10.15468/dl.q7c8u5
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polycarpaea carnosa"
 ]
}

 The dataset includes 95 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001328-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5v5b124
title: Data from: A range-wide domino effect and resetting of the annual cycle in a migratory songbird

description: Latitudinal differences in timing of breeding are well documented but how
 such differences carry over to influence timing of events in the annual
 cycle of migratory birds is not well understood. We examined geographic
 variation in timing of events throughout the year using light-level
 geolocator tracking data from 133 migratory tree swallows (Tachycineta
 bicolor) originating from 12 North American breeding populations. A
 swallow’s breeding latitude influenced timing of breeding, which then
 carried over to affect breeding ground departure. This resulted in
 subsequent effects on the arrival and departure schedules at fall stopover
 locations and timing of arrival at non-breeding locations. This “domino
 effect” between timing events was no longer apparent by the time
 individuals departed for spring migration. Our range-wide analysis
 demonstrates the lasting impact breeding latitude can have on migration
 schedules but also highlights how such timing relationships can reset when
 individuals reside at non-breeding sites for extended periods of time.
description: Gow et al. tres timing
 data supplementgow et al. tres timing data
 supplement.csv
DOI: 10.13140/rg.2.2.21485.86246
title: OFA for general anesthesia, deep and awake sedation. 1 Good luck and keep it simple! 2025 "OFAM (opioid free general anesthesia mixture) (Mulimix)
DOI: 10.5061/dryad.5mr10r5
title: Data from: On again, off again: acute stress response and negative feedback together predict resilience to experimental challenges

description: 1. Individuals often vary markedly in their ability to cope with
 stressors, but the drivers of this variation remain poorly understood.
 Many studies have tested relationships among individual variation in
 glucocorticoid levels and the response to challenges – often finding
 inconsistent patterns; however, few have addressed whether variation in
 the capacity to terminate the stress response through negative feedback is
 associated with stress resilience. 2. While conceptual models predict that
 interactions among different components of hypothalamic-pituitary-adrenal
 (HPA) axis regulation may be important predictors of the phenotypic and
 fitness effects of stress, we are aware of no previous experimental tests
 of this hypothesis. 3. We investigate whether individual variation in HPA
 axis regulation is related to resilience to experimental challenges in
 free-living tree swallows (Tachycineta bicolor). We mimicked salient
 natural challenges by temporarily reducing flight efficiency or increasing
 perceived predation risk during incubation, and determined whether HPA
 axis responsiveness prior to treatments predicted resilience. 4. Females
 that exhibited both a robust HPA axis activation and strong negative
 feedback were less likely to abandon nests during incubation. 5. Our
 results suggest that exhibiting a strong HPA axis activation coupled with
 effective negative feedback may predict stress resilience. Therefore, the
 ability to turn on and then off the HPA axis efficiently may be important
 for fitness. 6. Our results also suggest that the interactions between
 different components of the HPA axis may provide greater insight into
 differences in stress coping capacity.
description: Data CORT Incub
 AbandonCorticosterone data at
 first capture and nest abandonment statusData CORT Time
 serieCorticosterone data for
 each sample (baseline, stress-induced, post-dex)Data Mass
 changeBody mass data at first
 capture and second capture in females that did not
 abandoned.Data Dex
 validationCorticosterone data for
 dexamethasone validation experiment.
DOI: 10.5061/dryad.pg6qq10
title: Data from: Rapid comeback of males: evolution of male-killer suppression in a green lacewing population

description: Evolutionary theory predicts that the spread of cytoplasmic sex ratio
 distorters leads to the evolution of host nuclear suppressors, although
 there are extremely few empirical observations of this phenomenon. Here,
 we demonstrate that a nuclear suppressor of a cytoplasmic male killer has
 spread rapidly in a population of the green lacewing Mallada desjardinsi.
 An M. desjardinsi population, which was strongly female-biased in 2011
 because of a high prevalence of the male-killing Spiroplasma endosymbiont,
 had a sex ratio near parity in 2016, despite a consistent Spiroplasma
 prevalence. Most of the offspring derived from individuals collected in
 2016 had 1:1 sex ratios in subsequent generations. Contrastingly,
 all-female or female-biased broods appeared frequently from crossings of
 these female offspring with males derived from a laboratory line founded
 by individuals collected in 2011. These results suggest near-fixation of a
 nuclear suppressor against male killing in 2016 and reject the notion that
 a non-male-killing Spiroplasma variant has spread in the population.
 Consistently, no significant difference was detected in mitochondrial
 haplotype variation between 2011 and 2016. These findings, and earlier
 findings in the butterfly Hypolimnas bolina in Samoa, suggest that these
 quick events of male recovery occur more commonly than is generally
 appreciated.
description: Raw data of M.
 desjardinsi samples collected in MatsudoRawData0215.xlsx
DOI: 10.5061/dryad.2q0t408
title: Data from: Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)

