cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v2b8t
title: Data from: The costs and benefits of tolerance to competition in Ipomoea purpurea, the common morning glory

description: Tolerance to competition has been hypothesized to reduce the negative
 impact of plant-plant competition on fitness. Although competitive
 interactions are a strong selective force, an analysis of net selection on
 tolerance to competition is absent in the literature. Using fifty-five
 full/half-sibling families from 18 maternal lines in the crop weed Ipomoea
 purpurea we measured fitness and putative tolerance traits when grown with
 and without competition in an agricultural field. We tested for the
 presence of genetic variation for tolerance to competition and determined
 if there were costs and benefits of this trait. We also assessed
 correlations between tolerance and potential tolerance traits. We
 uncovered a fitness benefit of tolerance in the presence of competition
 and a cost in its absence. We failed to detect evidence of additive
 genetic variation underlying tolerance, but did uncover the presence of a
 significant maternal line effect for tolerance, which suggests its
 evolutionary trajectory is not easily predicted. The cost of tolerance is
 likely due to later initiation of flowering of tolerant individuals in the
 absence of competition, whereas relative growth rate was found to
 positively covary with tolerance in the presence of competition, and can
 thus be considered a tolerance trait.
description: Tolerance to Competition
 Field Experiment Datatoldat.csvR script for Tolerance to Competition Analysistolcomp.R
DOI: 10.5061/dryad.bs621
title: Data from: Is biotic resistance enhanced by natural variation in diversity?

description: Theories linking diversity to ecosystem function have been challenged by
 the widespread observation of more exotic species in more diverse native
 communities. Few studies have addressed the underlying processes by
 dissecting how biotic resistance to new invaders may be shaped by the same
 environmental influences that determine diversity and other community
 properties. In grasslands with heterogeneous soils, we added invaders and
 removed competitors to analyze the causes of invasion resistance. Abiotic
 resistance was measured using invader success in the absence of the
 resident community. Biotic resistance was measured as the reduction in
 invader success in the presence of the resident community. Invaders were
 most successful where biotic resistance was lowest and abiotic resistance
 was highest, confirming the dominant role of biotic resistance. Contrary
 to theory, though, biotic resistance was highest where both species
 richness and functional diversity were lowest. In the multivariate
 framework of a structural equation model, biotic resistance was
 independent of community diversity, and was highest where fertile soils
 led to high community biomass. Seed predation slightly augmented biotic
 resistance without qualitatively changing the results. Soil-related
 genotypic variation in the invader also did not affect the results. We
 conclude that in natural systems, diversity may be correlated with
 invasibility and yet have little effect on biotic resistance to invasion.
 More generally, the environmental causes of variation in diversity should
 be considered when examining the potential functional consequences of
 diversity.
description: Grace et al 2017
 Appendix_S3-Data
DOI: 10.15468/dl.qaa5fa
title: Occurrence Download

description: A dataset containing 562462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-73.44 46.36,-47.12 46.36,-47.12 60.71,-73.44 60.71,-73.44 46.36))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 562462 records from 360 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001077-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.81b74
title: Data from: Hacking the Bell test using classical light in energy-time entanglement–based quantum key distribution

description: Photonic systems based on energy-time entanglement have been proposed to
 test local realism using the Bell inequality. A violation of this
 inequality normally also certifies security of device-independent quantum
 key distribution (QKD) so that an attacker cannot eavesdrop or control the
 system. We show how this security test can be circumvented in energy-time
 entangled systems when using standard avalanche photodetectors, allowing
 an attacker to compromise the system without leaving a trace. We reach
 Bell values up to 3.63 at 97.6% faked detector efficiency using tailored
 pulses of classical light, which exceeds even the quantum prediction. This
 is the first demonstration of a violation-faking source that gives both
 tunable violation and high faked detector efficiency. The implications are
 severe: the standard Clauser-Horne-Shimony-Holt inequality cannot be used
 to show device-independent security for energy-time entanglement setups
 based on Franson’s configuration. However, device-independent security can
 be reestablished, and we conclude by listing a number of improved tests
 and experimental setups that would protect against all current and future
 attacks of this type.
description: Experimental
 measurementsThese are the
 measurement results for the faking of the Bell violation in the Franson
 interferometer. Filenames starting with A are Alice's measurement
 results. Filenames starting with B are Bob's measurement results. The
 three last characters of the filename show the settings of the source and
 analysis station in multiples of pi/4. The first character is the early
 setting, the middle is the late setting and the last character is the
 phase shift in the analysis station. The character N stands for no pulse.
 The data files are counts, each row is one second of data. Each column is
 one detector (plus or minus). The first half of each file is the early
 timeslot, the second half is the late timeslot. The detectors used in the
 experiment are commercial products from Princeton Lightwave. These
 detectors are InGaAs avalanche photodiodes (APDs) that use Geiger and
 biased pulse modes at the operating temperature 218 K. The detection
 wavelength range is 1300 to 1550 nm, giving a maximum detection efficiency
 of 20 % at 1550 nm. The dark count rate is 5e−5 per nanosecond
 .Franson
 experiment.zip
DOI: 10.15468/dl.tp52jm
title: Occurrence Download

