cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.67fp5
title: Data from: Silent oceans: ocean acidification impoverishes natural soundscapes by altering sound production of the world’s noisiest marine invertebrate

description: Soundscapes are multidimensional spaces that carry meaningful information
 for many species about the location and quality of nearby and distant
 resources. Because soundscapes are the sum of the acoustic signals
 produced by individual organisms and their interactions, they can be used
 as a proxy for the condition of whole ecosystems and their occupants.
 Ocean acidification resulting from anthropogenic CO2 emissions is known to
 have profound effects on marine life. However, despite the increasingly
 recognised ecological importance of soundscapes, there is no empirical
 test of whether ocean acidification can affect biological sound
 production. Using field recordings obtained from three geographically
 separated natural CO2 vents, we show that forecasted end-of-century ocean
 acidification conditions can profoundly reduce biological sound quantity
 and quality. Snapping shrimps were among the noisiest marine organisms and
 the suppression of their sound production at vents was responsible for the
 vast majority of the soundscape alteration observed. To assess mechanisms
 that could account for these observations, we tested whether long-term
 exposure (2-3 months) to elevated CO2 induced a similar reduction in the
 snapping behaviour (loudness and frequency) of snapping shrimps. The
 results indicated that the soniferous behaviour of these animals was
 substantially reduced in both frequency and sound level of snaps produced.
 As coastal marine soundscapes are dominated by biological sounds produced
 by snapping shrimps, the observed suppression of this component of
 soundscapes could have important and possibly pervasive ecological
 consequences for organisms that use soundscapes as a source of
 information. This trend towards silence could be of particular importance
 for those species whose larval stages use sound for orientation towards
 settlement habitats.
description: Rossi et al. 2016 Proc B
 - datasetThe excel file contains
 8 sheets. The first four sheets contain the data used for a specific
 figure in the manuscript. The name of the sheet identifies which figure
 the data represent (Fig. 1A,1B,2,3). The last four sheets contain the
 water chemistry data reported in table S1.Proc B - soundscape OA - TRossi
 dataset.xlsx
DOI: 10.5061/dryad.q9m45
title: Data from: Energetic constraints on species coexistence in birds

description: The association between species richness and ecosystem energy availability
 is one of the major geographic trends in biodiversity. It is often
 explained in terms of energetic constraints, such that coexistence among
 competing species is limited in low productivity environments. However, it
 has proven challenging to reject alternative views, including the null
 hypothesis that species richness has simply had more time to accumulate in
 productive regions, and thus the role of energetic constraints in limiting
 coexistence remains largely unknown. We use the phylogenetic relationships
 and geographic ranges of sister species (pairs of lineages who are each
 other’s closest extant relatives) to examine the association between
 energy availability and coexistence across an entire vertebrate class
 (Aves). We show that the incidence of coexistence among sister species
 increases with overall species richness and is elevated in more productive
 ecosystems, even when accounting for differences in the evolutionary time
 available for coexistence to occur. Our results indicate that energy
 availability promotes species coexistence in closely related lineages,
 providing a key step toward a more mechanistic understanding of the
 productivity–richness relationship underlying global gradients in
 biodiversity.
description: Data for Figure
 1A-DThis dataset contains
 the cell values (for NPP, species richness, sister coexistence and sister
 age) used in Figure 1A-D.Data for figure
 1.xlsxData for Figure
 2A-BThis file contains two
 datasheets. The first sheet provides the underlying sister species, and
 their values of coexistence and NPP from a single exemplar tree used to
 plot Figure 2A. The second sheet provides the numerical values plotted in
 Figure 2B.Data for figure
 2.xlsxData for Figure
 3This
 file contains the individual numeric values plotted in Figure
 3.Data for
 figure 3.xlsxData for Figure
 4A-DThis file contains 4
 datasheets providing the individual numeric values plotted in Figure
 4A-D.Data
 for figure 4.xlsxData for Figure
 5This
 file provides the cell values (species richness and coexistence) and realm
 assignments used in Figure 5.Data for figure
 5.xlsxData for Figure
 S2A-BThis file contains the
 cell values (species richness, sister species richness and coexisting
 richness) used in Figure S2A-B.Data for figure
 S2.xlsxData for Figure
 S4This file contains the
 observed and estimated vales of σ and ε for different sister species age
 distributions plotted in Figure S2.Data for figure
 S4.xlsx
DOI: 10.5061/dryad.537fs
title: Data from: Genetic variation in bitter taste receptor genes influences the foraging behavior of plateau zokor (Eospalax baileyi)