description: Whole genome duplication (WGD), the doubling of the nuclear DNA of a
 species, contributes to biological innovation by creating genetic
 redundancy. One mode of WGD is allopolyploidization, wherein each genome
 from two ancestral species becomes a 'subgenom' of a polyploid
 descendant species. The evolutionary trajectory of a duplicated gene that
 arises from WGD is influenced both by natural selection, creating new or
 partitioning functions, and by gene silencing (pseudogenization). Here, we
 explored how these two phenomena varied over time and within allopolyploid
 genomes in several allotetraploid clawed frog species (Xenopus). Our
 analysis demonstrates that, across these polyploid genomes, purifying
 selection was greatly relaxed compared to a diploid outgroup, was
 asymmetric between each subgenome, and that coding regions are shorter in
 the subgenome with more relaxed purifying selection. As well, we found
 that the rate of gene loss was higher in the subgenome under weaker
 purifying selection and has remained relatively consistent over time after
 WGD. Our findings provide perspective from vertebrates on the evolutionary
 forces that likely shape allopolyploid genomes on other branches of the
 tree of life.
description: code
DOI: 10.5061/dryad.r7c23
title: Data from: No evidence that plant-soil feedback effects of native and invasive plant species under greenhouse conditions are reflected in the field

description: Plant–soil feedback (PSF) may affect above-ground higher trophic levels in
 glasshouse experiments, but evidence from field studies on the relevance
 of these multitrophic interactions for plant performance is lacking.
 Therefore, we examined whether PSF effects of several native and invasive
 plant species occur also in the field and influence plant damage by
 above-ground herbivores. Root zone soil from an abandoned urban field was
 used as inocula for the PSF experiment. First, we grew eight urban
 grassland plant species (five natives and three invasive species)
 separately in a glasshouse, with soil biota communities conditioned by the
 respective species itself (‘home soil’) or by a mixture of all other
 species (‘foreign soil’). After 13 weeks, one cohort of the plants was
 placed on an urban field in Berlin to assess damage by naturally
 colonizing herbivores, while another cohort of the plants stayed in the
 glasshouse. We observed that the extent of the PSF effects differed
 between the field and glasshouse cohorts of plants. While we found
 positive PSF responses for five of the eight plant species in the
 glasshouse, we found no PSF effects in the field. Further, there was no
 trend that invasive or native species differed in the direction or extent
 of PSF responses. Concerning the leaf damage by herbivores of the field
 plants, we found no evidence that the soil history (home vs. foreign soil)
 affected the effects of above-ground herbivores on the plants. Synthesis.
 We conclude that PSF effects are more likely to be found under glasshouse
 conditions. In the field, PSFs seem to play a minor role for the selected
 urban grassland species. More generally, our study highlights the need to
 focus on PSFs under natural conditions and in natural communities
 (including higher trophic levels), which is often overlooked in PSF
 research.
description: Plant biomass data from
 the experiment.Plant biomass data in a
 tab-separated txt-file. Species name abbreviations correspond to the
 paper.biomass_data.txtPlant damage dataPlant damage data of field plants in a tab-separated txt-file. Species name abbreviations correspond to the paper.damage_data.txt
DOI: 10.5061/dryad.88365
title: Data from: Foraging responses of sheep to plant spatial micro-patterns can cause diverse associational effects of focal plant at individual and population levels

description: 1. Multiple-scale foraging decisions by large herbivores can cause
 associational effects of focal plant individuals neighbored with different
 species. Spatial micro-patterns between the focal plant and its
 neighboring species within patches can affect herbivore foraging
 selectivity at within- and between-patch scale, which may consequently
 lead to associational plant effects occurring at both plant individual and
 population levels. However, these associational effects have not been
 explored together in the plant-herbivore interaction studies. 2. We aim to
 evaluate how plant spatial micro-pattern within different quality patches
 mediate herbivore foraging selectivity, thereby affecting the
 associational effects of focal plant individuals and population. 3. Using
 sheep as the model herbivore and a medium preferred species as the focal
 plant, we conducted a manipulative experiment by allowing sheep grazing
 freely among three different quality patches, each of which consisted of
 preferred, un-preferred and focal plant species with different abundances
 forming spatially aggregated or dispersed micro-patterns. 4. Results
 showed that, compared with the aggregated plant micro-pattern, dispersed
 plant micro-patterns within different quality patches increased sheep
 within-patch selectivity, and caused diverse associational effects of
 focal plant individuals. Focal plant individuals experienced neighbor
 contrast defense (i.e. got protection in the high quality patch) and
 associational defense (i.e. got protection in the low quality patch),
 respectively, when plants dispersedly distributed in the low and high
 quality patch. Focal plant individuals simultaneously experienced
 associational susceptibility (i.e. got damage in the high quality patch)
 and neighbor contrast susceptibility (i.e. got damage in the low quality
 patch) when plants dispersedly distributed in the medium quality patch.
 Furthermore, dispersed plant micro-patterns reduced sheep foraging
 selectivity between patches, and led to a lower consumption of focal plant
 population compared with the aggregated plant micro-pattern. 5. Herbivore
 adopt different within- and between-patch foraging decisions to maintain a
 high intake of the preferred species in response to various plant
 micro-patterns, and consequently cause diverse associational effects of
 both focal plant individuals and population. These associational effects
 have important implications for understanding the species coexistence and
 plant community assembly in the grazing ecosystems.
description: JAE-2017-00477