description: A dataset containing 58 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'CN'
 AND GBIF_WITHIN('POLYGON((103.19070 20.98250,124.36243 20.98250,124.36243 29.44757,103.19070 29.44757,103.19070 20.98250))', occurrence.decimallatitude, occurrence.decimallongitude) = TRUE
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.occurrencestatus = 'PRESENT'
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '2473545', TRUE)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 58 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001096-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b7k60
title: Data from: Reinterpretation of a previously described Jehol bird clarifies early trophic evolution in the Ornithuromorpha

description: STM35-3 from the Yixian Formation is the only Early Cretaceous
 ornithuromorph preserving direct evidence of granivory. The crop contains
 numerous seeds and the preservation of gastroliths presumably within the
 ventriculus indicates this diet was paired with the presence of a gastric
 mill as in living granivorous birds. STM35-3 was originally referred to
 Hongshanornis longicresta, member of a diverse clade of small, basal
 ornithuromorphs with elongate hindlimbs known as the Hongshanornithidae.
 Hindlimb proportions suggest that hongshanornithids were wading birds, an
 ecological inference somewhat in conflict with direct evidence suggesting
 Hongshanornis fed on seeds. However, close inspection of STM35-3 reveals
 that the specimen represents a new species not closely related to
 hongshanornithids, distinguished by large forelimbs that exceed the length
 of the hindlimbs, robust and narrow coracoids, and a delicate edentulous
 rostrum. In contrast, all hongshanornithids have hindlimbs that far exceed
 the length of the forelimbs, coracoids with wide sternal margins, and
 small teeth throughout the upper and lower jaws. Reinterpretation of this
 new taxon, Eogranivora edentulata gen. et sp. nov, helps to clarify
 trophic driven patterns of tooth loss within the Ornithuromorpha. Apparent
 loss of the hallux may represent the first such occurrence in a Mesozoic
 bird and suggests a highly terrestrial lifestyle.
description: SI zheng etal
 eogranivoradata matrix for
 cladistic analysis
DOI: 10.5061/dryad.383q87q
title: Data from: Transient growth-enhancing effects of elevated maternal thyroid hormones at no apparent oxidative cost during early postnatal period

description: Maternal thyroid hormones (THs) have been proven crucial for embryonic
 development in humans, but their influence within the natural variation on
 wild animals remains unknown. So far the only two studies that
 experimentally investigated the potential fitness consequences of maternal
 THs in birds found inconsistent results. More studies are thus required to
 assess the general effects of maternal THs and their influences on more
 behavioral and physiological parameters. In this study, we experimentally
 elevated yolk TH content in a wild migratory passerine species, the
 collared flycatcher (Ficedula albicollis), to investigate the effects on
 hatching success, nestling growth and oxidative stress. We found that
 TH-injected eggs had a higher hatching success, and the nestlings hatched
 from TH-injected eggs were heavier and larger than control nestlings, but
 only during the early postnatal period. These differences vanished by
 fledging. Nestlings from TH-injected eggs exhibited lower activity of the
 glutathione-s-transferase, a major antioxidant enzyme, than control
 nestlings at day 12, a few days before fledging, but they did not differ
 in oxidative damage and overall intracellular oxidative state. These
 results suggest that the early growth-enhancing effects incurred no
 observable oxidative stress. We hypothesize that such a transient
 growth-enhancing effect might be adaptive in advancing the development and
 maturation of the offspring so they are well-prepared in time for the
 upcoming migration. Further studies investigating whether such advancing
 effects can influence long-term fitness, will be more than valuable.
description: Data and R codes for
 transient effects of maternal THsThe compressed folder
 contains all data and R codes used to produce the results in the
 associated paper.Transient effects of maternal
 THs_Hsu_etal_JAV.zip
DOI: 10.5061/dryad.r14ch
title: Data from: The evolutionary origin of variation in song length and frequency in the avian family Cettiidae