description: The ability to detect bitter tastes is important for animals; it can help
 them to avoid ingesting harmful substances. Bitter taste perception is
 mainly mediated by bitter taste receptor proteins, which are encoded by
 members of the Tas2r gene family and vary with the dietary preference of a
 specific species. Although individuals with different genotypes differ in
 bitterness recognition capability, little is known about the relationship
 between genetic variation and food selection tendencies at the
 intraspecific level. In this study, we examined the relationship between
 genotypes and diet in plateau zokor (Eospalax baileyi), a subterranean
 rodent endemic to the Qinghai-Tibet Plateau that caches food for the
 winter. We assayed the composition and taste profile of each plant
 contained in temporary caches and vicinity quadrats, which were
 representative of selected and available food, respectively. Bitter plant
 selection indices (Ebitter) were estimated. We also sequenced 26 candidate
 Tas2r genes from zokors and determined their relationships with the
 Ebitter of their caches. We identified four key results: (1) zokors varied
 considerably in both bitter food preference and Tas2r sequences; (2) five
 genes (zTas2r115, zTas2r119, zTas2r126, zTas2r134, and zTas2r136)
 exhibited allelic variation that was significantly associated with
 Ebitter; (3) synonymous SNPs, nonsynonymous SNPs, and pseudogenization are
 involved in the genotype–phenotype relationship; (4) the minor genotypes
 of zTas2r115, zTas2r134, and zTas2r136 and the major genotypes of
 zTas2r119 and zTas2r126 cached more bitter plants. Our results link Tas2r
 variation with food selection behavior at the population level for the
 first time.
description: File
 S1The
 original sequence alignments of 56 zokors respectively for the 26 Tas2r
 genes.Table
 S1-S6Table S1 GenBank
 accession numbers for human and mouse Tas2r sequences that were used for
 blast researching the zokor Tas2r genes. Table S2 Primers (5’ to 3’) for
 amplifying and sequencing the Tas2r genes of zokors. Table S3 Plants found
 in zokor over-winter caches or vicinity quadrats and their tastes as well
 as overall appearance frequencies in the 56 burrow systems. Table S4
 Composition (weight percentage) of plants with different tastes in caches
 and quadrats. Table S5 Food selection and genotype distribution at the DNA
 level of the 56 zokors. The major genotype and minor genotype(s) were
 marked as 1 and 0, respectively. Table S6 Food selection and genotype
 distribution at the AA level of the 56 zokors. The major genotype and
 minor genotype(s) were marked as 1 and 0, respectively.
DOI: 10.5061/dryad.3s6j7
title: Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials

description: Background: Little is known about publication agreements between industry
 and academic investigators in trial protocols and the consistency of these
 agreements with corresponding statements in publications. We aimed to
 investigate (i) the existence and types of publication agreements in trial
 protocols, (ii) the completeness and consistency of the reporting of these
 agreements in subsequent publications, and (iii) the frequency of
 co-authorship by industry employees. Methods and Findings: We used a
 retrospective cohort of randomized clinical trials (RCTs) based on
 archived protocols approved by six research ethics committees between 13
 January 2000 and 25 November 2003. Only RCTs with industry involvement
 were eligible. We investigated the documentation of publication agreements
 in RCT protocols and statements in corresponding journal publications. Of
 647 eligible RCT protocols, 456 (70.5%) mentioned an agreement regarding
 publication of results. Of these 456, 393 (86.2%) documented an industry
 partner’s right to disapprove or at least review proposed manuscripts; 39
 (8.6%) agreements were without constraints of publication. The remaining
 24 (5.3%) protocols referred to separate agreement documents not
 accessible to us. Of those 432 protocols with an accessible publication
 agreement, 268 (62.0%) trials were published. Most agreements documented
 in the protocol were not reported in the subsequent publication (197/268
 [73.5%]). Of 71 agreements reported in publications, 52 (73.2%) were
 concordant with those documented in the protocol. In 14 of 37 (37.8%)
 publications in which statements suggested unrestricted publication
 rights, at least one co-author was an industry employee. In 25
 protocol-publication pairs, author statements in publications suggested no
 constraints, but 18 corresponding protocols documented restricting
 agreements. Conclusions: Publication agreements constraining academic
 authors’ independence are common. Journal articles seldom report on
 publication agreements, and, if they do, statements can be discrepant with
 the trial protocol.
description: Protocol
 characteristicsProtocol characteristics
 on individual trial protocol levelPROT_EXPORT.xlsxMerged dataset of protocol and publicationMerged datasets of protocols and resulting journal publications on individual trial level.PROT_PUBL_MERGE_EXPORT.xlsx
DOI: 10.5061/dryad.7s7r1
title: Data from: Seed size predicts community composition and carbon storage potential of tree communities in rainforest fragments in India’s Western Ghats

description: Fragmentation is ubiquitous across tropical forests and drives marked
 shifts in tree community composition by differentially affecting species’
 dispersal, establishment and survival. Such compositional shifts can
 potentially alter ecosystem-level properties such as above-ground carbon
 storage, but our understanding of the factors linking compositional shifts
 to carbon storage is limited. We compared tree communities of contiguous
 and fragmented tropical rainforests in the Western Ghats (India) and
 assessed the ability of various plant functional traits associated with
 seed dispersal, establishment and survival processes to predict species’
 responses to fragmentation. Further, we assessed relationships between
 functional traits that predict tree community turnover and those that
 govern carbon storage to examine how fragmentation effects on species’
 composition can alter the ability of tree communities to store carbon.
 Seed size, as indexed by seed length, was the best predictor of species’
 responses, with larger-seeded species declining in fragments. Across
 species, seed length was positively correlated with maximum attainable
 height, which decreased by 10% on average at the community level in
 fragments. Such shifts towards smaller-seeded communities could decrease
 forest stature and reduce above-ground carbon stocks by 8%. Synthesis and
 applications. Our study highlights a previously undescribed mechanism by
 which fragmentation-driven declines of large-seeded tree species can
 reduce above-ground carbon stocks by promoting shorter-statured forests.
 These results imply that strict protection alone might be insufficient,
 and that a multi-pronged conservation strategy would be required to
 sustain carbon stocks in tropical forest fragments. Such interventions
 will need to combine restoration programmes for large-seeded tree species
 in fragments with broader-scale efforts to maintain hospitable and
 well-connected landscapes for their seed dispersers.
description: Vegetation plot data
 from contiguous and fragmented rainforests in the Western Ghats,
 IndiaPlot size: 30m X 30m.
 Min DBH: 3cm.Osuri_Sanakran_2016_JAE_plot_data.csv
DOI: 10.5061/dryad.g5510
title: Data from: Local and regional determinants of vascular epiphyte mortality in the Andean mountains of Colombia