description: Aspects of bird song have been shown to correlate with morphological and
 ecological features, including beak and body size, and habitat. Here we
 study evolution of song length and song frequency among 30 species
 belonging to the Cettiidae. Frequency is negatively correlated with body
 size, and song length increases with latitude. Although migration distance
 correlates with latitude, the association of song length with latitude is
 only present within the non-migratory species, implying the association is
 not a consequence of migration. We place these correlations in a
 historical framework to show that the body size-frequency association
 arose early in the group, but the latitude-song length association is more
 evolutionarily labile. We suggest that latitudinal correlates of song
 length may reflect increased importance of sexual selection by female
 choice.
description: Data for Cettiidae song
 evolution studyRaw song measurements as
 well as the ecology traits data (i. e. breeding latitude, migration and
 morphology) for 30 species in Cettiidae are provided.cettiidaedata.xlsx
DOI: 10.5061/dryad.ck5c0
title: Data from: Better the devil you know: common terns stay with a previous partner although pair bond duration does not affect breeding output

description: In a monogamous species two partners contribute to the breeding process.
 We study pair formation as well as the effect of pair bond length and age
 on breeding performance, incorporating individual heterogeneity, based on
 a high-quality dataset of a long-lived seabird, the common tern (Sterna
 hirundo). To handle missing information and model the complicated
 processes driving reproduction, we use a hierarchical Bayesian model of
 the steps that lead to the number of fledglings, including processes at
 the individual and the pair level. The results show that the age of both
 partners is important for reproductive performance, with similar patterns
 for both sexes and individual heterogeneity in reproductive performance,
 but pair bond length is not. The terns are more likely to choose a former
 partner independent of the previous breeding outcome with that partner,
 which suggests a tendency to retain the partner chosen at the beginning of
 the breeding career.
description: RebkeBeckerColchero_ProceedingsB_All_DataThis folder includes the following files: RebkeBeckerColchero_ProceedingsB_Data.csv - This is the main data file used for the paper. It includes the individual-based data of common terns (Sterna hirundo). RebkeBeckerColchero_ProceedingsB_AddData_Ringed.csv - This is an additional data file used for the paper. It includes a list of partners appearing in the main data file in the column PartnerID, that were marked by ring only and not by transponder. RebkeBeckerColchero_ProceedingsB_AddData_Nests.csv - This is an additional data file used for the paper. It includes a list of the breeding year and the corresponding number of nests in the colony.
DOI: 10.5061/dryad.2mv5722
title: Data from: Stream community richness predicts apex predator occupancy dynamics in riparian systems

description: Streams and adjacent riparian habitats represent linked terrestrial and
 aquatic ecosystems that exchange materials and energy. Recognized
 relationships among apex predators and ecosystem biodiversity led us to
 hypothesize that these predators in riparian-stream systems were more
 likely to be found in sites with high stream quality, defined as increased
 ecosystem function and integrity. In our freshwater study system, river
 otter (Lontra canadensis) and mink (Neovison vison) play critical roles as
 apex predators. We used multi-season occupancy modelling across 3 sampling
 years (2012-2014) to compare aspects of the stream communities that
 explain occupancy dynamics of river otter and mink, including their
 interactions with other semi-aquatic mammals. We surveyed for semi-aquatic
 mammals at 77 sites in 12 major watersheds in southern Illinois, USA
 (44,526 km2). Naïve occupancy differed among years but generally increased
 for river otter, and remained high (≥93.5%) for mink. Increasing substrate
 availability increased detectability of river otter, whereas mink
 detection varied by survey period. Occupancy of river otter during the
 initial survey period was higher in sites closer to reintroduction points.
 Probability of colonization of river otter was positively associated with
 macroinvertebrate index of biotic integrity, fish species richness, and
 beaver presence. Sites with high species richness of fish families
 preferred by river otter also had increased river otter persistence. Mink
 occupied sites with increased fish richness, muskrat presence, and mussel
 community index. Taken together, our results show occupancy of both mink
 and river otter were predicted by aspects of prey diversity and presence,
 indicating the importance of community composition in occupancy dynamics
 of riparian predators. Ultimately, these relationships suggest that
 habitat heterogeneity and system stability are important to apex predator
 site use. However, the relative role of bottom-up and top-down forcing in
 stream systems remains to be resolved.
description: READ_ME_Holland_etal_apex_predText file containing meta data for all csv files in data package.Holland_etal_apex_pred_OtterMatrixCSV file with detection matrix for river otter data, in southern Illinois 2012-2014. Additional information available in readme file.Holland_etal_apex_pred_MinkMatrixCSV file with detection matrix for mink data, in southern Illinois 2012-2014. Additional information available in readme file.Holland_etal_apex_pred_DectDataCSV file with detection data from top models for occupancy of mink and river otter in southern Illinois, 2012-2014.Holland_etal_apex_pred_SiteDataCSV file with site variables used in top models of initial occupancy, colonization, or extinction aspects of multi-season occupancy models for mink and river otter in southern Illinois, 2012-2014.Holland_etal_apex_pred_SeasDataCSV with seasonal variables from top models for multi-season occupancy of river otter and mink in southern Illinois, 2012-2014.
DOI: 10.5061/dryad.v6f74
title: Data from: Risk factors for bloodborne viral hepatitis in healthcare workers of Pakistan: a population based case–control study