description: 1. We present the first large-scale assessment of vascular epiphyte
 mortality in the neotropics. Our goals were to explore the primary types
 of vascular epiphyte death and to identify local and regional determinants
 of epiphyte mortality in natural forests located 60 to 2900 m a.s.l. in
 the Colombian Andes. 2. Based on two consecutive annual surveys, we
 followed the fate of 4247 epiphytes to estimate the epiphyte mortality
 rate on 116 host trees at nine sites. A logistic regression analysis for
 proportional data with a binomial distribution of the error was applied to
 determine the probability of epiphyte death in relation to local and
 regional explanatory variables. 3. The overall epiphyte mortality rate was
 7.5 ± 1.1% yr−1 (mean ± standard error). Non-mechanical factors, such as
 desiccation, accounted for a mortality rate of 1.9 ± 0.3% yr−1. Mechanical
 factors, such as falling branches, accounted for a mortality rate of 5.6 ±
 1.1% yr−1. According to generalized linear modelling analyses, both local
 and regional factors played key roles in determining epiphyte mortality.
 The actual evapotranspiration (regional factor) and the mean epiphyte
 attachment height (local factor) were both consistently positively
 associated with the probability of epiphyte death. Additional variables
 identified as possible determinants of the epiphyte mortality were the
 temperature seasonality, annual temperature range, the height and number
 of branches of the tree, and the abundance of large trees (DBH ≥ 10 cm).
 4. Synthesis. The recorded high mortality rate indicates that natural
 epiphyte assemblages must be highly dynamic to avoid local extinction of
 species. Our study identifies actual evapotranspiration as an important
 driver of epiphyte mortality, and we highlight its importance in
 determining the fate tropical epiphyte communities may experience if
 evapotranspiration increases due to climate change. We hope our study
 addresses the paucity of research on non-tree growth forms, typically
 ignored in vegetation dynamics, and encourages their inclusion in future
 studies that investigate the function of tropical ecosystems.
description: EpihyteMortalityData
DOI: 10.5061/dryad.6n018
title: Data from: Publication and reporting of clinical trial results: cross sectional analysis across academic medical centers

description: Objective: To determine rates of publication and reporting of results
 within two years for all completed clinical trials registered in
 ClinicalTrials.gov across leading academic medical centers in the United
 States. Design: Cross sectional analysis. Setting: Academic medical
 centers in the United States. Participants: Academic medical centers with
 40 or more completed interventional trials registered on
 ClinicalTrials.gov. Methods: Using the Aggregate Analysis of
 ClinicalTrials.gov database and manual review, we identified all
 interventional clinical trials registered on ClinicalTrials.gov with a
 primary completion date between October 2007 and September 2010 and with a
 lead investigator affiliated with an academic medical center. Main outcome
 measures: The proportion of trials that disseminated results, defined as
 publication or reporting of results on ClinicalTrials.gov, overall and
 within 24 months of study completion. Results: We identified 4347
 interventional clinical trials across 51 academic medical centers. Among
 the trials, 1005 (23%) enrolled more than 100 patients, 1216 (28%) were
 double blind, and 2169 (50%) were phase II through IV. Overall, academic
 medical centers disseminated results for 2892 (66%) trials, with 1560
 (35.9%) achieving this within 24 months of study completion. The
 proportion of clinical trials with results disseminated within 24 months
 of study completion ranged from 16.2% (6/37) to 55.3% (57/103) across
 academic medical centers. The proportion of clinical trials published
 within 24 months of study completion ranged from 10.8% (4/37) to 40.3%
 (31/77) across academic medical centers, whereas results reporting on
 ClinicalTrials.gov ranged from 1.6% (2/122) to 40.7% (72/177).
 Conclusions: Despite the ethical mandate and expressed values and mission
 of academic institutions, there is poor performance and noticeable
 variation in the dissemination of clinical trial results across leading
 academic medical centers.
description: Publication and
 Reporting-Compiled Data TablesCompiled data tables for
 each institution including data from the manual review for publications
 along with results reporting data and trial characteristics from
 ClinicalTrials.govCompiledDataTables-final-clean.xlsx
DOI: 10.5061/dryad.86bq5
title: Data from: Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease

description: Detecting loci under selection is an important task in evolutionary
 biology. In conservation genetics detecting selection is key to
 investigating adaptation to the spread of infectious disease. Loci under
 selection can be detected on a spatial scale, accounting for differences
 in demographic history among populations, or on a temporal scale, tracing
 changes in allele frequencies over time. Here we use these two approaches
 to investigate selective responses to the spread of an infectious
 cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the
 Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction
 site associated DNA’ (RAD) markers from populations pre- and post DFTD
 arrival, and DFTD free populations, we infer loci under selection due to
 DFTD and investigate signatures of selection that are incongruent among
 methods, populations, and times. The lack of congruence among populations
 influenced by DFTD with respect to inferred loci under selection, and the
 direction of that selection, fail to implicate a consistent selective role
 for DFTD. Instead genetic drift is more likely driving the observed allele
 frequency changes over time. Our study illustrates the importance of
 applying methods with different performance optima e.g. accounting for
 population structure and background selection, and assessing congruence of
 the results.
description: Tasmanian devil RAD
 dataThe data file consists
 of 4 parts (1999, 2004, 2009 and 2013) each representing a sampling year
 for Tasmanian devils.
DOI: 10.5281/zenodo.18387339
title: TIS_dataset

description: TIS_dataset for psychometrics analysis
DOI: 10.5281/zenodo.18387338
title: TIS_dataset

description: TIS_dataset for psychometrics analysis
DOI: 10.15468/dl.pu77d6
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paphia costata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 16 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001441-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b754g
title: Data from: Targeted reforestation could reverse declines in connectivity for understory birds in a tropical habitat corridor

description: Re-establishing connectivity between protected areas isolated by habitat
 clearing is a key conservation goal in the humid tropics. In northeastern
 Costa Rica, payments for environmental services (PES) and a government ban
 on deforestation have subsidized forest protection and reforestation in
 the San Juan–La Selva Biological Corridor (SJLSBC), resulting in a decline
 in mature forest loss and the expansion of tree plantations. We use field
 studies and graph models to assess how conservation efforts have altered
 functional connectivity over the last 25 years for four species of
 insectivorous understory birds. Field playback studies assessed how
 reforestation habitat quality affected the willingness of Myrmeciza exsul,
 Henicorhina leucosticta, Thamnophilus atrinucha, and Glyphorynchus
 spirurus to travel outside forest habitat for territorial defense.
 Observed travel distances were greatest in nonnative and native tree
 plantations with high understory stem density, regardless of overstory
 composition. In contrast, tree plantations with low stem density had
 travel responses comparable to open pasture for three of the four bird
 species. We modeled landscape connectivity for each species using graph
 models based on varying possible travel distances in tree plantations,
 gallery forests, and pastures. From 1986 to 2011, connectivity for all
 species declined in the SJLSBC landscape (5825 km2) by 14% to 21% despite
 only a 4.9% net loss in forest area and the rapid expansion of tree
 plantations over 2% of the landscape. Plantation placement in the
 landscape limited their potential facilitation of connectivity because
 they were located either far from forest cover or within already
 contiguous forest areas. We mapped current connectivity bottlenecks and
 identified priority areas for future reforestation. We estimate that
 reforestation of priority areas could improve connectivity by 2% with only
 a 1% gain in forest cover, an impressive gain given the small area
 reforested. Results indicate key locations where spatial targeting of PES
 within the SJLSBC study region would protect existing forest connectivity
 and enhance the connectivity benefits of reforestation.
description: Bird movement data in
 response to playbacks, Fagan et al. 2016This file contains the
 data for the experimental playback trials with four species of birds, as
 described in Fagan et al. 2016. See the readme for more details. If you
 want the control data for the subset of birds that responded to playbacks,
 please contact the author.uploaded_Dryad2015_con4paper_birds.zipLand cover maps for Fagan et al. 2016This contains the edited land cover maps used in Fagan et al. 2016, created from supervised classification of a 1986-2011 Landsat time series (a subset of path 15, row 53). Please cite Fagan et al. 2013 and Fagan et al. 2016 when using these maps, and see the read me and those publications for further details.uploaded_Dryad2015_con4paper_maps.zip