description: Objectives: A high prevalence of viral hepatitis B and C was found among
 healthcare workers during a province-wide screening in Sindh Province,
 Pakistan. A follow-up study was undertaken to identify risk factors for
 this high prevalence in healthcare workers. Design: Population based
 case–control design. Setting: Public sector healthcare facilities in a
 rural district of Pakistan. Participants: Healthcare workers who were
 screened for hepatitis B surface antigen (HBsAg) and hepatitis C virus
 (HCV) antibodies. 178 healthcare workers employed at the public sector
 clinics and hospitals of the district were approached, of which 14 refused
 to participate. Cases had detectable serum antibodies against HCV and the
 presence of HBsAg. Healthcare workers non-reactive to HCV antibodies and
 with no HBsAg were controls. These were matched in a ratio of 1:1. Outcome
 measure: Detectable serum HBsAg and HCV antibody titer were taken as
 outcome. OR for various exposures was calculated; those with p&lt;0.25
 were entered in a multivariate logistic regression model to find out
 significant predictors. Results: Needle stick injury (OR=6; CI95 1.4 to
 23), recapping the needle (OR=5.7; CI95 1.1 to 28), wound care at accident
 and emergency of a hospital (OR=5.5; CI95 1 to 28), female gender (OR=3.4;
 CI95 1 to 12) and more than 10 years of formal education (OR=0.25; CI95
 0.07 to 0.8) were associated with hepatitis C. Hepatitis B was found to be
 associated with trying to bend or break a needle after use (OR=4.9; CI95 1
 to 24). Conclusions: Healthcare workers in Pakistan are at additional risk
 of exposure to bloodborne pathogens. Bi-dimensional risk factors present
 at individual and broader health systems levels are responsible.
 Occupational safety, health trainings and redesigning of the curriculum
 for allied health professionals are required.
description: Risk Factors for
 Hepatitis in Health Workers of Sindh-PakistanThis data file is the
 about the risk factors for Viral Hepatitis B and C among the health care
 workers of district Jamshoro in Sindh, PakistanHep Data
 (Dyrad).sav
DOI: 10.5281/zenodo.18382309
title: Dataset and samples for Anonymous Submission
DOI: 10.5281/zenodo.18382308
title: Dataset and samples for Anonymous Submission
DOI: 10.5061/dryad.4g099
title: Data from: No effect of partner age and lifespan on female age-specific reproductive performance in blue tits

description: Studies of age-specific reproductive performance are fundamental to our
 understanding of population dynamics and the evolution of life-history
 strategies. In species with bi-parental care, reproductive ageing
 trajectories of either parent may be influenced by their partner's
 age, but this has rarely been investigated. We investigated
 within-individual age-specific performance (laying date and number of eggs
 laid) in wild female blue tits Cyanistes caeruleus and evaluated how the
 age and longevity of their male partner indirectly influenced the
 females' reproductive performance. Females showed clear
 age-dependence in both laying date and number of eggs laid. We found that
 female reproductive performance improved in early life, before showing a
 decline. Longer-lived females had an earlier laying date throughout their
 lives than shorter-lived females, but there was no difference in number of
 eggs laid between longer- and shorter-lived females. Within breeding
 pairs, the female's (age-specific) reproductive performance was not
 dependent on the age and longevity of the male partner. We conclude that
 the age and quality of the male partner may be of little importance for
 traits that are under direct female control.
description: Amininasab_etal_JAB_DryadThis data was used for analyses on manuscript entitled :No effect of partner age and lifespan on female age-specific reproductive performance in blue tits